bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods, Figures 1 - 3, and Table 1 from Noninvasive Quantification of Solid Tumor Microstructure Using VERDICT MRI
Authors: Panagiotaki Eletheria , Walker-Samuel Simon , Siow Bernard , Johnson S. Peter , Rajkumar Vineeth , Pedley R. Barbara , Lythgoe Mark F. , Alexander Daniel C.
Published: March 2023

PDF file - 1763KB, This supplemental material includes S1), a figure with the fit of the VERDICT model to the diffusion data from all the samples, S2), a figure demonstrating the quality of the diffusion images and the signal attenuation from an example sample of each cell line, TS1) a table with the orientation angle estimates of the VERDICT model, S3) a figure to demonstrate that VERDICT performs better than a tensor model, a two-tensor model and an isotropic version of the VERDICT model. We also include details of all the histological procedures as well as extra information about the choice of the vascular compartment in the VERDICT model.
Supplementary Figure 5 from The CXCL7/CXCR1/2 Axis Is a Key Driver in the Growth of Clear Cell Renal Cell Carcinoma
Authors: Grépin Renaud , Guyot Mélanie , Giuliano Sandy , Boncompagni Marina , Ambrosetti Damien , Chamorey Emmanuel , Scoazec Jean-Yves , Negrier Sylvie , Simonnet Hélène , Pagès Gilles
Published: March 2023

PDF file - 41K, SB225002 decreased the production of pro-angiogenic CXCL cytokines.
Supplementary Figure 1 from miR-30-5p Functions as a Tumor Suppressor and Novel Therapeutic Tool by Targeting the Oncogenic Wnt/β-Catenin/BCL9 Pathway
Authors: Zhao Jian-Jun , Lin Jianhong , Zhu Di , Wang Xujun , Brooks Daniel , Chen Ming , Chu Zhang-Bo , Takada Kohichi , Ciccarelli Bryan , Admin Samir , Tao Jianguo , Tai Yu-Tzu , Treon Steven , Pinkus Geraldine , Kuo Winston Patrick , Hideshima Teru , Bouxsein Mary , Munshi Nikhil , Anderson Kenneth , Carrasco Ruben
Published: March 2023

PDF file - 2673KB, MiR-30s target BCL9 in MM cells.
Data Supplement from High-Throughput Time-Resolved FRET Reveals Akt/PKB Activation as a Poor Prognostic Marker in Breast Cancer
Authors: Veeriah Selvaraju , Leboucher Pierre , de Naurois Julien , Jethwa Nirmal , Nye Emma , Bunting Tamara , Stone Richard , Stamp Gordon , Calleja Véronique , Jeffrey Stefanie S. , Parker Peter J. , Larijani Banafshé
Published: March 2023

Supplementary Figure 4: Quantification of endogenous pAkt (pT308) using whole IgG secondary antibodies in fixed FFPE human breast tumor by amplified FRET assay.
Supplementary Table S1 from ERBB3-Independent Activation of the PI3K Pathway in EGFR-Mutant Lung Adenocarcinomas
Authors: Song Xiaoling , Fan Pang-Dian , Bantikassegn Amlak , Guha Udayan , Threadgill David W. , Varmus Harold , Politi Katerina
Published: March 2023

Supplementary Table S1. List of mice treated with erlotinib.
Supplementary Figure 1 from The DREAM Complex Mediates GIST Cell Quiescence and Is a Novel Therapeutic Target to Enhance Imatinib-Induced Apoptosis
Authors: Boichuk Sergei , Parry Joshua A. , Makielski Kathleen R. , Litovchick Larisa , Baron Julianne L. , Zewe James P. , Wozniak Agnieszka , Mehalek Keith R. , Korzeniewski Nina , Seneviratne Danushka S. , Schöffski Patrick , Debiec-Rychter Maria , DeCaprio James A. , Duensing Anette
Published: March 2023

PDF file - 1731K, Supplemental Figure 1. SKP2 expression levels do not predict p27Kip1 levels after imatinib therapy.
Supplementary Methods, Figures 1 -2 from Identification of ATR–Chk1 Pathway Inhibitors That Selectively Target p53-Deficient Cells without Directly Suppressing ATR Catalytic Activity
Authors: Kawasumi Masaoki , Bradner James E. , Tolliday Nicola , Thibodeau Renee , Sloan Heather , Brummond Kay M. , Nghiem Paul
Published: March 2023

Supplementary Materials and Methods. Supplementary Figure S1: Cell viability in various concentrations of DNA-damaging agents and novel ATR pathway inhibitors. Supplementary Figure S2: Effects of novel and established ATR pathway inhibitors on Chk1 phosphorylation induced by hydroxyurea or cisplatin as assessed by flow cytometry.
Supplementary Figure S6 from Myostatin Gene Inactivation Prevents Skeletal Muscle Wasting in Cancer
Authors: Gallot Yann S. , Durieux Anne-Cécile , Castells Josiane , Desgeorges Marine M. , Vernus Barbara , Plantureux Léa , Rémond Didier , Jahnke Vanessa E. , Lefai Etienne , Dardevet Dominique , Nemoz Georges , Schaeffer Laurent , Bonnieu Anne , Freyssenet Damien G.
Published: March 2023

Serum levels of interferon (IFN)-γ, interleukin (IL)-1β, IL-6 and tumor necrosis (TNF)-α in wild-type (n=7) and Mstn-/- mice (n=8).
Supplementary Table 2 from BRG1/SMARCA4 Inactivation Promotes Non–Small Cell Lung Cancer Aggressiveness by Altering Chromatin Organization
Authors: Orvis Tess , Hepperla Austin , Walter Vonn , Song Shujie , Simon Jeremy , Parker Joel , Wilkerson Matthew D. , Desai Nisarg , Major Michael B. , Hayes D. Neil , Davis Ian J. , Weissman Bernard
Published: March 2023

Supplementary Table 2. Differentially expressed genes were identified between BRG1 mutant and BRG1 wild-type NSCLC cell lines, as described in Materials and Methods. Using an FDR threshold of .025, a total of 135 genes were down-regulated in the BRG1 mutant cell lines.
Supplementary Figure 5 from BRG1/SMARCA4 Inactivation Promotes Non–Small Cell Lung Cancer Aggressiveness by Altering Chromatin Organization
Authors: Orvis Tess , Hepperla Austin , Walter Vonn , Song Shujie , Simon Jeremy , Parker Joel , Wilkerson Matthew D. , Desai Nisarg , Major Michael B. , Hayes D. Neil , Davis Ian J. , Weissman Bernard
Published: March 2023

Supplementary Figure 5. This figure shows nucleosome positioning around 2 genes downregulated after Brg1 KD.
Data Supplement from IL4 Receptor ILR4α Regulates Metastatic Colonization by Mammary Tumors through Multiple Signaling Pathways
Authors: Venmar Katherine T. , Carter Kathy J. , Hwang Daniel G. , Dozier E. Ashley , Fingleton Barbara
Published: March 2023

Supplemental Figure 3: Immunohistochemical staining of immune infiltrates in R221a lung metastases
Data Supplement from A Novel Wnt Regulatory Axis in Endometrioid Endometrial Cancer
Authors: Zhao Yu , Yang Yihua , Trovik Jone , Sun Kun , Zhou Liang , Jiang Peiyong , Lau Tat-San , Hoivik Erling A. , Salvesen Helga B. , Sun Hao , Wang Huating
Published: March 2023

Supplemental Dataset. RNAseq analysis results of PCDH10 overexpressing HEC-1-B cells.
Data Supplement from Afatinib Enhances the Efficacy of Conventional Chemotherapeutic Agents by Eradicating Cancer Stem–like Cells
Authors: Wang Xiao-kun , He Jie-hua , Xu Jing-hong , Ye Sheng , Wang Fang , Zhang Hui , Huang Zhen-cong , To Kenneth Kin Wah , Fu Li-wu
Published: March 2023

Supplementary Table S2. Primer sequences for PCR.
Data Supplement from Afatinib Enhances the Efficacy of Conventional Chemotherapeutic Agents by Eradicating Cancer Stem–like Cells
Authors: Wang Xiao-kun , He Jie-hua , Xu Jing-hong , Ye Sheng , Wang Fang , Zhang Hui , Huang Zhen-cong , To Kenneth Kin Wah , Fu Li-wu
Published: March 2023

Supplementary figure legends
Supplementary Table 1 from A Regulatory Loop Involving miR-22, Sp1, and c-Myc Modulates CD147 Expression in Breast Cancer Invasion and Metastasis
Authors: Kong Ling-Min , Liao Cheng-Gong , Zhang Yang , Xu Jing , Li Yu , Huang Wan , Zhang Yi , Bian Huijie , Chen Zhi-Nan
Published: March 2023

PDF file - 75K, Oligonucleotide sequence of PCR primers and siRNA fragments.
Supplementary Figure 1 from Manganoporphyrins Increase Ascorbate-Induced Cytotoxicity by Enhancing H2O2 Generation
Authors: Rawal Malvika , Schroeder Samuel R. , Wagner Brett A. , Cushing Cameron M. , Welsh Jessemae L. , Button Anna M. , Du Juan , Sibenaller Zita A. , Buettner Garry R. , Cullen Joseph J.
Published: March 2023

PDF file - 123K, Supplementary Figure 1. AsPC-1 and Panc-1 cells treated with MnT2EPyP or MnTBAP in combination with AscH-.
Supplementary Figure 1 from A Regulatory Loop Involving miR-22, Sp1, and c-Myc Modulates CD147 Expression in Breast Cancer Invasion and Metastasis
Authors: Kong Ling-Min , Liao Cheng-Gong , Zhang Yang , Xu Jing , Li Yu , Huang Wan , Zhang Yi , Bian Huijie , Chen Zhi-Nan
Published: March 2023

PDF file - 30K, The effect of Sp1 and c-Myc overexpression or knockdown on CD147 expression detecting by western blot.
Supplementary Table 1 from The Cancer Stem Cell Marker Aldehyde Dehydrogenase Is Required to Maintain a Drug-Tolerant Tumor Cell Subpopulation
Authors: Raha Debasish , Wilson Timothy R. , Peng Jing , Peterson David , Yue Peng , Evangelista Marie , Wilson Catherine , Merchant Mark , Settleman Jeff
Published: March 2023

XLS file - 335KB, Gene expression comparison of KATO II cells and KATO II-derived DTPs.
Data Supplement from Molecular Homology and Difference between Spontaneous Canine Mammary Cancer and Human Breast Cancer
Authors: Liu Deli , Xiong Huan , Ellis Angela E. , Northrup Nicole C. , Rodriguez Carlos O. , O'Regan Ruth M. , Dalton Stephen , Zhao Shaying
Published: March 2023

Supplementary Table S1. Canine MC case information, including histopathological description, ER status, genomic-wide studies, notable genomic changes, age, breed and sex.
Data Supplement from Molecular Homology and Difference between Spontaneous Canine Mammary Cancer and Human Breast Cancer
Authors: Liu Deli , Xiong Huan , Ellis Angela E. , Northrup Nicole C. , Rodriguez Carlos O. , O'Regan Ruth M. , Dalton Stephen , Zhao Shaying
Published: March 2023

Supplementary Table S3. Supplementary data for mutation discovery in canine MCs by WES and RNA-seq analyses, including read mapping information, mutated gene listed, base substitution type, etc.
Supplemental Tables 1 - 3, Figure 1 from High Serum Iron Is Associated with Increased Cancer Risk
Authors: Wen Chi Pang , Lee June Han , Tai Ya-Ping , Wen Christopher , Wu Shiuan Be , Tsai Min Kuang , Hsieh Dennis P.H. , Chiang Hung-Che , Hsiung Chao Agnes , Hsu Chung Y. , Wu Xifeng
Published: March 2023

Supplemental Table 1. Hazard ratios for cancer incidence for different serum iron levels by smoking status. Supplemental Table 2. Cancer mortality risk for different serum iron levels Supplemental Table 3. Comparison of results of first and second test of serum iron. Supplemental Figure 1. J-shaped relationship between serum iron and cancer risk.
Supplementary Figure 2 from Gene Profiling of Canine B-Cell Lymphoma Reveals Germinal Center and Postgerminal Center Subtypes with Different Survival Times, Modeling Human DLBCL
Authors: Richards Kristy L. , Motsinger-Reif Alison A. , Chen Hsiao-Wei , Fedoriw Yuri , Fan Cheng , Nielsen Dahlia M. , Small George W. , Thomas Rachael , Smith Chris , Dave Sandeep S. , Perou Charles M. , Breen Matthew , Borst Luke B. , Suter Steven E.
Published: March 2023

PDF file - 843K, Unsupervised hierarchical clustering of cBCLs.
Supplementary Methods and Figure Legends from Mycoplasma Hyorhinis Infection Promotes NF-κB–Dependent Migration of Gastric Cancer Cells
Authors: Duan Hongying , Chen Ling , Qu Like , Yang Hua , Song Sonya Wei , Han Yong , Ye Meihua , Chen Wanyuan , He Xianglei , Shou Chengchao
Published: March 2023

Supplementary Methods and Figure Legends from Mycoplasma Hyorhinis Infection Promotes NF-κB–Dependent Migration of Gastric Cancer Cells
Supplementary Table 1 from Cellular Disposal of miR23b by RAB27-Dependent Exosome Release Is Linked to Acquisition of Metastatic Properties
Authors: Ostenfeld Marie Stampe , Jeppesen Dennis K. , Laurberg Jens R. , Boysen Anders T. , Bramsen Jesper B. , Primdal-Bengtson Bjarke , Hendrix An , Lamy Philippe , Dagnaes-Hansen Frederik , Rasmussen Mads H. , Bui Khan H. , Fristrup Niels , Christensen Erik I. , Nordentoft Iver , Morth Jens P. , Jensen Jørgen B. , Pedersen Jakob S. , Beck Martin , Theodorescu Dan , Borre Michael , Howard Kenneth A. , Dyrskjøt Lars , Ørntoft Torben Falck
Published: March 2023

miRNA profiling in exosomes and cells.
Supplementary Figure 3 from Cellular Disposal of miR23b by RAB27-Dependent Exosome Release Is Linked to Acquisition of Metastatic Properties
Authors: Ostenfeld Marie Stampe , Jeppesen Dennis K. , Laurberg Jens R. , Boysen Anders T. , Bramsen Jesper B. , Primdal-Bengtson Bjarke , Hendrix An , Lamy Philippe , Dagnaes-Hansen Frederik , Rasmussen Mads H. , Bui Khan H. , Fristrup Niels , Christensen Erik I. , Nordentoft Iver , Morth Jens P. , Jensen Jørgen B. , Pedersen Jakob S. , Beck Martin , Theodorescu Dan , Borre Michael , Howard Kenneth A. , Dyrskjøt Lars , Ørntoft Torben Falck
Published: March 2023

Analysis of RAB27A and RAB27B expression and genomic alterations in clinical samples. Effect of Rab27b knockdown on cell morphology and long-term growth kinetics.
Supplementary Figures S1-S6, Table S1-S2, and Materials and Methods from ISG15 Is a Critical Microenvironmental Factor for Pancreatic Cancer Stem Cells
Authors: Sainz Bruno , Martín Beatriz , Tatari Marianthi , Heeschen Christopher , Guerra Susana
Published: March 2023

Supplementary Figures S1-S6, Table S1-S2, and Materials and Methods. Figure S1 shows the distribution of macrophages and ISG15 expression in tissue from patient PDAC tumors, analyzed by IHC, and the expression of the CSC cell surface marker CD133 on PDAC cells cultured as adherent monolayers or as spheres. Figure S2 shows the growth of PDAC cells in vivo alone or with polarized human macrophages. Figure S3-S5 is a comprehensive IHC or IF analysis of ISG15 expression in multiple PDAC, breast and prostate cancer patient tumors. Figure S6 shows the migratory capacity of murine PDAC CSCs primed with control media or CM from M2-polarized ISG15+/+ or ISG15-/- murine macrophages. Table S1 lists the antibodies used in this study. Table S2 lists the sequences of the primers used for RTqPCR analysis.
Supplementary Figure 1 from Cellular Disposal of miR23b by RAB27-Dependent Exosome Release Is Linked to Acquisition of Metastatic Properties
Authors: Ostenfeld Marie Stampe , Jeppesen Dennis K. , Laurberg Jens R. , Boysen Anders T. , Bramsen Jesper B. , Primdal-Bengtson Bjarke , Hendrix An , Lamy Philippe , Dagnaes-Hansen Frederik , Rasmussen Mads H. , Bui Khan H. , Fristrup Niels , Christensen Erik I. , Nordentoft Iver , Morth Jens P. , Jensen Jørgen B. , Pedersen Jakob S. , Beck Martin , Theodorescu Dan , Borre Michael , Howard Kenneth A. , Dyrskjøt Lars , Ørntoft Torben Falck
Published: March 2023

NTA analysis, STR analysis, Pearson correlation values of miRNA expression in exosomes, correlation of miRNA and mRNA target abundance in cells vs. exosomes.
Supplementary Table 7 from Say No to DMSO: Dimethylsulfoxide Inactivates Cisplatin, Carboplatin, and Other Platinum Complexes
Authors: Hall Matthew D. , Telma Katherine A. , Chang Ki-Eun , Lee Tobie D. , Madigan James P. , Lloyd John R. , Goldlust Ian S. , Hoeschele James D. , Gottesman Michael M.
Published: March 2023

PDF file - 65KB, Peaks observed for ESI+ mass spectra of Pt complexes dissolved in DMSO, associated with Pt-DMSO adducts.
Supplementary Figure S3 from CtBP2 Modulates the Androgen Receptor to Promote Prostate Cancer Progression
Authors: Takayama Ken-ichi , Suzuki Takashi , Fujimura Tetsuya , Urano Tomohiko , Takahashi Satoru , Homma Yukio , Inoue Satoshi
Published: March 2023

Supplementary Figure S3. CtBP2 promotes androgen-dependent prostate cancer cell proliferation.
Supplementary Figure S2 from CtBP2 Modulates the Androgen Receptor to Promote Prostate Cancer Progression
Authors: Takayama Ken-ichi , Suzuki Takashi , Fujimura Tetsuya , Urano Tomohiko , Takahashi Satoru , Homma Yukio , Inoue Satoshi
Published: March 2023

Supplementary Figure S2. Effect of CTBP2 konckdown on androgen-mediated gene induction at early time point.
Supplementary Video #8 from Live-Cell Imaging of Invasion and Intravasation in an Artificial Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

Angiogenic sprouts and neighboring HMVECs oscillating in position relative to a cluster of MDA-MB-231 breast cancer cells.
Supplementary Video #7 from Live-Cell Imaging of Invasion and Intravasation in an Artificial Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

An HMVEC vessel under shear stress (12-15 dyne cm-2) extending an angiogenic sprout towards a cluster of MDA-MB-231 breast cancer cells.
Supplementary Video #6 from Live-Cell Imaging of Invasion and Intravasation in an Artificial Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

A single MDA-MB-231 breast cancer cell intravasating into an HMVEC vessel under shear stress (12-15 dyne cm-2).
Supplementary Video #3 from Live-Cell Imaging of Invasion and Intravasation in an Artificial Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

Multiple MDA-MB-231 breast cancer cells moving within a predefined matrix tunnel next to an HMVEC vessel under shear stress (12-15 dyne cm-2).
Supplemental Tables S1-S2 from Hedgehog Signaling Drives Radioresistance and Stroma-Driven Tumor Repopulation in Head and Neck Squamous Cancers
Authors: Gan Gregory N. , Eagles Justin , Keysar Stephen B. , Wang Guoliang , Glogowska Magdalena J. , Altunbas Cem , Anderson Ryan T. , Le Phuong N. , Morton J. Jason , Frederick Barbara , Raben David , Wang Xiao-Jing , Jimeno Antonio
Published: March 2023

Supplemental Tables S1-S2. Hirsch Score was calculated from tumors and their respective stroma from Figure 5 (S1); All potential flank implanted stromal:tumor and tumor:tumor combinations were measured bi-weekly to chart growth kinetics (S2).
Supplementary Video #2 from Live-Cell Imaging of Invasion and Intravasation in an Artificial Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

MDA-MB-231 breast cancer cells moving within a proteolytically degraded ECM track next to an HMVEC vessel under shear stress (12-15 dyne cm-2).
Supplementary Video #1 from Live-Cell Imaging of Invasion and Intravasation in an Artificial Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

Phase-contrast movie of a HUVEC microvessel under shear stress (12-15 dyne cm-2).
Supplemental Methods from Hedgehog Signaling Drives Radioresistance and Stroma-Driven Tumor Repopulation in Head and Neck Squamous Cancers
Authors: Gan Gregory N. , Eagles Justin , Keysar Stephen B. , Wang Guoliang , Glogowska Magdalena J. , Altunbas Cem , Anderson Ryan T. , Le Phuong N. , Morton J. Jason , Frederick Barbara , Raben David , Wang Xiao-Jing , Jimeno Antonio
Published: March 2023

Supplemental Methods. Description of additional methods and procedures used in the study.
Supplemental Table and Figure Legends from Transient SNAIL1 Expression Is Necessary for Metastatic Competence in Breast Cancer
Authors: Tran Hung D. , Luitel Krishna , Kim Michael , Zhang Kun , Longmore Gregory D. , Tran David D.
Published: March 2023

Supplemental Table and Figure Legends. Legends to the supplemental table and figures
Supplemental Material and Methods from Transient SNAIL1 Expression Is Necessary for Metastatic Competence in Breast Cancer
Authors: Tran Hung D. , Luitel Krishna , Kim Michael , Zhang Kun , Longmore Gregory D. , Tran David D.
Published: March 2023

Supplemental Material and Methods. Additional description of materials and methods used
Supplementary Figure 3 from Molecular Modulation of Estrogen-Induced Apoptosis by Synthetic Progestins in Hormone Replacement Therapy: An Insight into the Women's Health Initiative Study
Authors: Sweeney Elizabeth E. , Fan Ping , Jordan V. Craig
Published: March 2023

Supplementary Figure 3. MCF-7:WS8 cells were treated with Dex (A), MPA (B), or NETA (C), at concentrations ranging from 10-10 M to 10-6 M alone or in combination with 1µM 4-OHT, 1µM ICI 182,780, or 1µM RU486 for seven days, and DNA was quantified.
Supplementary Figures 1-19 from ALK-Dependent Control of Hypoxia-Inducible Factors Mediates Tumor Growth and Metastasis
Authors: Martinengo Cinzia , Poggio Teresa , Menotti Matteo , Scalzo Maria Stella , Mastini Cristina , Ambrogio Chiara , Pellegrino Elisa , Riera Ludovica , Piva Roberto , Ribatti Domenico , Pastorino Fabio , Perri Patrizia , Ponzoni Mirco , Wang Qi , Voena Claudia , Chiarle Roberto
Published: March 2023

Supplementary Figures 1-19. Supplementary Figure 1. Hypoxia pathways are enriched in ALCL. Supplementary Figure 2. Gene expression data on ALCL. Supplementary Figure 3. EML4-ALK NSCLC show enrichment in hypoxia pathway associated genes. Supplementary Figure 4. ALK regulates HIF-1ÃŽÂ± and HIF-2ÃŽÂ± expression in ALK-rearranged ALCL cell lines. Supplementary Figure 5. Oncogenic ALK regulates HIF-1ÃŽÂ± and HIF-2ÃŽÂ± expression levels in ALK-rearranged ALCL cell lines. Supplementary Figure 6. Oncogenic ALK-mediated control of HIF-1ÃŽÂ± and HIF-2ÃŽÂ± expression is not dependent on proteasome-dependent degradation. Supplementary Figure 7. ALK regulates HIF-1ÃŽÂ± and HIF-2ÃŽÂ± through STAT3 and C/EBPÃŽÂ². Supplementary Figure 8. STAT3 and C/EBPÃŽÂ² mediated regulation of HIFs in ALCL. Supplementary Figure 9. Ectopic expression of NPM-ALK in ALK negative ALCL. Supplementary Figure 10. Validation of shRNA against HIF-1ÃŽÂ± and HIF-2ÃŽÂ±. Supplementary Figure 11. HIF-2ÃŽÂ± is essential for the growth of ALK-rearranged ALCL in vivo. Supplementary Figure 12. HIF-1ÃŽÂ± and HIF-2ÃŽÂ± are not required for the growth of ALK-negative T cell lymphoma in vivo. Supplementary Figure 13. ALK regulates VEGFA mRNA expression and production in vitro. Supplementary Figure 14. Anti-angiogenic treatment in ALK negative ALCL. Supplementary Figure 15. Oncogenic ALK regulates HIF-1ÃŽÂ± and HIF-2ÃŽÂ± expression levels in EML4-ALK NSCLC. Supplementary Figure 16. HIF-ÃŽÂ± regulation in NSCLC is specifically dependent on ALK activity. Supplementary Figure 17. Oncogenic ALK activity up-regulates VEGF expression in NSCLC. Supplementary Figure 18. HIF-ÃŽÂ± knock-down does not affect the growth of K-RAS mutated NSCLC. Supplementary Figure 19. HIF-1ÃŽÂ± and HIF-2ÃŽÂ± are essential for metastasis formation in EML4-ALK NSCLC.
Supplemental Figure S1 from Targeted Noninvasive Imaging of EGFR-Expressing Orthotopic Pancreatic Cancer Using Multispectral Optoacoustic Tomography
Authors: Hudson Shanice V. , Huang Justin S. , Yin Wenyuan , Albeituni Sabrin , Rush Jamie , Khanal Anil , Yan Jun , Ceresa Brian P. , Frieboes Hermann B. , McNally Lacey R.
Published: March 2023

Supplemental Figure S1. Quantification of EGF-750 probe MSOT signal accumulation within S2VP10L tumor xenografts at various time points.
Supplementary Figure Legends from ALK-Dependent Control of Hypoxia-Inducible Factors Mediates Tumor Growth and Metastasis
Authors: Martinengo Cinzia , Poggio Teresa , Menotti Matteo , Scalzo Maria Stella , Mastini Cristina , Ambrogio Chiara , Pellegrino Elisa , Riera Ludovica , Piva Roberto , Ribatti Domenico , Pastorino Fabio , Perri Patrizia , Ponzoni Mirco , Wang Qi , Voena Claudia , Chiarle Roberto
Published: March 2023

Supplementary Figure Legends. File with Supplementary Figure Legends
pplementary Figure 1, Table 1 from Cell Surface Lactate Receptor GPR81 Is Crucial for Cancer Cell Survival
Authors: Roland Christina L. , Arumugam Thiruvengadam , Deng Defeng , Liu Shi He , Philip Bincy , Gomez Sobeyda , Burns William R. , Ramachandran Vijaya , Wang Huamin , Cruz-Monserrate Zobeida , Logsdon Craig D.
Published: March 2023

PDF file - 163K, Supplementary Figure 1: Lentiviral shRNA mediated knockdown or ectopic expression of GPR81. Supplementary Figure 2: Lentiviral shRNA mediated knockdown of GPR81 is associated with reduced levels of MCT1. Supplemental Table 1: Primer sequences for quantitative RT-PCR.
Supplementary Figures S1-S11 from Distinct Subpopulations of Head and Neck Cancer Cells with Different Levels of Intracellular Reactive Oxygen Species Exhibit Diverse Stemness, Proliferation, and Chemosensitivity
Authors: Chang Ching-Wen , Chen Yu-Syuan , Chou Shiu-Huey , Han Chia-Li , Chen Yu-Ju , Yang Cheng-Chieh , Huang Chih-Yang , Lo Jeng-Fan
Published: March 2023

Supplementary Figures S1-S11. The co-expression profile among ALDH activity, memGrp78 and Glut3 in SAS Sphere cells and cisplatin-resistant (cisPtR) SAS cells was examined by FACS (S1); Single-cell suspension from parental SAS or sphere SAS cells was stained with CellROX Deep Red reagent and DCF (S2); Enrichment of the drug-resistant population after in vitro drug treatment (S3); ROSLow cells were sorted using DCFDA staining from SAS sphere cells (S4); Differentially expressed genes of reactive oxygen species scavenging in Parental cells and Sphere cells under 2, 3, 5, or 9 weeks of cultivation with defined serum-free selection medium were collected and analyzed (S5); Treatment of sphere cells with catalase inhibitor 3AT reduced catalase activity (S6); Combinatorial treatment of ROS scavenger inhibitor and cisplatin induces apoptosis cell death (S7); Knockdown of CAT or SOD2 gene expression diminished spheres-forming capability, stemness marker expression of HN-CICs (S8); Overexpression of CAT in HNCICs promotes stemness properties (S9); Overexpression of CAT in HNSCC under defined serum-free selection medium promotes stemness properties (S10); Cell viability of drugs treated hematopoietic stem cells (S11).
Supplementary Video 3 from Deubiquitination of γ-Tubulin by BAP1 Prevents Chromosome Instability in Breast Cancer Cells
Authors: Zarrizi Reihaneh , Menard Julien Albert , Belting Mattias , Massoumi Ramin
Published: March 2023

Live cell microscopy of MDA-MB-468 inducibly expressing empty expression plasmid and transiently transfected with H2B-GFP. The movie shows anaphase bridge.
Supplementary Figures 1 - 6 from Deubiquitination of γ-Tubulin by BAP1 Prevents Chromosome Instability in Breast Cancer Cells
Authors: Zarrizi Reihaneh , Menard Julien Albert , Belting Mattias , Massoumi Ramin
Published: March 2023

Supplementary Figure 1. The cellular distribution of gamma-tubulin and BRCA1 in MCF10A cells, using immunofluorescence staining and confocal microscopy. Bars, 10 mm. Supplementary Figure 2. Confidence view screenshot from STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) shows known and predicted protein-protein interaction network of human BAP1 and UCHL1, as well as gamma tubulin (TUBG1) and BRCA1, which were used as inputs to the query. Supplementary Figure 3. (A)The subcellular distribution of endogenous BAP1 in MCF10A cells, using immunofluorescence staining and confocal microscopy.(B) The subcellular localization of BAP1 in MCF10A cells were biochemically divided into cytosolic (Cyto), Nuclear membrane (NM) and Nucleus (Nu) fractions and examined by Western blotting with an anti-BAP1 antibody. alpha-tubulin and Lamin B were used as molecular markers for the cytosolic and Nucleus fractions, respectively. Supplementary Figure 4. (A) Immunoprecipitation of endogenous alpha-tubulin from synchronized MCF10A cells and immunoblotting using UCHL1 and alpha-tubulin antibodies. The arrowhead points to a shift in size of alpha-tubulin corresponding to ubiquitinated alpha-tubulin.MCF10A cells were synchronized by double-thymidine block release and collected in G1, S and G2/M phases. (B) MCF10A cells were synchronized by a double thymidine block. Cells in mitotic phase were obtained by nocodazole treatment (M0) and released from nocodazole after 45 min (M1), 90 min (M2), and 180 min (M3). Cell extracts were immunoprecipitated with alpha-tubulin antibody and analyzed by Western blotting using antibodies against UCHL1, alpha-tubulin, and actin. The lysate (lower panel) shows an equal amount of protein used for immunoprecipitation. Supplementary Figure 5. (A) Western blot analysis of BAP1 and Actin expression in CAMA and T47D cells. (B) Immunoprecipitation of endogenous BAP1 from synchronized CAMA and T47D cells and immunoblotting using anti-BAP1 and alpha-tubulin antibodies. Cells were synchronized by double-thymidine block release and collected in mitosis by mitotic shake-off. Both asynchronous and synchronous cell extracts were used for immunoprecipitation. The lysate (lower panel) shows an equal amount of protein used for immunoprecipitation (C) Analysis of the levels of BAP1 and ubiquitinated alpha-tubulin in CAMA and T47D cells treated for three days with shRNA against BAP1 or empty expression plasmid (shCtrl). The arrowhead points to a shift in size of alpha-tubulin corresponding to ubiquitinated alpha-tubulin. Supplementary Figure 6. (A) Western blot analysis of wild-type, Flag-HA-BAP1, using HA antibody. (B) Western blot analysis of, Flag-BAP1-C91A, using flag antibody.
Data Supplement from Natural Killer Cells Eradicate Galectin-1–Deficient Glioma in the Absence of Adaptive Immunity
Authors: Baker Gregory J. , Chockley Peter , Yadav Viveka Nand , Doherty Robert , Ritt Michael , Sivaramakrishnan Sivaraj , Castro Maria G. , Lowenstein Pedro R.
Published: March 2023

Supplementary Figure S1. Plasmid map of the pCI-neo-mCitrine expression vector.
Table S2 from Oncogenic KRAS Confers Chemoresistance by Upregulating NRF2
Authors: Tao Shasha , Wang Shue , Moghaddam Seyed Javad , Ooi Aikseng , Chapman Eli , Wong Pak K. , Zhang Donna D.
Published: March 2023

Table S2. The percentage of mice with adenocarcinomas from each group.
Table S1 from Oncogenic KRAS Confers Chemoresistance by Upregulating NRF2
Authors: Tao Shasha , Wang Shue , Moghaddam Seyed Javad , Ooi Aikseng , Chapman Eli , Wong Pak K. , Zhang Donna D.
Published: March 2023

Table S1. Cisplatin toxicity as a function of KRAS, NRF2, KEAP1, and P53. The response to cisplatin-mediated toxicity of the listed NSCLC was measured by functional impairment of mitochondria using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. LD50s are listed. The coding regions of NRF2 and KRAS were sequenced and the status of each gene is listed. The mutation information for KEAP1 and TP53 was obtained from the literature. The references can be found in the supporting references according to the numbers in the table.
Data Supplement from TRIB1 Supports Prostate Tumorigenesis and Tumor-Propagating Cell Survival by Regulation of Endoplasmic Reticulum Chaperone Expression
Authors: Mashima Tetsuo , Soma-Nagae Taeko , Migita Toshiro , Kinoshita Ryoko , Iwamoto Atsushi , Yuasa Takeshi , Yonese Junji , Ishikawa Yuichi , Seimiya Hiroyuki
Published: March 2023

Supplementary Table 2 shows the candidate survival factors in prostate cancer spheroid as revealed by RNAi screening.
Supplemental Figure S3 from Aurora-A Inhibition Offers a Novel Therapy Effective against Intracranial Glioblastoma
Authors: Van Brocklyn James R. , Wojton Jeffrey , Meisen Walter H. , Kellough David A. , Ecsedy Jeffery A. , Kaur Balveen , Lehman Norman L.
Published: March 2023

Additional effects of Aurora-A inhibition on senescence, apoptosis and stem markers in GB neurospheres.
Supplementary Table 2 from Cancer-Associated Adipose Tissue Promotes Breast Cancer Progression by Paracrine Oncostatin M and Jak/STAT3 Signaling
Authors: Lapeire Lore , Hendrix An , Lambein Kathleen , Van Bockstal Mieke , Braems Geert , Van Den Broecke Rudy , Limame Ridha , Mestdagh Pieter , Vandesompele Jo , Vanhove Christian , Maynard Dawn , Lehuédé Camille , Muller Catherine , Valet Philippe , Gespach Christian P. , Bracke Marc , Cocquyt Veronique , Denys Hannelore , De Wever Olivier
Published: March 2023

F: forward primer, R: reverse primer.
Supplementary Methods and Figure legends from Reducing CD73 Expression by IL1β-Programmed Th17 Cells Improves Immunotherapeutic Control of Tumors
Authors: Chatterjee Shilpak , Thyagarajan Krishnamurthy , Kesarwani Pravin , Song Jin H. , Soloshchenko Myroslawa , Fu Jianing , Bailey Stefanie R. , Vasu Chenthamarkshan , Kraft Andrew S. , Paulos Chrystal M. , Yu Xue-Zhong , Mehrotra Shikhar
Published: March 2023

The document contains supplementary methods and figure legends for supplementary figure 1, 2 and 3.
Supplementary Fig. 2 from Metastasis Stimulation by Hypoxia and Acidosis-Induced Extracellular Lipid Uptake Is Mediated by Proteoglycan-Dependent Endocytosis
Authors: Menard Julien A. , Christianson Helena C. , Kucharzewska Paulina , Bourseau-Guilmain Erika , Svensson Katrin J. , Lindqvist Eva , Chandran Vineesh Indira , Kjellén Lena , Welinder Charlotte , Bengzon Johan , Johansson Maria C. , Belting Mattias
Published: March 2023

Figure S2. LDL induces the accumulation of LD-associated cholesteryl esters in hypoxic cells.
Data Supplement from A Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition
Authors: Carmona F. Javier , Davalos Veronica , Vidal Enrique , Gomez Antonio , Heyn Holger , Hashimoto Yutaka , Vizoso Miguel , Martinez-Cardus Anna , Sayols Sergi , Ferreira Humberto J. , Sánchez-Mut Jose V. , Morán Sebastián , Margelí Mireia , Castella Eva , Berdasco Maria , Stefansson Olafur A. , Eyfjord Jorunn E. , Gonzalez-Suarez Eva , Dopazo Joaquín , Orozco Modesto , Gut Ivo G. , Esteller Manel
Published: March 2023

Supplementary Figures S1-2 and Tables S1-6. Supplementary Figure S1. Expression changes measured by qRT-PCR of genes undergoing DNA methylation shifts in canine epithelial-to-mesenchymal transition. Supplementary Figure S2. Translation of the DNA methylation changes observed in the canine epithelial-to-mesenchymal transition model to human breast cancer. Supplementary Table S1. List of all DMRs (87,296) identified between MDCK-U and MDCK-T. Supplementary Table S2. List of differentially expressed genes between MDCK-U and MDCK-T. Supplementary Table S3. Genes undergoing differential expression between MDCK-U and MDCK-T in association with an intragenic DMR. Supplementary Table S4. Gene ontology analysis of DNA methylation associated transcriptional changes in the MDCK-EMT model. Supplementary Table S5. Gene promoters with consistent DNA methylation variation in canine and human EMT. Supplementary Table S6. Gene ontology analysis with the gene-expression changes observed for conserved DMRs.
Supplementary Figure S3 from β-Catenin Contributes to Lung Tumor Development Induced by EGFR Mutations
Authors: Nakayama Sohei , Sng Natasha , Carretero Julian , Welner Robert , Hayashi Yuichiro , Yamamoto Mihoko , Tan Alistair J. , Yamaguchi Norihiro , Yasuda Hiroyuki , Li Danan , Soejima Kenzo , Soo Ross A. , Costa Daniel B. , Wong Kwok-Kin , Kobayashi Susumu S.
Published: March 2023

Afatinib inhibits tyrosine-phosphorylation of EGFR.
Data Supplement from RB Family Tumor Suppressor Activity May Not Relate to Active Silencing of E2F Target Genes
Authors: Vormer Tinke L. , Wojciechowicz Kamila , Dekker Marleen , de Vries Sandra , van der Wal Anja , Delzenne-Goette Elly , Naik Sjalin H. , Song Ji-Ying , Dannenberg Jan-Hermen , Hansen Jacob B. , te Riele Hein
Published: March 2023

Supplementary Figure S4. Adipose deposits in RbN750/wtp130-/- and RbN750/wtp130+/- mice.
Data Supplement from RB Family Tumor Suppressor Activity May Not Relate to Active Silencing of E2F Target Genes
Authors: Vormer Tinke L. , Wojciechowicz Kamila , Dekker Marleen , de Vries Sandra , van der Wal Anja , Delzenne-Goette Elly , Naik Sjalin H. , Song Ji-Ying , Dannenberg Jan-Hermen , Hansen Jacob B. , te Riele Hein
Published: March 2023

Supplementary Materials and Methods. Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Figure 4 from Loss of Cdk2 and Cyclin A2 Impairs Cell Proliferation and Tumorigenesis
Authors: Gopinathan Lakshmi , Tan Shawn Lu Wen , Padmakumar V. C. , Coppola Vincenzo , Tessarollo Lino , Kaldis Philipp
Published: March 2023

PDF file - 1673KB, Premature senescence in Cdk2nullcyclin A2null MEFs and biochemical analysis of primary liver tumor cells.
Supplementary Figure 2 from Loss of Cdk2 and Cyclin A2 Impairs Cell Proliferation and Tumorigenesis
Authors: Gopinathan Lakshmi , Tan Shawn Lu Wen , Padmakumar V. C. , Coppola Vincenzo , Tessarollo Lino , Kaldis Philipp
Published: March 2023

PDF file - 1342KB, Tumorigenesis using transformed MEFs.
Supplementary Information from MPHOSPH1: A Potential Therapeutic Target for Hepatocellular Carcinoma
Authors: Liu Xinran , Zhou Yafan , Liu Xinyuan , Peng Anlin , Gong Hao , Huang Lizi , Ji Kaige , Petersen Robert B. , Zheng Ling , Huang Kun
Published: March 2023

Supplementary Information: provides experimental procedures in details, as well as two tables and one figure. Table S1. Features and relative expression levels of MPHOSPH1 of clinical samples. Table S2. Hepatic function assays of the orthotopic HCC xenograft animal model. Figure S1. In vivo knockdown of endogenous MPHOSPH1 inhibits orthotopic HCC xenograft growth. Tumor nodules are indicated with yellow arrows.
Supplmentary File 1 from Nuclear Factor of Activated T-cell Activity Is Associated with Metastatic Capacity in Colon Cancer
Authors: Tripathi Manish K. , Deane Natasha G. , Zhu Jing , An Hanbing , Mima Shinji , Wang Xiaojing , Padmanabhan Sekhar , Shi Zhiao , Prodduturi Naresh , Ciombor Kristen K. , Chen Xi , Washington M. Kay , Zhang Bing , Beauchamp R. Daniel
Published: March 2023

Supplmentary File 1. genes from the integrated colon cancer co-expression network
Supplementary Figure Legends and Experimental Procedures from TRAP1 Is Involved in BRAF Regulation and Downstream Attenuation of ERK Phosphorylation and Cell-Cycle Progression: A Novel Target for BRAF-Mutated Colorectal Tumors
Authors: Condelli Valentina , Piscazzi Annamaria , Sisinni Lorenza , Matassa Danilo Swann , Maddalena Francesca , Lettini Giacomo , Simeon Vittorio , Palladino Giuseppe , Amoroso Maria Rosaria , Trino Stefania , Esposito Franca , Landriscina Matteo
Published: March 2023

Supplementary Figure Legends and Experimental Procedures
Supplemental Figures 1 - 7 from Acquired Resistance to Fractionated Radiotherapy Can Be Overcome by Concurrent PD-L1 Blockade
Authors: Dovedi Simon J. , Adlard Amy L. , Lipowska-Bhalla Grazyna , McKenna Conor , Jones Sherrie , Cheadle Eleanor J. , Stratford Ian J. , Poon Edmund , Morrow Michelle , Stewart Ross , Jones Hazel , Wilkinson Robert W. , Honeychurch Jamie , Illidge Tim M.
Published: March 2023

Supplemental figure 1: Gating strategy for determining tumor cell PD-L1 expression. Supplemental figure 2: Impact of low-dose fractionated RT on PD-L1 expression by CD11b+GR1Hi cells. Supplemental figure 3: Dual blockade of PD-1 and PD-L1 does not further enhance efficacy of RT combination. Supplemental figure 4: Blockade of PD-1 / PD-L1 in combination with local RT is well tolerated in mice. Supplemental figure 5: PD-1 / PD-L1 blockade does not directly sensitise tumor cells to RT. Supplemental figure 6: Scheduling of RT and anti-PD-L1 is critical for anti-tumor activity. Supplemental figure 7: Only acute administration of anti-PD-L1 mAb may be required to achieve efficacy when delivered in combination with RT.
Supplementary Methods from Myeloid IKKβ Promotes Antitumor Immunity by Modulating CCL11 and the Innate Immune Response
Authors: Yang Jinming , Hawkins Oriana E. , Barham Whitney , Gilchuk Pavlo , Boothby Mark , Ayers Gregory D. , Joyce Sebastian , Karin Michael , Yull Fiona E. , Richmond Ann
Published: March 2023

Supplementary Methods
Supplemental Figures 1 - 5 from Myeloid IKKβ Promotes Antitumor Immunity by Modulating CCL11 and the Innate Immune Response
Authors: Yang Jinming , Hawkins Oriana E. , Barham Whitney , Gilchuk Pavlo , Boothby Mark , Ayers Gregory D. , Joyce Sebastian , Karin Michael , Yull Fiona E. , Richmond Ann
Published: March 2023

Figure S1: Myeloid Ikkβ is required for anti-tumorigenic immunity. Figure S2. Myeloid cell depletion alters tumor immunity. Figure S3. Ikkβ loss alters macrophage phagocytosis capacity. Figure S4. Myeloid Ikkβ deletion reduced the cytotoxicity of T cells Figure S5. Cytokines play a major role in orchestrating the cellular make-up of the tumor microenvironment.
Supp Table S16 from In Vivo Disruption of an Rb–E2F–Ezh2 Signaling Loop Causes Bladder Cancer
Authors: Santos Mirentxu , Martínez-Fernández Mónica , Dueñas Marta , García-Escudero Ramón , Alfaya Begoña , Villacampa Felipe , Saiz-Ladera Cristina , Costa Clotilde , Oteo Marta , Duarte José , Martínez Victor , Gómez-Rodriguez Ma José , Martín Ma Luisa , Fernández Manoli , Viatour Patrick , Morcillo Miguel A. , Sage Julien , Castellano Daniel , Rodriguez-Peralto Jose L. , de la Rosa Federico , Paramio Jesús M
Published: March 2023

Supp Table S16. Transcription factor analyzed by Chip Enrichment analysis of the upregulated genes in human recurrent bladder tumors.
Data Supplement from Armed Oncolytic Virus Enhances Immune Functions of Chimeric Antigen Receptor–Modified T Cells in Solid Tumors
Authors: Nishio Nobuhiro , Diaconu Iulia , Liu Hao , Cerullo Vincenzo , Caruana Ignazio , Hoyos Valentina , Bouchier-Hayes Lisa , Savoldo Barbara , Dotti Gianpietro
Published: March 2023

Supplementary Figure S1. NB cells infected with Ad5ÃŽ?24 do not upregulate GD2, Fas, TRAIL receptors and costimulatory molecules
Data Supplement from Armed Oncolytic Virus Enhances Immune Functions of Chimeric Antigen Receptor–Modified T Cells in Solid Tumors
Authors: Nishio Nobuhiro , Diaconu Iulia , Liu Hao , Cerullo Vincenzo , Caruana Ignazio , Hoyos Valentina , Bouchier-Hayes Lisa , Savoldo Barbara , Dotti Gianpietro
Published: March 2023

Supplementary Figure S3. Growth of CHLA-255 cells in control mice
Supplemental Table from Early Pregnancy Sex Steroids and Maternal Breast Cancer: A Nested Case–Control Study
Authors: Fortner Renée T. , Schock Helena , Kaaks Rudolf , Lehtinen Matti , Pukkala Eero , Lakso Hans-Åke , Tanner Minna , Kallio Raija , Joensuu Heikki , Grankvist Kjell , Zeleniuch-Jacquotte Anne , Toniolo Paolo , Lundin Eva , Surcel Helja-Marja
Published: March 2023

Doubling of Circulating Endogenous Hormones and Breast Cancer Risk, by Time Between First Birth and Diagnosis and Age at Diagnosis: Finnish Maternity Cohort (n=3,480).
Data Supplement from Armed Oncolytic Virus Enhances Immune Functions of Chimeric Antigen Receptor–Modified T Cells in Solid Tumors
Authors: Nishio Nobuhiro , Diaconu Iulia , Liu Hao , Cerullo Vincenzo , Caruana Ignazio , Hoyos Valentina , Bouchier-Hayes Lisa , Savoldo Barbara , Dotti Gianpietro
Published: March 2023

Supplementary Movie 1B. GD2.CAR-T cell
Data Supplement from Armed Oncolytic Virus Enhances Immune Functions of Chimeric Antigen Receptor–Modified T Cells in Solid Tumors
Authors: Nishio Nobuhiro , Diaconu Iulia , Liu Hao , Cerullo Vincenzo , Caruana Ignazio , Hoyos Valentina , Bouchier-Hayes Lisa , Savoldo Barbara , Dotti Gianpietro
Published: March 2023

Supplementary Movie 1C. Ad5ÃŽ?24 and control T cells
Supplemental Materials and Methods, Figure Legend, Figures S1-6 from SCCA1/SERPINB3 Promotes Oncogenesis and Epithelial–Mesenchymal Transition via the Unfolded Protein Response and IL6 Signaling
Authors: Sheshadri Namratha , Catanzaro Joseph M. , Bott Alex J. , Sun Yu , Ullman Erica , Chen Emily I. , Pan Ji-An , Wu Song , Crawford Howard C. , Zhang Jianhua , Zong Wei-Xing
Published: March 2023

Supplemental Materials and Methods, Figure Legend, Figures S1-6. Figure S1. SCCA1-expressing MCF10A cells become independent of the hormonal factors. Figure S2. Expression of SCCA1 leads to IL-6 production. Figure S3. The induction of UPR by SCCA1 is dependent on its protease inhibition function. Figure S4. Silencing of ATF6a and PERK leads to decreased IL-6 production and cell proliferation in MDA-MB-231 cells. Figure S5. Silencing of SCCA results in decreased UPR, IL-6 production, and cell growth. Figure S6. Elevated SCCA1 expression leads to UPR and IL-6 production in various cell lines.
Supplementary Tables 1 - 7 from Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery
Authors: Hudson Andrew M. , Yates Tim , Li Yaoyong , Trotter Eleanor W. , Fawdar Shameem , Chapman Phil , Lorigan Paul , Biankin Andrew , Miller Crispin J. , Brognard John
Published: March 2023

Supplementary Table 1A. Mutations that were only identified by CCLE in the comparison of sequencing data of 1630 genes across 568 cell lines from CCLE and COSMIC . Supplementary Table 1B. Mutations that were only identified by COSMIC in the comparison of sequencing data of 1630 genes across 568 cell lines from CCLE and COSMIC. Supplementary Table 2. Sequencing cold spots (larger than 100bp) in cancer consensus and kinase genes identified from sequencing data of 10 CCLE whole exome sequencing files (not hybrid capture). Supplementary Table 3. New mutations detected by CRUK Manchester Institute sequencing that were not reported by either CCLE or COSMIC. Supplementary Table 4. Proportion of missense mutations exclusively reported by one institute (CCLE or COSMIC) that were subsequently found by CRUK MI sequencing. Supplementary Table 5. Sequencing statistics for CRUK MI sequencing. Supplementary Table 6. List of kinase and Cancer Census genes that were analyzed to identify sequencing cold-spots in 10 CCLE whole exome sequencing files Supplementary Table 7 Read coverage in CCLE Hybrid Capture data at the midpoint of the 20 largest cold-spots identified in CCLE from 10 lung whole exome sequencing files (not hybrid capture).
Supplementary Figure S4 from Phosphoinositide Protein Kinase PDPK1 Is a Crucial Cell Signaling Mediator in Multiple Myeloma
Authors: Chinen Yoshiaki , Kuroda Junya , Shimura Yuji , Nagoshi Hisao , Kiyota Miki , Yamamoto-Sugitani Mio , Mizutani Shinsuke , Sakamoto Natsumi , Ri Masaki , Kawata Eri , Kobayashi Tsutomu , Matsumoto Yosuke , Horiike Shigeo , Iida Shinsuke , Taniwaki Masafumi
Published: March 2023

Supplementary Figure S4. A. BX-912 shows no cross-resistance with BTZ. BX-912 exerted its growth inhibitory effect on BTZ-resistant KMS-11/BTZ cells and OPM-2/BTZ cells (red lines) as effectively as on their respective parental cells (blue dotted lines). Cells were treated with the indicated concentrations of either BX-912 or BTZ for 48 hours. The viable cell number of untreated cells was considered to be 1.0. B. The combination of BX-912 and the NF-ÃŽÂºB inhibitor, BAY11-7085, exhibited an additive growth inhibitory effect on BTZ-resistant KMS-11/BTZ cells and OPM-2/BTZ cells. Shaded areas represent the additive effects of the two agents.
Supplementary Script B from Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery
Authors: Hudson Andrew M. , Yates Tim , Li Yaoyong , Trotter Eleanor W. , Fawdar Shameem , Chapman Phil , Lorigan Paul , Biankin Andrew , Miller Crispin J. , Brognard John
Published: March 2023

Groovy program script used to make the 568 cell line comparison
Supplementary Figure S1 from Phosphoinositide Protein Kinase PDPK1 Is a Crucial Cell Signaling Mediator in Multiple Myeloma
Authors: Chinen Yoshiaki , Kuroda Junya , Shimura Yuji , Nagoshi Hisao , Kiyota Miki , Yamamoto-Sugitani Mio , Mizutani Shinsuke , Sakamoto Natsumi , Ri Masaki , Kawata Eri , Kobayashi Tsutomu , Matsumoto Yosuke , Horiike Shigeo , Iida Shinsuke , Taniwaki Masafumi
Published: March 2023

Supplementary Figure S1. AMO-1 cells and NCI-H929 cells were seeded at 2 x 105 cells/ml on day 0, and were treated either by BX-912 or AR12 at their concentrations of 5, 10, or 20 microM for 24, 48, and 72 hours. Cells were directly stained by trypan blue, and viable cell numbers were counted under the inverted microscope. Results were mean{plus minus}SD of triplicate analyses.
Supplemental Methods and Legends from Phosphoinositide Protein Kinase PDPK1 Is a Crucial Cell Signaling Mediator in Multiple Myeloma
Authors: Chinen Yoshiaki , Kuroda Junya , Shimura Yuji , Nagoshi Hisao , Kiyota Miki , Yamamoto-Sugitani Mio , Mizutani Shinsuke , Sakamoto Natsumi , Ri Masaki , Kawata Eri , Kobayashi Tsutomu , Matsumoto Yosuke , Horiike Shigeo , Iida Shinsuke , Taniwaki Masafumi
Published: March 2023

Supplemental Methods and Legends
Supplemental Figure Legends from Homeoprotein Six2 Promotes Breast Cancer Metastasis via Transcriptional and Epigenetic Control of E-Cadherin Expression
Authors: Wang Chu-An , Drasin David , Pham Catherine , Jedlicka Paul , Zaberezhnyy Vadym , Guney Michelle , Li Howard , Nemenoff Raphael , Costello James C. , Tan Aik-Choon , Ford Heide L.
Published: March 2023

Supplemental Figure Legends. Legends for Supplemental Figures S1-S8. Also includes Supplemental Reference.