bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 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 Figure S2. Absolute numbers of CD3 cells per gram of tumor and normal colon tissue collected from MSS and MSI human CRC patients.
Data Supplement 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

PDF file 171K, Contains Supplementary Data and Methods
Supplementary Figure S1 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 Figure S1. Laser capture microdissection of FFPE tissue sections.
Supplementary Methods, Figures 1 - 5, Tables 1 - 5 from Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms
Authors: Diamond Eli L. , Durham Benjamin H. , Haroche Julien , Yao Zhan , Ma Jing , Parikh Sameer A. , Wang Zhaoming , Choi John , Kim Eunhee , Cohen-Aubart Fleur , Lee Stanley Chun-Wei , Gao Yijun , Micol Jean-Baptiste , Campbell Patrick , Walsh Michael P. , Sylvester Brooke , Dolgalev Igor , Aminova Olga , Heguy Adriana , Zappile Paul , Nakitandwe Joy , Ganzel Chezi , Dalton James D. , Ellison David W. , Estrada-Veras Juvianee , Lacouture Mario , Gahl William A. , Stephens Philip J. , Miller Vincent A. , Ross Jeffrey S. , Ali Siraj M. , Briggs Samuel R. , Fasan Omotayo , Block Jared , Héritier Sebastien , Donadieu Jean , Solit David B. , Hyman David M. , Baselga José , Janku Filip , Taylor Barry S. , Park Christopher Y. , Amoura Zahir , Dogan Ahmet , Emile Jean-Francois , Rosen Neal , Gruber Tanja A. , Abdel-Wahab Omar
Published: April 2023

Supplementary Figure 1. Somatic mutations detected in histiocytic neoplasms. Supplementary Figure 2. Frequencies of known activating kinase mutations in histiocytic neoplasms. Supplementary Figure 3. ARAF mutations and variants of unknown significance detected in BRAFV600E-wildtype, non-Langerhans Cell Histiocytic neoplasms. Supplementary Figure 4. Clinical and histological images of the non-Langerhans cell histiocytosis (non-LCH) lesions from index patients with kinase fusions identified by RNA-seq. Supplementary Figure 5. Gene expression analysis of histiocytic neoplasms by RNA-seq. Supplementary Table 1. Characteristics of patient samples with histiocytic neoplasms used in this study and genomic analysis utilized for each sample. Supplementary Table 2. Whole exome sequencing metrics. Supplementary Table 3. Somatic variants identified by whole exome and whole transcriptome sequencing and validated by droplet-digital PCR and/or custom-capture targeted next-generation sequencing with variant allele frequencies (VAFs). Supplementary Table 4. List of the top 1% of differentially expressed genes across histiocytic samples from mRNA sequencing. Supplementary Table 5. PCR primers with M13F2 and M13R2 tails (blue) for Sanger sequencing used in the targeted sequencing recurrence testing for MAP2K1 exons 2 and 3 and all coding regions of ARAF.
Supplementary Figure 7 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 7 - PDF file 111K, Characterization of myeloid cells in lung, tumor, spleen, and lymph nodes
Supplementary Figure 6 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 6 - PDF file 115K, IFN-gamma production in different myeloid cell subsets, and factors that mediate IFN-gamma production
Supplementary Data from MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Authors: Neupane Manish , Clark Allison P. , Landini Serena , Birkbak Nicolai J. , Eklund Aron C. , Lim Elgene , Culhane Aedin C. , Barry William T. , Schumacher Steven E. , Beroukhim Rameen , Szallasi Zoltan , Vidal Marc , Hill David E. , Silver Daniel P.
Published: April 2023

Analysis of Uterine Cancer Subtypes. This file contains analysis of mutual exclusivity relationship between MECP2 amplification and KRAS mutation in uterine cancer subtypes.
Supplementary Figures 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

PDF file 234K, This is a file containing the list of supplementary tables, the list of supplementary figures, as well as the 7 supplementary figures (S1 to S7) and their correspondent legends, mentioned in the main text
Supplementary Table S3 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

Differentially expressed genes (DEGs) identified from RNA-Seq by DeSeq between control and imatinib-treated GIST cell lines.
Supplementary Figure and Table Legends 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

Supplementary Figure and Table Legends
Supplementary Figure S3 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 S3 shows analysis for microvascularization (A), alcian blue staining of tissue sections (B), and ICAM-1 expression in human samples (C).
Supplementary Figure Legend 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

Figure legend to Supplementary Figure S1.
Supplementary Table S4 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

Co- and anti-occurrence of genomic alterations in lung adenocarcinoma.
Supplementary Methods 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 - 71KB
Supplementary Figure 1 from Inflammatory Myofibroblastic Tumors Harbor Multiple Potentially Actionable Kinase Fusions
Authors: Lovly Christine M. , Gupta Abha , Lipson Doron , Otto Geoff , Brennan Tina , Chung Catherine T. , Borinstein Scott C. , Ross Jeffrey S. , Stephens Philip J. , Miller Vincent A. , Coffin Cheryl M.
Published: April 2023

PDF file - 59KB, Schematic representation of the index patient's treatment history. A timeline detailing the index patient's diagnosis and subsequent systemic therapies is depicted. Time in months is shown below the arrow. The timeline starts at the patient's initial diagnosis.
Supplementary Figure 4 from Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Authors: Ye Jiangbin , Fan Jing , Venneti Sriram , Wan Ying-Wooi , Pawel Bruce R. , Zhang Ji , Finley Lydia W.S. , Lu Chao , Lindsten Tullia , Cross Justin R. , Qing Guoliang , Liu Zhandong , Simon M. Celeste , Rabinowitz Joshua D. , Thompson Craig B.
Published: April 2023

(A) Kelly cells stably expressing non-targeting shRNA (shNT) or SHMT2 shRNA (shSHMT2) were exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 24 hours. Total cellular DNA were extracted and relative mitochondria/nuclear DNA ratio were measured using Q-PCR. (Data represent Mean {plus minus} S.D of four independent experiments). (B) Kelly cells were exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 6h. ROS levels were measured using a flow cytometry-based MitoTracker Red CM-H2Ros assay. All values are normalized to normoxic shNT control cells (Data represent Mean {plus minus} S.D of three biological repeats, ***p<0.001, determined by Student's two-tailed t-test). (C) Knockdown of SHMT2 display swollen mitochondria upon hypoxic stress. Kelly cells was exposed to normoxia (Nor) or 0.5% O2 (Hyp) for 24 hours. Cells were fixed and pictures were taken under electronic microscope (EM) (25000X). Arrows indicate mitochondria.
Supplementary Table 1 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 57K, Supplementary table and legend. Evaluation of the PD-L1 expression in tumor samples carrying EGFR mutations
Supplementary Figure S4 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 783K, Supplementary Figure S4. PI3K inhibition does not decrease P-ERK in RAS-mutant cells. Related to main Figure 4
Supplementary Figures 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 2020K, Supplementary figures 1-11. For the mouse experiments tumor bearing lungs were classified as mildly sick and severely sick based on the tumor burden as determined by right lung lobe weights. Oncogene induced immunosuppressive environment manifested as compromised T cell function, elevation in the levels of tumor promoting cytokines, and changes in lung hematopoietic population was observed in the mildy sick mice in addition to the severely sick EGFR mutant mice. Anti PD-1 antibody treatment did not show efficacy in the Kras driven tumors despite the expression of the PD-1 ligand
Supplementary Figure S1 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 3213K, Figure S1. BAY 80-6946 is a potent and selective PI3K inhibitor. PI3K inhibition induces more apoptosis than AKT inhibition. Related to main Figure 1
Supplementary Table 3 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Table 3 - PDF file 119K, Comparison of differentially expressed genes in COR cell lines with the EMT signature of Byers et al. (2013)
Supplementary Table 1 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Table 1 - PDF file 114K, Kinase selectivity profiling of CO-1686
Supplementary Figure 3 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 3 - PDF file 295K, Activity of CO-1686 against rare lung-cancer associated EGFR mutants
Supplementary Figure S2 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 S2 - PDF file 19K, Fig.S2. DFMO triggers an increase in HT-29 cells of 5-methyltetrahydrofolate, the essential cofactor for support of methionine regeneration from homocysteine. Identification of 5-methyltetrahydrofolate was based on empirical formula assignment, considering accurate mass and MFG scores (see Methods) and neutral loss of glutamate due to in-source fragmentation. Relative quantification is based on measured ion intensities. Note that without DFMO treatment, detection of 5-methyltetraydrofolate was below the limit of quantification (*p < 0.05)
Supplementary Figure S1 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 S1 - PDF file 174K, Fig S1. Technical reproducibility of LC-MS-based metabolite profiling in the HT-29 colorectal cancer cell line. Panel A: Overlay of total ion chromatograms acquired by 24 repeated analyses of a single HT-29 colorectal cancer cell extract, assessing the consistency of measurements. Panel B: Profile plot overlay of normalized ion intensities for 624 distinct metabolites, quantified as a function of injection number for the 24 repeated analyses depicted in panel A. Results show flat run-to-run variation (mean CV = 7.99%) in the levels of the 624 metabolites with repeated analysis. Panel C: Peak overlay of 24 repeated assessments of extracted ion chromatograms for detection of some metabolites that are relevant to the present study, demonstrating reproducibility of quantification
Supplementary Figures S1 - S9 from The Androgen-Regulated Protease TMPRSS2 Activates a Proteolytic Cascade Involving Components of the Tumor Microenvironment and Promotes Prostate Cancer Metastasis
Authors: Lucas Jared M. , Heinlein Cynthia , Kim Tom , Hernandez Susana A. , Malik Muzdah S. , True Lawrence D. , Morrissey Colm , Corey Eva , Montgomery Bruce , Mostaghel Elahe , Clegg Nigel , Coleman Ilsa , Brown Christopher M. , Schneider Eric L. , Craik Charles , Simon Julian A. , Bedalov Antonio , Nelson Peter S.
Published: April 2023

Supplementary Figure S1. TMPRSS2 expression is associated with androgen receptor (AR) levels and is regulated by androgens in vivo. Supplementary Figure S2. Characterization of the differentiation status, Tmprss2 and AR expression in Tmprss2+/+ TRAMP and Tmprss2 -/- TRAMP mice. Supplementary Figure S3. Suppression of TMPRSS2 inhibits cell proliferation and invasion. Supplementary Figure S4. TMPRSS2 influences tumor cell clearance and growth in metastatic sites. Supplementary Figure S5. Comparison of cleavage specificities for type II transmembrane serine proteases expressed in prostate epithelium. Supplementary Figure S6. Identification of putative TMPRSS2 substrates based on peptide cleavage specificities determined by PS-SCL. Supplementary Figure S7. Assessment of TMPRSS2 substrate activity. Supplementary Figure S8. Characterization of TMPRSS2 chemical inhibitors. Supplementary Figure S9. Bromhexine suppresses prostate cancer cell invasion but but does not influence proliferation in vitro.
Supplementary Figure S1 Details from Co-occurring Genomic Alterations Define Major Subsets of KRAS-Mutant Lung Adenocarcinoma with Distinct Biology, Immune Profiles, and Therapeutic Vulnerabilities
Authors: Skoulidis Ferdinandos , Byers Lauren A. , Diao Lixia , Papadimitrakopoulou Vassiliki A. , Tong Pan , Izzo Julie , Behrens Carmen , Kadara Humam , Parra Edwin R. , Canales Jaime Rodriguez , Zhang Jianjun , Giri Uma , Gudikote Jayanthi , Cortez Maria A. , Yang Chao , Fan Youhong , Peyton Michael , Girard Luc , Coombes Kevin R. , Toniatti Carlo , Heffernan Timothy P. , Choi Murim , Frampton Garrett M. , Miller Vincent , Weinstein John N. , Herbst Roy S. , Wong Kwok-Kin , Zhang Jianhua , Sharma Padmanee , Mills Gordon B. , Hong Waun K. , Minna John D. , Allison James P. , Futreal Andrew , Wang Jing , Wistuba Ignacio I. , Heymach John V.
Published: April 2023

Supplementary Figure S1 Details. Expression levels of 384 genes selected for the NMF algorithm in the three KRAS-mutant LUAC subsets.
Table S5 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 S5 - XLS file 30K, Supplementary table 5 show the list of genes overlapped with published database
Table S3 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 S3 - XLS file 71K, Supplementary table 3 shows the expression profiles of PIK3CA/E545K-regulated genes in HEK-Vector, -PDK1, -Myc and -E545K cells
Table S1 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 S1 - XLS file 316K, Supplementary table 1 shows the expression profiles of PDK1-regulated genes in HEK-Vector, -PDK1, -Myc and -E545K cells
Supplementary Movie 2 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 normal breast tissue.
Supplementary Figure 4 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 - 114k, Supporting western blot analysis and drug treatment in prostate cancer cell lines.
Supplementary Figure 2 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 - 2951K, Olaparib induces a differing response in vivo depending on the genetic background.
Supplementary Table 2 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

Genes that are occupied by RNF2 and show changed expression in HMEL-RNF2WT cells. This file provides the gene names of those genes that show change in expression in HMEL-RNF2WT cells compared to HMEL-GFP cells and contain RNF2 binding site in their promoter.
Supplementary Methods, Figure Legends, Table Legends 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

This file contains supplementary methods, supplementary figure legends, supplementary table legends and supplementary references.
Supplementary Table 6 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

Selective alteration enrichment. This table shows the results of applying Fisher's Exact Test to a tabulated set of predicted damaging somatically altered genes in responders compared to non-responders. A Benjamini-Hochberg/FDR q-value is reported for genes with the minimum number of events necessary to be considered for a theoretically significant p-value of {less than or equal to} 0.01 (n = 6). The results are sorted by p-value (lowest to highest).
Supplementary Table 2 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

All alterations in responders and non-responders. All somatic mutations and short insertion/deletions are listed, with additional annotations regarding genomic coordinates, protein change, allelic fractions, and validation status (if available).
Supplementary Figures 1 - 4 from Somatic ERCC2 Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma
Authors: Van Allen Eliezer M. , Mouw Kent W. , Kim Philip , Iyer Gopa , Wagle Nikhil , Al-Ahmadie Hikmat , Zhu Cong , Ostrovnaya Irina , Kryukov Gregory V. , O'Connor Kevin W. , Sfakianos John , Garcia-Grossman Ilana , Kim Jaegil , Guancial Elizabeth A. , Bambury Richard , Bahl Samira , Gupta Namrata , Farlow Deborah , Qu Angela , Signoretti Sabina , Barletta Justine A. , Reuter Victor , Boehm Jesse , Lawrence Michael , Getz Gad , Kantoff Philip , Bochner Bernard H. , Choueiri Toni K. , Bajorin Dean F. , Solit David B. , Gabriel Stacey , D'Andrea Alan , Garraway Levi A. , Rosenberg Jonathan E.
Published: April 2023

Supplementary Figure 1. Mutation rates by cohort. Supplementary Figure 2. ERCC2 mutations. Supplementary Figure 3. ERCC2 mutation status and overall survival. Supplementary Figure 4. ERCC2 mutations occur in highly conserved regions.
Supplementary Methods 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 Methods PDF file - 123K, This file contains the Supplementary materials and methods linked to the manuscript. In addition the references associated with the materials are reported
Supplementary Figure 7 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 7 PDF file - 205K, This Figure shows that pharmacological inhibition of FAK results in suppression of NSCLC in vivo
Supplementary Figure S6 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 95K, Data demonstrating that siRNA mediated downregulation of ST6GalNAc2 expression in human and mouse cell lines promotes tumor cell aggregation in vivo
Supplementary Figures S1 - S9 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 Figures S1-S9. Figure S1. PARP1 is a partner of the RAP80-BRCA1 complex and promotes BRCA1 PARsylation. Figure S2. In vitro PARP1-driven PARsylation of BRCA1 fragments. Figure S3. Identification of a BRCA1 sequence required for optimal mono- and poly- ADP-ribosylation of the BRCA1 F3.7 fragment. Figure S4. The BRCA1 D5 sequence is not required for IRIF localization of BRCA1 in S/G2 phase nuclei. Figure S5. Olaparib treatment leads to increased BRCA1 chromatin association at sites near an I-SceI induced DSB. Figure S6. (a) RAP80 depletion and/or Olaparib treatment does not interfere with the interaction between BARD1 and BACH1, CtIP or RAD51. (b) The BRCA1-D5 sequence is required for a stable interaction between BRCA1 and RAP80 after IR, but not for the interaction between BRCA1 and BACH1 or CtIP. (c) RAP80 is not required for BRCA1 PARsylation in cells. (d) The RAP80-BRCA1 complex contains both PARsylated and unmodified BRCA1 molecules. Figure S7. PID is required for efficient RAP80 binding to PAR and PARsylated BRCA1, but not required for RAP80 IRIF localization. Figure S8. PARP1 activity is required for normal HRR tuning. Figure S9. Effects of RAD51 or EXO1/DNA2L depletion on STGC of cells expressing endogenous BRCA1, BRCA1-WT or BRCA1-D5, or depleted of BRCA1.
Supplementary Methods 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 Methods.
Supplementary Figure 3 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 Figure 3. HEK293 cells were transiently transfected with either CV or L2HGDH cDNA and TET1 cDNA. Protein lysates were harvested and immunoblotted for the indicated proteins.
Supplementary Figure 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 Figure 2. HK-2 and HEK293 cells were transiently cotransfected with the indicated siRNA and TET1 cDNA. Protein lysates were harvested and immunoblotted for the indicated proteins.
Supplementary Methods and Legends from First-in-Humans Trial of an RNA Interference Therapeutic Targeting VEGF and KSP in Cancer Patients with Liver Involvement
Authors: Tabernero Josep , Shapiro Geoffrey I. , LoRusso Patricia M. , Cervantes Andres , Schwartz Gary K. , Weiss Glen J. , Paz-Ares Luis , Cho Daniel C. , Infante Jeffrey R. , Alsina Maria , Gounder Mrinal M. , Falzone Rick , Harrop Jamie , White Amy C. Seila , Toudjarska Iva , Bumcrot David , Meyers Rachel E. , Hinkle Gregory , Svrzikapa Nenad , Hutabarat Renta M. , Clausen Valerie A. , Cehelsky Jeffrey , Nochur Saraswathy V. , Gamba-Vitalo Christina , Vaishnaw Akshay K. , Sah Dinah W.Y. , Gollob Jared A. , Burris Howard A.
Published: April 2023

Supplementary Methods and Legends PDF file - 72K, Includes detailed methods for 5' RACE assay and DCE-MRI scans, as well as figure legends for the six supplementary figures
Supplementary Figure 2 from Brain Tumor Cells in Circulation Are Enriched for Mesenchymal Gene Expression
Authors: Sullivan James P. , Nahed Brian V. , Madden Marissa W. , Oliveira Samantha M. , Springer Simeon , Bhere Deepak , Chi Andrew S. , Wakimoto Hiroaki , Rothenberg S. Michael , Sequist Lecia V. , Kapur Ravi , Shah Khalid , Iafrate A. John , Curry William T. , Loeffler Jay S. , Batchelor Tracy T. , Louis David N. , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

STEAM cocktail staining specifically identifies GBM cells.
Supplementary Table S1 from The ALK/ROS1 Inhibitor PF-06463922 Overcomes Primary Resistance to Crizotinib in ALK-Driven Neuroblastoma
Authors: Infarinato Nicole R. , Park Jin H. , Krytska Kateryna , Ryles Hannah T. , Sano Renata , Szigety Katherine M. , Li Yimei , Zou Helen Y. , Lee Nathan V. , Smeal Tod , Lemmon Mark A. , Mossé Yael P.
Published: April 2023

PF-06463922 is potent against ALK-mutated NB cell lines in vitro. Mean (n=3) IC50 values ({plus minus} SD) for crizotinib and PF-06463922 are listed for 10 NB cell lines harboring the indicated ALK aberrations, plus one NSCLC cell line (NCI-H3122). Fold increases in the IC50 values with crizotinib over those measured for PF-06463922 are also listed in the right-most column.
Supplementary Methods, Figure Legends, Table S1 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

Supplemental Table S1. List of antibodies used for flow cytometry.
Supplementary Methods 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 Methods
Supplementary Figure Legends from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Figure Legends
Supplementary Table Legend 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 Table Legend
Supplementary Figures 1 - 7 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 Figures 1 - 7. Supplementary Figure 1. Immunoblot analysis of IL-15 in normal donor CD4+ T-cells, SS patient CD4+ T-cells and patient derived cell lines. Supplementary Figure 2. Representative flow cytometric histogram is shown for CD3 expression in mononuclear cells from skin of WT and IL-15 tg mice. Supplementary Figure 3. Immunoblot analysis of HDAC1 in normal donor CD4+ T-cells, SS patient CD4+ T-cells and patient derived cell line, Hut78. Protein lysates were probed for expression of HDAC1; β-Actin was used as housekeeping control. Supplementary Figure 4. Immunoblot analysis for expression of p21 protein in normal donor CD4+ cells following ten days of incubation in IL-15 compared to unstimulated normal donor CD4+ T-cells. Supplementary Figure 5. Pie chart showing the distribution of HDAC1 occupancy in normal donor CD4+ T-cells (upper left) compared to patient CD4+ T-cells (upper right) and normal donor CD4+ T-cells stimulated with 100ng/ml IL-15 for 24 hours (lower left). Supplementary Figure 6. High magnification and (B) low magnification histological analysis of IL-15 Tg skin. Supplementary Figure 7. The CTCL mouse disease severity scoring system is on a 0 to 100 scale, with 100 being the highest (most severe) score.
Supplementary Methods, Figure Legends, Table Legend from Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia
Authors: Trinquand Amélie , dos Santos Nuno R. , Tran Quang Christine , Rocchetti Francesca , Zaniboni Benedetta , Belhocine Mohamed , Da Costa de Jesus Cindy , Lhermitte Ludovic , Tesio Melania , Dussiot Michael , Cosset François-Loïc , Verhoeyen Els , Pflumio Françoise , Ifrah Norbert , Dombret Hervé , Spicuglia Salvatore , Chatenoud Lucienne , Gross David-Alexandre , Hermine Olivier , Macintyre Elizabeth , Ghysdael Jacques , Asnafi Vahid
Published: April 2023

Supplementary Methods, Figure Legends, Table Legend
Supplementary Figures 1 - 3 from RICTOR Amplification Defines a Novel Subset of Patients with Lung Cancer Who May Benefit from Treatment with mTORC1/2 Inhibitors
Authors: Cheng Haiying , Zou Yiyu , Ross Jeffrey S. , Wang Kai , Liu Xuewen , Halmos Balazs , Ali Siraj M. , Liu Huijie , Verma Amit , Montagna Cristina , Chachoua Abraham , Goel Sanjay , Schwartz Edward L. , Zhu Changcheng , Shan Jidong , Yu Yiting , Gritsman Kira , Yelensky Roman , Lipson Doron , Otto Geoff , Hawryluk Matthew , Stephens Philip J. , Miller Vincent A. , Piperdi Bilal , Perez-Soler Roman
Published: April 2023

Supplementary Figure 1 shows RICTOR amplification/overexpression in the index patient by FISH and IHC. Supplementary Figure 2 shows analysis of TCGA database for RICTOR alteration in all types of cancers, including NSCLC. Supplementary figure 3A shows the gene alterations in each individual with RICTOR-amplified tumors. 3B shows the absolute and relative frequency of each gene alteration found in RICTOR-amplified lung cancer samples from FM NGS database.
Supplementary Figure Legends from Safety and Antitumor Activity of the Multitargeted Pan-TRK, ROS1, and ALK Inhibitor Entrectinib: Combined Results from Two Phase I Trials (ALKA-372-001 and STARTRK-1)
Authors: Drilon Alexander , Siena Salvatore , Ou Sai-Hong Ignatius , Patel Manish , Ahn Myung Ju , Lee Jeeyun , Bauer Todd M. , Farago Anna F. , Wheler Jennifer J. , Liu Stephen V. , Doebele Robert , Giannetta Laura , Cerea Giulio , Marrapese Giovanna , Schirru Michele , Amatu Alessio , Bencardino Katia , Palmeri Laura , Sartore-Bianchi Andrea , Vanzulli Angelo , Cresta Sara , Damian Silvia , Duca Matteo , Ardini Elena , Li Gang , Christiansen Jason , Kowalski Karey , Johnson Ann D. , Patel Rupal , Luo David , Chow-Maneval Edna , Hornby Zachary , Multani Pratik S. , Shaw Alice T. , De Braud Filippo G.
Published: April 2023

Supplementary Figure Legends
Supplementary Methods, Figure Legends, Table Legends 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 Methods, Supplementary References, Supplementary Table Legends, and Supplementary Figure Legends.
Supplementary Figure 3 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

Response of BPDCN and AML cells to navitoclax and A-1331852. (A) MTT assay results for the indicated cell lines after 72 hours of exposure to the indicated doses of navitoclax (combined BCL-2/BCL-XL inhibitor). (B) MTT assay results for the indicated cell lines after 72 hours of exposure to the indicated doses of A-1331852 (BCL-XL only inhibitor). In both panels, data points represent mean of 3 replicates +/- SEM, line represents non-linear regression (curve fit).
Supplementary Figure S1 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 S1. Effects on haptotaxis are independent of effects on cell velocity.
Supplementary Figure Legends 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 Legends
Supplementary Table S7 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

Primer and oligonucleotide sequences.
Supplementary Table S1 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

ctDNA patient list.