bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB153: Inhibiting BRD4 as a proposed alternative therapeutic strategy for HPV16-associated head and neck squamous cell carcinoma
Authors: Suresh Dhruthi , Mohanty Chitrasen , Wang Albert R. , Kendziorski Christina , Iyer Gopal
Published: April 2023

Integration of Human Papilloma Virus (HPV) 16 into human genomes is an integral event for cancer progression in Head and Neck Squamous Cell Carcinoma (HNSCC). There is a need to differentiate treatment for HPV-16 integrated HNSCC from other subtypes. We hypothesize that by inhibiting Bromodomain Extra Terminal (BET) protein BRD4, a transcriptional co-regulator of host and viral genes can advance treatment in patients with the integrated subtype of HPV16 associated HNSCC. Through small molecule inhibition and knockdown of BRD4 in seven model HPV-16 integrated cell lines, we demonstrated that BRD4 down-regulates the expression of viral genes E6, E7, independent of viral E2 type of integration. Given that E6 expression is mediated by BRD4, E6-p53 interactions was abrogated as revealed through increased expression of p53. Furthermore, BRD4 inhibition caused downregulation of c-Myc. This result also suggests the function of BRD4 in the regulation of proteins in cell cycle regulation, including E2F1 and p21. BRD4 inhibition was also shown to delay DNA damage response (DDR) by reducing the expression of RAD51 in 6 out of 7 cell lines. RNA-sequencing results give further insight regarding the downregulation of genes involved in DDR – RAD51, BRCA1 and BRCA2 in all cell lines. RNA-sequencing data also gives us an understanding of the implication of BRD4-inhibition in other genes involved in cell cycle regulation. Knockdown of BRD4 done through small hairpin RNA (shRNA) constructs phenocopied the effects shown through inhibition of BRD4. Additionally, treating the above-mentioned cell lines with BRD4 inhibitor (JQ1) followed by radiation showed further downregulation of viral oncogenes E6, and E7. This suggests that combining radiation and JQ1 treatment can be a viable combination treatment. De-escalating radiation treatment with BRD4 inhibition has potential to be an effective combination treatment for HPV16 integrated HNSCC.

Citation Format: Dhruthi Suresh, Chitrasen Mohanty, Albert R. Wang, Christina Kendziorski, Gopal Iyer. Inhibiting BRD4 as a proposed alternative therapeutic strategy for HPV16-associated head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB153.
Abstract LB155: In vivo imaging of vascular pathology in mouse orthotopic glioma model using functional ultrasound
Authors: Rytkönen Jussi , Lehtimäki Kimmo , Stenius Taina-Kaisa , Immonen Riikka , Suhonen Ari , Shatillo Artem
Published: April 2023

Neovascularization together with aberrant vasculature is a hallmark of glioblastomas. Understanding tumor vasculature can have a pivotal role in planning therapeutics approaches. The objective of this study was to investigate morphological, vasculature and blood flow changes induced by aggressive tumor growth, using in vivo imaging - magnetic resonance imaging (MRI) and functional ultrasound (fUS) imaging in a mouse model of orthotopic glioma. Female NMRI nude mice were xenografted orthotopically with U-87 MG, a human glioblastoma, cells (5 × 104) at the age of 8 weeks. Four weeks after implantation the mice we anesthetized with isoflurane and scanned with 11.7 T small animal MRI (Bruker) for tumor volumetry. Thereafter, the mice were imaged with Iconeus One imaging system (Iconeus, Paris, France) for structural information of brain vasculature and relative cerebral blood volume (rCBV) changes. High resolution vascular imaging was performed after intravenous injection of microbubble contrast agent (SonoVue, sulphur hexafluoride microbubbles). The average tumor size was 58.8 ± 27.6 mm3 (mean ± SD, n=7) four weeks after implantation. Aberrant vasculature could be visualized with structural fUS imaging as and the necrotic core of the tumor could be observed. A reduced rCBF was observed in ipsilateral hemisphere on the relative power doppler signal timeseries as a lower amplitude and faster decay compared to contralateral side. As a summary, in vivo fUS imaging is a noninvasive tool to visualize vascular changes induced by aggressive brain tumor growth which are not detectable with conventional imaging methods (CT, MRI, PET, SPECT) and can provide a novel readout for efficacy studies.

Citation Format: Jussi Rytkönen, Kimmo Lehtimäki, Taina-Kaisa Stenius, Riikka Immonen, Ari Suhonen, Artem Shatillo. In vivo imaging of vascular pathology in mouse orthotopic glioma model using functional ultrasound [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB155.
Abstract LB160: Mdm2 regulates metastasis and associated cellular processes through modulation of Sprouty4 in a p53-independent manner
Authors: de Queiroz Rafaela Muniz , Efe Gizem , Guzman Asja , Hashimoto Naoko , Kawashima Yusuke , Tanaka Tomoaki , Rustgi Anil K. , Prives Carol
Published: April 2023

Mdm2 and its homologue MdmX form an E3-ligase complex that is best understood as the major regulator of p53. Yet Mdm2 and MdmX have functions in cells that are independent of their ability to degrade p53. Amongst the functions regulated by Mdm2 is cell migration, although the molecular mechanism(s) involved have not been well characterized. We show, in a p53 null model, that either siRNA knockdown of Mdm2 or MdmX as well as pharmacological inhibition of the Mdm2/X complex E3-ligase can reduce migration of cells grown as monolayer or invasion of cells from pre-formed spheroids into collagen-based matrices. This is consistent with our observation that Mdm2 ablation or inhibition leads to decreased cell spreading and attachment of cells to the extracellular matrix. In line with these findings, we found that modulation of Mdm2, MdmX or the Mdm2/X complex impacts focal adhesion (FA) formation, a main step in cell attachment, spreading and migration. Physiologically, Mdm2 silencing leads to decreased metastatic burden in mouse models. Mechanistically, we have discovered that Mdm2 modulates the RNA levels of Sprouty4 and that Sprouty4 is needed for the effects of Mdm2 knockdown on cell migration, FA formation and metastasis. Taken together, we have discovered a pathway by which Mdm2, through the activity of the Mdm2/X complex, mitigates FA formation, migration and ultimately metastasis by regulation of Sprouty4 independently of p53. Our findings suggest that blocking Mdm2 or the Mdm2/X complex might be a potential target to prevent metastasis.

Citation Format: Rafaela Muniz de Queiroz, Gizem Efe, Asja Guzman, Naoko Hashimoto, Yusuke Kawashima, Tomoaki Tanaka, Anil K. Rustgi, Carol Prives. Mdm2 regulates metastasis and associated cellular processes through modulation of Sprouty4 in a p53-independent manner [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB160.
Abstract LB169: Machine learning-based approach for glioblastoma drug repurposing on real-world patient data
Authors: Lin Ko-Hong , Kim Yejin , Lee Dung-Fang , Jiang Xiaoqian
Published: April 2023

Glioblastoma (GBM) is the most aggressive and deadly type of brain cancer. The poor survival rate of GBM is often attributed to the low therapeutic efficiency of current front-line therapy, treatment resistance, and high recurrence rate. Sizeable clinical data of cancer patients preserve a great potential for drug discovery and drug repurposing research, enabling comprehensive screening of treatment effects among frequently-prescribed medications. To efficiently characterize potent drug candidates and develop novel treatment strategies for GBM, we designed a machine-learning-based pipeline that predicts repurposable drug combinations from large-scale patient claims data. Our pipeline first identified pseudo-randomized drug-user and non-user cohorts from heterogeneous clinical records and balanced the confounding effects using the Inverse Probability of Treatment Weighting (IPTW) method. Next, our model computed the averaged treatment effect on the treated (ATT) values to determine the treatment effects of our candidates. Our methodology identified several promising drug combinations that have been found to be effective in inhibiting GBM in cell line experiments. This research was conducted by integrating computational and experimental approaches to identify drug combinations, providing a promising strategy for the development of new treatments for GBM.

Citation Format: Ko-Hong Lin, Yejin Kim, Dung-Fang Lee, Xiaoqian Jiang. Machine learning-based approach for glioblastoma drug repurposing on real-world patient data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB169.
Abstract LB172: Improved T-cell and B-cell receptor repertoire profiling and immunophenotyping for biomarker discovery
Authors: Chenchik Alex , Makhanov Mikhail , Liu Tianbing , Hu Dongfang , Diehl Paul , Kobzik Lester
Published: April 2023

T-cell receptor (TCR) and B-cell receptor (BCR) repertoire profiling, also referred to as adaptive immune receptor repertoire (AIRR) profiling, holds great potential for the understanding of disease mechanisms and for the development of new treatments in infectious disease, autoimmunity, and immuno-oncology. This potential could be greatly improved by combining information about receptor clonotypes with immunophenotypes of T- and B- cells. A new technology we developed that combines profiling of all human TCR and BCR variable regions with phenotypic characterization of immune cells using the same workflow could be particularly useful. The TCR and BCR immunophenotyping method proposed involves RT-PCR amplification and sequencing of the CDR3 regions of the TCR and BCR genes, and subsequently determining the expression levels of the most informative T- and B-cell phenotyping genes. Preliminary results show that this method allows for comprehensive profiling of all seven TCR and BCR chains from a single sample, in a highly reproducible manner, directly from micro-samples including cancer tissue, whole blood, sorted cells and more. Bioinformatic analysis of the next-generation sequencing (NGS) data from the TCR and BCR clonotypes profile combined with RNA expression profiling of the same samples results in a richer data set that includes the identification of major immune cell subtypes and their activation status. Data from human cancer tissue and whole blood samples will be presented.

Citation Format: Alex Chenchik, Mikhail Makhanov, Tianbing Liu, Dongfang Hu, Paul Diehl, Lester Kobzik. Improved T-cell and B-cell receptor repertoire profiling and immunophenotyping for biomarker discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB172.
Abstract LB183: Network biology approach reveals multiple non-essential helper genes to target cancer cell lethality
Authors: Li Yongsheng , Sahni Nidhi , Yi S. Stephen
Published: April 2023

Understanding the determinants of human gene essentiality is critical for developing anticancer therapeutics. Here, we systematically analyzed the human essentialome from a network perspective. We found that essential genes are mostly context-specific and predicted synthetic lethal interactions based on analysis of context-specific essentiality in distinct genetic backgrounds. The predicted gene pairs are significantly overlapped with known synthetic lethality and further validated across more than 300 cancer cell lines. Moreover, analysis of synthetic lethal interactions among actionable genes helps prioritizing rational drug combinations. Surprisingly, genes in human essentialome (especially spliceosome, RNA transport and cell cycle genes) are enriched for cancer mutations with high functional impact and disease risks. Our network analyses suggest that protein interactome topology and neighborhood community integrated with gene expression, are highly predictive of gene essentiality. Thus, we devised network-based method (SYE-NET) to systematically prioritize the essentialome, which is further validated by functional screens in independent cell lines. Taken together, our study provides a holistic insight into molecular determinants for cell fate and implicates potential biomarkers for synthetic lethality and drug combinations in cancer, a critical step towards precision medicine.

Citation Format: Yongsheng Li, Nidhi Sahni, S. Stephen Yi. Network biology approach reveals multiple non-essential helper genes to target cancer cell lethality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB183.
Abstract LB195: Immunotherapies that repolarize macrophages and CD4 T cells enhance the effect of chemotherapy in high-grade serous ovarian cancer
Authors: Elorbany Samar , Berlato Chiara , Carnevalli Larissa , Maniati Eleni , Wang Jun , Barry Simon , Manchanda Ranjit , Kzhyshkowska Julia , Balkwill Frances
Published: April 2023

We asked if single-cell RNA sequencing (scRNA-seq) analysis of tumor immune cells in high-grade serous ovarian cancer (HGSOC) would reveal ways to enhance effects of neo-adjuvant chemotherapy (NACT). Analysis of 64,097 immune cells from seven HGSOC omental metastases showed that positive effects of NACT on immune responses were counterbalanced by induction of immunosuppressive mechanisms, especially related to antigen presentation and Treg activity. We identified stabilin-1 (Clever-1) on macrophages and FOXP3 in Tregs as targets and validated actions of their inhibitors in vitro. ScRNA-seq analysis of 69,781 cells from chemotherapy-treated syngeneic mouse HGSOC tumors showed significant agreement with the patient results. Combinations of chemotherapy with anti-stabilin1 antibody and/or FOXP3 inhibitor (AZD8701), FOXP3i, significantly increased median survival of mice with established peritoneal disease. Long-term survivors (300 days+) were resistant to tumor rechallenge. Analysis of bulk RNA sequencing data from treated murine tumors confirmed our hypothesis and suggested potential mechanisms to explain the anti-tumor response seen in the murine models. Tumors treated with chemotherapy plus anti-stabilin1 antibody showed significant enrichment of anti-tumor macrophage signature and antigen presentation pathway compared to chemotherapy alone. Tumors treated with chemotherapy plus FOXP3i in combination with anti-stabilin1 antibody showed significant upregulation of antigen presentation, T cell activation and cytotoxicity and T helper 1 differentiation pathways. There was significant reduction in FOXP3 positive cells and significant increase of Tbet positive cells in FOXP3i treated murine tumors suggesting repolarization of naive T cells in the tumor microenvironment towards a more anti-tumor T helper phenotype. As there are early phase clinical trials of FOXP3 inhibitor and anti-stabilin1 (Clever-1) antibody in patients with advanced cancer, these results suggest ways of improving response to chemotherapy not only in HGSOC but in other cancers that are treated by NACT.

Citation Format: Samar Elorbany, Chiara Berlato, Larissa Carnevalli, Eleni Maniati, Jun Wang, Simon Barry, Ranjit Manchanda, Julia Kzhyshkowska, Frances Balkwill. Immunotherapies that repolarize macrophages and CD4 T cells enhance the effect of chemotherapy in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB195.
Abstract LB224: STC-1010 a new therapeutic vaccine promotes tumor cell death
Authors: Bessede Alban , Alzeeb George , Tortorelli Corinne , Guegan Jean-Philippe , Rey Christophe , Chalus Lionel , Pinteur Benoit , Bravetti Paul , Italiano Antoine
Published: April 2023

BACKGROUND Colorectal cancer (CRC) is the third most commonly diagnosed cancer (10% of new cases in 2020) and the second leading cause of cancer-related death (9.4%) worldwide. CRC is often detected at late stages, with 38% of metastasis cases at diagnosis. This makes the development of efficient treatments crucial. Recent tremendous progress sets immunotherapy as a treatment option and opens multiple ways to address therapeutic challenges in CRC. Accordingly, we have previously developed therapeutic cancer vaccine based on stimulated tumor cells (STC) technology, that have already shown efficacy in immunocompetent mouse models. Same strategy was used in this study to generate the STC-1010 therapeutic vaccine, a novel human therapeutic CRC vaccine derivate from 3 human CRC cell lines, HCT116, HT29 and LOVO exposed to irradiation, heat shock, chemotherapy agents and haptenized.

METHODS We evaluate STC-1010 for its potential to favor an immune stimulatory response on human monocytes-derived dendritic cells (moDCs) from 2 different donors through i) a derived Mixed Lymphocyte Reaction (dMLR) assay, ii) the assessment of their cytokine profile, iii) the evaluation of their capacity to activate autologous CD8+ T cells and finally iv) to promote apoptosis of three CRC cell lines (HCT116, HT29 and LS-174T).

RESULTS We showed that STC-1010 induced IL-8 and IL-12 production, and reduced IL-10 during moDCs maturation. In addition, dendritic cells (DCs) exposed to STC-1010 during the maturation enhanced Interferon gamma (IFNg) production by CD8+ T cells (p=0,06 for donor 1 and p=0,0004 for donor 2) and amplified their anti-tumor activity, in combination with LPS/IFNg and CD40L. CD8+ T cells primed with STC-1010-treated DCs promote massive apoptosis of HCT116 and HT29 cells compared to the condition without STC-1010 (p<0,001 for all donors). The benefit of STC-1010 was not detectable with LS174T cells characterized by a low expression of HLA-ABC and used as negative control in this study.

CONCLUSION Taken together, our results showed that Brenus STC-1010 human vaccine is an efficient strategy to educate immune system and promote the CRC cells death in vitro lending further support in favor of STC technology based on physical or chemical stimulation and haptenization to generate human cancer therapeutic vaccine.

Citation Format: Alban Bessede, George Alzeeb, Corinne Tortorelli, Jean-Philippe Guegan, Christophe Rey, Lionel Chalus, Benoit Pinteur, Paul Bravetti, Antoine Italiano. STC-1010 a new therapeutic vaccine promotes tumor cell death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB224.
Abstract LB228: Replication stress activates the DNA damage response and contributes to lapatinib resistance in HER2-positive SK-BR-3 cells
Authors: Kim So Hyeon , Min Ahrum , Kim Seongyeong , Kim Yu Jin , Ham Sujin , Hwang Hae Min , Lee Minyoung , Lee Changyun , Kim Jinyong , Lee Dae-Won , Lee Kyung-Hun , Im Seock-Ah
Published: April 2023

Background: Lapatinib is a small molecular inhibitor of HER2 and EGFR tyrosine kinases, which is approved for HER2-positive metastatic breast cancer as second line treatment. Significant proportion of patients experience disease progression due to acquired resistance. Activation of DNA damage repair (DDR) is one of the drug-resistance mechanism, however, the impact of DDR on sensitivity to lapatinib is unclear. Thus, lapatinib resistance mechanism was explored from the standpoint of DDR activation.

Methods: Acquired lapatinib-resistant (LR) SK-BR-3 cell lines were generated by continuously exposing to lapatinib, starting with 30 nmol/L and incrementally increasing to 10 μmol/L over 7 months. MTT assay was used to confirm lapatinib sensitivity. Cell cycle progression was analyzed using BrdU assay. Replication fork speed and stalled fork were analyzed by DNA fiber assay. Expression of the molecules was examined using Western blotting, immunofluorescence assay and transcriptome data analysis. DNA strand breaks and repair efficacy were evaluated through alkaline comet assay.

Results: G1/S phase transition was increased and early/late S phase population was increased in SK-BR-3 LR cells. Replication fork speed was accelerated and replication stress are elevated in SK-BR-3 LR cells. p-Chk1, Rad51, Rad51B, Rad51C and XRCC3 were upregulated in SK-BR-3 LR cells. After irradiation or treatment with ATR inhibitor, γ-H2AX was continuously increased in parental cells. In contrast, γ-H2AX did not change significantly in SK-BR-3 LR cells, and Chk1 was activated after irradiation or treatment with ATR inhibitor. Tail of comet disappeared at early time point in in SK-BR-3 LR cells after induction of DNA damage compared with parental cells. These results demonstrated that DDR was activated and DNA damage repair capacity was enhanced in LR cells.

Conclusion: Replication stress is elevated in SK-BR-3 LR cells. Up-regulation of molecules involved in the homologous recombination repair pathway was observed in SK-BR-3 LR cells. Moreover, DNA repair capacity was increased in SK-BR-3 LR cells. These data suggested that activation of DNA damage repair pathway caused by replication stress contributes to lapatinib resistance.

Citation Format: So Hyeon Kim, Ahrum Min, Seongyeong Kim, Yu Jin Kim, Sujin Ham, Hae Min Hwang, Minyoung Lee, Changyun Lee, Jinyong Kim, Dae-Won Lee, Kyung-Hun Lee, Seock-Ah Im. Replication stress activates the DNA damage response and contributes to lapatinib resistance in HER2-positive SK-BR-3 cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB228.
Abstract LB232: Targeting MEK activity in pancreatic tumors resistant to the combination of 5FU, irinotecan, and oxaliplatin promotes response to immunotherapy
Authors: Pham Thao D. , Metropulos Anastasia E. , Mubin Nida , Shah Dhavan N. , Spaulding Christina , Shields Mario , Bentrem David J. , Munshi Hidayatullah G.
Published: April 2023

FOLFIRINOX, a chemotherapy regimen consisting of 5FU, Leucovorin, Irinotecan, and Oxaliplatin, has been a first-line standard of care for patients with pancreatic adenocarcinoma (PDAC) for the last decade. However, low patient survival rates following treatment highlight frequent occurrence of resistance. Hence there is increasing interest in developing appropriate models of FOLFIRINOX resistance to identify subsequent line therapies. We have generated PDAC cell lines that exhibit acquired resistance to a combination of 5FU (F), Irinotecan (I), and Oxaliplatin (O) (FIO) in vitro. In mice, they form tumors that resemble FOLFIRINOX neoadjuvant-treated PDAC patients in regard to immune cell infiltration and a lack of response to single-agent anti-PD-1 therapy. We also show that similar to human PDAC tumors treated with neoadjuvant FOLFIRINOX, FIO-resistant tumors exhibit increased ERK1/2 phosphorylation. We demonstrate that the MEK inhibitor Trametinib reprograms the FIO-resistant tumors, but not the parental tumors, towards a less immunosuppressive tumor immune microenvironment. Importantly, Trametinib sensitizes FIO-resistant tumors to anti-PD-1 therapy, with the combination treatment significantly enhancing the cytolytic activity of the infiltrating CD8 + T cells and increasing tumor cell death. Taken together, our findings identify enhanced MEK/ERK signaling as a therapeutic target in FOLFIRINOX-resistant PDAC tumors, and suggest evaluating the combination of Trametinib and anti-PD-1 therapy in patients who progress on FOLFIRINOX.

Citation Format: Thao D. Pham, Anastasia E. Metropulos, Nida Mubin, Dhavan N. Shah, Christina Spaulding, Mario Shields, David J. Bentrem, Hidayatullah G. Munshi. Targeting MEK activity in pancreatic tumors resistant to the combination of 5FU, irinotecan, and oxaliplatin promotes response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB232.
Abstract LB250: Multiplex screening of PBMCs with DNA barcoded peptide exchanged MHC trimers to identify peptide-specific paired VDJ TCRs at single cell level
Authors: Delcommenne Marc , Hou Xiaohong , Poluektov Yuri , Pan Wenjing , Sims Emily , Byrne-Steele Miranda
Published: April 2023

Elucidation of the paired TCR receptor-antigen synapse is important both for vaccine development and for targeted therapy. Linkage of T cell responses with specific antigenic peptides will not only guide the development of immunotherapies but also enable treatment response monitoring. Currently, single cell sequencing technology is well established, but the identification of specific pathogenic peptides and associated TCR in single cell level is still challenging. In most cases, ascertaining T cell responses to pathogenic peptides is based on the screening of pooled peptides that do not give the knowledge of corresponding responsive TCR to a particular peptide. We therefore developed a technique that uses DNA barcoded peptide exchanged MHC trimers to stain PBMCs. With this technique, multiple peptide-loaded trimers can be used to stain a PBMC sample in one test tube. Single cells positive for trimers are sorted, amplified, and sequenced together with the DNA barcode. Specific peptides can be identified with the DNA barcodes which are co-amplified with TCRs. Applying this technique, we screened one PBMC sample with several peptide-loaded trimers in one reaction. Utilizing the CDR3 identity of known clones against each of these peptides, we were able to demonstrate and validate that a multi-peptide screen using DNA barcodes is feasible. Further optimization is in progress to reduce background and to increase the multiplexing of barcoded peptide-trimers.

Citation Format: Marc Delcommenne, Xiaohong Hou, Yuri Poluektov, Wenjing Pan, Emily Sims, Miranda Byrne-Steele. Multiplex screening of PBMCs with DNA barcoded peptide exchanged MHC trimers to identify peptide-specific paired VDJ TCRs at single cell level [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB250.
Abstract LB253: Long-read single-cell sequencing of liver cancer
Authors: Luo Jian-Hua , Liu Silvia , Ren Bao-Guo , Yu Yan-Ping
Published: April 2023

The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Protein mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.

Citation Format: Jian-Hua Luo, Silvia Liu, Bao-Guo Ren, Yan-Ping Yu. Long-read single-cell sequencing of liver cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB253.
Abstract LB269: Inhibition Of C-C chemokine receptor 7 extends survival rate in murine model of T-cell acute lymphoblastic leukemia
Authors: Sanchez Anahi , Vazquez Aaron E. , Valenzuela Janet M. , Stanley Savannah , Bill Colin A. , Vines Charlotte M.
Published: April 2023

C-C Chemokine Receptor 7 (CCR7) expression in pediatric T-cell acute lymphoblastic leukemia (T-ALL) promotes entry of leukemic cells into the central nervous system (CNS), where the disease finds sanctuary from systemic chemotherapies. To confirm that Notch1 drives expression of CCR7, we modified the ROSA26-PRDM14 ([PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ (retinoblastoma interacting zinc finger) homology domain containing 14]) MX-1 Cre inducible CD8+ T-ALL mouse model. This model, upon induction with polyI:C, expresses NOTCH1 downstream of PRDM14, and the T-ALL cells enter the CNS during leukemogenesis. We crossed these mice with ROSA26-Luc2 mice, which allows for tracking of T-ALL cells during disease progression. We questioned if these T-ALL cells expressed CCR7. We found that not only do the T-ALL cells express CCR7 and enter the CNS, but that a CCR7 antagonist, CCL198-83 administered during leukemogenesis doubles the mean survival of the CCL198-83 treated mice from 45 to 90 days. These studies provide a novel platform for a potential therapeutic that can be used to limit CNS entry and potentially recycling through the CNS.

Citation Format: Anahi Sanchez, Aaron E. Vazquez, Janet M. Valenzuela, Savannah Stanley, Colin A. Bill, Charlotte M. Vines. Inhibition Of C-C chemokine receptor 7 extends survival rate in murine model of T-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB269.
Abstract LB270: LINGO2-microRNA cluster controls oral cancer stemness ability and cancer progression
Authors: Chang Wei-Min , Li Li-Jie , Lin Che-Hsuan , Hsiao Michael , Chang Peter Mu-Hsin
Published: April 2023

Cancer recurrence and metastasis are the primary reasons for treatment failure in late-stage oral cancer. Cancer stem cells are the root of cancer recurrence and metastasis. By using the microRNAome analysis of Taiwan OSCC cohort, we found miR-876-3p was highly correlated to OSCC recurrence. The precursor miR-876 promoted in vitro OSCC cell proliferation, migration, and cancer stemness and regulated several cancer stemness-relative genes such as NANOG, OCT4, and LIN28A expression. miR-876 and miR-873 are located in the second intron of the 5’-untransalation region (5’-UTR) at the alternative variant leucine-rich repeat and Ig domain containing 2 (LINGO2). Interestingly, only OSCC cells presented LINGO2 protein expression but did not show in primary oral keratinocytes (HOK). The unique CpG islands at the alternative transcription start site of LINGO2 hinted at crucial epigenetic regulation that controls LINGO2 activation. Silencing of LINGO2 expression reduced OSCC cell growth and cancer stemness abilities. LINGO2 expression was higher in OSCC tumor tissue than in adjacent normal tissue in both Taiwan and The Cancer Genome Atlas (TCGA) head and neck cancer cohorts. Moreover, LINGO2 also served as a poor prognostic marker in cancer patients' overall and recurrent free survival time. In summary, we found a novel LINGO2-microRNA cluster that regulates OSCC stemness and metastasis abilities. Those cancer specific expressions may provide a new therapy niche in OSCC cancer therapy.

Citation Format: Wei-Min Chang, Li-Jie Li, Che-Hsuan Lin, Michael Hsiao, Peter Mu-Hsin Chang. LINGO2-microRNA cluster controls oral cancer stemness ability and cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB270.
Abstract LB281: HIRA suppression is a mechanism of chemotherapy resistance in ovarian cancer
Authors: Yasukawa Maya , Drapela Stanislav , Ilter Didem , Shahzad Mian M. , Gomes Ana P.
Published: April 2023

Ovarian cancer accounts for the fifth most common cause of cancer death among women, despite being relatively rare. This is in large because majority of cases are diagnosed at advanced stage and frequently recur after primary treatment. Despite numerous efforts to develop effective targeted therapies and immunotherapies for ovarian cancer the standard of care remains chemotherapies. We postulate that part of the problem is the paucity of preclinical research and clinical trials focused on dormant persister ovarian cancer cells that remain after chemotherapy treatments. Emerging evidence supports the idea that persister cancer cells undergo a period of dormancy following chemotherapy which enables their survival and drive late recurrence. Thus, there is dire need to understand the pathways that empower the establishment of dormancy following chemotherapies in ovarian cancer. Epigenetic reprogramming is notoriously known to enable cell fate transitions and the establishment of drug resistance. An important layer of epigenetic regulation frequently overlooked in cancer is the regulation of nucleosome composition via histone variants. Importantly, analysis of data from the human protein atlas revealed that histone H3.3 chaperone, Histone Regulator Protein A (HIRA) expression inversely correlated with poor prognosis, suggesting that HIRA suppression might play a role in the development of chemotherapy resistance. Here, we demonstrate that HIRA is a major regulator of cell fate transitions in ovarian cancer cells in response to chemotherapies. Our data indicates that HIRA levels are suppressed in response chemotherapies in cancer cells. Genetic suppression of HIRA in ovarian cancer cells triggered a non-poliferative state characterized by the induction of canonical dormancy markers (p27, an increase in p38 phosphorylation) and cell cycle arrest. Accordingly, HIRA suppression in these cancer cells renders them less sensitive to the standard of care chemotherapy agent paclitaxel. Together, our data demonstrates that HIRA levels play an important role in controlling cell fate decisions in ovarian cancer and regulate chemotherapy sensitivity.

Citation Format: Maya Yasukawa, Stanislav Drapela, Didem Ilter, Mian M. Shahzad, Ana P. Gomes. HIRA suppression is a mechanism of chemotherapy resistance in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB281.
Abstract LB317: Discovery and characterization of a next-generation FGFR inhibitor overcoming FGFR resistant mutations
Authors: Ying Haiyan , Xin Wenqun , Deng Haibing , Zhao Yuan , Yu Hongping , Chen Zhui , Xu Yao-chang
Published: April 2023

Introduction: FGFRs play important roles in cancer development and inhibition of FGFR could disrupt tumor cell proliferation and growth. Four selective FGFR inhibitors have been approved (erdafitinib, pemigatinib, infigratinib, and futibatinib) and several others are in clinical development. Unfortunately upon treatment with these first-generation FGFR inhibitors, acquired resistance often develops and is frequently associated with the emergence of secondary FGFR2/3 kinase domain mutations. Therefore, selectively targeting FGFR2/3 as well as their resistant mutations may render a second-generation treatment approach for the refractory/relapsed patients. Using advanced computation-aided structural analysis and medicinal chemistry design, we have discovered a novel, next-generation, and highly selective FGFR inhibitor, ABSK121. This novel inhibitor demonstrated robust anti-tumor activity in FGFR-dependent tumor models with strong activities against not only de novo but also acquired resistant mutations.

Method: ABSK121 was evaluated in biochemical and cellular proliferation experiments for its inhibition on wile type FGFR enzymatic activity and FGFR-dependent cancer cell proliferation. Its potency against FGFR mutations was also analyzed in relevant biochemical and cellular experiments. Efficacy studies were conducted in multiple tumor models to confirm its in vivo activities. Preliminary selectivity profile and ADME profiles were also evaluated.

Results: ABSK121 inhibited wild type FGFRs with IC50<10 nM in biochemical assay. ABSK121 also displayed great potency against resistant kinase domain mutations. In cell lines harboring FGFR amplification, fusions, or resistant mutations, ABSK121 demonstrated strong anti-proliferation activity as well as strong inhibition of FGFR downstream signaling activities. In preclinical in vivo studies, oral administration of ABSK121 strongly inhibited the growth of subcutaneous xenograft tumors dependent on wild type or resistant mutant FGFR. Suppression of tumor growth was dose-dependent and well correlated with pharmacodynamic inhibition of FGFR signaling. ABSK121 also showed great kinase selectivity with no CYP or hERG inhibition.

Conclusion: ABSK121, presented here by Abbisko Therapeutics, is a highly potent, selective, and next-generation small molecule FGFR inhibitor with great potency against resistant FGFR mutations. Its superior profile supports fast-track preclinical and clinical development.

Citation Format: Haiyan Ying, Wenqun Xin, Haibing Deng, Yuan Zhao, Hongping Yu, Zhui Chen, Yao-chang Xu. Discovery and characterization of a next-generation FGFR inhibitor overcoming FGFR resistant mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB317.
Abstract LB326: Combined inhibition of BRD4 and FAK1 as a novel therapeutic strategy for neurofibromatosis type 2 related schwannomas
Authors: Gonzalez Maria Alejandra , Kissil Joseph , Troutman Scott
Published: April 2023

Neurofibromatosis type 2 (NF2) is a rare disorder that is inherited in an autosomal-dominant manner and is attributed to the loss of heterozygosity (LOH) of the NF2 gene, which encodes for the tumor suppressor protein Merlin. Patients affected by the disease develop vestibular schwannomas (VS), meningiomas, and ependymomas resulting in high morbidity and premature mortality. To date, neurofibromatosis type 2 has no FDA-approved drug-based treatment. Merlin plays a central role in mediating cell contact inhibition (CI) of proliferation. Loss of Merlin leads to abnormal activation of multiple signaling pathways, including those regulated by small G-proteins Ras/Rac/cdc42 and the Hippo-YAP pathway. The Hippo-YAP pathway plays a major role in cell growth and organ size control and at its core is comprised of a kinase cascade that regulates the transcriptional regulator YAP. The function of YAP is crucial for VS development, and there are several mechanisms by which YAP regulates transcription. Some of these functions have been shown to involve the Bromodomain and Extra-Terminal domain (BET) proteins acting as co-factors. We have previously shown that the BET inhibitor JQ1 can selectively reduce the growth of the NF2-null schwannoma and Schwann cells in vitro and tumorigenesis in vivo. Additionally, evidence has shown that Merlin loss can lead to increased cell proliferation that it requires the activity of Focal Adhesion Kinase 1 (FAK1). We have previously demonstrated that FAK1 inhibition via Crizotinib has antiproliferative effects in NF2-null Schwann cells, and is currently in phase II clinical trials in NF2-related VS. In this study, wild-type and NF2-null Schwann cells and schwannoma cell lines were used to determine the impact on cell growth by employing the treatment with the BET inhibitor JQ1 and the FAK1 inhibitor Crizotinib. Our analysis in NF2-null Schwann cells and schwannoma cell lines shows that the combined inhibition exerts an antineoplastic effect at nanomolar concentrations. Moreover, this combination resulted in selective inhibition of NF2-null Schwann cell proliferation when compared to wild-type Schwann cells in vitro, when compared to either drug alone. Our preliminary data suggest that combined targeting of BET and FAK1 may offer a potential therapeutic option for the treatment of NF2-related schwannomas.

Citation Format: Maria Alejandra Gonzalez, Joseph Kissil, Scott Troutman. Combined inhibition of BRD4 and FAK1 as a novel therapeutic strategy for neurofibromatosis type 2 related schwannomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB326.
Abstract LB335: Establishment of the effective dose of the STAT3 inhibitor WP1066 used in combination with STING activation for reprograming the preclinical glioma microenvironment
Authors: Najem Hinda , Tripathi Shashwat , Sooreshjani Moloud , Hurley Lisa , Dussold Corey , Arrieta Victor , Ott Martina , Wei Jun , Curran Michael , Marisetty Anantha , Priebe Waldemar , Platanias Leondias C. , Lesniak Maciej S. , James Charles D. , Horbinski Craig , Ashley David M. , Heimberger Amy B.
Published: April 2023

Purpose: Trials of immunotherapy in diffuse glioma patients have been mostly unsuccessful. We therefore sought to determine the combined effects of the signal transducer and activator of transcription 3 (STAT3) inhibitor WP1066 and the STING agonist IACS-8803 in a preclinical model of glioma.

Experimental Design: C57BL/6 mice (n=9-10/group) with orthotopically engrafted GL261 cells were treated orally with WP1066, a blood-brain-barrier penetrant inhibitor of STAT3, in combination with the STING agonist IACS-8803 administered directly into the tumor. Analysis of treatment effects included immunoblots, ubiquitination, multiplex immunohistochemistry, and NanoString immune phenotyping of glioma-infiltrating immune cells.

Results: The STING agonist 8803 at 2.5µg/mouse, in combination with WP1066 dosed at 30mg/kg with a 12-hour delay, increased animal subject median survival (MS) to 58 days, in contrast to monotherapy (WP1066=25 days, 8803=29 days) or control (25 days) (p=0.002 of combo relative to all other groups). Dose escalation of WP1066 to 60 mg/kg, administered simultaneously with 8803, completely abrogated the therapeutic combinatorial effect. Five ubiquitin-binding domains were predicted on STING using the UbPred program; concentrations of 5µM or higher of WP1066 induced polyubiquitination of phosphorylated STING. Immune profiling during the therapeutic window demonstrated a multi-pathway induction of anti-tumor immunity.

Conclusions: Co-administration of a reduced effective dose of WP1066 is necessary with STING agonist 8803 to effectively enhance the anti-glioma immune reactivity in the tumor microenvironment.

Citation Format: Hinda Najem, Shashwat Tripathi, Moloud Sooreshjani, Lisa Hurley, Corey Dussold, Victor Arrieta, Martina Ott, Jun Wei, Michael Curran, Anantha Marisetty, Waldemar Priebe, Leondias C. Platanias, Maciej S. Lesniak, Charles D. James, Craig Horbinski, David M. Ashley, Amy B. Heimberger. Establishment of the effective dose of the STAT3 inhibitor WP1066 used in combination with STING activation for reprograming the preclinical glioma microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB335.
Abstract LB341: Single-cell CRISPR screens in primary human T cells identify regulators of Th2 cell skewing
Authors: Loregger Anke , Irnstorfer Johanna , Untermoser Nicole , Vinko Nikola , Krejci Adam , Schmidt Henrik , Bürckstümmer Tilmann
Published: April 2023

CRISPR screens have become the primary discovery engine in modern biology. However, many screening workflows are still performed in cancer cell lines and coupled to simplistic read-outs such as cellular fitness. At Myllia Biotechnology, we combine CRISPR screening with single-cell RNA sequencing, leveraging two transformative technologies to enable genetic screening for complex phenotypes. We utilize the CRISPR screening workflow to map the impact of thousands of genetic perturbations on the global transcriptome at single-cell resolution. Our powerful approach has broad applications in identifying novel drug targets or elucidating unknown mechanisms of actions of drugs.

Primary human T cells are currently of great interest in the scientific community. They are not only key players in autoimmunity and other inflammatory diseases, but also represent attractive targets for immunotherapy of cancer. To enable the discovery of novel targets, we built a workflow that utilizes CD4+ T cells from peripheral blood and allows functional genomic screens in these cells. Upon activation, naïve CD4+ T cells proliferate and differentiate into specific T helper cell subsets, such as Th1, Th2, or Th17 cells. Here, we present data of an experiment in which we screened for regulators of T helper cell differentiation and skewed cells towards the Th2 subset. We aimed to identify genes whose knockout boosts or attenuates the ability of primary naïve CD4+ T cells to become Th2 cells. Th2 cells support the humoral immune response, and their dysfunction has been linked to inflammatory diseases, including asthma.

In our screen, the different T cell subsets could be captured using curated transcriptomic signatures. Importantly, several gene KOs introduced in a pooled fashion using CRISPR/Cas9 accumulated in distinct subpopulations, suggesting that these genes regulate the differentiation of naïve T cells into the various T helper cell subsets.

Overall, our pooled screening approach in primary human T cells allows for novel insights in the plasticity of T cells and identifies genes that could serve as drug targets in autoimmunity, inflammation and immuno-oncology.

Citation Format: Anke Loregger, Johanna Irnstorfer, Nicole Untermoser, Nikola Vinko, Adam Krejci, Henrik Schmidt, Tilmann Bürckstümmer. Single-cell CRISPR screens in primary human T cells identify regulators of Th2 cell skewing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB341.