bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB133: An orally bioavailable degrader targeting androgen receptor and the splice variant in castration resistant prostate cancer
Authors: Hung Chiu-Lien , Wang Ling-Yu , Fu Chih-Wei , Hsu Hung-Chih , Kung Hsin-Jien
Published: April 2023

The development and progression of prostate cancer depends on androgen receptor (AR) whose sustained activity albeit the use of anti-androgen drugs accounts for one of the major mechanisms leading to drug resistance. As such, the clinical benefits of current therapeutic agents remain rather limited for the advanced prostate cancer. Given that expression of constitutively active AR variants (AR-Vs) that lack the ligand-binding domain (LBD) clinically associates with the drug resistance and poor survival, targeting both AR and the LBD-truncated AR-Vs is anticipated an effective approach to overcome therapy resistance. Here, we present Proteolysis Targeting Chimeras (PROTAC) compound ITRI-148, capable of effectively degrading both full-length and LBD-truncated AR by targeting the proteins via the N-terminal domain to Cereblon-mediated ubiquitination and degradation. Degradation of AR and AR-V7 suppresses target gene expression, and inhibits cell proliferation with accompanied apoptosis activation in AR-V7-expressing castration-resistant prostate cancer (CRPC) cell models. In vivo, this compound displays good pharmacokinetics profiles and oral bioavailability with strong antitumor efficacy towards castration-, enzalutamide-resistant CWR22Rv1 and VCaP xenograft models. These data provide compelling evidence that by targeting AR NTD for induced degradation of active AR protein variants, ITRI-148 is a promising agent for the intervention of advanced therapy-resistant prostate cancers.

Citation Format: Chiu-Lien Hung, Ling-Yu Wang, Chih-Wei Fu, Hung-Chih Hsu, Hsin-Jien Kung. An orally bioavailable degrader targeting androgen receptor and the splice variant in castration resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB133.
Abstract LB151: Exploring the tumor microenvironment in a spatial context with SpaCET
Authors: Ru Beibei , Huang Jinlin , Zhang Yu , Aldape Kenneth , Jiang Peng
Published: April 2023

Uncovering the composition and structure of the tumor microenvironment is critical to a mechanistic understanding of tumorigenesis and therapeutic resistance. Spatial transcriptomics (ST) technology has enabled profiling the molecular features of tumor tissue with position information. However, the spatial probe of various ST strategies with a 10~100 μm diameter might capture a mixture of transcripts from multiple cells or cell lineages. Cell type deconvolution in ST data of tumor tissues remains challenging for existing methods, which are designed to decompose general ST or bulk data. We develop the Spatial Cellular Estimator for Tumors (SpaCET) to infer cell identities from tumor ST data. Without the need of inputting cell references, SpaCET estimates malignant and non-malignant cell abundance by using a gene pattern dictionary of copy number alterations in common malignancies and a hierarchical atlas of immune/stromal cells, respectively. SpaCET provides higher accuracy than existing methods based on eight ST datasets on seven cancer types with matched double-blind histopathology annotations as ground truth. Furthermore, SpaCET can reveal the potential intercellular interactions at the tumor-immune interface by integrating inferred cell fractions with the ligand-receptor interaction network. We expect that SpaCET will be a valuable tool for spatial cancer biology.

Citation Format: Beibei Ru, Jinlin Huang, Yu Zhang, Kenneth Aldape, Peng Jiang. Exploring the tumor microenvironment in a spatial context with SpaCET [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB151.
Abstract LB159: Deregulation of CTC-associated RPL/RPS protein expression inhibits melanoma brain metastasis
Authors: Bowley Tetiana Yuriyivna , Merkley Seth , Lagutina Irina , Marchetti Dario
Published: April 2023

Melanoma brain metastasis (MBM) is associated with poor prognosis and low survival rates. MBM is diagnosed clinically in up to 60% of melanoma patients and in up to 80% of patients at autopsy. Circulating Tumor Cells (CTCs) are “seeds” of fatal metastasis and the smallest functional units of cancer. Our previous studies have employed a multilevel approach to identify a common CTC signature for ribosomal protein large/small subunits (RPL/RPS) which is linked to MBM development and progression1. Here, we hypothesized that targeting ribosomal biogenesis prevents MBM onset in CTC-derived xenografts. First, we treated CTC-injected MBM mice with RPL15 inhibitor omacetaxine to monitor metastatic progression. Second, parallel cohorts of mice were treated with CDK4/CDK6 inhibitor palbociclib with or without omacetaxine to assess effects of cell proliferation. Total flux of MBM signal was measured by IVIS and found to be higher in untreated mice. Mouse necropsies revealed decreased levels of MBM, along with metastatic dissemination to other organs. Third, collected mouse blood was analyzed by the FDA-approved ParsortixTM platform to enumerate CTC/CTC clusters (IHC), and evaluate their gene expression (RNA-seq). Lastly, metabolic profiling of inhibitor-treated versus untreated MBM CTC-derived clones was performed in vitro. Collectively, our findings indicate that the deregulation of ribosomal proteins inhibits MBM progression. This implicates a specific vulnerability of aggressive CTC subsets with high RPL/RPS content in MBM patients. RPL/RPS genetic screening could be a prognostic indicator of MBM severity and clinical outcomes. Our work promotes the concept that therapies targeting RPL/RPS proteins merit exploration as potential suppressors of metastatic progression in general, MBM in particular. 1. Bowley T, Lagutina I, Francis C, Sivakumar S, Selwyn R, Taylor E, et al. The RPL/RPS gene signature of melanoma updates CTCs associates with brain metastasis. Cancer Research Communications 2022;2: 1445-57.

Citation Format: Tetiana Yuriyivna Bowley, Seth Merkley, Irina Lagutina, Dario Marchetti. Deregulation of CTC-associated RPL/RPS protein expression inhibits melanoma brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB159.
Abstract LB177: Tumor sideomics: spatial characteristics and functional deregulation in colorectal cancer
Authors: Burgman Brandon , Pan Xingxin , Yi S. Stephen
Published: April 2023

Clinical evidence suggests that right-sided colorectal cancer (CRC) tends to have a worse prognosis compared to left-sided CRC. The distinct functional mechanisms underlying this “sidedness” remain cryptic and poorly understood. Thus, molecular classification of CRC is of paramount in targeting specific subtypes and personalizing treatment for patients. To identify targetable molecular features to improve treatment regimens, we performed multi-faceted network analyses of hundreds of CRC patients. In our network model, epigenetic features, differential expression of transcript abundance, and mutational frequency were used to identify widespread gene dysregulation and perturbed pathways to reveal disrupted networks distinct to right or left sided colorectal cancer. We discovered histone related genes and distinct epigenetic signals are at play in right-sided CRC. Additionally, our studies reveal “at risk” patient characteristics suggestive of survival differences, to improve diagnostic predictors based on CRC sidedness. Overall, our integrative approach serves to link molecular profiles distinct between left and right sided colorectal cancer, while improving upon previous models of CRC and paving the way towards identifying more effective treatment alternatives from a previously overlooked, readily characterized subtype of colorectal cancer.

Citation Format: Brandon Burgman, Xingxin Pan, S. Stephen Yi. Tumor sideomics: spatial characteristics and functional deregulation in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB177.
Abstract LB182: Targeting arginine methylation for improved therapy in triple negative breast cancer
Authors: Li Yang , McGrail Daniel J. , Awasthi Sharad , Yi S. Stephen , Bedford Mark T. , Sahni Nidhi
Published: April 2023

Since the discovery of DNA repair deficiency as risk factors for breast cancer, our knowledge of their function in maintaining human genomic integrity and a normal biological function has greatly advanced, ultimately culminating in development of PARP inhibitors that can specifically target patients who harbor these mutations. However, to date PARP inhibitors have demonstrated only modest clinical success as monotherapy in triple-negative breast cancer. In addition, conventional therapies are often coupled with severe toxicity. Therefore, there is a dire need to develop more effective combination therapies. Although there are many existing tools to predict possible actionable targets, it remains challenging to effectively and systematically identify drug combinations for better breast cancer therapeutics. This is because most tumors carry multiple genetic alterations that cannot be suppressed with mono-therapies; and diverse confounding factors such as intra-tumor and inter-tumor heterogeneity exist across patient populations. Our preliminary proteomics study has revealed a new protein mark called arginine methylation as a novel target for breast cancer. We found that inhibition of arginine methylation can sensitize cancer cells for PARP inhibition treatment. We further assessed and validated this actionable and synergistic drug combination in patient-derived xenograft models. Together, our novel target combinations discovered here may serve as important biomarkers to help develop more effective combination therapy. Furthermore, our results help uncover patient-specific signaling mechanisms, a critical step towards precision medicine in breast cancer therapy, which is a benefit and potential long-term outcome.

Citation Format: Yang Li, Daniel J. McGrail, Sharad Awasthi, S. Stephen Yi, Mark T. Bedford, Nidhi Sahni. Targeting arginine methylation for improved therapy in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB182.
Abstract LB194: A small molecular-weight anti-lag-3 peptide inhibits colon tumor growth
Authors: Alahmari Mohammed , Mamani Umar-Farouk , Guo Yuhan , Lin Chien-Yu , Ibrahim Mohammed Nurudeen , Li Yongren , Cheng Kun
Published: April 2023

Lymphocyte activation gene-3 (LAG-3) has emerged as a promising target for cancer immunotherapy. It is expressed on activated CD4+ and CD8+ T cells, and on the surface of B cells, natural killer cells, and dendritic cells (DC). It has also been found to be highly expressed on activated T cells upon treatment with monoclonal antibodies targeting the PD-1/PD-L1 pathway, which may explain the resistance mechanism of monotherapy. Several anti-LAG-3 antibodies are being examined in clinical trials to treat different types of cancers. Despite their specificity and affinity, antibody-based checkpoint inhibitors are hampered by poor tumor permeability and high production costs. In this study, we aimed to discover a small peptide-based anti-LAG-3 inhibitor using a novel biopanning technique developed in our laboratory. We discovered several anti-LAG-3 inhibitor peptides, and the CMA16 peptide showed the highest stability and blocking efficacy. The peptides were synthesized by the solid-phase peptide synthesis using PurePepTM Chorus synthesizer (Gyros Protein Technologies, Tucson, AZ). The molecular weights and purity were confirmed by mass spectrometry and HPLC, respectively. To evaluate the function of the CMA16 peptide, a series of in vitro functional assays including binding ELISA, serum stability and cell viability assays were performed. In vivo anti-tumor activity of the peptides was examined in five-week-old C57BL/6 mice bearing MC38 cells. CMA16 significantly inhibited the growth of MC38 tumors. Quantification of CD8+ tumor-infiltrating cells revealed a significant increase in this type of immune cells in the group of mice treated with CMA16. These findings support the further development of the CMA16 peptide as potential anti-LAG-3 inhibitor for cancer immunotherapy.

Citation Format: Mohammed Alahmari, Umar-Farouk Mamani, Yuhan Guo, Chien-Yu Lin, Mohammed Nurudeen Ibrahim, Yongren Li, Kun Cheng. A small molecular-weight anti-lag-3 peptide inhibits colon tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB194.
Abstract LB213: Identification of DM004, a first-in-class anti-5T4/MET bispecific antibody-drug conjugate
Authors: Han Zhenyan , Shang Chengzhang , Dai Wenjuan , An Gao , Zhang Ellen , Lin Qingcong , Yang Yi
Published: April 2023

Aberrant MET signaling is frequently found in various types of solid tumors, and is correlated with oncogenic transformation, treatment resistance and poor prognosis. While MET remains an attractive therapeutic target, it is widely expressed on the surface of epithelial and endothelial cells, including normal tissues and tumors. To date, MET-targeting agents are associated with adverse clinical effects, including hypoalbuminemia, peripheral edema and pneumonitis, indicating that alternate treatments and/or modalities are needed. Intriguingly, MET antigen is commonly co-expressed with the oncofetal antigen 5T4 in various cancer types, including head and neck, lung and pancreatic cancer. While 5T4 is highly expressed on primary and metastatic cancers and is associated with adverse clinical outcomes in solid tumors, expression on normal adult tissues is very limited. Although several therapeutic agents targeting 5T4 antigen are currently being evaluated in human clinical studies, none have yet entered the market. To address these challenges, we hypothesized that targeting both MET and 5T4 with a bispecific antibody-drug conjugate (BsADC) could provide a more targeted therapeutic strategy to effectively eliminate tumor cells and reduce systemic toxicity. Here, we report that we have successfully generated two bispecific antibody candidates targeting both 5T4 and MET. The candidates were conjugated with monomethyl auristatin E (MMAE) via a protease-cleavable linker to generate DM004 BsADCs, i.e., Top1-MMAE and Top2-MMAE. In vitro, DM004 BsAbs demonstrated enhanced internalization in the NCI-H226 cell line compared to its parental monoclonal and monovalent anti-5T4 and anti-MET antibodies. In vivo, DM004 BsADCs exhibited robust anti-tumor activity in cell line-derived and patient-derived xenografts of gastric cancer and lung cancer, respectively. In particular, DM004 Top2-MMAE outperformed benchmark ADCs in lung BP0508 PDX models. In summary, we have identified a novel BsADC which may be a promising future treatment for cancers co-expressing 5T4 and MET.

Citation Format: Zhenyan Han, Chengzhang Shang, Wenjuan Dai, Gao An, Ellen Zhang, Qingcong Lin, Yi Yang. Identification of DM004, a first-in-class anti-5T4/MET bispecific antibody-drug conjugate [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB213.
Abstract LB220: S095029: a novel clinical-stage Fc-silenced NKG2A-blocking antibody with best-in-class potential
Authors: Melander Maria , Laugel Bruno
Published: April 2023

NKG2A and its ligand HLA-E are increasingly recognized as an important immune checkpoint restraining multiple lymphocyte populations involved in cancer immunity. Initially described as an NK cell inhibitory receptor, NKG2A’s role in regulating T-cell functions has recently come to the fore and is increasingly viewed as a key component of its immune suppressive functions. In addition, clinical studies have also provided proof-of-concept evidence for the superiority of dual NKG2A/PD-L1 blockade over anti-PD-L1 monotherapy. As of now clinical safety and efficacy results are only available for a single NKG2A-blocking antibody. This is in contrast with other immune checkpoint receptors (e.g., PD-1) where multiple blocking agents with different pharmacological properties have been assessed in the clinic, thereby providing a broad assessment of the target therapeutic potential and benefit to patients.

Here, we report the generation and preclinical characterization of a novel monoclonal antibody (mAb) disrupting the NKG2A/HLA-E interaction. The Fc-attenuated IgG1 mAb S095029 binds NKG2A with a nM-range affinity and reverses the inhibitory effects of the NKG2A/HLA-E interaction in several experimental models, both in vitro and in vivo. As a single agent S095029 enhanced the killing activity and cytokine secretion of NK and γδ T-cells in co-culture with cancer cell lines of multiple tissue origins. We also show that S095029 increased the antibody-dependent cellular cytotoxicity (ADCC) mediated by Fc-competent mAbs in different antigen systems with high HLA-E expression. Of note, these immune-activating properties of S095029 compared favorably in benchmarking experiments with other clinical-stage anti-NKG2A mAbs. Finally, S095029 combination with PD-1 blocking agents, with or without an additional ADCC mAb component, conferred superior anti-tumor activity compared to treatments without NKG2A blockade.

Overall, our in vitro and in vivo data support the clinical development of S095029 in tumor settings with adequate HLA-E expression and suggest potential differentiating characteristics compared to other anti-NKG2A mAbs. S095029 is currently being evaluated in phase 1 dose escalation studies as a single agent or in combination with anti-PD-1 therapy (NCT05162755).

Citation Format: Maria Melander, Bruno Laugel. S095029: a novel clinical-stage Fc-silenced NKG2A-blocking antibody with best-in-class potential [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB220.
Abstract LB223: Intratumoral administration of modified vaccinia Ankara expressing a tumor associated antigen and the costimulatory molecules IL-12 and 4-1BBL induces potent systemic long-term immune responses against murine tumors
Authors: Langbein Cigdem Atay , Giessel Raphael , Housni Mahmad Ismail , Lämmermann Kerstin , Bathke Barbara , Riedl André , Hausmann Jürgen , Kalla Markus , Chaplin Paul , Hochrein Hubertus , Medina-Echeverz José , Hinterberger Maria
Published: April 2023

In the last decade, immunotherapy has revolutionized cancer treatment. However, the lack of potent therapy-induced immune responses against solid tumors due to the immune-suppressive tumor microenvironment (TME) is still a major drawback. One approach to reprogram TME is virotherapy, which can target tumors via destruction of infected tumor cells as well as activating immune cell populations in the TME. A versatile and safe tool for virotherapy is modified vaccinia virus Ankara (MVA), which has already been approved by the FDA as a non-replicating vaccine against smallpox and monkeypox and is also in clinical trials against other infectious diseases and cancer. In the current study, we deciphered the anti-tumorigenic effect of a novel MVA vector encoding a tumor associated antigen (TAA) and the costimulatory molecules IL-12 and 4-1BBL, called MVA-TAA-4-1BBL-IL12. We could show that repetitive intratumoral (IT) injection of MVA-TAA-4-1BBL-IL12 resulted in strong tumor growth control, shrinkage and/or complete elimination of tumors and induction of tumor-specific CD8 T cell response. Furthermore, MVA-TAA-4-1BBL-IL12 treatment promoted a systemic anti-tumor immune response not only against the treated tumor but also untreated, distant tumors. Importantly, local virotherapy also resulted in the generation of tumor-specific memory response, which protected mice against local recurrence after rechallenge. As a conclusion, our findings show that MVA-TAA-4-1BBL-IL12 IT treatment induces an effective anti-tumorigenic immune response in different solid tumor models, which gives rise to long-term protection against cancer recurrence.

Citation Format: Cigdem Atay Langbein, Raphael Giessel, Mahmad Ismail Housni, Kerstin Lämmermann, Barbara Bathke, André Riedl, Jürgen Hausmann, Markus Kalla, Paul Chaplin, Hubertus Hochrein, José Medina-Echeverz, Maria Hinterberger. Intratumoral administration of modified vaccinia Ankara expressing a tumor associated antigen and the costimulatory molecules IL-12 and 4-1BBL induces potent systemic long-term immune responses against murine tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB223.
Abstract LB229: Tinengotinib, a novel fibroblast growth factor receptor (FGFR) inhibitor, is potent against resistance mutations in FGFR1/2/3
Authors: Qiang Xiaoyan , Yu Qi , Fan Jean , Wu Frank , Sun Caixia , Peng Peng
Published: April 2023

Dysregulated FGFR alterations (FGFRalt), including gene amplification, hot spot mutations, and gene fusion or rearrangement, have been reported in 7% of solid tumors, functioning as oncogenic drivers independent of tumor types. First generation of FGFR inhibitors, such as erdafitinib and pemigatinib, have already demonstrated promising efficacy on multiple cancers with prespecified FGFRalt. However, certain kinase mutations identified in the clinics, including gatekeeper mutations and some molecular brake mutations, may cause resistance to first generation FGFR inhibitors and remain challenging for current FGFR inhibitor development. Tinengotinib potently inhibited multiple FGFR1/2/3 resistant mutations both in vitro and in vivo. In the biochemical and cellular assays, tinengotinib exhibited potent inhibitory activities against FGFR2 gatekeeper mutation V564F, and molecular brake mutation N549K, which were known to cause resistance to the first generation FGFR inhibitors in cholangiocarcinoma patients with FGFR2 fusion or rearrangement. Binding kinetics was measured using surface plasmon resonance (SPR) on FGFR2, and tinengotinib demonstrated very tight binding to the target. To understand the underlying mechanism, we conducted co-crystallization of tinengotinib and wild type kinase domain of FGFR2. The resulting high-resolution X-ray diffraction structure revealed a very unique binding mode of tinengotinib in the ATP-binding site of FGFR2 comparing to other FGFR inhibitors. In addition, homology model demonstrated similar binding mode of tinengotinib to FGFR 1 and 3. This is consistent with the finding of tinengotinib showing excellent potency to FGFR 1/3 gatekeeper mutations. Tinengotinib is well tolerated in the clinical trials. Retrospective analysis showed early promising efficacy in treating patients with various solid tumors bearing FGFRalt. It provides an opportunity to investigate tinengotinib as a tumor agnostic therapy in patients with prespecified FGFR 1/2/3 alterations (pan-FGFRalt).

Citation Format: Xiaoyan Qiang, Qi Yu, Jean Fan, Frank Wu, Caixia Sun, Peng Peng. Tinengotinib, a novel fibroblast growth factor receptor (FGFR) inhibitor, is potent against resistance mutations in FGFR1/2/3 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB229.
Abstract LB230: Critical role for DAXX in triple negative breast cancer
Authors: Osipo Clodia , Wyatt Debra
Published: April 2023

Breast cancer is the most common diagnosed cancer and second cause of mortality in women. In particular, triple negative breast cancer, a subtype with few targeted therapies, frequently presents with metastatic disease and drug resistance. Nearly half of women with triple negative breast cancer will have metastatic disease. New targets and therapies are needed to prevent drug resistance and metastatic disease. We identified a novel protein, DAXX, in a biomarker window trial as a potent inhibitor of breast cancer stem cells (BCSC). BCSC are responsible for drug resistance, metastases, and tumor relapse. In this current study, the role of DAXX in sensitivity to cytotoxic chemotherapy was investigated in the setting of triple negative breast cancer. DAXX depletion using RNAi increased the proliferative capacity of three triple negative breast cancer cell lines (MDA-MB-231, BT549, and MDA-MB-468). This corresponded with increased PARylation of cellular proteins and PARP-1. DAXX was required to limit cell cycle progression through S-phase. Knockdown of DAXX modulated sensitivity to carboplatin, doxorubicin, and paclitaxel in vitro. Survival of female nude mice-bearing MDA-MB-231 DAXX-depleted tumors was 100% upon paclitaxel treatment compared to vehicle control-treated mice where the survival rate was 0% after 30 days. This survival advantage was not due to differences in tumor burden or tumor growth rates. These results suggest that DAXX is a critical growth regulator of triple negative breast cancer and possible predictor of response to paclitaxel.

Citation Format: Clodia Osipo, Debra Wyatt. Critical role for DAXX in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB230.
Abstract LB239: Downregulation of spliceosomal proteins hnRNPH1 and H2 in WM266-4 melanoma cells induces immune signaling
Authors: Sultan Maab , Diez Juan , Smalley Keiran S.M. , Beljanski Vladimir , Nathonson Lubov , Minond Dmitriy
Published: April 2023

This study aims to determine the effect of hnRNPH1/H2 (H1/H2) downregulation on immune-related genes in vitro. Due to the molecular heterogeneity of melanoma, it is difficult to treat it, which necessitates new approaches. We discovered compounds that selectively kill melanoma cells by binding to spliceosomal proteins hnRNPH1/H2. RNAseq of melanoma cells treated with H1/H2 siRNA showed upregulation of immune pathways. To validate this effect of genomic modulation of H1/H2 on immune gene expression, we used NanoString method. We treated both WM266-4 cell line and melanocytes with H1/H2 siRNA and scrambled siRNA to knockdown our target gene. Then, RNA was extracted and analyzed by NanoString. Analysis data of melanoma cell line showed a significant difference between RNA samples treated with scrambled and the one treated with siRNA in upregulating immune-related genes. In contrast, data of melanocytes revealed no significant difference between scrambled and siRNA samples and did not show upregulation of these genes. This implies the specificity of this response to melanoma cells. In conclusion, we hypothesize that downregulation of spliceosomal proteins H1/H2 can upregulate immune-related genes, which in turn can improve melanoma patients’ survival. Consequently, H1/H2 can be targeted as a novel therapeutic approach.

Citation Format: Maab Sultan, Juan Diez, Keiran S.M. Smalley, Vladimir Beljanski, Lubov Nathonson, Dmitriy Minond. Downregulation of spliceosomal proteins hnRNPH1 and H2 in WM266-4 melanoma cells induces immune signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB239.
Abstract LB258: Therapeutic advantage of targeting lysosome as signaling hub for metabolic conditions in malignant gliomas
Authors: Jing Yongwei , Kobayashi Masahiko , Hirao Atsushi
Published: April 2023

Lysosome, as the digestive system of the cell, participated in numerous cell biological processes, such as macromolecular degradation, cell adhesion/migration, and apoptosis by regulating metabolic status and pro-growth signaling. Therefore, lysosome could be a promising therapeutic target for cancer therapy, but it remains unclear how lysosome is involved in cancer malignancy. In this study, to investigate the roles of function lysosomes in the regulation of malignant status, we evaluated the proteolytic activity of lysosomes using BODIPY-dye conjugated BSA (DQ-BSA) in malignant gliomas characterized by high aggressivity, destructivity, and invasiveness, glioblastoma multiforme (GBM). While most GBM patient-derived cells showed higher lysosomal proteolytic activity than an immortalized human neural progenitor cell line derived from the embryonic brain, levels of lysosome activity positively co-related with sphere formation. Multi-omics analysis demonstrated that the level of lysosomal proteolytic activity was co-related with metabolic status, including activated mitochondria biogenesis and amino acid transport. The orthotopic xenograft model revealed that lysosome activity in vitro is a critical biomarker representing malignant phenotypes of GBM. We found that the MiT/TFE family, a master regulator of lysosomal biogenesis, controlled the malignant progression of GBM, including therapy resistance, indicating that quality control of lysosomes is a critical determinant for the malignant properties of gliomas. To develop a novel therapeutic approach for targeting lysosomal function, we performed screening of FDA-approved compounds and found that lysosomotropic agents, which induced galectin-3 punctation as an indicator of lysosomal membrane damage, efficiently suppressed tumor growth. Ifenprodil, a clinically available drug that acts as a lysosomotropic agent, increased intracellular Ca2+ levels, resulting in mitochondrial reactive oxygen species-mediated cytotoxicity. Furthermore, we found that the efficacy of ifenprodil was remarkably enhanced by metabolic modifications, such as amino acid restriction, in vitro and in vivo. Collectively, these data indicate that lysosomes as signaling hubs for metabolic conditions play critical roles in the regulation of the malignant status of GBM patients. Our findings propose that lysosomal biogenesis is a promising target to develop a novel therapeutic approach for GBM.

Citation Format: Yongwei Jing, Masahiko Kobayashi, Atsushi Hirao. Therapeutic advantage of targeting lysosome as signaling hub for metabolic conditions in malignant gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB258.
Abstract LB263: An in vivo unbiased screen identifies clathrin adaptor protein complex-2 as a novel tumor suppressor
Authors: Zimmerman Seth Parker , Counter Christopher M.
Published: April 2023

Pancreatic ductal adenocarcinoma (PDAC) is almost uniformly lethal. It is thus imperative to find new therapeutic approaches to treat this disease. While whole genome CRISPR/Cas9 screens have successfully identified new vulnerabilities in PDAC cell lines, it is becoming increasingly clear that cell culture do not faithfully recapitulate the complex nature of tumorigenesis in vivo, and hence may fail to identify the full spectrum of potential therapeutic targets to be explored in this devastating disease. As previous screens we performed identified phosphatidylinositol (Ptdlns) metabolism as important for pancreatic cell growth, I generated a custom sgRNA library targeting this entire form of metabolism. To identify vulnerabilities specific to tumor growth, I screened this library in five different human PDAC cell lines grown in culture versus as xenograft tumors. I found that sgRNAs targeting two genes encoding separate subunits of the Adaptor Protein complex-2 (AP2), a regulator of clathrin mediated endocytosis, were negatively enriched in all five PDAC cell lines when grown in culture. In agreement, AP2 subunit genes are considered common essential by DepMap. Paradoxically however, the same sgRNAs were positively enriched in three of these five cell lines when grown as xenograft tumors. This begs the question how the loss of a supposably essential complex behaves like a tumor suppressor and instead enhances tumor growth when disrupted. Here, I will present data that loss of AP2 results in a substantial restructuring the plasma membrane proteome, which in cultured cells results in the loss of iron transport, one of the main functions of this complex, and cell death. Conversely, this restructuring in vivo retains receptors and adhesion proteins on the cell surface, where transcriptome and proteomic analysis indicate enhances proliferative signaling. These data support AP2 promoting cell viability of cultured cells through active iron transport, but suppresses tumor growth in vivo by endocytosing the very receptors needed for tumor growth.

Citation Format: Seth Parker Zimmerman, Christopher M. Counter. An in vivo unbiased screen identifies clathrin adaptor protein complex-2 as a novel tumor suppressor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB263.
Abstract LB272: Spatial cellular architecture predicts prognosis in glioblastoma
Authors: Zheng Yuanning , Carrillo-Perez Francisco , Pizurica Marija , Gevaert Olivier
Published: April 2023

Intra-tumoral heterogeneity and cell-state plasticity are key drivers for the therapeutic resistance of glioblastoma (GBM). Studies based on single-cell RNA-seq and spatial transcriptomics have classified GBM cells into distinct transcriptional phenotypes. However, how the transcriptional diversity and spatial cellular organization are associated with patient prognosis remains incompletely resolved. Here, we developed a deep learning model to predict spatially resolved transcriptional programs from histology images. The model was trained on spatial transcriptomics data and validated in external testing cohorts. Applying the model to two separate patient cohorts led to the discovery of conserved relationships between tumor architecture and prognosis. Patient with poor prognosis had higher proportions of GBM cells expressing a hypoxia-induced transcriptional program. In addition, high clustering patterns of reactive astrocytes were associated with a poor prognosis. Conversely, when the reactive astrocytes were dispersed and connected to other cell types, the risk was decreased. To validate our results, we developed a separate deep learning model that used histology images to predict prognosis. Applying the model to spatial transcriptomics data discovered survival-associated regional gene expression programs. Genes related to glycoprotein metabolism and injury response were significantly upregulated in tumor cells with high aggressiveness. Our studies established a scalable approach to resolve the transcriptional heterogeneity of GBM and linked the spatial cellular architecture to clinical outcomes.

Citation Format: Yuanning Zheng, Francisco Carrillo-Perez, Marija Pizurica, Olivier Gevaert. Spatial cellular architecture predicts prognosis in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB272.
Abstract LB284: CLAUDIN-1 targeting antibody ALE.C04 drives single activity and restores anti-PD1 efficacy in solid tumors
Authors: Toso Alberto , Teixeira Geoffrey , Zimmermann Tina , Gill Stefanie Gill , Schmitter Daniela , Meyer Markus , Muller Marion , Mailly Laurent , Baumert Thomas , Manenti Luigi , Iacone Roberto
Published: April 2023

Claudin 1 (CLDN1) is a protein confined within the normal epithelial tight junctions of different tissues. Upon malignant transformation, CLDN1 is overxpressed and epitopes become exposed outside the tight junctions (non-Junctional CLDN1). ALE.C04 is a highly specific humanized monoclonal antibody that recognizes a unique CLDN1 exposed epitope in different solid tumors. Herein we show that non-Junctional CLDN1 (NJ-CLDN1) is frequently overexpressed in solid tumors. Pre-clinically, ALE.C04 drives tumor growth inhibition in different CDXs and PDX in vivo tumor models. Notably, CLDN1 expression on tumor cells positively correlates with T cell exclusion, a mechanism described to hinder the efficacy of Checkpoint inhibitors (CPIs). On this line, the overexpression of Cldn1 in mouse tumor cells promoted T-cell exclusion and resistance to anti-PD1 treatment. Importantly, ALE.C04 restored both T-cell infiltration and anti-PD1 efficacy in tumors. Mechanistically, NJ-CLDN1 interacts with different components involved in extracellular matrix remodeling, thus establishing a physical barrier that exclude immune cells from the tumor nest. ALE.C04 perturbs the interface between CLDN1+ tumor cells and the stroma, thus restoring immune cell infiltration. Our pre-clinical data showed that: i) NJ-CLDN1 is a novel and druggable target in solid tumors ii) ALE.C04 is a selective anti-CLDN1 antibody capable of driving anti-tumor activity as both single agent and in combination with anti-PD1.

Citation Format: Alberto Toso, Geoffrey Teixeira, Tina Zimmermann, Stefanie Gill Gill, Daniela Schmitter, Markus Meyer, Marion Muller, Laurent Mailly, Thomas Baumert, Luigi Manenti, Roberto Iacone. CLAUDIN-1 targeting antibody ALE.C04 drives single activity and restores anti-PD1 efficacy in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB284.
Abstract LB293: The evolution of MRD assays: Moving beyond the tumor-Informed bespoke NGS panel
Authors: Labrousse Paul , Stetson Daniel , Hadfield James , Abbosh Chris , Zehir Ahmet , Barrett Carl , Dougherty Brian , Hodgson Darren
Published: April 2023

The non-invasive detection of circulating tumor DNA (ctDNA) from plasma has been shown to have clinical value for detection of minimal residual disease (MRD), identification of emerging resistance to treatment, and predicting treatment response. The ability to detect MRD following curative treatment allows for the stratification of patients with higher risk of disease recurrence. Multiple studies, across hundreds of patients in different indications, including lung and colon cancer, have shown that tumor-informed personalized assays have high sensitivity to detect recurrence. The tumor-informed bespoke panels utilize sequencing of the tumor tissue to identify clonal somatic variants, which are then used to generate a personalized panel to track the variants in patient plasma. Next-generation MRD technologies are aiming to provide greater sensitivity by expanding methods beyond the small, personalized panels. Utilization of increased numbers of somatic variants is predicted to achieve a greater level of sensitivity for detection of MRD.

Here we describe, C2I Genomics which provides a novel platform that exploits whole genome sequencing of the tumor tissue and plasma to define a somatic variant signature. An important difference of this method is that it develops a personalized bioinformatic signature rather than a personalized NGS panel. To understand the potential of this novel methodology, we utilized a set of 54 contrived clinical sample dilutions from three indications, with an expected (or engineered) VAF range of 0.2-0.002%, that have commutability to the intended use population.

We found that C2I Genomics technology is highly sensitive, where for all returned samples, the assay routinely achieved detection down to the lowest dilution of 0.002% allelic frequency. Overall, the assay resulted in an average detection rate of 93% across all dilutions (n = 54). The aggregate detection rate of several tumor-informed assays, examining the same dilutions, yielded a detection rate of 68%.

In summary, the C2I Genomics assay showed robust detection from contrived samples which are representative of clinical trial samples in both cfDNA yields and allele frequency.

Citation Format: Paul Labrousse, Daniel Stetson, James Hadfield, Chris Abbosh, Ahmet Zehir, Carl Barrett, Brian Dougherty, Darren Hodgson. The evolution of MRD assays: Moving beyond the tumor-Informed bespoke NGS panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB293.
Abstract LB322: Antitumor activity of 1st-in-class pan-RAS inhibitor ADT-1004 in mouse models of pancreatic ductal adenocarcinoma
Authors: Maxuitenko Yulia Y. , Foote Jeremy B. , Keeton Adam B. , Chen Xi , Berry Kristy , Fadlalla Khalda , Valiyaveettil Jacob , Huang Chung-Hui , Moore Austin M. , Graff Emily C. , Nagaraju Ganji P. , Carstens Julienne L. , El-Rayes Bassel F. , Buchsbaum Donald J. , Piazza Gary A.
Published: April 2023

Pancreatic ductal adenocarcinoma (PDA) is the 4th leading cause of cancer death in the U.S. with only about a 10% five-year survival rate and an estimated 60,000 deaths/year by 2030. Poor survival is frequently due to advanced disease at the time of diagnosis, as well as the high prevalence of KRAS driver mutations. Currently, approved KRAS-targeted therapeutics are designed to covalently inactivate only KRAS-G12C mutants, whereas the most common mutations in PDA are KRAS-G12D, KRAS-G12V, and KRAS-G12R. Thus, the need for novel RAS-targeted therapeutics with efficacy in tumors with these more common mutations is of utmost urgency to reduce PDA disease burden. We have synthesized a novel chemical class of pan-RAS inhibitors with unique biological properties and attractive drug-like properties. As a prodrug, ADT-1004, generates an active metabolite, ADT-007, that potently inhibits the growth of human and murine PDA cell lines in vitro with single-digit nM IC50 irrespective of specific RAS mutational codon or isozyme by inhibiting activated RAS and signaling downstream of KRAS (ERK1/2 and AKT phosphorylation). ADT-1004 is well tolerated with no discernable toxicity at oral dosages of up to 175 mg/kg bid. Pharmacokinetic studies demonstrated that ADT-1004 produces sustained plasma concentrations of ADT-007 ~50-fold above IC50 values, with even higher concentrations in both subcutaneous and orthotopic pancreatic tumors. Once daily oral administration of ADT-1004 significantly inhibited the growth of orthotopically implanted PDA tumors with a corresponding reduction in RAS/MAPK signaling. ADT-1004 represents a 1st-in-class pan-RAS inhibitor with potential advantages over mutant-specific KRAS inhibitors for greater efficacy and ability to avert mechanisms of resistance. These data support future clinical trials of ADT-1004 as a monotherapy for the treatment of patients with PDA regardless of the underlying mutation.

Citation Format: Yulia Y. Maxuitenko, Jeremy B. Foote, Adam B. Keeton, Xi Chen, Kristy Berry, Khalda Fadlalla, Jacob Valiyaveettil, Chung-Hui Huang, Austin M. Moore, Emily C. Graff, Ganji P. Nagaraju, Julienne L. Carstens, Bassel F. El-Rayes, Donald J. Buchsbaum, Gary A. Piazza. Antitumor activity of 1st-in-class pan-RAS inhibitor ADT-1004 in mouse models of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB322.
Abstract LB354: 9p arm loss is an important predictor of immune evasion in several human cancers
Authors: Bianchi Joy
Published: April 2023

The identification of biomarkers that predict patient response to immune checkpoint blockade (ICB) is a key focus of current cancer research. We and others have found that high levels of Somatic Copy Number Alterations (SCNAs) in tumors are associated with decreased infiltration by cytotoxic immune cells and predict patient’s response to ICB. Recently, we predicted that the strongest SCNA driver of cytotoxic T cell depletion in HPV-negative oral cancer, was the loss of the entire 9p arm and that it was a marker of poor survival in recurrent oral cancers treated by anti-PD1 therapy. 9p arm loss is among the most common SCNAs in solid tumors and we revealed its importance beyond 9p21.3 deletion (i.e., CDKN2A and the IFNA cluster).To systematically investigate the immune-related role of 9p deletion and other SCNAs in cancer, we have developed a computational pipeline to identify the genes altered by SCNAs predicting the strongest risk of cancer immune evasion. We analyzed 7 solid tumor types and identified thousands of tumor-specific SCNAs predicting an immune cold phenotype but only ~100 SCNAs were conserved across all tumor types. Strikingly, 60% of the conserved deletions were localized on the 9p arm and the strongest 9p candidates included some known cancer drivers but also new candidates such as RANBP6 and TOPORS, that have been suggested to decrease proinflammatory and pro-immunogenic molecules. We have identified a 17-gene cluster deletion in 9p13 composed mostly of genes involved in proteasomal degradation or membrane trafficking, suggesting that its deletion might disturb MHC-mediated antigen presentation. We are now engineering human and mouse oral cancer cell lines to recapitulate 9p deletion and decipher its role in immune evasion through in vitro and in vivo immunological assays. We are also using the parameters we determined in our computational pipeline to develop a machine learning method improving our prediction of SCNAs driving immune evasion. Our findings identified 9p deletion as a novel biomarker for predicting clinical benefit of ICB and will allow a better understanding of the SCNA-mediated mechanisms suppressing tumor immune response.

Citation Format: Joy Bianchi. 9p arm loss is an important predictor of immune evasion in several human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB354.