bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1517: Genetic characterization of normal pancreas tissue using single-cell technology
Authors: Karnoub Elias-Ramzey R. , Zhang Haochen , Umeda Shigeaki , Masilionis Ignas , Chaligné Ronan , Iacobuzio-Donahue Christine
Published: April 2023

Mechanisms behind the evolution of normal pancreas tissue into pancreatic ductal adenocarcinoma (PDAC) are still poorly understood. More thorough characterization of mutational processes and development of clones is possible with single-cell DNA sequencing (scDNA-seq) of normal pancreas tissue. We developed a custom panel with 596 amplicons targeting over 200 genes known to be important in PDAC for use with Mission Bio’s Tapestri platform. We have recently optimized this method with nuclei which have been extracted from thirty frozen normal pancreas tissues, each from a different patient. Of these tissues, twenty-five were derived from rapid autopsies of patients with brain tumors to minimize the possibility of tumor cells being present in the pancreas. Normal pancreas tissue was verified by hematoxylin and eosin staining. Nuclei were extracted using the S2 Genomics Singulator 100 and counted with DAPI using the Countess 3 FL to ensure the concentration was adequate and that the sample was clean without excessive debris before library preparation and sequencing. Bulk whole exome sequencing (WES) and digital droplet polymerase chain reaction (ddPCR) were performed on several of these sample to validate certain mutations seen in scDNA-seq. Patients of a variety of ages ranging from five to 74 and with various risk factors including smoking and diabetes were chosen to better understand the impact on clonal expansion and genetic patterns present in normal pancreas tissue. For each of the thirty samples, an average of 2464 good quality nuclei were sequenced with over 70 reads per cell per amplicon on average. Mutations that were present in high quantities of cells were confirmed with WES and ddPCR. We found that older patients and patients that either smoke or those with diabetes had not only an increased number of mutations, but each individual cell, on average, had a significantly higher mutation count. The associated clones were also much greater in size in the higher-risk patients’ tissues. Furthermore, there was an increase in heterogeneity in the form of mutually exclusive clusters of cells. These results highlight the effects of various risk factors on normal pancreas tissue and potentially describe novel mechanisms of tumorigenesis.

Citation Format: Elias-Ramzey R. Karnoub, Haochen Zhang, Shigeaki Umeda, Ignas Masilionis, Ronan Chaligné, Christine Iacobuzio-Donahue. Genetic characterization of normal pancreas tissue using single-cell technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1517.
Abstract 1531: Human anti-CD40 agonistic antibodies with enhanced FcgR engagement activate immune cell and promote anti-tumor efficacy
Authors: Wang Linya , Yuan Tom Z. , Villalta Mouna , Han Zhen , Wadhwa Hansika , Chan Kara Y. , Yang Marisa , Htoy Tammy , VanDyke Paul , Holliday Carson , Franco Hector , Giang Hoa , Axelrod Fumiko , Sato Aaron
Published: April 2023

Checkpoint inhibitors represent a major advance in cancer immunotherapy, and combinatorial immunotherapies with secondary drivers of anti-tumor immunity provide beneficial effects for patients that do not show a strong endogenous immune response. CD40 is a member of the TNF family of receptors that has been shown to play a crucial role in enhancing B cell and dendritic cell activity and fostering anti-tumor immune responses. Engagement of the inhibitory Fcg-receptor (FcgR) IIb is an absolute requirement for in vivo antitumor activity of agonistic anti-CD40 monoclonal antibodies, and Fc region mutant designs of anti-CD40 antibodies had been discovered to enhance FcgRIIb engagement. With Twist’s precision DNA writing technologies, we have created phage display VHH and scFv libraries with diversity greater than 1 × 1010 for optimal discovery. In this study, we performed high affinity binding of the antibodies by SPR and cell surface binding. The leads are reformatted on human IgG1, IgG4, and IgG1 mutant. The in vitro properties of the CD40 agonistic antibodies demonstrate enhanced FcgRIIb engagement by NFkB activation. B cell activation is also detected by upregulation of CD86 and IL6 secretion. In humanized hCD40 mice model, we observed the engineered anti-CD40 agonists enhance anti-tumor immune function in vivo. These studies suggest that our antibodies can be potential drug for cancer immunotherapy.

Citation Format: Linya Wang, Tom Z. Yuan, Mouna Villalta, Zhen Han, Hansika Wadhwa, Kara Y. Chan, Marisa Yang, Tammy Htoy, Paul VanDyke, Carson Holliday, Hector Franco, Hoa Giang, Fumiko Axelrod, Aaron Sato. Human anti-CD40 agonistic antibodies with enhanced FcgR engagement activate immune cell and promote anti-tumor efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1531.
Abstract 1628: A small-molecule inhibitor of WRN selectively kills MSI-H cancer cells and phenocopies WRN genetic defects
Authors: Rao Yanhua , Srivatsan Anjana , Liimatta Marya , Munoz Diana , Quirit Jeanne , Shi Jianxia , Nguyen An , Linghu Xin , Federowicz Federowicz , Jones Brian , Fleury Melissa , Newby Zach , Dillon Michael P. , Barsanti Paul A. , Lackner Mark R. , White Michael A. , Lee Yang , Landis Phil , Peng Yang , Cicchini Michelle , Cottom Josh , Nickels Leng , Brnardic Ed , DeMartino Michael , Taygerly Josh
Published: April 2023

Werner syndrome protein (WRN) is a RecQ-family helicase involved in the maintenance of genome integrity. Germline mutations in WRN cause premature aging and cancer predisposition. Analysis of systematic RNAi and CRISPR screening data has previously revealed that WRN is essential for the survival of cancer cell lines with high microsatellite instability (MSI-H). We have developed potent and selective small-molecule inhibitors of WRN helicase (WRNi) and showed that pharmacological inhibition of WRN causes lethality and induction of DNA damage markers selectively in MSI-H cancer cell lines compared to microsatellite-stable (MSS) cell lines. Screening of WRNi across a large panel of pooled, barcoded cell lines in the PRISM format revealed selective sensitivity in MSI-H cell lines and showed that pharmacological inhibition of WRN is highly correlated with genetic ablation of WRN across this panel, confirming selectivity for WRN. In vivo evaluation demonstrated robust and MSI-selective tumor regressions. These data provide pharmacological proof-of-concept for the WRN/MSI-H synthetic lethal relationship and support WRN inhibition as a novel therapeutic approach for the treatment of MSI-H cancers.

Citation Format: Yanhua Rao, Anjana Srivatsan, Marya Liimatta, Diana Munoz, Jeanne Quirit, Jianxia Shi, An Nguyen, Xin Linghu, Federowicz Federowicz, Brian Jones, Melissa Fleury, Zach Newby, Michael P. Dillon, Paul A. Barsanti, Mark R. Lackner, Michael A. White, Yang Lee, Phil Landis, Yang Peng, Michelle Cicchini, Josh Cottom, Leng Nickels, Ed Brnardic, Michael DeMartino, Josh Taygerly. A small-molecule inhibitor of WRN selectively kills MSI-H cancer cells and phenocopies WRN genetic defects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1628.
Abstract 163: Establishment of pancreatic ductal adenocarcinoma organoids model using endoscopic ultrasonography-guided fine needle biopsy: a new window into understanding pancreatic ductal adenocarcinoma tumor biology
Authors: Kim Hyemin , Cha Hongui , Lee Se-Hoon , Park Joo Kyung
Published: April 2023

Background & Aims: Tumor biology studies of pancreatic ductal adenocarcinoma (PDAC) used surgical specimens, even though most PDACs are unresectable. The aims of the study were to 1) establish PDAC organoids platform from endoscopic ultrasonography (EUS)-guided fine needle biopsy (FNB), 2) investigate clinicopathologic and genomic characterization, and 3) find out the clinical applicability of the patient-derived PDAC organoids model from PDAC diagnosis to treatment timeline.

Methods: The patients with suspected PDACs were enrolled prospectively, and PDAC minimal specimens were acquired from EUS-guided FNB at Samsung Medical Center from 2015 to 2019.

Results: Ninety-four PDAC organoids were successfully established (94/113, 83.2%) via EUS-guided FNB within 8.2±2.6 days. Clinical factors were also analyzed associated with the success rate in establishing PDAC organoids; specimens with high cellularity (>10 clusters) were an independent factor in multivariate analysis. Whole exome sequencing showed the high concordance between primary PDAC and its organoid and more enriched genetic alterations in organoids. In addition, the high-throughput screening (HTS) drug test revealed that the clinical correlation with real-world data was 12 out of 15 between PDAC organoids and the chemotherapeutic response of the study patients. Whole-transcriptome sequencing identified genes and pathways associated with the drug responses.

Conclusions: We have achieved the PDAC organoid platform in a high success rate via EUS-guided FNB, and the concordance between primary PDAC and its organoid seems very high. More importantly, the HTS drug test showed that PDAC organoids may well reflect clinical chemotherapeutic response and may also be used as the “Patient Avatar Model” in clinical practice on time.

Citation Format: Hyemin Kim, Hongui Cha, Se-Hoon Lee, Joo Kyung Park. Establishment of pancreatic ductal adenocarcinoma organoids model using endoscopic ultrasonography-guided fine needle biopsy: a new window into understanding pancreatic ductal adenocarcinoma tumor biology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 163.
Abstract 1630: Development of a prodrug for treating renal cancer carcinoma
Authors: Hamilton Ross , Castan Leniher , Vega Stephanie , Varadhachary Atul , Chatterjee Dev
Published: April 2023

Improved characterization of the etiology and biology of cancer cells have led to the development of targeted chemotherapeutics, which rely on alterations of particular molecules in cancer cells to exert therapeutic effects. As heterogeneity is an important characteristic of cancer, precision medicine has become a core strategy in treating cancer patients. One approach for targeted therapeutics is the delivery of prodrugs designed to be activated by tumor-associated enzymes (TAEs). SULT1A1, a sulfotransferase enzyme, is overexpressed in about 5-15% of cancer patients including breast, prostate, and renal cell carcinoma (RCC); however, it is either not expressed or expressed at low levels in most normal tissue. Bioinformatic analyses revealed that SULT1A1 overexpression in tumors is correlated with worse patient prognosis. We have identified a new compound, FIS103, which is a small molecule anti-cancer prodrug that is activated by SULT1A1. This class of compounds, N-benzyl indole carbinols (N-BICs), cause rapid cell death by inducing widespread non-specific covalent alkylation of proteins in the cancer cell. Here, we show FIS103, an N-BIC analog, has potent antitumor activity in SULT1A1 high-expressing RCC cell lines (A498 and Caki-1) and has no effect in the SULT1A1 low-expressing cells (786-O and ACHN), indicating low toxicity in the absence of SULT1A1. In silico modeling validated the SULT1A1-FIS103 interaction. Furthermore, FIS103 demonstrates potent SULT1A1-dependent antitumor activity in NU/J mouse xenografts injected with A498 (RCC) cells. Remarkably, the tumors in mice became non-detectable 14 days post-FIS103 treatment and remained absent through the study conclusion (41 days). Since only a subset of patients will express this enzyme, it is critical to identify those who are more likely to respond. Thus, a companion diagnostic to screen for patients whose tumors overexpress SULT1A1 is essential to the success of this approach. Collectively, targeted therapeutics aims to ultimately move patient care away from broadly toxic, non-specific chemotherapies, and towards more rationally designed treatments. By developing our drug and the companion diagnostic, we believe we can provide an effective therapeutic option for the treatment of cancers in a subset of patients who fail standard chemotherapy - either as a standalone therapy, or in rationale combination with other drug options. Therefore, the development of FIS103 has the potential to improve survival as well as quality of life of RCC patients and may have application in other SULT1A1 expressing cancers.

Citation Format: Ross Hamilton, Leniher Castan, Stephanie Vega, Atul Varadhachary, Dev Chatterjee. Development of a prodrug for treating renal cancer carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1630.
Abstract 176: Generation and maintenance of anaplastic thyroid cancer spheroids from human cancer cells
Authors: Hu Jiangnan , Ghosh Chandrayee , Kebebew Electron
Published: April 2023

Background: Anaplastic thyroid cancer (ATC) is the most aggressive thyroid cancer. Despite advances in tissue culture techniques, a robust model for thyroid cancer spheroid culture is yet to be developed. Here, we described a protocol to generate tumor spheroids from human ATC cells and excising cell lines.

Methods: Using four established ATC cell lines (8505C, SW1736, C643 and THJ-16T) and one clinical tumor sample derived ATC cells, we created an efficient and cost-effective 3D culture system that can enhance our understanding of ex vivo treatment response.

Results: We found that all four cell lines can readily form spheroids in culture with unique morphology, size, and cytoskeletal organization. We observed both cohesive (dense and solid structures) and dis-cohesive (irregularly shaped structures) spheroids within the same culture condition across different cell lines. BRAFWT ATC spheroids grew in a cohesive pattern, while BRAFV600E- mutant ATC spheroids show dis-cohesive organization. In the patient-derived spheroids (BRAFV600E- mutant ATC), we observed both growth patterns with mostly the dis-cohesive type. Phase-contrast images taken over time suggest that the cohesive ATC spheroids seem to be clonally derived, allowing the study of tumor heterogeneity. Furthermore, the ATC spheroids we established can maintain the 3D structures in the culture medium.

Conclusion: Our study describes the development of a robust spheroid system from established ATC cell lines and freshly acquired patient tumor samples. We show that combining 3D culture with traditional 2D methods provides a complementary and powerful approach to the future drug screening and mechanism studies in the ATC.

Citation Format: Jiangnan Hu, Chandrayee Ghosh, Electron Kebebew. Generation and maintenance of anaplastic thyroid cancer spheroids from human cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 176.
Abstract 1760: ADI-PEG20 and GC7 as a novel anti-metabolite strategy for the treatment of malignant pleural mesothelioma
Authors: Carpentier Joséphine , Szlosarek Peter W. , Martin Sarah Anne
Published: April 2023

Malignant pleural mesothelioma (MPM) is a highly aggressive cancer with less than 10% of patients surviving 5-years from diagnosis. Arginine deprivation using pegylated arginine deiminase (ADI-PEG20) is a novel treatment for mesothelioma deficient in the arginine biosynthetic enzyme ASS1. However, resistance to ADI-PEG20 in MPM is a significant problem and is characterized in part by reprogramming of the urea and polyamine metabolism pathway (Locke et al., 2016). We sought to identify a targeted metabolism-based therapy to overcome the emerging resistance and increase the efficiency of ADI-PEG20 treatment for patients with MPM.

New models of ADI-PEG20 resistance were generated by constant exposure of MPM cell lines to arginine deprivation for 6 months. ADI-PEG20 resistant and sensitive MPM cell lines were treated with a panel of polyamine targeting molecules. Metabolome alterations were studied by targeted metabolomics and glucose flux analyses.

Our results confirmed the up-regulation of ASS1 expression from (50 to 3000-fold) alongside upregulation of polyamine catabolism and upon generation of ADI-PEG20 resistance. Treatment of ADI-PEG20 resistant cell lines with a range of different polyamine inhibitors demonstrated that ADI-PEG20 resistant cell lines were significantly more sensitive to the spermidine-analogue GC7 than their respective ASS1-ve parental cell lines. Moreover, the combination of GC7 and ADI-PEG20 prevented the emergence of resistant cells in vitro. We observed a significant synergistic effect of GC7 and ADI-PEG20 in both ASS1-ve and ASS1+ve cell lines in 2D and 3D cell culture models as well as in our mice in vivo model. Metabolomics analysis revealed that GC7 treatment significantly impaired the TCA cycle. We hypothesize that GC7 is repurposing the fate of Acetyl-CoA to polyamine catabolism therefore shutting down the TCA cycle. Our findings provide novel insights into a polyamine targeted therapy that may prevent resistance to ADI-PEG20 treatment in MPM and related arginine-auxotrophic cancers.

Citation Format: Joséphine Carpentier, Peter W. Szlosarek, Sarah Anne Martin. ADI-PEG20 and GC7 as a novel anti-metabolite strategy for the treatment of malignant pleural mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1760.
Abstract 1887: Preclinical development of BB-1701, a HER2-tageting eribulin-containing ADC with potent bystander effect and ICD activity
Authors: Wang Yang , Xia Bing , Cao Lixia , Yang Jianfeng , Feng Cui , Jiang Fangdun , Li Chen , Gu Lixia , Yang Yifan , Tian Jing , Cheng Cindy , Furuuchi Keiji , Fulmer James , Verdi Arielle , Rybinski Katherine , Soto Allis , Albone Earl , Uenaka Toshimitsu , Gong Likun , Liu Tingting , Qin Qiuping , Wei Ziping , Zhou Yuhong
Published: April 2023

Several HER2-targeting antibody-drug conjugates (ADC) have gained market approval for the treatment of HER2-expressing metastasis. However, these ADC drugs still face challenges of acquired resistance and/or severe adverse effects associate with their payload toxins. Eribulin, a market approval agent for the treatment of metastatic breast cancer and liposarcoma , is a new choice of ADC payload with distinct mechanism of action (MOA). Here we report preclinical studies of BB-1701, a novel HER2-tageting eribulin-containing ADC. BB-1701 exhibited potent and specific cytotoxicity activities to various types of cancer cells where HER2-exprssing levels vary in large ranges. BB-1701 induced tumor-growth suppression, even regression in in vivo models with a single dose of 1-5 mg/kg dosage. In comparison with other HER2-targeting ADCs with different toxin payloads (DM1, MMAE and Dxd), eribulin-containing ADC demonstrated higher potency to cancer cell lines with low HER2 expressing levels (with lower IC50). BB-1701 also showed effective tumor suppression in models insensitive to T-DM1 or T-Dxd. Mode of action studies revealed significant bystander cytotoxicity of BB-1701 to HER2-low cells when co-cultured with HER2-high cells. Additionally, BB-1701 treatment increased ATP releasing and Calreticulin expression, both were deemed immunogenic cell death (ICD) markers. Lastly, repeat dose pharmacokinetic and toxicology studies in nonhuman primates revealed favorable PK and safety profiles of BB-1701 in the clinical intend dosage route and schedule. In conclusion, these comprehensive preclinical data have strongly supported BB-1701 as a potent antitumor agent to cancers including HER2-low expressing and/or cancers insensitive to other HER2-targeting ADCs. A phase I clinical study of BB-1701 in those patients is ongoing.

Citation Format: Yang Wang, Bing Xia, Lixia Cao, Jianfeng Yang, Cui Feng, Fangdun Jiang, Chen Li, Lixia Gu, Yifan Yang, Jing Tian, Cindy Cheng, Keiji Furuuchi, James Fulmer, Arielle Verdi, Katherine Rybinski, Allis Soto, Earl Albone, Toshimitsu Uenaka, Likun Gong, Tingting Liu, Qiuping Qin, Ziping Wei, Yuhong Zhou. Preclinical development of BB-1701, a HER2-tageting eribulin-containing ADC with potent bystander effect and ICD activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1887.
Abstract 1890: Bispecific T cell engagers targeting TrkB
Authors: Bijlsma Jetta , Desikan Srinidhi , Miller Timothy , Thom Allie , Bath Jennifer , Roodink Ilse
Published: April 2023

Tropomyosin kinase B (TrkB) plays an important role in survival, differentiation, and proliferation of neural cells. It belongs to the family of receptor tyrosine kinases and its specific ligands are NT-4/5 and BDNF. The (over)expression of TrkB and (over)activation of the BDNF/TrkB signaling pathway is implicated in various solid malignancies and associated with poor prognosis due to the role of TrkB in suppressing anoikis and promoting epithelial-mesenchymal transition. Here we present the development and characterization of novel T cell engagers targeting TrkB. A panel of 41 sequence unique antibodies were selected from human phage display libraries and B cells of TrkB-ECD immunized chicken. Following recombinant expression, the panel of antibodies was analyzed for off-rate, binding reactivity to plate-immobilized and cell-expressed TrkB, cross-reactivity to other tropomyosin kinase family members, and competition with BDNF. Based on their characteristics, two targeting arms were prioritized for the generation of T cell engagers using a standard bispecific knob-into-hole approach. Apart from a commercial CD3 targeting arm, three proprietary CD3 targeting arms were also analyzed. After successful production of the bispecifics , the molecules were validated to bind to plate-immobilized TrkB and CD3 separately and cell-associated TrkB and CD3 simultaneously. In addition, our TrkB T cell engagers were able to induce varying levels of T cell activation in vitro. Our data suggests that these TrkB/CD3 bispecific molecules could be interesting candidates for further development into immuno-oncology therapeutics.

Citation Format: Jetta Bijlsma, Srinidhi Desikan, Timothy Miller, Allie Thom, Jennifer Bath, Ilse Roodink. Bispecific T cell engagers targeting TrkB [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1890.
Abstract 190: Personalized identification of cancer treatments in real-time: TumOC - a tumor organoid-on-chip platform for online cell vitality measurements
Authors: Flechner Marie , Loskutov Juergen , Nadolny Madeleine , Pfohl Ulrike , Regenbrecht Christian R. , Uhlig Katja , Wedeken Lena
Published: April 2023

Enhanced, physiologically relevant in-vitro tumor models significantly increase the success rate in new drug development, reduce the number of animal experiments and result finally in better therapies for cancer patients. Furthermore, they have the potential to offer new approaches to personalized oncology. In recent years, 3D cell cultures were established as relevant preclinical cancer models, suitable for high-throughput-screening. However, their capacity to model and/or measure physiological processes can still be enhanced. Colorectal carcinomas (CRC) are one of the most common malignant tumors. Due to its heterogeneity and high probability to metastasize, the disease is often incurable and novel, improved therapies are urgently needed. In this project, we developed a tumor organoid-on-chip platform (TumOC) by combining most recent technological advances: We integrated CRC patient-derived 3D cell cultures (organoids) and microsensor particles that enable assessment of cell vitality in real time by measuring oxygen concentration in a microfluidic system. The resulting TumOC platform allows for defined exposition of cytostatic drugs including dynamic and combination treatments. Measurements of cell vitality in real time enables analysis of not only the final effect of a drug treatment, but also the kinetics of drug response. At the same time, utilizing organoids allows for recapitulating tumor architecture and heterogeneity. Using the TumOC platform, we measured the cell vitality in real time over several days during treatment with classic chemotherapeutics or targeted cancer drugs and compared the results to end-point measurements on the same organoids in a static system. We assessed the effect of intra- and intertumoral heterogeneity and developed a protocol for treatment with clinically used combination regimes. In conclusion, our TumOC platform with its ability to recapitulate tumor heterogeneity in combination with dynamic treatments and real-time cell vitality assessment is an in-vitro tumor model closely recapitulating the physiological situation in a patient. TumOC provides an impressive opportunity to test and, consequently, predict the effectiveness of anti-cancer therapies. Therefore, this system is of interest not only for pre-clinical drug development but also for personalized oncology.

Citation Format: Marie Flechner, Juergen Loskutov, Madeleine Nadolny, Ulrike Pfohl, Christian R. Regenbrecht, Katja Uhlig, Lena Wedeken. Personalized identification of cancer treatments in real-time: TumOC - a tumor organoid-on-chip platform for online cell vitality measurements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 190.
Abstract 192: A novel and rapid patient-derived organoid breast cancer platform for precision medicine
Authors: Graham David M. , Rupprecht Gabrielle , Bankaitis Eric D. , Force Jeremy M. , Watlington Wylie , Metzger Steven W. , Shen Xiling , Hsu David
Published: April 2023

An increasing number of studies performing correlative drug screens on patient-derived organoids (PDO) are revealing enormous potential for these models in predicting patient response to therapy. Despite this, their future use in a clinical setting is hindered by intrinsic limitations of PDO models, namely low success rates in establishing growing cell cultures from tumor tissue samples and long return times for drug response data that fall outside timescales of clinical actionability. To address these limitations, we leveraged technological advances in emulsion-based microfluidics and droplet generators to develop MicroOrganoSpheres (MOS) - microscale environments containing tumorspheres that retain structural, cellular, and genetic properties of an individual patient’s diseased tissue. Here, we focused on generating MOS from breast cancer tissue biopsies and resections across different subtypes of breast cancer. We established over 30 unique patients’ breast MOS samples at an average of 80% success, with the majority of these samples being hormone receptor positive (ER+/PR+) - the most clinically lethal and challenging subtype to establish. We evaluated MOS dose-responses across several first line standard of care chemotherapies for breast cancer. For this, we created a semi-automated workflow paired with high-content imaging for quantifying dose responses and tracking longitudinal cell dynamics during dosing. We generated dose response data for MOS samples, being able to move from primary tissue samples to MOS to drug dosing data within a clinically relevant timescale of 2-3 weeks. We conclude that our platform demonstrates the feasibility of 1) efficiently establishing MOS from breast cancer patient tumor samples from different subtypes and 2) performing drug dosing studies on these samples with improved turnaround times that enable clinical actionability for the patient. Together, these findings provide a foundation for evaluating this technology as a diagnostic tool in future clinical settings.

Citation Format: David M. Graham, Gabrielle Rupprecht, Eric D. Bankaitis, Jeremy M. Force, Wylie Watlington, Steven W. Metzger, Xiling Shen, David Hsu. A novel and rapid patient-derived organoid breast cancer platform for precision medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 192.
Abstract 1922: PhyloFrame: A machine learning framework for ancestry agnostic disease signatures
Authors: Smith Leslie A. , Cahill James A. , Graim Kiley
Published: April 2023

Rapid advancements in genomic sequencing technologies have catalyzed the molecular identification and treatment of previously elusive diseases. Despite these genomic advancements, disparities in precision medicine access and data have resulted in disparate impacts on different socioeconomic groups. Many of the gold standard datasets largely exclude minority populations, compounding their exclusion from medical research. This has resulted in a restricted understanding of cancer and other complex diseases. We demonstrate the effects of ancestral bias in gold standard genomics datasets through ancestral analysis of cancer-related genes in the Cancer Gene Census, spanning 17 ancestral populations. Additionally, we present a machine learning framework, PhyloFrame, that incorporates population genomics data to correct for ancestral bias by creating disease signatures representative of all ancestries. Our ancestral analysis results show that while a majority of the current cancer-related genes in the Cancer Gene Census have below average mutation frequency in non-European populations, there are peaks of ancestrally enriched mutations in ancestry-specific genes related to cancer, which can be targeted using PhyloFrame. PhyloFrame prioritizes gene expression from the cancer genes with high frequency mutations in a given human population in order to capture genes driving disease in each ancestry. It builds on existing disease gene signatures and big-data functional interaction networks to identify ancestry-relevant genes related to a disease, outputing an ancestry-agnostic disease signature. We test PhyloFrame on TCGA cancers with diverse patient populations, such as breast cancer, and compare PhyloFrame's disease signature output to the disease signature output of elastic net runs on cancer samples from a single ancestry. Our results demonstrate that the incorporation of ancestral information allows PhyloFrame to recapitulate disease signatures trained on only one ancestry in a dataset with individuals from many unquantified ancestries. With the incorporation of ancestral information, PhyloFrame is able to create disease signatures with genes pertinent to each ancestral population, even when individuals from those populations are not included in the training data. This work offers a quick and cheap alternative to the mass sequencing that would be required to capture disease-driving genes in minority populations in hopes to contribute to equitable representation in medical research.

Citation Format: Leslie A. Smith, James A. Cahill, Kiley Graim. PhyloFrame: A machine learning framework for ancestry agnostic disease signatures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1922.
Abstract 2007: Evaluation of the antitumor activity of ca102l, a hyaluronic acid and lenalidomide conjugate, in multiple myeloma
Authors: Tchaparian Eskouhie , Lin Star
Published: April 2023

Multiple Myeloma (MM) is a rare and incurable hematological malignancy. Despite emerging treatments, there is still an unmet medical need for novel therapeutics to target the inherent and acquired drug resistance associated with MM. CA102L is a conjugate of hyaluronic acid and an anticancer drug designed to deliver its payload, Lenalidomide (Len), to MM cells via the CD44 receptor. Lenalidomide is used as a front-line therapy in MM; The CD44 receptor is highly expressed in MM and is associated with advanced clinical stages and poor survival. In addition to the enhancement of the therapeutic efficacy of Len, a reduction in off-target toxicity is suggested. The present study was designed to evaluate the efficacy of CA102L in MM and identify its potential mechanism of action. The antitumor efficacy of CA102L was tested (in vitro and in vivo) in two MM cancer models, IM-9 and NCI-H929. Protein expression was used to identify the potential targets of CA102L in MM. Both in in vitro and in vivo investigations, CA102L as a single agent displayed an improvement in potency in MM models. In CB-17 SCID mice bearing either IM-9 or NCI-H929 cells, tumor growth inhibition was significantly higher (P< 0.05) in the CA102L (25 mg/kg) treated group compared to that of Len (25 mg/kg). Further, CD31 and hematoxylineosin (H&E) staining of tumor sections from the IM-9 xenograft mice treated with CA102L resulted in greater antiangiogenic and antiproliferative effects compared to the other groups. Prolonged survival was also observed in CA102L monotherapy in H929 models relative to Len (56% vs 11%). Interestingly, in H929 cell viability studies, CA102L and Len at 400μM showed comparable cytotoxicity with a 60% cell growth inhibition, while superior activity was noted against IM-9-treatments (CA102L 60%, Len 20%). Western blot studies confirmed CRBN as the primary target of CA102L. In summary CA102L as a single agent, exhibited greater efficacy than Len in preclinical MM models, thus representing a promising potential therapeutic strategy for MM. Studies presently are ongoing to further evaluate CA102L’s preclinical profile to advance the candidate into the clinic.

Citation Format: Eskouhie Tchaparian, Star Lin. Evaluation of the antitumor activity of ca102l, a hyaluronic acid and lenalidomide conjugate, in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2007.
Abstract 201: Establishment of 3D co-culture spheroid model for in- vitro drug screening
Authors: Nelson Christella J. , Cheriyan Vino T. , Pandit Abhishek , Francis Joseph , Tackett Alan
Published: April 2023

Melanoma is an aggressive form of skin cancer that accounts for 75% of deaths of all skin cancers in the United States. Moreover, the number of cases is increasing at an alarming rate than any other cancer worldwide. But what is more alarming is the lack of chemo preventive or therapeutic drugs that are easily accessible to people and the absence of an efficient, effective and reliable model or platform for drug screening. A growing scientific and observational analyses suggests that antioxidants contain in blueberry inhibit tumor growth, and help slow down esophageal, lung, mouth, pharynx, endometrial, pancreatic, prostate, and colon cancers. Lately, the use of 3D multicellular spheroid culture has become a potential link to bridge the gap between monolayer culture and animal model. The treatment of blueberry extract (1mg) on the spheroids of A375 cells showed a disintegration of these spheroids and reduction in their growth. To optimize the culture conditions further herein, we used a novel three-dimensional (3D) coculture system with melanoma (A375), human fibroblast (HF-1) and Human umbilical endothelial cells (HUVECs) to study the effectiveness of drug in vitro. The multicellular nature of the coculture spheroid stimulates the microenvironment of the original tumor which makes it more efficient in drug screening process. The immunofluorescence assay on the 3D spheroid co-culture shows the interactions among these three cells which mimics the tumor microenvironment. We further analyzed the combination of blueberry extract and resveratrol which proved the effectiveness of blueberry extract as a potential chemosensitizer with resveratrol for skin cancer therapy. The complementary effect on the inhibition of A375 cell proliferation were observed when treated with 8 mg blueberry and 10 mM of resveratrol. The results of MTT assay indicates that the blueberry extracts showed potential cytotoxic activity against A375 cell line. 3D spheroid assay and 3D spheroid co-culture assays further confirmed the effectiveness of blueberry and resveratrol combination. Therefore, this platform could be applied for in vitro based drug screening studies. To conclude cytotoxic effects of the blueberry extract in human melanoma cells make them good candidates for further pharmacological studies to discover effective drugs for melanoma therapy.

Citation Format: Christella J. Nelson, Vino T. Cheriyan, Abhishek Pandit, Joseph Francis, Alan Tackett. Establishment of 3D co-culture spheroid model for in- vitro drug screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 201.
Abstract 2066: Visualization and analysis of cancer genomics data using UCSC Xena
Authors: Goldman Mary , Craft Brian , Zhu Jingchun , Haussler David
Published: April 2023

UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Private data are kept on the researcher's computer and are never uploaded to our public servers. We support Mac, Windows, and Linux.

Questions Xena can help you answer:

* Is overexpression of this gene associated with lower/higher survival?

* What genes are differentially expressed between these two groups of samples?

* What is the relationship between mutation, copy number, expression, etc for this gene?

Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, GDC, PCAWG, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data: SNPs, INDELs, copy number variation, gene expression, ATAC-seq, DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotype information, subtype classifications and biomarkers. All of our data is available for download via python or R APIs, or using our URL links.

Our signature Visual Spreadsheet view shows multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. We also have dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, differential gene expression analysis, charts, statistical analyses, genomic signatures, and the ability to generate URLs to live views. We link out to the UCSC Genome Browser as well as MuPIT/CRAVAT and TumorMap.

New features include:

* Genome-wide differential gene expression analysis

* Select samples directly from the screen for filtering and creating subgroups

* Violin plots on any numerical data

* Loading of Microsoft Excel files

Our beta prototype site for visualizing single-cell data delivers million-cell-scale multi-omics data for interactive visualization in a web browser. Contact us for access to our beta prototype site.

If you use us please cite our publication in Nature Biotechnology: https://www.nature.com/articles/s41587-020-0546-8

Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. Visualization and analysis of cancer genomics data using UCSC Xena [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2066.
Abstract 2071: Detecting somatic DNA copy number differences with DiNAMIC.Duo
Authors: Walter Vonn , Choi Hyo Young , Zhao Xiaobei , Gao Yan , Holt Jeremiah , Hayes D. Neil
Published: April 2023

Somatic DNA copy number alterations (CNAs) arise in tumor tissue because of underlying genomic instability. Recurrent CNAs that occur in the same genomic region across multiple independent samples are of interest to researchers because they may contain genes that contribute to the cancer phenotype. However, differences in copy number states between cancers are also commonly of interest, for example when comparing tumors with distinct morphologies in the same anatomic location. Current methodologies are limited by their inability to perform direct comparisons of CNAs between tumor cohorts, and thus they cannot formally assess the statistical significance of observed copy number differences or identify regions of the genome where these differences occur. We introduce the DiNAMIC.Duo R package that can be used to identify recurrent CNAs in a single cohort or recurrent copy number differences between two cohorts, including when neither cohort is copy neutral. The TCGA studies of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) identified statistically significant CNAs in many known cancer-related genes, including gains of EGFR and losses of CDKN2A in each tumor type separately. By directly comparing the two cohorts, DiNAMIC.Duo detects statistically significant copy number differences for CDKN2A, thus suggesting that losses are more pronounced in LUSC; in contrast, differences for EGFR are not statistically significant, which suggests similar levels of gain. Existing methods that detect recurrent CNAs in a single cohort cannot make this distinction. Recent studies have leveraged TCGA data to find known cancer genes in chr3q, chr14q13, and chr20q11 that are differentially expressed in LUAD vs. LUSC. DiNAMIC.Duo identifies statistically significant copy number differences in these regions, which suggests that the observed expression changes may be driven by underlying differences in copy number.

Citation Format: Vonn Walter, Hyo Young Choi, Xiaobei Zhao, Yan Gao, Jeremiah Holt, D. Neil Hayes. Detecting somatic DNA copy number differences with DiNAMIC.Duo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2071.
Abstract 2082: DNAfusion: An R/Bioconductor package for increased sensitivity of detecting EML4-ALK gene fusions in liquid biopsies from cancer patients
Authors: Maansson Christoffer Trier , Andersen Emma Roger , Ulhoi Maiken Parm , Meldgaard Peter , Sorensen Boe Sandahl
Published: April 2023

EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC). Liquid biopsies containing circulating tumor DNA (ctDNA), including EML4-ALK, can be used to study tumor dynamics with next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection in liquid biopsies varies between different pipelines and analysis tools. We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. 48 blood samples from a training cohort consisting of 41 stage IV EML4-ALK positive NSCLC patients and 7 healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples compared to AVENIO (sensitivity = 61.0% vs. 36.6%, P = 0.046). The newly identified EML4-ALK positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK positive and 24 EML4-ALK negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort compared to AVENIO (sensitivity = 62.5% vs. 29.2%, P = 0.042). DNAfusion demonstrated a specificity of 100% in both the training and the validation cohorts. Monitoring EML4-ALK variants with AVENIO and DNAfusion in serial blood samples from 24 stage IV EML4-ALK positive patients during treatment (n = 72), revealed that DNAfusion can detect EML4-ALK variants at clinically critical timepoints, otherwise missed by AVENIO. Here we present DNAfusion, which increases sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The high sensitivity of DNAfusion is a necessity for analytical tools used to monitor ctDNA in serial plasma samples in order to implement liquid biopsies in the clinic. The simplistic way of operating the R package makes it easy to set up in the clinical setting enabling wider expansion of liquid biopsy and NGS based diagnostics.

Citation Format: Christoffer Trier Maansson, Emma Roger Andersen, Maiken Parm Ulhoi, Peter Meldgaard, Boe Sandahl Sorensen. DNAfusion: An R/Bioconductor package for increased sensitivity of detecting EML4-ALK gene fusions in liquid biopsies from cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2082.