bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1-S8 from Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial–Mesenchymal Transition
Authors: Fang Liang , Zhang Li , Wang Mengran , He Yuhao , Yang Jiao , Huang Zengjin , Tan Ying , Fang Ke , Li Jun , Sun Zhiyuan , Li Yanping , Tang Yisen , Liang Weizheng , Cui Huanhuan , Zhu Qionghua , Wu Zhe , Li Yiming , Hu Yuhui , Chen Wei
Published: March 2024

Figure S1-S8
Data from Body Weight Correlates with Molecular Variances in Patients with Cancer
Authors: Huang Fengyuan , Xu Peng , Yue Zongliang , Song Yuwei , Hu Kaili , Zhao Xinyang , Gao Min , Chong Zechen
Published: March 2024

Abstract
Overweight and obesity are identified by a high body mass index (BMI) and carry significant health risks due to associated comorbidities. Although epidemiologic data connect overweight/obesity with 13 cancer types, a better understanding of the molecular mechanisms underlying this correlation is needed to improve prevention and treatment strategies. In this study, we conducted a comprehensive analysis of molecular differences between overweight or obese patients and normal weight patients across 14 different cancer types from The Cancer Genome Atlas. Using the propensity score weighting algorithm to control for confounding factors, obesity-specific mutational features were identified, such as higher mutation burden in rectal cancer and biased mutational signatures in other cancers. Differentially expressed genes (DEG) in tumors from patients with overweight/obesity were predominantly upregulated and enriched in inflammatory and hormone-related pathways. These DEGs were significantly associated with survival rates in various cancer types, highlighting the impact of elevated body fat on gene expression profiles and clinical outcomes in patients with cancer. Interestingly, while high BMI seemed to have a negative impact on most cancer types, the normal weight–biased mutational and gene expression patterns indicated overweight/obesity may be beneficial in endometrial cancer, suggesting the presence of an “obesity paradox” in this context. Body fat also significantly impacted the tumor microenvironment by modulating immune cell infiltration, underscoring the importance of understanding the interplay between weight and immune response in cancer progression. Together, this study systematically elucidates the molecular differences corresponding to body weight in multiple cancer types, offering potentially critical insights for developing precision therapy for patients with cancer.
Significance:
Elucidation of the complex interplay between body weight and the molecular landscape of cancer could potentially guide tailored therapies and improve patient management amid the global obesity crisis.
Data from Adipose Triglyceride Lipase Is a Therapeutic Target in Advanced Prostate Cancer That Promotes Metabolic Plasticity
Authors: Awad Dominik , Cao Pham Hong Anh , Pulliam Thomas L. , Spradlin Meredith , Subramani Elavarasan , Tellman Tristen V. , Ribeiro Caroline F. , Muzzioli Riccardo , Jewell Brittany E. , Pakula Hubert , Ackroyd Jeffrey J. , Murray Mollianne M. , Han Jenny J. , Leng Mei , Jain Antrix , Piyarathna Badrajee , Liu Jingjing , Song Xingzhi , Zhang Jianhua , Klekers Albert R. , Drake Justin M. , Ittmann Michael M. , Coarfa Cristian , Piwnica-Worms David , Farach-Carson Mary C. , Loda Massimo , Eberlin Livia S. , Frigo Daniel E.
Published: March 2024

Abstract
Lipid metabolism plays a central role in prostate cancer. To date, the major focus has centered on de novo lipogenesis and lipid uptake in prostate cancer, but inhibitors of these processes have not benefited patients. A better understanding of how cancer cells access lipids once they are created or taken up and stored could uncover more effective strategies to perturb lipid metabolism and treat patients. Here, we identified that expression of adipose triglyceride lipase (ATGL), an enzyme that controls lipid droplet homeostasis and a previously suspected tumor suppressor, correlates with worse overall survival in men with advanced, castration-resistant prostate cancer (CRPC). Molecular, genetic, or pharmacologic inhibition of ATGL impaired human and murine prostate cancer growth in vivo and in cell culture or organoids under conditions mimicking the tumor microenvironment. Mass spectrometry imaging demonstrated that ATGL profoundly regulates lipid metabolism in vivo, remodeling membrane composition. ATGL inhibition induced metabolic plasticity, causing a glycolytic shift that could be exploited therapeutically by cotargeting both metabolic pathways. Patient-derived phosphoproteomics identified ATGL serine 404 as a target of CAMKK2–AMPK signaling in CRPC cells. Mutation of serine 404 did not alter the lipolytic activity of ATGL but did decrease CRPC growth, migration, and invasion, indicating that noncanonical ATGL activity also contributes to disease progression. Unbiased immunoprecipitation/mass spectrometry suggested that mutation of serine 404 not only disrupts existing ATGL protein interactions but also leads to new protein–protein interactions. Together, these data nominate ATGL as a therapeutic target for CRPC and provide insights for future drug development and combination therapies.
Significance:
ATGL promotes prostate cancer metabolic plasticity and progression through both lipase-dependent and lipase-independent activity, informing strategies to target ATGL and lipid metabolism for cancer treatment.
Table S4 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

Sequences of sgRNAs used for induction of ERBB4 transcription by CRISPR activation technique.
Figure S9 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 S9. 5-FU treatment induced immune response in MC38 syngeneic tumors and caspase inhibition did not affect the activity of 5-FU.
Figure S5 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 S5. PUMA was induced by p53 and required for necroptosis induction in LoVo cells treated with antimetabolites.
Figure S2 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 S2. Analysis of 30 anticancer drugs revealed that 5-FU and Gemcitabine induced necroptosis in LoVo cells.
Figure S8 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

Levels of p-AKT (A, top) and p-ERK (B, bottom) were determined by phospho-flow cytometry upon 1µM of idelalisib. Density plots show the median MFI values of two replicates, negative control (dotted black), parental (grey), resistant (red). (B) Images on the left show the expression of pRELA by immunofluorescence upon 1µM of idelalisib (right) or control (DMSO, left) in parental and resistant (4hr exposure). Boxplot on the right represents the protein quantification from the immunofluorescence experiments. Data derived from two independent experiments. Three representative fields were evaluated from each independent experiment.
P-values from Welch Two Sample test performed on mean MFI values.
Figure S1 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 S1. No association was found between RIP1 and MLKL expression and CRC patient survival.
Figure S18 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

Expression of let-7c (A) and miR-29c (B) miRNAs was evaluated in Karpas1718 parental and resistant lines by real time PCR upon previous exposure to DMSO (control, grey), decitabine (100nM, yellow) or tazemetostat (5µM, red). RQ values calculated by the DDCt method, RNU6 was used as housekeeping miRNA. Data derived from three independent experiments.
Figure S16 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

Cell viability was evaluated by MTT assay (72h). Karpas1718 parental (A) or resistant (B) were exposed to DMSO (control, black) or decitabine (100nM, red), given concomitantly (continuous lines) or 72 hours before idelalisib (pre DMSO in dashed black or pre decitabine in dashed red). Error bars correspond to standard deviation of the mean. Data derived from two independent experiments. Statistically significant differences were evaluated by moderated t-test comparing each treatment to control (DMSO).
Figure S15 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

Resistant in parallel with parental clones of Karpas1718 cell line were exposed to a library of 348 compounds alone (single, 1µM) or in combination with 1µM idelalisib (combo) for 72h. Cell viability was measured by MTT assay (72h). Yellow for benefit in combo, purple benefit in single treatment.
Figure S1 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

Multi-drug resistance phenotype was ruled out by the expression of MDR1 (left) and MDR2 (right) genes by real time PCR. RQ values calculated by the DDCt method. Karpas1718 (K1718) parental lines in grey and resistant in red. Data derived from two independent experiments; error bars represent standard deviation of the mean.
Figure S3 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 S3 shows confirmation of AKT expression and knockdown in additional cell lines. A, Immunoblotting analysis of WM793 and HT144 cells treated with each siRNA alone or in combination showed effective knockdown of individual paralogs using antibodies against total AKT1, AKT2, and AKT3. B, Expression of each AKT paralog in MTG001 and MTG004 using RT-PCR.
Table 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

Differentially expressed proteins identified from the total proteomic analysis in SUDHL5 and RIVA treated with NBI-961 relative to DMSO vehicle control using log2 fold change greater than or equal to 1 and less than or equal to -1.
Table S8 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 total proteomic analysis in RIVA treated with NBI-961 relative to DMSO vehicle control.
Table 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

DLBCL patient characteristics.
Table S1 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

Short Tandem Repeat (STR) analysis of the DLBCL and benign B cell lines.
Supplementary Data - Tables 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

supplemental tables S1, 4, and 6-12
Supplemental methods 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

Supplemental Methods: Gene Expression by Quantitative PCR
Figure S2 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

1H NMR spectra of NBI-961. Purity of NBI-961 was determined by
1H NMR after dissolved in methanol. Spectra was recorded using an Agilent HPLC with a run time of 15.01 mins and a flow rate of 0.8 mL/min.
Tables S1 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

The DXd concentration in the culture media of human cell lines.
Figure S10 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 does not alter FLT3 expression or its downstream substrate with greater cytotoxicity than sorafenib. (A) Western blot analysis of FLT3 in NBI-961 treated SUDHL5 in lysates from the same three independent experiments showing NEK2 degradation in Figure 4A. (B) Western blot analysis of phosphorylated mTOR (a known downstream substrate of FLT3) in newly NBI-961 treated SUDHL5 lysates from three independent experiments. NEK2 degradation was confirmed. Quantification of p-mTOR band intensity normalized to ACTIN is shown below. (C) Cell viability curves after 96 h NBI-961 treatment of RIVA (red dashed line) and SUDHL5 (blue dashed line) DLBCL cells compared to sorafenib treatment (solid lines) at a higher serial dilution (40 – 0.039 M; left panel) and at the same serial dilution as NBI-961 (2 – 0.00195 M; right panel). Sorafenib GI50 (95% C.I.): RIVA, 4.15 M (3.24 – 5.31); SUDHL5, 3.32 M (2.43 – 4.54).
Figure S5 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

The concentration of R-DXd and total Ab in monkey plasma.
Figure S4 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

ADCC and CDC activity of R-DXd.
Fig. S24 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. S24
Fig. S2 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. S2
Fig. S16 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. S16
Fig. S10 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. S10
Abstract A006: Reckless mitotic entry as a novel chemosensitization approach for alkylating agents
Authors: Lang Fengchao , Cornwell James , Kaur Karambir , Elmogazy Omar , Zhang Wei , Zhang Meili , Song Hua , Sun Zhonghe , Wu Xiaolin , Aladjem Mirit I. , Aregger Michael , Cappell Steven , Yang Chunzhang
Published: March 2024

The cell cycle is tightly regulated by checkpoints, playing a vital role in controlling its progression and timing. Cancer cells exploit the G2/M checkpoint, which serves as a resistance mechanism against genotoxic anti-cancer treatments, allowing for DNA repair prior to cell division. Therefore, manipulating cell cycle timing has emerged as a potential strategy to augment the effectiveness of DNA damage-based therapies such as alkylating agents and radiation. In this study, we conducted a forward genome wide CRISPR/Cas9 screening with repeated exposure to the alkylating agent temozolomide (TMZ) to investigate the mechanisms underlying tumor cell survival under genotoxic stress. Our findings revealed that canonical DNA repair pathways, including ATM/Fanconi and mismatch repair, determine cell fate under genotoxic stress. Notably, we identified the critical role of the membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase, known as Myt1 (encoded by PKMYT1), in ensuring cell survival. Depletion of PKMYT1 led to overwhelming TMZ-induced cytotoxicity in cancer cells. Isobologram analysis demonstrated potent drug synergy between TMZ and other clinically used alkylating agents, such as carmustine, busulfan, and dacarbazine, when combined with a novel Myt1 kinase inhibitor, RP-6306. Mechanistically, inhibiting Myt1 forced G2/M-arrested cells into an unscheduled transition to the mitotic phase without complete resolution of DNA damage, as indicated by a substantial increase in γH2AX-positive cells in mitosis. Moreover, RP-6306 dramatically altered cell cycle timing, reducing the threshold time for mitotic entry. This forced entry into mitosis, along with persistent DNA damage, resulted in severe mitotic abnormalities, including unaligned and partially condensed chromosomes, lagging chromosomes, chromosome bridges, and multipolar spindles. Ultimately, these aberrations led to mitotic exit with substantial apoptosis. Importantly, preclinical animal studies demonstrated that the combination regimen involving TMZ and RP-6306 prolonged the overall survival of glioma-bearing mice. Collectively, our findings highlight the potential of targeting cell cycle timing through Myt1 inhibition as a novel strategy to enhance the efficacy of current standard cancer therapies, potentially leading to improved disease outcomes.

Citation Format: Fengchao Lang, James Cornwell, Karambir Kaur, Omar Elmogazy, Wei Zhang, Meili Zhang, Hua Song, Zhonghe Sun, Xiaolin Wu, Mirit I. Aladjem, Michael Aregger, Steven Cappell, Chunzhang Yang. Reckless mitotic entry as a novel chemosensitization approach for alkylating agents [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 A006.
Abstract A008: Disruption of SLFN5 enhances vulnerability to APR-246, a mutant p53 reactivator in glioblastoma
Authors: Perez Ricardo E. , Eckerdt Frank , Platanias Leonidas C.
Published: March 2024

Glioblastoma multiforme (GBM) or grade 4 IDHWT glioma is the most malignant brain tumor with a median survival of ~15 months. Current treatment options are limited to a combination of surgery, radiation, and the alkylating agent temozolomide (TMZ). However, despite this aggressive treatment regimen, patients inevitably develop recurrent tumors, which depict a high degree of resistance to DNA damage induced by TMZ and irradiation. Therefore, it is imperative to better understand cellular signals contributing to GBM tumorigenesis and therapy resistance. We have previously established potential roles for members of the protein family of schlafens (SLFNs) in GBM. SLFNs have established roles in cell differentiation, cell proliferation, immune responses, and an expanding role in cancer biology. Several human SLFNs have been linked to chemosensitivity in various cancer types. In particular, SLFN5 mRNA levels progressively increased from grade 2 to grade 4 glioma suggesting a possible therapeutic target for GBM. Therefore, in an effort to better understand the role of SLFN5 in GBM tumorigenesis, CRISPR/Cas9-mediated SLFN5 knockout glioblastoma cell lines and PDX lines were generated. Cells lacking expression of SLFN5 showed increased DNA damage signaling, as judged by elevated basal levels of the DNA damage marker γH2AX and persistent phosphorylation of Chk2. Gene ontology analysis indicated increased expression of p53 pathway components in SLFN5 knockout cells. In GBM, p53 activity is commonly deregulated due to high mutations in the p53 pathway. In line with this, SLFN5 knockout cells depicted increased sensitivity to the mutant p53 reactivator APR-246 correlating with p53 mutational status. APR-246 induced PARP cleavage in SLFN5 knockout cells was rescued by the ROS scavenger N-acetyl-D-cysteine (NAC). Our results suggest increased DNA damage signaling in SLFN5 deficient cells. Furthermore, mutant p53 reactivator APR-246 induced apoptosis is dependent on ROS signaling. In summary, we provide evidence for a protective role of SLFN5 to limit DNA damage and ROS signaling in GBM.

Citation Format: Ricardo E. Perez, Frank Eckerdt, Leonidas C. Platanias. Disruption of SLFN5 enhances vulnerability to APR-246, a mutant p53 reactivator in glioblastoma [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 A008.
Abstract A020: Neural stem cells expressing PTEN-L suppress glioblastoma invasion in vivo
Authors: Lorimer Ian A. , Lui Margarita , Lavictoire Sylvie J. , Coulombe Josee
Published: March 2024

Purpose: The purpose of this study is to evaluate the therapeutic potential of neural stem cells expressing PTEN-L (a variant of the tumor suppressor PTEN that can transfer between cells) in preclinical glioblastoma models. Experimental procedures: Human neural stem cells derived by direct reprogramming of peripheral blood erythroblasts were used. Using lentiviral transduction, these were engineered for doxycycline-inducible expression of a modified version of PTEN-L with optimized expression and enhanced cell-to-cell transfer properties. Expression of PTEN-L was assayed by Western blot analysis. These engineered neural stem cells were evaluated in an orthotopic mouse xenograft model in which human glioblastoma cells show extensive invasion into the uninjected hemisphere. Neural stem cells and glioblastoma cells were co-injected and mice were then randomized to chow with or without doxycycline. Mice were evaluated for overall survival and for invasion of glioblastoma cells into the uninjected hemisphere. Results: When injected intracerebrally into immunocompromised mice, peripheral blood-derived neural stem cells persisted for over four months and showed an ability to spontaneously migrate to sites distant from the injection site. When co-injected with human glioblastoma cells from patients, the neural stem cells co-migrated with glioblastoma cells along the corpus callosum and to distant sites. Peripheral blood-derived neural stem cells transduced with lentiviral vectors for doxycycline-inducible PTEN-L efficiently secreted PTEN-L. In the orthotopic mouse xenograft glioblastoma model, expression of PTEN-L by neural stem cells did not significantly improve survival in mice (log rank P = 0.5) but did significantly repress glioblastoma cell invasion into the uninjected hemisphere (two-tailed t-test P = 0.02). Conclusions. Peripheral blood-derived neural stem cells show good persistence and migrate with human glioblastoma cells in vivo. They can be engineered to efficiently secret functional PTEN-L. Peripheral blood-derived neural stem cells expressing PTEN-L do not increase survival in the one patient model tested but do repress invasion. This initial evidence for bioactivity supports further studies evaluating the ability of neural stem cells expressing PTEN-L to sensitize glioblastoma to therapeutics for which PTEN loss has been implicated in resistance.

Citation Format: Ian A. Lorimer, Margarita Lui, Sylvie J. Lavictoire, Josee Coulombe. Neural stem cells expressing PTEN-L suppress glioblastoma invasion in vivo [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 A020.
Abstract B013: In vitro stability and in vivo pharmacokinetic behavior of panobinostat in mouse models for the treatment of CNS tumors
Authors: Zhang Wenqiu , Oh Ju-Hee , Zhang Wenjuan , Sirianni Rachael W. , Elmquist William F.
Published: March 2024

Aberrant alterations of histone deacetylases (HDACs), an epigenetic regulator, are common in central nervous system (CNS) tumors and HDAC inhibitors have been found to have therapeutic potential for the treatment of CNS tumors. Panobinostat is a pan-HDAC inhibitor that has shown potency against multiple CNS tumors. Panobinostat has a hydroxamic acid side chain, a structural element reported to be susceptible to esterase activity in multiple compounds. Therefore, in vitro stability of panobinostat may allow the prediction of in vivo pharmacokinetic behavior. The objective of this study is to discover the mechanisms influencing the in vitro stability of panobinostat in multiple matrices and evaluate the in vivo pharmacokinetics in mouse models. In vitro stability studies in mouse plasma at different temperatures showed that panobinostat was unstable in mouse plasma and the decomposition rate was temperature-dependent. Meanwhile, panobinostat was stable in phosphate-buffered saline (PBS, pH7.4) tested at the same incubation conditions. Therefore, we propose that enzymatic activity is a contributor of the in vitro instability of panobinostat. Panobinonstat stability was also measured in plasma from different species. Data show that panobinostat was stable in human, monkey and dog plasma while unstable in mouse and rat plasma. The species difference observed was in line with the carboxylesterase 1c (Ces1c) expression among these species, where rodent plasma has abundant Ces1c expression while the other species have no Ces1c in plasma. With this in mind, we evaluated the impact of Ces1c removal from the matrices. We found that panobinostat was stable in plasma collected from Ces1c knockout mice (B6.Cg-Ces1ctm1.1Loc/J), indicating that Ces1c is contributing to the in vitro instability of panobinostat in plasma. To evaluate the influence of Ces1c on its pharmacokinetic behaviors, we studied the plasma and CNS distribution of panobinostat in wild-type C57BL6/J mice and Ces1c knockout mice following an intravenous bolus dose of 10 mg/kg via tail vein. Despite improved in vitro stability of panobinostat in plasma from Ces1c knockout mice compared with that in plasma from wild-type C57BL6/J, in vivo plasma concentration-time profiles were superimposable between these two genotypes. In addition, the CNS delivery of panobinostat was not influenced by the lack of Ces1c. Studies are ongoing to find potential in vivo mechanisms that are protecting the compound from robust in vitro degradation in the plasma.

Citation Format: Wenqiu Zhang, Ju-Hee Oh, Wenjuan Zhang, Rachael W. Sirianni, William F. Elmquist. In vitro stability and in vivo pharmacokinetic behavior of panobinostat in mouse models for the treatment of CNS 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 B013.
Abstract B018: Epigenetic targeting improves glioblastoma cell sensitivity to chemotherapy
Authors: Tehrani Golnaz Asaadi , Kubick Becca , Datta Meenal
Published: March 2024

Histone deacetylase inhibitors (HDACi) have emerged as a new class of anti-tumor agents for various types of cancers, including glioblastoma (GBM). Recent studies have shown that targeting the GBM epigenome can enhance the effects of standard clinical therapies. Here, we utilized the human U87-GBM cell line to evaluate the cytotoxic properties of three blood-brain-barrier-penetrating HDACi, suberoylanilide hydroxamic acid (SAHA, or Vorinostat), valproic acid (VPA), and CAY10603, both as monotherapies and in combination with the chemotherapeutic agent temozolomide (TMZ). Combination Index (CI) was quantified by MTT assay and human normal astrocytes (HNAs, SV40T) were used as cytotoxic controls. We found that HDACi significantly reduced cell viability and increased cell death of human GBM cells, but not HNAs. Combination therapy of HDACi with TMZ generated increased cytotoxic activity in comparison to TMZ monotherapy, with the combination of VPA and TMZ having the strongest effect (30% viability following VPA/TMZ treatment, compared to 42% SAHA/TMZ, 45% CAY10603/TMZ, and 85% TMZ alone). In contrast, when evaluating epi-drugs as monotherapies, at intermediate concentrations, 1.9 μM CAY10603 was most effective in decreasing U87-GBM cell viability (27%) particularly at micromolar concentrations, compared to 3.7 μM SAHA (36%) and 1.5 mM VPA (51%). In HNAs, CAY10603, SAHA, and VPA decreased cell viability to 80%, 87%, and 90%, respectively.These findings suggest that HDACi synergize with TMZ to enhance its cytotoxicity. The promising anti-tumor effects these HDACi-s warrant preclinical studies.

Citation Format: Golnaz Asaadi Tehrani, Becca Kubick, Meenal Datta. Epigenetic targeting improves glioblastoma cell sensitivity to chemotherapy [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 B018.
Abstract B029: A novel lupus-associated antibody that inhibits the growth of aggressive high-grade glioma orthotopic xenografts and enhances radiotherapy via a unique mechanism
Authors: Johns Terrance G. , Kuchibhotla Mani , O'Sullivan Kim , Ng Zi Ying , Palanisamy Ranjith , Campbell James , Dubljevic Valentina , Endersby Raelene
Published: March 2024

A major immune dysregulation in lupus patients is the generation of autoantibodies targeting a range of self-molecules. Some of these lupus antibodies may have anti-tumor activity in high-grade glioma (HGG). An autoantibody, 3E10, was isolated from a mouse model of lupus that has high affinity for DNA. Two different humanized forms of 3E10 were generated, PAT-DX1 (a di-scFV) and PAT-DX3 (a humanized IgG1). Neither DX1 nor DX3 inhibited the in vitro growth of HGG patient-derived cell lines, either alone or in combination with radiotherapy (RT). In contrast, both antibody constructs inhibited the growth of GBM6 orthotopic xenografts in mice as single agents, consistent with our data showing uptake of labelled DX1 in HGG xenografts. Interestingly, despite its larger molecular weight, DX3 displayed greater anti-tumor activity than DX1, possibly due to improved tumor localization. DX1 showed at least additive anti-tumor activity in combination with RT against GBM6 xenografts, significantly extending survival. Neutrophils produce NETs, a proinflammatory form of cell death that generates web-like structures composed of various injurious enzymes and DNA. NET release promotes a favorable tumor environment through induction of cellular proliferation and angiogenesis. NETs cause resistance to therapeutics in a variety of cancers and their inhibition improves response to these therapeutics. Our published data shows that DX1 inhibits the formation of NETs in neutrophils, suggesting this could be its mechanism of action and is consistent with the lack of DX1 in vitro activity. Large scale production of DX1 has been optimized and toxicology and safety studies in rats and non-human primates have not identified any concerns. A first in human Phase 1 clinical trial of DX1 is planned in 2024 and will include HGG patients.

Citation Format: Terrance G. Johns, Mani Kuchibhotla, Kim O'Sullivan, Zi Ying Ng, Ranjith Palanisamy, James Campbell, Valentina Dubljevic, Raelene Endersby. A novel lupus-associated antibody that inhibits the growth of aggressive high-grade glioma orthotopic xenografts and enhances radiotherapy via a unique mechanism [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 B029.
Abstract B031: A brain penetrant Nicotinamide-adenine dinucleotide mimetic impedes de novo guanylate synthesis and glioblastoma growth
Authors: Chen Yu-Jung , Iyer Swathi V. , David Hsieh Chun-Cheng , Wang Tao , Li Jing , Lien Michelle C. , Ganbold Mungunsarnai , Xie Xuanhua P. , Jayewickreme Chenura , Brady Sean F , Lim Kyun , Parada Luis F
Published: March 2024

Glioblastoma is a malignant disease with dire prognosis and in urgent need of improved therapeutics. We identify a small compound, Gliocidin, that kills glioblastoma cells while sparing replicative mouse embryonic fibroblasts. Gliocidin activity reveals a de novo purine synthesis pathway metabolic vulnerability in glioblastoma caused by indirect inhibition of inosine monophosphate dehydrogenase 2 (IMPDH2). Gliocidin mediated IMPDH2 blockade reduces intracellular guanine nucleotide levels causing nucleotide imbalance, replication stress, and tumor cell death. Gliocidin is a prodrug anabolized into its tumoricidal metabolite by the enzyme nicotinamide nucleotide adenylyltransferase (NMNAT1) of the NAD+ salvage pathway. In vivo, Gliocidin penetrates the blood brain barrier and extends orthotopic murine GBM mouse survival. The DNA alkylating agent, Temozolomide (TMZ), induces Nmnat1 expression causing a synergistic tumor killing effect and additional survival benefit in patient-derived xenograft (PDX) orthotopic mouse models. This study brings Gliocidin to light as a prodrug that can improve the survival of GBM patients.

Citation Format: Yu-Jung Chen, Swathi V. Iyer, Chun-Cheng David Hsieh, Tao Wang, Jing Li, Michelle C. Lien, Mungunsarnai Ganbold, Xuanhua P. Xie, Chenura Jayewickreme, Sean F Brady, Kyun Lim, Luis F Parada. A brain penetrant Nicotinamide-adenine dinucleotide mimetic impedes de novo guanylate synthesis and glioblastoma growth [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 B031.
Abstract B038: Accurate quantitative profiling of rna modifications and their associations with glioblastoma
Authors: Morales Shnaider Frank A , Eddings Coston , Simpson Jennifer , Tannous Bakhos A. , Chiu Norman
Published: March 2024

Every chemical group that is added to one of the canonical ribonucleotides, i.e., RNA modification, in a specific transcript can potentially alter the RNA folding as well as the RNA-protein interactions. Hence, RNA modifications are considered as post-transcriptional regulators for RNA splicing, RNA stability, and translation, just to name a few. Today, 170+ different RNA modifications have been identified, but only half a dozen of them are linked to glioblastoma (GBM). On the other hand, other RNA biology studies indicated the interplays between RNA modifications within a specific epitranscriptome could play a regulatory role in cellular activities. Although suitable methods for profiling RNA modifications in a specific epitranscriptome are available, the lack of ribonucleoside standards has prohibited the accurate quantification of each detectable RNA modification. To address this analytical challenge, our group has recently developed a mass spectrometric method that can achieve accurate quantitative profiling of untargeted RNA modifications without using any standards. Using the developed method, all the RNA modifications in patient-derived GBM cell lines could be profiled with high accuracy. In total, 31 different RNA modifications were detected in the GBM epitranscriptomes. By comparing with the profile detected in healthy human brain tissues, a unique set of upregulated RNA modifications is associated with the development of GBM. These findings are supported by the upregulated gene expression data obtained from GBM patients that are available in The Cancer Genome Atlas program.

Citation Format: Frank A Morales Shnaider, Coston Eddings, Jennifer Simpson, Bakhos A. Tannous, Norman Chiu. Accurate quantitative profiling of rna modifications and their associations with glioblastoma [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 B038.
Abstract IA016: Metabolic reprogramming and cancer progression in patients
Authors: DeBerardinis Ralph J.
Published: March 2024

Many human diseases, including cancer, involve alterations of cellular metabolism caused either directly or indirectly by mutations in genes that regulate the metabolic network. In cancer, reprogrammed metabolic activities arising from mutations in tumor suppressors and oncogenes are thought to contribute both to cancer initiation and progression, particularly metastasis. Many factors intrinsic or extrinsic to the cancer cell impact metabolic properties within tumors and influence vulnerabilities that could presumably be exploited to suppress cancer progression. Although many insights about metabolic regulation have been derived from reductionist models of cancer cell growth in culture, these models do not incorporate all of the factors – particularly cancer cell-extrinsic factors – that contribute to cancer progression. I will describe approaches to assess cancer metabolism within intact tumors, including in cancer patients. We use a multidisciplinary approach to infuse 13C-labeled nutrients (13C-glucose, 13C-acetate, 13C-glutamine) during surgical tumor resection in patients with malignancies in the brain, lung, kidney and other organs. Isotope labeling in metabolites extracted from tumors and adjacent, nonmalignant tissue provides information metabolic pathways activated or repressed in the tumors. By following clinical outcomes over time, we have identified labeling features and pathways that correlate with metastasis and early demise. I will discuss how these features reflect the evolution of metabolic properties and liabilities during human cancer progression, and how parallel studies in mice have allowed us to define mechanisms by metabolism supports metastasis.

Citation Format: Ralph J. DeBerardinis. Metabolic reprogramming and cancer progression in patients [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 IA016.
Abstract IA026: Metabolic dependencies of brain metastases
Authors: Pacold Michael E
Published: March 2024

Cells require nutrients to make biomolecules required for growth and proliferation, and restricted availability of these nutrients prevents cell growth. Nutrient limits are imposed by the extracellular environment, such as the brain interstitial fluid, which maintains low levels of amino acids such as serine and glycine. These amino acids serve as neurotransmitters, and are needed to make proteins, nucleotides, and antioxidants. Cells also make some metabolites, such as coenzymes, in limiting quantities. Both acute and chronic nutrient depletion and hypoxia contribute to the pathogenesis of many diseases including autoimmune disease, cardiac disease, and cancer. Cells entering, growing, or proliferating in the brain or other low-nutrient environments must find other sources of serine, glycine, and coenzymes or synthesize their own, and prioritize the efficient use of nutrients and oxygen. We are interested in discovering the metabolic adaptations needed for cells to enter the brain, determining if cells acquire these adaptations before they enter the brain or adapt following entry into the brain, and targeting these adaptations with small molecule inhibitors.

Citation Format: Michael E Pacold. Metabolic dependencies of 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 IA026.