bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 617: MEK inhibitor rescued the efficacy of PD-1 blocker in STK11/LKB1 mutated colorectal cancer model
Authors: Liu Demi X. , Zhou Jun , Nie Chenpan , An Annie X. , Li Henry Q.X. , Wang Jingjing 
Published: June 2022

Abstract
Introduction: The mechanism of action of primary resistance to PD-1 blockade is largely unknown, however STK11/LKB1 alterations have been reported to have a significant role in primary resistance to PD-1/PD-L1 axis inhibitors in KRAS-mutant lung adenocarcinoma. It is importsnt to identify treatments which can rescue the efficacy of PD-1 blocker in STK11/LKB1-mutant patients. We have developed a STK11 knockout (KO) model using the CT26 colorectal cancer syngeneic line which harbors a KRAS mutation and evaluated the response to checkpoint inhibitor alone and in combination with MEK inhibitors.
Method: CT26-STK11KOwas developed by CRISPR/Cas9 technology and STK11/LTB1 deletion was verified by Western Blot. To test the response of the cell line to anti-PD-1 treatment (10mg/kg), we engrafted CT26-WT and CT26-STK11KO tumor lines into BALB/c mice. Tumor growth inhibition (TGI) was assessed as TGI%=(1-Ti/Vi) x100%; Ti as the mean tumor volume of the treatment group on the measurement day; Vi as the mean tumor volume of control group at the measurement day. At termination FACS analysis of different major types of immune cells was performed. Combination with MEK inhibitors, including Trametinib (1mg/kg) was also evaluated.
Results: In comparison to CT26-WT tumor growth, PD-1 blocker could not inhibit CT26-STK11KO tumor progression. However, Combinational treatment of Trametinib and anti-PD-1 antibody delayed CT26-STK11KO tumor growth. In CT26-WT tumor bearing mice, anti-PD-1 monotherapy increased total CD45+ immune cells, suggesting an ongoing immune response; significantly increased the ratio between M1 and M2, which might be an indicator for enhanced type I T cell response. CD8+ T cell infiltration in CT26-STK11KO tumors was dramatically decreased associated with increased percentage of G-MDSC which may have contributed to the loss of response to anti-PD-1 treatment. MET inhibitor, Trametinib, decreased G-MDSC and restored CD8+ T cell infiltration and PD-1 blocker efficacy in CT26-STK11KO tumor.
Conclusions: We successfully generated a CT26-STK11KO cell line which was valuable for evaluation of PD-1 blocker and MEK inhibitor in STK11/LTB1 deficient tumor, in which Trametinib could rescue the efficacy of PD-1 treatment in CT26-STK11KO tumor via inhibiting G-MDSC. Taken together, our data suggest that altered immune cell infiltration, particularly increased G-MDSCs, in tumor microenvironment might be the reason for poor PD-1 blocker efficacy in CT26-STK11KO tumor.
Citation Format: Demi X. Liu, Jun Zhou, Chenpan Nie, Annie X. An, Henry Q.X. Li, Jingjing Wang. MEK inhibitor rescued the efficacy of PD-1 blocker in STK11/LKB1 mutated colorectal cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 617.
Abstract 6171: A single-cell solution for solid tumors to detect mutations and quantify copy number variations
Authors: Parikh Saurabh , Patel Khushali , Li Alex , Parikh Anup 
Published: June 2022

Abstract
Cancer is a highly heterogeneous disease characterized by the presence of chromosomal structural copy number variation (CNV) and driver gene mutation events, which appear somatically at the early stages of oncogenesis and can drive tumor progression. Previously, we have developed a high throughput single cell DNA analysis platform that leverages droplet microfluidics and a multiplex-PCR based targeted DNA sequencing approach. It demonstrates high sensitivity detection of SNVs and indels in the same cells and generation of high resolution maps of clonal architecture based on mutational profiling. Here we expand upon the same approach and create an algorithm to accurately quantify CNVs along with genetic mutations from the same single cells. To estimate the CNV the amplicon read counts were corrected for artefacts related to cell to cell variability due sequencing efficiencies along with amplicon to amplicon variability that occur due to amplification efficiency differences. We used a spiked in diploid cell line as a reference to normalize all the cells. The spiked cell line was identified using its mutational profile. We validated the system using cell lines with known CNVs and found that we could at least accurately estimate copy numbers ranging from 0 through 5. Some of the regions were also validated orthogonally using droplet digital PCR. Another set of validation was performed using well characterized cell lines from NIST. We enable multiple visualizations of the copy number estimates in karyotype plots and line plots projected on SNV clones. With improved biochemistry, panel design and novel data analysis algorithms we develop a complete solution to detect amplification or loss of function in oncogenes and tumor suppressors reliably. Integration of CNVs and SNVs facilitates more accurate reconstruction of tumor evolution to better understand cancer progression mechanisms as well for quality control of gene edited cells, to further advance cancer research and therapy.
Citation Format: Saurabh Parikh, Khushali Patel, Alex Li, Anup Parikh. A single-cell solution for solid tumors to detect mutations and quantify copy number variations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6171.
Abstract 6175: Developing antibody-drug conjugates against cholangiocarcinoma using a novel molecular target
Authors: Zhu Bing , Yao Shi-Li , Wang Xin-Yan , Xu Rui , Guo Peng , Ying Jie-Er 
Published: June 2022

Abstract
As a rare malignancy, cholangiocarcinoma (CCA) is a lethal disease with a 5-year overall survival rate of merely 5%. Highly invasive and asymptomatic characteristics of CCA cause most patients diagnosed at advanced stages, severely deteriorating their clinical outcomes. The drug treatment options for CCA are limited and surgical resection of CCA frequently suffers from a high recurrence rate of 66%. Albeit Pemigatinib, a FGFR2 inhibitor, has recently been approved by FDA as the first CCA-targeted therapeutic, only less than 10% of patients with CCA carry FGFR2 fusion mutations that can benefit from this drug. Ivosidenib, another targeted drug against IDH1 mutation, only works for 13% CCA patients carrying this mutation. Therefore, discovering new molecular targets and developing associated targeted drugs remain a significant and unmet medical need in CCA therapy. In this study, we first screened potential molecular targets for CCA by comparing the expression levels of a panel of cancer-related cell membrane antigens between human CCA cells and normal human intrahepatic biliary epithelial cells through flow cytometry. CD54 was identified as a remarkable molecular target of CCA with strong binding force to its antibodies and high endocytosis efficiency by flow cytometry and confocal fluorescent microscopy. Meanwhile, we confirmed that CD54 was absent in most normal human tissues but was highly upregulated in CCA tumor tissues through immunohistochemical (IHC) staining. Based on this newly discovered CCA target, we constructed a series of CD54 antibody-drug conjugates (ADCs) using different chemical linkers and payloads. We next evaluated and compared the half maximum inhibitory concentrations (IC50s) of each ADC in ablating human CCA cells in vitro in order to identify an optimized ADC formulation. Furthermore, we validated its anti-tumor efficacy against primary and peritoneal metastatic CCA tumors in vivo in comparison with conventional chemotherapy. Eventually, we determined the biodistribution and safety profile of this CD54 ADC in order to ensure that it is well-tolerated under the effective dose. In general, we identified CD54 as a novel molecular target for CCA through antibody library screening, and explored its potential in the development of CCA-targeted ADCs, providing a promising targeted therapeutic for clinical treatment of CCA.
Citation Format: Bing Zhu, Shi-Li Yao, Xin-Yan Wang, Rui Xu, Peng Guo, Jie-Er Ying. Developing antibody-drug conjugates against cholangiocarcinoma using a novel molecular target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6175.
Abstract 6193: TWIST2 promotes tumor progression and represses myogenic differentiation in rhabdomyosarcoma
Authors: Shah Akansha , Guo Lei , Jaichander Priscilla , Chen Kenian , Hernandez Karla Cano , Xu Lin , Bassel-Duby Rhonda , Olson Eric , Liu Ning 
Published: June 2022

Abstract
Rhabdomyosarcoma (RMS) is an aggressive pediatric soft tissue sarcoma of myoblast origin. RMS tumors are unable to terminally differentiate into syncytial muscle despite elevated expression of the muscle master regulators, MyoD and Myf5. Fusion-positive RMS (FP-RMS) and fusion-negative RMS (FN-RMS) have emerged as the two major RMS subtypes. The pathogenesis of FP-RMS is commonly defined by the balanced translocation of chromosomes 2 and 3 resulting in the misexpression of a chimeric PAX3/7-FOXO1 oncoprotein that derails normal differentiation pathways. However, the molecular basis of FN-RMS is poorly understood as single nucleotide variations in genes like KRAS, NRAS, and TP53 have limited recurrence (less than 10% of all patient tumors). In contrast, DNA copy number variations are highly recurrent and the genes they encode represent vulnerabilities in FN-RMS. Strikingly, we discovered that 72% of FN-RMS patient tumors harbor copy number amplifications at loci of TWIST1, TWIST2, or both, resulting in the upregulation of TWIST gene expression. We demonstrated that depletion of TWIST2 using a doxycycline inducible shRNA system caused cell cycle arrest and increased myogenic differentiation in xenograft models of FN-RMS. To interrogate whether TWIST2 can directly regulate the expression of these genes, we performed RNA-seq and ChIP-seq for TWIST2, H3K27Ac, and MYOD in TWIST2 knockdown and control FN-RMS cells. Utilizing this genome-wide data of chromatin binding, we comprehensively demonstrated that TWIST2 competes with MYOD preferentially at a subset of enhancers required for myogenic differentiation, causing repression of these loci. Interestingly, while MYOD binding is gained at myogenic loci in the absence of TWIST2, binding of MYOD is not lost at growth-promoting, oncogenic enhancers despite a decrease in their associated gene expression. This suggests that TWIST2 interacts with a different slew of transcription factors or chromatin regulators to activate gene expression. To interrogate this possibility, we are characterizing the TWIST2 protein interactome in FN-RMS cells using BioID as well as motifs enriched at TWIST2-regulated peaks. By studying TWIST2-associated pathways that affect RMS growth and differentiation, we see an opportunity to unlock novel therapeutic strategies for RMS.
Citation Format: Akansha Shah, Lei Guo, Priscilla Jaichander, Kenian Chen, Karla Cano Hernandez, Lin Xu, Rhonda Bassel-Duby, Eric Olson, Ning Liu. TWIST2 promotes tumor progression and represses myogenic differentiation in rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6193.
Abstract 6200: MANGO: pipeline for identifying genomic translocations with key biological significance in inflammatory breast cancer
Authors: Morales-Rivera Carlos S. , Driscoll Emilia R. , Peterson-Peguero Esther A. 
Published: June 2022

Abstract
Genomic instability in cancer is essential for aberrant gene expression and translocation events that potentiate oncogenesis. Thus gene fusions, nonsense mutations and gene deregulation are key contributors to oncogenic phenotypes. Certain genomic translocations have been linked to cancer subtypes, such BCR—ABL1 for chronic myeloid leukemia (CML) serving as potential onco-biomarkers. Inflammatory breast cancer (IBC) is the rarest and most lethal subtype of breast cancer with a 5-year survival rate below 50%. Ethnic disparities for breast cancer exist; negative estrogen (ER) and progesterone (PR) hormone receptor status is more frequent in Hispanic and African American women. In addition, inflammatory breast cancer lacks defined molecular markers limiting its early onset detection which leads to poorer overall prognosis. Thus, we hypothesized that profiling IBC translocations, including its subtypes, show valuable insights to better understand this complex disease. We developed MANGO, a pipeline that leverages STAR, STAR-Fusion, FusionInspector, and Trinity to identify, visualize and assemble gene fusions from IBC sequencing data. Using the SUM149PT cell line as a model for IBC, we identified and experimentally validated a model fusion gene ZDHHC5—EPB41L5. Fusion unaware sequence assemblies cross-validated the fusion and its multiple splice sites, one of which encodes a fusion peptide. Differential gene expression between SUM149PT and SUM190PT, an IBC cell line without evidence for the identified translocation, showed loss of expression of ZDHHC5 but no change in EPB41L5, suggesting the latter retained its expression in its new genomic localization. Furthermore, in-silico functional predictions for experimental results reveals an in-frame fusion peptide with transmembrane signals in EPB41L5. Genomic translocation mapping reveals triple-negative IBC diverges from traditional breast cancer translocation patterns. In short, MANGO serves as a powerful tool to identify biologically significant translocations involved in IBC and other cancer classifications.
Citation Format: Carlos S. Morales-Rivera, Emilia R. Driscoll, Esther A. Peterson-Peguero. MANGO: pipeline for identifying genomic translocations with key biological significance in inflammatory breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6200.
Abstract 624: Classifying cGAS-STING activity links chromosomal instability with immunotherapy response in metastatic bladder cancer
Authors: Sokac Mateo 
Published: June 2022

Abstract
The cGAS-STING pathway serves a critical role in anti-cancer therapy. Particularly, response to immunotherapy is likely driven by both active cGAS-STING signaling that attracts immune cells, and by the presence of cancer neoantigens that presents as targets for cytotoxic T-cells. Chromosomal instability (CIN) is a hallmark of cancer, but also leads to an accumulation of cytosolic DNA that in turn results in increased cGAS-STING signaling. To avoid triggering the cGAS-STING pathway, it is commonly disrupted by the cancer cells, either through mutations in the pathway or through transcriptional silencing. Given its effect on the immune system, determining the cGAS-STING activation status prior to treatment initiation is likely of clinical relevance, but to date no robust method has been developed. Here, we used combined expression data from 2307 tumors from five cancer types from The Cancer Genome Atlas (TCGA) to define a novel cGAS-STING activity score based on eight genes with a known role in the pathway. Using unsupervised clustering, four distinct categories of cGAS-STING activation were identified. In multivariate models, the cGAS-STING active tumors show improved prognosis. Importantly, in an independent bladder cancer immunotherapy treated cohort, patients without cGAS-STING activation showed very limited response to treatment, while patients with strong cGAS-STING activation showed improved response and improved prognosis, particularly among patients with high CIN and high numbers of neoantigens. In a multivariate model, a significant interaction was observed between CIN, neoantigens, and cGAS-STING activation. Together, this supports a role of cGAS-STING activity as a predictive biomarker in combination with measures of CIN and neoantigens for the application of immunotherapy.
Citation Format: Mateo Sokac. Classifying cGAS-STING activity links chromosomal instability with immunotherapy response in metastatic bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 624.
Abstract 6241: Macc1 regulates breast cancer progression and metastasis via remodeling tumor immune microenvironment
Authors: Son Hye-Youn , Heo Woo Hang , Li Song Bin , Quan Mingji , Her Yu Jeong , Lee Kyu-Jin , Kim Ju Hee , Lee Han-Byoel , Han Wonshik , Moon Hyeong-Gon 
Published: June 2022

Abstract
Although the established cancer cell lines exhibit less degrees of intratumoral heterogeneity when compared to human solid tumors, studies have suggested that, even within the same cancer cell line, substantial degree of heterogeneity may exist. In this study, we have performed single cell cloning experiment using 4T1 mouse mammary carcinoma cell line and compared the phenotypes of different clones. When compared to the parental 4T1 cell line, one clone (C12) showed markedly different phenotype by exhibiting less aggressive features in vitro and significantly slower tumor growth and metastasis in vivo. The tumor tissue of the C12 showed significant alteration in immune microenvironment as higher number of recruited immune cells including T and B cells. RNA sequencing of the C12 clones and parental 4T1 cells identified Macc1 as a significantly up-regulated gene in parental 4T1 cells. Metastasis-associated colon cancer 1 (MACC1) has been associated with poor prognosis and the promotion of metastasis within several types of cancer, especially colon cancer. The gene encoding the hepatocyte growth factor (HGF) receptor, MET, is a transcriptional target of MACC1. Next, we established Macc1-silenced 4T1 cells using the parental 4T1 cells and observed that Macc1-silencing resulted in a similar phenotype seen in the C12 clone; decreased cell proliferation and migration in vitro and slow tumor growth and metastasis in vivo. To mimic the metastasis in vitro, intravasation was determined as which tumor cells were co-cultured with HUVEC, human umbilical vein endothelial cells. We discovered tumor cell penetration into HUVEC cells was blocked in Macc1-silencing 4T1 group. According to CD45, CD3, and CD19 immunohistochemistry, we also defined immune cells, especially T and B cells, were highly infiltrated in Macc1-silencing tumor like as C12 clone tumor. These results were also reconstructed in EMT6, another TNBC mouse cell line model. In this study, we show that MACC1 can regulate tumor progression and metastasis by remodeling of immune microenvironment.
Citation Format: Hye-Youn Son, Woo Hang Heo, Song Bin Li, Mingji Quan, Yu Jeong Her, Kyu-Jin Lee, Ju Hee Kim, Han-Byoel Lee, Wonshik Han, Hyeong-Gon Moon. Macc1 regulates breast cancer progression and metastasis via remodeling tumor immune microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6241.
Abstract 6243: RAR gamma interactome and cistrome guide the androgen receptor enhancer usage in prosate cancer
Authors: Wani Sajad A. , Gray Jaimie S. , Campbell Moray J. 
Published: June 2022

Abstract
Epigenetic mechanisms in prostate cancer (PCa) alter androgen receptor (AR) enhancer access resulting in re-wired AR signaling and cancer progression and/or therapy resistance. Previously, we established miR-96 targets RARγ and its coactivator TACC1, which in turn impacts AR signaling associated with PCa progression. In the current study we sought to define the RARγ complex, its interactions with the AR, and in turn how this controls gene expression. Increased RARγ levels through miR-96 treatments increased both ENZA antiproliferative sensitivity associated with an increase in G1 and G2/M. IMPACT-seq identified miR-96 recognition elements (MREs) in HPr1AR (~1950 at 24h) and LNCaP cells (~ 350) with ~ 150 shared. In parallel, m6A-Seq revealed that the epitranscriptome mark m6A differed significantly between cells. For example, m6A was more significantly enriched on TACC1 mRNA in LNCaP compared to HPr1AR and m6A-marked MRE resulted in genes being more signficantly down-regulated by miR96, including TACC1. RIME revealed that RARγ significantly interacts miR-96 differentially expressed transcripts (DETs) and proteins (DEPs) including m6A regulators (METTL3) and QSER1 complex that protects against enhancer methylation. Reflecting this, restoring RARγ levels in 22Rv1 cells, increased AR genomic binding 12-fold to greater than 9,500 sites and further by TACC1. These gained AR sites were enriched for GATA and Homeobox motifs, significantly overlapped with H3K27ac and super-enhancers, and also ChromHMM-defined Poised Enhancers (logPV = 163) and Transcribed regions (logPV = 179). RNA-Seq experiments revealed that RARγ/TACC1 significantly altered the frequency and fold change of DHT-regulated genes. Finally, miR-96 antagomir/ENZA treatments drove a unique transcriptome that triggered cell cycle arrest and significantly associated with worse survival in the SU2C cohort. To summarize these data suggest that miR-96 is directed to control the RARγ/TACC1 complex in part by m6A marks. Restoring the RARγ/TACC1 complex increased association with potential bookmarking factor like QSER1 and redirects AR to active enhancers that promote ENA-regulated genes and increase propensity for cells to undergo cell arrest.
Citation Format: Sajad A. Wani, Jaimie S. Gray, Moray J. Campbell. RAR gamma interactome and cistrome guide the androgen receptor enhancer usage in prosate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6243.