bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1707: YAP-driven epigenetic reprogramming in head and neck cancer
Authors: Officer Adam , Faraji Farhoud , Ramirez Sydney , Goren Alon , Tamayo Pablo , Gutkind J. Silvio
Published: March 2024

The ability to measure tumor evolution is difficult due to a lack of model systems able to capture tumor initiation, development, and invasion. We have developed a Dox-inducible spatiotemporally controlled HPV- and YAP-driven model of head and neck squamous cell carcinoma (HNSCC) with a well-defined cancer stem cell population. In order to better understand the epigenetic reprogramming associated with tumorigenesis we have systematically characterized the chromatin accessibility, histone landscape and YAP binding sites in this model.

Cell lines were generated from tongue epithelia of normal and Dox-induced tumor-containing mice. Gene expression was measured using RNA-seq and chromatin accessibility was measured using ATAC-seq. CUT&Tag for H3K27me3, H3K27ac, and YAP was used to measure epigenetic reprogramming and YAP-DNA interactions.

Differential gene expression shows that genes involved in hormone signaling, glutathione-related metabolism, fatty acid metabolism and p53 signaling were highly enriched in the normal tongue suggesting a change in metabolism upon tumorigenesis.Differential ATAC-seq peaks with higher binding levels in the normal tongue showed enrichment for p53 motifs as well as homebox motifs including Otx2, GSC and CRX suggesting p53 signaling is lost upon carcinogenesis and lineage determination is altered. Motifs for TEAD, AP-1, and KLF5 were enriched in the tumor-specific ATAC-seq peaks showing that YAP is involved in chromatin accessibility changes. CUT&Tag for YAP shows clear YAP binding near canonical YAP target genes including Axl, Ccn1, Ccn2 and Birc3. YAP peaks with higher binding in the normal tongue cell line were enriched for RUNX2 and p63 motifs and peaks higher in the tumor contained KLF5 motifs showing YAP is directly involved in the reprogramming of lineage determination. Multi-omics integration shows YAP-driven chromatin remodeling is associated with differential expression of genes involved in keratin production, EGFR and ER signaling.

Direct epigenetic characterization of YAP involvement in tumor initiation is key to understanding the mechanisms of tumorigenesis in head and neck cancer. This work shows that YAP directly binds and affects the expression of genes involved in lineage determination and growth factor signaling to induce cancer progression and generate a cancer stem cell population.

Citation Format: Adam Officer, Farhoud Faraji, Sydney Ramirez, Alon Goren, Pablo Tamayo, J. Silvio Gutkind. YAP-driven epigenetic reprogramming in head and neck 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 1707.
Abstract 1747: The mutational landscape and its longitudinal dynamics in relapsed and refractory Hodgkin lymphoma
Authors: Witte Hanno , Künstner Axel , Hahn Thomas , Bernard Veronica , Stoelting Stephanie , Kusch Kathrin , Nagarathinam Kumar , von Bubnoff Nikolas , Khandanpour Cyrus , Bauer Arthur , Grunert Michael , Arndt Annette , Steinestel Konrad , Merz Hartmut , Busch Hauke , Feller Alfred , Gebauer Niklas
Published: March 2024

Introduction: In classical Hodgkin-lymphoma (cHL), only a few cases recur, and only a limited fraction of patients is primary-refractory to standard-polychemotherapy. Underlying genomic features of unfavorable clinical courses remain sparsely characterized. Here, we investigated the genomic characteristics of primary-refractory/relapsed cHL in contrast with long-term-responders (LTR).

Methods: Therefore, ultra-deep next-generation panel-sequencing was performed on a total of 59 samples (20 LTR, 26 relapsed (rHL: 11 initial-diagnosis, 15 relapse) and 13 primary-refractory (prHL: 8 initial-diagnosis, 5 progression) from 44 cHL-patients applying a hybrid-capture approach. We compared samples associated with distinct disease courses concerning their oncogenic drivers, mutational signatures, and perturbed pathways.

Results: Compared to LTRs, mutations in genes such as PMS2, PDGFRB, KAT6A, EPHB1, and HGF were detected more frequently in prHL/rHL. Additionally, we observed that in rHL or prHL, BARD1-mutations occur, whereas ETV1, NF1, and MET-mutations were eliminated through clonal selection. A significant enrichment of non-synonymous variants was detected in prHL compared to LTRs and a significant selection process in favor of NOTCH-pathway mutations driving rHL or prHL was observed.

Conclusion: This study delineates distinct mutational signatures between LTR and rHL/prHL, whilst illustrating longitudinal dynamics in mutational profiles using paired samples. Further, several exploitable therapeutic vulnerabilities for rHL and prHL were identified.

Citation Format: Hanno Witte, Axel Künstner, Thomas Hahn, Veronica Bernard, Stephanie Stoelting, Kathrin Kusch, Kumar Nagarathinam, Nikolas von Bubnoff, Cyrus Khandanpour, Arthur Bauer, Michael Grunert, Annette Arndt, Konrad Steinestel, Hartmut Merz, Hauke Busch, Alfred Feller, Niklas Gebauer. The mutational landscape and its longitudinal dynamics in relapsed and refractory Hodgkin lymphoma [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 1747.
Abstract 1826: New inhibitors of oncology targets discovered using the affinity-mediated selection of DNA-encoded chemical libraries followed by machine-learning
Authors: Keefe Anthony D. , AbouZleikha Mohamed , Baghaie AJ , Clark Matthew A. , Guie Marie-Aude , Guilinger John P. , Walsh Ryan , Zhang Ying
Published: March 2024

X-Chem’s DNA-Encoded Chemical Library platform generates a large amount of binding data for each target it is screened against. Here, we report the application of machine learning to these large datasets with case studies that include the identification of novel inhibitors of two oncology targets. One, ERα, is an estrogen-activated receptor that controls transcription and stimulates breast cell proliferation including in breast cancer. The second, DCAF1, is the substrate-recognition component of an E3 ligase complex that is associated with the proliferation of colon cancer cells. Over 100 billion DNA-Encoded compounds were synthesized and screened for their affinity to each target. The selection output data was then featurized and used to train multiple machine-learned models. Models with demonstrated predictive power were then used to score virtual catalogue compounds which were subsequently acquired and tested. A range of successful data-science strategies will be described including those that lead to double-digit nM inhibitors of each of DCAF1 and ERα.

Citation Format: Anthony D. Keefe, Mohamed AbouZleikha, AJ Baghaie, Matthew A. Clark, Marie-Aude Guie, John P. Guilinger, Ryan Walsh, Ying Zhang. New inhibitors of oncology targets discovered using the affinity-mediated selection of DNA-encoded chemical libraries followed by machine-learning [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 1826.
Abstract 1838: Advancing cancer research with Next-Generation Protein Sequencing™ on Platinum™ by Quantum-Si
Authors: Nguyen Khanh Dinh
Published: March 2024

Protein sequencing has the potential of playing a crucial role in advancing cancer research by providing insights into the specific proteins involved in cancer pathways. New discoveries from protein sequencing advance our understanding of cancer and potential targeted therapies. Here, we demonstrate the power of next-generation protein sequencing™ using the insight-generating Platinum™ platform. Individual peptides are digested from proteins and immobilized on a semiconductor chip and probed by dye-labeled N-terminal amino acid (NAA) recognizers, followed by subsequent aminopeptidase cleavage to expose each NAA in the peptide for recognition. By recording and analyzing fluorescent intensity, lifetime, and binding kinetics of each NAA binding event, we can decipher single amino acid substitutions and modifications.

To demonstrate the versatility of this methodology across proteins associated with cellular biology, we sequenced a series of interleukins: IL4, IL6, IL7, IL13, IL20, and IL34. Interleukins, a group of cytokines that play a vital role in cancer by modulating immune responses, promoting inflammation, and influencing tumor microenvironment, impacting tumor growth and the efficacy of treatments. We have successfully sequenced all the mentioned interleukins individually or within protein mixtures. Furthermore, we were able to sequence IL6 that was enriched through immunoprecipitation from human serum. Finally, we demonstrated the unique potential of Platinum in detecting post-translational modifications (PTMs) relevant to cancer, as exemplified by the successful identification of arginine citrullination in vimentin, an onco-protein that promotes cancer cell mobility and invasion into surround tissues.

These results demonstrate the transformative potential of next-generation protein sequencing using Platinum™ in enabling the identification of proteins in complex mixtures and biofluids, as well as the detection of critical PTMs implicated in human pathophysiology, offering valuable insights into cancer research.

Citation Format: Khanh Dinh Nguyen. Advancing cancer research with Next-Generation Protein Sequencing™ on Platinum™ by Quantum-Si    [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 1838.
Abstract 1859: Diverse CD28-binding IgG and heavy chain-only antibodies for T-cell engager development
Authors: Lam Katherine , Zhi Shirley , Kraft Lucas , Vigano Elena , Wei  , Faralla Cristina , Odekunle Esther , Bullock Kelly , Marshall Erin , Cid Melissa , Leung Grace , DeVorkin Lindsay , Duncan Sherie
Published: March 2024

Engagement of the CD28 co-receptor by T-cell engager (TCE) molecules can enhance activation, proliferation, and anti-tumor activities, particularly in immunosuppressive tumor microenvironments. In this study, we present data on a diverse panel of CD28-binding IgG and heavy chain-only (HCAb) antibodies for T-cell co-stimulation. Our diverse panel of CD28-binding antibodies add co-stimulatory building blocks to our TCE repertoire. Using single B cell-screening, we identified fully human IgG and HCAb binders to human and non-human primate CD28 with a high degree of sequence diversity. We selected a subset of antibodies for expression and assessed binding to both human and cynomolgus CD28-expressing cells. These antibodies displayed a wide range of binding avidities in the sub-nanomolar to micromolar range, and epitope binning analysis identified seven epitope communities. Co-stimulatory activity for a subset of molecules was assessed in vitro. Antibodies displayed a wide range of crosslinked T-cell activation with the majority showing no activation independent of crosslinking. Data presented here describe a diverse set of CD28-binding antibodies ready for engineering into co-stimulatory TCEs. Combining these molecules with our TCE platform or other T-cell activating strategies will enable development of novel TCE modalities with co-stimulatory function for diverse tumor targets.

Citation Format: Katherine Lam, Shirley Zhi, Lucas Kraft, Elena Vigano, Wei, Cristina Faralla, Esther Odekunle, Kelly Bullock, Erin Marshall, Melissa Cid, Grace Leung, Lindsay DeVorkin, Sherie Duncan. Diverse CD28-binding IgG and heavy chain-only antibodies for T-cell engager development [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 1859.
Abstract 194: Single-cell mechanical analysis reveals that astrocytes and glioblastoma cells have similar viscoelastic properties
Authors: Najera Julian , Onwudiwe Killian , Holen Luke , Burchett Alice A. , Rodriguez Dorielis , Zarodniuk Maksym , Siri Saeed , Datta Meenal
Published: March 2024

Despite recent advances in treatment, the survival rate of glioblastoma (GBM) patients remains low due to the cancer’s resistance to current treatment modalities. Solid tumors like GBM are known to harbor physical abnormalities at the tissue and cell level. An understanding of GBM cell mechanics may therefore lead to the identification of novel disease mechanisms, biomarkers, and therapeutic strategies to improve treatment outcomes. In this study, we aimed to compare the mechanics of human GBM cells and their normal counterpart, immortalized human astrocytes (IHAs). To accomplish this, we used a parallel-plate flow system to expose single cells to physiological fluid shear stress and recorded the resulting deformation using a camera-coupled microscope. We then utilized digital image correlation analysis to create strain-time profiles of individual cells and fit the profiles with a three-parameter generalized Maxwell model to characterize their nuclear and cytoplasmic viscoelastic properties. We also used fluorescence microscopy and atomic force microscopy to quantify actin density and alignment and adhesion energy in both cell types, respectively. Our results showed that, contrary to extracranial cancer cells, the viscoelastic properties of GBM cells are similar to their normal counterpart. This may explain why metastasis in GBM patients is rare and conventional treatment options are unsuccessful. We also found that actin organization and localization and adhesion energy is different between GBM cells and IHAs. Thus, future research which links the genetic and microenvironmental factors that modulate these unique mechanical features may lead to the development of rational and novel clinical strategies against GBM.

Citation Format: Julian Najera, Killian Onwudiwe, Luke Holen, Alice A. Burchett, Dorielis Rodriguez, Maksym Zarodniuk, Saeed Siri, Meenal Datta. Single-cell mechanical analysis reveals that astrocytes and glioblastoma cells have similar viscoelastic properties [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 194.
Abstract 1947: Studies on pMEK inhibitors for the treatment of RAS-mutant cancers as a single agent or combinations
Authors: Lv Xiaobing , Xu Min , Hu Yong , Zhao Lanjiao , Chen Xiuquan , Chen Youqin , Yang Chen , Li Jizhi , Chen Chen
Published: March 2024

RAS mutations are the most common oncogene in human cancers and KRAS has the highest frequency in non-small cell lung cancer (NSCLC) and pancreatic cancer (PDAC). KRAS G12C inhibitors have been approved to treat NSCLC patients. However, drug-resistance is eventually developed for these treatments. Preclinical studies suggested MAPK pathway reactivation is one possible mechanism. Among many MEK inhibitors in clinical development, CH5126766 binds to MEK1 inactive conformation and blocks its phosphorylation and activation. We believe this compound should prevent MAPK “paradoxical activation” commonly observed in most RAF and MEK inhibitors such as vemurafenib and cobimetinib. We studied this compound in various in vitro assays and found its potential in combating the paradoxical activation, which might be the cause of drug-resistance for MAPK signal pathway inhibitors, including RAS-, RAF- MEK- and ERK-inhibitors, as a single agent or in combination with above-mentioned inhibitors. In addition, we are developing a series of compounds based on CH5126766, by improving the inhibition of MEK1/2 kinase activity in addition to its activation. In summary, studies on the pMEK inhibitor demonstrated that this class of compounds might mitigate the MAPK pathway reactivation and prolong drug efficacies in clinical. Detailed research results will be discussed.

Citation Format: Xiaobing Lv, Min Xu, Yong Hu, Lanjiao Zhao, Xiuquan Chen, Youqin Chen, Chen Yang, Jizhi Li, Chen Chen. Studies on pMEK inhibitors for the treatment of RAS-mutant cancers as a single agent or combinations [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 1947.
Abstract 1952: Co-alterations in PIK3CA and ARID1A lead to enhanced sensitivity to PI3K inhibition
Authors: Udgata Shirsa , Stoecker Jordan N. , Lippert Anna L. , Pasch Cheri A. , Deming Dustin A.
Published: March 2024

Background: There is increasing interest in developing precision medicine strategies for cancers with PIK3CA mutations. Co-alterations in PIK3CA and ARID1A (AD) occur in ~1% of all cancers. Previously, patients with co-alterations in PIK3CA and AD have shown both an improved objective response rate and improved progression free survival following copanlisib (cop) treatment compared to cancers with PIK3CA mutations and wild-type AD. Here we evaluate potential mechanisms for this enhanced clinical benefit.

Methods: AD was knocked out in SW48 and SW48PIK3CA-H1047R (SW48PK) human 2D colorectal cancer cell lines using CRISPR (SW48AD; SW48PKAD). Knockouts were confirmed using PCR genotyping, amplicon sequencing, and western blot (WB). A cell proliferation assay (WST-1) was performed at increasing doses of cop for 48hrs to determine cell viability. WBs were performed at 6hrs and 24hrs after cop treatment to determine levels of phosphorylation of AKT, S6, and 4EBP1 and levels of apoptosis-related proteins (MCL-1, BCL-xL, BCL-2, PARP). Athymic nude mice were flank injected with SW48PK and SW48PKAD and treated with cop (10mg/kg in PEG400/acidified water (0.1N HCl, pH 3.5; 20/80, v/v) or vehicle for 25 days or until moribund.

Results: WST-1 assay showed highest sensitivity to cop in SW48PKAD cells compared to SW48, SW48PK and SW48AD. At 10nM (p=0.01), there was a significant difference in cell viability between SW48PK and SW48PKAD. No significant difference was seen in the phosphorylation (p) of AKT, S6, or 4EBP1 between SW48PK and SW48PKAD. Expression of MCL-1 protein decreased in SW48PKAD compared to SW48PK. No difference was seen in levels of BCL-xL and BCL-2. On treatment with cop, there was a greater reduction in pS6 in SW48PKAD at 24 hours compared to SW48PK, but no significant difference in pAKT and p4EBP1. There was a gradual increase in MCL-1, BCL-xL, and cleaved PARP in SW48PKAD overtime following cop treatment compared to SW48PK. In vivo, untreated SW48PKAD tumors grew more quickly than the SW48PK tumors (8-fold increase in tumor size in SW48PKAD compared to 5-fold increase in SW48PK by day 25, p=0.06). SW48PKAD mice had significant tumor reduction (p=0.002) on cop treatment by day 25; however, SW48PK mice did not.

Conclusions: ARID1A loss along with PIK3CA mutation leads to greater PI3K inhibition response most likely due to enhanced induction of apoptosis. Further confirmation of this enhanced sensitivity is required with better in vitro models such as patient-derived cancer organoids.

Citation Format: Shirsa Udgata, Jordan N. Stoecker, Anna L. Lippert, Cheri A. Pasch, Dustin A. Deming. Co-alterations in PIK3CA and ARID1A lead to enhanced sensitivity to PI3K inhibition [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 1952.
Abstract 1992: A novel RB1 E3 ligase TRIM37 contributes to palbociclib resistance in breast cancer
Authors: You Chanping , Tsoi Ho , Man Pui Sum , Chow Larry Ka Yue , Dai Wei , Khoo Ui Soon
Published: March 2024

The tripartite motif-containing 37 (TRIM37) is a RING finger E3 ubiquitin ligase and is a poor prognostic factor in breast cancer patients. The gene is located in chromosome 17q23, a region amplified in up to 40% of breast cancers. We observed that activation of androgen receptor (AR) could induce resistance to the CDK4/6 inhibitor Palbociclib, the mechanism yet to be clarified. ChIP-sequencing data suggested that AR binds to the TRIM37 promoter, with AR activation resulting in TRIM37 expression. We hypothesized that TRIM37 might be involved in Palbociclib resistance. Using an ER+ve cell line MCF7 and a TNBC cell line MDA-MB 453, we found that overexpression of TRIM37 could induce Palbociclib resistance. TRIM37 overexpression resulted in RB1 protein downregulation, which is the primary downstream target of CDK4/6, while TRIM37 knockdown enhanced RB1 protein expression. Ubiquitination assay demonstrated TRIM37 overexpression increased the level of RB1 protein ubiquitination. The co-immunoprecipitation (Co-IP) assay confirmed that TRIM37 protein could interact with the RB1 protein. These results suggest that TRIM37 could be the E3 ligase that regulates RB1 degradation. Various deletion mutants of TRIM37 were cloned for Co-IP experiments between these mutants and RB1. Results show that the MATH and c-terminal domains of TRIM37 was the essential region for the interaction. Overexpression of the mutant with the TRIM37 MATH and c-terminal domains (TRIM37-MATH/C) could enhance RB1 protein level. This might be due to competition of TRIM37-MATH/C with wild-type TRIM37 for RB1 binding. Our findings suggest TRIM37 is a novel RB1 E3 ligase, and it binds to the RB1 protein via the MATH and C-terminal domains to regulate protein degradation. Our study also suggests that high expression of TRIM37 mediated by AR activation could deplete RB1, which is the target of Palbociclib, eventually leading to resistance. These findings are supportive of the contribution of AR activation to Palbociclib resistance.

Citation Format: Chanping You, Ho Tsoi, Pui Sum Man, Larry Ka Yue Chow, Wei Dai, Ui Soon Khoo. A novel RB1 E3 ligase TRIM37 contributes to palbociclib resistance in breast 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 1992.
Abstract 2082: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Authors: Cook Ashley L. , Sur ojit , Dobbyn Laura , Watson Evangeline , Cohen Joshua D. , Ptak Blair , Lee Bum Seok , Paul Suman , Hsiue Emily , Popoli Maria , Vogelstein Bert , Papadopoulos Nickolas , Bettegowda Chetan , Gabrielson Kathy , Zhou Shibin , Kinzler Kenneth , Wyhs Nicolas
Published: March 2024

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen revealed disruption of kinase SMG1’s phosphorylation of UPF1 as a potent disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro. Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases.

Citation Format: Ashley L. Cook, ojit Sur, Laura Dobbyn, Evangeline Watson, Joshua D. Cohen, Blair Ptak, Bum Seok Lee, Suman Paul, Emily Hsiue, Maria Popoli, Bert Vogelstein, Nickolas Papadopoulos, Chetan Bettegowda, Kathy Gabrielson, Shibin Zhou, Kenneth Kinzler, Nicolas Wyhs. Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape [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 2082.
Abstract 2092: Genomic and proteomic analysis of glioblastoma recurrences during TTFields exposure
Authors: Cianci Francesca , Rey Guido , Krex Dietmar , Ceresa Davide , Malatesta Paolo , Mazzanti Michele
Published: March 2024

Glioblastoma (GB) is the most aggressive type of brain tumor, and current treatments are generally ineffective in preventing recurrence. Tumor Treating Fields (TTFields) are an innovative treatment that has been shown to improve patients' life expectancy in the last two decades. TTFields therapy has an antitumoral effect that involves different mechanisms and is an optional add-on to standard maintenance temozolomide. Although TTFields therapy initially slows tumor progression, it does not prevent tumor relapse in most patients. In the present investigation, we run a genomic and proteomic analysis of surgical material from 10 patients treated with TTFields. GB tissues were obtained from the primary tumor mass and from a second surgery after tumor relapse. All the patients, in addition to brain tumor standard therapies, were treated with TTFields for eighteen hours a day, the time span of treatment application was dependent on GB recurrence. Control samples were obtained from primary and secondary surgeries of 5 patients treated with standard therapy alone. The GB tissue extracts were analyzed with an RNAseq routine, and the results from the secondary surgery were compared with the data obtained from tumor specimens of the primary surgery. A common feature of transcripts among all the patients was the alterations of several pathways promoting the increase of intracellular oxidation and cell cycle regulation. In parallel with the analysis of patient specimens, we developed an in vitro GB cell relapse model. This was instrumental in investigating the beneficial contribution of TTFields action during tumor relapse, but also in uncovering the limitation of this therapeutic procedure. GB primary cultures obtained from patients' surgery were exposed for up to 12 days with 200 kHz TTFields stimulation using the inovitro™ system. After 12 days of continuous TTFields application, GB cells showed an average depolarization of the resting membrane potential, increasing oxidation, and acidification of the cytoplasm. Genomic analysis of treated cells compared with wild-type primary culture, denoted an increase of tumor stem cell markers, activation of several metabolic pathways, and upregulation of different ion channel protein transcripts. Our final goal is to identify specific molecular features enhanced by TTFields treatment to be used as a parallel therapy to fight GB recurrence.

Citation Format: Francesca Cianci, Guido Rey, Dietmar Krex, Davide Ceresa, Paolo Malatesta, Michele Mazzanti. Genomic and proteomic analysis of glioblastoma recurrences during TTFields exposure [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 2092.
Abstract 2097: ABT co-dose accelerated target validation with a fit-for-purpose HPK1 inhibitor tool
Authors: Methot Joey L. , Chen Joanna L. , Yu Elsie , Otte Ryan D. , Xu Haiyan , Xu Zangwei , Lacey Brian , Laskey Jason , Mcleod Robbie , Smith Dustin , Pasternak Alexander
Published: March 2024

Target validation can be challenging when mouse efficacy studies require achieving a high therapeutic exposure of a tool compound, ideally with a low peak-to-trough (P/T) ratio to avoid Cmax-induced toxicity. Herein, we describe the daily co-administration of the CYP inhibitor aminobenzotriazole (ABT) as a well-tolerated PK enhancer for medium-term efficacy studies in mice, enabling faster decision-making in the early space with imperfect tools. Genetic studies in mice have suggested that HPK1 inhibition would lead to enhanced effector T-cell function, decreased tumor growth and enhanced αPD-L1 efficacy. However, it remains unknown whether immune activation by pharmacological inhibition of HPK1 will recapitulate the genetic deletions. We developed a fit for purpose tool compound with picomolar HPK1 potency, excellent kinome selectivity (98% >100x, ATP-Km corrected), dose-dependent inhibition of pSLP76, sustained IL2 elevation in PBMCs, and IL6/TNFa elevation in dendritic cells. The mouse PK for this tool was inadequate, having a low exposure (AUC 16 uM-hr at 100 mg/kg po) and a high P/T ratio of 13 that could lead to an erosion of kinome selectivity in vivo; complicating efficacy interpretation and limiting overall tolerability. However, when co-dosed with ABT (50 mg/kg po 2 h prior to the HPK1 inhibitor), improved exposure of our tool was achieved (AUC 63 uM-hr at 100 mg/kg po), 90% inhibition of pSLP76 was maintained at C(trough), and the P/T ratio was reduced to 3 to avoid Cmax-induced toxicity. The inhibitor was well-tolerated co-dosed with ABT for three weeks in mice, enabling studies sooner to probe HPK1 pharmacological inhibition in cancer immunotherapy as a monotherapy as well as in combination with a mouse anti-PD-1 antibody.

Citation Format: Joey L. Methot, Joanna L. Chen, Elsie Yu, Ryan D. Otte, Haiyan Xu, Zangwei Xu, Brian Lacey, Jason Laskey, Robbie Mcleod, Dustin Smith, Alexander Pasternak. ABT co-dose accelerated target validation with a fit-for-purpose HPK1 inhibitor tool [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 2097.
Abstract 210: Carcinogenic influence of e-cigarette aerosols on breast and lung cancer models
Authors: Begum Rizwana , Thota Shilpa , Chintala Naveen , Sapkota Biplov , Pandit Abhishek , Francis Joseph
Published: March 2024

Background and Purpose: With the rising popularity of E-cigarettes among the youth, there is an urgent need to understand their long-term health implications, particularly the potential for carcinogenesis. Although tobacco smoking is established as a major cancer risk factor, the carcinogenic potential of E-cigarettes remains underexplored. Given that metastatic cancer accounts for most cancer-related deaths in the United States, elucidating the biological impacts of E-cigarette aerosols on cancer progression is critical for developing effective interventions. This study aims to address this critical gap by exploring the effects of E-cigarette aerosols on cellular models pertinent to breast and lung cancer.

Methods: Mouse breast epithelial cells (HC11), triple-negative breast cancer cells (4T1), and human lung adenocarcinoma cells (Calu-3) were exposed to E-cigarette aerosol at the air-liquid interface for one hour, followed by a 24-hour recovery period.

Results: Our study revealed that E-cigarette aerosols with mint flavor induce epithelial-to-mesenchymal transition (EMT) in both normal mammary epithelial and breast cancer cells. Furthermore, we also observed activation of the TGF pathway and an increased expression of stemness-related markers (OCT4, SOX2, NANOG, KLF4, and c-MYC) in 4T1 cells exposed to mint and menthol-flavored E-cigarette aerosols in both 2D and 3D cell culture environments. Microscopic examination at a 10X magnification level revealed that 4T1 and Calu-3 cells exposed to menthol-flavored E-cigarette aerosols exhibited signs of cellular disassociation and detachment whereas the control cells maintained discoidal aggregate morphology.

Conclusion: The data presented here illuminate a potential link between E-cigarette use and carcinogenic processes, challenging the notion of E-cigarettes as a safe smoking alternative. This research is of paramount importance to cancer research as it unveils possible new avenues for tumor progression, emphasizing the necessity for a critical evaluation of E-cigarette products.

Citation Format: Rizwana Begum, Shilpa Thota, Naveen Chintala, Biplov Sapkota, Abhishek Pandit, Joseph Francis. Carcinogenic influence of e-cigarette aerosols on breast and lung cancer models [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 210.
Abstract 2102: Understanding the mechanism of action of rigosertib in recessive dystrophic epidermolysis bullosa-associated squamous cell carcinoma through single cellanalysis
Authors: South Andrew P. , Han Suhao , Fortina Paolo
Published: March 2024

The allosteric inhibitor rigosertib (an experimental therapeutic) was previously identified as an effective inducer of G2M arrest and apoptosis in squamous cell carcinoma (SCC) keratinocytes isolated from patients with the rare genetic disease recessive dystrophic epidermolysis bullosa (RDEB), both in vitro and in vivo. Early clinical trial data treating RDEB-associated SCC with rigosertib has shown remarkable efficacy in a sub-set of patients and understanding the mechanism of action of rigosertib in this lethal cancer would provide rationale for patient stratification. Multiple mechanisms of action were previously attributed to rigosertib, including polo-like kinase-1 (PLK1), PI3-kinase, activated RAS and microtubule polymerization inhibition. Our published data comparing PLK1 siRNA with PI3-Kinase inhibitors, MAPK inhibitors and microtubule disruption favored PLK1 as a mechanism of action without definitive conclusion. We therefore sought to determine the mechanism of action using transcriptomic profiling. Flow cytometry experiments identified three main categories of time to increase G2M in nine separate RDEB SCC keratinocyte populations in culture ranging from 1 to 6 hours after exposure to 1uM rigosertib. Bulk-RNA sequencing of representative populations from time to G2M groupings failed to identify consistent transcriptional change after exposure to rigosertib. However, single cell sequencing was able to identify increases in sub-populations of cells associated with G2M as well as transient emergence of unique populations that were specific to individual patient populations after exposure to rigosertib in culture. Of note a transient population of RDEB SCC keratinocytes only present after 1 hour of exposure to rigosertib was characterized by increased expression of the potassium regulator KCNRG which has previously been associated with apoptosis in chronic lymphocytic leukemia. Ongoing work is determining the role this gene may play in the mechanism of apoptosis induction in RDEB SCC keratinocytes after exposure to rigosertib.

Citation Format: Andrew P. South, Suhao Han, Paolo Fortina. Understanding the mechanism of action of rigosertib in recessive dystrophic epidermolysis bullosa-associated squamous cell carcinoma through single cellanalysis [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 2102.
Abstract 2157: Evaluating cervical and lung cancer risk among Hispanic and Non-Hispanic Black women in three urban Texas counties
Authors: Chu Megan L. , Jayesh Irene E.
Published: March 2024

This study examines if there is a statistically significant difference in the risk of being diagnosed with cervical and lung cancer between Hispanic and Non-Hispanic Black (NHB) women in Tarrant, Dallas, and Bexar county.

Pulling from the National Cancer Institute’s Surveillance, Epidemiology, and End Results (SEER) Program, 2000-2020 trends in cancer diagnosis were measured by age-adjusted annual percent change (APC). Data was sorted by county and race/ethnicity and statistically insignificant measures were removed. APC measures were ranked relative to counties across Texas and the US. APC measures with 95% confidence intervals for Hispanic and NHB women in Tarrant, Dallas, and Bexar county were compared for a significant difference. Results from a previous study indicated that the slowest decreases in cervical cancer rates are found among Hispanic and African-American women in Tarrant and Dallas County. We built upon this study to assess if there was a statistically significant difference in the risk of developing cervical and lung cancer between these two groups. In Tarrant County (TC), the cervical cancer APC of Hispanic women was -1.8 [-3.4,0.1] and NHB women was -1.2 [-3.7, 1.3]. In Dallas County, the cervical cancer APC of Hispanic women was -2.1 [-3.4, -0.8] and NHB women was -1.8 [-3, -0.5]. This indicates that for both cities, Hispanic women saw a greater decrease in the APC in cervical cancer rates than NHB women.

In Tarrant County (TC), the lung cancer APC of Hispanic women was -2.7 [-4.5, -0.9] and NHB women was -2.1[-3.1, -1.1]. In Dallas County, the lung cancer APC of Hispanic women was -2.3 [-4.2, -0.4] and NHB women was -1.8 [-2.5, -1]. This indicates that for both cities, while Hispanic women saw a greater decrease in the APC in lung cancer rates than NHB women, the decrease is not statistically significant due to the overlap of the confidence intervals. Even though the confidence interval (CI) overlaps indicates insignificance, the APC can still provide valuable information regarding diagnostic trends seen in urban cities. The results showed that there is no significant difference between these two groups, suggesting that other county-level factors may play a role in diagnostic disparities seen between these two racial groups.

Citation Format: Megan L. Chu, Irene E. Jayesh. Evaluating cervical and lung cancer risk among Hispanic and Non-Hispanic Black women in three urban Texas counties [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 2157.
Abstract 22: Development and characterization of human tumor specific cytotoxic lymphocytes for preclinical drug development
Authors: Rohleff Ina , Gröne Lea , Lashuk Kanstantsin , Schueler Julia B.
Published: March 2024

Heterogeneity within a tumor allows it to better adapt to changing conditions and can have therefore a negative impact on a patient’s prognosis, response to treatment and overall health. Breast cancer is a highly heterogeneous disease caused by distinct genetic mutations in mammary epithelial cells, resulting in significantly different forms of the disease and a need for highly personalized treatment schemes for patients. Hence, it is important to develop and improve (immuno)therapies for breast cancer patients. Adoptive T-cell therapy with autologous CD8+ cytotoxic T cell lymphocytes (CTL) is a promising method that has already shown promising effects in melanoma patients. Unfortunately, there is almost no information about the use in breast cancer patients. We developed an in vitro protocol to generate tumor-specific CTLs by priming on HER2+ breast cancer cell lines JIMT-1 and SKBR-3. Subsequently, these primed CTLs were tested in 2D and 3D immune cell killing assays in a life cell imaging device in combination with an endpoint viability assay. The activity was compared with unspecific CD8+T cells activated by phytohemagglutinin (PHA) or αCD2/αCD3/αCD28, HER2-peptide specific T cells and HER2-CAR T cells serving as a positive control. We investigated the feasibility to freeze CTLs for use in subsequent studies and validated the relevance of HER2 as the main druggable target in the tumor lines using an siRNA approach. The CTLs were most effective on JIMT-1 in a 3D setting, whereas the SKBR-3 CTLs displayed similar activity in 2D and in 3D. The respective CTLs were tumor line specific, as SKBR-3 CTLs did not kill efficiently the JIMT-1 cells and vice versa. The same CTLs displayed the same efficacy pattern after thawing but less pronounced. Thus, within one experimental set-up it is recommended to use either one. The Her2 knockdown in the target cells reduced the killing activity of the CTLs slightly. However, this effect was not statistically significant proving the importance of CTLs as treatment option as well as neoantigens as targets in drug development. In summary, the CTLs proved to capture the respective tumor heterogeneity showing high killing rates in both SK-BR3 and JIMT-1 being more active than HER2-peptide specific T cells. The availability of CTLs in a preclinical setting facilitates screening approaches for combinational studies. Beyond that they can serve as starting material to develop cancer vaccines and identify highly immunogenic neoantigens.

Citation Format: Ina Rohleff, Lea Gröne, Kanstantsin Lashuk, Julia B. Schueler. Development and characterization of human tumor specific cytotoxic lymphocytes for preclinical drug development [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 22.
Abstract 2243: A multi-ethnic population-based pilot study of multiple myeloma disparities
Authors: Rolon Angelica M. , Vang April P. , Quino J. Elizabeth , Estrada Ana , Stewart Eric , Cress Rosemary D. , Carvajal-Carmona Luis , Arana Alexa Morales
Published: March 2024

To understand multiple myeloma (MM) disparities we established the Precision MEDicine, EqUity and Disparities Research in MultipLe MyeLomA (MEDULLA) study, a population-based study in California. Our study contacted, via the Cancer Registry of Greater California (CRGC), 100 adult MM patients from four racial/ethnic groups: Non-Hispanic Black (NHB), Non-Hispanic White (NHW), Latinos, and Asians. Data collection included variables reported to the CRGC, a self-administered survey, and biospecimen saliva collection. The survey focused on demographics, risk factors, cancer treatment, family history, quality of life, and social determinants of health. Of the 400 MM patients, we had 95 patients who responded to the survey, giving a response rate of 24%. 44% of those who responded were NHW, 21% NHB, 19% Latinos, and 16% Asians. Those that provided a response tend to be living in a census tract location with lower proportions of poverty (p=0.0004), higher proportion of adults ages 25 years or over with a college degree (p=0.0011), higher median household income (p=0.0048), lower proportion of adults ages 25 years or over without a high school diploma (p<0.0001), and a lower proportion of individuals ages 16 or over who are unemployed (p<0.006). All respondents also have a lower comorbidity count and expressed being in good health. For minorities, we identified a trend where a higher response rate is seen if they live in an area where median household income is higher (p=0.0108). For every 1% increase in poverty rates, NHW living in such neighborhoods were 3% less likely to respond to the survey (p=0.04). For every 10% increase in the proportion of individuals having a college degree, response rate increased by 1.17 for minorities in that neighborhood (p=0.07). Minorities living in neighborhoods with high proportions of adults without a high school diploma and high unemployment rates are less likely to respond (p=0.02 and p=0.047, respectively). In conclusion, we found significantly lower participation rates among minority groups, with socio-economic factors affecting response rates. Our findings, therefore, suggest that future studies must develop improved community-focused and culturally tailored strategies to engage and meaningfully understand MM etiology and survivorship in such populations.

Citation Format: Angelica M. Rolon, April P. Vang, J. Elizabeth Quino, Ana Estrada, Eric Stewart, Rosemary D. Cress, Luis Carvajal-Carmona, Alexa Morales Arana. A multi-ethnic population-based pilot study of multiple myeloma disparities [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 2243.
Abstract 226: Effect of MCL-1 inhibitor on organoids derived from cholangiocarcinoma patients with IDH1 mutation
Authors: Suzuki Shiho , Matsuzaki Juntaro , Muramatsu Toshihide , Kanai Yae , Saito Yoshimasa
Published: March 2024

Cholangiocarcinomas are highly aggressive malignancies with a poor prognosis. The global incidence of cholangiocarcinoma patients appears to be on the rise. While surgical resection remains the curative option for cholangiocarcinoma patients, the majority of cases are diagnosed at an advanced stage, resulting in poor outcomes. Patients with inoperable cholangiocarcinomas typically undergo chemotherapy regimens, including Gemcitabine, but their efficacy is limited, leading to low 5-year survival rates. Recent advancements in organoid culture technology allow for the in vitro replication of tissue structures by culturing tissue stem cells in three dimensions, offering great promise for personalized medicine. Utilizing patient-derived organoids has proven effective in predicting the outcomes of therapeutic drugs. We have successfully established organoids using cancer tissue derived from cholangiocarcinoma patients, and stably culturing and maintaining them, promoting their application to personalized medicine (Saito Y et al. Cell Rep. 27, 1265, 2019, Saito Y et al. Cancer Cell 40, 226, 2022). IDH1 mutations have been identified in approximately 15% of intrahepatic cholangiocarcinomas and are known to convert α-ketoglutarate (α-KG) in the TCA cycle to produce 2-hydroxyglutarate (2-HG), which is observed in gliomas and acute myeloid leukemia. 2-HG acts as an antagonist to α-KG-dependent dioxygenases, promoting cancer development. This study aims to develop a novel treatment for cholangiocarcinomas with IDH1 mutations. Metabolomic analysis of patient-derived cholangiocarcinoma organoids revealed 2-HG accumulation and reduced ATP production in IDH1-mutated cholangiocarcinoma organoids compared to IDH1 wild-type cholangiocarcinoma organoids. This may suppress the protein synthesis of MCL-1 and mTOR signaling through the activation of AMPK kinase, suggesting that further inhibition of MCL-1 could be lethal in IDH1-mutated cholangiocarcinoma organoids. Indeed, exposure to S63845, an MCL-1 inhibitor, significantly inhibited cell proliferation in IDH1-mutated cholangiocarcinoma organoids, unlike in IDH1 wild-type cholangiocarcinoma organoids. Furthermore, the combination of MCL-1 inhibitor and BCL-XL inhibitor demonstrated a synergistic and potent growth inhibitory effect on cholangiocarcinoma organoids. These findings indicate that the MCL-1 inhibitor holds promise as a new therapeutic agent for cholangiocarcinoma patients with IDH1 mutations.

Citation Format: Shiho Suzuki, Juntaro Matsuzaki, Toshihide Muramatsu, Yae Kanai, Yoshimasa Saito. Effect of MCL-1 inhibitor on organoids derived from cholangiocarcinoma patients with IDH1 mutation [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 226.