bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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&lt;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&lt;0.0001) 37.8% (p=0.0386) 55.4% (p=0.0258) 46.8% (p=0.0007) 7.2% (p&lt;0.0001) Lung (n=452) 8.8% (p=0.0004) 50.2% (p&lt;0.0001) 24.6% (p=0.0003) 8.4% (p&lt;0.0001) 5.5% (p&lt;0.0001) Colorectal (n=342) 9.9% (p=0.0027) 51.5% (p&lt;0.0001) 25.1% (p=0.0008) 16.4% (p=0.0147) 8.2% (p&lt;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

Abstract
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 (&gt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.