tbuckley/cabot-search huggingface dataset:
Abstract 1534: The tumor immune microenvironment at different stages of non-small cell lung cancer
Authors: Mackenzie Hansen, Qin Zhou, Yoko S. DeRose, Magdalena Kovacsovics, Benjamin Brintz, Benjamin L. Witt, Kim L. O'Neill, Siwen Hu-Lieskovan
Journal: Cancer Research (2024)

Abstract Introduction: To better understand the immune microenvironment in non-small cell lung cancer (NSCLC), we evaluated immune cell populations within the tumor parenchyma and their interaction at the periphery of the tumors at different stages of disease. Methods: 27 whole tumor slides were collected from NSCLC patients of all stages after surgical resection. Tissue slides were stained with multiplex Opal immunofluorescence for CD8, CD68, CK, PD-1, PD-L1, FoxP3, and DAPI using a Leica Bond automated stainer. Slides were scanned at 20x magnification by Akoya Polaris whole slide scanner and spectrally unmixed. Spatial analyses were performed on the HALO software. Results: Density of CD8 T cells, T regulatory (Treg) cells, and macrophages were significantly higher (p=0.001) in the interface region compared to the tumor and stroma. There is abundant CD8 T cell infiltration in the tumor at early stage I and this decreased significantly (p=0.05) at higher stages. PD-1− CD8 T cells significantly dropped with higher stage, while PD-1+ CD8 T cells did not. On the other hand, macrophage infiltration increased as stage increased, with most of the increase driven by PD-L1− macrophages. No statistically significant trends were observed in Treg cells across stages, but they appeared to be higher in stage II. No differences in immune infiltration were observed between the NSCLC subtypes adenocarcinoma and squamous cell carcinoma. No correlation was found between proximity of immune cell subsets to tumor cells and stage. Conclusion: The tumor microenvironment in NSCLC is rich in CD8+ cells at early stage and their density decreases as the stage of the disease increases, while macrophage infiltration increases as the disease stage progresses. Citation Format: Mackenzie Hansen, Qin Zhou, Yoko S. DeRose, Magdalena Kovacsovics, Benjamin Brintz, Benjamin L. Witt, Kim L. O'Neill, Siwen Hu-Lieskovan. The tumor immune microenvironment at different stages of 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 1534.
Abstract 1291: ASPIRE: Advocates and Scientists Partner in Research Education
Authors: Laurie Betts, Jennifer Potter, Veronica Carlisle, Patricia A. Spears
Journal: Cancer Research (2024)

Abstract UNC Lineberger Comprehensive Cancer Center (LCCC) has a robust and growing cancer patient advocacy community. UNC Lineberger is the flagship publicly funded comprehensive cancer center in North Carolina. We are constantly looking for ways to educate patient and community advocates on recent advances in cancer biology research and clinical trials. Our advocates are also valuable partners for our basic and clinical researchers that may be early in their career. We developed and implemented an inaugural research education program for new advocates. We model this program partly on the highly successful and popular AACR Scientist Survivor Program that recently celebrated it’s 25th anniversary. Some of the UNC LCCC advocates participate in the SSP and were motivated to develop our own local program. We will showcase our pilot 2024 ASPIRE education program that brings together cancer patient and community advocates and cancer researchers to learn from each other. The basic itinerary of the ASPIRE program is: 1.Three separate one-hour online presentations by UNC Lineberger researchers with a patient advocate moderator. The topics covered are: Cancer 101 : cancer biology, diagnosis, staging, treatment. Clinical Trials 101: clinical trials, phases, patient protection, progress with for example accrual of representative populations. Research 101: bench research, bioinformatic, AI, how research works and how it may lead to new treatments. To showcase a tissue donation program being developed by UNC Patient Advocates that will benefit researchers. 2.The lecture series is followed by a breakfast roundtable discussion for all the participants to discuss their experiences. There will be short presentations and discussions in small groups of researchers and cancer patient advocates. We will summarize our ASPIRE pilot experience, how our participation in the SSP program motivated this local program, and how we plan to incorporate feedback from participants to inform future programs. We hope this will lead to more informed patient advocates that can then be even more powerful in research advocacy. Citation Format: Laurie Betts, Jennifer Potter, Veronica Carlisle, Patricia A. Spears. ASPIRE: Advocates and Scientists Partner in Research Education [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 1291.
Abstract 2800: Shotgun metagenomics of COPD-associated lung cancer tissue microbiome
Authors: Atsushi Matsuoka, Kazuhiko Shien, Shuta Tomida, Daisuke Mizuno, Masayoshi Ohki, Ryo Yoshichika, Tomohiro Higashihara, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Ken Suzawa, Hiromasa Yamamoto, Shinichi Toyooka
Journal: Cancer Research (2024)

Abstract The gut microbiome plays a crucial role in the development of multiple chronic diseases. Several solid tumors including lung cancer are also implicated in the gut microbiome in cancer initiation and progression, possibly affecting signaling pathways in the tumor microenvironment. However, the microbiome in the peripheral lung tissue is unexplored and their relationship to the lung tumor microenvironment is still unknown. Thus, to explore the relationship between the microbiome and the tumor microenvironment of lung cancer, we performed shotgun metagenomic sequencing of the lung cancer tissue, especially in lung cancer patients accompanied by chronic obstructive pulmonary disease (COPD). We confirmed the presence of a diverse microbiome in peripheral lung cancer tissue. Next, we focused on individual species. We observed significant differences in the relative abundance of several species between COPD and non-COPD patients, and cancer and non-cancer tissue. Then, we focused on the metagenomic diversity between samples. The number of species in COPD patients and cancer tissue were decreased. And the bacterial total abundance in each sample were observed similar trend. On the other hand, alpha diversity in each sample were showed different trend to them. In the analysis of beta diversity using Principal Coordinate Analysis (PCoA), clusters were formed in each group. These findings suggest that microbiome imbalance known as dysbiosis in the peripheral lung tissue may affect the tumor microenvironment resulting in cancer progression. Citation Format: Atsushi Matsuoka, Kazuhiko Shien, Shuta Tomida, Daisuke Mizuno, Masayoshi Ohki, Ryo Yoshichika, Tomohiro Higashihara, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Ken Suzawa, Hiromasa Yamamoto, Shinichi Toyooka. Shotgun metagenomics of COPD-associated lung cancer tissue microbiome [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 2800.
Abstract 4468: Elucidating the phosphoinositide-modulatory function of INPP5B in regulating cancer stemness and tumorigenesis in liver cancer
Authors: Linglin Liu, Yifei Wang, Yunong Xie, Man Tong
Journal: Cancer Research (2024)

Abstract Hepatocellular carcinoma (HCC) represents a major global health challenge, characterized by its heterogeneity and aggressive nature. Solid evidence has now suggested that tumor growth is driven by subpopulations of tumor cells with less differentiated cell states, called cancer stem cells (CSCs), which govern therapeutic resistance and tumor recurrence. Therefore, characterization of CSCs and their associated oncogenic signaling pathways is crucial to the development of more specific and sensitive HCC prognostic markers and to the design of novel targeted therapies against CSCs for HCC treatment. In search of the altered genes and pathways that are tightly associated with cancer stemness trait in HCC, we exploited the stemness and oncogenic dedifferentiation signature to mine the HCC dataset of the Cancer Genome Atlas. Phosphoinositide signaling was identified to be enriched and downregulated in the transcriptomes of HCC patients with strong stemness and dedifferentiated signature. Subsequent clinical correlation analysis found inositol polyphosphate-5-phosphatase B (INPP5B) to be the top downregulated gene in phosphoinositide signaling with its expression correlated with poor survival in HCC patients. Functional studies showed that INPP5B overexpression reversed the oncogenic and stemness properties while INPP5B knockout promoted tumor growth in immunocompetent mice. Subsequent RNA sequencing and molecular assays revealed INPP5B deregulation to be associated with lipid metabolism remodeling. Collectively, our results suggest an intricate relationship between phosphoinositide signaling and lipid metabolism through the regulation of INPP5B in HCC. The findings may open new avenue for future research aimed at devising targeted therapies to interfere with liver CSCs and enhance the prognosis of HCC patients. Citation Format: Linglin Liu, Yifei Wang, Yunong Xie, Man Tong. Elucidating the phosphoinositide-modulatory function of INPP5B in regulating cancer stemness and tumorigenesis in liver 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 4468.
Abstract 5813: AI-driven identification and validation of novel synthetic lethal gene pairs through deep mining of cancer dependency data
Authors: Daniel S. Miller, Oliver Vipond, Alfie Brennan, Anna Hercot
Journal: Cancer Research (2024)

Abstract The targeting of synthetic lethal (SL) gene pairs is emerging as a new paradigm in precision oncology, with the potential to deliver treatments with higher efficacy and fewer side-effects. However, existing approaches have focused on a few well-validated pairs, and there is a clear need to expand the toolbox of potential SL targets. We have performed deep mining of cancer dependency data using a suite of machine learning tools and AI algorithms underpinned by robust statistical analysis to identify the next generation of SL gene pairs. To ensure robust, high confidence validation of multiple SL pairs simultaneously, we have used three cell lines and orthogonal assay formats. This has led to the confirmation of new druggable SL genes suitable for clinical development. We have identified the cancer subtypes with the strongest evidence of SL vulnerabilities and quantified patient populations who would most benefit from novel therapeutic agents. For one gene pair, we have generated novel best-in-class inhibitors of the target of interest, with exceptional selectivity over the SL partner, and used these chemical tools to validate the SL relationship in 2D and 3D models. Citation Format: Daniel S. Miller, Oliver Vipond, Alfie Brennan, Anna Hercot. AI-driven identification and validation of novel synthetic lethal gene pairs through deep mining of cancer dependency data [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 5813.
Abstract 1952: Co-alterations in <i>PIK3CA</i> and ARID1A lead to enhanced sensitivity to PI3K inhibition
Authors: Shirsa Udgata, Jordan N. Stoecker, Anna L. Lippert, Cheri A. Pasch, Dustin A. Deming
Journal: Cancer Research (2024)

Abstract Background: There is increasing interest in developing precision medicine strategies for cancers with PIK3CA mutations. Co-alterations in PIK3CA and ARID1A (AD) occur in ~1% of all cancers. Previously, patients with co-alterations in PIK3CA and AD have shown both an improved objective response rate and improved progression free survival following copanlisib (cop) treatment compared to cancers with PIK3CA mutations and wild-type AD. Here we evaluate potential mechanisms for this enhanced clinical benefit. Methods: AD was knocked out in SW48 and SW48PIK3CA-H1047R (SW48PK) human 2D colorectal cancer cell lines using CRISPR (SW48AD; SW48PKAD). Knockouts were confirmed using PCR genotyping, amplicon sequencing, and western blot (WB). A cell proliferation assay (WST-1) was performed at increasing doses of cop for 48hrs to determine cell viability. WBs were performed at 6hrs and 24hrs after cop treatment to determine levels of phosphorylation of AKT, S6, and 4EBP1 and levels of apoptosis-related proteins (MCL-1, BCL-xL, BCL-2, PARP). Athymic nude mice were flank injected with SW48PK and SW48PKAD and treated with cop (10mg/kg in PEG400/acidified water (0.1N HCl, pH 3.5; 20/80, v/v) or vehicle for 25 days or until moribund. Results: WST-1 assay showed highest sensitivity to cop in SW48PKAD cells compared to SW48, SW48PK and SW48AD. At 10nM (p=0.01), there was a significant difference in cell viability between SW48PK and SW48PKAD. No significant difference was seen in the phosphorylation (p) of AKT, S6, or 4EBP1 between SW48PK and SW48PKAD. Expression of MCL-1 protein decreased in SW48PKAD compared to SW48PK. No difference was seen in levels of BCL-xL and BCL-2. On treatment with cop, there was a greater reduction in pS6 in SW48PKAD at 24 hours compared to SW48PK, but no significant difference in pAKT and p4EBP1. There was a gradual increase in MCL-1, BCL-xL, and cleaved PARP in SW48PKAD overtime following cop treatment compared to SW48PK. In vivo, untreated SW48PKAD tumors grew more quickly than the SW48PK tumors (8-fold increase in tumor size in SW48PKAD compared to 5-fold increase in SW48PK by day 25, p=0.06). SW48PKAD mice had significant tumor reduction (p=0.002) on cop treatment by day 25; however, SW48PK mice did not. Conclusions: ARID1A loss along with PIK3CA mutation leads to greater PI3K inhibition response most likely due to enhanced induction of apoptosis. Further confirmation of this enhanced sensitivity is required with better in vitro models such as patient-derived cancer organoids. Citation Format: Shirsa Udgata, Jordan N. Stoecker, Anna L. Lippert, Cheri A. Pasch, Dustin A. Deming. Co-alterations in PIK3CA and ARID1A lead to enhanced sensitivity to PI3K inhibition [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 1952.
Abstract 5797: Next generation antibody drug conjugates: Multi-payload conjugates targeting multiple mechanisms of cell killing
Authors: Richard L. Kendall, Marco Lobba, Saurabh Johri, Chanez Symister, Devin Trinter, Maxwell Nguyen, Daniel Gutierrez, Samantha Brady, Andrew Lau, Matthew B. Francis
Journal: Cancer Research (2024)

Abstract Introduction: ADCs have had tremendous impact on patient outcomes in breast cancer and are now second line therapy for stage IV HER2 positive metastatic breast cancer. However, many patients fail to respond or relapse after treatment with ADC therapies due to tumor heterogeneity and resistance to ADC payloads. We are developing next generation ADCs that deliver targeted combination chemotherapies with a single molecule. Method: CatenaBio has developed a novel system capable of attaching distinct payloads at different sites to the same antibody, enabling the production of highly stable single-molecule targeted combination therapies, Multi-Payload-Conjugates (MPCs), with a well-defined drug-antibody ratio (DAR). Results: We screened combinations of different payloads targeting several different mechanisms of cell division attached to trastuzumab at different DARs to optimize tumor cell killing. These targeted combination ADCs demonstrated robust killing in both HER2 high and low tumor cell lines. Additionally, these novel MPCs show potent inhibition of tumor growth in a HER2+ xenograft model of cancer. Conclusion: Antibody Drug Conjugates have revolutionized the treatment of high HER2 positive breast cancer. More recently advances have been made in the design of ADCs to expand indications to include HER2 low as well as HER2 negative patients. Multi-payload Conjugates® offer the next step in ADC design and allow for the combination of multiple mechanisms of action in a single MPC that are highly effective across multiple breast cancer cell lines and HER2 expression levels. These molecules offer the potential to circumvent tumor resistance pathways and deliver deeper and more durable responses. Citation Format: Richard L. Kendall, Marco Lobba, Saurabh Johri, Chanez Symister, Devin Trinter, Maxwell Nguyen, Daniel Gutierrez, Samantha Brady, Andrew Lau, Matthew B. Francis. Next generation antibody drug conjugates: Multi-payload conjugates targeting multiple mechanisms of cell killing [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 5797.
Abstract 58: Immunocytokines with specificity for invariant region of CAR molecules enhance effector function of multiple CAR T cell therapies
Authors: J T. Keane, Oula K. Dagher, Fang Liu, Avery D. Posey
Journal: Cancer Research (2024)

Abstract The effector functions of CAR T cells can be enhanced through delivery of immunostimulatory cytokines, such as IL-12, IL-18, or IL-23. However, systemic delivery of recombinant cytokines or paracrine secretion by CAR T cells can elicit toxicities due to non-specific targeting of the cytokines. Here, we designed immunocytokines with antibodies specific for the invariant linker peptides that join variable domains in the CAR scFv and immunostimulatory cytokines. The immunocytokines were capable of targeting CAR molecules agnostic of target antigen, demonstrating broad applicability without the need for further genetic engineering of CAR therapies, such as co-expression of a surrogate molecule (tEGFR, etc.). The addition of immunocytokines enhanced CAR T cell cytolytic activity and secretion of type I cytokines, even at low concentrations of immunocytokine. In a stringent Nalm6 xenograft model, the addition of immunocytokines delivering IL-12 enhanced the anti-tumor activity of anti-CD19 CAR T cells and overall survival compared to controls of antibody alone or PBS. This technological development presents the opportunity to specifically enhance the activity of multiple CAR T cell therapies in the absence of non-specific toxicities. Citation Format: J T. Keane, Oula K. Dagher, Fang Liu, Avery D. Posey. Immunocytokines with specificity for invariant region of CAR molecules enhance effector function of multiple CAR T cell therapies [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 58.
Abstract 1292: ProTALKS: A community outreach project founded by a graduate of the CaRE2 Community Scientist Research Advocacy training program, Mrs. Lynn Jones-Turpin
Authors: Lynn Jones-Turpin, Ileana Guzman, Brooke Hensel, Fern Webb
Journal: Cancer Research (2024)

Abstract ProTALKS was created and led by a community member committed to reducing prostate cancer health disparities. ProTALKS stands for Prostate Cancer Outreach, Opinions, and Opportunities and is designed to increase awareness of prostate cancer prevention, research, and treatment as well as highlight the health disparities observed in Black communities. According to the Florida Department of Health, prostate cancer incidence and mortality rates among Black men living in Duval County are higher compared to men of other races and ethnicities. Therefore, there is a need for programs like ProTALKS that focus on early detection strategies and promoting community resources. In collaboration with the Prostate Health Education Network (PHEN), The American Legion Post 197, and Florida Blue, ProTALKS has increased access to services such as prostate cancer screening and evidence-based information. Community events implemented by ProTALKS bring together oncologists, researchers, key community leaders, health educators, and providers to educate and promote positive health behavior changes among high-risk communities. In addition to hosting health fairs, ProTalks has hosted grilling competitions and community awareness walks to further educate the community about prostate cancer prevention, screening, and research. ProTALKS also shares information through the local newspaper, The Jacksonville Free Press, The Lynn &amp; Friends radio show, and social media platforms. Since its start in 2021, with support from the Florida-California Cancer Research, Education, and Engagement (CaRE2) Health Equity Center, ProTALKS has implemented more than 10 community events with over 1,000 community members from Jacksonville, Florida. ProTALKS, in collaboration with CaRE2, continues to disseminate information about cancer screening, the importance of clinical trial participation, and donating biospecimens for cancer research. Although ProTALKS has been successful in its mission, there have been challenges throughout its implementation. For example, one challenge has been increasing the number of community members attending events and using appropriate marketing techniques to promote ProTALKS’ activities. Future implications to avoid challenges include recruiting more volunteers, and partnering with other community organizations in Duval County. Citation Format: Lynn Jones-Turpin, Ileana Guzman, Brooke Hensel, Fern Webb. ProTALKS: A community outreach project founded by a graduate of the CaRE2 Community Scientist Research Advocacy training program, Mrs. Lynn Jones-Turpin [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 1292.