bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods, Figures S1 - S9 from Access to Follicular Dendritic Cells Is a Pivotal Step in Murine Chronic Lymphocytic Leukemia B-cell Activation and Proliferation
Authors: Heinig Kristina , Gätjen Marcel , Grau Michael , Stache Vanessa , Anagnostopoulos Ioannis , Gerlach Kerstin , Niesner Raluca A. , Cseresnyes Zoltan , Hauser Anja E. , Lenz Peter , Hehlgans Thomas , Brink Robert , Westermann Jörg , Dörken Bernd , Lipp Martin , Lenz Georg , Rehm Armin , Höpken Uta E.
Published: April 2023

Figure S1. Gating strategy to characterize and quantitate CD19+CD5+ leukemia Emu-Tcl1 cell frequencies and homeostatic chemokine receptor expression on splenic, LN, PB, and BM derived CD19+CD5+ gated Emu-Tcl1 tumor cells. This Figure complements Figure 1. Figure S2. Surface marker expression of murine Emu-Tcl1 leukemia cells is shown. Human primary B-CLL cells share characteristic expression of CXCR5. This Figure complements Figure 1. Figure S3. Enrichment plots of seven proliferation-related signatures are presented. Short term transfer of CXCR5+/+Emu-Tcl1 or CXCR5-/-Emu-Tcl1 tumor cells shows upregulation of the gene encoding the cell-cycle inhibitor p21 in CXCR5-deficient leukemia cells. Growth and activation delay of CXCR5-/- Emu-Tcl1 tumor cells can be reversed by direct contacts with stromal cells in vitro. This Figure complements Figure 2. Figure S4. (A) shows that CCR7-deficiency on leukemia cells does not affect their migratory behavior and complements Figure 3. (B) Ebi2-/-Emu-Tcl1 leukemia cells enter B cell follicles and the GC light zone area in a pattern comparable to Ebi2++Emu-Tcl1 leukemia cells, as presented in Figure 4, and (C) tumor growth of Ebi2-/-Emu-Tcl1 mice is unaltered compared to Wt Emu-Tcl1 mice. Figure S5. Human primary B-CLLs exhibit a characteristic FDC staining. This Figure complements Figure 4. Figure S6. Pertussis toxin (PTX) treatment induces apoptosis in Emu-Tcl leukemia cells co-cultured with FDC-HK stroma cells. This Figure complements Figure 4. Figure S7. Intravital application of anti-CD21/CD35 Fab fragments stains specifically GC light zone localized FDCs. These stainings complement Figure 5. Figure S8. Challenge of Rag2-/- mice with Emu-Tcl1 leukemia B cells induces FDC networks and a tumor cell-promoting cytokine and chemokine secretion. This Figure accompanies Figure 6. Figure S9. Abrogation of LTbetaR-signaling leads to disappearance of characteristic stromal elements within the B cell follicle; however, CD31+ blood vessels are not affected. In accordance with Figure 7, Ltalpha -/- Emu-Tcl1 mice exhibit substantially delayed leukemia growth and progression.
Supplementary Data from PTEN-Deficient Tumors Depend on AKT2 for Maintenance and Survival
Authors: Chin Y. Rebecca , Yuan Xin , Balk Steven P. , Toker Alex
Published: April 2023

PDF file 1017K, Figure S1 shows the functions of Akt1 and Akt2 in the proliferation and migration of prostate tumor cells. Figure S2 demonstrates that all three Akt isoforms play a critical role in MDA-MB-468 breast cancer cell proliferation and formation of tumor spheroids. Figure S3 shows that Akt2 does not play a critical role in the survival of tumor cells with wild-type PTEN. Figure S4 shows the expression and phosphorylation levels of Akt1 and Akt2 in prostate tumor cells. Figure S5 demonstrates a critical role of p21 in Akt2-mediated cell cycle progression. Figure S6 shows that Bax does not play a role in Akt2-mediated spheroid survival. Figure S7 shows the volume of individual tumors measured in the xenograft studies for Fig. 6A
Supplementary Figure 9 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 9 - PDF file 150K, Gating strategy, sorting efficiency, and TbetaRII expression in myeloid cell subsets
Supplementary Figure 3 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 3 - PDF file 76K, IFN-gamma production by T cells and its effect on tumor growth in Tgfbr2MyeKOand Tgfbr2flox/flox control mice
Supplementary Figure 2 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 2 - PDF file 42K, The effect of myeloid specific deletion of Tgfbr2 on tumor growth and metastasis
Supplementary Table S7 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

Variants identified from WES of 92 tumors after filtering.
Supplementary Table 3 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 3. Analysis of the statistical significance of mutations.
Supplementary Fig. 3 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

PDF file 124K, Involvement of LUBAC in CBM complex mediated NF-kappaB activation, related to main figure 3
Supplementary Fig. 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

PDF file 283K, RNF31 DNA sequence electropherograms for the region corresponding to the single nucleotide polymorphisms (SNPs)
Supplementary Tables from CD74–NRG1 Fusions in Lung Adenocarcinoma
Authors: Fernandez-Cuesta Lynnette , Plenker Dennis , Osada Hirotaka , Sun Ruping , Menon Roopika , Leenders Frauke , Ortiz-Cuaran Sandra , Peifer Martin , Bos Marc , Daßler Juliane , Malchers Florian , Schöttle Jakob , Vogel Wenzel , Dahmen Ilona , Koker Mirjam , Ullrich Roland T. , Wright Gavin M. , Russell Prudence A. , Wainer Zoe , Solomon Benjamin , Brambilla Elisabeth , Nagy-Mignotte Hélène , Moro-Sibilot Denis , Brambilla Christian G. , Lantuejoul Sylvie , Altmüller Janine , Becker Christian , Nürnberg Peter , Heuckmann Johannes M. , Stoelben Erich , Petersen Iver , Clement Joachim H. , Sänger Jörg , Muscarella Lucia A. , la Torre Annamaria , Fazio Vito M. , Lahortiga Idoya , Perera Timothy , Ogata Souichi , Parade Marc , Brehmer Dirk , Vingron Martin , Heukamp Lukas C. , Buettner Reinhard , Zander Thomas , Wolf Jürgen , Perner Sven , Ansén Sascha , Haas Stefan A. , Yatabe Yasushi , Thomas Roman K.
Published: April 2023

XLSX file 75K, This is an excel file containing 9 sheets, one for each of the 9 supplementary tables (S1 to S9) mentioned in the main text
Figure S7 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 856K, KRas is required for proliferation before and after the induction of EMT
Figure S5 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 1151K, ErbB3 and NRG1 promote Akt activity in H441 and H2122 cells and ErbB3 knockdown reduces serum-independent proliferation
Supplementary Table S4 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

Gene expression levels in GIST cell lines.
Figure S2 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 838K, The effects of TGF-beta1 are specific to epithelial cells and lead to reduced serum-independent proliferation
Figure S1 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 921K, Akt inhibition reduces serum-independent proliferation
Supplementary Table 1 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 Table 1. Complete list of somatic mutations and copy number alterations detected by IMPACT in 79 stage IV SQCLC patients with clinical annotation.
Supplementary Figures 1 - 2 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 1. Copy number pattern in paired lung cancer primaries and brain metastases from patients PP1, PP2, and PP4. Red, blue, and white indicate gain, loss, neutral states, respectively. The total number of shared cytobands (percent shared) between the primary and brain metastases are indicated at the bottom. Supplementary Figure 2A. Genome-wide copy number profile of the PP1 brain metastasis (A) and lung primary (B). Total log-copy ratio (logR) in the tumor versus normal and minor allele frequency (MAF) in the tumor are plotted. Yellow line represents joint segmentation of logR and MAF. Supplementary Figure 2B. Genome-wide copy number profile of the PP4 brain metastasis (A) and lung primary (B). Supplementary Figure 2C. Genome-wide copy number profile of the PP2 brain metastasis (A) and lung primary (B). Pooled normal was used to generate the logR plot. Supplementary Figure 2D. Genome-wide copy number profile of the PP3 brain metastasis (A) and PP5 brain metastasis (B).
Supplementary Figure 3 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 152K, Histological analysis reveals characteristics of metastasis in RapidCaP
Supplementary Figures 1 -11 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 - 326K, This file contains 11 supplementary figures with biochemistry, computational analysis, in vitro and in vivo studies to support the role of targeting MYCN in neuroblastoma with BETi.
Supplementary Figure Legend 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 - 35K
Supplementary Figure 1 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 428K, Virus injection delivers target genes to epithelial prostate without immune reaction
Supplementary Figure 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 Figure S1. Pharmacokinetic profile of Sym004.
Supplementary Figure Legends, Table Legends 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 - 77KB
Supplementary Figure Legends 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 92K, Legends to supplementary figures 1-11
Supplementary Table 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 Table 2. Lung cell lines homozygotes for KDM4A SNP-A482 are not enriched for mutations that could be linked to sensitivity to PI3K/mTOR inhibitors.
Supplementary Figure Legends 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 Legends
Supplementary Figure 8 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 8 - PDF file 215K, Photomicrographs of CO-1686 resistant NCI-H1975 cell (COR) clones and quantification of EGFR siRNA knockdown in COR clones
Supplementary Figure S4 from Unbiased Metabolite Profiling Indicates That a Diminished Thymidine Pool Is the Underlying Mechanism of Colon Cancer Chemoprevention by Alpha-Difluoromethylornithine
Authors: Witherspoon Mavee , Chen Qiuying , Kopelovich Levy , Gross Steven S. , Lipkin Steven M.
Published: April 2023

Supplementary Figure S4 - PDF file 23K, Fig S4. DFMO Normal Human Colon Tissue. Normal human colon tissues were treated with DFMO(300nM) for 4 days. After treatment metabolites were extracted and analyzed by LC MS/MS. S-adenosine methionine(SAM) downstream products methythioadenosine(MTA) and methionine were significantly reduced by DFMO treatment (N=5) p-value <0.01
Supplementary Figure 4 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 4 - PDF file 103K, Pharmacokinetic analysis of CO-1686 in nu/nu mice
Supplementary Figure S5 from Suppression of CHK1 by ETS Family Members Promotes DNA Damage Response Bypass and Tumorigenesis
Authors: Lunardi Andrea , Varmeh Shohreh , Chen Ming , Taulli Riccardo , Guarnerio Jlenia , Ala Ugo , Seitzer Nina , Ishikawa Tomoki , Carver Brett S. , Hobbs Robin M. , Quarantotti Valentina , Ng Christopher , Berger Alice H. , Nardella Caterina , Poliseno Laura , Montironi Rodolfo , Castillo-Martin Mireia , Cordon-Cardo Carlos , Signoretti Sabina , Pandolfi Pier Paolo
Published: April 2023

Supplementary Figure S5. ERG overexpression induces p53 activation through excessive DNA damage.
Supplementary Figure S2 from Suppression of CHK1 by ETS Family Members Promotes DNA Damage Response Bypass and Tumorigenesis
Authors: Lunardi Andrea , Varmeh Shohreh , Chen Ming , Taulli Riccardo , Guarnerio Jlenia , Ala Ugo , Seitzer Nina , Ishikawa Tomoki , Carver Brett S. , Hobbs Robin M. , Quarantotti Valentina , Ng Christopher , Berger Alice H. , Nardella Caterina , Poliseno Laura , Montironi Rodolfo , Castillo-Martin Mireia , Cordon-Cardo Carlos , Signoretti Sabina , Pandolfi Pier Paolo
Published: April 2023

Supplementary Figure S2. ETV1 represses CHK1 expression.
Supplementary Figure S1 from Suppression of CHK1 by ETS Family Members Promotes DNA Damage Response Bypass and Tumorigenesis
Authors: Lunardi Andrea , Varmeh Shohreh , Chen Ming , Taulli Riccardo , Guarnerio Jlenia , Ala Ugo , Seitzer Nina , Ishikawa Tomoki , Carver Brett S. , Hobbs Robin M. , Quarantotti Valentina , Ng Christopher , Berger Alice H. , Nardella Caterina , Poliseno Laura , Montironi Rodolfo , Castillo-Martin Mireia , Cordon-Cardo Carlos , Signoretti Sabina , Pandolfi Pier Paolo
Published: April 2023

Supplementary Figure S1. ERG downregulation of CHK1 is AR independent.
Table S6 from PDK1 Signaling Toward PLK1–MYC Activation Confers Oncogenic Transformation, Tumor-Initiating Cell Activation, and Resistance to mTOR-Targeted Therapy
Authors: Tan Jing , Li Zhimei , Lee Puay Leng , Guan Peiyong , Aau Mei Yee , Lee Shuet Theng , Feng Min , Lim Cheryl Zihui , Lee Eric Yong Jing , Wee Zhen Ning , Lim Yaw Chyn , Karuturi R.K. Murthy , Yu Qiang
Published: April 2023

Table S6 - XLS file 22K, Supplementary table 6 shows primers used for quantitative RT-PCR analysis
Supplementary Table 1 from Immune Cell–Poor Melanomas Benefit from PD-1 Blockade after Targeted Type I IFN Activation
Authors: Bald Tobias , Landsberg Jennifer , Lopez-Ramos Dorys , Renn Marcel , Glodde Nicole , Jansen Philipp , Gaffal Evelyn , Steitz Julia , Tolba Rene , Kalinke Ulrich , Limmer Andreas , Jönsson Göran , Hölzel Michael , Tüting Thomas
Published: April 2023

XLS file 28K, List of top 50 interferon alpha induced gene across five humane melanoma cell lines
Supplementary Figures 1-2 from Immune Cell–Poor Melanomas Benefit from PD-1 Blockade after Targeted Type I IFN Activation
Authors: Bald Tobias , Landsberg Jennifer , Lopez-Ramos Dorys , Renn Marcel , Glodde Nicole , Jansen Philipp , Gaffal Evelyn , Steitz Julia , Tolba Rene , Kalinke Ulrich , Limmer Andreas , Jönsson Göran , Hölzel Michael , Tüting Thomas
Published: April 2023

PDF file 309K, Results of repeated dose acute toxicity study
Supplementary Figures S1-S19 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 615K, This file contains a series of additional experiments and analyses related to Main Figures 1-5, including more extensive transcript/drug sensitivity correlations, mRNA-expression validation experiments,IHC controls, confirmation of drug sensitivity predictions and perturbation experiments
Supplementary Figure 7 from Vulnerabilities of PTEN–TP53-Deficient Prostate Cancers to Compound PARP–PI3K Inhibition
Authors: González-Billalabeitia Enrique , Seitzer Nina , Song Su Jung , Song Min Sup , Patnaik Akash , Liu Xue-Song , Epping Mirjam T. , Papa Antonella , Hobbs Robin M. , Chen Ming , Lunardi Andrea , Ng Christopher , Webster Kaitlyn A. , Signoretti Sabina , Loda Massimo , Asara John M. , Nardella Caterina , Clohessy John G. , Cantley Lewis C. , Pandolfi Pier Paolo
Published: April 2023

PDF - 138K, Survival curves of the in vivo treatment of Olaparib and BKM120.
Supplementary Movie 4 from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: April 2023

Real-time intravital two-photon microscopy showing phagocytosis of a large, granular clump of bisphosphonate by a single tumour-associated macrophage.
Supplementary Figure 5 from Vulnerabilities of PTEN–TP53-Deficient Prostate Cancers to Compound PARP–PI3K Inhibition
Authors: González-Billalabeitia Enrique , Seitzer Nina , Song Su Jung , Song Min Sup , Patnaik Akash , Liu Xue-Song , Epping Mirjam T. , Papa Antonella , Hobbs Robin M. , Chen Ming , Lunardi Andrea , Ng Christopher , Webster Kaitlyn A. , Signoretti Sabina , Loda Massimo , Asara John M. , Nardella Caterina , Clohessy John G. , Cantley Lewis C. , Pandolfi Pier Paolo
Published: April 2023

PDF - 632K, Preclinical assessment of Olaparib and BKM120 treatment in vivo.
Supplementary Movie 1 from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: April 2023

Real-time intravital two-photon microscopy showing distribution of bisphosphonate in 4T1 breast tumour.
Supplementary Figure 3 from Vulnerabilities of PTEN–TP53-Deficient Prostate Cancers to Compound PARP–PI3K Inhibition
Authors: González-Billalabeitia Enrique , Seitzer Nina , Song Su Jung , Song Min Sup , Patnaik Akash , Liu Xue-Song , Epping Mirjam T. , Papa Antonella , Hobbs Robin M. , Chen Ming , Lunardi Andrea , Ng Christopher , Webster Kaitlyn A. , Signoretti Sabina , Loda Massimo , Asara John M. , Nardella Caterina , Clohessy John G. , Cantley Lewis C. , Pandolfi Pier Paolo
Published: April 2023

PDF - 14407K, Supporting histology for Olaparib treatment in vivo.
Supplementary Figures S1 - S3 from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: April 2023

Supplementary Figure S1. Fluorescently-labelled bisphosphonate is present in the macrophage-rich region of 4T1 mammary tumours in vivo. Supplementary Figure S2. N-BP colocalises with microcalcifications, detected by calcein labelling in 4T1 mammary tumours. Supplementary Figure S3. TAMs do not take up N-BP as efficiently in the B16.F10 melanoma model compared to the 4T1 mammary tumour model.
Supplementary Figure 1 from Vulnerabilities of PTEN–TP53-Deficient Prostate Cancers to Compound PARP–PI3K Inhibition
Authors: González-Billalabeitia Enrique , Seitzer Nina , Song Su Jung , Song Min Sup , Patnaik Akash , Liu Xue-Song , Epping Mirjam T. , Papa Antonella , Hobbs Robin M. , Chen Ming , Lunardi Andrea , Ng Christopher , Webster Kaitlyn A. , Signoretti Sabina , Loda Massimo , Asara John M. , Nardella Caterina , Clohessy John G. , Cantley Lewis C. , Pandolfi Pier Paolo
Published: April 2023

PDF - 546K, Olaparib induces a differing response in vitro depending on the genetic background.
Supplementary Methods, Table S1 - 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 Methods. Supplementary Table S1. Clinical data of analysed patients. Supplementary Table S2. List of genes significantly associated with the DTC status. Supplementary Table S3. Summary of data sets used for in silico validation. Supplementary Table S4. Multivariate analysis of RAI2 gene expression in diffrent breast cancer data sets. Supplementary Table S5. List of primers used for qPCR analysis.
Supplementary Table 3 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

Description of states in 45-state chromatin state model.This table describes the biological annotation of each chromatin state in 50-state chromatin model from HMEL-BRAFV600E cells from ChromHMM program.
Supplementary Table 1 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

Binding sites for RNF2 in HMEL-RNF2WT cells. This file contains list of all chromosomal locations that show enrichment by MACS for RNF2 binding by V5 ChIP-Seq in HMEL-RNF2 cells.
Supplementary Figure S3 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 S3. qPCR verification of RAI2 expression and correlative analysis of RAI2 mRNA expression in primary breast tumors.
Supplementary Methods, Figure Legends from First Selective Small Molecule Inhibitor of FGFR4 for the Treatment of Hepatocellular Carcinomas with an Activated FGFR4 Signaling Pathway
Authors: Hagel Margit , Miduturu Chandra , Sheets Michael , Rubin Nooreen , Weng Weifan , Stransky Nicolas , Bifulco Neil , Kim Joseph L. , Hodous Brian , Brooijmans Natasja , Shutes Adam , Winter Christopher , Lengauer Christoph , Kohl Nancy E. , Guzi Timothy
Published: April 2023

Supplementary Methods and Figure Legends
Supplementary Figure S1 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 S1. Survival analysis in extreme quartiles of RAI2 expression in lung colon and ovarian cancer data sets.
Supplementary Figures S1 - S6, Tables S1 - S2 from First Selective Small Molecule Inhibitor of FGFR4 for the Treatment of Hepatocellular Carcinomas with an Activated FGFR4 Signaling Pathway
Authors: Hagel Margit , Miduturu Chandra , Sheets Michael , Rubin Nooreen , Weng Weifan , Stransky Nicolas , Bifulco Neil , Kim Joseph L. , Hodous Brian , Brooijmans Natasja , Shutes Adam , Winter Christopher , Lengauer Christoph , Kohl Nancy E. , Guzi Timothy
Published: April 2023

Supplementary Figure S1. Potency against FGFR family and kinome selectivity. Supplementary Figure S2. Kinases with a cysteine at the equivalent position to Cys552 in FGFR4. Supplementary Figure S3. MALDI Mass Spectrometry of FGFR4. Supplementary Figure S4. Induction of Caspase 3/7 activity in Hep 3B cells. Supplementary Figure S5. FGFR4 turnover rates in Hep 3B cells. Supplementary Figure S6. Analysis of TCGA HCC samples. Supplementary Table S1. Kinetic parameters of FGFR4 inhibition by BLU9931. Supplementary Table S2. Pharmacokinetic parameters for BLU9931.
Supplementary Table S1 from PI3′-Kinase Inhibition Forestalls the Onset of MEK1/2 Inhibitor Resistance in BRAF-Mutated Melanoma
Authors: Deuker Marian M. , Marsh Durban Victoria , Phillips Wayne A. , McMahon Martin
Published: April 2023

Supplementary Table S1. Pathway targeted inhibitors that were used to interrogate the role of class I PI3'-kinase isoforms in BRAFV600E-driven melanoma.
Supplementary Table 5 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

Damaging scores for alterations. This table shows the damaging scores (Methods) for nonsynonymous alterations (missense, nonsense, splice site, frame shift) studied in this cohort. The damaging score was derived as follows: missense mutations were scored using the Polyphen2 score(41) for the amino acid substitution. Nonsense mutations, splice site mutations, and short insertion/deletions were automatically assigned a damaging score of 1. "Unavailable" damaging scores are those that are missense mutations without a PolyPhen2 score.
Supplementary Figure Legends from PI3′-Kinase Inhibition Forestalls the Onset of MEK1/2 Inhibitor Resistance in BRAF-Mutated Melanoma
Authors: Deuker Marian M. , Marsh Durban Victoria , Phillips Wayne A. , McMahon Martin
Published: April 2023

Supplementary Figure Legends
Supplementary Methods from Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis
Authors: Parmenter Tiffany J. , Kleinschmidt Margarete , Kinross Kathryn M. , Bond Simon T. , Li Jason , Kaadige Mohan R. , Rao Aparna , Sheppard Karen E. , Hugo Willy , Pupo Gulietta M. , Pearson Richard B. , McGee Sean L. , Long Georgina V. , Scolyer Richard A. , Rizos Helen , Lo Roger S. , Cullinane Carleen , Ayer Donald E. , Ribas Antoni , Johnstone Ricky W. , Hicks Rodney J. , McArthur Grant A.
Published: April 2023

PDF file 658K, Supplementary Methods
Supplementary Table 3 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 the combined cohort. MutSigCV ranked list of significantly mutated genes across the entire cohort (n = 50 patients). Entries are sorted by q values. Entries with significant q values that failed manual review in Integrated Genomics Viewer (IGV) were marked as "Blacklist" in the Notes column and excluded from the final results (see Methods).
Supplementary Data 2 from Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis
Authors: Parmenter Tiffany J. , Kleinschmidt Margarete , Kinross Kathryn M. , Bond Simon T. , Li Jason , Kaadige Mohan R. , Rao Aparna , Sheppard Karen E. , Hugo Willy , Pupo Gulietta M. , Pearson Richard B. , McGee Sean L. , Long Georgina V. , Scolyer Richard A. , Rizos Helen , Lo Roger S. , Cullinane Carleen , Ayer Donald E. , Ribas Antoni , Johnstone Ricky W. , Hicks Rodney J. , McArthur Grant A.
Published: April 2023

XLS file 118K, Table listing gene sets identified by GSEA as significantly enriched in control versus vemurafenib treated A375 cells (FDR>0.25)
Supplementary Table 1 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

Treatment information and sequencing metrics for all patients The treatment information and raw sequencing metrics, including mean target coverage, for each case is listed here. In addition, the mutation rate data referred to in the Results and represented in Supplementary Figure 1 is listed here by synonymous rate, non-synonymous rate, and total number of mutations per patient. *Cases that were included in the TCGA effort (UC-0296 and UC-0234). (dd = dose dense, GC = gemcitabine/cisplatin, MVAC = methotrexate, vinblastine, doxorubicin, cisplatin). Unavailable cases for Fluidigm Validation (due to inadequate remaining DNA or technical failure) are also denoted (n = 15).
Supplementary Data 1 from Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis
Authors: Parmenter Tiffany J. , Kleinschmidt Margarete , Kinross Kathryn M. , Bond Simon T. , Li Jason , Kaadige Mohan R. , Rao Aparna , Sheppard Karen E. , Hugo Willy , Pupo Gulietta M. , Pearson Richard B. , McGee Sean L. , Long Georgina V. , Scolyer Richard A. , Rizos Helen , Lo Roger S. , Cullinane Carleen , Ayer Donald E. , Ribas Antoni , Johnstone Ricky W. , Hicks Rodney J. , McArthur Grant A.
Published: April 2023

XLS file 72K, Table describing the 300 genes whose mRNA expression were most significantly changed by vemurafenib treatment in A375 cells
Supplementary Figure and Table Legends 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

Supplementary Figure and Table Legends from Somatic ERCC2 Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma
Supplementary Movie S2 from An In Vivo Functional Screen Identifies ST6GalNAc2 Sialyltransferase as a Breast Cancer Metastasis Suppressor
Authors: Murugaesu Nirupa , Iravani Marjan , van Weverwijk Antoinette , Ivetic Aleksandar , Johnson Damian A. , Antonopoulos Aristotelis , Fearns Antony , Jamal-Hanjani Mariam , Sims David , Fenwick Kerry , Mitsopoulos Costas , Gao Qiong , Orr Nick , Zvelebil Marketa , Haslam Stuart M. , Dell Anne , Yarwood Helen , Lord Christopher J. , Ashworth Alan , Isacke Clare M.
Published: April 2023

MOV file 2886K, Video showing dynamic flow adhesion assays of ZR75.1 shNTC and shST6 cells on a HUVEC monolayer in the presence of the galectin-3 inhibitor GCS-100
Supplementary Figure S5 from An In Vivo Functional Screen Identifies ST6GalNAc2 Sialyltransferase as a Breast Cancer Metastasis Suppressor
Authors: Murugaesu Nirupa , Iravani Marjan , van Weverwijk Antoinette , Ivetic Aleksandar , Johnson Damian A. , Antonopoulos Aristotelis , Fearns Antony , Jamal-Hanjani Mariam , Sims David , Fenwick Kerry , Mitsopoulos Costas , Gao Qiong , Orr Nick , Zvelebil Marketa , Haslam Stuart M. , Dell Anne , Yarwood Helen , Lord Christopher J. , Ashworth Alan , Isacke Clare M.
Published: April 2023

PDF file 299K, Additional characterization of human breast cancer cell lines; immunofluorescence analysis and lung retention assays
Supplementary Figure 2 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 2 PDF file - 182K, This Figure shows the activation status of RhoA and Rac1 in mouse lungs and validation of RhoA-GTP antibody on mouse lung tissue by IHC
Supplementary Figure S2 from An In Vivo Functional Screen Identifies ST6GalNAc2 Sialyltransferase as a Breast Cancer Metastasis Suppressor
Authors: Murugaesu Nirupa , Iravani Marjan , van Weverwijk Antoinette , Ivetic Aleksandar , Johnson Damian A. , Antonopoulos Aristotelis , Fearns Antony , Jamal-Hanjani Mariam , Sims David , Fenwick Kerry , Mitsopoulos Costas , Gao Qiong , Orr Nick , Zvelebil Marketa , Haslam Stuart M. , Dell Anne , Yarwood Helen , Lord Christopher J. , Ashworth Alan , Isacke Clare M.
Published: April 2023

PDF file 325K, Additional validation of ST6GalNAc2 as a metastasis suppressor including in a spontaneous metastasis assay using the parental 4T1 cells
Supplementary Methods, Figures S1 - S7 from PtdIns(3,4,5)P3-Dependent Activation of the mTORC2 Kinase Complex
Authors: Liu Pengda , Gan Wenjian , Chin Y. Rebecca , Ogura Kohei , Guo Jianping , Zhang Jinfang , Wang Bin , Blenis John , Cantley Lewis C. , Toker Alex , Su Bing , Wei Wenyi
Published: April 2023

Figure S1. The Sin1-PH domain binds the mTOR kinase domain to inhibit mTOR kinase activity, Related to Figure 1. Figure S2. The PH domain is a unique and physiological functional PH domain, Related to Figure 2. Figure S3. PI(3,4,5)P3 binds the Sin1-PH motif to activate mTORC2, Related to Figure 3. Figure S4. The presence of PIP3 species leads to attenuated Sin1-PH domain interaction with mTOR-KD, Related to Figure 4. Figure S5. The Sin1-PH motif mainly interacts with PI(3,4,5)P3 through three critical residues including R393, K428 and K464, Related to Figure 5. Figure S6. The cancerous Sin1-PH mutant lose binding with the mTOR-kinase domain, leading to elevated Akt-S473 phosphorylation and enhanced oncogenic activities, Related to Figure 6. Figure S7. C-terminal tagging of KRas-CAAX to Sin1 could partially rescue the deficiency of the Sin1-CAA mutant in membrane recruitment and mTORC2 activation, Related to Figure 7.
Supplementary Methods, Figure Legends from PARP1-Driven Poly-ADP-Ribosylation Regulates BRCA1 Function in Homologous Recombination–Mediated DNA Repair
Authors: Hu Yiduo , Petit Sarah A. , Ficarro Scott B. , Toomire Kimberly J. , Xie Anyong , Lim Elgene , Cao Shiliang A. , Park Eunyoung , Eck Michael J. , Scully Ralph , Brown Myles , Marto Jarrod A. , Livingston David M.
Published: April 2023

This file includes supplementary figure legends, supplementary methods, and supplementary references.
Supplementary Table 1 from Loss of MIG6 Accelerates Initiation and Progression of Mutant Epidermal Growth Factor Receptor–Driven Lung Adenocarcinoma
Authors: Maity Tapan K. , Venugopalan Abhilash , Linnoila Ilona , Cultraro Constance M. , Giannakou Andreas , Nemati Roxanne , Zhang Xu , Webster Joshua D. , Ritt Daniel , Ghosal Sarani , Hoschuetzky Heinz , Simpson R. Mark , Biswas Romi , Politi Katerina , Morrison Deborah K. , Varmus Harold E. , Guha Udayan
Published: April 2023

Supplementary Table 1. Identification of mice used is Western blots and immunoprecipitation experiments (M1-M20) and the mice used for the early time periods upon doxycycline induction.
Supplementary Methods, Figure Legends from Loss of MIG6 Accelerates Initiation and Progression of Mutant Epidermal Growth Factor Receptor–Driven Lung Adenocarcinoma
Authors: Maity Tapan K. , Venugopalan Abhilash , Linnoila Ilona , Cultraro Constance M. , Giannakou Andreas , Nemati Roxanne , Zhang Xu , Webster Joshua D. , Ritt Daniel , Ghosal Sarani , Hoschuetzky Heinz , Simpson R. Mark , Biswas Romi , Politi Katerina , Morrison Deborah K. , Varmus Harold E. , Guha Udayan
Published: April 2023

Supplementary Methods, Figure Legends
Supplementary Table 2 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 2. VHL Genotyping in High L-2HG Tumors.
Supplementary Figure Legends, Tables S1 - S3 from Heterogeneity Underlies the Emergence of EGFRT790 Wild-Type Clones Following Treatment of T790M-Positive Cancers with a Third-Generation EGFR Inhibitor
Authors: Piotrowska Zofia , Niederst Matthew J. , Karlovich Chris A. , Wakelee Heather A. , Neal Joel W. , Mino-Kenudson Mari , Fulton Linnea , Hata Aaron N. , Lockerman Elizabeth L. , Kalsy Anuj , Digumarthy Subba , Muzikansky Alona , Raponi Mitch , Garcia Angel R. , Mulvey Hillary E. , Parks Melissa K. , DiCecca Richard H. , Dias-Santagata Dora , Iafrate A. John , Shaw Alice T. , Allen Andrew R. , Engelman Jeffrey A. , Sequist Lecia V.
Published: April 2023

Supplementary Figure Legends. Supplementary Table S1. Patient characteristics. Supplementary Table S2. Tissue genotyping analyses. Supplementary Table S3. Allelic Fraction of T790M and maximum reduction in tumor volume in response to rociletinib.
Supplementary Table S1 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 70K, This table contains the IC50 values of in vitro cell survival assay for crizotinib or ceritinib in engineered EML4-ALK mutant Ba/F3 cells corresponding to Fig 4A