bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2633: Discovery of novel, highly selective inhibitors of PLK4 that demonstrate in vivo regressions in TRIM37 high xenografts
Authors: Edgar Kyle A. , Young Amy , Moore Jared , Chen Xi , Fang Wei , Chang Jae H. , Kong Wayne , Long Jason E. , Pankov Aleksandr , Daemen Anneleen , Shore Daniel G. , Warne Robert , Gibbons Paul , Ndubaku Chudi O. , Junttila Melissa R. , Friedman Lori S.
Published: June 2022

Amplification and copy number alterations of the 17q23 amplicon are common in breast cancer and neuroblastoma and have been associated with early relapse and poor prognosis. Recent work identified a key vulnerability associated with amplicon-driven overexpression of TRIM37 in these tumor types (Meitinger et al. 2020; Yeow et al. 2020). High levels of TRIM37 prevent acentrosomal spindle assembly and render cells mitotically vulnerable to inhibition of polo-like kinase 4 (PLK4), a serine/threonine protein kinase that controls centrosome duplication.

We have discovered potent small molecule inhibitors of PLK4 that are highly selective against the kinome, including against the closely related aurora kinases and PLK1-3. Self-regulation of PLK4 protein levels occurs through proteasomal degradation induced by PLK4 trans-autophosphorylation. ORIC PLK4 inhibitors blocked trans-autophosphorylation leading to stabilization of PLK4, thus directly demonstrating target inhibition in cells. Importantly, PLK4 inhibitor induced PLK4 protein stabilization correlated with cell viability, providing a quantifiable pharmacodynamic (PD) association with antitumor activity. Cell viability assessment across a cancer cell line panel revealed that the highly selective ORIC PLK4 inhibitors showed greater potency in TRIM37 high cancer cell lines as compared to TRIM37 low cell lines. In contrast, less selective compounds, including from the clinical literature, did not display differential potency in TRIM37 high versus low cancer cell lines. Importantly, cell potency in TRIM37 high cancer cells was rescued with knockdown of TRIM37, illustrating that selective PLK4 inhibitors are synthetic lethal with TRIM37 amplification. Oral administration of ORIC PLK4 inhibitors resulted in regressions of TRIM37 high xenograft tumors, with corresponding PD effects and no body weight loss.

In summary, we have discovered novel, potent, highly selective small molecule inhibitors of PLK4 that are orally bioavailable and confirmed the potential for this new target in treating tumors with high levels of TRIM37.

Citation Format: Kyle A. Edgar, Amy Young, Jared Moore, Xi Chen, Wei Fang, Jae H. Chang, Wayne Kong, Jason E. Long, Aleksandr Pankov, Anneleen Daemen, Daniel G. Shore, Robert Warne, Paul Gibbons, Chudi O. Ndubaku, Melissa R. Junttila, Lori S. Friedman. Discovery of novel, highly selective inhibitors of PLK4 that demonstrate in vivo regressions in TRIM37 high xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2633.
Abstract 2652: Efficacy of a small molecule MCT1 and MCT4 transporter inhibitor in cancer
Authors: Sharma Sambad , Goreczny Gregory , Bowman Nicole , Duffy Jennifer , Banerjee Daliya , Wijerathna Sanath , Dzuris John , Wu Kerui , Wu Shih-Ying , Tyagi Abhishek , Watabe Kounosuke , Escobedo Jaime , Sandanayaka Vincent
Published: June 2022

Targeting metabolic pathways has been a major clinical interest to effectively treat cancer patients. FDA approval of TIVSOVO(R) (IDH1 inhibitor) has validated the clinical importance of targeting tumor metabolism in cancer. Although MCT1-targeting small molecule inhibitor is currently under investigation for lymphoid cancers, the therapeutic efficacy of this compound is compromised by compensatory overexpression of MCT4 by tumor cells. Therefore, there is a need for a dual MCT1/4 inhibitor to target cancer. We have developed a first-in-class orally bioavailable small molecule inhibitor that targets lactate transport through MCT1 and MCT4 transporters. In 4T1 syngeneic model, we observed a significant dose-dependent reduction of tumor growth by NGY-B treatment that also correlated with serum lactate levels. Immunoprofiling of tumors revealed that NGY-B promoted anti-tumor immune response in 4T1 tumor bearing mice indicating simultaneous immune activation. Also, the combination of NGY-B with a checkpoint inhibitor led to greater efficacy and overall survival in this model suggesting a potential combination therapy in the clinic. Furthermore, we demonstrated the direct tumor cell killing effect of NGY-B in multiple human CDX and PDX models. Therefore, NGY-B intervenes two key hallmarks of cancer - tumor metabolism and anti-tumor immunity, and provides a novel modality to therapeutically target cancer.

Citation Format: Sambad Sharma, Gregory Goreczny, Nicole Bowman, Jennifer Duffy, Daliya Banerjee, Sanath Wijerathna, John Dzuris, Kerui Wu, Shih-Ying Wu, Abhishek Tyagi, Kounosuke Watabe, Jaime Escobedo, Vincent Sandanayaka. Efficacy of a small molecule MCT1 and MCT4 transporter inhibitor in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2652.
Abstract 2669: ERAS-007 (ERK inhibitor) + ERAS-601 (SHP2 inhibitor) exhibit nonclinical combination activity across KRAS mutated NSCLC, CRC, and PDAC tumor models
Authors: Martin Leenus , Lew Erin D. , Patel Roopal , Oh Joanne , Zhang Jingchuan , Nevarez Robin , Congdon Taylor , Lin Wei , Brail Les , Shoemaker Robert
Published: June 2022

KRAS mutations occur in about 25% of all cancers and promote oncogenesis via constitutive activation of the RAS/MAPK pathway. Targeting KRAS mutant tumors by inhibiting individual nodes in the RAS/MAPK pathway, including SHP2, SOS1, KRAS, RAF, MEK, and ERK, has shown early clinical activity, but the rapid emergence of resistance limits the benefit of monotherapy. Resistance is often mediated by reactivation of RAS/MAPK pathway signaling, which can occur by increased activation of upstream of the RAS/MAPK pathway (e.g., EGFR activation) and/or activation of RAS/MAPK pathway nodes (e.g., oncogenic BRAF and MEK mutations). Inhibiting both upstream and downstream RAS/MAPK pathway nodes has the potential to more robustly prevent reactivation relative to inhibition of a single node alone. We are currently exploring the combination of an inhibitor of an upstream node, SHP2, with ERAS-601 and the terminal downstream node, ERK1/2, with ERAS-007 (our first “MAPKlamp”) in nonclinical models. We evaluated this MAPKlamp in NSCLC, CRC, and pancreatic tumor models that harbored KRAS mutations in vitro and in vivo. In 14-day clonogenic assays in KRAS mutant NSCLC, CRC, and PDAC cell lines, this MAPKlamp inhibited colony growth more potently than ERAS-601 or ERAS-007 alone. In KRAS mutant CDX and PDX models, this MAPKlamp’s in vitro activity was observed in vivo where it achieved superior tumor growth inhibition and tumor regression relative to ERAS-601 and ERAS-007 monotherapy. This MAPKlamp showed in vitro and in vivo combination activity in KRAS mutant tumors, and these results support its clinical evaluation in RAS/MAPK pathway-driven tumors.

Citation Format: Leenus Martin, Erin D. Lew, Roopal Patel, Joanne Oh, Jingchuan Zhang, Robin Nevarez, Taylor Congdon, Wei Lin, Les Brail, Robert Shoemaker. ERAS-007 (ERK inhibitor) + ERAS-601 (SHP2 inhibitor) exhibit nonclinical combination activity across KRAS mutated NSCLC, CRC, and PDAC tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2669.
Abstract 267: Xenograft models of non-metastatic non-small cell lung cancer reveals micrometastasis-associated single cell composition
Authors: Suvilesh Kanve Nagaraj , Nussbaum Yulia I. , Radhakrishnan Vijay , Manjunath Yariswamy , Avella Diego M. , Staveley-O’Carroll Kevin F. , Kimchi Eric T. , Chaudhuri Aadel A. , Shyu Chi-Ren , Li Guangfu , Pantel Klaus , Warren Wesley C. , Mitchem Jonathan B. , Kaifi Jussuf T.
Published: June 2022

Background: Circulating tumor cells (CTCs) represent micrometastatic disease and may offer unique insights into future recurrences in lethal malignancies, including non-small cell lung cancer (NSCLC). Due to CTC rarity and limited stability, no CTC-derived xenograft (CDX) models have ever been generated from non-metastatic NSCLC patients directly. Alternative strategies are needed to molecularly characterize CTCs in this potentially curable patient group.

Methods: Surgically resected NSCLC primary tumor tissues were implanted in immunodeficient mice to establish ten patient-derived xenografts (PDXs). CTCs from 2/10 PDX models led to generation of two stable metastatic models that were studied by single cell sequencing.

Results: Single cell analysis revealed an additional alveolar epithelial type II (AT2) population in metastatic tumors, besides a common AT2 cluster in PDX/metastatic tumors. This was consistent with an external validation set analysis in primary and metastatic NSCLC patient tumors. Further, AT2 clusters of metastatic tumors expressed higher cancer stemness genes versus primary PDX tumor that was recapitulated in patients primary and metastatic tumors.

Conclusions: Stable metastatic models from early stage NSCLC patients can be generated with CTCs from PDX models. The distinct AT2 population identified in CDX tumors with cancer stemness features might be critical mediator of metastasis that deserves further study to discover personalized strategies against NSCLC micrometastases.

Citation Format: Kanve Nagaraj Suvilesh, Yulia I. Nussbaum, Vijay Radhakrishnan, Yariswamy Manjunath, Diego M. Avella, Kevin F. Staveley-O’Carroll, Eric T. Kimchi, Aadel A. Chaudhuri, Chi-Ren Shyu, Guangfu Li, Klaus Pantel, Wesley C. Warren, Jonathan B. Mitchem, Jussuf T. Kaifi. Xenograft models of non-metastatic non-small cell lung cancer reveals micrometastasis-associated single cell composition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 267.
Abstract 27: Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues
Authors: Crawford David Robert , Sinha Sanju , Nair Nishanth U. , Ryan Bríd M. , Barnholtz-Sloan Jill , Mount Stephen M. , Erez Ayelet , Adalpe Kenneth , Castle Philip E. , Rajagopal Padma S. , Day Chi-Ping , Schäffer Alejandro A. , Ruppin Eytan
Published: June 2022

Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 170 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-matched cancer-AID incidence rate sex bias data pairs, we find that the sex biases observed in the incidence of AIDs and cancers that occur in the same tissue are positively correlated across human tissues. Second, we find that the sex bias in the expression of the 37 genes encoded in the mitochondrial genome stands out as the common key factor whose levels across human tissues are most strongly and positively associated with these incidence rate sex biases.

Citation Format: David Robert Crawford, Sanju Sinha, Nishanth U. Nair, Bríd M. Ryan, Jill Barnholtz-Sloan, Stephen M. Mount, Ayelet Erez, Kenneth Adalpe, Philip E. Castle, Padma S. Rajagopal, Chi-Ping Day, Alejandro A. Schäffer, Eytan Ruppin. Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 27.
Abstract 2706: Ultra-Low Input High-Fidelity (ULI-HiFi) long-reads uncover variants in genomic dark matter from pre-cancer polyp and tumor samples
Authors: Lee Hayan , Erwin Graham , Horning Aaron , Kirtikar Raushun , Griffin-Baldwin Emmett , Rowell William , Li Philip , Kingan Sarah , Snyder Michael P.
Published: June 2022

Long-read sequencing technologies have been constrained by high error rates and large sample input requirements. The recent introduction of HiFi sequencing has enabled highly accurate detection of single-nucleotide variants (SNVs) from long reads (10-15 kb). However, a major limiting factor is the amount of sample input required, where current protocols require ≥15 micrograms of DNA. Here we report Ultra-Low Input High Fidelity Sequencing (ULI-HiFi), an amplification-based library preparation that reduces this input to 10 nanograms of DNA, a more than 10,000-fold reduction in sample input. When the ultra-low input method was tested using a benchmark genome, HG002, we observed high precision and improved recall of structural variants compared to a ground truth dataset from the Genome in a Bottle Consortium. We also benchmarked small variants and reported the accurate analysis of many variants in clinically important genes that are unmappable with short reads. We used this strategy to sequence tumor and polyp samples from a patient with familial adenomatous polyposis, a hereditary form of colon cancer, which revealed SNVs and structural variants not detected by short-read techniques. This strategy will enable the improved characterization of genetic variants from limited clinical samples.

Citation Format: Hayan Lee, Graham Erwin, Aaron Horning, Raushun Kirtikar, Emmett Griffin-Baldwin, William Rowell, Philip Li, Sarah Kingan, Michael P. Snyder. Ultra-Low Input High-Fidelity (ULI-HiFi) long-reads uncover variants in genomic dark matter from pre-cancer polyp and tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2706.
Abstract 2709: Transcriptomic meta-analysis of non-Hodgkin’s B-cell lymphomas reveals reliance on pathways associated with extracellular matrix
Authors: Rapier-Sharman Naomi , Pickett Brett E.
Published: June 2022

We report here the results of a transcriptomic meta-analysis of public data for B-cell Non-Hodgkin’s Lymphomas (BCNHL). In 2016, there were 461,000 cases of Non-Hodgkin’s lymphoma worldwide, resulting in 240,000 deaths that year. BCNHLs pose a significant disease burden worldwide, making up 85-90% of BCNHL cases. BCNHL subtypes include Burkitt’s lymphoma, marginal-zone B-cell lymphomas, follicular lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma. There is a growing need to understand the mechanisms of BCNHL pathology. The scientific community has spent a great deal of time and effort to identify the hallmarks of cancer. Since cancers of different subtypes can be considered parallel systems, we have performed a meta-analysis including as many BCNHL subtypes as possible to determine common underlying mechanisms. We performed a transcriptomic meta-analysis of publicly available RNA-sequencing data for BCNHL, consisting of 322 relevant samples across seven distinct studies in the NCBI Gene Expression Omnibus (GEO). To our knowledge, no BCNHL meta-analysis of this magnitude has previously been performed. We found ~10,400 significant differentially expressed genes (FDR p-value <= 0.05) and 33 significantly modulated pathways (FDR p-value <= 0.05). We observed potential common mechanisms for BCNHL’s differentially expressed genes and signaling pathways. Our findings include a significant class of proteoglycans not previously associated with lymphomas as well as significant upregulation of extracellular matrix-associated proteins. This meta-analysis offers fresh insights into the inner workings and mechanisms of B-cell lymphomas that could give rise to improved diagnostics and/or therapeutics.

Citation Format: Naomi Rapier-Sharman, Brett E. Pickett. Transcriptomic meta-analysis of non-Hodgkin’s B-cell lymphomas reveals reliance on pathways associated with extracellular matrix [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2709.
Abstract 272: Effective treatment of colorectal peritoneal metastases by exploiting a molecular subtype specific vulnerability
Authors: Bootsma Sanne , Dings Mark P. , Moreno Leandro Ferreira , Lenos Kristiaan J. , Vermeulen Louis , Bijlsma Maarten F.
Published: June 2022

In colorectal cancer, peritoneal metastases (PMs) associate with severe morbidity and dismal prognosis. Given the incidence of this disease and the lack of adequate treatments currently available, PMs pose a large unmet clinical need. Although PMs can be accompanied by more widespread metastatic disease, it often occurs as the only sign of dissemination. This implies that the route of metastatic spread to the peritoneum differs from that to distant organs. PMs are thought to result from cancer cells that spill into the abdominal cavity, and are able to attach to the peritoneal lining and form tumor deposits. This cascade places specific demands on the cancer cells.

Here, we report that colorectal cancers that present with PMs almost universally classify as consensus molecular subtype 4 (CMS4). This previously recognized disease entity is characterized by mesenchymal features, poor prognosis, and resistance to therapies currently used against peritoneal metastases, which explains their limited efficacy. By leveraging disease models that capture CMS4-specific features, including the ability to form PMs in vivo, we identified elesclomol as a highly effective agent. Elesclomol kills cancer cells in a copper-dependent fashion by targeting the oxidative phosphorylation machinery, which we found to be a specific vulnerability of CMS4 cancers. Elesclomol-Cu2+ was effective following only minutes of exposure to CMS4 cell lines and organoids, supporting its use in intra-abdominal treatment procedures. It is therefore a promising candidate for the local treatment of peritoneal metastases of colorectal cancer.

Citation Format: Sanne Bootsma, Mark P. Dings, Leandro Ferreira Moreno, Kristiaan J. Lenos, Louis Vermeulen, Maarten F. Bijlsma. Effective treatment of colorectal peritoneal metastases by exploiting a molecular subtype specific vulnerability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 272.
Abstract 2740: Stochastic modeling uncovers the interplay between early cancer progression and adaptive immune-specific cancer escape
Authors: George Jason T.
Published: June 2022

The lack of durable therapeutic interventions continues to limit cancer treatment efficacy. While breakthroughs in immunotherapy have improved patient survival for some disease subtypes, immune escape is an unfortunate and common hallmark of cancer evasion. Understanding the dynamic interplay between an evolving and heterogeneous malignant population and the adaptive immune system, consisting of millions of unique T cells, is therefore required for designing optimized treatment strategies. We begin by describing the implications of cancer escape via durable evasion events, such as major histocompatibility antigen presentation down-regulation. Durable escape is then applied to relate observed cancer age-specific incidence to physiologic impairments in T cell turnover and diversity. We then discuss a more generalized stochastic process that enables transient escape and recurrent recognition via distinct T cell subclones. This co-evolutionary model predicts repeated immune recognition and cancer evasion prior to disease manifestation. Using this model, we find that T cell turnover and cancer mutation rates explain differences in early age incidence data across nearly all cancer types. Lastly, we introduce a modeling approach for understanding the extent of optimality occurring in cancer evasion via tumor-associated antigen downregulation, emphasizing the utility of foundational modeling frameworks for optimizing cancer T cell immunotherapy.

Citation Format: Jason T. George. Stochastic modeling uncovers the interplay between early cancer progression and adaptive immune-specific cancer escape [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2740.
Abstract 2772: A novel bio-physical based CDA approach for evaluating lung cancer therapeutic responses
Authors: Wu Junjie , Zou Zixiu , Du Xuedong , Lin Yue , Tang Xing , Chen Jie , Peng Lan , Yu Chris
Published: June 2022

Background: Lung cancer is the world's highest mortality and incidence rate of malignancy, and the prognosis survival rate is significantly lower than other tumors. A novel bio-physics based multi (pan)-cancer test technology named Cancer Differentiation Analysis Technology (CDA) has been developed and investigated for evaluating and monitoring lung cancer therapeutic responses.

Methods: A total of 686 patients diagnosed with different sub-types of lung cancer were included in this study. CDA levels were concurrently measured in peripheral blood obtained from 686 patients during the treatment. According to the response evaluation criteria in solid tumors (RECIST) 1.1 standard, the efficacy of 686 patients after treatment was evaluated, and the diagnostic efficacy of CDA technology was evaluated by receiver operating characteristic (ROC) curve.

Results: Clinical pathological parameters of the patients are listed in Table 1. The higher the CDA value, the worse the curative effect. CDA value of lung cancer in CR (complete response) group was significantly lower than that in other 3 groups (p<0.05). CDA value of adenocarcinoma lung cancer in CR group were significantly lower than that in SD (stable disease) group (p<0.05). For non - metastatic lung cancer, CDA value in CR group was significantly lower than that in SD group (p<0.05) The receiver ROC analysis showed that the area under curve (AUC) of lung cancer group, NSCLC group, adenocarcinoma lung cancer group, were 0.756, 0.772, and 0.792, respectively. The AUC of early lung cancer group, and non - metastatic lung cancer group were 0.794, and 0.851.

Conclusions: CDA appears to have the ability to predict and monitor therapeutic responses to lung cancer surgery and chemotherapy treatments. In most cases, the CDA of CR patients is low, and there is a good correlation between CDA and curative effect in early lung cancer. CDA could be a potential candidate for evaluating lung cancer, especially for early stage lung cancer therapeutic response.

Citation Format: Junjie Wu, Zixiu Zou, Xuedong Du, Yue Lin, Xing Tang, Jie Chen, Lan Peng, Chris Yu. A novel bio-physical based CDA approach for evaluating lung cancer therapeutic responses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2772.
Abstract 2832: Identifying tumor specific surface protein markers for glioblastoma immunotherapy by single-nuclei RNA-seq
Authors: Ibrahim Omar M. , Wang Liang-Bo , Yao Lijun , Caravan Wagma , Deen Nataly Naser Al , Jayasinghe Reyka G. , Chheda Milan G. , Ding Li
Published: June 2022

Glioblastoma (GBM) is one of the deadliest adult brain tumors, in which the typical treatments of surgery, chemotherapy, and/or radiotherapy yield generally poor median survival. GBM is categorized into IDH-mutant subtype and IDH-wildtype subtype, which is subcategorized into proneural, classical, and mesenchymal subtypes, yet few personalized treatment options are available. The use of genetically modified chimeric antigen receptor T cells (CAR-T), such as CD19 CAR-T, has shown significant clinical efficacy in the treatment of hematological malignancies due to specific antitumor response; however, CAR-T response in GBM has been poor. Single nuclei RNA-seq (snRNA-seq) technology offers high-resolution profiling of different cell populations and their specific differential patterns. Accordingly, we developed a robust genomic analysis pipeline that can be applied to external datasets, tumor, and healthy samples. This was followed by unbiased systematic analysis of GBM tumor-specific cell surface markers using 18 single nuclei RNA sequencing (snRNA-seq) samples to identify GBM specific CAR-T targets allowing efficient tumor cells targeting and minimum off-target effects by CAR-T (1). We identified key potential targetable cell surface-specific markers and we also identified subtype-specific targets. Our findings provide insights into tumor-specific cell surface proteins that may be potential targets for engineered immunotherapy. References:(1) Wang, Liang-Bo, Alla Karpova, Marina A. Gritsenko, Jennifer E. Kyle, Song Cao, Yize Li, Dmitry Rykunov, et al. "Proteogenomic and metabolomic characterization of human glioblastoma." Cancer cell 39, no. 4 (2021): 509-528.

Citation Format: Omar M. Ibrahim, Liang-Bo Wang, Lijun Yao, Wagma Caravan, Nataly Naser Al Deen, Reyka G. Jayasinghe, Milan G. Chheda, Li Ding. Identifying tumor specific surface protein markers for glioblastoma immunotherapy by single-nuclei RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2832.
Abstract 2866: BAY 3375968: An afucosylated anti-CCR8 antibody depleting activated intratumoral regulatory T cells as a cancer immunotherapy
Authors: Roider Helge , Tseng Su-Yi , Hoff Sabine , Berndt Sandra , Filarski Katharina , Gritzan Uwe , Stelte-Ludwig Beatrix , Nadler Wiebke M. , Grudzinska-Goebel Joanna , Ellinger Philipp , Trautwein Mark , Gorjanacz Matyas
Published: June 2022

Regulatory T cells (Tregs) play an indispensable role in mediating peripheral tolerance to self-antigens. They can also promote tumor growth by suppressing the function of effector CD8+ and CD4+ T cells in the tumor microenvironment (TME). Furthermore, Tregs are identified as one of the key resistance mechanisms hampering the efficacy of immune checkpoint inhibitors (ICIs) across many tumor types. Therefore, there is a high need for safe and effective agents that would specifically deplete tumor-infiltrating Tregs while sparing both peripheral Tregs and effector T cells.

Chemokine receptor 8 (CCR8) is predominantly expressed on activated tumor-infiltrating Tregs and marks the most suppressive and proliferative Treg population. CCR8+ Tregs are associated with high tumor grade and poor overall survival across many tumor types such as lung, breast, or head-neck cancer. Thus, unlike other approaches directed against Tregs, targeting CCR8 offers the opportunity to specifically deplete intra-tumoral Tregs without impacting peripheral Tregs or other immune cells.

BAY 3375968 is a non-internalizing fully human glycoengineered (afucosylated) monoclonal IgG1 antibody, which in vitro selectively depleted human CCR8+ Tregs via antibody dependent cellular cytotoxicity (ADCC) and antibody dependent cellular phagocytosis (ADCP). In vivo efficacy studies using mouse surrogate antibodies showed strong monotherapeutic efficacy across a variety of murine tumor models with clear correlation of intratumoral CCR8+ Treg depletion and CD8+ T cell increase. The monotherapeutic efficacy of CCR8 depleting antibodies was further enhanced by combinations with ICIs. BAY 3375968 also showed a good safety profile in cynomolgus monkeys. In conclusion, CCR8 is a novel Treg depleting immunotherapy target, and due to its highly tumor-restricted expression profile, BAY 3375968 may provide superior clinical safety and efficacy profile comparing to other less specific Treg targeting approaches.

Based on the promising pre-clinical data, preparations for a phase I clinical trial investigating the safety, tolerability, pharmacokinetics, pharmacodynamics, and preliminary anti-tumor activity of BAY 3375968 are underway.

Citation Format: Helge Roider, Su-Yi Tseng, Sabine Hoff, Sandra Berndt, Katharina Filarski, Uwe Gritzan, Beatrix Stelte-Ludwig, Wiebke M. Nadler, Joanna Grudzinska-Goebel, Philipp Ellinger, Mark Trautwein, Matyas Gorjanacz. BAY 3375968: An afucosylated anti-CCR8 antibody depleting activated intratumoral regulatory T cells as a cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2866.
Abstract 2926: Structure-based design of quadruplex-binding small molecule compounds: The essential role of water molecules
Authors: Neidle Stephen
Published: June 2022

The compounds CM03 and SOP1812 are tri- and tetra-substituted naphthalene diimide derivatives with high affinity for several human DNA quadruplexes. They have been designed by computer modelling based on co-crystal structures of 1st-generation substituted naphthalene diimides with human intramolecular telomeric quadruplexes. CM03 and SOP1812 have single-digit 1-20 nM anti-proliferative activity in a panel of human pancreatic ductal adenocarcinoma (PDAC) cell lines (Marchetti et al., J. Med. Chem, 2018, 61, 2500-2517: Ahmed et al., ACS Med Chem Lett, 2020, 11, 1634-1644) and significant anti-tumor activity in the MIA-PACA2 xenograft model for PDAC as well as in the more demanding KPC model. SOP1812 is bio-available at therapeutic doses and is well tolerated at these levels in animal models. It is currently being evaluated as a candidate for clinical development by Qualigen Therapeutics Inc. The role of water in protein-drug binding is well documented and known to be important for accurate estimates of drug binding energies and for docking/virtual screening studies. To date this factor has not been seriously considered in studies of ligand-quadruplex interactions even though virtual screening has emerged as an important tool for finding new chemotypes and optimizing compound libraries in silico. A high-resolution crystal structure of a naphthalene diimide quadruplex complex (PDB id 3UYH: Micco et al., J. Med. Chem., 2013, 56, 2959-2974) has now been analyzed in detail. Patterns of water molecules have been found in each of the four quadruplex grooves, associated with the cationic side chains. Only a nitrogen atom on each N-methyl-piperazine cationic end groups is in direct hydrogen bonded contact with a phosphate group. The morpholino groups each have a small and well-defined cluster of water molecules mediating between cationic nitrogen atom and phosphate group. The rest of each groove is filled by a second cluster of waters, suggesting that larger substituents can be accommodated. Data from a library of naphthalene diimide derivatives is being examined to validate the role of these waters, especially with respect to their relative mobilities and ease of displacement.

Citation Format: Stephen Neidle. Structure-based design of quadruplex-binding small molecule compounds: The essential role of water molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2926.
Abstract 2931: Optical genome mapping workflow for identification and annotation of variants in hematological diseases
Authors: Hauenstein Jennifer , Pang Andy , Chaubey Alka , Hastie Alex
Published: June 2022

Guidelines from WHO, NCCN and others, for the genetic analysis of hematological malignancies included structural variation analysis. Traditionally, this has relied on a combination of three cytogenetic technologies for structural variation analysis: karyotyping, FISH, and microarray, are used to detect copy number variants, translocations, inversions. Next generation sequencing is also applied for mutation analysis but has not been successful for structural variation analysis. These traditional methods have many very manual aspects and require extensive expertise. Optical genome mapping (OGM) consolidates assays into a single laboratory assay in which the output provides the visualization of structural and copy number variants at one time. OGM is able to comprehensively detect structural variations genome wide down to 5% variant allele fraction for CNVs, inversions, and translocations from blood and bone marrow aspirates making it an attractive choice for hematologic malignancy genomic analysis. Preanalytical and analytical steps require approximately 4-5 days from sample to processed data with structural variation calls. Dynamic filtering in the user interface can be configured to remove most polymorphic variants and prioritize relevant variants. In addition, the OGM graphical user interface software, Bionano Access 1.7, allows for the user to assign classification/relevance to the variants for each case. For example, an ALL sample with t(9;22), deletion of CDKN2A, and whole chromosome gains of 4,6, and 10 can be easily visualized with the Circos plot and, then, can be further examined and annotated as needed. A second analyst can repeat the process blind to the first analysis and a supervisor can adjudicate the classifications. A variety of cases with hallmark abnormalities from various leukemias will be presented with the filtering and prioritization workflow used to derive them. This comprehensive technology allows for a quicker, more reliable output than traditional cytogenetic approaches.

Citation Format: Jennifer Hauenstein, Andy Pang, Alka Chaubey, Alex Hastie. Optical genome mapping workflow for identification and annotation of variants in hematological diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2931.
Abstract 2943: Acoustic cell separation platform for efficient preparation of single cell/nuclei suspension from complex samples for genomics analysis
Authors: Yu Liping
Published: June 2022

Preparing a single cell suspension is a critical step in any solid tissue for genomics analysis as the presence of cellular debris, dead cells and free RNA will cause incorrect cell count, noise in sequencing read and possibly clogging of the microfluidic chip. Single cell preparation not only involves the tissue dissociation process but the “clean-up” step of the dissociation product. Current methods for removing dead cells and debris use magnetic beads and density gradient centrifugation, which are lengthy and costly, and often result in low cell recovery. Here we present a high-speed acoustic cell separation platform—MARS® Sample Preparation system. The system has three independent modules and each has an acoustic cell processing chip (CPC) which creates different moving trajectory of live cells, dead cells, and cellular debris in the acoustic field to achieve high efficiency of single cell separation. MARS® sample preparation provides fast, gentle, and label-free protocol to separate single cells and single nuclei from various types of organs and dissociation processes including manual enzymatic approach and automatic platform. Separated single cells and nuclei demonstrate compatibility with the downstream single cell genomics platform. We here report the separation of live single cells and nuclei from mouse brain tissue dissociation with over 99% removal of myelin and other debris, and 60%-80% recovery of cells and nuclei. Those results were obtained on the MARS® with 0.8mL/min flow rate and three samples in parallel process. Samples before and after MARS® acoustic process were analyzed with both flow cytometry and imaging-based cell counter. The performance of “clean-up” of the acoustic process was compared to conventional Percoll based centrifugation method and showed significant advantage. The results of separating kidney cells/nuclei, lung cells/nuclei, as well as spleen cells also demonstrated high debris removal and cell recovery over several samples processed in multiple batches. MARS® sample preparation platform and its acoustic technology provide a powerful new tool for single cell preparation for expanded application of single cell genomics.

Citation Format: Liping Yu. Acoustic cell separation platform for efficient preparation of single cell/nuclei suspension from complex samples for genomics analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2943.
Abstract 2947: Surveying the tumor suppressive genetic network underlying chr4p deletion in TNBC
Authors: Corpo Joseph Del , Dandage Rohan , Harrington Lea , Kuzmin Elena
Published: June 2022

Triple negative breast cancer (TNBC) is a breast cancer subtype lacking targetable biomarkers, resulting in the worst prognosis compared to other breast cancer subtypes. TNBC is characterized by many large copy number variants that result in the deletion and amplifications of many genes, with TP53 being the only common oncogenic driver. Using TCGA data and in-depth functional genomic analysis of TNBC patient-derived xenografts (PDX), our group showed that chr4p is a recurrently deleted region in basal breast cancer, which TNBC is an enriched subtype. This correlated with poor prognosis and a highly proliferative state. Here, we set out to survey the tumor suppressive genetic network underlying the TNBC-specific chr4pdeletion. Using an arrayed CRISPR-enCas12 screening approach, I will generate a panel of mutant cell lines deleted for all protein-coding genes residing within chr4p. MCF10A series of cell lines will be used for mutant cell line construction, because it is an established normal human breast epithelial model system with a normal karyotype to ensure the diploid state ofchr4p and includes other derivatives (MCF10A(-E7-Bcl2)) that show basal anchorage independent growth in 3D to assess cell transformation. The resulting panel of single gene deletion mutant cell lines will be characterized for their effects on proliferation, apoptosis, cell transformation and senescence. Additionally, the tumor suppressive genetic interaction network of chr4p will be mapped using a multiplexed CRISPR-enCas12 screening methodology. A dual guide-RNA library will be generated for all protein-coding genes to test all pairwise combinations for tumor suppressive genetic interactions. The proliferation due to double gene deletions will be monitored and compared to single gene deletions to identify tumor suppressive interactions. This study will be the first to systematically identify tumor suppressor genetic network underlying chr4p. Ultimately, it will provide an in-depth understanding of the genetic network of large copy number variants in TNBC and insight into new avenues for precision oncology.

Citation Format: Joseph Del Corpo, Rohan Dandage, Lea Harrington, Elena Kuzmin. Surveying the tumor suppressive genetic network underlying chr4p deletion in TNBC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2947.
Abstract 2976: Associate Professor
Authors: Hua Fang , Hao Wenzhuo , Wang Lingyan , Li Shitao
Published: June 2022

Epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that instigates several signaling cascades, including NF-κB signaling pathway, to induce cell differentiation and proliferation. Overexpression and mutations of EGFR are found in up to 30% of solid tumors and correlate with a poor prognosis. Although it is known that EGFR-mediated NF-κB activation is involved in tumor development, the signaling axis is not well elucidated. Here, we found that plakophilin 2 (PKP2) and the linear ubiquitin chain assembly complex (LUBAC) were required for EGFR-mediated NF-κB activation. Upon EGF stimulation, EGFR recruited PKP2 to the plasma membrane, and PKP2 bridged HOIP, the catalytic E3 ubiquitin ligase in the LUBAC, to the EGFR complex. The recruitment activated the LUBAC complex and the linear ubiquitination of NEMO, leading to IκB phosphorylation and subsequent NF-κB activation. Furthermore, EGF-induced linear ubiquitination was critical for tumor cell proliferation and tumor development. Knockout of HOIP impaired EGF-induced NF-κB activity and reduced cell proliferation. HOIP knockout also abrogated the growth of A431 epidermal xenograft tumors in nude mice by more than 70%. More importantly, the HOIP inhibitor, HOIPIN-8, inhibited EGFR-mediated NF-κB activation and cell proliferation of A431, MCF-7, and MDA-MB-231 cancer cells. Overall, our study reveals a novel linear ubiquitination signaling axis of EGFR, and perturbation of HOIP E3 ubiquitin ligase activity is potential targeted cancer therapy.

Citation Format: Fang Hua, Wenzhuo Hao, Lingyan Wang, Shitao Li. Associate Professor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2976.
Abstract 298: Targeting KRAS mutant non-small cell lung cancer with EGFR aptamer displaying 3WJ pRNA nanoparticles
Authors: Yang Linlin , Li Zhefeng , Guo Peixuan , Williams Terence M.
Published: June 2022

Background and Purpose: KRAS mutations are one of the most common oncogenic mutations in human cancers, including non-small cell lung cancer (NSCLC), and have established roles in cancer pathogenesis and therapeutic resistance. Development of effective inhibitors of mutant KRAS represent a significant challenge. The field of three-way junction (3WJ) based RNA nanoparticles has advanced rapidly and shows promise as an effective in vivo siRNA delivery system. This aim of this study is to explore the potential of 3WJ-pRNA nanoparticles for specific and efficient delivery of KRASG12C siRNA to NSCLC cells harboring a KRASG12C mutation to effectively silence KRAS oncogenic activity.

Experimental design: Multifunctional EGFRapt-3WJ-siKRASG12C nanoparticles were prepared using bottom-up self-assembly approach, and characterized by agarose gel shift assay, dynamic light scattering (DLS), and temperature gradient gel electrophoresis system (TGGE). Three NSCLC cell lines, H2122 and H2030 carrying KRASG12C, and H1299 with wild type KRAS were used in this study. Binding specificity and delivery efficiency of EGFRapt-3WJ-siKRASG12C nanoparticles in NSCLC cells were evaluated in vitro and in vivo. Biological effects of KRAS mutant silencing were assessed by in vitro functional assays, and in vivo tumor xenograft experiments.

Results: Characterization of EGFRapt-3WJ-siKRASG12C by DLS showed 7.2 ± 0.5 nm average size, and TGGE indicated a melting temperature (Tm) of 51.77°C. Flow cytometry, IVIS lumina imaging assay, real-time quantitative PCR, western blot, and KRAS activity assay confirmed that EGFRapt-3WJ-siKRASG12C potently and selectively depleted cellular KRAS expression, resulting in suppression of downstream MAPK pathway signaling in KRASG12C NSCLC cells and in heterotopic tumor models. In addition, in vitro cell proliferation, migration/invasion, and chemotherapy and radiotherapy sensitivity assays, demonstrated that KRAS silencing by EGFRapt-3WJ-siKRASG12C suppressed NSCLC cell growth, migration/invasion ability, and sensitized NSCLC cells to chemotherapy or radiotherapy. In vivo, these nanoparticles led to regression of tumor growth in heterotopic models.

Conclusions: Together, this study suggests that 3WJ pRNA based platform has clinical potential to suppress mutant KRAS activity for the treatment of KRAS driven human cancers, and warrants further development.

Citation Format: Linlin Yang, Zhefeng Li, Peixuan Guo, Terence M. Williams. Targeting KRAS mutant non-small cell lung cancer with EGFR aptamer displaying 3WJ pRNA nanoparticles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 298.
Abstract 3032: Selenoprotein Sepp1 determines cysteine dependence in pancreatic cancer
Authors: Amer Arslan , Alothaim Tahiyat , Tang Xiaohu
Published: June 2022

Pancreatic cancer (PaCa) represents the fourth leading cause of overall cancer death, despite its relatively low incidence compared to other malignancies (Lung, prostate, breast, etc.). Approximately 57,600 people were estimated to be diagnosed with pancreatic cancer in the USA, and 47,050 were estimated to die of the disease in 2020 reported by The American Cancer Society. Novel effective therapeutic strategies are urgently needed. Metabolic changes are typically associated with tumor development to support fast cell proliferation and malignant transition. Such metabolic deregulations differentiate tumor cells from normal cells and act as potential targets of anticancer therapies. Previous studies have shown cysteine dependence often presents in various cancers, since cysteine metabolism supplies glutathione - an important substrate for the cellular reactive oxygen species (ROS) cleanup cycle. Studies in breast and kidney cancers have shown that such cysteine-dependence is a prominent feature in the cancer subtypes with a mesenchymal cell phenotype, instead of in the epithelial subtype. We found that cysteine dependence exists in pancreatic cancer as well. Mesenchymal PaCa cells, in contrast to the epithelial tumor cells, appear to be more sensitive to cysteine depletion with extensive induction of ferroptosis, a programmed cell death pathway involving iron and lipid peroxidation. Gene expression analysis revealed the selenium transporter protein Sepp1 to be absent in the mesenchymal PaCa cells. Knockdown of Sepp1 expression in cysteine-independent cells renders cells dependent on cysteine. Selenium is a micronutrient required for the synthesis of selenoproteins including GPX4 and Sepp1. The addition of selenium alleviated cell reliance on cysteine and caused resistance to GPX4 inhibitor-induced ferroptosis. We observed that Sepp1 regulates the thioredoxin pathway to rescue the cells under the glutathione deficiency. Interestingly, the conditioned media assay also revealed that Sepp1 protects cells from ROS stress by a symbiotic mechanism. Our findings suggest that Sepp1 could serve as a biomarker of tumor cysteine-dependency and a potential molecular target for therapeutic strategies to overcome drug resistance in pancreatic cancer.

Citation Format: Arslan Amer, Tahiyat Alothaim, Xiaohu Tang. Selenoprotein Sepp1 determines cysteine dependence in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3032.