bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5855: Spatial transcriptomics deciphers the cellular society of advanced colorectal cancer
Authors: Hashimoto Masahiro , Ozato Yuki , Nakano Yusuke , Abe Tadashi , Hisamastu Yuichi , Toshima Takeo , Yonemura Yusuke , Uemura Mamoru , Masuda Takaaki , Yamamoto Hirofumi , Mori Masaki , Eguchi Hidetoshi , Doki Yuichiro , Mimori Koshi 
Published: April 2023

Abstract
Introduction: In recent years, single-cell RNA sequencing (scRNA-seq) and high-dimensional spatial transcriptomics (ST-seq) have contributed significantly to our understanding of the tumor microenvironment (TME) in many cancers. This is essential for understanding the tumor-stromal crosstalk. Thus, integrating scRNA-seq data with ST-seq data will facilitate understanding intercellular communication in TMEs.
Material and Method: We performed and combined ST-seq in CRC with public scRNA-seq. And, immunohistochemistry (IHC) (HLA-G, CD68, and SPP1) was performed on 20 CRC surgical specimens collected in our hospital. To verify this, we knocked out H2-M3 (HLA-G in humans) in mouse CRC cell lines (MC-38 cells) using the CRISPR/Cas9 system and examined H2-M3 KO tumor volume in xenograft mouse models.
Results: We identified co-localized cells with CRC cells at the invasive front and those in the center based on the spatial distribution estimated by an analytical pipeline, Cell2location. At the invasive front, CRC cells co-localized more frequently with SPP1+ macrophages than other cells. To dissect the molecular machinery and cell types inducing SPP1+ macrophages, we found ligand activity by another pipeline, NicheNet. The prominent signal to SPP1+ macrophages was mediated by several ligand-receptor pairs including HLA-G- immunoglobulin-like transcript (ILT)2/ILT4. Next, we disclosed the effect on CD8+ cells, and SPP1+ macrophages secrete IL-10 suppressing the immune activity of CD8+ T cells. And the ratio of HLA-G-positive cancer cells was predominantly higher in areas with more SPP1+ macrophages by IHC in CRC. In vivo analysis, H2-M3 KO reduced CRC tumor volume and tumor tissue from H2-M3 KO cells exhibited higher SPP1 and CD68 staining compared with wild type cells.
Conclusion: SPP1+ macrophages and cancer cells secreting high levels of HLA-G may represent targets to improve the prognosis of patients with CRC. Further analysis is currently underway with a focus on early-stage cancer in carcinoma in adenoma.
Citation Format: Masahiro Hashimoto, Yuki Ozato, Yusuke Nakano, Tadashi Abe, Yuichi Hisamastu, Takeo Toshima, Yusuke Yonemura, Mamoru Uemura, Takaaki Masuda, Hirofumi Yamamoto, Masaki Mori, Hidetoshi Eguchi, Yuichiro Doki, Koshi Mimori. Spatial transcriptomics deciphers the cellular society of advanced colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5855.
Abstract 5879: Defining the cancer Immunogram using multimodal analysis to guide immunotherapy in diffuse large B cell lymphoma
Authors: Mattie Michael D. , Perbost Regis , Turcan Sarah , Danan Corinne , Locke Frederick L. , Neelapu Sattva S. , Miklos David B. , Jacobson Caron A. , Lekakis Lazaros J. , Lin Yi , Ghobadi Armin , Kim Jenny J. , Wang Zixing , Xue Allen , Filosto Simone , Scholler Nathalie , Galon Jerome 
Published: April 2023

Abstract
(a) Expansion of therapeutic strategies against diffuse large B-cell lymphoma (DLBCL) offers new opportunities to fight aggressive non-Hodgkin's lymphoma. Therapy approaches, such as R-CHOP and stem cell transplant, and CAR-T cell therapies are now available for the treatment of DLBCL. While the role of the tumor microenvironment (TME) during the therapeutic response is now recognized, the spatial organization and the communication between the diverse factors that compose the TME remains to be fully understood. In this study, we describe a new immunogram tool to help clinical researchers measure the tumor microenvironment contribution to drug efficacy or toxicity in DLBCL context.
(b) In a previous work, using a high-quality testing and innovative multimodal and integrative approach, we constructed the first Veracyte Biopharma Atlas for DLBCL lesions. Based on this knowledge and the understanding of the immune contexture of tumors, we constructed an immunogram using the scoring of clinically relevant biomarkers. Our immunogram scoring approach is composed of key features driving computational derivation of DLBCL Atlas clusters, which include immune gene signatures, immune cell phenotyping combined with spatial information, and genomic and clinical parameters.
(c) Patterns that strongly associated with CAR-T treatment response were determined. In addition, promising results have been obtained in the prediction to CAR-T toxicity related to T-regulatory cells or R-CHOP response with transcriptomic signature.
(d) Retrospective analysis of CAR-T clinical trial data and tumor biopsies highlighted the Veracyte Immunogram as a powerful tool to score the patient probability of response to CAR-T. This work provides the framework for identification of predictors of response to therapy, potential targets of interest or biomarkers that could be applied in future clinical trials.
Citation Format: Michael D. Mattie, Regis Perbost, Sarah Turcan, Corinne Danan, Frederick L. Locke, Sattva S. Neelapu, David B. Miklos, Caron A. Jacobson, Lazaros J. Lekakis, Yi Lin, Armin Ghobadi, Jenny J. Kim, Zixing Wang, Allen Xue, Simone Filosto, Nathalie Scholler, Jerome Galon. Defining the cancer Immunogram using multimodal analysis to guide immunotherapy in diffuse large B cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5879.
Abstract 5992: Cells rapidly adapt to CDK2 inhibitors via plasticity of the CDK2/4/6-Rb-E2F axis
Authors: Arora Mansi , Moser Justin , Hoffman Timothy E. , Watts Lotte P. , Min Mingwei , Musteanu Monica , Rong Yao , Schneider Jordan , Ill C Ryland , Nangia Varuna , Sanclemente Manuel , Lapek John , Nguyen Lisa , Niessen Sherry , Dann Stephen , van Arsdale Todd , Barbacid Mariano , Miller Nichol , Spencer Sabrina L. 
Published: April 2023

Abstract
CDK2 is a core cell-cycle enzyme that phosphorylates a variety of substrates to drive progression through the cell cycle. CDK2 is hyperactivated in multiple cancers and is therefore an attractive therapeutic target. Here, application of a novel small molecule CDK2/4/6 inhibitor, PF-06873600, enabled in-depth interrogation of CDK2 substrate phosphorylation, cell-cycle progression, and drug adaptation in preclinical models. CDK2-specific inhibition leads to rapid loss of substrate phosphorylation, but unexpectedly, CDK2 substrate phosphorylation rebounds within several hours. Whereas CDK1 is known to compensate for loss of CDK2 in Cdk2-/- mice, here we demonstrate an early dependence on CDK4/6 activity. CDK2 inhibition reveals latent CDK4/6 activity throughout S phase that backstops the proliferative program by maintaining Rb1 hyperphosphorylation, active E2F transcription, and Cyclin A2 expression, enabling re-activation of CDK2. Our results augment our understanding of CDK plasticity and indicate that co-inhibition of CDK2 and CDK4/6 is required to suppress adaptation to CDK2 inhibitors.
Citation Format: Mansi Arora, Justin Moser, Timothy E. Hoffman, Lotte P. Watts, Mingwei Min, Monica Musteanu, Yao Rong, Jordan Schneider, C Ryland Ill, Varuna Nangia, Manuel Sanclemente, John Lapek, Lisa Nguyen, Sherry Niessen, Stephen Dann, Todd van Arsdale, Mariano Barbacid, Nichol Miller, Sabrina L. Spencer. Cells rapidly adapt to CDK2 inhibitors via plasticity of the CDK2/4/6-Rb-E2F axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5992.
Abstract 6020: The role of TP53 mutation status in the response to DNA methyltransferase inhibitor treatment
Authors: Omar Khadra K. , Grundy Erin E. , Cox Olivia , Hadley Melissa , Chiappinelli Katherine B. 
Published: April 2023

Abstract
The purpose of this study was to understand the effect of p53 mutation status in ovarian cancer cells on the expression of repetitive elements (REs) following epigenetic treatment. High-grade serous ovarian carcinoma is the most aggressive subtype of ovarian cancer and the 5 year survival rate has remained unchanged for over two decades. Over 90% of high-grade serous ovarian carcinoma (OC) patients have a mutation in the TP53 gene, which encodes the p53 protein. P53 is a transcription factor primarily involved in maintaining genome integrity, but it can also regulate the expression of REs in the genome. REs account for more than half of the genome and these repetitive genomic elements are epigenetically silenced in healthy cells to prevent genome instability. The expression of some REs, such as long interspersed nuclear elements and endogenous retroviruses, are upregulated in human OC patients and cell lines. The mechanism by which p53 regulates expression of REs is not well-understood; the literature documents some instances of p53 activating RE transcription and others of p53 repressing RE transcription, depending on the target elements. We have previously shown that RE expression can be induced by treating OC cells with low doses of DNA methyltransferase inhibitors (DNMTis). Recently, we showed that OC cell lines with mutant p53 have higher baseline expression of REs compared to wild type (WT) cell lines. Treatment of TP53 mutant OC cell lines with DNMTis had a muted effect on RE expression compared to treatment of WT OC cell lines. To explore the relationship between TP53 mutation status and RE expression after DNMTi treatment, OC cell lines with different p53 mutation statuses were treated with 500 nM of the DNMTi 5-azacytidine. We then analyzed the expression of several REs via RT-qPCR and western blot. We hypothesized that TP53 mutant cell lines would have lower DNMTi upregulation of REs than TP53 WT cell lines. While at the RNA level RE expression was variable, at the protein level, we found that DNMTi treatment increased protein levels of several REs in TP53 WT and mutant, but not null, OC cell lines. Future work will examine the feasibility of utilizing these RE proteins as immunotherapy targets in OC.
Citation Format: Khadra K. Omar, Erin E. Grundy, Olivia Cox, Melissa Hadley, Katherine B. Chiappinelli. The role of TP53 mutation status in the response to DNA methyltransferase inhibitor treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6020.
Abstract 6039: ELOVL5 affects prostate cancer cell proliferation and modulates the AR pathway
Authors: Rodrigues Silvia D. , Ribeiro Caroline , Teixeira Isadora , Pakula Hubert , Fanelli Giuseppe N. , Socciarelli Fabio , Butler Lisa , Swinnen Johannes , Loda Massimo 
Published: April 2023

Abstract
Prostate cancer (PCa) is characterized by alterations in lipid metabolism, exemplified by increased rates of de novo lipogenesis and elongation by fatty acid elongase enzymes known as ELOVLs (elongation of very long chain fatty acids). We have previously shown that the ELOVL family members ELOVL2, 5, and 7 are Androgen Receptor (AR)-regulated proteins; and that ELOVL5 is overexpressed in both primary and castration-resistant prostate cancer. To confirm the role of ELOVL5 activity in prostate carcinogenesis, we generated genetically engineered mouse models (GEMM) with deletion of Elovl5, validated by immunohistochemistry, in combination with the overexpression of c-Myc, an oncogene known to affect lipid metabolism in cancer cells. As expected, we observed alterations in the lipid profile of the murine prostate with the partial deletion of Elovl5, as determined by a significant reduction in levels of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) with long-chain fatty acids (22 carbons) and increased levels of PE with short-chain fatty acids (14 carbons), suggesting an overall shortening on acyl chains of the most common phospholipid species. Interestingly, we also observed that the heterozygous deletion of Elovl5 reduced the expression levels of the AR on the anterior lobe of the murine prostate, in comparison to tissue from Elovl5 wild type mice. Preliminary data also indicates a modulation in prostate volume when Elovl5 is genetically deleted in comparison to tissue from wild type mice. Heterozygous Elovl5 deletion did not affect healthy tissue.To explore biological effects, we generated a 3D organoid line derived from the prostate of mice with homozygous deletion of Elovl5 and overexpression of c-Myc. We found that Elovl5 knock-out decreased organoid diameter and proliferation of c-Myc-driven cells compared to Elovl5 WT. This effect was potentiated when organoids were treated with Enzalutamide, suggesting that targeting Elovl5 may sensitize prostate cells to anti-androgen therapy.Our findings suggest lipid elongation via ELOVL5 as a potential therapeutic target for PCa.
Citation Format: Silvia D. Rodrigues, Caroline Ribeiro, Isadora Teixeira, Hubert Pakula, Giuseppe N. Fanelli, Fabio Socciarelli, Lisa Butler, Johannes Swinnen, Massimo Loda. ELOVL5 affects prostate cancer cell proliferation and modulates the AR pathway. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6039.
Abstract 604: Hybrid quantification of SILAC-barcoded interacting tumor and T cells
Authors: Molero Sofía Ibáñez , Atmopawiro Alisha , Terry Alex , Altelaar Maarten , Peeper Daniel , Stecker Kelly 
Published: April 2023

Abstract
Therapeutic interference of cell-cell communication mechanisms has allowed the clinical development of multiple cancer treatments. For example, the therapeutic intervention of T cell-tumor cell interactions of PD-1 and PD-L1, respectively, by immune checkpoint blockade (ICB) has improved the clinical outcome of cancer patients. However, only a minority of patients are currently benefiting from ICB. Thus, there is an urgent need to improve our understanding of the T cell-tumor cell interplay. Recently developed algorithms serve to deconvolute gene expression of physically interacting cells (PIC). However, such approaches are limited for proteomics (MS) and phosphoproteomics (pMS), which are required to get molecular insight into protein functionality. Here, we present a new method: Hybrid quantification of SILAC-barcoded interacting cells (HySic). Briefly, we use Stable Isotope Labelling by Amino acids in Cell culture (SILAC) to differentiate between two cell types of interest: T cells and tumor cells. We co-cultured the cells allowing to engage in functional interactions and without the need to separate them, and subsequently performed a label-free quantification (LFQ) LC-MS analysis. After initial bioinformatic analysis and validation with independent techniques, we used HySic to unravel protein mechanisms contributing to functional T cell-tumor cell interactions. We used established interaction mechanisms like those mediated by IFNγ signaling proteins to benchmark HySic, while this analysis also brought new protein pathways to light, which will be presented. In conclusion, we have established and validated HySIC as a new method to study protein signaling dynamics in physically interacting cells. Our data shows the effectiveness and applicability of HySIC to study cell-cell interactions, which could be easily extended to other biological systems.
Citation Format: Sofía Ibáñez Molero, Alisha Atmopawiro, Alex Terry, Maarten Altelaar, Daniel Peeper, Kelly Stecker. Hybrid quantification of SILAC-barcoded interacting tumor and T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 604.
Abstract 6049: Exogenous serine promotes cancer stem cells in oral squamous cell carcinoma
Authors: Jankowski Stacy Ann , Hardy Nina C. , Kukuruzinska Maria A. 
Published: April 2023

Abstract
Cancer development and progression is associated with metabolic reprogramming of tumor cells required to meet their proliferative, bioenergetic and survival challenges. Some metabolites, including a non-essential amino acid, serine, have been shown to play a role in tumorigenesis by promoting aggressive cell states, such as cancer stem cells (CSCs). Previous studies from our laboratory showed that the nuclear branch of the Wnt/β-catenin signaling pathway, the β-catenin/CBP/MLL1 axis, enhanced CSC states during oral squamous cell carcinoma (OSCC) evolution through H3K4 trimethylation (H3K4me3) and epigenetic remodeling of the chromatin landscape. Given that metabolism has also been shown to modulate cell plasticity via epigenomic modifications, we have aimed to decode the relationship between serine synthesis and cell identity in OSCC.
We have shown that under serine starvation conditions, OSCC cells upregulate steady-state mRNA and protein levels of serine synthesis pathway enzymes. The latter is associated with an increase in the by-product, alpha-ketoglutarate (αKG), a co-substrate for nuclear αKG-dependent dioxygenases, which demethylate histone marker H3K27me3 and de-repress differentiation-associated genes. Furthermore, increased production of αKG is associated with downregulation of the β-catenin/CBP/MLl1 complex and CSC-associated H3K4me3.
In this study, we used human OSCC cell lines CAL27 and HSC3, derived from a primary tongue tumor and a metastatic site, respectively. Each cell line was cultured in either complete medium or serine starvation medium. Serine starvation conditions led to a downregulation of H3K27me3 along with H3K4me3, promoting a switch from cancer stem cell to differentiation-enhancing chromatin landscape. The observed changes in cell plasticity were further investigated through tumorsphere formation, a surrogate assay for cancer stem cells. We found that OSCC CAL27 and HSC3 cells readily formed tumorspheres replete with stem cell markers BMI1, KRT14 and SOX2, under non-adhesive conditions when grown in complete media, supporting our findings that utilization of exogenous serine enables OSCC cells to maintain stemness. Our findings suggest that a switch from exogenous serine uptake to the endogenous serine biosynthesis promotes OSCC cell differentiation concomitant with the loss of CSC identity.
Citation Format: Stacy Ann Jankowski, Nina C. Hardy, Maria A. Kukuruzinska. Exogenous serine promotes cancer stem cells in oral squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6049.
Abstract 605: Single cell RNA sequencing reveals tumor immune microenvironment and T cell receptor diversity in epidermal growth factor receptor (EGFR) mutated lung cancer
Authors: Chakrabarti Turja , Wu Wei , Kerr Daniel L. , Allegakoen Paul , Bivona Trever G. , Blakely Collin M. 
Published: April 2023

Abstract
Background:
Somatic alterations in the Epidermal Growth Factor Receptor (EGFR) gene represent a common subset of oncogene-driven lung cancer. Patients who receive EGFR-targeted tyrosine kinase inhibitor (TKI) therapy inevitably develop treatment resistance with limited options after disease progression, with immune checkpoint inhibitor therapy (ICI) typically ineffective. Tumor Immune Microenvironment (TME) characteristics, including T-cell receptor (TCR) sequencing and clonality have been incompletely explored in this population.
Methods:
We further analyzed our group’s available data from a previous study on therapy-induced evolution of human lung cancer (Maynard et. al, PMID: 32822576). Tumor samples were sorted and subjected to smartseq-based single-cell RNA sequencing. A total of 7495 cells were derived from 17 samples from 10 patients with tumors that harbored EGFR driver gene mutations. This included 1322 gene marker-annotated T-cells. Samples were grouped into three treatment conditions: treatment naïve (TN), residual disease (RD), and progressive disease (PD). We then used the TraCeR tool to infer the TCR α, β, and the complementarity-determining region 3 (CDR3) sequences.
Results:
T-cells were enriched in RD (55.2%) relative to TN (12.8%) and PD (31.9%) (p&lt;0.0001, Chi-square test) with cytotoxic T-cells as the predominant phenotype across treatment conditions. Increased expression of CTLA4, and LAG3 occurred in PD (p&lt;0.0001, Kruskal-Wallis test). Single-cell TCR analysis revealed increased TCR clonal diversity in PD (Shannon Diversity Index: 0.261 PD &gt; 0.255 TN &gt; 0.205 RD) while increased clonal expansion occurred in RD (32 clones from 4 patients) as compared to TN (17 clones from 1 patient) and PD (14 clones from 1 patient) (p&lt;0.0001, Chi-square test).
Conclusion:
T-cell infiltration is greatest in RD, while immunosuppressive genes were significantly expressed in PD. Increased TCR clonal expansion with less clonal diversity in RD suggests the presence of tumor-specific TCR clones and that this may be the optimal time to initiate ICI treatment. Future directions will include the identification of clonally expanded TCR and matched neoantigens to provide potential tailored immunotherapies for patients with TKI-resistant tumors.
Citation Format: Turja Chakrabarti, Wei Wu, Daniel L. Kerr, Paul Allegakoen, Trever G. Bivona, Collin M. Blakely. Single cell RNA sequencing reveals tumor immune microenvironment and T cell receptor diversity in epidermal growth factor receptor (EGFR) mutated lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 605.