bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2214: Impacts of habitual and recent alcohol intake on gut microbiome diversity and composition among Black Americans
Authors: Liu Lili , Nguyen Sang , Cai Qiuyin , Shrubsole Martha , Zheng Wei , Yu Danxia
Published: March 2024

Background: Alcohol intake can alter the gut microbiome, which may play a role in the development of cancer and other chronic diseases. However, there have been limited population-based studies investigating the associations of habitual and recent alcohol intake with the gut microbiome, particularly among Black Americans.

Methods: We investigated the association of alcohol intake with the gut microbiome among 538 Black American participants of the Southern Community Cohort Study (150 men and 388 women). Habitual and recent alcohol intake was assessed at cohort baseline (2002-2009) and stool collection (2018-2021), respectively. DNA was extracted from fecal samples for gut microbiome profiling using shotgun metagenomic sequencing. Generalized linear models were employed to evaluate the associations between alcohol intake and gut microbiome diversity and composition, with adjustments for sociodemographic characteristics, other lifestyle factors, and comorbidities. False discovery rate (FDR)<0.1 was considered statistically significant.

Results: The mean age at enrollment was 53.2 ± 7.7 years, with a mean interval of 13.8 years (range: 9.0-18.1 years) between baseline and stool collection. Neither habitual nor recent alcohol intake was associated with microbiome diversity indices, and recent alcohol intake was not associated with microbial taxa abundance either. However, habitual alcohol intake, both total amount and subtypes, showed significant associations with microbial taxa abundance primarily in men, including Actinobacteria, Proteobacteria, Firmicutes, and classes Bacilli and Clostridia within these phyla (all FDR<0.1). Specifically, total alcohol and red wine intakes were inversely associated with genus MGYG-HGUT-02719 in class Clostridia; beer consumption was inversely associated with genus Anaerostipes; white wine intake showed negative associations with order RF32 and genus Eubacterium and a positive association with genus Paenibacillus. Most of these associations remained significant after adjusting for BMI and history of cardiometabolic diseases or cancer.

Conclusion: We identified gut microbiome taxa associated with habitual alcohol intake among Black American men, including several with anti- or pro-gastrointestinal-cancer properties. However, the magnitudes of these associations were generally small. Further research is needed to determine if these bacteria play a mediating or modifying role in alcohol-disease relationships.

Citation Format: Lili Liu, Sang Nguyen, Qiuyin Cai, Martha Shrubsole, Wei Zheng, Danxia Yu. Impacts of habitual and recent alcohol intake on gut microbiome diversity and composition among Black Americans [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 2214.
Abstract 2248: Diminished survival in patients with pancreatic ductal adenocarcinoma is linked with residence in redlined neighborhoods
Authors: Vudatha Vignesh , Freudenberger Devon , Liu Christopher , Fernandez Leopoldo , Trevino Jose
Published: March 2024

Redlining refers to the practice of classifying neighborhoods with racial minorities and low-income residents as “hazardous” for investors. This discriminatory practice by the Home Owners’ Loan Corporation (HOLC) has been shown to impact patient cancer incidence and outcomes in breast, lung, cervical, and colorectal cancers. In this study, we evaluate the impact of HOLC status on pancreatic ductal adenocarcinoma (PDAC) outcomes in Virginia. The Virginia Department of Health Cancer Registry was queried for adult patients diagnosed with pancreatic ductal adenocarcinoma from 2009-2018. The HOLC grade (A: best, B: still desirable, C: definitely declining, D: hazardous) of each patient’s address was determined using the University of Richmond Inequality map. Patient demographics, treatment, and survival data were compared by HOLC Grade via descriptive statistics, bivariate and multivariate analysis. 394 patients were identified (A: 24 (6.1%), B: 54 (13.7%), C: 198 (50.3%), D: 118 (29.9%)). There was no association between patient age, sex, insurance status, receipt of therapy, or smoking history and HOLC status. Patient race was significantly associated with HOLC status with more Black patients living in areas with worse HOLC grades compared to White patients (p<0.001). Survival analysis demonstrated that lack of surgery and chemotherapy (p<0.0001), metastatic disease (p<0.0001), and residential status in areas of HOLC grade D (p=0.012) were associated with worse survival. Based on Cox regression analysis, patients who lived in areas with HOLC grade B (adjusted HR 0.70; CI 0.49-0.98) and C (adjusted HR 0.74; CI 0.58-0.95) had improved survival compared to those living in areas with HOLC grade D. Additionally, age greater than 65, metastatic disease, and lack of treatment were associated with worse survival. Residence in a redlined neighborhoods can play a significant role in pancreatic ductal adenocarcinoma outcomes. Location in a “hazardous” area in Virginia is associated with worse survival in PDAC patients. Disparities in socioeconomics, housing, education, and food accessibility in these areas likely play a role in shaping these outcomes. Future studies are warranted to further investigate this disparity in care.

Citation Format: Vignesh Vudatha, Devon Freudenberger, Christopher Liu, Leopoldo Fernandez, Jose Trevino. Diminished survival in patients with pancreatic ductal adenocarcinoma is linked with residence in redlined neighborhoods [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 2248.
Abstract 2298: Optimization of high-volume cell free DNA extraction and end-to-end automation for TSO 500 ctDNA library prep
Authors: Prasad Nripesh , Rock Rachel , Beatty Rebecca , Robinson Melanie , Wildman Dineen , Sykes Michael , Umylny Boris , Halsey Thomas
Published: March 2024

Liquid biopsy such as plasma, has emerged as one of the most valuable sample types for profiling circulating tumor DNA (ctDNA) for screening, response to treatment, and monitoring relapse in oncology patients. Due to the diffuse nature of ctDNA however, both extraction and library preparation must be optimized for the efficient downstream next-generation sequencing (NGS) application. We initially addressed the optimization of quality and quantity of cfDNA recovery from healthy and various oncology patients by evaluating QIAsymphony DSP Circulating DNA Kit and Apostle MiniMax cfDNA isolation kits. Overall, the cfDNA yields from Apostle MiniMax kit were approximately 12X higher. We then optimized high-volume automated cfDNA extraction from 1ml, 3ml and 6ml plasma samples using the Biomek i7 for Apostle MiniMax kit. Colorectal, Gastric and Ovarian cancer gave the highest yield of cfDNA whereas, Esophageal, Lung and Kidney cancers were the lowest cfDNA yielding samples. We then analyzed ctDNA from plasma from healthy donors, colorectal, kidney, Breast, and endometrial cancer patients along with Oncospan and Seraseq ctDNA mutation mix (5-0.5% AF) to evaluate the mutation detection efficacy, repeatability, and reproducibility by targeted NGS using TSO 500ctDNA assay ay 10ng, 20ng, and 30ng inputs. For library preparation batches of 48 samples were prepared using a fully automated processes for the library prep, Hybridization capture and post capture enrichment on the Beckman i5 robot. Libraries were sequenced on NovaSeq 6000 at 600M Paired-end depth. This method demonstrates an overall concordance of inter-run and intra-run accuracy of variant detection to be 90% demonstrating that this method run as described produces highly repeatable and reproducible variant detection to sub-1% allele frequencies. The inter-run, lot-to-lot, and operator-to-operator variability was ≥99%. Down-sample analysis demonstrated high levels of assay performance with sample inputs of 30 ng with ≥96% sample passing Illumina cut-off metrics at 150M PE read depth as compared to Illumina recommended 420M PE reads. Taken together, we provide a high-volume automated solution for cfDNA extraction from plasma samples, additionally these data demonstrate a robust, reproducible, and highly accurate targeted DNA sequencing method that can be used for low allele frequency variant detection in cfDNA.

Citation Format: Nripesh Prasad, Rachel Rock, Rebecca Beatty, Melanie Robinson, Dineen Wildman, Michael Sykes, Boris Umylny, Thomas Halsey. Optimization of high-volume cell free DNA extraction and end-to-end automation for TSO 500 ctDNA library prep [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 2298.
Abstract 230: Deep learning embedding-based segmentation for morphological analysis in organoids
Authors: Sureshkumar Akash , Bisht Shilpa , Easwaran Hariharan
Published: March 2024

Background: The organoid model is a useful tool for modeling the cellular microenvironment of the organ from which they are derived. Organoids recapitulate the self-organization of heterogenous cell types and the microenvironment. Quantifying the morphological features of organoids can provide valuable insights into cellular organizational defects and growth characteristics, which can facilitate drug discovery. Measurement of these characteristics in live organoids can be performed quickly and easily directly in culture using widefield microscopy. The current state-of-the-art method to detect and identify the shape of individual organoids in brightfield images uses the U-Net Convolutional Neural Network (CNN) with a watershed transform to label pixels. However, this method yields jagged shape proposals and cannot detect overlapping regions. We propose the use of an embedding-based segmentation network based on the Branched ERF-Net to solve these issues.

Methods: Organoids were established from the proximal colon of BrafV600E heterozygous mice, and 50 phase-contrast images of the organoids were acquired at 2.5x and 4x magnification. Organoids present in acquired images were labeled manually. The network was trained on this collection of manually labeled images and validated on a separate validation dataset.

Results: The network accurately labels organoids. Overlapping organoids are segmented correctly and shape proposals are smoother. Detection of overlapping organoids with the Branched ERF-Net architecture yields an accurate organoid count, verified against manual counting. Smoother shape proposals also enable the use of convexity defects to measure organoid budding.

Conclusions: Deep-learning analysis of widefield images enables the rapid assessment of morphological characteristics, such as size, count, and budding, which are key to understanding proliferation and differentiation changes. The modified Branched ERF-Net architecture we propose for organoid segmentation is a robust and versatile method to quantify organoid morphology.

Citation Format: Akash Sureshkumar, Shilpa Bisht, Hariharan Easwaran. Deep learning embedding-based segmentation for morphological analysis in organoids [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 230.
Abstract 2351: Genomics annotation and interpretation in somatic oncology using structured data from a clinical knowledgebase
Authors: Li Jian , Niu Lili , krishna Shuba , Kinshuk Fnu , Jones Martin , Hernandez Carlos , Clark Michael , Balladares Sandra
Published: March 2024

Accurate and comprehensive interpretation of genomic variants has become a bottleneck in clinical sequencing applications due to the accelerating precision oncology and biomedical information explosion. This motivated us to build Ephesus, a framework enabling curation of predictive, prognostic and diagnostic evidence for clinical biomarkers in cancers. Currently Ephesus is the primary content source for Roche navify Mutation Profiler (nMP).

The Ephesus’ data model ensures adherence to best practices in clinical genomic content curation. Variant classification follows the AMP guidelines for somatic variant interpretation. Variant interpretations are derived from international regulatory approvals and clinical practice guidelines (FDA, EMA, TGA, eVIQ, etc.) and recommendations (NCCN, ESMO). The data model is mapped to a set of relational tables. To enforce data integrity and validity, strategies such as data normalization based on standard nomenclatural ontologies, a submit-review-approval workflow, and biological constraints are adopted. Ephesus is deployed as a web application used by curators inside and outside Roche. The UI allows users to conduct edits, filtering, sorting and bulk operations on entities by attributes. In order to minimize manual effort and maximize content coverage, inference rules are applied before ingesting into nMP.

Currently Ephesus is developed for data collection, browsing and summarizing primary entities such as biomarkers, evidence items, genes, variants, variant groups, and drugs. The content from the 2023-Aug snapshot contains 11,596 directly curated biomarker profiles (including biomarker combinations), and 6M+ expanded profiles for 41 major cancer types. To evaluate the clinical reporting value of the curated knowledge, ~160k real cancer patient samples of the AACR GENIE project were queried on Ephesus. Compared with three other major knowledgebases, Ephesus/NMP is observed showing the highest performance.

Table 1. Percentage of patients or biomarkers with at least one interpretation from each knowledgebase CGI (2022-10-17) CIVIC(2023-09-01) ClinVar(2023-09-09) NMP(2023-08-11) AACR-Genie-v14.0 Total patient % with any interpretation 25% (40,545) 46% (73,835) 81% (130,882) 89% (142,905) 160,965 biomarker % (including combos) with any interpretation 0.03% (256) 0.06% (526) 13.26% (122,424) 73.79% (681,128) 923,093

Citation Format: Jian Li, Lili Niu, Shuba krishna, Fnu Kinshuk, Martin Jones, Carlos Hernandez, Michael Clark, Sandra Balladares. Genomics annotation and interpretation in somatic oncology using structured data from a clinical knowledgebase [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 2351.
Abstract 2361: A PD1-antibody-attenuated IL-2 fusion protein activates immune cells leading to the inhibition of tumor growth in ex vivo human 3D tumor models
Authors: Satchi-Fainaro Ronit , Avramoff Opal , Katyal Anshika , Yeini Eilam , Krinsky Anne , Liubomirski Yulia , Dulberg Shai , Tiram Galia , Kaminitz Ayelet , Gill Jason , Pedersen Jessica , Bar-On Dana , Tamir Ayala , Ayton Paul , Taura Tetsuya , Wilson David , Madi Asaf
Published: March 2024

IL-2 has been prescribed to effectively treat malignancies, mainly melanoma, for decades. Its use has waned in recent years due to significant toxicity and a narrow therapeutic index. To overcome the limitations of systemic administration of IL-2, we have generated a modified IL-2 (IL2Att) with specific substitutions to reduce the binding affinity with the IL-2R. The attenuated cytokine was fused to a high-affinity anti-PD1 antibody that does not block PD-1 binding with its ligands (PD-L1 and PD-L2). The resulting antibody-cytokine fusion, anti-PD1-IL2Att, allows selective delivery of IL-2 to tumor-reactive PD1+ T cells, with limited potential to activate PD1− cells. To evaluate the effect of anti-PD1-IL2Att in a human tumor microenvironment (TME), we established a unique human 3D multi-cellular cancer system. This model system includes neoplastic and somatic cells that make up the TME, further supplemented with peripheral blood mononuclear cells (PBMC). We found that the anti-PD1-IL2Att reduced tumor cell survival more effectively in several types of these 3D cancer models (melanoma, glioblastoma, ovarian and colon cancer) than standard immune checkpoint inhibitors pembrolizumab or nivolumab. Combination treatments of anti-PD1-IL2Att with either of these agents resulted in improved immune activation and tumor cell killing. Our findings suggest that tumor-targeted attenuated cytokines such as IL-2 can promote robust tumor killing while minimizing systemic toxicity.

Citation Format: Ronit Satchi-Fainaro, Opal Avramoff, Anshika Katyal, Eilam Yeini, Anne Krinsky, Yulia Liubomirski, Shai Dulberg, Galia Tiram, Ayelet Kaminitz, Jason Gill, Jessica Pedersen, Dana Bar-On, Ayala Tamir, Paul Ayton, Tetsuya Taura, David Wilson, Asaf Madi. A PD1-antibody-attenuated IL-2 fusion protein activates immune cells leading to the inhibition of tumor growth in ex vivo human 3D tumor models [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 2361.
Abstract 2438: A retrospective pilot study to validate the utility of proteomic biomarkers in the blood for diagnosis of breast cancer
Authors: Jung So-Youn , Lee Eun-Gyeong , Han Jai Hong , Lee Seeyoun , Shin Soyeon , Lee Ju Yeon , Kim Sung-Soo , Kim Yumi , Noh Dong-Young
Published: March 2024

Background: Previously, three-protein signature (Mastocheck®, Bertis Inc.) from plasma has been launched to overcome the limitation of low accuracy of mammography. In addition, nine-protein signature from serum was newly developed to improve the accuracy of three-protein signature as a blood-based diagnostic tool. This study aimed to validate the diagnostic utility for breast cancer of nine-protein signature with comparison with three-protein signature.

Methods: A blood-based test using multiple reaction monitoring (MRM) by mass spectrometry to quantify nine proteins (APOC1, CHL1, FN1, VWF, PPBP, CLU, PRDX6, PRG4, and MMP9) in serum and three proteins (APOC1, CHL1, CA1; Mastocheck®) in plasma was investigated using blood of 30 health women and 30 breast cancer patients. Using the cut-off values confirmed by AI-based deep learning model, we evaluated the sensitivity, specificity, and accuracy of nine- and three-protein signature for detecting breast cancer.

Results: Among 60 cases, the sensitivity and specificity of nine-protein signature was 87.9% and 80.7% for diagnosis of breast cancer. These values were 20% and 10% higher than those of three-protein signature, respectively (66.7% of sensitivity and 70.0% of specificity). The accuracy of nine-and three-protein signature was 83.3% and 68.3%.

Conclusion: This study demonstrated that nine-protein signature could be a more accurate and effective tool for detecting breast cancer compare to three-protein signature). For a confirmatory study, we need to perform a large scaled validation study in future. Grants: This research was supported by Bertis, Republic of Korea (grant number: NCC 2341770-1)

Citation Format: So-Youn Jung, Eun-Gyeong Lee, Jai Hong Han, Seeyoun Lee, Soyeon Shin, Ju Yeon Lee, Sung-Soo Kim, Yumi Kim, Dong-Young Noh. A retrospective pilot study to validate the utility of proteomic biomarkers in the blood for diagnosis of breast 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 2438.
Abstract 2451: Investigation of SIRT6 usefulness as a novel biomarker for oral cancer
Authors: Yoshii Haruka , Shimoda Ami , Mitsudo Kenji , Kioi Mitomu
Published: March 2024

Introduction: SIRT6 is one of the seven human sirtuin genes and is known to function as an onco-suppressor gene in colorectal and ovarian cancers, although it is up-regulated in other cancers. Thus, SIRT6 is considered performing both tumor-suppressing and promoting roles. However, the association of SIRT6 with oral squamous cell carcinoma (OSCC) and its role in OSCC pathogenesis are currently unclear. Currently, SCC or CYFRA are used as a tumor marker to assist in the diagnosis of OSCC in a clinical setting whereas its sensitivity is low. Therefor the development of a novel biomarker for early diagnosis and identification of new therapeutic targets is critical to resolve the pressing clinical issues related to the management of OSCC. This study aimed to investigate the expression and the relevance of SIRT6 in patients with OSCC and its potential as a biomarker for early detection and prognosis prediction.

Materials and Methods: This study enrolled 78 patients with OSCC and 9 patients with carcinoma in situ (CIS). The OSCC patients had undergone surgery or chemoradiotherapy (51 surgery and 27 chemoradiotherapy). The CIS patients had undergone surgery. Samples were also obtained from 10 patients with oral potentially malignant disorders (OPMDs). Biopsied or surgical resected samples were used for the study. We obtained 21 noncancerous tissues as normal tissues from the adjacent noncancerous tissues after tumor resection. Immunohistochemistry, quantitative real-time RT-PCR, and microarray analyses were performed to determine SIRT6 expression and its association with clinicopathological features in OSCC, CIS, and OPMDs using clinical paraffin embedded specimens.

Results: SIRT6 mRNA levels were higher in OSCC tissues than those in noncancerous tissues (p<0.05). And SIRT6 protein expression levels were higher in OSCC, CIS and OPMDs tissues than those in noncancerous tissues (p<0.05). SIRT6 expression was predominant in patients aged ≥65 years and significantly correlated with shorten overall survival. In the microarray analysis, some SIRT6-associated genes, such as ANXA2 was significantly up-regulated, and PIGC and RGPD4 were down-regulated in OSCC.

Conclusion: SIRT6 plays a role in tumor homeostasis, leading to a poor prognosis in OSCC. SIRT6 may represent a novel target not only for the treatment, but also as a prognostic marker in OSCC.

Citation Format: Haruka Yoshii, Ami Shimoda, Kenji Mitsudo, Mitomu Kioi. Investigation of SIRT6 usefulness as a novel biomarker for oral 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 2451.
Abstract 2565: Vitamin D deficiency and outcomes in prostate cancer patients: A real-world database
Authors: Hart Lowell L. , Reeves James , Garofalo Stacey , Amick William
Published: March 2024

Introduction: Vitamin D is essential for many bodily functions, including bone health and the prevention of osteoporosis and rickets. In recent years, the importance of vitamin D metabolism in immune system regulation and cancer prevention has been studied with increased focus. With the advent of cancer immunotherapies this has become more important. Multiple recent publications document that vitamin D deficiency is prevalent in cancer patients. This has also been observed specifically in prostate cancer patients, with a high percentage of these deficient patients being of African- American ancestry. It has been theorized that high levels of vitamin D deficiency among African American prostate cancer patients could contribute to worse cancer outcomes and increased health disparities. However, routine vitamin D testing has not been commonly performed in the oncologic community. We hypothesized that deficient levels of vitamin D could lead to inferior prostate cancer outcomes in men with a wide range of ethnic and socio-economic backgrounds. In this project we recorded vitamin D levels in prostate cancer patients at a large community oncology group and evaluated them by stage, pathologic data, survival, race/ethnicity, and other clinical features.

Methods: This study is a retrospective, observational study of the data from the electronic medical records of patients with prostate cancer who received vitamin D level testing at Florida Cancer Specialists & Research Institute from 2008- 2023, throughout the state of Florida. All data used in this study will constitute secondary data, it will have been collected originally for clinical use in the general oncology practice setting. No date parameters or patient limits will be applied to this study, and all eligible patients are included.

Results: 451 patients with prostate cancer had determination of vitamin D levels, out of a total of 27,772 prostate cancer patients in the database. 38% of the prostate cancer patients analyzed had low 25-OH vitamin D levels (<32 ng/ml). Patients with low vitamin D levels had an average Gleason score of 7.46. Patients with low vitamin D levels who died had an average survival of 144 months. Patients with low vitamin D levels who presented with localized disease had a 35% chance of eventually developing castrate-resistant disease. 45% of the low vitamin D group developed metastatic disease during their course of treatment. Further comparisons of vitamin D levels with pathologic data, survival/longevity, race/ethnicity, and clinical course will be evaluated and presented.

Citation Format: Lowell L. Hart, James Reeves, Stacey Garofalo, William Amick. Vitamin D deficiency and outcomes in prostate cancer patients: A real-world database [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 2565.
Abstract 2580: Targeting chromatin in ovarian cancer stem cells
Authors: Wang Yinu , Frederick Jane , Zhang Yaqi , Bartom Elizabeth Thomas , Bauer Greta , Tanner Edward , Backman Vadim , Matei Daniela
Published: March 2024

The dynamic organization of chromatin, governed by epigenetic modifiers, critically regulates cell plasticity and determines cell fate in both normal and malignant stem cells. We hypothesized that chromatin architecture plays a role in regulating transcriptional heterogeneity in ovarian cancer stem cells (OCSCs) to maintain stemness and chemoresistance. PWS microscopy showed that ALDH+ OCSCs derived displayed higher nuclear fractal dimension D signals (P<0.05) than ALDH- non-OCSCs, indicating that chromatin in OCSCs possesses higher packing compared to non-OCSCs. Cut & TAG Sequencing showed that of the 3606-histone repressive H3K27m3 enriched regions (P<0.05, fold change >2), 3208 were detected in OCSCs while 398 peaks were present in non-OCSCs, consistent with findings supporting high D features in OCSCs. The active mark H3K4me3 was enriched at the promoter of stemness-associated genes, including SOX2, ALDH1A3, and FZD7 in OCSCs; and the repressive histone mark H3K27me3 was enriched at the promoter of the epithelial cell marker CDH1 in OCSCs. These results support that the chromatin of OCSCs contains open genomic regions, corresponding to stemness-associated genes and repressed regions associated with genes related to differentiation. RNA sequencing indicated that the coefficient of variance (COV) reflecting transcriptional heterogeneity in OCSCs was higher than in non-OCSCs at baseline. In response to platinum, genes with low baseline expression in OCSCs were most upregulated, supporting increased transcriptional heterogeneity in response to chemotherapy. Inhibitors of epigenetic modifiers (DNMTi, EZH2i, and Dot1Li) induced chromatin re-organization in OCSCs and promoted OCSCs transition toward differentiation, supporting that stemness-associated chromatin structure is targetable. We demonstrated that a Dot1L inhibitor (Dot1Li) targeted OCSCs by decreasing chromatin packing D, resulting in decreased transcriptional heterogeneity. In conclusion, OCSCs harbor highly packed chromatin, contributing to chemoresistance and cell plasticity. Epigenetic modifiers (such as Dot1Li) inhibit stemness by regulating chromatin organization and transcriptional malleability.

Citation Format: Yinu Wang, Jane Frederick, Yaqi Zhang, Elizabeth Thomas Bartom, Greta Bauer, Edward Tanner, Vadim Backman, Daniela Matei. Targeting chromatin in ovarian cancer stem cells [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 2580.
Abstract 2621: Preclinical Efficacy of DM002, a bispecific HER3 × MUC1 antibody-drug conjugate with a novel DNA topoisomerase I inhibitor, in solid tumor models
Authors: Zhang Yifu , Shang Chengzhang , Wang Nannan , An Gao , Guo Chaoshe , An W. Frank , Yang Yi
Published: March 2024

MUC1 is a known tumor-associated antigen (TAA), but previous anti-MUC1 agents have shown limited clinical efficacy due to neutralization by the soluble N-terminal autoproteolytic product of MUC1. More recently, HER3-targeted ADCs, such as Patritumab deruxtecan, have shown encouraging early clinical activity in a variety of tumors. However, the majority of patients did not exhibit response to paritumab deruxtecan treatment. Therefore, improved therapies targeting these TAAs are needed.

As HER3 and MUC1 are co-expressed in a wide range of cancer types, we hypothesized that simultaneous targeting of HER3 and MUC1 with a bispecific antibody-drug conjugate (bsADC) could potentially lead to increased efficacy, reduced resistance and improved safety in the clinical setting. We generated an anti-HER3 × MUC1 bispecific antibody using the fully human common light chain antibody transgenic mice (RenLite®).

The HER3 × MUC1 bsAb showed improved cell binding and internalization in vitro compared to the parental mAb, suggesting synergy between the two arms. We then conjugated the HER3xMUC1 bsAb with vcMMAE for proof-of-concept studies, or with our novel DNA topoisomerase I inhibitor linker/payload conjugates (BLD1102) to make DM002-BLD1102 bsADC. Both bsADCs potently inhibited the growth of HER3+MUC1+ PDX tumors. DM002-vcMMAE also showed greater in vivo efficacy than its parental mAb ADCs, consistent with their in vitro internalization activity. DM002-BLD1102 also showed strong anti-tumor activity in DM002-vcMMAE resistant PDX models, suggesting the superiority of this new DNA topoisomerase I inhibitor linker/payload over the classical vcMMAE linker/payload. In conclusion, the HER3 × MUC1 bsAb is a promising agent for the treatment of HER3 and MUC1 positive tumors.

Citation Format: Yifu Zhang, Chengzhang Shang, Nannan Wang, Gao An, Chaoshe Guo, W. Frank An, Yi Yang. Preclinical Efficacy of DM002, a bispecific HER3 × MUC1 antibody-drug conjugate with a novel DNA topoisomerase I inhibitor, in solid tumor models [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 2621.
Abstract 2635: An epigenetic regulation targeting inhibitory receptors and attenuates CD8 T cell exhaustion in breast cancer
Authors: Lin You-Zhe , Wu Wan-Rong , Chung Feng-Chi , Shen Yi-Chun , Lee Chuan-Chun , Li Hong-Wei , Lin Guang-Jan , Chengx Wei-Chung , Wang Shao-Chun
Published: March 2024

T cell exhaustion is a state of dysfunctional T cell response characterized by prolonged antigen exposure and diminished effector functions, a significant cause of tumor tolerance, and poor response to immune checkpoint blockade (ICB) therapy. T cell exhaustion is a highly dynamic process involved with a network of genetic and epigenetic regulation that program the T cell functions. Epigenetic regulation by microRNAs targets multiple genes involved in T cell function and is expected to be a major contributor to the functional programming of tumor-associated T cells. However, the underlying causal mechanisms remain to be determined. Here, we show that the microRNA miR-379-5p is a critical epigenetic regulator for promoting T cell function and suppressing exhaustion induced by chronic stimulation. The microRNA is identified by integrating bioinformatic interrogation of the miRNA databases cross-referencing with the TCGA database for genes involved in T cell functioning and their correlation with clinical outcomes, coupled with molecular profiling of miRNAs in experimental T exhaustion. Notably, the expression levels of miR-379-5p in tumor tissues, which encompass cancer cells and the surrounding stromal components, including immune cells, are closely associated with favorable prognosis of various cancer types. Further molecular and cellular characterization of miR-379-5p entailing cell culture, animal models, and patient-derived tumor organoids shows that it exerts suppressive effects by targeting specific sequences in the 3’ untranslated region (UTR) of critical immune checkpoint genes in T cells, thereby enhances the effector functions of cytotoxic T cells for tumor clearance. Ectopic expression of miR-379-5p shifts the evolution of primary T cells toward memory-like effector cells while silencing miR-379-5p induces exhaustion and abrogates the cytotoxic activity of primary T cells. We further demonstrate that transcriptional downregulation of miR-379-5p in T cells by a nuclear receptor transcription factor which is responsible for initiating the exhausting process impairs the tumor suppression function of T cells. Our studies indicate that miR-379-5p can function as a tumor suppressor by protecting T cells from exhaustion and bears the potential for developing novel strategies to improve the response to ICB therapy in breast cancer.

Citation Format: You-Zhe Lin, Wan-Rong Wu, Feng-Chi Chung, Yi-Chun Shen, Chuan-Chun Lee, Hong-Wei Li, Guang-Jan Lin, Wei-Chung Chengx, Shao-Chun Wang. An epigenetic regulation targeting inhibitory receptors and attenuates CD8 T cell exhaustion in breast 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 2635.
Abstract 2656: The selective IKZF2 molecular glue degrader, PVTX-405, counters Treg immune suppression,shows significant tumor growth delay as single agent and synergistic response with immune checkpoint therapies (ICTs)
Authors: Dhruv Harshil D. , McEachern Donna , Bai Longchuan , Zhang Xuqing , Chen Zhixiang , Nagilla Rakesh , Behshad Elham , Han Bomie , Orth Peter , Rej Rohan , Kirchhoff Paul , Shin Niu , Jolivette Larry , Strickland Corey , Sui Zhihua , Priestley Scott , Wang Shaomeng , Mohammad Helai
Published: March 2024

Immunosuppressive regulatory T-cells (Tregs) are key modulators of tumor immune evasion and resistance to immune checkpoint therapies (ICTs). IKZF2 (Helios) is a transcription factor that is selectively expressed by Treg and has been shown to be essential for maintaining function and stability of Tregs in the face of inflammatory conditions that include autoimmune disease as well as cancer. Here we describe the discovery of PVTX-405, a potent and selective IKZF2 molecular glue degrader (DC50=6.3 nM). Our molecular glue degrader promotes a productive ternary complex with the E3 ubiquitin ligase substrate receptor cereblon (CRBN) to selectively degrade IKZF2 while sparing other CRBN neosubstrates (IKZF1/3, GSPT1, CK1a). PVTX-405 demonstrates rapid and selective degradation of IKZF2 in Jurkat cells in vitro, human PBMC derived Tregs ex vivo, and in cynomolgus monkeys in vivo. Degradation of IKZF2 in Jurkat cells leads to dose dependent increase in production of inflammatory cytokine IL-2. In ex vivo co-cultures of Tregs and effector T-cells, PVTX-405 reduces the suppressive activity of Tregs. To determine whether the relief of Treg suppressive activity observed in vitro and ex vivo can translate to anti-tumor activity in vivo we utilized CRBNI391V(humanized CRBN) mice. We developed a novel MC38 syngeneic tumor model to test both monotherapy and combination efficacy in an immune-competent setting. Once daily oral administration of PVTX-405 as single agent significantly delays the growth of MC38 tumors. Further, in vivo treatment of PVTX-405 in combination with ICTs, anti-PD1 or anti-LAG3, significantly increased animal survival and led to durable tumor regressions compared to ICTs alone. Together, these results demonstrate a strong synergy between ICTs and Treg destabilization through pharmacological degradation of IKZF2 and represent a promising combination strategy for treatment of cancer.

Citation Format: Harshil D. Dhruv, Donna McEachern, Longchuan Bai, Xuqing Zhang, Zhixiang Chen, Rakesh Nagilla, Elham Behshad, Bomie Han, Peter Orth, Rohan Rej, Paul Kirchhoff, Niu Shin, Larry Jolivette, Corey Strickland, Zhihua Sui, Scott Priestley, Shaomeng Wang, Helai Mohammad. The selective IKZF2 molecular glue degrader, PVTX-405, counters Treg immune suppression,shows significant tumor growth delay as single agent and synergistic response with immune checkpoint therapies (ICTs) [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 2656.
Abstract 2679: Myeloid olfactory receptors in melanoma
Authors: Benson Elayne M. , Ley Klaus , Orecchioni Marco , Hedrick Catherine C.
Published: March 2024

Olfactory receptors are commonly found in the nasal cavity and function to detectodorants. However, very recent studies have determined that innate immune cells,including monocytes and macrophages, express olfactory receptors. OLFR2 (OR6A2 inhumans), was recently linked to atherosclerosis development through interaction with itsligand, octanal. Increased levels of octanal are considered as a risk factor foratherosclerosis. Conversely, octanal levels are associated with lower cancer incidence,suggesting that OLFR2 may play a protective role in cancer. Indeed, data from TheCancer Genome Atlas for liver and brain cancers show that OLFR2 expression isassociated with increased patient survival. Here, we utilized an orthotopic melanomamouse model using B16 cancer cells in C57/BL6 mice that had been transplanted witheither wild type or OLFR2 knockout bone marrow to directly test the role of OLFR2 onimmune cells in regulating tumor growth. We found that hematopoietic deletion of OLFR2exacerbated melanoma tumor growth in these mice; again, supporting the notion thatOLFR2 is anti-tumoral. The OLFR2+ cells present in the tumor were myeloid cells.Monocytes, non-classical monocytes specifically, function to detect cancer cells in tumorseeding sites, and recruit NK cells for tumor cell destruction. OLFR2-deficientmacrophages were found to migrate less to tumor cells in an in vitro assay, suggestingthat OLFR2 is involved in the sensing of newly seeding tumor cells, likely through sensingoctanal. Studies are ongoing to determine the exact functions of OLFR2+ monocytes andmacrophages in the tumor microenvironment. OLFR2 may be one of several olfactoryreceptors that is utilized by myeloid cells as a defense mechanism for detection of newlyseeding or metastatic tumor cells. As olfactory receptors are easily druggable targets,understanding their role in cancer prevention could lead to emerging newimmunotherapies for cancer.

Citation Format: Elayne M. Benson, Klaus Ley, Marco Orecchioni, Catherine C. Hedrick. Myeloid olfactory receptors in melanoma [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 2679.
Abstract 2684: Pan-cancer neutrophil profiling illuminates anti-tumor antigen-presenting potency
Authors: Wu Ying Cheng , Ma Jiaqiang , Gao Qiang
Published: March 2024

Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing functions across cancer types. However, given their short half-life and fragile proliferation, it remains challenging to explore how neutrophils adapt to specific fates in cancer. Here we generated and integrated single-cell neutrophil transcriptomes from 17 cancer types (225 samples, 143 patients). Neutrophils exhibited extraordinary complexity, with 10 distinct cell states along differentiation paths including inflammation, angiogenesis, and antigen presentation. Notably, the antigen-presenting program was associated with favorable survival in most cancers and could be evoked by leucine metabolism and subsequent histone H3K27ac modification. These neutrophils could further invoke both (neo)antigen-specific and antigen-independent T-cell responses. Neutrophil delivery or leucine diet fine-tuned the immune balance to boost anti-PD-1 therapy in various murine cancers. In summary, these data not only unravel the neutrophil divergence across cancers, but also offer therapeutic opportunities such as antigen-presenting neutrophil delivery.

Citation Format: Ying Cheng Wu, Jiaqiang Ma, Qiang Gao. Pan-cancer neutrophil profiling illuminates anti-tumor antigen-presenting potency [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 2684.
Abstract 2765: Novel WNT-RIP1-GDF15 pathway promotes migration and invasion of colorectal cancer cells
Authors: Kang A-Ram , Kim Do Hoon , Park Jong Kuk
Published: March 2024

Growth-differentiation factor 15 (GDF15) is a member of the transforming growth factor β (TGF-β) family protein, also known as NSAID-activated gene 1 (NAG-1) or macrophage inhibitory cytokine 1 (MIC-1), and is a major cause of cancer cachexia, cardiovascular disease, and various inflammatory diseases. Roles of GDF15 as major inflammatory response factor also have been demonstrated in animal models, and it has also showed various malignant functions such as regulating metabolism, promoting metastasis by inducing EMT in cancer. Here, we revealed a novel potential role for RIP1 in colorectal cancer (CRC) in enhancing metastasis by controlling WNT-RIP1-GDF15 signaling. We showed that WNT3A treatment increased the expression of GDF15 and GFRAL. Immunohistochemical analysis of human CRC tissue arrays consisting of primary cancer and metastatic cancer also confirmed that the expression of GDF15 and GFRAL was increased in metastatic cancer. Human XL cytokine assay, western blot, and ELISA results confirmed that GDF15 expression was reduced in cell lines in which RIP1 was knocked down. Reduction of GDF15 expression and secretion by RIP1 knockdown showed suppression of EMT induction resulting to decrease of migration and invasion of CRC cells. Taken together, these results suggest a novel EMT-enhancing role for RIP1 in the WNT pathway and suggest a novel WNT-RIP1-GDF15 pathway contributing to CRC malignancy by promoting EMT.

Citation Format: A-Ram Kang, Do Hoon Kim, Jong Kuk Park. Novel WNT-RIP1-GDF15 pathway promotes migration and invasion of colorectal cancer cells [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 2765.
Abstract 2767: Exploring ADAR1 dependencies in breast cancer brain-metastases
Authors: Sposito Teresa , Klacking Emma E. , Ruiz Antonio W. , Pham Jessica , Jamieson Catriona
Published: March 2024

Background: Adenosine deaminase acting on double-stranded RNA (ADAR1) is a recognized driver of epitranscriptomic (post-transcriptional) remodeling and tumor progression. Changes in amino acid sequence, mRNA splicing, and/or polyadenylation sites are only some of the adenosine-to-inosine (A-to-I) RNA editing effects. Under physiological conditions, ADAR1 activity prevents autoinflammation by inhibiting the accumulation of endogenous immunostimulatory double-stranded RNA and by suppressing the Z-RNA sensor ZBP1. Such mechanisms are exploited by cancer cells to desensitize tumor response to therapies, therefore augmenting aggressiveness. Approximately 10 to 20% of patients diagnosed with breast cancer (BC) will develop metastatic disease, which remains the leading cause of death in individuals with BC. We have hypothesized that ADAR1 and its interferon-inducible p150 isoform, play a pivotal role in promoting BC metastases since high levels of ADAR1 are associated with a worse prognosis in patients with high grade BC, especially in the triple-negative BC subgroup (TNBC), which is the most likely to develop brain metastases.

Methods: We established a humanized mouse model of breast cancer brain metastases (BC-BrM) using neonatal intracerebroventricular inoculation of MDA-MD-231 TNBC cells and primary patient derived metastatic cells in Rag2−/−γc−/− mice. Before implantation, MDA-MD-231 cells were transduced with a nanoluc-GFP reporter for tracing ADAR1 enzymatic activity in the brain metastatic niche. Lentiviral shRNA knockdown vectors targeting ADAR1, combined with over-expression vectors of full-length ADAR1 or the p150 deleted isoform were adopted to detect editing changes in the metastatic model through RNA-sequencing of BC-BrM.

Results: BrM derived from MDA-MD-231 implants display upregulation of ADAR1 p150 and activation of the WNT/β-catenin pathway compared to the non-implanted cell lines. Upon shRNA knockdown of ADAR1, decreased expression of BC stem cell markers was detected via FACS in MDA-MD-231 ADAR1 knocked-down versus control BC-BrM isolated cells. We are now exploring molecular pathways affected by ADAR1 loss/overexpression in establishing BrM.

Future Directions: We have developed a biorepository of primary patient-derived metastatic breast cancer samples and have begun the process of tracking metastatic kinetics and ADAR1 activation with the ADAR1 reporter in an orthotopic mouse model. Overall, this study will provide new insights into the molecular role of ADAR1 deaminase activity in establishing and maintaining metastatic niches.

Citation Format: Teresa Sposito, Emma E. Klacking, Antonio W. Ruiz, Jessica Pham, Catriona Jamieson. Exploring ADAR1 dependencies in breast cancer brain-metastases [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 2767.