bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2368: Intratumoral delivery of HER-2-CD3hFc mRNA-LNP inhibits ovarian tumor growth
Authors: Golubovskaya Vita M. , Sienkiewicz John , Sun Jinying , Zhang Shiming , Huang Yanwei , Hu Liang , Zhou Hua , Harto Hizkia , Xu Shirley , Berahovich Robert , Wu Lijun 
Published: March 2024

Abstract
Her-2 is a well-known driver of carcinogenesis that is overexpressed in breast, ovarian and other tumors. Immunotherapy with bispecific antibodies is a promising cancer therapy approach. Her-2 (Herceptin) antibody was used to test bispecific antibody against ovarian cancer cells. First, Her-2-CAR-T cells with Her-2 (4D5) ScFv and 4-1BB costimulatory domain were generated and tested using in vitro killing and IFN-gamma assays, and in vivo efficacy SKOV-3 xenograft NSG mouse model. Her-2-CAR-T cells killed SKBR-3 breast and SKOV-3 ovarian cancer cells and stopped SKOV-3 xenograft tumor growth. This Her-2-ScFv was used to generate bispecific Her-2 ScFv-CD3-ScFv human Fc antibody using in vitro transcribed mRNA. The 5’capped Her-2-CD3-hFc mRNA with 5’UTR, 3’UTR and poly A tail was generated by in vitro transcription using DNA template. The mRNA was embedded into lipid nanoparticles (LNP) using microfluidic PreciGenome Flex S NanoGenerator. Western blotting detected &gt;160 kDa bispecific antibody secreted from A1847 and 293 cells transfected with mRNA-LNPs. The bispecific antibody was binding Her-2-positive A1847 ovarian cancer cell lines and T cells by FACS analysis. The Her-2-CD3-hFc bispecific antibody with T cells effectively killed Her-2-positive target cells in a dose-dependent manner in RTCA assay and produced high level of IFN-gamma. Moreover, intratumoral delivery of Her-2-CD3-hFc mRNA-LNP with intravenous injection of T cells completely blocked A1847 xenograft tumor growth. In conclusion. intratumoral delivery of Her-2-CD3 mRNA-LNP blocks ovarian xenograft tumor growth and provides a solid basis for future pre-clinical and clinical studies.
Citation Format: Vita M. Golubovskaya, John Sienkiewicz, Jinying Sun, Shiming Zhang, Yanwei Huang, Liang Hu, Hua Zhou, Hizkia Harto, Shirley Xu, Robert Berahovich, Lijun Wu. Intratumoral delivery of HER-2-CD3hFc mRNA-LNP inhibits ovarian tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2368.
Abstract 2378: The triple-specific antibody KA-3003, targeting PSMA, CD28, and 4-1BB, is developed for the treatment of prostate cancer by enhancing T cell activity within the tumor
Authors: Wu Guojin , Guo Zhengcheng , Peng Hao , Hao Feng , Liu Tongtong , Ning Jinying 
Published: March 2024

Abstract
Immunotherapy, revolutionizing the treatment of advanced solid tumors by blocking PD1 signaling, has encountered a challenge in prostate cancer, exhibiting a low response ratio to anti-PD-1 therapy. Furthermore, cancer immunotherapy using 4-1BB agonists faces limited clinical development due to dose-limiting toxicity. Here, we developed a tri-specific antibody, KA-3003, targeting PSMA, CD28, and 4-1BB, with the goal of enhancing T cell activation in the tumor microenvironment. This antibody was created using our common light chain bispecific antibody discovery platform and nanobody antibody discovery platform with knob-into-hole technology. KA-3003, in IgG1 format, features mutations in the Fc domain to eliminate ADCC, ADCP, and CDC activity. It contains two identical nanobodies at the C-terminal against 4-1BB, while binding to PSMA and CD28 with two Fabs at the N-terminal, sharing an identical light chain. KA-3003 exhibits high affinity for PSMA and relatively lower affinity for CD28 and CD137. In the presence of a low concentration of CD3 antibody to stimulate T cell activation, co-culture of tumor cells expressing PSMA with primary T cells isolated from human PBMC enhances T cell activation and proliferation. In PBMC humanized immunodeficient mouse tumor models, KA-3003 effectively suppresses the growth of 22Rv1 tumors with or without a PD1 antagonist antibody. Additionally, KA-3003 has a half-life of more than five days in the blood of Balb/c mice. Finally, we assessed the developability of this antibody with different treatments such as high concentration, low pH, repeated freezing and thawing, and high temperature. KA-3003 shows neither aggregation nor degradation. In conclusion, the tri-specific antibody KA-3003, developed with our common light chain antibody discovery platform, stands out as a promising pre-clinical candidate drug for the treatment of prostate cancer.
Citation Format: Guojin Wu, Zhengcheng Guo, Hao Peng, Feng Hao, Tongtong Liu, Jinying Ning. The triple-specific antibody KA-3003, targeting PSMA, CD28, and 4-1BB, is developed for the treatment of prostate cancer by enhancing T cell activity within the tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2378.
Abstract 244: Patient-derived organoids: A pre-clinical model to assess infection and killing capacity of viral vectors for cancer therapy
Authors: Morales-Rodriguez Francisco , Sasso Maria Stella , Bezhaeva Taya , Bailey-Bucktrout Samantha , Lai Ka Wai , Gkogkou Foteini , Boj Sylvia 
Published: March 2024

Abstract
HUB’s patient-derived organoids (PDOs) are in vitro models that preserve tissue morphology and original cellular complexity. Additionally, PDOs are compatible with (high) throughput screening methods, enabling informed decision-making early in the drug development pipeline and significantly improving the odds of positive outcomes in clinical trials. Akamis Bio has developed experimental viral vector-based tumour gene therapies that have the potential to treat a variety of solid tumours by driving the expression of immunologically active biomolecules and therapeutic proteins hampering tumour immune evasion. These vectors are based on a replication competent, chimeric group B adenovirus backbone that selectively replicates and expresses transgene payloads in tumor cells, and additionally exerts oncolytic activity. To evaluate the efficacy of such a virus-based gene delivery strategy, HUB set up a proof-of-concept study to assess the propagation capability of Akamis Bio’s viral vectors in tumour PDOs. Intact PDOs from primary pancreatic tumours were infected with several viral loads, ranging from 0.1 viral particles per cell (PPC) to 100 PPC. The viral vector encoded a GFP reporter gene to identify infected cells using fluorescence imaging. The cultures were imaged daily for 14 days, allowing the assessment of cytotoxicity and infection efficiency and dynamics. Independently of PPC, infections always started in the exterior of PDOs in a few GFP-positive cells. The gradual increase over time in GFP-signal toward the interior of PDOs suggests the high likelihood of secondary infection events. Crucially, GFP intensity was correlated with cell death in PDOs, as evidenced by morphological features detected in brightfield images. Moreover, the infection dynamics were dose-dependent, as the GFP intensity peak arose later with decreasing PPC. These results show the capacity of HUB PDOs to study the infection dynamics of Akamis viral vectors. This pre-clinical platform permits rapid and efficient screening and dose evaluation for oncolytic virotherapies. Unique access to extensive tumour PDO biobanks with characterized genomic landscapes allows best-in-class stratification of treatment response based on tumour type and genetic heterogeneity.
Citation Format: Francisco Morales-Rodriguez, Maria Stella Sasso, Taya Bezhaeva, Samantha Bailey-Bucktrout, Ka Wai Lai, Foteini Gkogkou, Sylvia Boj. Patient-derived organoids: A pre-clinical model to assess infection and killing capacity of viral vectors for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 244.
Abstract 2464: Defective NMD promotes aberrant intron retention in clear cell renal cell carcinoma
Authors: Zhou Mi , Giri Gilbert , Kim William Y. , Dominguez Daniel 
Published: March 2024

Abstract
Clear cell renal cell carcinoma (ccRCC) is the 8th most common cancer in the United States, constituting 75% of all kidney cancer cases. Clear cell RCC (ccRCC) along with melanoma has traditionally been viewed as an immunotherapy responsive disease with a storied history of immunotherapy treatments including high dose interleukin 2 (IL2), interferon, and allogeneic stem cell transplant. Indeed, RCC was one of the first tumor types to garner FDA approval for PD1 immune checkpoint inhibition (ICI). However, unlike melanoma, most RCC tumors do not have a high tumor mutational burden (TMB) to potentially explain their immunotherapy responsiveness. We and others have sought to explain this unanswered question and have demonstrated that non-canonical tumor associated antigens like endogenous retroviruses (ERVs) may in part explain ICI response in RCC. We have noted that ccRCC tumors have the highest level of retained introns (RI) across all TCGA tumors, that RI levels are secondary to suppressed non-sense mediated decay (NMD) activity, and that one can subset ccRCC into RI-high and normal-like tumors. Moreover, we have found that mTOR signaling plays a key role in regulating NMD and intron retention and that mTOR inhibition can promote intron retention. We hypothesized that these aberrantly retained introns could serve as a rich source of highly foreign, tumor associated neoantigens and that of retained intron neoantigens, the ones not observed in normal tissue would be the most immunogenic. We derived a so called “Neo-RI-antigen burden” that represents the burden of retained intron neoantigens not found in normal tissues and demonstrate that the Neo-RI-antigen burden of complete responders is numerically higher than those with partial response or progressive disease in a dataset of immunotherapy treated melanoma patients. Our work suggests the possibility of using NMD-targeting drugs as a potential therapeutic in combination with ICI to enhance the overall treatment response.
Citation Format: Mi Zhou, Gilbert Giri, William Y. Kim, Daniel Dominguez. Defective NMD promotes aberrant intron retention in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2464.
Abstract 250: Sex differences in cancer stemness among individuals with early onset colorectal cancer
Authors: Aladelokun Oladimeji , Sumigray Kaelyn , Khan Sajid A. , Johnson Caroline 
Published: March 2024

Abstract
Since 1990, the overall incidence and mortality rates of late onset colorectal cancer (LOCRC ≥50 years) have been decreasing due to improvements in access to screening and available treatment options. However, the rates for early onset CRC (EOCRC ≤ 49 years) have steadily increased in men and women. Less than 30% of LOCRC patients present with late-stage tumors (clinical stages III or IV) at the time of diagnosis compared to 70% of EOCRC patients. Despite this, the cellular and molecular mechanisms underlying the incidence and stage are unclear, as are appropriate strategies for prevention of recurrence in men and women with EOCRC. Effective prognostic markers are therefore urgently needed. To address this issue, we performed a detailed bioinformatics analysis based on Gene Expression Omnibus database (GSE39582; n=585 patients), wherein we identified 7 prognostic biomarkers for EOCRC: KRAS, LGR5, CTNNB1, MYC, BMI1, CD44 and ASNS. Importantly, Kaplan Meier analysis revealed tumor onset at a younger age was significantly (p = 0.0082) associated with poorer 5-year survival in men with EOCRC only, after adjusting for KRAS status. CTNBB1 and CD44 transcript levels were higher in men with EOCRC versus men with LOCRC. Conversely, female EOCRC had a higher frequency of KRAS mutations (52.6%) compared to their LOCRC counterpart (38.8%), and an increased expression of markers of tumor stem cell and metabolic reprogramming including LGR5, MYC, BMI, and ASNS. A single CRISPR-Cas9 deletion of ASNS in HCT116 cell lines, a pre-clinical model of EOCRC, caused an inhibition of 3D spheroid formation compared to HCT116 ASNS wild type cells. In vivo study using a cell line derived R2G2 mouse xenograft model showed that ASNS disruption caused a reduction in tumor burden that was accompanied by low Lgr5 and Myc transcripts compared to the ASNS wild type group, indicating that ASNS may regulate cancer stemness. Together, this data suggests a unique molecular fingerprint for EOCRC and highlights sex-specific influences on cellular metabolism during EOCRC progression.
Citation Format: Oladimeji Aladelokun, Kaelyn Sumigray, Sajid A. Khan, Caroline Johnson. Sex differences in cancer stemness among individuals with early onset colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 250.
Abstract 252: Functional and lineage atlas of salivary gland regeneration charted by rapid in vivo gene targeting
Authors: Gan Qiwen , Ying Zhe 
Published: March 2024

Abstract
The crucial function of the salivary gland of keeping the oral cavity lubricated to facilitate breathing, swallowing, and lingual communication is often compromised following cancer radiotherapies. Due to the ultra-high radiosensitivity and low regeneration potential of the salivary epithelium, radiation-induced damage is largely permanent, representing a major clinical challenge. To solve this problem, we have developed a scalable rapid gene targeting system in the murine salivary gland using in-utero injection of lentiviruses. This allows us to transduce ectodermal progenitors of salivary glands with high efficiency and full randomness. Barcoded lentiviral lineage tracing suggests that every major salivary gland originated from a defined number of progenitors, each progenitor-derived clone has relatively equal expansion potential during development and equally contributes to regeneration post radiation challenge. This observation indicates that the major salivary glands of a single mouse can be used as a platform to study lineage dynamics or test up to ~2600 different genetic conditions during regeneration. With this robust approach in hand, we identified major barriers to salivary gland regeneration from among hundreds of differentially regulated signaling pathways and genes post-irradiation. Based on these discoveries, we are currently in the process of 1) Understanding the molecular mechanisms underlying the top regeneration barriers; 2) Dissecting the cell fate dynamics of salivary gland regeneration with or without regeneration barriers; and 3) Testing if we can restore the salivary gland in situ via combinatorial removal of regeneration barriers. Our work will provide unbiased functional and lineage roadmaps of post-irradiation salivary gland regeneration and potentially serve as the cornerstones of future therapeutic interventions.
Citation Format: Qiwen Gan, Zhe Ying. Functional and lineage atlas of salivary gland regeneration charted by rapid in vivo gene targeting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 252.
Abstract 2532: Deciphering multiple protein complexes in BCL2 family to measure apoptotic dependencies in acute myeloid leukemia
Authors: Lee Hongwon , Chun Changju , Choi Byungsan , Hong Saem , Lee Yunseo , Koh Youngil , Yoon Tae-Young 
Published: March 2024

Abstract
The BCL2 protein family controls apoptosis by shifting the dynamic equilibrium state of complex formation. BH3 mimetics disrupt this balance by disturbing the interaction of a specific anti-apoptotic protein, leading to the initiation of apoptosis. However, relying solely on molecular data for the specific anti-apoptotic protein can be challenging due to the functional redundancy within the BCL2 protein family and their complex interaction network. Therefore, comprehensive profiling information considering protein complexes is essential to determine apoptotic dependencies, particularly in a clinical context. In this study, we adapted a Single-molecule Protein Interaction Detection (SPID) platform that can assess levels of protein complexes in a quantitative manner. Out of the 47 metrics included in our Apoptosis Signaling 47 panel, we utilized 22 assays to measure apoptosis dependencies in acute myeloid leukemia (AML) cells obtained from 32 patients. By combining these metrics, we developed a predictive model for the ex vivo response to ABT-199 treatment, focusing on three key biomarkers: BCL2-BAX complex, BCL2-BIM binding potential, and BCLxl-BAK level. From a receiver operating curve (ROC) analysis, the model exhibited high accuracy with a value of 0.94 area under the curve (AUC). We further validated our model by comparing the predicted response to the therapeutic outcomes in 10 AML patients according to the 2017 ELN guidelines, and achieved 100% sensitivity (4 out of 4 identified correctly) and 83.3% specificity (5 out of 6 identified correctly). Overall, our platform provides an effective method to explore apoptosis dependencies in clinical samples based on the information regarding protein complexes within the BCL2 protein family. Three key molecular biomarkers can be translated into a gauge for predicting therapeutic outcomes of BH3 mimetics, suggesting an improvement of precision medicine in AML treatment.
Citation Format: Hongwon Lee, Changju Chun, Byungsan Choi, Saem Hong, Yunseo Lee, Youngil Koh, Tae-Young Yoon. Deciphering multiple protein complexes in BCL2 family to measure apoptotic dependencies in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2532.
Abstract 2536: Multimodal stratification of predictive biomarkers in head and neck cancers: A focus on cytokine-based immunotherapy
Authors: Ramos Corinne , Ruez Richard , Delebecq Sandra , Senechal Victor 
Published: March 2024

Abstract
Background Immunotherapy, particularly cytokine-based therapy, has been gaining traction in the treatment of head and neck cancers. Cytokines are small proteins that play a crucial role in the immune response to cancer. However, not all patients respond to cytokine-based immunotherapies, and some may experience severe side effects. The ability to predict which patients are most likely to benefit from these therapies could greatly improve the efficacy and tolerability of treatment. In this context, the study of predictive biomarkers, such as the expression of immune checkpoint molecules like PD-L1 and TIGIT, and the profiling of cytokines within the tumor microenvironment, has become crucial. These biomarkers could provide valuable information about the patient's immune response to the tumor and their likelihood of responding to cytokine-based immunotherapies.
Method A multimodal approach to stratify predictive biomarkers in head and neck cancers was used. The methodology was founded on combining metabolic, transcriptomic, and proteomic data to offer a comprehensive understanding of potential biomarkers. The data from different modalities were integrated using bioinformatics and machine learning algorithms. This comprehensive dataset was analyzed to identify multimodal biomarker signatures that could predict patient responses to cytokine-based therapies.
Result Preliminary finding showed significant heterogeneity in the expression of PD-L1, TIGIT, and various cytokines across the tumor microenvironment. This underscored the complexity of head and neck cancers. Certain multimodal biomarker signatures, which included specific patterns of immune checkpoint molecule expression, cytokine profiles, and immune cell infiltration, correlated robustly with patient responses to cytokine-based therapies.
Conclusion Our study demonstrates the considerable potential of a multimodal stratification approach in deciphering the complexity of head and neck cancers and predicting responses to cytokine-based immunotherapies. By integrating metabolomic, transcriptomic, and proteomic data, we identified unique biomarker signatures that strongly correlated with therapy responses. This work underscores the invaluable role of integrated predictive biomarker profiles in enhancing the precision of immunotherapy.
Citation Format: Corinne Ramos, Richard Ruez, Sandra Delebecq, Victor Senechal. Multimodal stratification of predictive biomarkers in head and neck cancers: A focus on cytokine-based immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2536.