bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Appendix from The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen
Authors: Malta Tathiane M. , Sabedot Thais S. , Morosini Natalia S. , Datta Indrani , Garofano Luciano , Vallentgoed Wies , Varn Frederick S. , Aldape Kenneth , D'Angelo Fulvio , Bakas Spyridon , Barnholtz-Sloan Jill S. , Gan Hui K. , Hasanain Mohammad , Hau Ann-Christin , Johnson Kevin C. , Cazacu Simona , deCarvalho Ana C. , Khasraw Mustafa , Kocakavuk Emre , Kouwenhoven Mathilde C.M. , Migliozzi Simona , Niclou Simone P. , Niers Johanna M. , Ormond D. Ryan , Paek Sun Ha , Reifenberger Guido , Sillevis Smitt Peter A. , Smits Marion , Stead Lucy F. , van den Bent Martin J. , Van Meir Erwin G. , Walenkamp Annemiek , Weiss Tobias , Weller Michael , Westerman Bart A. , Ylstra Bauke , Wesseling Pieter , Lasorella Anna , French Pim J. , Poisson Laila M. , Woehrer Adelheid , Lowman Allison K , deCarvalho Ana C , Castro Ana Valeria , Transou Andrea , Brodbelt Andrew R , Hau Ann-Christin , Lasorella Anna , Golebiewska Anna , Walenkamp Annemiek , Molinaro Annette M , Iavarone Antonio , Ismail Azzam , Westerman Bart A , Ylstra Bauke , Bock Christoph , Ormond D. Ryan , Brat Daniel J , Kocakavuk Emre , Van Meir Erwin G , Barthel Floris P , Varn Frederick S , D'Angelo Fulvio , Finocchiaro Gaetano , Rao Ganesh , Zadeh Gelareh , Reifenberger Guido , ngNg Ho Keu , Kim Hoon , Noushmehr Houtan , Miletic Hrvoje , Gan Hui K , Datta Indrani , Rock Jack , Snyder James M , Huse Jason T , Connelly Jennifer M , Barnholtz-Sloan Jill S , Niers Johanna M , deGroot John F , Akdemir Kadir C , Kannan Kasthuri S , Ligon Keith L , Aldape Kenneth , Bulsara Ketan R , Johnson Kevin C , Alfaro Kristin D , Poisson Laila M , Garofano Luciano , Stead Lucy F , Nasrallah MacLean P , Smits Marion , van den Bent Martin J , Kouwenhoven Mathilde CM , Weller Michael , Hasanain Mohammad , Khasraw Mustafa , Gould Peter V , Smitt Peter A Sillevis , LaViolette Peter S , Tatman Philip D , Wesseling Pieter , French Pim J , Beroukhim Rameen , Verhaak Roel G.W. , Migliozzi Simona , Niclou Simone P , Bakas Spyridon , Kalkanis Steven , Paek Sun Ha , Short Susan C , Ghazaleh Tabatabai , Malta Tathiane M , Sabedot Thais S , Weiss Tobias , Walbert Tobias , Baid Ujjwal , Vallentgoed Wies , Yung W. K. Alfred , Verhaak Roel G.W. , Iavarone Antonio , Noushmehr Houtan
Published: March 2024

List of collaborator authors
Supplementary Figure5 from Adipocyte Precursor-Derived NRG1 Promotes Resistance to FGFR Inhibition in Urothelial Carcinoma
Authors: Hosni Sana , Kilian Viola , Klümper Niklas , Gabbia Daniela , Sieckmann Katharina , Corvino Dillon , Winkler Anja , Saponaro Miriam , Wörsdörfer Karin , Schmidt Doris , Hahn Oliver , Zanotto Ilaria , Bertlich Marina , Toma Marieta , Bald Tobias , Eckstein Markus , Hölzel Michael , Geyer Matthias , Ritter Manuel , Wachten Dagmar , De Martin Sara , Alajati Abdullah
Published: March 2024

Supplementary Figure5
Table S2 from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms
Authors: Arribas Alberto J. , Napoli Sara , Cascione Luciano , Barnabei Laura , Sartori Giulio , Cannas Eleonora , Gaudio Eugenio , Tarantelli Chiara , Mensah Afua A. , Spriano Filippo , Zucchetto Antonella , Rossi Francesca M. , Rinaldi Andrea , Castro de Moura Manuel , Jovic Sandra , Bordone Pittau Roberta , Stathis Anastasios , Stussi Georg , Gattei Valter , Brown Jennifer R. , Esteller Manel , Zucca Emanuele , Rossi Davide , Bertoni Francesco
Published: March 2024

Panel of antibodies used in flow cytometry experiments.
Figure S8 from PUMA/RIP3 Mediates Chemotherapy Response via Necroptosis and Local Immune Activation in Colorectal Cancer
Authors: Chen Dongshi , Ermine Kaylee , Wang Yi-Jun , Chen Xiaojun , Lu Xinyan , Wang Peng , Beer-Stolz Donna , Yu Jian , Zhang Lin
Published: March 2024

Figure S8. 5-FU-induced cell-surface translocation of calreticulin and DC phagocytosis of CRC cells are mediated by p53/PUMA/RIP3-dependent necroptosis.
Figure S4 from Genetic Silencing of AKT Induces Melanoma Cell Death via mTOR Suppression
Authors: Parkman Gennie L. , Turapov Tursun , Kircher David A. , Burnett William J. , Stehn Christopher M. , O'Toole Kayla , Culver Katie M. , Chadwick Ashley T. , Elmer Riley C. , Flaherty Ryan , Stanley Karly A. , Foth Mona , Lum David H. , Judson-Torres Robert L. , Friend John E. , VanBrocklin Matthew W. , McMahon Martin , Holmen Sheri L.
Published: March 2024

Supplementary Figure S4 demonstrates that siAKT1-3 is specific for human AKT. A, The cell confluency assay of YUMM1.1 mouse melanoma cells under genetic inhibition demonstrated no effect on cell death with siAKT1, siAKT2, siAKT3, or any combination. Error bars indicate standard error of the mean of triplicate wells. B, Immunoblotting of YUMM1.1 cells treated with siCtrl vs siAKT1-3. No knockdown of P-AKT (Ser473) or P-PRAS40 (T246) indicated the specificity of the siRNAs for human AKT.
Supplementary Methods 1 from Palazestrant (OP-1250), A Complete Estrogen Receptor Antagonist, Inhibits Wild-type and Mutant ER-positive Breast Cancer Models as Monotherapy and in Combination
Authors: Parisian Alison D. , Barratt Susanna A. , Hodges-Gallagher Leslie , Ortega Fabian E. , Peña Guadalupe , Sapugay Judevin , Robello Brandon , Sun Richard , Kulp David , Palanisamy Gopinath S. , Myles David C. , Kushner Peter J. , Harmon Cyrus L.
Published: March 2024

Supplementary text including supplementary materials and methods and references.
Table S5 from Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma
Authors: McCrury Mason , Swafford Kennith , Shuttleworth Sydnye L. , Mehdi Syed Hassan , Acharya Baku , Saha Debasmita , Naceanceno Kevin , Byrum Stephanie D. , Storey Aaron J. , Xu Ying-Zhi , Doshier Claire , Patel Vijay , Post Ginell R. , De Loose Annick , Rodriguez Analiz , Shultz Leonard D. , Zhan Fenghuang , Yoon Donghoon , Frett Brendan , Kendrick Samantha
Published: March 2024

Growth inhibitory concentrations (GI50) of NBI-961, doxorubicin and vincristine.
Table S11 from Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma
Authors: McCrury Mason , Swafford Kennith , Shuttleworth Sydnye L. , Mehdi Syed Hassan , Acharya Baku , Saha Debasmita , Naceanceno Kevin , Byrum Stephanie D. , Storey Aaron J. , Xu Ying-Zhi , Doshier Claire , Patel Vijay , Post Ginell R. , De Loose Annick , Rodriguez Analiz , Shultz Leonard D. , Zhan Fenghuang , Yoon Donghoon , Frett Brendan , Kendrick Samantha
Published: March 2024

Differentially expressed proteins identified from the phospho-proteomic analysis in RIVA treated with NBI-961 relative to DMSO vehicle control.
Figure S9 from Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma
Authors: McCrury Mason , Swafford Kennith , Shuttleworth Sydnye L. , Mehdi Syed Hassan , Acharya Baku , Saha Debasmita , Naceanceno Kevin , Byrum Stephanie D. , Storey Aaron J. , Xu Ying-Zhi , Doshier Claire , Patel Vijay , Post Ginell R. , De Loose Annick , Rodriguez Analiz , Shultz Leonard D. , Zhan Fenghuang , Yoon Donghoon , Frett Brendan , Kendrick Samantha
Published: March 2024

NBI-961 causes loss of NEK2 and NEK2 phosphorylation. A, B, Western blot analysis of NEK2 and phosphorylated NEK2 (p-NEK2) protein expression in NBI-961 treated RIVA (A) and U2932 (B) cell lines after 24 h. Quantification of band intensity normalized to ACTIN as mean ± SEM from three independent experiments shown as a bar graph below each blot. Adjusted P-values as determined by a one-way ANOVA with Dunnett’s multiple test correction for comparisons to DMSO vehicle treated control (VTC). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001
Supplementary FIgure S2 from Dual CAR-T Cells Targeting CD19 and CD37 Are Effective in Target Antigen Loss B-cell Tumor Models
Authors: Imai Kanae , Takeuchi Yuki , Terakura Seitaro , Okuno Shingo , Adachi Yoshitaka , Osaki Masahide , Umemura Koji , Hanajiri Ryo , Shimada Kazuyuki , Murata Makoto , Kiyoi Hitoshi
Published: March 2024

Supplemental Figure S2. Evaluation of cytokine production against tumor cells isolated from patients who relapsed after CAR-T cell therapy.
A, Expression of CD19, CD20, and CD37 in diffuse large B-cell lymphoma cells from a relapsed patient after a treatment with tisagenlecleucel. B, Intracellular IL-2 or IFN-γ positive cells after stimulation with the patient tumor cells at an E:T ratio 1:1 for 4 h.
Figure S3 from Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma
Authors: McCrury Mason , Swafford Kennith , Shuttleworth Sydnye L. , Mehdi Syed Hassan , Acharya Baku , Saha Debasmita , Naceanceno Kevin , Byrum Stephanie D. , Storey Aaron J. , Xu Ying-Zhi , Doshier Claire , Patel Vijay , Post Ginell R. , De Loose Annick , Rodriguez Analiz , Shultz Leonard D. , Zhan Fenghuang , Yoon Donghoon , Frett Brendan , Kendrick Samantha
Published: March 2024

Original blot images from Figures 2E and 2F in the main text. (A) Uncropped blot of Figure 2E immunoblotted with a mixture of anti-NEK2 and anti-TBP primary antibodies and imaged as a composite of both Dylight 650 and 800 channels. (B) Uncropped blot of Figure 2F immunoblotted with a mixture of anti-NEK2 and anti-ACTIN primary antibodies. The blot is shown as imaged in each individual channel. Both blots were resolved with a mixture of Dylight 650 and Dylight 800 secondary antibodies and imaged using the BioRad ChemiDoc MP as described in the Methods.
Table S2 from Raludotatug Deruxtecan, a CDH6-Targeting Antibody–Drug Conjugate with a DNA Topoisomerase I Inhibitor DXd, Is Efficacious in Human Ovarian and Kidney Cancer Models
Authors: Suzuki Hirokazu , Nagase Shotaro , Saito Chiemi , Takatsuka Atsuko , Nagata Motoko , Honda Kokichi , Kaneda Yuki , Nishiya Yumi , Honda Tomoyo , Ishizaka Tomomichi , Nakamura Kensuke , Nakada Takashi , Abe Yuki , Agatsuma Toshinori
Published: March 2024

PK parameters in mice and monkeys.
Fig. S3 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S3
Fig. S22 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S22
Fig. S19 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S19
Figure S1 from Improving Intracellular Delivery of an Antibody–Drug Conjugate Targeting Carcinoembryonic Antigen Increases Efficacy at Clinically Relevant Doses In Vivo
Authors: Nessler Ian , Rubahamya Baron , Kopp Anna , Hofsess Scott , Cardillo Thomas M. , Sathyanarayan Nalini , Donnell Jennifer , Govindan Serengulam V. , Thurber Greg M.
Published: March 2024

SE-HPLC Plot CEA-IgG. Size-exclusion HPLC (SE-HPLC) of CEA IgG, M85151a (XAb in our description), product #l0-C10C, from Fitzgerald Industries International. HPLC detection at 280 nm, the antibody absorbance region.
Abstract A001: Silencing of EYA4 regulates stemness in H3K27M-mutant diffuse midline glioma
Authors: Barravecchia Ivana , Sharma Monika , Magnuson Brian , Ferris Sarah F. , Apfelbaum April , Koschmann Carl , Lyssiotis Costas A. , Ljungman Mats , Galban Stefanie
Published: March 2024

Therapeutic resistance remains a major obstacle to preventing progression of H3K27M-altered Diffuse Midline Glioma (DMG). Resistance is driven in part by ALDH-positive cancer stem cells (CSC), with high ALDH1A3 expression observed in H3K27M-mutant DMG biopsies. We hypothesized that ALDH-mediated stemness and resistance may in part be driven by the oncohistone itself. Upon deletion of H3K27M, ALDH1A3 expression decreased dramatically and was accompanied by a gain in astrocytic marker expression and a loss of neurosphere forming potential, indicative of changes in differentiation. Here we show that the oncohistone regulates histone acetylation through ALDH1A3 in a Wnt-dependent manner and that loss of H3K27M expression results in re-sensitization of DMGs to radiotherapy. The observed elevated Wnt signaling in H3K27M-altered DMG likely stems from a dramatic suppression of mRNA and protein expression of the Wnt inhibitor EYA4 driven by the oncohistone. Thus, our findings identify EYA4 as a bona fide tumor suppressor in DMG that upon suppression, results in aberrant Wnt signaling to orchestrate stemness and differentiation. Future studies will therefore explore whether overexpression of EYA4 in DMG can impede growth and invasion. In summary, we have gained mechanistic insight into H3K27M-mediated regulation of cancer stemness and differentiation, which provides rationale for exploring new therapeutic targets for DMG.

Citation Format: Ivana Barravecchia, Monika Sharma, Brian Magnuson, Sarah F. Ferris, April Apfelbaum, Carl Koschmann, Costas A. Lyssiotis, Mats Ljungman, Stefanie Galban. Silencing of EYA4 regulates stemness in H3K27M-mutant diffuse midline glioma [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr A001.
Abstract A017: Cell-specific photodynamic therapy for high grade gliomas
Authors: Arias Alberto Guillermo
Published: March 2024

High grade gliomas (HGG) are infiltrative tumors. Surgery is the initial treatment, aiming to alleviate intracranial pressure and reduce tumor volume. Additional treatment includes radiotherapy and chemotherapy with Temozolomide. Despite these interventions, the 5-year survival rate for HGG patients remains below 10%, with a median survival of less than 2 years. Thus, there is an urgent need for novel therapeutic approaches In this talk I will present in vitro studies on a novel therapeutic approach using cell-specific Photodynamic Therapy. This therapy uses a drug that is activated by light exposure, called photosensitizer, generating reactive oxygen species capable of inducing cell death. This type of treatment has been used in clinical practice for decades, but its use in cancer treatment is rather new and is currently being evaluated in clinical trials in different cancer types. Here, we used a new cyclic peptide obtained through in vivo panning that can bind selectively to HGG cell lines. This peptide was coupled to the photosensitizer "Verteporfin". In vitro studies showed high toxicity and specificity of this peptide using different conditions, doses and incubation periods. Using immunodeficient mice with intracranial and also subcutaneous tumor induction, we studied the biodistribution of this peptide, showing higher accumulation in the tumor than in the healthy brain. These preliminary results set the ground for upcoming in vivo preclinical studies. Furthermore, we seek to explore the diagnostic and therapeutic potential of our HGG-specific peptide by coupling it to the radionuclide Lutetium 177.

Citation Format: Alberto Guillermo Arias. Cell-specific photodynamic therapy for high grade gliomas [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr A017.
Abstract A021: Exosome delivered combinatorial treatment for malignant brain tumors
Authors: Thomas Sydney , Gourishetti Karthik , Rangavajhula Karthik , Bhere Deepak
Published: March 2024

Glioblastoma (GBM), a World Health Organization (WHO) Grade IV astrocytoma, is a highly aggressive brain tumor with poor prognosis. Current therapeutic approaches, which include surgery, chemotherapy, and radiation therapy, are largely ineffective and often result in tumor recurrence. Several characteristics of the tumors make them challenging to treat, including their protection by the blood-brain barrier, which hinders effective treatment delivery. Our research addresses this issue by using exosomes, which are small cell-derived vesicles, as delivery vehicles for microRNA (miR) therapies. Dysregulation of miR expression has been implicated in tumorigenesis, and targeting these dysregulated miRs is emerging as a promising approach to tumor treatment. In particular, miR-7 and miR-124 have been identified as tumor-suppressive miRs that are downregulated in various tumors, including GBM. In this study, stem cell-derived exosomes loaded with miR-7 and miR-124 have been evaluated as a combinatorial approach for treating GBM. In our work, human adipose stem cells (ADSCs) were transduced with the target miR-7 and miR-124 plasmids and cultured in exosome-depleted FBS. The miR-containing exosomes from the ADSCs were then isolated, purified, quantified, and characterized for use in subsequent studies. Murine and human GBM cells as well as primary patient-derived primary GBM cells were treated with miR-7 and miR-124 exosomes, and the efficacy of exosome treatment was determined using cell viability assays and microscopy. The mechanisms of miR modulation of cell proliferation and cell death pathways were analyzed with time-course western blot analysis. Orthotopic animal models of GBM will be used to assess the effectiveness of our methods in vivo. Our results have demonstrated successful delivery of miR-7 and miR-124 to GBM cells via stem cell-derived exosomes. Data show that treatment with these tumor-suppressive miRs halts GBM growth in vitro by modulating multiple pathways involved in tumor growth and progression. While we await results of our in vivo studies, our preliminary data demonstrate that delivery of miR-7 and miR-124 via stem cell-derived exosomes is a promising therapeutic approach for treating GBM.

Citation Format: Sydney Thomas, Karthik Gourishetti, Karthik Rangavajhula, Deepak Bhere. Exosome delivered combinatorial treatment for malignant brain tumors [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr A021.
Abstract A035: Radiation-induced senescence as a driver of glioblastoma recurrence
Authors: Jordan Ben R. , Tomimatsu Nozomi , Di Cristofaro Luis Macedo , Kanji Suman , Mukherjee Bipasha , Burma Sandeep
Published: March 2024

Glioblastomas (GBM) are treated with high doses of ionizing radiation (IR), yet these tumors inevitably recur, and the recurrent tumors are highly therapy resistant. An understanding of mechanisms driving GBM recurrence is critical for improving therapy. During GBM therapy, both the tumor and normal brain tissue surrounding the tumor are treated with up to 60 Gy of IR. IR is a potent inducer of senescence, and senescent stromal cells can promote the growth of neighboring tumor cells by secreting matrix metalloproteinases, chemokines, cytokines, and growth factors that create a senescence-associated secretory phenotype (SASP). We have shown previously that IR-induced senescence of astrocytes in the brain leads to the secretion of SASP factors that promote the growth and invasiveness of tumor cells in mouse models of GBM (Fletcher-Sananikone, et al, Cancer Research, 2021). Following up on this study, we irradiated a panel of GBM cell lines and found that a significant fraction of these senesced rapidly in a p21-dependent manner. Senescent glioma cells upregulated SASP genes in a NF-kB-dependent manner, prominently, the interleukin IL6, which is an activator of the JAK-STAT pathway. Conditioned media from senescent GBM cells activated the JAK-STAT pathway in non-senescent GBM cells as well as promoted tumor cell proliferation and radioresistance. Interestingly, conditioned media from senescent GBM cells could also activate the NF-kB pathway and induce SASP in non-senescent cells. These results indicate that senescent GBM cells can activate pro-tumorigenic pathways in their non-senescent counterparts and SASP can spread from senescent to non-senescent cells. Bioinformatic analyses of the transcriptomic profiles of irradiated GBM cells and publicly available data from the TCGA database revealed that the inhibitor of apoptosis protein cIAP2 is a critical survival factor for senescent glioma cells. We find that targeting cIAP2 using Smac mimetics triggers apoptosis of senescent GBM cells with minimal toxicity towards normal brain cells, like astrocytes. Upregulation of cIAP2 in irradiated tumor cells was also observed in PDX models of GBM. Using these PDX models, we are currently validating novel senolytic-based therapeutic approaches to mitigate tumor recurrence after radiotherapy. In sum, our findings illustrate how senescence of both stromal and tumor cells promote GBM recurrence via different mechanisms and underscore the potential utility of adjuvant senolytic therapy for blunting GBM recurrence after radiotherapy.

Citation Format: Ben R. Jordan, Nozomi Tomimatsu, Luis Macedo Di Cristofaro, Suman Kanji, Bipasha Mukherjee, Sandeep Burma. Radiation-induced senescence as a driver of glioblastoma recurrence [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr A035.
Abstract IA004: Targeting clonal heterogeneity in treatment-refractory Glioblastoma with novel and empiric immunotherapies
Authors: Singh Sheila K
Published: March 2024

Despite aggressive multimodal therapy, glioblastoma (GBM) remains the most common malignant primary brain tumor in adults. With the advent of therapies that revitalize the anti-tumor immune response, several immunotherapeutic modalities have been developed for the treatment of GBM. In this talk, we summarize recent clinical and pre-clinical efforts to develop immunotherapeutic and chimeric antigen receptor (CAR) T cell treatment strategies for GBM recurrence, including challenges in the form of fundamental mechanisms of therapy evasion by tumor cells, such as immense intratumoral heterogeneity, suppression of the tumor immune microenvironment, and low mutational burden. Insights from these advances and challenges have shaped our development of a translational research pipeline from initial target discovery, through target validation and exploration of mechanism, to building new biotherapeutics against novel cancer targets, and preclinical testing in our patient-derived animal models of treatment-resistant GBM. We have tracked GBM cell populations that undergo clonal evolution as a result of selective pressures exerted by standard treatments to identify the cellular composition of the recurrence, to allow us to determine the intracellular signaling pathways that drive GBM relapse. Ultimately, we will design rational combinations of therapeutics that can reignite the anti-tumor immune response, effectively and specifically target tumor cells, and reliably decrease tumor burden for GBM patients.

Citation Format: Sheila K Singh. Targeting clonal heterogeneity in treatment-refractory Glioblastoma with novel and empiric immunotherapies [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr IA004.
Abstract IA007: Distinct immune landscapes characterize highly and minimally invasive brain metastases
Authors: Siegel Peter
Published: March 2024

Background: Cancer metastasis to the brain is a common complication of advanced disease with limited therapeutic options. Inefficient treatment is influenced, in part, by the unique composition of the brain microenvironment. Brain metastases (BrM) grow in two distinct patterns, either as minimally invasive (MI) masses with well-defined borders, or as tumors with highly invasive (HI) growth into surrounding brain tissue. HI BrM are associated with poor prognoses compared to MI BrM; however, differences in the tumor immune microenvironments (TIME) between these two lesion types remain largely unknown. Here, we investigate how the TIME differs between HI and MI BrM. Methods: We use Nanostring Digital Spatial Profiling coupled with the Cancer Transcriptome Atlas panel on 5 MI and 15 HI BrM patient samples (lung and breast cancer). This technique enables specific isolation of cancer cells at the tumor-brain interface and quantification of 1,825 cancer-specific RNA targets. Additionally, we perform imaging mass cytometry (IMC) on 119 BrM samples (lung cancer, breast cancer, melanoma, other) from 46 patients, encompassing over 350,000 cells. Samples represent BrM from various primary sites, including cancers of the lung, breast, and skin, and include patient-matched samples from the brain-tumor interface (‘margin’) or the centre of the metastatic lesion (‘core’). Results: The Nanostring Digital Spatial Profiling revealed a list of 106 and 73 differentially expressed genes in MI vs HI breast and lung BrM, respectively. Gene set enrichment analyses revealed that an interferon gamma (IFNγ) pathway signature was enriched in MI BrM and lost in HI BrM, which was confirmed by immunohistochemical staining for pSTAT1, consistent with an “immune hot” TIME in MI BrM when compared to HI lesions. Using IMC technology, we identified 20 different cell types, activation states, and spatially-defined cellular neighborhoods across our BrM patient samples. In comparison to MI samples, HI BrM have lower numbers of B cells, CD4+ T cells, and CD4- CD8- T cells in both the core and margin samples, and lower numbers of CD8+ T cells and regulatory T cells in the margin samples only. Conclusion: These data suggest that HI BrM invade into an immunosuppressed microenvironment while MI BrM are characterized by an active anti-tumor immune infiltrate. Together, this work suggests potential immune regulation of BrM invasion, which warrants further investigation.

Citation Format: Peter Siegel. Distinct immune landscapes characterize highly and minimally invasive brain metastases [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr IA007.
Abstract PR-004: Targeting EPHB2/ABL1 restores anti-tumor immunity in a preclinical model of ependymoma
Authors: Uccello Taylor P. , Ren Jun , Amoozgar Zohreh , Zhao Yuhui , Lei Pin-Ji , Ho William W. , Roberge Sylvie , Huang Peigen , Duda Dan G. , Xu Lei , Jain Rakesh K.
Published: March 2024

Purpose: Ependymoma (EPN) is a common type of brain tumor in children and is often resistant to available cytotoxic therapies. Molecular profiling studies have led to a better understanding of unique EPN subtypes and revealed a critical role of EPHB2. However, the immune system's role in tumor progression and treatment response remains poorly understood. New treatments for EPN are desperately needed and should be developed in a molecular subtype-specific fashion. Experimental Design: We developed a syngeneic mouse model using subtype-specific EPHB2-driven genetically engineered EPN tumor cells. Druggable targets were identified by matching transcriptomic signatures with the target spectrum of FDA-approved drugs. After identifying dasatinib as a potentially effective agent, we measured the changes in the immune microenvironment during EPN growth and after dasatinib treatment. Results: Transcriptomic profiling of EPHB2-driven EPN and analysis of a human EPN dataset revealed multiple protein kinases as potential druggable targets. We found that the multikinase inhibitor dasatinib potently inhibited the growth of EPN both in vitro and in vivo, mainly through blocking EPHB2 and ABL1 signaling. We found an increased frequency of immunosuppressive M2-like tumor-associated macrophages (TAMs), which proportionally increased with tumor size during tumor progression. However, treatment with dasatinib reprogrammed the EPN immune microenvironment by polarizing the TAMs toward an anti-tumor M1-like phenotype and increasing CD8 T cell activation. Furthermore, dasatinib treatment induced complete regression of established EPN tumors in 78% of the animals and protected survivors against tumor recurrence. Depletion of CD8 T cells compromised the durability of EPN responses and reduced overall survival. Conclusions: These data indicate that dasatinib may be an effective therapy for EPHB2-driven molecular subgroup of EPNs by activating the anti-tumor immune response and support further investigations of dasatinib in clinical trials.

Citation Format: Taylor P. Uccello, Jun Ren, Zohreh Amoozgar, Yuhui Zhao, Pin-Ji Lei, William W. Ho, Sylvie Roberge, Peigen Huang, Dan G. Duda, Lei Xu, Rakesh K. Jain. Targeting EPHB2/ABL1 restores anti-tumor immunity in a preclinical model of ependymoma [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr PR-004.
Abstract A024: High throughput screen for identifying inducers of Autophagic Cell Death in Ovarian Carcinoma
Authors: Hanjra Pahul , Liu Andrea , Ferrer Marc , Sood Anil K. , Wen Yunfei
Published: March 2024

Ovarian carcinoma continues to have the highest associated mortality among gynecologic malignancies. Despite surgery and chemotherapy, relapse and drug-resistant disease remains common. Thus, new therapeutic targets and improved combination regimens are needed. Autophagy is a conserved process cells use to remove and recycle old or damaged contents and maintain homeostasis, especially in times of cellular stress. Prolonged autophagy can result in cell death independently of apoptosis in a process known as autophagy cell death (ACD). This offers an alternative therapeutic strategy to target cancer cells, which are often resistant to apoptosis. In this study, we performed a high-throughput screen using the Mechanism Interrogation PlatE (MIPE) oncology library in HeyA8 and SKOV3 spheroids to identify drugs with high potential to induce ACD. Screening was performed in two phases: 1) Enrichment for compounds that decreased cell viability; 2) Enrichment for compounds able to induce autophagic flux in SKOV3 spheroids. We used a pft-LC3-RFP-GFP construct which was stably expressed in SKOV3 cells before 3-D culture as an autophagy index, and the accumulation of LC3-RFP in SKOV3 spheroids was measured in response to the treatments from MIPE compounds versus compared to control. An analog of the top hit of the screen results was the SIRT1 inhibitor, EX-527. We next performed a pharmacodynamic study in OVCA432-ip1-luc tumor-bearing mice to identify potential biomarkers of drug activity. We found that expression of the autophagy-related protein, LC3B, increased in tumors in a dose-dependent manner, forming loci indicative of autophagy flux at 20 mg/kg. Work is ongoing to identify rational combinations for use of EX-527 in management of ovarian carcinoma, and to characterize its mechanism of action.

Citation Format: Pahul Hanjra, Andrea Liu, Marc Ferrer, Anil K. Sood, Yunfei Wen. High throughput screen for identifying inducers of Autophagic Cell Death in Ovarian Carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A024.
Abstract A047: Modeling the role of the fallopian tube in the prevention and spread of high grade serous cancer using a multi-organ platform
Authors: Burdette Joanna
Published: March 2024

It is now recognized that a large percentage of high grade serous ovarian cancers arise in the fallopian tube and colonize the ovary as the primary metastatic step. One of the risk factors associated with ovarian cancer is the lifetime number of ovulations. Few models are currently available that allow the process of ovulation and the development of ovarian cancer to be studied. To address this gap, our team developed a microphysiological platform called PREDICT-multi-organ-system (MOS). PREDICT-MOS contains 30 wells for culturing organs and 60 pumps with precisely controlled flow rates. Human fallopian tube tissue can be grown in an air-liquid interface, while murine ovaries can be engineered to ovulate while producing and secreting physiological concentrations of hormones and proteins over the entire process of ovulation. Importantly, these secreted factors are contained in the device within the media and can therefore precisely model local concentration gradients and temporal exposure of the human fallopian tube tissues. First, we uncovered that the ovary secretes versican during the cycle to enhance ovarian migration, adhesion, and expansion within the ovarian microenvironment. We revealed that fallopian tube tumor cells stimulate the ovary to produce testosterone, which enhanced fallopian tube invasion and stem cell marker expression. Next, we profiled the expression of secreted extracellular vesicles that are produced by the fallopian tube on the platform. Extracellular vesicles may provide a new form of liquid biopsy, but understanding the cargo expressed from normal cells is critical for understanding the importance of cancer EV’s during progression. Finally, we have engineered the platform to allow for real-time invasion using an insert technology and a modified pump that allows for interaction between the organs. Overall, the integration of organ-on-chip technology with key human tissues allows for the in-depth analysis of the role of ovulation in the onset and spread of high-grade serous cancer from the fallopian tube.

Citation Format: Joanna Burdette. Modeling the role of the fallopian tube in the prevention and spread of high grade serous cancer using a multi-organ platform [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A047.
Abstract B032: Probing the molecular crosstalk between ovarian cancer and omentum
Authors: Haughan Monica A. , Lusk Hannah , Bergsten Tova M. , Levy Sarah E. , Klingelhutz Aloysius J. , Sanchez Laura M. , Burdette Joanna E.
Published: March 2024

Ovarian cancer (OC) is the 5th leading cause of cancer death in women despite being considered rare, highlighting the critical need to better understand the mechanisms of pathogenesis and progression. High grade serous OC, the most prevalent OC subtype, frequently metastasizes to the omentum. Building off previous work using an imaging mass spectrometry (IMS) co-culture system to uncover metabolomic changes in primary metastasis, we are now probing the molecular crosstalk between the omentum and OC cells. Our IMS co-culture system identifies molecules produced in co-culture of tumorigenic MOE PTENshRNA or vector control MOE PTENSCR cells and explants. IMS revealed multiple signals, including epinephrine (EPI), unique to the MOE PTENshRNA + omentum condition. Clinical data shows stress and increased expression of ADRβ2, an EPI receptor, are correlated with poorer survival. However, no significant changes were observed in EPI (10mM) treated MOE PTENshRNA invasiveness investigated via Boyden chamber assay. EPI signaling through ADRβ2 can induce lipolysis and propranolol treatment, antagonizing ADRβ2, has shown partial deactivation of OC stimulated lipolysis. We hypothesize EPI may be an autocrine signal produced by the omentum liberating fatty acids and driving tumor progression. To test this, we began examining an immortalized, human pre-adipocyte line (VNPAD 30315) for mechanistic studies. VNPAD 30315 can be differentiated into adipocytes and forms spheroids more accurately simulating in vivo fatty tissues compared to 2D culture. Successfully differentiated spheroids have been generated and spheroid conditioned media (CM) increases invasion like omentum CM. Preliminary results suggest spheroids produce results similar to murine and human omentum explants in IMS co-culture. Currently we are exploring the effects of EPI on the spheroids and adipocyte CM on tumorigenic models. Overall, we are working to identify signals in omental metastasis with our IMS co-culture system and to determine their mechanisms in vitro with a 3D adipocyte model.

Citation Format: Monica A. Haughan, Hannah Lusk, Tova M. Bergsten, Sarah E. Levy, Aloysius J. Klingelhutz, Laura M. Sanchez, Joanna E. Burdette. Probing the molecular crosstalk between ovarian cancer and omentum [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B032.
Abstract B055: Identifying compounds to promote apoptotic cell death in clear cell ovarian cancer
Authors: Shay Brendan , Handly-Santana Abram , Qin Xingping , Choniere Jonathan , Sarosiek Kristopher , Brugge Joan S. , Stover Elizabeth H.
Published: March 2024

Clear cell ovarian cancer is a rare subtype of ovarian cancer with a poor prognosis in advanced-stage disease and increased resistance to standard-of-care treatments including platinum chemotherapy. Previously, we found that multiple clear cell ovarian cancer cell lines are sensitive to inhibition of BCL-XL, a pro-survival member of the BCL-2 family of proteins that control mitochondrial apoptosis. Adding a BCL-XL inhibitor also enhances cell death in clear cell ovarian cancer cell lines treated with standard-of-care drugs including cisplatin, paclitaxel, and poly(ADP-ribose) polymerase (PARP) inhibitor olaparib. To more broadly identify compounds that affect the viability of clear cell ovarian cancer cell lines, either alone or in combination with BCL-XL inhibition, we applied a chemical screening approach. We designed an anchor screen strategy in which a chemical library of clinically relevant compounds (Selleck bioactive compound library; 1,902 compounds) was screened against clear cell ovarian cancer cell lines in two sets: library compounds only, or library compounds combined with BCL-XL inhibitor A1331852 at a fixed concentration (IC25 for each cell line). Fold-change in cell number compared to controls and Z-scores were calculated to identify compounds with single-agent activity in clear cell ovarian cancer and/or with enhanced activity in the presence of A1331852. Initial screening data from JHOC5 and OVISE cell lines identified compounds with targets such as SYK and other tyrosine kinases, PI3K/AKT, and BCL2, as well as chemotherapies, which demonstrated increased activity in the presence of BCL-XL inhibition. Screening of additional cell lines and validation of candidate hits is ongoing to identify agents that are active alone or in combination with BCL-XL inhibition against clear cell ovarian cancer.

Citation Format: Brendan Shay, Abram Handly-Santana, Xingping Qin, Jonathan Choniere, Kristopher Sarosiek, Joan S. Brugge, Elizabeth H. Stover. Identifying compounds to promote apoptotic cell death in clear cell ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B055.
Abstract B076: Targeting cancer glycomes sensitizes ovarian tumors to immunotherapy
Authors: Nie Hao , Saini Pratima , Liu Heng , Zhou Wei , Wang Chen , Claiborne Daniel , Zhang Nan , Abdel-Mohsen Mohamed , Zhang Rugang
Published: March 2024

Aberrant glycans on tumor cell surface contribute to immune escape. The purpose of this study is to establish novel immunotherapeutic strategies for HGSOC tumors by targeting glycans-mediated immune escape in high-grade serous ovarian cancer (HGSOC). Here, we performed in vivo screens targeting 96 glycan structures among a series of mouse HGSOC tumors with different genotypes. We identified β1, 6-GlcNAc branched N-glycan as a major determinant of immune escape in a homologous recombination (HR)-proficiency dependent manner in HGSOCs. Mechanistically, BRCA1/2 transcriptionally suppresses the expression of MGAT5 that produces β1, 6-GlcNAc branched glycans. Using in vitro T cell killing assay, we observed that removal of β1, 6-GlcNAc branched glycans by a small molecule inhibitor or genetically knocking down MGAT5, sensitizes HR-proficient human HGSOC cells to T cells assault. Consistently, using orthotopic syngeneic mouse models, we observed that inhibition of β1, 6-GlcNAc branched glycans sensitizes and synergizes with anti-PD-L1 in HR-proficient, but not HR-deficient HGSOCs. In summary, we identified β1, 6-GlcNAc branched N-glycan as a key mediator of immune escape in HR-proficient HGSOCs. Our findings indicate that MGAT5 represents a therapeutic target to overcome immune escape in a HR-status dependent manner and inhibition of β1, 6-GlcNAc branched glycans sensitizes HR-proficient HGSOCs to immune checkpoint blockades.

Citation Format: Hao Nie, Pratima Saini, Heng Liu, Wei Zhou, Chen Wang, Daniel Claiborne, Nan Zhang, Mohamed Abdel-Mohsen, Rugang Zhang. Targeting cancer glycomes sensitizes ovarian tumors to immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B076.
Abstract IA007: Tumor heterogeneity in ovarian clear cell carcinoma
Authors: Huang Ruby Yun-Ju
Published: March 2024

Ovarian clear cell carcinoma (OCCC) is a gynecologic cancer showing high incidence in East Asia with critical unmet needs for novel therapeutic options. It is a histological subtype with distinct pathological features, molecular profiles, and biological functions. At the bulk transcriptomic level, there are distinct epithelial (EpiCC) and mesenchymal (MesCC) subtypes and immune-related gene expression signatures (irGES) in OCCC tumors. The MesCC subtype or Immune-Hot features are shown to associate with worse clinical outcomes across several cohort studies. During disease progression from early to advanced OCCC, there is a switch from EpiCC to MesCC subtypes and Immune-Cold to Immune-Hot features. Therefore, the landscapes of tumor heterogeneity in early versus advanced OCCC are different. Bulk and spatial profiling revealed that most early OCCC tumors exhibited Immune-Cold features associated with a non-CTLA4 irGES subtype, no tumor infiltrating immune cells (TIIs), and non-immune mimic tumor cells. A subset of early OCCC tumors acquired Immune-Hot features that were associated with a CTLA4 irGES subtype, and TIIs situated adjacent to immune mimic tumor cells. Two translational studies TGOG-4001 and TGOG-4002 have been launched to validate clinical assays for the stratification of Immune-Hot tumors. In advanced OCCC, certain metastatic sites showed high degrees of heterogeneity in spatial transcriptomics with subregions close to the tumor periphery or invasion fronts at the tumor-stromal interface showing inflammatory and EMT-like signals. The primary sites with subregions situated at the tumor core predominantly showed oxidative phosphorylation and low EMT signals. Collectively, OCCC is an ovarian cancer with immense degree of tumor heterogeneity. Comprehensive and in-depth multi-dimensional analysis could facilitate the design of better patient stratification strategies.

Citation Format: Ruby Yun-Ju Huang. Tumor heterogeneity in ovarian clear cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr IA007.
Abstract IA021: Mutational processes as determinants of immune evasion in ovarian cancer
Authors: Shah Sohrab P.
Published: March 2024

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, tumor heterogeneity and intraperitoneal spread. Immunotherapies have had limited efficacy in HGSOC, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumor foci determine the immunological states of the tumor microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumor sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumors harbored inflammatory signaling and ongoing immunoediting, reflected in loss of HLA diversity and tumor infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumors exhibited elevated immunosuppressive TGFβ signaling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumors and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

Citation Format: Sohrab P. Shah. Mutational processes as determinants of immune evasion in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr IA021.
Table S3 from Next-generation Multi-target Stool DNA Panel Accurately Detects Colorectal Cancer and Advanced Precancerous Lesions
Authors: Gagrat Zubin D. , Krockenberger Martin , Bhattacharya Abhik , Gagrat Bridget Z. , Leduc Christine M. , Matter Michael B. , Fourrier Keith D. , Mahoney Douglas W. , Edwards V David K. , Lidgard Graham P. , Limburg Paul J. , Johnson Scott C. , Domanico Michael J. , Kisiel John B.
Published: March 2024

Table S3: Overall test performance for marker selection study for novel multi-target stool DNA panel.
Figure S13 from Neutralizing Antibodies Impair the Oncolytic Efficacy of Reovirus but Permit Effective Combination with T cell–Based Immunotherapies
Authors: Groeneveldt Christianne , Kinderman Priscilla , Griffioen Lisa , Rensing Olivia , Labrie Camilla , van den Wollenberg Diana J.M. , Hoeben Rob C. , Coffey Matt , Loghmani Houra , Verdegaal Els M.E. , Welters Marij J.P. , van der Burg Sjoerd H. , van Hall Thorbald , van Montfoort Nadine
Published: March 2024

Figure S13. Frequency and activation of circulating myeloid cells during Reo preexposure.
Figure S1 from Neutralizing Antibodies Impair the Oncolytic Efficacy of Reovirus but Permit Effective Combination with T cell–Based Immunotherapies
Authors: Groeneveldt Christianne , Kinderman Priscilla , Griffioen Lisa , Rensing Olivia , Labrie Camilla , van den Wollenberg Diana J.M. , Hoeben Rob C. , Coffey Matt , Loghmani Houra , Verdegaal Els M.E. , Welters Marij J.P. , van der Burg Sjoerd H. , van Hall Thorbald , van Montfoort Nadine
Published: March 2024

Figure S1. Bodyweight during preexposure and clodronate liposome treatment.
Table S1 from Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer
Authors: Zhang Han , Lee Sanghoon , Muthakana Renee R. , Lu Binfeng , Boone David N. , Lee Daniel , Wang Xiao-Song
Published: March 2024

Table S1. Datasets analyzed in the study
Supplementary Tables from LILRB3 Supports Immunosuppressive Activity of Myeloid Cells and Tumor Development
Authors: Huang Ryan , Liu Xiaoye , Kim Jaehyup , Deng Hui , Deng Mi , Gui Xun , Chen Heyu , Wu Guojin , Xiong Wei , Xie Jingjing , Lewis Cheryl , Homsi Jade , Yang Xing , Zhang Chengcheng , He Yubo , Lou Qi , Smith Caroline , John Samuel , Zhang Ningyan , An Zhiqiang , Zhang Cheng Cheng
Published: March 2024

Supplementary Tables 1-4