tbuckley/cabot-search huggingface dataset:
Abstract 5491: Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level
Authors: Karmen Aguirre, Christine Yiwen-Yeh, Olivia Laveroni
Journal: Cancer Research (2024)

Abstract Immune exclusion and evasion are central barriers to the success of immunotherapies and cell therapies in solid tumors. Here we applied single cell spatial and perturbational transcriptomics alongside clinical,histological, and genomic profiling to elucidate immune exclusion and evasion in high-grade serous tubo-ovarian cancer (HGSC). Using high-plex spatial transcriptomics we profiled more than 1.3 million cells from 95 tumors and 60 patients, revealing generalizable principles in HGSC tumor tissue organization.Our data demonstrates that effector T cells resist stroma-mediated trapping and sequestration. However, upon infiltration into the tumor, T cells, as well as Natural Killer (NK) cells, preferentially co-localize only with a subset of malignant cells that manifest a distinct transcriptional cell state. The latter consists of dozens of co-regulated genes and is repressed under various copy number alterations. Performing CRISPR Perturb-seq screens in ovarian cancer cells, we identified functionally diverse genetic perturbations - including knockout of the insulin sensing repressor PTPN1 and the epigenetic regulator ACTR8 - that de-repress the proposed immunogenic malignant cell state identified in patients and indeed sensitize ovarian cancer cells to T cell and NK cell cytotoxicity. Taken together, our study uncovered a profound connection between somatic genetic aberrations, malignant cell transcriptional dysregulation, and immune evasion at the cellular and tissue level, allowing us to identify targets that reprogram malignant cell states as an avenue to unleash anti-tumor immune responses. Citation Format: Karmen Aguirre, Christine Yiwen-Yeh, Olivia Laveroni. Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level [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 5491.
Abstract 7081: Comprehensive investigation of NAT10’s catalytic and non-catalytic functions in cancer cell proliferation
Authors: Sweta Pradeep Raikundalia, Mahmood Hassan Dalhat, Emmely A. Patrasso, Adam Suh, Daniel Arango
Journal: Cancer Research (2024)

Abstract N-acetyltransferase 10 (NAT10) is emerging as an oncoprotein in multiple cancers including acute myeloid leukemia and liver cancer. In addition, my preliminary studies show that NAT10 is a stress response that promotes the resilience of cancer cells to anti-tumor drugs. However, the underlying mechanisms by which NAT10 promotes cancer growth and drug resistance are unknown. NAT10 is an RNA acetyltransferase, where it acetylates cytidines in rRNA, tRNA, mRNA, and lncRNAs. Our previous work demonstrated that NAT10 promotes translation efficiency and mRNA stability through the acetylation of cytidines in mRNA. However, NAT10 is a multifunctional protein. Besides acetylating RNA, NAT10 also acetylates proteins at lysine residues, has RNA helicase activity, and can serve as a scaffold in ribonucleoprotein complexes. Based on this complexity, it is imperative to elucidate whether NAT10 exerts its oncogenic activity via RNA acetylation, protein acetylation, disruption of RNA structures, or non-catalytic functions. Strikingly, our preliminary results indicate that the acetyltransferase function of NAT10 is dispensable for cell proliferation. To evaluate NAT10’s oncogenic activity unbiasedly, we are now performing a deep mutagenesis scanning (DMS) assay. For this purpose, we generated a library of mutants in hundreds of NAT10 residues. This library was transduced in multiple cell lines from acute myeloid leukemia and liver cancer carrying a PROTAC system, which allow us to deplete NAT10 in a rapid and controlled manner while expressing ectopically thousands of NAT10 mutants. In this conference, I will talk about, my results, how DMS is a powerful tool to delineate the molecular functions of candidate oncoproteins, and the implications of our results for the potential drugging of NAT10 in cancer. Keywords: Cell proliferation, NAT10, RNA modifications, Deep mutagenesis scanning. Citation Format: Sweta Pradeep Raikundalia, Mahmood Hassan Dalhat, Emmely A. Patrasso, Adam Suh, Daniel Arango. Comprehensive investigation of NAT10’s catalytic and non-catalytic functions in cancer cell proliferation [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 7081.
Abstract 4025: A phase II trial of neoadjuvant gemcitabine, cisplatin plus tislelizumab followed by concurrent chemoradiotherapy in locoregionally advanced nasopharyngeal carcinoma: Clinical efficacy, safety and the biomarker analysis
Authors: Xiao-Yun Li, Si-Yi Xie, Qiu-Yan Chen, Hai-Qiang Mai, Lin-Quan Tang
Journal: Cancer Research (2024)

Abstract Immune checkpoint inhibitors (ICIs) have been widely used in recurrent or metastatic nasopharyngeal carcinoma (NPC), but the addition of ICIs to chemoradiotherapy in locoregionally advanced (LA) NPC requires further investigation. We conducted a phase II, single-arm trial to evaluate the efficacy and safety of neoadjuvant gemcitabine, cisplatin (GP) plus tislelizumab followed by concurrent chemoradiotherapy (CCRT) in LA-NPC. All participants received 3 cycles of GP chemotherapy plus tislelizumab (200 mg) followed by 3 cycles of cisplatin-based CCRT. The primary endpoint was the clinical complete response rate (CR) after neoadjuvant chemoimmunotherapy (NAT). The secondary endpoints include pathological CR rate, progression-free survival (PFS), overall survival (OS), locoregional relapse-free survival (LRRFS), distant metastasis-free survival (DMFS), etc. Pretreatment blood samples and paired (pre-/post-NAT) tissue biopsies were collected to perform full-spectrum peripheral T-cell profiling, PD-L1 and tertiary lymphoid structures (TLS) staining. Among all 63 participants, the CR rate after NAT reached 41.3% (95% CI, 28.8%-53.8%), far exceeding our hypothesized CR rate of 22%. The objective response rate (ORR) and pCR rate after NAT were 88.9% (95% CI, 80.9% to 96.9%) and 74.6% (95% CI, 62.1% to 84.7%), respectively. As of July 15th, 2023, after the median follow-up of 25 months, the 2-year PFS and OS were 98.4% and 100%. The incidence of grade 3-4 immunotherapy-related adverse events was 1.6%. The compliance of CCRT was not compromised. Patients who achieved CR had significantly more circulating CD4+ and CD8+ effector memory T cells (Tem), regulatory T cells (Treg) and follicular helper T cells (Tfh). The peripheral abundance of LAG3+ Tem and Tfh were independently predictive of NAT response. The number and maturation of TLS significantly increased after NAT in the CR group, but not in the Non-CR group. GP chemotherapy plus tislelizumab followed by CCRT was highly therapeutic and safe in treating LA-NPC, further randomized phase III studies are awaited. Citation Format: Xiao-Yun Li, Si-Yi Xie, Qiu-Yan Chen, Hai-Qiang Mai, Lin-Quan Tang. A phase II trial of neoadjuvant gemcitabine, cisplatin plus tislelizumab followed by concurrent chemoradiotherapy in locoregionally advanced nasopharyngeal carcinoma: Clinical efficacy, safety and the biomarker analysis [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 4025.
Abstract 2608: Hu2G10 antibody-drug conjugates selectively target cleaved-activated Trop-2 in cancer cells and show therapeutic efficacy against multiple human cancers
Authors: Saverio Alberti, Marco Trerotola, Antonino Moschella, Raffaella Giavazzi, Emanuela Guerra
Journal: Cancer Research (2024)

Abstract Trop-2 is a transmembrane calcium signal transducer which activates growth-signaling networks that converge on Akt, ERK, Cyclin D1, NFkB (1). Trop-2 cleavage by ADAM10 was shown to be an activator switch for induction of cancer growth and metastatic diffusion (2). We devised a strategy to obtain monoclonal antibodies (mAb) capable of recognizing ADAM10-exposed sites in cancer cells. We succeeded at obtaining mAb that efficiently bound Trop-2 expressing cancer cells and were able to inhibit cell growth in vitro. We humanized the 2G10 mAb as the IgG1/k Hu2G10 antibody. Hu2G10 binds cancer-specific, cleaved/activated Trop-2 with Kd 10−12 M. On the other hand, it binds uncleaved/wtTrop-2 in normal cells with Kd 3.16 × 10−8 M, thus promising an unprecedented therapeutic index in patients. Antibody-drug conjugates (ADC) of Hu2G10 were obtained using stable linkers, multiple conjugation chemistries and different payloads, among them topoisomerase I inhibitors, bleomycin, RNA polymerase inhibitor, MMAE and calicheamicin. Hu2G10-ADC selectively killed Trop-2-expressing cells in vitro. Dose-response curves were obtained for the BxPC-3 pancreatic cancer, DU-145 prostate cancer, HT29 colon cancer cell lines and KM12SM/Trop2 colon cancer transfectants, reaching EC50 values as low as 5.05 × 10−10 M. Hu2G10-ADC drove high anticancer effectiveness on cell- and patient-derived xenografts from colon, pancreas, prostate and ovarian cancer. Effectiveness followed a gradient of payload potency, with correspondingly high therapeutic indexes. Consistently, neither detectable toxic effects nor weight loss were observed in any subgroup of treated xenotransplant-bearing mice. Taken together these findings candidate anti-Trop-2 Hu2G10-ADC for best-in-class anticancer therapy. (1) E. Guerra et al., The Trop-2 signaling network in cancer growth. Oncogene 32, 1594-1600 (2013).(2) M. Trerotola et al., Trop-2 cleavage by ADAM10 is an activator switch for cancer growth and metastasis. Neoplasia 23, 415-428 (2021). Citation Format: Saverio Alberti, Marco Trerotola, Antonino Moschella, Raffaella Giavazzi, Emanuela Guerra. Hu2G10 antibody-drug conjugates selectively target cleaved-activated Trop-2 in cancer cells and show therapeutic efficacy against multiple human cancers [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 2608.
Abstract 2532: Deciphering multiple protein complexes in BCL2 family to measure apoptotic dependencies in acute myeloid leukemia
Authors: Hongwon Lee, Changju Chun, Byungsan Choi, Saem Hong, Yunseo Lee, Youngil Koh, Tae-Young Yoon
Journal: Cancer Research (2024)

Abstract The BCL2 protein family controls apoptosis by shifting the dynamic equilibrium state of complex formation. BH3 mimetics disrupt this balance by disturbing the interaction of a specific anti-apoptotic protein, leading to the initiation of apoptosis. However, relying solely on molecular data for the specific anti-apoptotic protein can be challenging due to the functional redundancy within the BCL2 protein family and their complex interaction network. Therefore, comprehensive profiling information considering protein complexes is essential to determine apoptotic dependencies, particularly in a clinical context. In this study, we adapted a Single-molecule Protein Interaction Detection (SPID) platform that can assess levels of protein complexes in a quantitative manner. Out of the 47 metrics included in our Apoptosis Signaling 47 panel, we utilized 22 assays to measure apoptosis dependencies in acute myeloid leukemia (AML) cells obtained from 32 patients. By combining these metrics, we developed a predictive model for the ex vivo response to ABT-199 treatment, focusing on three key biomarkers: BCL2-BAX complex, BCL2-BIM binding potential, and BCLxl-BAK level. From a receiver operating curve (ROC) analysis, the model exhibited high accuracy with a value of 0.94 area under the curve (AUC). We further validated our model by comparing the predicted response to the therapeutic outcomes in 10 AML patients according to the 2017 ELN guidelines, and achieved 100% sensitivity (4 out of 4 identified correctly) and 83.3% specificity (5 out of 6 identified correctly). Overall, our platform provides an effective method to explore apoptosis dependencies in clinical samples based on the information regarding protein complexes within the BCL2 protein family. Three key molecular biomarkers can be translated into a gauge for predicting therapeutic outcomes of BH3 mimetics, suggesting an improvement of precision medicine in AML treatment. Citation Format: Hongwon Lee, Changju Chun, Byungsan Choi, Saem Hong, Yunseo Lee, Youngil Koh, Tae-Young Yoon. Deciphering multiple protein complexes in BCL2 family to measure apoptotic dependencies in acute myeloid leukemia [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 2532.
Abstract 6721: AI-guided generation of novel GUCY2C-targeting T-cell engagers for the treatment of colorectal cancer
Authors: Liang Tian, Jinxiu Hou, Chenpeng Su, Xiaoou Xu, Xiaoqian Chen, Dandan Liu, Jiyuan Tian, Rui Shen, Yi Pan, Yuan Yuan, Lisha Dong, Tingting Gu, Jian Peng
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) ranks as one of the most lethal cancers worldwide. Given the advances in immunotherapy and targeted therapy, the survival time in CRC has been improving recently. However, the development of novel and effective therapies for CRC still remains an unmet medical need. Guanylyl cyclase C (GUCY2C) is a transmembrane receptor expressed on the surface of intestinal epithelial cells. Recent studies have demonstrated that GUCY2C is causally linked to intestinal inflammation, dysbiosis, and tumorigenesis. To this end, GUCY2C has emerged as a promising target for immunotherapy and a diagnostic marker of primary and metastatic cancer. Here we describe the discovery and optimization of a novel panel of GUCY2C-targeting T cell engagers (TCEs) developed via our streamlined AI-guided TCE development platform. We have identified a number of anti-GUCY2C antibodies with various binding epitopes on GUCY2C, and subsequently generated a panel of novel GUCY2C-targeting multispecific antibodies with favorable developability and functionalities via our AI-driven engineering technology. Our data demonstrate that a biparatopic GUCY2C x CD3 TCE engineered as an asymmetric ‘1+2’ format can recognize two distinct epitopes on GUCY2C. This biparatopic GUCY2C x CD3 TCE shows enhanced tumor cell binding affinity and superior T cell-mediated cytotoxicity compared to the ‘1+1’ GUCY2C x CD3 TCE and ‘1+2’ bivalent GUCY2C x CD3 TCE where the two GUCY2C targeting arms can only bind to an identical epitope on GUCY2C. In addition, we have engineered a novel GUCY2C × CD3 x CD28 trispecific TCE, in which the CD3-targeting arm in tandem with the co-stimulating CD28-targeting arm mediate the interaction with T cells. This anti-GUCY2C trispecific TCE induces favorable synergistic T cell activation and tumor cell killing in vitro compared to the bispecific counterparts. In vivo anti-tumor activity assessments of these multispecific TCE molecules in various tumor xenograft mouse models are currently ongoing. Citation Format: Liang Tian, Jinxiu Hou, Chenpeng Su, Xiaoou Xu, Xiaoqian Chen, Dandan Liu, Jiyuan Tian, Rui Shen, Yi Pan, Yuan Yuan, Lisha Dong, Tingting Gu, Jian Peng. AI-guided generation of novel GUCY2C-targeting T-cell engagers for the treatment of colorectal 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 6721.
Abstract 1566: Cancer metastasis and stemness: The metastasis-inducer MACC1 regulates LGR5 to promote cancer stem cell-like properties in colorectal cancer
Authors: Müge Erdem, Kyung Hwan Lee, Markus Hardt, Joseph Regan, Dennis Kobelt, Wolfgang Walther, Christian Regenbrecht, Ulrike S. Stein
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. The high mortality is directly associated with metastatic disease which is thought to be initiated by colon cancer stem cells according to cancer stem cell (CSC) model. Consequently, early identification of those patients who are at high risk for metastasis is crucial for improved treatment and patient outcome. Metastasis-associated in colon cancer 1 (MACC1) is a novel prognostic biomarker for tumor progression and metastasis formation independent of tumor stage. We previously showed an involvement of MACC1 in cancer stemness in the mouse intestine of our transgenic mouse models. However, the expression of MACC1 in human CSCs and possible implications remain elusive. Here, we explored the molecular mechanisms by which MACC1 regulates stemness and CSC-associated invasive phenotype based on patient-derived 3D cell culture models (PD3D), patient-derived xenografts (PDX) and human CRC cell lines. We showed that CD44-enriched CSCs from PD3D models express significantly higher levels of MACC1 and display higher tumorigenicity in immunocompromised mice. Similarly, RNA sequencing performed on PD3D and PDX models demonstrated significantly increased MACC1 expression in ALDH1(+) CSCs, highlighting its involvement in cancer stemness. We further showed the correlation of MACC1 with CSC markers CD44, NANOG and LGR5 in PD3D models as well as established cell lines. Additionally, MACC1 increased stem cell gene expression, clonogenicity and sphere formation. Strikingly, we showed that MACC1 binds as a transcription factor to the LGR5 gene promoter uncovering the long-known CSC marker LGR5 as novel essential signaling mediator used by MACC1 to induce CSC-like properties in human CRC patients. Our in vitro findings were further substantiated by significant positive correlation of MACC1 and LGR5 in CRC cell lines as well as CRC patient tumors. Taken together, this study indicates that the metastasis-inducer MACC1 act as a cancer stem cell-associated marker. Interventional approaches targeting MACC1 would potentially improve further targeted therapies for colorectal cancer patients to eradicate CSCs, prevent cancer recurrence and distant metastasis formation. Citation Format: Müge Erdem, Kyung Hwan Lee, Markus Hardt, Joseph Regan, Dennis Kobelt, Wolfgang Walther, Christian Regenbrecht, Ulrike S. Stein. Cancer metastasis and stemness: The metastasis-inducer MACC1 regulates LGR5 to promote cancer stem cell-like properties in colorectal 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 1566.
Abstract 3493: Read-level methylation pattern extraction for high-multiplex large-scale targeted NGS assay
Authors: Mingda Jin, Masatomo Kaneko, Steven Cen, Hongtao Li, Wei Guo, Xinyi Zhou, Atsuko Fujihara, Tsuyoshi Iwata, Lorenzo Storino Ramacciotti, Divyangi Paralkar, Giovanni E Cacciamani, Manju Aron, Osamu Ukimura, Inderbir S. Gill, Gangning Liang, Andre L. Abreu, Jeffrey Bhasin, Xiaojing Yang, Xi-Yu Jia
Journal: Cancer Research (2024)

Abstract The abnormal changes in DNA methylation are linked to the early stages of carcinogenesis. Identifying these epigenetic changes in circulating tumor DNA (ctDNA) can reveal potential biomarkers for the early diagnosis of various cancers. However, analyzing such data poses bioinformatics challenges due to the lack of sensitivity in detecting the low abundance ctDNA signals in biopsy samples, which are often overwhelmed by the complexity of libraries containing hundreds of targeted regions. Read-level methylation analysis holds the promise of more in-depth DNA methylation detection due to the wide coverage and high sensitivity of rare signals. However, this approach is hindered by the absence of a standardized workflow capable of generating interpretable reports suitable for both bench scientists and professional bioinformaticians. Here, we present a bioinformatics workflow that examines next-generation sequencing (NGS) data and characterizes the read-level methylation patterns of amplicons. Compared to other currently available tools, our method is designed to work with high-multiplex, large-scale targeted assays. It effectively eliminates the undesired noise derived from sequencing byproducts such as false CpG calls, dimers, and off-target alignments. Additionally, to accommodate the substantial volume of data generated by state-of-the-art NGS platforms, the workflow enables parallel processing of samples compatible with both cloud-based and on-premises computing resources. This workflow provides a comprehensive per-sample visualization of DNA methylation patterns and reports read-level methylation results in a “pattern-as-a-feature” table. In this table, the occurrence of an amplicon epiallelic haplotype (pattern) for every sample is represented as a “feature column” and is aggregated with all patterns discovered in the experiment. These read-level patterns, along with other information, can be used to develop machine learning algorithms to reiteratively harvest true predictive features and penalize confounding signals in predicting cancer diagnosis. Citation Format: Mingda Jin, Masatomo Kaneko, Steven Cen, Hongtao Li, Wei Guo, Xinyi Zhou, Atsuko Fujihara, Tsuyoshi Iwata, Lorenzo Storino Ramacciotti, Divyangi Paralkar, Giovanni E Cacciamani, Manju Aron, Osamu Ukimura, Inderbir S. Gill, Gangning Liang, Andre L. Abreu, Jeffrey Bhasin, Xiaojing Yang, Xi-Yu Jia. Read-level methylation pattern extraction for high-multiplex large-scale targeted NGS 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 3493.