tbuckley/cabot-search huggingface dataset:
Abstract 2194: Association of metabolic syndrome conditions with risk of second primary cancer of any organ in breast cancer survivors
Authors: Amrita Mukherjee, Zheng Gu, Lie Hong Chen, Arnold L. Potosky, Reina Haque
Journal: Cancer Research (2024)

Abstract Purpose: Breast cancer survivors are at increased risk of developing second primary cancers; however, factors attributing to increased risk of second primary cancer in breast cancer survivors are under-studied. We evaluated the association of metabolic syndrome conditions with second primary cancer of any organ in breast cancer survivors. Methods: In this retrospective cohort study, we included 37,222 patients diagnosed with breast cancer between 2008-2020 at Kaiser Permanente Southern California (KPSC), an integrated healthcare system. We extracted data on cancer-related variables, sociodemographic and clinical variables from KPSC’s cancer registry and electronic health records. Among the metabolic conditions, we identified diabetes, hypertension, and dyslipidemia using ICD-10 diagnosis codes at or 1-year prior to breast cancer diagnosis; obesity was based on body mass index (BMI≥30kg/m2). We included metabolic syndrome as a categorical variable: 0, 1-2, and 3+ metabolic conditions. We followed patients electronically from breast cancer diagnosis until patients developed second primary cancer of any organ, died, disenrolled from the health plan, or reached study’s end (12/31/2021), whichever occurred first. Proportional hazards regression was used to report association [HR (95%CI)] between metabolic conditions and any second primary cancer. Results: During a median (IQR) follow-up of 5.17 (2.75-8.58) years, 1701 (4.6%) patients developed any second primary cancer. More than half (53.1%) of the breast cancer survivors had 1-2 metabolic conditions at baseline; 19.4% had 3+ metabolic conditions, and the rest 27.5% did not have any metabolic condition. Hypertension was the most common metabolic condition (45.5%), followed by obesity (38.9%), dyslipidemia (36.5%), and diabetes (19.0%). Survivors with 0 and 1-2 metabolic conditions were 35% and 19% less likely to develop any second primary cancer than survivors with 3+ metabolic conditions, respectively [crude HR (95%CI): 0.65 (0.57-0.75) and 0.81 (0.72-0.91), respectively]. Reduced risk in survivors with 1-2 metabolic conditions persisted adjusting for age, race and ethnicity, breast cancer diagnosis year, breast tumor SEER summary stage, breast tumor estrogen-progesterone status, smoking status, and breast tumor treatment [adjusted HR (95%CI): 0.87 (0.77-0.99)]. Conclusion: Risk of second primary cancer of any organ was elevated in breast cancer survivors with three or more metabolic conditions. Citation Format: Amrita Mukherjee, Zheng Gu, Lie Hong Chen, Arnold L. Potosky, Reina Haque. Association of metabolic syndrome conditions with risk of second primary cancer of any organ in breast cancer survivors [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 2194.
Abstract 1397: Metabolic CRISPR-Cas9 screening identifies loss of mitochondria<i>Gene M</i>in triple-negative breast cancer to promote lung metastasis via immune modulation
Authors: Shu-Ting Chou, Xiaoyong Wang, Deanna N. Edwards, Jin Chen
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer (TNBC) is a heterogenous breast cancer characterized by an aggressive phenotype and high risk of metastatic occurrence. Metastasis is a multifaceted process that involves metabolic reprogramming, selection, and adaptation. Although studies have shown that alterations of metabolic processes can influence TNBC phenotype and sensitivity to treatments, less is known about how changes in metabolic enzymes in the tumor cells affect crosstalk between tumor and immune cells during metastasis. Here, we performed a high-throughput CRISPR-Cas9 screening of metabolic genes in an orthotopic basal-like mammary carcinoma 4T1 mouse model to identify key metabolic enzymes in the tumor cells that are associated with TNBC lung metastasis by affecting the tumor microenvironment (TME). The CRISPR-Cas9 screening showed an enrichment of sgRNA for mitochondria Gene M in the metastasized lungs of wild-type mice but not Rag1−/− mice, indicating that loss of Gene M could modulate adaptive immune cells in the TME or distant organs to promote 4T1 lung metastasis. Further pilot experiments revealed that loss of Gene M in 4T1 cells increased murine basal-like carcinoma lung metastasis in vivo and decreased population of B cells, CD4+ T cells, M2 macrophages, monocytes, and CXCR2+ neutrophils in the metastasized lungs without affecting the growth rate of the primary tumors. Overall, our preliminary results demonstrated that Gene M deficiency in 4T1 cells affects immune cell profile and drives lung metastasis of murine basal-like carcinoma cells, but the molecular and cellular mechanisms by which loss of Gene M grant tumor cells with metastatic advantage requires further investigation. Citation Format: Shu-Ting Chou, Xiaoyong Wang, Deanna N. Edwards, Jin Chen. Metabolic CRISPR-Cas9 screening identifies loss of mitochondriaGene Min triple-negative breast cancer to promote lung metastasis via immune modulation [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 1397.
Abstract 3774: Evaluation of FibraChek™ for non-invasive detection of hepatic fibrosis and hepatocellular carcinoma
Authors: Sunao Tanaka, Guoxiang Xie, Hideki Furuya, Wei Jia, Charles J. Rosser
Journal: Cancer Research (2024)

Abstract Introduction and Objectives: The incidence of hepatocellular carcinoma (HCC) has almost tripled since the early 1980s in the United States where it is the fastest rising cause of cancer-related deaths. Advanced liver fibrosis and cirrhosis are ones of major risk factors for HCC. The recent evidence demonstrates that successfully treating the cause of early to moderate hepatic fibrosis may reverse most. For this reason, detecting hepatic fibrosis in an early stage is crucial. Liver biopsy is currently the gold standard for the assessment of hepatic fibrosis in clinical practice. Thus, there is an urgent clinical need for the development of non-invasive blood-based tests because of its ease of obtaining biological material. Previously, we developed FibraChek™, non-invasive blood-based tests. In this study, we tested the performance of FibraChek™ on detecting hepatic fibrosis and HCC in the US. Methods: The performance of FibraChek™ was evaluated in a single-institutional cohort of 14 prospectively collected subjects presenting for chronic liver disease (NAFLD/NASH) patients with hepatic fibrosis, 19 prospectively collected subjects diagnosed with HCC, and 12 prospectively collected controls from the US. The algorithm uses weighted value of the 5 biomarkers: AST, ALT, Platelet, Taurocholic Acid (TCA) &amp; Tyrosine plus age to derive a risk score. The ability of the test to identify patients harboring hepatic fibrosis or HCC was assessed. Hepatic fibrosis status was confirmed by tissue biopsy or definitive surgery. Diagnostic performance was assessed using AUC. Results: FibraChek™ provided an AUC of 0.923 with an overall sensitivity of 93.9%, specificity of 81.8%, NPV 91.2% and PPV 81.8%. Interestingly, risk scores in HCC cohort indicated higher than those in patients with hepatic fibrosis. Thus, FibraChek™ may be also able to use for HCC detection. Conclusions: Serum levels of a biomarker panel enabled the accurate discrimination of hepatic fibrosis and controls. The FibraChek™ test can achieve the easy, efficient, and accurate detection of hepatic fibrosis and HCC in a non-invasive patient setting. Citation Format: Sunao Tanaka, Guoxiang Xie, Hideki Furuya, Wei Jia, Charles J. Rosser. Evaluation of FibraChek™ for non-invasive detection of hepatic fibrosis and hepatocellular carcinoma [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 3774.
Abstract 5504: Integrating ultrahigh-plex spatial phenotyping: From discovery to clinical applications
Authors: Aditya Pratapa, Ning Ma, Niyati Jhaveri
Journal: Cancer Research (2024)

Abstract Background The journey from discovering predictive spatial biomarkers (known as spatial signatures) for immunotherapy responses to their clinical application necessitates a cohesive approach bridging ultrahigh-plex discovery experiments with high-throughput translational studies. This study focuses on integrating Akoya Biosciences spatial multiplexed imaging technologies with advanced data analysis techniques for comprehensive spatial phenotyping across the discovery-to-clinical continuum. Methods Human formalin-fixed, paraffin-embedded (FFPE) cancer tissues were profiled using ultrahigh-plex PhenoCode™ Discovery panels to examine cell lineage, immune activation, and checkpoint markers via the PhenoCycler®-Fusion spatial biology platform. The subsequent use of PhenoCode™ Signature panels targeted specific biomarkers of immune profile, immune contexture, tumor-infiltrating lymphocytes (TIL), macrophage polarization, and T cell status via the PhenoImager® HT platform. Open-source whole slide image analysis software QuPath was employed for precise image analysis, including ROI segmentation, cell detection, classification, exploration of spatial interactions, and identification of distinct spatial signatures. Results Our analysis revealed distinct spatial relationships within various tumor types, quantifying immune cell distributions and their interactions. The ultrahigh-plex data correlated with high-throughput signature panel analyses, thus paving a new simplified way for targeted identification and development of predictive spatial signatures for immunotherapy outcomes. Conclusions The combined use of ultrahigh-plex discovery panels, high-throughput signature panels, and deep-learning image analysis provides a comprehensive understanding of cellular interactions in the tumor microenvironment. This integrated approach, utilizing Akoya's end-to-end workflows, accelerates the identification of predictive spatial biomarker signatures across various human tissue samples. Citation Format: Aditya Pratapa, Ning Ma, Niyati Jhaveri. Integrating ultrahigh-plex spatial phenotyping: From discovery to clinical applications [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 5504.
Abstract 3074: Regulating lactate levels in triple negative breast cancer presents a promising avenue for therapeutic intervention
Authors: Chandra Prakash Prasad, Sheikh Mohammad Umar, Arundhathi Dev J. R., Akanksha Kashyap, Meetu Rathee
Journal: Cancer Research (2024)

Abstract Introduction: Among all subtypes of breast cancer, triple-negative breast cancer (TNBC) is associated with the most unfavorable prognosis, emphasizing the critical need to pinpoint therapeutic targets tailored to TNBCs. Lactate, produced as a by-product of aerobic glycolysis, acts as an oncometabolite and plays a substantial role in promoting tumor aggressiveness, particularly in TNBCs. In our ongoing laboratory investigations, we are actively exploring strategies to mitigate the influence of lactate on TNBCs. Methods: The experiments utilized two triple-negative breast cancer (TNBC) cell lines, i.e., MDA-MB231 and MDA-MB468. The inhibitors employed in this study are FOXY5, XAV939, PFK15, and Quercetin. Protein expression was examined using Western blotting and Immunofluorescence assays. Trans-well and wound healing assays were employed to assess cell migration and invasion. Colony formation assays (CFU) were utilized to investigate stem cell potential and proliferation. In vivo experiments were conducted using 4T1-orthotopic Balb/c mice. Results: Using triple-negative breast cancer (TNBC) cells, we have demonstrated the pivotal role of the WNT/β-catenin signaling pathway in promoting the generation of extracellular lactate, thus driving the progression and metastasis of TNBCs. Additionally, we have shown that inhibiting lactate production in TNBC cells, and consequently impeding cell migration and invasion, can be achieved by using recombinant WNT5A or its mimicking hexa-peptide FOXY5. Similarly, employing a β-catenin inhibitor such as XAV939 can yield comparable outcomes in relation to TNBC cells. In an alternative approach, we conducted inhibition experiments targeting PFKFB3 (6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase), a key regulator of aerobic glycolysis in cancer cells. Our findings indicate that a combined approach involving siPFKL and iPFKFB3 is more promising in suppressing lactate production in TNBCs when compared to the effects of individual iPFKFB3 treatment. Conclusions: Our present investigations suggest that employing inhibitors targeting the WNT/β-catenin signaling pathway, PFKP, and PFKEB3 could be a promising therapeutic strategy to effectively reduce lactate levels in TNBCs. Citation Format: Chandra Prakash Prasad, Sheikh Mohammad Umar, Arundhathi Dev J. R., Akanksha Kashyap, Meetu Rathee. Regulating lactate levels in triple negative breast cancer presents a promising avenue for therapeutic intervention [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 3074.
Abstract 2745: Sequential tracking of PD-L1 expression on circulating epithelial tumor cells (CETCs) in men with primary non-metastatic prostate cancer
Authors: Dorothea Schott, Monika Pizon, Ulrich Pachmann, Katharina Pachmann, Matthias Mäurer
Journal: Cancer Research (2024)

Abstract Background: Radiotherapy (RT) is an essential component of multimodality therapy in the primary or postoperative treatment of prostate cancer with curative intent by preventing local recurrence and distant metastases, indicating its impact on residual occult tumor, such as circulating tumor cells. Immunogenic changes in cancer cells induced by RT can lead to adaptive up-regulation of PD-L1 expression. As immune checkpoint inhibition plays an increasingly important role in prostate cancer, radiogenic PD-L1 upregulation may be of therapeutic importance. The aim of this study was to determine PD-L1 status on CETCs before and during RT. Methods: Peripheral blood samples were collected from 52 primary non-metastatic prostate cancer patients. CETCs were enumerated and analyzed for PDL-L1 expression prior to (baseline), 3 and 6 weeks after the start of RT using fluorescence scanning microscopy. Results: PD-L1 expression was detectable in CETCs and localized in the membrane and/or cytoplasm. We found a correlation between PD-L1 status in CETCs and aggressiveness of cancer disease prior to RT. The frequency of PD-L1 positive CETCs depended on the grading and Gleason score of the primary tumor. Patients with a high Gleason score and G3 tumors had significantly more PD-L1 positive CETCs compared to patients with a low Gleason Score and G1 tumors. Moreover, patients in stage I/II had significantly less PD-L1 positive CETCs compared to patients in stage III/IV (mean 54.25 vs. mean 69.65; p&amp;lt;0.05). A higher number of PD-L1 positive CETCs were detected in patients who had radical prostatectomy before start of RT than in those who had no surgical intervention (mean 66.24 vs. mean 47.46; p&amp;lt;0.01). Interestingly, the fraction of PD-L1 positive CETCs decreased significantly during RT only in patients with G3 tumors and a high Gleason Score. Conclusion: Our results indicated that PD-L1 in CETCs is closely related to the aggressiveness of the primary tumor and may be a co-factor associated with the progression of prostate cancer. PD-1/PD-L1 blockade combined with RT represents a novel and promising treatment strategy that could contribute to improve the treatment efficacy of prostate cancer. Citation Format: Dorothea Schott, Monika Pizon, Ulrich Pachmann, Katharina Pachmann, Matthias Mäurer. Sequential tracking of PD-L1 expression on circulating epithelial tumor cells (CETCs) in men with primary non-metastatic prostate 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 2745.
Prevalence estimates of tuberculosis infection in adults in Denmark: a retrospective nationwide register-based cross-sectional study, 2010 to 2018
Authors: Anne Ahrens Østergaard, Troels Lillebaek, Inge Petersen, Andreas Fløe, Eliza H Worren Bøkan, Ole Hilberg, Inge K Holden, Lone Larsen, Ada Colic, Christian Wejse, Pernille Ravn, Bente Mertz Nørgård, Stephanie Bjerrum, Isik Somuncu Johansen
Journal: Eurosurveillance (2024)

BackgroundTuberculosis (TB) elimination requires identifying and treating persons with TB infection (TBI).AimWe estimate the prevalence of positive interferon gamma release assay (IGRA) tests (including TB) and TBI (excluding TB) in Denmark based on TBI screening data from patients with inflammatory bowel disease (IBD) or inflammatory rheumatic disease (IRD).MethodsUsing nationwide Danish registries, we included all patients with IBD or IRD with an IGRA test performed between 2010 and 2018. We estimated the prevalence of TBI and positive IGRA with 95% confidence intervals (CI) in adolescents and adults aged 15-64 years after sample weighting adjusting for distortions in the sample from the background population of Denmark for sex, age group and TB incidence rates (IR) in country of birth.ResultsIn 13,574 patients with IBD or IRD, 12,892 IGRA tests (95.0%) were negative, 461 (3.4%) were positive and 221 (1.6%) were indeterminate, resulting in a weighted TBI prevalence of 3.2% (95% CI: 2.9-3.5) and weighted positive IGRA prevalence of 3.8% (95% CI: 3.5-4.2) among adults aged 15-64 years in the background population of Denmark. Unweighted TBI prevalence increased with age and birthplace in countries with a TB IR higher than 10/100,000 population.ConclusionEstimated TBI prevalence is low in Denmark. We estimate that 200,000 persons have TBI and thus are at risk of developing TB. Screening for TBI and preventive treatment, especially in persons born in high TB incidence countries or immunosuppressed, are crucial to reduce the risk of and eliminate TB.
Abstract 4908: Comprehensive tool for pan-cancer consensus data mining of drugs, targets and biomarkers
Authors: Sukjoon Yoon
Journal: Cancer Research (2024)

Abstract The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the discovery of drug targets and biomarkers. For this purpose, we have developed a convenient tool, Q-omics software, for general researchers and cancer scientists to carry out customized data mining without bioinformatics background. Q-omics provides a comprehensive interface and smart functions for facilitating pan cancer-wide association studies on mutations, RNA expression, protein abundance, shRNA/CRISPR efficacy, drugs, tumor-infiltrating cells, patient survival, clinical info. etc. Furthermore, consensus scores on associated data pairs from heterogeneous samples, help to predict the reproducibility of data mining results. Q-omics (download: http://qomics.io) improves the utility of cancer omics big data for non-computational scientists at all levels of cancer research. Citation Format: Sukjoon Yoon. Comprehensive tool for pan-cancer consensus data mining of drugs, targets and biomarkers [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 4908.
Abstract 6574: UCHL1 is a molecular indicator and a therapeutic target for neuroendocrine carcinomas
Authors: Shiqin Liu, Timothy Chai, Fernando Marques, Qingqing Yin, En-Chi Hsu, Michelle Shen, Angus Toland, Abel Bermudez, Alifiani B. Hartono, Christopher F. Massey, Chung S. Lee, Liwei Zheng, Maya Baron, Caden J. Denning, Merve Aslan, Holly Nguyen, Rosalie Nolley, Amina Zoubeidi, Millie Das, Christian Kunder, Brooke Howitt, H Tom Soh, Irving L. Weissman, Michael A. Liss, Arnold I. Chin, James D. Brooks, Eva Corey, Sharon Pitteri, Jiaoti Huang, Tanya Ivanova Stoyanova
Journal: Cancer Research (2024)

Abstract Neuroendocrine carcinomas, such as neuroendocrine prostate cancer (NEPC), small cell lung cancer (SCLC), and neuroblastoma, share common histological features, including expression of neuroendocrine markers, rapid relapse after treatment, and poor prognosis. Due to the poor clinical outcome of patients with neuroendocrine carcinomas, there is a critical need to identify new drivers, therapeutic targets, and effective therapeutic strategies for these malignancies. Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a protease that has a dual function in regulating protein stability. We demonstrated that UCHL1 is significantly elevated in tissues from patients with NEPC, SCLC, and neuroblastoma. Loss of UCHL1 decreases tumor growth and inhibits metastasis of these malignancies. UCHL1 maintains neuroendocrine differentiation and promotes cancer progression by regulating nucleoporin, POM121, and p53. UCHL1 binds, deubiquitinates, and stabilizes POM121 to regulate POM121-associated nuclear transport of key transcriptional factors, E2F1 and c-MYC. Conversely, UCHL1 binds p53 and promotes p53 degradation. Importantly, treatment with UCHL1 inhibitors significantly reduces tumor growth and metastasis of neuroendocrine carcinomas. The combination of UCHL1 inhibitors with cisplatin, the standard of care used for neuroendocrine carcinomas, halts tumor growth in pre-clinical settings. Our study reveals new mechanisms of UCHL1 function in neuroendocrine carcinomas tumorigenesis and identifies UCHL1 as a therapeutic target and potential molecular indicator for diagnosis and monitoring treatment responses in neuroendocrine carcinomas. Citation Format: Shiqin Liu, Timothy Chai, Fernando Marques, Qingqing Yin, En-Chi Hsu, Michelle Shen, Angus Toland, Abel Bermudez, Alifiani B. Hartono, Christopher F. Massey, Chung S. Lee, Liwei Zheng, Maya Baron, Caden J. Denning, Merve Aslan, Holly Nguyen, Rosalie Nolley, Amina Zoubeidi, Millie Das, Christian Kunder, Brooke Howitt, H Tom Soh, Irving L. Weissman, Michael A. Liss, Arnold I. Chin, James D. Brooks, Eva Corey, Sharon Pitteri, Jiaoti Huang, Tanya Ivanova Stoyanova. UCHL1 is a molecular indicator and a therapeutic target for neuroendocrine carcinomas [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 6574.