bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S2 from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

Antibody validation panel and distinct intracellular localization by IHC
Supporting Information: Tables from Targeted Degradation of BET Proteins in Triple-Negative Breast Cancer
Authors: Bai Longchuan , Zhou Bing , Yang Chao-Yie , Ji Jiao , McEachern Donna , Przybranowski Sally , Jiang Hui , Hu Jiantao , Xu Fuming , Zhao Yujun , Liu Liu , Fernandez-Salas Ester , Xu Jing , Dou Yali , Wen Bo , Sun Duxin , Meagher Jennifer , Stuckey Jeanne , Hayes Daniel F. , Li Shunqiang , Ellis Matthew J. , Wang Shaomeng
Published: March 2023

This file include supporting tables from SI. Table 1 to Table 6.
Supplementary Figure S1 from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

PACE4 mRNA splicing analysis and primer design
Supporting Information: Methods from Targeted Degradation of BET Proteins in Triple-Negative Breast Cancer
Authors: Bai Longchuan , Zhou Bing , Yang Chao-Yie , Ji Jiao , McEachern Donna , Przybranowski Sally , Jiang Hui , Hu Jiantao , Xu Fuming , Zhao Yujun , Liu Liu , Fernandez-Salas Ester , Xu Jing , Dou Yali , Wen Bo , Sun Duxin , Meagher Jennifer , Stuckey Jeanne , Hayes Daniel F. , Li Shunqiang , Ellis Matthew J. , Wang Shaomeng
Published: March 2023

This file contains supporting information of methods including compound syntheses, molecular modeling, reagents, proteomic & transcriptome profiling and QPCR primers.
Supporting Information: Figures from Targeted Degradation of BET Proteins in Triple-Negative Breast Cancer
Authors: Bai Longchuan , Zhou Bing , Yang Chao-Yie , Ji Jiao , McEachern Donna , Przybranowski Sally , Jiang Hui , Hu Jiantao , Xu Fuming , Zhao Yujun , Liu Liu , Fernandez-Salas Ester , Xu Jing , Dou Yali , Wen Bo , Sun Duxin , Meagher Jennifer , Stuckey Jeanne , Hayes Daniel F. , Li Shunqiang , Ellis Matthew J. , Wang Shaomeng
Published: March 2023

This file includes all supporting figures from SI Fig.1 to SI Fig. 23.
Supplementary figure 7-8 and Table 2 from Prominent Oncogenic Roles of EVI1 in Breast Carcinoma
Authors: Wang Hui , Schaefer Thorsten , Konantz Martina , Braun Martin , Varga Zsuzsanna , Paczulla Anna M. , Reich Selina , Jacob Francis , Perner Sven , Moch Holger , Fehm Tanja N. , Kanz Lothar , Schulze-Osthoff Klaus , Lengerke Claudia
Published: March 2023

Gene expression patterns associated with EVI1 knockdown or overexpression in BC, schematic illustration of potential EVI1 binding sites in the KISS1 promotor and control experiments for ChIP analyses; note included primer sequences.
Supplementary figure 6 from Prominent Oncogenic Roles of EVI1 in Breast Carcinoma
Authors: Wang Hui , Schaefer Thorsten , Konantz Martina , Braun Martin , Varga Zsuzsanna , Paczulla Anna M. , Reich Selina , Jacob Francis , Perner Sven , Moch Holger , Fehm Tanja N. , Kanz Lothar , Schulze-Osthoff Klaus , Lengerke Claudia
Published: March 2023

Effect of EVI1 knockdown on tumorigenicity in vivo and clonogenicity in vitro.
Supplementary figure 5 from Prominent Oncogenic Roles of EVI1 in Breast Carcinoma
Authors: Wang Hui , Schaefer Thorsten , Konantz Martina , Braun Martin , Varga Zsuzsanna , Paczulla Anna M. , Reich Selina , Jacob Francis , Perner Sven , Moch Holger , Fehm Tanja N. , Kanz Lothar , Schulze-Osthoff Klaus , Lengerke Claudia
Published: March 2023

MAPK inhibition modulates BC cell cycle progression and abrogates estrogen-mediated growth rescue in EVI1 knockdown cells.
Supplementary Figures 1-7 from FLT3 and JAK2 Mutations in Acute Myeloid Leukemia Promote Interchromosomal Homologous Recombination and the Potential for Copy Neutral Loss of Heterozygosity
Authors: Gaymes Terry J. , Mohamedali Azim , Eiliazadeh Anthony L. , Darling David , Mufti Ghulam J.
Published: March 2023

Figure 1:Localisation of PZD-GFP-Puro Figure 2:iHR events in FLT3-ITD line, MOLM-13 Figure 3:Localisation of PZD-DR1/DR2-puro Figure 4: HR events in FLT3-ITD cells Figure 5: HR/ROS activity in FLT3-ITD cells Figure 6: SCE in FLT3-ITD cells Figure 7: HR in G0 arrested FLT3-ITD cells
Supplemental Table S3 from The NCI-60 Methylome and Its Integration into CellMiner
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Rajapakse Vinodh , Luna Augustin , Kohn Kurt W. , Stevenson Holly , Wang Yonghong , Heyn Holger , Nogales Vanesa , Moran Sebastian , Goldstein David J. , Doroshow James H. , Meltzer Paul S. , Esteller Manel , Pommier Yves
Published: March 2023

Linear regression analysis of 15,798 genes with with transcript expression, DNA methylation, and DNA copy number data available.
Supplementary Figure 1 and Table 1 from Prominent Oncogenic Roles of EVI1 in Breast Carcinoma
Authors: Wang Hui , Schaefer Thorsten , Konantz Martina , Braun Martin , Varga Zsuzsanna , Paczulla Anna M. , Reich Selina , Jacob Francis , Perner Sven , Moch Holger , Fehm Tanja N. , Kanz Lothar , Schulze-Osthoff Klaus , Lengerke Claudia
Published: March 2023

Analysis of EVI1 expression within a BC patient cohort.
Supplementary Methods and References from A Transposon-based Analysis Reveals RASA1 Is Involved in Triple-Negative Breast Cancer
Authors: Suárez-Cabrera Cristian , Quintana Rita M. , Bravo Ana , Casanova M. Llanos , Page Angustias , Alameda Josefa P. , Paramio Jesús M. , Maroto Alicia , Salamanca Javier , Dupuy Adam J. , Ramírez Angel , Navarro Manuel
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplemental Figure S1 from The NCI-60 Methylome and Its Integration into CellMiner
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Rajapakse Vinodh , Luna Augustin , Kohn Kurt W. , Stevenson Holly , Wang Yonghong , Heyn Holger , Nogales Vanesa , Moran Sebastian , Goldstein David J. , Doroshow James H. , Meltzer Paul S. , Esteller Manel , Pommier Yves
Published: March 2023

Methylation gene probe selection and correlation to expression level.
Supplemental Figure Legends from The NCI-60 Methylome and Its Integration into CellMiner
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Rajapakse Vinodh , Luna Augustin , Kohn Kurt W. , Stevenson Holly , Wang Yonghong , Heyn Holger , Nogales Vanesa , Moran Sebastian , Goldstein David J. , Doroshow James H. , Meltzer Paul S. , Esteller Manel , Pommier Yves
Published: March 2023

Legends for Supplemental Figures S1-S2.
Supplementary Table S2 from The Histone Methyltransferase DOT1L Promotes Neuroblastoma by Regulating Gene Transcription
Authors: Wong Matthew , Tee Andrew E.L. , Milazzo Giorgio , Bell Jessica L. , Poulos Rebecca C. , Atmadibrata Bernard , Sun Yuting , Jing Duohui , Ho Nicholas , Ling Dora , Liu Pei Yan , Zhang Xu Dong , Hüttelmaier Stefan , Wong Jason W.H. , Wang Jenny , Polly Patsie , Perini Giovanni , Scarlett Christopher J. , Liu Tao
Published: March 2023

Supplementary Table S2. Multivariable Cox regression analysis of DOT1L expression in tumor tissues as a factor prognostic for outcome in 476 neuroblastoma patients
Supplemental Methods and Supplemenal Figures 1 through 5 from [18F](2S,4R)4-Fluoroglutamine PET Detects Glutamine Pool Size Changes in Triple-Negative Breast Cancer in Response to Glutaminase Inhibition
Authors: Zhou Rong , Pantel Austin R. , Li Shihong , Lieberman Brian P. , Ploessl Karl , Choi Hoon , Blankemeyer Eric , Lee Hsiaoju , Kung Hank F. , Mach Robert H. , Mankoff David A.
Published: March 2023

Supplemental Methods. SI-Fig 1 HPLC chromatogram of [18F]4F-Glu and [18F]4F-Gln mixture. SI-Fig 2 Comparison of T/B values obtained by two readers. SI-Fig 3 Comparison of T/B ratios obtained from different tumor ROI methods. SI-Fig 4 Comparison of T/B ratios between single and multiROI approach. SI-Fig 5 Estimation of [18F]4F-Gln distribution volume (DV) by kinetic analyses of PET data.
Supplementary Materials and Methods, Figures, Figure Legends - Revised from The Histone Methyltransferase DOT1L Promotes Neuroblastoma by Regulating Gene Transcription
Authors: Wong Matthew , Tee Andrew E.L. , Milazzo Giorgio , Bell Jessica L. , Poulos Rebecca C. , Atmadibrata Bernard , Sun Yuting , Jing Duohui , Ho Nicholas , Ling Dora , Liu Pei Yan , Zhang Xu Dong , Hüttelmaier Stefan , Wong Jason W.H. , Wang Jenny , Polly Patsie , Perini Giovanni , Scarlett Christopher J. , Liu Tao
Published: March 2023

Supplementary Materials and Methods, Figures, Figure Legends. Fig. S1, N-Myc up-regulates ODC1 and E2F2. Fig. S2, DOT1L and N-Myc do not regulate HIF1α and VEGF. Fig. S3, knocking down DOT1L gene expression does not induce neuroblastoma cell death. Fig. S4, knocking down DOT1L reduces ODC1 and E2F2 expression in neuroblastoma tissues in mice. Fig. S5, DOT1L expression correlates with ODC1 and E2F2 expression in human neuroblastoma tissues.
Supplementary Materials and Methods, Supplementary Schemes 1 through 3, Supplementary Figures 1 through 6 and Supplementary Table 1 from A Novel Platinum(II)–Based Bifunctional ADC Linker Benchmarked Using 89Zr-Desferal and Auristatin F–Conjugated Trastuzumab
Authors: Sijbrandi Niels J. , Merkul Eugen , Muns Joey A. , Waalboer Dennis C.J. , Adamzek Kevin , Bolijn Marije , Montserrat Veronica , Somsen Govert W. , Haselberg Rob , Steverink Paul J.G.M. , Houthoff Hendrik-Jan , van Dongen Guus A.M.S.
Published: March 2023

Description of additional methods and procedures used in the study. Description of the synthesis of the drug-linkers used in the study. Supplementary Scheme S1. Synthetic route towards Cl-Lx-DFO-Fe(III), Supplementary Scheme S2. Synthetic route towards Cl-Lx-AF and Supplementary Scheme S3. Synthetic route towards Mal-AF. Supplementary Figure S1 Consistency of Lx-DFO coupling to different mAbs, Supplementary Figure S2. Assessment of Lx-DFO binding throughout the mAb molecule, Supplementary Figure S3. Assessment of Lx-AF binding throughout the mAb molecule, Supplementary Figure S4. In vitro serum stability, Supplementary Figure S5. Kaplan-Meier survival curves and Supplementary Figure S6. Model compound study. Supplementary Table S1. In vitro In vitro cell viability values.
Supplemental figure legends from Emergence of High-Avidity Melan-A–Specific Clonotypes as a Reflection of Anti–PD-1 Clinical Efficacy
Authors: Simon Sylvain , Vignard Virginie , Varey Emilie , Parrot Tiphaine , Knol Anne-Chantal , Khammari Amir , Gervois Nadine , Lang Francois , Dreno Brigitte , Labarriere Nathalie
Published: March 2023

Legends of supplemental figures S1, S2, S3 and S4
Figure S4 from Emergence of High-Avidity Melan-A–Specific Clonotypes as a Reflection of Anti–PD-1 Clinical Efficacy
Authors: Simon Sylvain , Vignard Virginie , Varey Emilie , Parrot Tiphaine , Knol Anne-Chantal , Khammari Amir , Gervois Nadine , Lang Francois , Dreno Brigitte , Labarriere Nathalie
Published: March 2023

Figure S4 shows 41-BB, PD-1, TIGIT, and PD-1/TIGIT expression on all the main Melan-A-specific VÃŸ subtypes, upon TCR activation.
Supplementary figure legends from Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma
Authors: Sadahiro Hirokazu , Kang Kyung-Don , Gibson Justin T. , Minata Mutsuko , Yu Hai , Shi Junfeng , Chhipa Rishi , Chen Zhihong , Lu Songjian , Simoni Yannick , Furuta Takuya , Sabit Hemragul , Zhang Suojun , Bastola Soniya , Yamaguchi Shinobu , Alsheikh Hebaallah , Komarova Svetlana , Wang Jun , Kim Sung-Hak , Hambardzumyan Dolores , Lu Xinghua , Newell Evan W. , DasGupta Biplab , Nakada Mitsutoshi , Lee L. James , Nabors Burt , Norian Lyse A. , Nakano Ichiro
Published: March 2023

Supplementary figure legends and materials and methods
Figure S1 from Emergence of High-Avidity Melan-A–Specific Clonotypes as a Reflection of Anti–PD-1 Clinical Efficacy
Authors: Simon Sylvain , Vignard Virginie , Varey Emilie , Parrot Tiphaine , Knol Anne-Chantal , Khammari Amir , Gervois Nadine , Lang Francois , Dreno Brigitte , Labarriere Nathalie
Published: March 2023

Figure S1 illustrates the robustness and reproducibility of the methodolgy used to sort and amplify Melan-A specific T cells from HLA-A2 PBMC.
Figure S5 from Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma
Authors: Sadahiro Hirokazu , Kang Kyung-Don , Gibson Justin T. , Minata Mutsuko , Yu Hai , Shi Junfeng , Chhipa Rishi , Chen Zhihong , Lu Songjian , Simoni Yannick , Furuta Takuya , Sabit Hemragul , Zhang Suojun , Bastola Soniya , Yamaguchi Shinobu , Alsheikh Hebaallah , Komarova Svetlana , Wang Jun , Kim Sung-Hak , Hambardzumyan Dolores , Lu Xinghua , Newell Evan W. , DasGupta Biplab , Nakada Mitsutoshi , Lee L. James , Nabors Burt , Norian Lyse A. , Nakano Ichiro
Published: March 2023

Supplementary Figure S5. BGB324 treatment decreases PD-L1 expression in tumors.
Supplementary Materials and Methods from Cell-Specific Computational Modeling of the PIM Pathway in Acute Myeloid Leukemia
Authors: Silverbush Dana , Grosskurth Shaun , Wang Dennis , Powell Francoise , Gottgens Berthold , Dry Jonathan , Fisher Jasmin
Published: March 2023

Supplementary Materials and Methods: Cell line treatment Gene expression microarray Whole exome DNA sequencing Theranostics health reverse phase protein array Protein array data transformation for executable network model construction PhosphoScan phosphorylation proteomics Qualitative networks (QN) Construction of a cell-specific AML model
Figure S4 from Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma
Authors: Sadahiro Hirokazu , Kang Kyung-Don , Gibson Justin T. , Minata Mutsuko , Yu Hai , Shi Junfeng , Chhipa Rishi , Chen Zhihong , Lu Songjian , Simoni Yannick , Furuta Takuya , Sabit Hemragul , Zhang Suojun , Bastola Soniya , Yamaguchi Shinobu , Alsheikh Hebaallah , Komarova Svetlana , Wang Jun , Kim Sung-Hak , Hambardzumyan Dolores , Lu Xinghua , Newell Evan W. , DasGupta Biplab , Nakada Mitsutoshi , Lee L. James , Nabors Burt , Norian Lyse A. , Nakano Ichiro
Published: March 2023

Supplementary Figure S4. Identification of T cells subpopulation in GBM dissociated tumor via CyTOF.
Supplementary Figures 1 through 6 and Tables 1 through 5 from Cell-Specific Computational Modeling of the PIM Pathway in Acute Myeloid Leukemia
Authors: Silverbush Dana , Grosskurth Shaun , Wang Dennis , Powell Francoise , Gottgens Berthold , Dry Jonathan , Fisher Jasmin
Published: March 2023

Figure S1. A schematic representation for the method of transforming the log2 linear RPPA values to a 5 point categorical scale suitable for BMA modeling. Figure S2. Differential AML signaling responses to single agent PIM inhibition with AZD1208 and combination with FLT3 inhibitor AC220 Figure S3. Synergic combinations of drugs are sought to increase sensitivity. Figure S4. Susceptibility identified in AZD1208 Resistant Cells. Figure S5. Generation of a Boolean model to predict phosphorylation events, responses to single treatment and synergistic combinations of treatments. Figure S6. Generation of an AND/OR model to predict phosphorylation events, responses to single treatment and synergistic combinations of treatments. Table S1. Categorized RPPA. RPPA results for MOLM16, MV411, KG1A and EOL1 cells, categorized to 5 point scale from 0-4 Table S2. PhosphoScan MassSpec. LC-MS/MS phosphorylation proteomic in MOLM16 cells treated with 2 uM AZD1208 for 3 hours Table S3. QMN RPPA. Quadrant median normalized (QMN) calculated for RPPA protein levels for MOLM16, MV411, KG1A and EOL1 cells. Table S4. RPPA Stats. Calling statistically significant total protein and phosphorylation changes (determined by log2 QMN differences greater than or equal to 0.5 and Wilcoxon Rank Sum Tests p-values less than or equal to 0.1) Table S5. Exome. Whole exome DNA sequencing
Supplementary Figures from CBX8 Exhibits Oncogenic Activity via AKT/β-Catenin Activation in Hepatocellular Carcinoma
Authors: Zhang Chris Zhiyi , Chen Shi-Lu , Wang Chun-Hua , He Yang-Fan , Yang Xia , Xie Dan , Yun Jing-Ping
Published: March 2023

Supplementary Figures contain the following contents: The expression of Chromobox genes in HCC (Figure S1). Data analysis from TCGA database (Figure S2). The expression of CBX8 in several types of tumors (Figure S3). The prognostic value of CBX8 in HCC (Figure S4). The protein expression of CBX8 in HCC (Figure S5). The effect of CBX8 on cell proliferation and migration (Figure S6). Tumor weight in xenograft models (Figure S7). Expression of CBX8 and vimentin in lung metastasis (Figure S8). Analysis of gene microarray (Figure S9). Pathway enrichment analyses of RNA-seq (Figure S10). The effects of β-catenin and MAPK pathways on CBX8-mediated phenotypes (Figure S11). The association of CBX8 and EGR1 in HCC (Figure S12). The effect of PRC1 on CBX8-mediated phenotypes (Figure S13). Effects of EGR1 siRNAs (Figure S14). The requirement of EGR1 for CBX8-mediated malignances (Figure S15). Bioinformatics for miR-365a-3p (Figure S16). The CBX8-mediated regulation of EGR1 and miR-365a-3p (Figure S17). The effects of CBX1, CBX4, CBX7 and CBX8 on HCC cell proliferation and migration (Figure S18). The modulation of CBX8 by miR-410-3p (Figure S19).
Supplementary Figures and Tables from OCTN1 Is a High-Affinity Carrier of Nucleoside Analogues
Authors: Drenberg Christina D. , Gibson Alice A. , Pounds Stanley B. , Shi Lei , Rhinehart Dena P. , Li Lie , Hu Shuiying , Du Guoqing , Nies Anne T. , Schwab Matthias , Pabla Navjotsingh , Blum William , Gruber Tanja A. , Baker Sharyn D. , Sparreboom Alex
Published: March 2023

This file contains supplementary information regarding materials and methods including: chemicals and reagents, early drug uptake, NCI60 correlation analysis, quantitative determination of ergothioneine, and culturing keratinocytes.
Extended Methods, Reagents and Antibodies used, from SKP2 Activation by Thyroid Hormone Receptor β2 Bypasses Rb-Dependent Proliferation in Rb-Deficient Cells
Authors: Xu Xiaoliang L. , Li Zhengke , Liu Aihong , Fan Xianqun , Hu Dan-ning , Qi Dong-Lai , Chitty David W. , Jia Renbing , Qui Jianping , Wang Justin Q. , Sharaf Jake , Zou Jun , Weiss Rebecca , Huang Hongyan , Joseph Walter J. , Ng Lily , Rosen Richard , Shen Binghui , Reid Mark W. , Forrest Douglas , Abramson David H. , Singer Samuel , Cobrinik David , Jhanwar Suresh C.
Published: March 2023

Supplementary Information. This file contains Extended Experimental Procedures including Table S1 (pLKO lentiviral shRNAs), Table S2 (Antibodies used in this study), and Table S3 (qPCR primers).
Table S2 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

DNA array results for control and ZDHHC3 ablated MDA-MB-231 cells
Supplementary Methods from Differential Regulation of the Melanoma Proteome by eIF4A1 and eIF4E
Authors: Joyce Cailin E. , Yanez Adrienne G. , Mori Akihiro , Yoda Akinori , Carroll Johanna S. , Novina Carl D.
Published: March 2023

This file contains Materials and Methods related to supplementary data.
Supplementary Figures from Differential Regulation of the Melanoma Proteome by eIF4A1 and eIF4E
Authors: Joyce Cailin E. , Yanez Adrienne G. , Mori Akihiro , Yoda Akinori , Carroll Johanna S. , Novina Carl D.
Published: March 2023

Supplementary Figures - Figure S1. Representative western blots demonstrating knockdown and overexpression of elF4A1 and elF4# in MSTC and A375. Figure S2. Western blots validating factor-specific and commonly regulated proteins using primary and secondary siRNAs. Figure S3. Knockdown of eIF4A1 or eIF4E for 48h does not increase apoptosis. Figure S4. Survival data for individual cell cycle proteins. Figure S5. Inhibition of the electron transport chain reduces A375 invasion. Figure S6. Cell Cycle and TCA/ETC pathways are less enriched at the mRNA level than at the protein level. Figure S7. mRNA determinants of direct regulation by eIF4A1 and eIF4E are not shared by indirect targets. Figure S8. Increased density of CERT motifs in 5'UTR and 3'UTR of transcripts that are positively regulated by eIF4E. Figure S9. Ribosomal subunit mRNA, not protein, levels are increased with eIF4E depletion. Figure S10. Reduced general translation upon eIF4A1 and eIF4E depletion is rescued by miRNA-target interactions.
Figure S4 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

The figure shows that Conditioned media from DHHC3 ablated cells chemoattracts model M1 macrophages. It also shows that DHHC3 ablation alters TXNIP protein levels.
Figure S3 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

The figure shows that DHHC3 ablation affects oxidative stress and senescence
Figure S2 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

Validation of shRNA knockdown and DHHC3 ablation effects on mammary tumor cell growth and invasion are shown.
Supplementary Methods and References from Long Noncoding RNA LINC00092 Acts in Cancer-Associated Fibroblasts to Drive Glycolysis and Progression of Ovarian Cancer
Authors: Zhao Linjie , Ji Gaili , Le Xiaobing , Wang Chenlu , Xu Lian , Feng Min , Zhang Yaguang , Yang Huiliang , Xuan Yu , Yang Yanfei , Lei Lingzi , Yang Qilian , Lau Wayne Bond , Lau Bonnie , Chen Yi , Deng Xiangbing , Yao Shaohua , Yi Tao , Zhao Xia , Wei Yuquan , Zhou Shengtao
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplemental References.
Supplementary Figures S1-S11 from Long Noncoding RNA LINC00092 Acts in Cancer-Associated Fibroblasts to Drive Glycolysis and Progression of Ovarian Cancer
Authors: Zhao Linjie , Ji Gaili , Le Xiaobing , Wang Chenlu , Xu Lian , Feng Min , Zhang Yaguang , Yang Huiliang , Xuan Yu , Yang Yanfei , Lei Lingzi , Yang Qilian , Lau Wayne Bond , Lau Bonnie , Chen Yi , Deng Xiangbing , Yao Shaohua , Yi Tao , Zhao Xia , Wei Yuquan , Zhou Shengtao
Published: March 2023

CAFs promote peritoneal metastasis of ovarian cancer (S1); CSIOVDB analysis of CXCL14 expression in ovarian cancer (S2); CXCL14 inhibition attenuates ovarian cancer metastasis in vivo (S3); LINC00092 silencing induced increase of cleaved caspase-3 in specimens of ovarian cancer peritoneal metastasis model in nude mice (S4); Enhanced LINC00092 expression in ovarian cancer cells could offset the metastasis-attenuating effects of CXCL14 knockdown in CAFs (S5); RIP experiments were performed using an antibody against EZH2 on extracts from A2780s cell line (S6); Correlation between LINC00092 level and PFKFB2 expression in ovarian cancer (S7); PFKFB2 in the maintenance of metastatic phenotype of ovarian cancer (S8); Enhanced LINC00092 expression in ovarian cancer cells could offset the metastasis-attenuating effects of CXCL14 knockdown in CAFs (S9); The necessity and sufficiency of CAF-secreted CXCL14, LINC00092 in ovarian cancer cells and PFKFB2 in ovarian cancer cells in the process of metastasis formation in ovarian cancer (S10); A schematic model summarizing the proposed mechanistic model of the a positive feedback loop between CXCL14-positive CAFs and ovarian cancer cells favorable for cancer metastasis by manipulating Warburg effect (S11).
Supplementary Tables from Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia
Authors: Ding Ling-Wen , Sun Qiao-Yang , Tan Kar-Tong , Chien Wenwen , Thippeswamy Anand Mayakonda , Eng Juh Yeoh Allen , Kawamata Norihiko , Nagata Yasunobu , Xiao Jin-Fen , Loh Xin-Yi , Lin De-Chen , Garg Manoj , Jiang Yan-Yi , Xu Liang , Lim Su-Lin , Liu Li-Zhen , Madan Vikas , Sanada Masashi , Fernández Lucia Torres , Preethi Hema , Lill Michael , Kantarjian Hagop M. , Kornblau Steven M. , Miyano Satoru , Liang Der-Cherng , Ogawa Seishi , Shih Lee-Yung , Yang Henry , Koeffler H. Phillip
Published: March 2023

Supplementary Table 1. Samples used for whole exome and targeted sequencing. Supplementary Table 2. Clinical information of patients. Supplementary Table 3. 560 Genes screened in the targeted sequencing. Supplementary Table 4. Sequences of shRNA or CRISPR-Cas9 sgRNA used in this study. Supplementary Table 5. Sequences of real-time PCR primers used in this study. Supplementary Table 6. Sequences of primers used for Sanger validation of CRISPR-Cas9 indel. Supplementary Table 7. Mutations of KRAS identified in this study have been found in a variety of cancers. Supplementary Table 8. Mutations of PTPN11 in other cancers occurring in the same location as in our ALL cohort. Supplementary Table 9. Recurrent mutation sites of FLT3 in different cancers. Supplementary Table 10. Cell lines or cancer samples harboring either E1099K or T1150A hotspot mutation of WHSC1. Supplementary Table 11. R1446 mutations of CREBBP recurrently occurred in a variety of cancers. Supplementary Table 12. Mutational hotspot (D1399) of EP300 occurring in other cancers occurring in the same location as in our ALL cohort.Supplementary Table 13. Rare mutations occurring in our ALL cohort (mutated in one individual each), but these mutations have been recurrently documented in the COSMIC cancer mutations database. Supplementary Table 14. Mutations of genes involved in DNA repair pathway in relapse samples.
Supplementary Figure legends from Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia
Authors: Ding Ling-Wen , Sun Qiao-Yang , Tan Kar-Tong , Chien Wenwen , Thippeswamy Anand Mayakonda , Eng Juh Yeoh Allen , Kawamata Norihiko , Nagata Yasunobu , Xiao Jin-Fen , Loh Xin-Yi , Lin De-Chen , Garg Manoj , Jiang Yan-Yi , Xu Liang , Lim Su-Lin , Liu Li-Zhen , Madan Vikas , Sanada Masashi , Fernández Lucia Torres , Preethi Hema , Lill Michael , Kantarjian Hagop M. , Kornblau Steven M. , Miyano Satoru , Liang Der-Cherng , Ogawa Seishi , Shih Lee-Yung , Yang Henry , Koeffler H. Phillip
Published: March 2023

Legends for Supplementary Figures
Supplementary Tables 1 and 2 from ESE3 Inhibits Pancreatic Cancer Metastasis by Upregulating E-Cadherin
Authors: Zhao Tiansuo , Jiang Wenna , Wang Xiuchao , Wang Hongwei , Zheng Chen , Li Yang , Sun Yan , Huang Chongbiao , Han Zhi-bo , Yang Shengyu , Jia Zhiliang , Xie Keping , Ren He , Hao Jihui
Published: March 2023

Supplementary Table 1. Antibodies and primers Supplementary Table 2. Clinicopathologic characteristics of TMA
Supplemenetary Figures 1 through 4 from ESE3 Inhibits Pancreatic Cancer Metastasis by Upregulating E-Cadherin
Authors: Zhao Tiansuo , Jiang Wenna , Wang Xiuchao , Wang Hongwei , Zheng Chen , Li Yang , Sun Yan , Huang Chongbiao , Han Zhi-bo , Yang Shengyu , Jia Zhiliang , Xie Keping , Ren He , Hao Jihui
Published: March 2023

Figure S1. Effects of Methylation-reducing agent and ESE3 on pancreatic cancer growth and migration in vitro. Figure S2. The basal expression of ESE3 in four PDAC cell lines by Western blotting experiment. Figure S3. Regulation of EMT marker expression by ESE3. Figure S4. Impact of altered expression of ESE3 on pancreatic tumor growth in nude mice.
Supplementary Information from Prolactin Receptor–Mediated Internalization of Imaging Agents Detects Epithelial Ovarian Cancer with Enhanced Sensitivity and Specificity
Authors: Sundaram Karthik M. , Zhang Yilin , Mitra Anirban K. , Kouadio Jean-Louis K. , Gwin Katja , Kossiakoff Anthony A. , Roman Brian B. , Lengyel Ernst , Piccirilli Joseph A.
Published: March 2023

The supplemental file contains additional data from the analysis of the tissue microarray and additional experimental results related to conjugation, cell culture experiments, and animal imaging studies
Supplementary Fig 1 from Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia
Authors: Ding Ling-Wen , Sun Qiao-Yang , Tan Kar-Tong , Chien Wenwen , Thippeswamy Anand Mayakonda , Eng Juh Yeoh Allen , Kawamata Norihiko , Nagata Yasunobu , Xiao Jin-Fen , Loh Xin-Yi , Lin De-Chen , Garg Manoj , Jiang Yan-Yi , Xu Liang , Lim Su-Lin , Liu Li-Zhen , Madan Vikas , Sanada Masashi , Fernández Lucia Torres , Preethi Hema , Lill Michael , Kantarjian Hagop M. , Kornblau Steven M. , Miyano Satoru , Liang Der-Cherng , Ogawa Seishi , Shih Lee-Yung , Yang Henry , Koeffler H. Phillip
Published: March 2023

Supplementary Fig. 1. Mutational spectrum of pediatric ALL.
Supplemental Figure S3 from RelB Expression Determines the Differential Effects of Ascorbic Acid in Normal and Cancer Cells
Authors: Wei Xiaowei , Xu Yong , Xu Fang Fang , Chaiswing Luksana , Schnell David , Noel Teresa , Wang Chi , Chen Jinfei , St. Clair Daret K. , St. Clair William H.
Published: March 2023

The subgroups of the animal experiment were analyzed using Kaplan-Meier survival curves with the log-rank test.
Supplemental Figure S2 from RelB Expression Determines the Differential Effects of Ascorbic Acid in Normal and Cancer Cells
Authors: Wei Xiaowei , Xu Yong , Xu Fang Fang , Chaiswing Luksana , Schnell David , Noel Teresa , Wang Chi , Chen Jinfei , St. Clair Daret K. , St. Clair William H.
Published: March 2023

After treatment with AA, the expression of RelB, Bcl-xL, and Bax in PC3 and PZ cells was quantified by western blots by RT-PCR.
Supplemental Figure S1 from RelB Expression Determines the Differential Effects of Ascorbic Acid in Normal and Cancer Cells
Authors: Wei Xiaowei , Xu Yong , Xu Fang Fang , Chaiswing Luksana , Schnell David , Noel Teresa , Wang Chi , Chen Jinfei , St. Clair Daret K. , St. Clair William H.
Published: March 2023

The effect of PEG-CAT on radiosensitization of AA in PC3 cells was determined by MTT assay.
Supplementary Table 2 from Systematic In Vivo Inactivation of Chromatin-Regulating Enzymes Identifies Setd2 as a Potent Tumor Suppressor in Lung Adenocarcinoma
Authors: Walter David M. , Venancio Olivia S. , Buza Elizabeth L. , Tobias John W. , Deshpande Charuhas , Gudiel A. Andrea , Kim-Kiselak Caroline , Cicchini Michelle , Yates Travis J. , Feldser David M.
Published: March 2023

Supplementary Table 2: Ingenuity Pathway Analysis results for Setd2 vs. GFP tumors.
Supplementary Table S4 from Constitutive NOTCH3 Signaling Promotes the Growth of Basal Breast Cancers
Authors: Choy Lisa , Hagenbeek Thijs J. , Solon Margaret , French Dorothy , Finkle David , Shelton Amy , Venook Rayna , Brauer Matthew J. , Siebel Christian W.
Published: March 2023

Gene lists related to Fig. 6E. Y axis = DAPT vs. DMSO. (Y-axis only; X-axis genes same as in Fig. 6D).
Supplementary Figures 1-10. from Systematic In Vivo Inactivation of Chromatin-Regulating Enzymes Identifies Setd2 as a Potent Tumor Suppressor in Lung Adenocarcinoma
Authors: Walter David M. , Venancio Olivia S. , Buza Elizabeth L. , Tobias John W. , Deshpande Charuhas , Gudiel A. Andrea , Kim-Kiselak Caroline , Cicchini Michelle , Yates Travis J. , Feldser David M.
Published: March 2023

Supplementary Figure 1: Locations and types of chromatin regulator mutations found in human lung adenocarcinomas. Supplementary Figure 2: Identification of high efficiency Brg1, Arid1a and Setd2 sgRNAs using a fluorescent reporter-based sensor assay. Supplementary Figure 3: Examples of tumors with mixed expression of Brg1, Arid1a and H3K36me3. Supplementary Figure 4: Proliferative and apoptotic rates of KrasG12D/+ tumors targeted with sgRNAs against GFP, Brg1, Arid1a, or Setd2. Supplementary Figure 5: Identification of chromatin regulator expression status and measurement of tumor cell purity in RNA-Seq samples. Supplementary Figure 6: Ingenuity Pathway Analysis of top 10 enriched canonical pathways in Arid1a and Setd2 deficient tumors. Supplementary Figure 7: Proliferative and apoptotic rates of KrasG12D/+;p53-/- tumors targeted with sgRNAs against GFP, Brg1, Arid1a, or Setd2. Supplementary Figure 8: Analysis of markers of tumor cell identity in early and late KrasG12D/+;p53-/- tumors. Supplementary Figure 9: Representative images of tumors from KrasG12D/+;p53flox/flox mice, and the distinct morphology of Setd2 deficient tumors. Supplementary Figure 10: Analysis of multinucleate giant cells, aberrant mitoses and DNA damage in Setd2 deficient tumors.
Supplementary Table S2 from Constitutive NOTCH3 Signaling Promotes the Growth of Basal Breast Cancers
Authors: Choy Lisa , Hagenbeek Thijs J. , Solon Margaret , French Dorothy , Finkle David , Shelton Amy , Venook Rayna , Brauer Matthew J. , Siebel Christian W.
Published: March 2023

Gene lists related to Fig. 6C. X axis = anti-N3.A13 vs. DAPT, Y axis = anti-gD vs. DAPT.
Supplementary Figure Legends from Systematic In Vivo Inactivation of Chromatin-Regulating Enzymes Identifies Setd2 as a Potent Tumor Suppressor in Lung Adenocarcinoma
Authors: Walter David M. , Venancio Olivia S. , Buza Elizabeth L. , Tobias John W. , Deshpande Charuhas , Gudiel A. Andrea , Kim-Kiselak Caroline , Cicchini Michelle , Yates Travis J. , Feldser David M.
Published: March 2023

Figure legends for supplementary figures.
Supplementary Figures 1-3 from Constitutive NOTCH3 Signaling Promotes the Growth of Basal Breast Cancers
Authors: Choy Lisa , Hagenbeek Thijs J. , Solon Margaret , French Dorothy , Finkle David , Shelton Amy , Venook Rayna , Brauer Matthew J. , Siebel Christian W.
Published: March 2023

Supplementary Figures 1-3 Supplementary Figure 1. NOTCH3 schematic (not to scale) showing residues for the furin (S1), metalloprotease (S2) and gamma-secretase (S3) cleavages. HD, heterodimerization; TM, transmembrane. Human S3 cleavage regions for NOTCH1 (P46531), NOTCH2 (Q04721), and NOTCH3 (Q9UM47) are aligned with the antigen sequence used to generate anti-V1662. Supplementary Figure 2. NOTCH3, but not other receptors or JAG1, modulates basal cell growth in soft agar. As in Fig. 4 for (A) MDA-MB-468 or (B) HCC70 cells. Supplementary Figure 3. NOTCH3 agonism stimulates tumor growth, whereas NOTCH3 antagonism slows tumor growth in vivo. As in Fig. 5B using HCC70 cells.
Supplementary Figure S1-7 from Radiation Resistance in KRAS-Mutated Lung Cancer Is Enabled by Stem-like Properties Mediated by an Osteopontin–EGFR Pathway
Authors: Wang Meng , Han Jing , Marcar Lynnette , Black Josh , Liu Qi , Li Xiangyong , Nagulapalli Kshithija , Sequist Lecia V. , Mak Raymond H. , Benes Cyril H. , Hong Theodore S. , Gurtner Kristin , Krause Mechthild , Baumann Michael , Kang Jing X. , Whetstine Johnathan R. , Willers Henning
Published: March 2023

Fig. S1. Importance of mutant KRAS status for cellular and clinical radioresistance. Fig. S2. Characterization of the CSC-like features of KRAS mutant NSCLC cells. Fig. S3. Pathway analysis of differentially expressed genes in KRAS mutant vs wild-type NCI-H1703 cells. Fig. S4. Factors influencing the radioresistance of NSCLC cell lines with mutant KRAS. Fig. S5. Role of SPP1/osteopontin expression in KRAS mutant and wild-type NSCLC cell lines and tumors. Fig. S6. Characterization of MLCC alterations in KRAS mutant NSCLC. Fig. S7. BIM regulation and importance of p53/p16 alterations in KRASmut NSCLC.
Legends to Supplementary Figures from Radiation Resistance in KRAS-Mutated Lung Cancer Is Enabled by Stem-like Properties Mediated by an Osteopontin–EGFR Pathway
Authors: Wang Meng , Han Jing , Marcar Lynnette , Black Josh , Liu Qi , Li Xiangyong , Nagulapalli Kshithija , Sequist Lecia V. , Mak Raymond H. , Benes Cyril H. , Hong Theodore S. , Gurtner Kristin , Krause Mechthild , Baumann Michael , Kang Jing X. , Whetstine Johnathan R. , Willers Henning
Published: March 2023

Fig. S1. Importance of mutant KRAS status for cellular and clinical radioresistance. Fig. S2. Characterization of the CSC-like features of KRAS mutant NSCLC cells. Fig. S3. Pathway analysis of differentially expressed genes in KRAS mutant vs wild-type NCI-H1703 cells. Fig. S4. Factors influencing the radioresistance of NSCLC cell lines with mutant KRAS. Fig. S5. Role of SPP1/osteopontin expression in KRAS mutant and wild-type NSCLC cell lines and tumors. Fig. S6. Characterization of MLCC alterations in KRAS mutant NSCLC. Fig. S7. BIM regulation and importance of p53/p16 alterations in KRASmut NSCLC.
Supplementary Tables S1-S5 from Bone Marrow Adipocytes Facilitate Fatty Acid Oxidation Activating AMPK and a Transcriptional Network Supporting Survival of Acute Monocytic Leukemia Cells
Authors: Tabe Yoko , Yamamoto Shinichi , Saitoh Kaori , Sekihara Kazumasa , Monma Norikazu , Ikeo Kazuho , Mogushi Kaoru , Shikami Masato , Ruvolo Vivian , Ishizawa Jo , Hail Numsen , Kazuno Saiko , Igarashi Mamoru , Matsushita Hiromichi , Yamanaka Yasunari , Arai Hajime , Nagaoka Isao , Miida Takashi , Hayashizaki Yoshihide , Konopleva Marina , Andreeff Michael
Published: March 2023

Clinical characteristics of AMoL patients (S1); Quantitative expression of metabolites in U937 cells after BM-adipocyte co-culture and etomoxir treatment (S2); Genes whose expression was altered in U937 cells co-cultured with MSCs or BM-adipocytes and treated with etomoxir (S3); Genes whose expression was altered most often in U937 and THP1 cells by BM-adipocyte co-culture and treatment with etomoxir (S4); Proteins whose expression was altered in U937 cells by BM-adipocyte co-culture (S5).
Figure S5-S6 from New Generation Nanomedicines Constructed from Self-Assembling Small-Molecule Prodrugs Alleviate Cancer Drug Toxicity
Authors: Wang Hangxiang , Lu Zhongjie , Wang Lijiang , Guo Tingting , Wu Jiaping , Wan Jianqin , Zhou Liqian , Li Hui , Li Zhen , Jiang Donghai , Song Penghong , Xie Haiyang , Zhou Lin , Xu Xiao , Zheng Shusen
Published: March 2023

In vivo drug plasma concentration-time profile and drug tissue biodistribution
Figure S4 from New Generation Nanomedicines Constructed from Self-Assembling Small-Molecule Prodrugs Alleviate Cancer Drug Toxicity
Authors: Wang Hangxiang , Lu Zhongjie , Wang Lijiang , Guo Tingting , Wu Jiaping , Wan Jianqin , Zhou Liqian , Li Hui , Li Zhen , Jiang Donghai , Song Penghong , Xie Haiyang , Zhou Lin , Xu Xiao , Zheng Shusen
Published: March 2023

Systemic toxicity of pSNMs in healthy ICR mice
Supplementary Procedures from Wnt5a Drives an Invasive Phenotype in Human Glioblastoma Stem-like Cells
Authors: Binda Elena , Visioli Alberto , Giani Fabrizio , Trivieri Nadia , Palumbo Orazio , Restelli Silvia , Dezi Fabio , Mazza Tommaso , Fusilli Caterina , Legnani Federico , Carella Massimo , Di Meco Francesco , Duggal Rohit , Vescovi Angelo L.
Published: March 2023

Supplementary Procedures
Figure S2 from New Generation Nanomedicines Constructed from Self-Assembling Small-Molecule Prodrugs Alleviate Cancer Drug Toxicity
Authors: Wang Hangxiang , Lu Zhongjie , Wang Lijiang , Guo Tingting , Wu Jiaping , Wan Jianqin , Zhou Liqian , Li Hui , Li Zhen , Jiang Donghai , Song Penghong , Xie Haiyang , Zhou Lin , Xu Xiao , Zheng Shusen
Published: March 2023

In vitro cytotoxicity of nanodrugs against human breast cancer MDA-MB-231 cells and human colorectal carcinoma LoVo cells
Supplementary Figures from Wnt5a Drives an Invasive Phenotype in Human Glioblastoma Stem-like Cells
Authors: Binda Elena , Visioli Alberto , Giani Fabrizio , Trivieri Nadia , Palumbo Orazio , Restelli Silvia , Dezi Fabio , Mazza Tommaso , Fusilli Caterina , Legnani Federico , Carella Massimo , Di Meco Francesco , Duggal Rohit , Vescovi Angelo L.
Published: March 2023

Suppl Fig S1: Levels of Wnt5a expression in brain tumors correlate to aggressiveness or outcome; Suppl Fig S2: Wnt5a overexpression sustains TPCs invasive capability; Suppl Fig S3: Elevated Wnt5a expression promotes migratory capability in otherwise poorly motile U87MG, both in vitro and in vivo; Suppl Fig S4: Pathways enrichment of invasive TPCs progeny based on Wnt5a levels; Suppl Fig S5: Mesenchymal hGBM TPCs are endowed with enhanced dispersal ability to distribute widely in the brain as compared to classical TPCs; Suppl Fig S6: Hypothetical mechanism of Wnt5a regulation that confers the infiltratory phenotype in hGBM TPCs;
Supplementary methods from PI-273, a Substrate-Competitive, Specific Small-Molecule Inhibitor of PI4KIIα, Inhibits the Growth of Breast Cancer Cells
Authors: Li Jiangmei , Gao Zhen , Zhao Dan , Zhang Lunfeng , Qiao Xinhua , Zhao Yingying , Ding Hong , Zhang Panpan , Lu Junyan , Liu Jia , Jiang Hualiang , Luo Cheng , Chen Chang
Published: March 2023

informations for experiments
Supplemental Figure 3 from Selective Reversible Inhibition of Autophagy in Hypoxic Breast Cancer Cells Promotes Pulmonary Metastasis
Authors: Dower Christopher M. , Bhat Neema , Wang Edward W. , Wang Hong-Gang
Published: March 2023

Inhibition of autophagy promotes cell migration and fibronectin deposition
CTLA4 is epressed in human B cell lymphoma and multiple myeloma cells from CTLA4 Promotes Tyk2-STAT3–Dependent B-cell Oncogenicity
Authors: Herrmann Andreas , Lahtz Christoph , Nagao Toshikage , Song Joo Y. , Chan Wing C. , Lee Heehyoung , Yue Chanyu , Look Thomas , Mülfarth Ronja , Li Wenzhao , Jenkins Kurt , Williams John , Budde Lihua E. , Forman Stephen , Kwak Larry , Blankenstein Thomas , Yu Hua
Published: March 2023

Suppl. Fig. S1 showing CTLA4 expression and CD86 cellular internalization by human BCL and human MM cells acquired by flow cytometry.
Supplementary Materials and Methods from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks
Authors: Kelley Dylan Z. , Flam Emily L. , Izumchenko Evgeny , Danilova Ludmila V. , Wulf Hildegard A. , Guo Theresa , Singman Dzov A. , Afsari Bahman , Skaist Alyza M. , Considine Michael , Welch Jane A. , Stavrovskaya Elena , Bishop Justin A. , Westra William H. , Khan Zubair , Koch Wayne M. , Sidransky David , Wheelan Sarah J. , Califano Joseph A. , Favorov Alexander V. , Fertig Elana J. , Gaykalova Daria A.
Published: March 2023

Description of Supplemental Materials and Methods
CTLA4 expression by tumor associated B cells from CTLA4 Promotes Tyk2-STAT3–Dependent B-cell Oncogenicity
Authors: Herrmann Andreas , Lahtz Christoph , Nagao Toshikage , Song Joo Y. , Chan Wing C. , Lee Heehyoung , Yue Chanyu , Look Thomas , Mülfarth Ronja , Li Wenzhao , Jenkins Kurt , Williams John , Budde Lihua E. , Forman Stephen , Kwak Larry , Blankenstein Thomas , Yu Hua
Published: March 2023

Suppl. Fig. S3 showing CTLA4 expression by tumor associated CD19 B cells
Supplemental File 2 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks
Authors: Kelley Dylan Z. , Flam Emily L. , Izumchenko Evgeny , Danilova Ludmila V. , Wulf Hildegard A. , Guo Theresa , Singman Dzov A. , Afsari Bahman , Skaist Alyza M. , Considine Michael , Welch Jane A. , Stavrovskaya Elena , Bishop Justin A. , Westra William H. , Khan Zubair , Koch Wayne M. , Sidransky David , Wheelan Sarah J. , Califano Joseph A. , Favorov Alexander V. , Fertig Elana J. , Gaykalova Daria A.
Published: March 2023

The script for ChIP-Seq and RNA-Seq data integration
Supplementary Materials and Methods, Supplementary Figures 1 through 6, and Supplementary Tables 1 through 8 from Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells
Authors: Neubert Natalie J. , Tillé Laure , Barras David , Soneson Charlotte , Baumgaertner Petra , Rimoldi Donata , Gfeller David , Delorenzi Mauro , Fuertes Marraco Silvia A. , Speiser Daniel E.
Published: March 2023

Supplementary Materials and Methods. Supplementary Figures: Fig. S1. Sorting strategy and purity. Fig. S2. Comparison of the two batches of NanoString experiments shown in Fig. 1 and Fig. 4. Fig. S3. Melanoma cells respond to CTL attack with gene expression changes. Fig. S4. CTL-induced gene expression changes are driven by IFNgamma and TNFalpha. Fig. S5. Representative histograms of protein expression regulated by cytokines. Fig. S6. Characterization of untreated and CTL-exposed melanocytes. Supplementary Tables: Table S1. Source of the 17 melanoma cell lines used in this study. Table S2. Antibodies (including isotype-matched controls) used to assess protein expression by flow cytometry. Table S3. Differential expression of genes that are part of the enriched gene sets in Supplementary Figs. S3C and S3E. Table S4. Selection of genes for 181-gene panel. Table S5. Differential expression of genes in melanoma cell lines after 24h treatment. Table S6. Protein expression of melanoma cells after 48h culture in presence or absence of IFNgamma and TNFalpha. Table S7. Differential expression of genes in melanocyte cell lines after 24h treatment. Table S8. Genes that have statistically different fold-changes (MelanA-specific CTLs/untreated) between melanoma cell lines and melanocyte lines. Supplementary References.
Legends for supplemental figures and table from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks
Authors: Kelley Dylan Z. , Flam Emily L. , Izumchenko Evgeny , Danilova Ludmila V. , Wulf Hildegard A. , Guo Theresa , Singman Dzov A. , Afsari Bahman , Skaist Alyza M. , Considine Michael , Welch Jane A. , Stavrovskaya Elena , Bishop Justin A. , Westra William H. , Khan Zubair , Koch Wayne M. , Sidransky David , Wheelan Sarah J. , Califano Joseph A. , Favorov Alexander V. , Fertig Elana J. , Gaykalova Daria A.
Published: March 2023

Legends for supplemental figures S1-S15 and tables S1-S11
Table S1 from Blocking Myristoylation of Src Inhibits Its Kinase Activity and Suppresses Prostate Cancer Progression
Authors: Kim Sungjin , Alsaidan Omar Awad , Goodwin Octavia , Li Qianjin , Sulejmani Essilvo , Han Zhen , Bai Aiping , Albers Thomas , Beharry Zanna , Zheng Y. George , Norris James S. , Szulc Zdzislaw M. , Bielawska Alicja , Lebedyeva Iryna , Pegan Scott D. , Cai Houjian
Published: March 2023

Primer sequences used for cloning Src/Fyn mutants, shRNAs, and RT-PCR
Figures S1-S6, Table S1-S3 from Sustained Adrenergic Signaling Promotes Intratumoral Innervation through BDNF Induction
Authors: Allen Julie K. , Armaiz-Pena Guillermo N. , Nagaraja Archana S. , Sadaoui Nouara C. , Ortiz Tatiana , Dood Robert , Ozcan Merve , Herder Danielle M. , Haemmerle Monika , Gharpure Kshipra M. , Rupaimoole Rajesha , Previs Rebecca A. , Wu Sherry Y. , Pradeep Sunila , Xu Xiaoyun , Han Hee Dong , Zand Behrouz , Dalton Heather J. , Taylor Morgan , Hu Wei , Bottsford-Miller Justin , Moreno-Smith Myrthala , Kang Yu , Mangala Lingegowda S. , Rodriguez-Aguayo Cristian , Sehgal Vasudha , Spaeth Erika L. , Ram Prahlad T. , Wong Stephen T.C. , Marini Frank C. , Lopez-Berestein Gabriel , Cole Steve W. , Lutgendorf Susan K. , De Biasi Mariella , Sood Anil K.
Published: March 2023

Fig. S1. Sustained adrenergic signaling increases nerve counts in tumors. Fig. S2. Characterization of tumoral innervation. Fig. S3. NE induces BDNF expression. Fig. S4. NE-induced BDNF expression is mediated by ADRB3/Epac/Jnk. Fig. S5. BDNF increases nerve counts. Fig. S6. Adrenergic-mediated mTrkB activation leads to increased in vivo tumor nodule counts. Table S1. Alteration in pathways associated with neuronal growth and function after NE treatment (HeyA8 and SKOV3ip1 cells). Table S2. Association of Clinicopathologic variables with BDNF protein expression. Table S3. Association of Clinicopathologic variables with Nerve Counts.
Supplemental Methods and Figure Legends from Blocking Myristoylation of Src Inhibits Its Kinase Activity and Suppresses Prostate Cancer Progression
Authors: Kim Sungjin , Alsaidan Omar Awad , Goodwin Octavia , Li Qianjin , Sulejmani Essilvo , Han Zhen , Bai Aiping , Albers Thomas , Beharry Zanna , Zheng Y. George , Norris James S. , Szulc Zdzislaw M. , Bielawska Alicja , Lebedyeva Iryna , Pegan Scott D. , Cai Houjian
Published: March 2023

Supplemental Methods and Figure legends