bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S1 from Chemotherapy-Resistant Human Acute Myeloid Leukemia Cells Are Not Enriched for Leukemic Stem Cells but Require Oxidative Metabolism
Authors: Farge Thomas , Saland Estelle , de Toni Fabienne , Aroua Nesrine , Hosseini Mohsen , Perry Robin , Bosc Claudie , Sugita Mayumi , Stuani Lucille , Fraisse Marine , Scotland Sarah , Larrue Clément , Boutzen Héléna , Féliu Virginie , Nicolau-Travers Marie-Laure , Cassant-Sourdy Stéphanie , Broin Nicolas , David Marion , Serhan Nizar , Sarry Audrey , Tavitian Suzanne , Kaoma Tony , Vallar Laurent , Iacovoni Jason , Linares Laetitia K. , Montersino Camille , Castellano Rémy , Griessinger Emmanuel , Collette Yves , Duchamp Olivier , Barreira Yara , Hirsch Pierre , Palama Tony , Gales Lara , Delhommeau François , Garmy-Susini Barbara H. , Portais Jean-Charles , Vergez François , Selak Mary , Danet-Desnoyers Gwenn , Carroll Martin , Récher Christian , Sarry Jean-Emmanuel
Published: April 2023

(1) Clinical characteristics of 27 AML patients used in this study for engraftment in NSG mice, including the 25 ones treated in vivo with 60 mg/kg/d cytarabine (AraC) for 5 days. (2) Clinical and mutational characteristics of AML cell lines used in this study.
Supplementary Table 1 from AZD9291, an Irreversible EGFR TKI, Overcomes T790M-Mediated Resistance to EGFR Inhibitors in Lung Cancer
Authors: Cross Darren A.E. , Ashton Susan E. , Ghiorghiu Serban , Eberlein Cath , Nebhan Caroline A. , Spitzler Paula J. , Orme Jonathon P. , Finlay M. Raymond V. , Ward Richard A. , Mellor Martine J. , Hughes Gareth , Rahi Amar , Jacobs Vivien N. , Brewer Monica Red , Ichihara Eiki , Sun Jing , Jin Hailing , Ballard Peter , Al-Kadhimi Katherine , Rowlinson Rachel , Klinowska Teresa , Richmond Graham H.P. , Cantarini Mireille , Kim Dong-Wan , Ranson Malcolm R. , Pao William
Published: April 2023

PDF file - 89KB, Additional biochemical and cellular profiling data for AZD9291 and metabolites.
Supplementary Figure 5 from AZD9291, an Irreversible EGFR TKI, Overcomes T790M-Mediated Resistance to EGFR Inhibitors in Lung Cancer
Authors: Cross Darren A.E. , Ashton Susan E. , Ghiorghiu Serban , Eberlein Cath , Nebhan Caroline A. , Spitzler Paula J. , Orme Jonathon P. , Finlay M. Raymond V. , Ward Richard A. , Mellor Martine J. , Hughes Gareth , Rahi Amar , Jacobs Vivien N. , Brewer Monica Red , Ichihara Eiki , Sun Jing , Jin Hailing , Ballard Peter , Al-Kadhimi Katherine , Rowlinson Rachel , Klinowska Teresa , Richmond Graham H.P. , Cantarini Mireille , Kim Dong-Wan , Ranson Malcolm R. , Pao William
Published: April 2023

PDF file - 182KB, Pharmacokinetic analysis of AZD9291, AZ5104 and AZ7550 total plasma concentrations vs time following single oral dose of 25mg/kg AZD9291 in mice.
Supplementary Figure 2 from AZD9291, an Irreversible EGFR TKI, Overcomes T790M-Mediated Resistance to EGFR Inhibitors in Lung Cancer
Authors: Cross Darren A.E. , Ashton Susan E. , Ghiorghiu Serban , Eberlein Cath , Nebhan Caroline A. , Spitzler Paula J. , Orme Jonathon P. , Finlay M. Raymond V. , Ward Richard A. , Mellor Martine J. , Hughes Gareth , Rahi Amar , Jacobs Vivien N. , Brewer Monica Red , Ichihara Eiki , Sun Jing , Jin Hailing , Ballard Peter , Al-Kadhimi Katherine , Rowlinson Rachel , Klinowska Teresa , Richmond Graham H.P. , Cantarini Mireille , Kim Dong-Wan , Ranson Malcolm R. , Pao William
Published: April 2023

PDF file - 151KB, Activity of AZD9291 and metabolites against cellular phospho-HER2 assays.
Supplementary Figure 1 from AZD9291, an Irreversible EGFR TKI, Overcomes T790M-Mediated Resistance to EGFR Inhibitors in Lung Cancer
Authors: Cross Darren A.E. , Ashton Susan E. , Ghiorghiu Serban , Eberlein Cath , Nebhan Caroline A. , Spitzler Paula J. , Orme Jonathon P. , Finlay M. Raymond V. , Ward Richard A. , Mellor Martine J. , Hughes Gareth , Rahi Amar , Jacobs Vivien N. , Brewer Monica Red , Ichihara Eiki , Sun Jing , Jin Hailing , Ballard Peter , Al-Kadhimi Katherine , Rowlinson Rachel , Klinowska Teresa , Richmond Graham H.P. , Cantarini Mireille , Kim Dong-Wan , Ranson Malcolm R. , Pao William
Published: April 2023

PDF file - 107KB, Mass Spectrometry study showing covalent binding of AZD9291 to cysteine 797 in EGFR T790M.
Supplementary Tables 10 - 14 from Deconstruction of a Metastatic Tumor Microenvironment Reveals a Common Matrix Response in Human Cancers
Authors: Pearce Oliver M.T. , Delaine-Smith Robin M. , Maniati Eleni , Nichols Sam , Wang Jun , Böhm Steffen , Rajeeve Vinothini , Ullah Dayem , Chakravarty Probir , Jones Roanne R. , Montfort Anne , Dowe Tom , Gribben John , Jones J. Louise , Kocher Hemant M. , Serody Jonathan S. , Vincent Benjamin G. , Connelly John , Brenton James D. , Chelala Claude , Cutillas Pedro R. , Lockley Michelle , Bessant Conrad , Knight Martin M. , Balkwill Frances R.
Published: April 2023

Supplementary Tables 10 - 14
Figures S1 - S6 from Deconstruction of a Metastatic Tumor Microenvironment Reveals a Common Matrix Response in Human Cancers
Authors: Pearce Oliver M.T. , Delaine-Smith Robin M. , Maniati Eleni , Nichols Sam , Wang Jun , Böhm Steffen , Rajeeve Vinothini , Ullah Dayem , Chakravarty Probir , Jones Roanne R. , Montfort Anne , Dowe Tom , Gribben John , Jones J. Louise , Kocher Hemant M. , Serody Jonathan S. , Vincent Benjamin G. , Connelly John , Brenton James D. , Chelala Claude , Cutillas Pedro R. , Lockley Michelle , Bessant Conrad , Knight Martin M. , Balkwill Frances R.
Published: April 2023

Supplemental Figures and Supplemental Methods
Supplemental Table from TCR Repertoire Intratumor Heterogeneity in Localized Lung Adenocarcinomas: An Association with Predicted Neoantigen Heterogeneity and Postsurgical Recurrence
Authors: Reuben Alexandre , Gittelman Rachel , Gao Jianjun , Zhang Jiexin , Yusko Erik C. , Wu Chang-Jiun , Emerson Ryan , Zhang Jianhua , Tipton Christopher , Li Jun , Quek Kelly , Gopalakrishnan Vancheswaran , Chen Runzhe , Vence Luis M. , Cascone Tina , Vignali Marissa , Fujimoto Junya , Rodriguez-Canales Jaime , Parra Edwin R. , Little Latasha D. , Gumbs Curtis , Forget Marie-Andrée , Federico Lorenzo , Haymaker Cara , Behrens Carmen , Benzeno Sharon , Bernatchez Chantale , Sepesi Boris , Gibbons Don L. , Wargo Jennifer A. , William William N. , Swisher Stephen , Heymach John V. , Robins Harlan , Lee J. Jack , Sharma Padmanee , Allison James P. , Futreal P. Andrew , Wistuba Ignacio I. , Zhang Jianjun
Published: April 2023

Table S1. Patient demographics and characteristics.
Supplementary Figure S3 from Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade
Authors: Gu Yi-Feng , Cohn Shannon , Christie Alana , McKenzie Tiffani , Wolff Nicholas , Do Quyen N. , Madhuranthakam Ananth J. , Pedrosa Ivan , Wang Tao , Dey Anwesha , Busslinger Meinrad , Xie Xian-Jin , Hammer Robert E. , McKay Renée M. , Kapur Payal , Brugarolas James
Published: April 2023

Validation of Villin-Cre;Vhl;Bap1/Pbrm1 and Sglt2-Cre;Vhl;Bap1/Pbrm1 mice.
Supplemental Tables from Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling
Authors: Chaudhuri Aadel A. , Chabon Jacob J. , Lovejoy Alexander F. , Newman Aaron M. , Stehr Henning , Azad Tej D. , Khodadoust Michael S. , Esfahani Mohammad Shahrokh , Liu Chih Long , Zhou Li , Scherer Florian , Kurtz David M. , Say Carmen , Carter Justin N. , Merriott David J. , Dudley Jonathan C. , Binkley Michael S. , Modlin Leslie , Padda Sukhmani K. , Gensheimer Michael F. , West Robert B. , Shrager Joseph B. , Neal Joel W. , Wakelee Heather A. , Loo Billy W. , Alizadeh Ash A. , Diehn Maximilian
Published: April 2023

Supplemental Tables S1-S12
Supplemental Methods from Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling
Authors: Chaudhuri Aadel A. , Chabon Jacob J. , Lovejoy Alexander F. , Newman Aaron M. , Stehr Henning , Azad Tej D. , Khodadoust Michael S. , Esfahani Mohammad Shahrokh , Liu Chih Long , Zhou Li , Scherer Florian , Kurtz David M. , Say Carmen , Carter Justin N. , Merriott David J. , Dudley Jonathan C. , Binkley Michael S. , Modlin Leslie , Padda Sukhmani K. , Gensheimer Michael F. , West Robert B. , Shrager Joseph B. , Neal Joel W. , Wakelee Heather A. , Loo Billy W. , Alizadeh Ash A. , Diehn Maximilian
Published: April 2023

Supplemental methods
Supplementary Movie 1 from ER Translocation of the MAPK Pathway Drives Therapy Resistance in BRAF-Mutant Melanoma
Authors: Ojha Rani , Leli Nektaria M. , Onorati Angelique , Piao Shengfu , Verginadis Ioannis I. , Tameire Feven , Rebecca Vito W. , Chude Cynthia I. , Murugan Sengottuvelan , Fennelly Colin , Noguera-Ortega Estela , Chu Charleen T. , Liu Shujing , Xu Xiaowei , Krepler Clemens , Xiao Min , Xu Wei , Wei Zhi , Frederick Dennie T. , Boland Genevieve , Mitchell Tara C. , Karakousis Giorgos C. , Schuchter Lynn M. , Flaherty Keith T. , Zhang Gao , Herlyn Meenhard , Koumenis Constantinos , Amaravadi Ravi K.
Published: April 2023

ERK translocation from cytosol to the ER
Supplementary Figures & Tables from BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor
Authors: Ozer Hatice Gulcin , El-Gamal Dalia , Powell Ben , Hing Zachary A. , Blachly James S. , Harrington Bonnie , Mitchell Shaneice , Grieselhuber Nicole R. , Williams Katie , Lai Tzung-Huei , Alinari Lapo , Baiocchi Robert A. , Brinton Lindsey , Baskin Elizabeth , Cannon Matthew , Beaver Larry , Goettl Virginia M. , Lucas David M. , Woyach Jennifer A. , Sampath Deepa , Lehman Amy M. , Yu Lianbo , Zhang Jiazhong , Ma Yan , Zhang Ying , Spevak Wayne , Shi Songyuan , Severson Paul , Shellooe Rafe , Carias Heidi , Tsang Garson , Dong Ken , Ewing Todd , Marimuthu Adhirai , Tantoy Christina , Walters Jason , Sanftner Laura , Rezaei Hamid , Nespi Marika , Matusow Bernice , Habets Gaston , Ibrahim Prabha , Zhang Chao , Mathé Ewy A. , Bollag Gideon , Byrd John C. , Lapalombella Rosa
Published: April 2023

Supplementary Figures S1-S7 with captions and Supplementary Tables
Table S2 from Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer
Authors: Tiriac Hervé , Belleau Pascal , Engle Dannielle D. , Plenker Dennis , Deschênes Astrid , Somerville Tim D. D. , Froeling Fieke E. M. , Burkhart Richard A. , Denroche Robert E. , Jang Gun-Ho , Miyabayashi Koji , Young C. Megan , Patel Hardik , Ma Michelle , LaComb Joseph F. , Palmaira Randze Lerie D. , Javed Ammar A. , Huynh Jasmine C. , Johnson Molly , Arora Kanika , Robine Nicolas , Shah Minita , Sanghvi Rashesh , Goetz Austin B. , Lowder Cinthya Y. , Martello Laura , Driehuis Else , LeComte Nicolas , Askan Gokce , Iacobuzio-Donahue Christine A. , Clevers Hans , Wood Laura D. , Hruban Ralph H. , Thompson Elizabeth , Aguirre Andrew J. , Wolpin Brian M. , Sasson Aaron , Kim Joseph , Wu Maoxin , Bucobo Juan Carlos , Allen Peter , Sejpal Divyesh V. , Nealon William , Sullivan James D. , Winter Jordan M. , Gimotty Phyllis A. , Grem Jean L. , DiMaio Dominick J. , Buscaglia Jonathan M. , Grandgenett Paul M. , Brody Jonathan R. , Hollingsworth Michael A. , O'Kane Grainne M. , Notta Faiyaz , Kim Edward , Crawford James M. , Devoe Craig , Ocean Allyson , Wolfgang Christopher L. , Yu Kenneth H. , Li Ellen , Vakoc Christopher R. , Hubert Benjamin , Fischer Sandra E. , Wilson Julie M. , Moffitt Richard , Knox Jennifer , Krasnitz Alexander , Gallinger Steven , Tuveson David A.
Published: April 2023

Table S2
Supplementary Tables 1 and 2 from Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility
Authors: Kaur Amanpreet , Ecker Brett L. , Douglass Stephen M. , Kugel Curtis H. , Webster Marie R. , Almeida Filipe V. , Somasundaram Rajasekharan , Hayden James , Ban Ehsan , Ahmadzadeh Hossein , Franco-Barraza Janusz , Shah Neelima , Mellis Ian A. , Keeney Frederick , Kossenkov Andrew , Tang Hsin-Yao , Yin Xiangfan , Liu Qin , Xu Xiaowei , Fane Mitchell , Brafford Patricia , Herlyn Meenhard , Speicher David W. , Wargo Jennifer A. , Tetzlaff Michael T. , Haydu Lauren E. , Raj Arjun , Shenoy Vivek , Cukierman Edna , Weeraratna Ashani T.
Published: April 2023

Tables of proteomics and CD4/8 staining
Supplementary Movie 5 from Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility
Authors: Kaur Amanpreet , Ecker Brett L. , Douglass Stephen M. , Kugel Curtis H. , Webster Marie R. , Almeida Filipe V. , Somasundaram Rajasekharan , Hayden James , Ban Ehsan , Ahmadzadeh Hossein , Franco-Barraza Janusz , Shah Neelima , Mellis Ian A. , Keeney Frederick , Kossenkov Andrew , Tang Hsin-Yao , Yin Xiangfan , Liu Qin , Xu Xiaowei , Fane Mitchell , Brafford Patricia , Herlyn Meenhard , Speicher David W. , Wargo Jennifer A. , Tetzlaff Michael T. , Haydu Lauren E. , Raj Arjun , Shenoy Vivek , Cukierman Edna , Weeraratna Ashani T.
Published: April 2023

Supplementary Movie 5
Supplementary Movie 2 from Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility
Authors: Kaur Amanpreet , Ecker Brett L. , Douglass Stephen M. , Kugel Curtis H. , Webster Marie R. , Almeida Filipe V. , Somasundaram Rajasekharan , Hayden James , Ban Ehsan , Ahmadzadeh Hossein , Franco-Barraza Janusz , Shah Neelima , Mellis Ian A. , Keeney Frederick , Kossenkov Andrew , Tang Hsin-Yao , Yin Xiangfan , Liu Qin , Xu Xiaowei , Fane Mitchell , Brafford Patricia , Herlyn Meenhard , Speicher David W. , Wargo Jennifer A. , Tetzlaff Michael T. , Haydu Lauren E. , Raj Arjun , Shenoy Vivek , Cukierman Edna , Weeraratna Ashani T.
Published: April 2023

Supplementary Movie 2
Supplementary Movie 11 from Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility
Authors: Kaur Amanpreet , Ecker Brett L. , Douglass Stephen M. , Kugel Curtis H. , Webster Marie R. , Almeida Filipe V. , Somasundaram Rajasekharan , Hayden James , Ban Ehsan , Ahmadzadeh Hossein , Franco-Barraza Janusz , Shah Neelima , Mellis Ian A. , Keeney Frederick , Kossenkov Andrew , Tang Hsin-Yao , Yin Xiangfan , Liu Qin , Xu Xiaowei , Fane Mitchell , Brafford Patricia , Herlyn Meenhard , Speicher David W. , Wargo Jennifer A. , Tetzlaff Michael T. , Haydu Lauren E. , Raj Arjun , Shenoy Vivek , Cukierman Edna , Weeraratna Ashani T.
Published: April 2023

Supplementary Movie 11
Supplementary Figures 1-10 from Suppression of Adaptive Responses to Targeted Cancer Therapy by Transcriptional Repression
Authors: Rusan Maria , Li Kapsok , Li Yvonne , Christensen Camilla L. , Abraham Brian J. , Kwiatkowski Nicholas , Buczkowski Kevin A. , Bockorny Bruno , Chen Ting , Li Shuai , Rhee Kevin , Zhang Haikuo , Chen Wankun , Terai Hideki , Tavares Tiffany , Leggett Alan L. , Li Tianxia , Wang Yichen , Zhang Tinghu , Kim Tae-Jung , Hong Sook-Hee , Poudel-Neupane Neermala , Silkes Michael , Mudianto Tenny , Tan Li , Shimamura Takeshi , Meyerson Matthew , Bass Adam J. , Watanabe Hideo , Gray Nathanael S. , Young Richard A. , Wong Kwok-Kin , Hammerman Peter S.
Published: April 2023

Supplementary Figures 1-10 and corresponding legends
Figure S4 from Exploiting Drug Addiction Mechanisms to Select against MAPKi-Resistant Melanoma
Authors: Hong Aayoung , Moriceau Gatien , Sun Lu , Lomeli Shirley , Piva Marco , Damoiseaux Robert , Holmen Sheri L. , Sharpless Norman E. , Hugo Willy , Lo Roger S.
Published: April 2023

Supplementary Figure S4. Caspase 3-independence of the cell-death predominant MAPKi-addiction phenotype
Figure S3 from Exploiting Drug Addiction Mechanisms to Select against MAPKi-Resistant Melanoma
Authors: Hong Aayoung , Moriceau Gatien , Sun Lu , Lomeli Shirley , Piva Marco , Damoiseaux Robert , Holmen Sheri L. , Sharpless Norman E. , Hugo Willy , Lo Roger S.
Published: April 2023

Supplementary Figure S3. Mitochondrial dysfunctions induced by MAPKi withdrawal in R-lines
Supplementary Methods from Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma
Authors: Pectasides Eirini , Stachler Matthew D. , Derks Sarah , Liu Yang , Maron Steven , Islam Mirazul , Alpert Lindsay , Kwak Heewon , Kindler Hedy , Polite Blase , Sharma Manish R. , Allen Kenisha , O'Day Emily , Lomnicki Samantha , Maranto Melissa , Kanteti Rajani , Fitzpatrick Carrie , Weber Christopher , Setia Namrata , Xiao Shu-Yuan , Hart John , Nagy Rebecca J. , Kim Kyoung-Mee , Choi Min-Gew , Min Byung-Hoon , Nason Katie S. , O'Keefe Lea , Watanabe Masayuki , Baba Hideo , Lanman Rick , Agoston Agoston T. , Oh David J. , Dunford Andrew , Thorner Aaron R. , Ducar Matthew D. , Wollison Bruce M. , Coleman Haley A. , Ji Yuan , Posner Mitchell C. , Roggin Kevin , Turaga Kiran , Chang Paul , Hogarth Kyle , Siddiqui Uzma , Gelrud Andres , Ha Gavin , Freeman Samuel S. , Rhoades Justin , Reed Sarah , Gydush Greg , Rotem Denisse , Davison Jon , Imamura Yu , Adalsteinsson Viktor , Lee Jeeyun , Bass Adam J. , Catenacci Daniel V.
Published: April 2023

Supplementary Methods
Supplementary Figure Legends from Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma
Authors: Pectasides Eirini , Stachler Matthew D. , Derks Sarah , Liu Yang , Maron Steven , Islam Mirazul , Alpert Lindsay , Kwak Heewon , Kindler Hedy , Polite Blase , Sharma Manish R. , Allen Kenisha , O'Day Emily , Lomnicki Samantha , Maranto Melissa , Kanteti Rajani , Fitzpatrick Carrie , Weber Christopher , Setia Namrata , Xiao Shu-Yuan , Hart John , Nagy Rebecca J. , Kim Kyoung-Mee , Choi Min-Gew , Min Byung-Hoon , Nason Katie S. , O'Keefe Lea , Watanabe Masayuki , Baba Hideo , Lanman Rick , Agoston Agoston T. , Oh David J. , Dunford Andrew , Thorner Aaron R. , Ducar Matthew D. , Wollison Bruce M. , Coleman Haley A. , Ji Yuan , Posner Mitchell C. , Roggin Kevin , Turaga Kiran , Chang Paul , Hogarth Kyle , Siddiqui Uzma , Gelrud Andres , Ha Gavin , Freeman Samuel S. , Rhoades Justin , Reed Sarah , Gydush Greg , Rotem Denisse , Davison Jon , Imamura Yu , Adalsteinsson Viktor , Lee Jeeyun , Bass Adam J. , Catenacci Daniel V.
Published: April 2023

Supplementary Figure Legends
Figure S7 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Gating strategy for immune profile analyses in this study
Supplementary Table 14 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

Differential Gene Expression and Enrichment Analysis Between Control and shSRSF6-Treated JURKAT Cells
Supplementary Table 11 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

Protein List and Enrichment Analysis of USP7-IP-MS
Table S2 from ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer
Authors: Huang Yun-Han , Hu Jing , Chen Fei , Lecomte Nicolas , Basnet Harihar , David Charles J. , Witkin Matthew D. , Allen Peter J. , Leach Steven D. , Hollmann Travis J. , Iacobuzio-Donahue Christine A. , Massagué Joan
Published: April 2023

Table S2
Figure S7 from ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer
Authors: Huang Yun-Han , Hu Jing , Chen Fei , Lecomte Nicolas , Basnet Harihar , David Charles J. , Witkin Matthew D. , Allen Peter J. , Leach Steven D. , Hollmann Travis J. , Iacobuzio-Donahue Christine A. , Massagué Joan
Published: April 2023

Figure S7
Figure S6 from ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer
Authors: Huang Yun-Han , Hu Jing , Chen Fei , Lecomte Nicolas , Basnet Harihar , David Charles J. , Witkin Matthew D. , Allen Peter J. , Leach Steven D. , Hollmann Travis J. , Iacobuzio-Donahue Christine A. , Massagué Joan
Published: April 2023

Figure S6
Supplementary Video S1 from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

Supplementary Video S1
Supplementary Table S5 from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

Antibodies
Supplementary Table S1 from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

List of Models
Supplementary Figures from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

Supplementary Figures and Legends
Supplementary Data from Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization
Authors: Liu Zhaoqi , Yoshimi Akihide , Wang Jiguang , Cho Hana , Chun-Wei Lee Stanley , Ki Michelle , Bitner Lillian , Chu Timothy , Shah Harshal , Liu Bo , Mato Anthony R. , Ruvolo Peter , Fabbri Giulia , Pasqualucci Laura , Abdel-Wahab Omar , Rabadan Raul
Published: April 2023

Supplementary Figure S1-S13 and Figure captions and Supplementary methods
Supplementary Data from Tuning the Antigen Density Requirement for CAR T-cell Activity
Authors: Majzner Robbie G. , Rietberg Skyler P. , Sotillo Elena , Dong Rui , Vachharajani Vipul T. , Labanieh Louai , Myklebust June H. , Kadapakkam Meena , Weber Evan W. , Tousley Aidan M. , Richards Rebecca M. , Heitzeneder Sabine , Nguyen Sang M. , Wiebking Volker , Theruvath Johanna , Lynn Rachel C. , Xu Peng , Dunn Alexander R. , Vale Ronald D. , Mackall Crystal L.
Published: April 2023

Supplemental Table 1 Supplementary Figures 1-10
Supplementary Table S3 from Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer
Authors: Hou Pingping , Kapoor Avnish , Zhang Qiang , Li Jiexi , Wu Chang-Jiun , Li Jun , Lan Zhengdao , Tang Ming , Ma Xingdi , Ackroyd Jeffrey J. , Kalluri Raghu , Zhang Jianhua , Jiang Shan , Spring Denise J. , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

shRNA and sgRNA information
Supplementary Figures S1-9 from Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer
Authors: Hou Pingping , Kapoor Avnish , Zhang Qiang , Li Jiexi , Wu Chang-Jiun , Li Jun , Lan Zhengdao , Tang Ming , Ma Xingdi , Ackroyd Jeffrey J. , Kalluri Raghu , Zhang Jianhua , Jiang Shan , Spring Denise J. , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Supplementary Figures S1-9
Supplementary Methods from The INPP4B Tumor Suppressor Modulates EGFR Trafficking and Promotes Triple-Negative Breast Cancer
Authors: Liu Hui , Paddock Marcia N. , Wang Haibin , Murphy Charles J. , Geck Renee C. , Navarro Adrija J. , Wulf Gerburg M. , Elemento Olivier , Haucke Volker , Cantley Lewis C. , Toker Alex
Published: April 2023

Supplementary Methods
Supplementary reagents from Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock
Authors: Dong Zhen , Zhang Guoxin , Qu Meng , Gimple Ryan C. , Wu Qiulian , Qiu Zhixin , Prager Briana C. , Wang Xiuxing , Kim Leo J.Y. , Morton Andrew R. , Dixit Deobrat , Zhou Wenchao , Huang Haidong , Li Bin , Zhu Zhe , Bao Shideng , Mack Stephen C. , Chavez Lukas , Kay Steve A. , Rich Jeremy N.
Published: April 2023

Supplementary reagents showing information of reagents used in this manuscript
Supplemental Text and Figures from A Mutation in Histone H2B Represents a New Class of Oncogenic Driver
Authors: Bennett Richard L. , Bele Aditya , Small Eliza C. , Will Christine M. , Nabet Behnam , Oyer Jon A. , Huang Xiaoxiao , Ghosh Rajarshi P. , Grzybowski Adrian T. , Yu Tao , Zhang Qiao , Riva Alberto , Lele Tanmay P. , Schatz George C. , Kelleher Neil L. , Ruthenburg Alexander J. , Liphardt Jan , Licht Jonathan D.
Published: April 2023

Supplemental materials and methods and Supplemental Figures 1-7
Figure S6 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S6 shows exogenous AA, but not DHA promotes the growth of BrM cells.
Supplemental Figures from Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases
Authors: Fischer Grant M. , Jalali Ali , Kircher David A. , Lee Won-Chul , McQuade Jennifer L. , Haydu Lauren E. , Joon Aron Y. , Reuben Alexandre , de Macedo Mariana P. , Carapeto Fernando C. L. , Yang Chendong , Srivastava Anuj , Ambati Chandrashekar R. , Sreekumar Arun , Hudgens Courtney W. , Knighton Barbara , Deng Wanleng , Ferguson Sherise D. , Tawbi Hussein A. , Glitza Isabella C. , Gershenwald Jeffrey E. , Vashisht Gopal Y. N. , Hwu Patrick , Huse Jason T. , Wargo Jennifer A. , Futreal P. Andrew , Putluri Nagireddy , Lazar Alexander J. , DeBerardinis Ralph J. , Marszalek Joseph R. , Zhang Jianjun , Holmen Sheri L. , Tetzlaff Michael T. , Davies Michael A.
Published: April 2023

Figs. S1-S14
Supplementary Data from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Supplementary Data
Figure S1 from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Figure S1
Supplementary Video2 from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes
Authors: Miyabayashi Koji , Baker Lindsey A. , Deschênes Astrid , Traub Benno , Caligiuri Giuseppina , Plenker Dennis , Alagesan Brinda , Belleau Pascal , Li Siran , Kendall Jude , Jang Gun Ho , Kawaguchi Risa Karakida , Somerville Tim D.D. , Tiriac Hervé , Hwang Chang-Il , Burkhart Richard A. , Roberts Nicholas J. , Wood Laura D. , Hruban Ralph H. , Gillis Jesse , Krasnitz Alexander , Vakoc Christopher R. , Wigler Michael , Notta Faiyaz , Gallinger Steven , Park Youngkyu , Tuveson David A.
Published: April 2023

Confocal z-stack imaging of immunofluorescent (IF) images of mStrawberry-hM1A grafts 2 weeks after IGO transplantation
Figure S1 from Oncogenic KRAS Induces NIX-Mediated Mitophagy to Promote Pancreatic Cancer
Authors: Humpton Timothy J. , Alagesan Brinda , DeNicola Gina M. , Lu Dan , Yordanov Georgi N. , Leonhardt Carl S. , Yao Melissa A. , Alagesan Priya , Zaatari Maya N. , Park Youngkyu , Skepper Jeremy N. , Macleod Kay F. , Perez-Mancera Pedro A. , Murphy Michael P. , Evan Gerard I. , Vousden Karen H. , Tuveson David A.
Published: April 2023

Supp figure 1
Supplementary Figure S2 from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes
Authors: Miyabayashi Koji , Baker Lindsey A. , Deschênes Astrid , Traub Benno , Caligiuri Giuseppina , Plenker Dennis , Alagesan Brinda , Belleau Pascal , Li Siran , Kendall Jude , Jang Gun Ho , Kawaguchi Risa Karakida , Somerville Tim D.D. , Tiriac Hervé , Hwang Chang-Il , Burkhart Richard A. , Roberts Nicholas J. , Wood Laura D. , Hruban Ralph H. , Gillis Jesse , Krasnitz Alexander , Vakoc Christopher R. , Wigler Michael , Notta Faiyaz , Gallinger Steven , Park Youngkyu , Tuveson David A.
Published: April 2023

Compared to OGO-derived tumors, IGO-derived tumors have less active TGF-β signaling and better resemble the Progenitor subtype of PDAC.
Supplementary Data from Innate αβ T Cells Mediate Antitumor Immunity by Orchestrating Immunogenic Macrophage Programming
Authors: Hundeyin Mautin , Kurz Emma , Mishra Ankita , Rossi Juan Andres Kochen , Liudahl Shannon M. , Leis Kenna R. , Mehrotra Harshita , Kim Mirhee , Torres Luisana E. , Ogunsakin Adesola , Link Jason , Sears Rosalie C. , Sivagnanam Shamilene , Goecks Jeremy , Islam K.M. Sadeq , Dolgalev Igor , Savadkar Shivraj , Wang Wei , Aykut Berk , Leinwand Joshua , Diskin Brian , Adam Salma , Israr Muhammad , Gelas Maeliss , Lish Justin , Chin Kathryn , Farooq Mohammad Saad , Wadowski Benjamin , Wu Jingjing , Shah Suhagi , Adeegbe Dennis O. , Pushalkar Smruti , Vasudevaraja Varshini , Saxena Deepak , Wong Kwok-Kin , Coussens Lisa M. , Miller George
Published: April 2023

Supp Figures 1-7 and Legends
Supp Table 1 from Innate αβ T Cells Mediate Antitumor Immunity by Orchestrating Immunogenic Macrophage Programming
Authors: Hundeyin Mautin , Kurz Emma , Mishra Ankita , Rossi Juan Andres Kochen , Liudahl Shannon M. , Leis Kenna R. , Mehrotra Harshita , Kim Mirhee , Torres Luisana E. , Ogunsakin Adesola , Link Jason , Sears Rosalie C. , Sivagnanam Shamilene , Goecks Jeremy , Islam K.M. Sadeq , Dolgalev Igor , Savadkar Shivraj , Wang Wei , Aykut Berk , Leinwand Joshua , Diskin Brian , Adam Salma , Israr Muhammad , Gelas Maeliss , Lish Justin , Chin Kathryn , Farooq Mohammad Saad , Wadowski Benjamin , Wu Jingjing , Shah Suhagi , Adeegbe Dennis O. , Pushalkar Smruti , Vasudevaraja Varshini , Saxena Deepak , Wong Kwok-Kin , Coussens Lisa M. , Miller George
Published: April 2023

Supp Table 1
Supplementary_Methods_Revision.pdf from Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy
Authors: Chen Gregory M. , Chen Changya , Das Rajat K. , Gao Peng , Chen Chia-Hui , Bandyopadhyay Shovik , Ding Yang-Yang , Uzun Yasin , Yu Wenbao , Zhu Qin , Myers Regina M. , Grupp Stephan A. , Barrett David M. , Tan Kai
Published: April 2023

Supplementary Methods
Supplementary Table S3 from Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy
Authors: Chen Gregory M. , Chen Changya , Das Rajat K. , Gao Peng , Chen Chia-Hui , Bandyopadhyay Shovik , Ding Yang-Yang , Uzun Yasin , Yu Wenbao , Zhu Qin , Myers Regina M. , Grupp Stephan A. , Barrett David M. , Tan Kai
Published: April 2023

Supplementary Table S3. Gene sets for the TCF7 regulon and interferon response. For each gene set, three annotations are provided: the Ensembl gene id, the Entrez gene id, and HGNC symbol based on annotation from Ensembl version 94.
Figure S3 from Oncogenic KRAS Recruits an Expansive Transcriptional Network through Mutant p53 to Drive Pancreatic Cancer Metastasis
Authors: Kim Michael P. , Li Xinqun , Deng Jenying , Zhang Yun , Dai Bingbing , Allton Kendra L. , Hughes Tara G. , Siangco Christian , Augustine Jithesh J. , Kang Ya'an , McDaniel Joy M. , Xiong Shunbin , Koay Eugene J. , McAllister Florencia , Bristow Christopher A. , Heffernan Timothy P. , Maitra Anirban , Liu Bin , Barton Michelle C. , Wasylishen Amanda R. , Fleming Jason B. , Lozano Guillermina
Published: April 2023

Supplementary Figure 3
Figure S2 from Oncogenic KRAS Recruits an Expansive Transcriptional Network through Mutant p53 to Drive Pancreatic Cancer Metastasis
Authors: Kim Michael P. , Li Xinqun , Deng Jenying , Zhang Yun , Dai Bingbing , Allton Kendra L. , Hughes Tara G. , Siangco Christian , Augustine Jithesh J. , Kang Ya'an , McDaniel Joy M. , Xiong Shunbin , Koay Eugene J. , McAllister Florencia , Bristow Christopher A. , Heffernan Timothy P. , Maitra Anirban , Liu Bin , Barton Michelle C. , Wasylishen Amanda R. , Fleming Jason B. , Lozano Guillermina
Published: April 2023

Supplementary Figure 2
Supplementary Table S6 from Discovery of Candidate DNA Methylation Cancer Driver Genes
Authors: Pan Heng , Renaud Loïc , Chaligne Ronan , Bloehdorn Johannes , Tausch Eugen , Mertens Daniel , Fink Anna Maria , Fischer Kirsten , Zhang Chao , Betel Doron , Gnirke Andreas , Imielinski Marcin , Moreaux Jérôme , Hallek Michael , Meissner Alexander , Stilgenbauer Stephan , Wu Catherine J. , Elemento Olivier , Landau Dan A.
Published: April 2023

Description of analyzed TCGA data.
Supplementary Table S3 from Discovery of Candidate DNA Methylation Cancer Driver Genes
Authors: Pan Heng , Renaud Loïc , Chaligne Ronan , Bloehdorn Johannes , Tausch Eugen , Mertens Daniel , Fink Anna Maria , Fischer Kirsten , Zhang Chao , Betel Doron , Gnirke Andreas , Imielinski Marcin , Moreaux Jérôme , Hallek Michael , Meissner Alexander , Stilgenbauer Stephan , Wu Catherine J. , Elemento Olivier , Landau Dan A.
Published: April 2023

Benchmarked methods DNAme drivers.
Supplementary Data from Discovery of Candidate DNA Methylation Cancer Driver Genes
Authors: Pan Heng , Renaud Loïc , Chaligne Ronan , Bloehdorn Johannes , Tausch Eugen , Mertens Daniel , Fink Anna Maria , Fischer Kirsten , Zhang Chao , Betel Doron , Gnirke Andreas , Imielinski Marcin , Moreaux Jérôme , Hallek Michael , Meissner Alexander , Stilgenbauer Stephan , Wu Catherine J. , Elemento Olivier , Landau Dan A.
Published: April 2023

Supplementary Figure S1 to S7 and Supplementary Notes.
Supplementary Table S2 from Simultaneous Inhibition of LSD1 and TGFβ Enables Eradication of Poorly Immunogenic Tumors with Anti–PD-1 Treatment
Authors: Sheng Wanqiang , Liu Yi , Chakraborty Damayanti , Debo Brian , Shi Yang
Published: April 2023

Tumor cell-derived factors with immune suppressive effects
Supplementary Data from Calnexin Impairs the Antitumor Immunity of CD4+ and CD8+ T Cells
Authors: Chen Yichen , Ma Da , Wang Xi , Fang Juan , Liu Xiangqi , Song Jingjing , Li Xinye , Ren Xianyue , Li Qiusheng , Li Qunxing , Wen Shuqiong , Luo Liqun , Xia Juan , Cui Jun , Zeng Gucheng , Chen Lieping , Cheng Bin , Wang Zhi
Published: April 2023

Supplementary Figures and Tables
Supplementary Figure 1, Tables 1 - 3 from Increased Frequency of ICOS+ CD4 T Cells as a Pharmacodynamic Biomarker for Anti-CTLA-4 Therapy
Authors: Ng Tang Derek , Shen Yu , Sun Jingjing , Wen Sijin , Wolchok Jedd D. , Yuan Jianda , Allison James P. , Sharma Padmanee
Published: April 2023

PDF file - 103K, Supplemental Figure 1. An increased frequency of ICOS+ CD4 T-cells can be consistently detected on activated T-cells. Supplemental Table 1. Frequency of ICOS+ CD4 T-cells before and after in vitro activation. Supplemental Table 2. Reproducibility of flow cytometric assay to measure frequency of ICOS+ CD4 T-cells before and after in vitro activation in fresh and frozen samples. Supplemental Table 3. Intra-assay variability assessed for ICOS+ CD4 T-cells measured in samples obtained from anti-CTLA-4 treated patients.
Supplementary Figure Legend from Phosphatidylserine-Targeting Antibody Induces M1 Macrophage Polarization and Promotes Myeloid-Derived Suppressor Cell Differentiation
Authors: Yin Yi , Huang Xianming , Lynn Kristi D. , Thorpe Philip E.
Published: April 2023

PDF file - 110K
Supplementary Table S3 from Tumor PDCD1LG2 (PD-L2) Expression and the Lymphocytic Reaction to Colorectal Cancer
Authors: Masugi Yohei , Nishihara Reiko , Hamada Tsuyoshi , Song Mingyang , da Silva Annacarolina , Kosumi Keisuke , Gu Mancang , Shi Yan , Li Wanwan , Liu Li , Nevo Daniel , Inamura Kentaro , Cao Yin , Liao Xiaoyun , Nosho Katsuhiko , Chan Andrew T. , Giannakis Marios , Bass Adam J. , Hodi F. Stephen , Freeman Gordon J. , Rodig Scott J. , Fuchs Charles S. , Qian Zhi Rong , Nowak Jonathan A. , Ogino Shuji
Published: April 2023

Multivariable ordinal logistic regression analysis to assess the association of tumor PDCD1LG2 (PD-L2) expression (predictor) with Crohn's-like lymphoid reaction (outcome)
Supplementary Figures 1 - 3 from CD4 T Cells Require ICOS-Mediated PI3K Signaling to Increase T-Bet Expression in the Setting of Anti-CTLA-4 Therapy
Authors: Chen Hong , Fu Tihui , Suh Woong-Kyung , Tsavachidou Dimitra , Wen Sijin , Gao Jianjun , Ng Tang Derek , He Qiuming , Sun Jingjing , Sharma Padmanee
Published: April 2023

PDF file - 441K, Supplementary Figure 1. (A) Schema for clinical trial whereby patients received treatment with anti-CTLA-4. (B) Unsupervised hierarchical clustering of RPPA data obtained from 7 matched pre- and post-therapy samples. (C) Representative figure to demonstrate how ICOShi and ICOSlow CD4 T cells were sorted from patients' blood samples. (D) Representative figure to demonstrate similar frequency of CD25+ T cells in the ICOShi and ICOSlow CD4 T cell subsets. (E) Similar frequencies of CD28+ CD4 T cells were observed in pre- and post-therapy samples from a single patient treated with anti-CTLA-4 (Right Panel); Summary data from 7 different patients showing similar frequencies of CD28+ T cells in pre- and post-therapy blood samples (Left Panel); and the expression of CD28 was similar in post-therapy CD4+ICOShi and CD4+ICOSlow T cells (Lower Panel). MFI=mean fluorescence intensity. Supplementary Figure 2. (A) Schema to indicate when cells were obtained from the spleen, the tumor-draining lymph nodes (DLN) and the tumor-infiltrating lymphocytes (TILs) of tumor-bearing mice that received treatment with anti-CTLA-4. (B) Tumor-bearing WT and ICOS-/- mice have similar frequency of CD28+ CD4 T cells. (C) After 48 hrs of in vitro stimulation, CD4 T cells from both WT and ICOS-/- mice had similarly increased expression of proteins indicative of PI3K-signaling (pAKT, Bcl-Xl, cyclin B1 and pS6) and T-bet protein as compared to unstimulated T cells (0 hr). Supplementary Figure 3. (A) After tumor-bearing mice were treated with anti-CTLA-4 therapy, greater expression of proteins indicative of PI3K-signaling was found in CD4+ICOShi T cells from WT mice as compared to CD4+ICOSlow T cells from WT mice or CD4+ICOShi and CD4+ICOSlow T cells from ICOS-YF mice.
Supplementary Tables from Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures
Authors: Zeng Dongqiang , Li Meiyi , Zhou Rui , Zhang Jingwen , Sun Huiying , Shi Min , Bin Jianping , Liao Yulin , Rao Jinjun , Liao Wangjun
Published: April 2023

Table-S1: Basic information of series used for estimating fractions of tumor microenvironment cells; Table-S2: Relative Fractions of tumor microenvironment cells of 1524 gastric cancer patients with overall survival informations; Table-S3: Kmeans cluster and Hazard ratios of tumor microenvironment cells in gastric cancer; Table-S4: Cellular interaction of tumor microenvironment cells; Table-S5: Clinical infromation, TMEcluster, TMEscore and fractions of Tumor microenvironment cells of GC patients in the ACRG cohort; Table-S6: P-values of Pairwise comparison ; Table-S7: Differentially expressed genes of TMEclusters in the ACRG cohort; Table-S8: TME signature genes A and B; Table-S9: Functional and pathway enrichment analyses (Gene Ontology-Biological process) of TME signature genes A and B; Table-S10: Other gene Signatures enrolled in this study; Table-S11: Enrichment analysis of TME gene cluster A and C (Hallmark gene sets of Broad Institude); Table-S12: TMEscore of all gastric cancer patients with survival informations; Table-S13: TMEscore of patients from TCGA with survival informations; Table-S14: TMEscore of patients treated with immunotherapy
Supplementary Figure 3 from PD-L1 Expression in Triple-Negative Breast Cancer
Authors: Mittendorf Elizabeth A. , Philips Anne V. , Meric-Bernstam Funda , Qiao Na , Wu Yun , Harrington Susan , Su Xiaoping , Wang Ying , Gonzalez-Angulo Ana M. , Akcakanat Argun , Chawla Akhil , Curran Michael , Hwu Patrick , Sharma Padmanee , Litton Jennifer K. , Molldrem Jeffrey J. , Alatrash Gheath
Published: April 2023

PDF file - 76K, Supplementary figure 3. T cell Proliferation is decreased after co-culture with MDA-MB-157 breast cancer cells following PTEN knockdown. In addition to MDA-MB-231 cells, PTEN knockdown induced PD-L1 expression in MDA-MB-157 breast cancer cell line also decreases T cell proliferation. (A) Representative histogram of carboxyfluorescein succinimidyl ester (CFSE) assays shows decreased T cell proliferation when PBMC were co-cultured with MDA-MB-157 breast cancer cells transduced with PTEN shRNA in comparison with co-culture with parental MDA-MB-157 cells or MDA-MB-157 cells transduced with non-targeting shRNA. Unstimulated PBMC and stimulated PBMC alone were used as negative controls. CFSE analysis was performed on CD4+ or CD8+ cells. (B) Graphical analysis of CFSE data from a representative experiment performed in triplicate. Significance was determined using an ANOVA test (*P<0.01)
Supplementary Table S4 from MicroRNA MIR21 and T Cells in Colorectal Cancer
Authors: Mima Kosuke , Nishihara Reiko , Nowak Jonathan A. , Kim Sun A. , Song Mingyang , Inamura Kentaro , Sukawa Yasutaka , Masuda Atsuhiro , Yang Juhong , Dou Ruoxu , Nosho Katsuhiko , Baba Hideo , Giovannucci Edward L. , Bowden Michaela , Loda Massimo , Giannakis Marios , Bass Adam J. , Dranoff Glenn , Freeman Gordon J. , Chan Andrew T. , Fuchs Charles S. , Qian Zhi Rong , Ogino Shuji
Published: April 2023

Associations of MIR21 expression and CD8+ T-cell density in colorectal cancer tissue with patient mortality
Supplementary Methods from MicroRNA MIR21 and T Cells in Colorectal Cancer
Authors: Mima Kosuke , Nishihara Reiko , Nowak Jonathan A. , Kim Sun A. , Song Mingyang , Inamura Kentaro , Sukawa Yasutaka , Masuda Atsuhiro , Yang Juhong , Dou Ruoxu , Nosho Katsuhiko , Baba Hideo , Giovannucci Edward L. , Bowden Michaela , Loda Massimo , Giannakis Marios , Bass Adam J. , Dranoff Glenn , Freeman Gordon J. , Chan Andrew T. , Fuchs Charles S. , Qian Zhi Rong , Ogino Shuji
Published: April 2023

MIR21 expression after adjusting for cellularity in colorectal cancer tissue and statistical analysis
Supplementary Figure 5 from Restoring Retinoic Acid Attenuates Intestinal Inflammation and Tumorigenesis in APCMin/+ Mice
Authors: Penny Hweixian Leong , Prestwood Tyler R. , Bhattacharya Nupur , Sun Fionna , Kenkel Justin A. , Davidson Matthew G. , Shen Lei , Zuniga Luis A. , Seeley E. Scott , Pai Reetesh , Choi Okmi , Tolentino Lorna , Wang Jinshan , Napoli Joseph L. , Engleman Edgar G.
Published: April 2023

Failure of injected RA to reverse the proinflammatory phenotype of APCMin/+LPDCs.
Supplementary Figure S4 from Generation of Mouse Pluripotent Stem Cell–Derived Proliferating Myeloid Cells as an Unlimited Source of Functional Antigen-Presenting Cells
Authors: Zhang Rong , Liu Tian-Yi , Senju Satoru , Haruta Miwa , Hirosawa Narumi , Suzuki Motoharu , Tatsumi Minako , Ueda Norihiro , Maki Hiroyuki , Nakatsuka Ryusuke , Matsuoka Yoshikazu , Sasaki Yutaka , Tsuzuki Shinobu , Nakanishi Hayao , Araki Ryoko , Abe Masumi , Akatsuka Yoshiki , Sakamoto Yasushi , Sonoda Yoshiaki , Nishimura Yasuharu , Kuzushima Kiyotaka , Uemura Yasushi
Published: April 2023

In vivo safety of pMC-DC treatment.
Supplementary Figure S2 from Generation of Mouse Pluripotent Stem Cell–Derived Proliferating Myeloid Cells as an Unlimited Source of Functional Antigen-Presenting Cells
Authors: Zhang Rong , Liu Tian-Yi , Senju Satoru , Haruta Miwa , Hirosawa Narumi , Suzuki Motoharu , Tatsumi Minako , Ueda Norihiro , Maki Hiroyuki , Nakatsuka Ryusuke , Matsuoka Yoshikazu , Sasaki Yutaka , Tsuzuki Shinobu , Nakanishi Hayao , Araki Ryoko , Abe Masumi , Akatsuka Yoshiki , Sakamoto Yasushi , Sonoda Yoshiaki , Nishimura Yasuharu , Kuzushima Kiyotaka , Uemura Yasushi
Published: April 2023

Morphology and proliferation of mouse ES- or iPS-pMCs under different culture conditions.
Supplementary Figure S1 from Generation of Mouse Pluripotent Stem Cell–Derived Proliferating Myeloid Cells as an Unlimited Source of Functional Antigen-Presenting Cells
Authors: Zhang Rong , Liu Tian-Yi , Senju Satoru , Haruta Miwa , Hirosawa Narumi , Suzuki Motoharu , Tatsumi Minako , Ueda Norihiro , Maki Hiroyuki , Nakatsuka Ryusuke , Matsuoka Yoshikazu , Sasaki Yutaka , Tsuzuki Shinobu , Nakanishi Hayao , Araki Ryoko , Abe Masumi , Akatsuka Yoshiki , Sakamoto Yasushi , Sonoda Yoshiaki , Nishimura Yasuharu , Kuzushima Kiyotaka , Uemura Yasushi
Published: April 2023

Morphology and surface phenotype of mouse ES- or iPS-pMCs.