bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 424: RTK inhibitor resistance in NSCLC harboring MED12 mutation is overcome by only blocking MEK signaling, not AKT due to mutated MED12-induced YAP-PTEN dysregulation
Authors: Ryu Hyun-Min , Kim Deokhoon , Yoon Shinkyo , Lee Ho-Su , Lee Eunjin , Lee Chang Hoon , Kim Wanlim , Seo Seyoung , Jung Kyung Hae , Park Sook Ryun , Kim Sang-We , Park Kang-Seo , Lee Dae Ho
Published: April 2023

The advent of receptor tyrosine kinase inhibitors (RTKi) are important contributions to treat NSCLC patients harboring genetic aberration effectively. Nevertheless, the emergence of acquired or intrinsic RTKi resistance by other RTK activation bypass finally limits their efficacy. First of all, in this study, we identified MED12 mutation in TKI-resistant NSCLC cells based-on NGS analysis. Although MED12 was known to controls the response to multiple cancer drugs through regulation of TGF-beta receptor signaling reportedly, we additionally found that MED12 mutation activates not only TGF-beta receptor not also other ones, such as EGFR, meaning that blocking TGF-beta receptor or EGFR alone may not effective to overcome MED12 mutation-induced RTKi resistance. To overcome the RTKi resistance in NSCLC harboring MED12 mutation, we elaborated the two downstream signaling of RTK in MED12 knock-out NSCLC cells and observed that PI3K/AKT signaling is downregulated but MEK/ERK signaling is upregulated. We observed that only MEK inhibitor (MEKi), not PI3K/mTOR inhibitor, shows effective anti-cancer effect. Therefore, we explored why MEKi alone is effective in RTKi resistant NSCLC cells harboring MED12 mutation and presented that MED12 mutation directly suppressed activation of YAP via blocking a large mediator complex of MED12, MED13, CDK8 and CCNC, thereby increasing PTEN expression by inhibition of miR-29 expression. Increased PTEN inhibits reactivation of PI3K/AKT pathway. In conclusion, we first identified that MED12 mutation induces RTKi resistance though activating other RTKs, such as TGF-beta receptor or EGFR, and blocks PI3K/AKT pathway via dysregulation of YAP/PTEN/AKT interaction. Therefore, among two downstream signaling of RTK, activated MEK/ERK pathway can be a definitive target enough to overcome RTKi resistant NSCLC patients harboring MED12 mutation and MEKi could be a primary treatment option for resistant patients harboring MED12 mutation among NSCLC patients with repetitive recurrence of RTKi resistance by another RTK activation bypass.

Citation Format: Hyun-Min Ryu, Deokhoon Kim, Shinkyo Yoon, Ho-Su Lee, Eunjin Lee, Chang Hoon Lee, Wanlim Kim, Seyoung Seo, Kyung Hae Jung, Sook Ryun Park, Sang-We Kim, Kang-Seo Park, Dae Ho Lee. RTK inhibitor resistance in NSCLC harboring MED12 mutation is overcome by only blocking MEK signaling, not AKT due to mutated MED12-induced YAP-PTEN dysregulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 424.
Abstract 4281: Data driven refinement of gene signatures for enrichment analysis and cell state characterization
Authors: Wenzel Alexander T. , Tamayo Pablo , Mesirov Jill P.
Published: April 2023

The use of gene expression data has been crucial to the functional characterization of changes in molecular pathway activity and for identifying targets for novel treatments. However, the interpretation of this data is complicated by its high dimensionality and the difficulty of identifying biological signals within a list of differentially expressed genes. Gene Set Enrichment Analysis (GSEA) is a standard method for identifying pathway enrichment in gene expression data by testing whether a set of genes whose expression would indicate the activity of a specific process or phenotype are coordinately up- or downregulated more than would be expected by chance. As GSEA relies on high quality gene sets with coordinately regulated member genes, we maintain the Molecular Signatures Database (MSigDB) which contains 9 collections of curated gene sets representing different biological pathways and processes. Over time, we have observed that some of the MSigDB gene sets, especially those that are manually curated or defined in a very specific biological context, may not provide a sensitive and specific enough co-regulation signature. In response, we have created a data-driven, matrix-factorization-based refinement method to build more sensitive and specific gene sets. This method incorporates large-scale datasets from multiple sources such as the Cancer Dependency Map as well as curated protein-protein interaction networks. We will present the initial results of this refinement method and our ongoing work which will yield a new collection of refined gene sets that will be made freely available in MSigDB for use with GSEA and many other applications.

Citation Format: Alexander T. Wenzel, Pablo Tamayo, Jill P. Mesirov. Data driven refinement of gene signatures for enrichment analysis and cell state characterization. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4281.
Abstract 4306: Identifying genetic dependencies of replication stress using interpretable artificial intelligence
Authors: Zhao Xiaoyu , Singhal Akshat , Ideker Trey
Published: April 2023

Rapid proliferation is a hallmark of tumor cells, associated with sensitivity to chemicals that cause DNA replication stress (RS). Due to sustained proliferative signaling and/or defective DNA repair, cancer cells undergo persistent RS making them strongly dependent on the replication stress response (RSR). A consequence of this dependency is that RS becomes an exploitable therapeutic vulnerability in cancer treatment. Classical RS drugs work predominantly by interfering with DNA replication in dividing cells. Recently, an increasing number of drugs have been designed to specifically target RSR proteins. However, molecular pathways responsible for drug response are incompletely understood. Here we build an interpretable deep-learning model aimed at understanding mechanisms of susceptibility and resistance to replicative stress. Instead of associating genetic alterations with drug responses directly, our approach is to project individual mutations on a map of protein complexes and larger molecular assemblies with prior evidence for involvement in cancer. This approach is prompted and supported by the concept that cancer is a network-based disease arising from the action of hallmark cancer pathways. Through systematic interpretation, the model identifies 37 complexes that integrate rare alterations in hundreds of genes for accurate response prediction. The complexes, which cover roles in transcription, DNA repair, cell-cycle checkpoint, and immunity, are further investigated by directed genetic perturbations, validating 24 for which RS effects are phenocopied by CRISPR guide RNAs. For complexes with poorly characterized functions, further insights are obtained via their profiles of in-silico activation across RS agents. This study creates a library of system-level genetic vulnerabilities governing replication stress, with implications for drug selection and combination.

Citation Format: Xiaoyu Zhao, Akshat Singhal, Trey Ideker. Identifying genetic dependencies of replication stress using interpretable artificial intelligence. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4306.
Abstract 4378: Risk factors for death in the emergency department for melanoma patients
Authors: Hsiung Jayla , Taneja Kamil , Patel Karan , Diaz Michael , Wolfe Jared , Toloza Eric M.
Published: April 2023

Introduction: Many cancer deaths are related to melanoma. While there have been many studies that have identified risk factors for death in these patients, very few of them have analyzed the risk factors for death in melanoma patients in the emergency department (ED).

Methods: We utilized the 2006-2012 Nationwide Emergency Department Sample to characterize melanoma patients who die in the ED. Multivariate logistic regression was used to identify patient and hospital characteristics that were significantly associated with a higher chance of death. A p-value ≤0.05 was considered significant.

Results: From 2006 to 2012, 239,956 melanoma patients presented to the ED, and 2.1% of these melanoma patients died. Most melanoma patients who died in the ED were over the age of 70 years (60.0%), male (63.8%), Medicare beneficiaries (65.6%), of the highest income quartile (31.0%), presenting to a hospital in the South (35.3%), presenting to non-trauma hospitals (48.3%), and presenting to metropolitan non-teaching hospitals (43.4%). The most common reasons for patients who died upon presentation to the ED were a secondary malignancy (20.7%), septicemia (10.8%), acute cerebrovascular disease (7.5%), pneumonia (5.2%), and congestive heart failure (2.6%). The top 3 factors associated with high risk of death were septicemia (odds ratio (OR)=7.39, 95% confidence interval (CI)=5.79-9.43; p<0.001), acute cerebrovascular disease (OR=3.44, 95%CI=2.62-4.51; p<0.001), and age >70 years (OR=2.50, 95%CI=1.24-5.03; p=0.010). Table 1 lists all risk factors associated with a higher risk of death.

Conclusion: Melanoma patients over the age of 70, with septicemia, acute cerebrovascular disease, or pneumonia, and of male sex are at higher risk for death in the ED. Clinicians should be aware of these risk factors when melanoma patients present to the ED.

Risk Factors Associated with Death for Melanoma Patients in the Emergency Department Risk Factor Odds Ratio (95% Confidence Interval) p-value Septicemia 7.39 (5.79-9.43) <0.001 Acute Cerebrovascular Disease 3.44 (2.62-4.51) <0.001 Age >70 2.50 (1.24-5.03) 0.010 Charlson Comorbidity Index of 3 or More 2.32 (1.89-2.84) <0.001 Pneumonia 1.76 (1.27-2.45) 0.001 Charlson Comorbidity Index of 1 1.64 (1.40-1.93) <0.001 Charlson Comorbidity Index of 2 1.63 (1.31-2.03) <0.001 Medicaid 1.63 (1.19-2.23) 0.002 Metropolitan Teaching Hospital 1.33 (1.05-1.68) 0.017

Citation Format: Jayla Hsiung, Kamil Taneja, Karan Patel, Michael Diaz, Jared Wolfe, Eric M. Toloza. Risk factors for death in the emergency department for melanoma patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4378.
Abstract 439: From foe to friend: In vivo reprogramming of tumor-associated macrophages to an anti-cancer phenotype by modulating N-myristoyltransferase activity
Authors: Kallemeijn Wouter W. , Spear Sarah , Walton Josephine , Bussi Claudio , Soudy Christelle , Flynn Helen R. , Skehel Mark , Carling David , Solari Roberto , McNeish Iain A. , Tate Edward W.
Published: April 2023

Tumor-associated macrophages (TAMs) play a central role in cancer by driving tumor growth, metastasis, therapy failure and cancer recurrence. Macrophage plasticity and diversity allows classification along a M1-M2 polarization axis, where TAMs have a M2-like polarization, associated with a pro-tumoral phenotype, whereas M1 macrophages exhibit anti-tumor functions. Reprogramming TAMs to a M1-like anti-cancer phenotype is an increasingly coveted therapeutic strategy in oncology. Here, we report TAMs can be favorably reprogrammed by modulating N-myristoyltransferase (NMT) activity using on-target, drug-like inhibitors (NMTi). We identified >100 N-myristoylated proteins differentially expressed by macrophages along the M1-M2 polarization axis. In TAM-like M2 macrophages, 42 N-myristoylated proteins exhibited higher NMTi sensitivity as compared to other polarizations, and these NMT substrates significantly enriched in anti-inflammatory, immunity- and metabolism-related pathways. Unique to TAM-like M2 macrophages, NMT modulation by NMTi induces significant transcriptomic and proteomic changes, effectively switching the polarization towards a M1-like anti-cancer phenotype that is characterized by a M1-like spindle morphology, a M1-like glycolytic state, and induction of a pro-inflammatory secretome exhibiting potent anti-tumoral activity towards ovarian cancer spheroids in vitro. In vivo proof-of-principle was established in the syngeneic, macrophage-driven ID8 mouse model for human ovarian cancer, where NMTi treatment significantly reprogrammed murine M2-like TAMs into a M1-like anti-cancer phenotype, concomitantly reducing tumor burden without observable side-effects, and significantly extending median survival by 16 days. We are currently further investigating the intricacies that N-myristoylation plays in macrophage polarization, as well as further establishing the scope of NMTi-driven in vivo reprogramming of TAMs beyond ovarian cancer.

Citation Format: Wouter W. Kallemeijn, Sarah Spear, Josephine Walton, Claudio Bussi, Christelle Soudy, Helen R. Flynn, Mark Skehel, David Carling, Roberto Solari, Iain A. McNeish, Edward W. Tate. From foe to friend: In vivo reprogramming of tumor-associated macrophages to an anti-cancer phenotype by modulating N-myristoyltransferase activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 439.
Abstract 4486: Proof of principle for pharmacogenomic-guided precision oncology for pediatric malignancy
Authors: Lee Gi Ju , Choi Seung-Won , Choi Seung Ah , Cho Hee-Jin , Gartrell Robyn , Lee Ji Won , Kim Joo Whan , Her Nam-Gu , Rabadan Raul , Sung Ki Woong , Nam Do-Hyun , Kim Seung-Ki
Published: April 2023

Childhood cancers are rare and clinically diverse. They are typically associated with few driver mutational events than adult cancers, constituting potential targets for patient-specific precision therapy approaches. Here, we evaluated the feasibility of using a patient-derived tumor cell (PDC) based drug screening system and integrated multi-omics data to achieve precision oncology for pediatric patients. We established a PDC library derived from a few passage-cultured tumor cells from surgically resected tumor specimens and conducted chemical screening, which composed of various target agents of major oncogenic pathways (e.g. receptor tyrosine kinase inhibitor, proteasome inhibitor and histone deacetylase etc.). Next Generation Sequencing was performed to characterize the genomic and transcriptomic traits of tumors. Overall, success of establishing PDCs of pediatric cancers was high (80.4%) and comparable to adult cancers. The amount of obtained tissue was an important factor for the success of PDC establishment; the estimated optimal weight for PDC establishment was small (1.14g) and it is noteworthy that a small amount of tumor sample is sufficient to identify the potential hit(s) of parental tumors. The platform provided therapeutic options to pediatric tumors regardless of actionable targets. Our PDC approach identified several potential gene-drug associations, including anti-PI3K/Akt agents for neuroblastomas and anti-SHH agents for sarcomas with EWSR1 fusion. Given that a considerable proportion of pediatric tumors still lack actionable targets with matched treatment options, PDC-based drug screening profiles can be an optimal therapeutic strategy for these cases. Collectively, our analysis confirmed the feasibility of PDC-based in vitro drug screening systems to guide the therapeutic strategy for pediatric patients. This approach will accelerate the preclinical research for pediatric tumors to understand their pathophysiology and investigate the potential therapeutic strategies to fulfill the future precision oncology.

Citation Format: Gi Ju Lee, Seung-Won Choi, Seung Ah Choi, Hee-Jin Cho, Robyn Gartrell, Ji Won Lee, Joo Whan Kim, Nam-Gu Her, Raul Rabadan, Ki Woong Sung, Do-Hyun Nam, Seung-Ki Kim. Proof of principle for pharmacogenomic-guided precision oncology for pediatric malignancy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4486.
Abstract 4495: A mechanistic study of the TFE3-splicing machinery gene fusions reveals a new druggable target for translocation renal cell carcinoma
Authors: Damayanti Nur , Orsi Sabrina , Cordova Ricardo , Rupert Christopher , Shen Li , Linehan William Marston , Staschke Kirk , Hollenhorst Peter , Heppner David , Pili Roberto
Published: April 2023

TFE3 is a member of basic helix-loop-helix leucine zipper MiT transcription factor family and its chimeric proteins are associated with translocation renal cell carcinoma (tRCC). Despite the variety of genes fusions, most of TFE3 fusions partner genes are linked to spliceosome machinery. Dissecting the function of TFE3 fused to spliceosome machinery factors (TFE3-SF) could direct the development of effective therapies for this lethal disease, which is refractory to standard treatments for kidney cancer. Here, by using a combination of in silico structure prediction, molecular cloning, next generation transcriptomics, FRET technology, mutagenesis, proteomics, and high-throughput high-content screening (HTHCS) we interrogated a series of oncogenic mechanisms of TFE3-SF-containing fusions, including spontaneous nuclear translocation, nuclear paraspeckle occupancy, enhanced in vitro proliferation and in vivo growth, transcriptome remodeling, alternative splicing reprogramming, and novel dimer partner recruitment. Molecular inhibition of TFE3-SF dimerization reverses its oncogenic activity and represents a potential new target for therapeutic intervention. By using HTHCS combined with FRET technology we screened FDA approved drugs library (LOPAC) and small molecule library (Microsource) and identified hits compounds which inhibit TFE3-SF dimerization. Hits compounds were validated in 2D and 3D models utilizing patient derived xenolines expressing TFE3-SF. Ouabain and terfenadine demonstrated decreased cell proliferation, reduced spheroid growth and in vivo tumor growth. Overall, our results unmask synthetic vulnerabilities of TFE3-SF dimerization for novel therapeutic strategies in patients with this aggressive type of kidney cancer.

Citation Format: Nur Damayanti, Sabrina Orsi, Ricardo Cordova, Christopher Rupert, Li Shen, William Marston Linehan, Kirk Staschke, Peter Hollenhorst, David Heppner, Roberto Pili. A mechanistic study of the TFE3-splicing machinery gene fusions reveals a new druggable target for translocation renal cell carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4495.
Abstract 4553: How do shiitake and reishi mushrooms work on lung cancer?: A high throughput screening of 3D cell culture
Authors: Yang Mihi , Jang Hee-Kyung , Kang Huiwon
Published: April 2023

Shiitake (Lentinula edodes) and reishi mushrooms (Ganoderma sichuanense) have been noticed for desirable chemoprevention, such as improving immunity, overcoming anticancer drug resistance, etc. Particularly, beta-glucans have been mostly mentioned as the active component of the mushrooms. However, the right preparation and effective usage of the mushrooms for cancers are unclear, yet. Thus, we screened various extractions of the two mushrooms and combinations of the extracts, using a high throughput screening of 3D cell culture system on 384-pillar plates with various cancer cells and Cell Titer-Glo 3D cell viability assay kit (Promega). We also quantified the beta-glucans in all extractions with the Megazyme Mushroom and Yeast Beta-Glucan kit (K-YBGL) by excluding the alpha-glucans content from the total-glucans. As results, most of the extracts showed cytotoxicity on the lung cancer cells, A549 cells, rather than on the other cells, such as HepG2 (N=9 for each treatment). The extracts of reishi mushroom in 60% of methanol (dose range, 0.21-2.3 mg/ml) showed the strongest cytotoxicity on the lung cells, IC50=0.90 +/- 0.01 mg/ml, among the extracts of different methanol contents (10-60%) or different temperatures (50-90 °C) of hot water. However, the 60 % of methanol reishi extracts included relatively low levels of beta-glucans, compared to other extracts (18.57 +/- 0.31 vs. 22.42 +/- 5.56 % w/w). In addition, the levels of beta-glucans in all of reishi mushroom extracts were lower than those in all of the shiitake extracts (17.70 +/- 1.89 % vs. 27.05 +/- 4.21 % w/w: p<0.01). Moreover, there was no association between the levels of beta-glucans and IC50 in A549 cells. Interestingly, the combination (1:1) of the above 60% of methanol extracts of reishi mushroom and the 30% methanol extracts of shiitake (dose range, 0.30-3.26 mg/ml) showed synergic effects, i.e., 2-7 fold stronger effects (average of IC50=0.40 mg/ml) than every single treatment (average of IC50=0.90-2.63 mg/ml). Taken together, the reishi mushroom may have other strong chemopreventive materials rather than beta-glucans, while the shiitake may have a potentiation effect, when combined with the reishi mushroom. In conclusion, our 3D cell culture system showed high throughput performance to find the right preparation and effective usage of the two mushrooms and provided useful information for the next clinical studies for lung cancer.

Citation Format: Mihi Yang, Hee-Kyung Jang, Huiwon Kang. How do shiitake and reishi mushrooms work on lung cancer?: A high throughput screening of 3D cell culture. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4553.
Abstract 4673: Therapeutic potential of polatuzumab vedotin for the treatment of diffuse large B-cell lymphoma
Authors: Qi Hui , Wang Fuyang , Han Bingrui , Wang Xiaomin , Qiang Xiangnan , Zhang Zhixiang , Gu Qiangyang
Published: April 2023

Background Diffuse large B-cell lymphoma (DLBCL) is typically treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). Although most patients can be cured with R-CHOP, up to one-third of them relapses with a dismal outcome in most cases. Numerous approaches have been attempted to improve the treatment outcomes with R-CHOP. Polatuzumab vedotin is an antibody-drug conjugate targeting CD79b, which is ubiquitously expressed on over 90% of B-cell NHL malignancies, including DLBCL. To determine the potential of polatuzumab vedotin as a therapeutic agent, we evaluate its potency across a series of DLBCL patient derived xenograft (PDX) models.

Method We established and characterized a series of DLBCL lymphoma PDX models. Eight DLBCL PDX models were selected for polatuzumab vedotin efficacy study, of which three are GCB DLBCL. Gene expression analysis of these lymphoma PDX models was performed using an Illumina NovaSeq 6000 system following Illumina-provided protocols for 2 × 150 paired-end sequencing. The expression status of CD79b on these DLBCL PDX models was also evaluated by IHC.

Conclusion Our data showed that a single dose of polatuzumab vedotin at just 2 mg/kg could reached a comparable effect with R-CHOP and no significant body weight loss was observed. Our result showed that there is no apparent correlation between polatuzumab vedotin responses (TGI) and the CD79b expression (IHC Score). Although polatuzumab vedotin demonstrated encouraging activity in the treatment of DLBCL, some of the PDX models are also resistant to polatuzumab vedotin treatment. To further investigate the molecular parameters of the relative sensitivity of polatuzumab vedotin. Gene expression profiling of those PDX models and their sensitivity to polatuzumab vedotin were conducted, we found that the expression level of BCL-XL was correlated with reduced sensitivity to polatuzumab vedotin.

Citation Format: Hui Qi, Fuyang Wang, Bingrui Han, Xiaomin Wang, Xiangnan Qiang, Zhixiang Zhang, Qiangyang Gu. Therapeutic potential of polatuzumab vedotin for the treatment of diffuse large B-cell lymphoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4673.
Abstract 4814: Compensatory interplay of p97 segregase and HSP70 chaperone protect cancer cells from heat-induced proteotoxicity
Authors: Skrott Zdenek , Chroma Katarina , Muller Petr , Panacek Ales , Bartek Jiri , Mistrik Martin
Published: April 2023

Due to malignant transformation, cancer cells are characterized by elevated levels of genotoxic, replication or proteotoxic stresses, which makes them vulnerable to various external conditions, including increased temperature. Thus, hyperthermia represents a very effective therapeutic modality usually combined with standard chemotherapy or radiation. Moreover, the elevated temperature is often used in experimental studies related to protein aggregation, cellular heat shock response and other proteostasis mechanisms relevant to cancer progression and treatment. Recently, we developed a single-cell method to inflict defined, subcellular thermal damage, adopting the plasmon resonance principle. Dose-defined heat causes protein damage in subcellular compartments, rapid heat-shock chaperone recruitment, and ensuing engagement of the ubiquitin-proteasome system, providing unprecedented insights into spatiotemporal response to protein damage relevant to cancer. Using this versatile method, we discovered so-far unsuspected compensatory interplay of p97 translocase, the ubiquitin-proteasome system and heat shock protein chaperones in the processing of heat-damaged proteins. As both, p97 and heat shock proteins, represent potential cancer-relevant drug targets, these results can contribute to the development and better implementation of related therapies in cancer treatment.

Citation Format: Zdenek Skrott, Katarina Chroma, Petr Muller, Ales Panacek, Jiri Bartek, Martin Mistrik. Compensatory interplay of p97 segregase and HSP70 chaperone protect cancer cells from heat-induced proteotoxicity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4814.
Abstract 4815: TMEM9 decreases ER stress-induced misfolded proteins via lysosomal protein degradation
Authors: Wi Dong-Han , Jung Su-Rin , Lee Seong-Ju , Jeon Ye-seul , Jung Youn-Sang , Park Jae-Il
Published: April 2023

The endoplasmic reticulum (ER) contributes to various protein modifications such as protein folding. Also, the ER-associated degradation (ERAD) complex removes defective proteins, which prevents the accumulation of misfolded proteins to avoid abnormality of physiological activity. Several physiological and pathological stimuli, such as hypoxia and nutrient starvation lead to unfolded protein responses (UPRs). Given that hyper-proliferation causes hypoxia and glucose shortening, cancer cells might induce UPRs resulting in misfolded protein accumulation and aggregation. Although the ERAD complex removes defective proteins, the capacity of the proteasomal degradation pathway is not enough to completely clear defective proteins in hyper-proliferative cancer cells. Thus, it is likely that cancer cells require additional misfolded protein degradation systems. Transmembrane protein 9 (TMEM9) has been identified as a vesicular acidification amplifier, which is upregulated in cancer cells for Wnt/β-catenin signaling activation via lysosomal protein degradation. In this study, TMEM9 downregulated ER stress-induced misfolded proteins that decrease cancer cell proliferation and viability. ERAD inhibitor declined cancer cell proliferation, reverted by TMEM9. Intriguingly, TMEM9 decreased ERAD-induced apoptosis instead of promoted autophagic cell death under glucose shorten conditions. Here we suggest that lysosomal protein degradation is an additional protein degradation system for the removal of defective proteins and contributes to stable cancer cell proliferation via the clearing of garbage proteins.

Citation Format: Dong-Han Wi, Su-Rin Jung, Seong-Ju Lee, Ye-seul Jeon, Youn-Sang Jung, Jae-Il Park. TMEM9 decreases ER stress-induced misfolded proteins via lysosomal protein degradation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4815.
Abstract 4820: The disassembly of amyloid-bodies
Authors: Kirk Chloe , Bokros Michael , Grunfeld Alex , Lee Stephen
Published: April 2023

The ability of cells to adapt to a wide variety of stress conditions plays a critical role in various physiological and pathological settings, including development, cancer and neurological disorders. We recently reported the discovery of stress-induced low complexity noncoding RNA derived from stimuli-specific loci of the ribosomal intergenic spacer (rIGSRNA); an enigmatic region of the human genome historically dismissed as “junk” DNA. We showed that low complexity rIGSRNA activate a physiological amyloidogenic program that converts the nucleolus into Amyloid-bodies: a molecular prison of immobilized proteins in an amyloid-like state. This conserved post-translational regulatory pathway enables cells to rapidly and reversibly store an array of endogenous proteins in Amyloid-bodies and enter a dormant-like phenotype in response to severe environmental insults. While many membrane-less compartments have been described as liquid-like (e.g., stress granules, P-bodies, germ cell granules), our discovery of Amyloid-bodies provided evidence of an amyloidogenic process that can physiologically transition biological matter to a solid-like state. The ability of mammalian cells to efficiently dissemble Amyloid-bodies raises a fundamental question: Are mammalian cell disaggregases involved in Amyloid-body disassembly? Here, we show that Amyloid-bodies undergo a solid-to-liquid-phase transition to release sequestered proteins and restore nucleolar functions. An RNAi screened identified key Heat Shock Proteins (Hsps) that remodel Amyloid-bodies back to the liquid nucleoli on stress termination. The composition of mammalian disaggregases differs considerably from non-metazoans and those involved in disassembly of pathological amyloids in vitro. Activation of mammalian disaggregases and Amyloid-body disassembly is dependent on ATP concentration. Conceptually, this work identifies metazoan disaggregases challenging the widely accepted paradigm that the amyloid state is irreversible in mammalian cells. The data also provides alternative insights into pathogenic amyloids by examining their disassembly in cellular systems.

Citation Format: Chloe Kirk, Michael Bokros, Alex Grunfeld, Stephen Lee. The disassembly of amyloid-bodies. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4820.
Abstract 4847: Investigating the transcriptional regulation by estrogen-related receptor alpha (ERRα) under different metabolic conditions
Authors: Hua Brittney A. , Chen Chien-yu , Li Yang , He Lina , Stiles Bangyan , Slarve Ielyzaveta
Published: April 2023

Estrogen-related receptors (ERRs) are orphan nuclear receptors identified based on their high sequence similarity to estrogen receptors (ERs), but ERRs do not have a known endogenous ligand. ERRs play a primary role in regulating the transcription of genes involved in mitochondrial and lipid metabolism and are abundantly expressed across tissues. Because of ERR’s role in metabolism, it is suggested that they may also play a role in tumor metabolism, where dysfunction in lipid metabolism promotes tumor cell growth. The ERR subfamily is comprised of three isoforms: ERRα, ERRβ, and ERRγ. Studies targeting the ERR isoforms found that the absence of ERRα presents obesity and insulin resistance with an increase in bone mass, deletion of ERRβ causes placental abnormalities and embryonic lethality, and deletion of ERRγ leads to mitochondrial dysfunction. Together, these studies strongly suggest that ERRs, particularly ERR α and γ, function primarily as metabolic regulators, with ERRα being the predominant isoform expressed in the liver. In addition, the mechanisms leading to lipid accumulation vary under different feeding conditions. Previous studies from our lab showed that PTEN and PI3K/AKT signaling regulates ERRa expression and its function. Furthermore, we demonstrated that inhibiting ERRα blocks liver steatosis and steatohepatitis developed in a mouse model where loss of tumor suppressor PTEN drives both steatosis and cancer development. In addition, we found that ERR-PA, a small molecule inhibitor for ERR, attenuated cancer cell growth and proliferation in both mouse hepatocytes and human cancer cell lines. Here, we report transcriptome network regulated by ERRα under different metabolic conditions and further explored its regulation by the PI3K/AKT pathway. A better understanding of the role ERRα plays in physiology will allow further development of ERR-PA as a potential therapy for liver steatohepatitis, which progresses to end stage cirrhosis and ultimately liver cancer.

Citation Format: Brittney A. Hua, Chien-yu Chen, Yang Li, Lina He, Bangyan Stiles, Ielyzaveta Slarve. Investigating the transcriptional regulation by estrogen-related receptor alpha (ERRα) under different metabolic conditions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4847.
Abstract 4945: Inhibition of wild-type PI3Kα signaling is required for durable efficacy in PI3Kα mutant cancer cells due to robust re-activation of wild-type PI3Kα signaling
Authors: MacDougall John R. , Zhong Mengqi , Merritt Hanne , Cid Joselyn S. Del , Bradley John , Mak Raymond , Dhawan Neil , Chen Wei
Published: April 2023

PI3Kα is the most mutated oncogene with a high mutation rate in breast, lung, colorectal, gastric, bladder, and other tumor types. However, current inhibitors have had little efficacy in the clinic due to their inability to achieve maximal PI3Kα target engagement in a highly specific and durable manner. Contributing to this is that most PI3Kα mutant cancer cells are prone to robust pathway feedback and re-activation of remaining wild type PI3Kα signaling upon initial inhibition. We have analyzed pathway feedback in a variety of PI3Kα mutant cancer cell lines across multiple diverse indications and found this to be a common trait among PI3Kα mutant cancer cells. Additionally, when the mutant PI3Kα protein alone is targeted in these cells using mutant-specific inhibitors, we observed robust pathway re-activation and tumor cell proliferation. In contrast, TOS-358, a highly selective first-in-class covalent PI3Kα inhibitor, achieved complete inhibition of both PI3Kα mutant and wild type signaling and this correlated with the induction of cell cycle arrest and cell death across a wide variety of PI3Kα mutant tumor types. Furthermore, stimulation of PI3Kα signaling with serum rapidly re-activated the PI3K-AKT pathway in the presence of reversible and mutant specific inhibitors. Covalent molecules (namely TOS-358) achieved complete inhibition of pathway signaling in this format. Overall, this reveals the need to achieve sustained inhibition of both PI3Kα mutant and wild type signaling to achieve durable efficacy in PI3Kα mutant tumors.

Citation Format: John R. MacDougall, Mengqi Zhong, Hanne Merritt, Joselyn S. Del Cid, John Bradley, Raymond Mak, Neil Dhawan, Wei Chen. Inhibition of wild-type PI3Kα signaling is required for durable efficacy in PI3Kα mutant cancer cells due to robust re-activation of wild-type PI3Kα signaling. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4945.
Abstract 4951: Proteasome inhibitor carfilzomib induces apoptosis via downregulation of AKT pathway in HPV negative HNSCC
Authors: Jeong Woo-Jin , Kim Jiyeong , Lee Hye-Yeon , Wang Zhiyong , Amornphimoltham Walt , Gutkind Silvio
Published: April 2023

Background Head and neck squamous cell carcinoma (HNSCC) presents in heterogenous sites, varied etiology and risk factors, and has diverse genetic background which confer dissimilar response to treatments, including chemotherapy. Here we tested the hypothesis that investigation of HPV presence in a HNSCC cell line would identify pathway contributing to oncogenesis of other HNSCC. We sought to identify pathways that differentially affect HNSCC according to the genetic background, therefore identifying targets and suitable candidate for treatment. We used genetic and pharmacological approaches to inhibit AKT pathway in HNSCC cell lines.

Materials & methods Chemical genetic library screening against 6 HNSCC cell lines were performed. The high throughput combinatorial small molecule screening for cell viability and apoptosis was carried out. Candidate agents were validated in both CAL-27 (HPV-negative) and UM-SCC-47 (HPV-positive) cell lines. Identified pathways and representative targeted agents were validated in vitro. Expression of related protein were confirmed by western blot assay.

Results EGFR, PIK3CA, mTOR, CDK1, HSP90AB1, HDAC1, and PSMD1 pathways were identified to be susceptible pathways in HNSCC using high throughput chemical genetic library screening. In vitro validation of carfilzomib showed IC50 of 7.07nM in CAL-27 cells and IC50 of 26.3nM in UM-SCC-47 cells. Knockdown of PSMD1 transcripts by transfected siRNAs reduced CAL-27 cells viability. Carfilzomib regulates the AKT pathway by decreasing t-AKT, p-AKT, p-ERK, p-S6 proteins and increasing p21 in CAL-27.

Conclusion Inhibition of AKT pathway treatment with proteasome inhibitor carfilzomib is effective in HPV-negative HNSCC cells. Taken together, our findings reveal carfilzomib induced the apoptotic pathway and suggest that carfilzomib, the representative of a new class of chemotherapeutic drug, may be utilized for overcoming cisplatin-resistance in human SCC.

Citation Format: Woo-Jin Jeong, Jiyeong Kim, Hye-Yeon Lee, Zhiyong Wang, Walt Amornphimoltham, Silvio Gutkind. Proteasome inhibitor carfilzomib induces apoptosis via downregulation of AKT pathway in HPV negative HNSCC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4951.
Abstract 4970: TNG462 is a potential best-in-class MTA-cooperative PRMT5 inhibitor for the treatment of MTAP-deleted solid tumors
Authors: Briggs Kimberly J. , Tsai Alice , Zhang Minjie , Tonini Matthew R. , Haines Brian , Huang Alan , Cottrell Kevin M.
Published: April 2023

MTAP deletions occur in 10-15% of all human cancers, which provides one of the largest precision oncology patient populations. MTA-cooperative PRMT5 inhibitors leverage the well-characterized synthetic lethal relationship between PRMT5 inhibition and MTAP deletion. TNG908 is a clinical stage MTA-cooperative PRMT5 inhibitor for the treatment of MTAP-deleted solid tumors. TNG462 is an investigational stage MTA-cooperative PRMT5 inhibitor with significantly enhanced potency, selectivity, and extended target coverage designed to be a best-in-class treatment for patients with MTAP-deleted cancer. In vitro, TNG462 is 45X selective for MTAP-deleted cancer cell lines over isogenic MTAP WT cell lines and has marked selectivity for MTAP-deleted cancer cell lines independent of lineage in a large, diverse cell line panel. Oral administration of TNG462 drives dose-dependent antitumor activity including durable tumor regressions and complete responses in cell line- and patient-derived xenograft models representative of clinically relevant histologies. Preclinical data suggest a low risk for drug-drug interactions, supporting clinical combination strategies. With enhanced potency and selectivity for MTAP-deleted cancer cells and improved pharmacokinetic properties to extend target coverage, TNG462 has the potential for broader and deeper clinical activity in MTAP-deleted solid tumors than the MTA-cooperative PRMT5 currently being evaluated in clinical trials.

Citation Format: Kimberly J. Briggs, Alice Tsai, Minjie Zhang, Matthew R. Tonini, Brian Haines, Alan Huang, Kevin M. Cottrell. TNG462 is a potential best-in-class MTA-cooperative PRMT5 inhibitor for the treatment of MTAP-deleted solid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4970.
Abstract 5056: ABN401 demonstrates robust anti-tumor efficacy in orthotopic PDX models of MET-driven NSCLC brain metastases in a pre-clinical study
Authors: Rajasekaran Nirmal , Park Kyung Eui , Lee Saehyung , Kim Na Young , Chung Suk-Jae , Shin Young Kee , Choi Jun Young
Published: April 2023

Background Brain metastases (BM) are manifested in approximately 30-50% of patients with non-small cell lung cancer (NSCLC) and are associated with catastrophic implications on prognosis and survival. The development of blood-brain barrier-penetrant therapies for brain metastases of NSCLC is imperative and is a major clinical hurdle. ABN401, a highly potent and selective c-MET inhibitor, shows promising anti-tumor activity without significant safety concerns in patients with advanced NSCLC. Here, we report that ABN401 exhibits potent anti-tumor efficacy in pre-clinical orthotopic patient-derived xenografts (PDXs) derived from MET-driven NSCLC brain metastases.

Methods Anti-tumor efficacy of ABN401 was assessed in two lung cancer PDXs (LU5349 and LU5406) from BM models harboring high-level MET amplification grown in NOD/SCID mice. Subcutaneous PDXs (n=14/group) were treated with ABN401 (60 mg/kg QD, 125 mg/kg QD, and 165 mg/kg QD) or control groups. Established PDXs were orthotopically implanted into the brain (n=14/group) and were treated with ABN401 (125mg/kg QD), or control groups. The tumor volume of orthotopic model was monitored using magnetic resonance imaging (MRI). Brain, plasma, and tumor samples were collected for pharmacokinetics (PK) and pharmacodynamics (PD) correlation analysis.

Results The efficacy of ABN401(125 mg/kg QD) was confirmed in the subcutaneous PDX models (LU5349 and LU5406). Treatment with ABN401 showed up to 95% and 99% tumor growth inhibition in the LU5349 and LU5406 models, respectively. ABN401 (125 mg/kg QD) treatment induced complete or near-complete tumor growth regressions in the orthotopic tumor model. ABN401 also showed a desirable PK and safety profile with no significant changes in body weight.

Conclusions ABN401 treatment showed robust anti-tumor efficacy in PDX models of MET-driven NSCLC brain metastases. Our findings suggest that ABN401 has excellent potential for treating NSCLC patients with BM and supports its ongoing clinical development.

Citation Format: Nirmal Rajasekaran, Kyung Eui Park, Saehyung Lee, Na Young Kim, Suk-Jae Chung, Young Kee Shin, Jun Young Choi. ABN401 demonstrates robust anti-tumor efficacy in orthotopic PDX models of MET-driven NSCLC brain metastases in a pre-clinical study. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5056.
Abstract 5101: Inhibition of Notch reverses immunosuppression in basal-like breast cancer
Authors: Shen Qiang , Murakami Kiichi , Ohashi Pamela , Reedijk Michael
Published: April 2023

Aberrant Notch activation is a defining feature of basal-like breast cancer (BLBC), which has poor prognosis compared to other breast cancer molecular subtypes. Despite the clinical success of immune checkpoint blockade (ICB) in many malignancies including melanoma and small cell lung cancer, ICB has failed to demonstrate similar response in BLBCs, where most cases are highly infiltrated by tumor-associated macrophages (TAMs). There is increasing evidence that Notch is decisive in regulating intercellular communication in the tumor immune microenvironment (TIME). This includes the recruitment of TAMs which contribute to an immunosuppressive TIME, illuminating the potential of Notch-inhibition as adjuvant immunotherapy in BLBC. To examine the immune phenotype and therapeutic response of BLBC to combined Notch-inhibition and ICB, we employed an in vivo tumorgraft model using murine basal-like mammary tumor 4T1 cells. Briefly, tumor cells were orthotopically injected into the mammary fat pads of BALB/c mice. Using a crossover design, mice were randomly allocated to treatment with either Notch inhibitor (γ-secretase inhibitor, LY411575), anti-PD1 (RMP1-14), or control treatment for 12-days (stage-1), followed by randomization to a second 12-day period (stage 2) with the same, or one of the other treatments. Results: Despite the low response rate of BLBC to ICB alone, Notch inhibition reduced TAMs and induced responsiveness to sequential ICB. This response was characterized by increased cytotoxic T lymphocytes (GrB+, CTL) infiltration of the primary tumor. Similar results were observed when Notch-regulated cytokines (IL-1β and CCL2), crucial to TAM recruitment, were inhibited. Moreover, a more impressive therapeutic effect of sequential treatment was observed in lung metastasis, whereby TAM depletion and increased CTL infiltration were accompanied with near-complete abolition of metastases. Mechanistically, tumor cell Notch signaling upregulates a group of circulating cytokines including IL-1β and CCL2, which prime the lung for metastases. Additionally, compared to primary tumor cells, PD ligand 1 is up-regulated in lung metastases, rendering them profoundly sensitive to sequential ICB treatment. These findings highlight the potential of sequential Notch inhibition and ICB as a novel immunotherapeutic strategy in BLBC.

Citation Format: Qiang Shen, Kiichi Murakami, Pamela Ohashi, Michael Reedijk. Inhibition of Notch reverses immunosuppression in basal-like breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5101.