bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 1 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

Clinical association of CTC frequency
Supplementary Figure 5 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

Immunohistologic and DNA-FISH analysis of tumor cells and CTCs from a patient with metastatic GBM.
Supplementary Figure 4 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

Unsupervised hierarchical clustering analysis of patient and xenograft single cell qRT-PCR expression data.
Supplementary Table S1.5 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

Validation hits.
Supplementary Figure 1 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

GBM8 and GBM24 growth in culture.
Supplementary Tables and Legend from Efficacy of Intermittent Combined RAF and MEK Inhibition in a Patient with Concurrent BRAF- and NRAS-Mutant Malignancies
Authors: Abdel-Wahab Omar , Klimek Virginia M. , Gaskell Alisa A. , Viale Agnes , Cheng Donavan , Kim Eunhee , Rampal Raajit , Bluth Mark , Harding James J. , Callahan Margaret K. , Merghoub Taha , Berger Michael F. , Solit David B. , Rosen Neal , Levine Ross L. , Chapman Paul B.
Published: April 2023

PDF file 103K, Supplementary tables and supplementary figure legends
Supplementary Figure 4 from Efficacy of Intermittent Combined RAF and MEK Inhibition in a Patient with Concurrent BRAF- and NRAS-Mutant Malignancies
Authors: Abdel-Wahab Omar , Klimek Virginia M. , Gaskell Alisa A. , Viale Agnes , Cheng Donavan , Kim Eunhee , Rampal Raajit , Bluth Mark , Harding James J. , Callahan Margaret K. , Merghoub Taha , Berger Michael F. , Solit David B. , Rosen Neal , Levine Ross L. , Chapman Paul B.
Published: April 2023

PDF file 338K, Phospho-flow data
Supplementary Figure 2 from Efficacy of Intermittent Combined RAF and MEK Inhibition in a Patient with Concurrent BRAF- and NRAS-Mutant Malignancies
Authors: Abdel-Wahab Omar , Klimek Virginia M. , Gaskell Alisa A. , Viale Agnes , Cheng Donavan , Kim Eunhee , Rampal Raajit , Bluth Mark , Harding James J. , Callahan Margaret K. , Merghoub Taha , Berger Michael F. , Solit David B. , Rosen Neal , Levine Ross L. , Chapman Paul B.
Published: April 2023

PDF file 7489K, CT scans
Supplementary Table S1.2 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 KS.
Supplementary Table S1.1 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 100 shRNAs.
Supplementary Table S4 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

Total numbers and percentage of hematopoietic subsets in young Pax5+/- and wild type mice.
Supplementary Table S2 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

Differentially expressed genes in bone marrow tumors from Pax5+/- mice compared to wild-type B220+ bone marrow B cells.
Supplementary Table 1 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

Complete Data for Genetic Analysis of ctDNA and Tumor Tissue for All Samples.
Supplementary Tables 1 - 4 from Mesothelin-Targeted CARs: Driving T Cells to Solid Tumors
Authors: Morello Aurore , Sadelain Michel , Adusumilli Prasad S.
Published: April 2023

Supplementary Tables 1 - 4. Supplementary Table 1. Proposed Antigen targets of interest for CAR T-cell therapy investigation in solid tumors. Supplementary Table 2. Publications characterizing MSLN expression in solid tumors. Supplementary Table 3. Incidence estimated for patients with solid tumors expressing MSLN. Supplementary Table 4. Prevalence estimated for patients with solid tumors expressing MSLN.
Supplementary Table S3 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

sgRNAs Used in Validation Experiment: Table of sgRNA IDs, sequences and chromosomal locations.
Supplementary Table S2 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

Cell Essential Control Genes: Table of cell essential control genes used in this manuscript.
Supplementary Figures S1 - S7 from Real-Time Imaging Reveals Local, Transient Vascular Permeability, and Tumor Cell Intravasation Stimulated by TIE2hi Macrophage–Derived VEGFA
Authors: Harney Allison S. , Arwert Esther N. , Entenberg David , Wang Yarong , Guo Peng , Qian Bin-Zhi , Oktay Maja H. , Pollard Jeffrey W. , Jones Joan G. , Condeelis John S.
Published: April 2023

Supplementary Figure S1. TMEM formation with tumor stage in PyMT. Supplementary Figures S2. Tumor cell intravasation occurs at TMEM along with local, transient blood vessel permeability. Supplementary Figure S3. Tumor cell intravasation occurs at TMEM with local, transient blood vessel permeability in a human patient-derived xenograft model of triple negative breast cancer. Supplementary Figure S4. The sliding window measurement. Supplementary Figure S5. 155 kDa dextran-TMR does not extravasate. Supplementary Figure S6. VEGFAHi TEMs are enriched at TMEM and sites of pericyte depletion. Supplementary Figure S6. Vascular VE-Cadherin is decreased in the presence of Tie2Hi/VEGFAHi macrophages in TMEM in human breast cancer.
Supplementary Figures S1 - S15 from Obesity-Induced Inflammation and Desmoplasia Promote Pancreatic Cancer Progression and Resistance to Chemotherapy
Authors: Incio Joao , Liu Hao , Suboj Priya , Chin Shan M. , Chen Ivy X. , Pinter Matthias , Ng Mei R. , Nia Hadi T. , Grahovac Jelena , Kao Shannon , Babykutty Suboj , Huang Yuhui , Jung Keehoon , Rahbari Nuh N. , Han Xiaoxing , Chauhan Vikash P. , Martin John D. , Kahn Julia , Huang Peigen , Desphande Vikram , Michaelson James , Michelakos Theodoros P. , Ferrone Cristina R. , Soares Raquel , Boucher Yves , Fukumura Dai , Jain Rakesh K.
Published: April 2023

Supplementary Figures S1 - S15. Supplementary Figure S1. Effect of obesity on tumor initiation. Supplementary Figure S2. Adipose tissue - tumor interaction. Supplementary Figure S3. Correlation of collagen-I levels with tumor size, co-expression of collagen-I and hyaluronan in PSCs, and impact of obesity on desmoplasia and tumor hyaluronan levels. Supplementary Figure S4. Additional Western blotting data from PAN02 tumors. Supplementary Figure S5. Additional effects of AT-1 inhibition on obesity-aggravated desmoplasia, perfusion and drug delivery. Supplementary Figure S6. Additional data on the effect of obesity on immune cell infiltration in tumors. Supplementary Figure S7. Effects of TAN depletion on vessel perfusion in obese mice. Supplementary Figure S8. Effect of obesity on cytokine profile in AK4.4 tumors. Supplementary Figure S9. Effects of TAN depletion on tumor cytokine expression in obese mice. Supplementary Figure S10. Additional effects of losartan on the tumor immune microenvironment. Supplementary Figure S11. Distribution of PDAC patients according to their BMI. Supplementary Figure S12. Effect of obesity on the expression of AT1, Ly6g, and AT1/Ly6g double positivity in PAN02 tumors. Supplementary Figure S13. Representative picture of AT1 expression in cancer-associated adipocytes (arrows) in PAN02 tumors. Supplementary Figure S14. Additional effects of AT1 inhibition on obesity-aggravated microenvironment. Supplementary Figure S15. Prevalance of hypertesion in PDAC patients.
Supplementary Figures S1 - S10 from APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability
Authors: Sansregret Laurent , Patterson James O. , Dewhurst Sally , López-García Carlos , Koch André , McGranahan Nicholas , Chao William Chong Hang , Barry David J. , Rowan Andrew , Instrell Rachael , Horswell Stuart , Way Michael , Howell Michael , Singleton Martin R. , Medema René H. , Nurse Paul , Petronczki Mark , Swanton Charles
Published: April 2023

Supplementary Figure S1: Using reversine to cause chromosome segregation errors and p53-dependent aneuploidy tolerance. Supplementary Figure S2: Validation of APC/C subunits using siRNA deconvolution experiments in RPE1 and HCT116 cells, and how subunit knock-down rescues proliferation when the spindle assembly checkpoint is impaired. Supplementary Figure S3: APC/C subunit knock-down reduces segregation errors caused by SAC defects. Supplementary Figure S4: CRISPR-mediated disruption of TP53 and CDC27, and resistance to Mps1 inhibitors. Supplementary Figure S5: Functional testing of CDC27 mutations in Schizosaccharomyces pombe. Supplementary Figure S6: Cell division, microtubule attachment errors and tetraploidy. Supplementary Figure S7: CRISPR-mediated disruption of TP53 in RPE1 cells. Supplementary Figure S8: APC/C partial inhibition does not rescue structural anaphase defects caused by pre-mitotic replicative stress. Supplementary Figure S9: Spindle microtubule stability using photoactivation. Supplementary Figure S10: Adaptation of RPE1/p53ko populations to Mps1 inhibitors is accompanied by a mitotic delay.
Supplementary Figure Legends, Table Legends from APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability
Authors: Sansregret Laurent , Patterson James O. , Dewhurst Sally , López-García Carlos , Koch André , McGranahan Nicholas , Chao William Chong Hang , Barry David J. , Rowan Andrew , Instrell Rachael , Horswell Stuart , Way Michael , Howell Michael , Singleton Martin R. , Medema René H. , Nurse Paul , Petronczki Mark , Swanton Charles
Published: April 2023

Supplementary Legends
Supplementary Methods, Figure Legends, Table Legends 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 Methods, Figure Legends, Table Legends
Supplementary Figure Legends 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

Supplementary Figure Legends
Supplementary Figures 1 - 3, Tables 1 - 3 from Molecular Heterogeneity and Receptor Coamplification Drive Resistance to Targeted Therapy in MET-Amplified Esophagogastric Cancer
Authors: Kwak Eunice L. , Ahronian Leanne G. , Siravegna Giulia , Mussolin Benedetta , Borger Darrell R. , Godfrey Jason T. , Jessop Nicholas A. , Clark Jeffrey W. , Blaszkowsky Lawrence S. , Ryan David P. , Lennerz Jochen K. , Iafrate A. John , Bardelli Alberto , Hong Theodore S. , Corcoran Ryan B.
Published: April 2023

Supplementary Figure S1. Absence of ALK or ROS1 rearrangements in Patient #3. Supplementary Figure S2. CT images for Patient #5. Supplementary Figure S3. Interlesional heterogeneity in a HER2-amplified EGC patient. Supplementary Table S1. 40 gene clinical targeted exome sequencing panel. Supplementary Table S2. Emergence of KRASG12D mutation by ddPCR. Supplementary Table S3. Time to progression on MET inhibitor therapy.
Supplementary Video S2 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 Video S2. MenaINV drives haptotaxis via its interaction with alpha5beta1 in vivo.
Supplementary Figure S5 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 S5. Mena isoform expression does not affect Integrin alphav, beta1 or FAK levels.
Supplementary Table S4 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

Summary of fusion isoforms.
Supplementary Table S2 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

Cell viability and Ln(IC50) for 885 cancer cell lines treated with dasatinib and saracatinib over nine doses.
Supplementary Methods, Figures S1 - S5, Tables S7 - S8 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

Supplementary Figure S1. Verification of MYBL1 Translocation in Genomic DNA. Supplementary Figure S2. Expression of Recombinant c-Myb and A-Myb Fusion Proteins. Supplementary Figure S3. Gene Expression Analysis. Supplementary Figure S4. Gene Set Enrichment Analysis. Supplementary Figure S5. Heatmap of Genes Correlated to Combined MYB and MYBL1 Levels. Supplementary Table S7. Gene Ontology Analysis. Supplementary Table S8. GO analysis of genes whose expression is either positively (Top) or negatively (Bottom) correlated with combined MYB and MYBL1 expression.
Supplementary Figures S1 - S8 from Hif1a Deletion Reveals Pro-Neoplastic Function of B Cells in Pancreatic Neoplasia
Authors: Lee Kyoung Eun , Spata Michelle , Bayne Lauren J. , Buza Elizabeth L. , Durham Amy C. , Allman David , Vonderheide Robert H. , Simon M. Celeste
Published: April 2023

Supplementary Figure S1. HIF1α is dispensable for pancreas development. Supplementary Figure S2. Additional characterization of KrasG12D;Hif1αKO animals. Supplementary Figure S3. Disease spectrum of KrasG12D and KrasG12D;Hif1αKO mice. Supplementary Figure S4. Additional characterization of immune cell infiltration in KrasG12D and KrasG12D;Hif1αKO pancreata. Supplementary Figure S5. HIF1α deficiency increases the proportion of B1b cells in spleen. Supplementary Figure S6. B cell depletion inhibits development of microinvasive neoplasms in KrasG12D;Hif1αKO pancreata. Supplementary Figure S7. Characterization of pancreatic immune infiltrates following αCD20 mAb administration. Supplementary Figure S8. Effects of HIF1α on expression of cytokines and chemokines.
Supplementary Table S4 from CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas
Authors: Jiang Yanwen , Ortega-Molina Ana , Geng Huimin , Ying Hsia-Yuan , Hatzi Katerina , Parsa Sara , McNally Dylan , Wang Ling , Doane Ashley S. , Agirre Xabier , Teater Matt , Meydan Cem , Li Zhuoning , Poloway David , Wang Shenqiu , Ennishi Daisuke , Scott David W. , Stengel Kristy R. , Kranz Janice E. , Holson Edward , Sharma Sneh , Young James W. , Chu Chi-Shuen , Roeder Robert G. , Shaknovich Rita , Hiebert Scott W. , Gascoyne Randy D. , Tam Wayne , Elemento Olivier , Wendel Hans-Guido , Melnick Ari M.
Published: April 2023

A list of CREBBP mutations in cohorts 1 and 2.
Supplementary Table S3 from CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas
Authors: Jiang Yanwen , Ortega-Molina Ana , Geng Huimin , Ying Hsia-Yuan , Hatzi Katerina , Parsa Sara , McNally Dylan , Wang Ling , Doane Ashley S. , Agirre Xabier , Teater Matt , Meydan Cem , Li Zhuoning , Poloway David , Wang Shenqiu , Ennishi Daisuke , Scott David W. , Stengel Kristy R. , Kranz Janice E. , Holson Edward , Sharma Sneh , Young James W. , Chu Chi-Shuen , Roeder Robert G. , Shaknovich Rita , Hiebert Scott W. , Gascoyne Randy D. , Tam Wayne , Elemento Olivier , Wendel Hans-Guido , Melnick Ari M.
Published: April 2023

Patient info for cohorts 1 and 2.
Supplementary Methods, Tables S1 - S2 from Clinical Response of Carcinomas Harboring the BRD4–NUT Oncoprotein to the Targeted Bromodomain Inhibitor OTX015/MK-8628
Authors: Stathis Anastasios , Zucca Emanuele , Bekradda Mohamed , Gomez-Roca Carlos , Delord Jean-Pierre , de La Motte Rouge Thibault , Uro-Coste Emmanuelle , de Braud Filippo , Pelosi Giuseppe , French Christopher A.
Published: April 2023

Supplementary data on genomic alterations and BRD4-NUT fusion sequences. Supplementary Table S1. Genomic alterations identified by OncoPanel. Supplementary Table S2. BRD4-NUT fusion sequences identified by OncoPanel.
Supplementary Figure 4 from GM-CSF Mediates Mesenchymal–Epithelial Cross-talk in Pancreatic Cancer
Authors: Waghray Meghna , Yalamanchili Malica , Dziubinski Michele , Zeinali Mina , Erkkinen Marguerite , Yang Huibin , Schradle Kara A. , Urs Sumithra , Pasca Di Magliano Marina , Welling Theodore H. , Palmbos Phillip L. , Abel Ethan V. , Sahai Vaibhav , Nagrath Sunitha , Wang Lidong , Simeone Diane M.
Published: April 2023

Supplementary Figure 4. Differential secretion of cytokines by CA-MSC and CAFs from four different patients.
Supplementary Figure S1 from Clinical Response of Carcinomas Harboring the BRD4–NUT Oncoprotein to the Targeted Bromodomain Inhibitor OTX015/MK-8628
Authors: Stathis Anastasios , Zucca Emanuele , Bekradda Mohamed , Gomez-Roca Carlos , Delord Jean-Pierre , de La Motte Rouge Thibault , Uro-Coste Emmanuelle , de Braud Filippo , Pelosi Giuseppe , French Christopher A.
Published: April 2023

MYC and beta-catenin expression patterns in Patient 2 biopsies.
Supplementary Figure 2 from GM-CSF Mediates Mesenchymal–Epithelial Cross-talk in Pancreatic Cancer
Authors: Waghray Meghna , Yalamanchili Malica , Dziubinski Michele , Zeinali Mina , Erkkinen Marguerite , Yang Huibin , Schradle Kara A. , Urs Sumithra , Pasca Di Magliano Marina , Welling Theodore H. , Palmbos Phillip L. , Abel Ethan V. , Sahai Vaibhav , Nagrath Sunitha , Wang Lidong , Simeone Diane M.
Published: April 2023

Supplementary Figure 2. Pancreatic cancer associated MSCs promote tumor cell growth and invasion. A. GFP-labeled tumor cells were grown alone or co-cultured with CA-MSCs or CAFs. GFP-labeled tumor cells were grown in growth media, in combination with conditioned media (CM) from CA-MSCs and CM from CAFs. Increased tumor cell numbers when co-cultured with CA-MSC (A) or CA-MSC CM (A) demonstrate the ability of CA-MSCs to induce proliferation in the cancer cells. *p <0.05 vs growth medium for direct culture with CA-MSC and *p <0.0001 vs growth medium for culture with CA-MSC CM. B. Invasion assays demonstrating the impact of CA-MSCs (red) or CM from CA-MSCs on tumor cell (green) migration. Double headed arrows indicate extent of migration. *p <0.05 vs growth medium.
Supplementary Table S2 from Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance
Authors: Jeong Youngtae , Hoang Ngoc T. , Lovejoy Alexander , Stehr Henning , Newman Aaron M. , Gentles Andrew J. , Kong William , Truong Diana , Martin Shanique , Chaudhuri Aadel , Heiser Diane , Zhou Li , Say Carmen , Carter Justin N. , Hiniker Susan M. , Loo Billy W. , West Robert B. , Beachy Philip , Alizadeh Ash A. , Diehn Maximilian
Published: April 2023

Supplementary Table S2. Genotyping results for NSCLC patients treated with radiotherapy.
Supplementary Methods, Figure Legends, Table Legends, Table S1, Tables S3 - S4 from Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance
Authors: Jeong Youngtae , Hoang Ngoc T. , Lovejoy Alexander , Stehr Henning , Newman Aaron M. , Gentles Andrew J. , Kong William , Truong Diana , Martin Shanique , Chaudhuri Aadel , Heiser Diane , Zhou Li , Say Carmen , Carter Justin N. , Hiniker Susan M. , Loo Billy W. , West Robert B. , Beachy Philip , Alizadeh Ash A. , Diehn Maximilian
Published: April 2023

Supplementary Table S1. In vivo limiting dilution analyses of P-LSCC and K/P-LSCC. Supplementary Table S3. Likely zygosity and functional effects of KEAP1 mutations in NSCLC patients in Fig. 7A. Supplementary Table S4. Clinical characteristics of a validation cohort of stage I-III NSCLC patients treated with curative intent RT and analyzed for KEAP1/NRF2 mutation status using targeted next generation sequencing. Antibodies used in this study.
Supplementary Figures S1 - S9 from Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance
Authors: Jeong Youngtae , Hoang Ngoc T. , Lovejoy Alexander , Stehr Henning , Newman Aaron M. , Gentles Andrew J. , Kong William , Truong Diana , Martin Shanique , Chaudhuri Aadel , Heiser Diane , Zhou Li , Say Carmen , Carter Justin N. , Hiniker Susan M. , Loo Billy W. , West Robert B. , Beachy Philip , Alizadeh Ash A. , Diehn Maximilian
Published: April 2023

Supplementary Figure S1. Loss of Keap1 or Trp53 promotes airway basal stem cell self-renewal. Supplementary Figure S2. Lineage tracing method for airway basal stem cells. Supplementary Figure S3. Characterization of LSCCs derived from Keap1-/-;Trp53-/- or Trp53-/- tracheal cells. Supplementary Figure S4. Airway basal stem cells are the cell of origin for Trp53-/- and Keap1-/-;Trp53-/- LSCCs. Supplementary Figure S5. Gene expression analysis of P-LSCC and K/P-LSCC tumors. Supplementary Figure S6. Loss of Keap1 in LSCCs leads to protection from oxidative stress. Supplementary Figure S7. Loss of Keap1 in LSCCs leads to protection from ionizing irradiation. Supplementary Figure S8. Inhibition of xCT sensitizes radioresistant K/P-LSCCs. Supplementary Figure S9. TP53 mutation status is not associated with local failure after radiotherapy in human NSCLC patients.
Supplementary Video S1 from BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance
Authors: Tasdemir Nilgun , Banito Ana , Roe Jae-Seok , Alonso-Curbelo Direna , Camiolo Matthew , Tschaharganeh Darjus F. , Huang Chun-Hao , Aksoy Ozlem , Bolden Jessica E. , Chen Chi-Chao , Fennell Myles , Thapar Vishal , Chicas Agustin , Vakoc Christopher R. , Lowe Scott W.
Published: April 2023

Co-culture of NK cells and P/shRen IMR90 cells.
Supplementary Table S1 from Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation
Authors: Elf Shannon , Abdelfattah Nouran S. , Chen Edwin , Perales-Patón Javier , Rosen Emily A. , Ko Amy , Peisker Fabian , Florescu Natalie , Giannini Silvia , Wolach Ofir , Morgan Elizabeth A. , Tothova Zuzana , Losman Julie-Aurore , Schneider Rebekka K. , Al-Shahrour Fatima , Mullally Ann
Published: April 2023

Supplementary Table S1. Pre-ranked GSEA statistics between mutant and wild-type CALR 24 hours post-IL-3 withdrawal amongst STAT5, STAT3 and JAK2 inhibitor signatures from MSiGDB and literature.
Supplementary Methods, Figure Legends, Table Legends from Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation
Authors: Elf Shannon , Abdelfattah Nouran S. , Chen Edwin , Perales-Patón Javier , Rosen Emily A. , Ko Amy , Peisker Fabian , Florescu Natalie , Giannini Silvia , Wolach Ofir , Morgan Elizabeth A. , Tothova Zuzana , Losman Julie-Aurore , Schneider Rebekka K. , Al-Shahrour Fatima , Mullally Ann
Published: April 2023

Supplementary Data
Supplementary Table S2 from BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance
Authors: Tasdemir Nilgun , Banito Ana , Roe Jae-Seok , Alonso-Curbelo Direna , Camiolo Matthew , Tschaharganeh Darjus F. , Huang Chun-Hao , Aksoy Ozlem , Bolden Jessica E. , Chen Chi-Chao , Fennell Myles , Thapar Vishal , Chicas Agustin , Vakoc Christopher R. , Lowe Scott W.
Published: April 2023

Lists of BRD4-gained TEs and SEs.
Supplementary Figure S5 from Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation
Authors: Elf Shannon , Abdelfattah Nouran S. , Chen Edwin , Perales-Patón Javier , Rosen Emily A. , Ko Amy , Peisker Fabian , Florescu Natalie , Giannini Silvia , Wolach Ofir , Morgan Elizabeth A. , Tothova Zuzana , Losman Julie-Aurore , Schneider Rebekka K. , Al-Shahrour Fatima , Mullally Ann
Published: April 2023

Supplementary Figure S5. Immunoblotting of Calr-immunoprecipitated proteins and whole cell lysates from Ba/F3-Cas9 and Ba/F3-MPL-Cas9 cells targeted with Calr-directed CRISPR gene editing using a control guide, Calr guide m1, or Calr guide m2 demonstrates increased binding between MPL and mutant Calr (lane 3 - 4 (m1) and lane 5 -6 (m2)) as compared to wild type Calr (lane 2).
Supplementary Methods, Figure Legends from BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance
Authors: Tasdemir Nilgun , Banito Ana , Roe Jae-Seok , Alonso-Curbelo Direna , Camiolo Matthew , Tschaharganeh Darjus F. , Huang Chun-Hao , Aksoy Ozlem , Bolden Jessica E. , Chen Chi-Chao , Fennell Myles , Thapar Vishal , Chicas Agustin , Vakoc Christopher R. , Lowe Scott W.
Published: April 2023

Supplementary Methods, Figure Legends, References.
Supplementary Figure S2 from Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation
Authors: Elf Shannon , Abdelfattah Nouran S. , Chen Edwin , Perales-Patón Javier , Rosen Emily A. , Ko Amy , Peisker Fabian , Florescu Natalie , Giannini Silvia , Wolach Ofir , Morgan Elizabeth A. , Tothova Zuzana , Losman Julie-Aurore , Schneider Rebekka K. , Al-Shahrour Fatima , Mullally Ann
Published: April 2023

Supplementary Figure S2. Schema of CRISPR/Cas9 gene-editing targeting of exon 9 of Calr.
Supplementary Figure S7. Pathway to Pten/ Trp53 deficient prostate metastasis and therapy resistance. from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure S7. Pathway to Pten/ Trp53 deficient prostate metastasis and therapy resistance. Pten-loss triggers PIP3 signaling to activate AKT, which prompts activation of the p53/ p21/ p16 tumor suppressors and senescence arrest. Suppression and loss of p53 in this context results in cell proliferation and Il6 secretion. Il6 signals both auto and paracrine to activate Myc via the Jak/Stat pathway. Myc induces the Phlpp2 phosphatase which creates a negative feedback loop by dampening Akt activation. Metastases (and castration-resistant tumors) select for increased Myc expression (and gene amplification, and Akt inactivation, demonstrating that Myc supersedes the need for Akt in lethal prostate cancer.
Supplementary Tables 1 - 7 from Efficacy and Safety of Abemaciclib, an Inhibitor of CDK4 and CDK6, for Patients with Breast Cancer, Non–Small Cell Lung Cancer, and Other Solid Tumors
Authors: Patnaik Amita , Rosen Lee S. , Tolaney Sara M. , Tolcher Anthony W. , Goldman Jonathan W. , Gandhi Leena , Papadopoulos Kyriakos P. , Beeram Muralidhar , Rasco Drew W. , Hilton John F. , Nasir Aejaz , Beckmann Richard P. , Schade Andrew E. , Fulford Angie D. , Nguyen Tuan S. , Martinez Ricardo , Kulanthaivel Palaniappan , Li Lily Q. , Frenzel Martin , Cronier Damien M. , Chan Edward M. , Flaherty Keith T. , Wen Patrick Y. , Shapiro Geoffrey I.
Published: April 2023

Supplementary Table 1. Summary of 33 Patients Treated with Abemaciclib in Dose Escalation. Supplementary Table 2. Baseline patient and disease characteristics. Supplementary Table 3. Possibly related treatment-emergent adverse events (>10% all grades) for hormone receptorpositive breast cancer cohort (n=19) receiving combination therapy with abemaciclib plus fulvestrant. Supplementary Table 4. Summary of abemaciclib pharmacokinetic parameters following a single oral administration. Supplementary Table 5. Summary of abemaciclib pharmacokinetic parameters following repeated once-daily (Q24H) or twice-daily (Q12H) oral administration. Supplementary Table 6. Efficacy for NSCLC cohort, overall and by KRAS status. Supplementary Table 7. Efficacy for other tumor-specific cohorts.
Supplementary Figure S5. IHC analysis of wild type lung and primary and metastatic tumors. from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure S5. IHC analysis of wild type lung and primary and metastatic tumors. (A) Wild type lung do not show increased Myc, pAktS473 or Phlpp2 staining comparing to metastatic lungs. Scale Bar, 100 Î¼m. (B) Il6 analysis of PC metastasis to lung revealed that metastatic nodules expressed Il6. Staining levels varied between 22.5% and 72.8% positive cells per nodule. (C) No Il6 activation is found in the p53-null setting and the Pten-null glands that were free of hyperplasia/ neoplasia, while the glands with proliferating cells showed Il6, consistent with their breaking of the p53 response in parts of the tissue (see the positive gland in the right bottom corner of Ptenpc-/-).
Supplementary Figure S4. Activation of Stat3/Myc signaling is specific to Ptenpc-/-; Trp53pc-/-prostate and leads to stromal expansion. from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure S4. Activation of Stat3/Myc signaling is specific to Ptenpc-/-; Trp53pc-/-prostate and leads to stromal expansion. (A) H&E analysis of prostates from all studied genotypes reveals massive stromal expansion after co-deletion of Pten and Trp53. IHC analysis confirms stromal pStat3/ Myc activation specifically in Ptenpc-/-; Trp53pc-/- prostate. Note that pAkt activation is restricted to gland, consistent with triggering paracrine Il6/Stat3/Myc activation. Scale Bars, 100 Î¼m. (B) Pten is present in the stroma of Ptenpc-/-; Trp53pc-/- prostates confirming that the expansion of stroma is not driven by spurious Pten/Trp53 recombination. (C) Proliferation in the Ptenpc-/- glands correlates with Akt activation, in contrast to Ptenpc-/-; Trp53pc-/- glands, where it correlates with Stat3/ Myc staining.
Supplementary Table 4 from A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma
Authors: Mirabello Lisa , Koster Roelof , Moriarity Branden S. , Spector Logan G. , Meltzer Paul S. , Gary Joy , Machiela Mitchell J. , Pankratz Nathan , Panagiotou Orestis A. , Largaespada David , Wang Zhaoming , Gastier-Foster Julie M. , Gorlick Richard , Khanna Chand , de Toledo Silvia Regina Caminada , Petrilli Antonio S. , Patiño-Garcia Ana , Sierrasesúmaga Luis , Lecanda Fernando , Andrulis Irene L. , Wunder Jay S. , Gokgoz Nalan , Serra Massimo , Hattinger Claudia , Picci Piero , Scotlandi Katia , Flanagan Adrienne M. , Tirabosco Roberto , Amary Maria Fernanda , Halai Dina , Ballinger Mandy L. , Thomas David M. , Davis Sean , Barkauskas Donald A. , Marina Neyssa , Helman Lee , Otto George M. , Becklin Kelsie L. , Wolf Natalie K. , Weg Madison T. , Tucker Margaret , Wacholder Sholom , Fraumeni Joseph F. , Caporaso Neil E. , Boland Joseph F. , Hicks Belynda D. , Vogt Aurelie , Burdett Laurie , Yeager Meredith , Hoover Robert N. , Chanock Stephen J. , Savage Sharon A.
Published: April 2023

Associations of the top GWAS and imputed SNP with metastasis at diagnosis in the discovery stage (European ancestry) by inheritance model.
Supplementary Figure Legends from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure Legends from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Supplementary Tables S1 - S5, Figures S1 - S5 from A Large Multiethnic Genome-Wide Association Study of Prostate Cancer Identifies Novel Risk Variants and Substantial Ethnic Differences
Authors: Hoffmann Thomas J. , Van Den Eeden Stephen K. , Sakoda Lori C. , Jorgenson Eric , Habel Laurel A. , Graff Rebecca E. , Passarelli Michael N. , Cario Clinton L. , Emami Nima C. , Chao Chun R. , Ghai Nirupa R. , Shan Jun , Ranatunga Dilrini K. , Quesenberry Charles P. , Aaronson David , Presti Joseph , Wang Zhaoming , Berndt Sonja I. , Chanock Stephen J. , McDonnell Shannon K. , French Amy J. , Schaid Daniel J. , Thibodeau Stephen N. , Li Qiyuan , Freedman Matthew L. , Penney Kathryn L. , Mucci Lorelei A. , Haiman Christopher A. , Henderson Brian E. , Seminara Daniela , Kvale Mark N. , Kwok Pui-Yan , Schaefer Catherine , Risch Neil , Witte John S.
Published: April 2023

Supplementary Table S1. Descriptive factors for KP study population, broken down by study. Supplementary Table S2. Genome-wide significant SNPs found in our cohort. Supplementary Table S3. Cis-eQTL expression of rs4646284. Supplementary Table S4. Results at the 105 loci previously found to be associated with prostate cancer. Supplementary Table S5. Risk score of and variance explained by the 105 previously reported hits. Supplementary Figure S1. Manhattan and Q-Q plots of each race/ethnicity and meta-analysis. Supplementary Figure S2. Local plots of novel replicated rs4646284 and suggestive rs2659124. Supplementary Figure S3. Cis-eQTL of SLC22A1 and SLC22A3. Supplementary Figure S4. Comparison of ORs of KP to previous reports by race/ethnicity. Supplementary Figure S5. KP AUC estimates.
Supplementary Figures S1 - S16 from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer
Authors: Anagnostou Valsamo , Smith Kellie N. , Forde Patrick M. , Niknafs Noushin , Bhattacharya Rohit , White James , Zhang Theresa , Adleff Vilmos , Phallen Jillian , Wali Neha , Hruban Carolyn , Guthrie Violeta B. , Rodgers Kristen , Naidoo Jarushka , Kang Hyunseok , Sharfman William , Georgiades Christos , Verde Franco , Illei Peter , Li Qing Kay , Gabrielson Edward , Brock Malcolm V. , Zahnow Cynthia A. , Baylin Stephen B. , Scharpf Robert B. , Brahmer Julie R. , Karchin Rachel , Pardoll Drew M. , Velculescu Victor E.
Published: April 2023

Supplementary Figure S1. Computed Tomographic (CT) findings in patient CGLU116. Supplementary Figure S2. CT findings in patient CGLU127. Supplementary Figure S3. CT findings in patient CGLU161. Supplementary Figure S4. Tumor burden kinetics. Supplementary Figure S5. Neoantigen-specific TCR expansion in stimulated T cell cultures for patient CGLU127. Supplementary Figure S6. Neoantigen-specific TCR expansion in stimulated T cell cultures for patient CGLU161. Supplementary Figure S7. Loss of heterozygosity analyses for patient CGLU116. Supplementary Figure S8. Loss of heterozygosity analyses for patient CGLU117. Supplementary Figure S9. Loss of heterozygosity analyses for patient CGLU127. Supplementary Figure S10. Loss of heterozygosity analyses for patient CGLU161. Supplementary Figure S11. TCR clonality analyses for patients CGLU127 and CGLU161. Supplementary Figure S12. TCR clonality analyses for a responder and a non-responder to PD-1 blockade. Supplementary Figure S13. PD-L1 expression in responsive and resistant tumors. Supplementary Figure S14. Eliminated mutations for case CGHN2. Supplementary Figure S15. Comparison of five methods for estimation of tumor purity. Supplementary Figure S16. CD8+ T cell density in resistant tumors.
Supplementary Figure Legends from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer
Authors: Anagnostou Valsamo , Smith Kellie N. , Forde Patrick M. , Niknafs Noushin , Bhattacharya Rohit , White James , Zhang Theresa , Adleff Vilmos , Phallen Jillian , Wali Neha , Hruban Carolyn , Guthrie Violeta B. , Rodgers Kristen , Naidoo Jarushka , Kang Hyunseok , Sharfman William , Georgiades Christos , Verde Franco , Illei Peter , Li Qing Kay , Gabrielson Edward , Brock Malcolm V. , Zahnow Cynthia A. , Baylin Stephen B. , Scharpf Robert B. , Brahmer Julie R. , Karchin Rachel , Pardoll Drew M. , Velculescu Victor E.
Published: April 2023

Supplementary Figure Legends
Supplementary Figures 1 - 5 from Neutrophils Suppress Intraluminal NK Cell–Mediated Tumor Cell Clearance and Enhance Extravasation of Disseminated Carcinoma Cells
Authors: Spiegel Asaf , Brooks Mary W. , Houshyar Samin , Reinhardt Ferenc , Ardolino Michele , Fessler Evelyn , Chen Michelle B. , Krall Jordan A. , DeCock Jasmine , Zervantonakis Ioannis K. , Iannello Alexandre , Iwamoto Yoshiko , Cortez-Retamozo Virna , Kamm Roger D. , Pittet Mikael J. , Raulet David H. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 1. Systemic neutrophilia in tumor bearing mice. Supplementary Figure 2. Increased metastasis does not result from increased intravasation or post-extravasation events. Supplementary Figure 3. NK-mediated clearance of B16-F10-GFP+ cells. Supplementary Figure 4. Ly6G+ neutrophils are more abundant in spleens of 4T1 bearing mice. Supplementary Figure 5. Splenocyte conditioned medium activates endothelial cells and induces MMP-9 secretion.
Supplementary Figure Legends from Neutrophils Suppress Intraluminal NK Cell–Mediated Tumor Cell Clearance and Enhance Extravasation of Disseminated Carcinoma Cells
Authors: Spiegel Asaf , Brooks Mary W. , Houshyar Samin , Reinhardt Ferenc , Ardolino Michele , Fessler Evelyn , Chen Michelle B. , Krall Jordan A. , DeCock Jasmine , Zervantonakis Ioannis K. , Iannello Alexandre , Iwamoto Yoshiko , Cortez-Retamozo Virna , Kamm Roger D. , Pittet Mikael J. , Raulet David H. , Weinberg Robert A.
Published: April 2023

Supplementary Figure Legends
Supplementary Figure Legends from Response to MET Inhibitors in Patients with Stage IV Lung Adenocarcinomas Harboring MET Mutations Causing Exon 14 Skipping
Authors: Paik Paul K. , Drilon Alexander , Fan Pang-Dian , Yu Helena , Rekhtman Natasha , Ginsberg Michelle S. , Borsu Laetitia , Schultz Nikolaus , Berger Michael F. , Rudin Charles M. , Ladanyi Marc
Published: April 2023

Supplementary Figure Legends
Supplementary Figure S3 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

In vivo efficacy studies comparing PF-06463922 treatment at 10 mg/kg/day (5 mg/kg BID) and 3 mg/kg/day (1.5 mg/kg BID) with crizotinib treatment at 100 mg/kg QD in: A, Felix-PDX xenografts and B, SH-SY5Y xenografts.
Supplementary Figure S2 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

In vivo effects of crizotinib and PF-06463922 on event-free survival (EFS) in neuroblastoma PDX and xenograft models.
Supplementary Figure S1 from Acquired METD1228V Mutation and Resistance to MET Inhibition in Lung Cancer
Authors: Bahcall Magda , Sim Taebo , Paweletz Cloud P. , Patel Jyoti D. , Alden Ryan S. , Kuang Yanan , Sacher Adrian G. , Kim Nam Doo , Lydon Christine A. , Awad Mark M. , Jaklitsch Michael T. , Sholl Lynette M. , Jänne Pasi A. , Oxnard Geoffrey R.
Published: April 2023

Supplementary Figure S1 shows presence of the known EGFR exon 19 deletion and high level MET amplification, both of which had been present on prior tumor NGS.
Supplementary Figure Legends, Table Legend 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

Supplementary Figure Legends, Table Legend