bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S4 from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma
Authors: Van Allen Eliezer M. , Wagle Nikhil , Sucker Antje , Treacy Daniel J. , Johannessen Cory M. , Goetz Eva M. , Place Chelsea S. , Taylor-Weiner Amaro , Whittaker Steven , Kryukov Gregory V. , Hodis Eran , Rosenberg Mara , McKenna Aaron , Cibulskis Kristian , Farlow Deborah , Zimmer Lisa , Hillen Uwe , Gutzmer Ralf , Goldinger Simone M. , Ugurel Selma , Gogas Helen J. , Egberts Friederike , Berking Carola , Trefzer Uwe , Loquai Carmen , Weide Benjamin , Hassel Jessica C. , Gabriel Stacey B. , Carter Scott L. , Getz Gad , Garraway Levi A. , Schadendorf Dirk
Published: April 2023

PDF file, 12065K, Supplementary Table S4. Complete listing of all somatic mutations seen in all tumors. This table provides details on every non-synonymous mutation or short insertion/deletion observed in this cohort, with data on genomic coordinates, protein change, protein region affected, and read counts for each event. Many additional annotations are provided (e.g. cDNA change, RefSeq number)
Supplementary Table S3 from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma
Authors: Van Allen Eliezer M. , Wagle Nikhil , Sucker Antje , Treacy Daniel J. , Johannessen Cory M. , Goetz Eva M. , Place Chelsea S. , Taylor-Weiner Amaro , Whittaker Steven , Kryukov Gregory V. , Hodis Eran , Rosenberg Mara , McKenna Aaron , Cibulskis Kristian , Farlow Deborah , Zimmer Lisa , Hillen Uwe , Gutzmer Ralf , Goldinger Simone M. , Ugurel Selma , Gogas Helen J. , Egberts Friederike , Berking Carola , Trefzer Uwe , Loquai Carmen , Weide Benjamin , Hassel Jessica C. , Gabriel Stacey B. , Carter Scott L. , Getz Gad , Garraway Levi A. , Schadendorf Dirk
Published: April 2023

XLSX file 261K, Supplementary Table S3. Mutations seen in patients with tumors at one time point. For patients with whole exome sequencing data on either pre-treatment (for early resistance cases) or after relapse (for acquired resistance cases), this table summarizes the complete set of non-synonymous mutations and short insertion/deletions called. Alterations in this table met the additional criteria of at least 30X coverage in the tumor and an allelic fraction of at least 0.05. Each column is a patient, each row is a gene, and each non-blank entry denotes the protein change that results from the mutation seen
Supplementary Table S1 from Systematic Interrogation of 3q26 Identifies TLOC1 and SKIL as Cancer Drivers
Authors: Hagerstrand Daniel , Tong Alexander , Schumacher Steven E. , Ilic Nina , Shen Rhine R. , Cheung Hiu Wing , Vazquez Francisca , Shrestha Yashaswi , Kim So Young , Giacomelli Andrew O. , Rosenbluh Joseph , Schinzel Anna C. , Spardy Nicole A. , Barbie David A. , Mermel Craig H. , Weir Barbara A. , Garraway Levi A. , Tamayo Pablo , Mesirov Jill P. , Beroukhim Rameen , Hahn William C.
Published: April 2023

Supplementary Table S1 - XLSX file 54K, Gene suppression induced by shRNAs determined by quantitative real time PCR in MCF7 cells
Supplementary Table S2 from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma
Authors: Van Allen Eliezer M. , Wagle Nikhil , Sucker Antje , Treacy Daniel J. , Johannessen Cory M. , Goetz Eva M. , Place Chelsea S. , Taylor-Weiner Amaro , Whittaker Steven , Kryukov Gregory V. , Hodis Eran , Rosenberg Mara , McKenna Aaron , Cibulskis Kristian , Farlow Deborah , Zimmer Lisa , Hillen Uwe , Gutzmer Ralf , Goldinger Simone M. , Ugurel Selma , Gogas Helen J. , Egberts Friederike , Berking Carola , Trefzer Uwe , Loquai Carmen , Weide Benjamin , Hassel Jessica C. , Gabriel Stacey B. , Carter Scott L. , Getz Gad , Garraway Levi A. , Schadendorf Dirk
Published: April 2023

XLSX file 327K, Supplementary Table S2. Mutations seen exclusively in resistant tumors. For patients with whole exome sequencing data on both pre-treatment and resistant tumors (n = 32), this table summarizes the complete set of non-synonymous mutations and short insertion/deletions called only in the resistant but not pre-treatment tumors. Alterations in this table met the additional criteria of at least 30X coverage in the tumor and an allelic fraction of at least 0.05. Each column is a patient, each row is a gene, and each non-blank entry denotes the protein change that results from the mutation.
Supplementary Legends from Systematic Interrogation of 3q26 Identifies TLOC1 and SKIL as Cancer Drivers
Authors: Hagerstrand Daniel , Tong Alexander , Schumacher Steven E. , Ilic Nina , Shen Rhine R. , Cheung Hiu Wing , Vazquez Francisca , Shrestha Yashaswi , Kim So Young , Giacomelli Andrew O. , Rosenbluh Joseph , Schinzel Anna C. , Spardy Nicole A. , Barbie David A. , Mermel Craig H. , Weir Barbara A. , Garraway Levi A. , Tamayo Pablo , Mesirov Jill P. , Beroukhim Rameen , Hahn William C.
Published: April 2023

Supplementary Legends - PDF file 122K, Legends for all Supplementary information
Supplementary Table S1 from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma
Authors: Van Allen Eliezer M. , Wagle Nikhil , Sucker Antje , Treacy Daniel J. , Johannessen Cory M. , Goetz Eva M. , Place Chelsea S. , Taylor-Weiner Amaro , Whittaker Steven , Kryukov Gregory V. , Hodis Eran , Rosenberg Mara , McKenna Aaron , Cibulskis Kristian , Farlow Deborah , Zimmer Lisa , Hillen Uwe , Gutzmer Ralf , Goldinger Simone M. , Ugurel Selma , Gogas Helen J. , Egberts Friederike , Berking Carola , Trefzer Uwe , Loquai Carmen , Weide Benjamin , Hassel Jessica C. , Gabriel Stacey B. , Carter Scott L. , Getz Gad , Garraway Levi A. , Schadendorf Dirk
Published: April 2023

XLSX file 51K, Supplementary Table S1. Patient characteristics. Clinical characteristics for each patient are listed in this table, along with mean target coverage data for germline, pre-treatment, and resistant tumors (if available)
Supplementary Figure 3 from Systematic Interrogation of 3q26 Identifies TLOC1 and SKIL as Cancer Drivers
Authors: Hagerstrand Daniel , Tong Alexander , Schumacher Steven E. , Ilic Nina , Shen Rhine R. , Cheung Hiu Wing , Vazquez Francisca , Shrestha Yashaswi , Kim So Young , Giacomelli Andrew O. , Rosenbluh Joseph , Schinzel Anna C. , Spardy Nicole A. , Barbie David A. , Mermel Craig H. , Weir Barbara A. , Garraway Levi A. , Tamayo Pablo , Mesirov Jill P. , Beroukhim Rameen , Hahn William C.
Published: April 2023

Supplementary Figure 3 - PDF file 20K, 3q26 copy number in cancer cell lines
Supplementary Figure 2 from Systematic Interrogation of 3q26 Identifies TLOC1 and SKIL as Cancer Drivers
Authors: Hagerstrand Daniel , Tong Alexander , Schumacher Steven E. , Ilic Nina , Shen Rhine R. , Cheung Hiu Wing , Vazquez Francisca , Shrestha Yashaswi , Kim So Young , Giacomelli Andrew O. , Rosenbluh Joseph , Schinzel Anna C. , Spardy Nicole A. , Barbie David A. , Mermel Craig H. , Weir Barbara A. , Garraway Levi A. , Tamayo Pablo , Mesirov Jill P. , Beroukhim Rameen , Hahn William C.
Published: April 2023

Supplementary Figure 2 - PDF file 17K, SKIL induces Matrigel invasion
Supplementary Figure 1 from Systematic Interrogation of 3q26 Identifies TLOC1 and SKIL as Cancer Drivers
Authors: Hagerstrand Daniel , Tong Alexander , Schumacher Steven E. , Ilic Nina , Shen Rhine R. , Cheung Hiu Wing , Vazquez Francisca , Shrestha Yashaswi , Kim So Young , Giacomelli Andrew O. , Rosenbluh Joseph , Schinzel Anna C. , Spardy Nicole A. , Barbie David A. , Mermel Craig H. , Weir Barbara A. , Garraway Levi A. , Tamayo Pablo , Mesirov Jill P. , Beroukhim Rameen , Hahn William C.
Published: April 2023

Supplementary Figure 1 - PDF file 25K, Correlation between TLOC1 suppression and cell proliferation
Supplementary Figure 5 from Dominant Role of Oncogene Dosage and Absence of Tumor Suppressor Activity in Nras-Driven Hematopoietic Transformation
Authors: Xu Jin , Haigis Kevin M. , Firestone Ari J. , McNerney Megan E. , Li Qing , Davis Elizabeth , Chen Shann-Ching , Nakitandwe Joy , Downing James , Jacks Tyler , Le Beau Michelle M. , Shannon Kevin
Published: April 2023

Supplementary Figure 5 - PDF file 30K, Figure showing RAS expression in hematopoietic cancer cell lines and human pediatric AML samples
Supplementary Figure 3 from Dominant Role of Oncogene Dosage and Absence of Tumor Suppressor Activity in Nras-Driven Hematopoietic Transformation
Authors: Xu Jin , Haigis Kevin M. , Firestone Ari J. , McNerney Megan E. , Li Qing , Davis Elizabeth , Chen Shann-Ching , Nakitandwe Joy , Downing James , Jacks Tyler , Le Beau Michelle M. , Shannon Kevin
Published: April 2023

Supplementary Figure 3 - PDF file 125K, Data demonstrating that NrasG12D dosage does not affect the biochemical sensitivity of macrophages to the the MEK inhibitor PD0325901
Supplementary Methods, Tables S1 - S2 from MET-Driven Resistance to Dual EGFR and BRAF Blockade May Be Overcome by Switching from EGFR to MET Inhibition in BRAF-Mutated Colorectal Cancer
Authors: Pietrantonio Filippo , Oddo Daniele , Gloghini Annunziata , Valtorta Emanuele , Berenato Rosa , Barault Ludovic , Caporale Marta , Busico Adele , Morano Federica , Gualeni Ambra Vittoria , Alessi Alessandra , Siravegna Giulia , Perrone Federica , Di Bartolomeo Maria , Bardelli Alberto , de Braud Filippo , Di Nicolantonio Federica
Published: April 2023

Supplementary Table S1. List of genes and exons analyzed by targeted next-generation sequencing. Supplementary Table S2. Summary of molecular data from the ISH and sequencing analyses conducted on both the pre-treatment primary tumor and the liver biopsy obtained after progression on panitumumab plus vemurafenib treatment. List of abbreviations: IHC, immunohistochemistry; ND, not done; SISH, dual-color silver in-situ hybridization; FISH, fluorescence in-situ hybridization.
Supplementary Table S2-S5 from PD-1hi Identifies a Novel Regulatory B-cell Population in Human Hepatoma That Promotes Disease Progression
Authors: Xiao Xiao , Lao Xiang-Ming , Chen Min-Min , Liu Rui-Xian , Wei Yuan , Ouyang Fang-Zhu , Chen Dong-Ping , Zhao Xiao-Yu , Zhao Qiyi , Li Xue-Feng , Liu Chuan-Lu , Zheng Limin , Kuang Dong-Ming
Published: April 2023

Supplementary Table S2 shows characteristics of patients contributing samples. Supplementary Tables S3 - S5 list antibodies used in FACS, IHC, IF, and immunoblotting.
Supplementary Figures S1 - S3 from MET-Driven Resistance to Dual EGFR and BRAF Blockade May Be Overcome by Switching from EGFR to MET Inhibition in BRAF-Mutated Colorectal Cancer
Authors: Pietrantonio Filippo , Oddo Daniele , Gloghini Annunziata , Valtorta Emanuele , Berenato Rosa , Barault Ludovic , Caporale Marta , Busico Adele , Morano Federica , Gualeni Ambra Vittoria , Alessi Alessandra , Siravegna Giulia , Perrone Federica , Di Bartolomeo Maria , Bardelli Alberto , de Braud Filippo , Di Nicolantonio Federica
Published: April 2023

Supplementary Figure S1. Copy number increase of MDM2 gene at progression after vemurafenib+panitumumab. Supplementary Figure S2. Representative examples of colorectal carcinomas bearing BRAF mutations and MET gene copy number gain. Supplementary Figure S3. Untreated WiDr parental cells exhibit similar levels of activated RAS-GTP protein compared to their MET-amplified resistant derivatives treated with encorafenib+cetuximab+alpelisib (E+C+A).
Supplementary Figure Legends from MET-Driven Resistance to Dual EGFR and BRAF Blockade May Be Overcome by Switching from EGFR to MET Inhibition in BRAF-Mutated Colorectal Cancer
Authors: Pietrantonio Filippo , Oddo Daniele , Gloghini Annunziata , Valtorta Emanuele , Berenato Rosa , Barault Ludovic , Caporale Marta , Busico Adele , Morano Federica , Gualeni Ambra Vittoria , Alessi Alessandra , Siravegna Giulia , Perrone Federica , Di Bartolomeo Maria , Bardelli Alberto , de Braud Filippo , Di Nicolantonio Federica
Published: April 2023

Supplementary Figure Legends
Supplementary Figure S1 - S10 from PD-1hi Identifies a Novel Regulatory B-cell Population in Human Hepatoma That Promotes Disease Progression
Authors: Xiao Xiao , Lao Xiang-Ming , Chen Min-Min , Liu Rui-Xian , Wei Yuan , Ouyang Fang-Zhu , Chen Dong-Ping , Zhao Xiao-Yu , Zhao Qiyi , Li Xue-Feng , Liu Chuan-Lu , Zheng Limin , Kuang Dong-Ming
Published: April 2023

Supplementary Figure S1 shows association of PD-1+ and PD-1high B cells in tumor tissue with disease recurrence, plasma HBV DNA and cytokines in HCC patients, and surface markers on HCC B cells. Supplementary Figure S2 shows gating strategies for FACS, and the phenotypic and functional features of the B cell subsets. Supplementary Figure S3 expands data on factors that modulate PD-1 expression on B cells in HCC. Supplementary Figure S4 expands data on roles of Bcl-6 and STAT6 in B cell PD-1 regulation. Supplementary Figure S5 expands data on effects of PD-1 agonist on B cells. Supplementary Figure S6 expands data on effects of PD-1 triggering by PD-L1-expressing cells. Supplementary Figure S7 expands data on triggering PD-1 in B cells suppresses tumor-specific immunity. Supplementary Figure S8 shows graphical abstract for the results. Supplementary Figure S9 shows Isotype staining of FACS and immunohistochemistry (IHC) using clinical samples. Supplementary Figure S10 shows the negative expression of monocyte subset markers in tumor B cells.
Supplementary Table S3 from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer
Authors: Bishop Jennifer L. , Thaper Daksh , Vahid Sepideh , Davies Alastair , Ketola Kirsi , Kuruma Hidetoshi , Jama Randy , Nip Ka Mun , Angeles Arkhjamil , Johnson Fraser , Wyatt Alexander W. , Fazli Ladan , Gleave Martin E. , Lin Dong , Rubin Mark A. , Collins Colin C. , Wang Yuzhuo , Beltran Himisha , Zoubeidi Amina
Published: April 2023

Gene Profiling data of CRPC cells with BRN2 over-expression.
Supplementary Table S2 from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer
Authors: Bishop Jennifer L. , Thaper Daksh , Vahid Sepideh , Davies Alastair , Ketola Kirsi , Kuruma Hidetoshi , Jama Randy , Nip Ka Mun , Angeles Arkhjamil , Johnson Fraser , Wyatt Alexander W. , Fazli Ladan , Gleave Martin E. , Lin Dong , Rubin Mark A. , Collins Colin C. , Wang Yuzhuo , Beltran Himisha , Zoubeidi Amina
Published: April 2023

NEPC signature for GSEA analysis.
Supplementary Figure Legends, Table Legends, Figures S1 - S5 from Stromal Expression of miR-143/145 Promotes Neoangiogenesis in Lung Cancer Development
Authors: Dimitrova Nadya , Gocheva Vasilena , Bhutkar Arjun , Resnick Rebecca , Jong Robyn M. , Miller Kathryn M. , Bendor Jordan , Jacks Tyler
Published: April 2023

Supplementary Figure S1. Targeting strategy and initial characterization of miR-143/145-deficient mice. Supplementary Figure S2. Investigating tumor suppressive functions of miR-143/145 in vitro. Supplementary Figure S3. Effect of miR-143/145 deficiency on the growth of subcutaneous tumors. Supplementary Figure S4. Effect of miR-143/145 deficiency on tumor stroma. Supplementary Figure S5. Dissecting the stromal contribution of miR-143/145.
Supplementary Table S1 from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer
Authors: Bishop Jennifer L. , Thaper Daksh , Vahid Sepideh , Davies Alastair , Ketola Kirsi , Kuruma Hidetoshi , Jama Randy , Nip Ka Mun , Angeles Arkhjamil , Johnson Fraser , Wyatt Alexander W. , Fazli Ladan , Gleave Martin E. , Lin Dong , Rubin Mark A. , Collins Colin C. , Wang Yuzhuo , Beltran Himisha , Zoubeidi Amina
Published: April 2023

RNAseq of ENZ-resistant cells.
Supplementary Methods, Figure Legends from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer
Authors: Bishop Jennifer L. , Thaper Daksh , Vahid Sepideh , Davies Alastair , Ketola Kirsi , Kuruma Hidetoshi , Jama Randy , Nip Ka Mun , Angeles Arkhjamil , Johnson Fraser , Wyatt Alexander W. , Fazli Ladan , Gleave Martin E. , Lin Dong , Rubin Mark A. , Collins Colin C. , Wang Yuzhuo , Beltran Himisha , Zoubeidi Amina
Published: April 2023

Supplementary methods, figure legends, and primer lists.
Supplementary Tables S2 - S8 from Polarization of Tissue-Resident TFH-Like Cells in Human Hepatoma Bridges Innate Monocyte Inflammation and M2b Macrophage Polarization
Authors: Chen Min-Min , Xiao Xiao , Lao Xiang-Ming , Wei Yuan , Liu Rui-Xian , Zeng Qiu-Hui , Wang Jun-Cheng , Ouyang Fang-Zhu , Chen Dong-Ping , Chan Ka-Wo , Shi Dai-Chao , Zheng Limin , Kuang Dong-Ming
Published: April 2023

Supplementary Table S2. Clinical Characteristics of the 293 HCC Patients. Supplementary Table S3. Clinical Characteristics of the 16 Gastric Cancer Patients. Supplementary Table S4. Relationships between Peritumoral Stromal IL-21+ Cells and Clinicopathological Characteristics. Supplementary Table S5. Univariate and Multivariate Analyses of Factors Associated with Survival and Recurrence. Supplementary Table S6. Antibodies for Immunoblotting. Supplementary Table S7. Fluorochrome-Conjugated Antibodies Used in Flow Cytometry. Supplementary Table S8. Primers for Real-Time PCR.
Supplementary Figure S1 - S8 from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer
Authors: Bishop Jennifer L. , Thaper Daksh , Vahid Sepideh , Davies Alastair , Ketola Kirsi , Kuruma Hidetoshi , Jama Randy , Nip Ka Mun , Angeles Arkhjamil , Johnson Fraser , Wyatt Alexander W. , Fazli Ladan , Gleave Martin E. , Lin Dong , Rubin Mark A. , Collins Colin C. , Wang Yuzhuo , Beltran Himisha , Zoubeidi Amina
Published: April 2023

Supplementary Figure S1. Generation of ENZR Xenografts and Cell Lines. Supplementary Figure S2. AR non-driven ENZR cells display a NE differentiation signature. Supplementary Figure S3. BRN2 expression is associated with PCa progression and a NE phenotype in human tumors. Supplementary Figure S4. BRN2 expression is inversely related to AR activity and is required for ENZ-induced NE marker expression in CRPC. Supplementary Figure S5. BRN2 overexpression induces NE marker expression and reciprocally regulates AR. Supplementary Figure S6. BRN2 activity and markers of NE differentiation are suppressed by androgens in CRPC and ENZR cells. Supplementary Figure S7. SOX2 expression is induced by ENZ and suppressed by androgens. Supplementary Figure S8. BRN2 is required for neuroendocrine marker expression and aggressive growth of CRPC cells in vitro.
Supplementary Methods from Polarization of Tissue-Resident TFH-Like Cells in Human Hepatoma Bridges Innate Monocyte Inflammation and M2b Macrophage Polarization
Authors: Chen Min-Min , Xiao Xiao , Lao Xiang-Ming , Wei Yuan , Liu Rui-Xian , Zeng Qiu-Hui , Wang Jun-Cheng , Ouyang Fang-Zhu , Chen Dong-Ping , Chan Ka-Wo , Shi Dai-Chao , Zheng Limin , Kuang Dong-Ming
Published: April 2023

Supplementary Methods. Isolation of Mononuclear Cells from Peripheral Blood and Tissues; Flow Cytometry (FACS); ELISA; Real-Time PCR; Construction of Viral Vectors; Ex Vivo Plasma Cell Induction; Statistical Analysis.
Supplementary Methods, Tables S1 - S3, Figure Legends from Combination Therapy Targeting Ribosome Biogenesis and mRNA Translation Synergistically Extends Survival in MYC-Driven Lymphoma
Authors: Devlin Jennifer R. , Hannan Katherine M. , Hein Nadine , Cullinane Carleen , Kusnadi Eric , Ng Pui Yee , George Amee J. , Shortt Jake , Bywater Megan J. , Poortinga Gretchen , Sanij Elaine , Kang Jian , Drygin Denis , O'Brien Sean , Johnstone Ricky W. , McArthur Grant A. , Hannan Ross D. , Pearson Richard B.
Published: April 2023

This document contains additional materials and methods details, tables of antibody and primer details and supplementary data figure legends.
Supplementary Figures S1 - S7 from Polarization of Tissue-Resident TFH-Like Cells in Human Hepatoma Bridges Innate Monocyte Inflammation and M2b Macrophage Polarization
Authors: Chen Min-Min , Xiao Xiao , Lao Xiang-Ming , Wei Yuan , Liu Rui-Xian , Zeng Qiu-Hui , Wang Jun-Cheng , Ouyang Fang-Zhu , Chen Dong-Ping , Chan Ka-Wo , Shi Dai-Chao , Zheng Limin , Kuang Dong-Ming
Published: April 2023

Supplementary Figure S1. Identification of IL-21 + Tissue-Resident T FH -Like Cells in Human HCC. Supplementary Figure S2. Monocytes/MÏ† Polarize IL-21 + T FH -Like Cells in Cancer Microenvironments. Supplementary Figure S3. Innate Monocyte Activation Is Essential for IL-21 + T FH -Like Cell Differentiation. Supplementary Figure S4. Effects of Inflammatory Cytokines on STAT1 and STAT3 Activation. Supplementary Figure S5. High Density of IL-21 + T FH -like Cells Predicts Poor Survival of HCC Patients and Induces M2b MÏ† Polarization. Supplementary Figure S6. Efficiency of IgG Depletion by Protein G. Supplementary Figure S7. Summary of Results.
Supplementary Figure S4 from Combination Therapy Targeting Ribosome Biogenesis and mRNA Translation Synergistically Extends Survival in MYC-Driven Lymphoma
Authors: Devlin Jennifer R. , Hannan Katherine M. , Hein Nadine , Cullinane Carleen , Kusnadi Eric , Ng Pui Yee , George Amee J. , Shortt Jake , Bywater Megan J. , Poortinga Gretchen , Sanij Elaine , Kang Jian , Drygin Denis , O'Brien Sean , Johnstone Ricky W. , McArthur Grant A. , Hannan Ross D. , Pearson Richard B.
Published: April 2023

This figure shows supplementary data pertinent to Figure 4 including protein and cell death analysis data.
Supplementary Figure S3 from Combination Therapy Targeting Ribosome Biogenesis and mRNA Translation Synergistically Extends Survival in MYC-Driven Lymphoma
Authors: Devlin Jennifer R. , Hannan Katherine M. , Hein Nadine , Cullinane Carleen , Kusnadi Eric , Ng Pui Yee , George Amee J. , Shortt Jake , Bywater Megan J. , Poortinga Gretchen , Sanij Elaine , Kang Jian , Drygin Denis , O'Brien Sean , Johnstone Ricky W. , McArthur Grant A. , Hannan Ross D. , Pearson Richard B.
Published: April 2023

This figure shows supplementary data pertinent to Figure 3 including protein and cell immunofluorescence analysis data.
Supplementary Figure S2 from Combination Therapy Targeting Ribosome Biogenesis and mRNA Translation Synergistically Extends Survival in MYC-Driven Lymphoma
Authors: Devlin Jennifer R. , Hannan Katherine M. , Hein Nadine , Cullinane Carleen , Kusnadi Eric , Ng Pui Yee , George Amee J. , Shortt Jake , Bywater Megan J. , Poortinga Gretchen , Sanij Elaine , Kang Jian , Drygin Denis , O'Brien Sean , Johnstone Ricky W. , McArthur Grant A. , Hannan Ross D. , Pearson Richard B.
Published: April 2023

This figure shows supplementary data pertinent to Figure 2 including cell death and tumour cell analysis data.
Supplementary Methods, Figure Legends from STAT5 Is a Key Regulator in NK Cells and Acts as a Molecular Switch from Tumor Surveillance to Tumor Promotion
Authors: Gotthardt Dagmar , Putz Eva M. , Grundschober Eva , Prchal-Murphy Michaela , Straka Elisabeth , Kudweis Petra , Heller Gerwin , Bago-Horvath Zsuzsanna , Witalisz-Siepracka Agnieszka , Cumaraswamy Abbarna A. , Gunning Patrick T. , Strobl Birgit , Müller Mathias , Moriggl Richard , Stockmann Christian , Sexl Veronika
Published: April 2023

Supplementary Methods, Figure Legends
Supplementary Methods, Figure Legends from Bruton Tyrosine Kinase–Dependent Immune Cell Cross-talk Drives Pancreas Cancer
Authors: Gunderson Andrew J. , Kaneda Megan M. , Tsujikawa Takahiro , Nguyen Abraham V. , Affara Nesrine I. , Ruffell Brian , Gorjestani Sara , Liudahl Shannon M. , Truitt Morgan , Olson Peter , Kim Grace , Hanahan Douglas , Tempero Margaret A. , Sheppard Brett , Irving Bryan , Chang Betty Y. , Varner Judith A. , Coussens Lisa M.
Published: April 2023

Supplementary Methods and Figure Legends
Supplementary Figures S1 - S8 from STAT5 Is a Key Regulator in NK Cells and Acts as a Molecular Switch from Tumor Surveillance to Tumor Promotion
Authors: Gotthardt Dagmar , Putz Eva M. , Grundschober Eva , Prchal-Murphy Michaela , Straka Elisabeth , Kudweis Petra , Heller Gerwin , Bago-Horvath Zsuzsanna , Witalisz-Siepracka Agnieszka , Cumaraswamy Abbarna A. , Gunning Patrick T. , Strobl Birgit , Müller Mathias , Moriggl Richard , Stockmann Christian , Sexl Veronika
Published: April 2023

Supplementary Figure S1. Stat5 expression correlates with the expression of anti-apoptotic genes. Supplementary Figure S2. STAT5-deficient NK cells possess aberrant transcription factors expression. Supplementary Figure S3. Loss of STAT5 alters granzyme, perforin and IFN-gamma production. Supplementary Figure S4. STAT5-deficient NK cells induce tumor promotion. Supplementary Figure S5. Loss of STAT5 increases expression of the pro-angiogenic factor VEGF-A. Supplementary Figure S6. Peripheral splenic NK cells produce VEGF-A which does not impact NK cell numbers, proliferation or maturation but enhances tumor progression in lymphoid tumor models. Supplementary Figure S7. Tumor-infiltrating NK cells and macrophages are localized around blood vessels. Supplementary Figure S8. IL-2 stimulated human NK cells mirror the murine data.
Supplementary Table S7 from Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression
Authors: Wang Guocan , Lu Xin , Dey Prasenjit , Deng Pingna , Wu Chia Chin , Jiang Shan , Fang Zhuangna , Zhao Kun , Konaparthi Ramakrishna , Hua Sujun , Zhang Jianhua , Li-Ning-Tapia Elsa M. , Kapoor Avnish , Wu Chang-Jiun , Patel Neelay Bhaskar , Guo Zhenglin , Ramamoorthy Vandhana , Tieu Trang N. , Heffernan Tim , Zhao Di , Shang Xiaoying , Khadka Sunada , Hou Pingping , Hu Baoli , Jin Eun-Jung , Yao Wantong , Pan Xiaolu , Ding Zhihu , Shi Yanxia , Li Liren , Chang Qing , Troncoso Patricia , Logothetis Christopher J. , McArthur Mark J. , Chin Lynda , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

The 39-gene signatures curated from literatures.
Supplementary Table S6 from Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression
Authors: Wang Guocan , Lu Xin , Dey Prasenjit , Deng Pingna , Wu Chia Chin , Jiang Shan , Fang Zhuangna , Zhao Kun , Konaparthi Ramakrishna , Hua Sujun , Zhang Jianhua , Li-Ning-Tapia Elsa M. , Kapoor Avnish , Wu Chang-Jiun , Patel Neelay Bhaskar , Guo Zhenglin , Ramamoorthy Vandhana , Tieu Trang N. , Heffernan Tim , Zhao Di , Shang Xiaoying , Khadka Sunada , Hou Pingping , Hu Baoli , Jin Eun-Jung , Yao Wantong , Pan Xiaolu , Ding Zhihu , Shi Yanxia , Li Liren , Chang Qing , Troncoso Patricia , Logothetis Christopher J. , McArthur Mark J. , Chin Lynda , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Detailed information for the YAP1 IHC staining in human prostate cancers.
Supplementary Table S3 from Epigenetic Reprogramming Sensitizes CML Stem Cells to Combined EZH2 and Tyrosine Kinase Inhibition
Authors: Scott Mary T. , Korfi Koorosh , Saffrey Peter , Hopcroft Lisa E.M. , Kinstrie Ross , Pellicano Francesca , Guenther Carla , Gallipoli Paolo , Cruz Michelle , Dunn Karen , Jorgensen Heather G. , Cassels Jennifer E. , Hamilton Ashley , Crossan Andrew , Sinclair Amy , Holyoake Tessa L. , Vetrie David
Published: April 2023

Supplementary Table S3. Pathway analysis of mRNA expression changes resulting from treatment of CML CD34+ cells with EZH2i (GSK343).
Supplementary Table S4 from Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression
Authors: Wang Guocan , Lu Xin , Dey Prasenjit , Deng Pingna , Wu Chia Chin , Jiang Shan , Fang Zhuangna , Zhao Kun , Konaparthi Ramakrishna , Hua Sujun , Zhang Jianhua , Li-Ning-Tapia Elsa M. , Kapoor Avnish , Wu Chang-Jiun , Patel Neelay Bhaskar , Guo Zhenglin , Ramamoorthy Vandhana , Tieu Trang N. , Heffernan Tim , Zhao Di , Shang Xiaoying , Khadka Sunada , Hou Pingping , Hu Baoli , Jin Eun-Jung , Yao Wantong , Pan Xiaolu , Ding Zhihu , Shi Yanxia , Li Liren , Chang Qing , Troncoso Patricia , Logothetis Christopher J. , McArthur Mark J. , Chin Lynda , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Table S4. Genes upregulated in GFP+ tumors cells from Ptenpc-/-Smad4pc-/- mice as compared to Tomato+ cells ({greater than or equal to}4 fold).
Supplementary Table S2 from Epigenetic Reprogramming Sensitizes CML Stem Cells to Combined EZH2 and Tyrosine Kinase Inhibition
Authors: Scott Mary T. , Korfi Koorosh , Saffrey Peter , Hopcroft Lisa E.M. , Kinstrie Ross , Pellicano Francesca , Guenther Carla , Gallipoli Paolo , Cruz Michelle , Dunn Karen , Jorgensen Heather G. , Cassels Jennifer E. , Hamilton Ashley , Crossan Andrew , Sinclair Amy , Holyoake Tessa L. , Vetrie David
Published: April 2023

Supplementary Table S2. mRNA expression changes in CML and normal CD34+ cells resulting from treatment of EZHi (GSK343) (EMTAB-2893, MTAB-3552; Affymetrix HuGe 1.0 ST).
Supplementary Table S1 from Epigenetic Reprogramming Sensitizes CML Stem Cells to Combined EZH2 and Tyrosine Kinase Inhibition
Authors: Scott Mary T. , Korfi Koorosh , Saffrey Peter , Hopcroft Lisa E.M. , Kinstrie Ross , Pellicano Francesca , Guenther Carla , Gallipoli Paolo , Cruz Michelle , Dunn Karen , Jorgensen Heather G. , Cassels Jennifer E. , Hamilton Ashley , Crossan Andrew , Sinclair Amy , Holyoake Tessa L. , Vetrie David
Published: April 2023

Supplementary Table S1. Genome-wide analysis of mRNA expression levels in HPCs, HSCs, LSCs and LPCs (E-MTAB-2581, Affymetrix HuGe 1.0 ST).
Supplementary Figures S1 - S17 from Epigenetic Reprogramming Sensitizes CML Stem Cells to Combined EZH2 and Tyrosine Kinase Inhibition
Authors: Scott Mary T. , Korfi Koorosh , Saffrey Peter , Hopcroft Lisa E.M. , Kinstrie Ross , Pellicano Francesca , Guenther Carla , Gallipoli Paolo , Cruz Michelle , Dunn Karen , Jorgensen Heather G. , Cassels Jennifer E. , Hamilton Ashley , Crossan Andrew , Sinclair Amy , Holyoake Tessa L. , Vetrie David
Published: April 2023

Supplementary Figure S1. mRNA levels of PRC2 components in CML and normal samples used in this study. Supplementary Figure S2. Effect of TKI treatment on mRNA levels of PRC2 components on CML cells in vitro. Supplementary Figure S3. Analysis of promoters reprogrammed for H3K27me3 levels at promoters. Supplementary Figure S4. Relationship between changes in levels of H3K27me3 and changes in mRNA expression at H3K27me3 targets. Supplementary Figure S5. EZH2i treatment of CML and normal CD34+ cells. Supplementary Figure S6. EZH2i treatment of CML CD34+CD38- cells (LSCs). Supplementary Figure S7. Validation of EZH2 shRNAs in a CML cell line. Supplementary Figure S8. The effect of treatment of CML or normal CD34+ cells with EZH2i (GSK343; 1000 nM) on the global mRNA levels of H3K27me3 and H3K27me1 targets. Supplementary Figure S9. Both imatinib and EZH2i selectively target upregulation of H3K27me3 target genes. Supplementary Figure S10. Nilotinib, dasatinib and EZH2i selectively target upregulation of H3K27me3 target genes. Supplementary Figure S11. mRNA expression levels for H3K27me3 target genes in HSC and LSCs and their behaviour after TKI treatment. Supplementary Figure S12. mRNA expression levels for H3K27me3 target genes in HPC and LPCs (â‰^ CML CD34+) and their behaviour after EZH2i treatment. Supplementary Figure S13. Primary CML cells engrafted in NSG mice treated in vivo with EZH2i and TKI, alone and in combination. Supplementary Figure S14. Validation of mRNA expression changes determined by Affymetrix GeneChip analysis (E-MTAB-2581, Affymetrix HuGe 1.0 ST). Supplementary Figure S15. PRC2 mis-regulation in the three CML patient samples used for Affymetrix GeneChIP and ChIP-sequencing in this study. Supplementary Figure S16. Determining thresholds for identifying H3K27me3 target genes. Supplementary Figure S17. Validation of seqMiner(3) promoter classifications.
Supplementary Figure S8 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S8. Anti-CD96 and anti-PD1 therapy does not induce significant toxicities in B16F10 tumor bearing mice.
Supplementary Figure Legends from IL35-Producing B Cells Promote the Development of Pancreatic Neoplasia
Authors: Pylayeva-Gupta Yuliya , Das Shipra , Handler Jesse S. , Hajdu Cristina H. , Coffre Maryaline , Koralov Sergei B. , Bar-Sagi Dafna
Published: April 2023

Supplementary Figure Legends
Supplementary Figure S6 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S6. Anti-CD96 combines with anti-CTLA4, anti-PD1 or doxorubicin to increase survival and reduce metastases in mice bearing 4T1.2 spontaneous metastases.
Supplementary Figure S5 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S5. Anti-CD96 combines with anti-CTLA4 or anti-PD1 to enhance survival following challenge with experimental lung metastases.
Supplementary Figure 6 from Targeting Translation Initiation Bypasses Signaling Crosstalk Mechanisms That Maintain High MYC Levels in Colorectal Cancer
Authors: Wiegering Armin , Uthe Friedrich W. , Jamieson Thomas , Ruoss Yvonne , Hüttenrauch Melanie , Küspert Maritta , Pfann Christina , Nixon Colin , Herold Steffi , Walz Susanne , Taranets Lyudmyla , Germer Christoph-Thomas , Rosenwald Andreas , Sansom Owen J. , Eilers Martin
Published: April 2023

Supplementary Figure 6. BEZ235 does not alter proliferation or MYC levels in wild type or APC deficient intestinal enterocytes.
Supplementary Figure S3 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S3. Cd96-/- mice are resistant to EO771 spontaneous lung metastases and treatment with anti-CD96 mAb does not increase anti-metastatic effect.
Supplementary Figure 5 from Targeting Translation Initiation Bypasses Signaling Crosstalk Mechanisms That Maintain High MYC Levels in Colorectal Cancer
Authors: Wiegering Armin , Uthe Friedrich W. , Jamieson Thomas , Ruoss Yvonne , Hüttenrauch Melanie , Küspert Maritta , Pfann Christina , Nixon Colin , Herold Steffi , Walz Susanne , Taranets Lyudmyla , Germer Christoph-Thomas , Rosenwald Andreas , Sansom Owen J. , Eilers Martin
Published: April 2023

Supplementary Figure 5. Additional characterization of translation in colon carcinoma.
Supplementary Figure S2 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S2. Anti-metastatic activity of anti-CD96 is dependent on NK cells and IL-12p35, but independent of T cells.
Supplementary Figure S1 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S1. CD96 and CD226 have opposite roles in the control of experimental lung tumor metastases.
Supplementary Methods, Figure Legends, Tables S1 - S3 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

Supplementary Table S1. Patient characteristics of the single-agent anti-PD-1 cohort. Supplementary Table S2. List of primers used for gene expression analysis by real-time PCR. Supplementary Table S3. List of autophagy-related genes for overexpressing experiment.
Supplementary Figure S7 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

Improved antitumor activity can be achieved by combining the PI3Kbeta inhibitor and immune checkpoint blockers.
Supplementary Table S5 from Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles
Authors: Kim Eejung , Ilic Nina , Shrestha Yashaswi , Zou Lihua , Kamburov Atanas , Zhu Cong , Yang Xiaoping , Lubonja Rakela , Tran Nancy , Nguyen Cindy , Lawrence Michael S. , Piccioni Federica , Bagul Mukta , Doench John G. , Chouinard Candace R. , Wu Xiaoyun , Hogstrom Larson , Natoli Ted , Tamayo Pablo , Horn Heiko , Corsello Steven M. , Lage Kasper , Root David E. , Subramanian Aravind , Golub Todd R. , Getz Gad , Boehm Jesse S. , Hahn William C.
Published: April 2023

L1000 gene expression data of 1036 ORFs.
Supplementary Figure S6 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

The effect of PI3Kbeta inhibitor on melanoma with PTEN loss.
Supplementary Figure S5 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

Autophagy activity regulated by the PI3K pathway plays a critical role in T cell-induced tumor apoptosis.
Supplementary Table S4 from Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles
Authors: Kim Eejung , Ilic Nina , Shrestha Yashaswi , Zou Lihua , Kamburov Atanas , Zhu Cong , Yang Xiaoping , Lubonja Rakela , Tran Nancy , Nguyen Cindy , Lawrence Michael S. , Piccioni Federica , Bagul Mukta , Doench John G. , Chouinard Candace R. , Wu Xiaoyun , Hogstrom Larson , Natoli Ted , Tamayo Pablo , Horn Heiko , Corsello Steven M. , Lage Kasper , Root David E. , Subramanian Aravind , Golub Todd R. , Getz Gad , Boehm Jesse S. , Hahn William C.
Published: April 2023

Composition of cells and tumors from the in vivo screen.
Supplementary Figure S4 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

List of genes which are differentially expressed in melanomas with PTEN loss.
Supplementary Table S3 from Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles
Authors: Kim Eejung , Ilic Nina , Shrestha Yashaswi , Zou Lihua , Kamburov Atanas , Zhu Cong , Yang Xiaoping , Lubonja Rakela , Tran Nancy , Nguyen Cindy , Lawrence Michael S. , Piccioni Federica , Bagul Mukta , Doench John G. , Chouinard Candace R. , Wu Xiaoyun , Hogstrom Larson , Natoli Ted , Tamayo Pablo , Horn Heiko , Corsello Steven M. , Lage Kasper , Root David E. , Subramanian Aravind , Golub Todd R. , Getz Gad , Boehm Jesse S. , Hahn William C.
Published: April 2023

Pool composition of in vivo screen.
Supplementary Figure S1 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

PTEN loss in melanoma promotes resistance to T cell-mediated anti-tumor activity in the context of concurrent a selective inhibitor for mutant BRAF.
Supplementary Figures S1 - S3, Table S1 from Efficacy and Biological Correlates of Response in a Phase II Study of Venetoclax Monotherapy in Patients with Acute Myelogenous Leukemia
Authors: Konopleva Marina , Pollyea Daniel A. , Potluri Jalaja , Chyla Brenda , Hogdal Leah , Busman Todd , McKeegan Evelyn , Salem Ahmed Hamed , Zhu Ming , Ricker Justin L. , Blum William , DiNardo Courtney D. , Kadia Tapan , Dunbar Martin , Kirby Rachel , Falotico Nancy , Leverson Joel , Humerickhouse Rod , Mabry Mack , Stone Richard , Kantarjian Hagop , Letai Anthony
Published: April 2023

Supplementary Table S1. Overall activity and predictors of treatment failure (PD or less than partial response by IWG criteria). Supplementary Figure S1. BCL-2 family protein index at screening. Supplementary Figure S2. Mean (+ SD) venetoclax plasma concentration-time profile at week 6 day 1 (800 mg). Supplementary Figure S3. Study design.
Supplementary Figure Legends from ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors
Authors: Shen Jianfeng , Peng Yang , Wei Leizhen , Zhang Wei , Yang Lin , Lan Li , Kapoor Prabodh , Ju Zhenlin , Mo Qianxing , Shih Ie-Ming , Uray Ivan P. , Wu Xiangwei , Brown Powel H. , Shen Xuetong , Mills Gordon B. , Peng Guang
Published: April 2023

Supplementary Figure Legends from ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors
Supplementary Figure 7 from Macrophage PI3Kγ Drives Pancreatic Ductal Adenocarcinoma Progression
Authors: Kaneda Megan M. , Cappello Paola , Nguyen Abraham V. , Ralainirina Natacha , Hardamon Chanae R. , Foubert Philippe , Schmid Michael C. , Sun Ping , Mose Evangeline , Bouvet Michael , Lowy Andrew M. , Valasek Mark A. , Sasik Roman , Novelli Francesco , Hirsch Emilio , Varner Judith A.
Published: April 2023

Effect of macrophage secrete factors on PDAC cell migration in vitro.
Supplementary Figure 6 from Macrophage PI3Kγ Drives Pancreatic Ductal Adenocarcinoma Progression
Authors: Kaneda Megan M. , Cappello Paola , Nguyen Abraham V. , Ralainirina Natacha , Hardamon Chanae R. , Foubert Philippe , Schmid Michael C. , Sun Ping , Mose Evangeline , Bouvet Michael , Lowy Andrew M. , Valasek Mark A. , Sasik Roman , Novelli Francesco , Hirsch Emilio , Varner Judith A.
Published: April 2023

Immune checkpoint characterization of PDAC tumors.
Supplementary Figure 5 from Macrophage PI3Kγ Drives Pancreatic Ductal Adenocarcinoma Progression
Authors: Kaneda Megan M. , Cappello Paola , Nguyen Abraham V. , Ralainirina Natacha , Hardamon Chanae R. , Foubert Philippe , Schmid Michael C. , Sun Ping , Mose Evangeline , Bouvet Michael , Lowy Andrew M. , Valasek Mark A. , Sasik Roman , Novelli Francesco , Hirsch Emilio , Varner Judith A.
Published: April 2023

Immune expression profile of macrophages isolated from PDAC tumors.
Supplementary Figure 5 from In Vivo Role of INPP4B in Tumor and Metastasis Suppression through Regulation of PI3K–AKT Signaling at Endosomes
Authors: Li Chew Chen , Lunardi Andrea , Gulluni Federico , Ruan Daniel T. , Chen Ming , Salmena Leonardo , Nishino Michiya , Papa Antonella , Ng Christopher , Fung Jacqueline , Clohessy John G. , Sasaki Junko , Sasaki Takehiko , Bronson Roderick T. , Hirsch Emilio , Pandolfi Pier Paolo
Published: April 2023

Supplementary Figure 5. Loss of INPP4B results in increased AKT2 activation.