bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1925: Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers
Authors: Sealover Nancy E. , Finniff Bridget , Hughes Jacob , Lee Hyun , Kortum Robert L.
Published: March 2024

Single-agent targeting of RAS-mutated cancers using RAF/MEK/ERK or PI3K/AKT pathway inhibitors is ineffective; blocking one pathway relieves negative feedback control of RTK signaling and hyperactivates parallel effector pathways. While combined MEK and PI3K inhibition is effective in preclinical models, toxicity of this combination prevents its clinical use. Alternative strategies for treating RAS-mutated cancers are essential. Therapeutics directly targeting mutated RAS proteins have the potential to spare normal cellular function thereby lessening overall toxicity. Unfortunately, direct RAS inhibition as a monotherapy does not fully block RAS effector signaling. RAS proteins show differential activation of RAF and PI3K pathways: KRAS potently activates RAF but poorly activates PI3K, whereas HRAS effectively activates PI3K but poorly activates RAF. Further, mutant RAS inhibition relieves negative feedback controls leading to rapid hyperactivation of RTK−WT RAS signaling. A more comprehensive understanding of the interplay between mutant RAS and RTK−WT RAS signaling is essential to developing rational therapeutic approaches to treat RAS-mutated cancers. We found that WT RAS enhanced mutant RAS-driven transformation by activating RAS effectors poorly engaged by mutated RAS. Further, inhibition of RAS effectors activated poorly by mutant RAS synergized with and limited resistance to mutant HRAS and KRAS inhibitors. The mutant HRAS inhibitor tipifarnib blocked PI3K signaling and synergized with MEK inhibitors in HRAS-mutated cancer cell lines; covalent KRASG12C inhibitors blocked MEK signaling and synergized with PI3K inhibitors in KRASG12C- mutated cell lines. Synergy between inhibitors of mutant RAS and RAS effectors was dependent on intact RTK/WT RAS signaling and was lost in both RASless or SOSless MEFs. Dual knock-out of WT RAS isoforms in KRAS- and HRAS-mutated cancer cell lines reduced PI3K signaling in KRAS-mutant cell lines and MAPK signaling in HRAS-mutant cell lines and reduced proliferation, confirming our findings in MEF cells. Overall, our data highlight the critical role of WT RAS isoforms in supporting mutant RAS signaling and should be considered when designing combination therapies in RAS-mutated cancers.

Citation Format: Nancy E. Sealover, Bridget Finniff, Jacob Hughes, Hyun Lee, Robert L. Kortum. Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers [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 1925.
Abstract 1999: DCAF7 acts as a scaffold to recruit USP10 for G3BP1 deubiquitylation and facilitates chemoresistance and metastasis in nasopharyngeal carcinoma
Authors: Li Qing-Jie , Fang Xue-Liang , Li Ying-Qin , Lin Jia-Yi , Huang Cheng-Long , He Shi-Wei , Huang Sheng-Yan , Li Jun-Yan , Gong Sha , Chen Kai-Lin , Liu Na , Ma Jun , Zhao Yin , Tang Ling-Long
Published: March 2024

Though docetaxel plus cisplatin and 5-fluorouracil (TPF) induction chemotherapy becomes the standard care for locoregionally advanced nasopharyngeal carcinoma (NPC), some patients could not benefit from this therapy. The underlying mechanisms remain unclear. We found that DCAF7 was highly expressed in TPF resistant NPC patients, and promoted the cisplatin resistance and metastasis of NPC cells. Mechanistically, DCAF7 facilitates the interaction between USP10 and G3BP1, resulting in the removal of K48-linked ubiquitylation of G3BP1 at Lys76 mediated by USP10, thus preventing the degradation of G3BP1 through ubiquitin-proteasome pathway, and facilitates the stress granule (SG)-like structures formation. Moreover, knockdown of G3BP1 successfully reversed the SG-like structures formation and oncogenic effects exerted by DCAF7. Importantly, NPC patients with elevated DCAF7 expression exhibited high risks of metastasis, and is associated with a poor prognosis. This study identifies DCAF7 as a pivotal cisplatin resistance gene, and sheds light on the underlying mechanism of TPF resistance in NPC patients. The DCAF7-USP10-G3BP1 axis provides potential therapeutic targets and biomarker for NPC treatment.

Citation Format: Qing-Jie Li, Xue-Liang Fang, Ying-Qin Li, Jia-Yi Lin, Cheng-Long Huang, Shi-Wei He, Sheng-Yan Huang, Jun-Yan Li, Sha Gong, Kai-Lin Chen, Na Liu, Jun Ma, Yin Zhao, Ling-Long Tang. DCAF7 acts as a scaffold to recruit USP10 for G3BP1 deubiquitylation and facilitates chemoresistance and metastasis in nasopharyngeal 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 1999.
Abstract 2007: Neurolysin: A novel architect of the prostate cancer microenvironment and therapeutic resistance
Authors: Wang Choushi , Mu Ping
Published: March 2024

Introduction: Prostate cancer is the second leading cause of cancer-related death in American men, primarily driven by its ability to evade therapeutic interventions. This study uncovers a novel paradigm where neurolysin, a peptidase previously ascribed to neuronal function, orchestrates the tumor microenvironment (TME) by interfacing with cellular motor proteins. This interaction precipitates a series of events that not only fortify the cancer cells' survival but also underpin the resistance to antiandrogen therapies.

Experimental Procedures: We deployed advanced prostate cancer models to delve into the extra-neuronal influence of neurolysin, probing its role in the orchestration of the TME. An exhaustive suite of transcriptomic and proteomic analyses, complemented by comprehensive patient cohort studies, laid the foundation for unraveling the complex interplay between neurolysin, motor proteins, and the TME dynamics.

Results: Our data elucidates that neurolysin's depletion correlates with an altered TME, conducive to cancer proliferation and resilience against targeted therapies. This shift is mediated through neurolysin's interaction with cellular motor proteins, a liaison that appears to be a cornerstone in TME modulation. A significant subset of prostate cancer cases exhibits a neurolysin deficiency, paralleling more aggressive disease and therapeutic defiance, highlighting its role as a critical biomarker and a novel target for intervention.

Conclusions: Neurolysin steps into the limelight as a pivotal modulator of the TME, operating through mechanisms distinct from its known neuronal functions. Its interplay with motor proteins opens a novel avenue in prostate cancer biology, providing a unique perspective on the regulation of the TME and subsequent therapeutic resistance. Targeting this newly discovered regulatory axis presents a promising therapeutic strategy that could potentially redefine the clinical approach to managing prostate cancer and may have implications for other malignancies driven by similar TME alterations.

Citation Format: Choushi Wang, Ping Mu. Neurolysin: A novel architect of the prostate cancer microenvironment and therapeutic resistance [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 2007.
Abstract 2029: Investigation of anti-tumor activity of porcine myeloperoxidase for urothelial carcinoma of the bladder
Authors: Liu Junnan , Allen Robert C. , Stephens Jackson T. , Shah Paras , Huang Haojie
Published: March 2024

Introduction: Porcine myeloperoxidase (pMPO) is a cationic enzyme secreted by granulocytic leukocytes capable of selectively binding cancer cells due to their negative surface charge. In the presence of hydrogen peroxide (H2O2) and sodium chloride (NaCl), MPO catalyzes the production of electronically excited singlet molecular oxygen, which exerts focused cytotoxic activity against cancer cells.

Methods: Human bladder non-cancer (SV-HUC1) and cancer cells (T24 and 5637) were used to assess differential cytotoxic activity of pMPO. pMPO was combined with associated reagents, including H2O2, NaCl, and L-proline and glycine for 45 minutes to support the generation of singlet oxygen. MTS assay was used to assessed cell viability at day 3 post-treatment. Non-cancer and cancer cells were labeled with GFP and mCherry, respectively, via infection with lentivirus and cultured in tandem to allow for simultaneous treatment of both cell types. After the treatment, flow cytometry and microscopy were used to monitor the growth of the cells.

Results: No cytotoxicity was noted when SV-HUC1 cells were cultured with individual reagents pMPO, NaCl, L-Proline, or Glycine, and limited cytotoxicity was observed with H2O2. Notably, cell viability was nearly maximally preserved for SV-HUC1 cells. The combination of pMPO with associated reagents resulted in killing of 5637 and T24 cells, with tumoricidal activity maintained across increasing tumor cell density, with cell viability preserved for SV-HUC1 cells. Within the cell co-culture system, simultaneous treatment of both cell types with the pMPO treatment resulted in selective killing of tumor cells and preservation of SV-HUC1 cells. Mechanistic studies confirm specificity of pMPO binding to tumor cells, and further, high levels of expression of gammaH2AX and phospho-ATM in 5637 and T24 cells following treatment.

Conclusion: pMPO demonstrates selective and efficient killing of bladder cancer cells with minimal cytotoxicity against non-cancer urothelial cells. Given its reliance on direct surface contact with tumor cells for activity, pMPO may be developed as an intravesical therapy for treatment of non-muscle invasive bladder cancers.

Acknowledgements: This work was partially supported by Mayo funds provided to Dr. Haojie Huang.

Citation Format: Junnan Liu, Robert C. Allen, Jackson T. Stephens, Paras Shah, Haojie Huang. Investigation of anti-tumor activity of porcine myeloperoxidase for urothelial carcinoma of the bladder [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 2029.
Abstract 2046: Targeting cellular models of glioblastoma versus non-target and off-target cell populations using U87-MG membrane lipid-modified nanoliposomes
Authors: Janton Kaylee , Baamir Duha , Patel Aesha , Boco Sheren , Campbell Robert
Published: March 2024

Background: Glioblastoma Multiform (GBM) is an aggressive and malignant form of brain cancer known for its invasiveness and significant heterogenicity. The majority of GBM cases are linked to genetic mutations (ie. TP53, EGFR, and PTEN), which disrupt the normal regulation of cell growth and division, resulting in uncontrolled cell proliferation. The utilization of nanoparticles presents a promising approach for addressing the complexities associated with selective drug delivery to GMB and treatment. The purpose of this study was to investigate the effect of including U87-MG membrane lipid extracts in nanoliposomes using target, non-target, and normal healthy cellular populations in vitro.

Methods: The nanoliposomes employed for the experiments included various ratios of U87-MG lipid extracts (lipids derived from U87-MG cells), DOPC, Cholesterol, and DPPE-Rhodamine for fluorescence studies. The particle size and zeta potential values were measured and monitored throughout for consistency. Fluorescence intensity values (arbitrary units) were used to assess extent of cell binding, and uptake at the various time points. In vitro studies were employed to evaluate the cellular uptake activity of U87-MG-modified nanoliposome preparations using mixed ratios and compositions of lipid materials. Cell lines employed were, LN-18 (human glioma), T98G (human glioma), U87-MG (human glioma), 4TI (murine breast), and HBEC-5i (normal healthy) cells.

Results: The average size for the nanoliposomes (with and without lipid extract) fell within the range of 110 to 220 nm, while the zeta potential for the CLENs was negatively-charged. In vitro studies revealed that the inclusion of U87MG lipid extract in nanoliposomes increased cellular uptake in glioma cells when compared to control. Current investigations focus on different microenvironments, including non-target and off target cell populations. The findings from the cellular uptake analyses to date suggest that the in vitro cellular uptake of the CLENs varied in accordance with the total lipid extract content for all cell lines.

Citation Format: Kaylee Janton, Duha Baamir, Aesha Patel, Sheren Boco, Robert Campbell. Targeting cellular models of glioblastoma versus non-target and off-target cell populations using U87-MG membrane lipid-modified nanoliposomes [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 2046.
Abstract 2059: An image-based real time method to measure antibody-dependent cellular phagocytosis
Authors: Wang Jianyong , Shi Yongchang , Sun Yonglian , Koerber James T. , Seki Akiko , Rutz Sascha
Published: March 2024

Antibody-dependent cellular phagocytosis (ADCP) is an important mechanism of action of therapeutic antibodies. In vitro quantification of macrophage phagocytosis has been technically challenging. Flow cytometry assays were traditionally used for ADCP activity measurements, these methods were static measurements at certain time point, thus provide no information about engulfment kinetics. Moreover, the flow cytometry assays require lifting the macrophage cells from the labware which may affect macrophage activities. We have developed a real time ADCP assay using a live cell analysis system. The target cells labeled with a pH sensitive dye only fluoresce when they are engulfed in acidic phagosomes in the presence of specific antibodies. Our assay is a plate-based with a simple mix and read protocol without disturbing the macrophages. The new method is quantitative and robust, can be readily used for high-throughput screening for functional antibodies. By studying the ADCP activities of different subtypes of macrophages, we found M2 microphages showed the strongest ADCP activity compare to M0 and M1 macrophages, due to their different expression levels of FcgRs. The assay is highly sensitive to differentiate the antibody variants with enhanced Fc function. It can also be used to study the kinetics and mechanisms of ADCP.

Citation Format: Jianyong Wang, Yongchang Shi, Yonglian Sun, James T. Koerber, Akiko Seki, Sascha Rutz. An image-based real time method to measure antibody-dependent cellular phagocytosis [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 2059.
Abstract 2064: Unveiling the correlation between gemtuzumab-ozogamicin efficacy and CD33+ expression in AML primary samples using the novel AML vitroscreen
Authors: Gilardi Mara , Kaushik Garima , Walling Brandon , Schiavini Paolo , Cairo Stefano , Zipeto Marianna
Published: March 2024

Acute myeloid leukemia (AML) poses a significant therapeutic challenge, with a rising incidence in recent times. This clonal hematopoietic disorder of progenitor and stem cells exhibits aggressive behavior, and despite initial remission, recurrence is common1. The conventional shift from chemotherapy to monoclonal antibodies and antibody-drug conjugates (ADCs) has been hindered by the absence of AML-specific antigens. Notably, CD33, expressed strongly in 80-90% of AML cells, has become a target for gemtuzumab-ozogamicin (Mylotarg), the sole FDA approved ADC for AML treatment2. While advancements in understanding AML molecular mechanisms have influenced clinical approaches, the lack of clinically representative models hinders therapeutic progress. Existing models, both in vivo and ex vivo, struggle to capture the heterogeneity and complexity of AML3. Addressing this, we present our proprietary assay, Champions AML VitroScreen®4, designed for testing therapeutic candidates in primary AML samples. Our diverse bank of deeply characterized AML samples encompasses multiple subtypes, allowing evaluation of therapeutic responses through cell viability, proliferation, and clonal composition analyses. To validate our novel assay, we employed the VitroScreen platform to test Mylotarg across various AML subtypes, considering CD33 expression levels. By assessing more than 20 AML models, we determined the IC50 for Mylotarg and observed dose-dependent responses, where sensitivity to the drugh correlated with CD33 expression. Through multiple endpoints, including viability, proliferation, apoptosis, and phenotyping, we categorized primary AML models as responders, low responders, or resistant, establishing a strong positive correlation between Mylotarg sensitivity and CD33 expression. Our innovative approach, utilizing deeply characterized AML patient samples in the AML VitroScreen® platform, facilitates high-throughput drug testing. This system, serving as an ideal clinical translational setting in preclinical research, holds promise for developing tailored therapeutic strategies. Ultimately, this approach could significantly impact patient outcomes by offering improved strategies for both primary and recurrent AML cases.

Citation Format: Mara Gilardi, Garima Kaushik, Brandon Walling, Paolo Schiavini, Stefano Cairo, Marianna Zipeto. Unveiling the correlation between gemtuzumab-ozogamicin efficacy and CD33+ expression in AML primary samples using the novel AML vitroscreen [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 2064.
Abstract 2071: Pre-clinical evidence for new camptothecin-peptide conjugates in the treatment of sortilin-positive colorectal cancers
Authors: Das Sanjoy , Currie Jean-Christophe , Demeule Michel , Charfi Cyndia , Zgheib Alain , Nayyar Amit , Nguyen Anh Minh Thao , Danalache Bogdan Alexandru , Beliveau Richard , Marsolais Christian , Annabi Borhane
Published: March 2024

Limitations in current colorectal cancer (CRC) camptothecin (CPT)-based chemotherapy have mostly been attributed to low specificity and high systemic cytotoxic side effects. More effective therapies are therefore required to improve the clinical outcomes of patients with CRC. Here, we developed a selective and better anticancer drug delivery of CPT through conjugation to a peptide (TH19P01) that targets Sortilin (SORT1), a scavenging receptor expressed in various tumor tissues including CRC. In the current study, significant SORT1 expression was detected in various CRC cell lines as well as that of irinotecan analogs efflux pump (ABCG2) in LoVo and HT-29 cells. Considering this result, we used our proprietary peptide conjugation SORT1 technology to increase cell targeting selectivity and cell delivery efficacy of CPT analogs. Different peptide drug conjugates (PDCs) were generated linking the TH19P01 peptide to SN-38 (an irinotecan metabolite) or exatecan, which are two main CPT derivatives used in recent antibody drug conjugates (ADC) as payloads. In vitro, immunonofluorescent microscopy revealed that TH19P01 was rapidly internalized (<15 min) in a SORT1-positive human HT-29 CRC cell model. These PDCs also inhibited CRC cell proliferation at low nM concentrations (3-90 nM). In vivo, weekly administration of TH2101 (SN-38) and of TH2303 (exatecan) conjugates were well tolerated as they had little impact on mouse body weight but caused a more potent growth inhibition of the HT-29 CRC tumor xenograft model than did either unconjugated irinotecan or exatecan molecules. In fact, at their maximum tolerable dose, irinotecan and exatecan caused a tumor growth inhibition of only 48% and 45% whereas TH2101 and TH2303 inhibited the growth of HT-29 tumors by 83% and 91%, respectively. These results provide strong pre-clinical evidence for the future development of novel CPT PDCs therapeutics with targeting of SORT1-positive CRC cells.

Citation Format: Sanjoy Das, Jean-Christophe Currie, Michel Demeule, Cyndia Charfi, Alain Zgheib, Amit Nayyar, Anh Minh Thao Nguyen, Bogdan Alexandru Danalache, Richard Beliveau, Christian Marsolais, Borhane Annabi. Pre-clinical evidence for new camptothecin-peptide conjugates in the treatment of sortilin-positive colorectal cancers [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 2071.
Abstract 2128: Surufatinib treatment in pancreatic cancer: unveiling the role of GPR34 in TAMs and enhancing immunotherapy efficacy
Authors: Guo Xiaofan , Liu Yuxiao , Song Yuning , Huang Jing , Zhu Wenbo , Xu Peijun , Yu Jun , Gao Song , Hao Jihui
Published: March 2024

Background: Pancreatic cancer, often resistant due to its immunologically "cold" nature and tumor-associated macrophages (TAMs), presents challenges in chemotherapy and immunotherapy. This study uses single-cell transcriptomics to assess TAM subsets in response to surufatinib, an inhibitor targeting CSF-1R, FGFR1, and VEGFR1-3.

Methods: Surufatinib-treated patient samples were analyzed using single-cell RNA sequencing to identify altered macrophage subsets. Additional techniques, such as flow cytometry, tissue microarrays, co-culture assays, and macrophage-specific knockout mice, were used for further study. Western blot and immunofluorescence clarified the molecular functions of TAMs, and the impact of targeting these TAMs on PD-1 therapy was evaluated in a pancreatic cancer mouse model.

Results: Single-cell RNA sequencing revealed macrophage subsets with increased GPR34 expression following surufatinib treatment. The Gpr34fl/flLYZ2Cre mouse orthotopic-transplanted tumor model, treated with gemcitabine and albumin-bound paclitaxel, showed significantly reduced tumor growth compared to the control group, with notably lower percentages of exhausted T (Tex) cells and regulatory T (Treg) cells, and a significant increase in cytotoxic T cells in tumor tissue. LysoPS, produced by chronically injured pancreatic cancer cells, promotes the differentiation of bone marrow-derived monocytes (BMDM) into an immunosuppressive phenotype, an effect abolished after siGpr34 transfection. The LysoPS-GPR34 axis can significantly activate the NF-κB signaling pathway in BMDMs, potentially inducing the senescence-related secretory phenotype (SASP) and contributing to the macrophages' immunosuppressive phenotype. Combining a GPR34 antagonist with αPD-1 and PD-L1 inhibitors significantly curbed tumor growth and enhanced the immune environment in KPC mice.

Conclusions: Elevated GPR34 in TAMs enhances immunosuppression via the NF-κB pathway, affecting T cell distribution. GPR34's role could be key in optimizing surufatinib treatment for pancreatic cancer, indicating new therapeutic avenues.

Citation Format: Xiaofan Guo, Yuxiao Liu, Yuning Song, Jing Huang, Wenbo Zhu, Peijun Xu, Jun Yu, Song Gao, Jihui Hao. Surufatinib treatment in pancreatic cancer: unveiling the role of GPR34 in TAMs and enhancing immunotherapy efficacy [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 2128.
Abstract 2175: Multiple exposures to antibiotics and increased risk of colorectal cancer
Authors: Jani Niti , Richardson Maredith , Hogan Kristen , Pena Maria M.
Published: March 2024

Colorectal cancer (CRC) is the second leading cause of cancer related deaths in the United States and worldwide. In 2023, approximately 153,020 individuals will be diagnosed with CRC and 52,550 will die, including 19,550 cases and 3750 deaths in patients under 50 years of age. CRC in younger patients (less than 55 years) is known as early onset colorectal cancer (EOCRC). It is a growing global phenomenon whose incidence and mortality has incidence from 11% to 20% between 1995 to 2019 and is expected to increase by 140% by 2030. While it has been linked to known and established risks for CRC, the underlying causes and mechanisms are poorly understood. Based on our current knowledge of the disease, we propose that EOCRC results from exposure of children and young adults to exposome factors that have been increasing globally in the last four decades that may impact the microbiome causing dysbiosis and inflammation in the distal colon and rectum, the anatomical site of EOCRC. Among the likely factors is the use of antibiotics, particularly in infants and children. In this study we hypothesized that early life exposure to antibiotics causes dysbiosis and inflammation in the distal colon and rectum leading to increased mutations and epigenetic events that promote EOCRC development. Specifically, we examined the effect of the most commonly prescribed pediatric antibiotics on the gut microbiota and inflammatory environment in the colon, and their impact on tumor development upon exposure to a carcinogen. We treated A/J mice with multiples rounds of antibiotics and then exposed them to azoxymethane, a carcinogen to determine the effect on tumor development in the colon. The results showed that antibiotic exposure caused dysbiosis and inflammation in the colon of antibiotic treated mice as well as systemic inflammation in mice treated with antibiotics. Treatment with azoxymethane, a carcinogen in the presence of antibiotic-induced dysbiosis led to increased tumor burden in the distal colon. These results suggest a possible involvement of antibiotics on increased risk of EOCRC.

Citation Format: Niti Jani, Maredith Richardson, Kristen Hogan, Maria M. Pena. Multiple exposures to antibiotics and increased risk of 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 2175.
Abstract 2186: Bacterial lung cancer therapeutics from soil bacteria in New York City
Authors: Deb Dhruba , Danino Tal
Published: March 2024

The microbiome's diverse functions in human health have generated increasing interest in using live bacteria for cancer therapy. Due to their natural presence in colon, lung and breast tissue, bacterial therapies have been augmented using synthetic biology in order to treat infections, inflammation, and cancer. One major challenge is finding safe and effective host species and therapeutic payloads for a particular type of cancer. Here we explored the vast diversity of microbial isolates in the environment as a valuable source of novel therapeutic compounds that can be expressed by bacteria. Specifically, we isolated and identified soil bacteria from 25 local parks, and investigated their secreted compounds for anti-cancer activity using monolayer and 3D-spheroid cultures of lung cancer. Through metagenomic analysis, toxicology assays, varied growth conditions, and bacteria-cancer co-culture experiments, we found Bacillus spp. isolates from Manhattan parks' soil that secreted products with high, dose-dependent cytotoxicity against lung cancer models. We also demonstrate that Bacillus subtilis, a model organism for gram-positive bacteria, can colonize lung cancer tumor spheroids, pointing to its use as a viable strain for bacteria cancer therapy. The work presented here underscores the potential of harnessing environmental microbial diversity for the development of gram positive species and their compounds as cancer therapeutics.

Citation Format: Dhruba Deb, Tal Danino. Bacterial lung cancer therapeutics from soil bacteria in New York City [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 2186.
Abstract 2247: Cellular senescence as a potential mechanism underlying differences in chemoresistance between lung cancer cell lines derived from African-American and Caucasian patients
Authors: Semenova Nina , Robertson Camille C. , Yakisich Juan S. , Ayscue Robyn R. , Iyer Anand K. , Azad Neelam
Published: March 2024

Lung cancer remains the leading cause of cancer-related deaths world-wide. Statistical data reveals significant difference in both lung cancer incidence and death rate between African-American (AA) and Caucasian (CA) populations in the United States. Although these disparities can be partially attributed to socio-economical reasons, the biological mechanisms underlying them are poorly understood. In this study, we compared the chemoresistance of cell lines derived from tumor tissues obtained from AA patients (H23, H292) versus CA patients (A549, H460). The cell lines were treated with FDA-approved anti-cancer drugs as well as with cardenolide analogues previously reported by our group to have anti-cancer properties. Irrespectively of drug class, cellular senescence appeared to develop more abundantly in cells derived from AA patients. However, AA-derived cell lines manifested higher drug resistance in comparison to CA-derived ones, especially to cardenolide analogues. Recovery experiments in drug-free media revealed faster and more efficient re-growth after long-term (2 weeks) drug treatment in AA-derived cell lines. Taken together, the data provides a potential role for cellular senescence as mechanism of the differential chemoresistance observed between AA and CA lung cancer cell lines, revealing new potential targets for anti-cancer therapy.

Citation Format: Nina Semenova, Camille C. Robertson, Juan S. Yakisich, Robyn R. Ayscue, Anand K. Iyer, Neelam Azad. Cellular senescence as a potential mechanism underlying differences in chemoresistance between lung cancer cell lines derived from African-American and Caucasian patients [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 2247.
Abstract 2261: A scalable comparison of tumor immune atlases
Authors: Yang Jing , Liu Qi , Shyr Yu
Published: March 2024

Large single-cell atlases can serve as references for the analysis of smaller-scale studies. However, there are strong biases among atlases due to their varying sample sources, conditions, cell type annotation strategies and resolutions. Selecting appropriate atlas for future or smaller-scale studies is complicated due to unclear understanding of atlases, that limits the future or smaller-scale studies take advantage of the wealth of data that such atlases provide. For example, the tumor-infiltrating immune cell atlases including pan-cancer and cancer type-specific atlases provide comprehensive profiling of immune cells, which desperately facilitates future single-cell studies. However, lack of a comprehensive assessment and comparison of tumor immune cell atlases with standardized benchmarks blocked the application of the most appropriate atlas for smaller-scale study. In this study, we compared pan-cancer immune cell atlases including TICA, pan-cancer T cells and pan-cancer blueprint atlases, and cancer-type specific immune cell atlases containing ABTC, HCC and STAD atlases. We quantified the correlations of cell types and observed similar heterogeneity among atlases and unique immune cell populations in TICA as well. Then, we assessed the performance of atlases on accurately annotating immune cell types in the widely studied PBMC datasets—in which cell types were well annotated. Comparative analysis revealed the complementarity within atlases on mapping success, accuracy, clustering, annotatability and stability by benchmarking reference-based populations to reference-free de novo clustering on real immunotherapy datasets. We identified potential indicators of immune response and found that reference-based populations outperformed reference-free clusters in recognizing immunotherapy-related cell states. Our study can be easily extended to future atlases.

Citation Format: Jing Yang, Qi Liu, Yu Shyr. A scalable comparison of tumor immune atlases [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 2261.
Abstract 2276: Comprehensive analysis of the genomic landscape of thyroid cancer
Authors: Im SooHyun , Park Jong-Lyul , Kim Jae-Yoon , Jung Chan-Kwon , Kim Seon-Young
Published: March 2024

Thyroid cancer, the most common endocrine malignancy, has a high incidence worldwide. Meanwhile, the incidence of thyroid cancer ranks first in Korea. To assess the possible influence of ethnicity on the molecular profile of thyroid cancer, we compared the genomic features of South Korean thyroid cancer with European thyroid cancer. In this study, we performed whole genome sequencing profiling (WGS) for 459 Korean thyroid cancer patients, including papillary thyroid carcinoma (PTC, n = 274), noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP, n =18), follicular thyroid carcinoma (FTC, n = 16), follicular thyroid adenoma (FTA, n = 63), Hürthle cell adenoma (HCA, n = 22), and invasive encapsulated follicular variant papillary thyroid carcinoma (IEFVPTC, n = 19). We assessed the single nucleotide variant (SNV) and insertions and deletions using Mutect2, Varscan2, and Strelka2. For mutation signature and copy number alterations analysis, we used the Maftools and GISTIC2.0 packages, respectively. Our results revealed that most somatic mutations were similar between the Korean thyroid cancer dataset and the cancer genome atlas program (TCGA). However, the Korean cohort (1%) had a much lower NRAS mutation frequency than the TCGA cohort (8%). Mutation signature analysis showed that SBS6 and SBS2 were highly associated with the TCGA and Korean cohort. SBS6 is related to defective DNA mismatch repair, and SBS2 is characterized predominantly by CC > TT doublet base substitutions. In addition, we identified the NIFTP-specific somatic mutations such as KEAP1 and ZFP36L2. This study presents insights into the genomic landscape of Korean thyroid cancer and reveals some similarities and differences with European thyroid cancer at the molecular level.

Citation Format: SooHyun Im, Jong-Lyul Park, Jae-Yoon Kim, Chan-Kwon Jung, Seon-Young Kim. Comprehensive analysis of the genomic landscape of thyroid 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 2276.
Abstract 2325: NUWA-ms: A network-based method to infer quantification of missing proteins using multi-cohort proteomics profiles
Authors: Cao Lihua , Xie Yuhao , Chen Jiale , Wang Man , Zhao Tingting , Yang Heli , Du Yang , Yang Yang , Bu Zhaode , Ji Jiafu , Wu Jianmin
Published: March 2024

Although mass spectrometry is powerful for proteomic quantification, the inherent issue of missing values remains a significant challenge. We found a prevalent lack of quantification of valuable proteins (e.g., immune cell markers and drug targets) in published datasets, limiting the functional utilities of quantitative proteomic profiles. This was exemplified by the substantial lack of quantification of immune cell marker, which impede the dissection of tissue-infiltrating immune cells by deconvolution analysis of cancer proteomic profiles. Thus, we introduce a network-based method NUWA-ms for robust abundance inference of missing proteins using multi-cohort proteomic profiles. By evaluating 561 tumors with paired proteomic and transcriptomic profiles, a significant improvement of deconvolution performance was shown with the aid of NUWA-ms. This was further validated by the comparison between scRNA-seq and proteomic analyses of a same gastric cancer tumor tissue. NUWA-ms applications to cancer proteomic profiles facilitated the inference of CD8+ T cell markers and effector proteins, enabling the associations of CD8+ T cell infiltration with MSI status in colorectal cancer and anti-PD-1 therapy response in melanoma. These findings demonstrated the utilities of NUWA-ms in depicting infiltrating lymphocytes in the tumor microenvironment using proteomic profiles. Furthermore, based on the proteomic profiles of six patient-derived tumor organoids (PDOs), NUWA-ms application helped identifying PDOs sensitive to a targeted therapeutic agent including the ones neglected by the raw MS quantification, and aided in revealing the resistant mechanism. Together, NUWA-ms could enable a robust inference of protein abundance, to help identifying protein biomarkers and therapeutic targets for cancer and other complex diseases.

Citation Format: Lihua Cao, Yuhao Xie, Jiale Chen, Man Wang, Tingting Zhao, Heli Yang, Yang Du, Yang Yang, Zhaode Bu, Jiafu Ji, Jianmin Wu. NUWA-ms: A network-based method to infer quantification of missing proteins using multi-cohort proteomics profiles [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 2325.
Abstract 2379: The bispecific antibody KA-3007 against B7H3 and CD28 enhances T cell activation in solid tumors
Authors: Wu Guojin , Guo Zhengcheng , Peng Hao , Hao Feng , He Feng , Ning Jinying
Published: March 2024

Immunotherapy, revolutionizing the treatment of advanced solid tumors by blocking PD1 signaling, faces challenges as most cancers remain unresponsive to anti-PD-1 therapy. CD28, a key immune co-stimulatory receptor on T cells, often lacks ligands expressed on tumor cells. B7H3 is highly expressed in various solid tumors. In this study, we developed a bispecific antibody (BsAb) named KA-3007, targeting B7H3 and human CD28 to activate T cells in the tumor microenvironment. KA-3007, featuring an identical light chain, was developed using our common light chain bispecific antibody discovery platform with knob-into-hole technology. This BsAb is in regular IgG1 format with mutations in the Fc domain to eliminate ADCC, ADCP, and CDC activity. Its two Fabs bind to B7H3 with high affinity and CD28 with relatively low affinity. Co-culturing T cells with tumor cells expressing B7H3 enhances T cell activation. In PBMC humanized immunodeficient mouse tumor models, KA-3007 effectively suppresses the growth of NCI-H292 tumors, with or without a PD1 antagonist antibody. Furthermore, this antibody exhibits a half-life of more than five days in the blood of Balb/c mice. Finally, we assessed the developability of KA-3007 with different treatments such as high concentration, low pH, repeated freezing and thawing, and high temperature, and it shows neither aggregation nor degradation. In conclusion, the BsAb KA-3007, developed with our common light chain antibody discovery platform, emerges as a promising pre-clinical candidate drug for the treatment of solid cancers.

Citation Format: Guojin Wu, Zhengcheng Guo, Hao Peng, Feng Hao, Feng He, Jinying Ning. The bispecific antibody KA-3007 against B7H3 and CD28 enhances T cell activation in solid tumors [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 2379.
Abstract 2477: Selective IL-21 and IFN-alpha immunocytokines engineered using the AlphaSeq platform
Authors: Lin Charles , Shikany Colleen , Homad Leah , Fint Jessica , Bansal Ruchi , Goodnight Davis , Adamo Jeff , Van Citters Danielle , Swanson Ryan , Lopez Randolph
Published: March 2024

Although cytokine therapies have demonstrated curative effects in some cancer patients, clinical use remains limited due to undesired toxicity profiles accompanying systemic administration. Next generation cytokine approaches include conditional signaling focused on sites of interest, such as the tumor microenvironment or specific immune cell populations. Here, we share a novel approach for generating detuned cytokine therapeutic candidates using the AlphaSeq platform, which involves the re-engineering of yeast agglutination and mating to quantitatively measure protein-protein interactions at a library-on-library scale. Engineering interferon-alpha (IFNα) and interleukin-21 (IL-21), we show how AlphaSeq measures cytokine-receptor interactions and identifies cytokine variants with a broad range of affinities. A saturated mutational library was created for IFNα and IL-21and subsequently screened against a second library consisting of human IFNAR2 or human IL-21R, species orthologs and off-target receptors. AlphaSeq enabled identification of hundreds of detuned IFNα and IL-21 variants against both human and mouse receptors in parallel assays. Cytokine variants with lower affinity than parental IFNα or IL-21 were recombinantly expressed as Fc fusion proteins to orthogonally measure affinity with biolayer interferometry and characterize potency with an in vitro human PBMC phosflow assay, which showed strong correlation with AlphaSeq affinity measurements. Finally, detuned cytokine candidates were fused to anti-CD8 and other localizing antibodies to demonstrate cell population-specific signaling. Candidate molecules showed 1000-fold or greater potency in the targeted cell population than non-targeted populations. Our results show the AlphaSeq platform can accurately quantitate thousands of cytokine variant affinities simultaneously against multiple relevant receptors, enabling the selection of candidate immunocytokine antibody fusion proteins with targeted cell biased signaling. AlphaSeq’s rapid, comprehensive affinity determination is being used to develop clinically relevant IFNα and IL-21 therapeutic immunocytokines with accompanying preclinical data.

Citation Format: Charles Lin, Colleen Shikany, Leah Homad, Jessica Fint, Ruchi Bansal, Davis Goodnight, Jeff Adamo, Danielle Van Citters, Ryan Swanson, Randolph Lopez. Selective IL-21 and IFN-alpha immunocytokines engineered using the AlphaSeq platform [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 2477.
Abstract 2503: The role of APOBEC in early stage-EGFR mutant non-small cell lung cancer
Authors: Jung Hyun Ae , Lim Jinyeong , Choi Yoon-La , Park Sehhoon , Sun Jong-Mu , Ahn Myung-Ju , Lee Se-Hoon
Published: March 2024

Background: The APOBEC family of zinc-coordinating enzymes converts cytosines to uracils in single-strand DNA. APOBEC plays a crucial role in the mutation process of non-small cell lung cancer (NSCLC) and is essential for both adaptive and innate immune responses. This study aims to evaluate the role of the APOBEC mutation signature in early-stage non-small cell lung cancer (NSCLC).

Methods: We conducted whole-exome sequencing and whole-transcriptome sequencing using fresh tissue or formalin-fixed paraffin-embedded samples from 100 patients diagnosed with pathologic stage II-IIIA non-squamous NSCLC, all of whom underwent complete resection between January 2014 and December 2020 at Samsung Medical Center. This study aimed to assess the impact of APOBEC enrichment on disease-free survival (DFS), progression-free survival (PFS) of EGFR-TKI, and overall survival following recurrence.

Results: Median follow-up duration was 58.2 months (range, 11.3-141.1). Of the patients, 74% were never-smokers, and 52% had stage III disease. Among the 100 patients, 18 (18%) exhibited APOBEC enrichment (≥ 2). The median RFS was 25.2 months (95% CI, 17.3-33.2). Notably, APOBEC enrichment did not show a significant association with DFS (P=0.14). Among the 76 patients who experienced radiological recurrence, 69 received EGFR-TKI as first-line treatment. The median PFS for EGFR-TKI was 22.9 months (95% CI, 13.0-32.8). However, within this group, patients with APOBEC enrichment showed a shorter PFS compared to those without APOBEC enrichment (8.1 months vs. 24.6 months, P=0.014). In multivariate analysis, poor PFS of EGFR-TKI was associated with the type of EGFR mutation (L858R vs. exon 19 deletion, HR=1.9, P=0.04), TP53 mutation (mutation vs. wild type, HR=2.1, P=0.03), and APOBEC enrichment (≥ 2 vs. <2, HR=2.2, P=0.02). Overall survival from the starting EGFR-TKI was 61.1 months and 21.7 months for patients with APOBEC enrichment or patients without APOBEC enrichment, respectively (P=0.027).

Conclusions: APOBEC mutation signature may be presented at initial diagnosis of early-stage EGFR mutant NSCLC and it was associated with poor PFS of EGFR-TKI and overall survival.

Citation Format: Hyun Ae Jung, Jinyeong Lim, Yoon-La Choi, Sehhoon Park, Jong-Mu Sun, Myung-Ju Ahn, Se-Hoon Lee. The role of APOBEC in early stage-EGFR mutant non-small cell lung 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 2503.
Abstract 2517: The amplification of TPX2 is a potential biomarker of oxaliplatin-sensitivity of colorectal cancers (CRCs) with CIN phenotype
Authors: Ueno Shohei , Isobe Taichi , Taguchi Ryosuke , Tsuchihashi Kenji , Akashi Koichi , Baba Eishi
Published: March 2024

The amplification of Chr20q11.21 harboring TPX2 gene is the most frequent copy number alteration among the cases of colorectal cancers (CRCs), especially left-sided ones. We retrospectively examined 2828 cases of CRC patients who took cancer-genome panel tests in Japan between June 2019 and November 2022. The time to first-line treatment failure was longer with regimen with oxaliplatin than with those with irinotecan in CRC patients with Chr20q11,21 amplification (12.2 versus 9.2 months, p=0.0481). Oxaliplatin induces double-strand breaks (DSBs) and then cellular apoptosis. A key event of the DNA damage response to DSBs for cellular survival is the extensive phosphorylation of Ser139 of Histone H2AX adjacent to the chromosomal break. TPX2 whose gene resides in Chr20q11,21 has been reported to repress the phosphorylation of H2AX upon ionizing radiation. The purpose of this study is to identify the relationship between the amplification of TPX2 and oxaliplatin sensitivity in human CRCs. The knockdown of TPX2 decreased the oxaliplatin-susceptibility of COLO320 and Caco-2, CIN phenotype CRC cell lines which highly expressed TPX2. However, TPX2 knockdown did not reduce the oxaliplatin sensitivity of HCT-116, an MSI phenotype CRC cell line with low-level of TPX2 expression. The knockdown of TPX2 in CIN phenotype CRC cells, not in the MSI phenotype CRC cells, enhanced the phosphorylation of H2AX upon the DNA-damage induced by oxaliplatin. These findings suggest that amplification of TPX2 contributes to the oxaliplatin-susceptibility of CRCs with CIN phenotype through DNA repair machinery.

Citation Format: Shohei Ueno, Taichi Isobe, Ryosuke Taguchi, Kenji Tsuchihashi, Koichi Akashi, Eishi Baba. The amplification of TPX2 is a potential biomarker of oxaliplatin-sensitivity of colorectal cancers (CRCs) with CIN phenotype [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 2517.