bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2730: Metronomic dose-finding approach of oral chemotherapy by experimentally-driven integrated mathematical modeling
Authors: Kweon Seho , Jeong Yoo-Seong , Ko Yoon Gun , Chung Seung Woo , Lee Ha Kyeong , Chung Suk-Jae , Byun Youngro , Kim Sang Yoon
Published: June 2022

Conventional chemotherapy with maximum tolerated dose (MTD) has shown confident anti-cancer effect and when combined with targeted therapy, immunotherapy. Yet, understanding about how the MTD regimen is optimized has lacked due to its high tumor burdens. In this study, the oral doxorubicin (DOX) formulation was shown to improve oral bioavailability by 12.1% and sustain the metronomic concentration through the flexible protocol. Since the optimizing dose and schedules of DOX in metronomic chemotherapy (MCT) is essential to maximize efficacy and minimize toxicity, which is determined by the exposure of drugs based on pharmacokinetic-pharmacodynamic (PK/PD) correlation, we developed an integrated systemic mathematical model that can evaluate the anti-tumor effect and the toxicity of oral DOX formulation simultaneously. Oral physiologically-based pharmacokinetic (PBPK) models were established with dose dependency, and creatine kinase-MB (CK-MB) and tumor growth profiles were assessed as markers for toxicodynamic (TD) and PD models, respectively. Each model was validated and then integrated into the PK-TD/PD model and the effects of various oral metronomic regimens were predicted. In conclusion, the finalized oral metronomic dosing regimen (10 mg/kg, QD) showed 83.3% tumor growth inhibition without cardiotoxicity. In this study, we defined the MCT regimen using a mathematical model and suggested a dose selection method for developing oral drugs from injections, to efficiently utilize the preclinical results and apply to clinical practice.

Citation Format: Seho Kweon, Yoo-Seong Jeong, Yoon Gun Ko, Seung Woo Chung, Ha Kyeong Lee, Suk-Jae Chung, Youngro Byun, Sang Yoon Kim. Metronomic dose-finding approach of oral chemotherapy by experimentally-driven integrated mathematical modeling [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 2730.
Abstract 2733: A computational model of cellular metabolism with mutation data predicts metabolites associated with somatic mutations in cancers
Authors: Lee Sang Mi , Lee GaRyoung , Lee Sungyoung , Song Hyojin , Yoon Sung Soo , Yun Hongseok , Koh Youngil , Kim Hyun Uk
Published: June 2022

Metabolic reprogramming is considered a hallmark of cancers, which plays an important role in cancer progression and development, partly as a consequence of somatic mutations. A representative product of metabolic reprogramming in cancers is oncometabolites that show abnormal accumulation in a cancer cell, induce malignancy, and are generated upon mutations in a metabolic gene, often IDH1, SDH or FH. Identification of novel mutation-associated metabolites will facilitate developing biomarkers and treatment strategies for cancers, as in the case of ivosidenib, an FDA approved drug for treating acute myeloid leukemia (AML) having the IDH1 mutant. To this end, we develop a computational workflow that predicts so-called metabolite-gene-pathway sets (MGPs) that present metabolites and metabolic pathways significantly associated with gene mutations in cancers. The computational workflow uses cancer patients’ mutation data and a computational model of cellular metabolism called a genome-scale metabolic models (GEM). In this study, the computational workflow was demonstrated using 943 cancer patient-specific GEMs representing 24 different cancer types based on the Pan-Cancer Analysis of Whole Genomes (PCAWG) data [1], which, as a result, predicted 4,135 MGPs for these multiple cancer types. The computational workflow was shown to generate biologically meaningful MGPs on the basis of multi-omics data from 17 AML samples collected in this study as well as previous published studies. For the AML samples, metabolites of the MGPs predicted using the computational workflow showed significantly different intracellular concentrations, depending on mutation of genes involved in the MGP. Moreover, for the 115 MGPs predicted for CNS-GBM/Oligo that are associated with mutation of CIC, EGFR, IDH1 or TP53, 69% of the MGPs were supported by previous studies. This two-level validation indeed showed that it is possible to characterize metabolic pathways and their metabolites that are affected in response to somatic mutations in a cancer cell. Our computational workflow and its prediction outcomes will help better understand the mutation-associated metabolic reprogramming in cancers, and serve as a valuable resource for further extended studies on cancer metabolism. [1] The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82-93

Citation Format: Sang Mi Lee, GaRyoung Lee, Sungyoung Lee, Hyojin Song, Sung Soo Yoon, Hongseok Yun, Youngil Koh, Hyun Uk Kim. A computational model of cellular metabolism with mutation data predicts metabolites associated with somatic mutations in cancers [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 2733.
Abstract 28: New onset of type 2 diabetes after colorectal cancer diagnosis: Results from three prospective US cohort studies, systematic review, and meta-analysis
Authors: Zeng Hongmei , Yuan Chen , Morze Jakub , Fu Ruiying , Wang Kai , Wang Liang , Sun Feng , Ji John S. , Giovannucci Edward L. , Song Mingyang
Published: June 2022

Background: Limited data indicate that patients with colorectal cancer (CRC) are at higher risk of developing type 2 diabetes (T2D). We prospectively examined the risk of T2D between individuals with and without CRC in three large cohorts and conducted a meta-analysis.

Methods: We assessed the diagnosis of CRC and T2D among 111 485 women from the Nurses' Health Study, 112 958 women from the Nurses' Health Study II, and 46 581 men from the Health Professionals Follow-up Study. We used multivariable Cox regression with time-varying covariates to calculate the hazard ratio (HR) of T2D in relation to CRC diagnosis. We further performed a systematic review and meta-analysis of cohort studies.

Findings: Up to 36 years of follow-up (6.9 million person-years), we documented 3402 incident CRC cases and 26 469 T2D cases. Compared to non-CRC individuals, those with CRC were more likely to develop T2D (multivariable-adjusted HR 1.20, 95% CI 1.05-1.38). The association was most evident for individuals with fewer risk factors for T2D. In the meta-analysis of seven cohort studies (1 061 744 participants), CRC was associated with higher T2D risk (meta-analysis HR 1.21, 95% CI 1.11-1.31, I2=57.9%). By CRC duration, a statistically significant association was observed in the first 10 years but not after 10 years of CRC diagnosis (≤5 years, meta-analysis HR 1.32, 95% CI 1.27-1.36; 5.1-10 years, 1.14 [1.04-1.25]; >10 years, 1.14 [0.91-1.37]).

Interpretations: CRC was associated with increased T2D risk, especially in the first ten years after CRC diagnosis. Our findings highlight the importance of T2D prevention for CRC survivorship care.

Citation Format: Hongmei Zeng, Chen Yuan, Jakub Morze, Ruiying Fu, Kai Wang, Liang Wang, Feng Sun, John S. Ji, Edward L. Giovannucci, Mingyang Song. New onset of type 2 diabetes after colorectal cancer diagnosis: Results from three prospective US cohort studies, systematic review, and meta-analysis [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 28.
Abstract 2800: Use of an optimized machine learning algorithm to develop DNA methylation markers for detecting colorectal cancer (CRC)
Authors: Kang Jun-Kyu , Kim Su Yeon , Lim Yoojoo , Kim Hwang-Phill , Kim Tae-You
Published: June 2022

Introduction: Epigenetic changes including methylation occur early in tumorigenesis and are known to be highly pervasive across a tumor type. The DNA methylation pattern can vary between individuals with or without cancer and also in patients with cancer of different origins. In this study, we investigated the discovery of comprehensive markers and validation of the diagnostic and prognostic potential of colorectal cancer.

Methods: Patients with various stage of colorectal cancer were eligible for the current study, mainly stage III. We generated genome-wide methylation data from 379 colorectal cancer (CRC) tissues and 330 available paired adjacent normal mucosa tissues from Korean patients by Illumina EPIC Human Methylation microarray targeting 860,000~ CpG sites. A machine learning algorithm was used to build an optimized prediction model and select the tumor specific markers based on through theses CpG sites. Then, the risk score was devised for prognosis using this marker set. Finally, in order to validate the rule of CpG sites, the genomic location and pathway enrichment analysis was performed by CHROMHMM and Metascape.

Results: 379 colorectal cancer tissues and 330 paired adjacent normal mucosal tissues were included for analysis. Clinical stages of the included patients were, III in N (61.2%), II in N (19.5%), and IV in N (11.9%). A total of 305 methylation markers that showed statistically significant differences between normal and cancer tissues were selected. Our model could accurately identify CRC (areas under the curve for the training and validation cohorts: 0.968 and 0.984, respectively). Using our prediction model, the colorectal cancer patients were predicted as colorectal cancer accurately in the methylation data from TCGA (COREAD; colorectal cancer tissue DNA) and GEO dataset (plasma cfDNA from colorectal cancer patients). The risk score comprising the subset of 305 methylation markers was calculated, and poor prognosis was predicted in the high-risk score group (overall survival P <0.1, progression-free survival P < 0.01). Gene ontology (GO) enrichment analysis showed that the 305 CpG sites were enriched in transcription regulatory regions (160/305, 52.5%) and were associated with developmental process and carcinogenesis (GO: 0032502, P <0.001; C4721208, P <0.001).

Conclusions: In summary, the performance of our prediction model with these 305 CpG sites was highly accurate for CRC diagnosis, and the optimized risk score could predict the prognosis of Korean CRC patients

Citation Format: Jun-Kyu Kang, Su Yeon Kim, Yoojoo Lim, Hwang-Phill Kim, Tae-You Kim. Use of an optimized machine learning algorithm to develop DNA methylation markers for detecting colorectal cancer (CRC) [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 2800.
Abstract 2806: High sensitivity qPCR microsatellite instability detection in FFPE tissue
Authors: Yan Yan Helen , Young Blake , Wang Zhiheng , Yaseen Adam , Pinto Alessandro , Zhang David
Published: June 2022

Microsatellite instability (MSI) refers to genetic instability in short nucleotide repeats (e.g., 1-6bp tandem repeats), where a cell comprises a different number of repeats as compared to what was inherited from a progenitor cell. This genetic instability is often observed in tumor cells with impaired mismatch repair (MMR), especially in colorectal cancer (CRC) and endometrial cancer. MSI-high tumors can help identify patients that would benefit from additional genetic testing to diagnose Lynch Syndrome. Additionally, MSI can potentially be used as a biomarker to predict response to treatment with immunotherapy and CRC patients with MSI have a significantly better prognosis compared to those with intact mismatch repair. Here we present the VarTrace® MSI Research qPCR Assay, which enables high sensitivity detection of microsatellite instability. The assay uses NuProbe’s PCR-based Blocker Displacement Amplification (BDA) technology to enable the selective amplification of MSI unstable alleles with 1% analytical limit of detection. The assay is intended for the qualitative detection of mutations in 5 MSI loci (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) without the need of matched normal, and reports MSI-high (MSI-H), MSI-low (MSI-L) and Microsatellite Stable (MSS). Analytical validation of the assay has been completed on Horizon MSI/MSS formalin-fixed, paraffin-embedded (FFPE) DNA reference standard, SeraCare MSI AF5% reference panel mix, and 50 CRC FFPE samples. One FFPE section with as little as 2ng of input DNA is enough for this assay. The high sensitivity potentially allows for the detection of MSI status in liquid biopsy.

Citation Format: Yan Helen Yan, Blake Young, Zhiheng Wang, Adam Yaseen, Alessandro Pinto, David Zhang. High sensitivity qPCR microsatellite instability detection in FFPE tissue [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 2806.
Abstract 2847: Simultaneous TCR and transcriptomic sequencing of single Tcells defines biological subtypes in pancreatic cancer for adoptive Tcell therapy
Authors: Schalck Aislyn , Sakellariou-Thompson Donastas , Forget Marie-Andrée , Sei Emi , Hughes Tara , Bai Shanshan , Hu Min , Kumar Tapsi , Hurd Mark , Katz Matthew , Tzeng Chine-Wei , Pant Shubham , Javle Milind , Maitra Anirban , Haymaker Cara , Kim Michael , Navin Nicholas , Bernatchez Chantale
Published: June 2022

Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal tumor-type with very few effective treatment strategies. Attempts to improve outcomes using immune checkpoint blockade therapy have also failed, likely because the overall Tcell infiltration in this tumor-type is low. Despite this, the presence of CD3+CD8+ tumor-infiltrating lymphocytes (TIL) in PDAC is associated with improved survival outcomes, suggesting that other immune-based strategies could be more successful. Here, we examine ex vivo tumor-infiltrating Tcell expansion for adoptive Tcell therapy (ACT) as a potential strategy for treating PDAC. The focus of this study is to understand the transcriptional states of Tcells in the pancreas and PDACs and how they change with ex vivo expansion and re-infusion into patients as treatment strategy. We have performed both single cell transcriptome and TCR sequencing (scRNA-TCRseq) on 54,579 Tcells from 8 human PDAC samples and the ex vivo grown TIL from a subset of 6 patients and found 13 purported substates. Through TCR tracking of the Tcell clonotypes, we find that the expansion protocol is able to expand Tcells found in many different Tcell states in the primary tumor. Furthermore, we compared our thirteen tumor-infiltrating substates with 41,935 Tcells from two other independent single cell studies across 71 samples, and confirmed our substates to be present across all datasets.

Citation Format: Aislyn Schalck, Donastas Sakellariou-Thompson, Marie-Andrée Forget, Emi Sei, Tara Hughes, Shanshan Bai, Min Hu, Tapsi Kumar, Mark Hurd, Matthew Katz, Chine-Wei Tzeng, Shubham Pant, Milind Javle, Anirban Maitra, Cara Haymaker, Michael Kim, Nicholas Navin, Chantale Bernatchez. Simultaneous TCR and transcriptomic sequencing of single Tcells defines biological subtypes in pancreatic cancer for adoptive Tcell therapy [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 2847.
Abstract 2881: Proper priming of T cells is crucial for the anti-tumor effect of mPTX-35, an anti-TNFRSF25 agonist antibody
Authors: Sarhan Dareen , Rabah Lara , Tahiliani Vikas , Trinh Anh M. , Jasuja Rahul R. , Dixon Eric P. , Seavey Matthew , Verma Vivek , Gupta Seema , Khleif Samir N.
Published: June 2022

TNFRSF25, also known as Death Receptor 3 (DR3), is a cell surface receptor of the tumor necrosis factor receptor superfamily (TNFRSF) which is expressed on T cells, innate lymphoid cells, and B cells. Upon binding with TL1A ligand, this co-stimulatory molecule induces T cell activation, leading either to inflammation or cell death. Mouse PTX-35 (mPTX-35) is a TNFRSF25 functional agonist derived from a CDR that was humanized and affinity matured, then fused to a mouse IgG1-Fc backbone. Since costimulatory agonist antibodies have shown limited efficacy in clinical trials, our aims were to (i) determine the anti-tumor efficacy of mPTX-35, (ii) elucidate any mechanisms of resistance, and (iii) identify immune conditions that provide effective anti-tumor immune responses to mPTX-35 treatment. We studied the anti-tumor immune effects of mPTX-35 in both cold and hot tumor models. In a TC-1 cold tumor, we found that treatment with an anti-TNFRSF25 agonist antibody does not affect tumor growth or survival. In contrast, vaccination with an E7 antigen-specific vaccine leads to an environment that reverses primary resistance to the agonist antibody, inhibiting the tumor growth, and enhancing overall survival. Interestingly, we found that similar to other co-stimulatory agonist molecules, the immune effects of the anti-TNFRSF25 agonist are dose-dependent with lower (0.2 mg/kg) and higher (5 mg/kg) doses of mPTX-35 showing a reduced anti-tumor response than a dose of 1 mg/kg, resulting in a bell-shaped response in all tumor models. Similar immune-mediated anti-tumor effects of mPTX-35 were found in a CT26 (hot) tumor model. In conclusion, these results show that anti-TNFRSF25 agonist antibody demonstrates high anti-tumor efficacy in tumors that are infiltrated with T cells while the absence of properly antigen activated CD8 T cells (such as in cold tumors) incurs primary resistance to TNFRSF25 agonist that is reversed by proper priming of CD8 T cells. These results highlight the importance of optimal priming to limit primary resistance mechanisms and drive an efficacious immune response via the TNSFR25 axis.

Citation Format: Dareen Sarhan, Lara Rabah, Vikas Tahiliani, Anh M. Trinh, Rahul R. Jasuja, Eric P. Dixon, Matthew Seavey, Vivek Verma, Seema Gupta, Samir N. Khleif. Proper priming of T cells is crucial for the anti-tumor effect of mPTX-35, an anti-TNFRSF25 agonist antibody [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 2881.
Abstract 2889: Novel bispecific humanized BCMA-CD3 antibodies specifically target multiple myeloma cells
Authors: Huang Yanwei , Sienkiewicz John , Sun Jinying , Guiang Liselle , Li Feng , Yang Liming , Wu Lijun , Golubovskaya Vita M.
Published: June 2022

BCMA antigen is overexpressed in multiple myeloma cells and has been shown to be a promising target for novel cellular and antibody therapeutics. The humanized BCMA (clone 4C8A) antibody that effectively targeted multiple myeloma in a CAR (chimeric antigen receptor) format was used for designing several formats of bispecific BCMA-CD3 antibodies. Several different designs including univalent and bivalent BCMA-CD3 CrossMAB; triple chain BCMA-FAB-CD3 ScFv-Fc and tetravalent BCMA ScFv-CD3 ScFv-Fc antibodies were tested for affinity and binding with BCMA-positive cells and T cells. Real time cytotoxic activity (RTCA) and IFN-gamma secretion were also tested with multiple myeloma and CHO-BCMA target cells. All BCMA bispecific antibody designs demonstrated specific affinity with CHO-BCMA but not CHO cells in the nanoM range of 0.3-33 nM; all designs bound to T cells by FACS. The triple chain BCMA-FAB-CD3 ScFv-Fc designs had the highest Kd of binding with CHO-BCMA cells (Kd=0.3 nM) and with multiple myeloma MM1S, and H929 cells (0.1 and 0.3 nM, respectively). All antibodies with T cells specifically killed CHO-BCMA and multiple myeloma cells in a dose-dependent manner but not CHO or K562 cells, measured by RTCA assay. The bivalent BCMA-CD3 CrossMAB and triple chain BCMA FAB CD3scFv-Fc antibodies with T cells secreted IFN-gamma with EC50 =0.01-0.02 nM. In addition, the BCMA bispecific antibodies had high in vivo efficacy using a MM1S xenograft NSG mouse model.

Significance: This data demonstrates high efficacy of novel hBCMA-CD3 antibodies with multiple myeloma cells and provides a basis for future pre-clinical and clinical development.

Citation Format: Yanwei Huang, John Sienkiewicz, Jinying Sun, Liselle Guiang, Feng Li, Liming Yang, Lijun Wu, Vita M. Golubovskaya. Novel bispecific humanized BCMA-CD3 antibodies specifically target multiple myeloma cells [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 2889.
Abstract 2934: Pattern of PIK3CA co-alterations in endometrial cancer
Authors: Paul Madhuri , Scarpa Frank J. , Daringer Rachel , Agersborg Sally , Funari Vincent Anthony , Blocker Forrest
Published: June 2022

Purpose: Aberrant PI3K pathway activation drives tumor proliferation and survival. The aim of this study was to identify PI3K pathway activation patterns in endometrial cancer by profiling mutational prevalence and co-mutation with PTEN and TP53.

Methods: Molecular profiles of 1,180 unique cancer (endometrial, breast, lung, and colorectal) patients’ formalin-fixed paraffin-embedded tissue samples were analyzed. Samples were evaluated using a 323 gene NGS panel utilizing the QIAseq targeted DNA chemistry. Fisher's exact test was used for statistics.

Results: The most frequent PIK3CA mutations were found in the kinase domain (KD) in both endometrial and breast cancers (predominately p.H1047). In lung and colorectal cancers, helical domain alterations were predominant. There were significantly more PIK3CA adaptor binding domain mutations and PIK3CA/PTEN co-mutations in endometrial cancer compared to other tumor types. Among PIK3CA/PTEN co-mutations in endometrial cancer, there were significantly fewer TP53 mutations when compared to those with no PTEN co-mutation (17.2% vs. 70.7%; p<0.0001).

Conclusions: In endometrial cancer, PTEN is more frequently mutated upon PI3K/AKT pathway hyperactivation, abrogating its normal inhibitory effect on PI3K resulting in increased cell proliferation and survival. When PTEN is not mutated, alternations downstream of AKT, such as TP53 mutations, may serve as alternative cell survival regulators. This may account for the relationship between PTEN/PIK3CA KD co-mutation and TP53 mutation. While PIK3CA KD mutations are similarly predominant in breast and endometrial cancer, the PTEN feedback loop is disrupted in endometrial cancer. This study provides insight into the patterns of molecular alterations present within PIK3CA-mutated patients, which could be instrumental in stratifying patient populations.

PIK3CA Mutation Prevalence Adapter binding domain Helical domain Kinase domain Hotspot H1047 PTEN co-mutation + any PIK3CA mutation Endometrial (n=99) 21.2% 26.3% 42.4% 27.3% 58.6% Breast (n=278 ) 3.6% (p<0.0001) 37.8% (p=0.0386) 55.4% (p=0.0258) 46.8% (p=0.0007) 7.2% (p<0.0001) Lung (n=452) 8.8% (p=0.0004) 50.2% (p<0.0001) 24.6% (p=0.0003) 8.4% (p<0.0001) 5.5% (p<0.0001) Colorectal (n=342) 9.9% (p=0.0027) 51.5% (p<0.0001) 25.1% (p=0.0008) 16.4% (p=0.0147) 8.2% (p<0.0001)

Citation Format: Madhuri Paul, Frank J. Scarpa, Rachel Daringer, Sally Agersborg, Vincent Anthony Funari, Forrest Blocker. Pattern of PIK3CA co-alterations in endometrial 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 2934.
Abstract 2935: Whole genome sequence of triple negative breast cancer (TNBC) tumors of African descent
Authors: Ahuno Samuel Terkper , Shah Yajas , Martini Rachel , Sboner Andrea , Robine Nicolas , Elemento Olivier , Imielinski Marcin , Newman Lisa , Davis Melissa
Published: June 2022

In the US, BC incidence has recently converged among self-reported European Americans (EA) and African Americans (AA), however BC mortality remains approximately 40% higher among AA compared to EA and other SRR groups. The initial divergence in mortality curves between these groups occurred at the advent of hormone receptor (HR) targeted treatment options, unmasking the heterogeneity of BC diagnoses. Here, we present Whole Genomes Sequencing of 30 Triple Negative Breast Cancers of African women presenting to the clinics in New York. These were collected as part of the ICSBCS cohort to identify ancestry related mutational signatures including complex structural variants which could help better explain etiology of cancer in these population and that we may leveraged for treatment or prognostic purposes. Somatic mutational landscape included higher frequency of TP53 (73%), BRCA1 (40%), ATK1 (37%), CDH1(37%), and CTCF (33%). We confirmed African ancestry of patients through ADMIXTURE and observed (>70%) African ancestry. Comparison between our cohort and TCGA BRCA showed higher tumor mutational burden in our cohort which could be accounted for by greater sensitivity in our updated sequencing technology and analysis pipelines. Mutational signature analysis showed cosmic Signature 3 suggesting evidence of defective homologous recombination and signature 16 with unknown etiology. In addition, we also observed evidence deletions and structural variants such as rigma, pyrgo and typhonas. Ongoing efforts are investigating complex structural variants in our cohort compared to similar populations from other studies while waiting on additional samples.

Citation Format: Samuel Terkper Ahuno, Yajas Shah, Rachel Martini, Andrea Sboner, Nicolas Robine, Olivier Elemento, Marcin Imielinski, Lisa Newman, Melissa Davis. Whole genome sequence of triple negative breast cancer (TNBC) tumors of African descent [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 2935.
Abstract 2937: Mutational analysis of ORF-8 of SARS-CoV-2 - a window to immunotherapy
Authors: Trieu Gopika , Mehta Nikita , Park Jeffrey , Ionescu Andrew , Asgari Lily , Trieu Vuong
Published: June 2022

Background: TGF-Beta plays an important role in immune evasion in oncology. Similarly, SARS-Cov-2, the causal agent of the COVID-19 pandemic, also has an immune evasion function. This is mediated by ORF-8 through its interaction with multiple immune regulatory elements, including TGF-beta. This is a mutational analysis of ORF-8.

Methods: We took advantage of the database of millions of SARS-CoV-2 genomes are archived and organized in phylogenetic relationships to show the evolution of ORF-8. Site numbering and genome structure use Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 8 × 10^-4 subs per site per year. ( https://nextstrain.org/). The epidemiological data provided at https://ourworldindata.org/coronavirus was used to determine the property of the variants using mortality and infectivity data at the site.

Results: Scan of ORF-8 revealed a high rate of mutation at aa119 and aa120. More importantly, the mutation at 120 or 119 that resulted in null ORF8 clearly delineates the pre-Delta and Delta SARS-Cov-2. In fact, all the delta lineages exhibited the null mutation at 119/120. This region is important for the dimerization of ORF-8 and possibly its interaction with host TGF-beta. All other variants, including the alpha variants, are wild type (aa120 = F). Monitoring the mutations over the last several months indicated that the delta variants have now picked up the wild type F at aa120 (Faa120) in Egypt or the L at aa 120 (Laa120) in India. The epidemiology of Egypt and India indicates that the Faa120 is more immune evasive and suggestive that more infectious but not more lethal.

Conclusions: This is an opportunity to monitor in real-time the evolution of ORF-8 and how it is interacting with the host immune system. Additionally, since our current clinical trial on TGF-beta inhibitors is in India and Latin America, it is an opportunity to correlate clinical findings to molecular and epidemiological data for these variants. If we are correct, the Faa120 will emerge as the dominant variant in the next wave of COVID-19.

Citation Format: Gopika Trieu, Nikita Mehta, Jeffrey Park, Andrew Ionescu, Lily Asgari, Vuong Trieu. Mutational analysis of ORF-8 of SARS-CoV-2 - a window to immunotherapy [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 2937.
Abstract 2946: Perturb-seq analysis of TNFα-induced transcriptional response
Authors: Tedesco Donato , Chenchik Alex , Liu Tianbing , Hu Dongfang , Isachenko Nadya , Dolganov Nadia
Published: June 2022

We performed a single-cell Perturb-seq screen on HEK293 cells with a ~100 sgRNA pooled library, aimed at identifying genes involved in TNFα-induced transcriptional response. As a reference, a parallel screen was performed with cells transduced in arrayed format with the same set of sgRNAs as the pooled library. For the pooled library screen, cells were transduced with the pooled sgRNA library, selected and expanded for 10 days, split into 2 samples for 72h TNFα treatment/mock-treatment. After treatment, cells were loaded on the 10X Genomics instrument according to manufacturer’s specifications at 2000, 7500 and 15,000 cells/sample/lane. For the arrayed screen, cells were transduced with individual sgRNAs in arrayed format, selected and expanded for 10 days, split into 2 samples for 72h TNFα treatment/mock treatment. After treatment ~10,000 from each sample were harvested for RNA purification. For both pooled library single-cell and arrayed screens, genome-wide transcriptome analysis was assayed using the DriverMap Targeted RNA-Seq assay. Both screens identified TNFRSF1A and IKBKG as top mediators of TFNα transcriptional response.

Citation Format: Donato Tedesco, Alex Chenchik, Tianbing Liu, Dongfang Hu, Nadya Isachenko, Nadia Dolganov. Perturb-seq analysis of TNFα-induced transcriptional response [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 2946.
Abstract 2949: Enabling single cell analysis of copy number variation in breast cancer
Authors: Parikh Saurabh , Paula Arnaud Da Cruz , Bhaloo Shirin Issa , Li Alex , Weigelt Britta , Patel Khushali , Wronski Ania , Parikh Anup , Patel Khushali , Reis-Filho Jorge
Published: June 2022

Breast cancer is arguably one of the solid tumors most comprehensively analyzed by massively parallel sequencing. Although the repertoire of clonal somatic genetic alterations in primary and metastatic breast cancers has been characterized, a complete characterization of the subclonal genetic alterations present in these cancers, as well as their clonal composition and clonal dynamics remain to be fully defined. Addressing these knowledge gaps is germane to the successful personalization of treatments for breast cancer patients. Single cell sequencing is uncovering many insights into the clonal evolution and heterogeneity of breast cancers and how this can be leveraged for clinical and therapeutic benefit. Bulk next generation sequencing has primarily focused on mutation profiling; however, there are several lines of evidence to demonstrate the biological and clinical importance of accurately detecting copy number alterations. Previous single cell sequencing studies focusing on copy number alterations were based on whole-genome amplification methods or could not concurrently define the repertoire of somatic mutations and copy number alterations in single cells. Here we report on a novel single cell DNA sequencing approach leveraging the Tapestri device and Insights bioinformatic pipeline to detect both copy number alterations and somatic mutations in individual cells derived from breast cancer specimens. The identification of targeted somatic genetic alterations at single cell resolution provides novel insights about the development, progression and therapeutic resistance of breast cancers, and enables the development of novel diagnostic tools and predictive biomarkers.

Citation Format: Saurabh Parikh, Arnaud Da Cruz Paula, Shirin Issa Bhaloo, Alex Li, Britta Weigelt, Khushali Patel, Ania Wronski, Anup Parikh, Khushali Patel, Jorge Reis-Filho. Enabling single cell analysis of copy number variation in 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 2949.
Abstract 2954: Chromatin accessibility dynamics in CDK4/6 inhibitor-induced senescence
Authors: Rendleman Justin , Yeung Joanna , Pagane Nicole , Duba Irene , Scortea Andrew , Koff Andrew , Risca Viviana I.
Published: June 2022

Liposarcomas are a rare cancer that often undergo amplification of the 12q13-15 locus, which includes the gene encoding the cyclin-dependent kinase CDK4; CDK4/6 inhibitors therefore offer a promising targeted therapy to halt proliferation in these tumors where therapeutic options are scarce once surgical resection is no longer possible. CDK4/6 inhibition can lead to either reversible or irreversible exit from the cell cycle (quiescence or senescence, respectively), but the underlying mechanisms are not well understood. Applying ATAC-seq in a liposarcoma cell line model of therapy-induced senescence, we have assayed alterations in the chromatin landscape that arise in response to CDK4/6 inhibitor treatment to identify epigenetic changes that drive this cell fate decision. Additionally, we have compared this with cells that undergo senescence due to DNA damage induced by the drug doxorubicin, an anthracycline that is the standard first-line chemotherapy for liposarcoma. In CDK4/6 inhibition, we identified dynamic patterns of accessibility as cells transition from quiescence to senescence over 28 days of treatment. NF-kB motifs in promoter-proximal regions displayed increased accessibility as cells commit to the senescence state, and ATAC-seq peaks with AP-1 transcription factor family motifs exhibit dynamic accessibility. We characterized the DNA damage response by gamma-H2AX and 53BP1 immunofluorescence and found that for CDK4/6 inhibition there is minimal DNA damage and only at late senescence time points, in marked contrast with doxorubicin treatment. We observed differences in accessibility between CDK4/6 inhibitor- and doxorubicin-induced senescence in a region on chromosome 6 that contains the gene FRK. This gene encodes a tyrosine kinase in the Src family that negatively regulates cell proliferation and has been implicated as a tumor suppressor through upregulation of p21, which may reinforce restriction of phosphorylation on Rb in parallel with CDK4/6 inhibition. These findings provide further evidence of the epigenetic impact of CDK4/6 inhibitors in cancer cells, and highlight shared and specific mechanisms that lead to therapy-induced senescence.

Citation Format: Justin Rendleman, Joanna Yeung, Nicole Pagane, Irene Duba, Andrew Scortea, Andrew Koff, Viviana I. Risca. Chromatin accessibility dynamics in CDK4/6 inhibitor-induced senescence [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 2954.
Abstract 2962: The oncogenic role of epigenetic factor, SNF2L in PCa
Authors: Brown LaKendria K. , Li Guoliang , Kanagasabai Thanigaivelan , Chen Zhenbang
Published: June 2022

Prostate cancer (PCa) is the second-leading cause of cancer mortality in the United States and is the most commonly diagnosed malignancy in African American men. Epigenetic regulation including chromatin remodeling plays a crucial role in the development and progression of many human diseases such as cancers. Epigenetic alterations contribute to the development and progression of PCa. These alterations may cause drug resistance to readily available treatment options for human cancers including PCa. Nucleosome-remodeling factor (NURF) consists of bromodomain-PHD finger transcription factor (BPTF), sucrose non-fermenting-2-like (SNF2L), and pRBAP46/48, controls the chromatin remodeling machinery. One of NURF’s major function is to regulate histone modifications and gene expression. Epigenetic factor, SNF2L, serves as the energy transducing subunit in NURF and is encoded by the SMARCA1 gene. SNF2L is a ubiquitously expressed transcription activator and its elevation is associated with cancer development. However, the role of SNF2L on PCa progression is still elusive. Therefore, there are unmet needs to understand the role of SNF2L in PCa in order to develop effective therapeutic approaches of controlling this malignancy. The objective of this project is to assess the impact of SNF2L loss on PCa progression. We hypothesized that SNF2L knockout (KO) will inhibit the proliferation of androgen-sensitive and castration-resistant PCa cells and targeting SNF2L or SMARCA-1 gene may be beneficial for controlling cancer progression. We have generated SNF2L KO PCa cells with CRISPR-Cas9 technology and inhibited SMARCA-1 gene via transient transfection application. Our results showed that SNF2L loss resulted in a reduced proliferation and altered morphology of PCa cells. SNF2L KO destabilizes the NURF complex and impairs chromatin remodeling and histone modifications for cell growth and survival. Thereby, targeting SNF2L may serve as a novel therapeutic regime in PCa control.

Citation Format: LaKendria K. Brown, Guoliang Li, Thanigaivelan Kanagasabai, Zhenbang Chen. The oncogenic role of epigenetic factor, SNF2L in PCa [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 2962.
Abstract 2968: Interrogating the function of histone methyltransferases in MYC-driven medulloblastoma
Authors: Mercier Audrey L. , Stripay Jennifer L. , Bilokapic Silvija , Williams Justin , Nance Stephanie , Liu Jingjing , Philips Steven , Kandikonda Suresh , Morfouace Marie , Bramoulle Aude , Advedissian Tamara , Yu Jiyang , Peng Junmin , Ansari Aseem , Halic Mario , Durbin Adam , Vakoc Christopher , Roussel Martine F.
Published: June 2022

Medulloblastoma (MB) is the most common malignant pediatric brain tumor of the cerebellum, with four distinct molecular subgroups, each carrying different clinical prognoses. Group 3 (G3) is the most aggressive subgroup and is associated with amplifications of the MYC gene. MYC expression and function are controlled in part by epigenetic regulation, and interestingly, the few mutations that are found in G3 medulloblastoma are mostly located in genes encoding epigenetic regulators. Surprisingly, many tumors had no mutations raising the question as to whether non-mutated or non-amplified epigenetic regulators may be drivers of G3MB tumorigenesis. We previously found that dysregulation of the H3K27 methyltransferase EZH2 cooperates with MYC in G3MB, indicating that epigenetic regulators may provide a source of potential therapeutic targets. Therefore, to identify novel epigenetic drivers in G3MB, we performed an unbiased shRNA screen of 243 known chromatin regulators. The most intriguing candidate was SMYD3, a multidomain-containing protein with histone H4-lysine 5 (H4K5) methyltransferase activity. Knockdown of SMYD3 suppressed G3MB proliferation in vitro and tumor progression in vivo. SMYD3 protein is nuclear and associated with the MYC promoter. Deletion of SMYD3 results in loss of MYC, G2/M and epithelial-to-mesenchymal target gene expression. Using a multi-omics approach including CUT&RUN sequencing, RNA-seq, DNA methylation, cryo-electron microscopy (cryo-EM) and proteomics we aim to elucidate how SMYD3 controls G3MB tumorigenesis. These results highlight the role of a potentially targetable new epigenetic regulator of tumorigenesis in G3MB.

Citation Format: Audrey L. Mercier, Jennifer L. Stripay, Silvija Bilokapic, Justin Williams, Stephanie Nance, Jingjing Liu, Steven Philips, Suresh Kandikonda, Marie Morfouace, Aude Bramoulle, Tamara Advedissian, Jiyang Yu, Junmin Peng, Aseem Ansari, Mario Halic, Adam Durbin, Christopher Vakoc, Martine F. Roussel. Interrogating the function of histone methyltransferases in MYC-driven medulloblastoma [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 2968.
Abstract 2973: Rac inhibitors for cancer therapy
Authors: Crespo Grace Enid Velez , Hernandez Eliud , Dharmawardhane Suranganie , Vlaar Cornelis , Castillo Linnette , Kucheryavykh Lilia
Published: June 2022

Among all cancers worldwide, breast cancer is the first cause of death in women. One of the most aggressive subtypes of breast cancer is the triple negative form, which account for the 10-15% of breast cancer cases. Due to its complex heterogeneity triple negative breast cancer available treatments are limited, being chemotherapy in the first line of use. Despite advances in the search for new treatments, there is still a lack of effective therapies, being the metastatic disease the principal cause of breast cancer mortality. Therefore, it is critical to develop a new and effective strategies to inhibit metastasis. The Rho GTPase Rac has been identified as a promising target for anti-metastatic cancer therapy as it has been shown to play key roles in metastatic cancer cells dynamics as: cellular adhesion, migration, proliferation, survival and invasion. To this extent, in an effort to find a compound with increased Rac inhibitory capacity our group developed Ehop-016 derivatives HV-107 and HV-118. Previously we have reported HV-107 and HV-118 to affect cell viability promoting a G2-M cell cycle arrest with a sub-G1 population indicative of cell death in MDA-MB-231. Also, an increase of caspases activity validating apoptosis as a mechanism of cell death was shown. In addition, a decrease in tumor growth and metastasis by ~35 to 40% in an in vivo study using HV-118 at 1 mg/kg body weightwas also reported. Currently, through pulldown assays we have showed HV-107 and HV-118 to inhibit Rac activity at~500-2000 nM and 10 nM respectively in MDA-MB-231 and MDA-MB-468 breast cancer cells. Using trypan blue excision assay HV-107(>500 nM) and HV-118(>50 nM) were shown to affect cell viability promoting a G2-M cell cycle arrest in MDA-MB-468. We also demonstrated HV-107 and HV-118 to inhibit the direct downstream effector of Rac, PAK at >500 nM(HV-107) and >50 nM(HV-118) in MDA-MB-231 cells. In addition, HV-107 was also shown to increase Rho activity at concentrations significantly higher than the effective for Rac inhibition. Rho activity up-regulation has been reported to negatively affect migration of cancerous cells. Finally, we tested HV-107 in a mouse model of metastatic breast cancer. A decrease of ~ 40% in liver metastasis was shown for mice treated with 5 mg/kg BW HV-107. Taken together, our results indicate HV-107 and HV-118 are approximately 4-100 times more efficient than the parent compound Ehop-016 and have potential as anti-breast cancer metastasis therapeutics.

This study is supported by NIH Grant 1SC1GM122691, and PRINBRE P20GM103475 from NIGMS of the NIH to GVC

Citation Format: Grace Enid Velez Crespo, Eliud Hernandez, Suranganie Dharmawardhane, Cornelis Vlaar, Linnette Castillo, Lilia Kucheryavykh. Rac inhibitors for cancer therapy [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 2973.
Abstract 3026: Inhibition of glutaminolysis overcomes metabolic adaptation to devimistat treatment
Authors: Lang Liwei , Wang Fang , Shay Chloe , Ke Yonggang , Saba Nabil , Teng Yong
Published: June 2022

The identification and development of reagents that can limit preferential metabolic effectors in tumors as well as trigger unfavorable tumoral metabolic cues is of tremendous importance for suppressing malignancy. However, insufficient blocking of critical metabolic dependencies of cancer allows the development of metabolic bypasses, which significantly dampens therapeutic benefits of selective agents that target a single metabolic enzyme or pathway. We report here that head and neck squamous cell carcinoma (HNSCC) cells display strong addiction to glutamine. Devimistat, a novel lipoate analog, redirects cellular activity towards tumor-promoting glutaminolysis, leading to low anticancer efficacy in HNSCC cells. Mechanistically, devimistatinhibits the tricarboxylic acid cycle by blocking the enzyme activities of pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, which upregulates GLS1 and eventually promotes the compensatory role of glutaminolysis in cancer cell survival. Most importantly, the addition of a GLS1 inhibitor CB-839 to devimistat treatment abrogates the metabolic dependency of HNSCC cells on glutamine, achieving a synergistic anticancer effect in glutamine-addicted HNSCC. These novel and significant findings could lay a scientific foundation for developing more effective treatments targeting the metabolic requirements of HNSCC.

Citation Format: Liwei Lang, Fang Wang, Chloe Shay, Yonggang Ke, Nabil Saba, Yong Teng. Inhibition of glutaminolysis overcomes metabolic adaptation to devimistat treatment [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 3026.