bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S2 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map
Authors: Martins Maria M. , Zhou Alicia Y. , Corella Alexandra , Horiuchi Dai , Yau Christina , Rakhshandehroo Taha , Gordan John D. , Levin Rebecca S. , Johnson Jeff , Jascur John , Shales Mike , Sorrentino Antonio , Cheah Jaime , Clemons Paul A. , Shamji Alykhan F. , Schreiber Stuart L. , Krogan Nevan J. , Shokat Kevan M. , McCormick Frank , Goga Andrei , Bandyopadhyay Sourav
Published: April 2023

Supplementary Table S2. Drugs and their concentrations used in the isogenic drug screen.
Supplementary Figure 8 from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 1842K, GSK-3 inhibition leads to a decrease in TAK1 levels and p100-p52 processing in a statistically significant manner. All data obtained with independent experiments with Panc-1 and MiaPaCa-2, treated with GSK-3 inhibitor for 24 hours (right panel) or transiently transfected with indicated siRNA's for 72 hours (left panel) were quantified by densitometric analyses and is expressed as mean�SD. Statistical evaluation of the differences were calculated using students two-tailed t test and P value < 0.05 was considered significant.
Supplementary Figure 5 from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 63K, GSK-3 inhibition inhibits TAK1 mediated signaling. Panc-1 cells were treated with GSK-3 inhibitor, AR-A014418 (30M) for 24 hours and whole cell lysates immunoblotted for indicated antibodies.
Supplementary Figure 1 from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 308K, Left: AR-A014418 inhibits GSK-3 activity in a dose dependent mannerPanc-1 cells were treated with increasing concentrations of GSK-3 inhibitor, AR-A014418, like in Fig.1A. Whole cells extracts were prepared and immunoblotted for specified antibodies. p-Glycogen synthase is a downstream substrate of GSK-3 and thus an indicator of its kinase activity. Right: GSK-3 regulates apoptosis in MiaPaCa-2 cells. . Panc-1 and MiaPaCa-2 cells were transiently transfected with indicated siRNAs for 72 hours. Whole cell extracts were immunoblotted for specified antibodies.
Supplementary File 1 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Authors: Brastianos Priscilla K. , Carter Scott L. , Santagata Sandro , Cahill Daniel P. , Taylor-Weiner Amaro , Jones Robert T. , Van Allen Eliezer M. , Lawrence Michael S. , Horowitz Peleg M. , Cibulskis Kristian , Ligon Keith L. , Tabernero Josep , Seoane Joan , Martinez-Saez Elena , Curry William T. , Dunn Ian F. , Paek Sun Ha , Park Sung-Hye , McKenna Aaron , Chevalier Aaron , Rosenberg Mara , Barker Frederick G. , Gill Corey M. , Van Hummelen Paul , Thorner Aaron R. , Johnson Bruce E. , Hoang Mai P. , Choueiri Toni K. , Signoretti Sabina , Sougnez Carrie , Rabin Michael S. , Lin Nancy U. , Winer Eric P. , Stemmer-Rachamimov Anat , Meyerson Matthew , Garraway Levi , Gabriel Stacey , Lander Eric S. , Beroukhim Rameen , Batchelor Tracy T. , Baselga José , Louis David N. , Getz Gad , Hahn William C.
Published: April 2023

Supplementary File 1. Power for detection of somatic point mutations in coding exons of TARGET genes. The description for the plots in Supplementary File 1 can be found in the Legend of Supplementary Figure S1.
Supplementary Table S4 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 Table S4. Sequences of oligonucleotides used for qRT-PCR, RT-PCR, and 3C.
Supplementary Tables from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Authors: Lui Vivian W.Y. , Hedberg Matthew L. , Li Hua , Vangara Bhavana S. , Pendleton Kelsey , Zeng Yan , Lu Yiling , Zhang Qiuhong , Du Yu , Gilbert Breean R. , Freilino Maria , Sauerwein Sam , Peyser Noah D. , Xiao Dong , Diergaarde Brenda , Wang Lin , Chiosea Simion , Seethala Raja , Johnson Jonas T. , Kim Seungwon , Duvvuri Umamaheswar , Ferris Robert L. , Romkes Marjorie , Nukui Tomoko , Kwok-Shing Ng Patrick , Garraway Levi A. , Hammerman Peter S. , Mills Gordon B. , Grandis Jennifer R.
Published: April 2023

Supplementary Tables - PDF file 207K, Five supplementary tables denoting clinical characteristics of tumors, statistical correlations between PI3K mutational status, HPV status, cancer gene mutation status, and significance of pathway and gene mutation rates compared to background mutation rates, normalized to bases covered by exome sequencing
Supplementary Table 6 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Authors: Wagle Nikhil , Van Allen Eliezer M. , Treacy Daniel J. , Frederick Dennie T. , Cooper Zachary A. , Taylor-Weiner Amaro , Rosenberg Mara , Goetz Eva M. , Sullivan Ryan J. , Farlow Deborah N. , Friedrich Dennis C. , Anderka Kristin , Perrin Danielle , Johannessen Cory M. , McKenna Aaron , Cibulskis Kristian , Kryukov Gregory , Hodis Eran , Lawrence Donald P. , Fisher Sheila , Getz Gad , Gabriel Stacey B. , Carter Scott L. , Flaherty Keith T. , Wargo Jennifer A. , Garraway Levi A.
Published: April 2023

XLSX file 31K, Coverage and Metrics
Supplementary Table S2 from The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints
Authors: Llosa Nicolas J. , Cruise Michael , Tam Ada , Wicks Elizabeth C. , Hechenbleikner Elizabeth M. , Taube Janis M. , Blosser Richard L. , Fan Hongni , Wang Hao , Luber Brandon S. , Zhang Ming , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Sears Cynthia L. , Anders Robert A. , Pardoll Drew M. , Housseau Franck
Published: April 2023

Supplementary Table S2. Exome sequencing of MSS tumor outlier.
Supplementary Item 1 from The Basic Principles of Chimeric Antigen Receptor Design
Authors: Sadelain Michel , Brentjens Renier , Rivière Isabelle
Published: April 2023

Supplementary Item 1 - PDF file 70K, Complete references for citations listed in Table 1
Supplementary Tables S1 - S3 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

Supplementary Tables S1 - S3: Table S1. Expression of triglyceride synthesis genes in primary ccRCC (n=480) compared to normal kidney (n=69) samples. Table S2. Expression of cholesterol synthesis genes in primary ccRCC (n=480) compared to normal kidney (n=69) samples. Table S3. Relative concentration of acyl-carnitines in 20 primary ccRCC tumors compared to matched adjacent normal kidney samples.
Supplementary Movie 1 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

Supplementary Movie S1. Follicular motility of Emu-Tcl1 leukemia cells. The Movie complements Figure 4J.
Supplementary Table 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 Table S2. Summary of variant calls from WES analysis of matched pre-treatment and post-progression biopsies.
Supplementary Table 1 from Evolution of DNA Methylation Is Linked to Genetic Aberrations in Chronic Lymphocytic Leukemia
Authors: Oakes Christopher C. , Claus Rainer , Gu Lei , Assenov Yassen , Hüllein Jennifer , Zucknick Manuela , Bieg Matthias , Brocks David , Bogatyrova Olga , Schmidt Christopher R. , Rassenti Laura , Kipps Thomas J. , Mertens Daniel , Lichter Peter , Döhner Hartmut , Stilgenbauer Stephan , Byrd John C. , Zenz Thorsten , Plass Christoph
Published: April 2023

XLSX file 47K, Supplementary table 1: Clinical and biological features of all samples and timepoints used in the study including all genetic alterations found per sample
Supplementary Figures 1-10 from Evolution of DNA Methylation Is Linked to Genetic Aberrations in Chronic Lymphocytic Leukemia
Authors: Oakes Christopher C. , Claus Rainer , Gu Lei , Assenov Yassen , Hüllein Jennifer , Zucknick Manuela , Bieg Matthias , Brocks David , Bogatyrova Olga , Schmidt Christopher R. , Rassenti Laura , Kipps Thomas J. , Mertens Daniel , Lichter Peter , Döhner Hartmut , Stilgenbauer Stephan , Byrd John C. , Zenz Thorsten , Plass Christoph
Published: April 2023

PDF file 1498K, Supplemental figures 1-10: Methylation analysis of CLL and healthy donor samples using 450k arrays, WGBS and targeted BS-seq, including technical evaluations of the methods used
Supplementary Figure S5 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 S5. Role of ARAF Q489L and MEK F53L in resistance.
Supplementary Figure 8 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 8 - PDF file 84K, Immune cell profiling and IFN-gamma production in CD8 T cells in tumor tissues between Tgfbr2flox/flox and Tgfbr2MyeKO mice bearing 4T1 tumors
Supplementary Figure S1 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 S1. KRAS FISH analysis of parental and resistance cell lines.
Supplementary Figure 5 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 5 - PDF file 382K, Analysis of percentage or number in B cells, T cells, or myeloid cell subsets in the lungs between Tgfbr2MyeKO and control littermates under normal or tumor conditions
Supplementary Figure 4 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 4 - PDF file 129K, Validation of over expression of TGFbeta1, IL-4, IL10, as well as Arginase1 and iNOS in Tgfbr2
Supplementary Figure Legends 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 Legends
Supplementary Table S18 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 of 4 subsequent relapses.
Supplementary Table S16 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 11 cell lines after filtering.
Supplementary Methods, Figure Legends, Figures S1 - S6, Tables S1, S3 - S6, S8 - S15, S17 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

This file contains supplementary methods, supplementary references, supplementary figures S1-S6, supplementary tables S1, S3-S6, S8-S15, and S17, and legends for all supplementary figures and tables. Supplementary Figure S1. Summary of Ewing sarcoma tumor and cell line cohorts. Supplementary Figure S2. RNASeq validation of mutations identified by WES and WGS. Supplementary Figure S3. Power calculations for the detection of significantly mutated genes. Supplementary Figure S4. Copy number variants in Ewing sarcoma tumors. Supplementary Figure S5. ETS1 deletions associated with EWS/FLI rearrangements. Supplementary Figure S6. Copy number variants in diagnostic vs. treated Ewing sarcoma tumors. Supplementary Figure S7. SCNAs in paired Ewing sarcoma tumor samples. Supplementary Table S1. Tissue samples. Supplementary Table S3. Multiply mutated genes. Supplementary Table S4. Rearrangements and fusions detected by WGS and RNASeq. Supplementary Table S5. Mutational significance for tumor/normal pairs. Supplementary Table S6. Rate of coding mutations in Ewing sarcoma tumors. Supplementary Table S8. Mutational significance for all tumors. Supplementary Table S9. Gene set enrichment analyses of mutated genes. Supplementary Table S10. Significance of arm-level SCNAs. Supplementary Table S11. Multiply mutated genes of interest in all sample cohorts. Supplementary Table S12. Immunohistochemical staining of STAG2 in Ewing sarcoma tumors. Supplementary Table S13. Gene set enrichment analyses of STAG2 expressing vs. STAG2 loss. Supplementary Table S14. Gene and gene-fragment RPKM Values for EWS and ETS genes. Supplementary Table S15. ETS1 copy-number changes. Supplementary Table S17. Gene set enrichment analyses of tumors vs. cell lines.
Supplementary Table 5 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

STAG2 mutation in three cases that show a reduction of STAG2-immunopositive cells at disease recurrence.
Supplementary Table 2 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 42K, Co-occurrence of RNF31 SNPs with other genetic lesions in ABC DLBCL cases
Supplementary Table 2 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 2 provides a summary (a), list of structural variants (b), list of copy number alterations (c), list of Tier 1 single nucleotide variants (d), indels (e), and purity analyses (f).
Supplementary Fig. 4 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 149K, RNF31 peptides internalized equivalently in ABC DLBCL cells
Supplementary Table 1 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 1 describes the clinical characteristics of patients.
Supplementary Figures 1 - 5 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 Figure 1. Representative CIRCOS plots. Supplementary Figure 2. Scheme of copy number alterations. Indicates the copy number alterations in Ewing sarcoma. Supplementary Figure 3. Mutation spectrum in Ewing sarcoma. Indicates the proportion of each somatic base changes in Ewing sarcoma. Supplementary Figure 4. CDKN2A analysis across cell lines. RT-QPCR and western blot results in cell lines. Supplementary Figure 5. CDKN2A analysis across the extended cohort. QPCR analysis of the CDKN2A locus across the whole series of patients.
Supplementary Fig. 2 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 73K, Constitutive linear ubiquitination of NEMO in ABC comparing to GCB DLBCL cells
Supplementary Figure S2 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 S2 shows analysis for macrophages in cytokeratin-19 positive regions of ADM (A), and analysis for ICAM-1, macrophages and cytokeratin-19 in PanIN lesions (B).
Supplementary Table S1 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

Previously characterized MET exon 14 alterations.
Supplementary Figure 2 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 - 106KB, Schematic representation of the study design. 37 IMT tumor samples from 33 patients were collected under IRB approved protocols. ALK immunohistochemistry (IHC) was performed on each of the 37 cases as standard of clinical care. Targeted next-generation sequencing (NGS) using the FoundationOne was completed in each case. 22/26 ALK IHC+ and 11/11 ALK IHC- samples were evaluable. ALK kinase fusions were detected in 20/22 (91%) of the ALK IHC+ cases. In the ALK IHC- cases, 2/11 (18%) harbored ALK fusions, 2/11 (18%) harbored PDGFRβ fusions, and 4/11 (36%) harbored ROS1 fusions. Overall, therapeutically actionable kinase fusions were detected in 28/33 (85%) of cases.
Supplementary Table S1.3 from Metabolic and Functional Genomic Studies Identify Deoxythymidylate Kinase as a Target in LKB1-Mutant Lung Cancer
Authors: Liu Yan , Marks Kevin , Cowley Glenn S. , Carretero Julian , Liu Qingsong , Nieland Thomas J.F. , Xu Chunxiao , Cohoon Travis J. , Gao Peng , Zhang Yong , Chen Zhao , Altabef Abigail B. , Tchaicha Jeremy H. , Wang Xiaoxu , Choe Sung , Driggers Edward M. , Zhang Jianming , Bailey Sean T. , Sharpless Norman E. , Hayes D. Neil , Patel Nirali M. , Janne Pasi A. , Bardeesy Nabeel , Engelman Jeffrey A. , Manning Brendan D. , Shaw Reuben J. , Asara John M. , Scully Ralph , Kimmelman Alec , Byers Lauren A. , Gibbons Don L. , Wistuba Ignacio I. , Heymach John V. , Kwiatkowski David J. , Kim William Y. , Kung Andrew L. , Gray Nathanael S. , Root David E. , Cantley Lewis C. , Wong Kwok-Kin
Published: April 2023

Top 200 genes by W2ndB.
Supplementary Figure 4 from Phase IB Study of Vemurafenib in Combination with Irinotecan and Cetuximab in Patients with Metastatic Colorectal Cancer with BRAFV600E Mutation
Authors: Hong David S. , Morris Van K. , El Osta Badi , Sorokin Alexey V. , Janku Filip , Fu Siqing , Overman Michael J. , Piha-Paul Sarina , Subbiah Vivek , Kee Bryan , Tsimberidou Apostolia M. , Fogelman David , Bellido Jorge , Shureiqi Imad , Huang Helen , Atkins Johnique , Tarcic Gabi , Sommer Nicolas , Lanman Richard , Meric-Bernstam Funda , Kopetz Scott
Published: April 2023

68-gene panel for which mutation, amplification, deletion, and fusion profiling was available.
Supplementary Figure Legends, Table Legends, Figures S1 - S3 from Infection Exposure Is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility
Authors: Martín-Lorenzo Alberto , Hauer Julia , Vicente-Dueñas Carolina , Auer Franziska , González-Herrero Inés , García-Ramírez Idoia , Ginzel Sebastian , Thiele Ralf , Constantinescu Stefan N. , Bartenhagen Christoph , Dugas Martin , Gombert Michael , Schäfer Daniel , Blanco Oscar , Mayado Andrea , Orfao Alberto , Alonso-López Diego , Rivas Javier De Las , Cobaleda César , García-Cenador Maria Begoña , García-Criado Francisco Javier , Sánchez-García Isidro , Borkhardt Arndt
Published: April 2023

The PDF includes legends for Supplementary Tables S1 - S5 as well as legends for Supplementary Figures S1 - S3. Supplementary Figure S1 indicates pathogens detected in mice held in the SPF and conventional animal facility. Supplementary Figure S2 represents flow cytometric, histological and gene set enrichment characterization in Pax5+/- mice. Supplementary Figure S3 refers to in vivo growth of Ba/F3 cells expressing Jak3V670A and Jak3R653H mutations, respectively.
Supplementary Figure 2 from Phase IB Study of Vemurafenib in Combination with Irinotecan and Cetuximab in Patients with Metastatic Colorectal Cancer with BRAFV600E Mutation
Authors: Hong David S. , Morris Van K. , El Osta Badi , Sorokin Alexey V. , Janku Filip , Fu Siqing , Overman Michael J. , Piha-Paul Sarina , Subbiah Vivek , Kee Bryan , Tsimberidou Apostolia M. , Fogelman David , Bellido Jorge , Shureiqi Imad , Huang Helen , Atkins Johnique , Tarcic Gabi , Sommer Nicolas , Lanman Richard , Meric-Bernstam Funda , Kopetz Scott
Published: April 2023

Trends in cfDNA fraction (black) and radiographic changes (red) for ten other patients on study.
Supplementary Figures S1 - S9 from Improved Efficacy of Neoadjuvant Compared to Adjuvant Immunotherapy to Eradicate Metastatic Disease
Authors: Liu Jing , Blake Stephen J. , Yong Michelle C.R. , Harjunpää Heidi , Ngiow Shin Foong , Takeda Kazuyoshi , Young Arabella , O'Donnell Jake S. , Allen Stacey , Smyth Mark J. , Teng Michele W.L.
Published: April 2023

Supplementary Figure S1. Neoadjuvant immunotherapy is more effective at reducing metastatic burden. Supplementary Figure S2. Late neoadjuvant Treg depletion is more effective than adjuvant Treg depletion in eradicating metastatic disease. Supplementary Figure S3. Efficacy of neoadjuvant immunotherapy is dependent on surgical resection of the primary tumor. Supplementary Fig. S4. Neoadjuvant compared to adjuvant chemotherapy does not lead to improved survival benefit. Supplementary Figure S5. Long-term survivors following neoadjuvant immunotherapy treatment are tumor free and display immunological memory. Supplementary Figure S6. Efficacy of neoadjuvant Treg depletion depends on T and NK cells. Supplementary Figure S7. Kinetics of gp70 tumor-specific CD8+ T cells in peripheral blood following neoadjuvant or adjuvant Treg depletion. Supplementary Figure S8. Neoadjuvant immunotherapy increases tumor-specific CD8+ T cells in the peripheral organs and primary tumor. Supplementary Figure S9. Neoadjuvant compared to adjuvant immunotherapy increases the number of tumor-specific CD8+ T cells with effector phenotype.
Supplementary Figures 1 - 6 from Polyclonal Secondary FGFR2 Mutations Drive Acquired Resistance to FGFR Inhibition in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma
Authors: Goyal Lipika , Saha Supriya K. , Liu Leah Y. , Siravegna Giulia , Leshchiner Ignaty , Ahronian Leanne G. , Lennerz Jochen K. , Vu Phuong , Deshpande Vikram , Kambadakone Avinash , Mussolin Benedetta , Reyes Stephanie , Henderson Laura , Sun Jiaoyuan Elisabeth , Van Seventer Emily E. , Gurski Joseph M. , Baltschukat Sabrina , Schacher-Engstler Barbara , Barys Louise , Stamm Christelle , Furet Pascal , Ryan David P. , Stone James R. , Iafrate A. John , Getz Gad , Porta Diana Graus , Tiedt Ralph , Bardelli Alberto , Juric Dejan , Corcoran Ryan B. , Bardeesy Nabeel , Zhu Andrew X.
Published: April 2023

Supplementary Figure S1. Confirmation of secondary point mutation in FGFR2-ZMYM4 allele. Supplementary Figure S2. Homology between FGFR2 and FGFR3 proteins. Supplementary Figure S3. FGFR2-OPTN fusion detected in all autopsy lesions. Supplementary Figure S4. FoundationOne analysis of autopsy lesions. Supplementary Figure S5. PTEN loss of heterozygosity (LOH) identified in Patient #2. Supplementary Figure S6. Mutational analysis of original resection specimen from Patient #2.
Supplementary Table S1 from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Authors: Aguirre Andrew J. , Meyers Robin M. , Weir Barbara A. , Vazquez Francisca , Zhang Cheng-Zhong , Ben-David Uri , Cook April , Ha Gavin , Harrington William F. , Doshi Mihir B. , Kost-Alimova Maria , Gill Stanley , Xu Han , Ali Levi D. , Jiang Guozhi , Pantel Sasha , Lee Yenarae , Goodale Amy , Cherniack Andrew D. , Oh Coyin , Kryukov Gregory , Cowley Glenn S. , Garraway Levi A. , Stegmaier Kimberly , Roberts Charles W. , Golub Todd R. , Meyerson Matthew , Root David E. , Tsherniak Aviad , Hahn William C.
Published: April 2023

Sample Information: Table with cell line identities and relevant information for this manuscript.
Supplementary Figures S6 - S10 from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Authors: Aguirre Andrew J. , Meyers Robin M. , Weir Barbara A. , Vazquez Francisca , Zhang Cheng-Zhong , Ben-David Uri , Cook April , Ha Gavin , Harrington William F. , Doshi Mihir B. , Kost-Alimova Maria , Gill Stanley , Xu Han , Ali Levi D. , Jiang Guozhi , Pantel Sasha , Lee Yenarae , Goodale Amy , Cherniack Andrew D. , Oh Coyin , Kryukov Gregory , Cowley Glenn S. , Garraway Levi A. , Stegmaier Kimberly , Roberts Charles W. , Golub Todd R. , Meyerson Matthew , Root David E. , Tsherniak Aviad , Hahn William C.
Published: April 2023

Supplementary Figure S6. Representative example of complex amplified locus showing a CRISPR-CN correlation. Supplementary Figure S7. Comparative analysis of the relationship of CRISPR-Cas9 guide scores to the predicted number of CRISPR-Cas9-induced DNA cuts based on either copy number or total predicted perfect-match on- and off-target alignments. Supplementary Figure S8. Comprehensive analysis of CRISPR-Cas9 sensitivity correlated to the total predicted number of DNA cuts conferred by each sgRNA. Supplementary Figure S9. (A) PANC-1 infection efficiency corresponding to Figure 6 in vitro validation experiment measuring short-term proliferation and viability response of PANC-1 cells transduced at high multiplicity of infection. (B) Immunoblot of protein from PANC-1 cells harvested 48 hours after infection at high MOI with the indicated sgRNAs targeting inside (19q8) or outside (19q4) the PANC-1 19q13 amplicon shown in Figure 6A. Supplementary Figure S10. CRISPR-Cas9 targeting of amplified regions or multiple genomic loci induces DNA damage and a G2 cell cycle arrest in CAL120 cells.
Supplementary Figure 2 from Tumor Cell–Independent Estrogen Signaling Drives Disease Progression through Mobilization of Myeloid-Derived Suppressor Cells
Authors: Svoronos Nikolaos , Perales-Puchalt Alfredo , Allegrezza Michael J. , Rutkowski Melanie R. , Payne Kyle K. , Tesone Amelia J. , Nguyen Jenny M. , Curiel Tyler J. , Cadungog Mark G. , Singhal Sunil , Eruslanov Evgeniy B. , Zhang Paul , Tchou Julia , Zhang Rugang , Conejo-Garcia Jose R.
Published: April 2023

Estrogen-dependent MDSC mobilization in response to tumor-conditioned media.
Supplementary Figure 1 from Tumor Cell–Independent Estrogen Signaling Drives Disease Progression through Mobilization of Myeloid-Derived Suppressor Cells
Authors: Svoronos Nikolaos , Perales-Puchalt Alfredo , Allegrezza Michael J. , Rutkowski Melanie R. , Payne Kyle K. , Tesone Amelia J. , Nguyen Jenny M. , Curiel Tyler J. , Cadungog Mark G. , Singhal Sunil , Eruslanov Evgeniy B. , Zhang Paul , Tchou Julia , Zhang Rugang , Conejo-Garcia Jose R.
Published: April 2023

Expression of ESR1 by PCR and lack of responsiveness of tumor cells used in vivo.
Supplementary Figure Legends from Mechanism, Consequences, and Therapeutic Targeting of Abnormal IL15 Signaling in Cutaneous T-cell Lymphoma
Authors: Mishra Anjali , La Perle Krista , Kwiatkowski Sonya , Sullivan Laura A. , Sams Gregory H. , Johns Jessica , Curphey Douglas P. , Wen Jing , McConnell Kathleen , Qi Jun , Wong Henry , Russo Giandomenico , Zhang Jianying , Marcucci Guido , Bradner James E. , Porcu Pierluigi , Caligiuri Michael A.
Published: April 2023

Supplementary Figure Legends
Supplementary Tables S1 - S3 from EGFR Fusions as Novel Therapeutic Targets in Lung Cancer
Authors: Konduri Kartik , Gallant Jean-Nicolas , Chae Young Kwang , Giles Francis J. , Gitlitz Barbara J. , Gowen Kyle , Ichihara Eiki , Owonikoko Taofeek K. , Peddareddigari Vijay , Ramalingam Suresh S. , Reddy Satyanarayan K. , Eaby-Sandy Beth , Vavalà Tiziana , Whiteley Andrew , Chen Heidi , Yan Yingjun , Sheehan Jonathan H. , Meiler Jens , Morosini Deborah , Ross Jeffrey S. , Stephens Philip J. , Miller Vincent A. , Ali Siraj M. , Lovly Christine M.
Published: April 2023

Supplementary Tables S1 - S3. Supplementary Table S1. Summary of EGFR alterations in NSCLC identified by FoundationOne. Supplementary Table S2. Summary of genomic coordinates for the kinase fusions identified in this study. Supplementary Table S3. Results of MTT curve fitting from Prism.
Supplementary Figures S1 - S10 from EGFR Fusions as Novel Therapeutic Targets in Lung Cancer
Authors: Konduri Kartik , Gallant Jean-Nicolas , Chae Young Kwang , Giles Francis J. , Gitlitz Barbara J. , Gowen Kyle , Ichihara Eiki , Owonikoko Taofeek K. , Peddareddigari Vijay , Ramalingam Suresh S. , Reddy Satyanarayan K. , Eaby-Sandy Beth , Vavalà Tiziana , Whiteley Andrew , Chen Heidi , Yan Yingjun , Sheehan Jonathan H. , Meiler Jens , Morosini Deborah , Ross Jeffrey S. , Stephens Philip J. , Miller Vincent A. , Ali Siraj M. , Lovly Christine M.
Published: April 2023

Supplementary Figures S1 - S10. Supplementary Figure S1. Additional information for Patient 1. Supplementary Figure S2. Additional information for Patient 2. Supplementary Figure S3. Additional information for Patient 3. Supplementary Figure S4. Additional clinical information for Patient 4. Supplementary Figure S5. Characterization of EGFR-RAD51 in NR6 cells. Supplementary Figure S6. Relative stability of EGFR-WT, -L858R, and -RAD51. Supplementary Figure S7. Structural model of EGFR-RAD51 filaments. Supplementary Figure S8. On-target inhibition of EGFR-RAD51 by EGFR TKI. Supplementary Figure S9. Cetuximab inhibits ligand-induced activation of downstream signaling pathways in cells expressing EGFR-RAD51. Supplementary Figure S10. cDNA sequence of EGFR-RAD51.
Supplementary Table 3 from Synthetic Lethal Approaches Exploiting DNA Damage in Aggressive Myeloma
Authors: Cottini Francesca , Hideshima Teru , Suzuki Rikio , Tai Yu-Tzu , Bianchini Giampaolo , Richardson Paul G. , Anderson Kenneth C. , Tonon Giovanni
Published: April 2023

Supplementary Table 3. The 5 most enriched pathways in the K2 MM patient subgroup in the BIOCARTA MSigDB collection (high expression levels in K2).
Supplementary Table 2 from Synthetic Lethal Approaches Exploiting DNA Damage in Aggressive Myeloma
Authors: Cottini Francesca , Hideshima Teru , Suzuki Rikio , Tai Yu-Tzu , Bianchini Giampaolo , Richardson Paul G. , Anderson Kenneth C. , Tonon Giovanni
Published: April 2023

Supplementary Table 2. The 5 most enriched pathways in the K2 MM patient subgroup in the KEGG MSigDB collection (high expression levels in K2).
Supplementary Figure 6 from Blastic Plasmacytoid Dendritic Cell Neoplasm Is Dependent on BCL2 and Sensitive to Venetoclax
Authors: Montero Joan , Stephansky Jason , Cai Tianyu , Griffin Gabriel K. , Cabal-Hierro Lucia , Togami Katsuhiro , Hogdal Leah J. , Galinsky Ilene , Morgan Elizabeth A. , Aster Jon C. , Davids Matthew S. , LeBoeuf Nicole R. , Stone Richard M. , Konopleva Marina , Pemmaraju Naveen , Letai Anthony , Lane Andrew A.
Published: April 2023

Additional pharmacodynamic data showing in vivo PDX response to venetoclax. PD assessment of percent human CD45+CD123+ cells in the peripheral blood (PB), spleen, and bone marrow (BM) of six animals bearing PDX1 after 21 days of treatment with vehicle (n=3) or venetoclax (n=3).
Supplementary Figure 5 from Blastic Plasmacytoid Dendritic Cell Neoplasm Is Dependent on BCL2 and Sensitive to Venetoclax
Authors: Montero Joan , Stephansky Jason , Cai Tianyu , Griffin Gabriel K. , Cabal-Hierro Lucia , Togami Katsuhiro , Hogdal Leah J. , Galinsky Ilene , Morgan Elizabeth A. , Aster Jon C. , Davids Matthew S. , LeBoeuf Nicole R. , Stone Richard M. , Konopleva Marina , Pemmaraju Naveen , Letai Anthony , Lane Andrew A.
Published: April 2023

Time and dose-dependent response of primary BPDCN to venetoclax in vitro. (A) Cell death measurement by flow cytometry at 4 and 8 hours after addition of venetoclax at the indicated doses in a primary BPDCN, represented as change in Annexin V positivity relative to vehicle. (B) Dose response of primary BPDCNs and AMLs to venetoclax in vitro measured as in (A).
Supplementary Figure S4 from Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression
Authors: Oudin Madeleine J. , Jonas Oliver , Kosciuk Tatsiana , Broye Liliane C. , Guido Bruna C. , Wyckoff Jeff , Riquelme Daisy , Lamar John M. , Asokan Sreeja B. , Whittaker Charlie , Ma Duanduan , Langer Robert , Cima Michael J. , Wisinski Kari B. , Hynes Richard O. , Lauffenburger Douglas A. , Keely Patricia J. , Bear James E. , Gertler Frank B.
Published: April 2023

Supplementary Figure S4. Deletion of LERER in MenaINV affects tumor growth in a xenograft model.
Supplementary Methods, Figure Legends, Figures S1 - S7, Table S1 - Supplementary Figure S1 from The APC/C E3 Ligase Complex Activator FZR1 Restricts BRAF Oncogenic Function
Authors: Wan Lixin , Chen Ming , Cao Juxiang , Dai Xiangpeng , Yin Qing , Zhang Jinfang , Song Su-Jung , Lu Ying , Liu Jing , Inuzuka Hiroyuki , Katon Jesse M. , Berry Kelsey , Fung Jacqueline , Ng Christopher , Liu Pengda , Song Min Sup , Xue Lian , Bronson Roderick T. , Kirschner Marc W. , Cui Rutao , Pandolfi Pier Paolo , Wei Wenyi
Published: April 2023

Depletion of FZR1 leads to BRAF stabilization and subsequent ERK activation. Supplementary Figure S2. Depletion of FZR1 triggers the onset of premature senescence in primary melanocytes. Supplementary Figure S3. APCFZR1 promotes BRAF ubiquitination and subsequent degradation in a D-box dependent manner. Supplementary Figure S4. FZR1 disrupts the BRAF dimerization process. Supplementary Figure S5. Phosphorylation of FZR1 N-terminus by ERK and CYCLIN D1/CDK4 inhibits the APCFZR1 E3 ubiquitin ligase activity. Supplementary Figure S6. Pharmacologically inhibiting BRAF/ERK and CDK4 restores the APCFZR1 E3 ligase activity. Supplementary Figure S7. Depletion of FZR1 co-operates with PTEN deficiency to promote co-activation of BRAF/ERK and AKT oncogenic signaling both in vitro and in vivo. Supplementary Table S1. Mutation and deletion of FZR1 and 14 APC core complex subunits identified in melanoma patients from the TCGA melanoma dataset (cbioportal.org).
Supplementary Table S6 from Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor–Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma
Authors: Brayer Kathryn J. , Frerich Candace A. , Kang Huining , Ness Scott A.
Published: April 2023

Differentially Expressed Genes, Group 2 vs Normal.
Supplementary Table S5 from Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma
Authors: Saha Supriya K. , Gordan John D. , Kleinstiver Benjamin P. , Vu Phuong , Najem Mortada S. , Yeo Jia-Chi , Shi Lei , Kato Yasutaka , Levin Rebecca S. , Webber James T. , Damon Leah J. , Egan Regina K. , Greninger Patricia , McDermott Ultan , Garnett Mathew J. , Jenkins Roger L. , Rieger-Christ Kimberly M. , Sullivan Travis B. , Hezel Aram F. , Liss Andrew S. , Mizukami Yusuke , Goyal Lipika , Ferrone Cristina R. , Zhu Andrew X. , Joung J. Keith , Shokat Kevan M. , Benes Cyril H. , Bardeesy Nabeel
Published: April 2023

Source and cell culture information for cell lines.
Supplementary Table S5 from Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor–Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma
Authors: Brayer Kathryn J. , Frerich Candace A. , Kang Huining , Ness Scott A.
Published: April 2023

Differentially Expressed Genes, Group 1 vs Normal.
Supplementary Table S4 from Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma
Authors: Saha Supriya K. , Gordan John D. , Kleinstiver Benjamin P. , Vu Phuong , Najem Mortada S. , Yeo Jia-Chi , Shi Lei , Kato Yasutaka , Levin Rebecca S. , Webber James T. , Damon Leah J. , Egan Regina K. , Greninger Patricia , McDermott Ultan , Garnett Mathew J. , Jenkins Roger L. , Rieger-Christ Kimberly M. , Sullivan Travis B. , Hezel Aram F. , Liss Andrew S. , Mizukami Yusuke , Goyal Lipika , Ferrone Cristina R. , Zhu Andrew X. , Joung J. Keith , Shokat Kevan M. , Benes Cyril H. , Bardeesy Nabeel
Published: April 2023

Peptide quantification from MIB column isolation of the active kinome in DMSO- versus dasatinib-treated HuCCT1, RBE, and SNU-1079 cells.
Supplementary Table S3 from Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma
Authors: Saha Supriya K. , Gordan John D. , Kleinstiver Benjamin P. , Vu Phuong , Najem Mortada S. , Yeo Jia-Chi , Shi Lei , Kato Yasutaka , Levin Rebecca S. , Webber James T. , Damon Leah J. , Egan Regina K. , Greninger Patricia , McDermott Ultan , Garnett Mathew J. , Jenkins Roger L. , Rieger-Christ Kimberly M. , Sullivan Travis B. , Hezel Aram F. , Liss Andrew S. , Mizukami Yusuke , Goyal Lipika , Ferrone Cristina R. , Zhu Andrew X. , Joung J. Keith , Shokat Kevan M. , Benes Cyril H. , Bardeesy Nabeel
Published: April 2023

IC50 values for dasatinib in nM of nine ICC cell lines and the immortalized human cholangiocyte cell line MMNK-1.
Supplementary Table S3 from Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor–Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma
Authors: Brayer Kathryn J. , Frerich Candace A. , Kang Huining , Ness Scott A.
Published: April 2023

PCR Details.
Supplementary Table S1 from Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma
Authors: Saha Supriya K. , Gordan John D. , Kleinstiver Benjamin P. , Vu Phuong , Najem Mortada S. , Yeo Jia-Chi , Shi Lei , Kato Yasutaka , Levin Rebecca S. , Webber James T. , Damon Leah J. , Egan Regina K. , Greninger Patricia , McDermott Ultan , Garnett Mathew J. , Jenkins Roger L. , Rieger-Christ Kimberly M. , Sullivan Travis B. , Hezel Aram F. , Liss Andrew S. , Mizukami Yusuke , Goyal Lipika , Ferrone Cristina R. , Zhu Andrew X. , Joung J. Keith , Shokat Kevan M. , Benes Cyril H. , Bardeesy Nabeel
Published: April 2023

Median centered Ln(IC50) values for 17 BTC cell lines screened against 122 drugs.
Supplementary Table S4 from Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma
Authors: Girotti Maria Romina , Gremel Gabriela , Lee Rebecca , Galvani Elena , Rothwell Dominic , Viros Amaya , Mandal Amit Kumar , Lim Kok Haw Jonathan , Saturno Grazia , Furney Simon J. , Baenke Franziska , Pedersen Malin , Rogan Jane , Swan Jacqueline , Smith Matthew , Fusi Alberto , Oudit Deemesh , Dhomen Nathalie , Brady Ged , Lorigan Paul , Dive Caroline , Marais Richard
Published: April 2023

40 Gene Miseq primers.
Supplementary Table S3 from Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma
Authors: Girotti Maria Romina , Gremel Gabriela , Lee Rebecca , Galvani Elena , Rothwell Dominic , Viros Amaya , Mandal Amit Kumar , Lim Kok Haw Jonathan , Saturno Grazia , Furney Simon J. , Baenke Franziska , Pedersen Malin , Rogan Jane , Swan Jacqueline , Smith Matthew , Fusi Alberto , Oudit Deemesh , Dhomen Nathalie , Brady Ged , Lorigan Paul , Dive Caroline , Marais Richard
Published: April 2023

PDXs and WES list.