bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5875: Rab37 mediates intracellular trafficking and membrane presentation of PD-1 in T cells to foster an immunosuppressive microenvironment in lung cancer
Authors: Kuo Wan-Ting , Kuo I-Ying , Wu Shih-Ting , Su Wu-Chou , Wang Yi-Ching 
Published: April 2023

Abstract
Programmed cell death protein 1 (PD-1) expressed on the surface of CD8+ T cells is known as an immune checkpoint protein. High expression of PD-1 leads to T-cell dysfunction in the tumor microenvironment (TME). Our published studies show that Rab37 small GTPase-mediated vesicular trafficking of cell surface proteins and cytokines is critical in immunosuppressive TME. Here, we identify novel mechanisms of intracellular trafficking and plasma membrane presentation of PD-1 mediated by Rab37. Confocal immunofluorescence (IF) and vesicles isolation data demonstrated that PD-1 colocalized with Rab37-specific vesicles in T cells in a GTP-dependent manner. Total internal reflection fluorescence imaging, membrane fractionation, and flow cytometric analyses confirmed the dynamic trafficking and membrane presentation of PD-1 by Rab37. In addition, sucrose density gradient centrifugation and IF revealed that the level of glycosylated wild-type PD-1 in membrane compartment was more than glycosylation mutant PD-1, suggesting that glycosylation mutant PD-1 delayed in recruitment to the Rab37 vesicles and thus stalled in membrane presentation. Furthermore, T cell proliferation and activity were downregulated in Rab37 wild-type splenocytes co-cultured with cancer cells compared to those from Rab37 knockout mice using various T cell functional assays. Clinically, the multiplex IF-immunohistochemical assay indicated that the tumor infiltrated Rab37+/PD1+/TIM-3+/CD8+ exhaustion T cells were more in late staged lung cancer patients compared to those in early staged patients. Importantly, patients with Rab37+/PD-1+/TIM-3+/CD8+ tumor infiltrated T cells expression profile correlated with poor overall survival. Our results provide first trafficking mode of PD-1 mediated by Rab37 small GTPase and novel evidence of the tumor promoting function of Rab37/PD-1 axis in T cells of the tumor microenvironment.
Citation Format: Wan-Ting Kuo, I-Ying Kuo, Shih-Ting Wu, Wu-Chou Su, Yi-Ching Wang. Rab37 mediates intracellular trafficking and membrane presentation of PD-1 in T cells to foster an immunosuppressive microenvironment in 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 5875.
Abstract 5880: The role of SOAT1 on CD8+T cells-mediated immune response in ovarian cancer
Authors: He Jiangnan , Siu Michelle K.Y. , Long Runying , Zhang Ruiqian , Yung Mingo M.H. , Ngan Hextan Y. S. , Chan Karen K.L. 
Published: April 2023

Abstract
Introduction: Sterol-O acyltransferase 1 (SOAT1) functions by converting cholesterol and acyl-CoA into cholesterol ester and coA-SH. High SOAT1 expression with its mediated tumorigenesis has been shown in multiple cancers. Studies showed that SOAT1 inhibition by its inhibitors augmented the outcome of immunotherapies, in terms of the immune checkpoint blockades, cancer vaccines, and CAR-T cells, by boosting the function of T cells. However, in order to have a better understanding of the role played by SOAT1 in the tumor microenvironment of ovarian cancer (OC) and optimize strategies of combination immunotherapy, it’s necessary to detect the role of SOAT1 in OC cells on T cell-mediated immune response.
Methods: SOAT1 knockdown was manipulated by siRNAs transfection. SOAT1 was inhibited by avasimibe and OC cells were treated in different doses of avasimibe. qPCR was performed to detect gene expressions in ovarian cancer cells. T cells, isolated and activated from healthy donors, were cocultured with SOAT1-silenced and avasimibe pre-treated OC cells and their tumor-conditioned medium (TCM). Flow cytometry analysis was used to measure cytotoxic secretory molecules of human T cells, like IFN-r, TNF-a, and Granzyme B.
Results: The downregulation of intracellular cytotoxic cytokines was shown in the T cells cocultured with SOAT1-silenced and avasimibe-pretreated OC cells or treated by their TCM, thereby impairing the cytotoxic capacity of T cells, compared to the corresponding control group. qPCR results showed that several immunosuppressive cytokines, like IL-6, IL-8, TGF- were upregulated in the SOAT1-silenced or avasimibe-treated OC cells.
Conclusion: SOAT1 inhibition in ovarian tumor cells impairs CD8+ T cell cytotoxic function, to some extent, via the upregulation of immunosuppressive-related cytokines.
Citation Format: Jiangnan He, Michelle K.Y. Siu, Runying Long, Ruiqian Zhang, Mingo M.H. Yung, Hextan Y. S. Ngan, Karen K.L. Chan. The role of SOAT1 on CD8+T cells-mediated immune response in ovarian 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 5880.
Abstract 5901: Microbiome and genomic profiling in rectal adenocarcinoma
Authors: Hein David , Coughlin Laura , Poulides Nicole , Koh Andrew , Sanford Nina 
Published: April 2023

Abstract
Introduction: Recent studies have identified bacteria associated with colorectal cancer (CRC), with some data supporting causality in preclinical CRC models. We examined the gut microbiome composition and tumor genomic profiles in a diverse cohort of rectal cancer patients.
Methods: Twenty-two patients with newly-diagnosed, Stage II-IV rectal cancer without pathogenic germline mutations (mismatch repair genes, MUTYH) were included in the study. Gut microbiome profiling was performed on genomic DNA extracted from collected fecal samples (16S rRNA sequencing, V4 region). Tumor specimens were tested for somatic and germline mutations using the Tempus xT 648-gene panel and whole transcriptome RNA sequencing, providing information on tumor mutation burden (TMB), pathogenic KRAS mutation status and consensus molecular subtype (CMS). We then assessed differential abundance of microbial taxa (using ANCOM-BC) between the following groups: high vs low TMB (dichotomized at median, 3.7 mut/MB), presence versus absence of pathogenic KRAS mutation, and CMS subtype.
Results: The median age of study subjects was 49 years (range 37-78). Racial/ethnic breakdown was as follows: 2 non-Hispanic Asian, 4 non-Hispanic Black, 5 non-Hispanic White, and 11 White Hispanic. Twelve tumors carried a pathogenic KRAS variant and the median TMB was 3.7 m/MB (range 0.5-8.9 m/MB). Among 20 tumors that underwent whole transcriptome RNA sequencing, 1 was categorized as CMS1, 8 CMS2, 3 CMS3, 7 CMS4, and 2 CMS undetermined. There were no statistically significant differences in gut bacteria taxa abundance by KRAS mutation status or among CMS subtypes. The group with greater than median TMB, however, had statistically significant enrichment of Pepostreptococcus stomatis (18.4 fold increase, p=0.039 after Benjamini-Hotchberg adjustment with FDR = 0.05).
Conclusions: In this pilot study, we found that CRC patients with higher TMB had an enrichment of Peptostreptococcus stomatis, a bacteria associated with colonic dysplasia in mouse models and enriched in CRC patients as compared to healthy controls. (PMID 28823860, 35292756) Higher TMB is a predictive biomarker for response to immunotherapy across cancer types including CRC. Since the gut microbiome is potentially modifiable, further research is needed to better elucidate the connection between microbiome and CRC carcinogenesis including specific mutation profiles, which could pave the way for microbiome-related risk reduction or therapeutic strategies in CRC.
Citation Format: David Hein, Laura Coughlin, Nicole Poulides, Andrew Koh, Nina Sanford. Microbiome and genomic profiling in rectal adenocarcinoma. [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 5901.
Abstract 5985: Cyclin dependent kinase 9 (CDK9) inhibition increased efficacy of programmed cell death protein 1 (PD-1) blockade for hepatocellular carcinoma (HCC) through decreasing programmed death-ligand 1 (PD-L1) expression
Authors: Chen Ching-Tso , Shao Yu-Yun , Hsu Hung-Wei , Wo Rita R. , Wang Han-Yu , Cheng Ann-Lii , Hsu Chih-Hung 
Published: April 2023

Abstract
Background: PD-1 blockade has been approved as treatment for advanced HCC. We previously demonstrated the efficacy of CDK9 inhibition in reducing the expression of inducible proteins and as a treatment for HCC (Shao et al. Oncology 2022). We thus examined the influence of CDK9 inhibition on the expression of PD-L1 in HCC and the potential of improving the efficacy of PD-1 blockade with the combination of CDK9 inhibitors.
Methods: We first examined the influence of specific CDK9 inhibitors, AZD4573 and atuveciclib, on interferon-γ (IFN-γ) induced PD-L1 expression of human HCC cell lines HuH7 and Hep3B. Overexpression of CDK9 and siRNA to CDK9 were used to confirm the findings. Similar experiments were repeated in the mouse HCC cell line BNL. To test the in vivo efficacy, we orthotopically implanted BNL cells in the subcapsular area of BALB/c mice, which were then treated with vehicle, CDK9 inhibitors, anti-PD-L1 antibodies, or their combination. To compare with tumor sizes, all mice were sacrificed after 14 days of treatment. To compare survival, the mice were only sacrificed if they met the criteria of animal euthanasia.
Results: Both HuH7 and Hep3B cells had minimal PD-L1 expression, which however could be induced using IFN-γ. AZD4573 and atuveciclib decreased the IFN-γ induced PD-L1 expression of HuH7 and Hep3B cells in a dose dependent manner. The flow cytometry results confirmed that membrane PD-L1 expression was also decreased by CDK9 inhibition. Overexpression of CDK9 decreased the influence of these CDK9 inhibitors on PD-L1 expression. CDK9 knockdown using siRNA reduced the IFN-γ induced PD-L1 expression. AZD4573 and atuveciclib also reduce the PD-L1 expression in BNL cell lines. In the orthotopic animal model, the tumors of the sacrificed mice were significantly smaller in mice treated with atuveciclib and an anti-PD-L1 antibody than mice treatment with either alone. The survival of mice treated with the combination was also longer than mice treated with each therapy alone.
Conclusion: We demonstrated that CDK9 inhibition could reduce the IFN-γ induced PD-L1 expression of HCC cells. Combination of CDK9 inhibitors and anti-PD-L1 antibodies was more effective than either therapy alone.
Citation Format: Ching-Tso Chen, Yu-Yun Shao, Hung-Wei Hsu, Rita R. Wo, Han-Yu Wang, Ann-Lii Cheng, Chih-Hung Hsu. Cyclin dependent kinase 9 (CDK9) inhibition increased efficacy of programmed cell death protein 1 (PD-1) blockade for hepatocellular carcinoma (HCC) through decreasing programmed death-ligand 1 (PD-L1) expression. [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 5985.
Abstract 5988: A non-canonical CDK9 complex mediates endocycling in polyaneuploid cancer cell (PACC) state
Authors: Lee Cheng-fan , Loycano Michael , LOFTUS Luke , Kostecka Laurie , Li Melvin , Amend Sarah , Pienta Kenneth 
Published: April 2023

Abstract
Once prostate cancer has spread from its primary site, treatment is limited to systemically administered therapy. While tumors initially respond to these therapies, eventually, all therapies fail, and the tumor recurs. Ours and others' recent studies have shown the presence of a universal mechanism of resistance: accession of the polyaneuploid cancer cell (PACC) state. The PolyAneuploid Transition (PAT) is initiated when a cancer cell is subjected to external stress, including therapy (we have tested three classes of chemotherapy and radiation), and accesses an alternative non-mitotic cell cycle known as endocycling, resulting in a greater-than-G2 polyploidization of the aneuploid genome (polyaneuploidy). While in this pro-survival PACC state, we have shown that cells are resistant to all forms of cytotoxic therapy. Initial RNA sequencing of cells that have accessed the PACC state in response to multiple classes of chemotherapy, including docetaxel and cisplatin, demonstrate a remodeled transcriptional profile that is distinct from control cultures. We hypothesize that accession of the resistance-mediating PACC state requires transcriptional remodeling. Our data show that cells in the PACC state had increased overall transcriptional activity. The multi protein complex pTEFB (positive transcription elongation factor) is a critical driver of RNA Polymerase II function and is composed of multiple subunits, including CDK9, a cyclin regulatory subunit, and a transcription factor. CDK9 phosphorylation was significantly elevated during accession and persistence in the PACC state. Genetic inhibitionof CDK9 by siRNA led to decreased expression of cyclin A which plays a role in S phase, both in the mitoticcycle and in the PACC endocycle. Interestingly, despite increased CDK9 levels, known CDK9 pTEFb complex members cyclin T1 and BRD4 were both decreased in cells in the PACC state. We treated cancer cells induced to enter the PACC state upon exposure to cisplatin with pharmaceutical inhibitors of CDK9, Flavopiridol and Fadraciclib. Combination of CDK9 inhibition with chemotherapy showed a suppressive effect on the PACC population. Our findings therefore suggest that a non-canonical CDK9 complex could be critical role for the endocycling to access and maintain the PACC state and represents a therapeutic candidate to eliminate the resistance-mediating PACC state.
Citation Format: Cheng-fan Lee, Michael Loycano, Luke LOFTUS, Laurie Kostecka, Melvin Li, Sarah Amend, Kenneth Pienta. A non-canonical CDK9 complex mediates endocycling in polyaneuploid cancer cell (PACC) state. [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 5988.
Abstract 6011: Methylation profiling reveals the role of PRC2 in regulating DNA methylome changes in malignant peripheral nerve sheath tumors
Authors: Stehn Christopher M. , Bhunia Minu , Williams Kyle B. , Larsson Alex T. , Largaespada David A. 
Published: April 2023

Abstract
Neurofibromatosis type 1 (NF1) syndrome is an autosomal dominant cancer predisposition syndrome defined by germline deletion of one NF1 allele. Somatic loss of heterozygosity in the remaining NF1 allele in Schwann lineage cells gives rise to benign tumors known as plexiform neurofibromas. These tumors have a high risk of developing into cancerous lesions known as malignant peripheral nerve sheath tumors (MPNST) through the sequential deletion of CDKN2A/B followed by recurrent mutations in SUZ12 or EED, constituting the inactivation of polycomb repressor complex 2 (PRC2). PRC2 is a transcriptional repressor complex involved in the silencing of several genes throughout cell development and differentiation. Loss of this complex leads to a depletion in trimethylation marks on Histone H3 Lysine 27 (H3K27me3) and the subsequent gain of acetylation marks on the same lysine residue (H3K27Ac). However, full range of epigenetic consequences of these events are currently not well characterized, especially with respect to MPNST formation and development. The Largaespada lab has developed Schwann cell lines engineered to harbor deletions in NF1 and either SUZ12 or EED and assayed the methylation status of 850,000 CpG sites using the EPIC array. The resulting methylation profiles reveal a large degree of change in promoter methylation between cell lines with and without PRC2 inactivation. These changes, however, appear to be inconsistent. To further understand this phenomenon, I have analyzed differential methylation patterns between lines with SUZ12/EED deletions on top of NF1 deletion compared to those with NF1 deletion alone. Pathway analysis of genes whose promoters are differentially methylated upon PRC2 reveals a bias towards developmental modules such as morphogenesis and neuronal differentiation, suggesting that DNA methylation is a mechanism by which PRC2 loss promotes stemness in Schwann lineage cells prior to MPNST formation. Additionally, differentially methylated regions were overlapped with functional non-coding elements in the genome to understand potential ripple effects in the epigenome. These findings underline the importance of DNA methylation in contributing to tumor formation and define unique functions by which PRC2 specifically leverages diverse methylation states to drive malignant transformation in Schwann lineage cells.
Citation Format: Christopher M. Stehn, Minu Bhunia, Kyle B. Williams, Alex T. Larsson, David A. Largaespada. Methylation profiling reveals the role of PRC2 in regulating DNA methylome changes in malignant peripheral nerve sheath tumors. [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 6011.
Abstract 6012: Comparison of pre-analytical methods for DNA methylation analysis of cfDNA
Authors: Tanic Miljana , Emiloju Oluwadunni , Dhami Pawan , Beck Stephan 
Published: April 2023

Abstract
Liquid biopsies in the form of cell-free circulating tumor DNA (ctDNA) isolated from blood plasma or serum have shown great promise to be used as minimally-invasive markers in cancer patients providing an insight into the composition of both primary tumor and metastases, and an opportunity to assess clonal dynamics throughout the course of disease. CtDNA carries not only tumor- specific changes in its sequence but also distinctive epigenetic marks, namely DNA methylation patterns similar to the patterns in the primary tumor. Deregulation of tissue-specific DNA methylation patterns is an early event in carcinogenesis holding great promise to be exploited for early detection of cancer. However, in contrast to mutation detection, targeted DNA methylation sequencing of cfDNA remains a challenge due to low concentration and heavy fragmentation. The limiting step in detection of any analyte is the recovery of the DNA molecules. The pre-analytical steps in the DNA methylation detection pipeline include extraction of cfDNA molecules and their conversion using sodium bisulfite. Bisulfite conversion is a harsh chemical reaction that induces further fragmentation and degradation of already scarce cfDNA. In this study we compared commercial methods for cfDNA extraction and for bisulfite conversion to evaluate the yield, degradation and procedural loss. We compared five commercial kits for cfDNA extraction from blood plasma, three column-based (Qiagen’s QIAamp Circulating nucleic acids kit, Norgen’s Plasma/Serum Cell-Free Circulating DNA Purification and Macherey-Nagel’s NucleoSpin® Plasma XS) and two based on magnetic beads cleanup (Bioo Scientific’s Next Prep magnetic Cell-Free Circulating DNA isolation kitand Applied Biosystems’ Magmax Cell-Free Circulating DNA isolation kit. The kits used for bisulfite conversion were Zymo EZ DNA Methylation Lightning with column based purification and with magnetic beads purification, Zymo EZ DNA Methylation Direct with column based purification and with magnetic bead purification, Qiagen Epitect Fast DNA Bisulfite and Diagenode Premium Bisulfite kits. Same samples were processed by each of the kits, Sample degradation was determined using Agilent Bioanalyzer dsDNA kit. Yield was evaluated by Picogreen, absolute qPCR for single-copy gene and for contamination of gDNA by a B-cell specific assay, while procedural loss was determined based on the recovery of a synthetic spike-in.
Citation Format: Miljana Tanic, Oluwadunni Emiloju, Pawan Dhami, Stephan Beck. Comparison of pre-analytical methods for DNA methylation analysis of cfDNA. [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 6012.
Abstract 6022: The importance of DNA methylation to breast cancer cell phenotype and its role in the anticancer activity of withaferin-A
Authors: Brane Andrew , Tollefsbol Trygve O. 
Published: April 2023

Abstract
Breast Cancer (BC) is a widespread malignancy that affects the lives of millions of women each year. Prevention of BC through administration of epigenetically active dietary phytochemicals has received increased interest in recent years due to its relatively low cost, few side effects and potential to reduce the financial and healthcare burdens associated with BC. Many phytochemicals’ anticancer functions are thought to arise from their effects on the epigenome, although the relative importance of specific genes’ epigenetic states remain unclear. To elucidate this, we utilized human BC cell lines in combination with CRISPR-dCas technology tied to methylation modifiers to explore the importance of gene specific DNA methylation to cancer cell phenotype in both naïve BC cells and BC cells treated with the phytochemical Withaferin A (WA). We found that demethylation of promoters of the tumor suppressors p21 and p53 results in increased gene expression, while methylation of the promoter of the oncogene CCND1 results in decreased in gene expression. Additionally, changes to biological processes were associated with tumor suppressor promoter methylation state, including increases in cell cycle arrest for a demethylated p21 promoter and decreases in cell viability for a demethylated p53 promoter. We also found that downregulation of p21 through targeting DNMT3A to its promoter was able to ablate the anticancer function of WA in both MDA-MB-231 and MCF-7 cells. Taken together, these results highlight the potential importance of DNA methylation changes for cancer cell phenotype and a possible mechanism of action for the phytochemical WA in BC prevention.
Citation Format: Andrew Brane, Trygve O. Tollefsbol. The importance of DNA methylation to breast cancer cell phenotype and its role in the anticancer activity of withaferin-A [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 6022.