bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1603: The effect of dickkopf-1 (DKK-1) on prostate cancer growth and bone metastasis using the canine osteoblastic Probasco cell line
Authors: Yuan Shiyu , Hoggard Nathan K. , Kantake Noriko , Hildreth Blake E. , Rosol Thomas J.
Published: April 2023

Osteoblastic bone metastasis is the predominant phenotype observed in advanced prostate cancer and is associated with high patient mortality and morbidity. WNT signaling is necessary for both bone formation and tumor progression. Dickkopf-1 (DKK-1), a secretory antagonist of the canonical WNT/β-catenin signaling pathway, plays a complex role in bone tumors since it can either promote or decrease tumor occurrence and metastasis. The present study explored the molecular role of DKK-1 in prostate tumor progression, metastasis, and tumor-bone interactions using the osteoblastic canine prostate cancer cell line, Probasco. Previously, we found that DKK-1 can inhibit bone mineralization of mouse calvaria by Probasco conditioned medium (CM). Now we stably expressed DKK-1 in Probasco cells (Probasco-DKK-1), which were injected into the tibias or left ventricle of athymic mice. Bone metastases were monitored by bioluminesent imaging, microCT, and histopathology. Our results showed that Probasco-DKK-1 bone metastases had increased tumor growth, increased osteoclastic bone resorption, and decreased intramedullary woven bone formation in vivo. In vitro, DKK-1 had an autocrine effect on Probasco cells, which altered the cell morphology, increased cell proliferation, and induced EMT. Mechanistically, DKK-1 had little effect on the canonical WNT/β-catenin signaling while dramatically down-regulated the non-canonical WNT/JNK signaling, which inhibited caspase-dependent apoptosis in Probasco-DKK-1 cells. To investigate the effect of Probasco-DKK-1 on bone cells, primary osteoblasts and osteoclasts were treated by CM collected from cancer cells. We found that DKK-1 did not inhibit the mineralization of osteoblasts nor stimulate the activity of osteoclasts directly, but the expression of RNAKL was significantly higher in Probasco-DKK-1 CM-treated osteoblasts. Therefore, the Probasco-DKK-1 cells enhanced the activity of osteoclasts indirectly via the regulation of osteoblasts, which induced bone resorption. In conclusion, we showed that DKK-1 promoted prostate tumor growth by stimulating cell proliferation and inhibiting apoptosis in a canonical WNT-independent manner and attenuated the osteoblastic activity of prostate cancer. These findings provide new insights into the molecular mechanisms of DKK-1 in tumor progression.

Citation Format: Shiyu Yuan, Nathan K. Hoggard, Noriko Kantake, Blake E. Hildreth, Thomas J. Rosol. The effect of dickkopf-1 (DKK-1) on prostate cancer growth and bone metastasis using the canine osteoblastic Probasco cell line [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 1603.
Abstract 1618: A highly selective and potent TLR8 agonist ZG0895 in preclinical studies of anti-tumor activities
Authors: Cui Dawei , Liu Ruifeng , Yang Huanyi , Zhu Bing , Sheng Zelin , Lv Binhua
Published: April 2023

Toll-like receptor 8 (TLR8) recognizes ssRNA fragments from pathogens and initiate both innate and adaptive immune responses. TLR8 activation can reverse Treg and myeloid-derived suppressor cells (MDSC) mediated immune suppression by tumors that lead to a restore of immune response to inhibit tumor growth. ZG0895 is a potent and novel TLR agonist that shows a highly selective activation of TLR8 and has a more than 300-fold potency over TLR7 in EC50 values. The agonist screening results further confirmed that ZG0895 without activation of TLR isoforms like TLR2, 4 or 9 in cells. In pharmacokinetics and pharmacodynamics, ZG0895 has a preferable ADME and PK profile and can activate immune system via subcutaneous (s.c.) administration. For in vivo anti-tumor efficacy studies, ZG0895 at 1~30 mg/kg exhibited significant dose-dependent inhibition of tumor growth in immunocompetent myeloid-sufficient murine models with CT26, EMT6 or HH subcutaneous xenografts. Furthermore, ZG0895 administration resulted in a complete tumor regression by ZG0895 at high dose via s.c. injection. Mechanism studies of ZG0895 in ex vivo human PBMC assay showed a strong induction of TLR8 related cytokines. In vivo study in tumor-bearing mouse demonstrated that pro-inflammatory cytokines, such as TNFα, IL12p40, IL6 and IL10, were quickly released after ZG0895 treatment but soon returned to normal that can avoid continuous activation of systemic immunity and reduce the risk of cytokine release storm. Consistently, in vivo cynomolgus monkey study by consecutive treatments with ZG0895 (day 30) resulted in a significant increase of immune system cells including intermediate monocytes, non-classic monocytes, cDCs and NK cells, along with notable decrease of classical monocytes but unchanged pDCs, suggesting a possible reversion of tumor-initiated MDSC via TLR8 activation. All these changes were back to normal after period of recovery (day 57), indicated the immune effect of ZG0895 was restrained. These preclinical results support that ZG0895 as a highly TLR8-selective agonist inhibits tumor growth via the activation of TLR8 eliciting immune responses but under a better safety than other conventional TLR8 agonists, and it is worth to be further explored as an anti-cancer drug candidate.

Citation Format: Dawei Cui, Ruifeng Liu, Huanyi Yang, Bing Zhu, Zelin Sheng, Binhua Lv. A highly selective and potent TLR8 agonist ZG0895 in preclinical studies of anti-tumor activities [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 1618.
Abstract 1730: A novel chimeric virus-like drug conjugate (VDC) for the potential treatment of HPV-positive tumors
Authors: Kines Rhonda C. , Savinainen Anneli , Pinos Elisabet de los , Schiller John T.
Published: April 2023

Introduction: Human papillomavirus (HPV) virus-like particles (VLPs) bind to a wide variety of tumor types via modified glycosaminoglycans (GAGs) found on the tumor cell surface. This finding led to the development of the investigational virus-like drug conjugate (VDC) belzupacap sarotalocan (bel-sar, formerly AU-011), an HPV-derived VLP conjugated to a light-activated cytotoxic payload. When activated by near-infrared light, bel-sar induced rapid tumor necrosis resulting in pro-immunogenic cell death, release of tumor neoantigens and long-term anti-tumor immunity in the TC-1 tumor model. When E6 and E7 expressing TC-1 mouse tumors were treated with the VDC, E7-specific T-cells were detected in the absence of provided tumor antigens. A novel chimeric VDC (cVDC) is now in development, in which E6 and E7 are fused to the L2 capsid protein as a means to potentially further enhance the observed anti-tumor response. This cVDC could allow for the targeted cytotoxicity of HPV-positive tumors in addition to the release of supplemental tumor antigens E6 and E7 within the now pro-immunogenic tumor milieu, potentially leading to a long term anti-tumor response.

Methods: The detoxified sequences of E6 and E7 were engineered as one fusion polypeptide on the C-terminus of the L2 minor capsid protein. Both L2/E6/E7 and L2/E7/E6 protein expression vectors were generated to determine if the order of the proteins impacted L2’s ability to co-assemble with L1, the major capsid protein. The plasmids were co-expressed alongside L1 using the mammalian 293TT expression system.

Results: Both the L2/E6/E7 and L2/E7/E7 fusion proteins were expressed and co-assembled with L1 into chimeric VLPs. Fusion protein expression was validated by western blots for L2, E6 and E7, and VLPs were confirmed by electron microscopy.

Conclusions: Preliminary data indicate that chimeric VDCs containing E6 and E7 can successfully be generated using the 293TT mammalian expression system. Studies evaluating the cytotoxicity and E6 and E7 immunogenicity of the cVDC as well as the impact on tumor targeting are underway.

Citation Format: Rhonda C. Kines, Anneli Savinainen, Elisabet de los Pinos, John T. Schiller. A novel chimeric virus-like drug conjugate (VDC) for the potential treatment of HPV-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 1730.
Abstract 1746: Broad-spectrum kinome profiling identifies CDK6 upregulation as a driver of lenvatinib resistance in hepatocellular carcinoma
Authors: Leung Carmen Oi , Yang Yang , So Karl Kam , Zhao Qian , Lee Terence Kin
Published: April 2023

Lenvatinib is the FDA-approved targeted drug for advanced hepatocellular carcinoma (HCC), but the efficacy is modest due to drug resistance. Tumor kinome re-wiring governs drug resistance in resistant cancer cells, which is an obstacle for efficient cancer therapy. Therefore, identification of the kinases critical for this rewiring process in HCC is crucial. Upon mass spectrometry analysis using a lysine-targeted sulfonyl fluoride probe named XO44, CDK6 was identified to be the most upregulated kinase in lenvatinib-resistant HCC cell lines. Lentiviral-based overexpression and knockdown approaches were performed to characterize functional roles of CDK6 in regulation of cancer stemness and lenvatinib resistance. The upregulation of CDK6 in lenvatinib-resistant HCC cells is found to be mediated by the ERK/YAP signaling cascade. CDK6 is crucial in the regulation of acquired lenvatinib resistance via augmentation of cancer stemness and the overexpression of CDK6 led to poorer patient survival. We identified a novel noncanonical pathway of CDK6 in which it binds and regulates the activity of GSK3β, leading to activation of the Wnt/β-catenin signaling pathway. CDK6 inhibition by CDK4/6 inhibitor palbociclib or CDK6 degradation by proteolysis targeting chimeras (PROTACs) is highly synergistic with lenvatinib in vitro. Interestingly, palbociclib not only exerts the maximal growth suppressive effect with lenvatinib in lenvatinib-resistant HCC xenografts and Trp53KO/MYCOE-induced HCC models but also reshapes the tumor immune microenvironment. CDK6 blockade impedes the lenvatinib-induced activation of the ERK/YAP/CDK6/β-catenin signaling cascade. Targeting CDK6 with palbociclib in combination with lenvatinib may be a novel therapeutic strategy against HCC.

Citation Format: Carmen Oi Leung, Yang Yang, Karl Kam So, Qian Zhao, Terence Kin Lee. Broad-spectrum kinome profiling identifies CDK6 upregulation as a driver of lenvatinib resistance in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1746.
Abstract 1769: A combination approach of a cellular library and single cell microfluidics analysis for the rapid selection of CAR-T cells
Authors: Boga Eren , Berger Luisa , De Roia Alice , Zörnig Inka , Embacher Robert , Eichmüller Stefan B. , Jäger Dirk , Harbottle Richard , Schmidt Patrick
Published: April 2023

Within the last decade CAR-T cells have changed the landscape of treatment regimen for leukemia and myeloma, which is reflected by the first FDA approval of this class of living drugs in 2017. As of today, the clinical trial situation aims on CAR-T applicability in solid tumors, which is more arduous due to antigen heterogeneity and limited CAR-T persistence. More personalized and multi-target oriented cellular products may offer a solution to overcome these problems but then CAR identification and selection display the major bottleneck in the drug development process. Usually, matching scFvs are selected from targeting screens of a phage-display library and hits are subsequently cloned in CAR backbones and tested for functionality and possible limiting factors as the occurrence of tonic signaling. This makes the whole process very time consuming and laborious. Within this project, we propose a novel CAR-T selection method that rapidly shortens the discovery procedure. We have developed a full length CAR library in nS/MARt DNA vectors that is electroporated in a Jurkat reporter cell line reflecting entirely its full diversity. By this, we can quickly identify the amount of tonic signaling CARs and exclude them from further selection. For on-target selection we first perform a bulk pre-selection followed by a single cell functionality screening using the Berkeley Lights Lightning™ device. This allows us to export hits as clonal viable cells that undergo long length Nanopore CAR-RNA sequencing. Our findings show the feasibility of our approach and that it can shorten the timeframe needed for the full selection process from weeks to days.

Citation Format: Eren Boga, Luisa Berger, Alice De Roia, Inka Zörnig, Robert Embacher, Stefan B. Eichmüller, Dirk Jäger, Richard Harbottle, Patrick Schmidt. A combination approach of a cellular library and single cell microfluidics analysis for the rapid selection of CAR-T 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 1769.
Abstract 178: Establishment of patient-derived organoid of breast cancer
Authors: Ryu Won-Ji , Park Shinyoung , Lee Jeong Dong , Hwang Yumi , Jo Seongyeon , Yong Kweon Tae , Koo Ja Seung , Kim Min Hwan , Sohn Joo Hyuk , Park Hyung Seok
Published: April 2023

A patient-derived organoid (PDO) is an in vitro three-dimensional model which shows similar features in phenotypic and genetic aspects with primary tissue from patients. PDOs are useful for preclinical studies including drug sensitivity tests of tumors from individual patients as well as development of novel targeted agents. Collectively, PDOs are recently introduced as an emerging platform for personalized medicine. We obtained a total of 100 surgical specimens from 100 patients with breast cancer at the Yonsei Cancer Center, Severance Hospital, Seoul, Korea. One of the tissue specimens was acquired from a breast cancer patient-derived xenograft model. We dissociated the tissues and isolated breast cancer primary tumor cells from the samples, and then the cells were cultured in basement membrane-like matrix in 3D manner with growth medium with supplements. We defined successful establishment of PDOs as continuous growth after 3 passaging. Among all 100 cases, 32 cases failed to culture or passage, however, 41 cases were successfully cultured over 3 passages. In addition, the remaining 27 cases are still in progress of establishment. Success rate of PDO was 68% (68/100). Subtypes of primary tumors of the PDO were 33.8% (23/68) of luminal A, 26.5% (18/68) of luminal B, 26.5% (18/68) of triple-negative, 5.9% (4/68) of triple-positive and 7.4% (5/68) of HER2-enriched. Success rates of each subtype were 69.7% (23/33) of luminal A, 72.0% (18/25) of luminal B, 66.7% (18/27) of triple-negative, 66.7% (4/6) of triple-positive and 55.6% (5/9) of HER2-enriched. Pathologic evaluation using immunohistochemistry revealed that PDOs showed similar morphologic and immunohistochemical features with primary tumors. The selective sensitivity of PARP inhibitor, olaparib, was confirmed in PDOs harboring mutant BRCA1/2 compared with BRCA1/2 wild-type PDOs. Overall, PDOs can be used as a real-time platform for drug sensitivity and screening analyses, and a robust tool for preclinical studies in breast cancer.

Citation Format: Won-Ji Ryu, Shinyoung Park, Jeong Dong Lee, Yumi Hwang, Seongyeon Jo, Kweon Tae Yong, Ja Seung Koo, Min Hwan Kim, Joo Hyuk Sohn, Hyung Seok Park. Establishment of patient-derived organoid of breast cancer [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 178.
Abstract 1793: Single-cell RNA analysis reveal effector-like CD8+ CAR-T cell subpopulations associated with response in lymphoma patients
Authors: Sarén Tina , Ramachandran Mohanraj , Gammelgård Gustav , Lövgren Tanja , Wikström Kristina , Hashemi Jamileh , Freyhult Eva , Mirabello Claudio , Björklund Åsa K , Ahlström Håkan , Amini Rose-Marie , Hagberg Hans , Loskog Angelica , Enblad Gunilla , Essand Magnus
Published: April 2023

Although CD19-targeting CAR T cell therapy has shown remarkable success against B cell malignancies there is still room for improvement. To improve long-term responses amongst lymphoma patients, mechanisms underlying initial response and tumor relapses must be addressed. Recent studies have highlighted the importance of the quality of the starting cell material for CAR T cell production and the composition of the CAR T cell infusion product for clinical response. In our study, we have evaluated the clinical response to third generation anti-CD19 CAR T cell therapy in 23 patients with B cell lymphoma. Further, we evaluated the CAR T cell infusion products using targeted single-cell RNA sequencing and multi-color flow cytometry to find potential T cell subsets associating with clinical response. Patients were divided into responders (CR + PR) and non-responders (SD + PD) at the 1-month follow-up after treatment. The CAR T cell products of both responding and non-responding patients were dominated by CD8+ CAR T cells. When comparing cells from the two patient groups we found that the presence of effector-like CD8+ CAR T cells with a high cytotoxic and cytokine secretion and low dysfunction gene expression profile were associated with clinical response. Furthermore, CD8+ CAR T cells of responders displayed a higher polyfunctional gene expression profile, which has previously been shown to associate with clinical response. In contrast, CD8+ CAR T cells from the infusion products of non-responders displayed an elevated dysfunction gene expression profile. Our study reveals that single-cell RNA expression analysis of individual CAR T cell infusion product can identify subsets of effector cells correlating with clinical response. This can be used as a guidance in the CAR T cell production processes, to obtain CAR T cells with the desired characteristics.

Citation Format: Tina Sarén, Mohanraj Ramachandran, Gustav Gammelgård, Tanja Lövgren, Kristina Wikström, Jamileh Hashemi, Eva Freyhult, Claudio Mirabello, Åsa K Björklund, Håkan Ahlström, Rose-Marie Amini, Hans Hagberg, Angelica Loskog, Gunilla Enblad, Magnus Essand. Single-cell RNA analysis reveal effector-like CD8+ CAR-T cell subpopulations associated with response in lymphoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1793.
Abstract 1800: An oral triple inhibitor of PI3Kδ/γ and DNA-PK elicits anticancer immunity and potentiates therapeutic efficacy of immune checkpoint blockade
Authors: Lee Seung Joon , Lee Won Suk , Go Eun-Jin , Yang Hannah , Kim Hong Ro , Kim Bong-Seog , Kim Chan , Chon Hong Jae
Published: April 2023

Background: PI3Kδ and PI3Kγ are mainly expressed in leukocytes, indicating that they are involved in immune modulation of the tumor microenvironment (TME). Additionally, DNA-dependent protein kinase (DNA-PK) plays a pivotal role as a mediator in repairing DNA damage in cancer cells. Here, we developed a triple inhibitor of PI3Kδ/γ and DNA-PK, BR101801, to promote antitumor immune responses and thereby enhance therapeutic efficacy of the PD-1 immune checkpoint inhibitor.

Methods: CT26 and MC38 colon tumor-bearing immunocompetent mice were treated with BR101801 (50 mg/kg, PO) daily and/or anti-PD-1 (8 mg/kg, IP) twice a week. The tumors were comprehensively analyzed using flow cytometry, multiplex tissue imaging, and NanoString profiling methods.

Results: Oral administration of BR101801 suppressed tumor growth without significant toxicities. The optimal schedule for BR101801 was determined by activation of T cell immunity in the TME. BR101801 monotherapy significantly increased CD8+ cytotoxic T cells and decreased CD4+CD25+Foxp3+ regulatory T cells, while no changes were observed in tumor-associated macrophages. Moreover, BR101801 increased AH-1+ tumor-specific CD8+ T cells within BR101801-treated CT26 tumors. BR101801 induced extensive immune remodeling of the TME by altering immune-related genes. Notably, gene signatures related to DNA damage and inflammatory responses were more enriched in BR101801-treated tumors. Furthermore, the combination immunotherapy of BR101801 and anti-PD-1 antibody strongly suppressed tumor growth and improved antitumor immunity within the TME, leading to complete tumor regression.

Conclusion: Our study demonstrates that BR101801, an oral triple inhibitor of PI3Kδ/γ and DNA-PK, effectively elicited anticancer immune responses within the TME and potently inhibited tumor progression in combination with immune checkpoint blockade.

Citation Format: Seung Joon Lee, Won Suk Lee, Eun-Jin Go, Hannah Yang, Hong Ro Kim, Bong-Seog Kim, Chan Kim, Hong Jae Chon. An oral triple inhibitor of PI3Kδ/γ and DNA-PK elicits anticancer immunity and potentiates therapeutic efficacy of immune checkpoint blockade [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 1800.
Abstract 1821: Discovery of XNW21015, a novel, potent HPK1 inhibitor with excellent immune modulatory activity
Authors: Wu Yuchuan , Hao Rui , Chen Xi , Liu Xiao , Xie Yonghua , Wang Shihua , Gao Bingquan , Wen Jichun , Wu Zhenwei , Wang Wengui , Wei Haiyang , Hu Yonghan , Liu Xiaojun , Le Meijie , Qiang Jing
Published: April 2023

Hematopoietic progenitor kinase 1 (HPK1), also known as MAP4K1, is a member of the STE20 family of serine/threonine kinases, and restrictedly expressed in hematopoietic cells. In T cells, HPK1 negatively regulated TCR signaling by phosphorylating the adaptor protein SLP76 on Ser376, which leads to the dissociation of the SLP-76/LAT signalosomes and downregulation of T cell priming and activation. HPK1 knockout (KO) or kinase-inactive (KI) mice spontaneously reject tumors with an enhanced immune response compared to wild-type ones. Thus, HPK1 is a novel immuno-oncology (I/O) target. In this work, we described the discovery of a potent HPK1 inhibitor starting from comprehensive SAR-based design with guidance from X-ray crystallography and computational modeling. These efforts led to identification of the potent azaindole inhibitor XNW21015, with excellent kinase selectivity and promising PK profile of low clearance and sufficient exposure for in vivo animal studies. XNW21015 dose-dependently inhibited phosphorylation of SLP76(Ser376) in vitro and in vivo in response to anti-CD3 agonist antibody, with concomitant enhancement in T cell activation. Oral administration of XNW21015 in mouse syngeneic tumor models showed favorable PK profile and robust anti-tumor activity as both single agent and in combination with immune checkpoint inhibitors. In a humanized PDX (patient-derived xenograft) model, XNW21015 enhanced tumor-infiltrated lymphocytes (TIL). In summary, we have discovered a novel, highly potent and selective HPK1 inhibitor XNW21015 as promising small molecule I/O agent, as monotherapy or in combination with immune checkpoint inhibitors.

Citation Format: Yuchuan Wu, Rui Hao, Xi Chen, Xiao Liu, Yonghua Xie, Shihua Wang, Bingquan Gao, Jichun Wen, Zhenwei Wu, Wengui Wang, Haiyang Wei, Yonghan Hu, Xiaojun Liu, Meijie Le, Jing Qiang. Discovery of XNW21015, a novel, potent HPK1 inhibitor with excellent immune modulatory activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1821.
Abstract 1876: NAV-001, a high-efficacy antibody-drug conjugate targeting mesothelin with improved delivery of potent payload by counteracting MUC16/CA125 effects
Authors: Grasso Luigi , Kline J. Bradford , Nicolaides Nicholas C.
Published: April 2023

Subsets of tumor-produced proteins, referred to as Humoral Immuno-Oncology (HIO) factors, can bind to IgG1 antibodies and suppress their immune-effector activities. Antibody-drug conjugates (ADCs) targeting tumor cell surface antigens can internalize and kill target cells upon liberation of their cytotoxic payload. Binding of the antibody component of an ADC by a HIO factor may potentially hamper the efficacy of a bound ADC. To assess any suppression of ADC’s activity by HIO factors, we evaluated the efficacy of a HIO-refractory ADC, NAV-001, and a HIO-bound ADC, SS1, both targeting mesothelin. The HIO factor MUC16/CA125 protein, which binds to SS1 ADC, was shown to have a negative effect on its internalization and tumor cell killing. The MUC16/CA125 refractory NAV-001 ADC was shown to have robust killing of tumor cells regardless of MUC16/CA125 expression in vitro (EC50 ~20 pM) as well as in vivo at single, sub-mg/kg dosing. Moreover, NAV-001-PNU, which contains the PNU-159682 topoisomerase II inhibitor as a payload, demonstrated good stability in vitro and in vivo as well as robust bystander activity against tumor and stromal cells not expressing the target antigen mesothelin, while maintaining a tolerable safety profile in vivo. Single-dose NAV-001-PNU demonstrated robust tumor regression of a number of patient-derived xenograft models from different tumor types regardless of MUC16/CA125 expression. These findings suggest that identification of HIO-refractory antibodies to be used in ADC format may improve therapeutic efficacy as observed for NAV-001 and warrants NAV-001-PNU’s advancement to human clinical trials as a monotherapy to treat mesothelin-positive cancers.

Citation Format: Luigi Grasso, J. Bradford Kline, Nicholas C. Nicolaides. NAV-001, a high-efficacy antibody-drug conjugate targeting mesothelin with improved delivery of potent payload by counteracting MUC16/CA125 effects [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 1876.
Abstract 1980: Integrating common and rare genetic variants to predict cancer risks in diverse populations
Authors: Elmas Abdulkadir , Kittrell Hannah , Huang Kuan-lin
Published: April 2023

Inherited germline genetic factors contribute substantially to cancer risk. Large-scale DNA-Sequencing (DNA-Seq) studies have identified rare pathogenic variants in 5~10% of adult cancer cases, while genome-wide association studies (GWAS) have revealed hundreds of common variants that require aggregation using polygenic risk scores (PRS). However, rare and common genetic variants are often assessed separately and prohibit accurate risk assessments. Here, we developed methods to combine common and rare variants for improved cancer risk predictions using the diverse Mount Sinai BioMe population cohort of 49,854 individuals, including 22% African Americans, 1.9% Asian, 34% Latinx/Hispanic, 32% Europeans, and 11% of Other self-reported ancestries. By linking and analyzing EHR data, we identified over 4,000 cancer cases and another 815 individuals with family history, and analyzed 14 solid tumor types with at least 50 cases with pass-QC whole-exome sequencing (WES) data. The landscape of pathogenic variants differs across ancestries and highlighted multiple founder variants, while PRSs predict cancer risks in major cancer types across different ancestries. Notably, we detect significant interactions of common and rare genetic variants contributing to risks of selected cancer types. Machine learning models that combine both common and rare variants show higher predictive accuracy than using common or rare variants alone. Overall, our study underscores the importance of jointly considering common and rare genetic factors to provide accurate cancer risk assessment for diverse individuals.

Citation Format: Abdulkadir Elmas, Hannah Kittrell, Kuan-lin Huang. Integrating common and rare genetic variants to predict cancer risks in diverse populations [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 1980.
Abstract 1990: Targeting cancer stem cells is an answer to the curing lung cancer
Authors: Song Keum-Soo , Nimse Satish Balasaheb , Kim Taisun
Published: April 2023

Lung cancer is the leading cause of cancer-related mortality worldwide. Mainly, non-small cell lung cancer (NSCLC, about 80% of cases) and small cell lung cancer (SCLC, about 20% of cases) are the major types of lung cancer. Adenocarcinoma (30-50%) and squamous cell carcinoma (30%) are the major subtypes of NSCLC. Even though there are considerable advancements in the drugs against lung cancer, the 5-year survival rate is meager. Unfortunately, the drug resistance for currently available anticancer drugs results in a 5-year survival of only 5%. The remarkable lung cancer recurrence despite definitive local and/or systemic therapy indicate that residual cancer stem cells (CSCs) possess tumorigenic potential. Therefore, drugs targeting the CSCs and killing them quickly can cure lung cancer without any relapse and improve the 5-year survival rate. Herein, we present the application of the recently reported ID-Checker technology (Journal of Medicinal Chemistry 2022 65 (19), 12883-12894) for killing lung cancer stem cells (LCSC). The ID-Checker that is decorated with the glucose tag allows highly specific absorption and macroscale delivery of anticancer drugs to the LCSC through the GLUT channels. ID-Checker inhibits the microtubule formation resulting in the cell cycle arrest in the G2/M phase followed by apoptosis. The inhibition of microtubule formation by ID-Checker also leads to the inhibition of GLUT channel deployment in the LCSC. Thus, the glucose-deprived LCSC undergoes apoptosis within 72 hours of ID-Checker treatment. Hence, we believe the ID-Check technology presented here can kill the LCSC and completely cure lung cancer.

Citation Format: Keum-Soo Song, Satish Balasaheb Nimse, Taisun Kim. Targeting cancer stem cells is an answer to the curing lung cancer [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 1990.
Abstract 2038: Epstein-Barr virus shapes the tumor microenvironment in classical Hodgkin lymphoma
Authors: Pourmaleki Maryam , Jones Caitlin J. , Mellinghoff Sabrina D. , Greenstein Brian , Kumar Priyadarshini , Roshal Mikhail , Hollmann Travis J. , Socci Nicholas D. , Dogan Ahmet , Mellinghoff Ingo K.
Published: April 2023

The histopathologic appearance of classical Hodgkin lymphoma (cHL) is characterized by rare multinucleated malignant Hodgkin Reed-Sternberg (HRS) cells within a rich inflammatory tumor microenvironment (TME). A subset of cHL cases are associated with Epstein-Barr virus (EBV) infection, which is considered to play a part in cHL pathogenesis. Since EBV+ and EBV- cHL exhibit differing mechanisms of pathogenesis, we hypothesized that the composition and spatial architecture of the TME in EBV-associated cHL differs from that of EBV- cHL, with implications for stratifying patients for specific treatment regimens based on EBV positivity. Here, we designed a multimodal approach using spatially resolved multiplexed protein profiling, flow cytometry, immunohistochemistry, and transcriptomics to profile EBV positive and EBV negative cHL tumors. We measured over 27 million single cells and 1,000 unique proteomic cell states derived using 29 proteins in addition to the transcriptome in 43 patient tumors. We uncovered significant differences between EBV+ and EBV- cHL in relative abundance of specific immune cell types, immune activation state, and spatial organization of the HRS cell neighborhoods. We present a multidimensional characterization of cHL in relation to EBV with implications for therapeutic stratification of patients with virus-associated cHL.

Citation Format: Maryam Pourmaleki, Caitlin J. Jones, Sabrina D. Mellinghoff, Brian Greenstein, Priyadarshini Kumar, Mikhail Roshal, Travis J. Hollmann, Nicholas D. Socci, Ahmet Dogan, Ingo K. Mellinghoff. Epstein-Barr virus shapes the tumor microenvironment in classical Hodgkin lymphoma [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 2038.
Abstract 2039: Predicting abundance and expression of immune cells in patients’ head & neck tumor microenvironment from blood single-cell transcriptomics
Authors: Cao Yingying , Chang Tiangen , Schischlik Fiorella , Sinha Sanju , Wang Kun , Jiang Peng , Ruppin Eytan
Published: April 2023

The tumor microenvironment (TME) is a key determinant of immunotherapy efficacy, yet, not readily accessible. Here, we ask if the immune cell fractions (ICFs) and gene expression patterns in the TME can be predicted from the blood single-cell RNA sequencing (scRNA-Seq) data. To the best of our knowledge, the immune status of the TME has not been comprehensively evaluated and predicted from the blood previously. Addressing this challenge, we analyzed 26 paired head and neck squamous cell carcinoma (HNSCC) patients matched blood and tumor samples with CD45+ scRNA-Seq data and clinical information. We developed a machine learning predictor of ICFs and gene expression levels of major immune cell types in the TME from the matching blood transcriptomics and pertaining clinical information, termed the Tumor Immune MicroEnvironment Predictor (TIMEP). We find that the ICFs, all 11 major immune cell types in the TME were predictable from the blood. 17-47% genes expressed in different immune cells were predictable from the blood, with the highest coverage in dendritic cells and helper, cytotoxic and regulatory T cells. Furthermore, the ICF ratio (ICFR) signature of (Treg - Bmemory)/(Treg + Bmemory) in the TME, as predicted from the blood, can robustly predict the response to immune checkpoint blockade (AUC > 0.72 on three independent single-cell and bulk expression datasets). These results are the first to demonstrate the feasibility of employing single-cell transcriptomics liquid biopsy to predict the immune status in patients TME in patients, facilitating future personalized cancer precision therapy.

Citation Format: Yingying Cao, Tiangen Chang, Fiorella Schischlik, Sanju Sinha, Kun Wang, Peng Jiang, Eytan Ruppin. Predicting abundance and expression of immune cells in patients’ head & neck tumor microenvironment from blood single-cell transcriptomics [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 2039.
Abstract 2055: Prevalent focal amplification of oncogene in lung adenocarcinomas without canonical driver alterations
Authors: Park Seongyeol , Lim Joonoh , Yi Kijong , Yi Boram , Kim Ryul , Koo Jaemo , Na Kwon Joong , Park Samina , Park In Kyu , Kang Chang Hyun , Lee Jeong Seok , Ju Young Seok , Kim Young Tae
Published: April 2023

Lung adenocarcinoma (LADC) is the most common type of lung cancer and a leading cause of death worldwide. Typical oncogenes that drive LADCs when mutated (referred to as canonical drivers) include EGFR (30-60%), KRAS (10-30%), and fusion oncogenes (~10%) involving ALK, RET, and ROS1. However, approximately 30% of lung adenocarcinomas lack canonical drivers, implying unseen kinds of genomic alterations. Here, we explore alterations beyond the scope of canonical drivers in LADCs (referred to as non-canonical drivers) using large-scale whole-genome sequencing (WGS) of LADCs. We gathered total 183 WGS of LADCs, 138 of which were from our previous study (Lee et al. Cell. 2019) and 45 were newly sequenced from surgically resected LADCs. For raw data processing, we used a standard WGS analysis pipeline from read mapping to variant calling. Variant filtering and downstream analyses were performed using in-house scripts. Genomic variants analyzed in this study include single-base substitution (SBS), indel, structural variation (SV), and copy number variation (CNV). As a result, we found that 53 cases (29%) had no canonical drivers (ND group). Intriguingly, LADCs without canonical drivers had a contrasting genomic landscape compared to LADCs with canonical drivers (CD group). First, the point-mutation burden was ~3-fold higher in the ND group than in the CD group (52,500 vs. 17,900 for SNVs, p<0.001). Mutational signature analysis revealed that these additional mutations are attributable mainly to tobacco smoking (by mutational signature SBS4) and APOBEC-mediated mutagenesis (SBS12 and SBS13) and that they are more enriched in the ND group (4,800 vs 2,600, p=0.03). Second, the ND group harbored more frequent focal amplifications. Recurrently amplified genes include TERT, IL7R, NKX2-1, CCND1, CCND3, CCNE1, and EGFR. The pattern of SVs suggest that the amplifications occurred through the formation of extra-chromosomal DNA involving multiple chromosomes or following chromothripsis. Overall, this study broadens our understanding of non-canonical drivers of LADCs. Similar analyses of thousands of cancers with clinical information of the patient will likely yield the functional impact of these driver mutations and may offer more opportunities for LADC treatment in the future.

Citation Format: Seongyeol Park, Joonoh Lim, Kijong Yi, Boram Yi, Ryul Kim, Jaemo Koo, Kwon Joong Na, Samina Park, In Kyu Park, Chang Hyun Kang, Jeong Seok Lee, Young Seok Ju, Young Tae Kim. Prevalent focal amplification of oncogene in lung adenocarcinomas without canonical driver alterations [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 2055.
Abstract 2060: The exploratory analysis of dysregulated transcription factor FOXC1 in pan-cancer
Authors: Brown Alanna , Wu Zexun , Cao Huan , Falzarano Sara M. , Buxbaum Sarah G. , Rhie Suhn K.
Published: April 2023

FOXC1 is a transcription factor that is reported to play a key role in the development of cancer. For example, we showed that epigenetic dysregulation of FOXC1 is associated with meningioma progression. Moreover, we reported that FOXC1 is overexpressed in drug-resistant bladder cancer cells. To further characterize the molecular mechanisms of FOXC1 in carcinogenesis of different cancer types, we analyzed DNA-seq and RNA-seq datasets of over 30 cancer types generated from The Cancer Genome Atlas (TCGA) and Oncology Research Information Exchange network (ORIEN) consortia, using cBioportal. cBioportal is a tool that is used to visualize and analyze large-scale cancer genomic data. When we analyzed whole exome sequencing and DNA array datasets to search genetic alterations such as mutation, amplification, and deletion events that occur in the FOXC1 gene, we revealed that over 10 cancer types have genetic alterations. By analyzing RNA sequencing datasets through the cBioportal, we found that more than 10 cancer types have overexpression of FOXC1. Unlike TCGA, ORIEN has generated whole exome sequencing and RNA sequencing datasets from cancer patients who are treated. We are currently in the process of analyzing ORIEN data to determine FOXC1 alterations and its association with drug resistance in different cancer types. Moreover, we are evaluating the relationship between FOXC1 dysregulation and cancer patient survival. Overall, this analysis will denote the key role that FOXC1 plays in different cancer types and supply valuable knowledge for drug resistance.

Citation Format: Alanna Brown, Zexun Wu, Huan Cao, Sara M. Falzarano, Sarah G. Buxbaum, Suhn K. Rhie. The exploratory analysis of dysregulated transcription factor FOXC1 in pan-cancer [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 2060.
Abstract 2087: Sherlock-Genome: a R shiny app for genomic analysis and visualization
Authors: Klein Alyssa , Landi Maria Teresa , Zhang Tongwu
Published: April 2023

Over the last few decades, next generation sequencing technologies, including whole genome sequencing (WGS), have been increasingly used in cancer genomics studies. However, there is no efficient way to manage, visualize and integratively analyze sample-level WGS results across different bioinformatic pipelines, particularly for non-bioinformaticians. This greatly limits the usability of WGS data for biological discovery. Following the FAIR principles (findability, accessibility, interoperability, and reusability), we developed Sherlock-Genome, a R Shiny app designed for data harmonization, visualization and integrative analyses for WGS-based cancer genomics studies. Specifically, Sherlock-Genome provides pipelines for WGS analyses coupled with detailed guidelines on data preparation. The users can download the pipelines on their local computer, run the analyses and then upload the sample-level results into the Sherlock-Genome for data harmonization and integrative analyses across different genomic features. Sherlock-Genome also implements rigorous WGS-related data QC steps based on NGSpurity, a workflow that estimates the tumor purity, ploidy and clonal architecture by integrating somatic copy number alterations (SCNA), single nucleotide variants (SNV) and cancer cell fraction. Currently, Sherlock-Genome includes a few independent modules that allow users to generate a variety of interactive data inspection and visualization images, and perform many integrative analyses also using clinical and epidemiological data. These modules include study information and sample-level data QC (study overview, manifest information, NGSpurity), summaries of major genomics alterations (mutations, SCNA, structural variants), reports of advanced genomics analyses (mutational signatures, genomic landscape, clonal evolution) and functions related to different types of integrative analyses (survival analysis, integrative analysis). In addition, all plots in the Sherlock-Genome app can be downloaded as publication-ready figures from each module. Sherlock-Genome can be deployed in both local and cloud environments, allowing users to share sample-level analytical results together with the related publications. Sherlock-Genome has the potential to be widely used in cancer genomics allowing sample-level integrative analyses across multiple WGS and additional multi-omics features. A Sherlock-Genome demo with major module functions could be presented to allow users to know about this new interactive user-friendly tool for data analysis and visualization that can greatly advance biological discoveries.

Citation Format: Alyssa Klein, Maria Teresa Landi, Tongwu Zhang. Sherlock-Genome: a R shiny app for genomic analysis and visualization [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 2087.
Abstract 2228: Genome-wide mapping of SMYD3 in HPV-negative head and neck squamous cell carcinoma
Authors: Saeed Abbas , Sevilla Samantha , Saloura Vassiliki
Published: April 2023

HPV-negative head and neck squamous cell carcinoma (HNSCC) carries a particularly poor prognosis and novel therapeutic targets are thus urgently needed. We recently found that SET and MYND domain-containing 3 (SMYD3), a protein methyltransferase which has been reported to regulate global levels of trimethylated H3K4 (H3K4me3), an activating mark, and H4K20 (H4K20me3), a repressive mark, is overexpressed in HPV-negative HNSCC. Furthermore, we found that SMYD3 depletion impaired the colony formation capacity, cell cycling and the proliferation of HPV-negative HNSCC cell lines. Additionally, SMYD3 KO cell lines demonstrated decreased migratory potential. Accordingly, NSG xenograft mouse models of SMYD3 KO cell lines exhibited significantly decreased tumor growth compared to a parental HPV-negative HNSCC cell line. Based on the above preliminary results, this study aims to elucidate the specific mechanism(s) through which SMYD3 regulates the proliferative and migratory capacity of HPV-negative HNSCC cells. Nuclear/cytoplasmic fractionation of a panel of HPV-negative HNSCC cell lines showed that SMYD3 is expressed both in the nuclear as well as the cytoplasmic compartments. siRNA-mediated knockdown of SMYD3 for 6 days induced A 40% decrease in global H3K4me3 and more than 80% decrease in global H4K20me3 levels. Genome-wide mapping of SMYD3, H3K4me3 and H4K20me3 was pursued using CUT&RUN assays in parental and SMYD3 KO cell lines. The GoPeaks software was utilized to call significant peaks affected by 30% (p.adj<0.05). 515 genes were annotated to H3K4me3 peaks and were found to have significantly decreased H3K4me3 peaks with concordant mRNA downregulation by more than 30%. 185 genes were annotated to H4K20me3 peaks and were found to have significantly decreased H4K20me3 peaks with concordant mRNA upregulation by more than 30%. Amongst these genes, cell cycle regulators and EMT genes were identified. SMYD3 peaks were called successfully and analysis of its genome-wide mapping is ongoing, with particular focus on cell cycle and EMT genes. To assess whether SMYD3 regulates the global H3K4me3 and H4K20me3, mass spectrometry analysis in SMYD3 KO cells has been conducted and analysis is ongoing. Validation of candidate genes directly regulated by SMYD3, H3K4me3 and H4K20me3 is planned by qPCR and Western blotting. This study is the first to report genome-wide mapping results of human SMYD3, and provides mechanistic insights into the oncogenic function of SMYD3 in HPV-negative HNSCC.

Citation Format: Abbas Saeed, Samantha Sevilla, Vassiliki Saloura. Genome-wide mapping of SMYD3 in HPV-negative head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2228.