tbuckley/cabot-search huggingface dataset:
Abstract 4429: Plasma metabolic profiles in association with subsequent risk of colorectal cancer in the UK Biobank cohort
Authors: Fangcheng Yuan, Guochong Jia, Wanqing Wen, Wei Zheng
Journal: Cancer Research (2024)

Abstract Background: Dysregulation of metabolic processes contributes to colorectal cancer (CRC) etiology. We aimed to comprehensively evaluate the prospective associations between pre-diagnostic metabolic biomarkers and CRC risk in 230,420 UK Biobank participants. Methods: A total of 249 metabolic biomarkers were measured by nuclear magnetic resonance spectroscopy from baseline plasma samples. Cox proportional hazard models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the associations of metabolic biomarkers with CRC risk after adjusting for potential confounders. Subgroup analyses were performed by sex and CRC subsites (i.e., proximal colon, distal colon, rectum). We also conducted factor analyses to identify latent factors and examined their associations with CRC risk. Results: During a median follow-up time of 9.7 years, 2,410 incident primary CRC cases were identified after excluding participants diagnosed with CRC within two years after blood collection. After correcting for multiple testing, 50 metabolic biomarkers, including lipids and lipoproteins, fatty acids, ketone bodies, and inflammation, were significantly associated with incident CRC risk. No statistically significant differences were observed for the biomarker-CRC associations by sex and CRC subsite. In the sensitivity analysis, excluding cholesterol-lowering medication users did not alter the main findings. In factor analyses, we identified a significant association of CRC risk (HR = 1.08; 95% CI = 1.04-1.13; P-value = 6.89×10-5) with a metabolite pattern which was positively correlated with triglycerides and inversely correlated with relative concentrations of omega-6 fatty acids and polyunsaturated fatty acids. Conclusion: We identified multiple metabolic biomarkers and a metabolite pattern associated with CRC risk in a large prospective cohort. These findings suggest lipid metabolism may contribute to carcinogenesis of the colorectum. Citation Format: Fangcheng Yuan, Guochong Jia, Wanqing Wen, Wei Zheng. Plasma metabolic profiles in association with subsequent risk of colorectal cancer in the UK Biobank cohort [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 4429.
Abstract 4631: Evaluation of the impact of homozygous MTAP truncations on the activity and selectivity of MTA-cooperative PRMT5 inhibitors
Authors: Matthew R. Tonini, Andre A. Mignault, Douglas A. Whittington, Steven A. Lombardo, Binzhang Shen, Hannah Stowe, Satoshi Yoda, Shangtao Liu, Minjie Zhang, Kevin M. Cottrell, Samuel R. Meier, Heidi Rego, Jennifer Morawiak, Ellen Hooper, Yi Yu, Heather DiBenedetto, Adam S. Crystal, None Teng, Kimberly Briggs
Journal: Cancer Research (2024)

Abstract Homozygous deletion of the MTAP gene occurs in 10-15% of all human cancers. To benefit this large and diverse patient population, MTA-cooperative PRMT5 inhibitors, including TNG908 and TNG462, have been developed to leverage the synthetic lethal relationship between MTAP deletion and PRMT5 inhibition. MTA-cooperative PRMT5 inhibitors selectively bind the PRMT5-MTA complex driving selective inhibition of PRMT5 in MTAP-deleted cancers while sparing normal, MTAP-proficient cells. Our PRMT5 inhibitors are currently in Phase I/II clinical trials (NCT05275478 and NCT05732831), and eligibility is restricted to patients with tumors with confirmed MTAP loss either detected by next-generation sequencing (NGS) or immunohistochemistry. MTAP gene loss occurs in cancers because of its chromosomal proximity to one of the most common genetically altered tumor suppressor genes, CDKN2A, but the chromosomal 9p breakpoints for the co-deletion are not uniform. Indeed, while clinical NGS testing and preclinical data confirm that homozygous intragenic MTAP breakpoints occur, the functional consequence of any given breakpoint on MTAP enzymatic activity and protein function remains unknown. Given the potential implications for homozygous intragenic MTAP deletions to impact the clinical response to MTA-cooperative PRMT5 inhibitors, we have started to evaluate the loss-of-function phenotype of various MTAP truncations to determine whether they retain MTAP activity. Here, we present our initial functional genomics analysis of this important diagnostic biomarker using in vitro cDNA reconstitution approaches for MTAP activity combined with analysis of PRMT5 inhibitor sensitivity. Ultimately, these data may help refine patient enrollment on clinical trials to drive the maximum benefit for patients with MTAP-deleted cancers. Citation Format: Matthew R. Tonini, Andre A. Mignault, Douglas A. Whittington, Steven A. Lombardo, Binzhang Shen, Hannah Stowe, Satoshi Yoda, Shangtao Liu, Minjie Zhang, Kevin M. Cottrell, Samuel R. Meier, Heidi Rego, Jennifer Morawiak, Ellen Hooper, Yi Yu, Heather DiBenedetto, Adam S. Crystal, Teng, Kimberly Briggs. Evaluation of the impact of homozygous MTAP truncations on the activity and selectivity of MTA-cooperative PRMT5 inhibitors [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 4631.
Abstract 28: A CRISPR/Cas9 screening platform ImmuT Finder® enables in vivo T cell functional screening and identification of potent immunoregulatory targets for next-generation T cell therapy
Authors: Jingwei Sun, Jiahui Jin, Jingman Wang, Yao Sheng, Fei Li, Lingyun Chen, Yongchao Tan, Zhao Xu, Yanbin Liu, Ke Liu, Yarong Liu
Journal: Cancer Research (2024)

Abstract Insufficient tumor infiltration and the presence of various immunosuppressive mechanisms in tumor microenvironment (TME) are two major challenges compromising the anti-tumor efficacy of T cell therapy post infusion. PD-1/PD-L1 blockade has been proven to benefit a portion of late-stage solid tumor patients, however KO of PD-1 may impact the long-term persistence of CAR-T cells, indicating target selection strategies for gene editing of cell therapy products may differ from antibody drugs. To discover potent and/or novel immunoregulatory targets that could maximize the function of T cell therapy, we established an in vivo CRISPR/Cas9 screening platform, ImmuT Finder®, to identify functional gene targets in primary mouse T cells. Notably, T cells carrying sgRNA library have been collected at different harvest time points post transfer based on different screening purposes; library size has been rationally designed to ensure good coverage of the whole library in harvest samples. We selected top targets from in vivo screening and quickly validated their function in primary human T cells in a 96-well array. Then, the top targets that showed significant enhancement in proliferation and function of human T cells were further selected, and their combinational effects on human peripheral T cells and TIL were tested both in vitro and in vivo. Finally, GT307 stands out as the most potent KO combination, which significantly improves serial tumor killing of TCR-T and CAR-T as well as autologous tumor cytotoxicity of TIL in vitro. Furthermore, GT307 KO TCR-T and TIL demonstrated significantly improved tumor control in mouse models than their unedited counterparts and promoted long-term persistence with low support of IL-2. In summary, these data demonstrated that our ImmuT Finder® platform enables discovery of potent and/or novel targets for the development of T cell product and supports the clinical assessment of GT307 as a next-generation T cell therapy. Citation Format: Jingwei Sun, Jiahui Jin, Jingman Wang, Yao Sheng, Fei Li, Lingyun Chen, Yongchao Tan, Zhao Xu, Yanbin Liu, Ke Liu, Yarong Liu. A CRISPR/Cas9 screening platform ImmuT Finder® enables in vivo T cell functional screening and identification of potent immunoregulatory targets for next-generation T cell therapy [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 28.
Abstract 5667: Intratumoral heterogeneity in gastric cancer related with survival and tumor microenvironment
Authors: Do-eon Gu, Woo Sun Kwon, Sun Young Rha, Woong-Yang Park
Journal: Cancer Research (2024)

Abstract Gastric cancer (GC), often diagnosed at an advanced stage, poses a significant therapeutic challenge due to its resistance to treatment. The understanding of intratumoral heterogeneity, crucial for tumor cell survival, remains limited in GC. We conducted a comprehensive analysis of three patient groups (intraperitoneal metastasis [IM], hematogenous metastasis [HM], and both metastasis [HIM]) undergoing immunotherapy (IO) and chemotherapy. Utilizing single-cell RNA sequencing and TCR sequencing, we examined 11 adjacent normal, 10 HM, 8 IM, and 5 HIM primary GC samples. In epithelial cells, three distinct tumor clusters (Tumor_1, Tumor_2, and Tumor_3) were identified. Trajectory analysis revealed the differentiation of chief cells into Tumor_1, subsequently dividing into more malignant cell types, Tumor_2 and Tumor_3. Tumor_2 was enriched in IM, while Tumor_1 was enriched in HM and HIM. Patients grouped by Tumor_1, 2, 3 levels showed varying survival outcomes. Surprisingly, high Tumor_2 levels correlated with increased survival, attributed to elevated HLA and PDL1 expression, promoting immune cell recruitment and robust response to IO therapy. Conversely, Tumor_3 high patients exhibited worse survival, with enrichment in metabolic pathways associated with glycolysis and hypoxia, linking to metastasis. We observed the proportion of T cells that increased presence of CD8 effector cells among patients exhibiting high levels of Tumor_1 and Tumor_2. Through TCR analysis, we found heightened clonality in both CD8 effector cells and exhausted T cells in patients with elevated Tumor_1 and Tumor_2 levels. This suggests that the activated CD8 effector T cells in these patients may enhance their ability to effectively target and attack cancer cells. In summary, this study provides a comprehensive picture of intratumoral heterogeneity in GC can impact the survival and tumor microenvironment. The unexpected high survival in Tumor_2 patients emphasizes the potential of targeting specific pathways for improved therapeutic outcomes. Additionally, the observed T cell dynamics and clonality in Tumor_1 and 2 underscore the importance of understanding the immune microenvironment for effective cancer attack. Citation Format: Do-eon Gu, Woo Sun Kwon, Sun Young Rha, Woong-Yang Park. Intratumoral heterogeneity in gastric cancer related with survival and tumor microenvironment [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 5667.
Abstract 3020: The tumor suppressive role of methylthioadenosine phosphorylase in melanoma
Authors: Jennifer J. Hsiao, Pedro Andreu-Perez, Lajos V. Kemény, Miroslav Hejna, Jérémie Nsengimana, Jennifer Allouche, Abdullah Al Emran, D. Timothy Bishop, Göran B. Jönsson, Julia Newton-Bishop, Jun Song, David E. Fisher
Journal: Cancer Research (2024)

Abstract Methylthioadenosine phosphorylase (MTAP) is an enzyme that is expressed in virtually all tissues but lost in many cancers. MTAP deficiency can be due to either deletion of the MTAP gene or methylation of the MTAP promoter. In normal cells, MTAP catalyzes the conversion of methylthioadenosine (MTA), produced during polyamine biosynthesis, to adenine and 5-methylthioribose-1-phosphate, which is subsequently converted to methionine. MTAP deficiency results in intracellular accumulation of MTA. Although recent genome wide association studies (GWAS) have associated the MTAP locus with melanoma risk, the molecular mechanisms linking MTAP loss to increased tumorigenesis are not yet fully understood. In this study, we hypothesized that loss of MTAP and the resulting accumulation of MTA would dysregulate microphthalmia transcription factor (MITF), a master transcriptional regulator of melanocytes that is also an amplified or mutated oncogene in melanoma. We identify a novel signaling mechanism in which MTA accumulation from MTAP deficiency aberrantly induces MITF expression via inhibition of the cAMP phosphodiesterase PDE4D3 in melanocytes. Inhibition of PKA abolishes this MITF induction, suggesting that the PKA pathway is hyperactivated upon MTAP deficiency. Downregulation of MTAP leads to increased proliferation of melanoma cells in vitro and increased melanoma tumor growth in vivo. We also show that MTAP deficient melanoma cells are more resistant to the BRAF inhibitor vemurafenib and observe MTAP downregulation in BRAF inhibitor resistant melanoma clinical specimens. Furthermore, MTAP downregulation via decreased expression and/or genomic loss corresponds to significantly worse outcomes in early-stage cutaneous melanomas from multiple datasets, thereby identifying a clinically important sub-category of “thin-lethal” tumors. Citation Format: Jennifer J. Hsiao, Pedro Andreu-Perez, Lajos V. Kemény, Miroslav Hejna, Jérémie Nsengimana, Jennifer Allouche, Abdullah Al Emran, D. Timothy Bishop, Göran B. Jönsson, Julia Newton-Bishop, Jun Song, David E. Fisher. The tumor suppressive role of methylthioadenosine phosphorylase 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 3020.
Abstract 3811: Impact of antiviral treatment status on risk of extrahepatic cancers in patients with chronic hepatitis C
Authors: Menghua Tao, Jia Li, Trueman Wu, Stuart C. Gordon, Loralee B. Rupp, Sheri Trudeau, Scott D. Holmberg, Anne C. Moorman, Philip R. Spradling, Eyasu H. Teshale, Mark A. Schmidt, Yihe G. Daida, Mei Lu
Journal: Cancer Research (2024)

Abstract Background: Eradiation of hepatitis C virus (HCV) infection has been shown to reduce risk of liver cancer among HCV patients; however, there has been spare data on the effect of antiviral treatment on the risk of extrahepatic cancers. Using data from the Chronic Hepatitis Cohort Study (CHeCS), we investigated whether antiviral therapy impacts the risk of extrahepatic cancers among patients with HCV. Methods: 17,485 HCV patients were included in the study, and they were followed until incidence of cancer including lung cancer, non-Hodgkin lymphoma (NHL), breast cancer or prostate cancer, death, or last follow-up. An extended landmark modeling approach was considered, which included time-varying covariates and propensity score justification for treatment selection bias and used generalized estimating equations (GEE) with a link function as multinominal distribution for a discrete time-to-event data. Death was considered a competing risk. Results: Compared to untreated patients, patients with HCV treatment had significantly lower risk of lung cancer for direct-acting antiviral (DAA) treatment (hazard ratio (HR) = 0.47, 95% CI, 0.30-0.72) and for interferon-based treatment (IFN) (HR = 0.33, 95% CI, 0.20-0.50). The risk of NHL was only reduced among patients receiving DAA treatment. There were no significant associations between HCV treatment and risks of breast and prostate cancer. Conclusion: Both DAA and IFN antiviral treatment independently reduce the risk of lung cancer, while the protective association with NHL was limited among HCV patients with DAA treatment. Our findings support the importance of timely initiation antiviral therapy in chronic HCV-infected patients. Citation Format: Menghua Tao, Jia Li, Trueman Wu, Stuart C. Gordon, Loralee B. Rupp, Sheri Trudeau, Scott D. Holmberg, Anne C. Moorman, Philip R. Spradling, Eyasu H. Teshale, Mark A. Schmidt, Yihe G. Daida, Mei Lu. Impact of antiviral treatment status on risk of extrahepatic cancers in patients with chronic hepatitis C [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3811.
Abstract 3015: HD-PTP mediates tumor suppression via modulation of anti-tumor immunity
Authors: Chenxu Guo, Sheng Sun, Nayana Thimmiah, Agustina Maccio, Siang Koh, Leif Ellisen
Journal: Cancer Research (2024)

Abstract The role of circulating extracellular vesicles in cancer biology is an area of intense research interest. Here, we reveal a tumor suppressor mechanism of HD-PTP (His Domain Protein Tyrosine Phosphatase, encoded by PTPN23), a protein associated with ESCRT (endosomal sorting complex required for transport), a complex that controls endosome sorting and exosome secretion. While loss of HD-PTP is known to be tumorigenic in mice and is frequently observed in human cancers including Triple Negative Breast Cancer (TNBC), the relevant pathways have remained obscure. We find that inhibition of HD-PTP in vivo promotes tumor progression selectively in a syngeneic, immune-competent TNBC model but not in a matched immune-deficient model. Through systematic profiling of the exosomal proteome in HD-PTP proficient and deficient cells, we identify PD-L1 as a key exosomal cargo selectively enriched due to loss of HD-PTP. Mechanistically, we show that inhibition of HD-PTP results in PD-L1 stabilization, its co-localization with the exosomal marker CD63, the enrichment of endosomal PD-L1 and subsequent increase in ExoPD-L1 release. Exosomes produced post HD-PTP loss inhibits antigen-dependent T cell activity in vitro, and HD-PTP inhibition in a syngeneic TNBC model promotes non-cell-autonomous, exosome- and PD-L1-dependent tumor progression, associated with reduced T cell infiltration and altered macrophage polarization. Consistent with these findings, low HD-PTP levels in human solid tumors are associated with decreased tumor infiltrating lymphocytes, poor response to immune checkpoint inhibition and inferior overall survival. Taken together, our studies unveil a novel tumor suppressor pathway controlling PD-L1 trafficking and ExoPD-L1 secretion, highlighting the critical roles of HD-PTP and ESCRT in anti-tumor immunity. Citation Format: Chenxu Guo, Sheng Sun, Nayana Thimmiah, Agustina Maccio, Siang Koh, Leif Ellisen. HD-PTP mediates tumor suppression via modulation of anti-tumor immunity [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 3015.
Abstract 4456: <i>De novo</i> pyrimidine synthesis is a druggable vulnerability for chemotherapy resistant nasopharyngeal carcinoma with wild type IDH1
Authors: Yingqin Li, Yuheng Zhao, Wuqi Zhang, Chunxian Ou, Jiaxi Shen, Jun Ma
Journal: Cancer Research (2024)

Abstract Chemotherapy resistance is a major obstacle to treat nasopharyngeal carcinoma (NPC), and strategies to overcome this resistance are required. Using proteomic analysis, we found that NPC patients resistant to gemcitabine plus cisplatin (GP) induction chemotherapy were characterized by abundant metabolic pathways. NPC with high expression of wild-type isocitrate dehydrogenase 1 (wtIDH1) was hyperdependent on de novo pyrimidine nucleotide synthesis and resistant to GP. Knockdown of IDH1 augmented the inhibition of de novo pyrimidine nucleotide synthesis induced by gemcitabine and cisplatin but reversed the suppression of purine nucleotide synthesis, which leading to DNA damage caused by nucleotide pool imbalance. IDH1 facilitated transcription of dihydroorotate dehydrogenase (DHODH), a rate-limiting enzyme for de novo pyrimidine nucleotide synthesis, through promoting chromatin accessibility by ALKBH5 in an α-ketoglutaric acid dependent manner. DHODH inhibitor, BAY2402234 significantly sensitized NPC cells to gemcitabine plus cisplatin chemotherapy. Collectively, these results reveal that wtIDH1-induced increase in de novo pyrimidine nucleotide represents a metabolic vulnerability that can be exploited pharmacologically, highlighting BAY2402234 as a promising strategy to enhance the efficacy of chemotherapy against NPC. Citation Format: Yingqin Li, Yuheng Zhao, Wuqi Zhang, Chunxian Ou, Jiaxi Shen, Jun Ma. De novo pyrimidine synthesis is a druggable vulnerability for chemotherapy resistant nasopharyngeal carcinoma with wild type IDH1 [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 4456.
Abstract 3203: Extravasation and metastasis dynamics are cytoplasmically controlled by the epitranscriptome
Authors: Olivia R. Grafinger, Gobi Thillainadesan, Boyang Su, Yulin Mo, Xin Xu, Sara Mar, Minzhi Sheng, Sumaitha Al Islam, Jennifer Geddes-McAllister, Marc G. Coppolino, Hansen H. He, Gang Zheng, Katarzyna J. Jerzak, Hon S. Leong
Journal: Cancer Research (2024)

Abstract Non-coding RNA (ncRNA) and RNA binding proteins (RBPs) primarily reside in the nucleus to regulate splicing, transcription, and transcript stability. However, their role(s) in the cytoplasm were unclear until now. Evidence now suggests that ncRNAs within the cytoplasm play an important role in cancer invasion. In concert with MT1-MMP, a protease involved in invadopodia formation, long non-coding RNAs (lncRNAs) and RBPs form cytoplasmic complexes with MT1-MMP, which we termed “R-bodies” and are abundant in invasive breast cancer cells. RNA immunoprecipitation sequencing (RIP-seq) of only the cytoplasm identified the RNA at the core of these complexes to be metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a lncRNA which has been previously described as playing a fundamental role in cancer but only within the nucleus. Further investigation revealed that R-body-associated-MALAT1 was m6A-epigenetically marked. Depletion of any component of R-bodies and inhibition of m6A epigenetic marking of MALAT1 halted R-body formation and subsequent cell invasion. Importantly, we demonstrate that this cytoplasmic complex can be functionally targeted using RNA therapy against m6A-MALAT1 as well as drugs which inhibit the methyltransferase responsible for the m6A methylation of MALAT1. The identification of R-bodies has far-reaching implications and links the roles of cytoplasmic ncRNA and RBPs to the progression of disease. Citation Format: Olivia R. Grafinger, Gobi Thillainadesan, Boyang Su, Yulin Mo, Xin Xu, Sara Mar, Minzhi Sheng, Sumaitha Al Islam, Jennifer Geddes-McAllister, Marc G. Coppolino, Hansen H. He, Gang Zheng, Katarzyna J. Jerzak, Hon S. Leong. Extravasation and metastasis dynamics are cytoplasmically controlled by the epitranscriptome [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 3203.