tbuckley/cabot-search huggingface dataset:
Abstract 1928: Targeting FAK to improve the therapy of KRAS G12C mutant cancers
Authors: Shuang Liu, Junfen Shi, Chang Lu, Miao Zhang, Ying Xin, Yan Zhu, Jijun Li, Hong Luo, Yinghui Sun
Journal: Cancer Research (2024)

Abstract Despite the pivotal role of KRAS G12C in tumor initiation and progression, currently available KRAS G12C inhibitors have relatively modest activity compared to other approved therapies targeting other classic oncogenic drivers. Fortunately, efforts to improve the anti-tumor response to KRAS G12C targeted therapy have benefited from the use of combination approaches. Here, we found that treatment with KRAS G12C inhibitors induces sustained activation of focal adhesion kinase (FAK) in KRAS G12C mutant cell lines from various cancer types, including non-small cell lung cancer, colorectal cancer, and pancreatic cancer. These results suggest a potential role for FAK in adaptive resistance to KRAS G12C inhibition and encourage us to explore the anticancer effects of combining the KRAS G12C inhibitor SY-5933 with a FAK inhibitor, CT-707. The cell viability and clonogenic assays using various KRAS G12C mutant cancer cell lines showed that the combination of SY-5933 and CT-707 synergistically inhibited cell growth. Mechanistically, this enhanced anti-proliferative effect is associated with a significant decrease in FAK activity and a more pronounced induction of cell cycle arrest and apoptosis. In vivo efficacy studies in multiple cell line derived xenograft (CDX) models, the combination of SY-5933 plus CT-707 consistently induced a more potent anti-tumor response than either monotherapy alone. In conclusion, our results demonstrate that CT-707 has the potential to enhance the efficacy of SY-5933 by suppressing adaptive FAK activation under KRAS G12C inhibition. This provides a rationale for an innovative combination therapy to improve outcomes in patients with KRAS G12C mutated cancers. Citation Format: Shuang Liu, Junfen Shi, Chang Lu, Miao Zhang, Ying Xin, Yan Zhu, Jijun Li, Hong Luo, Yinghui Sun. Targeting FAK to improve the therapy of KRAS G12C mutant 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 1928.
Abstract 4897: Personalized cell surface target identification from pan-cancer RNA-seq and proteomics profiling of tumors
Authors: Giacomo B. Marino, Eden Z. Deng, Daniel J.B. Clarke, Weiping Ma, Pei Wang, Adam C. Resnick, Avi Ma'ayan
Journal: Cancer Research (2024)

Abstract In its third phase, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program collected pan-cancer data from 1,069 patients profiling the transcriptome, proteome, and phospho-proteome of tumors and adjacent tissues from ten cancer types. To identify potential immunotherapeutic candidates from this CPTAC cohort, we searched for cell-surface proteins that are highly expressed in tumor subtypes compared to their expression in normal tissues and cell types from ARCHS4 and the Genotype-Tissue Expression (GTEx) resources. For each cancer type, tumor samples were first clustered into subtypes based on RNA-seq data, and then cell surface targets were prioritized for each cluster. These targets were subsequently confirmed for high protein expression in the tumor subtypes. Tumor samples were also processed by their classification into immune subtypes to identify targets specific to hot (CD8+/IFNG+) and cold (CD8-/IFNG-) tumors of each cancer type. For each cancer type, the computational pipeline identified ~30 cell surface proteins that are highly expressed in the tumor and lowly expressed across tissues and cell types in both the ARCHS4 and GTEx backgrounds. Many of these targets are also robustly differentially expressed at the proteome level. Several targets were shared across tumor types, including VTCN1 and TMPRSS4. Altogether, this rational approach to identify potential targets demonstrates a pipeline that can be applied for personalized cancer diagnosis and therapeutic development. Citation Format: Giacomo B. Marino, Eden Z. Deng, Daniel J.B. Clarke, Weiping Ma, Pei Wang, Adam C. Resnick, Avi Ma'ayan. Personalized cell surface target identification from pan-cancer RNA-seq and proteomics profiling of 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 4897.
Abstract 4918: Cancer mutations converge on a constellation of molecular assemblies to predict resistance to replication stress agents
Authors: Xiaoyu Zhao, Akshat Singhal, SungJoon Park, JungHo Kong, Robin Bachelder, Trey Ideker
Journal: Cancer Research (2024)

Abstract Rapid proliferation is a hallmark of tumor cells, associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ensemble of predictive models that elucidate how cancer mutations impact the response to common RS-inducing (RSi) agents. The models implement recent advances in deep learning to facilitate multi-drug prediction and mechanistic interpretation. Instead of associating individual genetic alterations with RSi drug responses directly, the strategy is to project these alterations on a map of protein complexes and larger molecular assemblies associated with cancer. Initial studies in tumor cells identify 41 molecular assemblies that integrate alterations in hundreds of genes for accurate drug response prediction. These cover roles in transcription, repair, cell-cycle checkpoints, and growth signaling, of which 30 are shown by loss-of-function genetic screens to regulate drug sensitivity or replication restart. The model translates to cisplatin-treated cervical cancer patients, highlighting an RTK-JAK-STAT assembly governing resistance. This study defines a compendium of mechanisms by which mutations affect therapeutic responses, with implications for drug selection and combination. Citation Format: Xiaoyu Zhao, Akshat Singhal, SungJoon Park, JungHo Kong, Robin Bachelder, Trey Ideker. Cancer mutations converge on a constellation of molecular assemblies to predict resistance to replication stress agents [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 4918.
Abstract 6984: Investigating the function of the OSM-OSMR axis in pancreatic ductal adenocarcinoma (PDAC)
Authors: Yuan Sui, Tony Hunter
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal forms of cancer, characterized by a low survival rate and a significant global mortality impact. The interaction between PDAC and the immune system is complex and plays a crucial role in the progression of the disease. PDAC creates an immunosuppressive tumor microenvironment, which hampers the ability of immune cells to effectively infiltrate the tumor and mount an anti-cancer immune response. Additionally, there is an imbalance of cytokines, with an overabundance of immunosuppressive factors and a deficiency in pro-inflammatory cytokines. This hostile immunological landscape contributes to the aggressive nature of PDAC and hinders the success of immunotherapies and adjuvant treatments. One cytokine of particular interest is oncostatin M (OSM), a member of the interleukin-6 (IL-6) family. OSM has been implicated in the regulation of cancer and has been associated with poor overall survival in pancreatic cancer and other malignancies. Similar to other cytokines, OSM is secreted by immune cells and acts as a regulator of the inflammatory microenvironment surrounding the tumor. The levels of OSM in this milieu can potentially influence cancer development and regulation through multiple mechanisms. Despite the growing understanding of cytokines in cancer, research on the role of OSM in PDAC is still limited and requires further investigation to identify potential therapeutic targets. Therefore, there is a critical need to delve deeper into the functions of OSM and its receptor, oncostatin M receptor (OSMR), in the initiation and progression of pancreatic cancer. As such, our goal is to examine the functions of OSM and its receptor (OSMR) in initiating and advancing pancreatic cancer to better comprehend the role of the OSM-OSMR axis in PDAC, both in vivo and in vitro. Citation Format: Yuan Sui, Tony Hunter. Investigating the function of the OSM-OSMR axis in pancreatic ductal adenocarcinoma (PDAC) [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 6984.
Abstract 6979: Uncovering the BRAF interactome to identify novel therapeutic targets for BRAF driven melanoma and lung cancer
Authors: Kayla T. OToole
Journal: Cancer Research (2024)

Abstract BRAF protein kinases act downstream of RAS-GTP and upstream of MEK&amp;gt;ERK MAP Kinase signaling. Notably, mutational activation of BRAF is a driver of approximately 8% of all cancers, with a particular prevalence in lung cancer, thyroid cancer, and melanoma. Importantly, melanoma is responsible for the largest number of skin cancer deaths per year. Patients whose melanoma is driven by mutationally-activated BRAF account for ~50% of cutaneous melanoma cases. The most common mutational alteration is BRAFT1799A, which encodes the BRAFV600E oncoprotein kinase. Combined inhibition of BRAFV600E plus MEK1/2 has been approved for the treatment of BRAFV600E-driven melanoma and lung cancer. Although patients with mutationally-activated BRAF often have a significant response to BRAFV600E-targeted therapeutics, many patients develop lethal drug-resistant disease. The BRAFV600E oncoprotein kinase is proposed to be a monomer, yet many questions remain regarding the biochemistry of these signaling interactions. Thus, we aim to better understand the molecular mechanisms driving BRAFV600E-mediated melanoma and lung cancer cell growth. Preliminary data using gel filtration chromatography and immunoblotting analysis indicates that BRAFV600E is detected in a large multiprotein complex. Interestingly, the addition of a BRAFV600E inhibitor, vemurafenib, shifted the elution of complexes with BRAFV600E into lower molecular weight fractions. Based on these preliminary results, we characterized the components of these complexes to advance our understanding of how mutationally activated BRAF exists in melanoma cells; and thus, provide future insight into how we can better therapeutically target BRAFV600E. Moreover, in order to further elucidate BRAF interactions, we employed a novel form of proximity labeling, TurboID, to unbiasedly identify novel BRAF interactors and better understand how drug treatments change the BRAF interactome. The top ten statistically significant interactors are being investigated to understand how BRAF complexes are formed within the cell, how the complexes are influenced by drug treatments, and how important the individual components are in the formation of complexes with BRAF. Here, we investigate an interaction between BRAFV600E and the tumor suppressor, TP53. Moreover, elucidating the molecular architecture of BRAFV600E signaling complexes could highlight new therapeutic options for patients who display either primary or acquired resistance to inhibitors of BRAFV600E signaling. Citation Format: Kayla T. OToole. Uncovering the BRAF interactome to identify novel therapeutic targets for BRAF driven melanoma and 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 6979.
Abstract 5572: Microneedle-guided lymphatic delivery of a natural immune modulator toxin for enhanced cancer immunotherapy
Authors: Su Yeon Lim, Byung Deok Kim, PIN LIU, Ju hwa Shin, Ji Hoon Jeong
Journal: Cancer Research (2024)

Abstract Cancer immunotherapy has demonstrated significant potential as a cancer treatment by enhancing the immune system's ability to recognize and eliminate cancer cells. However, its efficacy can be limited by factors such as tumor heterogeneity, immunosuppressive tumor microenvironments, and systemic toxicities. Recent advances in drug delivery systems have facilitated the development of more targeted and personalized cancer therapies. Microneedles have emerged as a promising platform for non-invasive and highly localized drug delivery, directly administering drugs, vaccines, and other therapeutic agents to the skin. In this study, we designed dissolving microneedles (dMN) based on a biocompatible amphiphilic tri-block copolymer, which enables the self-assembly of nano-micelles containing hydrophobic drugs when applied to the skin. We used the dMN technology to formulate SKKU-06, a hydrophobic natural immune modulator toxin derived from fungi, which exhibits anti-cancer and immunomodulatory properties in melanoma (SKKU-06@dMN). After intratumoral application of SSKU-06@dMN to skin tumors, the drug-loaded nano-micelles can migrate to tumor-draining lymph nodes (TDLN). The dMN-guided delivery of SKKU-06 to skin tumors and TDLN induced immunogenic cell death and stimulated the activation and maturation of antigen-presenting cells (APCs), promoting the development of humoral and cellular anti-tumor immunity. Furthermore, the immunomodulatory effects of SSKU-06@dMN were enhanced when combined with anti-PD-1 treatment, impacting the tumor microenvironment through increased intratumoral CD8+ T cell infiltration and reduced Treg populations. This resulted in efficient growth inhibition of established skin cancer and metastatic cancer, as well as prolonged survival. The dMN-guided lymphatic delivery of SKKU-06 demonstrates the potential for treating metastatic solid tumors and improving cancer immunotherapy efficacy by modulating the tumor microenvironment. Citation Format: Su Yeon Lim, Byung Deok Kim, PIN LIU, Ju hwa Shin, Ji Hoon Jeong. Microneedle-guided lymphatic delivery of a natural immune modulator toxin for enhanced cancer 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 5572.
Abstract 2749: DHX36 may promote the growth and metastasis of lung cancer
Authors: Ting Li, Na Luo, Jiewen Fu, Chunli Wei, Junjiang Fu
Journal: Cancer Research (2024)

Abstract Introduction: Helicase is a kind of protein molecular motor that widely exists in eukaryotic cells, viruses and bacterial cells, and participates in DNA replication, transcription and other life activities. DHX36, a kind of helicase, is a new homologous gene of human DNA/RNA helicase cloned by our laboratory by homologous molecular cloning which used the sequence of the maleless gene (mle) of Drosophila. Studies have shown that DHX36 upregulates the expression of proto oncogene and promotes the occurrence of cancer. At present, there are few studies on DHX36 in lung cancer. This study aims to clarify the relationship between DHX36 and lung cancer and provide a new molecular target for the diagnosis, treatment and prognosis of lung cancer. Methods: Twenty-eight pairs of clinical tumor samples from lung adenocarcinoma and adjacent tissues were collected, and the protein expression of DHX36 in different tissues was detected by western blot. Correlation between DHX36 expression and survival prognosis of lung cancer patients was analyzed by online database. Over-expression of DHX36 in A549 and H460 cells and knockdown of DHX36 in A549 and H1975 cell lines, then the migration, invasion and growth index of cells were analyzed by real-time cell analyzer. After DHX36 stable knock-down cell line was established in H1975 cells, they were injected into nude mice by subcutaneous injection and tail vein injection respectively at the same time as the control cells, and the growth of subcutaneous tumors and the metastasis of lung tissues in nude mice were recorded and collected respectively. The tissues were analyzed by histology, immunohistochemistry, and western blot. Results: In 28 pairs of clinical lung cancer tumor samples, we found that DHX36 was higher in cancer tissues than in adjacent tissues in 23 pairs, which indicated that DHX36 might be a kind of proto oncogene to promote the occurrence and development of lung cancer. Bioinformatics analysis revealed that the high expression of DHX36 was related to the low survival of lung cancer patients. The results of RTCA showed that the abilities of growth, invasion and migration of cells in the over-expressed DHX36 groups were higher than those in the control groups. After DHX36 was knocked down, the growth, invasion and invasion of lung cancer cells were inhibited. Conclusion: DHX36 is expected to be a new molecular target of lung cancer. Next, we will knock out DHX36 in lung cancer cells to observe the tumor growth and lung metastasis in mice. Citation Format: Ting Li, Na Luo, Jiewen Fu, Chunli Wei, Junjiang Fu. DHX36 may promote the growth and metastasis of 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 2749.
Evaluation of chemical disposition in skin by stimulated Raman scattering microscopy
Authors: Panagiota Zarmpi, Dimitrios Tsikritsis, Jean-Luc Vorng, Natalie A. Belsey, Annette L. Bunge, Timothy J. Woodman, M. Begoña Delgado-Charro, Richard H. Guy
Journal: Journal of Controlled Release (2024)

Tracking drug disposition in the skin in a non-destructive and at least semi-quantitative fashion is a relevant objective for the assessment of local (cutaneous) bioavailability. Confocal Raman spectroscopy has been shown potentially useful in this regard and, importantly, recent advances have enabled the presence of applied chemicals in the viable epidermis below the stratum corneum (SC) to be determined without ambiguity and having addressed the challenges of (a) background signals from endogenous species and noise and (b) signal attenuation due to absorption and scattering. This study aimed to confirm these observations using a different vibrational spectroscopy approach - specifically, stimulated Raman scattering (SRS) microscopy - and the more conventional in vitro skin penetration test (IVPT). SRS is a nonlinear optical imaging technique which enables more precise location of the skin surface and enhanced skin depth resolution relative to confocal Raman microscopy. The method can also probe larger areas of the sample under investigation and identify the localization of the permeating chemical in specific structural components of the skin. Here, SRS was shown capable of tracking the uptake and distribution of 4-cyanophenol (CP), the same model compound used in the recent confocal Raman investigation, at depths beyond the SC following skin treatment with different vehicles and for different times. The SRS results correlated well with those from the confocal Raman experiments, and both were consistent with independent IVPT measurements. Acquired images clearly delineated CP preference for the intercellular lipid layers of the SC relative to the corneocytes. The stage is now set to apply these and other correlative techniques to examine commercial drug products.
Abstract 523: Aronia berry and oligomeric proanthocyanidins synergistically exhibit anticancer effects in colorectal cancer by inhibiting LMNB1
Authors: Yuan Li, Caiming Xu, Ajay Goel
Journal: Cancer Research (2024)

Abstract Background: Colorectal cancer (CRC) is one of the most common and recurrent diseases globally, ranking as the second leading cause of mortality. The high mortality rates associated with this disease are largely due to the ineffectiveness of current treatments and the development of chemotherapeutic resistance to conventional therapies. In recent years, several natural agents, such as Aronia berry extract (ABE) and oligomeric proanthocyanidins (OPCs), have shown promise in providing a safe, cost-effective, and synergistically multi-targeted treatment approach across various cancers. Herein, we hypothesized that the combined treatment with ABE and OPCs may synergistically regulate multiple oncogenic pathways, thereby presenting a more potent anti-cancer activity, particularly targeting CRC. Methods: We performed a series of cell culture experiments to evaluate the synergistic anticancer effect of the combination of ABE and OPCs in CRC cell lines. By performing genome-wide transcriptomic profiling, we identified specific growth-signaling pathways targeted by the combined treatment and subsequently validated these findings in cell lines and patient-derived 3D organoids. Results: The combined treatment with ABE and OPCs exhibited superior synergistic anti-tumor potential, affecting cell viability, proliferation, migration, and invasion in CRC cells. The transcriptomic analysis identified that LMNB1, associated with the cell apoptosis pathway Fold enrichment [FC]: 4.29, P =0.005), plays a crucial role in the anti-tumorigenic effects of these two natural products. Moreover, the combination of ABE and OPCs significantly altered the expression of key proteins involved in cell apoptosis and suppressed the expression level of LMNB1 in HCT116 (Combination vs. ABE, FC= 0.28; Combination vs. OPCs, FC= 0.24) and SW480 (Combination vs. ABE, FC= 0.65; Combination vs. OPCs, FC= 0.47), thereby inhibiting downstream Akt phosphorylation. Finally, we successfully demonstrated that the combined treatment displayed a superior anti-cancer activity in 3D organoids, significantly reducing both their number and size (P &amp;lt; 0.05). Conclusion: We present novel evidence for the synergistic anticancer effects of ABE and OPCs in CRC cells, which are in part achieved by regulating cellular apoptosis and the oncogene LMNB1 within the Akt signaling pathway. Citation Format: Yuan Li, Caiming Xu, Ajay Goel. Aronia berry and oligomeric proanthocyanidins synergistically exhibit anticancer effects in colorectal cancer by inhibiting LMNB1 [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 523.