bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental Figures 1 - 8 from Loss of Estrogen-Regulated microRNA Expression Increases HER2 Signaling and Is Prognostic of Poor Outcome in Luminal Breast Cancer
Authors: Bailey Shannon T. , Westerling Thomas , Brown Myles
Published: March 2023

Supplementary Figure 1. Normalized NanoString counts for clusters differentially expressed in MCF7 vs. MCF7:2A cells. Supplementary Figure 2. ER binding is lower at binding sites found near differentially regulated miRNAs. Supplementary Figure 3. The expression of the individual miRNAs in the let-7c/miR-99a/miR-125b cluster is correlated in patient samples. Supplementary Figure 4. Kaplan-Meier plot examining the expression of let-7c, miR-99a, and miR-125b in the luminal B, Her2, basal, and normal-like PAM50 subsets. Supplementary Figure 5. Kaplan-Meier plots demonstrating that the luminal A low patient subset has survival similar to patients with luminal B tumors. Supplementary Figure 6. HER2 mRNA is slightly reduced in response to miRNA treatment. Supplementary Figure 7. Let-7c indirectly targets the HER2 UTR and regulates Dicer. Supplementary Figure 8. miR-125b expression is not negatively correlated with HER2 protein expression or activity in patients with breast cancer.
Supplementary Tables S1-S4 from Genetic and Pharmacological Screens Converge in Identifying FLIP, BCL2, and IAP Proteins as Key Regulators of Sensitivity to the TRAIL-Inducing Anticancer Agent ONC201/TIC10
Authors: Allen Joshua E. , Prabhu Varun V. , Talekar Mala , van den Heuvel A. Pieter J. , Lim Bora , Dicker David T. , Fritz Jennifer L. , Beck Adam , El-Deiry Wafik S.
Published: March 2023

Supplementary Tables S1-S4. Kinase regulators of ONC201 sensitivity (S1); Validation of kinase regulators of ONC201 sensitivity (S2); ONC201 and sorafenib combinatorial activity in HCC and RCC (S3); Combination indices for ONC201 and sorafenib activity (S4).
Supplemental Table 2 from Host Age Is a Systemic Regulator of Gene Expression Impacting Cancer Progression
Authors: Beheshti Afshin , Benzekry Sébastien , McDonald J. Tyson , Ma Lili , Peluso Michael , Hahnfeldt Philip , Hlatky Lynn
Published: March 2023

Supplemental Table 2. Biofunctions predicted to be activated or inhibited in the course of tumor progression
Supplemental Figure S6 from Akt Inhibition Enhances Expansion of Potent Tumor-Specific Lymphocytes with Memory Cell Characteristics
Authors: Crompton Joseph G. , Sukumar Madhusudhanan , Roychoudhuri Rahul , Clever David , Gros Alena , Eil Robert L. , Tran Eric , Hanada Ken-ichi , Yu Zhiya , Palmer Douglas C. , Kerkar Sid P. , Michalek Ryan D. , Upham Trevor , Leonardi Anthony , Acquavella Nicolas , Wang Ena , Marincola Francesco M. , Gattinoni Luca , Muranski Pawel , Sundrud Mark S. , Klebanoff Christopher A. , Rosenberg Steven A. , Fearon Douglas T. , Restifo Nicholas P.
Published: March 2023

Supplemental Figure S6. 8.Akt inhibition of murine CD8+ T cells increased expression of CD62L and CD27, and decreased expression of CD44.
Supplementary Figure Legends from miR-124 and Androgen Receptor Signaling Inhibitors Repress Prostate Cancer Growth by Downregulating Androgen Receptor Splice Variants, EZH2, and Src
Authors: Shi Xu-Bao , Ma Ai-Hong , Xue Lingru , Li Meimei , Nguyen Hao G. , Yang Joy C. , Tepper Clifford G. , Gandour-Edwards Regina , Evans Christopher P. , Kung Hsing-Jien , deVere White Ralph W.
Published: March 2023

Legend for Supplementary Figures S1-S5.
Supplemental Figure S3 from Akt Inhibition Enhances Expansion of Potent Tumor-Specific Lymphocytes with Memory Cell Characteristics
Authors: Crompton Joseph G. , Sukumar Madhusudhanan , Roychoudhuri Rahul , Clever David , Gros Alena , Eil Robert L. , Tran Eric , Hanada Ken-ichi , Yu Zhiya , Palmer Douglas C. , Kerkar Sid P. , Michalek Ryan D. , Upham Trevor , Leonardi Anthony , Acquavella Nicolas , Wang Ena , Marincola Francesco M. , Gattinoni Luca , Muranski Pawel , Sundrud Mark S. , Klebanoff Christopher A. , Rosenberg Steven A. , Fearon Douglas T. , Restifo Nicholas P.
Published: March 2023

Supplemental Figure S3. Surface phenotype of Akti-treated and vehicle TIL isolated from patient with melanoma and expanded to clinical scale for 30 days prior to adoptive-transfer into humanized mouse model.
Supplementary Materials and Methods from Constitutive Activation of Myosin-Dependent Contractility Sensitizes Glioma Tumor-Initiating Cells to Mechanical Inputs and Reduces Tissue Invasion
Authors: Wong Sophie Y. , Ulrich Theresa A. , Deleyrolle Loic P. , MacKay Joanna L. , Lin Jung-Ming G. , Martuscello Regina T. , Jundi Musa A. , Reynolds Brent A. , Kumar Sanjay
Published: March 2023

Supplementary Materials and Methods. Description of additional methods and procedures used in the study.
Supplementary Figure S2 from Constitutive Activation of Myosin-Dependent Contractility Sensitizes Glioma Tumor-Initiating Cells to Mechanical Inputs and Reduces Tissue Invasion
Authors: Wong Sophie Y. , Ulrich Theresa A. , Deleyrolle Loic P. , MacKay Joanna L. , Lin Jung-Ming G. , Martuscello Regina T. , Jundi Musa A. , Reynolds Brent A. , Kumar Sanjay
Published: March 2023

Supplementary Figure S2. BMP4-induced differentiation alters tumor-initiating cell spread area, but not motility.
Supplementary Methods, Table 1 and Figure 1 from In Vivo Radioimaging of Bradykinin Receptor B1, a Widely Overexpressed Molecule in Human Cancer
Authors: Lin Kuo-Shyan , Pan Jinhe , Amouroux Guillaume , Turashvili Gulisa , Mesak Felix , Hundal-Jabal Navjit , Pourghiasian Maral , Lau Joseph , Jenni Silvia , Aparicio Samuel , Bénard François
Published: March 2023

Supplementary Methods, Table 1 and Figure 1. Supplementary Methods: Peptide synthesis Table 1: detailed biodistribution data. Supplementary Figure 1: Structure of the radiolabeled peptides evaluated in this study: 68Ga-P03083 (top), 68Ga-SH01078 (middle) and 68Ga-P03034 (bottom).
Supplementary Figure S3 from UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas
Authors: Wong Stephen Q. , Waldeck Kelly , Vergara Ismael A. , Schröder Jan , Madore Jason , Wilmott James S. , Colebatch Andrew J. , De Paoli-Iseppi Ricardo , Li Jason , Lupat Richard , Semple Timothy , Arnau Gisela Mir , Fellowes Andrew , Leonard J. Helen , Hruby George , Mann Graham J. , Thompson John F. , Cullinane Carleen , Johnston Meredith , Shackleton Mark , Sandhu Shahneen , Bowtell David D.L. , Johnstone Ricky W. , Fox Stephen B. , McArthur Grant A. , Papenfuss Anthony T. , Scolyer Richard A. , Gill Anthony J. , Hicks Rodney J. , Tothill Richard W.
Published: March 2023

CD3+ (Combined TIL grade) between MCV negative (V-MGG) versus MCV-positive (V+MGG) MCCs. n.s., not significant.
Supplementary Tables S1-S2 from Targeting a Plk1-Controlled Polarity Checkpoint in Therapy-Resistant Glioblastoma-Propagating Cells
Authors: Lerner Robin G. , Grossauer Stefan , Kadkhodaei Banafsheh , Meyers Ian , Sidorov Maxim , Koeck Katharina , Hashizume Rintaro , Ozawa Tomoko , Phillips Joanna J. , Berger Mitchel S. , Nicolaides Theodore , James C. David , Petritsch Claudia K.
Published: March 2023

List of antibodies used for immunostaining and flow cytometry/FACS (S1); List of primers (5'-3') used for RT-qPCR (S2).
Supplementary Figure S2 from Radiation Sensitivity in a Preclinical Mouse Model of Medulloblastoma Relies on the Function of the Intrinsic Apoptotic Pathway
Authors: Crowther Andrew J. , Ocasio Jennifer K. , Fang Fang , Meidinger Jessica , Wu Jaclyn , Deal Allison M. , Chang Sha X. , Yuan Hong , Schmid Ralf , Davis Ian , Gershon Timothy R.
Published: March 2023

Additional histologic studies.
Supplementary Figure S7 from Targeting a Plk1-Controlled Polarity Checkpoint in Therapy-Resistant Glioblastoma-Propagating Cells
Authors: Lerner Robin G. , Grossauer Stefan , Kadkhodaei Banafsheh , Meyers Ian , Sidorov Maxim , Koeck Katharina , Hashizume Rintaro , Ozawa Tomoko , Phillips Joanna J. , Berger Mitchel S. , Nicolaides Theodore , James C. David , Petritsch Claudia K.
Published: March 2023

Effect of combined inhibition of BRAFV600E and PLK1 on CD133+ cells.
Supplementary Figure S1 from Bortezomib Improves Adoptive T-cell Therapy by Sensitizing Cancer Cells to FasL Cytotoxicity
Authors: Shanker Anil , Pellom Samuel T. , Dudimah Duafalia F. , Thounaojam Menaka C. , de Kluyver Rachel L. , Brooks Alan D. , Yagita Hideo , McVicar Daniel W. , Murphy William J. , Longo Dan L. , Sayers Thomas J.
Published: March 2023

Increase in the number of lung metastases following the suppressive regimen of bortezomib.
Supplementary Figure Legends from Targeting a Plk1-Controlled Polarity Checkpoint in Therapy-Resistant Glioblastoma-Propagating Cells
Authors: Lerner Robin G. , Grossauer Stefan , Kadkhodaei Banafsheh , Meyers Ian , Sidorov Maxim , Koeck Katharina , Hashizume Rintaro , Ozawa Tomoko , Phillips Joanna J. , Berger Mitchel S. , Nicolaides Theodore , James C. David , Petritsch Claudia K.
Published: March 2023

Legends for Supplementary Figures S1-S7.
Supplementary Tables S1-S8, Figures S1-S4 from Whole-Exome Sequencing Reveals Frequent Genetic Alterations in BAP1, NF2, CDKN2A, and CUL1 in Malignant Pleural Mesothelioma
Authors: Guo Guangwu , Chmielecki Juliann , Goparaju Chandra , Heguy Adriana , Dolgalev Igor , Carbone Michele , Seepo Sara , Meyerson Matthew , Pass Harvey I.
Published: March 2023

Supplementary Tables S1-S8, Figures S1-S4. Table S1. Clinical characteristics of the 22 MPM patients. Table S2. Primer sequences of PIK3C2B, RDX, and TAOK1 for validation experiment. Table S3. A list of all somatic mutations detected in 22 MPMs (shown in separate excel file). Table S4. The average mutation rates of different cancer types in previously reported cancer genome studies. Table S5. Recurrently mutated genes that harbored much higher mutations than the background with significant threshold of P <0.01. Table S6. List of significant focal copy number alterations in the 22 MPMs (shown in separate excel file). Table S7. Pathways that are significantly enriched with genetic alterations in MPM. Table S8. Somatic mutations in the genes of Hippo signaling pathway(12) in MPMs. Figure S1. Spectrum of somatic point mutations identified in the 22 MPMs. Figure S2. Copy number alteration profiles of 22 MPMs using the whole exome sequencing data. Figure S3. Statistically significant focal deletions (blue) plotted along the genome for the MPM. Figure S4. A significant region of focal deletion at 9p21 containing CDKN2A/B and MIR31 (microRNA 31) in MPM rendered by the Integrative Genomics Viewer (IGV).
Supplementary Tables S1-S2 from SND1 Acts Downstream of TGFβ1 and Upstream of Smurf1 to Promote Breast Cancer Metastasis
Authors: Yu Lin , Liu Xin , Cui Kang , Di Yanbo , Xin Lingbiao , Sun Xiaoming , Zhang Wei , Yang Xi , Wei Minxin , Yao Zhi , Yang Jie
Published: March 2023

Supplementary Tables S1-S2. Primers used in the manuscript (S1); Expression of SND1 in Human Breast Tissues (S2).
Table S3 from Disseminated Tumor Cells Persist in the Bone Marrow of Breast Cancer Patients through Sustained Activation of the Unfolded Protein Response
Authors: Bartkowiak Kai , Kwiatkowski Marcel , Buck Friedrich , Gorges Tobias M. , Nilse Lars , Assmann Volker , Andreas Antje , Müller Volkmar , Wikman Harriet , Riethdorf Sabine , Schlüter Hartmut , Pantel Klaus
Published: March 2023

SILAC mass spectra overview
Table S2 from Disseminated Tumor Cells Persist in the Bone Marrow of Breast Cancer Patients through Sustained Activation of the Unfolded Protein Response
Authors: Bartkowiak Kai , Kwiatkowski Marcel , Buck Friedrich , Gorges Tobias M. , Nilse Lars , Assmann Volker , Andreas Antje , Müller Volkmar , Wikman Harriet , Riethdorf Sabine , Schlüter Hartmut , Pantel Klaus
Published: March 2023

SILAC identification details for BC-M1 and MDA-MB-468
Supplementary Figure Legends from SND1 Acts Downstream of TGFβ1 and Upstream of Smurf1 to Promote Breast Cancer Metastasis
Authors: Yu Lin , Liu Xin , Cui Kang , Di Yanbo , Xin Lingbiao , Sun Xiaoming , Zhang Wei , Yang Xi , Wei Minxin , Yao Zhi , Yang Jie
Published: March 2023

Supplementary Figure Legends. Legends for Supplementary Figures S1-S2.
Supplementary methods and supplementary figure Legends from Disseminated Tumor Cells Persist in the Bone Marrow of Breast Cancer Patients through Sustained Activation of the Unfolded Protein Response
Authors: Bartkowiak Kai , Kwiatkowski Marcel , Buck Friedrich , Gorges Tobias M. , Nilse Lars , Assmann Volker , Andreas Antje , Müller Volkmar , Wikman Harriet , Riethdorf Sabine , Schlüter Hartmut , Pantel Klaus
Published: March 2023

Supplementary methods and supplementary figure Legends
Supplemental Table S2 from Akt–Girdin Signaling in Cancer-Associated Fibroblasts Contributes to Tumor Progression
Authors: Yamamura Yumiko , Asai Naoya , Enomoto Atsushi , Kato Takuya , Mii Shinji , Kondo Yuji , Ushida Kaori , Niimi Kaoru , Tsunoda Nobuyuki , Nagino Masato , Ichihara Shu , Furukawa Koichi , Maeda Kengo , Murohara Toyoaki , Takahashi Masahide
Published: March 2023

Correlations between clinicopathological features and Girdin phosphorylation in CAF.
Figure S2 from Disseminated Tumor Cells Persist in the Bone Marrow of Breast Cancer Patients through Sustained Activation of the Unfolded Protein Response
Authors: Bartkowiak Kai , Kwiatkowski Marcel , Buck Friedrich , Gorges Tobias M. , Nilse Lars , Assmann Volker , Andreas Antje , Müller Volkmar , Wikman Harriet , Riethdorf Sabine , Schlüter Hartmut , Pantel Klaus
Published: March 2023

Quality control of the SILAC experiment
Supplemental Figure S2 from Akt–Girdin Signaling in Cancer-Associated Fibroblasts Contributes to Tumor Progression
Authors: Yamamura Yumiko , Asai Naoya , Enomoto Atsushi , Kato Takuya , Mii Shinji , Kondo Yuji , Ushida Kaori , Niimi Kaoru , Tsunoda Nobuyuki , Nagino Masato , Ichihara Shu , Furukawa Koichi , Maeda Kengo , Murohara Toyoaki , Takahashi Masahide
Published: March 2023

The arbitrary grading scale was developed to quantitate the phosphorylation of Girdin in CAF in tissue sections.
Supplemental Figure S1 from Akt–Girdin Signaling in Cancer-Associated Fibroblasts Contributes to Tumor Progression
Authors: Yamamura Yumiko , Asai Naoya , Enomoto Atsushi , Kato Takuya , Mii Shinji , Kondo Yuji , Ushida Kaori , Niimi Kaoru , Tsunoda Nobuyuki , Nagino Masato , Ichihara Shu , Furukawa Koichi , Maeda Kengo , Murohara Toyoaki , Takahashi Masahide
Published: March 2023

Effects of TGF-β1 stiumlation on α-SMA expression in fibroblasts isolated from WT and SA mice.
Supplemental Figures and Tables from Ly6E/K Signaling to TGFβ Promotes Breast Cancer Progression, Immune Escape, and Drug Resistance
Authors: AlHossiny Midrar , Luo Linlin , Frazier William R. , Steiner Noriko , Gusev Yuriy , Kallakury Bhaskar , Glasgow Eric , Creswell Karen , Madhavan Subha , Kumar Rakesh , Upadhyay Geeta
Published: March 2023

Table S1: List of qRT-PCR primers; Table. S2: Summary table of mRNA expression for Ly6K and Ly6E in normal and cancer samples in seven comparison; Fig. S1. Expression of Ly6K and Ly6E in human normal and breast cancer tissues; Fig. S2: The knockdown for Ly6K and Ly6E is specific; Fig. S3: Colony assay; Fig. S4: The Ly6K gene is required for intravasation, extravasation and colonization of cancer cells; Fig. S5: Comparison of CD274, CTLA4, IL2RA, LY6E and LY6K gene expression in clinical samples of breast cancer in indicated 6 analysis in three different datasets; Fig. S6: High expression of Ly6K and Ly6E impair NK cell binding to cancer cell; Fig. S7: Indicated cells (MDA-MB-231) were treated with 100ng/ml IFN-g overnight; Fig. S8: Rescue over expression phenotype.
Supplemental Table S3 from PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease
Authors: Li Zejuan , Chen Ping , Su Rui , Hu Chao , Li Yuanyuan , Elkahloun Abdel G. , Zuo Zhixiang , Gurbuxani Sandeep , Arnovitz Stephen , Weng Hengyou , Wang Yungui , Li Shenglai , Huang Hao , Neilly Mary Beth , Wang Gang Greg , Jiang Xi , Liu Paul P. , Jin Jie , Chen Jianjun
Published: March 2023

Distribution of target genes of MLL-fusion proteins in different sets of genes that are significantly differentially expressed between the three groups of samples.
Supplementary Figures 1 through 10 and Supplementary Tables 1 and 2 from HER2 Signaling Drives DNA Anabolism and Proliferation through SRC-3 Phosphorylation and E2F1-Regulated Genes
Authors: Nikolai Bryan C. , Lanz Rainer B. , York Brian , Dasgupta Subhamoy , Mitsiades Nicholas , Creighton Chad J. , Tsimelzon Anna , Hilsenbeck Susan G. , Lonard David M. , Smith Carolyn L. , O'Malley Bert W.
Published: March 2023

10 figures and 2 tables provided as supplementary material supporting the major conclusions of the manuscript and experimental details.
Supplemental Table S2 from PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease
Authors: Li Zejuan , Chen Ping , Su Rui , Hu Chao , Li Yuanyuan , Elkahloun Abdel G. , Zuo Zhixiang , Gurbuxani Sandeep , Arnovitz Stephen , Weng Hengyou , Wang Yungui , Li Shenglai , Huang Hao , Neilly Mary Beth , Wang Gang Greg , Jiang Xi , Liu Paul P. , Jin Jie , Chen Jianjun
Published: March 2023

List of the 1,022 genes that are expressed at a significantly lower level in Group 1 than in both Groups 2 and 3.
Supplementary Data 2 from HER2 Signaling Drives DNA Anabolism and Proliferation through SRC-3 Phosphorylation and E2F1-Regulated Genes
Authors: Nikolai Bryan C. , Lanz Rainer B. , York Brian , Dasgupta Subhamoy , Mitsiades Nicholas , Creighton Chad J. , Tsimelzon Anna , Hilsenbeck Susan G. , Lonard David M. , Smith Carolyn L. , O'Malley Bert W.
Published: March 2023

Spreadsheet containing Gene ID and ontology analysis for all transcripts downregulated with HER2 depletion.
Supplementary Data 1 from HER2 Signaling Drives DNA Anabolism and Proliferation through SRC-3 Phosphorylation and E2F1-Regulated Genes
Authors: Nikolai Bryan C. , Lanz Rainer B. , York Brian , Dasgupta Subhamoy , Mitsiades Nicholas , Creighton Chad J. , Tsimelzon Anna , Hilsenbeck Susan G. , Lonard David M. , Smith Carolyn L. , O'Malley Bert W.
Published: March 2023

Spreadsheet containing Gene ID and ontology analysis for all transcripts upregulated with HER2 depletion.
Supplemental Methods and References from PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease
Authors: Li Zejuan , Chen Ping , Su Rui , Hu Chao , Li Yuanyuan , Elkahloun Abdel G. , Zuo Zhixiang , Gurbuxani Sandeep , Arnovitz Stephen , Weng Hengyou , Wang Yungui , Li Shenglai , Huang Hao , Neilly Mary Beth , Wang Gang Greg , Jiang Xi , Liu Paul P. , Jin Jie , Chen Jianjun
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplemental References.
Supplemental Figure Legends from PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease
Authors: Li Zejuan , Chen Ping , Su Rui , Hu Chao , Li Yuanyuan , Elkahloun Abdel G. , Zuo Zhixiang , Gurbuxani Sandeep , Arnovitz Stephen , Weng Hengyou , Wang Yungui , Li Shenglai , Huang Hao , Neilly Mary Beth , Wang Gang Greg , Jiang Xi , Liu Paul P. , Jin Jie , Chen Jianjun
Published: March 2023

Legends for Supplemental Figures S1-S11.
Supplementary Figures 1 through 7 from miR-29b Mediates NF-κB Signaling in KRAS-Induced Non–Small Cell Lung Cancers
Authors: Langsch Stephanie , Baumgartner Ulrich , Haemmig Stefan , Schlup Cornelia , Schäfer Stephan C. , Berezowska Sabina , Rieger Gregor , Dorn Patrick , Tschan Mario P. , Vassella Erik
Published: March 2023

Supplementary Fig. 1: Ectopic PIK3CAH1047R expression induces a modest activation of the EGFR downstream signaling pathway in BEAS-2B clones. Supplementary Fig. 2: the steady state level of miR-29b and the relative copy number of the miR-29b2 locus are significantly correlated in KRAS/EGFR wildtype tumors. Supplementary Fig. 3: miR-138 expression is not induced by mutant KRAS or mutant EGFR in adenocarcinoma tissues. Supplementary Fig. 4: Inhibitors of the EGFR signaling pathway downregulate expression of key downstream effectors. Supplementary Fig. 5: miR-29b confers resistance to TNFalpha+ActD-induced apoptosis. Supplementary Fig. 6: TNFAIP3 is a target of miR-29b. Supplementary Fig. 7: miR-29b sensitizes A549 cells to cisplatin-induced apoptosis.
Supplementary Table S8 from PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells
Authors: Rahme Gilbert J. , Zhang Zhonghua , Young Alison L. , Cheng Chao , Bivona Eric J. , Fiering Steven N. , Hitoshi Yasuyuki , Israel Mark A.
Published: March 2023

Gene ontology analysis with Revigo clustering on upregulated genes with Dox addition.
Supplementary Table S7 from PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells
Authors: Rahme Gilbert J. , Zhang Zhonghua , Young Alison L. , Cheng Chao , Bivona Eric J. , Fiering Steven N. , Hitoshi Yasuyuki , Israel Mark A.
Published: March 2023

Gene ontology analysis with Revigo clustering on downregulated genes with Dox addition.
Supplementary Figure Legends from Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas
Authors: Hilvo Mika , de Santiago Ines , Gopalacharyulu Peddinti , Schmitt Wolfgang D. , Budczies Jan , Kuhberg Marc , Dietel Manfred , Aittokallio Tero , Markowetz Florian , Denkert Carsten , Sehouli Jalid , Frezza Christian , Darb-Esfahani Silvia , Braicu Elena Ioana
Published: March 2023

Supplementary Figure Legends
Supplementary Table S6 from PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells
Authors: Rahme Gilbert J. , Zhang Zhonghua , Young Alison L. , Cheng Chao , Bivona Eric J. , Fiering Steven N. , Hitoshi Yasuyuki , Israel Mark A.
Published: March 2023

Pearson correlation scores for RTK genes in TCGA 2008 GBM dataset.
Supplementary Table S2 from PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells
Authors: Rahme Gilbert J. , Zhang Zhonghua , Young Alison L. , Cheng Chao , Bivona Eric J. , Fiering Steven N. , Hitoshi Yasuyuki , Israel Mark A.
Published: March 2023

Primers used for qRT-PCR.
Supplementary Materials and Methods from PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells
Authors: Rahme Gilbert J. , Zhang Zhonghua , Young Alison L. , Cheng Chao , Bivona Eric J. , Fiering Steven N. , Hitoshi Yasuyuki , Israel Mark A.
Published: March 2023

Description of additional methods and procedures used in the study.
Supplementary Table 1 from The Deubiquitinase USP9X Maintains DNA Replication Fork Stability and DNA Damage Checkpoint Responses by Regulating CLASPIN during S-Phase
Authors: McGarry Edel , Gaboriau David , Rainey Michael D. , Restuccia Umberto , Bachi Angela , Santocanale Corrado
Published: March 2023

Protein groups identified by MaxQuant analysis.
Supplementary Figures from NADPH Oxidase 1 Activity and ROS Generation Are Regulated by Grb2/Cbl-Mediated Proteasomal Degradation of NoxO1 in Colon Cancer Cells
Authors: Joo Jung Hee , Oh Hyunjin , Kim Myungjin , An Eun Jung , Kim Rae-Kwon , Lee So-Young , Kang Dong Hoon , Kang Sang Won , Keun Park Cheol , Kim Hoguen , Lee Su-Jae , Lee Daekee , Seol Jae Hong , Bae Yun Soo
Published: March 2023

Supplementary Figure S1: Interaction between NoxO1 and Grb2 Supplementary Figure S2: Interaction domains between NoxO1 and Grb2 Supplementary Figure S3: Stability of Nox1 and NoxA1 Supplementary Figure S4: Target of ubiquitination is not p47phox Supplementary Figure S5: PKC-dependent NoxO1 phosphorylation Supplementary Figure S6: Subcellular localization of NoxO1 and NoxA1 Supplementary Figure S7: Effect of NoxO1 on Erkactivation
Supplementary materials from Abscopal Benefits of Localized Radiotherapy Depend on Activated T-cell Trafficking and Distribution between Metastatic Lesions
Authors: Poleszczuk Jan T. , Luddy Kimberly A. , Prokopiou Sotiris , Robertson-Tessi Mark , Moros Eduardo G. , Fishman Mayer , Djeu Julie Y. , Finkelstein Steven E. , Enderling Heiko
Published: March 2023

Derivation of the mathematical model and additional simulations.
Supplementary Figure S4 from RANK Signaling Blockade Reduces Breast Cancer Recurrence by Inducing Tumor Cell Differentiation
Authors: Yoldi Guillermo , Pellegrini Pasquale , Trinidad Eva M. , Cordero Alex , Gomez-Miragaya Jorge , Serra-Musach Jordi , Dougall William C. , Muñoz Purificación , Pujana Miguel-Angel , Planelles Lourdes , González-Suárez Eva
Published: March 2023

Constitutive deletion of RANK decreases tumor incidence in MMTv-PyMT
Supplementary Figure S3 from RANK Signaling Blockade Reduces Breast Cancer Recurrence by Inducing Tumor Cell Differentiation
Authors: Yoldi Guillermo , Pellegrini Pasquale , Trinidad Eva M. , Cordero Alex , Gomez-Miragaya Jorge , Serra-Musach Jordi , Dougall William C. , Muñoz Purificación , Pujana Miguel-Angel , Planelles Lourdes , González-Suárez Eva
Published: March 2023

RANKL treatment decreases apoptosis in MMTV-PyMT-derived tumor cells in vitro
Supplemental Figures and Tables from Caspase-9b Interacts Directly with cIAP1 to Drive Agonist-Independent Activation of NF-κB and Lung Tumorigenesis
Authors: Vu Ngoc T. , Park Margaret A. , Shultz Michael D. , Bulut Gamze B. , Ladd Amy C. , Chalfant Charles E.
Published: March 2023

Supplemental Figure 1: Larger legend table for symbols in fig 1A. Supplemental Figure 2: The expression of BIRC5, CDKN1A, CXCL1 and IER3 correlates with expression of C9b, but not C9a, in human NSCLC tissues. Supplemental Figure 3: Down-regulation of RIP1 abolishes the effect of C9b on IκBα level.. Supplemental Figure 4: The role of C9b in the NF-κB pathway is translational to other cell lines, H838 and HBEpC. Supplemental Figure 5: C9b activates the canonical NF-κB pathway in H838 cells and HBEpCs. Supplemental Figure 6: C9b level inversely correlates with IκBα level in NSCLC cells. Supplemental Figure 7: Down-regulation of cIAP2 has no effect on NF-κB activation and does not inhibit the effect of C9b on the NF-κB pathway. Supplemental Figure 8: Cleavage of C9b is not important for interaction with cIAP1. Supplemental Figure 9: Tumors formed from NSCLC cells stably expressing WT C9b have higher Ki-67 expression (cell proliferation) than tumors formed from control cells or cells expressing IBM-mutated (Mut) C9b. Supplemental Figure 10: The interaction with cIAP1 mediates the enhancing effect of C9b on the cell viability and survival/AIG of NSCLC cells and HBEpCs. Supplemental Figure 11: Suppression of the canonical NF-κB pathway by ectopically expressing the suppressor, IκBα, increases NIK level. Supplemental Figure 12: Down-regulation of NIK does not affect the survival/AIG of NSCLC cells. Supplemental Table 1: qPCR primers for NF-κB target genes utilized in the study Supplemental Table 2: List of NF-κB-related genes that expression was affected by down-regulation of C9b in A549 cells or up-regulation of C9b in HBEpC cells (identified by deep RNA sequencing). Supplemental Table 3: List of NF-κB target genes that expression is contrastingly affected by down-regulation of C9b in A549 cells versus by up-regulation of C9b in HBEpCs. Supplemental Table 4: NSCLC cell lines used in Figure 2D or Supplemental Figure 6. Supplemental Table 5: Sequences of negative control si-RNA and caspase-9a or -9b si-RNA utilized in the study.
Supplementary figure legends from SKAP2 Promotes Podosome Formation to Facilitate Tumor-Associated Macrophage Infiltration and Metastatic Progression
Authors: Tanaka Masamitsu , Shimamura Shintaro , Kuriyama Sei , Maeda Daichi , Goto Akiteru , Aiba Namiko
Published: March 2023

Figure legends of supplementary figure 1-7
Supplementary Table S3 from Identification of Patients with Recurrent Glioblastoma Who May Benefit from Combined Bevacizumab and CCNU Therapy: A Report from the BELOB Trial
Authors: Erdem-Eraslan Lale , van den Bent Martin J. , Hoogstrate Youri , Naz-Khan Hina , Stubbs Andrew , van der Spek Peter , Böttcher René , Gao Ya , de Wit Maurice , Taal Walter , Oosterkamp Hendrika M. , Walenkamp Annemiek , Beerepoot Laurens V. , Hanse Monique C.J. , Buter Jan , Honkoop Aafke H. , van der Holt Bronno , Vernhout René M. , Smitt Peter A.E. Sillevis , Kros Johan M. , French Pim J.
Published: March 2023

Individual patient characteristics.
Supplementary Figure S5 from Obesity-Induced Colorectal Cancer Is Driven by Caloric Silencing of the Guanylin–GUCY2C Paracrine Signaling Axis
Authors: Lin Jieru E. , Colon-Gonzalez Francheska , Blomain Erik , Kim Gilbert W. , Aing Amanda , Stoecker Brian , Rock Justin , Snook Adam E. , Zhan Tingting , Hyslop Terry M. , Tomczak Michal , Blumberg Richard S. , Waldman Scott A.
Published: March 2023

Daily calorie intake, body weights, and guanylin expression in Balb/c mice on lean or high fat (HF) diets.
Supplementary Figure S4 from Obesity-Induced Colorectal Cancer Is Driven by Caloric Silencing of the Guanylin–GUCY2C Paracrine Signaling Axis
Authors: Lin Jieru E. , Colon-Gonzalez Francheska , Blomain Erik , Kim Gilbert W. , Aing Amanda , Stoecker Brian , Rock Justin , Snook Adam E. , Zhan Tingting , Hyslop Terry M. , Tomczak Michal , Blumberg Richard S. , Waldman Scott A.
Published: March 2023

Daily calorie intake, body weights, and guanylin expression in wild type and obesity-resistant (HF-R) C57BL/6 mice on lean or high fat (HF) diets.
Supplementary Figures S1-S6 from Enhanced Survival with Implantable Scaffolds That Capture Metastatic Breast Cancer Cells In Vivo
Authors: Rao Shreyas S. , Bushnell Grace G. , Azarin Samira M. , Spicer Graham , Aguado Brian A. , Stoehr Jenna R. , Jiang Eric J. , Backman Vadim , Shea Lonnie D. , Jeruss Jacqueline S.
Published: March 2023

Micro-porous PCL scaffolds persist and maintain a space for extended times in vivo (S1); Host response following implantation of micro-porous PCL scaffolds in the dorsal subcutaneous space of an NSG mouse in vivo (S2); Dynamics of immune cell populations in the spleen of BALB/c mice with a PCL scaffold implant at day 0, 5, 10, and 15 post tumor inoculation (S3); Micro-porous PCL scaffolds enable recruitment of human MDA-MD-231BR cells in a chronic model of scaffold implantation (S4); Micro-porous PCL scaffolds do not significantly improve survival in a post-surgical model of breast cancer metastasis with day 6 post tumor inoculation resection (S5); Anti-Gr-1 depletion significantly reduces the presence of CD11b+Gr-1hiLy6C- MDSCs in the spleen primary tumor and scaffold (S6).
Supplementary Figure S4 from H3K27 Demethylase JMJD3 Employs the NF-κB and BMP Signaling Pathways to Modulate the Tumor Microenvironment and Promote Melanoma Progression and Metastasis
Authors: Park Woo-Yong , Hong Beom-Jin , Lee Jungsul , Choi Chulhee , Kim Mi-Young
Published: March 2023

STC1 and CCL2 expression are positively correlated with JMJD3 expression level in human malignant melanoma.
Supplementary Figure S3 from ΔNp63α Silences a miRNA Program to Aberrantly Initiate a Wound-Healing Program That Promotes TGFβ-Induced Metastasis
Authors: Rodriguez Calleja Lidia , Jacques Camille , Lamoureux François , Baud'huin Marc , Tellez Gabriel Marta , Quillard Thibaut , Sahay Debashish , Perrot Pierre , Amiaud Jerome , Charrier Celine , Brion Regis , Lecanda Fernando , Verrecchia Franck , Heymann Dominique , Ellisen Leif W. , Ory Benjamin
Published: March 2023

p63 and p73 regulate SMAD4 and TÎ²RII.
Supplementary Dataset 1 from H3K27 Demethylase JMJD3 Employs the NF-κB and BMP Signaling Pathways to Modulate the Tumor Microenvironment and Promote Melanoma Progression and Metastasis
Authors: Park Woo-Yong , Hong Beom-Jin , Lee Jungsul , Choi Chulhee , Kim Mi-Young
Published: March 2023

GSM numbers of each sample used in clinical sample analysis shown in Fig. 1D and 6G
supplemental Figure 2 from BAFF and APRIL from Activin A–Treated Dendritic Cells Upregulate the Antitumor Efficacy of Dendritic Cells In Vivo
Authors: Shurin Michael R. , Ma Yang , Keskinov Anton A. , Zhao Ruijing , Lokshin Anna , Agassandian Marianna , Shurin Galina V.
Published: March 2023

Activin A does not alter phenotypic maturation of DC.
Table S7 from Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas
Authors: Droog Marjolein , Nevedomskaya Ekaterina , Kim Yongsoo , Severson Tesa , Flach Koen D. , Opdam Mark , Schuurman Karianne , Gradowska Patrycja , Hauptmann Michael , Dackus Gwen , Hollema Harry , Mourits Marian J. , Nederlof Petra , van Boven Hester , Linn Sabine C. , Wessels Lodewyk , van Leeuwen Flora E. , Zwart Wilbert
Published: March 2023

Primer sequences corresponding with supplemental figure S5.
Table S2 from Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas
Authors: Droog Marjolein , Nevedomskaya Ekaterina , Kim Yongsoo , Severson Tesa , Flach Koen D. , Opdam Mark , Schuurman Karianne , Gradowska Patrycja , Hauptmann Michael , Dackus Gwen , Hollema Harry , Mourits Marian J. , Nederlof Petra , van Boven Hester , Linn Sabine C. , Wessels Lodewyk , van Leeuwen Flora E. , Zwart Wilbert
Published: March 2023

Patient characteristics of endometrioid adenocarcinomas used for ChIP-seq.
Table S1 from Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas
Authors: Droog Marjolein , Nevedomskaya Ekaterina , Kim Yongsoo , Severson Tesa , Flach Koen D. , Opdam Mark , Schuurman Karianne , Gradowska Patrycja , Hauptmann Michael , Dackus Gwen , Hollema Harry , Mourits Marian J. , Nederlof Petra , van Boven Hester , Linn Sabine C. , Wessels Lodewyk , van Leeuwen Flora E. , Zwart Wilbert
Published: March 2023

Clinicopathological parameters of patient samples in the TAMARISK-study. MC-UC = interval between breast cancer and endometrial cancer.
Supplementary Table 1 from Activation of Hematopoietic Stem/Progenitor Cells Promotes Immunosuppression Within the Pre–metastatic Niche
Authors: Giles Amber Jin , Reid Caitlin Marie , Evans Justin DeWayne , Murgai Meera , Vicioso Yorleny , Highfill Steven Lorenz , Kasai Miki , Vahdat Linda , Mackall Crystal Lee , Lyden David , Wexler Leonard , Kaplan Rosandra Natasha
Published: March 2023

Cytokines produced in tumor-conditioned media.
Figure S8 from Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas
Authors: Droog Marjolein , Nevedomskaya Ekaterina , Kim Yongsoo , Severson Tesa , Flach Koen D. , Opdam Mark , Schuurman Karianne , Gradowska Patrycja , Hauptmann Michael , Dackus Gwen , Hollema Harry , Mourits Marian J. , Nederlof Petra , van Boven Hester , Linn Sabine C. , Wessels Lodewyk , van Leeuwen Flora E. , Zwart Wilbert
Published: March 2023

Kaplan-Meier survival plot of endometrial cancer patients who were not treated with tamoxifen for their breast cancer, categorized as ERalpha+/FOXA1+, ERalpha+/FOXA1-, ERalpha-/FOXA1+ or ERalpha-/FOXA1-.
Supplementary Figure 3 from Activation of Hematopoietic Stem/Progenitor Cells Promotes Immunosuppression Within the Pre–metastatic Niche
Authors: Giles Amber Jin , Reid Caitlin Marie , Evans Justin DeWayne , Murgai Meera , Vicioso Yorleny , Highfill Steven Lorenz , Kasai Miki , Vahdat Linda , Mackall Crystal Lee , Lyden David , Wexler Leonard , Kaplan Rosandra Natasha
Published: March 2023

Myeloid-derived suppressor cells localize with spontaneous metastases
Supplementary figure legends 1-6 from CK2α' Drives Lung Cancer Metastasis by Targeting BRMS1 Nuclear Export and Degradation
Authors: Liu Yuan , Amin Elianna B. , Mayo Marty W. , Chudgar Neel P. , Bucciarelli Peter R. , Kadota Kyuichi , Adusumilli Prasad S. , Jones David R.
Published: March 2023

Legends for Supplementary Figures S1-S6.
Supplementary Figure Legends from Eradication of Acute Myeloid Leukemia with FLT3 Ligand–Targeted miR-150 Nanoparticles
Authors: Jiang Xi , Bugno Jason , Hu Chao , Yang Yang , Herold Tobias , Qi Jun , Chen Ping , Gurbuxani Sandeep , Arnovitz Stephen , Strong Jennifer , Ferchen Kyle , Ulrich Bryan , Weng Hengyou , Wang Yungui , Huang Hao , Li Shenglai , Neilly Mary Beth , Larson Richard A. , Le Beau Michelle M. , Bohlander Stefan K. , Jin Jie , Li Zejuan , Bradner James E. , Hong Seungpyo , Chen Jianjun
Published: March 2023

Legends for supplemental figures.
Supplementary Table 1 from Maximizing the Efficacy of MAPK-Targeted Treatment in PTENLOF/BRAFMUT Melanoma through PI3K and IGF1R Inhibition
Authors: Herkert Barbara , Kauffmann Audrey , Mollé Sandra , Schnell Christian , Ferrat Thomas , Voshol Hans , Juengert Janina , Erasimus Hélène , Marszalek Grégory , Kazic-Legueux Malika , Billy Eric , Ruddy David , Stump Mark , Guthy Daniel , Ristov Mitko , Calkins Keith , Maira Sauveur-Michel , Sellers William R. , Hofmann Francesco , Hall Michael N. , Brachmann Saskia M.
Published: March 2023

Supplementary information on the selectivity analysis shown in Figure 1A. (A) Representation of classes for all compounds used for the selectivity analysis. (B) Information on all significant hits showing selectivity for PTENLOF cell lines. The table summarizes the main target of the individual compound, the p value indicative of significant selectivity for sensitivity in the PTENLOF compared to the PTENWT cell line panel and the corresponding false discovery rate (FDR), the mean area over the curve (AOC) of the PTENLOF and PTENWT cell line panel, the total number of tested compounds with the same MoA and the rank of these additional compounds.
Supplementary Figure Legends from Mass Spectrometry–Based Metabolomics Identifies Longitudinal Urinary Metabolite Profiles Predictive of Radiation-Induced Cancer
Authors: Cook John A. , Chandramouli Gadisetti V.R. , Anver Miriam R. , Sowers Anastasia L. , Thetford Angela , Krausz Kristopher W. , Gonzalez Frank J. , Mitchell James B. , Patterson Andrew D.
Published: March 2023

Legend for Supplementary Figures S1-S5.
Supplementary Figure 3 from Phosphatase PTP4A3 Promotes Triple-Negative Breast Cancer Growth and Predicts Poor Patient Survival
Authors: den Hollander Petra , Rawls Kathryn , Tsimelzon Anna , Shepherd Jonathan , Mazumdar Abhijit , Hill Jamal , Fuqua Suzanne A.W. , Chang Jenny C. , Osborne C. Kent , Hilsenbeck Susan G. , Mills Gordon B. , Brown Powel H.
Published: March 2023

Supp Fig 3 - A-B) Average tumor growth of MDA MB231 shPTP4A3 and control tumors treated with doxycycline or vehicle. C) mRNA expression of MDA MB231 control tumors and PTP4A3 tumors treated with doxycycline or vehicle. D) Average tumor growth of MDA MB468 control tumors and PTP4A3 tumors treated with doxycycline or vehicle. D) Tumor growth rate is not reduced in tumors from the ER-positive breast cancer cell lines.E). Tumor growth slopes of MCF-7 control tumors and PTP4A3 tumors treated with doxycycline or vehicle.
Supplementary Table 3 from Cystine Deprivation Triggers Programmed Necrosis in VHL-Deficient Renal Cell Carcinomas
Authors: Tang Xiaohu , Wu Jianli , Ding Chien-Kuang , Lu Min , Keenan Melissa M. , Lin Chao-Chieh , Lin Chih-An , Wang Charles C. , George Daniel , Hsu David S. , Chi Jen-Tsan
Published: March 2023

Supplementary Table 3. Differential gene response of RCC4 VHL-deficient and -restored cells upon cystine deprivation
Supplementary Figures S1-S8 from Integrative Genome-Scale Analysis Identifies Epigenetic Mechanisms of Transcriptional Deregulation in Unfavorable Neuroblastomas
Authors: Henrich Kai-Oliver , Bender Sebastian , Saadati Maral , Dreidax Daniel , Gartlgruber Moritz , Shao Chunxuan , Herrmann Carl , Wiesenfarth Manuel , Parzonka Martha , Wehrmann Lea , Fischer Matthias , Duffy David J. , Bell Emma , Torkov Alica , Schmezer Peter , Plass Christoph , Höfer Thomas , Benner Axel , Pfister Stefan M. , Westermann Frank
Published: March 2023

Dendrogram and probability values for hierarchical clustering of 105 neuroblastomas based on genome-wide DNA methylation (S1); Kaplan-Meier estimates of overall survival for DNA methylation subgroups (S2); Genes whose hypermethylation and downregulation are associated with neuroblastoma high-risk disease are induced during neuronal differentiation of neuroblastoma cells (S3); Examples for genes whose hypermethylation and downregulation are associated with neuroblastoma high-risk disease and that are marked by both H3K27me3 and DNA methylation at putative regulatory regions in Be(2)-C cells (S4); MYCN deregulation is associated with activation of PRC2 components (S5); Genes whose hypermethylation and downregulation are associated with high-risk disease are H3K27me3-marked in a MYCN-dependent fashion (S6); Example for genes whose hypermethylation and downregulation are associated with neuroblastoma high-risk disease that significantly lost H3K27me3 and DNA methylation at putative regulatory regions upon treatment with DAC and EPZ-6438 in Be(2)-C cells (S7); Genes whose hypermethylation and downregulation are associated with high-risk disease are preferentially induced upon DAC/TSA treatment (S8).
Supplementary figure 2 from Estrogen Receptor α Promotes Breast Cancer by Reprogramming Choline Metabolism
Authors: Jia Min , Andreassen Trygve , Jensen Lasse , Bathen Tone Frost , Sinha Indranil , Gao Hui , Zhao Chunyan , Haldosen Lars-Arne , Cao Yihai , Girnita Leonard , Moestue Siver Andreas , Dahlman-Wright Karin
Published: March 2023

Metabolic profiles of breast cancer cells in response to estrogen treatment
Supplementary Table S1 from Expansion of a BDCA1+CD14+ Myeloid Cell Population in Melanoma Patients May Attenuate the Efficacy of Dendritic Cell Vaccines
Authors: Bakdash Ghaith , Buschow Sonja I. , Gorris Mark A.J. , Halilovic Altuna , Hato Stanleyson V. , Sköld Annette E. , Schreibelt Gerty , Sittig Simone P. , Torensma Ruurd , Duiveman-de Boer Tjitske , Schröder Christoph , Smits Evelien L. , Figdor Carl G. , de Vries I. Jolanda M.
Published: March 2023

A list of all molecules detected by antibody microarray (Multiplex analysis) with their UniPort entry name.
Supplementary Methods from Hyperthermia Synergizes with Chemotherapy by Inhibiting PARP1-Dependent DNA Replication Arrest
Authors: Schaaf Lea , Schwab Matthias , Ulmer Christoph , Heine Simon , Mürdter Thomas E. , Schmid Jens O. , Sauer Georg , Aulitzky Walter E. , van der Kuip Heiko
Published: March 2023

More detailed information on materials and methods
Supplemental Table 1 from G0S2 Suppresses Oncogenic Transformation by Repressing a MYC-Regulated Transcriptional Program
Authors: Yim Christina Y. , Sekula David J. , Hever-Jardine Mary P. , Liu Xi , Warzecha Joshua M. , Tam Janice , Freemantle Sarah J. , Dmitrovsky Ethan , Spinella Michael J.
Published: March 2023

Genes with altered expression in G0S2 null MEFs as compared to wild-type MEFs
Supplementary Table 4 from Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients
Authors: Osman Abdullah A. , Neskey David M. , Katsonis Panagiotis , Patel Ameeta A. , Ward Alexandra M. , Hsu Teng-Kuei , Hicks Stephanie C. , McDonald Thomas O. , Ow Thomas J. , Alves Marcus Ortega , Pickering Curtis R. , Skinner Heath D. , Zhao Mei , Sturgis Eric M. , Kies Merrill S. , El-Naggar Adel , Perrone Federica , Licitra Lisa , Bossi Paolo , Kimmel Marek , Frederick Mitchell J. , Lichtarge Olivier , Myers Jeffrey N.
Published: March 2023

Supplementary Table 4: Expression of genes associated with loss and gain of function phenotypes for ordinal regression analysis shown in Figure 3B and 3F.
Supplementary Figure 1 from Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients
Authors: Osman Abdullah A. , Neskey David M. , Katsonis Panagiotis , Patel Ameeta A. , Ward Alexandra M. , Hsu Teng-Kuei , Hicks Stephanie C. , McDonald Thomas O. , Ow Thomas J. , Alves Marcus Ortega , Pickering Curtis R. , Skinner Heath D. , Zhao Mei , Sturgis Eric M. , Kies Merrill S. , El-Naggar Adel , Perrone Federica , Licitra Lisa , Bossi Paolo , Kimmel Marek , Frederick Mitchell J. , Lichtarge Olivier , Myers Jeffrey N.
Published: March 2023

Supplementary Figure 1: Expression of p53 target genes is impaired following cisplatin treatment in HNSCC harboring mutant TP53.
Methods and Materials from Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients
Authors: Osman Abdullah A. , Neskey David M. , Katsonis Panagiotis , Patel Ameeta A. , Ward Alexandra M. , Hsu Teng-Kuei , Hicks Stephanie C. , McDonald Thomas O. , Ow Thomas J. , Alves Marcus Ortega , Pickering Curtis R. , Skinner Heath D. , Zhao Mei , Sturgis Eric M. , Kies Merrill S. , El-Naggar Adel , Perrone Federica , Licitra Lisa , Bossi Paolo , Kimmel Marek , Frederick Mitchell J. , Lichtarge Olivier , Myers Jeffrey N.
Published: March 2023

Methods and Materials. Quantitative Reverse Transcription PCR (RT-qPCR) Analyses; mRNA Expression Arrays; Orthotopic Nude Mouse Model of Oral Cavity Cancer; Patient Cohort and TP53 Sequencing;Supplementary References;Footnotes.
Supplementary Figures 1 through 8 from Targeting the WASF3–CYFIP1 Complex Using Stapled Peptides Suppresses Cancer Cell Invasion
Authors: Teng Yong , Bahassan Abdulaziz , Dong Dayong , Hanold Laura E. , Ren Xiaoou , Kennedy Eileen J. , Cowell John K.
Published: March 2023

Supplementary Figure S1. Real-time RT-PCR analysis shows that knockdown of CYFIP1 does not affect WASF1/2/3 transcript levels. Supplementary Figure S2. As a result of the knockdown for any of the three genes (shW1-1 and shW1-2 for WASF1, shW2-1 and shW2-2 for WASF2, shW3 and shW3-2 for WASF3), there was no change in proliferation compared to control knockdown cells (shGFP). Supplementary Figure S3. Expression levels of WASF3 (W3) are unchanged over a twenty-four hour period following treatment of MDA-MB-231 cells with either scrambled (SCR) or WAHM peptides. Supplementary Figure S4. Proliferation of MDA-MB-231 and PC3 cells are not significantly affected by treatment with either of the scrambled (SCR) peptides or WAHM peptides at two different concentrations, compared with vehicle alone treated (DMSO) cells. Supplementary Figure S5. In scratch wound assays (A) cell motility over 24 hours was recorded for four different cell lines; MDA-MB-231 and HS578T (breast cancer cells) and PC3 and DU145 (prostate cancer cells). Supplementary Figure S6. WAHM peptides suppress cell invasion in a dose-dependent manner. Supplementary Figure S7. Loss of phosphoactivated WASF3 in the absence of serum. MDA-MB-231 cells express high levels of WASF3 and PC3 cells express lower levels (input). Supplementary Figure S8. Rac2 is identified as a novel WASF3-interacting protein.
Supplemental Figure 1 from Jak1–STAT3 Signals Are Essential Effectors of the USP6/TRE17 Oncogene in Tumorigenesis
Authors: Quick Laura , Young Robert , Henrich Ian C. , Wang Xiaoke , Asmann Yan W. , Oliveira Andre M. , Chou Margaret M.
Published: March 2023

P-STAT3 IHC
Supplementary Tables S1-S7 from Downregulation of the TGFβ Pseudoreceptor BAMBI in Non–Small Cell Lung Cancer Enhances TGFβ Signaling and Invasion
Authors: Marwitz Sebastian , Depner Sofia , Dvornikov Dmytro , Merkle Ruth , Szczygieł Magdalena , Müller-Decker Karin , Lucarelli Philippe , Wäsch Marvin , Mairbäurl Heimo , Rabe Klaus F. , Kugler Christian , Vollmer Ekkehard , Reck Martin , Scheufele Swetlana , Kröger Maren , Ammerpohl Ole , Siebert Reiner , Goldmann Torsten , Klingmüller Ursula
Published: March 2023

Immunohistochemical analysis of patient material (S1); IHC score for TGF-beta pathway member from matched patient samples (S2); List of TGF-beta regulated genes (S3); List of EMT-related genes (S4); Results of paired t-tests for Microarray (S5); Patient information (S6); List of specific primers used for qRT-PCR gene expression analysis (S7).
Supplementary materials and methods from S-nitrosylation of the Mitochondrial Chaperone TRAP1 Sensitizes Hepatocellular Carcinoma Cells to Inhibitors of Succinate Dehydrogenase
Authors: Rizza Salvatore , Montagna Costanza , Cardaci Simone , Maiani Emiliano , Di Giacomo Giuseppina , Sanchez-Quiles Virginia , Blagoev Blagoy , Rasola Andrea , De Zio Daniela , Stamler Jonathan S. , Cecconi Francesco , Filomeni Giuseppe
Published: March 2023

Supplementary materials and methods