bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5879: Spatially-segmented single-cell transcriptomics by diffusional accessibility to a small-molecule dye
Authors: Morse David B. , Ceribelli Michele , De Jonghe Joachim , Michalowski Aleksandra , Muus Christoph , Vias Maria , Boyle Samantha , Weitz David A. , Brenton James , Buenrostro Jason D. , Thomas Craig , Knowles Tuomas P. 
Published: September 2020

Abstract
High-throughput single-cell RNA-seq (scRNA-seq) is used to describe complex tissues by characterizing transcriptional states of individual cells. Defining a cell's position, both in regard to tissue margins and its social context, is essential for understanding the intrinsic and extrinsic variables that effect the transcriptional identity of individual cells. Conventional high-throughput scRNA-seq assays, however, decouple cells from their original locations within tissues. In situ hybridization readouts of gene expression and in situ sequencing preserve spatial information in tissues, but currently have a lower total read threshold than NextGen sequencing – imposing a restriction on either cell throughput or transcriptional breadth. Combining the above methods or using regional barcodes to define 2D positions have spatially-reconstructed tissue regions but are seldom employed in unspecialized laboratories. We describe SEgmentation by Exogenous Perfusion (SEEP), a rapid, integrated, method for providing 3D spatial-segmentation to scRNA-seq data. Tissues are divided into layers based on accessibility of a fluorescent dye allowing sorted cells to be characterized by transcriptomic and regional identity. We use SEEP to explore how the transcriptional states of cells in high-grade serous ovarian cancer vary with respect to intratumoral position. We describe an integrated method for correlating 3D radial-spatial cell positions with scRNA-seq data. By employing a basic stain-and-sort method using an off-the-shelf live-dead stain, we are able to correlate transcriptional profiles with radial-spatial positions in both radially symmetric tissues (e.g., spheroids, organoids, spherical tumor masses) and linear tissue samples (e.g., punch biopsies). SEEP uses an imaging-based calibration step to inform the parameters of a FACS and sequencing based measurement step. Across spheroid, organoid, and PDX models of high-grade serous ovarian cancer, we find common positional transcriptomic profiles, ranging from single-gene proclivities to multi-gene-set enrichments across tissue layers.
Citation Format: David B. Morse, Michele Ceribelli, Joachim De Jonghe, Aleksandra Michalowski, Christoph Muus, Maria Vias, Samantha Boyle, David A. Weitz, James Brenton, Jason D. Buenrostro, Craig Thomas, Tuomas P. Knowles. Spatially-segmented single-cell transcriptomics by diffusional accessibility to a small-molecule dye [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5879.
Abstract 589: Immune biomarker profiling and safety evaluation response to 4-1BB antibody (Urelumab) in humanized 4-1BB mice
Authors: Xiang Jie , Li Dirui , Yang Hao , Ng Gary , Shen Yuelei 
Published: September 2020

Abstract
4-1BB (CD137) belongs to the TNFR superfamily and is expressed by activated CD4 helper T cells, B cells, natural killer cells, natural killer T cells, dendritic cells and Treg cells. 4-1BB is a potential therapeutic target as it enhances tumor rejection by upregulating T cells following activation and its engagement increases T cell proliferation and pro-inflammatory cytokine production. However, the liver toxicity associated with over immune activation has obstructed the clinical development of 4-1BB targeting therapies. To address the issue, Biocytogen has developed humanized B-h4-1BB mice as an efficient platform of both in vivo MOA and safety studies of 4-1BB antibody.
In B-h4-1BB mice, murine colon cancer MC38 cells were subcutaneously implanted. Biomarkers, such as, mCD45, mCD3, mCD4, mCD8, mNK, mFoxp3, mCD11b, and etc., were profiled after the treatment with an 4-1BB antibody (Urelumab). FACS, IHC, and IF data showed that Urelumab have increased the ratio of CD8+ T cell, but on the other hand decreased Treg cell, the PD-1 and Tim3 (T cell exhausted marker) upon treatment. Toxicity have also been with the treatment of Urelumab using this model. The blood chemistry assays showed that the high dose Urelumab had toxicity effects compared with the control group and WT C57BL/6 mice. Based on these findings, we conclude that the B-h4-1BB humanized mouse model is a powerful platform for both MOA (biomarker) discovery and safety evaluation of 4-1BB antibody.
Citation Format: Jie Xiang, Dirui Li, Hao Yang, Gary Ng, Yuelei Shen. Immune biomarker profiling and safety evaluation response to 4-1BB antibody (Urelumab) in humanized 4-1BB mice [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 589.
Abstract 5892: Whole-exome and RNA sequencing reveals chromosomal rearrangements associated with the recurrence of pulmonary carcinoid
Authors: Miyanaga Akihiko , Masuda Mari , Motoi Noriko , Tsuta Koji , Nakamura Yuka , Nishijima Nobuhiko , Watanabe Shun-ichi , Asamura Hisao , Tsuchida Akihiko , Seike Masahiro , Gemma Akihiko , Yamada Tesshi 
Published: September 2020

Abstract
Background: The majority of pulmonary carcinoid (PC) tumors can be cured by surgical resection alone, but a significant proportion of patients experience recurrence. As PC is insensitive to conventional chemotherapy and a significant proportion of patients develop metastases, further clarification of the molecular mechanisms of metastasis is needed in order to develop targeted therapeutics.
Material and Method: We performed comprehensive whole-exome sequencing (WES) of primary tumors and corresponding normal lung tissues from 14 PC patients (including 4 patients who developed postsurgical distant metastasis) and RNA sequencing of primary tumors from 6 PC patients (including 4 patients who developed postsurgical distant metastasis). Exon array-based gene expression analysis was performed in 25 cases of PC.
Results: We identified a total of 139 alterations in 136 genes. MUC6 and SPTA1 were recurrently mutated at a frequency of 21% (3/14) and 14% (2/14), respectively. Mucin protein family genes including MUC2, MUC4 and MUC6 were mutated in a mutually exclusive manner in 36% (5/14). Pathway analysis of the mutated genes revealed enrichment of genes involved in mitogen-activated protein kinase (MAPK) signaling, regulation of the actin cytoskeleton and focal adhesion, and transforming growth factor (TGF)-β signaling. RNA sequencing revealed a total of 8 novel fusion transcripts including one derived from a chromosomal translocation between the TRIB2 and PRKCE genes. All of the 8 fusion genes were detected in primary PCs that had developed metastasis after surgical resection. We identified 14 genes up-regulated in 5 PCs that had relapsed after surgical resection.
Conclusions: In this study we identified novel somatic mutations and chromosomal rearrangements in PC by examining clinically aggressive cases that had developed postsurgical metastasis. It will be essential to validate the clinical significance of these genetic changes in a larger independent patient cohort.
Citation Format: Akihiko Miyanaga, Mari Masuda, Noriko Motoi, Koji Tsuta, Yuka Nakamura, Nobuhiko Nishijima, Shun-ichi Watanabe, Hisao Asamura, Akihiko Tsuchida, Masahiro Seike, Akihiko Gemma, Tesshi Yamada. Whole-exome and RNA sequencing reveals chromosomal rearrangements associated with the recurrence of pulmonary carcinoid [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5892.
Abstract 590: Efficacy evaluation of bispecific antibodies in humanized mice after B cell depletion
Authors: Gan Tian , Li Dirui , Yang Hao , Ng Gary , Li Yanan , Lin Qingcong 
Published: September 2020

Abstract
The development of bifunctional/multifunctional therapeutics have gained tremendous traction in recent years. Preclinical efficacy evaluation of bi-functional antibody drugs faces two main problems: first is the often limited cross-reaction between the anti-human antibody and murine target in animals; second is the reduced efficacy as a result of neutralization of antibodies by anti-drug antibodies (ADA) in animals due to the high immunogenicity of some bi-specific antibodies.
To eliminate the ADA production against bi-specific therapeutic agents, Biocytogen developed a B cell depletion method based on humanized mouse syngeneic xenograft tumor model for preclinical efficacy evaluation of bispecific antibodies. To a syngeneic xenograft tumor model (PD-L1 humanized mice inoculated subcutaneously with MC38-hPD-L1 cells), CD20 antibody was injected to deplete B cells in the mice for the inhibition anti-antibody production. A model bi-specific agent against PD-L1 and TGF-β was sequentially injected to the mice. The tumor inhibitory effect of the bi-specific was assessed by tumor growth inhibition rate (TGI) calculated from measured tumor volume.
Blood samples were drawn from mice for B cell analysis. The clearance of B cells in the blood flow and the serum concentration (including ADA) in mice were analyzed by flow cytometry and ELISA, respectively. The results showed that B cells were effectively eliminated from the murine blood after injection of CD20 antibody. Despite of the absence of B cells, the tumor growth was inhibited upon the treatment with M7824 analog, compared with the control group. Corresponding to the efficacy results, the mice in B cells-depleted group maintained a normal drug concentration in the blood while reducing the production of anti-drug antibodies. In summary, the B cell depletion mice have been validated as a promising model for the efficacy evaluation of complex structure antibody (bi or multi-functional antibody).
Citation Format: Tian Gan, Dirui Li, Hao Yang, Gary Ng, Yanan Li, Qingcong Lin. Efficacy evaluation of bispecific antibodies in humanized mice after B cell depletion [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 590.
Abstract 5912: YTHDF1 amplification associates with clinicopathological featuresand predicts worse survival in breast cancer
Authors: Li Cheukfai , Zhang Guochun , Wang Yulei , Chen Bo , Li Kai , Cao Li , Ren Chongyang , Wen Lingzhu , Jia Minghan , Mok Hsiaopei , Lai Jianguo , Xiao Weikai , Li Xuerui , Liao Ning 
Published: September 2020

Abstract
N6-methyladenosine (m6A) is a common RNA modification on eukaryotic mRNA and several m6a regulatory proteins, which plays a crucial part in breast cancer. But the copy number variations (CNVs) for m6a regulatory proteins and their role in pathogenesis and progression in breast cancer is still unclear. By analyzing the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and the cancer genome atlas (TCGA database), we screened CNVs of ten m6A regulatory genes, including YTHDF3, YTHDF1, FTO, YTHDC1, ALKBH5, METTL3, WTAP, METTL14, YTHDF2, YTHDC2. Among them, YTHDF3 and YTHDF1 amplification had higher alteration rates among ten m6A regulatory genes. YTHDF1 and YTHDF3 amplification resulted in higher mRNA expression (P&lt;0.001). We found that YTHDF1 and YTHDF3 amplification presented a high correlation with worse cinlicopathological characteristics and overall survival (OS) in breast cancer patients. COX regression analysis showed YTHDF1 amplification was an independent risk factor for 10-year OS in breast cancer (HR=1.549, 95% CI: 1.408-1.705, P&lt;0.001, Table). Moreover, GSEA analysis revealed the downstream target of YTHDF1 may be related to MYC signaling regulation and T cell differentiation. In conclusion, we illustrated genetic alteration of m6A regulatory genes in breast cancer patients and found significant relationship between YTHDF1 amplification and worse clinical characteristics, indicating it a potential target for breast cancer treatment in epigenetic modification.
Univariate and multivariate Cox proportional hazard analysis for 10-year overall survivalUnivariateUnivariateHR95% CIP valueHR95% CIP valueNode status1.7181.566-1.885&lt;0.0011.5491.408-1.705&lt;0.001Tumor Size1.0161.013-1.019&lt;0.001ER status0.6200.530-0.725&lt;0.0010.5260.440-0.629&lt;0.001PR status0.6120.531-0.707&lt;0.001HER2 status1.7471.445-2.112&lt;0.0011.5171.234-1.866&lt;0.001Age1.0241.018-1.030&lt;0.0011.0331.026-1.039&lt;0.001YTHDF11.8111.419-2.313&lt;0.0011.5491.408-1.705&lt;0.001
Citation Format: Cheukfai Li, Guochun Zhang, Yulei Wang, Bo Chen, Kai Li, Li Cao, Chongyang Ren, Lingzhu Wen, Minghan Jia, Hsiaopei Mok, Jianguo Lai, Weikai Xiao, Xuerui Li, Ning Liao. YTHDF1 amplification associates with clinicopathological featuresand predicts worse survival in breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5912.
Abstract 5914: URI participates in cisplatin-induced DNA damage repair of gastric cancer cells via the ATM/CHK2 pathway
Authors: Bian Huiqin , Lu Yaojuan , Gu Yu , Zhang Xiaojing , Sun Lichun , Gu Junxia , Zheng Qiping 
Published: September 2020

Abstract
Gastric cancer is the most common gastrointestinal malignant tumor and also the second leading cause of cancer-related mortality worldwide. Given its high rate of non- symptoms at early stage, gastric cancer is usually diagnosed at middle or advanced stage with metastasis. Therefore, chemotherapy, including Cisplatin, becomes a main treatment option, in addition to surgery. However, it is not uncommon for patients to develop cisplatin resistance which limits its clinical applications. URI, a prefoldin family member and also an oncoprotein, has been shown to promote multiple cancer development, including gastric cancer. The aim of this study was to investigate how URI may participate in the DNA damage repair of gastric cancer cells induced by Cisplatin and its possible mechanism via the ATM/CHK2 pathway. URI knockdown cell lines from gastric cancer cells MGC-803 and SGC-7901 were established and treated with different concentrations of Cisplatin. Cell viability, proliferation and apoptosis were analyzed by CCK-8, EDU assay, and flow cytometry respectively. DNA injury marker H2AX were examined by qRT-PCR and Western blot analysis. Comet assay was used to detect the DNA damage. The results showed that URI knockdown reduces cell viability and proliferation, as well as the Cisplatin-induced apoptosis of gastric cancer cells. Cisplatin dose responsively induced DNA damage in gastric cancer cells and URI knockdown enhanced this damage as indicated by comet assay and increased γH2AX expression. We have also detected increased levels of P-ATM and P-CHK2 in gastric cancer cells treated with Cisplatin, while URI knockdown decreased the P-ATM and P-CHK2 expression after the cells were treated with cisplatin for 12 hours. Taken together, our results support that URI reduces DNA damage and promotes DNA repair of gastric cancer cells induced by cisplatin and therefore, enhances its resistance possibly via the ATM/CHK2 pathway
Citation Format: Huiqin Bian, Yaojuan Lu, Yu Gu, Xiaojing Zhang, Lichun Sun, Junxia Gu, Qiping Zheng. URI participates in cisplatin-induced DNA damage repair of gastric cancer cells via the ATM/CHK2 pathway [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5914.
Abstract 5924: A clock gene of TIM promotes colorectal cancer tumorigenesis through binding with myosin-9
Authors: Yuan Xiaoqin , Wang Yi , Wu Lei 
Published: September 2020

Abstract
Colorectal cancer (CRC) is a common tumor that is characterized by its high mortality rate. However, the underlying molecular mechanisms that drive CRC tumorigenesis are still not clear. Clock genes have been recognized as playing key roles in tumor development. In our present study, we found the expression of TIM (encoding protein of Timeless), one of the clock genes was up-regulated in CRC tissues comparing to the corresponding normal tissues by the results of IHC and its expression was closely associated with tumor clinical stage and poor overall survival of CRC patients through analysis of clinical CRC patients. Functional studies demonstrated that TIM promoted CRC cell proliferation, migration and invasion in vitro and in vivo. Mechanistic investigations showed that TIM plays a key role in EMT. Immunoprecipitation followed by mass spectrometry revealed that Timeless bound with Myosin-9. Furthermore, we also found TIM regulated the expression level of Myosin-9. And Myosin-9 knockdown retarded the migration and invasion of TIM-overexpressed CRC cells. Furthermore, we found the expression of TIM was regulated by histone acetylation at its promoter area. Our results show that TIM could regulate tumorigenesis of CRC by binding and regulating Myosin-9. Our results also implicate TIM as a potential prognostic biomarker and therapeutic target for CRC.
Citation Format: Xiaoqin Yuan, Yi Wang, Lei Wu. A clock gene of TIM promotes colorectal cancer tumorigenesis through binding with myosin-9 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5924.
Abstract 5943: The role of IL-6 family cytokines in gastrointestinal cancer
Authors: Taniguchi Koji , Kawazoe Tetsuro 
Published: September 2020

Abstract
The important effector of the Hippo pathway, YAP, is strongly activated in the majority of gastrointestinal cancer. However, the mechanism by which YAP is activated in gastrointestinal cancer remains unknown. Previously, we found that after intestinal injury, IL-6 family cytokines activate the Src family kinases (SFK)-YAP pathway, which enhances intestinal regeneration. Here, we found that in addition to β-catenin, loss of tumor suppressor adenomatous polyposis coli (APC) activates SFKs, YAP and STAT3, which are simultaneously activated in 60-70% of human colorectal cancer specimens. We also found that up-regulation of IL-6 signal transducer (IL-6ST/gp130), which is induced by YAP activation, causes the activation of SFKs, YAP and STAT3. We also found that leukemia inhibitory factor (LIF), one of the IL-6 family cytokines, plays an important role in human esophageal squamous cell carcinoma by activating the SFK-YAP pathway. The combination treatment of SFK and JAK inhibitors results in suppression of gastrointestinal tumors. These results suggest that these signaling pathways might be new attractive therapeutic targets in human gastrointestinal cancer.
Citation Format: Koji Taniguchi, Tetsuro Kawazoe. The role of IL-6 family cytokines in gastrointestinal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5943.
Abstract 5957: Roles for the cancer stem cell marker Aldh1A1 in Merlin null nervous system tumors
Authors: Hillson Lily , Laraba Liyam , Shivane Aditya G. , Edwards Philip , Bantukallu Ganesha , Simeonov Anton , Martinez Natalia J. , Yang Shyh-Ming , Parkinson David B. 
Published: September 2020

Abstract
Our lab is interested in the development and growth of schwannoma and meningioma tumors of the nervous system. Approximately 70% of these tumors arise due to loss of the tumor suppressor Merlin. In a mouse model of schwannoma (P0-CRE NF2fl/fl), we observed increased mRNA levels of the cancer stem cell marker Aldehyde dehydrogenase 1A1 (Aldh1A1) in Merlin-null Schwann cells. Immunostaining showed elevated levels of Aldh1A1 protein in this mouse model and in another mouse model (Postn-CRE NF2fl/fl), in which schwannoma tumors arise spontaneously within the vestibulocochlear nerve and dorsal root ganglia of the nervous system. Similarly, staining of human schwannoma samples also showed a strong elevation of Aldh1A1 protein in all tumor cells. Parallel analysis of meningioma tumor samples, in which Merlin loss also occurs, also showed a strong increase of Aldh1A1 protein levels. Western blotting enabled identification of the mechanism by which Merlin loss regulates Aldh1A1. Merlin/TAZ double knockout, but not Merlin/YAP double knockout, sciatic nerves show reduced Aldh1A1 expression. This implicates Hippo signalling through the TAZ effector as the mechanism of Aldh1A1 upregulation both in vitro and in vivo in both tumor types. Chemical inhibition with Aldh1a1-specific inhibitor (NCT-505) or shRNA knockdown of Aldh1A1 in Merlin-null schwannoma and meningioma cells in culture attenuated tumor cell growth, proving Aldh1A1 has a role in tumor cell proliferation; studies using Aldh1A1 null mice to test this in vivo are ongoing. A major target of Aldh1A1 signalling is the regulation of retinoic acid (RA) signalling. We are examining expression and activation of components of RA signalling in both schwannoma and meningioma tumor cells to identify whether this may be of therapeutic use in the future for these two tumor types. In conclusion, the TAZ-dependent upregulation of Aldh1A1 in Merlin-null schwannoma and meningioma tumor cells has a functional role in driving cell proliferation in these two clinically important tumor types. Further work will seek to identify the mechanism by which Aldh1A1 activity contributes to tumor growth.
Citation Format: Lily Hillson, Liyam Laraba, Aditya G. Shivane, Philip Edwards, Ganesha Bantukallu, Anton Simeonov, Natalia J. Martinez, Shyh-Ming Yang, David B. Parkinson. Roles for the cancer stem cell marker Aldh1A1 in Merlin null nervous system tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5957.
Abstract 598: Integrated computational and experimental design of a monobody targeting PDL1
Authors: Harrison Reed E. , Man Chi-Wei , Wang Yingxiao 
Published: September 2020

Abstract
Monobodies (Mb) are small, synthetic antibodies based on the human fibronectin type III domain that exhibit high thermodynamic stability without disulfide bonds. To explore suitability of these domains as cancer-targeting molecules, we apply computational and experimental methods to develop a Mb that targets programmed-death-ligand 1 (PDL1). As some tumors overexpress PDL1 to inhibit T-cell responses, a PDL1-binding Mb could be used to promote successful immunotherapy. More broadly, computational methods applied to developing a PDL1-binding Mb can also be applied to developing new Mbs that target cancer antigens. Starting from the G9 Mb (PDB: 1ttg), we grafted the CDR3 loop of a known PDL1-binder (PDB: 5jds) into the FG loop of the Mb. This design was displayed on the surface of yeast and shown to bind PDL1 better than the G9 Mb, though not as well as a high affinity variant of PD1, the cognate receptor of PDL1. Using molecular dynamics simulations, we evaluated structural features that are unlikely to contribute to PDL1-binding. Using this approach, we selected amino acid positions for site-saturated mutagenesis and constructed a yeast library displaying Mb isoforms. Through iterative rounds of selection, we identified a Mb isoform with further improved PDL1-binding.
Citation Format: Reed E. Harrison, Chi-Wei Man, Yingxiao Wang. Integrated computational and experimental design of a monobody targeting PDL1 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 598.