bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5495: Multiplexed analysis across cancers of diverse origins to unravel spatial interactions within the tumor microenvironment
Authors: Agrawal Vasundhara , Arvidson Lisa , Smith Michael J. , White Katie O. , Heil-Chapdelaine Richard A. , Jensen Samuel , BOSE ARINDAM
Published: March 2024

The tumor microenvironment (TME) is heterogeneous and is primarily composed of fibroblasts, extracellular matrix, immune cells, and blood vessels. Importantly, the tumor immune microenvironment (TIME) is a major source of cancer heterogeneity and influences both disease progression and response to therapeutic interventions. Malignant cells typically recruit various cell types such as vascular endothelial cells, cancer-associated fibroblasts (CAFs), and tumor-associated macrophages (TAMs) to promote tumor growth. Therefore, studying such a complex interplay among tumor, stromal cells, and immune cells within the TME necessitates a multiplexed analytical approach to investigate cancerous tissues from diverse origins, to ultimately predict clinical outcomes and design novel therapies. While numerous studies have been focused on investigating the expression patterns of immune-oncology markers within specific tissues, the extent to which such marker expression patterns are shared across tumors originating from various tissues is not adequately understood. In this study, we analyzed a large panel of Cell Signaling Technology (CST®) antibodies that are targeting immune, stromal, epithelial, and vascular markers in cancer tissues derived from various origins including lung, colon, and pancreas. Using multiplexed Cell DIVE imaging, key spatial interactions in the tumor microenvironment that are (1) tissue-specific, and (2) shared across tumors irrespective of origin were determined. Specifically, cluster analysis of a common panel of markers across tissues of different origins uncovered molecular signatures that are common to all cancer tissue types as well as those that are unique to specific tissue types to advance our understanding of the disease, and its progression, shedding light on the intricate interactions within the TME.

Citation Format: Vasundhara Agrawal, Lisa Arvidson, Michael J. Smith, Katie O. White, Richard A. Heil-Chapdelaine, Samuel Jensen, ARINDAM BOSE. Multiplexed analysis across cancers of diverse origins to unravel spatial interactions within the tumor microenvironment [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 5495.
Abstract 5503: Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response
Authors: Pratapa Aditya , Hernandez Lydia , Cheikh Bassem Ben , Jhaveri Niyati , Kulasinghe Arutha
Published: March 2024

Background Targeted immune checkpoint inhibitors (ICI) with anti-PD-1/PD-L1 therapy offer durable treatment of mucosal head and neck squamous cell cancer (HNSCC), in both human papillomavirus-positive (HPV+) and negative (HPV-) patients. However, currently available biomarker signatures for targeted ICI therapies have limited predictive value. Our recent ultrahigh-plex profiling of HNSCC tissue with 100+ cancer hallmarks of tumor and immunobiology uncovered distinct spatial domains that serve as defining factors for clinical response and resistance.

Methods Our unbiased analysis of whole-slide metastatic HNSCC tumors is from a clinical cohort of patients treated with Pembrolizumab/Nivolumab. The cohort consisted of patients with a range of outcomes from complete vs partial vs progressive disease responses to ICI therapy. We first characterized the tumor microenvironment using our ultrahigh-plex protein panel with 100+ antibodies on the PhenoCycler®-Fusion platform. To expand upon our biomarker discovery, we included multiomic cancer hallmarks with a multimodal protein/RNA detection panel. Targeted spatial RNA detection was performed to complement and augment the microenvironment characterization achieved by our protein panel. To further consolidate the multiomic data, we leveraged MaxFuse, a state-of-the art computational framework that integrates multimodal spatial and single-cell expression data.

Results Our multiomic spatial phenotyping uncovered diverse tumor regions, each with distinct biomarker expression that is reflected across modalities including protein, RNA, and metabolic activity, indicating regions likely associated with resistance to immunotherapy. Our multiomic data integration also revealed spatial signatures associated with different tissue compartments, such as the tumor and non-tumor associated tertiary lymphoid structures.

Conclusions We demonstrate a multi-pronged approach that incorporated both novel experimental and computational techniques for elucidating tumor microenvironment in HNSCC tissue prior to ICI-based immunotherapy. Our multiomic approach provides deeper characterization of the HNSCC at the transcriptomic and proteomic level incorporating depth across the entire transcriptome and single-cell spatial resolution of key protein determinants for predicting and furthering our understanding of immunotherapy response to ICI therapy.

Citation Format: Aditya Pratapa, Lydia Hernandez, Bassem Ben Cheikh, Niyati Jhaveri, Arutha Kulasinghe. Ultrahigh-plex spatial phenotyping of head and neck cancer tissue uncovers multiomic signatures of immunotherapy response [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 5503.
Abstract 5523: granulocyte-colony stimulating factor secreted from cancer associated fibroblasts initiates tumorigenesis and metastasis in triple negative breast cancer
Authors: Gotoh Noriko , Tacheuchi Yasuto , Murayama Takahiko , Kashimura Risa , Ikeda Kazuhiro , Horie Kuniko , Inoue Satoshi , Okamoto Koji
Published: March 2024

Although cancer stem-like cells (CSCs) interact with cancer-associated fibroblasts (CAFs), it remains obscure how it occurs and what are the functional roles of this interaction. When patient-derived breast cancer cells (BCCs) were co-cultured with CAFs, significantly more spheroids were formed compared to those cells cultured alone. This suggests that CAFs produce soluble factors that increase the tumor-initiating ability of CSCs. Transcriptome analysis revealed that the expression of granulocyte colony stimulating factor (G-CSF) was highly upregulated in the conditioned medium of CAFs co-cultured with BCCs. Tumor-initiating ability was increased in the presence of G-CSF. Furthermore, G-CSF neutralizing antibody treatment suppressed tumorigenesis and bone metastasis in the patient-derived xenograft (PDX) model. These findings indicate that G-CSF secreted by CAFs induces CSCs to initiate tumors and metastasis. Inhibition of G-CSF would be a novel therapeutic target for breast cancer.

Citation Format: Noriko Gotoh, Yasuto Tacheuchi, Takahiko Murayama, Risa Kashimura, Kazuhiro Ikeda, Kuniko Horie, Satoshi Inoue, Koji Okamoto. granulocyte-colony stimulating factor secreted from cancer associated fibroblasts initiates tumorigenesis and metastasis in triple negative 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 5523.
Abstract 5553: Glycan CA19-9 mediated immune modulation in the pancreatic tumor microenvironment
Authors: Hsu Jasper , Oh Tae Gyu , Peck Kristina L. , Rock Angelica E. , Bishop Garret , Okhovat Shira R. , Kaech Susan M. , Engle Dannielle D.
Published: March 2024

Pancreatic ductal adenocarcinoma (PDA) is an intractable common malignancy with a pro-tumorigenic and immunosuppressive microenvironment (ME) that often limits treatment efficacy. Only 10-15% of patients are eligible for surgical resection, which is the only cure for PDA. The glycan CA19-9 is used to follow treatment response in PDA patients, but its functional role in PDA remained unknown until recently because rodents lack the ability to produce this carbohydrate. CA19-9 elevation in a KRAS-mutant background results in increased tumor proliferation and ME remodeling in mice. The tumor ME is encompassed by hypovascularized stroma consisting of cancer associated fibroblasts (CAFs) and tumor associated macrophages (TAMs) that contribute to desmoplasia and immunosuppression. All prior work investigating the tumor ME in PDA mouse models was performed in CA19-9 negative context, potentially missing a key element of PDA biology. Elevation of CA19-9 in mice caused expansion of both antigen-presenting (ap)CAFs and TAMs. CA19-9 induction in KRAS-mutant organoids increased gene expression of M-CSF, IL1a, and TGFb and led to increased apCAF and TAM differentiation. This project aims to uncover the mediators of CA19-9-mediated ME remodeling. CA19-9-modified macrophage colony-stimulating factor (M-CSF) was identified via immunoprecipitation and mass spectrometry from KRAS-mutant CA19-9-inducible pancreatic organoids. CA19-9-M-CSF induced increased immunosuppressive TAM differentiation in vivo and in vitro using a novel Macrophage, Organoid, and Fibroblast (MOrF) co-culture platform. This project will identify the mechanisms by which CA19-9 directly contributes to PDA ME immune modulation and unveil essential molecular underpinnings of PDA biology that will inform effective therapies in the future.

Citation Format: Jasper Hsu, Tae Gyu Oh, Kristina L. Peck, Angelica E. Rock, Garret Bishop, Shira R. Okhovat, Susan M. Kaech, Dannielle D. Engle. Glycan CA19-9 mediated immune modulation in the pancreatic tumor microenvironment [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 5553.
Abstract 5556: An vascularized melanoma model for with unidirectional perfusion of circulating immune cells for advancing immune-oncology research
Authors: Torregrosa Manuel Caro , de Ruiter Sander , Burton Todd , Queiroz Karla , Allen Will , Komen Job , Trietsch Sebastiaan , Broek Lenie van den
Published: March 2024

Understanding the interactions between the tumor the vascular systems and circulating immune cells is crucial for elucidating mechanisms of immune cell recruitment in cancer and in exploring potential immunotherapeutic approaches. However, current in vitro models often lack the fidelity to replicate these intricate dynamics observed in vivo. The OrganoPlate Graft has been developed for perfusion of peripheral blood mononuclear cells (PBMCs) through a vascular bed with a melanoma monolayer (A375) to study aspects such as immune cell adhesion, extravasation and interaction with the tumor. The OrganoPlate Graft comprises 48 chips per plate, each designed to simulate the conditions of vascular beds. The device achieves flow through passive leveling, utilizing gravity to induce a pressure drop and unidirectional flow across the vascular bed in both positive and negative inclines. This approach avoids the complications and potential artifacts introduced by external pump, reduces complexity, and increases the throughput with up to 16 plates (768 chips) served by each OrganoFlow rocker. In experimental settings, formation of the vascular bed was seen to be consistent in plates and the introduction of the chemokine CXCL-12 led to the establishment of a gradient. Subsequently, PBMCs were observed to localize in clusters as a result of extravasation towards this gradient and the A375 monolayer. This behavior is consistent with known chemotactic responses in more complex in vivo environments. A notable observation was the sustained activity of PBMCs within the system. Cells continued to perfuse through the vascular bed for up to three days after seeding. In summary, the OrganoPlate Graft provides a platform for studying immune interactions in an immunocompetent vascular bed model. Its design and functionality allow for the exploration of immune cell behaviors in proximity to tumor cells, offering potential insights for immune-oncology research. The system's ability to mimic immune cell migration and extravasation in a controlled environment, and future potential to observe tumour killing makes it a valuable tool for advancing our understanding of immune-tumor interactions and may contribute to the development of novel immune-oncology therapeutic strategies.

Citation Format: Manuel Caro Torregrosa, Sander de Ruiter, Todd Burton, Karla Queiroz, Will Allen, Job Komen, Sebastiaan Trietsch, Lenie van den Broek. An vascularized melanoma model for with unidirectional perfusion of circulating immune cells for advancing immune-oncology research [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 5556.
Abstract 5572: Microneedle-guided lymphatic delivery of a natural immune modulator toxin for enhanced cancer immunotherapy
Authors: Lim Su Yeon , Kim Byung Deok , LIU PIN , Shin Ju hwa , Jeong Ji Hoon
Published: March 2024

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

Citation Format: Su Yeon Lim, Byung Deok Kim, PIN LIU, Ju hwa Shin, Ji Hoon Jeong. Microneedle-guided lymphatic delivery of a natural immune modulator toxin for enhanced cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5572.
Abstract 5578: Multi-omics approach reveals a SMAD4-deficiency signature, translational reprogramming and synthetic lethality in esophageal adenocarcinom
Authors: Milne Julia V. , Fujihara Kenji , Kusnadi Eric , Pechlivanis Maree , Thio Niko , Cabalag Carlos , Gulati Twishi , Gotovac Jovana , Simpson Kaylene , Duong Cuong , Furic Luc , Phillips Wayne , Clemons Nicholas
Published: March 2024

Esophageal adenocarcinoma (EAC) is a cancer of high mutation burden with negligible recurrent and druggable driver genes and, therefore, a paucity of options for targeted therapy. Mutation or loss of the tumor suppressor gene SMAD4 occurs in up to 20% of EAC cases, and we have previously shown that loss of SMAD4 is sufficient to promote EAC tumorigenesis in an in vivo xenograft model. The present study aimed to delineate the role of SMAD4 in EAC tumorigenesis and identify synthetic lethal interactions in SMAD4-deficient cancers as a novel approach for treating EAC.

Our multi-omics methodology integrated RNA-sequencing, proteomics, polysome-sequencing, reverse-phase protein arrays, and genome-wide CRISPR-Cas9 screening to unveil a SMAD4-deficiency signature and new therapeutic avenues for EAC. These data reveal a complex interplay between SMAD4 loss and regulation of mTOR signaling, with specific downstream effects to reprogram translation. SMAD4-deficient cells express decreased levels of 4E-BP1, the inhibitory binding partner of EIF4E, which is the rate-limiting component of the cap-dependent translation initiation complex. This was accompanied by increased mTOR activity, including phosphorylation and inactivation of 4E-BP1. We found that SMAD4-deficient cells exhibit vastly different polysome traces compared to their wildtype counterparts and preferentially upregulate cap-dependent translation, acquiring an addiction to translation of oncogenic mRNAs. Furthermore, perturbation of additional negative regulators of mTOR signaling in combination with SMAD4 knockout exacerbated these effects and accelerated tumorigenesis in vivo and growth of patient-derived organoids in vitro.

This work advances our knowledge of EAC tumorigenesis, provides new mechanistic insights into SMAD4-driven transformation as well as novel potential therapeutic avenues for SMAD4-deficient EAC.

Citation Format: Julia V. Milne, Kenji Fujihara, Eric Kusnadi, Maree Pechlivanis, Niko Thio, Carlos Cabalag, Twishi Gulati, Jovana Gotovac, Kaylene Simpson, Cuong Duong, Luc Furic, Wayne Phillips, Nicholas Clemons. Multi-omics approach reveals a SMAD4-deficiency signature, translational reprogramming and synthetic lethality in esophageal adenocarcinom [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 5578.
Abstract 560: IGF1 induces the expression of CYR61 in metastatic prostate cancer
Authors: Ortiz Hernandez Greisha L. , Walker Mya , Woods-Burnham Leanne , Kittles Rick A. , Casiano Carlos A. , Neuhausen Susan
Published: March 2024

The cysteine-rich angiogenic inducer 61 (CYR61) is a member of the cellular communication network (CCN) protein family that can be induced by growth factors. CYR61-specific functions are dependent on cellular context. In prostate cancer (PCa), CYR61 contributes to cell growth and survival through its interactions with extracellular ligands, such as integrins avb3 and a6b4, in the extracellular matrix space. Interestingly, CYR61 contains an insulin-like growth factor-binding protein domain suggesting that it may interact with insulin-like growth factor-I (IGF1). High serum levels of IGF1 are directly linked to PCa development and recently have been studied as a predictor of metastatic disease. Given the important roles that IGF1 and CYR61 play in PCa and their potential interaction, it is critical to investigate their molecular interplay. The correlation between PCa aggressiveness and circulating levels of CYR61 and IGF1 is poorly studied. Our goal was to assess the contribution of CYR61-IGF1 interaction to PCa cell proliferation. Their combined role may explain a proportion of aggressive PCa. This study was designed to characterize the role of IGF1-induced expression of CYR61 in metastatic PCa cellular models and to determine if this interaction contributes to aggressive tumor properties (e.g., proliferation, migration, tumorsphere formation). Using immunoblotting, we demonstrated that CYR61 is upregulated in the metastatic cell line PC3. Furthermore, optimized knockdown of CYR61 using siRNA significantly reduced PC3 cell proliferation, viability, and prostasphere formation. To examine the underlying mechanisms associated with IGF1 signaling, we assessed the activation of either the PI3/Akt and MAPK pathways in PC3 cells with CYR61 silencing. CYR61 siRNA-mediated knockdown decreased activation of the PI3/Akt pathway but did not affect the MAPK pathway. In addition, we found that IGF1 induces protein expression of CYR61 in a time-dependent manner, validated by both immunoblotting and confocal microscopy. In conclusion, these data provided evidence that CYR61 expression is induced by IGF1, and its inhibition decreased the capacity of metastatic PCa cells to proliferate, indicating a potential utilization of CYR61 inhibition in the therapy of metastatic PCa.

Citation Format: Greisha L. Ortiz Hernandez, Mya Walker, Leanne Woods-Burnham, Rick A. Kittles, Carlos A. Casiano, Susan Neuhausen. IGF1 induces the expression of CYR61 in metastatic prostate 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 560.
Abstract 5647: Investigating the role of AP-2α in melanomagenesis
Authors: Bartschat Nicholas , Chang Jeremy , Suraju Mohammed , Nagel Ryan , Li Zhijie , White Jeffrey , Kenny Colin , Weigel Ronald
Published: March 2024

Introduction: Transcription factor AP-2α (encoded by the TFAP2A gene) is a protein involved in the early development of multiple tissues, particularly the neural crest. Melanocytes are derived from the neural crest and their development appears to rely on AP-2α and its paralogues, along with master regulator MITF. Prior studies have indicated that AP-2α is a crucial regulator of melanoma metastasis. However, it is unclear if AP-2α plays a role in melanomagenesis. We sought to understand the role of AP-2α in melanomagenesis, hypothesizing that knock out (KO) of TFAP2A would suppress malignant potential in vitro and downregulate genetic pathways linked to malignant transformation.

Methods: TFAP2A KO was generated with a single-guide RNA CRISPR/Cas9 system targeting exon 3 of the gene in the human melanoma cell line A375. Tumorigenesis phenotype was assessed by evaluating contact-independent colony formation with the in vitro soft agar assay. To identify downstream regulatory programs controlled by TFAP2A, we then utilized RNA-seq and Gene Set Enrichment Analysis (GSEA, San Diego). RNA-seq was performed on four clones each for wildtype and TFAP2A KO samples and the resulting data was processed using GSEA to identify gene sets modified after TFAP2A KO.

Results: Targeting of TFAP2A with CRISPR/Cas9 effectively knocked out AP-2α protein expression in the A375 melanoma cell line. Colony formation on soft agar assay was significantly decreased after TFAP2A KO (P < 0.01). RNA-seq revealed significant differential expression of 11,195 genes after TFAP2A KO. Gene sets with negative enrichment after TFAP2A KO included those overall higher in tumors versus normal tissue (FWER P = 0.003) and multiple signaling pathways related to malignant transformation such as TGF-β (FWER P = 0.003), MYC (FWER P = 0.009), KRAS (FWER P = 0.03), and Notch (FWER P = 0.043).

Conclusions: Our data suggests that TFAP2A plays a role in cutaneous melanomagenesis. TFAP2A may represent a therapeutic target for melanoma, though further pre-clinical studies are needed. We plan to further test this hypothesis in a melanoma mouse model with conditional TFAP2A KO under the control of inducible Cre recombinase driven by the mouse tyrosinase gene promoter.

Citation Format: Nicholas Bartschat, Jeremy Chang, Mohammed Suraju, Ryan Nagel, Zhijie Li, Jeffrey White, Colin Kenny, Ronald Weigel. Investigating the role of AP-2α in melanomagenesis [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 5647.
Abstract 5662: PDCD1 and CD48 significantly impact cancer recurrence and survival in pediatric acute lymphoblastic leukemia
Authors: Alotaibi Shatha Fawaz , Abuhadi Lames , Alolyani Noura , Alotaibi Moureq R. , Alhoshani Ali R. , Sobeai Homood As
Published: March 2024

Introduction: Immune checkpoints (ICPs) play a critical role in modulating the immune response, maintaining self-tolerance, and preventing excessive immune system activation. Dysregulation of immune checkpoints has been implicated in cancer progression and treatment resistance. In this study, we aimed to screen for dysregulated immune checkpoint genes that might be associated with cancer recurrence in pediatric acute lymphoblastic leukemia (ALL) following a course of cancer treatment. We hypothesized that certain ICPs would be significantly dysregulated in relapsed ALL patients, potentially providing insights into the underlying mechanisms driving therapy resistance and disease recurrence.

Methods: 51 ICP genomic data (gene expression, copy number alterations (CNAs), and mutation) of133 patients with relapse information [relapse-free (n=29) and relapsed (n=104)] extracted from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) were examined in the study. Patient’s t-test (p-value < 0.05) was used to identify significant genetic factors between relapse-free and relapsed patients. Free and overall survival analyses were performed using log-rank test (p-value < 0.05) based on patient gene expression profiles.

Results: Among the 51 genes examined, PDCD1, PVR, CD70, and CD48 were significantly upregulated in relapsed patients compared with relapse-free patients (P < 0.05). No significant CNAs nor mutations were detected in these four genes. Patients with high expression profiles of PDCD1 and CD48 at diagnosis were 1.71 and 1.47 more likely to relapse compared to patients with low expression profiles, respectively (P < 0.05). Furthermore, the upregulation of PDCD1 (P= 0.0004, HR= 1.972) and CD48 (P= 0.0344, HR= 1.533) demonstrated significantly increased mortality rates in patients following treatment, as indicated by overall survival analyses.

Conclusion: The upregulation of PDCD1 and CD48 was significantly associated with relapse and survival of ALL patients. Promisingly, these two ICPs can potentially be used as prognostic biomarkers for relapse risk and rationale for alternative therapeutic strategies. Our study suggests that targeting PDCD1 and CD48 might be beneficial in enhancing the treatment efficiency and thereby reducing the recurrence risk. The study was funded by the Deputyship for Research and Innovation, Ministry of Education, Saudi Arabia (DRI-KSU-1273).

Citation Format: Shatha Fawaz Alotaibi, Lames Abuhadi, Noura Alolyani, Moureq R. Alotaibi, Ali R. Alhoshani, Homood As Sobeai. PDCD1 and CD48 significantly impact cancer recurrence and survival in pediatric acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5662.
Abstract 567: Fisetin sensitizes triple negative breast cancer cells to radiation
Authors: Khozooei Shayan , Veerappan Soundaram , Toulany Mahmoud
Published: March 2024

Triple negative breast cancer (TNBC) represents a highly aggressive subtype, constituting approximately 20% of all breast cancer cases. Y-box binding protein-1 (YB-1) is often overexpressed in various tumor types and has been implicated in conferring resistance to cell death induced by radiotherapy. Fisetin, a flavonoid compound with demonstrated anti-cancer properties, operates in part through inhibiting phosphorylation of YB-1 by p90 ribosomal S6 kinase (RSK). In this study, we investigated the potential synergistic effects of combining fisetin with radiotherapy in TNBC. The activation status of the RSK signaling pathway was assessed in both total cell lysate and subcellular fractions using Western blotting. A standard clonogenic assay was employed to evaluate post-irradiation cell survival. To investigate the frequency of double-strand breaks (DSBs) and chromosomal aberrations, γH2AX foci assay and 3-color fluorescence in situ hybridization analyses were conducted, respectively. The DSB repair pathways targeted by fisetin were examined in cells expressing genomically integrated reporter constructs by quantifying green fluorescence protein expression through flow cytometry. Apoptosis and autophagy were measured using flow cytometric quantification of sub-G1 cells and the assessment of LC3-II protein expression, respectively. Kinase array and phosphoproteomics analyses were carried out to study the potential impact of fisetin on the signaling involved in the DNA damage response (DDR) after irradiation. We demonstrated that fisetin mimics the effects of RSK pharmacological inhibitors in terms of effect on YB-1 phosphorylation. Treatment with fisetin increased frequency of DSB in non-irradiated cells and impaired repair of DSB after irradiation. Fisetin attenuated DSB repair by suppressing the classical non-homologous end-joining and homologous recombination repair pathways. The frequency of chromosomal aberration was enhanced by fisetin treatment. The effect of fisetin on inhibiting DSB repair was partially YB-1 dependent. Phosphoproteomic analysis revealed that fisetin inhibits DDR signaling, which leads to radiosensitization in TNBC cells, as shown in combination with single dose or fractionated doses irradiation. Fisetin neither inhibited DSB repair nor radiosensitized normal human fibroblast HSF7 cells. The radiosensitizing effect of fisetin was not attributed to enhancing apoptosis or modulating autophagy. In summary, combining fisetin with radiotherapy may enhance TNBC radiotherapy outcomes.

-This research was supported by a grant from the German Research Council (DFG,TO 685/2-3).

Citation Format: Shayan Khozooei, Soundaram Veerappan, Mahmoud Toulany. Fisetin sensitizes triple negative breast cancer cells to radiation [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 567.
Abstract 5676: Spatial 3D genome organization reveals intratumor heterogeneity in primary glioblastoma samples
Authors: Wang Qixuan , Wang Juan , Mathur Radhika , Youngblood Mark W. , Jin Qiushi , Hou Ye , Stasiak Lena A. , Luan Yu , Costello Joseph F. , Yue Feng
Published: March 2024

Glioblastoma (GBM) represents the most prevalent malignant primary brain tumor with highly unfavorable prognosis. Currently, most genomic studies are conducted at a single site of a tumor, which do not reflect the complete genetic or epigenetic information across the whole tumor. Furthermore, the intra-tumoral heterogeneity (ITH) of 3D genome organization has also not been studied yet. To address these gaps, we performed Hi-C experiments in 21 samples obtained from 9 GBM patients, with 15 of them being spatially mapped based on their 3D coordinates from the same patients. We identified extensive inter-tumoral and intra-tumoral heterogeneity in genome compartmentalization and chromatin interactions. Notably, in a patient with 9 spatially mapped samples from both temporal and frontal regions, we accumulated over 6 billion reads and defined high-resolution region-specific chromatin interactions, regulatory networks, and key regulators within the same patient. We detected structural variation (SV) and enhancer hijacking across all the samples, and identified recurrent events that affect known cancer-related genes such as CDKN2A/B. Finally, we introduce the concept of 'enhancer amputation', defined as the loss of enhancers due to SVs which lead to decreased expression of their original target genes. To our knowledge, this study represents the first large-scale exploration of the 3D genome in primary GBM patients and the first investigation of 3D genome organization in multiple regions of the same tumor. Our findings provide unprecedented insights into the ITH of GBM at the 3D genomic level, opening new avenues for understanding and potentially targeting this devastating disease.

Citation Format: Qixuan Wang, Juan Wang, Radhika Mathur, Mark W. Youngblood, Qiushi Jin, Ye Hou, Lena A. Stasiak, Yu Luan, Joseph F. Costello, Feng Yue. Spatial 3D genome organization reveals intratumor heterogeneity in primary glioblastoma samples [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 5676.
Abstract 5683: lncRNA-protein interactions that predict response to endocrine therapy in HR+ breast cancer
Authors: Waiters Kacie D. , Quttina Maram , Khan Ashfia F. , Karami Samaneh , Peidl Anthony S. , Babajide Funmi , Bawa-Khalfe Tasneem
Published: March 2024

Hormone receptor positive (HR+) breast cancer (BCa) is the most frequently diagnosed BCa type accounting for 70% of all breast cancer cases. A large population of HR+ BCa patients (30-40%) are resistant to mainstay endocrine therapy and develop incurable metastatic disease. Hence, it is imperative to identify viable biomarkers that stratify patients as drug responders or non-responders.

Emerging scientific literature highlights the essential role of long non-coding RNAs (lncRNA) in cancer drug resistance and metastatic transformation; lncRNA include RNAs over 200 nucleotides in length that do not encode protein. Major biological functions of lncRNA rely on association with select protein interactors. As lncRNA equally bind proteins with and without canonical RNA-binding motifs, it is unclear what facilitates this lncRNA-protein interaction. Our recent studies show that SUMO post-translational modification (or SUMOylation) of target proteins potentiates binding with lncRNA, particularly at the chromatin. Using a small-scale screening, we see that SUMO-modification works to enhance association with lncRNAs for proteins with and without a canonical RNA binding domain (RBD). SUMOylation of RBD-expressing heterochromatin protein 1 α (HP1α) drives interaction with multiple chromatin-associated lncRNA both within and outside canonical heterochromatin foci. Interaction with lncRNA supports SUMOylated HP1α’s unconventional function as a transcriptional repressor at select euchromatic loci. We now report an inverse relationship in which SUMOylated HP1α directs the stability of its lncRNA binding partner. Specifically, SUMO-modified HP1α directs cell-cycle dependent recruitment of the RNA degradation machinery to the chromatin and facilitates clearance of chromatin-bound lncRNA. This dynamic lncRNA degradation process is disturbed with cancer onset and instead favors aberrant cancer cell transformation. Consistently, restoring lncRNA degradation homeostasis decreases metastatic properties of HR+ BCa cells and increases sensitivity to targeted therapeutics currently in clinical trials.

Our studies define a fundamental mechanism that dictates lncRNA stability and/or degradation in BCa cells. In addition, we present viable biomarkers that predict sensitivity to ET and alternative targeted therapies.

Citation Format: Kacie D. Waiters, Maram Quttina, Ashfia F. Khan, Samaneh Karami, Anthony S. Peidl, Funmi Babajide, Tasneem Bawa-Khalfe. lncRNA-protein interactions that predict response to endocrine therapy in HR+ 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 5683.
Abstract 571: CRISPR/Cas9 screening identifies the proteasome subunit PSMC6 as key for the survival of cisplatin-resistant ovarian carcinoma cells
Authors: Costantino Matteo , D'arcy Padraig , Mirra Luca , Corno Cristina , Beretta Giovanni L. , Gubat Johannes , Pratesi Pietro , Ciniselli Chiara M. , Verderio Paolo , Linder Stig , Perego Paola
Published: March 2024

Ovarian carcinoma is a disease with poor prognosis, due to delays in diagnosis and the development of drug resistance. Since deregulation of the ubiquitin proteasome system may contribute to the development of drug resistance, the aim of this study was to investigate the interplay between expression of proteasome subunits and cisplatin resistance by utilizing a CRISPR/Cas9 dropout screen. Paired cisplatin-sensitive and -resistant cells (IGROV-1 and IGROV-1/Pt1) were transfected with Cas9 and transduced with gRNAs against proteasome components. Cells were collected at early (day 4) and late (day 21) time exposure and sequenced to identify genes necessary for survival. Various proteasome subunits were found to be essential for the survival of cisplatin-resistant ovarian carcinoma cells, including PSMA5, PSMC6, PSMD7, PSMD12 and PSMD14. Since PSMC6 knockout produced the greatest growth inhibitory effects, it was selected for functional studies utilizing conventional RNA interference. When IGROV-1 and IGROV-1/Pt1 cells were transfected with small interfering RNAs (siRNAs) targeting PSMC6, efficient down-regulation on the mRNA and protein level was observed. Phenotypic analyses of PSMC6 knockdown cells indicated reduced clonogenicity using both 2D and soft agar assays in parental and resistant cells associated with down-regulation of the canonical MAPK pathway. A slight but not significant increase in sensitivity to cisplatin was observed upon PSMC6 silencing in resistant cells using clonogenic assays. Finally, we carried out a pilot study using ovarian carcinoma specimens (n = 134) obtained through the institutional biobank. The samples were representative of the frequency occurrence of the various histological ovarian carcinoma subtypes. We found that PSMC6 expression, evaluated by qRT-PCR, was associated with tumor stage. These findings suggest that PSMC6 is linked to ovarian carcinoma aggressiveness and that PSMC6 targeting may be an interesting therapeutic strategy.

Citation Format: Matteo Costantino, Padraig D'arcy, Luca Mirra, Cristina Corno, Giovanni L. Beretta, Johannes Gubat, Pietro Pratesi, Chiara M. Ciniselli, Paolo Verderio, Stig Linder, Paola Perego. CRISPR/Cas9 screening identifies the proteasome subunit PSMC6 as key for the survival of cisplatin-resistant ovarian carcinoma cells [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 571.
Abstract 5717: CDK4 inhibition suppresses Rab11 mediated collective cell migration in colon cancer cells
Authors: Cheng Chun Pu , Ku Chia-En , Lee Shin-Ru , Wang Yu-Chun , Ching Yu-Chien , Chen Hui-Chun , Chao Wei-Ting
Published: March 2024

In tumor progression, cell proliferation and cell adhesion are critical for tumor growth and metastasis. It has been demonstrated cell division which associated with microtubule organization also has impact on tubulin mediated focal adhesion turnover, however, the mechanism is not clear in the cell cohort migration which is accompanied with both cell proliferation and cell migration. This study is to investigate the effect of cell cycle inhibition in the collective cell migration. HT-29 colon cancer cells were treated with CDK4 inhibitor CINK4, paclitaxel and focal adhesion inhibitor PF573228. The cell proliferation rate was determined by MTT assay, cell migration ability was analyzed by wound healing assay. Rab11, E-cadherin and focal adhesion kinase were revealed by immuno-confocal microscopy. When HT-29 cells were treated with lower dose of CDK4 inhibitor CINK4, cell migration was suppressed. Meanwhile, in the result of immunostaining, the recycling endosomal protein Rab11which is involved in E-cadherin turnover in collective cell migration was not distributed in the cell membrane after CINK4 treatment. Furthermore, when cellular FAK activity were inhibited by PF573228 and tubulin disassembly was inhibited by paclitaxel, the cell area was increased with stable attachment, however, the membrane translocation of Rab11 was not affected. This study demonstrated cell cycle inhibition in G1 phase affected Rab11 mediated collective cell migration through tubulin regulated focal adhesion turnover for cell attachment. Keywords: CDK4, cell cycle, focal adhesion kinase, paclitaxel, colon cancer

Citation Format: Chun Pu Cheng, Chia-En Ku, Shin-Ru Lee, Yu-Chun Wang, Yu-Chien Ching, Hui-Chun Chen, Wei-Ting Chao. CDK4 inhibition suppresses Rab11 mediated collective cell migration in colon cancer cells [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 5717.
Abstract 5771: Utilizing a photoreactive chloroalkane capture tag for target deconvolution
Authors: Uyeda Tetsuo , Hurst Robin , Levin Sergiy , Rosenblatt Mike , Zimmermann Kris , Ohana Rachel F.
Published: March 2024

Identifying the physiologically relevant targets of bioactive compounds is often the rate limiting step toward understanding their mechanism of action. To this end, we developed a streamlined chemical proteomic strategy that utilizes a novel photoreactive cleavable chloroalkane tag, which can be attached to bioactive compounds to isolate their respective cellular targets for identification by mass spectrometry. The tag does not significantly affect compounds potency and membrane permeability, allowing for binding interactions to be established within intact cells under appropriate physiological conditions. UV-induced covalent photo-crosslinking “freezes” the cellular interactions and prevents their dissociation upon cell lysis. Effective enrichment of the cellular targets is achieved through their selective covalent capture onto HaloTag coated particles and subsequent selective release by tag cleavage. Putative targets identified by mass spectrometry can be readily verified using resonance energy transfer. By exchanging the chloroalkane tag for a fluorophore, direct binding to the targets can be revealed through proximity of the fluorophore to a small NanoLuc luciferase genetically fused to the putative target. This approach was used to identify physiologically relevant targets for bioactive compounds including those with low affinity and/or low abundance as well as insoluble targets with multiple trans membrane domains.

Citation Format: Tetsuo Uyeda, Robin Hurst, Sergiy Levin, Mike Rosenblatt, Kris Zimmermann, Rachel F. Ohana. Utilizing a photoreactive chloroalkane capture tag for target deconvolution [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 5771.
Abstract 5811: Ultralong CDR3 engineered interleukin-15 antibody fusion for T and NK cell expansion
Authors: Huang Ruiqi , McGregor Duncan , Smider Vaughn
Published: March 2024

Interleukin (IL)-15 is a promising immunotherapeutic cytokine for cancer treatment because it can stimulate the proliferation and cytotoxicity of CD8+ T lymphocytes and nature killer (NK) cells, similar to the action of IL-2, which has been used to treat metastatic melanoma and renal cancer. IL-15 may have improved pharmacologic properties over IL-2 because it doesn’t cause vascular leak syndrome or stimulate regulatory T cells. However, IL-15 is difficult to express as a stable soluble protein and has a short half-life in vitro and in vivo. To solve the problem, we designed an IL-15 ultralong CDR3 humanized bovine antibody fusion. Bovine ultralong CDR3 antibodies have a unique “stalk and knob” structure in which two antiparallel β-strands support a disulfide bonded knob protruding out of the antibody surface and forms a mini antigen binding domain. By replacing the knob domain with IL-15, we have created a chimeric CDR3-IL-15 IgG which functions as IL-15 in vitro and in vivo but can be easily produced in mammalian cells with increased stability. Thus, the CDR3 can stabilize IL-15 in the absence of its high affinity receptor α (Rα) chain. Furthermore, as IL-15 utilizes Rα for increased trans signaling to the receptor β and γ subunits, one variant candidate (CDR3-IL-15_Rα) was produced by co-expressing Rα sushi domain with the chimeric IgG. Both constructs have been demonstrated to be highly active in stimulating proliferation of NK cells and CD8+ T cells in vitro as well as in stimulating proliferation of NK cells and CD8+ T cells in rats and non-human primates (NHP). Although the CDR3-IL-15_Rα exhibited higher in vitro signaling activity than CDR3-IL-15, both were equally potent in stimulating the proliferation of NK cells and CD4+ and CD8+ T cells in NHP without any immunogenicity detected. Moreover, in vivo studies in NHP indicated that CDR3-IL-15 acted faster than CDR3-IL-15_Rα in stimulating the proliferation of these lymphocytes. CDR3-IL-15 is the first thermodynamically stabilized variant of IL-15 produced in the absence of its Rα chain, is highly active in vivo, and has multiple potential cancer applications as an T and NK cell stimulating agent.

Citation Format: Ruiqi Huang, Duncan McGregor, Vaughn Smider. Ultralong CDR3 engineered interleukin-15 antibody fusion for T and NK cell expansion [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 5811.