bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Movie F from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

MOV file 45K, Cell undergoing a normal mitosis followed by cell death in the daughter cell (see Supplementary Figure 4 for movie stills)
Supplementary Figure S3 from Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma
Authors: Ryan Russell J.H. , Drier Yotam , Whitton Holly , Cotton M. Joel , Kaur Jasleen , Issner Robbyn , Gillespie Shawn , Epstein Charles B. , Nardi Valentina , Sohani Aliyah R. , Hochberg Ephraim P. , Bernstein Bradley E.
Published: April 2023

Supplementary Figure S3. Enhancer looping interactions and TF binding at BCL6 enhancers.
Supplementary Movie D from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

MOV file 1084K, Cell undergoing a normal mitosis followed by mitosis in the daughter cell (see Supplementary Figure 4 for movie stills)
Supplemental Table Legends from HIF2α-Dependent Lipid Storage Promotes Endoplasmic Reticulum Homeostasis in Clear-Cell Renal Cell Carcinoma
Authors: Qiu Bo , Ackerman Daniel , Sanchez Danielle J. , Li Bo , Ochocki Joshua D. , Grazioli Alison , Bobrovnikova-Marjon Ekaterina , Diehl J. Alan , Keith Brian , Simon M. Celeste
Published: April 2023

Supplemental Table Legends: Legends for all supplementary tables.
Supplementary Figure S3 from Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations
Authors: Ahronian Leanne G. , Sennott Erin M. , Van Allen Eliezer M. , Wagle Nikhil , Kwak Eunice L. , Faris Jason E. , Godfrey Jason T. , Nishimura Koki , Lynch Kerry D. , Mermel Craig H. , Lockerman Elizabeth L. , Kalsy Anuj , Gurski Joseph M. , Bahl Samira , Anderka Kristin , Green Lisa M. , Lennon Niall J. , Huynh Tiffany G. , Mino-Kenudson Mari , Getz Gad , Dias-Santagata Dora , Iafrate A. John , Engelman Jeffrey A. , Garraway Levi A. , Corcoran Ryan B.
Published: April 2023

Supplementary Figure S3. Copy number alterations for Patient #1.
Supplementary Figure S2 from Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations
Authors: Ahronian Leanne G. , Sennott Erin M. , Van Allen Eliezer M. , Wagle Nikhil , Kwak Eunice L. , Faris Jason E. , Godfrey Jason T. , Nishimura Koki , Lynch Kerry D. , Mermel Craig H. , Lockerman Elizabeth L. , Kalsy Anuj , Gurski Joseph M. , Bahl Samira , Anderka Kristin , Green Lisa M. , Lennon Niall J. , Huynh Tiffany G. , Mino-Kenudson Mari , Getz Gad , Dias-Santagata Dora , Iafrate A. John , Engelman Jeffrey A. , Garraway Levi A. , Corcoran Ryan B.
Published: April 2023

Supplementary Figure S2. KRAS mutation drives resistance to RAF inhibitor combinations.
Supplementary Figures S1 - S5 from A Genetic Platform to Model Sarcomagenesis from Primary Adult Mesenchymal Stem Cells
Authors: Guarnerio Jlenia , Riccardi Luisa , Taulli Riccardo , Maeda Takahiro , Wang Guocan , Hobbs Robin M. , Song Min Sup , Sportoletti Paolo , Bernardi Rosa , Bronson Roderick T. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Lunardi Andrea , Pandolfi Pier Paolo
Published: April 2023

Supplementary Figure S1. Candidate genes that couple with p53 loss to transform MSCs. Supplementary Figure S2. Lrf plays as oncosuppressor triggering tumorigenesis in MSCs. Supplementary Figure S3. Lrf expression does not affect the CFU-F capacities of MSCs nor it triggers MSCs to senescence or apoptosis. Supplementary Figure S4. Lrf regulates the differentiation process of MSCs through the repression of Dlk1. Supplementary Figure S5. Lrf plays a role as oncosuppressor in triggering the tumorigenesis of MSCs through Sox9 and Dlk1.
Supplementary Figure 10 from TGF-β Signaling in Myeloid Cells Is Required for Tumor Metastasis
Authors: Pang Yanli , Gara Sudheer Kumar , Achyut Bhagelu R. , Li Zhaoyang , Yan Hannah H. , Day Chi-Ping , Weiss Jonathan M. , Trinchieri Giorgio , Morris John C. , Yang Li
Published: April 2023

Supplementary Figure 10 - PDF file 82K, Time course study for in vivo cell trafficking; the expression of TGFbeta ligands and receptors in myeloid cells and subsets
Supplementary Figure 1 from TGF-β Signaling in Myeloid Cells Is Required for Tumor Metastasis
Authors: Pang Yanli , Gara Sudheer Kumar , Achyut Bhagelu R. , Li Zhaoyang , Yan Hannah H. , Day Chi-Ping , Weiss Jonathan M. , Trinchieri Giorgio , Morris John C. , Yang Li
Published: April 2023

Supplementary Figure 1 - PDF file 183K, Overproduction of immature myeloid cells in both tumor bearing mice and cancer patients, flow cytometry analysis and sorting
Supplementary Table S2 from The Genomic Landscape of Pediatric Ewing Sarcoma
Authors: Crompton Brian D. , Stewart Chip , Taylor-Weiner Amaro , Alexe Gabriela , Kurek Kyle C. , Calicchio Monica L. , Kiezun Adam , Carter Scott L. , Shukla Sachet A. , Mehta Swapnil S. , Thorner Aaron R. , de Torres Carmen , Lavarino Cinzia , Suñol Mariona , McKenna Aaron , Sivachenko Andrey , Cibulskis Kristian , Lawrence Michael S. , Stojanov Petar , Rosenberg Mara , Ambrogio Lauren , Auclair Daniel , Seepo Sara , Blumenstiel Brendan , DeFelice Matthew , Imaz-Rosshandler Ivan , Schwarz-Cruz y Celis Angela , Rivera Miguel N. , Rodriguez-Galindo Carlos , Fleming Mark D. , Golub Todd R. , Getz Gad , Mora Jaume , Stegmaier Kimberly
Published: April 2023

Mutations identified from WES and WGS of 26 tumors with paired normals.
Supplementary Tables S1 - S3 from MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Authors: Neupane Manish , Clark Allison P. , Landini Serena , Birkbak Nicolai J. , Eklund Aron C. , Lim Elgene , Culhane Aedin C. , Barry William T. , Schumacher Steven E. , Beroukhim Rameen , Szallasi Zoltan , Vidal Marc , Hill David E. , Silver Daniel P.
Published: April 2023

Supplementary Table S1. List of validated hits from N minus RAS screen. Supplementary Table S2. Amplicons in Human Cancer (from Broad Institute TCGA Copy Number Portal). Supplementary Table S3. Cancer cell lines used in current study with their MECP2 expression and RAS/MAPK/PI3K pathways mutation status (based on COSMIC, canSAR, ATCC, and CCLE databases).
Supplementary Methods from MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Authors: Neupane Manish , Clark Allison P. , Landini Serena , Birkbak Nicolai J. , Eklund Aron C. , Lim Elgene , Culhane Aedin C. , Barry William T. , Schumacher Steven E. , Beroukhim Rameen , Szallasi Zoltan , Vidal Marc , Hill David E. , Silver Daniel P.
Published: April 2023

Supplementary Methods from MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Supplementary Figures S1 - S6 from MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Authors: Neupane Manish , Clark Allison P. , Landini Serena , Birkbak Nicolai J. , Eklund Aron C. , Lim Elgene , Culhane Aedin C. , Barry William T. , Schumacher Steven E. , Beroukhim Rameen , Szallasi Zoltan , Vidal Marc , Hill David E. , Silver Daniel P.
Published: April 2023

Supplementary Figure S1. The Amplification of the MECP2 Gene Drives Its Expression, and the MECP2 Gene on the Active X Chromosome is Preferentially Amplified, Related to Figure 1. Supplementary Figure S2. MECP2 Overexpression Allows Soft Agar Growth of N minus RAS Cells in Two Different Types of Human Breast Epithelial Cells, and MECP2 Splicing Isoforms Differ In Their Ability to Confer Anchorage Independent Growth, Related to Figure 2A. Supplementary Figure S3: MECP2 Overexpression Allows Two Different Types of N minus RAS Breast Epithelial Cells To Grow As Tumor Xenograft In Nude Mice, Related to Figure 2E, 2F. Supplementary Figure S4. The MECP2 e2 Short Splicing Isoform Allows Sustained Activation of the MAPK Pathway after Prolonged Starvation in Minimal Medium without Growth Factors, Related to Figure 4A-C. Supplementary Figure S5. Both MECP2 Isoforms Activate the PI3K Pathway, Related to Figure 4D. Supplementary Figure S6. Additional human cancer cell lines with high level of MECP2 are growth-inhibited upon inhibition of MECP2 expression, Related to Figure 4E.
Supplementary Table 4 from Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations
Authors: Tirode Franck , Surdez Didier , Ma Xiaotu , Parker Matthew , Le Deley Marie Cécile , Bahrami Armita , Zhang Zhaojie , Lapouble Eve , Grossetête-Lalami Sandrine , Rusch Michael , Reynaud Stéphanie , Rio-Frio Thomas , Hedlund Erin , Wu Gang , Chen Xiang , Pierron Gaelle , Oberlin Odile , Zaidi Sakina , Lemmon Gordon , Gupta Pankaj , Vadodaria Bhavin , Easton John , Gut Marta , Ding Li , Mardis Elaine R. , Wilson Richard K. , Shurtleff Sheila , Laurence Valérie , Michon Jean , Marec-Bérard Perrine , Gut Ivo , Downing James , Dyer Michael , Zhang Jinghui , Delattre Olivier
Published: April 2023

Supplementary Table 4 provides the precise description of all STAG2 mutations in Ewing sarcoma.
Supplementary Table 1 from Essential Role of the Linear Ubiquitin Chain Assembly Complex in Lymphoma Revealed by Rare Germline Polymorphisms
Authors: Yang Yibin , Schmitz Roland , Mitala Joseph , Whiting Amanda , Xiao Wenming , Ceribelli Michele , Wright George W. , Zhao Hong , Yang Yandan , Xu Weihong , Rosenwald Andreas , Ott German , Gascoyne Randy D. , Connors Joseph M. , Rimsza Lisa M. , Campo Elias , Jaffe Elaine S. , Delabie Jan , Smeland Erlend B. , Braziel Rita M. , Tubbs Raymond R. , Cook James R. , Weisenburger Dennis D. , Chan Wing C. , Wiestner Adrian , Kruhlak Michael J. , Iwai Kazuhiro , Bernal Federico , Staudt Louis M.
Published: April 2023

Supplementary Table 1 PDF file 53K, Enrichment of two rare SNPs among ABC DLBCL tumors
Figure S8 from Epithelial-to-Mesenchymal Transition Rewires the Molecular Path to PI3K-Dependent Proliferation
Authors: Salt Megan B. , Bandyopadhyay Sourav , McCormick Frank
Published: April 2023

PDF 1842K, EMT alters sensitivity to inhibition of EGFR but does not affect sensitivity to PI3K inhibitors
Figure S3 from Epithelial-to-Mesenchymal Transition Rewires the Molecular Path to PI3K-Dependent Proliferation
Authors: Salt Megan B. , Bandyopadhyay Sourav , McCormick Frank
Published: April 2023

PDF 1555K, siRNAs targeting ErbB3 and NRG1 are efficient and on target and knockdown of autocrine TGF-alpha/EREG does not affect ErbB3-PI3K signaling
Supplemantary Figure S1 from FGFR-Mediated Reactivation of MAPK Signaling Attenuates Antitumor Effects of Imatinib in Gastrointestinal Stromal Tumors
Authors: Li Fang , Huynh Hung , Li Xiaoyan , Ruddy David A. , Wang Youzhen , Ong Richard , Chow Pierce , Qiu Shumei , Tam Angela , Rakiec Daniel P. , Schlegel Robert , Monahan John E. , Huang Alan
Published: April 2023

Expression of FGFR1-4, FGF1-23, KIT, ETV1, PRKCQ, ANO1, EGFR, ERBB2-4, MET, IGF1R, HGF, EGF and NRG1 in multiple primary tumor types and cancer cell lines.
Supplementary Figure 5 from Obligate Progression Precedes Lung Adenocarcinoma Dissemination
Authors: Caswell Deborah R. , Chuang Chen-Hua , Yang Dian , Chiou Shin-Heng , Cheemalavagu Shashank , Kim-Kiselak Caroline , Connolly Andrew , Winslow Monte M.
Published: April 2023

PDF file 128K, KT-Early and KT-Late mice have high total tumor burden
Supplementary Figure 4 from Next-Generation Sequencing of Stage IV Squamous Cell Lung Cancers Reveals an Association of PI3K Aberrations and Evidence of Clonal Heterogeneity in Patients with Brain Metastases
Authors: Paik Paul K. , Shen Ronglai , Won Helen , Rekhtman Natasha , Wang Lu , Sima Camelia S. , Arora Arshi , Seshan Venkatraman , Ladanyi Marc , Berger Michael F. , Kris Mark G.
Published: April 2023

Supplementary Figure 4. Heatmap of mRNA expression for clustered protocadherin gene families. A. gamma cluster and B. beta cluster in 178 TCGA lung squamous cell carcinomas and 5 MSKCC brain metastasis samples. Yellow ticks under the dendrogram indicate the brain metastasis samples.
Supplementary Figure 2 from Obligate Progression Precedes Lung Adenocarcinoma Dissemination
Authors: Caswell Deborah R. , Chuang Chen-Hua , Yang Dian , Chiou Shin-Heng , Cheemalavagu Shashank , Kim-Kiselak Caroline , Connolly Andrew , Winslow Monte M.
Published: April 2023

PDF file 320K, Similar total tumor burden and core genomic alterations in KPT-Early and KPT-Late mice
Supplementary Figure 3 from Next-Generation Sequencing of Stage IV Squamous Cell Lung Cancers Reveals an Association of PI3K Aberrations and Evidence of Clonal Heterogeneity in Patients with Brain Metastases
Authors: Paik Paul K. , Shen Ronglai , Won Helen , Rekhtman Natasha , Wang Lu , Sima Camelia S. , Arora Arshi , Seshan Venkatraman , Ladanyi Marc , Berger Michael F. , Kris Mark G.
Published: April 2023

Supplementary Figure 3. Photomicrographs of chromosome 5p FISH from PP1-PP4 brain metastases. Red signals correspond to 5p13.
Supplementary Figure 1 from Obligate Progression Precedes Lung Adenocarcinoma Dissemination
Authors: Caswell Deborah R. , Chuang Chen-Hua , Yang Dian , Chiou Shin-Heng , Cheemalavagu Shashank , Kim-Kiselak Caroline , Connolly Andrew , Winslow Monte M.
Published: April 2023

PDF file 2560K, Titratable induction of early and late stage lung cancer in KrasLSLG12D/+;p53flox/flox;R26tdTomato/+ (KPT) mice
Supplementary Methods, Figures S1 - S15 from CDKN2B Loss Promotes Progression from Benign Melanocytic Nevus to Melanoma
Authors: McNeal Andrew S. , Liu Kevin , Nakhate Vihang , Natale Christopher A. , Duperret Elizabeth K. , Capell Brian C. , Dentchev Tzvete , Berger Shelley L. , Herlyn Meenhard , Seykora John T. , Ridky Todd W.
Published: April 2023

Supplementary Figure S1. p15, p16, and Ki-67 expression in a benign BRAF(V600E) nevus. Supplementary Figure S2. Active CDK4 reverses BRAF(V600E)-mediated melanocyte growth arrest. Supplementary Figure S3. BRAF(V600E), p15, and p16 expression in normal and nevus MCs. Supplementary Figure S4. Engineered p15 and p16 expression in melanocytes. Supplementary Figure S5. Effects of p15 shRNA rescue and lentiCRISPRCAS9 mediated p15 loss in diBRAF(V600E) MCs. Supplementary Figure S6. Loss of CDKN2A and CDKN2B promotes proliferation in BRAF(V600E) Melanocytes. Supplementary Figure S7. p15 and p16 Expression in Benign Nevi and Melanoma. Supplementary Figure S8. p15 and p16 Expression in a Benign Nevus with Adjacent Melanoma. Supplementary Figure S9. Erk 1/2 Target EGR-1 is Upregulated in BRAFV600E Nevi. Supplementary Figure S10. BRAF(V600E) inhibitor PLX4720 prevents induction of p15- mediated growth arrest but is insufficient to reverse previously-established growth arrest. Supplementary Figure S11. BRAF(V600E) Induces Loss of Repressive Chromatin Marks at the CDKN2A/B Locus. Supplementary Figure S12. Effects of hTERT on p15 in BRAF(V600E) Melanocytes. Supplementary Figure S13. Senescence Marker Expression in human xenografts derived from Nevus-MCs. Supplementary Figure S14. Effects of p53(R248W) Transduction on Melanocytes. Supplementary Figure S15. p16 Loss Results in Partial Proliferation Rescue in BRAFV600E Nevus Melanocytes.
Supplementary Text from Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers
Authors: Pickering Curtis R. , Zhang Jiexin , Yoo Suk Young , Bengtsson Linnea , Moorthy Shhyam , Neskey David M. , Zhao Mei , Ortega Alves Marcus V. , Chang Kyle , Drummond Jennifer , Cortez Elsa , Xie Tong-xin , Zhang Di , Chung Woonbok , Issa Jean-Pierre J. , Zweidler-McKay Patrick A. , Wu Xifeng , El-Naggar Adel K. , Weinstein John N. , Wang Jing , Muzny Donna M. , Gibbs Richard A. , Wheeler David A. , Myers Jeffrey N. , Frederick Mitchell J.
Published: April 2023

Supplementary Text - PDF file 435K, This file contains supplementary methods, figure legends for supplementary figures S1-S5, descriptions for supplementary tables S1-S14, legends for supplementary methods figures SM1-SM15, supplementary references 1-7, and supplementary methods figures SM1-SM15
Supplementary Methods from Mutant KRAS–Induced Expression of ICAM-1 in Pancreatic Acinar Cells Causes Attraction of Macrophages to Expedite the Formation of Precancerous Lesions
Authors: Liou Geou-Yarh , Döppler Heike , Necela Brian , Edenfield Brandy , Zhang Lizhi , Dawson David W. , Storz Peter
Published: April 2023

Supplementary Methods
Supplementary Tables from Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers
Authors: Pickering Curtis R. , Zhang Jiexin , Yoo Suk Young , Bengtsson Linnea , Moorthy Shhyam , Neskey David M. , Zhao Mei , Ortega Alves Marcus V. , Chang Kyle , Drummond Jennifer , Cortez Elsa , Xie Tong-xin , Zhang Di , Chung Woonbok , Issa Jean-Pierre J. , Zweidler-McKay Patrick A. , Wu Xifeng , El-Naggar Adel K. , Weinstein John N. , Wang Jing , Muzny Donna M. , Gibbs Richard A. , Wheeler David A. , Myers Jeffrey N. , Frederick Mitchell J.
Published: April 2023

Supplementary Tables -XLSX file 2328K, This file contains supplemental tables S1-S14. These tables describe the clinical, pathological and genomic information for this study. Also included are GISTIC peak information, expression and copy number correlations, additional expression and methylation data, sequencing coverage and mutation data for patients and cell lines, and expanded pathway and targeted event information
Supplementary Figure S6 from Mutant KRAS–Induced Expression of ICAM-1 in Pancreatic Acinar Cells Causes Attraction of Macrophages to Expedite the Formation of Precancerous Lesions
Authors: Liou Geou-Yarh , Döppler Heike , Necela Brian , Edenfield Brandy , Zhang Lizhi , Dawson David W. , Storz Peter
Published: April 2023

Supplementary Figure S6 shows an analysis of ADM events in 3D explant culture in presence of the MMP inhibitor GM6001.
Supplementary Figure S5 from Mutant KRAS–Induced Expression of ICAM-1 in Pancreatic Acinar Cells Causes Attraction of Macrophages to Expedite the Formation of Precancerous Lesions
Authors: Liou Geou-Yarh , Döppler Heike , Necela Brian , Edenfield Brandy , Zhang Lizhi , Dawson David W. , Storz Peter
Published: April 2023

Supplementary Figure S5 shows the treatment schedule (A), additional controls (B), basic complete blood count tests (C), and analysis for T-cells and neutrophils (D) for Figure 3F.
Supplementary Figure 8 from RapidCaP, a Novel GEM Model for Metastatic Prostate Cancer Analysis and Therapy, Reveals Myc as a Driver of Pten-Mutant Metastasis
Authors: Cho Hyejin , Herzka Tali , Zheng Wu , Qi Jun , Wilkinson John E. , Bradner James E. , Robinson Brian D. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Trotman Lloyd C.
Published: April 2023

PDF file 63K, JQ1 suppresses Myc transcription in RapidCaP prostates and lymph nodes
Supplementary Figure 6 from RapidCaP, a Novel GEM Model for Metastatic Prostate Cancer Analysis and Therapy, Reveals Myc as a Driver of Pten-Mutant Metastasis
Authors: Cho Hyejin , Herzka Tali , Zheng Wu , Qi Jun , Wilkinson John E. , Bradner James E. , Robinson Brian D. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Trotman Lloyd C.
Published: April 2023

PDF file 218K, Histological analysis of castration resistant prostate cancer reveals the Akt-Myc switch
Supplementary Figure S1 from Mutant KRAS–Induced Expression of ICAM-1 in Pancreatic Acinar Cells Causes Attraction of Macrophages to Expedite the Formation of Precancerous Lesions
Authors: Liou Geou-Yarh , Döppler Heike , Necela Brian , Edenfield Brandy , Zhang Lizhi , Dawson David W. , Storz Peter
Published: April 2023

Supplementary Figure S1 shows the treatment scheme for GdCl3 (A), and analysis of tissue for T-cells and neutrophils (B), or for presence of PanIN lesions (C).
Supplementary Figure 5 from RapidCaP, a Novel GEM Model for Metastatic Prostate Cancer Analysis and Therapy, Reveals Myc as a Driver of Pten-Mutant Metastasis
Authors: Cho Hyejin , Herzka Tali , Zheng Wu , Qi Jun , Wilkinson John E. , Bradner James E. , Robinson Brian D. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Trotman Lloyd C.
Published: April 2023

PDF file 137K, Live monitoring of disease progression in castrated and mock castrated RapidCaP mice
Supplementary Tables 1 - 9 from Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition
Authors: Puissant Alexandre , Frumm Stacey M. , Alexe Gabriela , Bassil Christopher F. , Qi Jun , Chanthery Yvan H. , Nekritz Erin A. , Zeid Rhamy , Gustafson William Clay , Greninger Patricia , Garnett Matthew J. , McDermott Ultan , Benes Cyril H. , Kung Andrew L. , Weiss William A. , Bradner James E. , Stegmaier Kimberly
Published: April 2023

PDF file - 93K, This file contains 9 supplementary tables including the full primary screening data and secondary testing of BETi in neuroblastoma, supporting tables for the expression profiling analyses, and the list of Affymetrix probes (MYCN) and shRNA sequences for BRD4 and MYCN.
Supplementary Table S1 from Safety and Activity of the First-in-Class Sym004 Anti-EGFR Antibody Mixture in Patients with Refractory Colorectal Cancer
Authors: Dienstmann Rodrigo , Patnaik Amita , Garcia-Carbonero Rocio , Cervantes Andrés , Benavent Marta , Roselló Susana , Tops Bastiaan B.J. , van der Post Rachel S. , Argilés Guillem , Skartved Niels J.Ø. , Hansen Ulla H. , Hald Rikke , Pedersen Mikkel W. , Kragh Michael , Horak Ivan D. , Braun Stephan , Van Cutsem Eric , Tolcher Anthony W. , Tabernero Josep
Published: April 2023

Supplementary Table S1. Related adverse events (occurring in {greater than or equal to}10% of the patients) and related serious adverse events (all events) by system organ class and preferred term.
Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib
Authors: Wagle Nikhil , Grabiner Brian C. , Van Allen Eliezer M. , Hodis Eran , Jacobus Susanna , Supko Jeffrey G. , Stewart Michelle , Choueiri Toni K. , Gandhi Leena , Cleary James M. , Elfiky Aymen A. , Taplin Mary Ellen , Stack Edward C. , Signoretti Sabina , Loda Massimo , Shapiro Geoffrey I. , Sabatini David M. , Lander Eric S. , Gabriel Stacey B. , Kantoff Philip W. , Garraway Levi A. , Rosenberg Jonathan E.
Published: April 2023

PDF file 249K, Effect of pazopanib on S6K1 phosphorylation in cells expressing activating MTOR mutations
Data Supplement from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib
Authors: Wagle Nikhil , Grabiner Brian C. , Van Allen Eliezer M. , Hodis Eran , Jacobus Susanna , Supko Jeffrey G. , Stewart Michelle , Choueiri Toni K. , Gandhi Leena , Cleary James M. , Elfiky Aymen A. , Taplin Mary Ellen , Stack Edward C. , Signoretti Sabina , Loda Massimo , Shapiro Geoffrey I. , Sabatini David M. , Lander Eric S. , Gabriel Stacey B. , Kantoff Philip W. , Garraway Levi A. , Rosenberg Jonathan E.
Published: April 2023

PDF file 196K, The Data Supplement contains Supplementary Tables 1-3, which provide additional detail about the clinical trial as well as Supplementary Methods and References
Supplementary Table 1 from Inflammatory Myofibroblastic Tumors Harbor Multiple Potentially Actionable Kinase Fusions
Authors: Lovly Christine M. , Gupta Abha , Lipson Doron , Otto Geoff , Brennan Tina , Chung Catherine T. , Borinstein Scott C. , Ross Jeffrey S. , Stephens Philip J. , Miller Vincent A. , Coffin Cheryl M.
Published: April 2023

PDF file - 87KB, Changes in the indicated laboratory parameters after 3 cycles of crizotinib. HgB: hemoglobin, Hct: hematocrit, MCV: mean corpuscular volume, ESR: erythrocyte sedimentation rate, LDH: lactate dehydrogenase.
Supplementary Table S2 from Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors
Authors: Frampton Garrett M. , Ali Siraj M. , Rosenzweig Mark , Chmielecki Juliann , Lu Xinyuan , Bauer Todd M. , Akimov Mikhail , Bufill Jose A. , Lee Carrie , Jentz David , Hoover Rick , Ou Sai-Hong Ignatius , Salgia Ravi , Brennan Tim , Chalmers Zachary R. , Jaeger Savina , Huang Alan , Elvin Julia A. , Erlich Rachel , Fichtenholtz Alex , Gowen Kyle A. , Greenbowe Joel , Johnson Adrienne , Khaira Depinder , McMahon Caitlin , Sanford Eric M. , Roels Steven , White Jared , Greshock Joel , Schlegel Robert , Lipson Doron , Yelensky Roman , Morosini Deborah , Ross Jeffrey S. , Collisson Eric , Peters Malte , Stephens Philip J. , Miller Vincent A.
Published: April 2023

Summary of MET exon 14 alterations.
Supplementary Figure 5 from Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Authors: Ye Jiangbin , Fan Jing , Venneti Sriram , Wan Ying-Wooi , Pawel Bruce R. , Zhang Ji , Finley Lydia W.S. , Lu Chao , Lindsten Tullia , Cross Justin R. , Qing Guoliang , Liu Zhandong , Simon M. Celeste , Rabinowitz Joshua D. , Thompson Craig B.
Published: April 2023

Kelly cells stably expressing non-targeting shRNA (shNT) or SHMT2 shRNA (shSHMT2) were exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 48 hours incubated with glucose concentrations indicated, % cell viability was determined using Trypan Blue staining (Data represent Mean {plus minus} S.D from three biological repeats).
Supplementary Figures S1 - S10, Tables S1 - S3 from Mutation-Specific RAS Oncogenicity Explains NRAS Codon 61 Selection in Melanoma
Authors: Burd Christin E. , Liu Wenjin , Huynh Minh V. , Waqas Meriam A. , Gillahan James E. , Clark Kelly S. , Fu Kailing , Martin Brit L. , Jeck William R. , Souroullas George P. , Darr David B. , Zedek Daniel C. , Miley Michael J. , Baguley Bruce C. , Campbell Sharon L. , Sharpless Norman E.
Published: April 2023

Figure S1. Generation of the LSL-N-RasQ61R allele. Figure S2. Conditional expression of N-Ras mutants does not alter melanocyte morphology. Figure S3. In both the heterozygous and homozygous state, NRasG12D fails to induce melanoma formation. Figure S4. Melanocyte-specific N-RASQ61R expression causes high penetrance nevus formation. Figure S5. Characteristics of Ras-mutant murine melanocytes and melanomas. Figure S6. Establishment and validation of TpLN61R/61R tumor cell lines. Figure S7. Binding of NRAS61R-mant-GMPPNP to PI3Kγ and RAF-RBD. Figure S8. NRASG12D and NRASQ61R similarly bind BRAF as measured by isothermal titration calorimetry. Figure S9. Proliferation of NRAS mutant human melanoma cell lines is not codon-specific. Figure S10. Activation of ERK and AKT in melanocytes is not codon-specific. Table S1. Frequency of canonical RAS mutations in human cancer. Table S2. Comparative stability of GMPPCP- and GDP- bound NRAS variants. Table S3. Summary of prior RAS-driven murine melanoma models.
Supplementary Figure 3 from Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Authors: Ye Jiangbin , Fan Jing , Venneti Sriram , Wan Ying-Wooi , Pawel Bruce R. , Zhang Ji , Finley Lydia W.S. , Lu Chao , Lindsten Tullia , Cross Justin R. , Qing Guoliang , Liu Zhandong , Simon M. Celeste , Rabinowitz Joshua D. , Thompson Craig B.
Published: April 2023

(A) Immunoblots of N-Myc and c-Myc in the six cell lines. (B, C) H293T and HT1080 cells were exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 6 or 16 hours, (D) H1299 cells were exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 16 hours. mRNA levels were measured using Q-PCR and normalized to normoxia control.
Supplementary Figure 2 from Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Authors: Ye Jiangbin , Fan Jing , Venneti Sriram , Wan Ying-Wooi , Pawel Bruce R. , Zhang Ji , Finley Lydia W.S. , Lu Chao , Lindsten Tullia , Cross Justin R. , Qing Guoliang , Liu Zhandong , Simon M. Celeste , Rabinowitz Joshua D. , Thompson Craig B.
Published: April 2023

The hypoxic induction of SHMT2 depends on HIF-1alpha. SK-N-BE(2) cells stably expressing non-targeting shRNA or a shRNA against HIF-1alpha were exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 8 hours. mRNA levels were measured using Q-PCR and normalized to normoxia control.
Supplementary Materials and Methods from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 93K, This file contains detailed description of experimental procedures as well as reagents utilized
Supplementary Figure 1B from Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Authors: Ye Jiangbin , Fan Jing , Venneti Sriram , Wan Ying-Wooi , Pawel Bruce R. , Zhang Ji , Finley Lydia W.S. , Lu Chao , Lindsten Tullia , Cross Justin R. , Qing Guoliang , Liu Zhandong , Simon M. Celeste , Rabinowitz Joshua D. , Thompson Craig B.
Published: April 2023

Kaplan-Meier survival analysis in human breast cancer patients.
Supplementary Figure S7 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 1129K, Supplementary Figure S7. Combined MEK and AKT inhibition improves antitumor efficacy in vivo. Pulsatile administration of the PI3K inhibitor is effective. Related to main Figure 7
Supplementary Figure S6 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 40K, Supplementary Figure S6. Induction of apoptosis by PI3K inhibition in HER2-amplified cells. Related to main Figure 6
Supplementary Figure S5 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 1177K, Supplementary Figure S5. PI3K regulates the level of active RAS in RAS wild type cells. Related to main Figure 5
Supplementary Methods from Activation of the PD-1 Pathway Contributes to Immune Escape in EGFR-Driven Lung Tumors
Authors: Akbay Esra A. , Koyama Shohei , Carretero Julian , Altabef Abigail , Tchaicha Jeremy H. , Christensen Camilla L. , Mikse Oliver R. , Cherniack Andrew D. , Beauchamp Ellen M. , Pugh Trevor J. , Wilkerson Matthew D. , Fecci Peter E. , Butaney Mohit , Reibel Jacob B. , Soucheray Margaret , Cohoon Travis J. , Janne Pasi A. , Meyerson Matthew , Hayes D. Neil , Shapiro Geoffrey I. , Shimamura Takeshi , Sholl Lynette M. , Rodig Scott J. , Freeman Gordon J. , Hammerman Peter S. , Dranoff Glenn , Wong Kwok-Kin
Published: April 2023

- PDF file 306K, MRI tumor volume quantification, lists for all the antibodies used in the experiments, gating method for Flow cytometry analysis, and supplementary references
Supplementary Figure S3 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 778K, Supplementary Figure S3. Pan PI3K inhibitor GDC-0941 downregulates ERK phosphorylation. Related to main Figure 3
Supplementary Figure Legends from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 67K, This file contains legends for supplementary figures S1-S7. It describes in detail what's included in each figure
Supplementary Table 3 from A Coding Single-Nucleotide Polymorphism in Lysine Demethylase KDM4A Associates with Increased Sensitivity to mTOR Inhibitors
Authors: Van Rechem Capucine , Black Joshua C. , Greninger Patricia , Zhao Yang , Donado Carlos , Burrowes Paul d. , Ladd Brendon , Christiani David C. , Benes Cyril H. , Whetstine Johnathan R.
Published: April 2023

Supplementary Table 3. List of drugs and primary targets used for the study.
Supplementary Table 2 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Table 2 - PDF file 113K, Mutant EGFR cell panel profiling of CO-1686
Supplementary Materials and Methods from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Materials and Methods - PDF file 179K, Supplemental materials and methods for Walter et al. manuscript
Supplementary Figure 9 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Figure 9 - PDF file 168K, NCI-H1975 parental and CO-1686 resistant clones cluster into distinct groups using an RNA-based EMT signature
Supplementary Figure 3 from A Coding Single-Nucleotide Polymorphism in Lysine Demethylase KDM4A Associates with Increased Sensitivity to mTOR Inhibitors
Authors: Van Rechem Capucine , Black Joshua C. , Greninger Patricia , Zhao Yang , Donado Carlos , Burrowes Paul d. , Ladd Brendon , Christiani David C. , Benes Cyril H. , Whetstine Johnathan R.
Published: April 2023

Supplementary Figure 3. Rapamycin treatment reduces KDM4A protein levels.
Supplementary Figure 2 from A Coding Single-Nucleotide Polymorphism in Lysine Demethylase KDM4A Associates with Increased Sensitivity to mTOR Inhibitors
Authors: Van Rechem Capucine , Black Joshua C. , Greninger Patricia , Zhao Yang , Donado Carlos , Burrowes Paul d. , Ladd Brendon , Christiani David C. , Benes Cyril H. , Whetstine Johnathan R.
Published: April 2023

Supplementary Figure 2. KDM4A SNP-A482 associates with increased cellular sensitivity to drugs targeting the mTOR pathway.
Supplementary Figure 7 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Figure 7 - PDF file 352K, H&E and immunohistochemical (Ki67) staining of tumors derived from EGFR mutant GEM models
Supplementary Figure 1 from A Coding Single-Nucleotide Polymorphism in Lysine Demethylase KDM4A Associates with Increased Sensitivity to mTOR Inhibitors
Authors: Van Rechem Capucine , Black Joshua C. , Greninger Patricia , Zhao Yang , Donado Carlos , Burrowes Paul d. , Ladd Brendon , Christiani David C. , Benes Cyril H. , Whetstine Johnathan R.
Published: April 2023

Supplementary Figure 1. KDM4A SNP-A482 (rs586339) correlates with worse outcome in NSCLC patients.
Supplementary Figure 5 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Figure 5 - PDF file 134K, Schedule dependence of CO-1686 antitumor activity in NCI-H1975 mode
Supplementary Methods and Figures from NUP98–PHF23 Is a Chromatin-Modifying Oncoprotein That Causes a Wide Array of Leukemias Sensitive to Inhibition of PHD Histone Reader Function
Authors: Gough Sheryl M. , Lee Fan , Yang Fan , Walker Robert L. , Zhu Yeulin J. , Pineda Marbin , Onozawa Masahiro , Chung Yang Jo , Bilke Sven , Wagner Elise K. , Denu John M. , Ning Yi , Xu Bowen , Wang Gang Greg , Meltzer Paul S. , Aplan Peter D.
Published: April 2023

PDF file 601K, Supplementary Methods. Figure S1. The NUP98-PHF23 (NP23) transgene and peripheral blood (PB) characteristics of NP23 mice. Figure S2. NP23 AML and pre-T LBL. Figure S3. NP23 bi-clonal AML/pre-T LBL, B-ALL and erythroid leukemias. Figure S4.Impaired hematopoietic development in NP23 progenitor cell populations. Figure S5. Validation of differential gene expression in NP23 tissues. Figure S6. NP23 cells are sensitive to disulfiram, an inhibitor of PHD domain H3K4me3 binding
Supplementary Materials and Methods from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors
Authors: Konieczkowski David J. , Johannessen Cory M. , Abudayyeh Omar , Kim Jong Wook , Cooper Zachary A. , Piris Adriano , Frederick Dennie T. , Barzily-Rokni Michal , Straussman Ravid , Haq Rizwan , Fisher David E. , Mesirov Jill P. , Hahn William C. , Flaherty Keith T. , Wargo Jennifer A. , Tamayo Pablo , Garraway Levi A.
Published: April 2023

PDF file 272K, This file contains an extended description of the materials and methods used to generate steady-state protein expression, drug sensitivity, lysate generation and blotting techniques along with all DNA sequences for loss of function reagents
Supplementary Figures from A Novel AKT1 Mutant Amplifies an Adaptive Melanoma Response to BRAF Inhibition
Authors: Shi Hubing , Hong Aayoung , Kong Xiangju , Koya Richard C. , Song Chunying , Moriceau Gatien , Hugo Willy , Yu Clarissa C. , Ng Charles , Chodon Thinle , Scolyer Richard A. , Kefford Richard F. , Ribas Antoni , Long Georgina V. , Lo Roger S.
Published: April 2023

PDF file 1160K, This file contains all supplementary data including key controls experiments for IHC, IHC data quantification, PDGFRbeta IHCs, Western blots of a large melanoma cell line panel, presentation of DTP and DTPP concepts, PDGFRbeta expression analysis of live vs. dead sub-populations, and additional clonogenic assays and drug titrations
Supplementary Figure S5 from Suppression of Early Hematogenous Dissemination of Human Breast Cancer Cells to Bone Marrow by Retinoic Acid–Induced 2
Authors: Werner Stefan , Brors Benedikt , Eick Julia , Marques Elsa , Pogenberg Vivian , Parret Annabel , Kemming Dirk , Wood Antony W. , Edgren Henrik , Neubauer Hans , Streichert Thomas , Riethdorf Sabine , Bedi Upasana , Baccelli Irène , Jücker Manfred , Eils Roland , Fehm Tanja , Trumpp Andreas , Johnsen Steven A. , Klefström Juha , Wilmanns Matthias , Müller Volkmar , Pantel Klaus , Wikman Harriet
Published: April 2023

Supplementary Figure S5. Quantification of CAMA-1 cells with mesenchymal transformed cellular morphology.
Supplementary Figures 1 - 5 from Dual Roles of RNF2 in Melanoma Progression
Authors: Rai Kunal , Akdemir Kadir C. , Kwong Lawrence N. , Fiziev Petko , Wu Chang-Jiun , Keung Emily Z. , Sharma Sneha , Samant Neha S. , Williams Maura , Axelrad Jacob B. , Shah Amiksha , Yang Dong , Grimm Elizabeth A. , Barton Michelle C. , Milton Denai R. , Heffernan Timothy P. , Horner James W. , Ekmekcioglu Suhendan , Lazar Alexander J. , Ernst Jason , Chin Lynda
Published: April 2023

Supplementary Figure 1. Western blots. Supplementary Figure 2. Graphs showing tumor volume from mice following intradermal injection of (A) HMEL-BRAF^V600E cells, (B) WM115 cells, (C) 1205 Lu cells, and (D) pMEL-NRAS^G12D overexpressing GFP, RNF2 wild-type or catalytic mutant derivatives (R70C or I53S). Supplementary Figure 3. (A) RNF expression in the melanoma expression data for normal skin, nevi, and primary tumors. Supplementary Figure 4. (A) Heat map showing clustering of top 10 percent deregulated genes in duplicates of expression data from RNF2^WT overexpressing compared to GFP overexpressing HMEL-BRAF^V600E cells. Supplementary Figure 5. Chromatin state analysis on HMEL-BRAF^V600E cells.
Supplementary Table 4 from Somatic ERCC2 Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma
Authors: Van Allen Eliezer M. , Mouw Kent W. , Kim Philip , Iyer Gopa , Wagle Nikhil , Al-Ahmadie Hikmat , Zhu Cong , Ostrovnaya Irina , Kryukov Gregory V. , O'Connor Kevin W. , Sfakianos John , Garcia-Grossman Ilana , Kim Jaegil , Guancial Elizabeth A. , Bambury Richard , Bahl Samira , Gupta Namrata , Farlow Deborah , Qu Angela , Signoretti Sabina , Barletta Justine A. , Reuter Victor , Boehm Jesse , Lawrence Michael , Getz Gad , Kantoff Philip , Bochner Bernard H. , Choueiri Toni K. , Bajorin Dean F. , Solit David B. , Gabriel Stacey , D'Andrea Alan , Garraway Levi A. , Rosenberg Jonathan E.
Published: April 2023

Significantly altered genes in clinical subsets. MutSigCV ranked lists for significantly mutated genes in the non-responders only (n = 25), the responders only (n = 25), and the ERCC2WT responders only (n = 16).
Supplementary Figure 5 from RHOA-FAK Is a Required Signaling Axis for the Maintenance of KRAS-Driven Lung Adenocarcinomas
Authors: Konstantinidou Georgia , Ramadori Giorgio , Torti Francesca , Kangasniemi Kim , Ramirez Rachel E. , Cai Yiran , Behrens Carmen , Dellinger Michael T. , Brekken Rolf A. , Wistuba Ignacio I. , Heguy Adriana , Teruya-Feldstein Julie , Scaglioni Pier Paolo
Published: April 2023

Supplementary Figure 5 PDF file - 199K, This Figure shows that FAK is a critical target of RHOA in mutant KRAS;INK4a/ARF deficient NSCLC cells
Supplementary Figure 3 from RHOA-FAK Is a Required Signaling Axis for the Maintenance of KRAS-Driven Lung Adenocarcinomas
Authors: Konstantinidou Georgia , Ramadori Giorgio , Torti Francesca , Kangasniemi Kim , Ramirez Rachel E. , Cai Yiran , Behrens Carmen , Dellinger Michael T. , Brekken Rolf A. , Wistuba Ignacio I. , Heguy Adriana , Teruya-Feldstein Julie , Scaglioni Pier Paolo
Published: April 2023

Supplementary Figure 3 PDF file - 76K, This Figure shows the knockdown efficiency of shRNAs against KRAS and that MEK1/2 inhibition suppresses RHOA
Supplementary Figure Legends from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Authors: Bakhoum Samuel F. , Kabeche Lilian , Murnane John P. , Zaki Bassem I. , Compton Duane A.
Published: April 2023

Supplementary Figure Legends from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Supplementary Figure 1 from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Authors: Bakhoum Samuel F. , Kabeche Lilian , Murnane John P. , Zaki Bassem I. , Compton Duane A.
Published: April 2023

A, Example of an anaphase spindle with lagging chromosomes and the number of lagging chromosomes per anaphase spindle as a function of IR dose. B, Example of a multipolar anaphase spindle and the percentage of anaphase spindles with acentric chromatin as a function of IR dose. C, Example of an anaphase spindle with acentric chromatin fragments and the number of multipolar mitoses as a function of IR dose. Circles represent mean {plus minus} s.e.m, n = 150 cells, 3 experiments. Representative mitotic spindles are stained for Hec1 to denote kinetochores (green), DNA (blue), and microtubules (red). Scale bar 5-Î¼m.
Supplementary Table 1 from l-2-Hydroxyglutarate: An Epigenetic Modifier and Putative Oncometabolite in Renal Cancer
Authors: Shim Eun-Hee , Livi Carolina B. , Rakheja Dinesh , Tan Jubilee , Benson Daniel , Parekh Vishwas , Kho Eun-Young , Ghosh Arindam P. , Kirkman Richard , Velu Sadanan , Dutta Shilpa , Chenna Balachandra , Rea Shane L. , Mishur Robert J. , Li Qiuhua , Johnson-Pais Teresa L. , Guo Lining , Bae Sejong , Wei Shi , Block Karen , Sudarshan Sunil
Published: April 2023

Supplementary Table 1. Clinical Data on Tumor Samples.
Supplementary Figure Legend from The ALK Inhibitor Ceritinib Overcomes Crizotinib Resistance in Non–Small Cell Lung Cancer
Authors: Friboulet Luc , Li Nanxin , Katayama Ryohei , Lee Christian C. , Gainor Justin F. , Crystal Adam S. , Michellys Pierre-Yves , Awad Mark M. , Yanagitani Noriko , Kim Sungjoon , Pferdekamper AnneMarie C. , Li Jie , Kasibhatla Shailaja , Sun Frank , Sun Xiuying , Hua Su , McNamara Peter , Mahmood Sidra , Lockerman Elizabeth L. , Fujita Naoya , Nishio Makoto , Harris Jennifer L. , Shaw Alice T. , Engelman Jeffrey A.
Published: April 2023

PDF file 100K, Legends for the supplementary figures
Supplementary Figures from First-in-Humans Trial of an RNA Interference Therapeutic Targeting VEGF and KSP in Cancer Patients with Liver Involvement
Authors: Tabernero Josep , Shapiro Geoffrey I. , LoRusso Patricia M. , Cervantes Andres , Schwartz Gary K. , Weiss Glen J. , Paz-Ares Luis , Cho Daniel C. , Infante Jeffrey R. , Alsina Maria , Gounder Mrinal M. , Falzone Rick , Harrop Jamie , White Amy C. Seila , Toudjarska Iva , Bumcrot David , Meyers Rachel E. , Hinkle Gregory , Svrzikapa Nenad , Hutabarat Renta M. , Clausen Valerie A. , Cehelsky Jeffrey , Nochur Saraswathy V. , Gamba-Vitalo Christina , Vaishnaw Akshay K. , Sah Dinah W.Y. , Gollob Jared A. , Burris Howard A.
Published: April 2023

Supplementary Figures PDF file - 114K, Includes sequence information on KSP and VEGF siRNAs, murine Hep3B tumor model data with ALN-VSP, ALN-VSP Phase I study design, KSP and VEGF mRNA levels in tumor cell lines and normal liver, and comparison of ALN-VSP PK data in cancer patients and non-human primates