bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4420: Carbohydrate-CD11b engagement enhances differentiation of tumor-associated myeloid cells in immunotherapy of solid cancers
Authors: Zhang Mei
Published: June 2023

Background: Methods to perturb tumor-associated myeloid cell function are being actively pursued to overcome these challenges in immunotherapy and search for a cure. CD11b is a potential therapeutic target to modulate suppressive myeloid derived cells and induce tumor-reactive T-cell responses. However, CD11b can bind to multiple carbohydrate ligands that trigger a variety of myeloid cell functions like adhesion, migration, and even phagocytosis and proliferation. This has created a major challenge to understand the molecular basis by which CD11b converts differences in receptor-ligand binding into subsequent immune signaling responses, and to use this knowledge for therapeutic development.

Methods: This study investigated a previously reported carbohydrate ligand, BG34-200, that showed anti-tumor effect through modulating CD11b+ cells. Applying modern approaches of peptide microarray, multi-parameter FACS analysis, cellular/molecular immunological technology, advanced microscopic imaging, and transgenic mouse models of solid cancers, we studied the BG34-200-CD11b carbohydrate-protein engagement and immunological changes it triggered in the context of solid cancers including osteosarcoma, melanoma and pancreatic cancer.

Results: Our results show that BG34-200 can mediate direct, specific, multi-site and multivalent binding to integrin CD11b to trigger cellular differentiation in a suppressive tumor-associated myeloid cell subset. In melanoma, osteosarcoma, and pancreatic cancer, we detected this rare myeloid cell subset in blood, which displayed an inflammatory monocyte phenotype and exhibited immunosuppressive behavior. BG34-200-CD11b engagement could induce differentiation of these tumor-associated inflammatory monocytes into dendritic cells by inducing phagocytosis that effectively trigger F-actin cytoskeletal rearrangement and intrinsic ICAM-1 clustering important for antigen presentation and effector T cell stimulation.

Conclusions: Our findings improve understanding of molecular basis by which CD11b converts difference in carbohydrate ligands into subsequent immune signaling responses, may lead to development of safe and novel therapies modulating myeloid derived cell function for immunotherapy of solid cancers.

Citation Format: Mei Zhang. Carbohydrate-CD11b engagement enhances differentiation of tumor-associated myeloid cells in immunotherapy of solid cancers. [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 4420.
Abstract 4425: GlycoConnect™ immune cell engagers (GC™-ICEs). A non-genetic approach to targeted IL-15 immunotherapy
Authors: van Geel Remon , van Delft Floris
Published: June 2023

Engagement of T cell or NK cells to harness a patient’s immune system is a promising approach in immuno-oncology. An immunocytokine, i.e. a tumor-targeting antibody (fragment) genetically fused to an immunostimulatory cytokine, is specifically designed for this purpose. Fusion antibody-IL-15 immunocytokines, based on a variety of molecular architectures, are currently finding their way to the clinic with promising results.

Here we demonstrate how GlycoConnect™, a site-specific conjugation technology anchoring on the native antibody glycan, can be applied for attachment of IL-15 without prior antibody engineering. Moreover, the immunostimulatory activity of these GlycoConnect™ immune cell engagers (GC™-ICEs) can be modulated by tailoring linker design and payload stoichiometry. In particular, we demonstrate how a protease-cleavable mAb-IL-15 conjugate can be used to prevent systemic activation of the immune system, leading to a significantly improved therapeutic index in rodent models. In vitro and in vivo studies will be presented to showcase the biological activity of these GC™-ICEs in comparison to conventional immunocytokines obtained via genetic engineering.

Citation Format: Remon van Geel, Floris van Delft. GlycoConnect™ immune cell engagers (GC™-ICEs). A non-genetic approach to targeted IL-15 immunotherapy. [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 4425.
Abstract 4432: A highly differentiated A2AR inhibitor for potential use in cancer therapy
Authors: Venkateshappa Chandregowda , Narayanan Kishore , Nair Rashmi , AB Aravind , Putta Ramakishore VP , Nagaraj Jwala , Goyal Megha , Ahuja Vijay Kamal , Dhudashiya Amith A , DS Samiulla , Daginakatte Girish , Antony Thomas , Nellore Kavitha , Samajdar Susanta , Ramachandra Murali
Published: June 2023

As a potent immunosuppressor adenosine is essential for maintaining tissue homeostasis and preventing an overzealous immune response during inflammation and infection. However, adenosine generated within the tumor microenvironment by the action of ectonucleotides hinders the immune reaction towards cancer cells by signaling through adenosine receptors such as high affinity A2AR expressed on immune cells. Tumors evade the immune response by usurping pathways that negatively regulate normal immune responses. Resistance to inhibition of immune checkpoint targets arises because of an upregulation in the expression of the CD39-CD73 axis and the resulting increase in production of adenosine in the tumor microenvironment. Inhibition of either adenosine generation or signaling by inhibition of A2AR along with other immune activation strategies have been shown to be effective therapeutic approaches.

In view of this, we sought to discover and develop novel small molecule inhibitors that dually target A2AR and an immuno-suppressive ligand expressed in the tumor microenvironment. Aurigene’s dual inhibitors exhibit potent inhibition of both A2AR and an immuno-suppressive target of relevance in respective biochemical assays. Potent biochemical activity translated into rescue of chemokines and IL-2 in human PBMCs. Lead compounds exhibited desirable drug-like properties and excellent pharmacokinetic exposure in rodents. In a syngeneic tumor model, lead compounds demonstrated significant tumor growth inhibition. Anti-tumor efficacy correlated well with tumor drug levels and modulation of pharmacodynamic markers. In summary, we have identified first-in-class dual inhibitors with good drug like properties, which showed significant antitumor efficacy. Evaluation of these lead compounds in additional tumor models and in vivo toxicity studies will be presented.

Citation Format: Chandregowda Venkateshappa, Kishore Narayanan, Rashmi Nair, Aravind AB, Ramakishore VP Putta, Jwala Nagaraj, Megha Goyal, Vijay Kamal Ahuja, Amith A Dhudashiya, Samiulla DS, Girish Daginakatte, Thomas Antony, Kavitha Nellore, Susanta Samajdar, Murali Ramachandra. A highly differentiated A2AR inhibitor for potential use in cancer therapy. [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 4432.
Abstract 4434: A PD-1-targeted, receptor-masked IL-2 immunocytokine with maintained potential to engage endogenous IL-2Ra drives selective stimulation of PD-1+ T cells and robust anti-tumor efficacy
Authors: Wu Jiaxi , Bloch Nicolin , Chang Aaron , Bhavsar Ramandeep , Patel Supriya , Wang Qingqing , Ahmed Hassan Shakil , Garg Vidur , Amatulli Michael , Yan Yuetian , Wang Shunhai , Dudgeon Drew , Ramos Willy , Krueger Pamela , Rafique Ashique , Huang Tammy , Ullman Erica , Hermann Aynur , Olson William , Lin John , Smith Eric , Zhang Tong
Published: June 2023

Interleukin-2 (IL-2) is a key cytokine for T cell proliferation, differentiation, and effector function. Recombinant IL-2 has been used for the treatment of metastatic melanoma and renal cell carcinoma, and induced complete, durable tumor regression in some patients. ​However, its broader use in cancer immunotherapy has been limited by severe toxicity. A new generation of IL-2 therapies with decreased binding to IL-2 receptor α-chain (IL-2Rα) is being developed to reduce toxicity and Tregs expansion yet with limited clinical success so far. Here, we show that the ability to engage IL-2Rα is critical for maximal anti-tumor activity of a systemic IL-2 therapy, and an alternative approach to circumvent systemic toxicity is to deliver IL-2 specifically to tumor-reactive T cells. We developed REGN10597, a PD-1-targeted, receptor-masked IL-2 immunocytokine with attenuated systemic IL-2 activity but maintained capacity to engage endogenous IL-2Rα on PD-1+ T cells. Compared to WT IL-2, receptor masked IL-2 shows improved PK and diminished systemic toxicity in mice. REGN10597 shows PD1-targeting-dependent IL-2 activity in vitro and drives selective expansion of tumor-infiltrating PD-1+ CD8 T cells with vigorous effector functions in vivo. In preclinical syngeneic tumor models in PD-1 humanized mice, REGN10597 demonstrates robust anti-tumor efficacy both as a single agent and in combination with PD-1 or PD-L1 blocking antibodies. These findings highlight the therapeutic potential of REGN10597 as a novel targeted and receptor masked WT IL-2 therapy, supporting its clinical development for the treatment of cancer.

Citation Format: Jiaxi Wu, Nicolin Bloch, Aaron Chang, Ramandeep Bhavsar, Supriya Patel, Qingqing Wang, Hassan Shakil Ahmed, Vidur Garg, Michael Amatulli, Yuetian Yan, Shunhai Wang, Drew Dudgeon, Willy Ramos, Pamela Krueger, Ashique Rafique, Tammy Huang, Erica Ullman, Aynur Hermann, William Olson, John Lin, Eric Smith, Tong Zhang. A PD-1-targeted, receptor-masked IL-2 immunocytokine with maintained potential to engage endogenous IL-2Ra drives selective stimulation of PD-1+ T cells and robust 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 4434.
Abstract 445: A next generation TEAD inhibitor with refined isoform specificity for superior safety & efficacy
Authors: Muller Florian , Baloglu Erkan , Morley Andrew D. , Chakravarti Deepavali , Kunnimalaiyaan Selvi , Gyruis Jeno , Shacham Sharon
Published: June 2023

The Hippo pathway is an important regulator of cell proliferation and one of the last major oncogenic pathways not yet extensively targeted in precision oncology. The Hippo pathway is executed by the YAP1/TAZ (WWTR1) co-activators and the TEAD family of transcription factors, which consists of four paralogs (TEAD1-4) with both redundant and unique functions. The transcriptional targets of TEADs include genes playing tumor-promoting roles, including pro-proliferative, immunosuppressive, and anti-apoptotic genes. A growing body of research points to the central importance of the Hippo pathway as a key driver of oncogenesis and as key resistance mechanism to inhibitors of the MAPK pathway or its upstream activators, such as receptor tyrosine kinases. Sporos BioDiscovery has developed novel inhibitors that reversibly bind to the palmitoylation site of TEAD transcription factors to block Hippo pathway activity. Sporos BioDiscovery’s internal bioinformatic insights were leveraged to fine tune the inhibitory activity against the four TEAD paralogs, to maximize efficacy and minimize toxicity. Key characteristics of the SPR1 TEAD inhibitors: (i) low nM, single-agent activity against multiple TEAD-dependent cell lines in vitro in established Hippo-pathway hyperactive mesothelioma cell lines as well as in several non-mesothelioma, cell lines without any obvious lesions in the upstream components of the Hippo pathway. (ii) activity against multiple tumor models in vivo with tumor regression observed even in large established tumors, a feat not previously reported with any other TEAD inhibitor. (iii) strong interactions with inhibitors of the MAPK pathway and inhibitors of its upstream activators, such as RTKs. (iv) favorable ADME profile in rodents, dogs and NHPs, as well as a favorable safety profile. In sum, SPR1 presents monotherapy opportunities in ultra-responder populations based on internal bioinformatic insights, while broader potential exists as an adjuvant for precision oncology targeted therapies, particularly within the MAPK pathway and its upstream activators.

Citation Format: Florian Muller, Erkan Baloglu, Andrew D. Morley, Deepavali Chakravarti, Selvi Kunnimalaiyaan, Jeno Gyruis, Sharon Shacham. A next generation TEAD inhibitor with refined isoform specificity for superior safety & 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 445.
Abstract 4458: Single cell landscape of multicentric Castleman disease in identical twins
Authors: Chan Jason Yongsheng , Loh Jui Wan , Lim Jing Quan , Liany Herty , Lee Elizabeth Chun Yong , Lee Jing Yi , Kannan Bavani , Lim Boon Yee , Lim Kerry , Ha Jeslin Chian Hung , Ng Cedric Chuan-Young , Ko Tun Kiat , Huang Dachuan , Seow Dominique Yuan Bin , Cheng Chee Leong , Chan Sock Hoai , Ngeow Joanne , Teh Bin Tean , Lim Soon Thye , Ong Choon Kiat
Published: June 2023

Idiopathic Multicentric Castleman Disease (iMCD) is a rare IL-6-driven hematological disorder characterized by systemic lymphadenopathy, elevated immunoglobulin levels, and prominent plasmacytosis in the bone marrow and lymph nodes. An unusual occurrence of iMCD in identical twins provided a unique opportunity to answer genetic and molecular features of this disease, including the cell-of-origin of IL-6 signals, and the immune milieu within affected lymphoid organs and in circulation. Germline whole genome sequencing of the affected twins identified pathogenic homozygous mutations of NCOA4 c.G1322A and monoallelic mutations of TRAF3 c.G1504A - both genes recently implicated in IL-6 signaling and B-cell regulation. Their unaffected sister was heterozygous mutant for NCOA4 and homozygous wildtype for TRAF3 loci. Via single cell sequencing of 63,519 cells from bone marrow, lymph node, and peripheral blood mononuclear cells, we identified nodal endothelial cells and fibroblastic reticular cells (FRC) as the source of IL-6 signals. The latter are composed of mainly T-cell zone FRCs (CCL19+/CCL21+/IL7+/PDPN+/MADCAM1-) and a minor population of follicular dendritic cells (FDCs) (CD21+/CD35+/CXCL13+). An “inflammatory” peripheral monocytosis enriched for the expression of S100A family genes was evident in both twins, as well as a group of monocytes expressing cytotoxic gene signatures in the affected twin with milder clinical manifestations. Their unaffected sister mainly carried monocytes enriched for expression of major histocompatibility complex (MHC) class II genes. In conclusion, we provided evidence of a genetic cause of iMCD, identified the putative cell-of-origin of IL-6 signals in this rare disease, and described a distinct monocytic immune response phenotype.

Citation Format: Jason Yongsheng Chan, Jui Wan Loh, Jing Quan Lim, Herty Liany, Elizabeth Chun Yong Lee, Jing Yi Lee, Bavani Kannan, Boon Yee Lim, Kerry Lim, Jeslin Chian Hung Ha, Cedric Chuan-Young Ng, Tun Kiat Ko, Dachuan Huang, Dominique Yuan Bin Seow, Chee Leong Cheng, Sock Hoai Chan, Joanne Ngeow, Bin Tean Teh, Soon Thye Lim, Choon Kiat Ong. Single cell landscape of multicentric Castleman disease in identical twins. [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 4458.
Abstract 4743: Wnt/beta-catenin mediated epigenetic modifications drive age-dependent oral squamous cell carcinoma evolution
Authors: Fisher Emily R. , Spinella Anthony , Hardy Nina C. , Varelas Xaralabos , Bais Manish , Kukuruzinska Maria A.
Published: June 2023

Oral Squamous Cell Carcinoma (OSCC) is a devastating disease associated with high morbidity, poor survival, and few therapeutic options. This malignancy is driven, in part, by epigenetic reprogramming of the chromatin landscape directed by β-catenin in complex with CREB-binding protein (CBP) and mixed lineage leukemia methyltransferase 1 (MLL1). The β-catenin/CBP/MLL1 complex promotes an open chromatin structure by enabling transcription of genes associated with cell plasticity, including cancer stem cells and cells with partial EMT (p-EMT) phenotypes. Growing evidence indicates that cell plasticity and cellular senescence are integral processes shared by cancer and aging. Given that the median age of OSCC diagnosis is 66 years, it is likely that aging promotes OSCC evolution to advanced disease.

To examine the effects of aging on OSCC evolution, we adapted a syngeneic mouse model of tobacco-associated oral carcinogenesis. This model utilizes a mouse cell line, 4MOSC1, derived from 4-nitroquinoline-1 oxide- (4NQO)-induced tongue tumor which, when implanted into mouse tongues, generates tumors that recapitulate human OSCC mutanome. The growth of 4MOSC1 derived orthotopic tumors was studied in 6- and 80-week-old mice. Tumors were allowed to develop for 18 days, after which they were harvested and processed for single cell RNA sequencing, histopathology and immunofluorescence (IF) analyses.

Results showed that tumors grew at a faster rate and to a greater overall size in old mice compared to their young cohorts. OSCC harvested from the old mice displayed statistically significant reduction in membranous E-cadherin concomitant with increased Cbp and H3K4me3 abundance, suggesting an age-associated upregulation of β-catenin/Cbp/Mll1 epigenetic activity. Increased expression of Bmi1, keratin 14, and podoplanin supported increased cell plasticity in OSCC from aged mice. Further, these tumors exhibited augmented cellular senescence, as judged by the disruption of lamin B1-associated nuclear membrane integrity, and by an increased cell population with markers of senescence from single cell sequencing analyses.

These data suggest that aging is associated with increased β-catenin/Cbp/Mll1 epigenetic signaling, cell plasticity and cellular senescence, which collectively contribute to the evolution of OSCC.

Citation Format: Emily R. Fisher, Anthony Spinella, Nina C. Hardy, Xaralabos Varelas, Manish Bais, Maria A. Kukuruzinska. Wnt/beta-catenin mediated epigenetic modifications drive age-dependent oral squamous cell carcinoma evolution. [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 4743.
Abstract 4844: Development of an oxygen consumption rate assay for a standard plate reader
Authors: Marozas Ian , Zeng Zhiyang , Valley Mike , Vidugiriene Jolanta , Cali James , Zhou Wenhui
Published: June 2023

Cells generate ATP by two metabolic pathways, oxidative phosphorylation (OXPHOS) and glycolysis. Together, the amount of ATP generated by both OXPHOS and glycolysis define a cell’s metabolic phenotype and fitness. Researchers are interested in methods to characterize cellular metabolic fitness, which can be a powerful a selection criterion for cell-based therapies such as CAR-T cell therapy. Researchers are also interested in measuring the effects of drug treatment on metabolic fitness, to identify metabolic targets for cancer therapeutics and to determine mitochondrial toxicity of novel therapeutics. Here, we have developed a low-cost strategy for a standard plate reader to monitor the rate change of oxygen concentration, or the oxygen consumption rate (OCR), which is a measure of OXPHOS activity. In our assay, oxygen quenches a phosphorescent porphyrin dye in a concentration dependent manner, allowing one to calculate the oxygen concentration of the culture system with the Stern-Volmer relationship. The porphyrin dye is embedded within nanobeads that are suspended above the cell monolayer and the phosphorescence of the beads is measured from the bottom of the well with a standard plate reader. We found that the OCR increased with cell seeding density in three separate cell lines: HEP-G2, HCT-116, and K-562 suspension cells. We showed that inhibitors of the electron transport chain (ETC) decreased OCR, whereas an uncoupler of the electron transport chain, FCCP, increased OCR in a dose dependent manner. Lastly, mitochondrial fitness (e.g., spare respiratory capacity) was determined by sequentially dosing the mitochondria with poisons specific to the different ETC complexes.

Citation Format: Ian Marozas, Zhiyang Zeng, Mike Valley, Jolanta Vidugiriene, James Cali, Wenhui Zhou. Development of an oxygen consumption rate assay for a standard plate reader. [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 4844.
Abstract 4846: Mitochondria packaged from platelet-derived microvesicles modulate the metabolism and mitochondrial dynamics of breast cancer cells
Authors: Gauvin Vanessa L. , Veilleux Vanessa , Pichaud Nicolas , Robichaud Gilles A. , Boudreau Luc H.
Published: June 2023

The incidence of breast cancer among women far exceeds those of other cancers where metastasis accounts for the majority of deaths associated with the disease. It is well established that platelets play a prominent role in breast cancer malignancy and disease progression. Recently, activated platelets have been characterized to release platelet-derived microparticles (PMPs), which can also package functional mitochondria of platelet origin (termed mitoMPs). We recently demonstrated that mitoMPs can interact with breast cancer cells where they transfer their cargo (i.e., mitochondria) to recipient cancer cells upon their internalization. Given that metabolic reprogramming through mitochondrial dynamics represents a hallmark trait of cancer progression, the intercellular trafficking of foreign mitochondria provided by mitoMPs represent a new mechanistic avenue for cancer cell metabolic plasticity and disease progression.Therefore, the aim of this study was to evaluate the impact of mitoMP-packaged mitochondria on recipient breast cancer cell mitochondrial dynamics upon internalization. Technically, a series of breast cancer cell models (MB231, MCF7 and MCF10A) were co-cultured with mitoMPs and profiled for mitochondrial dynamics and function using complementing experimental approaches, such as flow cytometry, confocal microscopy, and RT-qPCR. We show that mitoMPs and their mitochondria cargo internalize primarily into the malignant MB231 cell model. To investigate the impact of mitoMP uptake by cancer cells on the mitochondrial dynamics, RT-qPCR and Western blot analyses were performed to profile the expression levels of several fusion and fission proteins, including OPA1, MFF, DRP1, MitoFusin 1 and MitoFusin 2. Finally, using fluorescent-based assays, we confirmed that mitoMPs modulated ATP production in MB231 breast cancer cells through upregulation of the OXPHOS pathway. Our research provides a new mechanism by which extracellular vesicles (mitoMPs) play an important role in cancer cell mitochondrial dynamics and function to support metabolic plasticity during the metastatic journey of cancer cells. The knowledge gained from these studies will further provide new avenues for strategic intervention to mitigate the morbidity and mortality associated with breast cancer disease.

Citation Format: Vanessa L. Gauvin, Vanessa Veilleux, Nicolas Pichaud, Gilles A. Robichaud, Luc H. Boudreau. Mitochondria packaged from platelet-derived microvesicles modulate the metabolism and mitochondrial dynamics of breast 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 4846.
Abstract 5018: PROTAC degraders of CDK8/CDK19 Mediator kinases potently suppress multiple myeloma proliferation
Authors: Zhang Li , Li Jing , Dowling Charles E. , Broude Eugenia V. , Roninson Igor B. , McInnes Campbell , Chen Mengqian
Published: June 2023

CDK8 and CDK19 are kinase components of the CDK module that comprises CDK8 or CDK19 together with their binding partner cyclin C (CCNC) and two other proteins; the CDK module is associated with transcriptional Mediator complex. CDK8/19 Mediator kinases potentiate transcription induced by different signals, regulate protein levels of Mediator complex components and protect CCNC from proteolytic degradation; the latter activity is exerted in a kinase-independent manner. CDK8/19 kinase inhibitors have entered clinical trials for solid tumors and leukemias. To extend the effects of CDK8/19 inhibition and to suppress their kinase-independent activities, we have developed three series of PROteolysis TArgeting Chimeras (PROTACs) based on different selective inhibitors of CDK8/19 kinases, connected via different linkers to a moiety binding cereblon (CRBN) E3 ligase. The most potent PROTACs degraded both CDK8 and CDK19 in different cell types with DC50s of 10-20 nM. RNA-Seq analysis of 293 cells treated with a CDK8/19 kinase inhibitor or PROTAC showed that the bulk of the PROTAC’s transcriptomic effects matched the effects of the kinase inhibitor. In contrast to the kinase inhibitors, CDK8/19-degrading PROTACs also induced CCNC degradation. Cancer Dependency Map (DepMap) analysis revealed that multiple myelomas (MM), where CRBN is an established therapeutic target, show greater dependency on CCNC than most of the tumor cell lines. We have tested two strongly CCNC-dependent MM cell lines and one CCNC-independent MM line for sensitivity to different CDK8/19 kinase inhibitors and PROTACs. Kinase inhibitors showed low to moderate anti-proliferative activity in all three MM lines, whereas CDK8/19 PROTACs were an order of magnitude more potent than the kinase inhibitors in the two CCNC-dependent MM lines (IC50s of 20-30 nM) but not in the CCNC-independent line. The effects of CDK8/19-degrading PROTACs were stronger than those of the CRBN-targeting drug pomalidomide (approved for MM), a CRBN-binding PROTAC acting on androgen receptor or a CDK8 degradation-inactive PROTAC analog containing CDK8/19- and CRBN-binding moieties. These results suggest the potential of CDK8/CDK19-degrading PROTACs for the treatment of MM.

Citation Format: Li Zhang, Jing Li, Charles E. Dowling, Eugenia V. Broude, Igor B. Roninson, Campbell McInnes, Mengqian Chen. PROTAC degraders of CDK8/CDK19 Mediator kinases potently suppress multiple myeloma proliferation. [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 5018.
Abstract 5021: Preclinical evaluation of immunomodulatory effects of aurora kinase inhibition in HPV+ cancers
Authors: Sinha Pragya , Ghosh Soma , Johnson Faye M. , Sastry Jagannadha K.
Published: June 2023

Human papillomavirus (HPV) is the causative agent of cervical cancer and some cancers of the penis, vulva, vagina, anus, and oropharynx. In an earlier study, we identified Aurora Kinase (AK) inhibitors from a large-scale drug screening as a unique class of reagents to induce selective apoptosis in HPV+ human tumor cells in vitro and in vivo (using HPV+ PDX mouse models). We tested the in vivo efficacy of alisertib, an Aurora Kinase A inhibitor, in an immunocompetent mouse model (mEER) for HPV+ oropharyngeal cancers. In preparation for this, we first tested 300 nM alisertib on 3 HPV+ murine cancer cell lines: TC-1, C3.43, and mEER for 48h. We observed that when compared to the vehicle (DMSO) control group, the level of phospho Aurora Kinase A was completely inhibited. Furthermore, in multiple HPV+ murine tumor cell lines we observed significant apoptosis as measured by annexin V 7-AAD staining along with higher cell surface expression of calreticulin (CRT), and high mobility group box 1 protein (HMGB1) which are markers for immunogenic cell death (ICD). Both CRT and HMGB1 serve as “eat me” signals that in turn trigger APC-mediated dead-cell antigen uptake, a crucial event for priming the responses from the innate immune system. In support of this, we observed that in a co-culture setting, the conditioned medium from alisertib-treated tumor cells increased the frequencies of CD8+ cells expressing GnzB as well as a significant decrease in the population of T regulatory cells (Tregs) (CD4+ FoxP3+). Additionally, we observed an increase in the innate immune natural killer cell subset. Future studies will explore the in vivo efficacy of Aurora Kinase inhibition along with immune checkpoint blockade and/or therapeutic vaccination. Our proposed research will have a positive impact because we will gain insight into the immune responses underlying the co-dependency of HPV+ cancers on Aurora kinase. Our research may lead to an increase in the rates of long-term, durable clinical responses or may allow for therapy de-escalation.

Citation Format: Pragya Sinha, Soma Ghosh, Faye M. Johnson, Jagannadha K. Sastry. Preclinical evaluation of immunomodulatory effects of aurora kinase inhibition in HPV+ cancers. [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 5021.
Abstract 522: Selective estrogen receptor a-UPR activators (SERA): a novel class of small molecules that eradicate estrogen receptor positive tumors
Authors: Mulligan Michael P. , Boudreau Matthew W. , Shapiro David J. , Fan Timothy M. , Hergenrother Paul J. , Barnhart Kerry , Azorsa David , Kiefer Jeff , Mousses Spyro
Published: June 2023

While therapy of estrogen receptor alpha positive (ERα+) breast cancer is often initially successful with ERα modulating or inhibiting drugs, eventual drug resistance is universal and such treatments are rarely curative. To address this considerable medical need, several generations of novel anti-tumor small molecule agents specifically targeting the estrogen-ERα interaction have been synthesized and characterized. We are pursuing an alternative approach, activation of an endogenous cell death pathway downstream of ERα with non-competitive Selective Estrogen Receptor Activators (SERAs). These compounds exhibit their effects by dysregulating calcium homeostasis in ERα+ tumor cells leading to hyper-activation of the anticipatory unfolded protein response (a-UPR) and necrotic cell death, a mechanism distinct from current breast cancer therapeutics. These molecules cause increases in P-EIF2a and P-AMPK, and cleavage of ATF6α, which are all hallmarks of the hyper-activation of a-UPR. SERA molecules cause death of ERα+ breast cancer cells in culture with 24hr IC50 values in the low nanomolar range, including breast cancer cell lines harboring ERα mutations known to contribute to acquired ERα modulator therapy resistance, while IC50 values in ERα-negative cells are orders of magnitude higher. In the MCF-7 ERα+ breast cancer xenograft model, once weekly IV injections of SERA2 at 10mg/kg cause durable, complete tumor regression, and SERA2 also has impressive activity in a challenging-to-treat PDX model that is resistant to fulvestrant and tamoxifen. SERAs are well-tolerated after multiple intravenous injections in mice, rats, and dogs, and clinical trial-compatible formulations have been developed. These findings suggest that SERA molecules can address the important unmet clinical need for more effective therapies for patients with ERα+ tumors who progress on conventional SERM, SERD, and targeted therapies.

Citation Format: Michael P. Mulligan, Matthew W. Boudreau, David J. Shapiro, Timothy M. Fan, Paul J. Hergenrother, Kerry Barnhart, David Azorsa, Jeff Kiefer, Spyro Mousses. Selective estrogen receptor a-UPR activators (SERA): a novel class of small molecules that eradicate estrogen receptor positive tumors [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 522.
Abstract 5284: Recurrent Middle Eastern differentiated thyroid carcinoma has worse outcome than persistent disease
Authors: Parvathareddy Sandeep K. , Siraj Abdul K. , Annaiyappanaidu Padmanaban , Siraj Nabil , Ahmed Saeeda O. , Qadri Zeeshan , Azam Saud , Al-Kuraya Khawla S.
Published: June 2023

Background: Differentiated Thyroid Cancer (DTC) is the most common endocrine malignancy. Despite its excellent prognosis, recurrent and persistent disease remain major challenges after initial treatment. Although most studies have considered persistence and recurrent as a single entity, emerging studies to differentiate recurrent and persistent disease are controversial and study on recurrent and persistent DTC from Middle Eastern ethnicity is lacking.

Methods: We retrospectively analyzed 1822 patients who underwent surgery ± I131 treatment for DTC with a median age of 38.9 years and median follow-up of 90 months.

Results: We found a similar prevalence rate of persistent and recurrent disease (16.4% vs. 16.6%) in Middle Eastern DTC patients. Relative to patients with persistent disease, patients with recurrent disease were significantly older (median age 36.1 vs. 45.8 years; p < 0.0001), were more likely to have ATA high risk tumors (p < 0.0001) and had a higher rate of distant metastasis (p < 0.0001). However, structural disease had an almost similar frequency in both recurrent and persistent disease (72.2% vs 73.3%). On multivariant logistic regression analysis, both T status and N status are independent predictors for both recurrent and persistent disease. However, older age, extrathyroidal extension and the presence of distant metastasis were independent predictors of only recurrent disease. In addition, patients with recurrent disease had significantly worse overall survival (OS; p < 0.0001) and cancer specific survival (CSS; p < 0.0001), which remained significant in multivariate Cox proportional hazard model (Hazard ratio = 2.72; 95% confidence interval = 1.20 - 7.01; p = 0.0153 for OS and Hazard ratio = 5.09; 95% confidence interval = 2.10 - 15.24; p = 0.0001 for CSS).

Conclusion: Although persistent and recurrent disease in Middle Eastern DTC have similar frequencies, recurrent disease had worse outcome compared to persistent disease. This has great potential clinical relevance to differentiate recurrene from persistence for therapeutic and follow-up approach for improving outcomes of DTC patients from Middle Eastern ethnicity.

Citation Format: Sandeep K. Parvathareddy, Abdul K. Siraj, Padmanaban Annaiyappanaidu, Nabil Siraj, Saeeda O. Ahmed, Zeeshan Qadri, Saud Azam, Khawla S. Al-Kuraya. Recurrent Middle Eastern differentiated thyroid carcinoma has worse outcome than persistent disease. [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 5284.
Abstract 5353: Graph representation learning of tumor topology from spatial imaging data
Authors: Ceglia Nicholas , Freeman Samuel S. , Pourmaleki Maryam , McPherson Andrew , Shah Sohrab P.
Published: June 2023

Recently, novel technologies have enabled spatially resolved multiplexed protein profiling of tumors; however, there is an unmet need for unbiased detection of spatial structures within the tissue. By encoding multiplexed images as a graph, we produce an efficient and well-studied graph representation that allows for the application of sophisticated machine learning methods, particularly graph neural networks (GNNs) and graph autoencoders (GAE). While GNNs have recently become popular tools in the analysis of spatial data, current GNN methods are limited by production of cell-level representations rather than graph-level representations. To understand patterns of local tissue structure and protein expression, we implemented a generalizable GAE framework that summarizes marker intensity and morphological values with the local topology of neighboring cells. In this way, each local cellular graph is represented as a single point in the lower dimensional space. We show that our framework generates low-dimensional features that reflect both cellular attributes and tissue structure. We demonstrate that clustering local structure in 318 fields of view from 22 tumor lesions across 7 patients with in-transit melanoma captured using multiplexed immunofluorescence (mpIF) can produce spatial motifs predictive of response to intralesional interleukin-2 (IL-2) immunotherapy. Additionally, we applied our framework to mpIF data of 146 high grade serous ovarian cancer tumors across 50 patients. We identify clusters with higher CD8+ T cell infiltration that associate with homologous recombination deficiency. Our method can be readily applied to various spatially resolved multiplexed imaging platforms, and the resulting embeddings provide a compressed representation of subgraphs that can be used in further classification or regression analysis of patient- and/or image-level histological, clinical, or genomic labels.

Citation Format: Nicholas Ceglia, Samuel S. Freeman, Maryam Pourmaleki, Andrew McPherson, Sohrab P. Shah. Graph representation learning of tumor topology from spatial imaging data. [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 5353.
Abstract 5365: Extracting novel knowledge from scientific literature to build a web portal for cancer researchers to keep up with the latest scientific discoveries
Authors: Pan Feng , Zhang Yuan , Sui Xin , Sun Donghu , Chung Menghan , Zhang Jinfeng
Published: June 2023

Millions of new papers are published in biomedical sciences every year. In many disciplines, it has become impossible to read all the published new papers to learn what is happening in the frontier of a particular area. This gap is widening as the publishing speed has been accelerating in recent years. To address this challenge, one can convert unstructured text data into a structured form, which can then support highly accurate information retrieval, information integration, and automated knowledge discovery. A plausible approach for such a task is to use named entity recognition (NER) and relation extraction (RE) methods to identify important biological entities and extract their relations to construct knowledge graphs (KGs). The LitCoin Natural Language Processing (NLP) Challenge was recently organized by NCATS of NIH and NASA to spur innovation by rewarding the most creative and high-impact uses of biomedical text to create KGs. In addition to entities and relations, the manually annotated LitCoin dataset also contains the annotations of relations being new discoveries or background knowledge. Our team participated in the challenge and ranked first place. The novelty prediction model of our pipeline has achieved an F1 score of 0.90. We have applied our model to all the PubMed abstracts published previously and the newly published ones to extract the novel discoveries in each article. A web portal has been created to allow scientists to view the latest discoveries in cancer research. The web portal is updated daily with versatile visualization tools for cancer researchers to quickly grasp the latest discoveries in a particular area. It also offers powerful functions to explore the existing literature and make sophisticated inferences about causal and indirect relationships.

Citation Format: Feng Pan, Yuan Zhang, Xin Sui, Donghu Sun, Menghan Chung, Jinfeng Zhang. Extracting novel knowledge from scientific literature to build a web portal for cancer researchers to keep up with the latest scientific discoveries. [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 5365.
Abstract 5366: Constructing the largest-scale biomedical knowledge graph using all PubMed articles and its application in automated knowledge discovery
Authors: Zhang Yuan , Pan Feng , Sui Xin , Sun Donghu , Chung Menghan , Zhang Jinfeng
Published: June 2023

The number of biomedical publications is growing at an accelerated speed. This ever-increasing amount of scientific literature has made reading all the published articles regularly impossible even for a very specific research area. A solid grasp of existing literature is essential for coming out with novel and plausible scientific ideas. To bridge the gap between the published scientific findings and our incapability of manually processing them, we need to convert the unstructured text into structured form to enable automated methods to use the structured, machine-readable information to generate novel hypotheses, which can then be manually validated. A plausible approach for converting unstructured text into structured form is to use named entity recognition (NER) and relation extraction (RE) methods to identify the biological entities and extract their relations to construct knowledge graphs (KGs). KGs can link concepts within existing research to allow researchers to find connections that may have been difficult to discover without them. The LitCoin Natural Language Processing (NLP) Challenge was recently organized by NCATS of NIH and NASA to spur innovation by rewarding the most creative and high-impact uses of biomedical, publication-free text to create KGs. Our team participated in the challenge and ranked first place. Using the pipelines developed for the LitCoin NLP challenge, we have constructed the largest-scale biomedical KG using all PubMed articles. We further develop advanced deep-learning methods to predict new links from the constructed KG. We demonstrate the power of this new framework using several examples important for drug discovery.

Citation Format: Yuan Zhang, Feng Pan, Xin Sui, Donghu Sun, Menghan Chung, Jinfeng Zhang. Constructing the largest-scale biomedical knowledge graph using all PubMed articles and its application in automated knowledge discovery. [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 5366.
Abstract 5390: Robust prediction of pan-cancer immune checkpoint blockade response using machine learning
Authors: Chang Tiangen , Dhruba Saugato R. , Cao Yingying , Morris Luc G. , Ruppin Eytan
Published: June 2023

Immune checkpoint blockade (ICB) has revolutionized our approach to cancer treatment. However, the response rate is still low. With the accumulation of data, efforts to use these data to build machine learning predictors of ICB response are rising. However, as most datasets are still quite small, pertaining machine learning models may often ‘overfit’ the data, i.e., have a much weaker performance on independent test data than on the data they were learned upon. Here we analyzed ~2000 patient samples from multiple cohorts across 16 solid tumor types. Based on 10 genomic & clinical features, we built different machine learning models, comparing their performance in terms of the Area Under ROC Curve (AUC) and importantly, in terms of the AUC difference between training vs validation sets, using a standard cross validation procedure. As a result, the Linear LASSO Regression (LLR) model outperformed all other models by having the highest AUC on the validation set (0.74) and notably, the smallest AUC difference between training and validation sets (0.02). In contrast, these two AUC values for the FDA approved tumor mutational burden (TMB) biomarker are 0.63 and 0.03. The highest predictive features were, receiving chemotherapy before ICB treatment or not, TMB, cancer type, blood albumin level, blood neutrophil-to-lymphocyte ratio, and patient age. The LLR score also consistently predicted overall survival and progression-free survival across all individual cancer types. More importantly, ICB response probability increased near-monotonically from 0% to > 43% with the LLR score, which is an important feature for patient exclusion. In contrast, ICB response probability is ~25% when TMB = 0 and not always higher with higher TMB. In summary, the LLR model identifies key features predicting pan-cancer ICB response and survival. The use of combined genomic and clinical features holds potential to further facilitate clinical ICB patient stratification beyond TMB.

Citation Format: Tiangen Chang, Saugato R. Dhruba, Yingying Cao, Luc G. Morris, Eytan Ruppin. Robust prediction of pan-cancer immune checkpoint blockade response using machine learning. [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 5390.