bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1708: Improving genotype specific chemotherapy response in ovarian cancer via cGAS-STING pathway activation
Authors: Shakfa Noor , Lightbody Elizabeth , Li Deyang , Wilson-Sanchez Juliette , Conseil Gwenaelle , Afriyie-Asante Afrakoma , Chenard Stephen , Hamade Ali , Koti Madhuri 
Published: July 2021

Abstract
High grade serous ovarian carcinoma (HGSC) is the most lethal gynecologic malignancy with high rates of chemotherapy resistance and poor outcomes. Our previous studies have demonstrated the variable tumor immune microenvironment states that associate with platinum chemotherapy response. We further showed the significance of the interferon (IFN) induced chemokine CXCL10 as a key mediator of tumor infiltrating immune cell recruitment. Using the ID8-Trp53−/− murine model of HGSC, we demonstrated the potential of Stimulator of Interferon Genes (STING) pathway activation in enhancing response of HGSC tumors to carboplatin chemotherapy and sensitizing them to immune checkpoint blockade therapy through a heightened type 1 IFN (IFN1) response. CXCL10 production via IFN1 is also governed by genes that regulate cellular DNA damage repair pathways. Evolving evidence indicates a role of BRCA1 and PTEN genes in mediating cellular IFN1 responses. Losses in the function of these genes is widely prevalent in a large proportion of HGSC tumors, where tumors with BRCA1 mutations (~25% of HGSC cases) have higher CD8+ T cell infiltration in contrast to those with loss of PTEN (~10% of cases). We hypothesized that HGSC tumors with loss of PTEN expression can be rendered susceptible to immune mediated killing via activating the STING pathway. Tumors generated from ID8-Trp53−/−; Brca1−/− cells and those from ID8-Trp53−/−; Pten−/− cells in C57BL6 mice showed significant immunologic differences through local and systemic immune profiling. The addition of STING agonist treatment significantly increased chemosensitivity and improved overall response in mice implanted with ID8-Trp53−/−; Pten−/− cells compared to those treated with carboplatin alone, altering immune responses. This study is foundational to inform rational combinations of STING pathway activating therapies in HGSC, augmenting responses to existing chemotherapy regimens and prolonging survival rates in patients.
Citation Format: Noor Shakfa, Elizabeth Lightbody, Deyang Li, Juliette Wilson-Sanchez, Gwenaelle Conseil, Afrakoma Afriyie-Asante, Stephen Chenard, Ali Hamade, Madhuri Koti. Improving genotype specific chemotherapy response in ovarian cancer via cGAS-STING pathway activation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1708.
Abstract 1718: Tumor eradicated by an effective in situ vaccine based on a TLR agonist and an agonistic anti-OX40 antibody
Authors: Chu Yanhong , Liu Qin , Liu Baorui 
Published: July 2021

Abstract
As cancers are antigenic, numerous efforts have been devoted to harnessing the exquisite specificity of the immune system to destruct tumors over the past two decades. In this study, we have employed a practical approach called in situ vaccination without the need to previously identify and isolate antigen targets. Intratumoral injection of a TLR7 ligand R837 and an agonistic anti-OX40 antibody showed impressive synergistic anti-tumor effects. R837 upregulated the expression of OX40 on CD4+ T cells in the treated tumor. Then, anti-OX40 antibody triggered systemic tumor-specific T cell responses, with one-fold increase of effector memory T cells properties and stronger toxicity of lymphocytes in spleen. Remarkably, both the injected tumor and the noninjected tumor in the distant lesion of the mice were eliminated after vaccination. IL-1α is a pro-inflammatory cytokine, however IL-10 is an important anti-inflammatory cytokine that plays a central role as a negative immune regulator. In the tumor microenvironment, we found that the level of IL-1α increased and IL-10 decreased after vaccination. From RNA-seq analysis, many immune-related pathways in the tumor microenvironment were activated after vaccination, such as TNF signaling pathway, NOD-like receptor signaling pathway, C-type lectin receptor signaling pathway, Toll-like receptor signaling pathway and so on. This in situ vaccine based on two low doses of immunoomdulators caused little harm to normal organs and provided long-term protection against the same syngeneic tumor rechallenge. It could be applied to various types of late stage solid tumors and worthy of further clinical research.
Citation Format: Yanhong Chu, Qin Liu, Baorui Liu. Tumor eradicated by an effective in situ vaccine based on a TLR agonist and an agonistic anti-OX40 antibody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1718.
Abstract 172: Computational analysis of the NEK family of proteins reveals unique structural features and interactions with other cancer-related proteins
Authors: Silva Andriele , Singh Shaneen 
Published: July 2021

Abstract
The human Never In Mitosis A-like kinase (NEK) protein family consists of serine/threonine kinases that are implicated in the assembly of the mitotic spindle, regulation of the disjunction of the centrosome, and the functioning of the primary cilium. Protein kinases that regulate the centrosome cycle are often abnormally controlled in tumor cells, as are NEK family members. NEK2 was first identified in pediatric solid tumors and also has elevated expression levels in breast, pancreatic and colorectal cancer. NEK1, NEK3, and NEK5 are highly expressed in thyroid tumors, NEK8 is overexpressed in primary human breast tumors, and NEK11's expression is upregulated in early-stage colorectal cancers. To effectively exploit NEKs as drug targets, it is critical to understand their structure-function relationships to help elucidate their mechanism of action. However, structural information for most NEKs and the range and breadth of their interactions with other proteins are still widely unknown. In this study, we use an integrated computational approach which includes the prediction of the 3D structure using homology modeling, threading, and ab initio techniques, the biophysical/biochemical characterization of the theoretical models, followed by in silico protein-protein predictions and docking analysis to present a comprehensive computational analysis of all eleven NEK proteins. Our results reveal unique structural features in some of NEK family members, such as the armadillo (ARM)-like fold in NEK10 and RCC1 repeats found in NEK8 and NEK9. In addition, we present detailed investigations of four predicted protein-protein interaction scenarios involving NEK1, NEK7, NEK8, and NEK9 using docking analysis. This analysis lends support to new, previously unreported interactions of these NEKs with other cancer-related proteins i.e., TNF alpha with NEK7, GEF2 with NEK9, LRRK2 with NEK1, and ARA9 with NEK8. The details of the residues involved in the interaction interfaces from our proposed interaction scenarios provide valuable data for designing rational experiments to validate these interactions. Overall, this study uncovers novel and intriguing information about the NEK protein family, unique protein-protein interaction predictions, and lays the groundwork for elucidating their molecular mechanism as well as for investigating their potential as therapeutic targets.
Citation Format: Andriele Silva, Shaneen Singh. Computational analysis of the NEK family of proteins reveals unique structural features and interactions with other cancer-related proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 172.
Abstract 1725: Short-term administration of high dose mIL-2/CD25 fusion protein elicits CD8+ T cell-driven anti-tumor immunity and memory
Authors: LaPorte Kathryn , Hernandez Rosmely , Malek Thomas 
Published: July 2021

Abstract
Recombinant IL-2 (rIL-2) promotes the differentiation, proliferation, and survival of antigen-activated T cells and induces potent anti-tumor activity. High dose (HD) rIL-2 broadly targets T effector (Teff) and NK cells. However, rIL-2 cancer therapy requires long-term infusions of high doses due to its short half-life and is associated with severe toxicities which limit efficacy. To circumvent these limitations, our lab has developed and is testing a new IL-2-based biologic, mIL-2/CD25, which can be used at high doses to promote anti-tumor immunity. mIL-2/CD25 is a fusion protein (FP) composed of mouse IL-2 fused to the mouse CD25 extracellular domain via a non-cleavable glycine-serine linker with selectivity toward the high affinity IL-2R. This FP has a much longer half-life (16 hr) than rIL-2 (15 min). At a low dose, mIL-2/CD25 selectively expands Tregs, but at a HD, Teff cells are also engaged. These properties allow for HD FP to readily expand activated endogenous tumor-reactive Teff cells, but not memory-phenotypic CD8+ T cells and NK cells. In the current study, we tested the extent short-term HD FP therapy activated tumor-reactive Teff cells to elicit efficacious anti-tumor immunity responses despite Treg stimulation. HD FP prolonged survival in mice bearing B16.F10 melanoma, MC-38 colon adenocarcinoma, or CT26 colon carcinoma. In the CT26 model, a significant increase in both the number and the frequency of CD8+ T cells was detected in the tumor microenvironment (TME) of treated mice. FP-dependent Treg expansion was observed in secondary lymphoid tissues but not the TME. This therapeutic approach, therefore, led to a higher CD8+ Teff to Treg ratio specifically in the TME. After FP treatment, CD8+ T cells isolated from the TME expressed lower levels of TOX, PD-1, and LAG-3, suggesting that they were less exhausted. T cell depletion studies using anti-CD8 revealed that CD8+ T cells are the major driver of the FP-induced anti-tumor response. Rechallenge of animals that had previously cleared CT26 due to FP treatment led to successful tumor rejection, showing that the FP supported anti-tumor memory. These findings demonstrate that mIL-2/CD25 amplifies recently activated tumor-reactive CD8+ Teff cells to generate efficacious anti-tumor responses that limit Treg-dependent negative regulation in the TME and lead to anti-tumor memory.
Citation Format: Kathryn LaPorte, Rosmely Hernandez, Thomas Malek. Short-term administration of high dose mIL-2/CD25 fusion protein elicits CD8+ T cell-driven anti-tumor immunity and memory [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1725.
Abstract 1734: Modulation of immune responses to cancer by bi-specific IL-2/IL-13 superkines
Authors: Merchant Fahar , To Minh 
Published: July 2021

Abstract
Introduction: The IL-2 pathway plays a vital role in stimulating a pro-inflammatory (Th1) response against cancer through expansion and activation of effector CD8 T and NK cells. In contrast, the IL-4/IL-13 pathway stimulates myeloid derived suppressor cells (MDSCs) and M2 skewing of tumor associated macrophage (TAM) to foster an anti-inflammatory (Th2) response that is often exploited by cancers as a means to dampen the effects of the Th1 pathway. Therefore, suppression of MDSC and M2 TAM through inhibition of the IL-4/IL-13 pathway together with stimulation of effector immune cells through activation of the IL-2 pathway have the potential to invigorate a pro-inflammatory response in an otherwise immune suppressive tumor microenvironment (TME). To achieve this goal, we leveraged the versatility of our IL-2 and IL-13 superkine platforms to engineer long-acting bi-specific constructs to co-target surface receptors of these respective pathways.
Experimental Procedure: Studies included binding analyses by BLI/Octet and Biacore/SPR, signaling analyses using IL-2 and IL-4/IL-13 reporter assays, signaling analysis in human PBMC, and in vitro M1/M2 macrophage polarization assay.
Summary of Data: sIL2M-Fc-sIL13M is a bi-specific superkine composed of an IL-2 super-agonist (sIL2M) and IL-13 super-antagonist (sIL13M) linked together by human IgG1 Fc. sIL2M binds CD122 with superior affinity over IL-2 but does not engage CD25, which is expressed on immune-suppressive Tregs. sIL13M has higher affinity than IL-13 for IL13Rα1, which together with IL-4Rα forms a functional receptor complex. In pSTAT5 assay using primary human PBMCs, sIL2M-Fc-sIL13M showed enhanced potency over IL-2 in the activation of CD8 T-cells and NK cells while exhibiting limited activity on Treg. In an IL-4/IL-13 dependent pSTAT6 reporter assay, sIL2M-Fc-sIL13M demonstrated dose-dependent antagonism against stimulatory activity of both IL-4 and IL-13. This antagonistic effect was further validated with inhibition of IL-13 induced M2 polarization of macrophages in vitro.
Conclusion: sIL2M-Fc-sIL13M is a bi-specific superkine capable of concomitantly stimulating a Th1 response through activation of the IL-2 pathway and suppressing a Th2 response through inhibition of the IL-4/IL-13 pathway. Additional bi-specific superkine constructs are currently under testing, including those designed to enable accumulation in TME by engaging the decoy IL-13Rα2 that is overexpressed on a number of different tumor types.
Citation Format: Fahar Merchant, Minh To. Modulation of immune responses to cancer by bi-specific IL-2/IL-13 superkines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1734.
Abstract 174: In-depth transcriptomic comparisons provide novel insights into cancer metastasis
Authors: LIU KE , Glicksberg Benjamin S. , Paithankar Shreya , Chen Bin 
Published: July 2021

Abstract
Comparison of the transcriptome between primary and metastatic cancer is frequently performed to study cancer metastasis; however, distilling plausible biology from the comparison results remains a big challenge. We show that in the differential expression (DE) analysis performed on bulk RNAseq data a large proportion of DE genes are identified due to technical issues instead of biological differences between primary and metastatic cancer cells. Next, we develop a computational pipeline DEBoost to minimize such artifacts and apply it to five cancer types. We perform comprehensive analysis on the retained tumor-intrinsic DE genes to explore the biological mechanisms underlying the metastasis of different cancer types. Many of the DE genes are associated with the progression of primary cancer, suggesting the differential expression may have already been established before metastasis. Clustering analysis on DE genes identifies CNVs that account for the transcriptomic change and we further confirm 19p13.12 amplification drives the metastasis of primary Basal-like breast cancer via activating NOTCH signaling pathway. We also find that cell cycling is more active in metastatic prostate cancer than in primary cancer, suggesting the difference of responses to treatment like cell cycling inhibitors. Finally, we show that some metastatic cancer cells tend to express genes whose expression is normally observed at the metastasis site and we experimentally validate this phenomenon in colorectal cancer liver metastasis. Our pan-cancer liver metastasis study provides novel biological insights into cancer metastasis and meanwhile demonstrates the feasibility of characterizing tumor-intrinsic DE genes in cancer metastasis using our computational pipeline.
Citation Format: KE LIU, Benjamin S. Glicksberg, Shreya Paithankar, Bin Chen. In-depth transcriptomic comparisons provide novel insights into cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 174.
Abstract 176: Detecting neoepitopes from tumor RNA sequencing datasets
Authors: Thompson Drew , Vaske Olena M. , Rao Arjun , Beale Holly C. 
Published: July 2021

Abstract
Epitopes are peptides that present on the surface of the cell and can be recognized by immune cells to initiate the immune response. Identification of neoepitopes – tumor-specific, MHC-bound epitopes recognized specifically by T-cells – is valuable for predicting response to immunotherapies, including checkpoint blockade therapies. Tumors with more neoepitopes tend to be more responsive to immune checkpoint therapies compared to tumors with fewer neoepitopes. ProTECT is a previously published computational method that uses Illumina whole genome and transcriptome sequencing data from tumor and matched normal tissues to identify neoepitopes. Tumor and normal whole genome sequencing data are used to infer a patient's HLA haplotypes, as well as annotate variants as either somatic or germline. While whole genome sequencing is comprehensive, it is quite costly and not available for many samples. Here we adapt ProTECT to use only tumor RNA sequencing data and HLA haplotype information available to the clinician to identify neoepitopes in a tumor sample. Prior to running ProTECT, we use the computational tools Opossum and Platypus for variant calling instead of Radia (which is designed for variant calling using both RNA and DNA sequencing data as input). To determine which variants are somatic and therefore could represent tumor neoepitopes, variants found in RNA are compared to a panel of normals, for example the Genome Aggregation Database (gnomAD; containing variants from 125,748 exome sequences and 15,708 whole-genome sequences). With the resulting somatic variants and the HLA type, ProTECT proceeds as usual, with translation of variants into proteins, MHC:Peptide binding predictions and neoepitope ranking. We find that high quality neoepitopes are identifiable using an RNA-only approach, when genomic data is absent. Future work will validate the sensitivity of our method by benchmarking it against the original ProTECT predictions in the TCGA Prostate Adenocarcinoma cohort.
Citation Format: Drew Thompson, Olena M. Vaske, Arjun Rao, Holly C. Beale. Detecting neoepitopes from tumor RNA sequencing datasets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 176.
Abstract 1760: Role of Batf-dependant Th17 immune response in PTEN-null mouse model
Authors: Zhang Qiuyang , Liu Sen , Zhang Bing 
Published: July 2021

Abstract
Basic leucine zipper transcription factor ATF-like (BATF) belongs to the activator protein 1 (AP-1) family of transcription factors and has been shown to be predominantly expressed in cells of hematopoietic origin, especially in T cells. Mice deficient for BATF were first described to lack T helper cell type 17 (Th17). Th17 cells are a distinct lineage of CD4+ T helper cells that provide protective immunity to infections but are also involved in chronic inflammation and autoimmunity. However, the role of Th17 response in prostate cancer remains controversial. In this study, we took a genetic approach to explore the role of BATF-dependent Th17 cells in prostate cancers by interbreeding BATF-deficient (Batf-/-) mice with mice that are conditionally mutant for PTEN, an established preclinical model for prostate cancer. Batf+/+;Pten-/- and Batf+/-;Pten-/- mice presented similar prostate phenotypes thus were put into one group (named Batf+), which were compared to the Batf-/-;Pten-/- group (named Batf-). We found that Batf- prostates were clearly smaller than Batf+ prostates at 30 weeks. The genitourinary bloc weight was significantly heavier in Batf+ mice than in Batf- mice at 12 and 30 weeks. Batf+ mice developed significantly higher percent of invasive adenocarcinomas in different prostate lobes at 9, 12, and 30 weeks, respectively compared to Batf- mice. Tumors in Batf- mice exhibited lower rates of cellular proliferation and higher apoptosis, as well as reduced inflammatory cell infiltration and angiogenesis in the prostatic stroma. Moreover, Batf- mice exhibited significantly reduced mRNA and protein levels of Th17 cytokines, AP-1 family members and IL-23R, and reduced NF-kB pathway activity in both spleen and prostate tissues. CD4+ T cells from Batf- mice cultured under Th17 conditions for 4 days, expressed reduced AP-1 family-regulated genes compared to Batf+ mice. Prostate cancer cells (LNCaP) with overexpression of BATF in vitro exhibited increased IL-23R expression. Prostate tissues from Batf- mice cultured under IL-6 or Th17 conditions for 4 days had reduced IL-23R expression compared to that from Batf+ mice. Taken together, our results suggest that Batf promotes the initiation and progression of prostate adenocarcinoma via Th17-mediated inflammatory immune responses and that the Batf-IL-23-IL-17 axis is a critical pathway that is needed for prostate adenocarcinoma development and progression.
This work was supported by the NIH-National Institute of General Medical Sciences COBRE on Aging and Regenerative Medicine (P20GM103629, PD: S. Michal Jazwinski; PI: Q.Z.) and the Carol Lavin Bernick Faculty Grant from Tulane University (PI: Q.Z.).
Citation Format: Qiuyang Zhang, Sen Liu, Bing Zhang. Role of Batf-dependant Th17 immune response in PTEN-null mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1760.