tbuckley/cabot-search huggingface dataset:
Abstract 2313: Multi-modal deep learning to predict cancer outcomes by integrating radiology and pathology images
Authors: Zhe Li, Yuming Jiang, Ruijiang Li
Journal: Cancer Research (2024)

Abstract Purpose: Cancer patients routinely undergo radiologic and pathologic evaluation for their diagnostic workup. These data modalities represent a valuable and readily available resource for developing new prognostic tools. Given their vast difference in spatial scales, effective methods to integrate the two modalities are currently lacking. Here, we aim to develop a multi-modal approach to integrate radiology and pathology images for predicting outcomes in cancer patients. Methods: We propose a multi-modal weakly-supervised deep learning framework to integrate radiology and pathology images for survival prediction. We first extract multi-scale features from whole-slide H&amp;E-stained pathology images to characterize cellular and tissue phenotypes as well as spatial cellular organization. We then build a hierarchical co-attention transformer to effectively learn the multi-modal interactions between radiology and pathology image features. Finally, a multimodal risk score is derived by combining complementary information from two images modalities and clinical data for predicting outcome. We evaluate our approach in lung, gastric, and brain cancers with matched radiology and pathology images and clinical data available, each with separate training and external validation cohorts. Results: The multi-modal deep learning models achieved a reasonably high accuracy for predicting survival outcomes in the external validation cohorts (C-index range: 0.72-0.75 across three cancer types). The multi-modal prognostic models significantly improved upon single-modal approach based on radiology or pathology images or clinical data alone (C-index range: 0.53-0.71, P&amp;lt;0.01). The multi-modal deep learning models were significantly associated with disease-free survival and overall survival (hazard ratio range: 3.23-4.46, P&amp;lt;0.0001). In multivariable analyses, the models remained an independent prognostic factor (P&amp;lt;0.01) after adjusting for clinicopathological variables including cancer stage and tumor differentiation. Conclusions: The proposed multi-modal deep learning approach outperforms traditional methods for predicting survival outcomes by leveraging routinely available radiology and pathology images. With further independent validation, this may afford a promising approach to improve risk stratification and better inform treatment strategies for cancer patients. Citation Format: Zhe Li, Yuming Jiang, Ruijiang Li. Multi-modal deep learning to predict cancer outcomes by integrating radiology and pathology images [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 2313.
Abstract 1520: A novel cluster of cytolytic alpha/beta TCR+CD4−CD8−T cells originating from CD8+T cells with potent innate-like T cell killing ability: implicating adoptive T cell transfer therapy for hepatocellular carcinoma
Authors: Cheng-Heng Wu, Te-Wei Tseng, Chen-Yang Huang, Ping-Hsun Ou, Yi-Chen Lin, Pin-Jung Chen, Po-Ting Lin, Chan-Keng Yang, Wei Teng, Tsung-Han Wu, Yung-Chang Lin, Chun-Yen Lin
Journal: Cancer Research (2024)

Abstract Tumor immunotherapies represent promising strategies for treating various cancers, including hepatocellular carcinoma. In this context, immune cells, including the adoptive T cell transfer treatment, become the focus of interests. Notably, alpha/beta TCR+CD4−CD8−T (DNT) cells is a subgroup of T cells that is ignored for a long time but was re-focused recently. These DNT cells are a group of cells with opposite functions in different condition, including pro-inflammatory or suppressive functions and possibly originated from over-stimulation of peripheral CD4+T cells/CD8+T cells or a special group of T cells formed in thymus. In our research results, we have found these DNT cells increased in murine hepatoma model, especially in the tumor microenvironment. In addition, these DNT cells from tumor microenvironment of murine hepatoma possessed potent tumor-killing ability. Furthermore, we analyzed the transcriptome profile of T cells in tumor microenvironment by single cell RNAseq approach (CITE-seq). We found DNT cells could be categorized into two main clusters, one is cytolytic DNT cells, resemble the potent CD8+T cells, and another is the CD4+T cell-like DNT cells. These cytolytic DNT cells are not exhausted but with high expression of cytolytic molecule and low hypoxia-inducible factor-1alpha (HIF-1a) expression. By trajectory analysis, cytolytic DNT cells come from the conventional CD8+T cells but following a unique developmental pathway that is different from the exhausted CD8+T cells. Interesting, these cytolytic DNT cells also expressed high level of Fcer1g molecule, a marker of innate CD8+T cells. In addition, these DNT cells could be generated and expanded in-vitro by IL-15 without TCR activation. In conclusion, we identified a cluster of cytolytic DNT cells, originated from CD8+T cells, exhibits innate T cells behavior and potent killing ability. In addition, these cytolytic DNT cells could be generated and expanded in-vitro for the adoptive T cell transfer treatment of hepatoma. Citation Format: Cheng-Heng Wu, Te-Wei Tseng, Chen-Yang Huang, Ping-Hsun Ou, Yi-Chen Lin, Pin-Jung Chen, Po-Ting Lin, Chan-Keng Yang, Wei Teng, Tsung-Han Wu, Yung-Chang Lin, Chun-Yen Lin. A novel cluster of cytolytic alpha/beta TCR+CD4−CD8−T cells originating from CD8+T cells with potent innate-like T cell killing ability: implicating adoptive T cell transfer therapy for 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 1520.
Abstract 1799: Regulation of epidermal stem cell proliferation and adhesion by ACSS2
Authors: Nicholas K. Chamberlain, Xiaomin Bao
Journal: Cancer Research (2024)

Abstract Acetyl-CoA Synthetase Short-Chain Family Member 2 (ACSS2) is an enzyme that converts acetate into acetyl-CoA, a crucial metabolite required for protein acetylation and lipogenesis. Acetyl-CoA is membrane-impermeable and must be synthesized in the compartment in which it will be used. Among ACSS enzymes, ACSS2 alone is found in the nucleocytoplasmic compartment rather than the mitochondria. This enzyme shows dynamic localization dependent on cell nutrient status, with nutrient stress promoting nuclear localization where ACSS2 activity promotes cell growth and survival. Emerging evidence suggests ACSS2 may also play roles in promoting metastasis, and has been proposed as a potential therapeutic target. However, the role of ACSS2 in controlling normal tissue homeostasis is understudied. Addressing this knowledge gap is critical to ensure safety and efficacy of cancer therapeutics. As 80% to 90% of human cancers originate from epithelial tissues, we have leveraged human epidermal stem cells to further interrogate the role of ACSS2. As progenitor keratinocytes differentiate, they detach from the basal lamina and migrate from the metabolically privileged basal layer to the more challenging environment at the surface of the epidermis. Using shRNA-mediated knockdown, we first found ACSS2 knockdown dramatically decreases progenitor keratinocyte clonogenicity, abolishing proliferative capacity. Analysis of RNA sequencing data following ACSS2 knockdown with five constructs showed significant increases in expression of genes related to cell adhesion, extracellular matrix organization, collagen catabolism, and cell migration, in addition to keratinocyte differentiation. Downregulated genes were associated with cell division, DNA repair, and DNA replication. Live cell imaging revealed knockdown cells show striking differences in cell adhesion compared to control. These results indicate a role for ACSS2 in regulating keratinocyte proliferation and adhesion during the maintenance of epidermal homeostasis. Citation Format: Nicholas K. Chamberlain, Xiaomin Bao. Regulation of epidermal stem cell proliferation and adhesion by ACSS2 [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 1799.
Abstract 1998: ABCB1 promotes uveal melanoma cell resistance to FR900359 and identifies a tumor cell subpopulation with a distinct gene expression signature
Authors: Sarina Dion Murray, Jesse D. Riordan, Eric R. Anderson, Michael D. Onken, Kendall J. Blumer, Adam J. Dupuy, Christopher S. Stipp
Journal: Cancer Research (2024)

Abstract Uveal melanoma (UM) is the leading form of intraocular cancer in adults and the second most common form of melanoma. Although rare, UM has a median survival rate of ~1 year after metastasis occurs. Metastatic UM is largely refractory to treatment and there are no effective pharmacological therapies, resulting in poor overall survival. In &amp;gt;90% UM cases, the oncogenic initiator proteins are constitutively active mutant GNAQ or GNA11 proteins (GNAQ/11). FR900359 (FR) is a natural compound that inhibits GNAQ/11 and has anti-proliferative effects on UM cells. To identify key oncogenic mechanisms downstream of mutant GNAQ/11, we performed a Sleeping Beauty (SB) transposon forward genetic screen to identify drivers of FR resistance. The SB screen identified ATP-binding cassette sub-family B member 1 (ABCB1) as one of the top genes upregulated by SB in FR-resistant UM cell populations. We determined that although ABCB1 does not provide immediate resistance to FR, the overexpression of ABCB1 leads to emergence of resistant colonies at a much higher rate than spontaneous resistance, validating ABCB1 as contributors to FR resistance. Unexpectedly, immunofluorescence revealed that a relatively small fraction of UM cells strongly expresses the transgenes after stable transfection. Immunoblotting confirmed that ABCB1 expression was initially modest in ABCB1-transfected populations but increased in the cells that developed resistance to FR. To examine the kinetics of FR resistance, population doubling versus time (PDVT) assays were performed in UM cells expressing ABCB1 or empty vector control treated with FR or vehicle. FR potently suppressed the proliferation of vector control cells. Drug-naïve ABCB1-transfected cells developed resistance to FR over time but accomplished fewer population doublings than vehicle-treated cells in the same time interval. Once transgenic populations emerged as resistant populations in FR, they grew similarly in drug or vehicle. Ongoing RNA-sequencing analysis from PDVT samples has identified distinct gene expression signatures associated with FR treatment and ABCB1 expression. These findings are expected to illuminate tumor cell heterogeneity amongst UM cell populations that may be related to drug resistance and metastasis. Citation Format: Sarina Dion Murray, Jesse D. Riordan, Eric R. Anderson, Michael D. Onken, Kendall J. Blumer, Adam J. Dupuy, Christopher S. Stipp. ABCB1 promotes uveal melanoma cell resistance to FR900359 and identifies a tumor cell subpopulation with a distinct gene expression signature [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 1998.
Abstract 6830: Xenium <i>in situ</i> analysis and reproducibility study of multiple carcinomas for clinical studies
Authors: Elim Cheung, Baowen Zhang, Lutong Zhang, Tong Lu, Rikita Gakhar, Vidyodhaya Sundaram
Journal: Cancer Research (2024)

Abstract 10x Genomics’ Xenium is the newest in situ spatial transcriptomics platform offering sub-cellular resolution in frozen and FFPE tissue sections for a deeper study of cellular mechanisms and interactions. Mapping RNA targets at high specificity with fully customizable assays and quick workflow, it uses rolling circle amplification and interpretation-ready data is available immediately after the run. At BioChain Institute, Inc. (BioChain), we are conducting validation studies for reproducibility of results with the Xenium platform using BioChain’s oncology biospecimen.FFPE tissues from BioChain’s repository were screened by our pathologist for tumor content above 30%. Four carcinoma tissues from Breast, Colon, Lung, and Kidney with high DV200 scores were selected. An array was constructed with these tissues to fit the Xenium slide’s imageable area. Two serial sections were used for the Xenium run per 10x Genomics’ protocol. The Off-the-shelf Human Multi-Tissue and Cancer Panel was used for targeting 377 genes. H&amp;E staining and imaging was performed, and the image was integrated with the data on the Xenium platform. The results were found to be reproducible between two different operators. For example, in the breast section, over 96,000 cells were detected and median transcripts per cell were 70 in both the runs. There were 20 clusters representing different cell types/states, 99% transcripts were within cells, and ~85% of the transcripts were found to be high quality. Furthermore, we are analyzing the expression of unique tumor type and immune transcripts to map the heterogeneity of the tissues, as well as sensitivity, and standard deviation between the runs. The Xenium platform is a powerful tool for the sub-cellular spatial transcriptomics study of tissues with targeted gene panels. However, one of the four tissues used here failed to show enough transcripts. Further investigation is underway to examine the issue and conclude best practices thereafter. Our future studies will include accuracy and concordance validation with Xenium run on different days and Visium whole transcriptome assay post- Xenium. Citation Format: Elim Cheung, Baowen Zhang, Lutong Zhang, Tong Lu, Rikita Gakhar, Vidyodhaya Sundaram. Xenium in situ analysis and reproducibility study of multiple carcinomas for clinical studies [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 6830.
Abstract 4560: Assessing cancer drug combination efficacy across 900+ PRISM cell lines in a multiplexed screening assay
Authors: Ashish Bino George, Shiker Nair, Mustafa Kocak, Ellen Nguyen, Alvin Kalathungal, Anthony Fazio, Cole Ponsi, Aydin Golabi, Melissa A. Ronan, Matthew G. Rees, Jennifer A. Roth
Journal: Cancer Research (2024)

Abstract Combination therapies are crucial in cancer care, yet identifying which combination will benefit a specific patient is challenging. The vast array of clinical, investigational, and tool anticancer agents and diverse cancer contexts makes investigating many drug combinations over a large number of cell lines infeasible. Here, we describe a multiplexed screening approach using the PRISM assay, where drug combinations are screened on &amp;gt;900 DNA-barcoded cancer cell lines. We analyze cell viability data in drug combinations and single agents using established metrics to describe the combined effects such as additivity, synergy, and antagonism. Quantifying and classifying combined effects will help prioritize specific combinations for follow-up investigations and provide biological and mechanistic insights, thus enabling rationally designed combination therapies. We illustrate our methodology through data from three drug combinations that exemplify synergy and antagonism. In the first combination, temozolomide+O6-benzylguanine (alkylating agent + MGMT inhibitor), we found that cell lines expressing MGMT were sensitized to temozolomide in the presence of O6-benzylguanine, thus illustrating synergy. In the second combination, we screened two anti-apoptosis compounds A-1331852+AZD5991 (BCL-xL + MCL1 inhibitor) and found that BCL-xL and MCL1 inhibition were also synergistic. In the third combination, ML210+ferrostatin-1 (GPX4 inhibitor inducing ferroptosis + ferroptosis inhibitor), we found that ferrostatin-1 antagonized the effects of ML210. Our analysis also reveals the importance of appropriate dose selection and analytical metrics for reliably measuring combined effects. In conclusion, the PRISM platform's multiplexed cell line screening is a robust method for characterizing rationally designed drug combinations, offering a systematic approach to enhance the precision of combination therapy development in cancer care. Citation Format: Ashish Bino George, Shiker Nair, Mustafa Kocak, Ellen Nguyen, Alvin Kalathungal, Anthony Fazio, Cole Ponsi, Aydin Golabi, Melissa A. Ronan, Matthew G. Rees, Jennifer A. Roth. Assessing cancer drug combination efficacy across 900+ PRISM cell lines in a multiplexed screening assay [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 4560.
Abstract 1975: Discovery of I-1000233, a potent, selective and brain permeable SHP2 allosteric inhibitor
Authors: Francesca Puca, Danilo Fabbrini, Alina Ciammaichella, Antonino Missineo, Monica Bisbocci, Martina Nibbio, Annalise Di Marco, Claudia Apicella, Fabrizio Colaceci, Romina Sasso, Daniela Natale, Francesco Scalabrì, Cristina Alli, Vincenzo Pucci, Christian Montalbetti, Alessia Petrocchi, Alessandro Carugo, Carlo Toniatti
Journal: Cancer Research (2024)

Abstract Background: SHP2 (Src homology region 2-containing protein tyrosine phosphatase 2) is a target of interest for cancer therapy due to its key role in the regulation of RAS/MAPK signal transduction downstream of Receptor Tyrosine Kinases (RTKs). We report here the identification of I-1000233, a novel, highly potent, orally available and brain permeable SHP2 allosteric inhibitor, with potential for the treatment of tumors with dysregulated RTK/RAS/ERK signaling pathways. Material and Methods: High-throughput biological, biochemical and pharmacodynamic (PD) assays were used to inform Structure Activity Relationship studies which led to the identification of a chemical series of potent SHP2 inhibitors. Iterative optimization of physicochemical and pharmacological properties resulted in the identification of I-1000233, an orally available SHP2 inhibitor that showed excellent drug-like properties in preclinical studies. Results: I-1000233 is a potent inhibitor of the SHP2 enzyme in vitro (IC50 = 2 nM) with an exceptionally long residence time on the target. When tested in cell lines, it exhibits significant anti-proliferation activity against brain tumor cells and multiple RAS or EGFR mutant models. It strongly inhibits pERK, a downstream marker of MAPK pathway activity, in a dose dependent manner. Further, in vivo preclinical data confirmed that I-1000233 penetrates the BBB and shows anti-tumor activity, supporting its potential in the treatment of CNS and brain-metastasized tumors. Conclusions: I-1000233 is a potent, selective and orally available SHP2 inhibitor with potential for once-a-day dosing and its brain permeability in humans makes it a promising therapeutic agent against SHP2i responsive brain tumors and metastases. Citation Format: Francesca Puca, Danilo Fabbrini, Alina Ciammaichella, Antonino Missineo, Monica Bisbocci, Martina Nibbio, Annalise Di Marco, Claudia Apicella, Fabrizio Colaceci, Romina Sasso, Daniela Natale, Francesco Scalabrì, Cristina Alli, Vincenzo Pucci, Christian Montalbetti, Alessia Petrocchi, Alessandro Carugo, Carlo Toniatti. Discovery of I-1000233, a potent, selective and brain permeable SHP2 allosteric inhibitor [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 1975.
Abstract 6858: PPARδ and type 1 interferon collaboratively regulate CIITA-MHCII pathway: Unveiling novel mechanisms of tumor Tregs
Authors: Qiyuan Yang, Yuqiong Liang, Ye Zheng
Journal: Cancer Research (2024)

Abstract Regulatory T cells (Tregs) play an essential role in suppressing anti-tumor immunity, often resulting in unfavorable clinical outcomes across numerous cancers. However, systemic Treg depletion, while augmenting anti-tumor responses, also triggers detrimental autoimmune disorders. Thus, dissecting the mechanisms by which Tregs navigate and exert their functions within the tumor microenvironment (TME) is pivotal for devising innovative Treg-centric cancer therapies. Our study highlights the role of peroxisome proliferator-activated receptor β/δ (PPARδ), a nuclear hormone receptor involved in fatty acid metabolism. Remarkably, PPARδ ablation in Tregs escalated tumor growth and augmented the immunosuppressive characteristics of the TME. This absence of PPARδ spurred an increased expression of genes central to antigen presentation, notably CIITA and MHCII. Our results showcase a novel association where the absence of CIITA in PPARδ-deficient Tregs bolsters anti-tumor responses, casting CIITA as a pivotal downstream regulator of PPARδ within Tregs. In vitro assays demonstrated that elevated CIITA levels enhance the suppressive capacity of Tregs, facilitated by an antigen-independent interaction between Treg-MHCII and Tconv-TCR/CD4/Lag3. A significant revelation was the role of type 1 interferon as a TME signal that promotes the genesis of MHCII+ Tregs; this process is accentuated by PPARδ deficiency. In conclusion, the co-regulation between TME cues and PPARδ signaling shapes the adaptive and suppressive roles of Treg cells through the CIITA-MHCII pathway. Strategically targeting the potent MHCII+ Treg population could open a new avenue for cancer therapies by boosting anti-tumor defenses while curbing autoimmune threats. Citation Format: Qiyuan Yang, Yuqiong Liang, Ye Zheng. PPARδ and type 1 interferon collaboratively regulate CIITA-MHCII pathway: Unveiling novel mechanisms of tumor Tregs [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 6858.