bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 904: Optimizing CAR T therapy via metabolic engineering for the treatment of glioblastoma
Authors: Ghosh Tanya , Chakraborty Avirup , Jin Linchun , Feier Diana , Silver Aryeh , Rahman Maryam , Flores Catherine , Sarkisian Matthew , Huang Jianping , Mitchell Duane A. , Deleyrolle Loic P.
Published: April 2023

Glioblastoma represent a great challenge and current therapies are negligibly effective, with disease recurrence being inevitable. T cell therapy has emerged as a viable treatment for brain malignancies. While promising, the efficacy of this approach is often limited by a complex immunosuppressive tumor microenvironment. These complexities mean that more sophisticated T cell products are required. The brain tumor microenvironment provides local restraints via metabolic competition suppressing antitumor immunity, specifically inhibiting infiltration and effector functions of host and adoptively transferred tumor-reactive T cells. The objective of this project is to test new treatments to reverse immune dysfunction in brain cancer through the regulation of T cell metabolic signaling. We propose that modulating glucose signaling can potentiate T cell anti-tumor activity. The glucose signaling pathway of T cells was modulated through overexpression of glucose transporters and the function of metabolically modified T cells was investigated using murine and human models. We revealed a competition for glucose between T cells and tumor cells, with tumor cells imposing glucose restriction mediating T cell hyporesponsiveness. Overexpression of glucose transporters such as Glut1 and Glut3 enhanced T cell glucose utilization and provided a survival/growth advantage and greater activation, specifically in glucose-restricted conditions. We established that glucose transporter overexpression improves intratumoral infiltration and expansion of adoptively transferred CAR T cells, resulting in improved survival. Our study integrates fundamental concepts of tumor and immune metabolism in the design of immunotherapy and confirms that immunometabolism represents a viable target for new cancer therapy to treat brain tumors.

Citation Format: Tanya Ghosh, Avirup Chakraborty, Linchun Jin, Diana Feier, Aryeh Silver, Maryam Rahman, Catherine Flores, Matthew Sarkisian, Jianping Huang, Duane A. Mitchell, Loic P. Deleyrolle. Optimizing CAR T therapy via metabolic engineering for the treatment of glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 904.
Supplementary Figure Legend from FBXW7 Mediates Chemotherapeutic Sensitivity and Prognosis in NSCLCs
Authors: Yokobori Takehiko , Yokoyama Yozo , Mogi Akira , Endoh Hideki , Altan Bolag , Kosaka Takayuki , Yamaki Ei , Yajima Toshiki , Tomizawa Kenji , Azuma Yoko , Onozato Ryoichi , Miyazaki Tatsuya , Tanaka Shigebumi , Kuwano Hiroyuki
Published: April 2023

PDF - 52KB, Legends for Supplementary Figures 1 and 2.
Supplementary Figure 6 from Inhibition of mTOR Pathway Sensitizes Acute Myeloid Leukemia Cells to Aurora Inhibitors by Suppression of Glycolytic Metabolism
Authors: Liu Ling-Ling , Long Zi-Jie , Wang Le-Xun , Zheng Fei-Meng , Fang Zhi-Gang , Yan Min , Xu Dong-Fan , Chen Jia-Jie , Wang Shao-Wu , Lin Dong-Jun , Liu Quentin
Published: April 2023

PDF file - 1113K, Aurora kinases inhibitors had no effect with mTOR inhibitors on PBMCs.
Supplementary Figure 3 from Inhibition of mTOR Pathway Sensitizes Acute Myeloid Leukemia Cells to Aurora Inhibitors by Suppression of Glycolytic Metabolism
Authors: Liu Ling-Ling , Long Zi-Jie , Wang Le-Xun , Zheng Fei-Meng , Fang Zhi-Gang , Yan Min , Xu Dong-Fan , Chen Jia-Jie , Wang Shao-Wu , Lin Dong-Jun , Liu Quentin
Published: April 2023

PDF file - 1100K, Combination of Aurora kinases inhibitors and 2DG had minimal effect on PBMCs.
Supplementary Tables 1 - 2, Figures 1 - 7 from Energy Management by Enhanced Glycolysis in G1-phase in Human Colon Cancer Cells In Vitro and In Vivo
Authors: Bao Yan , Mukai Kuniaki , Hishiki Takako , Kubo Akiko , Ohmura Mitsuyo , Sugiura Yuki , Matsuura Tomomi , Nagahata Yoshiko , Hayakawa Noriyo , Yamamoto Takehiro , Fukuda Ryo , Saya Hideyuki , Suematsu Makoto , Minamishima Yoji Andrew
Published: April 2023

PDF - 1735K, Table S1: Percentages of Fucci-HTC116 in S + G2 and G1 phases in mouse liver metastatic foci. Table S2: Numbers of MALDO-IMS measurement points in mouse liver metastatic foci. Figure S1: Frequency distribution of relative intensities of MALDI-IMS signal in mouse number 3. Figure S2: Synchronization Figure S3: Intracellular concentrations of metabolites Figure S4: Analysis of metabolites in HCT116 WT cells cultured under 1g/L glucose. Figure S5: Analysis of metabolites in HCT116 p53-null cells cultured under 3g/L glucose. Figure S6: Lactate efflux. Figure S7: Real-time RT-PCR analysis for monocarboxylate transporters (MCTs).
Supplementary Figure from MiR-335 Inhibits Small Cell Lung Cancer Bone Metastases via IGF-IR and RANKL Pathways
Authors: Gong Meng , Ma Junrong , Guillemette Ryan , Zhou Mingliang , Yang Yan , Yang Yujing , Hock Janet M. , Yu Xijie
Published: April 2023

PDF file, 131K, Down-regulation of miRNAs in SBC-5 cells.
Supplementary Figures 1 - 9 from RAS/MEK–Independent Gene Expression Reveals BMP2-Related Malignant Phenotypes in the Nf1-Deficient MPNST
Authors: Sun Daochun , Haddad Ramsi , Kraniak Janice M. , Horne Steven D. , Tainsky Michael A.
Published: April 2023

PDF file - 839K
Supplementary Methods from Fer Protein-Tyrosine Kinase Promotes Lung Adenocarcinoma Cell Invasion and Tumor Metastasis
Authors: Ahn Joseph , Truesdell Peter , Meens Jalna , Kadish Carli , Yang Xiaolong , Boag Alexander H. , Craig Andrew W.B.
Published: April 2023

PDF file - 87K
Supplementary Figure 3 from Fer Protein-Tyrosine Kinase Promotes Lung Adenocarcinoma Cell Invasion and Tumor Metastasis
Authors: Ahn Joseph , Truesdell Peter , Meens Jalna , Kadish Carli , Yang Xiaolong , Boag Alexander H. , Craig Andrew W.B.
Published: April 2023

PDF file - 196K, Fer promotes wound healing migration of H1299 cells.
Supplementary Methods and Figure Legend from Interleukin-6 and Oncostatin-M Synergize with the PI3K/AKT Pathway to Promote Aggressive Prostate Malignancy in Mouse and Human Tissues
Authors: Smith Daniel A. , Kiba Atsushi , Zong Yang , Witte Owen N.
Published: April 2023

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Supplementary Figure 1 from Interleukin-6 and Oncostatin-M Synergize with the PI3K/AKT Pathway to Promote Aggressive Prostate Malignancy in Mouse and Human Tissues
Authors: Smith Daniel A. , Kiba Atsushi , Zong Yang , Witte Owen N.
Published: April 2023

PDF file - 2722K, Expression of IL6 or OSM with loss of PTEN does not dramatically increase graft size or weight.
Supplementary Figure 6 from NF-YA Underlies EZH2 Upregulation and Is Essential for Proliferation of Human Epithelial Ovarian Cancer Cells
Authors: Garipov Azat , Li Hua , Bitler Benjamin G. , Thapa Roshan J. , Balachandran Siddharth , Zhang Rugang
Published: April 2023

PDF file - 106K, NF-YA knockdown suppresses EZH2 expression and inhibits the proliferation of human EOC cells.
Supplementary Figure 4 from NF-YA Underlies EZH2 Upregulation and Is Essential for Proliferation of Human Epithelial Ovarian Cancer Cells
Authors: Garipov Azat , Li Hua , Bitler Benjamin G. , Thapa Roshan J. , Balachandran Siddharth , Zhang Rugang
Published: April 2023

PDF file - 63K, NF-YA ChIP analysis on positive and negative controls.
Supplementary Figure 2 from NF-YA Underlies EZH2 Upregulation and Is Essential for Proliferation of Human Epithelial Ovarian Cancer Cells
Authors: Garipov Azat , Li Hua , Bitler Benjamin G. , Thapa Roshan J. , Balachandran Siddharth , Zhang Rugang
Published: April 2023

PDF file - 52K, Expression of NF-YA, EZH2 and H3K27Me3 in a panel of EOC cell lines.
Supplementary Methods, Figure Legend from Suppression of Ser/Thr Phosphatase 4 (PP4C/PPP4C) Mimics a Novel Post-Mitotic Action of Fostriecin, Producing Mitotic Slippage Followed by Tetraploid Cell Death
Authors: Theobald Benjamin , Bonness Kathy , Musiyenko Alla , Andrews Joel F. , Urban Gudrun , Huang Xizhong , Dean Nicholas M. , Honkanen Richard E.
Published: April 2023

PDF file - 128K
Supplementary Figure 4 from Systems Analysis of the NCI-60 Cancer Cell Lines by Alignment of Protein Pathway Activation Modules with “-OMIC” Data Fields and Therapeutic Response Signatures
Authors: Federici Giulia , Gao Xi , Slawek Janusz , Arodz Tomasz , Shitaye Amanuel , Wulfkuhle Julia D. , De Maria Ruggero , Liotta Lance A. , Petricoin Emanuel F.
Published: April 2023

PDF file - 1038K, Systems networks of AKT (A), apoptosis (B), IGF-1R (C) and mTOR (D) pathway activation. Node color: Violet - node representing the Pathway Score; Blue - phosphoproteins (linked to pathway score or to other proteins/genes at the protein level); Yellow - genes (linked to Pathway Score or to other proteins/genes at the mRNA level); Orange - microRNA; Dark green - drug; Light green - metabolite; Gray - other. Node shape: Diamond - Pathway Score node, or phosphoprotein that is used in calculating the Pathway Score; Circle - other nodes. Edge color & label: Brown - relationship inferred based on phosphoprotein level (either with level other phosphoprotein, or with Pathway Score); Gray - relationship inferred based on gene mRNA expression (either with mRNA of other gene, or with Pathway Score); Dark green - phosphoprotein level or gene expression (mRNA) is significantly correlated with drug's response measured as -log(GI50); Light green - phosphoprotein level or gene expression (mRNA) is significantly correlated with metabolite concentration; Red - phosphoprotein level or gene expression (mRNA) is significantly correlated with mutation of other gene. Arrow points from mutation gene to the mRNA gene; Pink - gene expression (mRNA) is significantly correlated with methylation of other gene. Arrow points from methylation gene to the mRNA gene; Dark blue - gene expression (mRNA) is significantly correlated with copy number of other gene. Arrow points from copy number gene to the mRNA gene; Orange - gene expression (mRNA) is significantly correlated with expression of microRNA. Edge line style: Solid - positive correlation; Dashed - negative correlation.
Supplementary Figure 2 from Systems Analysis of the NCI-60 Cancer Cell Lines by Alignment of Protein Pathway Activation Modules with “-OMIC” Data Fields and Therapeutic Response Signatures
Authors: Federici Giulia , Gao Xi , Slawek Janusz , Arodz Tomasz , Shitaye Amanuel , Wulfkuhle Julia D. , De Maria Ruggero , Liotta Lance A. , Petricoin Emanuel F.
Published: April 2023

PDF file - 150K, Identification and characterization of activated pathway modules by signal transduction representation: IGF-1R (A), apoptosis (C), mTOR (E), AKT (G) and EGFR (I) and unsupervised hierarchical clustering: IGF-1R (B), apoptosis (D), mTOR (F), AKT (H) and EGFR (J). For the pathway representation, the inhibitory phosphorylations considered in the analysis are shown in red and the activating phosphorylations in green. For the unsupervised hierarchical clustering, the complete panel of NCI-60 (vertical axis) is shown. Specific endpoint relative intensity values have been used to create the heatmaps. After overall score calculation, we highlighted the cell lines with the top 10 pathway scores (red), and the cell lines with the lowest 10 pathway activation scores (green).
Supplementary Methods, Figure Legends 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

PDF file - 155K
Supplementary Figure 2 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

PDF file - 4413K, Progression in CDKN2AB lung tumors.
Supplementary Fig. 1 from Transcription Factor Interactions Mediate EGF-Dependent COX-2 Expression
Authors: Xu Kaiming , Shu Hui-Kuo G.
Published: April 2023

Supplementary Fig. 1 - PDF file 91K, EGFRvIII expression correlates with elevated COX-2 levels
Supplementary Figure 2 from Tpl2 Kinase Impacts Tumor Growth and Metastasis of Clear Cell Renal Cell Carcinoma
Authors: Lee Hye Won , Joo Kyeung Min , Lim Joung Eun , Cho Hyun Jung , Cho Hee Jin , Park Min Chul , Seol Ho Jun , Seo Seong Il , Lee Jung-Il , Kim Sunghoon , Jeong Byong Chang , Nam Do-Hyun
Published: April 2023

PDF file - 34K, Tpl2 silencing delayed cell cycle progression in human ccRCC Caki-1 cells. *P<0.05
Supplementary Table 1 from Loss of a Negative Feedback Loop Involving Pea3 and Cyclin D2 Is Required for Pea3-Induced Migration in Transformed Mammary Epithelial Cells
Authors: Ladam Franck , Damour Isabelle , Dumont Patrick , Kherrouche Zoulika , de Launoit Yvan , Tulasne David , Chotteau-Lelievre Anne
Published: April 2023

PDF file - 22K, siRNA sequences used for the cyclin d2 AND pea3 knock-down experiments.
Supplementary Figure Legend from Loss of a Negative Feedback Loop Involving Pea3 and Cyclin D2 Is Required for Pea3-Induced Migration in Transformed Mammary Epithelial Cells
Authors: Ladam Franck , Damour Isabelle , Dumont Patrick , Kherrouche Zoulika , de Launoit Yvan , Tulasne David , Chotteau-Lelievre Anne
Published: April 2023

PDF file - 86K
Supplementary Figure 2 from Loss of a Negative Feedback Loop Involving Pea3 and Cyclin D2 Is Required for Pea3-Induced Migration in Transformed Mammary Epithelial Cells
Authors: Ladam Franck , Damour Isabelle , Dumont Patrick , Kherrouche Zoulika , de Launoit Yvan , Tulasne David , Chotteau-Lelievre Anne
Published: April 2023

PDF file - 283K, Wound healing assay for TAC-V and TAC-Pea3-V cells transfected with ctrl or pea3 siRNAs and treated or not with TGF-β1. Western blot analysis of p27kip1 protein expression.
Supplementary Figure 1 from Oncogenic MUC1-C Promotes Tamoxifen Resistance in Human Breast Cancer
Authors: Kharbanda Akriti , Rajabi Hasan , Jin Caining , Raina Deepak , Kufe Donald
Published: April 2023

PDF file - 504K, BT-474 cells were infected with a lentivirus expressing MUC1 shRNA(#2) with a targeting sequence distinct from that used for MUC1 silencing in the experiments shown in Fig. 1. A. Lysates from BT-474, BT-474/CshRNA and BT-474/MUC1shRNA(#2) cells were immunoblotted with the indicated antibodies (left). Lysates from BT-474/CshRNA and BT-474/MUC1shRNA(#2) were immunoblotted with the indicated antibodies (right). B. BT-474/MUC1shRNA(#2) cells were left untreated (Control) and treated with 5 μM tamoxifen on days 0 and day 2. The results (mean+SD of three replicates) are expressed as viable cell number as determined by trypan blue staining on day 4.
Supplementary Figure Legend 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

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Supplementary Table 4 from Tumor Suppressor Functions of miR-133a in Colorectal Cancer
Authors: Dong Yujuan , Zhao Junhong , Wu Chung-Wah , Zhang Lijing , Liu Xiaodong , Kang Wei , Leung Wing-Wah , Zhang Ning , Chan Francis K.L. , Sung Joseph J.Y. , Ng Simon S.M. , Yu Jun
Published: April 2023

PDF file - 81K, Clinicopathological correlation of miR-133a expression in CRC.
Supplementary Table 3 from Tumor Suppressor Functions of miR-133a in Colorectal Cancer
Authors: Dong Yujuan , Zhao Junhong , Wu Chung-Wah , Zhang Lijing , Liu Xiaodong , Kang Wei , Leung Wing-Wah , Zhang Ning , Chan Francis K.L. , Sung Joseph J.Y. , Ng Simon S.M. , Yu Jun
Published: April 2023

PDF file - 49K, DNA sequences of primers used in the study.
Supplementary Figure 2 from Tumor Suppressor Functions of miR-133a in Colorectal Cancer
Authors: Dong Yujuan , Zhao Junhong , Wu Chung-Wah , Zhang Lijing , Liu Xiaodong , Kang Wei , Leung Wing-Wah , Zhang Ning , Chan Francis K.L. , Sung Joseph J.Y. , Ng Simon S.M. , Yu Jun
Published: April 2023

PDF file - 54K, miR-133a expression levels in xenograft models.
Supplementary Figure 8 from Autophagy-Dependent Metabolic Reprogramming Sensitizes TSC2-Deficient Cells to the Antimetabolite 6-Aminonicotinamide
Authors: Parkhitko Andrey A. , Priolo Carmen , Coloff Jonathan L. , Yun Jihye , Wu Julia J. , Mizumura Kenji , Xu Wenping , Malinowska Izabela A. , Yu Jane , Kwiatkowski David J. , Locasale Jason W. , Asara John M. , Choi Augustine M.K. , Finkel Toren , Henske Elizabeth P.
Published: April 2023

PDF file - 42K, Parthenolide rescues proliferation in Tsc2-/- MEFs.
Supplementary Figure 2 from Autophagy-Dependent Metabolic Reprogramming Sensitizes TSC2-Deficient Cells to the Antimetabolite 6-Aminonicotinamide
Authors: Parkhitko Andrey A. , Priolo Carmen , Coloff Jonathan L. , Yun Jihye , Wu Julia J. , Mizumura Kenji , Xu Wenping , Malinowska Izabela A. , Yu Jane , Kwiatkowski David J. , Locasale Jason W. , Asara John M. , Choi Augustine M.K. , Finkel Toren , Henske Elizabeth P.
Published: April 2023

PDF file - 55K, Effect of chloroquine on the metabolome of Tsc2+/+ MEFs.
Supplementary Figure 1 from Autophagy-Dependent Metabolic Reprogramming Sensitizes TSC2-Deficient Cells to the Antimetabolite 6-Aminonicotinamide
Authors: Parkhitko Andrey A. , Priolo Carmen , Coloff Jonathan L. , Yun Jihye , Wu Julia J. , Mizumura Kenji , Xu Wenping , Malinowska Izabela A. , Yu Jane , Kwiatkowski David J. , Locasale Jason W. , Asara John M. , Choi Augustine M.K. , Finkel Toren , Henske Elizabeth P.
Published: April 2023

PDF file - 61K, Effect of chloroquine in Tsc2-deficient models.
Supplementary Methods 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

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Supplementary Figure 1 from Dysregulating IRES-Dependent Translation Contributes to Overexpression of Oncogenic Aurora A Kinase
Authors: Dobson Tara , Chen Juan , Krushel Les A.
Published: April 2023

PDF file - 67K, Sequence of the Aurora A mRNA 5' leader.
Supplementary Figure 2 from Balanced Tiam1-Rac1 and RhoA Drives Proliferation and Invasion of Pancreatic Cancer Cells
Authors: Guo Xingjun , Wang Min , Jiang Jianxin , Xie Chengchen , Peng Feng , Li Xu , Tian Rui , Qin Renyi
Published: April 2023

PDF file - 9152K, A. Wound healing assay for BxPC-3 cells after Tiam1 knock-down. B. Determination of BxPC-3 cell migration and invasiveness after Tiam1 knock-down using transwell assays. C. Determination of Panc-1 cell migration and invasiveness after Tiam1 knock-down using transwell assay. D. Transwell assays of invasiveness after treatment with NSC23766 and/or Y27632.
Supplementary Figure 4 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

PDF file - 101K, S4. Lentivirus-mediated silencing of TGF-alpha in LM8-PHD4 cells.
Supplementary Figure 3 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

PDF file - 108K, S3. VEGF levels are not changed in PHD4-overexpressing LM8 tumors.
Supplementary Figure Legend from Tumor-Secreted LOXL2 Activates Fibroblasts through FAK Signaling
Authors: Barker Holly E. , Bird Demelza , Lang Georgina , Erler Janine T.
Published: April 2023

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Supplementary Figures 1 - 12, Tables 1 - 6 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

PDF file - 7618K, S1. Analysis of the genetic interaction between 53BP1 and ATM in organismal growth and development. S2. Analysis of ploidy in Trp53bp1-/-/Atm-/- lymphomas. S3. Analysis of Trp53bp1-/-/Atm-/- thymic lymphomas by TCRα/δ locus FISH. S4. SKY analysis of two Trp53bp1-/-/Atm-/- lymphomas. S5. Cell cycle analysis of resting lymphocytes after IR. S6. Aberrant Vd2-Dd1/Dd2-Jd1 coding junctions are not detected in Trp53bp1-/-/Atm-/- mice. S7. Aberrant Vd5-Dd2 Recombination Signal Junctions are not detected in Trp53bp1-/-/Atm-/- mice. S8. Histograms showing the frequency distribution of deletions from each coding end (A-D) and signal end (E-F) analyzed. S9. Cell cycle analysis of activated (cycling) lymphocytes after IR. S10. Analysis of genomic stability in splenic B or T cells treated with olaparib. S11. Analysis of the G2/M checkpoint. α-CD40/IL-4-activated B cells were harvested one hour after exposure to 2 Gy of IR, stained with a FITC-labeled antibody to phospho(P)-histone H3 (Ser10) and propidium iodide (PI) and analyzed by flow cytometry. S12. A second primer set detects deletions at hybrid V(D)J recombination junctions in Trp53bp1-/-/Atm-/- thymic DNA from 7 day-old mice. Table S1. Mendelian ratios in liveborn mice from 53BP1+/-/ATM+/- intercrosses (n=19 litters) Table S2. Analysis of genomic stability in HU-treated B lymphocytes deficient for 53BP1 and/or ATM. Table S3. Analysis of genomic stability in α-CD40+IL-4activated B lymphocytes deficient for 53BP1 and/or ATM. Table S4. Analysis of genomic stability in α-CD40/IL-4 activated B cells deficient for 53BP1 and/or ATM. Metaphase spreads were obtained 24 hr after IR and stained with a telomere probe. Table S5. Analysis of genomic stability in LPS-activated B cells deficient for 53BP1 and/or ATM. Metaphases were obtained 24 hr after exposure to IR and stained with a telomere probe. Table S6. Analysis of genomic stability in T lymphocytes deficient for 53BP1 and/or ATM.
Supplementary Figure 1 from The Impact of miRNA-Based Molecular Diagnostics and Treatment of NRF2-Stabilized Tumors
Authors: Yamamoto Shinsuke , Inoue Jun , Kawano Tatsuyuki , Kozaki Ken-ichi , Omura Ken , Inazawa Johji
Published: April 2023

PDF file - 85K, Validation of the ARE-reporter system.
Supplementary Methods, Tables 1 - 4, Figures 1 - 7 from Human Lung Epithelial Cells Progressed to Malignancy through Specific Oncogenic Manipulations
Authors: Sato Mitsuo , Larsen Jill E. , Lee Woochang , Sun Han , Shames David S. , Dalvi Maithili P. , Ramirez Ruben D. , Tang Hao , DiMaio John Michael , Gao Boning , Xie Yang , Wistuba Ignacio I. , Gazdar Adi F. , Shay Jerry W. , Minna John D.
Published: April 2023

PDF file - 2798K, Supplementary Table S1. Primary antibodies used for immunoblotting. Supplementary Table S2. In vitro and in vivo characterization of soft agar clones derived from manipulated HBECs. Supplementary Table S3: Drug response phenotypes of isogenic clones of oncogenically manipulated HBECs. Supplementary Table S4: Significantly differentially expressed genes between tumorigenic (Clones 1, 5 and 11) and non-tumorigenic (Clones 6, 7, 8 and 9) soft agar clones of HBEC3p53,KRAS. Supplementary Figure S1: HBEC anchorage independent and dependent growth, induced senescence, phase contrast and cell cycle analyses of HBECs with and without mutant KRAS and other oncogenic manipulations. Supplementary Figure S2: Histology and immunohistochemical stains of xenograft tumors after oncogenic manipulation of HBECs, and soft agar colony formation after introduction of p53, KRAS, and c-myc oncogenic changes into HBECs. Supplementary Figure S3: Oncogenically manipulated HBECs tested for cell proliferation, stem cell and differentiation marker mRNA expression, and phase contrast morphology after growth in defined and serum containing medium, and TUNEL staining of xenograft HBEC tumors. Supplementary Figure S4: Southern blot analyses of clonal composition of oncogenically manipulated HBECs and tests of soft agar growth of individual clones. Supplementary Figure S5: Representative dose-response curves of HBEC3 and HBEC3p53,KRAS treated with standard lung cancer chemotherapy doublets. Supplementary Figure S6: Cell cycle analysis of soft agar clones of HBEC3p53,KRAS. Supplementary Figure S7: Microarray analysis of 203-probe mRNA gene signature differentially expressed between tumorigenic and non-tumorigenic soft agar clones of HBEC3p53,KRAS against clinical variables. Supplementary Figure S8: Full, uncut blots of immunoblots presented in main article.
Supplementary Figure 4 from Activation of the NF-κB Pathway by the STAT3 Inhibitor JSI-124 in Human Glioblastoma Cells
Authors: McFarland Braden C. , Gray G. Kenneth , Nozell Susan E. , Hong Suk W. , Benveniste Etty N.
Published: April 2023

PDF file - 82K, Effective inhibition of NF-κB using BAY-11 and shRNA knockdown.
Supplementary Figure 1 from CDCP1 Regulates the Function of MT1-MMP and Invadopodia-Mediated Invasion of Cancer Cells
Authors: Miyazawa Yuri , Uekita Takamasa , Ito Yuumi , Seiki Motoharu , Yamaguchi Hideki , Sakai Ryuichi
Published: April 2023

PDF File-118K, Expression of CDCP1 in invasive breast cancer cell lines.
Supplementary Tables 1 - 3 from HER-2/neu Mediates Oncogenic Transformation via Altered CREB Expression and Function
Authors: Steven André , Leisz Sandra , Massa Chiara , Iezzi Manuela , Lattanzio Rossano , Lamolinara Alessia , Bukur Jürgen , Müller Anja , Hiebl Bernhard , Holzhausen Hans-Jürgen , Seliger Barbara
Published: April 2023

PDF file - 101K, Supplementary Table 1. Summary of primers used Supplementary Table 2. Patients and tumor characteristics (n = 112) Supplementary Table 3. pCREB(ser133) status according to clinico-pathological parameters in T1-T2, N0 breast cancer patients (n = 112).
Supplementary Table from Inhibition of Cell Adhesion by a Cadherin-11 Antibody Thwarts Bone Metastasis
Authors: Lee Yu-Chen , Bilen Mehmet Asim , Yu Guoyu , Lin Song-Chang , Huang Chih-Fen , Ortiz Angelica , Cho Hyojin , Song Jian H. , Satcher Robert L. , Kuang Jian , Gallick Gary E. , Yu-Lee Li-Yuan , Huang Wilber , Lin Sue-Hwa
Published: April 2023

PDF file, 18K, Oligonucleotide sequences used in this study.
Supplementary Figure 6 from Hematopoietic Expression of Oncogenic BRAF Promotes Aberrant Growth of Monocyte-Lineage Cells Resistant to PLX4720
Authors: Kamata Tamihiro , Dankort David , Kang Jing , Giblett Susan , Pritchard Catrin A. , McMahon Martin , Leavitt Andrew D.
Published: April 2023

PDF file - 110K, S6. Imunohistochemistry of tissue sections from BrafV600E bone marrow recipients.
Supplementary Figure Legend from EGFR Inhibition Induces Proinflammatory Cytokines via NOX4 in HNSCC
Authors: Fletcher Elise V.M. , Love-Homan Laurie , Sobhakumari Arya , Feddersen Charlotte R. , Koch Adam T. , Goel Apollina , Simons Andrean L.
Published: April 2023

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Supplementary Table 3 from miRNA-145 Targets v-ets Erythroblastosis Virus E26 Oncogene Homolog 1 to Suppress the Invasion, Metastasis, and Angiogenesis of Gastric Cancer Cells
Authors: Zheng Liduan , Pu Jiarui , Qi Teng , Qi Meng , Li Dan , Xiang Xuan , Huang Kai , Tong Qiangsong
Published: April 2023

PDF file - 22K, Oligonucleotide sets for construct, inhibitor and siRNA
Supplementary Methods and Figure Legend from miRNA-145 Targets v-ets Erythroblastosis Virus E26 Oncogene Homolog 1 to Suppress the Invasion, Metastasis, and Angiogenesis of Gastric Cancer Cells
Authors: Zheng Liduan , Pu Jiarui , Qi Teng , Qi Meng , Li Dan , Xiang Xuan , Huang Kai , Tong Qiangsong
Published: April 2023

PDF file - 96K
Supplementary Figure 2 from PKCι Maintains a Tumor-initiating Cell Phenotype That Is Required for Ovarian Tumorigenesis
Authors: Wang Yin , Hill Kristen S. , Fields Alan P.
Published: April 2023

PDF file - 105K, S2. Knockdown of Ect2 or MMP10 in ES2 oncospheres inhibits TIC clonal expansion.
Supplementary Figure 1 from FoxM1 is Overexpressed in Helicobacter pylori–Induced Gastric Carcinogenesis and Is Negatively Regulated by miR-370
Authors: Feng Yimin , Wang Lixiang , Zeng Jiping , Shen Li , Liang Xiuming , Yu Han , Liu Shili , Liu Zhifang , Sun Yundong , Li Wenjuan , Chen Chunyan , Jia Jihui
Published: April 2023

Supplementary Figure 1 - PDF file 2120K, The representation of the pathway invovled in this manuscript
Supplementary Figure Legend from Inhibition of Hedgehog and Androgen Receptor Signaling Pathways Produced Synergistic Suppression of Castration-Resistant Prostate Cancer Progression
Authors: Gowda Pramod S. , Deng Jianhong D. , Mishra Sweta , Bandyopadhyay Abhik , Liang Sitai , Lin Shu , Mahalingam Devalingam , Sun Lu-Zhe
Published: April 2023

PDF file - 95K
Supplementary Figure 6 from The HER2- and Heregulin β1 (HRG)–Inducible TNFR Superfamily Member Fn14 Promotes HRG-Driven Breast Cancer Cell Migration, Invasion, and MMP9 Expression
Authors: Asrani Kaushal , Keri Ruth A. , Galisteo Rebeca , Brown Sharron A.N. , Morgan Sarah J. , Ghosh Arundhati , Tran Nhan L. , Winkles Jeffrey A.
Published: April 2023

PDF file - 30K, Figure S6. HRG1-β1 stimulation of MCF7 cells induces Fn14 mRNA expression.
Supplementary Figure 1 from The HER2- and Heregulin β1 (HRG)–Inducible TNFR Superfamily Member Fn14 Promotes HRG-Driven Breast Cancer Cell Migration, Invasion, and MMP9 Expression
Authors: Asrani Kaushal , Keri Ruth A. , Galisteo Rebeca , Brown Sharron A.N. , Morgan Sarah J. , Ghosh Arundhati , Tran Nhan L. , Winkles Jeffrey A.
Published: April 2023

PDF file - 308K, Figure S1. Analysis of Fn14 and EGFR family member expression in breast cancer cell lines.
Supplementary Table 1 from HD Chromoendoscopy Coupled with DNA Mass Spectrometry Profiling Identifies Somatic Mutations in Microdissected Human Proximal Aberrant Crypt Foci
Authors: Drew David A. , Devers Thomas J. , O'Brien Michael J. , Horelik Nicole A. , Levine Joel , Rosenberg Daniel W.
Published: April 2023

PDF file - 57KB, 105 mutations to 22 known tumor suppressors and proto-oncogenes were screened for each sample.
Table S1 from Mastermind-Like 3 Controls Proliferation and Differentiation in Neuroblastoma
Authors: Heynen Guus J.J.E. , Nevedomskaya Ekaterina , Palit Sander , Jagalur Basheer Noorjahan , Lieftink Cor , Schlicker Andreas , Zwart Wilbert , Bernards Rene , Bajpe Prashanth Kumar
Published: April 2023

Supplementary Table 1: List of genes that have a fold change in expression of at least log2FC > 1.5 and adjust
Supplementary Figure 1 from HD Chromoendoscopy Coupled with DNA Mass Spectrometry Profiling Identifies Somatic Mutations in Microdissected Human Proximal Aberrant Crypt Foci
Authors: Drew David A. , Devers Thomas J. , O'Brien Michael J. , Horelik Nicole A. , Levine Joel , Rosenberg Daniel W.
Published: April 2023

PDF file - 53KB, Suitable amplification of genomic loci from three microdissected ACF samples was accomplished using the Sequenom standard PCR protocol. Microdissected ACF DNA achieved the equivalent amplification levels obtained using 1 ng of input DNA. The loci amplified is a 462 nt region of RRBP1 using the following primers - F (exon) - 5'-AGATGGCGAAAACTCACCACC-3' and R (intron) - 5'- GCCTTTTTGCCCTGAGTAGT-3'. The primers span an intron-exon border to restrict amplification to the genomic DNA template.
Supplementary Table S1 from Glutamine Transporters Are Targets of Multiple Oncogenic Signaling Pathways in Prostate Cancer
Authors: White Mark A. , Lin Chenchu , Rajapakshe Kimal , Dong Jianrong , Shi Yan , Tsouko Efrosini , Mukhopadhyay Ratna , Jasso Diana , Dawood Wajahat , Coarfa Cristian , Frigo Daniel E.
Published: April 2023

List of siRNA, shRNA and primer sequences used in study.
2 Supplementary Tables and 8 Supplementary Figures with Legends from Deubiquitinase OTUD6B Isoforms Are Important Regulators of Growth and Proliferation
Authors: Sobol Anna , Askonas Caroline , Alani Sara , Weber Megan J. , Ananthanarayanan Vijayalakshmi , Osipo Clodia , Bocchetta Maurizio
Published: April 2023

Table ST1. List of oligonucleotides and siRNAs used in this study. Table ST2. List of antibodies used in this study. Figure S1. Sequence alignment of OTUD6A and OTUD6B (isoform 1) performed using Clustal omega software. Figure S2. RNA silencing to OTUD2 and OTUD5 in NSCLC cells does not affect the protein synthesis rate. Figure S3. Comassie blue staining of a representative SDS PAGE gel loaded with 40 μg of proteins obtained from total cell lysate (1), nuclear fraction (2), postmitochondrial fraction (3), postribosomal fraction (4) and ribosomes (5). Note the typical enrichment in low molecular weigh bands (ribosomal proteins) of the ribosomal fraction. Figure S4. OTUD6B coimmunoprecipitates with eIF4G and other eIF4F components. Figure S5. Schematic (Top) and sequence alignment (Bottom) of OTUD6B isoforms. Large spiral: coiled coil domain. Figure S6. Evidence of allelic mutation (arrow) of the OTUD6B catalytic core in HCC827. Figure S7. OTUD6B-1 and OTUD6B-2 cause cell death when overexpressed in NSCLC cells. Figure S8. Hematoxylin/Eosin staining of 8μm-thick, frozen slides of representative normal lung.
Suppl. Figure Legends from Dual Src Kinase/Pretubulin Inhibitor KX-01, Sensitizes ERα-negative Breast Cancers to Tamoxifen through ERα Reexpression
Authors: Anbalagan Muralidharan , Sheng Mei , Fleischer Brian , Zhang Yifang , Gao Yuanjun , Hoang Van , Matossian Margarite , Burks Hope E. , Burow Matthew E. , Collins-Burow Bridgette M. , Hangauer David , Rowan Brian G.
Published: April 2023

Legends for all supplementary figures
Figure S1 -S11 from Dual Src Kinase/Pretubulin Inhibitor KX-01, Sensitizes ERα-negative Breast Cancers to Tamoxifen through ERα Reexpression
Authors: Anbalagan Muralidharan , Sheng Mei , Fleischer Brian , Zhang Yifang , Gao Yuanjun , Hoang Van , Matossian Margarite , Burks Hope E. , Burow Matthew E. , Collins-Burow Bridgette M. , Hangauer David , Rowan Brian G.
Published: April 2023

Supplementary Figure S1. KX-01 at low dose inhibited phosphorylation of Src in MDA-MB-231 xenografts. Supplementary Figure S2. Effect of KX-01 on ERÃŽÂ± mRNA expression in Patient Derived Xenograft (PDX) tumors. Supplementary Figure S3. Effect of KX-01 and tamoxifen on ERÃŽÂ± regulated proteins c-myc, cyclin D1 and pS2 in MDA-MB-231 tumor lysates by Western blot analysis. Supplementary Figure S4. TUNEL immunofluorescence microscopy on MDA-MB-231 tumor sections from mice treated with VC, TAM, KX-01, KX-01 + TAM. Supplementary Figure S5. Effect of KX-01and tamoxifen co-treatment on growth of MDA-MB-157 breast tumor xenografts. Supplementary Figure S6. TUNEL immunofluorescence microscopy on MDA-MB-157 tumor sections from mice treated with VC, TAM, KX-01, KX-01 + TAM. Supplementary Figure S7. Effect of KX-01 withdrawal on ERÃŽÂ± expression and tamoxifen sensitivity in MDA-MB-231 tumors. Supplementary Figure S8. Effect of KX-01 on ERÃŽÂ± and E-cadherin protein expression in MDA-MB-231 xenografts measured by Western blot analysis of tumor lysates. Supplementary Figure S9. Effect of KX-01 on histone deacetylases (HDACs) activity in MDA-MB-231 tumors. Supplementary Figure S10. Low dose KX-01 had no effect on microtubule formation in MDA-MB-231 tumors. Supplementary Figure S11. ERÃŽÂ± mRNA expression induced by KX-01 in MDA-MB-231, MDA-MB-468 and MDA-MB-157 triple negative breast cancer cells.
Supplementary Methods, Figure Legends, Figures 1 - 4 from Functional Heterogeneity of PAX5 Chimeras Reveals Insight for Leukemia Development
Authors: Fortschegger Klaus , Anderl Stefanie , Denk Dagmar , Strehl Sabine
Published: April 2023

PDF file - 178K, Oligonucleotide and protein sequences; antibody list; Supplementary figures S1-S4 with legends Supplementary Figure S1. Subcellular localization of PAX5 fusion proteins in HeLa cells. Supplementary Figure S2. EMSA using CD79A probe. Supplementary Figure S3. Luciferase assays in NALM-6. Supplementary Figure S4. Protein levels of transduced 558LμM cells.
Supplementary Figure 3 from Delineation of a FOXA1/ERα/AGR2 Regulatory Loop That Is Dysregulated in Endocrine Therapy–Resistant Breast Cancer
Authors: Wright Tricia M. , Wardell Suzanne E. , Jasper Jeff S. , Stice James P. , Safi Rachid , Nelson Erik R. , McDonnell Donald P.
Published: April 2023

Supplementary Figure 3: Rescue of AGR2 specific proliferation with conditional AGR2 media.
Supplementary Figure 3 from Hypoxia Regulates Alternative Splicing of HIF and non-HIF Target Genes
Authors: Sena Johnny A. , Wang Liyi , Heasley Lynn E. , Hu Cheng-Jun
Published: April 2023

S3. HIF activity is sufficient to promote AS of HIF target genes.
Figure S4 from Dissecting LncRNA Roles in Renal Cell Carcinoma Metastasis and Characterizing Genomic Heterogeneity by Single-Cell RNA-seq
Authors: Li Xue , Meng Xianwen , Wei Cong , Zhou Yincong , Chen Hongjun , Huang He , Chen Ming
Published: April 2023

Figure S4. 173 differentially expressed lncRNAs profiling of all single cells.
Data Supplement from Unbiased Proteomic and Transcript Analyses Reveal that Stathmin-1 Silencing Inhibits Colorectal Cancer Metastasis and Sensitizes to 5-Fluorouracil Treatment
Authors: Wu Wei , Tan Xing Fei , Tan Hwee Tong , Lim Teck Kwang , Chung Maxey Ching Ming
Published: April 2023

Figure S1: Caspase 6 silencing in STMN1 KD cells abrogates 5FU sensitisation. Figure S2: Caspase 6 is the apical caspase in STMN1 silencing-induced 5FU sensitization.
Supplemental Table 8 from Expression of ANRIL–Polycomb Complexes–CDKN2A/B/ARF Genes in Breast Tumors: Identification of a Two-Gene (EZH2/CBX7) Signature with Independent Prognostic Value
Authors: Meseure Didier , Vacher Sophie , Alsibai Kinan Drak , Nicolas Andre , Chemlali Walid , Caly Martial , Lidereau Rosette , Pasmant Eric , Callens Celine , Bieche Ivan
Published: April 2023

Relationship between CBX7 transcripts levels and classical clinical biological parameters in a series of 456 breast cancers.
Sequence of primers from Increased Expression of Beige/Brown Adipose Markers from Host and Breast Cancer Cells Influence Xenograft Formation in Mice
Authors: Singh Rajan , Parveen Meher , Basgen John M. , Fazel Sayeda , Meshesha Meron F. , Thames Easter C. , Moore Brandis , Martinez Luis , Howard Carolyn B. , Vergnes Laurent , Reue Karen , Pervin Shehla
Published: April 2023

Sequence of various mouse and human primers used in this study.
Supplemental Table 7 from Expression of ANRIL–Polycomb Complexes–CDKN2A/B/ARF Genes in Breast Tumors: Identification of a Two-Gene (EZH2/CBX7) Signature with Independent Prognostic Value
Authors: Meseure Didier , Vacher Sophie , Alsibai Kinan Drak , Nicolas Andre , Chemlali Walid , Caly Martial , Lidereau Rosette , Pasmant Eric , Callens Celine , Bieche Ivan
Published: April 2023

Relationship between JARID2 transcripts levels and classical clinical biological parameters in a series of 454 breast cancers.
Supplemental Table 5 from Expression of ANRIL–Polycomb Complexes–CDKN2A/B/ARF Genes in Breast Tumors: Identification of a Two-Gene (EZH2/CBX7) Signature with Independent Prognostic Value
Authors: Meseure Didier , Vacher Sophie , Alsibai Kinan Drak , Nicolas Andre , Chemlali Walid , Caly Martial , Lidereau Rosette , Pasmant Eric , Callens Celine , Bieche Ivan
Published: April 2023

Relationship between SUZ12 transcripts levels and classical clinical biological parameters in a series of 456 breast cancers.
Pathological characteristics of human breast tumors from Increased Expression of Beige/Brown Adipose Markers from Host and Breast Cancer Cells Influence Xenograft Formation in Mice
Authors: Singh Rajan , Parveen Meher , Basgen John M. , Fazel Sayeda , Meshesha Meron F. , Thames Easter C. , Moore Brandis , Martinez Luis , Howard Carolyn B. , Vergnes Laurent , Reue Karen , Pervin Shehla
Published: April 2023

Human breast tumors used in this study were according to the stage/grade
Supplemental Table 15 from Expression of ANRIL–Polycomb Complexes–CDKN2A/B/ARF Genes in Breast Tumors: Identification of a Two-Gene (EZH2/CBX7) Signature with Independent Prognostic Value
Authors: Meseure Didier , Vacher Sophie , Alsibai Kinan Drak , Nicolas Andre , Chemlali Walid , Caly Martial , Lidereau Rosette , Pasmant Eric , Callens Celine , Bieche Ivan
Published: April 2023

Statistical analysis and correlation between ANRIL pathway genes in the series of 456 breast tumors.
Figure S7 from Linking Cancer Metabolism to DNA Repair and Accelerated Senescence
Authors: Efimova Elena V. , Takahashi Satoe , Shamsi Noumaan A. , Wu Ding , Labay Edwardine , Ulanovskaya Olesya A. , Weichselbaum Ralph R. , Kozmin Sergey A. , Kron Stephen J.
Published: April 2023

Histone demethylases mediate effects of alpha-KG.
Figure S6 from Linking Cancer Metabolism to DNA Repair and Accelerated Senescence
Authors: Efimova Elena V. , Takahashi Satoe , Shamsi Noumaan A. , Wu Ding , Labay Edwardine , Ulanovskaya Olesya A. , Weichselbaum Ralph R. , Kozmin Sergey A. , Kron Stephen J.
Published: April 2023

Enhancing TCA cycle results in persistent DNA damage.
Supplementary figure legends from Taxol Induces Brk-dependent Prosurvival Phenotypes in TNBC Cells through an AhR/GR/HIF–driven Signaling Axis
Authors: Regan Anderson Tarah M. , Ma Shihong , Perez Kerkvliet Carlos , Peng Yan , Helle Taylor M. , Krutilina Raisa I. , Raj Ganesh V. , Cidlowski John A. , Ostrander Julie H. , Schwertfeger Kathryn L. , Seagroves Tiffany N. , Lange Carol A.
Published: April 2023

Figure legends describing supplementary data
Figure S1 from Linking Cancer Metabolism to DNA Repair and Accelerated Senescence
Authors: Efimova Elena V. , Takahashi Satoe , Shamsi Noumaan A. , Wu Ding , Labay Edwardine , Ulanovskaya Olesya A. , Weichselbaum Ralph R. , Kozmin Sergey A. , Kron Stephen J.
Published: April 2023

IRIF persistence correlates with inhibition of PARP-regulated repair pathway.
Supplementary Figure 2 from Taxol Induces Brk-dependent Prosurvival Phenotypes in TNBC Cells through an AhR/GR/HIF–driven Signaling Axis
Authors: Regan Anderson Tarah M. , Ma Shihong , Perez Kerkvliet Carlos , Peng Yan , Helle Taylor M. , Krutilina Raisa I. , Raj Ganesh V. , Cidlowski John A. , Ostrander Julie H. , Schwertfeger Kathryn L. , Seagroves Tiffany N. , Lange Carol A.
Published: April 2023

TMA data derived from luminal, or adjacent 'normal' tissue, stained for total GR or phospho-GR expression.
Figure S3 from p53 Deletion or Hotspot Mutations Enhance mTORC1 Activity by Altering Lysosomal Dynamics of TSC2 and Rheb
Authors: Agarwal Stuti , Bell Catherine M. , Taylor Shirley M. , Moran Richard G.
Published: April 2023

Efficiency of transfection of HCT116 cells null for p53 with HA-TSC2 (A) and Flag-Sestrin2 (B).
Supplemental Data from FOXC1 Regulates FGFR1 Isoform Switching to Promote Invasion Following TGFβ-Induced EMT
Authors: Hopkins Alex , Coatham Mackenzie L. , Berry Fred B.
Published: April 2023

Supplemental Table 1 lists the primers used for qPCR analysis in this study. Supplemental Table 2 contains a list of RNA transcripts down regulated in the shFOXC1 cells compared to shEGFP cells. Genes selected for further analysis are presented in Figure 3. Supplemental Table 3 contains a list of RNA transcripts up regulated in shFOXC1 cells compared to shEGFP cells. Supplemental Figure 1 presents results of transient siRNA knockdown of Foxc1 in NMuMG cells. These data are complementary to the stable shRNA Foxc1 knockdown experiments presented in Figure 2. Supplemental Figure 2. This figure depicts expression of mesenchymal marker genes N-cadherin and Vimentin in shFOXC1 knock down NMuMG cells following TGF-β1 induced EMT events. Supplemental Figure 3 presents the localization of E-cadherin and β-actin in control and siFOXC1 NMuMG following TGF-β1 induced EMT. These data demonstrate siFOXC1 and Control cells undergo morphological alterations reminiscent of EMT events. Supplemental Figure 4 includes the entire membrane probed with anti-Foxc1 antibody used in Figure 2. This figure also includes an "no primary antibody" control demonstrating the non-specific bands observed are derived from the secondary antibody.
Supplementary Figure Legends, Table Legends, Figure 1, Tables 1 - 4 from Evaluating TBK1 as a Therapeutic Target in Cancers with Activated IRF3
Authors: Muvaffak Asli , Pan Qi , Yan Haiyan , Fernandez Rafael , Lim Jongwon , Dolinski Brian , Nguyen Thi T. , Strack Peter , Wu Stephen , Chung Rossana , Zhang Weiqun , Hulton Chris , Ripley Steven , Hirsch Heather , Nagashima Kumiko , Wong Kwok-Kin , Jánne Pasi A. , Seidel-Dugan Cynthia , Zawel Leigh , Kirschmeier Paul T. , Middleton Richard E. , Morris Erick J. , Wang Yan
Published: April 2023

PDF file - 1334KB, S1. IC50 values of TBK1 inhibitors Compound number 5, Compound number 4 and Compound number 3 from the selected PDAC, colorectal cancer and NSCLC cancer cell lines using are shown. Table 1S. List of shRNAs Targeting TBK1 Table 2S. RAS Gene Signature Score Correlation with Sensitivity to the TBK1i (Compound #1) and Meki (PD0325901) in NSCLC Cell Lines Table 3S. List of Cell Lines from 6-Cell Line Panels that were Used in TBK1 Inhibitor Screening in the 2-Dimensional Cell Viability Assay (NSCLC and Colorectal cancer panels) Table 4S. List of Cell Lines from 6-Cell Line Panels that were Used in TBK1 Inhibitor Screening in the 2-Dimensional Cell Viability Assay (Ovarian cancer, GBM and Lymphoma panels).
Suppl-Figure 5 from Pancreatic Neuroendocrine Tumors and EMT Behavior Are Driven by the CSC Marker DCLK1
Authors: Ikezono Yu , Koga Hironori , Akiba Jun , Abe Mitsuhiko , Yoshida Takafumi , Wada Fumitaka , Nakamura Toru , Iwamoto Hideki , Masuda Atsutaka , Sakaue Takahiko , Yano Hirohisa , Tsuruta Osamu , Torimura Takuji
Published: April 2023

Sphere formation assay.
Supplementary Materials and Methods and Supplementary Figures 1 through 11 from DDB2 Suppresses Tumorigenicity by Limiting the Cancer Stem Cell Population in Ovarian Cancer
Authors: Han Chunhua , Zhao Ran , Liu Xingluo , Srivastava Amit , Gong Li , Mao Hsiaoyin , Qu Meihua , Zhao Weiqiang , Yu Jianhua , Wang Qi-En
Published: April 2023

PDF - 899K, Supplementary Materials and Methods; S1. Manipulation of DDB2 expression does not change EMT of ovarian cancer cells. S2. DDB2 reduces the abundance of ALDH+ cells in ovarian cancer cell lines. S3. Effect of DDB2 on the ALDH1A1 protein expression in ovarian cancer cell lines S4. Downregulation of DDB2 increases the abundance of ALDH+ cells in ovarian cancer cell line 2008. S5. Overexpression of DDB2 reduces, while knockdown of DDB2 increases the percentage of CD44+CD117+ cells in ovarian cancer cell lines S6. Analysis of side population (SP) cells in CP70 and DDB2 overexpressed CP70 cells. S7. Isolation and characterization of CP70-ALDH+ cells. S8. Isolation and characterization of SKOV3-CSCs. S9. Isolation and characterization of 2008-CD44+CD117+ and 2008C13-CD44+CD117+ cells. S10. The correlation between DDB2 and IκB mRNA expression levels in ovarian serous cystadenocarcinomas. S11. Effects of DDB2 promoter methylation and DDB2 copy number alteration on the DDB2 mRNA level in ovarian serous cystadenocarcinomas
Suppl-Figure 1 from Pancreatic Neuroendocrine Tumors and EMT Behavior Are Driven by the CSC Marker DCLK1
Authors: Ikezono Yu , Koga Hironori , Akiba Jun , Abe Mitsuhiko , Yoshida Takafumi , Wada Fumitaka , Nakamura Toru , Iwamoto Hideki , Masuda Atsutaka , Sakaue Takahiko , Yano Hirohisa , Tsuruta Osamu , Torimura Takuji
Published: April 2023

Negative control for immunohistochemistry
Supplemental Figure Legends from Differential Expression of OATP1B3 Mediates Unconjugated Testosterone Influx
Authors: Sissung Tristan M. , Ley Ariel M. , Strope Jonathan D. , McCrea Edel M. , Beedie Shaunna , Peer Cody J. , Shukla Suneet , van Velkinburgh Jennifer , Reece Kelie , Troutman Sarah , Campbell Tessa , Fernandez Elena , Huang Phoebe , Smith Jordan , Thakkar Nilay , Venzon David J. , Brenner Stefan , Lee Wooin , Merino Maria , Luo Ji , Jager Walter , Price Douglas K. , Chau Cindy H. , Figg William D.
Published: April 2023

Supplemental Figure Legends 1-4