bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2975: Genome-scale CRISPR screen finds prostate lineage specific dependencies
Authors: Attari Adel , Misek Sean , Eser Pinar , Yeagley Alexa , Chen Yu , Boehm Jesse , (Moony) Tseng Yuen-Yi 
Published: July 2021

Abstract
Functional genomics has held great promise for mapping cancer dependencies and identifying new therapeutic targets in cancer cell lines. However, this remains a major challenge for prostate cancer (PCa) due to the lack of cancer cell models and efficient optimization of pooled genetic perturbation screens. The Broad Cancer Cell Line Factory (CCLF) is attempting to fulfill this unmet need by generating novel prostate cancer cell models and uncovering prostate specific lineage dependencies. Encouragingly, Dr. Yu Chen at Memorial Sloan Kettering Cancer Center has developed several 3D cancer organoids from advanced prostate cancer. Although the success rate needs improvement for primary PCa, over 12 long-term models have been established by this group. In collaboration with Chen Lab, we aim to expand the prostate cell model collection by using PCa organoids and patient-derived normal cells. We can then apply these models for genetic perturbation profiling to unravel prostate lineage specific dependencies. Many historical cancer cell lines and cancer organoids were not compatible with genome-scale CRISPR screening due to the slow cellular growth. Here we first optimized the media conditions in these PCa organoids by using empirical media screening assay conditions through our HYBRID technology. The HYBRID technology allows for the systemic evaluation of 64 media conditions at once, so that we can perform RNAseq analysis to identify the conditions most physiologically resembling the PCa environment with the maximum doubling time. We have further developed our high throughput screening strategies for organoid culture using an optimized protocol to study 3D growth patterns in a 96-well format using the Incucyte S3 System. Next, to map out all possible dependencies, we are testing the feasibility of a pooled genome scale CRISPR screen. In our preliminary assay development results, we demonstrated the reproducible viral infectibility in several organoids ranging from 40-70% infection rate. We anticipate that these genome-wide CRISPR data in PCa organoid and normal prostate cell models can be integrated and analyzed with 4 previous PCa cell lines screened in the Broad Dependency Map to point out more prostate lineage specific genetic vulnerabilities and possible therapeutic targets.
Citation Format: Adel Attari, Sean Misek, Pinar Eser, Alexa Yeagley, Yu Chen, Jesse Boehm, Yuen-Yi (Moony) Tseng. Genome-scale CRISPR screen finds prostate lineage specific dependencies [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 2975.
Abstract 3: Deep learning-based integration of esophageal cancer morphology with genomics
Authors: Verma Ruchika , Wu Wei , Kumar Neeraj , Yu Elizabeth , Choi Won-Tak , Umetsu Sarah , Bivona Trever 
Published: July 2021

Abstract
Esophageal cancer is a major cause of cancer mortality world-wide. Even with advanced treatment options available, patients with esophageal cancer have a poor 5-year survival rate of 16%. Genomic studies of esophageal cancer have revealed frequently mutated genes involved in different oncogenic pathways. In this study, we attempted to predict genomic alterations, pathological and clinical features directly from H&E-stained whole slide images (WSIs) of individual esophageal cancer cases by utilizing modern deep learning methods. We used WSIs with esophageal cancer obtained from TCGA and annotated cancerous epithelial and stromal components separately for esophageal adenocarcinoma (EAC) and squamous cell carcinoma (ESCC) (n= 25 cases for each) to create a training set. Subsequently, patches of size 256×256 pixels were extracted, and a U-Net convolutional neural network (CNN) was trained for semantic segmentation of tumor epithelium and stromal pixels. Tumor epithelium regions identified by the first U-Net CNN were fed into a Squeezenet model to learn to distinguish between EAC and ESCC in the training phase. Finally, for each subtype (EAC and ESCC), separate Densenet models were trained to predict gene mutation status. We also trained independent Densenet models to predict tumor stage, grade, and survival outcome from the tumor epithelial patches. After training, we tested these models on an independent validation set obtained from TCGA (n = 99) and UCSF (n = 25) patients, ensuring patient level separation between the training and the validation sets. We obtained an average AUC of 0.90 and 0.87 for epithelium vs. stromal and EAC vs. ESCC classification, respectively, on the validation datasets. These models enabled us to predict tumor stage, grade, and survival outcome with an accuracy of &gt; 0.9. TP53 gene alterations were detected in over 50% of esophageal cancer cases, and our model was able to predict TP53 gene mutation status on WSIs with an AUC of 0.91. Overall, this study demonstrates how deep learning algorithms can aid in better understanding and predicting key biological and clinical features of aggressive malignancies at both population and individual patient level. This integration of artificial intelligence with molecular and histopathologic features could also help to accelerate precision cancer diagnosis and treatment in the clinical setting.
Citation Format: Ruchika Verma, Wei Wu, Neeraj Kumar, Elizabeth Yu, Won-Tak Choi, Sarah Umetsu, Trever Bivona. Deep learning-based integration of esophageal cancer morphology with genomics [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 3.
Abstract 3003: In vitro and in vivo model for evaluation of novel therapeutic agents in patient -derived acute B-lymphoblastic leukemia (B-ALL)
Authors: Vishwakarma Bandana Ajay , Verma Bhavna , Wesa Amy 
Published: July 2021

Abstract
B-cell Acute Lymphoblastic Leukemia is a hematological malignancy with malignant transformation and proliferation of B-Cell progenitors. Young patients fare well with common therapeutic agents and hematopoietic stem cell transplant, but a subpopulation is chemo-resistant and has high relapse rate. Besides, prognosis in adult patient is worse than younger individuals. Thus, there is an increase need for development of novel and targeted therapeutics. Lack of suitable in vitro culture conditions for primary B-ALL cells severely impairs the evaluation of new therapeutics. We have established a short-term culture system that supports survival of primary B-ALL cells ex vivo for screening of candidate therapeutic agents. Different culture conditions were evaluated, and cell growth/viability was assessed using Cell titer-Glo assay. Out of 13 primary B-ALL models studied 5 models proliferated and 5 remain stable and viable till day 3. Flow cytometry study showed that all the models stably expressed CD19 and CD20 throughout the assay. The models were tested for sensitivity to chemotherapeutic drugs doxorubicin, vincristine, imatinib and cytarabine. Heterogeneous dose dependent responses were observed across the models (IC50 17nM - 0.3 µM doxorubicin), (IC50 3 - 79 nM vincristine) indicating a range of relative sensitivity to B-ALL models. Interestingly, BCR-ABL-ve models were resistant to imatinib and BCR-ABL+ve sensitive. Next ,to develop patient derived xenograft preclinical B-ALL model, two million PBMC from B-ALL patients (n=14) were intravenously transplanted into sub-lethally irradiated NCG mice. 100% engraftment(n=5,P1) was observed in all the models, but latency of engraftment(&gt;3%) in peripheral blood varied from 15 days to 3.5 months. The time of passage varied from 40 to 120 days. Flow cytometry analyses showed 30-95% of the bone marrow cells was hCD45+, hCD19+ cells. Splenomegaly was observed and infiltration of 40-98% of B-ALL cells was detected in spleen. Engrafted cells matched the immunophenotype of the corresponding patient. On serial transplantation (n=15) these models showed similar engraftment and immunophenotype. Thus, at Champions we have established a robust in vitro platform for screening new drugs for B-ALL and a passagable patient derived preclinical xenograft model for in vivo drug efficacy study.
Citation Format: Bandana Ajay Vishwakarma, Bhavna Verma, Amy Wesa. In vitro and in vivo model for evaluation of novel therapeutic agents in patient -derived acute B-lymphoblastic leukemia (B-ALL) [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 3003.
Abstract 3024: Targeting the RNA binding protein LIN28B in Group 3 medulloblastoma decreases proliferation and promotes apoptosis
Authors: Shahab Shubin W. , Rokita Jo Lynne , Juraschka Kyle , Kumar Sachin , Taylor Michael , Schnepp Robert W. , MacDonald Tobey J. , Kenney Anna M. 
Published: July 2021

Abstract
Medulloblastoma (MB) is the most common pediatric malignant brain tumor and is currently divided into WNT, SHH, Group 3 and Group 4 subtypes. Even with multimodal chemotherapy, radiotherapy and surgery, many children with Group 3 MBs do not survive. While the molecular aberrations underlying WNT- and SHH-driven MBs are relatively well understood, the oncogenic drivers that lead to Group 3/4 MBs are poorly defined, limiting therapeutic progress. In addition to genetic mutations and alterations, cancers display dysregulated transcription and translation. RNA-binding proteins (RBPs) play key roles in both transcription and translation, and a subset of RBPs are differentially expressed in many different cancers. Indeed, we have previously demonstrated an oncogenic role for the RBP LIN28B in neuroblastoma and it is known to be upregulated in Wilms tumor, hepatoblastoma, germ cell tumors, leukemia among others. LIN28B is a key regulator of let-7 family miRNAs, which in turn inhibit LIN28B and other oncogenes. We hypothesize that LIN28B plays an important role in Group 3 MB and that a better understanding of LIN28B and LIN28B-driven networks will reveal novel therapeutic vulnerabilities. In support of our hypothesis we find that among the four subtypes, LIN28B levels are highest in Group 3 MB, and that overexpression is associated with significantly worse survival. Down-regulation of LIN28B results in significant reduction in cell proliferation by CellTiter-Glo and increased apoptosis by Caspase-Glo (as well as induction of cleaved PARP on immunoblots). In contrast overexpression of LIN28B increases Group 3 cell proliferation and tumor sphere formation. In addition we find that PDZ-binding kinase (PBK) a downstream target of LIN28B is downregulated when LIN28B is depleted. PBK knock down also leads to decreased proliferation of Group 3 MB cells. Finally, in order to robustly define the signaling networks downstream from LIN28B that are involved in Group 3 MB metastasis, we have performed who transcriptome RNA-seq profiling of two group 3 cell lines following LIN28B depletion and plan to interrogate a subset of these based on expression change and functional relevance to LIN28B-mediated Group 3 MB metastasis. This work will help define the role for LIN28B in Group 3 MB aggressiveness and pave the way for similar studies in other cancers.
Citation Format: Shubin W. Shahab, Jo Lynne Rokita, Kyle Juraschka, Sachin Kumar, Michael Taylor, Robert W. Schnepp, Tobey J. MacDonald, Anna M. Kenney. Targeting the RNA binding protein LIN28B in Group 3 medulloblastoma decreases proliferation and promotes apoptosis [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 3024.
Abstract 3071: A method for infratentorial structures segmentation for tumor treating fields treatment planning
Authors: Glozman Yana , Shamir Reuben R. , Bomzon Zeev 
Published: July 2021

Abstract
Introduction: Tumor treating fields (TTFields) is an FDA approved treatment for the management of glioblastoma multiform (GBM) and mesothelioma (MPM) and is associated with a significant extension to patients' survival. We have developed software to optimize the location of the TTFields transducer arrays (TAs) on GBM patients' head to maximize the field in the tumor region. To that end, we first segment the patients' head MRIs into five normal and three abnormal tissues. However, the current method for head segmentation was found to be less accurate at the infratentorial regions, mark some sinuses with cerebrospinal fluid (CSF), and does not identify the cerebellum and brain-stem. Therefore, it is assuming the infratentorial structures have the same electrical properties as in the cerebrum.
Methods: We have developed a new method for segmentation of the head MRI that overcomes these limitations. As in the previous method, we have incorporated an atlas that is composed of an MRI image and tissue probability maps (TPM). The TPM assign each voxel in the atlas MRI with a value in the range of 0-1. This value reflects the probability that the specific tissue resides in that voxel. We have generated new customized TPMs for the cerebellum, brain stem and sinuses. Moreover, we have carefully revised the other TPMs to ensure best results. Last, we have incorporated these TPMs in a new atlas-based segmentation method. We have validated the method on 10 GBM patients T1w +gad head MRIs.
Results: The average Dice coefficient between gold-standard and algorithms' segmentation was 68.4% (SD=11.2%) that is similar to the value observed with the current method implemented in the treatment-planning software (67.8%; SD=10.6%). However, the new method presented here extends the current method with the cerebellum (average Dice = 84%) and brainstem (average Dice = 67%). Moreover, the sinuses are marked with air, and erroneous CSF segments in the sinuses were removed.
Conclusions: We have presented a novel method for the segmentation of the head that facilitates accurate infratentorial and supratentorial structures' segmentation. Moreover, the method eliminates erroneous CSF segmentation in the sinuses. These improvements pave the way for TTFields planning for infratentorial tumors.
Citation Format: Yana Glozman, Reuben R. Shamir, Zeev Bomzon. A method for infratentorial structures segmentation for tumor treating fields treatment planning [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 3071.
Abstract 3072: Clinically relevant MAPK pathway inhibition reverses stem cell fate defects and sensitize BRAF mutant glioma to immune modulatory therapies
Authors: Petritsch Claudia K. , Grossauer Stefan , Wang Wei , Barrette Anne Marie , Park Jongwhi 
Published: July 2021

Abstract
Pediatric low-grade gliomas (pLGG) are the most common central nervous system (CNS) tumor in children. Although the majority of pLGG has unregulated MAPK pathway activity, and clinical MAPK pathway inhibitors are available, pLGG treatment remains challenging. Tumor progression, rebound, and therapy resistance limit the success of MAPK pathway inhibitors, especially in high risk subgroups, such as BRAF V600E mutant CDKN2A deleted gliomas.To define mechanisms for progression and overcome resistance, we generated BRAF V600E mutant, CDKN2A deleted murine glioma models of different grades and drug sensitivities. Here, we use genetically engineered mice to target expression of BRAF V600E and deletion of CDKN2A to various germinal and non-germinal areas, assessing neuro-anatomical aspects of oncogene sensitivity. Using neural stem cell (NSC)- and astrocyte-, and oligodendrocyte progenitor cell (OPC)-selective driver line, we investigate the likely origin for pLGG and therapy resistant glioma stem cells, developing models that faithfully recapitulate human tumor development. Our numerous immunocompetent, orthotopic BRAF V600E mutant glioma model derived from endogenous tumors exhibit a range of sensitivities to MAPK inhibitor therapies, allowing us to define mechanisms for therapy resistance. In syngeneic, orthotopic BRAF V600E mutant CDKN2A deleted gliomas, we define MAPK pathway inhibitor-induced-changes in the tumor microenvironment, including the immune infiltrate, and investigate immune modulatory therapy as novel treatment strategy for children with BRAF mutant gliomas. Our numerous models for BRAF mutant glioma will facilitate research on tumor development, progression and the tumor-immune interactions. Collectively, our results describe genetic alteration- and microenvironment-based mechanisms for BRAF mutant tumor initiation and progression, and suggest therapeutic combination therapies for glioma.
Citation Format: Claudia K. Petritsch, Stefan Grossauer, Wei Wang, Anne Marie Barrette, Jongwhi Park. Clinically relevant MAPK pathway inhibition reverses stem cell fate defects and sensitize BRAF mutant glioma to immune modulatory therapies [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 3072.
Abstract 3083: Role of S100A10 in the metastatic colonization of breast cancer stem cells
Authors: Shimono Yohei , Yanagi Hisano , Watanabe Takashi , Nishimura Tatsunori , Hayashi Takanori , Okada Seiji , Suzuki Motoshi , Kawada Kenji , Minami Hironobu , Gotoh Noriko 
Published: July 2021

Abstract
Breast cancer is now the most frequently diagnosed cancer and the leading global cause of cancer death in women. Despite advances in the diagnosis and treatment of human breast cancer, advanced stage, metastatic breast cancers are difficult to cure. Among the common target organs for breast cancer metastasis, post recurrence survival is worst when multiple metastasis was observed in the liver. Cancer stem cells (CSCs) are a sub-population of the cells that retain high tumorigenic capacity and, at the same time, are able to sustain the formation of tumors that recreate the cellular diversity of the parent lesions from which they have been originally isolated. We and others have shown that in epithelial malignancies such as breast and colorectal cancers, self-renewal ability of cancer cells with CSC properties is epigenetically regulated by their expression of microRNAs, such as with miR-200c, miR-142 and miR-221. Because of their highly tumorigenic properties, CSCs with are associated with metastatic progression, especially at the initial steps of metastases. We have previously established the breast cancer patient-derived tumor xenograft (PDX) mouse model in which CSC marker CD44+ cancer cells formed spontaneous microscopic metastases in the liver. Comparison of gene expression profiles between the CD44+ human breast cancer cells metastasized to the liver (‘metastasized CSCs') and those in the primary site (‘primary CSCs') revealed that S100A10 was upregulated in metastasized CSCs than in primary CSCs. Knockdown of S100A10 in breast cancer cells reduced the matrix metalloproteinase activity and suppressed their invasion abilities in transwell cell invasion assays in which upper surface of transwell inserts were precoated with Matrigel. Knockdown of S100A10 suppressed, and overexpression of S100A10 enhanced the 3D organoid formation capacities of breast cancer PDX cells in vitro. Finally, constitutive knockdown of S100A10 significantly reduced their metastatic ability to the liver in vivo. Upregulation of S100 family protein expression is observed in many human cancers, including breast, lung, bladder and gastric cancers. These findings suggest that S100A10 functions as a metastasis promoter of breast CSCs by conferring both invasion ability and CSC properties in breast cancers.
Citation Format: Yohei Shimono, Hisano Yanagi, Takashi Watanabe, Tatsunori Nishimura, Takanori Hayashi, Seiji Okada, Motoshi Suzuki, Kenji Kawada, Hironobu Minami, Noriko Gotoh. Role of S100A10 in the metastatic colonization of breast cancer stem cells [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 3083.
Abstract 3093: Nix mediated mitophagy maintains ovarian cancer cell stemness
Authors: Khaket Tejinder Pal , Wang Qi-En 
Published: July 2021

Abstract
Ovarian cancer is the most frequent cause of death among gynecologic malignancies. Despite the availability of effective therapeutics against cancer, the overall 5-year survival rate of ovarian cancer is still ~30-40%. Most of the lethality are due to cancer relapse and drug resistance, where cancer stem cells (CSCs) are supposed to be the key regulators. CSCs also known as tumor-initiating cells, are a small subgroup of tumor cells that can develop tumors through their capability of self-renewal and differentiation. CSCs can canonically nurture therapeutic resistance, tumor invasion, metastasis, and recurrence, which tremendously attract the scientific community for the unique CSC-based cancer therapeutics. While changing phenotypical features of CSCs complicates their identification and thereby metabolism-based alternate strategy seems to be worthy anti CSC therapy. Though autophagic degradation of mitochondria (mitophagy) based mitochondrial dynamics endowed cancer cells with stemness, but wide informational gaps and missing mechanistic knowledge further necessitates the study on mitophagy dependent CSC regulation. In this study, we investigated the potential involvement of mitophagy in maintenance of cancer cell stemness. In our experimental conditions, FACS sorted CD117/44+/+, ALDHbr and ovarian cancer stem cell like cells (CSCLCs) from OVACR4 and OVCAR3 cells showed higher mitochondrial translocation of cytosolic LC3 that directly indicates the progression of mitophagy in these subpopulations. Reduced mitocontent in CSCLCs as compare to bulk cells also supports the mitochondrial degradation. To analyze the involvement of mitophagy in stemness, mitophagy has been targeted with mDIVI a well-known mitophagy inhibitor, which downregulate the sphere forming ability and protein levels of stemness marker such as SOX2 in ovarian cancer cells. Furthermore, the mechanistic detail of mitophagy involvement in cancer stemness were evaluated. Among different mitophagy proteins, BNIP3L/NIX is highly expressed in ALDHbr and CD117/44+/+ sorted cells as compare to ALDHdim and CD117/44-/- cells, respectively. The functional implication of NIX in ovarian CSCs was verified by gene silencing approach. NIX silencing diminished the sphere forming ability and stem cell marker OCT4 that supported its crucial involvement in ovarian cancer cells stemness. In summary, our findings provide a mechanistic detail of mitophagy underlying maintenance of the CSC population in ovarian cancer and suggest that targeting of NIX based mitophagy could be exploited for the eradication of CSC and thereby tumor recurrence and drug resistance in ovarian cancer.
Citation Format: Tejinder Pal Khaket, Qi-En Wang. Nix mediated mitophagy maintains ovarian cancer cell stemness [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 3093.