bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 7383: G2PT: Mechanistic genotype-phenotype translation using hierarchical transformers
Authors: Lee Ingoo , Park Sungjoon , Nam Hojung , Ideker Trey
Published: March 2024

Motivation: Many machine learning models have been proposed that use genotypes to predict various phenotypes. Recently, these models have focused not only on an accurate prediction but mechanistic interpretation, in that they attempt to describe the hierarchy of biological systems underlying the predicted phenotype. Such models still face major challenges, however, including how to robustly quantify the importance of systems mediating phenotypic outcomes and how to represent the bidirectional flow of information among genes, systems, phenotypes, and cell environment.

Results: To address these challenges we introduce G2PT, a general Genotype-to-Phenotype Transformer, which we apply here to the classic G2P problem of modeling tumor cell sensitivity to drugs. We show that the framework of hierarchical transformers can represent biological systems spanning a wide range of physical scales and provide a quantitative assessment of the interplay between biological components important for phenotype prediction. When used to analyze a high-throughput cell screen of 436 drugs exposed to 1,097 cell types, we show that the model achieves good performance in predicting cell sensitivity for 83% of drugs (⍴ > 0.5 in cross-validation). G2PT provides a robust and interpretable model with potential application to many challenges in genotype-phenotype translation.

Citation Format: Ingoo Lee, Sungjoon Park, Hojung Nam, Trey Ideker. G2PT: Mechanistic genotype-phenotype translation using hierarchical transformers [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 7383.
Abstract 7384: Regulation of phosphorylated VGLL1 by the positively charged binding pocket on the surface of TEAD4
Authors: Choi Jae Mun , Van Le Huong , Park Young Bin , Yun Yu Kyung , Kim Jun Hong , Wilianto Jonathan , Shadiev Nuzup , Sung Chul , Ku Bonsu , Chang Kwan-Young , Won Misun
Published: March 2024

Vestigial-like 1 (VGLL1) is a transcriptional co-activator that binds to TEA domain-containing transcription factors (TEADs), regulating hippo pathway. High expression of VGLL1 is associated with gastric cancer, breast cancer, and pancreatic cancers. VGLL1 is transcriptionally regulated by PI3K/β-catenin signaling and is phosphorylated by ribosomal S6 kinase 2 (RSK2) in the presence of TGF-β. It is clear that phosphorylation at S84 of the VGLL1 protein is critical for its interaction with TEAD4 to express their target genes involved in the proliferation and metastasis of cancer cells. In the isothermal titration calorimetry study, we observed S84-phosphorylated VGLL1 peptide bound to TEAD4. However, it is difficult to understand structure-based molecular mechanism of the phosphorylated VGLL1 at S84 due to lack of the detailed human VGLL1-TEAD4 complex structure for rational drug design. In this study, we modeled full-length human VGLL1-TEAD4 or YAP1-TEAD4 complexes and performed MMPBSA calculations or Kd/Ki predictions followed by MD simulations using Pharmaco-Net's CNN-based artificial intelligence model. Our study suggests that a positively charged binding pocket on the surface of TEAD4 can regulate interaction between Trp243 from YAP1 and phosphorylated-Ser84 from VGLL1. The newly identified binding pocket is composed of Lys297, Val414, and Tyr429, which can interact with phosphorylated Ser84 residue and maintain Omega loop-like structure shown in YAP1-TEAD4 complex. The computed binding energy for phosphorylated-VGLL1-TEAD was -134.80 +/- 8.20 Kcal/mol which was a similar binding energy to YAP1-TEAD4 complex. In addition, global peptide docking using S84-containing-VGLL1 peptide (SCVP) indicated that SCVP can bind to the same binding pocket with average 1.39 μM. This suggested that there could be a novel therapeutic approach targeting this interaction with SCVP, an agent that seems to mimic phosphor-VGLL1 interaction and thus demonstrates promise as a potential therapeutic intervention. Nevertheless, further experimental verification and clinical investigations are needed to validate these innovative findings.

Citation Format: Jae Mun Choi, Huong Van Le, Young Bin Park, Yu Kyung Yun, Jun Hong Kim, Jonathan Wilianto, Nuzup Shadiev, Chul Sung, Bonsu Ku, Kwan-Young Chang, Misun Won. Regulation of phosphorylated VGLL1 by the positively charged binding pocket on the surface of TEAD4 [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 7384.
Abstract 7435: PATTY: A bias estimation and correction model for bulk and single-cell CUT&Tag data
Authors: Hu Sheng'en Shawn , Chen Qingying , Grieco Megan , Zang Chongzhi
Published: March 2024

The accurate detection of transcription factor (TF) binding sites and histone modifications (HM) on the genome-wide scale is essential for studying functional epigenetics and gene regulation. Cleavage Under Targets & Tagmentation (CUT&Tag) is a low-cost and easy-to-implement epigenomic profiling method that can be performed on a low number of cells and on the single-cell level. CUT&Tag experiments use the hyperactive transposase Tn5 for tagmentation. We find that Tn5 is subject to intrinsic sequence insertion bias (intrinsic bias). Additionally, the preference of Tn5 insertion toward accessible chromatin also affects the distribution of CUT&Tag reads (open chromatin bias). Both types of biases can significantly confound bulk and single-cell CUT&Tag data analysis, which requires careful assessment and new analytical methods. To address this challenge, we present PATTY (Propensity Analyzer for Tn5 Transposase Yielded bias), a computational method for systematic characterization and correction of biases in CUT&Tag data. We demonstrate that histone modification signals (H3K27me3 and H3K27ac) detected from CUT&Tag data after bias correction using PATTY are better associated with orthogonal biological features such as gene expression. PATTY-corrected single-cell CUT&Tag signals for histone modification can better cluster cells into their true cell types. This new computational method can improve both bulk and single-cell CUT&Tag data analysis.

Citation Format: Sheng'en Shawn Hu, Qingying Chen, Megan Grieco, Chongzhi Zang. PATTY: A bias estimation and correction model for bulk and single-cell CUT&Tag data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7435.
Abstract 7445: Association between C-reactive protein and cognitive impairment in IDH-mutant gliomas
Authors: Kauss McKenzie C. , Wright Michelle L. , Raval Dhaivat , Hsieh Emory , Slattery Kaitlynn , Armstrong Terri S. , Mendoza Tito R. , Guedes Vivian A.
Published: March 2024

Cognitive impairment is common in primary brain tumor (PBT) patients, as a result of the disease and secondary damage from directed and systemic therapy. Recently, the risk in patients with IDH-mutant gliomas and role of interconnectivity of the tumor with neurons and the tumor microenvironment has heightened interest in exploration of biomarkers of impairment to inform care. Here, we investigate Montreal Cognitive Assessment (MoCA) scores and peripheral blood levels of C-reactive protein (CRP) in a cross-sectional cohort of 47 adult IDH-mutant PBT patients enrolled in a natural history study (NHS, NCT02851706: PI T. Armstrong). MoCA raw scores (range 0-30) were dichotomized (≤ 25 = cognitive dysfunction). Baseline CRP was quantified in banked serum samples in duplicate using (V-Plex/Vascular Injury Panel-2, Meso Scale Discovery [MSD], Rockville, MD) in a QuickPlex SQ 120 instrument (MSD). Lab personnel were blinded to diagnosis and clinical status. To reduce skewness in CRP raw values, we used log transformation. Descriptive statistics, Pearson’s correlation, and logistic regression were conducted using IBM SPSS and SAS Statistics software. The sample was predominately male (62%), white (70%), with high-grade gliomas (III/IV) (68%) and an average age at diagnosis of 36 years (SD: 9; median: 34; range: 20-53). The mean MoCA score was 25 (SD: 5; median: 26; range: 11-30). Dichotomizing MoCA scores showed that less than half (43%) of participants exhibited moderate-severe (≤ 25) cognitive impairment. MoCA binary group was negatively correlated with levels of CRP (r=-0.42, p<.003). The log mean concentration of CRP was higher in participants with cognitive impairment (7.99, SD=0.47 vs 7.57, SD=0.45, p<.003) than those without impairment. Finally, when controlling for age and sex, CRP remained predictive of cognitive impairment (OR 8.18, 95% CI 1.70,39.23). Higher levels of CRP were associated with lower MoCA scores in a cross-sectional sample of patients with IDH-mutant gliomas, suggesting an association between the severity of inflammation and cognitive impairment in IDH-mutant glioma patients. Further analysis in large, more diverse longitudinal cohorts will be needed to validate these findings in this population and compare to those with IDH-WT tumors and develop predictive models to inform biomarker development.

Citation Format: McKenzie C. Kauss, Michelle L. Wright, Dhaivat Raval, Emory Hsieh, Kaitlynn Slattery, Terri S. Armstrong, Tito R. Mendoza, Vivian A. Guedes. Association between C-reactive protein and cognitive impairment in IDH-mutant gliomas [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 7445.
Abstract 7461: Obesity promotes breast cancer progression via complement 1q
Authors: Zhang Tao , Liu Shimeng , Brown Myles
Published: March 2024

Obesity markedly impacts the onset and progression of various tumors. Yet, the mechanisms by which obesity-driven remodeling in macrophages modulates tumor progression are not yet fully elucidated. Using single-cell RNA sequencing and in vivo syngeneic murine models, we identified an enriched subset of macrophages expressing high levels of C1q complex genes in the adipose tissue of obese mice. Intriguingly, these C1q-positive macrophages are also prevalent within the tumor microenvironment. Our data suggest that obesity induces cell apoptosis in both adipocytes and tumor cells, and that macrophages engulf these apoptotic cells via a C1q-dependent pathway, thus promoting immunosuppression. Moreover, C1q deficiency in mice impairs tumor growth. Notably, C1q is upregulated in human breast cancer and is associated with poor prognosis. Our results suggest that targeting C1q could be an effective method for breast cancer treatment.

Citation Format: Tao Zhang, Shimeng Liu, Myles Brown. Obesity promotes breast cancer progression via complement 1q [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 7461.
Abstract 7477: Isoxanthohumol inhibits LPS-induced inflammatory responses in macrophages
Authors: Kao Tzu-Han , Li Chia-yang
Published: March 2024

Background: Pathogen infection, such as bacteria, viruses, and fungus, frequently leads to septicemia through a series of inflammatory responses that have very high fatality rates. And, servere inflammation may cause gene mutation which is beginning of cancer. Macrophages are a critical type of antigen-presenting cells that control both innate and adaptive immune responses. During pathogen infection, activated macrophages secret many proinflammatory mediators and cytokines, including nitric oxide (NO), TNF-α and IL-6 against pathogens; however, an overwhelming inflammatory response provokes abundant cells to undergo apoptosis. In the present study, we aimed to examine the anti-inflammatory effect of isoxanthohumol, a prenylflavonoid from hops and beer.

Method: We used lipopolysaccharide (LPS) as a pathogenic stimulus to induce inflammatory responses by J774A.1 macrophages. MTT assay was used to detect cell viability. The secretion of NO was analyzed by Griess reagent assay, while the production of TNF-α, IL-6, IL-1β was measured by enzyme-linked immunosorbent assay (ELISA). The expression of iNOS, COX-2, and MAPKs was examined by Western blotting. The activity of NF-κB was analyzed by promotor reporter assay. The activation of NLRP3 inflammasome was examined by ELISA and immunofluorescence staining. In addition to that, we explored the secretion of cytokines, IL-1β, in THP-1 cell.

Result: We found that isoxanthohumol significantly suppresses the secretion of NO and attenuates the production of TNF-α and IL-6 by LPS-induced macrophages. In addition, isoxanthohumol also inhibits the expression of iNOS and COX-2, suppresses the phosphorylation of JNK, and attenuates the activity of NF-κB by LPS-induced macrophages. Moreover, isoxanthohumol decreases the activation of NLRP3 inflammasome by reducing the production of IL-1β and repressing the ASC speck formation of NLRP3 inflammasome in LPS/ATP-induced macrophages.

Conclusion: Our experimental results demonstrated that isoxanthohumol effectively inhibits LPS-induced inflammatory responses in macrophages, suggesting that isoxanthohumol might have benefits for attenuating inflammation.

Citation Format: Tzu-Han Kao, Chia-yang Li. Isoxanthohumol inhibits LPS-induced inflammatory responses in macrophages [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 7477.
Abstract 7499: Circulating tumor cell enumeration and protein expression by CapioCyte and Allegro Plus imaging
Authors: Lim Ju-heon , Johnson Chassidy , Kaplan Tal , Poellmann Michael J. , Harari Yuval , Kfir Elad , Wang Andrew Z. , Hong Seungpyo
Published: March 2024

Radiation or chemoradiation followed by surgical resection is the current standard of therapy for many diseases. These treatments are increasingly supplemented with monoclonal antibodies, such as epidermal growth factor receptor (EGFR)-targeting and programmed death ligand 1 (PD-L1) checkpoint-blocking antibodies. The use of these therapies is typically dependent on solid tissue biopsy to confirm elevated expression of these markers in the solid tumor, which carries complications and may only be sampled at diagnosis. In contrast, a liquid biopsy may detect these markers with minimal invasiveness and at multiple points throughout treatment and recovery. Here, we describe the development of an automated and integrated workflow for circulating tumor cell (CTC) analysis. We previously demonstrated that the CapioCyte method is a highly sensitive approach for enrichment of CTCs using a combination of biomimetic rolling on recombinant E-selectin and antibody-mediated capture on a nanostructured polymer surface within a flow chamber for capture. Here we report a fully automated CapioCyte instrument for CTC purification and immunofluorescence staining using epithelial, white blood cell and nuclear makers to identify and distinguish CTCs from WBCs while also quantifying EGFR or PD-L1 presence on respective CTCs. The immunostaining conditions were developed and validated for high analytical sensitivity and specificity using cell lines and health donor white blood cells with known biomarker status. The final assay conditions were transferred to the CapioCyte for automated immunostaining. CapioCyte enriched and stained CTC samples are paired with the BioView Allegro Plus platform, an imaging and analysis solution using machine learning and customized algorithms for automated imaging and CTC candidate identification based on high-resolution Z-stack images. The reported comprehensive and automated workflow was used to enumerate CTCs in patients with non-small cell lung carcinoma (NSCLC) in a feasibility cohort. Median CTC counts from NSCLC patients was 7.5 CTC/ml (n=26, mean 51.7, range 0.3 - 406.2). Studies are on-going to expand the cohort including testing blood from head and neck cancer patients and respective EGFR and PD-L1 status. The combined and automated CapioCyte-Allegro Plus workflow shows great potential for routine quantification of CTCs and EGFR and PD-L1 status.

Citation Format: Ju-heon Lim, Chassidy Johnson, Tal Kaplan, Michael J. Poellmann, Yuval Harari, Elad Kfir, Andrew Z. Wang, Seungpyo Hong. Circulating tumor cell enumeration and protein expression by CapioCyte and Allegro Plus imaging [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 7499.
Abstract 7527: Investigating biomarkers for immune-related adverse events following immune checkpoint inhibitor therapy in recurrent lung cancer patients
Authors: Kudo Yujin , Matsubayashi Jun , Takahashi Satoshi , Hagiwara Masaru , Kakihana Masatoshi , Nagao Toshitaka , Ohira Tatsuo , Ikeda Norihiko
Published: March 2024

Background: The application of immune checkpoint inhibitors (ICIs) as adjuvant therapy post-lung cancer surgery is expected to confer significant benefits. However, the risk factors for severe immune-related adverse events (irAEs) remain incompletely understood, and managing irAEs may require long-term steroid use. The identification of biomarkers for irAEs in patients with surgically resected lung cancer is an urgent need.

Methods: We analyzed 43 lung cancer patients who received ICI treatment for recurrence postoperatively. Macrodissection of lung cancer lesions was performed on FFPE specimens from resected lungs, from which total RNA was extracted. We conducted gene expression analysis of 770 immune-related genes using the PanCancer Immune Profiling Panel (NanoString Technologies, Inc., Seattle, WA, USA). The relationship between gene expression changes and irAEs or the efficacy of ICI treatment was examined. For validation, immunostaining of proteins strongly associated with irAEs was performed to determine their expression status in tissue specimens.

Results: Among the 43 patients (30 males, 13 females, median age 68), 28 had adenocarcinoma, and 15 had squamous cell carcinoma. PD-L1 positivity was observed in 36 patients. The treatment regimens included pembrolizumab monotherapy for 18 patients and combination immunotherapy for 25 patients, with 25 patients responding to treatment and 7 developing irAEs. There was a marked difference in gene expression between adenocarcinoma and squamous cell carcinoma, with a notably higher number of tumor-infiltrating lymphocytes (TILs) in adenocarcinoma. An increase in TILs was observed in cases with irAEs across both cancer types. Additionally, an increased CD8/Treg ratio and CD8/exhausted T cell ratio were noted in adenocarcinomas with irAEs. A strong correlation between IRF5 gene expression and the occurrence of irAEs in adenocarcinoma was also confirmed by immunohistochemistry.

Conclusion: We have identified tumor immune microenvironments correlated with the onset of irAEs following ICI treatment in patients with postoperative recurrence of lung cancer. This discovery could contribute to perioperative treatment strategies and improve our understanding of tumor immune mechanisms.

Citation Format: Yujin Kudo, Jun Matsubayashi, Satoshi Takahashi, Masaru Hagiwara, Masatoshi Kakihana, Toshitaka Nagao, Tatsuo Ohira, Norihiko Ikeda. Investigating biomarkers for immune-related adverse events following immune checkpoint inhibitor therapy in recurrent lung cancer patients [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 7527.
Abstract 7534: Tobemstomig, a novel bispecific checkpoint inhibitory antibody to preferentially block PD-1 and LAG-3 on CD8 TILs over Tregs
Authors: Codarri-Deak Laura , Weber Patrick Aaron , Nicolini Valeria , Klein Christian , Umana Pablo , Seeber Stefan , Perro Mario , Leclair Stephane
Published: March 2024

Checkpoint inhibitors targeting PD-1 have shown unprecedented clinical efficacy in several cancer indications and therefore have, revolutionized the standard of care. However, despite this advancement, only ~20-30% of the patients derive durable benefit from such a treatment. One of the suggested reasons for this limited success is the expression/activation of compensatory inhibitory pathways such as LAG-3 on tumor-reactive T cells. Therefore, it is envisioned that simultaneous antagonism of PD-1 and LAG-3 receptors would overcome this adaptive resistance mechanism and allow a more profound reinvigoration of tumor-reactive T cells. LAG-3 is constitutively expressed by regulatory T cells (on Tregs) and it has been reported that its blockade increases Treg suppressive function which could potentially off-sets the benefit of blocking LAG-3 on tumor-reactive CD8 T cells.We therefore developed a 1+1 PD1-LAG3 bispecific antibody, Tobemstomig, with a unique PD-1 binder recognizing a glycoepitope and more than 20 fold higher affinity than the LAG-3 binder which recognizes a novel and differentiated binding epitope (E3). This difference in affinities allows for an avidity driven selectivity gain to PD-1 and LAG-3 double positive T cells over and the following advantages over monospecific and other bispecific aPD-1/-L1 and aLAG-3 antibodies:1.improved targeting to tumor-reactive T cells rather than Tregs due to the selectivity gain and different expression patterns of PD-1 and LAG-3 on these two T cell types, 2.reduced internalization, 3.resistance to drug-shaving by macrophages due to Fc -silencing via P329G LALA,4.increased in vitro T cell effector functions even in the presence of Tregs, 5.in-vivo targeting and expansion of CD8 TILs, including stem-like T cells, and increase in T cell effector functions and6.superior in vivo tumor control/eradication compared to combination of monospecific anti-PD1 and anti-LAG3 antibodies,in several mouse models including Panc02 in syngeneic huPD-1xhuLAG3 dtg mice and BXPC3, WSU, OCI-Ly18 and BC004 in humanized mice Tobemstomig has completed dose escalation and is currently tested in a composite proof of concept Ph2 trial in several solid tumor indications.

Citation Format: Laura Codarri-Deak, Patrick Aaron Weber, Valeria Nicolini, Christian Klein, Pablo Umana, Stefan Seeber, Mario Perro, Stephane Leclair. Tobemstomig, a novel bispecific checkpoint inhibitory antibody to preferentially block PD-1 and LAG-3 on CD8 TILs over 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 7534.
Abstract 7536: CD4+T cell exhaustion in the tumor microenvironment and antitumor immunity
Authors: Nagasaki Joji , Zhou Wenhao , Kawashima Shusuke , Ishino Takamasa , Kawase Katsushige , Ueda Youki , Yamashita Kazuo , Watanabe Tomofumi , Inozume Takashi , Togashi Yosuke
Published: March 2024

Background: Immune checkpoint inhibitors (ICIs) exert clinical efficacy against various types of cancer through reinvigoration of exhausted CD8+ T cells that attack cancer cells directly in the tumor microenvironment (TME). However, compared to CD8+ T cell exhaustion, the role of CD4+ T cell exhaustion in antitumor immunity remains unclear.

Methods and Results: From single-cell sequencing for tumor-infiltrating lymphocytes (TILs) from patients with melanoma and mouse models, we found that CXCL13, which is highly expressed in tumor-infiltrating exhausted CD8+ T cells, induces PD-1+CXCR5+CD4+ follicular helper T (TFH)-like cell infiltration, which could contribute to antitumor immunity. Furthermore, a part of the TFH-like cells in the TME exhibits cytotoxicity and directly attacks MHC-II-expressing tumors. RNA velocity and latent time analysis in single-cell sequencing for melanoma TILs showed that the differentiation of TFH-like cells from the naive CD4+ T cells were different from that of other CD4+ T cells. In addition, the TFH-like cytotoxic CD4+ T cells were at the late stage of differentiation and some non-cytotoxic TFH-like cells might differentiate into TFH-like cytotoxic CD4+ T cells. We additionally found considerable overlapped clonotypes between the cytotoxic and non-cytotoxic clusters. TFH-like cytotoxic CD4+ T cells have high LAG-3/BLIMP1 and low TCF1 expression without self-renewal ability, whereas non-cytotoxic TFH-like cells express low LAG-3/BLIMP1 and high TCF1 with self-renewal ability, closely resembling the relationship between terminally differentiated and stem-like progenitor exhaustion in CD8+ T cells, respectively.

Conclusion: Our findings provide novel insights into TFH-like CD4+ T cell exhaustion with helper progenitor and cytotoxic differentiated functions, which mediates antitumor immunity orchestrally with CD8+ T cells.

Citation Format: Joji Nagasaki, Wenhao Zhou, Shusuke Kawashima, Takamasa Ishino, Katsushige Kawase, Youki Ueda, Kazuo Yamashita, Tomofumi Watanabe, Takashi Inozume, Yosuke Togashi. CD4+T cell exhaustion in the tumor microenvironment and antitumor 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 7536.
Abstract 7547: Enhancers as targets for improvements in immunotherapy
Authors: Singh Anand , Kochat Veena , Arslan Emre , Satpati Suresh , Deng Wentao , Yadav Sandeep , Bataki Efthalia , Yee Cassian , Rai Kunal
Published: March 2024

Role of epigenetic elements in mediating tumor immune interaction remains poorly understood. We previously identified enrichment of active enhancer states on a set of genomic loci in non-responders to immune checkpoint blockade (ICB) therapy. We noted that the activated non-responder enhancers marked a group of key regulators of in melanoma cells that are known to mediate resistance to ICB therapy and several checkpoint receptors in T cells. Through spatial epigenomics (Spatial ATAC and CUT&Tag) approaches, we identified the tumor-immune niches harboring unique gene regulatory elements and transcription factors that could mediate melanoma-T cell interaction. Further, we aimed to identify functional epigenetic elements through custom CRISPRi screening of enhancers in patient tumor-derived melanoma and T cells. CRISPRi approaches identified novel functional enhancers that mediate T cell mediated killing. For example, we identified distal c-MET enhancers as important contributors to T cell mediated killing. In T cells, we identified enhancer hubs that target multiple genes. These hubs could be targeted to activate interferon gamma, reduce T cell exhaustion, and improve T cell mediated killing of melanoma cells. Such enhancer hubs could serve as targets in the ex vivo setting to improve adoptive T cell therapy. Overall, our results suggest that enhancers with unique spatial patterns in melanoma tumors contribute to the response to immunotherapy and could be novel targets for therapy.

Citation Format: Anand Singh, Veena Kochat, Emre Arslan, Suresh Satpati, Wentao Deng, Sandeep Yadav, Efthalia Bataki, Cassian Yee, Kunal Rai. Enhancers as targets for improvements in immunotherapy [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 7547.
Abstract 7561: Standardized conditions for growth of lung cancer tumoroids cultured reproducibly in 3D-cultures
Authors: Malmros Karina , Carlsén Daniel , Brunnström Hans
Published: March 2024

Background: Lung cancer is the most common cause of cancer-related death in Sweden with an estimated mortality of 3500 persons in 2021. Late diagnosis and heterogeneity of the disease lead to difficulty in predicting optimal treatment regime for each case. Further development of personalized therapy would be facilitated by reliable and efficient cultivation of cancer cell samples from patients in a clinical setting. A promising method is to grow the cells as 3D structures known as tumoroids, though the choice of extracellular matrix substrate or solid support most suitable for this purpose should be elucidated.

Aim: To assess which extracellular matrix substrates or solid supports which enable lung cancer tumoroid generation reproducibly without affecting the status or detection of genetic alterations and protein expression, using lung cancer cell lines.

Methods: Eight lung cancer cell lines, where of three adenocarcinoma and five squamous cell carcinomas, were included in this project. Each cell line was characterized with immunohistochemistry (IHC) for commonly expressed antigens in the two lung cancer types. Also, protein detection with Western Blots was performed. Cell lines found not expressing relevant antigens associated with the specific lung cancer variant were discarded. The remaining cell lines were cultivated in BIOFLOAT TC-Platte 96 well plate, Nunclon Sphera flasks, or GrowDex-T hydrogel, later transferred to a Corning Elplasia 6 well plate, and monitored for tumoroid generation.

Results: The lung squamous cell carcinomas HCC-95 and HCC-1588 were both positive for CK5 and p40, while H1703 was negative for both markers. The adenocarcinoma H1975 was positive for TTF-1, also, unexpectedly, seen for NCI-H1703, earlier defined as squamous cell carcinoma. The tested cell lines were successfully cultured as tumoroids in the BIOFLOAT TC- 96 well plate, Nunclon Sphera flasks, and GrowDex-T hydrogel. The mutational status of the tumoroids as compared to the original tumors is currently under evaluation.

Conclusion: We here show successful 3D culturing of cell lines with alternative substrates. Further fine-tuning of the chosen reproducible system's simplicity and cost is required before culturing tumoroids from lung cancer patients can be launched.

Citation Format: Karina Malmros, Daniel Carlsén, Hans Brunnström. Standardized conditions for growth of lung cancer tumoroids cultured reproducibly in 3D-cultures [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 7561.
Abstract 7563: Efficacy of JPI-547, novel dual PARP inhibitor, in endometrial cancer cell line
Authors: Lee Shin-Wha , Nam So-Hyun , Park Su-Bin
Published: March 2024

Objectives: PARP inhibitor is effective in treating DNA repair deficiency endometrial cancer. Endometrial cancer (EC) is one of the most common gynecological cancers in developed countries and its incidence is increasing, and the prognosis of patients with early stage and low-risk EC is very good, but the prognosis of progressive and recurrent EC is poor. Novel PARP inhibitor JPI-547 is a PARP and tankyrase dual inhibitor, and in cancer cells, tankyrase inhibitor plays an important role in DNA repair, telomere maintenance, and cell survival. This experiment was conducted to determine whether the reactivity of the PTEN mutant EEC was increased by using the Novel PARP inhibitor.

Method: Human endometrioid endometrial cancer cell lines, Hec-1A, Hec-1B and Ishikawa were obtained. Cell viability assay for the drugs Olaparib and JPI-547 were assessed. Colonies consisting of at least 50 cells were counted. The number of dead cells was counted in five different areas of the hemocytometer, and the experiment was performed three times. The percentage of dead cells was analyzed compared to the untreated group. We confirmed the efficacy by siRNA transfection and immunofluorescence.

Result: When treated with Olaparib, there was no change in cell viability in the rest of the cells except for Ishikawa cells, which are PTEN mutations. It decreased by 35.4% in Ishikawa cells, whereas when treated with JPI-547, all cell lines Hec-1A, Hec-1B, and Ishikawa cell viability decreased by 28%, 34.3%, and 48.7%, respectively. PTEN knock-down reduced cell visibility by 28% when treated with olaparib, whereas when treated with JPI-547, Hec-1A (siCont) and Hec-1A (siPTEN) decreased by 26% and 42%, respectively, in all cells regardless of whether PTEN knock-down is present. When treated with Olaparib, dead cells were identified only in PTEN knock-down cells, increasing by 22%. When treated with JPI-547, dead cells increased by 25.5% and 33% in all cells of Hec-1A (siCont) and Hec-1A (siPTEN), respectively. It was confirmed that JPI-547 can reduce cell viability regardless of the formation of Rad51 according to PTEN.

Conclusion: JPI-547, a novel PARP inhibitor, showed good efficacy in PTEN mutation and PTEN-wild-type EEC cell lines than in conventional PARP inhibitor. The effect of reducing survival of ECC cell line with JPI-547 was confirmed with or without PTEN mutation. Further evaluation and in vivo experiments are needed to prove the efficacy of JPI-547 in EC.

Citation Format: Shin-Wha Lee, So-Hyun Nam, Su-Bin Park. Efficacy of JPI-547, novel dual PARP inhibitor, in endometrial cancer cell line [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 7563.
Abstract 7564: DNA methylation profiling identifies two distinct groups of oligosarcoma, IDH-mutant with distinct genetic alterations and clinical outcomes
Authors: Zhang Kenan , Liu Lingyu , Liu Xing , Jiang Tao
Published: March 2024

DNA methylation has been extensively adopted for the classification of brain tumors and is endorsed by current neuropathology guidelines. Recently, oligosarcoma, IDH-mutant has been characterized as a distinct group of IDH mutant gliomas by DNA methylation classification. However, emerging studies revealed the variety in this group. Here, we employed DNA methylation-based t-SNE analysis to characterize oligosarcomas identified by the dkfz brain tumor classifier (v12.5). Thereby, we uncovered that oligosarcomas were segregated into two distinct groups, namely, subgroup A and subgroup B, which were further validated by genetic alterations and clinical outcomes. Next-generation Sequencing revealed subtype A tumors enriched with chr 1p/19q co-deletion, chr 6q loss, CDKN2A/B homogeneous deletion, TERT promoter mutation, and NF1 mutation, while subtype B tumors showed chr7 gaining and TP53 mutation. RNA sequencing and gene set enrichment analysis (GSEA) revealed that neuronal-tumor interaction and muscular progression pathways were more enriched in subtype A tumors. In contrast, subtype B tumors showed enrichment for angiogenesis and mTOR pathways. Additionally, inter-chromosomal fusion genes were more frequently found in subtype A tumors. Clinically, patients with subgroup A oligosarcomas manifested poorer survival and distinct imaging features in magnetic resonance imaging (MRI) compared to those with subgroup B. Collectively, we provided more cases of oligosarcoma, IDH-mutant, confirming the existence of this newly identified group, and revealed the subgroups harboring different genetic alterations and suffering different prognoses, providing new evidence for the molecular pathology in diffuse glioma.

Citation Format: Kenan Zhang, Lingyu Liu, Xing Liu, Tao Jiang. DNA methylation profiling identifies two distinct groups of oligosarcoma, IDH-mutant with distinct genetic alterations and clinical outcomes [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 7564.
Abstract 76: Correlated multi-scale 3D optical microscopy of tumor tissues
Authors: Zheng Jingtian , Lee Steve Seung-Young
Published: March 2024

Three-dimensional (3D) optical microscopy in combination with advanced tissue clearing methods permits the interrogation of intact large-sized tumor tissues. There are many optical microscopy methods (e.g. light-sheet and confocal microscopy) offering 3D tumor images at varying levels of spatial resolution (e.g. organ, tissue, cell, and molecule level). However, it is a challenge to correlatively integrate various resolution 3D images obtained by different optical microscopy of tumor tissue. In this project, we developed a correlated multi-scale 3D optical microscopy method that enables the acquisition of macroscopic to microscopic spatial information from a single tumor tissue in 3D. Firstly, we used light sheet microscopy to image a whole large-sized, cleared tumor tissue and analyzed the results to identify regions of interests (ROIs). After defining ROIs in the 3D whole tumor image, we added a UV-activatable visible dye, spiropyran, in the agarose gel surrounding the cleared tumor and exposed the sample to a UV light sheet horizontally at the height (z-axis) of the tumor where the ROIs present. The activated dye showed ‘purple’ colored lines in the agarose gel and we physically marked the gel along the visible colored lines. We further sectioned the tumor at the ROI positions using a vibratome after reversing tissue clearing process. After immunofluorescence staining and aqueous-based tissue clearing, confocal microscopy allowed the localization of various cell types in the ROIs of tumor macrosections. To validate the method for multi-scale evaluation of cancer immunotherapy, we tested it with control and DMXAA-treated mouse mammary tumor tissues. We successfully acquired the 3D images of whole tumors by capturing autofluorescence signals with a 633 nm excitation laser and its matched emission filter. Based on the autofluorescence tumor images, we defined two ROIs for each control and treated tumor and performed optical marking and physical sectioning of the tumors as described above. Next, we stained the macrosections (400 µm thick) with DAPI, CK8-DL488, CD45-DL550, and ER-TR7-DL680 to visualize cancer, immune, and stromal cells in the ROIs at cellular resolution. We quantitatively analyzed the correlated multi-scale 3D image data for assessment of the effects of DMXAA treatment on the tumor microenvironment including eradiation of cancer cells, immune infiltration, and remodeling of tumor stroma. In summary, this new microscopy method will provide comprehensive spatial information of tumor tissues and benefit a broad cancer research field such as the discovery of new tumor biomarkers and the development of effective cancer therapies.

Citation Format: Jingtian Zheng, Steve Seung-Young Lee. Correlated multi-scale 3D optical microscopy of tumor tissues [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 76.
Abstract 7603: Targeting MTAP-deleted tumor via synthetic lethality with a combination of a PRMT5i and an MAT2Ai
Authors: Zhang Guiping , Li Jiapeng , Li Jie Jack
Published: March 2024

MTAP (methylthioadenosine phosphorylase) is located adjacent to the tumor-suppressor gene CDKN2A (cyclin-dependent kinase inhibitor 2A) and sometimes co-deleted in 10-15% of all cancers, especially in glioblastoma, mesothelioma, and pancreatic cancers. Recent studies shown that MTAP deletions in cancer create vulnerability to synthetic lethal with the MAT2A/PRMT5/RIOK1 axis. Herein, we report the discovery of a PRMT5 inhibitor GH56, and an MAT2A inhibitor GH31, both showed promising single agent efficacy and synergy in MTAP loss tumor models. GH56 is an MTA-Cooperative PRMT5 inhibitor. In vitro, GH56 showed potent SDMA inhibition in MTAP-deleted cancer cells with an IC50 from 0.8‒3 nM. It also showed excellent selectivity with more than 100-folds in MTAP-WT cells. In a cell panel with more than 100 cell-lines, GH56 selectively inhibited the growth of cells with MTAP-deletion while separated the cells with MTAP-WT. In the safety panel and kinase panel, GH56 all showed good selectivity. In addition, GH56 had an IC50 > 10 μM for hERG. In vivo, GH56 showed dose-dependent efficacy in a series MTAP-deleted models and were well tolerated. In U87MG glioblastoma CDX model, NCI-H838 NSCLC CDX model, BXPC-3/HupT4 PDAC CDX models and RT112-84 BLCA model, TGI for GH56 at high dose were all >100%. On the other hand, GH31 is a potent and selective MAT2A inhibitor. GH31 also showed excellent selectivity with MTAP-deleted and MTAP-WT cell lines. The combination of GH56 and GH31 showed synergy both in vitro and in vivo. The low dose GH31 combination with low-dose GH56 achieved the similar efficacy as high dose GH56 and a more rapid tumor regression. In view of the delayed onset of the tumor response and high dose needed by PRMT5 inhibitor (reported by clinic stage compounds), the combination of PRMT5i and MAT2Ai will be advantageous. Furthermore, both GH56 and GH31 are brain penetrant, especially for GH31, with a Kpuu > 0.6 and B/P > 2. The combination of GH56 and GH31 in a brain metastasis model and a glioblastoma in situ model all showed strong synergy, demonstrated the potential for the treatment of glioblastoma and other cancer with brain metastasis. In summary, we discovered potent, selective and brain penetrant PRMT5 inhibitor GH56 and MAT2A inhibitor GH31. Both compounds are currently under evaluation in IND-enabling studies and will provide more options for MTAP-deleted cancers.

Citation Format: Guiping Zhang, Jiapeng Li, Jie Jack Li. Targeting MTAP-deleted tumor via synthetic lethality with a combination of a PRMT5i and an MAT2Ai [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 7603.
Abstract 7607: Single-cell genomics study before and after neoadjuvant therapy for triple-negative breast cancer
Authors: Shao Yingkuan , Xu Kailun
Published: March 2024

Breast cancer has become the most common malignant tumor globally. Neoadjuvant chemotherapy (NAC) has become an important treatment option for locally advanced breast cancer, capable of eliminating circulating tumor cells (micrometastases) and achieving downstaging objectives. However, even after completing neoadjuvant chemotherapy or receiving local treatment, some patients may still have residual lesions, which are a key factor in distant recurrence and metastasis. The existing clinical biomarker tests such as CEA, CA-153, and imaging methods are unable to accurately assess the condition early on. Although tissue pathology biopsy of tumor specimens is the gold standard for clinical pathological diagnosis, it also has certain limitations. Traditional high-throughput sequencing technology for breast cancer primarily identifies "driver genes" associated with the occurrence and development of breast cancer. However, it has limitations in identifying genomic structural changes and subclones of breast cancer, and it overlooks the heterogeneity among tumor cells. The emergence of single-cell RNA sequencing (scRNA-seq) technology can detect these heterogeneous individuals, decode the heterogeneity of breast cancer cells, refine molecular subtypes, and open up new pathways to overcome drug resistance. We collected samples from 6 patients with locally advanced triple-negative breast cancer (ER-, PR-, HER2-negative, defined as HER2 immunohistochemistry 0, 1+ or 2+ but FISH-negative). We compared the cell subgroups and their gene expression in biopsy specimens before neoadjuvant chemotherapy with those in post-treatment specimens obtained during surgery, analyzing changes in cell composition in the tumor microenvironment before and after immunotherapy to identify specific cell types potentially contributing to the outcome of immunotherapy, particularly cell subtypes associated with T-cell clonal proliferation. We found that in the group with good neoadjuvant treatment response (Miller-Payne grade 4-5), B cells, CD4+ T cells, CD8+ T cells, and Tregs cells were all significantly downregulated, while endothelial cells and aSMA-positive fibroblast cells were significantly upregulated. By comparing changes in the immune microenvironment between patients with and without T-cell clonal proliferation before and after treatment, we revealed the differentiation patterns of various immune cells in immunotherapy and potential mechanisms of action.

Citation Format: Yingkuan Shao, Kailun Xu. Single-cell genomics study before and after neoadjuvant therapy for triple-negative breast 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 7607.
Abstract 7650: An analysis of the prognostic role of sarcopenia derived with fully automated deep learning slice-based muscle estimation in patients with metastatic non-small cell lung cancer (NSCLC)
Authors: Safta Wiem , Santana-Davila Rafael , Paulucci David , Geese William J. , Grootendorst Diederik J.
Published: March 2024

Introduction: Sarcopenia, progressive and generalized loss of skeletal muscle mass, is difficult and labor intensive to directly measure as it requires manual segmentations by radiologists from computed tomography (CT) scans. Sarcopenia has been shown to be a prognostic factor in some metastatic cancers. We evaluated the impact of sarcopenia derived via an automated segmentation algorithm on outcomes in the Phase 3 NSCLC clinical trial, CheckMate 227 (NCT02477826)

Methods: The sarcopenia score assessment involves automated selection of the L3 vertebra level slice from abdominal or chest, abdomen, and pelvis (CAP) CT scans, followed by automated segmentation of the muscle area from that slice. Sarcopenia scores were derived from previously established definitions of sarcopenia, with values below 41 cm2/m2 for female patients (regardless of BMI) and below 43 cm2/m2 or 53 cm2/m2 for male (based on BMI < 25 kg/m2 or ≥ 25 kg/m2). Among the 967 patients with evaluable scans, sarcopenia at baseline was identified in 68.39% (n=329/481) patients receiving nivolumab (NIVO) with ipilimumab (IPI) and 70.2% (n=341/486) receiving chemotherapy (Chemo).

Results: There was a trend of worse overall survival (OS) in patients with baseline sarcopenia across both treatment arms (minimum follow up 49.4 months). In patients with baseline sarcopenia vs ITT, median OS was 16.5 mo vs. 21.8 mo (p= 0.219) within the NIVO + IPI arm and 12.9 mo vs.15.0 mo (p= 0.273) within the Chemo arm respectively. Any increase in muscle mass from baseline to week 12 was associated with better OS for patients treated with NIVO+IPI (n=98) with sarcopenia at baseline compared to those without an increase in muscle mass (median OS 45.3 mo vs.19.5 mo, p= 0.012). This was not seen in those who received Chemo (n=87). Weight and muscle mass were moderately correlated at baseline (r=0.60).

Conclusions: We found that in CheckMate 227, baseline sarcopenia is associated with numerically worse OS, regardless of treatment, leading to potential use as a negative prognostic biomarker. Patients with NSCLC receiving immunotherapy might benefit from changes in muscle mass being monitored during treatment. Validation of these findings in other studies and other tumor types is warranted.

Citation Format: Wiem Safta, Rafael Santana-Davila, David Paulucci, William J. Geese, Diederik J. Grootendorst. An analysis of the prognostic role of sarcopenia derived with fully automated deep learning slice-based muscle estimation in patients with metastatic non-small cell lung cancer (NSCLC) [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 7650.