bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3547: The ISB Cancer Gateway in the Cloud (ISB-CGC): Access, explore and analyze large-scale cancer data through the Google Cloud
Authors: Seidl Fabian , Hagen Lauren , Wilson Jacob , Aguilar Boris , Bleich Deena , Wolfe Lauren , Gundluru Poojitha , Venkatesan Prema , Tian Mi , Paquette Suzanne , Lee Elaine , Huffman Danna , Pot David , Longabaugh William
Published: March 2024

Rapid growth of cancer data in recent decades has made data discovery and wrangling difficult for the average cancer research lab. Our mission at the ISB Cancer Gateway in the Cloud (ISB-CGC), part of the NCI’s Cancer Research Data Commons ecosystem, is to democratize access to large cancer datasets. Funded by the NCI, we have performed ETL processes on data from GDC and PDC projects such as TCGA, TARGET, and CPTAC. We generated hundreds of BigQuery tables containing data such as mutations, gene expression, and protein abundance, which enable data analysis in the cloud via SQL. BigQuery analyses are inexpensive and rapid even when scaled to petabyte sized inputs, for example we ran 6.6 billion correlations in 2.5 hours with a total cost of about one dollar. These data can also be accessed affordably from Google Cloud VMs where researchers can develop analysis pipelines in Python, R, and workflow languages such as CWL. We present two recent collaborations: In one BigQuery was used to develop machine learning algorithms that calculated genetic risk scores from TCGA glioblastoma and ovarian cancer copy number variation. In another example researchers combined SQL queries of our BQ tables with data from the ISPY2 Trial initiative and generated an R shiny app that can dynamically create data visualizations for genes of interest in different TCGA cohorts.

Citation Format: Fabian Seidl, Lauren Hagen, Jacob Wilson, Boris Aguilar, Deena Bleich, Lauren Wolfe, Poojitha Gundluru, Prema Venkatesan, Mi Tian, Suzanne Paquette, Elaine Lee, Danna Huffman, David Pot, William Longabaugh. The ISB Cancer Gateway in the Cloud (ISB-CGC): Access, explore and analyze large-scale cancer data through the Google Cloud [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3547.
Abstract 3660: Plasma cell free DNA hydroxymethylation profiling reveals anti-PD1 treatment response and resistance biology in non-small cell lung cancer
Authors: Guler Gulfem D. , Ning Yuhong , Coruh Ceyda , Phillips Tierney , Nabiyouni Maryam , Hazen Kyle , Scott Aaron , Volkmuth Wayne , Levy Samuel
Published: March 2024

Background: Treatment with immune checkpoint inhibitors (ICIs) targeting programmed death-1 (PD-1) can yield durable anti-tumor responses, yet not all patients respond to ICIs. Current approaches to select patients who may benefit from anti-PD-1 treatment are insufficient. 5-hydroxymethylation (5hmC) analysis of plasma-derived cell free DNA (cfDNA) presents a novel non-invasive approach for identification of therapy response biomarkers which can tackle challenges associated with tumor biopsies such as tumor heterogeneity and serial sample collection.

Methods: 151 blood samples were collected from 31 non-small cell lung cancer (NSCLC) patients before therapy start and at multiple timepoints whilst on therapy. Blood samples were processed to obtain plasma-derived cfDNA, followed by enrichment of 5hmC-containing cfDNA fragments through biotinylation via a two-step chemistry and binding to streptavidin coated beads. 5hmC-enriched cfDNA and whole genome libraries were prepared in parallel and sequenced to obtain whole hydroxymethylome and whole genome plasma profiles, respectively.

Results: Comparison of on-treatment timepoint to matched pre-treatment samples from same patients revealed that anti-PD-1 treatment induced distinct changes in plasma cfDNA 5hmC profiles of responders, as judged by RECIST, relative to non-responders. In responders, 5hmC accumulated over genes involved in immune activation such as IFNγ and IFNα response, inflammatory response, and TNFα signaling, whereas in non-responders 5hmC increased over epithelial to mesenchymal transition genes. The Molecular Response to anti-PD-1 treatment, as measured by 5hmC changes in plasma cfDNA profiles were observed early, starting with the first cycle of treatment. Comparison of pre-treatment plasma samples revealed that anti-PD-1 treatment response- and resistance-associated genes can be captured by 5hmC profiling of plasma-derived cfDNA.

Conclusions: These results demonstrate that 5hmC profiling can identify response and resistance associated biological pathways in plasma samples, offering a novel method for non-invasive prediction and monitoring of immunotherapy response in NSCLC.

Citation Format: Gulfem D. Guler, Yuhong Ning, Ceyda Coruh, Tierney Phillips, Maryam Nabiyouni, Kyle Hazen, Aaron Scott, Wayne Volkmuth, Samuel Levy. Plasma cell free DNA hydroxymethylation profiling reveals anti-PD1 treatment response and resistance biology in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3660.
Abstract 3666: Multi-cancer early detection using metrics of DNA methylation based epigenetic instability
Authors: Thursby Sara-Jayne , Jin Zhicheng , Baylin Steve B. , Brock Malcolm , Pisanic Thomas , Easwaran Hariharan
Published: March 2024

Cancers present significant changes in DNA methylation, which has proven to be highly useful in cell-free DNA (cfDNA) based cancer detection. Cancer epigenomes are marked by a high degree of intra- and inter-tumor epigenetic variation, indicative of the high level of epigenetic instability. However, the nature of the regions with high epigenetic instability and its utility as biomarker has not been explored. Here we developed a novel methodology and metric to measure the degree of epigenetic perturbation, termed the Epigenetic Instability Index (EII), for multiple cancer screening through cfDNA. Our novel methodology provides a sample specific score of epigenetic perturbation in relation to the expected normal state as opposed to only looking at CpG sites that change between samples. Through machine learning, we have elucidated 269 CpG-island regions which sufficiently capture the epigenetic instability in cancers. We have built classifier models using the EII metrics of these 269 regions and demonstrate that they can efficiently identify breast and lung cancer cases from cfDNA methylation data. Particularly, the models can differentiate even Stage IA of NSCLC with ~75% sensitivity at 95% specificity and early-stage breast cancer at ~68% sensitivity and 95% specificity. The EII metrics perform significantly better than metrics that measure absolute DNA methylation levels. Our studies highlight the potential of measuring epigenetic instability from cfDNA in any given sample in addition to traditional methods of methylation measurement for non-invasive screenings via liquid biopsies.

Citation Format: Sara-Jayne Thursby, Zhicheng Jin, Steve B. Baylin, Malcolm Brock, Thomas Pisanic, Hariharan Easwaran. Multi-cancer early detection using metrics of DNA methylation based epigenetic instability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3666.
Abstract 3698: Characterization of circulating rare events in non-small cell lung cancer
Authors: Seo Jiyoun , Shishido Stephanie N. , Mason Jeremy , Velasco Carmen Ruiz , Mullin Jaden , Prabakar Rishvanth , Hicks James , Kuhn Peter
Published: March 2024

Non-small cell lung cancer (NSCLC) is the most frequent type of lung cancer, accounting for about 80 - 85% of all diagnoses. Unfortunately, 75% of NSCLC diagnoses are made when cancer has already spread and the prognosis is poor. Therefore, biomarker investigation that might allow for early detection of NSCLC is critical to improving patient outcomes. The purpose of this study is to demonstrate the feasibility of liquid biopsy to detect and identify circulating rare events, such as circulating tumor cells (CTCs), associated with NSCLC. Here we apply our non-enrichment-based High Definition Single Cell Assay (HDSCA) workflow which utilizes an immunofluorescence staining technique and an unsupervised rare event detection algorithm to identify the circulating rare cells and acellular events in samples collected from 206 NSCLC patients and 60 healthy individuals. We detected a heterogeneous population of circulating rare events in NSCLC, including epithelial, mesenchymal, and endothelial cells, as well as acellular events such as oncosomes. Cancer-associated circulating rare events with statistically significant prevalence in NSCLC compared to healthy individuals were observed. Molecular characterization using multiplexed targeted proteomics based on imaging mass cytometry and genomic analysis by single-cell copy number profiling confirmed the phenotypic heterogeneity and genomic profiles of the detected circulating rare events. In this study, our results demonstrate the use of the extended capabilities of liquid biopsy to identify a comprehensive overview of circulating rare events that can provide clinically valuable biomarkers in NSCLC.

Citation Format: Jiyoun Seo, Stephanie N. Shishido, Jeremy Mason, Carmen Ruiz Velasco, Jaden Mullin, Rishvanth Prabakar, James Hicks, Peter Kuhn. Characterization of circulating rare events in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3698.
Abstract 3721: EZH2 inhibition enhances PD-L1 protein stability through USP22-mediated deubiquitination in colorectal cancer
Authors: Yang Jianling , Huang Jiaqi , Yin Qianqian , Xue Lixiang
Published: March 2024

The regulation of PD-L1 is the key question which largely determines the outcome of the immune checkpoint inhibitors (ICIs) based therapy. The epigenetic mechanism is involved in transcriptional regulation towards PD-L1. However, besides the transcription level, the protein stability of PD-L1 is closely correlated to its function and has drawn more and more attention. In this study, EZH2 inhibition could enhance PD-L1 expression and protein stability, and the deubiquitinase ubiquitin-specific peptidase 22 (USP22) is identified as a key mediator in this process. EZH2 inhibition upregulates the expression of USP22 via canonical mechanism, and upregulated USP22 further stabilize PD-L1. Importantly, a combination of EZH2 inhibitors with anti-PD-1 immune checkpoint blockade therapy could improve the tumor microenvironment, promotes immune cell infiltration, enhances sensitivity to immunotherapy and exerts synergistic anti-cancer effects. In addition, knocking down USP22 could potentially enhance the therapeutic efficacy of EZH2 inhibitor on colon cancer. These findings unveil the novel role of EZH2 inhibitors (EZH2i) in tumor immune evasion by upregulating PD-L1. Although it may be one reason of EZH2i inefficacy due to the fact that it elicits the immune suppressive effect, appropriately utilizing this drawback to arouse PD-L1 expression may convert the tumor into more responsive upon ICI cancer therapy. In addition, the EZH2-USP22-PD-L1 regulatory axis could further facilitating to identify populations sensitive to immunotherapy or provide novel strategy for combined treatment. Therefore, these findings provide valuable insights into the intricate interplay between EZH2 and PD-L1, shedding light on the optimization of combining both immune checkpoint blockade and EZH2 inhibitor based epigenetic therapies to achieve more efficacies and accuracy in cancer treatment.

Citation Format: Jianling Yang, Jiaqi Huang, Qianqian Yin, Lixiang Xue. EZH2 inhibition enhances PD-L1 protein stability through USP22-mediated deubiquitination in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3721.
Abstract 3723: Hepatic arterial infusion chemotherapy prolongs patient survival in HCC after atezolizumab and bevacizumab failure
Authors: Sung Pil Soo
Published: March 2024

Background: Atezolizumab/bevacizumab is the first-line chemotherapy for unresectable hepatocellular carcinoma (HCC) patients. In our institute, if the patient is not feasible for or cannot afford the first-line systemic chemotherapy, hepatic artery infusion chemotherapy (HAIC) is proposed and used for treatment The purpose of the study was to compare the prognosis of HAIC treatment in newly diagnosed patients and patients who received HAIC after atezolizumab-bevacizumab treatment failure.

Methods: We retrospectively assessed 49 HCC patients who were treated with HAIC between January 2022 and August 2023. 35 patients were treated with HAIC at initial diagnosis and 14 patients were treated with HAIC after the first line chemotherapy Atezolizumab-bevacizumab combination chemotherapy. We evaluated tumor response, progression free survival (PFS), disease control rate (DCR) and overall survival (OS).

Results: There was a no significant difference in OS and PFS between HCC patients who were treated with HAIC at initial diagnosis and those who were treated after atezolizumab bevacizumab treatment failure. (P value = 0.0770, 0.6993 respectively) In addition, there was no significant difference in the treatment responses. (P=0.4330) Our analysis of the objective response rate (ORR) and disease control rate (DCR) also revealed no significant difference between the two treatment groups. (P=0.247 and 0.829 respectively).

Conclusion: There was no significant difference between the OS and PFS of advanced HCC patients who were treated with HAIC at initial diagnosis and those who were treated with HAIC after atezolizumab bevacizumab treatment failure. Hepatic arterial infusion chemotherapy may prolong patient survival in HCC after atezolizumab and bevacizumab failure.

Citation Format: Pil Soo Sung. Hepatic arterial infusion chemotherapy prolongs patient survival in HCC after atezolizumab and bevacizumab failure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3723.
Abstract 3758: Evaluation of breast cancer-derived extracellular vesicles as diagnostic indicator for HER2 status
Authors: Moon Sol , Kim Min Woo , Kim Young , Lee Suji , Lee Hyojung , Kim Joon Ye , Kim Seung Il , Kim Jee Ye
Published: March 2024

HER2-low is a new distinct type of breast cancer that is characterized by low levels of the HER2 protein. As treatment paradigms for HER2-low breast cancer are rapidly evolving with the approval of antibody-drug conjugates, identification of HER2-low breast cancer with more sensitive and reproducible HER2 assays is needed. We aimed to investigate the utility of liquid biopsy in isolating tumor-derived extracellular vesicles (TDEs) for diagnosis of HER2 status. We adopted an affinity-based approach to isolate TDEs and performed CNV analysis of the ERBB2/neu genes using the tumor DNA present in TDEs (etDNA). HER2 status of etDNA had been determined by droplet digital PCR using HER2/EIF2C ratio, a highly accurate method to quantify DNA copy number. In our study, we utilized a variety of breast cancer cell lines categorized as HER2-low (MDA-MB-231, MCF7, ZR-75-1) and HER2-high (MDA-MB-453, BT-474, SK-BR-3) to confirm HER2 expression in extracellular vesicles (EVs) by flow cytometry. This analysis successfully demonstrated that EVs effectively reflect the HER2 status of the tumor cells, evidenced by a strong Pearson correlation coefficient (r=0.987, p<0.001). Further clinical validation was conducted with plasma samples from 22 breast cancer patients. In the clinical study, we observed a significant correlation between the CNV of tumor DNA present in TDEs and the HER2 status of primary tumors (p<0.01). Additionally, the Receiver Operating Characteristic (ROC) analysis yielded an impressive area under the curve (AUC) value of 0.838 (p<0.01), demonstrating a high level of accuracy in differentiating between high and low HER2 groups, with a sensitivity of 55.6% and a specificity of 100%. In summary, we show potential diagnostic tools for real-time, less invasive determination of HER2 status in primary tumors, providing continuous monitoring methods for HER2 status. Although further validation in larger cohorts and prospective studies is needed, our study indicates that TDE analysis could contribute to the assays for identification of the HER2 status in breast cancer patients.

Citation Format: Sol Moon, Min Woo Kim, Young Kim, Suji Lee, Hyojung Lee, Joon Ye Kim, Seung Il Kim, Jee Ye Kim. Evaluation of breast cancer-derived extracellular vesicles as diagnostic indicator for HER2 status [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3758.
Abstract 3796: Investigating unbiased whole transcriptome high-resolution spatial interactions within tumor masses
Authors: Lee Marie M. , Wilhelmy Julie , Ong Thomas , Wang Wanxin , Yeung Bertrand , Chang Christina , Fan Christina
Published: March 2024

Tumor masses contain a diverse array of cell types, including both normal and tumor cells from different lineages, endothelial cells, and immune cells. Interactions among these cellular constituents and their spatial arrangements play a pivotal role in tumor development, progression, and metastasis. While single-cell analysis has provided valuable insights regarding the dissociated cellular composition of tumors, it falls short in elucidating the complex interplay of cell-cell interactions and spatial relationships that may drive tumor cellular behavior and gene expression.

We used the Curio Seeker Spatial Mapping Kits to uncover those spatial relationships in human tumor samples. The method captured whole transcriptomes and preserved the spatial locations of tumor cells, infiltrating immune cells, and normal cells by self segregating gene expression signatures and unbiased clustering. Amongst other findings by using Curio Seeker, we identified areas of immune cell infiltrates that were devoid of tumor cells, signifying zones of potential anti-tumor response.

The high spatial resolution, continuous gene expression maps from the Curio Seeker Spatial Mapping Kits reveal spatial interactions between different cellular populations that enable researchers to better understand how the interplay between tumor cell types and their cellular neighborhoods affect gene expression and tumor cell behavior.

Citation Format: Marie M. Lee, Julie Wilhelmy, Thomas Ong, Wanxin Wang, Bertrand Yeung, Christina Chang, Christina Fan. Investigating unbiased whole transcriptome high-resolution spatial interactions within tumor masses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3796.
Abstract 3805: Intestinal microbiome with chemotherapy response and RAS mutation in patients with advanced or metastatic colorectal cancer: a pilot, exploratory study
Authors: Kim Jwa Hoon , Kim Boyeon , Lee Soohyeon
Published: March 2024

Intestinal microbiomes interact with the tumor microenvironment, participating in inflammation and immune regulation, and are associated with the response to anticancer therapy. However, there has been limited research exploring the relationship between changes in the microbiome and treatment response in patients with metastatic colorectal cancer (mCRC) during chemotherapy and radiation therapy.This study included all 15 patients with mCRC treated with first-line systemic therapy between October 2021 and February 2023. We conducted 16S rRNA sequencing on baseline stool samples and investigated the association of intestinal microbiome with chemotherapy response and RAS mutation. The QIIME2 and R packages were used for analysis. As a results, Median age was 61 years (range, 35-73), and there were 8 patients with RAS-mutated mCRC. All patients were treated with first-line systemic therapy; FOLFOX (5-fluorouracil and oxaliplatin)-based (n=13) and FOLFIRI (5-fluorouracil and irinotecan)-based chemotherapy (n=2). Of them, 2 patients received short-course radiotherapy (ScRTx) to primary tumor before systemic chemotherapy, where pre- and post-ScRTx stool samples were collected. Among 15 patients, 9 patients (60%) achieved responses. Non-responders tend to exhibit higher alpha diversity (Chao1, Observed ASV) compared to responders. Firmicutes, Lactobacillus, Faecalibacterium, and the [Luminococcus]_gauvreauii_group were more prevalent in responders, whereas Bacteroidota, Prevotella, DTU089, Alistipes, Christensenellaceae_R-7_group, and Porphyromonas in non-responders. Despite no statistical significance, alpha diversity decreased in post-ScRTx compared to pre-ScRTx samples. Akkermansia, Prevotella, and Peptostreptococcus were more prevalent in the post-ScRTx compared to pre-ScRTx samples. Regarding the association of intestinal microbiome with RAS mutation, Bray curtis and weighted unifrac analyses revealed significant differences in beta diversity; higher incidence of Faecalibacterium, Lactobacillus, Prevotella, Anaerofilum, and UCG-005 in the RAS-wild type mCRC, while Bacteroides, Collinsella, Holdemanella, and Anaerostipes in RAS-mutated mCRC.This pilot study suggests the prognostic value of gut microbiomes and its association with RAS mutation in patients with mCRC treated with first line systemic therapy. A microbial functional study with immune cytokine change is planned to confirm these findings in future.

Citation Format: Jwa Hoon Kim, Boyeon Kim, Soohyeon Lee. Intestinal microbiome with chemotherapy response and RAS mutation in patients with advanced or metastatic colorectal cancer: a pilot, exploratory study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3805.
Abstract 3811: Impact of antiviral treatment status on risk of extrahepatic cancers in patients with chronic hepatitis C
Authors: Tao Menghua , Li Jia , Wu Trueman , Gordon Stuart C. , Rupp Loralee B. , Trudeau Sheri , Holmberg Scott D. , Moorman Anne C. , Spradling Philip R. , Teshale Eyasu H. , Schmidt Mark A. , Daida Yihe G. , Lu Mei
Published: March 2024

Background: Eradiation of hepatitis C virus (HCV) infection has been shown to reduce risk of liver cancer among HCV patients; however, there has been spare data on the effect of antiviral treatment on the risk of extrahepatic cancers. Using data from the Chronic Hepatitis Cohort Study (CHeCS), we investigated whether antiviral therapy impacts the risk of extrahepatic cancers among patients with HCV.

Methods: 17,485 HCV patients were included in the study, and they were followed until incidence of cancer including lung cancer, non-Hodgkin lymphoma (NHL), breast cancer or prostate cancer, death, or last follow-up. An extended landmark modeling approach was considered, which included time-varying covariates and propensity score justification for treatment selection bias and used generalized estimating equations (GEE) with a link function as multinominal distribution for a discrete time-to-event data. Death was considered a competing risk.

Results: Compared to untreated patients, patients with HCV treatment had significantly lower risk of lung cancer for direct-acting antiviral (DAA) treatment (hazard ratio (HR) = 0.47, 95% CI, 0.30-0.72) and for interferon-based treatment (IFN) (HR = 0.33, 95% CI, 0.20-0.50). The risk of NHL was only reduced among patients receiving DAA treatment. There were no significant associations between HCV treatment and risks of breast and prostate cancer.

Conclusion: Both DAA and IFN antiviral treatment independently reduce the risk of lung cancer, while the protective association with NHL was limited among HCV patients with DAA treatment. Our findings support the importance of timely initiation antiviral therapy in chronic HCV-infected patients.

Citation Format: Menghua Tao, Jia Li, Trueman Wu, Stuart C. Gordon, Loralee B. Rupp, Sheri Trudeau, Scott D. Holmberg, Anne C. Moorman, Philip R. Spradling, Eyasu H. Teshale, Mark A. Schmidt, Yihe G. Daida, Mei Lu. Impact of antiviral treatment status on risk of extrahepatic cancers in patients with chronic hepatitis C [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3811.
Abstract 3848: Comprehensive protein analysis to identify the proteins responsible for sarcopenia and their impact on antitumor immunotherapy in non-small cell lung cancer
Authors: Masuda Takaaki , Watanabe Satoshi , Wakabayashi Tomoya , Tanaka Susumu , Shono Kunihiro , Suzuki Ryo , Sekiya Tomoki , Yanagimura Naohiro , Arita Masashi , Ohtsubo Aya , Tanaka Tomohiro , Nozaki Koichiro , Saida Yu , Hokari Satoshi , Kondo Rie , Shima Kenjiro , Kimura Yosuke , Aoki Nobumasa , Ohshima Yasuyoshi , Koya Toshiyuki , Sakai Kazuko , Nishio Kazuto , Yamazaki Motohiko , Ishikawa Hiroyuki , Kikuchi Toshiaki
Published: March 2024

Background: Previous retrospective studies have shown that sarcopenia (Sar) is associated with poor outcome in cancer patients (pts) receiving immune checkpoint inhibitors (ICIs). We conducted a prospective study to determine whether Sar-related proteins induce Sar and reduce the efficacy of ICI.

Method: Non-small cell lung cancer (NSCLC) pts receiving ICI as first-line treatment at Niigata University Medical and Dental Hospital were eligible. Sar was diagnosed with physical performance and skeletal muscle mass. Comprehensive protein analysis of pre-treatment blood samples was performed to identify factors that correlate with muscle loss and ICI effects.

Result: 41 patients were enrolled from October 2019 through August 2022. PFS for Sar was 4.6 months, 6.7 months for Pre-Sar, and 16.7 months for Non-Sar (P=0.0028). OS for Sar was not reached, 15.7 months for Pre-Sar, and not reached for Non-Sar (P=0.0014). Leptin, IL-1β, IL-12, and Pentraxin 3 were significantly correlated with loss of muscle mass. In contrast, leptin, insulin, IGF-1, GDF-8, Activin A, IL-2Ra, IL-8, MMP-3, osteopontin, and Pentraxin-3 were significantly associated with poor OS. Pentraxin 3 and leptin were associated with both the effectiveness of immunotherapy and sarcopenia. A multivariate analysis that considered factors commonly associated with the effectiveness of immunotherapy, including age, PD-L1 expression rate, and neutrophil-lymphocyte ratio, Pentraxin 3 was determined to be an independent prognostic factor.

Conclusion: This study indicated that Sar-related proteins and inflammatory cytokines are involved in the development of Sar and ICI efficacy.

Citation Format: Takaaki Masuda, Satoshi Watanabe, Tomoya Wakabayashi, Susumu Tanaka, Kunihiro Shono, Ryo Suzuki, Tomoki Sekiya, Naohiro Yanagimura, Masashi Arita, Aya Ohtsubo, Tomohiro Tanaka, Koichiro Nozaki, Yu Saida, Satoshi Hokari, Rie Kondo, Kenjiro Shima, Yosuke Kimura, Nobumasa Aoki, Yasuyoshi Ohshima, Toshiyuki Koya, Kazuko Sakai, Kazuto Nishio, Motohiko Yamazaki, Hiroyuki Ishikawa, Toshiaki Kikuchi. Comprehensive protein analysis to identify the proteins responsible for sarcopenia and their impact on antitumor immunotherapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3848.
Abstract 3860: Characterizing peripheral immune correlates of tumor response in breast cancer patients immunized with the P10s-PADRE vaccine
Authors: Jousheghany Fariba , Lee John P. , Nounamo Bernice , Raj Vinay , Faulkner Jennifer L. , Siegel Eric , Makhoul Issam , Kieber-Emmons Thomas , Monzavi-Karbassi Behjatolah
Published: March 2024

Introduction: We demonstrated that vaccination of HR+/HER2− breast cancer subjects with P10s-PADRE cancer vaccine in combination with standard-of-care chemotherapy led to generation of antibodies (Ab), activation of Natural Killer (NK) and T cells, increases in IFNγ and TNFα, and increases in TILs and stromal CD3+ T cells. The current study was conducted to assess the vaccine's efficacy, particularly focusing on tumor shrinkage and pathologic Complete Response (pCR). Additionally, it aims to explore the association of specific peripheral-blood immune responses, such as antibody levels and NK and T-cell activation, with pCR and objective reduction in primary tumor size.

Methods: Blood samples collected at baseline and after treatment of at least 25 subjects were used in characterization of immune responses. Serum and plasma samples were used in ELISA, cytokine, and glycan-array assays to measure anti-peptide and anti-glycan antibodies and blood-cytokine levels. Peripheral blood mononuclear cells (PBMCs) were interrogated by RNA-seq, flow cytometry, and ELISpot assays.

Results: We observed that high levels of anti-peptide and anti-GD2 antibody responses correlated with pCR. Ab response was positively correlated with differential expression of CD56, GZMA, IFNγ, NKp46, and CD8b, among which GZMA and NKp46 showed a statistically significant association. Vaccine-induced functional cellular immune responses (measured by differential expression of IFNγ, GZMA, CD8, CD69, NKp46, CD56, and PRF1) correlated with reduction of primary tumor size. We also observed substantial differences among immune responders vs non-responders in immune gene expression and in cytokine production in post-immune PBMCs after specific and polyclonal stimulation.

Conclusions: The data suggest that immunization of HR+/HER2− breast cancer patients with P10s-PADRE in combination with chemotherapy leads to both humoral and cellular immune responses. While induction of a robust antibody response is a good marker for potential clinical efficacy, vaccine-associated increases of the ratio of CD8+ cells and the expression of CD69, CD8b, GZMA, IFNγ, NKp46, and PRF1 seem to serve as additional efficacy indicators. Future studies are underway to validate these findings and establish reliable prognostic biomarkers.

Citation Format: Fariba Jousheghany, John P. Lee, Bernice Nounamo, Vinay Raj, Jennifer L. Faulkner, Eric Siegel, Issam Makhoul, Thomas Kieber-Emmons, Behjatolah Monzavi-Karbassi. Characterizing peripheral immune correlates of tumor response in breast cancer patients immunized with the P10s-PADRE vaccine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3860.
Abstract 3872: Multi-ancestral origins of colorectal lesionsMulti-ancestral origins of colorectal lesions
Authors: Schenck Ryan O. , Khan Aziz , Horning Aaron , Esplin Edward D. , Van Egeren Debra ,   HTAN–FAP Consortium, Greenleaf William , Ford James M. , Snyder Michael P. , Curtis Christina
Published: March 2024

The widely accepted paradigm that cancer initiation is a monoclonal event has not been definitively resolved. In sporadic cancers this is due to the requirement for longitudinal sampling to study this occult process, which occurs over years to decades. Individuals with familial adenomatous polyposis (FAP) possess a germline APC mutation, leading to hundreds of colonic polyps in adolescence and a 100% lifetime risk of colorectal cancer. Resected colons from FAP patients contain normal mucosa, benign and dysplastic polyps that embed the natural history of colorectal tumorigenesis at different points of malignant progression. Through genome sequencing of 127 independent polyps or mucosa samples from six FAP patients, we characterized the genomic landscape, relative timing of somatic alterations, and clonal dynamics in normal, dysplastic, and invasive colon tissue. Comparison with multi-region sequencing data from FAP patients and sporadic colorectal adenomas and carcinomas indicates similar molecular profiles, with canonical cancer driver genes present across benign and dysplastic premalignant lesions and shared mutational orders. Pairwise sample comparisons and phylogenetic reconstructions revealed extensive heterogeneity and subclonal sharing within a patient’s benign and dysplastic lesions, irrespective of location in the colon. These data imply that polyps were initiated from multiple cells from distinct lineages whose most recent common ancestor arose during development. We corroborate these findings using a mechanistic mathematical model, which infers polyclonality in 100% of benign and 83% of dysplastic samples. Based on these findings, we propose a conceptual model of the multi-ancestral origin of intestinal malignancies.

Citation Format: Ryan O. Schenck, Aziz Khan, Aaron Horning, Edward D. Esplin, Debra Van Egeren, HTAN–FAP Consortium, William Greenleaf, James M. Ford, Michael P. Snyder, Christina Curtis. Multi-ancestral origins of colorectal lesionsMulti-ancestral origins of colorectal lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3872.
Abstract 390: Direct interaction of Pin1 with HIF-prolyl hydroxylase 2: Implications for breast cancer cell growth and survival
Authors: Quispe Yanymee Nimesia Guillen , Kim Su-Jung , Saeidi Soma , Choi Gyo-Jin , Chelakkot Chaithanya , Zhou Tianchi , Bang Sang-Beom , Kim Tae-Won , Shin Young-Kee , Surh Young-Joon
Published: March 2024

Prolyl hydroxylase domain 2 (PHD2) is the main hypoxia-inducible factor (HIF)-prolyl hydroxylase. PHD2 in normoxia hydroxylates specific proline residues in HIF-1α and HIF-2α, which facilitates their ubiquitination and proteasomal degradation. Although the activity of PHD2 is reduced in hypoxia, significant levels of residual activity of this monooxygenase are still detected under hypoxic conditions. However, its role under hypoxia is poorly understood. Peptidyl-prolyl isomerase (Pin1) binds to target proteins containing phosphorylated serine or threonine residues followed by proline (pS/T-P). As PHD2 harbors several pS/T-P motifs, it may be a potential substrate of Pin1. We found for the first time interaction between Pin1 and PHD2 in human breast cancer MDA-MB-231 cells in normoxic and hypoxic conditions. Additionally, the breast cancer tissue array showed elevated expression of PHD2 as well as Pin1 in tumors compared to adjacent normal tissues. LC-MS/MS spectrometry identified three amino acid residues (S125, T168, and S174) of PHD2 undergoing phosphorylation. Among these, serine 125 was found to be the principal site required for Pin1 binding. As a novel binding partner of Pin1, oncogenic PHD2 can be explored as a therapeutic target for the treatment of breast cancer.

Citation Format: Yanymee Nimesia Guillen Quispe, Su-Jung Kim, Soma Saeidi, Gyo-Jin Choi, Chaithanya Chelakkot, Tianchi Zhou, Sang-Beom Bang, Tae-Won Kim, Young-Kee Shin, Young-Joon Surh. Direct interaction of Pin1 with HIF-prolyl hydroxylase 2: Implications for breast cancer cell growth and survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 390.
Abstract 3926: ARF6-dependent endocytic trafficking of the interferon-gamma receptor drives adaptive immune resistance and response to immune checkpoint blockade
Authors: Wee Yinshen , Wang Junhua , Wilson Emily C. , Rich Coulson P. , Rogers Aaron , Tong Zhongzong , DeGroot Evelyn , Gopal Y.N. Vashisht , Davies Michael , Ekiz Huseyin Atakan , Tay Joshua K.H. , Stubben Chris , Boucher Kenneth M. , Oviedo Juan M. , Fairfax Keke C. , Williams Matthew A. , Holmen Sheri L. , Wolff Roger K. , Grossmann Allie H.
Published: March 2024

Interferon-gamma (IFNγ)-driven adaptive immune resistance (AIR) in cancer begins at the plasma membrane where cytokine signaling is initiated. Cytotoxic CD8+ T cells secrete IFNγ, eliciting tumor-intrinsic IFNγ signaling and expression of immunosuppressive genes, which are critical for effective therapeutic response to anti-PD-1 and anti-CTLA-4 immune checkpoint blockade (ICB). Although the IFNγ receptor (IFNγR) is expressed in all cell types, its surface density can determine a cell’s responsiveness to ligand. Mechanistic control over this process remains a mystery. Herein we report that the endocytic trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFNγ-driven AIR during primary tumor progression and in the setting of ICB therapy. The IFNγR1 subunit of the receptor is constitutively internalized in a ligand-independent manner. ARF6 is necessary for endocytic recycling of IFNγR1 and determines the steady-state surface density of the receptor. Loss of ARF6 results in lysosomal degradation of the receptor and controls IFNγR1 protein levels in melanoma, non-small cell lung cancer, colorectal cancer, and triple-negative breast cancer. IFNγ activates ARF6 in parallel with JAK1-STAT1 signaling, suggesting a positive feedback loop that allows tumor cells to dynamically respond to immune attack. Silencing ARF6 reduces tumor intrinsic IFNγ signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to systemic ICB therapy. Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent adaptive immunity, and support that ARF6-dependent endomembrane trafficking of the IFNγ receptor shapes clinical outcomes of ICB therapy.

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Citation Format: Yinshen Wee, Junhua Wang, Emily C. Wilson, Coulson P. Rich, Aaron Rogers, Zhongzong Tong, Evelyn DeGroot, Y.N. Vashisht Gopal, Michael Davies, Huseyin Atakan Ekiz, Joshua K.H. Tay, Chris Stubben, Kenneth M. Boucher, Juan M. Oviedo, Keke C. Fairfax, Matthew A. Williams, Sheri L. Holmen, Roger K. Wolff, Allie H. Grossmann. ARF6-dependent endocytic trafficking of the interferon-gamma receptor drives adaptive immune resistance and response to immune checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3926.
Abstract 4003: TBK1 inhibition enhances CAR-T cell efficacy against patient-derived organotypic tumor spheroids
Authors: Maggs Luke , Sun Yi , Cattaneo Giulia , Ventin Marco , Chen Feng , Rasmussen Martin Q. , Wang Xinhui , Ferrone Cristina R. , Ferrone Soldano , Jenkins Russell W.
Published: March 2024

Novel therapeutic strategies are needed to improve the efficacy of chimeric antigen receptor (CAR)-T cells in the treatment of solid tumors. Here, we set out to evaluate novel therapeutic strategies to improve the efficacy of B7-H3 (CD276) directed (B7-H3.CAR-T) using 3D microfluidic cultures of patient-derived organotypic tumor spheroids (PDOTS). PDOTS are generated from fresh patient tumor tissue and contain tumor cells, autologous immune cells and stromal cells, therefore recapitulating key features of the tumor microenvironment (TME), enabling the study of tumor-immune dynamics. We confirmed activity of B7-H3.CAR-T in PDOTS, although a strong correlation between B7-H3 expression and CAR-T efficacy was not observed. Mechanistic studies subsequently demonstrated dynamic upregulation of co-inhibitory receptors on CAR-T cells following target cell encounter leading to CAR-T cell dysfunction and limiting CAR-T efficacy in B7-H3 expressing tumors. PD-1 blockade restored CAR-T activity in monotypic and organotypic tumor spheroids with improved tumor control and upregulation of effector cytokines. Given the emerging role of TANK-binding kinase 1 (TBK1) as an immune evasion gene, we examined the effect of TBK1 inhibition on CAR-T efficacy. Similar to PD-1 blockade, TBK1 inhibition restored CAR-T activity in monotypic and organotypic tumor spheroids, prevented CAR-T cell dysfunction, and enhanced T cell proliferation. Inhibition or deletion of TBK1 also enhanced sensitivity of cancer cells to immune-mediated killing. Taken together, our results demonstrate the feasibility and utility of ex vivo profiling of CAR-T cells using PDOTS, and suggest that targeting TBK1 is a novel strategy to enhance CAR-T efficacy by overcoming tumor-intrinsic and -extrinsic resistance mechanisms.

Citation Format: Luke Maggs, Yi Sun, Giulia Cattaneo, Marco Ventin, Feng Chen, Martin Q. Rasmussen, Xinhui Wang, Cristina R. Ferrone, Soldano Ferrone, Russell W. Jenkins. TBK1 inhibition enhances CAR-T cell efficacy against patient-derived organotypic tumor spheroids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4003.
Abstract 4005: HER2 TKIs enhance the anti-tumor activity of HER2-targeting CAR-T and CAR-NK cells against NSCLC
Authors: Yang Yan , Nilsson Monique B. , Poteete Alissa , He Junqin , Huang Qian , Heymach John V.
Published: March 2024

Approximately 3% of non-small cell lung cancer (NSCLC) cases harbor ERBB2/HER2 mutations. Notably, the majority of actionable HER2 mutations in NSCLC are in-frame insertions in exon 20. Current HER2-targeting approaches, including antibody-drug conjugates (ADCs) such as trastuzumab deruxtecan, have shown promising response rates. To explore novel strategies for targeting HER2-positive NSCLC, we investigated chimeric antigen receptor (CAR)-based therapies to enhance the anti-tumor activity of immune effector cells. We engineered a series of HER2 CAR constructs utilizing scFvs derived from trastuzumab, pertuzumab, and FRP5, recognizing distinct domains of HER2. These scFvs were integrated into second-generation BB3z (with 4-1BB and CD3z intracellular domains) and third-generation 28BB3z (with CD28, 4-1BB, and CD3z intracellular domains) CAR backbones, which were subsequently transduced into activated T and natural killer (NK) cells to generate CAR-T and CAR-NK cells, respectively. High transduction efficiencies were achieved, with over 80% in CAR-T cells and over 50% in CAR-NK cells. We next evaluated their activity against a panel of NSCLC cell lines expressing varying levels of HER2 in vitro using firefly luciferase assays. All HER2 CAR-T cells demonstrated more than 90% killing against H2170 (HER2 high) and H322 (HER2 medium) at an effector:target (E:T) ratio of 10:1, whereas HER2 CAR-T cells yielded a killing effect of 35% against A549 (HER2 low) cells. HER2-targeting CAR-NK cells also displayed potent cytotoxicity against HER2-expressing NSCLC cells. Moreover, we observed that treatment of HER2 mutant and HER2 amplified NSCLC cells with low doses of HER2 tyrosine kinase inhibitors (TKIs) such as poziotinib enhanced the expression of HER2 on the cell surface. This upregulation resulted in enhanced activation of HER2 CAR-T and CAR-NK cells in coculture experiments as measured by CD107a expression on effector cells. Additionally, treatment with the HER2 TKI poziotinib potentiated the killing activity mediated by HER2 CAR-T and CAR-NK cells. Using a HER2 YVMA duplication patient-derived xenograft (PDX) NSCLC model, we observed that the in vivo combination of poziotinib with HER2 CAR-NK cells exhibited superior anti-tumor activity as compared to poziotinib treatment alone. In conclusion, HER2 CAR-T and CAR-NK cells effectively target HER2-mutant and HER2-positive NSCLC, and their combination with HER2 TKIs enhances vulnerability to HER2-targeting strategies.

Citation Format: Yan Yang, Monique B. Nilsson, Alissa Poteete, Junqin He, Qian Huang, John V. Heymach. HER2 TKIs enhance the anti-tumor activity of HER2-targeting CAR-T and CAR-NK cells against NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4005.
Abstract 4025: A phase II trial of neoadjuvant gemcitabine, cisplatin plus tislelizumab followed by concurrent chemoradiotherapy in locoregionally advanced nasopharyngeal carcinoma: Clinical efficacy, safety and the biomarker analysis
Authors: Li Xiao-Yun , Xie Si-Yi , Chen Qiu-Yan , Mai Hai-Qiang , Tang Lin-Quan
Published: March 2024

Immune checkpoint inhibitors (ICIs) have been widely used in recurrent or metastatic nasopharyngeal carcinoma (NPC), but the addition of ICIs to chemoradiotherapy in locoregionally advanced (LA) NPC requires further investigation. We conducted a phase II, single-arm trial to evaluate the efficacy and safety of neoadjuvant gemcitabine, cisplatin (GP) plus tislelizumab followed by concurrent chemoradiotherapy (CCRT) in LA-NPC. All participants received 3 cycles of GP chemotherapy plus tislelizumab (200 mg) followed by 3 cycles of cisplatin-based CCRT. The primary endpoint was the clinical complete response rate (CR) after neoadjuvant chemoimmunotherapy (NAT). The secondary endpoints include pathological CR rate, progression-free survival (PFS), overall survival (OS), locoregional relapse-free survival (LRRFS), distant metastasis-free survival (DMFS), etc. Pretreatment blood samples and paired (pre-/post-NAT) tissue biopsies were collected to perform full-spectrum peripheral T-cell profiling, PD-L1 and tertiary lymphoid structures (TLS) staining. Among all 63 participants, the CR rate after NAT reached 41.3% (95% CI, 28.8%-53.8%), far exceeding our hypothesized CR rate of 22%. The objective response rate (ORR) and pCR rate after NAT were 88.9% (95% CI, 80.9% to 96.9%) and 74.6% (95% CI, 62.1% to 84.7%), respectively. As of July 15th, 2023, after the median follow-up of 25 months, the 2-year PFS and OS were 98.4% and 100%. The incidence of grade 3-4 immunotherapy-related adverse events was 1.6%. The compliance of CCRT was not compromised. Patients who achieved CR had significantly more circulating CD4+ and CD8+ effector memory T cells (Tem), regulatory T cells (Treg) and follicular helper T cells (Tfh). The peripheral abundance of LAG3+ Tem and Tfh were independently predictive of NAT response. The number and maturation of TLS significantly increased after NAT in the CR group, but not in the Non-CR group. GP chemotherapy plus tislelizumab followed by CCRT was highly therapeutic and safe in treating LA-NPC, further randomized phase III studies are awaited.

Citation Format: Xiao-Yun Li, Si-Yi Xie, Qiu-Yan Chen, Hai-Qiang Mai, Lin-Quan Tang. A phase II trial of neoadjuvant gemcitabine, cisplatin plus tislelizumab followed by concurrent chemoradiotherapy in locoregionally advanced nasopharyngeal carcinoma: Clinical efficacy, safety and the biomarker analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4025.