bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 131: The role of p66ShcA in the melanoma oncogenesis process
Authors: Canedo Eduardo Cepeda , Rincon Sonia Del , Siegel Peter , Witcher Michael , Ursini-Siegel Josie 
Published: June 2022

Abstract
Background: The identification of crucial driver mutations that affect the MAPK signaling pathway (BRAF, NRAS, NF1) in melanomas, has allowed for the development of targeted therapies and shed light on the process of melanocyte transformation. Gain of function mutations in proteins within the Ras/MAPK pathway in melanocytes leads to the formation of benign neoplasms, or nevi. Multiple mechanisms prevent the transformation of nevi into invasive cancer, namely, oncogene-induced senescence (OIS) and immunosurveillance. Of interest to the melanomagenesis process is the p66ShcA redox protein. We have found that compared to other solid cancers, the majority of primary human melanomas, patient-derived xenografts and melanoma cell lines strongly overexpress p66ShcA, an adaptor protein that induces production of reactive oxygen species (ROS) in response to stress stimuli. Indeed, UV light, increases p66ShcA levels and p66ShcA-induced oxidative stress, which is relevant to this disease as sun exposure contributes significantly to melanoma development. We hypothesized that p66ShcA may play a crucial role in the early steps of melanocyte transformation, possibly by contributing to the overriding of OIS and immune surveillance.
Methods: Melanoma initiation and progression will be examined in a known transgenic mouse model (Tyr::CRE/brafCA/ptenlox/lox) either in the presence of endogenous levels of p66ShcA or in an inducible p66ShcA over-expression setting. The necessity of p66ShcA-high expression for melanocyte BRAFV600E-transformation will be tested in immortalized melanocytes. Lastly, to explore the potential selection advantage conferred by p66ShcA, its expression will be silenced in a panel of known melanoma cell lines. Clonogenic assays as well as mouse xenografts will be performed.
Results: TCGA melanoma datasets, immunoblot analysis of human melanoma cell lines (n&gt;10), and a collection of metastatic patient-derived xenografts (PDX) (n=6) indicate uniformly elevated p66ShcA levels compared to other cancer types. Knock-down of p66ShcA in multiple melanoma cell lines reduces their clonogenic potential. This reduction in colony formation is independent of driver mutation (e.g., BRAF, NRAS, NF1). Suggesting that p66ShcA may sustain melanoma proliferation. Furthermore, xenografts of the murine YUMM1.7 cell line (braf mutant, cdkn2a null and pten null) in immune-deficient and immune-competent mice indicate that loss of p66ShcA (YUMM1.7 p66ShcA-KO) delays tumor formation, specifically in mice with an intact immune system.
Citation Format: Eduardo Cepeda Canedo, Sonia Del Rincon, Peter Siegel, Michael Witcher, Josie Ursini-Siegel. The role of p66ShcA in the melanoma oncogenesis process [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 131.
Abstract 1319: Complement activation in pancreatic ductal adenocarcinoma
Authors: Bell Brett I. , Pandey Sanjay , Asp Patrik , Guha Chandan 
Published: June 2022

Abstract
The complement system is an innate immune cascade which recognizes and clears microbes and damaged host cells. Complement activation has been linked to the promotion of tumor growth and metastasis across various anatomical sites with context-dependent effects. We therefore aim to understand the role for complement activation in pancreatic cancer. We have generated a tamoxifen-inducible autochthonous mouse model of PDAC which recapitulates genetic mutations found in humans using LSL-KrasG12D/+; Tgfbr2fl/fl; Ptf1a-CreER (KTC) mice. Using these mice, we assessed for complement activation in pancreatic tumors by western blot and confocal immunofluorescence. Western blotting for neoepitopes generated upon cleavage of Complement Component 3 (C3) demonstrated significantly increased complement activation in KTC tumors when compared to normal pancreas from at least 4-7 months post-induction. Using confocal immunofluorescence, we observed deposition of complement fragments in tumor stroma and on ductal carcinoma cells identified by co-staining with cytokeratin 19. We therefore hypothesized complement blockade would reduce PDAC tumor growth and sought to test this using C3 knockout (C3 KO) mice which lack all downstream complement function due to the central role of C3. We assessed flank tumor growth using two Kras; Tp53 (KPC) mutant-derived tumor cell lines in wild type (WT) C57BL/6J and C3 KO mice yet did not find a biologically significant reduction in flank tumor growth between WT and C3 KO. To validate the knockout, we assessed C3 activation by western blot but surprisingly found increased complement activation in C3 KO tumors. RT-qPCR demonstrated local transcription of C3 mRNA in both WT and C3 KO tumors as well as transcription of C3 mRNA in KPC cells in culture. This demonstrates that KPC cells are capable of autocrine production of C3. Using immunocytochemistry and RT-qPCR we identified expression of the C3a receptor in KPC cells which we hypothesized could serve as a sensor for feedback to control local C3 production. We applied 10 nM recombinant C3a to KPCY cells in vitro and found a 20% reduction in C3 mRNA transcription 1-hour post-treatment. Pre-treatment with 500 nM C3aR Antagonist (SB290157) ablated this effect. In summary, complement activation is significantly increased in PDAC and appears to be activated in part by tumor cells themselves. Autocrine production of C3 by tumor cells is sufficient to produce complement activation in the absence of systemic C3. Additional experiments are warranted to determine the role of complement in PDAC using C3 mice crossed with KTC mice to assess tumorigenesis in the total absence of C3.
Citation Format: Brett I. Bell, Sanjay Pandey, Patrik Asp, Chandan Guha. Complement activation in pancreatic ductal adenocarcinoma [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 1319.
Abstract 1357: T cell memory and the critical effectors of successful anticancer immune response
Authors: Daniels Andrew , Damsky William , McGeary Meaghan , Iwasaki Akiko , Bosenberg Marcus 
Published: June 2022

Abstract
Despite the initial clinical success of immunotherapies in the treatment of melanoma, most patients fail to achieve long-term responses. While the majority of patients initially respond to these treatments, most go on to develop secondary resistance. The mechanisms underlying this failure of long-term response and successful responses is poorly understood.
To better understand the factors contributing to successful long-term anti-cancer immune responses, we utilized the YUMMER1.7 (YR1.7) melanoma line to develop a novel model for the evaluation of immunologic memory. We found that mice engrafted with a YR1.7 tumor can be cured by resection, and that subsequent challenge of these mice with the same tumor, even at 20x the cell number, led to expeditious rejection. Using depleting antibodies, we found that memory response were dependent on CD8 and CD4 T cells, and that CD4 depletion alone does not compromise initial responses, but leads to eventual failure of memory. We found no effect of natural killer cell (NK) depletion.
We performed single cell RNA sequencing on primary and rechallenge tumors from the same mouse, with the same tumor line. We found a phenotype of clonal replacement, in which the effective T cell clones seen in the memory response were non-overlapping with those found in the primary tumor. This implies an extra-tumoral location for these clones in the primary setting or the potential for additional priming of novel T cell clones upon re-challenge.
Together, these findings suggest a novel insights on the manner and location of T cells needed for anti-cancer memory responses.
Citation Format: Andrew Daniels, William Damsky, Meaghan McGeary, Akiko Iwasaki, Marcus Bosenberg. T cell memory and the critical effectors of successful anticancer immune 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 1357.
Abstract 1364: Spatially resolved T-cell receptor profiling elucidates relationships between TCR diversity, immune infiltration, and cancer-associated pathways
Authors: Kriner Michelle A. , van Raay Katrina , Reeves Jason W. , Fuhrman Kit A. , Klock Andrew , Kutchma Alecksandr , Piazza Erin , Beechem Joseph 
Published: June 2022

Abstract
As T-cells mature, genes encoding T-cell receptor (TCR) segments are somatically recombined to generate a diverse repertoire of receptors specific to unique antigens. The resultant TCR diversity, and subsequent clonal expansion events, are critical in understanding the adaptive immune response to pathogens and cancers. While many methods have been developed to determine specific clonotypes and overall TCR diversity present in various tissues, these methods to date have failed to capture spatial orientation and arrangement of T-cells engaging with their microenvironment. Tracking T-cell migration and infiltration into the tumor has thus been limited to post-hoc low-plex profiling methods. To better understand T-cell localization during tumor development, we have developed a TCR profiling panel for the GeoMx® Digital Spatial Profiler that can be combined with the GeoMx Cancer Transcriptome Atlas (CTA) or Human Whole Transcriptome Atlas (WTA). This novel spatial assay enables simultaneous quantification of all functional TCR constant, variable and joining segments in situ along with transcriptome-wide gene expression profiling in spatially defined regions of a tissue. We validated the performance of the TCR probe pool in inflamed tonsil and cell pellet arrays, demonstrating comparable sensitivity and specificity relative to orthogonal methods. We next used the GeoMx TCR spike-in panel to characterize intra- and inter-patient TCR heterogeneity in a cohort of 68 T-cell lymphomas to track clonal interactions between the malignant and non-malignant immune microenvironment. We demonstrate the ability to link the spatial context of TCR segment expression to activation of malignant signaling cascades as well as non-cancerous T-cell response to the presence of other immune cells and cancer-associated signaling. Together, the combination of our TCR spike-in panel with the CTA or WTA illuminates spatial distribution of T-cell clones paving the way for studies to comprehensively link TCR clonality changes to the tumor microenvironment.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
Citation Format: Michelle A. Kriner, Katrina van Raay, Jason W. Reeves, Kit A. Fuhrman, Andrew Klock, Alecksandr Kutchma, Erin Piazza, Joseph Beechem. Spatially resolved T-cell receptor profiling elucidates relationships between TCR diversity, immune infiltration, and cancer-associated pathways [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 1364.
Abstract 1380: Setdb1-loss reactivates ERV expression and interferon signaling to induce immune-mediated melanoma clearance
Authors: McGeary Meaghan K. , Damsky William , Daniels Drew , Micevic Goran , Song Eric , Lou Hua Jane , Calderwood Clotilde , Paradkar Sateja , Iwasaki Akiko , Calderwood David , Turk Benjamin , Bosenberg Marcus 
Published: June 2022

Abstract
While immunotherapies have been revolutionary for the treatment of many cancers including melanoma, most patients do not respond, or develop resistance to these therapies. Several epigenetic modulators have been identified as potential targets for augmenting anti-tumor immunity, however the full breadth of their role is not well-understood.
To identify modulators of anti-tumor immunity in melanoma, we performed a whole-genome CRISPR screen using the YUMMER-G model and identified members of the HUSH complex and its associated methyltransferase, Setdb1, as drop-out hits. To validate these findings, we used CRISPR-Cas9 to knockout Setdb1 individually and observed that Setdb1-/- tumors are cleared by their host mice in a CD8+ T-cell dependent manner.
To determine the source of immunogenicity in Setdb1-/- cells, we performed RNA-sequencing, cytokine profiling, and evaluated antigen presentation by flow cytometry. These assays revealed increased MHC-I levels, elevated secretion of Ifn-, and induction of an interferon-stimulated gene (ISG) expression program, consistent with the observed immunogenicity. We further determined that treating Setdb1-/- cells with IFNAR-blocking antibodies restores MHC-I levels to wild-type levels, suggestive of a tumor-intrinsic interferon loop.
We hypothesized that type-I interferon signaling is generated through sensing of expressed endogenous retroviral elements (ERVs), and consistently observe upregulation of ERVs in Setdb1-/- cells. Previous studies have described the potential for ERV-derived antigens to act as substrates for anti-tumor activity by CD8+ T cells. We identified T cells in the tumor microenvironment of Setdb1-/- tumors that bind tetramer carrying the P15E peptide derived from ERV envelope.
Together, these findings suggest that tumors lacking expression of Setdb1-/- upregulate ERV transcripts, driving expression of type-I interferons which generate an inflamed tumor microenvironment and potentiate efficient tumor clearance of Setdb1-/- tumors. Overall, this study emphasizes a critical role for regulators of ERV expression and type-I interferon expression, and suggests their potential as therapeutic targets for augmenting anti-cancer immune responses.
Citation Format: Meaghan K. McGeary, William Damsky, Drew Daniels, Goran Micevic, Eric Song, Hua Jane Lou, Clotilde Calderwood, Sateja Paradkar, Akiko Iwasaki, David Calderwood, Benjamin Turk, Marcus Bosenberg. Setdb1-loss reactivates ERV expression and interferon signaling to induce immune-mediated melanoma clearance [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 1380.
Abstract 1436: ABCF1 and ABCF2 genetic variants in association with hepatocellular carcinoma (HCC) risk
Authors: Yeung Philip Chun , Ng Kelvin Kwok Chai , Cheung Tan To , Chong Charing Ching-Ning , Lai Paul Bo San , Cheung Siu Tim 
Published: June 2022

Abstract
Background/Aims: ATP-binding cassette (ABC) transporters have been shown to regulate tumor initiating cells in various cancer types and specific genotype associated with cancer risk. ABCF1 was on priority among the ABC transporters because the gene located at 6p21, the chromosome region associated with a number of HCC risk genetic loci including the HLA genes. Its family member ABCF2 was also examined as their expression levels were highly correlated and associated with HCC recurrence.
Subjects and Methods: A total of 300 HCC and 300 healthy blood samples (99.3% and 94.7% Chinese respectively) were prospectively collected with informed consent. All patients had been diagnosed with primary HCC and underwent partial hepatectomy. Clinical information including sex, age, tumor stage and survival outcomes were collected prospectively. Genomic DNA were extracted from blood samples and SNPs were examined by TaqMan genotyping assay, Sequenom MassARRAY platform and direct sequencing.
Results: Sixteen SNPs and three INDELs were examined in ABCF1 and ABCF2 in the germline DNA of 300 HCCs and 300 healthy individuals. Among the 19 loci investigated, ABCF1 rs1264440 (916-99A&gt;G) and rs4148252 (*1delA), ABCF2 rs3823589 (-43+219C&gt;A) and rs75100208 (368-94C&gt;A) were significantly associated with HCC risk (OR: 1.424, 95%CI: 1.03-1.97, P=0.032; OR: 1.446, 95%CI: 1.04-2.00, P=0.026; OR: 1.635, 95%CI: 1.09-2.46, P=0.018; OR: 1.479, 95%CI: 1.09-2.18, P=0.049, respectively). Patients with any two of the four variant genotype, compared with those with all wild type, revealed elevated HCC risks (OR: 1.657, 95%CI: 1.16-2.37, P=0.006). Importantly, patients with all four variant genotypes demonstrated augmented HCC risk (OR: 2.295, 95%CI: 1.27-4.15, P=0.006).
Conclusions: ABCF1 genetic variants rs1264440, rs4148252 and ABCF2 genetic variants rs3823589, rs75100208 were associated with significantly increased HCC risk. Augmented cancer risk was observed among patients possessed all four variant genotypes in ABCF1 and ABCF2. Further mechanistic studies are warranted to comprehend the underlying mechanisms.
Citation Format: Philip Chun Yeung, Kelvin Kwok Chai Ng, Tan To Cheung, Charing Ching-Ning Chong, Paul Bo San Lai, Siu Tim Cheung. ABCF1 and ABCF2 genetic variants in association with hepatocellular carcinoma (HCC) risk [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 1436.
Abstract 1469: 14-3-3 binding during G1 stabilizes and sequesters PTOV1 to the cytoplasm
Authors: Pennington Katie L. , McEwan Colten M. , Woods James , Muir Colin M. , Sahankumari A G Pramoda , Eastmond Riley , Balasooriya Eranga R. , Egbert Christina M. , McCormack Katherine K. , Andersen Joshua L. 
Published: June 2022

Abstract
Cells must respond to changing environments by modulating signaling and gene expression patterns to maintain homeostasis, health, and viability. Inappropriate responses lead to disease processes, such as cancer. Despite improvements in targeted treatment options, cancer remains the second leading cause of death in the United States, illustrating the need to develop new highly effective targeted therapies. 14-3-3 interacts with a network of proteins to support signaling pathways promoting oncogenesis, metastasis, growth, cellular survival, and chemoresistance in a variety of cancers, including lung, prostate, and breast. We recently identified prostate tumor overexpressed 1 (PTOV1) as a novel 14-3-3 interacting protein promoting tumorigenic gene expression patterns. We showed that 14-3-3 binding sequesters PTOV1 in the cytoplasm and protects PTOV1 from proteasomal degradation. Using double thymidine block synchronization, we now demonstrate that both PTOV1 phosphorylation and total PTOV1 levels peak in G1, prior to PTOV1 translocating into the nucleus during S phase. These data support our model that 14-3-3-PTOV1 binding maintains PTOV1 in the cytoplasm during G1, where it is stabilized to carry out translational regulation. As the cell enters S phase, loss of phosphorylation and the accompanying loss of 14-3-3 binding allows PTOV1 to translocate into the nucleus, carry out relevant nuclear functions, and then be degraded via the proteasome.
Citation Format: Katie L. Pennington, Colten M. McEwan, James Woods, Colin M. Muir, A G Pramoda Sahankumari, Riley Eastmond, Eranga R. Balasooriya, Christina M. Egbert, Katherine K. McCormack, Joshua L. Andersen. 14-3-3 binding during G1 stabilizes and sequesters PTOV1 to the cytoplasm [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 1469.
Abstract 148: New conformational details help in clarifying Raf activation by dimerization
Authors: Zhang Mingzhen , Maloney Ryan , Jang Hyunbum , Nussinov Ruth 
Published: June 2022

Abstract
Raf is a family of serine/threonine kinases in the mitogen-activated protein kinase (MAPK) pathway for cell proliferation. The full activation of Raf requires the dimerization of the kinase domain. The dimer interface of Raf has been regarded as an important therapeutic target against cancer. The next generation paradox breakers target the Raf dimerization. Despite the clinical importance, it remains unclear that how the transverse side-to-side dimerization promotes the OFF-to-ON transition of Raf’s kinase domain, and how the activated ON-state kinase domain can be stabilized in the dimer for Raf signaling. In this work, we uncover an atomic-level mechanism of Raf activation through dimerization, addressing these questions. The mechanism shows that the replacement of the intramolecular π-π stacking by the intermolecular π-π stacking at the dimer interface promotes the Raf activation. It releases the structural constraint of the αC-helix, inducing a series of conformational changes for the OFF-to-ON transition, such as the disruption of the inhibitory hydrophobic interactions and the approach of phosphorylation sites in A-loop to HRD motif for cis-autophosphorylation. Once activated, the ON-state kinase domain can be stabilized by the N-terminal basic (NtB) motif in the dimer for Raf signaling. This work provides the high-resolution structural insights into the Raf activation, suggesting a new structural strategy for drug discovery against Raf dimerization. Funded by Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261201500003I.
Citation Format: Mingzhen Zhang, Ryan Maloney, Hyunbum Jang, Ruth Nussinov. New conformational details help in clarifying Raf activation by dimerization [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 148.
Abstract 1485: Identification and in vitro validation of miRNA biomarker candidates in head and neck squamous cell carcinoma using a network biology approach
Authors: Shah Laiba , Shah Maryam , Salam Abdus , Salim Khudeja , Khan Faisal F. 
Published: June 2022

Abstract
Micro-RNAs are small non-coding RNAs that are able to modulate the gene expression. Aberrant expression of micro-RNAs leads to different diseased conditions such as cancer. Head and Neck Squamous Cell Carcinoma (HNSCC) is the second most prevalent cancer in Pakistan and contributes to 9.1% of mortality annually due to late stage diagnosis and ineffective treatment. This research attempts to identify novel miRNAs candidates for their potential role as diagnostic, prognostics or therapeutic biomarkers in HNSCC patient-derived primary cells in the Pakistani population. miRNA species and their gene targets reported in HNSCC were identified using the miRbase, miRNet, and miRCancer databases, and a total of 69 miRNAs with differential expression levels in HNSCC were selected to seed a miRNA-Gene interaction network that was created using BioGrid and STRING data. Hub genes that were targeted by over-expressed miRNAs were predicted using miRTarbase. GO and KEGG analysis was carried out for the 181 interacting genes including TP53, SMAD4, PTEN, NOTCH2, and STAT3. Enrichment analysis demonstrated the increased involvement of these miRNAs in Cancer Pathways such as Hippo signaling Pathways and FoxO signaling pathways. We prioritized hub genes that were targeted by the highest number of tumor suppressor genes, and identified five miRNA species, including miR-21-5p, miR-16-5p, miR30a-5p, miR-93-5p, and miR106b-5p, as the best biomarker candidates for experimental validation. To validate the in silico findings, the top five microRNA candidates are being screened for expression in a library of local patient-derived primary cell lines from Pakistani HNSCC patients.
Citation Format: Laiba Shah, Maryam Shah, Abdus Salam, Khudeja Salim, Faisal F. Khan. Identification and in vitro validation of miRNA biomarker candidates in head and neck squamous cell carcinoma using a network biology approach [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 1485.