bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table from Epigenetic Regulation of Fanconi Anemia Genes Implicates PRMT5 Blockage as a Strategy for Tumor Chemosensitization
Authors: Du Changzheng , Li Steven W. , Singh Simranjit X. , Roso Kristen , Sun Michael A. , Pirozzi Christopher J. , Yang Rui , Li Jian-Liang , He Yiping
Published: April 2023

Supplementary Table from Epigenetic Regulation of Fanconi Anemia Genes Implicates PRMT5 Blockage as a Strategy for Tumor Chemosensitization
Supplementary Table from MIRO2 Regulates Prostate Cancer Cell Growth via GCN1-Dependent Stress Signaling
Authors: Furnish Madison , Boulton Dillon P. , Genther Victoria , Grofova Denisa , Ellinwood Mitchell Lee , Romero Lina , Lucia M. Scott , Cramer Scott D. , Caino M. Cecilia
Published: April 2023

Supplementary Table from MIRO2 Regulates Prostate Cancer Cell Growth via GCN1-Dependent Stress Signaling
Supplementary Figure from MIRO2 Regulates Prostate Cancer Cell Growth via GCN1-Dependent Stress Signaling
Authors: Furnish Madison , Boulton Dillon P. , Genther Victoria , Grofova Denisa , Ellinwood Mitchell Lee , Romero Lina , Lucia M. Scott , Cramer Scott D. , Caino M. Cecilia
Published: April 2023

Supplementary Figure from MIRO2 Regulates Prostate Cancer Cell Growth via GCN1-Dependent Stress Signaling
Supplementary Figure 7 from DCLK1-Short Splice Variant Promotes Esophageal Squamous Cell Carcinoma Progression via the MAPK/ERK/MMP2 Pathway
Authors: Ge Yang , Fan Xiaona , Huang Xuying , Weygant Nathaniel , Xiao Zeru , Yan Rui , Liu Heshu , Liu Jian , An Guangyu , Yao Jiannan
Published: April 2023

Figure S7 shows DCLK1 total expression in ESCC demonstrates EMT process activation and MAPK/ERK phosphorylation.
Supplementary Figure 6 from DCLK1-Short Splice Variant Promotes Esophageal Squamous Cell Carcinoma Progression via the MAPK/ERK/MMP2 Pathway
Authors: Ge Yang , Fan Xiaona , Huang Xuying , Weygant Nathaniel , Xiao Zeru , Yan Rui , Liu Heshu , Liu Jian , An Guangyu , Yao Jiannan
Published: April 2023

Figure S6 shows study workflow.
Supplementary Figure from DNA-PK Inhibitor Peposertib Amplifies Radiation-Induced Inflammatory Micronucleation and Enhances TGFβ/PD-L1 Targeted Cancer Immunotherapy
Authors: Carr Michael I. , Chiu Li-Ya , Guo Yige , Xu Chunxiao , Lazorchak Adam S. , Yu Huakui , Qin Guozhong , Qi Jin , Marelli Bo , Lan Yan , Sun Qing , Czauderna Frank , Zenke Frank T. , Blaukat Andree , Vassilev Lyubomir T.
Published: April 2023

Supplementary Figure from DNA-PK Inhibitor Peposertib Amplifies Radiation-Induced Inflammatory Micronucleation and Enhances TGFβ/PD-L1 Targeted Cancer Immunotherapy
Supplementary Figure from Ceramide Kinase Inhibition Drives Ferroptosis and Sensitivity to Cisplatin in Mutant KRAS Lung Cancer by Dysregulating VDAC-Mediated Mitochondria Function
Authors: Vu Ngoc T. , Kim Minjung , Stephenson Daniel J. , MacKnight H. Patrick , Chalfant Charles E.
Published: April 2023

Supplementary Figure from Ceramide Kinase Inhibition Drives Ferroptosis and Sensitivity to Cisplatin in Mutant KRAS Lung Cancer by Dysregulating VDAC-Mediated Mitochondria Function
Supplementary Figure from Circ_0001821 Affects Proliferation and the Cell Cycle in Esophageal Squamous Cell Carcinoma by Elevating BTRC-Mediated IKBA Ubiquitination
Authors: Lin Changjin , Wei Yujun , Duan Xinchun , Liu Chunquan , Du Yanlin , Wang Xiaoran , Luo Yi , Cui Yong
Published: April 2023

Supplementary Figure from Circ_0001821 Affects Proliferation and the Cell Cycle in Esophageal Squamous Cell Carcinoma by Elevating BTRC-Mediated IKBA Ubiquitination
Supplementary Tables 1-3, Figures 1-3 from Sohlh2 Regulates the Stemness and Differentiation of Colon Cancer Stem Cells by Downregulating LncRNA-H19 Transcription
Authors: Zhang Ruihong , Zhang Xiaoli , Zhang Wenfang , Cui Weiwei , Xiao Yunling , Liu Lanlan , Zhi Sujuan , Feng Xiaoning , Liu Xuyue , Shen Ying , Chai Jie , Hao Jing
Published: April 2023

Supplementary Table S1: Primer sequence for qPCR
Supplementary Table S2: LncRNAs regulated by Sohlh2 in colon cancer cells
Supplementary Table S3: The correlation of Sohlh2 expression and clinical characteristics
Supplementary Figure 1: The protein levels of Lgr5, CD133 were downregulated in Sohlh2-overexpressing CSC-derived xenografts, and the levels of TFF2 were upregulated.
Supplementary Figure S2: Sohlh2 downregulated the expression of β-catenin in xenograft tumors.
Supplementary Figure S3: Sohlh2 upregulated the expression of APC in HCT116 CSCs.
Supplementary Data from Disruption of β-Catenin–Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion
Authors: Chen George T. , Tifrea Delia F. , Murad Rabi , Habowski Amber N. , Lyou Yung , Duong Madeleine R. , Hosohama Linzi , Mortazavi Ali , Edwards Robert A. , Waterman Marian L.
Published: April 2023

Supplementary Data from Disruption of β-Catenin–Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion
Supplementary Table 1 from The Spatial Context of Tumor-Infiltrating Immune Cells Associates with Improved Ovarian Cancer Survival
Authors: Steinhart Benjamin , Jordan Kimberly R. , Bapat Jaidev , Post Miriam D. , Brubaker Lindsay W. , Bitler Benjamin G. , Wrobel Julia
Published: April 2023

Table S1. Median survival times (in days) for overall survival and disease-free survival outcomes, split by high and low B cell presence and high and low B cell-macrophage interaction.
Figure S8 from Bone Marrow Mesenchymal Stem Cells Induce Metabolic Plasticity in Estrogen Receptor–Positive Breast Cancer
Authors: Buschhaus Johanna M. , Rajendran Shrila , Chen Siyi , Wharram Bryan L. , Bevoor Avinash S. , Cutter Alyssa C. , Humphries Brock A. , Robison Tanner H. , Farfel Alex P. , Luker Gary D.
Published: April 2023

Figure S8. Single-cell metabolic responses over time. Cell type of interest is bolded in co-culture comparisons. Cumulative AUC changes in NADH lifetime over 30 minutes post-treatment in 10-minute intervals. For a single cell, each change is normalized to the initial NADH lifetime. Table shows changes in median values in picoseconds of NADH or CFP lifetime (ATP) after addition of each compound. Labels at the top of the table denote the relevant comparison in each column.
Figure S2 from Bone Marrow Mesenchymal Stem Cells Induce Metabolic Plasticity in Estrogen Receptor–Positive Breast Cancer
Authors: Buschhaus Johanna M. , Rajendran Shrila , Chen Siyi , Wharram Bryan L. , Bevoor Avinash S. , Cutter Alyssa C. , Humphries Brock A. , Robison Tanner H. , Farfel Alex P. , Luker Gary D.
Published: April 2023

Figure S2. NADH lifetime and ROS quantification for ER+ breast cancer cells with CM and MSCs in monoculture and co-culture. Cell type of interest is bolded in co-culture comparisons. A-B) Histograms of NADH lifetime for HS5 (A) and HS27a (B) in monoculture or co-culture with MCF7, T47D, and HCC1428 (HCC) ER+ breast cancer cells. C-E) Histograms of NADH lifetime for MCF7 (C), T47D (D), and HCC1428 (HCC, E) cells in co-culture and monoculture with control or CM from HS5 or HS27a MSCs. Dashed lines represent cancer cells in CM and solid lines represent cancer cells in monoculture or co-culture with MSCs. N>100 cells.
Supplementary Table 3 from Improved Delineation of Colorectal Cancer Molecular Subtypes and Functional Profiles with a 62-Gene Panel
Authors: Bhukdee Dhup , Nuwongsri Pattarin , Israsena Nipan , Sriswasdi Sira
Published: April 2023

Mutation rate and MSI status statistics for each subtype
Figure S6 from The Elongin BC Complex Negatively Regulates AXL and Marks a Differentiated Phenotype in Melanoma
Authors: Schieven Sebastiaan M. , Traets Joleen J.H. , Vliet Alex v. , Baalen Martijn v. , Song Ji-Ying , Guimaraes Marcos Da Silva , Kuilman Thomas , Peeper Daniel S.
Published: April 2023

Extended data on Figure 6: Low expression of ELOB/C is associated with dedifferentiation in human melanomas.
Supplementary Figures 1 and 2 from Exosomal lincROR Promotes Docetaxel Resistance in Prostate Cancer through a β-catenin/HIF1α Positive Feedback Loop
Authors: Jiang Xingkang , Xu Yong , Liu Ranlu , Guo Shanqi
Published: April 2023

S1. A. CCK-8 assay was used to detect the cytotoxicity of DTX in DTX-resistant PCa cells (PC3/DR and DU145/DR) and their parental sensitive cells (PC3 and DU145). B. The list of hypoxia-related lncRNAs from Pubmed and the top 80 upregulated lncRNAs in PC3/DR cells from RNA-seq (Jiang X, et al. Front Oncol, 2022). The data are presented as the mean ± S.D. of at least three independent experiments. *P < 0.05.
S2. A. The relative expression of lincROR was evaluated by qRT-PCR in PC3 and DU145 cells after being transfected with lincROR. B. DU145 cells were treated with different dosages of DTX (concentration of 0, 5, 10, 20, 40, and 80 nM) for 72 hours and cell viability was evaluated by a CCK-8 assay. C. The LDH release in the culture medium was detected in lincROR-transfected DU145 cells after DTX treatment. D. The expression of lincROR was evaluated in PC3/DR and DU145/DR cells after transfected with siROR #1 or #2. E. The cytotoxicity of DTX in DU145/DR cells was detected by CCK-8 assay after lincROR knockdown. F. The LDH release in culture medium was detected in lincROR-knockdown DU145/DR cells after DTX treatment. The data are presented as the mean ± S.D. of at least three independent experiments.
Supplementary Data Table S2 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: April 2023

Significant enriched pathways in JMJD6-KO MCF7 and MDA-MB231 cells
Figure S3 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: April 2023

Effect of Jmjd6 silencing in PyMT41C-cells. A) Real-Time PCR showing the levels of Jmjd6 in PyMT-41C cells transfected with non-targeting siRNA (siCtr) or specific for Jmjd6. Graph is the average of two independent experiments. Two-tailed unpaired t student test was applied to calculate statistical significance. B) Western blot performed on conditioned medium collected from PyMT-41C transfected as in A). Red Ponceau is shown as loading control. C) IF to detect ANXA1 levels and D) lipid droplet formation in cell transfected as in A).
Figure S2 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: April 2023

JMJD6 regulates lipid metabolism in MCF7 cells. A) Immunohistochemistry staining for ANXA1 (brown) combined with Oil red-O staining (pink) for lipid droplets visualization in wild-type MCF7 cells B) Gene set enrichment plot for 'Hallmark of Adipogenesis' found to be significantly downregulated in JMJD6 KO MCF7 cells compared to scramble control. C) List of 'Reactome Pathways' found to be regulated by the genes included in the gene set enrichment pathway of 'Hallmark of Adipogenesis' and present in the DEGs list of JMJD6 KO versus scramble MCF7 cells.
Figure S1 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: April 2023

Effect of JMJD6 KO in ER positive and negative cell lines. A) Western blot showing the expression of JMJD6 and ERα in wild-type, scramble or JMJD6 KO BT474 cells both in mass cultures (Left panel) and in single clones (right panel). Vinculin is shown as loading control. B) Volcano plot showing the most upregulated (red) and downregulated (green) genes between scramble and wild-type (parental) MCF7 (left) and MDA-MB231 (right) cells.
Supplementary Figures 1 and 2 from Quantitative In Vivo Imaging of the Androgen Receptor Axis Reveals Degree of Prostate Cancer Radiotherapy Response
Authors: Storey Claire M. , Altai Mohamed , Bicak Mesude , Veach Darren R. , Lückerath Katharina , Adrian Gabriel , McDevitt Michael R. , Kalidindi Teja , Park Julie E. , Herrmann Ken , Abou Diane , Zedan Wahed , Peekhaus Norbert , Klein Robert J. , Damoiseaux Robert , Larson Steven M. , Lilja Hans , Thorek Daniel , Ulmert David
Published: April 2023

S1. Hierarchical clustering based on Euclidean distance of RNA-seq data demonstrates separation of EBRT-treated (B1-3) and untreated (C1-3) samples.S2. Multi-dimensional scaling plot of RNA-seq data demonstrates separation of EBRT-treated (B1-3) and untreated (C1-3) samples.
Figure S2 from TBX3 Promotes Cervical Cancer Proliferation and Migration via HPV E6 and E7 Signaling
Authors: Khan Saif F. , Burmeister Carly A. , Scott David J. , Sinkala Musalula , Ramburan Amsha , Wu Hue-Tsi , Schäfer Georgia , Katz Arieh A. , Prince Sharon
Published: April 2023

HPV18 E6 and E7 oncogene mRNA expression in the E6, E7 and E6/E7 stably transfected cells compared to the wild type and empty vector controls.
Figure S1 from TBX3 Promotes Cervical Cancer Proliferation and Migration via HPV E6 and E7 Signaling
Authors: Khan Saif F. , Burmeister Carly A. , Scott David J. , Sinkala Musalula , Ramburan Amsha , Wu Hue-Tsi , Schäfer Georgia , Katz Arieh A. , Prince Sharon
Published: April 2023

Establishment of CaSki and HeLa cervical cancer cell culture model in which TBX3 was stably overexpressed.
Supplementary Tables 1-9 from Targeting Unc51-like Autophagy Activating Kinase 1 (ULK1) Overcomes Adaptive Drug Resistance in Acute Myelogenous Leukemia
Authors: Bhattacharya Seemana , Piya Sujan , Ma Huaxian , Sharma Priyanka , Zhang Qi , Baran Natalia , Ruvolo Vivian R. , McQueen Teresa , Davis R. Eric , Pourebrahim Rasoul , Konopleva Marina , Kantarjian Hagop , Cosford Nicholas D. P. , Andreeff Michael , Borthakur Gautam
Published: April 2023

Supplementary Table S1. Abbreviations of cell populations analyzed using Bloodspot.
Supplementary Table S2. Comparative analysis of significance based on survival curves generated using GraphPad.
Supplementary Table S3. Mutational profiles of AML cell lines and their sensitivity to SBI-0206965.
Supplementary Table S4. Mutational profiles of AML patient derived primary samples.
Supplementary Table S5. IC50 values of drug resistant cells.
Supplementary Table S6. Combinatorial Index (CI-value) of combination treatments.
Supplementary Table S7. Comparative analysis of significance based on survival curves generated using GraphPad (Ex vivo model).
Supplementary Table S8. List of Antibodies.
Supplementary Table S9. List of Primers.
Supplementary Figures 1-8 from Targeting Unc51-like Autophagy Activating Kinase 1 (ULK1) Overcomes Adaptive Drug Resistance in Acute Myelogenous Leukemia
Authors: Bhattacharya Seemana , Piya Sujan , Ma Huaxian , Sharma Priyanka , Zhang Qi , Baran Natalia , Ruvolo Vivian R. , McQueen Teresa , Davis R. Eric , Pourebrahim Rasoul , Konopleva Marina , Kantarjian Hagop , Cosford Nicholas D. P. , Andreeff Michael , Borthakur Gautam
Published: April 2023

S1. Effect of genetic abrogation of ULK1 in vitro and in vivo.
S2. ULK1 inhibitor SBI-0206965 has anti-leukemic activity and can overcome autophagic adaptation in drug-resistant cells.
S3. ULK1 inhibition reverses drug-resistance and synergizes with AML therapies.
S4. ULK1 inhibition changes signaling in AML cells.
S5. ULK1 inhibition hampers ROS.
S6. ULK1 inhibition accumulates dysfunctional mitochondria.
S7. ULK1 inhibition impairs colony forming ability and delays leukemia progression.
S8. In vitro and in vivo synergy of ULK1 inhibition with AML therapies.
Table S1 from Scaffolding Protein Connector Enhancer of Kinase Suppressor of Ras 1 (CNKSR1) Regulates MAPK Inhibition Responsiveness in Pancreas Cancer via Crosstalk with AKT Signaling
Authors: Li Dandan , Miermont Anne M. , Sable Rushikesh , Quadri Humair S. , Mathews Griner Lesley A. , Martin Scott E. , Odzorig Taivan , De Soumita , Ferrer Marc , Powers Astin S. , Hewitt Stephen M. , Rudloff Udo
Published: April 2023

Lists of cell lines, antibodies, RNAi kinome screen; and matrix drug combination.
Figure S1 from Scaffolding Protein Connector Enhancer of Kinase Suppressor of Ras 1 (CNKSR1) Regulates MAPK Inhibition Responsiveness in Pancreas Cancer via Crosstalk with AKT Signaling
Authors: Li Dandan , Miermont Anne M. , Sable Rushikesh , Quadri Humair S. , Mathews Griner Lesley A. , Martin Scott E. , Odzorig Taivan , De Soumita , Ferrer Marc , Powers Astin S. , Hewitt Stephen M. , Rudloff Udo
Published: April 2023

Resistance to MEK inhibition in YAPC cells is not due to reactivation of phospho-Extracellular-signal-regulated-kinases (ERK) levels.
Data from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: April 2023

Abstract
Breast cancer is the most common type of cancer in women worldwide, with the luminal subtype being the most widespread. Although characterized by better prognosis compared with other subtypes, luminal breast cancer is still considered a threatening disease due to therapy resistance, which occurs via both cell- and non–cell-autonomous mechanisms. Jumonji domain-containing 6, arginine demethylase and lysine hydroxylase (JMJD6) is endowed with a negative prognostic value in luminal breast cancer and, via its epigenetic activity, it is known to regulate many intrinsic cancer cell pathways. So far, the effect of JMJD6 in molding the surrounding microenvironment has not been explored.

Here, we describe a novel function of JMJD6 showing that its genetic inhibition in breast cancer cells suppresses lipid droplet formation and ANXA1 expression, via estrogen receptor alpha and PPARα modulation. Reduction of intracellular ANXA1 results in decreased release in the tumor microenvironment (TME), ultimately preventing M2-type macrophage polarization and tumor aggressiveness.
Implications:
Our findings identify JMJD6 as a determinant of breast cancer aggressiveness and provide the rationale for the development of inhibitory molecules to reduce disease progression also through the remodeling of TME composition.
Data from DNA Damage-Inducible Gene, Reprimo Functions as a Tumor Suppressor and Is Suppressed by Promoter Methylation in Gastric Cancer
Authors: Ooki Akira , Yamashita Keishi , Yamaguchi Kensei , Mondal Anupom , Nishimiya Hiroshi , Watanabe Masahiko
Published: April 2023

Abstract
In several types of human cancer, the gene expression of Reprimo, a highly glycosylated protein, is frequently silenced via methylation of its promoter. The aim of this study was to characterize the epigenetic inactivation of Reprimo and its biologic function and clinical relevance in gastric cancer. The correlation between Reprimo methylation and clinical relevance was assessed in 83 primary human gastric cancer tissues. The effects of Reprimo expression were also examined using in vitro and in vivo assays. Reprimo methylation was cancer specific and frequently observed. In two gastric cancer cell lines without Reprimo methylation, we observed faint or weak Reprimo expression under normal conditions and high expression under DNA-damaging conditions. In four gastric cancer cell lines with Reprimo methylation, however, Reprimo expression remained faint even under DNA-damaging conditions, with expression being restored in combination with agents that induce demethylation. Enforced Reprimo expression robustly inhibited cell proliferation and anchorage-independent colony formation and enhanced DNA damage-induced apoptosis. Inverse effects were observed via siRNA-mediated knockdown of endogenous Reprimo. Reprimo expression inhibited tumorigenesis in vivo. Reprimo methylation was also associated with a poor response in patients with gastric cancer treated with chemotherapy (P¼ 0.028), and a poor prognosis in patients with advanced gastric cancer (P¼ 0.03). In conclusion, Reprimo expression is normally induced in response to DNA damage, acting as a novel tumor suppressor in gastric cancer. However, Reprimo methylation abrogates its expression and effects. The clinical assessment of Reprimo promoter methylation may serve not only as a predictive marker for chemotherapy, but also as a marker for tumor aggressiveness. Mol Cancer Res; 11(11); 1362–74. ©2013 AACR.
Data from Nullifying the CDKN2AB Locus Promotes Mutant K-ras Lung Tumorigenesis
Authors: Schuster Katja , Venkateswaran Niranjan , Rabellino Andrea , Girard Luc , Peña-Llopis Samuel , Scaglioni Pier Paolo
Published: April 2023

Abstract
Lung cancer commonly displays a number of recurrent genetic abnormalities, and about 30% of lung adenocarcinomas carry activating mutations in the Kras gene, often concomitantly with inactivation of tumor suppressor genes p16INK4A and p14ARF of the CDKN2AB locus. However, little is known regarding the function of p15INK4B translated from the same locus. To determine the frequency of CDKN2AB loss in human mutant KRAS lung cancer, The Cancer Genome Atlas (TCGA) database was interrogated. Two-hit inactivation of CDKN2A and CDKN2B occurs frequently in patients with mutant KRAS lung adenocarcinoma. Moreover, p15INK4B loss occurs in the presence of biallelic inactivation of p16INK4A and p14ARF, suggesting that p15INK4B loss confers a selective advantage to mutant KRAS lung cancers that are p16INK4A and p14ARF deficient. To determine the significance of CDKN2AB loss in vivo, genetically engineered lung cancer mouse models that express mutant Kras in the respiratory epithelium were utilized. Importantly, complete loss of CDKN2AB strikingly accelerated mutant Kras–driven lung tumorigenesis, leading to loss of differentiation, increased metastatic disease, and decreased overall survival. Primary mutant Kras lung epithelial cells lacking Cdkn2ab had increased clonogenic potential. Furthermore, comparative analysis of mutant Kras;Cdkn2a null with Kras;Cdkn2ab null mice and experiments with mutant KRAS;CDKN2AB–deficient human lung cancer cells indicated that p15INK4B is a critical tumor suppressor. Thus, the loss of CDKN2AB is of biologic significance in mutant KRAS lung tumorigenesis by fostering cellular proliferation, cancer cell differentiation, and metastatic behavior.

Implications: These findings indicate that mutant Kras;Cdkn2ab null mice provide a platform for accurately modeling aggressive lung adenocarcinoma and testing therapeutic modalities. Mol Cancer Res; 12(6); 912–23. ©2014 AACR.
Data from Resveratrol and P-glycoprotein Inhibitors Enhance the Anti-Skin Cancer Effects of Ursolic Acid
Authors: Junco Jacob J. , Mancha Anna , Malik Gunjan , Wei Sung-Jen , Kim Dae Joon , Liang Huiyun , Slaga Thomas J.
Published: April 2023

Abstract
Ursolic acid, present in apples, rosemary, and other sources, is known to inhibit tumor formation and tumor cell viability in multiple systems, including skin. However, various cancers are resistant to ursolic acid treatment. Herein, skin carcinoma cells (Ca3/7) as compared with skin papilloma cells (MT1/2) displayed more resistance to ursolic acid-induced cytotoxicity. Interestingly, Ca3/7 cells had elevated levels of P-glycoprotein (P-gp), an ATP-dependent efflux pump that mediates resistance to chemotherapy in preclinical and clinical settings, and not only accumulated less but also more rapidly expelled the P-gp substrate rhodamine 123 (Rh123) indicating ursolic acid is transported by P-gp. To determine whether P-gp inhibition can enhance ursolic acid-mediated cytotoxicity, cells were challenged with P-gp inhibitors verapamil or cyclosporin A. Alternatively, cells were pretreated with the natural compound resveratrol, a known chemotherapy sensitizer. Verapamil and resveratrol enhanced the effects of ursolic acid in both cell lines, whereas cyclosporin A only did so in Ca3/7 cells. Similarly, verapamil inhibited Rh123 efflux in both lines, whereas cyclosporin A only inhibited Rh123 efflux in Ca3/7 cells. Resveratrol did not inhibit Rh123 efflux in either line, indicating the synergistic effects of resveratrol and ursolic acid are not manifest by inhibition of P-gp–mediated efflux of ursolic acid. These results indicate that the anti-skin cancer effects of ursolic acid are enhanced with P-gp inhibitors. In addition, resveratrol and ursolic acid interact synergistically, but not through inhibition of P-gp.

Implications: Resveratrol and/or p-glycoprotein inhibitors in combination with ursolic acid are an effective anti-skin cancer regimen. Mol Cancer Res; 11(12); 1521–9. ©2013 AACR.
Data from A Novel Germline Mutation in BAP1 Predisposes to Familial Clear-Cell Renal Cell Carcinoma
Authors: Farley Megan N. , Schmidt Laura S. , Mester Jessica L. , Peña-Llopis Samuel , Pavia-Jimenez Andrea , Christie Alana , Vocke Cathy D. , Ricketts Christopher J. , Peterson James , Middelton Lindsay , Kinch Lisa , Grishin Nick , Merino Maria J. , Metwalli Adam R. , Xing Chao , Xie Xian-Jin , Dahia Patricia L.M. , Eng Charis , Linehan W. Marston , Brugarolas James
Published: April 2023

Abstract
Renal cell carcinoma (RCC) clusters in some families. Familial RCC arises from mutations in several genes, including the von Hippel-Lindau (VHL) tumor suppressor, which is also mutated in sporadic RCC. However, a significant percentage of familial RCC remains unexplained. Recently, we discovered that the BRCA1-associated protein-1 (BAP1) gene is mutated in sporadic RCC. The BAP1 gene encodes a nuclear deubiquitinase and appears to be a classic two-hit tumor suppressor gene. Somatic BAP1 mutations are associated with high-grade, clear-cell RCC (ccRCC) and poor patient outcomes. To determine whether BAP1 predisposes to familial RCC, the BAP1 gene was sequenced in 83 unrelated probands with unexplained familial RCC. Interestingly, a novel variant (c.41T>A; p.L14H) was uncovered that cosegregated with the RCC phenotype. The p.L14H variant targets a highly conserved residue in the catalytic domain, which is frequently targeted by missense mutations. The family with the novel BAP1 variant was characterized by early-onset ccRCC, occasionally of high Fuhrman grade, and lacked other features that typify VHL syndrome. These findings suggest that BAP1 is an early-onset familial RCC predisposing gene.

Implications:BAP1 mutations may drive tumor development in a subset of patients with inherited renal cell cancer. Mol Cancer Res; 11(9); 1061–71. ©2013 AACR.
Data from Menin Directly Represses Gli1 Expression Independent of Canonical Hedgehog Signaling
Authors: Gurung Buddha , Feng Zijie , Hua Xianxin
Published: April 2023

Abstract
Multiple endocrine neoplasia type 1 (MEN-1), is a familial tumor syndrome resulting from mutations in the tumor suppressor gene menin (MEN1). Menin plays an essential role in both repressing and activating gene expression. However, it is not well understood how menin represses expression of multiple genes. Upon MEN1 excision, the transcription factor Gli1 and its target genes, including Ptch1 and c-Myc, were shown to be elevated in the absence of an apparent Hedgehog) pathway-activating ligand or when Smoothened (SMO), a key component of the pathway, is inhibited. Menin binds to the GLI1 promoter and recruits PRMT5, a histone arginine methyltransferase associated with transcriptional repression. Both PRMT5 binding and histone H4 arginine 3 methylation (H4R3m2s) are decreased at the GLI1 promoter in MEN1-excised cells. Moreover, MEN1 ablation resulted in increased binding of transcriptionally active Gli1 at the GLI1 promoter in a manner not influenced by the canonical Hedgehog signaling pathway. Inhibition of Gli1 by the small-molecule inhibitor GANT-61 led to decreased expression of Gli1 and its target genes in MEN1-depeleted cells. Furthermore, GANT-61 potently suppressed proliferation of MEN1-excised cells as compared with control cells. These findings uncover a novel epigenetic link whereby menin directly represses Gli1 expression, independent of the canonical Hedgehog signaling pathway, via PRMT5 and its repressive H4R3m2s mark.

Implications: Inhibition of GLI1 suppresses neuroendocrine tumors harboring mutations in the MEN1 gene. Mol Cancer Res; 11(10); 1215–22. ©2013 AACR.
Data from Comparative microRNA Profiling of Prostate Carcinomas with Increasing Tumor Stage by Deep Sequencing
Authors: Hart Martin , Nolte Elke , Wach Sven , Szczyrba Jaroslaw , Taubert Helge , Rau Tilman T. , Hartmann Arndt , Grässer Friedrich A. , Wullich Bernd
Published: April 2023

Abstract
MicroRNAs (miRNA) posttranscriptionally regulate gene expression and are important in tumorigenesis. Previous deep sequencing identified the miRNA profile of prostate carcinoma versus nonmalignant prostate tissue. Here, we generated miRNA expression profiles of prostate carcinoma by deep sequencing, with increasing tumor stage relative to corresponding nonmalignant and healthy prostate tissue, and detected clearly changed miRNA expression patterns. The miRNA profiles of the healthy and nonmalignant tissues were consistent with our previous findings, indicating a high fidelity of the method employed. In the tumors, quantitative real-time PCR (qRT-PCR) analysis of 40 paired samples of prostate carcinoma versus normal tissue revealed significant upregulation of miR-20a, miR-148a, miR-200b, and miR-375 and downregulation of miR-143 and miR-145. Hereby, miR-375 increased from normal to organ-confined tumors (pT2 pN0), slightly decreased in tumors with extracapsular growth (pT3 pN0), but was then expressed again at higher levels in lymph node metastasizing (pN1) tumors. The sequencing data for miR-375 were confirmed by Northern blotting and qRT-PCR. The regulation for other selected miRNAs could, however, not be confirmed by qRT-PCR in individual tumor stages. MiR-200b, in addition to miR-200c and miR-375 reduced the expression of SEC23A. Interestingly, miR-375, found by sequencing in pT2 upregulated by us and others in tumor versus normal tissue, and miR-15a, found by sequencing in pT2 and pT3 and in the metastasizing tumors, target the phosphatases PHLPP1 and PHLPP2, respectively. PHLPP1 and PHLPP2 dephosphorylate members of the AKT family of signal transducers, thereby inhibiting cell growth. Coexpression of miR-15a and miR-375 resulted in downregulation of PHLPP1/2 and strongly increased prostate carcinoma cell growth.

Implications: These genomic data reveal relevant miRNAs in prostate cancer that may have biomarker and therapeutic potential. Mol Cancer Res; 12(2); 250–63. ©2013 AACR.
Data from HDAC6 and SIRT2 Regulate the Acetylation State and Oncogenic Activity of Mutant K-RAS
Authors: Yang Moon Hee , Laurent Gaelle , Bause Alexandra S. , Spang Robert , German Natalie , Haigis Marcia C. , Haigis Kevin M.
Published: April 2023

Abstract
Activating point mutations in K-RAS are extremely common in cancers of the lung, colon, and pancreas and are highly predictive of poor therapeutic response. One potential strategy for overcoming the deleterious effects of mutant K-RAS is to alter its posttranslational modification. Although therapies targeting farnesylation have been explored, and have ultimately failed, the therapeutic potential of targeting other modifications remains to be seen. Recently, it was shown that acetylation of lysine 104 attenuates K-RAS transforming activity by interfering with GEF-induced nucleotide exchange. Here, the deacetylases HDAC6 and SIRT2 were shown to regulate the acetylation state of K-RAS in cancer cells. By extension, inhibition of either of these enzymes has a dramatic impact on the growth properties of cancer cells expressing activation mutants of K-RAS. These results suggest that therapeutic targeting of HDAC6 and/or SIRT2 may represent a new way to treat cancers expressing mutant forms of K-RAS.

Implications: This study suggests that altering K-RAS acetylation is a feasible approach to limiting tumorigenic potential. Mol Cancer Res; 11(9); 1072–7. ©2013 AACR.
Data from Alpha-CaMKII Plays a Critical Role in Determining the Aggressive Behavior of Human Osteosarcoma
Authors: Daft Paul G. , Yuan Kaiyu , Warram Jason M. , Klein Michael J. , Siegal Gene P. , Zayzafoon Majd
Published: April 2023

Abstract
Osteosarcoma is among the most frequently occurring primary bone tumors, primarily affecting adolescents and young adults. Despite improvements in osteosarcoma treatment, more specific molecular targets are needed as potential therapeutic options. One target of interest is α-Ca2+/calmodulin-dependent protein kinase II (α-CaMKII), a ubiquitous mediator of Ca2+-linked signaling, which has been shown to regulate tumor cell proliferation and differentiation. Here, we investigate the role of α-CaMKII in the growth and tumorigenicity of human osteosarcoma. We show that α-CaMKII is highly expressed in primary osteosarcoma tissue derived from 114 patients, and is expressed in varying levels in different human osteosarcoma (OS) cell lines [MG-63, N-methyl-N′-nitro-N-nitrosoguanidine (MNNG)/HOS, and 143B). To examine whether α-CaMKII regulates osteosarcoma tumorigenic properties, we genetically inhibited α-CaMKII in two osteosarcoma cell lines using two different α-CaMKII shRNAs delivered by lentiviral vectors and overexpressed α-CaMKII by retrovirus. The genetic deletion of α-CaMKII by short hairpin RNA (shRNA) in MG-63 and 143B cells resulted in decreased proliferation (50% and 41%), migration (22% and 25%), and invasion (95% and 90%), respectively. The overexpression of α-CaMKII in HOS cells resulted in increased proliferation (240%), migration (640%), and invasion (10,000%). Furthermore, α-CaMKII deletion in MG-63 cells significantly reduced tumor burden in vivo (65%), whereas α-CaMKII overexpression resulted in tumor formation in a previously nontumor forming osteosarcoma cell line (HOS). Our results suggest that α-CaMKII plays a critical role in determining the aggressive phenotype of osteosarcoma, and its inhibition could be an attractive therapeutic target to combat this devastating adolescent disease. Mol Cancer Res; 11(4); 349–59. ©2013 AACR.
Data from Transcriptional Regulation of CXCR4 in Prostate Cancer: Significance of TMPRSS2-ERG Fusions
Authors: Singareddy Rajareddy , Semaan Louie , Conley-LaComb M. Katie , St. John Jason , Powell Katelyn , Iyer Matthew , Smith Daryn , Heilbrun Lance K. , Shi Dongping , Sakr Wael , Cher Michael L. , Chinni Sreenivasa R.
Published: April 2023

Abstract
CXCR4 is a chemokine receptor that mediates invasion and metastasis. CXCR4 expression is transcriptionally regulated in cancer cells and is associated with aggressive prostate cancer phenotypes. Previously, we and others have shown that the transcription factor ERG regulates CXCR4 expression in prostate cancer cells and that androgens modulate CXCR4 expression via increasing ERG expression. Herein, the molecular mechanisms of ERG-mediated CXCR4 promoter activation, phosphorylation of ERG by intracellular kinases and subsequent CXCR4 expression, as well as the status of ERG and CXCR4 in human prostate cancer specimens were investigated. Using multiple molecular strategies, it was demonstrated that (i) ERG expressed in TMPRSS2-ERG fusion positive VCaP cells selectively binds to specific ERG/Ets bindings sites in the CXCR4 promoter; (ii) distal binding sites mediate promoter activation; (iii) exogenously expressed ERG promotes CXCR4 expression; (iv) ERG is phosphorylated at Serine-81 and -215, by both IKK and Akt kinases, and Akt mediates CXCR4 expression; (v) ERG-induced CXCR4 drives CXCL12-dependent adhesion to fibronectin; and (vi) ERG and CXCR4 were coexpressed in human prostate cancer tissue, consistent with ERG-mediated transcriptional activation of CXCR4. These data demonstrate that ERG activates CXCR4 expression by binding to specific ERG/Ets responsive elements and via intracellular kinases that phosphorylate ERG at discrete serine residues.

Implications: These findings provide a mechanistic link between TMPRSS2-ERG translocations and intracellular kinase-mediated phosphorylation of ERG on enhanced metastasis of tumor cells via CXCR4 expression and function in prostate cancer cells. Mol Cancer Res; 11(11); 1349–61. ©2013 AACR.
Data from PHD4 Stimulates Tumor Angiogenesis in Osteosarcoma Cells via TGF-α
Authors: Klotzsche-von Ameln Anne , Prade Ina , Grosser Marianne , Kettelhake Antje , Rezaei Maryam , Chavakis Triantafyllos , Flamme Ingo , Wielockx Ben , Breier Georg
Published: April 2023

Abstract
Solid tumor growth is intimately associated with angiogenesis, a process that is efficiently triggered by hypoxia. Therefore, oxygen-sensitive signaling pathways are thought to play a critical role in tumor angiogenesis and progression. Here, the function of prolyl hydroxylase-4 (PHD4), a relative of the prolyl hydroxylase domain proteins 1–3 that promote the degradation of hypoxia-inducible factors (HIF), was interrogated. To test the hypothesis that PHD4 might inhibit tumor angiogenesis, it was overexpressed in osteosarcoma cells, and unexpectedly, this manipulation led to increased tumor blood vessel density. However, the newly formed blood vessels were smaller than normal and appeared to be partially nonfunctional, as indicated by poor vessel perfusion. PHD4 overexpression in tumor cells stimulated the expression of TGF-α, which was necessary and sufficient to promote angiogenic sprouting of endothelial cells. On the other hand, PHD4 overexpression reduced HIF-2α protein levels, which in turn inhibited in vivo tumor growth. Combined, elevated PHD4 levels deregulate angiogenesis via increased TGF-α expression in vitro and in vivo. These data support the hypothesis that tumor growth can be uncoupled from vessel density and that the individual PHD family members exert distinct functions in tumors.

Implications: PHD4 influences tumor growth and vascularization through discrete mechanisms and molecular pathways that likely have therapeutic potential. Mol Cancer Res; 11(11); 1337–48. ©2013 AACR.
Data from 53BP1 Is Limiting for NHEJ Repair in ATM-deficient Model Systems That Are Subjected to Oncogenic Stress or Radiation
Authors: Rybanska-Spaeder Ivana , Reynolds Taylor L. , Chou Jeremy , Prakash Mansi , Jefferson Tameca , Huso David L. , Desiderio Stephen , Franco Sonia
Published: April 2023

Abstract
The DNA damage response (DDR) factors ataxia telangiectasia mutated (ATM) and p53 binding protein 1 (53BP1) function as tumor suppressors in humans and mice, but the significance of their mutual interaction to the suppression of oncogenic translocations in vivo has not been investigated. To address this question, the phenotypes of compound mutant mice lacking 53BP1 and ATM (Trp53bp1−/−/Atm−/−), relative to single mutants, were examined. These analyses revealed that loss of 53BP1 markedly decreased the latency of T-lineage lymphomas driven by RAG-dependent oncogenic translocations in Atm−/− mice (average survival, 14 and 23 weeks for Trp53bp1−/−/Atm−/− and Atm−/− mice, respectively). Mechanistically, 53BP1 deficiency aggravated the deleterious effect of ATM deficiency on nonhomologous end-joining (NHEJ)—mediated double-strand break repair. Analysis of V(D)J recombinase-mediated coding joints and signal joints in Trp53bp1−/−/Atm−/− primary thymocytes is, however, consistent with canonical NHEJ-mediated repair. Together, these findings indicate that the greater NHEJ defect in the double mutant mice resulted from decreased efficiency of rejoining rather than switching to an alternative NHEJ-mediated repair mechanism. Complementary analyses of irradiated primary cells indicated that defects in cell-cycle checkpoints subsequently function to amplify the NHEJ defect, resulting in more frequent chromosomal breaks and translocations in double mutant cells throughout the cell cycle. Finally, it was determined that 53BP1 is dispensable for the formation of RAG-mediated hybrid joints in Atm−/− thymocytes but is required to suppress large deletions in a subset of hybrid joints.

Implications: The current study uncovers novel ATM-independent functions for 53BP1 in the suppression of oncogenic translocations and in radioprotection.

Visual Overview: http://mcr.aacrjournals.org/content/11/10/1223/F1.large.jpg.

Mol Cancer Res; 11(10); 1223–34. ©2013 AACR.
Data from The Twist Box Domain Is Required for Twist1-induced Prostate Cancer Metastasis
Authors: Gajula Rajendra P. , Chettiar Sivarajan T. , Williams Russell D. , Thiyagarajan Saravanan , Kato Yoshinori , Aziz Khaled , Wang Ruoqi , Gandhi Nishant , Wild Aaron T. , Vesuna Farhad , Ma Jinfang , Salih Tarek , Cades Jessica , Fertig Elana , Biswal Shyam , Burns Timothy F. , Chung Christine H. , Rudin Charles M. , Herman Joseph M. , Hales Russell K. , Raman Venu , An Steven S. , Tran Phuoc T.
Published: April 2023

Abstract
Twist1, a basic helix-loop-helix transcription factor, plays a key role during development and is a master regulator of the epithelial–mesenchymal transition (EMT) that promotes cancer metastasis. Structure–function relationships of Twist1 to cancer-related phenotypes are underappreciated, so we studied the requirement of the conserved Twist box domain for metastatic phenotypes in prostate cancer. Evidence suggests that Twist1 is overexpressed in clinical specimens and correlated with aggressive/metastatic disease. Therefore, we examined a transactivation mutant, Twist1-F191G, in prostate cancer cells using in vitro assays, which mimic various stages of metastasis. Twist1 overexpression led to elevated cytoskeletal stiffness and cell traction forces at the migratory edge of cells based on biophysical single-cell measurements. Twist1 conferred additional cellular properties associated with cancer cell metastasis including increased migration, invasion, anoikis resistance, and anchorage-independent growth. The Twist box mutant was defective for these Twist1 phenotypes in vitro. Importantly, we observed a high frequency of Twist1-induced metastatic lung tumors and extrathoracic metastases in vivo using the experimental lung metastasis assay. The Twist box was required for prostate cancer cells to colonize metastatic lung lesions and extrathoracic metastases. Comparative genomic profiling revealed transcriptional programs directed by the Twist box that were associated with cancer progression, such as Hoxa9. Mechanistically, Twist1 bound to the Hoxa9 promoter and positively regulated Hoxa9 expression in prostate cancer cells. Finally, Hoxa9 was important for Twist1-induced cellular phenotypes associated with metastasis. These data suggest that the Twist box domain is required for Twist1 transcriptional programs and prostate cancer metastasis.

Implications: Targeting the Twist box domain of Twist1 may effectively limit prostate cancer metastatic potential. Mol Cancer Res; 11(11); 1387–400. ©2013 AACR.
Data from RASEF is a Novel Diagnostic Biomarker and a Therapeutic Target for Lung Cancer
Authors: Oshita Hideto , Nishino Ryohei , Takano Atsushi , Fujitomo Takashi , Aragaki Masato , Kato Tatsuya , Akiyama Hirohiko , Tsuchiya Eiju , Kohno Nobuoki , Nakamura Yusuke , Daigo Yataro
Published: April 2023

Abstract
Genome-wide gene expression profiling revealed that the Ras and EF-hand domain containing (RASEF) transcript was significantly transactivated in the majority of lung cancers. Using lung cancer cells, transient expression of RASEF promoted cell growth, whereas RASEF knockdown not only reduced its expression but resulted in growth suppression of the cancer cells. Immunohistochemical staining using tumor tissue microarrays consisting of 341 archived non–small cell lung cancers (NSCLC) revealed the association of strong RASEF positivity with poor prognosis (P = 0.0034 by multivariate analysis). Mechanistically, RASEF interacted with extracellular signal-regulated kinase (ERK) 1/2 and enhanced ERK1/2 signaling. Importantly, inhibiting the interaction between RASEF and ERK1/2 using a cell-permeable peptide that corresponded to the ERK1/2-interacting site of RASEF, suppressed growth of lung cancer cells. This study demonstrates that elevated RASEF promoted cell growth via enhanced ERK signaling and is associated with poor prognosis of NSCLC.

Implications: RASEF may play an important role in lung carcinogenesis and could serve as a vaiable prognostic biomarker and target for the development of new molecular therapies. Mol Cancer Res; 11(8); 937–51. ©2013 AACR.
Data from CYP1A1 Regulates Breast Cancer Proliferation and Survival
Authors: Rodriguez Mariangellys , Potter David A.
Published: April 2023

Abstract
Cytochrome P450-1A1 (CYP1A1) is an extrahepatic phase I metabolizing enzyme whose expression is suppressed under physiologic conditions but can be induced by substrates via the aryl hydrocarbon receptor (AhR). Recent studies have shown that the majority of breast cancer tumors constitutively express CYP1A1. These findings led us to test the hypothesis that CYP1A1 promotes breast cancer progression by evaluating the effects of CYP1A1 knockdown on the proliferation and survival of the MCF7 and MDA-MB-231 lines. Independently of estrogen receptor status, CYP1A1 knockdown decreased colony formation, decreased cell proliferation, blocked the cell cycle at G0-G1 associated with reduction of cyclin D1, and increased apoptosis associated with reduction of survivin. CYP1A1 knockdown markedly increased phosphorylation of AMP-activated protein kinase (AMPK) and decreased phosphorylation of AKT, extracellular signal-regulated kinases 1 and 2 (ERK1/2), and 70-kDa ribosomal protein S6 kinase (P70S6K). AMPK inhibition by compound C partially abrogated the proapoptotic effects of CYP1A1 knockdown, suggesting that effects of CYP1A1 knockdown are mediated in part through AMPK signaling. Consistent with CYP1A1 knockdown, pharmacologic reduction of CYP1A1 levels by the phytopolyphenol carnosol also correlated with impaired proliferation and induced AMPK phosphorylation. These results indicate that reduction of basal CYP1A1 expression is critical for inhibition of proliferation, which is not affected by α-naphthoflavone-mediated inhibition of CYP1A1 activity nor modulated by AhR silencing. This study supports the notion that CYP1A1 promotes breast cancer proliferation and survival, at least in part, through suppression of AMPK signaling and that reduction of CYP1A1 levels is a potential strategy for breast cancer therapeutics. Mol Cancer Res; 11(7); 780–92. ©2013 AACR.