bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S5 from Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML
Authors: Duy Cihangir , Teater Matt , Garrett-Bakelman Francine E. , Lee Tak C. , Meydan Cem , Glass Jacob L. , Li Meng , Hellmuth Johannes C. , Mohammad Helai P. , Smitheman Kimberly N. , Shih Alan H. , Abdel-Wahab Omar , Tallman Martin S. , Guzman Monica L. , Muench David , Grimes H. Leighton , Roboz Gail J. , Kruger Ryan G. , Creasy Caretha L. , Paietta Elisabeth M. , Levine Ross L. , Carroll Martin , Melnick Ari M.
Published: April 2023

Oligonucleotide sequences
Supplementary Table S2 from Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML
Authors: Duy Cihangir , Teater Matt , Garrett-Bakelman Francine E. , Lee Tak C. , Meydan Cem , Glass Jacob L. , Li Meng , Hellmuth Johannes C. , Mohammad Helai P. , Smitheman Kimberly N. , Shih Alan H. , Abdel-Wahab Omar , Tallman Martin S. , Guzman Monica L. , Muench David , Grimes H. Leighton , Roboz Gail J. , Kruger Ryan G. , Creasy Caretha L. , Paietta Elisabeth M. , Levine Ross L. , Carroll Martin , Melnick Ari M.
Published: April 2023

Frequency of recurrent mutations in the AML cohort
Supplementary Figures S1-S6 from Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML
Authors: Duy Cihangir , Teater Matt , Garrett-Bakelman Francine E. , Lee Tak C. , Meydan Cem , Glass Jacob L. , Li Meng , Hellmuth Johannes C. , Mohammad Helai P. , Smitheman Kimberly N. , Shih Alan H. , Abdel-Wahab Omar , Tallman Martin S. , Guzman Monica L. , Muench David , Grimes H. Leighton , Roboz Gail J. , Kruger Ryan G. , Creasy Caretha L. , Paietta Elisabeth M. , Levine Ross L. , Carroll Martin , Melnick Ari M.
Published: April 2023

Supplementary Figures S1-S6
Figure S7 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 7
Supplementary Table 6 from Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance
Authors: Pettitt Stephen J. , Frankum Jessica R. , Punta Marco , Lise Stefano , Alexander John , Chen Yi , Yap Timothy A. , Haider Syed , Tutt Andrew N.J. , Lord Christopher J.
Published: April 2023

Pathogenic neopeptide presentation scores
Supplementary Table 4 from Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance
Authors: Pettitt Stephen J. , Frankum Jessica R. , Punta Marco , Lise Stefano , Alexander John , Chen Yi , Yap Timothy A. , Haider Syed , Tutt Andrew N.J. , Lord Christopher J.
Published: April 2023

cBioPortal studies used
Supplemental Table 8 from Netrin G1 Promotes Pancreatic Tumorigenesis through Cancer-Associated Fibroblast–Driven Nutritional Support and Immunosuppression
Authors: Francescone Ralph , Barbosa Vendramini-Costa Débora , Franco-Barraza Janusz , Wagner Jessica , Muir Alexander , Lau Allison N. , Gabitova Linara , Pazina Tatiana , Gupta Sapna , Luong Tiffany , Rollins Dustin , Malik Ruchi , Thapa Roshan J. , Restifo Diana , Zhou Yan , Cai Kathy Q. , Hensley Harvey H. , Tan Yinfei , Kruger Warren D. , Devarajan Karthik , Balachandran Siddharth , Klein-Szanto Andres J. , Wang Huamin , El-Deiry Wafik S. , Vander Heiden Matthew G. , Peri Suraj , Campbell Kerry S. , Astsaturov Igor , Cukierman Edna
Published: April 2023

Amino Acid- Mass Spec
Supplementary Data from Glioma Stem Cell–Specific Superenhancer Promotes Polyunsaturated Fatty-Acid Synthesis to Support EGFR Signaling
Authors: Gimple Ryan C. , Kidwell Reilly L. , Kim Leo J.Y. , Sun Tengqian , Gromovsky Anthony D. , Wu Qiulian , Wolf Megan , Lv Deguan , Bhargava Shruti , Jiang Li , Prager Briana C. , Wang Xiuxing , Ye Qing , Zhu Zhe , Zhang Guoxin , Dong Zhen , Zhao Linjie , Lee Derrick , Bi Junfeng , Sloan Andrew E. , Mischel Paul S. , Brown J. Mark , Cang Hu , Huan Tao , Mack Stephen C. , Xie Qi , Rich Jeremy N.
Published: April 2023

Combined Supplementary Figures and Figure Legends
Table S6 from Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis
Authors: Taylor Justin , Sendino Maria , Gorelick Alexander N. , Pastore Alessandro , Chang Matthew T. , Penson Alexander V. , Gavrila Elena I. , Stewart Connor , Melnik Ella M. , Herrejon Chavez Florisela , Bitner Lillian , Yoshimi Akihide , Lee Stanley Chun-Wei , Inoue Daichi , Liu Bo , Zhang Xiao J. , Mato Anthony R. , Dogan Ahmet , Kharas Michael G. , Chen Yuhong , Wang Demin , Soni Rajesh K. , Hendrickson Ronald C. , Prieto Gorka , Rodriguez Jose A. , Taylor Barry S. , Abdel-Wahab Omar
Published: April 2023

Characteristics of XPO1 mutant and wild-type CLL patients that underwent RNA-sequencing analysis.
Table S5 from Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis
Authors: Taylor Justin , Sendino Maria , Gorelick Alexander N. , Pastore Alessandro , Chang Matthew T. , Penson Alexander V. , Gavrila Elena I. , Stewart Connor , Melnik Ella M. , Herrejon Chavez Florisela , Bitner Lillian , Yoshimi Akihide , Lee Stanley Chun-Wei , Inoue Daichi , Liu Bo , Zhang Xiao J. , Mato Anthony R. , Dogan Ahmet , Kharas Michael G. , Chen Yuhong , Wang Demin , Soni Rajesh K. , Hendrickson Ronald C. , Prieto Gorka , Rodriguez Jose A. , Taylor Barry S. , Abdel-Wahab Omar
Published: April 2023

Proteins with predicted or known nuclear export signals and significantly enhanced or reduced in nuclear export in XPO1 mutant versus wild-type from SILAC analysis.
Table S1 from Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis
Authors: Taylor Justin , Sendino Maria , Gorelick Alexander N. , Pastore Alessandro , Chang Matthew T. , Penson Alexander V. , Gavrila Elena I. , Stewart Connor , Melnik Ella M. , Herrejon Chavez Florisela , Bitner Lillian , Yoshimi Akihide , Lee Stanley Chun-Wei , Inoue Daichi , Liu Bo , Zhang Xiao J. , Mato Anthony R. , Dogan Ahmet , Kharas Michael G. , Chen Yuhong , Wang Demin , Soni Rajesh K. , Hendrickson Ronald C. , Prieto Gorka , Rodriguez Jose A. , Taylor Barry S. , Abdel-Wahab Omar
Published: April 2023

Number and frequency of XPO1 hotspot mutations found across cancer types.
Supplementary Table Captions from Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis
Authors: Taylor Justin , Sendino Maria , Gorelick Alexander N. , Pastore Alessandro , Chang Matthew T. , Penson Alexander V. , Gavrila Elena I. , Stewart Connor , Melnik Ella M. , Herrejon Chavez Florisela , Bitner Lillian , Yoshimi Akihide , Lee Stanley Chun-Wei , Inoue Daichi , Liu Bo , Zhang Xiao J. , Mato Anthony R. , Dogan Ahmet , Kharas Michael G. , Chen Yuhong , Wang Demin , Soni Rajesh K. , Hendrickson Ronald C. , Prieto Gorka , Rodriguez Jose A. , Taylor Barry S. , Abdel-Wahab Omar
Published: April 2023

Supplementary Table Captions for Tables S1-S6
Supplementary Methods from Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis
Authors: Taylor Justin , Sendino Maria , Gorelick Alexander N. , Pastore Alessandro , Chang Matthew T. , Penson Alexander V. , Gavrila Elena I. , Stewart Connor , Melnik Ella M. , Herrejon Chavez Florisela , Bitner Lillian , Yoshimi Akihide , Lee Stanley Chun-Wei , Inoue Daichi , Liu Bo , Zhang Xiao J. , Mato Anthony R. , Dogan Ahmet , Kharas Michael G. , Chen Yuhong , Wang Demin , Soni Rajesh K. , Hendrickson Ronald C. , Prieto Gorka , Rodriguez Jose A. , Taylor Barry S. , Abdel-Wahab Omar
Published: April 2023

Supplementary Methods
Supplementary Table 2 from The RNA m6A Reader YTHDF2 Maintains Oncogene Expression and Is a Targetable Dependency in Glioblastoma Stem Cells
Authors: Dixit Deobrat , Prager Briana C. , Gimple Ryan C. , Poh Hui Xian , Wang Yang , Wu Qiulian , Qiu Zhixin , Kidwell Reilly L. , Kim Leo J.Y. , Xie Qi , Vitting-Seerup Kristoffer , Bhargava Shruti , Dong Zhen , Jiang Li , Zhu Zhe , Hamerlik Petra , Jaffrey Samie R. , Zhao Jing Crystal , Wang Xiuxing , Rich Jeremy N.
Published: April 2023

Supplementary Table
Supplementary Table 2 from IFNγ Is Critical for CAR T Cell–Mediated Myeloid Activation and Induction of Endogenous Immunity
Authors: Alizadeh Darya , Wong Robyn A. , Gholamin Sharareh , Maker Madeleine , Aftabizadeh Maryam , Yang Xin , Pecoraro Joseph R. , Jeppson John D. , Wang Dongrui , Aguilar Brenda , Starr Renate , Larmonier Claire B. , Larmonier Nicolas , Chen Min-Hsuan , Wu Xiwei , Ribas Antoni , Badie Behnam , Forman Stephen J. , Brown Christine E.
Published: April 2023

Supplementary Table 2
Figure S6 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 6: Comparison between TCGA CRC and COSMIC signatures Cosine similarity heat map between de novo signatures found in TCGA (y axis) and COSMIC signatures (x axis). TCGA signatures were named after their closest COSMIC mutational process match (in bold)
Figure S15 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 15: MGMT promoter methylation status in TCGA COAD/ READ MGMT promoter methylation status in TCGA COAD/READ as predicted by the MGMT-STP27 model. The beta values of two probes (cg12434587 and cg12981137, resp. on the x and y axis) are plotted, as are the predicted methylated status.
Figure S1 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 1: Non-negative matrix factorization rank survey in NHS/HPFS Quality measures for Non-negative matrix factorization in NHS/ HPFS, as described in the R package "NMF". Arrows indicate the estimated rank of mutational signatures.
MEDI5752FINALSupplementaryMaterial.docx from Design and Efficacy of a Monovalent Bispecific PD-1/CTLA4 Antibody That Enhances CTLA4 Blockade on PD-1+ Activated T Cells
Authors: Dovedi Simon J. , Elder Matthew J. , Yang Chunning , Sitnikova Suzanne I. , Irving Lorraine , Hansen Anna , Hair James , Jones Des C. , Hasani Sumati , Wang Bo , Im Seock-Ah , Tran Ben , Subramaniam Deepa S. , Gainer Shelby D. , Vashisht Kapil , Lewis Arthur , Jin Xiaofang , Kentner Stacy , Mulgrew Kathy , Wang Yaya , Overstreet Michael G. , Dodgson James , Wu Yanli , Palazon Asis , Morrow Michelle , Rainey Godfrey J. , Browne Gareth J. , Neal Frances , Murray Thomas V. , Toloczko Aleksandra D. , Dall'Acqua William , Achour Ikbel , Freeman Daniel J. , Wilkinson Robert W. , Mazor Yariv
Published: April 2023

Supplementary Materials and Methods, and Supplementary Figures
TRACERx Consortium Members from Induction of APOBEC3 Exacerbates DNA Replication Stress and Chromosomal Instability in Early Breast and Lung Cancer Evolution
Authors: Venkatesan Subramanian , Angelova Mihaela , Puttick Clare , Zhai Haoran , Caswell Deborah R. , Lu Wei-Ting , Dietzen Michelle , Galanos Panagiotis , Evangelou Konstantinos , Bellelli Roberto , Lim Emilia L. , Watkins Thomas B.K. , Rowan Andrew , Teixeira Vitor H. , Zhao Yue , Chen Haiquan , Ngo Bryan , Zalmas Lykourgos-Panagiotis , Al Bakir Maise , Hobor Sebastijan , Grönroos Eva , Pennycuick Adam , Nigro Ersilia , Campbell Brittany B. , Brown William L. , Akarca Ayse U. , Marafioti Teresa , Wu Mary Y. , Howell Michael , Boulton Simon J. , Bertoli Cosetta , Fenton Tim R. , de Bruin Robertus A.M. , Maya-Mendoza Apolinar , Santoni-Rugiu Eric , Hynds Robert E. , Gorgoulis Vassilis G. , Jamal-Hanjani Mariam , McGranahan Nicholas , Harris Reuben S. , Janes Sam M. , Bartkova Jirina , Bakhoum Samuel F. , Bartek Jiri , Kanu Nnennaya , Swanton Charles
Published: April 2023

A complete list of investigators in the Tracking Non-Small Cell Lung Cancer Evolution through Therapy (TRACERx) Consortium
Supplementary Table from Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor
Authors: Huang Yung-Hsin , Chen Chun-Wei , Sundaramurthy Venkatasubramaniam , Słabicki Mikołaj , Hao Dapeng , Watson Caroline J. , Tovy Ayala , Reyes Jaime M. , Dakhova Olga , Crovetti Brielle R. , Galonska Christina , Lee Minjung , Brunetti Lorenzo , Zhou Yubin , Tatton-Brown Katrina , Huang Yun , Cheng Xiaodong , Meissner Alexander , Valk Peter J.M. , Van Maldergem Lionel , Sanders Mathijs A. , Blundell Jamie R. , Li Wei , Ebert Benjamin L. , Goodell Margaret A.
Published: April 2023

Supplementary Table from Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor
Supplementary Figure from Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor
Authors: Huang Yung-Hsin , Chen Chun-Wei , Sundaramurthy Venkatasubramaniam , Słabicki Mikołaj , Hao Dapeng , Watson Caroline J. , Tovy Ayala , Reyes Jaime M. , Dakhova Olga , Crovetti Brielle R. , Galonska Christina , Lee Minjung , Brunetti Lorenzo , Zhou Yubin , Tatton-Brown Katrina , Huang Yun , Cheng Xiaodong , Meissner Alexander , Valk Peter J.M. , Van Maldergem Lionel , Sanders Mathijs A. , Blundell Jamie R. , Li Wei , Ebert Benjamin L. , Goodell Margaret A.
Published: April 2023

Supplementary Figure from Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor
Supplementary Data PDF from Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis
Authors: Li Jun , Duran Mercedes A. , Dhanota Ninjit , Chatila Walid K. , Bettigole Sarah E. , Kwon John , Sriram Roshan K. , Humphries Matthew P. , Salto-Tellez Manuel , James Jacqueline A. , Hanna Matthew G. , Melms Johannes C. , Vallabhaneni Sreeram , Litchfield Kevin , Usaite Ieva , Biswas Dhruva , Bareja Rohan , Li Hao Wei , Martin Maria Laura , Dorsaint Princesca , Cavallo Julie-Ann , Li Peng , Pauli Chantal , Gottesdiener Lee , DiPardo Benjamin J. , Hollmann Travis J. , Merghoub Taha , Wen Hannah Y. , Reis-Filho Jorge S. , Riaz Nadeem , Su Shin-San Michael , Kalbasi Anusha , Vasan Neil , Powell Simon N. , Wolchok Jedd D. , Elemento Olivier , Swanton Charles , Shoushtari Alexander N. , Parkes Eileen E. , Izar Benjamin , Bakhoum Samuel F.
Published: April 2023

Supplementary Figures and Methods in PDF format
Supplementary Table S2 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy
Authors: DeStefano Shields Christina E. , White James R. , Chung Liam , Wenzel Alyssa , Hicks Jessica L. , Tam Ada J. , Chan June L. , Dejea Christine M. , Fan Hongni , Michel John , Maiuri Ashley R. , Sriramkumar Shruthi , Podicheti Ram , Rusch Douglas B. , Wang Hao , De Marzo Angelo M. , Besharati Sepideh , Anders Robert A. , Baylin Stephen B. , O'Hagan Heather M. , Housseau Franck , Sears Cynthia L.
Published: April 2023

Differential methylation values for methylation-binding domain sequencing (MBDseq) for sham and ETBF-colonized normal epithelium and tumors from Min and BRAFV600ELgr5CreMin (BLM) colons.
Supplementary Table S1 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy
Authors: DeStefano Shields Christina E. , White James R. , Chung Liam , Wenzel Alyssa , Hicks Jessica L. , Tam Ada J. , Chan June L. , Dejea Christine M. , Fan Hongni , Michel John , Maiuri Ashley R. , Sriramkumar Shruthi , Podicheti Ram , Rusch Douglas B. , Wang Hao , De Marzo Angelo M. , Besharati Sepideh , Anders Robert A. , Baylin Stephen B. , O'Hagan Heather M. , Housseau Franck , Sears Cynthia L.
Published: April 2023

Differential expression (DESeq2) tables of RNAseq of cell-sorted F4/80lowI-A/Elow (low) versus F4/80highI-A/Ehigh (high) cells from the mid-proximal colon of BRAFV600ELgr5Cre (BL) and wildtype (WT) mice 2 weeks after ETBF inoculation.
Supplementary Data from Bacterial Genotoxin Accelerates Transient Infection–Driven Murine Colon Tumorigenesis
Authors: Liu Yue , Fu Kai , Wier Eric M. , Lei Yifan , Hodgson Andrea , Xu Dongqing , Xia Xue , Zheng Dandan , Ding Hua , Sears Cynthia L. , Yang Jian , Wan Fengyi
Published: April 2023

Supplementary data contain Supplementary Table 1-3 and Supplementary Figures 1-11.
Supplementary Figures S1-S6, Table S4, Table S6 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy
Authors: DeStefano Shields Christina E. , White James R. , Chung Liam , Wenzel Alyssa , Hicks Jessica L. , Tam Ada J. , Chan June L. , Dejea Christine M. , Fan Hongni , Michel John , Maiuri Ashley R. , Sriramkumar Shruthi , Podicheti Ram , Rusch Douglas B. , Wang Hao , De Marzo Angelo M. , Besharati Sepideh , Anders Robert A. , Baylin Stephen B. , O'Hagan Heather M. , Housseau Franck , Sears Cynthia L.
Published: April 2023

Supplementary Figures 1-6; Table S4: Tumors from ETBF-colonized BRAFV600ELgr5CreMin (BLM) mice are MSI negative; Table S6: Primer sequences for qMSP and assays used for Taqman gene expression.
Supplementary Data from Loss of Optineurin Drives Cancer Immune Evasion via Palmitoylation-Dependent IFNGR1 Lysosomal Sorting and Degradation
Authors: Du Wan , Hua Fang , Li Xiong , Zhang Jian , Li Shasha , Wang Weichao , Zhou Jiajia , Wang Weimin , Liao Peng , Yan Yijian , Li Gaopeng , Wei Shuang , Grove Sara , Vatan Linda , Zgodziński Witold , Majewski Marek , Wallner Grzegorz , Chen Haoyan , Kryczek Ilona , Fang Jing-Yuan , Zou Weiping
Published: April 2023

Supplementary Figure S1-9 and Supplementary Tables S1-8
Table S6 from Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade
Authors: Gu Shengqing Stan , Zhang Wubing , Wang Xiaoqing , Jiang Peng , Traugh Nicole , Li Ziyi , Meyer Clifford , Stewig Blair , Xie Yingtian , Bu Xia , Manos Michael P. , Font-Tello Alba , Gjini Evisa , Lako Ana , Lim Klothilda , Conway Jake , Tewari Alok K. , Zeng Zexian , Sahu Avinash Das , Tokheim Collin , Weirather Jason L. , Fu Jingxin , Zhang Yi , Kroger Benjamin , Liang Jin Hua , Cejas Paloma , Freeman Gordon J. , Rodig Scott , Long Henry W. , Gewurz Benjamin E. , Hodi F. Stephen , Brown Myles , Liu X. Shirley
Published: April 2023

Effect of different drug treatment on the expression of genes encoding MHC-I, TAP1, PD-L1, and PD-L2
Table S5 from Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade
Authors: Gu Shengqing Stan , Zhang Wubing , Wang Xiaoqing , Jiang Peng , Traugh Nicole , Li Ziyi , Meyer Clifford , Stewig Blair , Xie Yingtian , Bu Xia , Manos Michael P. , Font-Tello Alba , Gjini Evisa , Lako Ana , Lim Klothilda , Conway Jake , Tewari Alok K. , Zeng Zexian , Sahu Avinash Das , Tokheim Collin , Weirather Jason L. , Fu Jingxin , Zhang Yi , Kroger Benjamin , Liang Jin Hua , Cejas Paloma , Freeman Gordon J. , Rodig Scott , Long Henry W. , Gewurz Benjamin E. , Hodi F. Stephen , Brown Myles , Liu X. Shirley
Published: April 2023

Information on the ICB treatment clinical cohorts used in this study
Supplementary Methods from AXL Inhibition in Macrophages Stimulates Host-versus-Leukemia Immunity and Eradicates Naïve and Treatment-Resistant Leukemia
Authors: Tirado-Gonzalez Irene , Descot Arnaud , Soetopo Devona , Nevmerzhitskaya Aleksandra , Schäffer Alexander , Kur Ivan-Maximilano , Czlonka Ewelina , Wachtel Carolin , Tsoukala Ioanna , Müller Luise , Schäfer Anna-Lena , Weitmann Maresa , Dinse Petra , Alberto Emily , Buck Michèle C. , Landry Jonathan JM. , Baying Bianka , Slotta-Huspenina Julia , Roesler Jenny , Harter Patrick N. , Kubasch Anne-Sophie , Meinel Jörn , Elwakeel Eiman , Strack Elisabeth , Quang Christine Tran , Abdel-Wahab Omar , Schmitz Marc , Weigert Andreas , Schmid Tobias , Platzbecker Uwe , Benes Vladimir , Ghysdael Jacques , Bonig Halvard , Götze Katharina S. , Rothlin Carla V. , Ghosh Sourav , Medyouf Hind
Published: April 2023

Supplementary Methods
Table S3 from Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade
Authors: Gu Shengqing Stan , Zhang Wubing , Wang Xiaoqing , Jiang Peng , Traugh Nicole , Li Ziyi , Meyer Clifford , Stewig Blair , Xie Yingtian , Bu Xia , Manos Michael P. , Font-Tello Alba , Gjini Evisa , Lako Ana , Lim Klothilda , Conway Jake , Tewari Alok K. , Zeng Zexian , Sahu Avinash Das , Tokheim Collin , Weirather Jason L. , Fu Jingxin , Zhang Yi , Kroger Benjamin , Liang Jin Hua , Cejas Paloma , Freeman Gordon J. , Rodig Scott , Long Henry W. , Gewurz Benjamin E. , Hodi F. Stephen , Brown Myles , Liu X. Shirley
Published: April 2023

Traf3-knockout signature derived from RNA-seq
Table S2 from Therapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade
Authors: Gu Shengqing Stan , Zhang Wubing , Wang Xiaoqing , Jiang Peng , Traugh Nicole , Li Ziyi , Meyer Clifford , Stewig Blair , Xie Yingtian , Bu Xia , Manos Michael P. , Font-Tello Alba , Gjini Evisa , Lako Ana , Lim Klothilda , Conway Jake , Tewari Alok K. , Zeng Zexian , Sahu Avinash Das , Tokheim Collin , Weirather Jason L. , Fu Jingxin , Zhang Yi , Kroger Benjamin , Liang Jin Hua , Cejas Paloma , Freeman Gordon J. , Rodig Scott , Long Henry W. , Gewurz Benjamin E. , Hodi F. Stephen , Brown Myles , Liu X. Shirley
Published: April 2023

RNA-seq and ATAC-seq of TRAF3-normal and -deficient B16F10 cells treated with vehicle control or IFNγ
Table S3 from Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium
Authors: Pikman Yana , Tasian Sarah K. , Sulis Maria Luisa , Stevenson Kristen , Blonquist Traci M. , Apsel Winger Beth , Cooper Todd M. , Pauly Melinda , Maloney Kelly W. , Burke Michael J. , Brown Patrick A. , Gossai Nathan , McNeer Jennifer L. , Shukla Neerav N. , Cole Peter D. , Kahn Justine M. , Chen Jing , Barth Matthew J. , Magee Jeffrey A. , Gennarini Lisa , Adhav Asmani A. , Clinton Catherine M. , Ocasio-Martinez Nicole , Gotti Giacomo , Li Yuting , Lin Shan , Imamovic Alma , Tognon Cristina E. , Patel Tasleema , Faust Haley L. , Contreras Cristina F. , Cremer Anjali , Cortopassi Wilian A. , Garrido Ruiz Diego , Jacobson Matthew P. , Dharia Neekesh V. , Su Angela , Robichaud Amanda L. , Saur Conway Amy , Tarlock Katherine , Stieglitz Elliot , Place Andrew E. , Puissant Alexandre , Hunger Stephen P. , Kim Annette S. , Lindeman Neal I. , Gore Lia , Janeway Katherine A. , Silverman Lewis B. , Tyner Jeffrey W. , Harris Marian H. , Loh Mignon L. , Stegmaier Kimberly
Published: April 2023

Reasons for not using recommended targeted therapy.
Table S2 from Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium
Authors: Pikman Yana , Tasian Sarah K. , Sulis Maria Luisa , Stevenson Kristen , Blonquist Traci M. , Apsel Winger Beth , Cooper Todd M. , Pauly Melinda , Maloney Kelly W. , Burke Michael J. , Brown Patrick A. , Gossai Nathan , McNeer Jennifer L. , Shukla Neerav N. , Cole Peter D. , Kahn Justine M. , Chen Jing , Barth Matthew J. , Magee Jeffrey A. , Gennarini Lisa , Adhav Asmani A. , Clinton Catherine M. , Ocasio-Martinez Nicole , Gotti Giacomo , Li Yuting , Lin Shan , Imamovic Alma , Tognon Cristina E. , Patel Tasleema , Faust Haley L. , Contreras Cristina F. , Cremer Anjali , Cortopassi Wilian A. , Garrido Ruiz Diego , Jacobson Matthew P. , Dharia Neekesh V. , Su Angela , Robichaud Amanda L. , Saur Conway Amy , Tarlock Katherine , Stieglitz Elliot , Place Andrew E. , Puissant Alexandre , Hunger Stephen P. , Kim Annette S. , Lindeman Neal I. , Gore Lia , Janeway Katherine A. , Silverman Lewis B. , Tyner Jeffrey W. , Harris Marian H. , Loh Mignon L. , Stegmaier Kimberly
Published: April 2023

Inhibitor Recommendation Usage Summary.
Table S1 from Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium
Authors: Pikman Yana , Tasian Sarah K. , Sulis Maria Luisa , Stevenson Kristen , Blonquist Traci M. , Apsel Winger Beth , Cooper Todd M. , Pauly Melinda , Maloney Kelly W. , Burke Michael J. , Brown Patrick A. , Gossai Nathan , McNeer Jennifer L. , Shukla Neerav N. , Cole Peter D. , Kahn Justine M. , Chen Jing , Barth Matthew J. , Magee Jeffrey A. , Gennarini Lisa , Adhav Asmani A. , Clinton Catherine M. , Ocasio-Martinez Nicole , Gotti Giacomo , Li Yuting , Lin Shan , Imamovic Alma , Tognon Cristina E. , Patel Tasleema , Faust Haley L. , Contreras Cristina F. , Cremer Anjali , Cortopassi Wilian A. , Garrido Ruiz Diego , Jacobson Matthew P. , Dharia Neekesh V. , Su Angela , Robichaud Amanda L. , Saur Conway Amy , Tarlock Katherine , Stieglitz Elliot , Place Andrew E. , Puissant Alexandre , Hunger Stephen P. , Kim Annette S. , Lindeman Neal I. , Gore Lia , Janeway Katherine A. , Silverman Lewis B. , Tyner Jeffrey W. , Harris Marian H. , Loh Mignon L. , Stegmaier Kimberly
Published: April 2023

MTT recommendation tiering system.
Supplementary Methods from Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium
Authors: Pikman Yana , Tasian Sarah K. , Sulis Maria Luisa , Stevenson Kristen , Blonquist Traci M. , Apsel Winger Beth , Cooper Todd M. , Pauly Melinda , Maloney Kelly W. , Burke Michael J. , Brown Patrick A. , Gossai Nathan , McNeer Jennifer L. , Shukla Neerav N. , Cole Peter D. , Kahn Justine M. , Chen Jing , Barth Matthew J. , Magee Jeffrey A. , Gennarini Lisa , Adhav Asmani A. , Clinton Catherine M. , Ocasio-Martinez Nicole , Gotti Giacomo , Li Yuting , Lin Shan , Imamovic Alma , Tognon Cristina E. , Patel Tasleema , Faust Haley L. , Contreras Cristina F. , Cremer Anjali , Cortopassi Wilian A. , Garrido Ruiz Diego , Jacobson Matthew P. , Dharia Neekesh V. , Su Angela , Robichaud Amanda L. , Saur Conway Amy , Tarlock Katherine , Stieglitz Elliot , Place Andrew E. , Puissant Alexandre , Hunger Stephen P. , Kim Annette S. , Lindeman Neal I. , Gore Lia , Janeway Katherine A. , Silverman Lewis B. , Tyner Jeffrey W. , Harris Marian H. , Loh Mignon L. , Stegmaier Kimberly
Published: April 2023

Supplementary Data file including supplementary methods and clinical case vignettes.
Supplementary Video 7 from Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling
Authors: Adamopoulos Christos , Ahmed Tamer A. , Tucker Maxwell R. , Ung Peter M.U. , Xiao Min , Karoulia Zoi , Amabile Angelo , Wu Xuewei , Aaronson Stuart A. , Ang Celina , Rebecca Vito W. , Brown Brian D. , Schlessinger Avner , Herlyn Meenhard , Wang Qi , Shaw David E. , Poulikakos Poulikos I.
Published: April 2023

Supplementary Video 7
Supplementary Figures from A Burned-Out CD8+ T-cell Subset Expands in the Tumor Microenvironment and Curbs Cancer Immunotherapy
Authors: Sanmamed Miguel F. , Nie Xinxin , Desai Shruti S. , Villaroel-Espindola Franz , Badri Ti , Zhao Dejian , Kim Anthony W. , Ji Lan , Zhang Tianxiang , Quinlan Edward , Cheng Xiaoxiao , Han Xue , Vesely Matthew D. , Nassar Ala F. , Sun Jingwei , Zhang Yu , Kim Tae Kon , Wang Jun , Melero Ignacio , Herbst Roy S. , Schalper Kurt A. , Chen Lieping
Published: April 2023

Figures S1-14 and Legends
Supplementary Video 6 from Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling
Authors: Adamopoulos Christos , Ahmed Tamer A. , Tucker Maxwell R. , Ung Peter M.U. , Xiao Min , Karoulia Zoi , Amabile Angelo , Wu Xuewei , Aaronson Stuart A. , Ang Celina , Rebecca Vito W. , Brown Brian D. , Schlessinger Avner , Herlyn Meenhard , Wang Qi , Shaw David E. , Poulikakos Poulikos I.
Published: April 2023

Supplementary Video 6
Supplementary Data from A Burned-Out CD8+ T-cell Subset Expands in the Tumor Microenvironment and Curbs Cancer Immunotherapy
Authors: Sanmamed Miguel F. , Nie Xinxin , Desai Shruti S. , Villaroel-Espindola Franz , Badri Ti , Zhao Dejian , Kim Anthony W. , Ji Lan , Zhang Tianxiang , Quinlan Edward , Cheng Xiaoxiao , Han Xue , Vesely Matthew D. , Nassar Ala F. , Sun Jingwei , Zhang Yu , Kim Tae Kon , Wang Jun , Melero Ignacio , Herbst Roy S. , Schalper Kurt A. , Chen Lieping
Published: April 2023

Supplementary Figure Legens
Supplementary Video 4 from Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling
Authors: Adamopoulos Christos , Ahmed Tamer A. , Tucker Maxwell R. , Ung Peter M.U. , Xiao Min , Karoulia Zoi , Amabile Angelo , Wu Xuewei , Aaronson Stuart A. , Ang Celina , Rebecca Vito W. , Brown Brian D. , Schlessinger Avner , Herlyn Meenhard , Wang Qi , Shaw David E. , Poulikakos Poulikos I.
Published: April 2023

Supplementary Video 4
Supplementary Video 3 from Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling
Authors: Adamopoulos Christos , Ahmed Tamer A. , Tucker Maxwell R. , Ung Peter M.U. , Xiao Min , Karoulia Zoi , Amabile Angelo , Wu Xuewei , Aaronson Stuart A. , Ang Celina , Rebecca Vito W. , Brown Brian D. , Schlessinger Avner , Herlyn Meenhard , Wang Qi , Shaw David E. , Poulikakos Poulikos I.
Published: April 2023

Supplementary Video 3
Supplementary Video 2 from Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling
Authors: Adamopoulos Christos , Ahmed Tamer A. , Tucker Maxwell R. , Ung Peter M.U. , Xiao Min , Karoulia Zoi , Amabile Angelo , Wu Xuewei , Aaronson Stuart A. , Ang Celina , Rebecca Vito W. , Brown Brian D. , Schlessinger Avner , Herlyn Meenhard , Wang Qi , Shaw David E. , Poulikakos Poulikos I.
Published: April 2023

Supplementary Video 2
Supplementary Figures from Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling
Authors: Adamopoulos Christos , Ahmed Tamer A. , Tucker Maxwell R. , Ung Peter M.U. , Xiao Min , Karoulia Zoi , Amabile Angelo , Wu Xuewei , Aaronson Stuart A. , Ang Celina , Rebecca Vito W. , Brown Brian D. , Schlessinger Avner , Herlyn Meenhard , Wang Qi , Shaw David E. , Poulikakos Poulikos I.
Published: April 2023

Supplementary Figures and Legends
Supplementary Table S5 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Marker genes for the monocyte-macrophage-DC subpopulations identified in Supplementary Figure 5H. Only genes with adjusted p-value < 0.01 and average log fold-change > 0.3 were included. gene, gene name; p_val, p-value calculated based on Wilcoxon test; avg_logFC, log fold-change of the average expression between the given cluster and all other clusters; pct.1, fraction of gene-expressing cells in the given cluster; pct.2, fraction of gene-expressing cells in all other clusters; pct.diff, Difference between the percentage of gene-expressing cells in the given cluster and all other clusters; p_val_adj, Bonferroni adjusted p-value; cluster, cluster annotation based on the gene markers identified; resolution, clustering resolution parameter used in Seurat.
Supplementary Table S2 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

List of genes differentially expressed in STK11mut vs STK11wt tumors.
Supplementary Table S4 from Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level
Authors: Wu Yingcheng , Yang Shuaixi , Ma Jiaqiang , Chen Zechuan , Song Guohe , Rao Dongning , Cheng Yifei , Huang Siyuan , Liu Yifei , Jiang Shan , Liu Jinxia , Huang Xiaowu , Wang Xiaoying , Qiu Shuangjian , Xu Jianmin , Xi Ruibin , Bai Fan , Zhou Jian , Fan Jia , Zhang Xiaoming , Gao Qiang
Published: April 2023

Supplementary Table S4. Macrophage phenotypic gene signature.
Supplementary Table S1 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Clinical activity with durvalumab plus tremelimumab in patients from Study 006 with STK11mut and STK11wt tumors, characterized by tumor cell PD-L1 expression (high [{greater than or equal to}25%] or low [<25%]) and TMB (high [{greater than or equal to}10 mut/Mb] or low [10 mut/Mb]).
Supplementary Table S3 from Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level
Authors: Wu Yingcheng , Yang Shuaixi , Ma Jiaqiang , Chen Zechuan , Song Guohe , Rao Dongning , Cheng Yifei , Huang Siyuan , Liu Yifei , Jiang Shan , Liu Jinxia , Huang Xiaowu , Wang Xiaoying , Qiu Shuangjian , Xu Jianmin , Xi Ruibin , Bai Fan , Zhou Jian , Fan Jia , Zhang Xiaoming , Gao Qiang
Published: April 2023

Supplementary Table S3. Differentially expressed genes between LM and CRC infiltrated MRC1+ CCL18+ macrophages & SPP1+ macrophages.
Supplementary Figure S8 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Antitumor efficacy of TNFRSF agonist immunotherapies in CT26 STK11wt or KO mice. Survival of mice engrafted with (A) CT26 WT or (B) CT26 STK11 KO clone 26C16 treated with isotype control antibodies, anti-PD-L1 plus anti-CTLA-4 mAbs or immune agonist Abs anti-OX40, anti-ICOS, or anti-CD137, as indicated.
Supplementary Table S1 from Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level
Authors: Wu Yingcheng , Yang Shuaixi , Ma Jiaqiang , Chen Zechuan , Song Guohe , Rao Dongning , Cheng Yifei , Huang Siyuan , Liu Yifei , Jiang Shan , Liu Jinxia , Huang Xiaowu , Wang Xiaoying , Qiu Shuangjian , Xu Jianmin , Xi Ruibin , Bai Fan , Zhou Jian , Fan Jia , Zhang Xiaoming , Gao Qiang
Published: April 2023

Supplementary Table S1. Clinical characteristics of patients included in this study.
Supplementary Figure S7 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Characterization of STAT3 phosphorylation in the CT26 STK11 KO model and from primary human NSCLC tumors. (A) Representative multispectral fluorescence imaging of phosphorylated murine STAT3 (pSTAT3), CD45, CD163, and nuclei (DAPI), as indicated, with quantification of positive cells per mm2 in CT26 tumors. 26C16 STK11 KI indicates CT26 STK11 KO clone 26C16 engineered to re-express WT STK11. (B) Normalized protein expression levels of human STAT3 phosphorylated at tyrosine 705 (Y705) from STK11mut and STK11wt samples based on RPPA data from the TCGA database (left). Levels of human STAT3 RNA expression in samples from TCGA (right). (C) pSTAT3 in tumor cells from primary human NSCLC PDX models. Mean percentages of pSTAT3+ cells were identified among human mitochondria-positive tumor cells from duplicate IHC samples for each STK11mut and STK11wt PDX sample as indicated (left). A statistically significant difference in the mean percentage of pSTAT3+ tumor cells was observed (right; two-tailed p-value calculated using a Mann-Whitney test). (D) IHC results from STK11mut NSCLC PDX sample LG0654 and STK11wt NSCLC PDX sample LG0567, which represented the extremes of tumor pSTAT3 IHC signal in tested samples.
Supplementary Figure S6 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Characterization of the adaptive T cell immune infiltrate and PD-L1 mRNA expression in CT26 STK11 KO tumors compared to CT26 WT. (A) Density of CD8+ T cells in tumors as indicated. (B) Representative micrographs of CD8 IHC. Bar indicates 200 Î¼m. (C) UMAP representation of the lymphocyte population identified within CD45+ cells, showing sub-populations as determined by Louvain clustering. (D) Percentage of lymphocyte sub-populations per sample. (E) Top highly expressed genes between lymphocyte sub-clusters used for annotation as labeled in C and D. (F) Comparison between median percentage of cells that are present in the activated CD8+ T cell cluster (CD8_T_activ) among CT26 WT and STK11 KO clones. (G) Comparison between median percentage of cells that are present in the resting CD8+ T cell cluster (T_rest) among CT26 WT and STK11 KO clones. (H) Density of CD4+ cells as determined by IHC. (I) Density of FoxP3+ cells (FoxP3+ Treg) determined by IHC. (J) Relative PD-L1 RNA expression levels from CT26 WT and CT26 STK11 KO tumors.
Supplementary Figure S4 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Characterization of CT26 tumor cell lines with CRISPR-mediated STK11 loss. (A) Western blotting of STK11, phosphorylated AMPK (p-AMPK), total AMPK, and actin in lysates from wild-type CT26 cells (CT26 WT), STK11 CRISPR knock-out clones 26C16, 26C10 and 26C4, and clone 26C16 cells engineered to re-express STK11 (26C16 KI STK11). The ratio of phosphorylated AMPK to total AMPK (p-AMPK/total AMPK) is shown at bottom. (B) In vitro growth of cells in tissue culture. *p < 0.01 for STK11 KO clones 26C4 and 26C10 vs CT26 WT, one-way ANOVA. (C) In vivo tumor growth rates. â€ p < 0.001 for STK11 KO clones 26C4, 26C10, and 26C16 each vs CT26 WT comparing tumor volumes at days 13-15, one-way ANOVA.
Supplementary Figure S3 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Association between STK11 mutation, TMB, PD-L1 expression and STK11 expression. (A) No differences in TMB were observed in baseline STK11mut vs STK11wt tumor samples from Study 006. (B) STK11mut tumors expressed lower baseline levels of PD-L1 than STK11wt tumors from Study 1108 and Study 006. (C) Patients with STK11 mutations had decreased baseline expression of STK11 in tumor biopsies from Study 1108 and Study 006. (D) No differential expression of CD8, CXCL9 or LAG3 was observed in STK11mut vs STK11wt tumors in pretreatment biopsies from Study 1108 and Study 006 analyzed by IHC. P-values indicate Wilcoxon t-test.
Supplementary Figure S2 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Association between STK11 mutation and patient prognosis. In TCGA, STK11 mutations do not predict NSCLC OS.
Supplementary Data from Targeting the p300/CBP Axis in Lethal Prostate Cancer
Authors: Welti Jonathan , Sharp Adam , Brooks Nigel , Yuan Wei , McNair Christopher , Chand Saswati N. , Pal Abhijit , Figueiredo Ines , Riisnaes Ruth , Gurel Bora , Rekowski Jan , Bogdan Denisa , West William , Young Barbara , Raja Meera , Prosser Amy , Lane Jordan , Thomson Stuart , Worthington Jenny , Onions Stuart , Shannon Jonathan , Paoletta Silvia , Brown Richard , Smyth Don , Harbottle Gareth W. , Gil Veronica S. , Miranda Susana , Crespo Mateus , Ferreira Ana , Pereira Rita , Tunariu Nina , Carreira Suzanne , Neeb Antje J. , Ning Jian , Swain Amanda , Taddei David , Schiewer Matthew J. , Knudsen Karen E. , Pegg Neil , de Bono Johann S.
Published: April 2023

Supplementary figures
Supplementary Data from Targeting the p300/CBP Axis in Lethal Prostate Cancer
Authors: Welti Jonathan , Sharp Adam , Brooks Nigel , Yuan Wei , McNair Christopher , Chand Saswati N. , Pal Abhijit , Figueiredo Ines , Riisnaes Ruth , Gurel Bora , Rekowski Jan , Bogdan Denisa , West William , Young Barbara , Raja Meera , Prosser Amy , Lane Jordan , Thomson Stuart , Worthington Jenny , Onions Stuart , Shannon Jonathan , Paoletta Silvia , Brown Richard , Smyth Don , Harbottle Gareth W. , Gil Veronica S. , Miranda Susana , Crespo Mateus , Ferreira Ana , Pereira Rita , Tunariu Nina , Carreira Suzanne , Neeb Antje J. , Ning Jian , Swain Amanda , Taddei David , Schiewer Matthew J. , Knudsen Karen E. , Pegg Neil , de Bono Johann S.
Published: April 2023

Supplementary tables
Supplementary Figure S11 from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Efficacy of anti-IL6 mAb in CT26 STK11 KO model. (A) Survival of mice engrafted with 26C16 and treated as indicated. Isotype vs anti-PD-L1 plus anti-CTLA-4, p = 0.0020; Isotype vs anti-IL6 plus anti-PD-L1 plus anti-CTLA-4, p = 0.034; anti-IL6 vs anti-IL6 plus anti-PD-L1 plus anti-CTLA-4, p = 0.055, log rank (Mantel-Cox) survival analysis. (B) Survival of mice engrafted with CT26 WT and treated as indicated.
Supplementary Appendix from Resistance to Durvalumab and Durvalumab plus Tremelimumab Is Associated with Functional STK11 Mutations in Patients with Non–Small Cell Lung Cancer and Is Reversed by STAT3 Knockdown
Authors: Pore Nabendu , Wu Song , Standifer Nathan , Jure-Kunkel Maria , de los Reyes Melissa , Shrestha Yashaswi , Halpin Rebecca , Rothstein Raymond , Mulgrew Kathy , Blackmore Stephen , Martin Philip , Meekin John , Griffin Matthew , Bisha Ina , Proia Theresa A. , Miragaia Ricardo J. , Herbst Ronald , Gupta Ashok , Abdullah Shaad E. , Raja Rajiv , Frigault Melanie M. , Barrett J. Carl , Dennis Phillip A. , Ascierto Maria Libera , Oberst Michael D.
Published: April 2023

Supplementary Appendix
Supplementary Table 1 from CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies
Authors: Wang Dongrui , Prager Briana C. , Gimple Ryan C. , Aguilar Brenda , Alizadeh Darya , Tang Hongzhen , Lv Deguan , Starr Renate , Brito Alfonso , Wu Qiulian , Kim Leo J.Y. , Qiu Zhixin , Lin Peng , Lorenzini Michael H. , Badie Behnam , Forman Stephen J. , Xie Qi , Brown Christine E. , Rich Jeremy N.
Published: April 2023

CRISPR screening reads on CAR T cells and GSCs
Supplementary Figure 2 from A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation
Authors: Lo Yuan-Hung , Kolahi Kevin S. , Du Yuhong , Chang Chiung-Ying , Krokhotin Andrey , Nair Ajay , Sobba Walter D. , Karlsson Kasper , Jones Sunny J. , Longacre Teri A. , Mah Amanda T. , Tercan Bahar , Sockell Alexandra , Xu Hang , Seoane Jose A. , Chen Jin , Shmulevich Ilya , Weissman Jonathan S. , Curtis Christina , Califano Andrea , Fu Haian , Crabtree Gerald R. , Kuo Calvin J.
Published: April 2023

Supplementary Figure 2