bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 1 and Table 2 from A Small-Molecule c-Rel Inhibitor Reduces Alloactivation of T Cells without Compromising Antitumor Activity
Authors: Shono Yusuke , Tuckett Andrea Z. , Ouk Samedy , Liou Hsiou-Chi , Altan-Bonnet Grégoire , Tsai Jennifer J. , Oyler Jennifer E. , Smith Odette M. , West Mallory L. , Singer Natalie V. , Doubrovina Ekaterina , Pankov Dmitry , Undhad Chandresh V. , Murphy George F. , Lezcano Cecilia , Liu Chen , O'Reilly Richard J. , van den Brink Marcel R.M. , Zakrzewski Johannes L.
Published: April 2023

PDF file 92K, Table 1. Characteristics of c-Rel inhibitor compounds; Table 2. Roles of c-Rel in T-cell responses and transplantation immunology
Supplementary Table 2 from Rare Mutations in RINT1 Predispose Carriers to Breast and Lynch Syndrome–Spectrum Cancers
Authors: Park Daniel J. , Tao Kayoko , Le Calvez-Kelm Florence , Nguyen-Dumont Tu , Robinot Nivonirina , Hammet Fleur , Odefrey Fabrice , Tsimiklis Helen , Teo Zhi L. , Thingholm Louise B. , Young Erin L. , Voegele Catherine , Lonie Andrew , Pope Bernard J. , Roane Terrell C. , Bell Russell , Hu Hao , Huff Chad D. , Ellis Jonathan , Li Jun , Makunin Igor V. , John Esther M. , Andrulis Irene L. , Terry Mary B. , Daly Mary , Buys Saundra S. , Snyder Carrie , Lynch Henry T. , Devilee Peter , Giles Graham G. , Hopper John L. , Feng Bing-Jian , Lesueur Fabienne , Tavtigian Sean V. , Southey Melissa C. , Goldgar David E.
Published: April 2023

PDF file 73K, Primers for RINT1 HRM
Supplementary Figure 6 from A Small-Molecule c-Rel Inhibitor Reduces Alloactivation of T Cells without Compromising Antitumor Activity
Authors: Shono Yusuke , Tuckett Andrea Z. , Ouk Samedy , Liou Hsiou-Chi , Altan-Bonnet Grégoire , Tsai Jennifer J. , Oyler Jennifer E. , Smith Odette M. , West Mallory L. , Singer Natalie V. , Doubrovina Ekaterina , Pankov Dmitry , Undhad Chandresh V. , Murphy George F. , Lezcano Cecilia , Liu Chen , O'Reilly Richard J. , van den Brink Marcel R.M. , Zakrzewski Johannes L.
Published: April 2023

PDF file 128KB, c-Rel-deficient T-cells are polarized towards Th2 responses during GVHD
Supplementary Figures S1 - S9, Table S1 from The Immune Microenvironment Confers Resistance to MAPK Pathway Inhibitors through Macrophage-Derived TNFα
Authors: Smith Michael P. , Sanchez-Laorden Berta , O'Brien Kate , Brunton Holly , Ferguson Jennifer , Young Helen , Dhomen Nathalie , Flaherty Keith T. , Frederick Dennie T. , Cooper Zachary A. , Wargo Jennifer A. , Marais Richard , Wellbrock Claudia
Published: April 2023

Supplementary Figures S1 - S9, Table S1. Supplementary Figure S1 (related to Figure 1) shows TNFR expression in melanoma cells. Supplementary Figure S2 (related to Figure 2) shows an NF-κBα binding site in the MITF promoter and MITF target gene expression. Supplementary Figure S3 (related to Figure 3) shows macrophage differentiation and their effect on melanoma cells, keratinocytes and fibroblasts. Supplementary Figure S4 (related to Figure 3) shows M1 and M2 macrophage marker expression in melanoma. Supplementary Figure S5 (related to Figure 4) shows that MEK inhibition does not affect the protective function of macrophages. Supplementary Figure S6 (related to Figure 4) BRAFi and MEKi induced changes in macrophage marker expression in vivo. Supplementary Figure S7 (related to Figure 6) shows that IKK inhibition and MEK inhibition synergise in vitro. Supplementary FigureS8 (related to Figure 6) shows that TNFα protects from BRAF inhibition and IKK and BRAF inhibition synergise in vitro. Supplementary Figure S9 (related to Figure 7) shows the expression of macrophage markers in IKKi treated allografts. Supplementary Table S1 lists patient details.
Supplementary Figure 1 from A Small-Molecule c-Rel Inhibitor Reduces Alloactivation of T Cells without Compromising Antitumor Activity
Authors: Shono Yusuke , Tuckett Andrea Z. , Ouk Samedy , Liou Hsiou-Chi , Altan-Bonnet Grégoire , Tsai Jennifer J. , Oyler Jennifer E. , Smith Odette M. , West Mallory L. , Singer Natalie V. , Doubrovina Ekaterina , Pankov Dmitry , Undhad Chandresh V. , Murphy George F. , Lezcano Cecilia , Liu Chen , O'Reilly Richard J. , van den Brink Marcel R.M. , Zakrzewski Johannes L.
Published: April 2023

PDF file 121K, IL-2 secretion is enhanced in irradiated recipients transplanted with allogeneic T-cells
Supplementary Legends from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
Authors: Shern Jack F. , Chen Li , Chmielecki Juliann , Wei Jun S. , Patidar Rajesh , Rosenberg Mara , Ambrogio Lauren , Auclair Daniel , Wang Jianjun , Song Young K. , Tolman Catherine , Hurd Laura , Liao Hongling , Zhang Shile , Bogen Dominik , Brohl Andrew S. , Sindiri Sivasish , Catchpoole Daniel , Badgett Thomas , Getz Gad , Mora Jaume , Anderson James R. , Skapek Stephen X. , Barr Frederic G. , Meyerson Matthew , Hawkins Douglas S. , Khan Javed
Published: April 2023

PDF file 92K, Supplementary Legends
Supplementary Figure S9 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
Authors: Shern Jack F. , Chen Li , Chmielecki Juliann , Wei Jun S. , Patidar Rajesh , Rosenberg Mara , Ambrogio Lauren , Auclair Daniel , Wang Jianjun , Song Young K. , Tolman Catherine , Hurd Laura , Liao Hongling , Zhang Shile , Bogen Dominik , Brohl Andrew S. , Sindiri Sivasish , Catchpoole Daniel , Badgett Thomas , Getz Gad , Mora Jaume , Anderson James R. , Skapek Stephen X. , Barr Frederic G. , Meyerson Matthew , Hawkins Douglas S. , Khan Javed
Published: April 2023

PDF file 258K, Genome wide copy number profile.
Supplementary Methods from Mechanism-Based Epigenetic Chemosensitization Therapy of Diffuse Large B-Cell Lymphoma
Authors: Clozel Thomas , Yang ShaoNing , Elstrom Rebecca L. , Tam Wayne , Martin Peter , Kormaksson Matthias , Banerjee Samprit , Vasanthakumar Aparna , Culjkovic Biljana , Scott David W. , Wyman Sarah , Leser Micheal , Shaknovich Rita , Chadburn Amy , Tabbo Fabrizio , Godley Lucy A. , Gascoyne Randy D. , Borden Katherine L. , Inghirami Giorgio , Leonard John P. , Melnick Ari , Cerchietti Leandro
Published: April 2023

Supplementary Methods - PDF file 100K, Reagents, gene expression profiling, RT-PCR, mice studies, clinical trial, patient samples, ex vivo treatments, immunohistochemistry and statistical analysis
Supplementary Figure S7 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
Authors: Shern Jack F. , Chen Li , Chmielecki Juliann , Wei Jun S. , Patidar Rajesh , Rosenberg Mara , Ambrogio Lauren , Auclair Daniel , Wang Jianjun , Song Young K. , Tolman Catherine , Hurd Laura , Liao Hongling , Zhang Shile , Bogen Dominik , Brohl Andrew S. , Sindiri Sivasish , Catchpoole Daniel , Badgett Thomas , Getz Gad , Mora Jaume , Anderson James R. , Skapek Stephen X. , Barr Frederic G. , Meyerson Matthew , Hawkins Douglas S. , Khan Javed
Published: April 2023

PDF file 186K, Loss of heterozygosity on Chromosome 11p15.5
Figures S7 - S9 from Mechanism-Based Epigenetic Chemosensitization Therapy of Diffuse Large B-Cell Lymphoma
Authors: Clozel Thomas , Yang ShaoNing , Elstrom Rebecca L. , Tam Wayne , Martin Peter , Kormaksson Matthias , Banerjee Samprit , Vasanthakumar Aparna , Culjkovic Biljana , Scott David W. , Wyman Sarah , Leser Micheal , Shaknovich Rita , Chadburn Amy , Tabbo Fabrizio , Godley Lucy A. , Gascoyne Randy D. , Borden Katherine L. , Inghirami Giorgio , Leonard John P. , Melnick Ari , Cerchietti Leandro
Published: April 2023

Figures S7, S8 and S9 - PDF file 206K, SMAD1 expression in patients and functional experiments
Supplementary Table S1 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 S1 shows characteristics of patients contributing samples.
Supplementary Methods 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

Flow Cytometry, ELISA, Construction of Viral Vectors, and PD-L1/PD-L2 Stable Cell Lines.
Supplementary Figures S1 - S6 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 Figure S1. B cells in human PDAC. Supplementary Figure S2. B cells and FcRgamma-positive cells regulate murine PDAC. Supplementary Figure S3. Leukocytes and BTK in human and murine PDAC. Supplementary Figure S4. Macrophage PI3Kgamma activates BTK to promote PDAC progression. Supplementary Figure S5. BTK and PI3Kgamma-inhibition decrease PDAC growth. Supplementary Figure S6. BTK inhibition improves gemcitabine response in late-stage PDAC.
Supplementary Table S3 from Immunogenomics of Hypermutated Glioblastoma: A Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy
Authors: Johanns Tanner M. , Miller Christopher A. , Dorward Ian G. , Tsien Christina , Chang Edward , Perry Arie , Uppaluri Ravindra , Ferguson Cole , Schmidt Robert E. , Dahiya Sonika , Ansstas George , Mardis Elaine R. , Dunn Gavin P.
Published: April 2023

Gene Fusions identified with INTEGRATE.
Supplementary Figures from Superenhancer Analysis Defines Novel Epigenomic Subtypes of Non-APL AML, Including an RARα Dependency Targetable by SY-1425, a Potent and Selective RARα Agonist
Authors: McKeown Michael R. , Corces M. Ryan , Eaton Matthew L. , Fiore Chris , Lee Emily , Lopez Jeremy T. , Chen Mei Wei , Smith Darren , Chan Steven M. , Koenig Julie L. , Austgen Kathryn , Guenther Matthew G. , Orlando David A. , Lovén Jakob , Fritz Christian C. , Majeti Ravindra
Published: April 2023

Supplementary Figure S1. Identification and refinement of cancer-specific super-enhancers in human AML. Supplementary Figure S2. Mapping of super-enhancers to genes. Supplementary Figure S3. AML SE profiles show pronounced variation in enhancers related to myeloid differentiation and enable de novo stratification into six distinct epigenomic subgroups. Supplementary Figure S4. Recapitulation of SE-defined clusters in AML data from the TCGA. Supplementary Figure S5 An SE is present at the RARA locus in a subset of AML samples. Supplementary Figure S6 SY-1425 is a selective and potent RARα agonist. Supplementary Figure S7 Comparison of SY-1425 response to RARA expression and enhancer score and the effect of an RARα antagonist. Supplementary Figure S8 SY-1425 in vivo pharmacokinetics. Supplementary Figure S9 SY-1425 survival and tissue effects on AML PDX models. Supplementary Figure S10 SY-1425 shows greater potency than ATRA in vitro and in vivo. Supplementary Figure S11 Induction of markers of myeloid differentiation in RARA-high AML cell lines upon SY-1425 treatment. Supplementary Figure S12 Comparison of SY-1425 expression and molecular response to APL. Supplementary Figure S13 SY-1425 expression and molecular response.
Supplementary Figure S7 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance
Authors: Miller Miles A. , Oudin Madeleine J. , Sullivan Ryan J. , Wang Stephanie J. , Meyer Aaron S. , Im Hyungsoon , Frederick Dennie T. , Tadros Jenny , Griffith Linda G. , Lee Hakho , Weissleder Ralph , Flaherty Keith T. , Gertler Frank B. , Lauffenburger Douglas A.
Published: April 2023

Supplementary Figure S7. Live-cell immunostaining shows relatively minor changes in ADAM10 and ADAM17 surface levels following MEKi. Measurements were taken 1, 2, and 3h following inhibitor treatment and averaged (*p=0.02, n=3).
Supplementary Figure S6 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance
Authors: Miller Miles A. , Oudin Madeleine J. , Sullivan Ryan J. , Wang Stephanie J. , Meyer Aaron S. , Im Hyungsoon , Frederick Dennie T. , Tadros Jenny , Griffith Linda G. , Lee Hakho , Weissleder Ralph , Flaherty Keith T. , Gertler Frank B. , Lauffenburger Douglas A.
Published: April 2023

Supplementary Figure S6. Validation of ADAM10 and ADAM17 siRNA knockdown in MDA-MB157 and MDA-MB231, assessed by live-cell immunostaining and confirmed at right by western blot in MDA-MB231 (*p<0.05).
Supplementary Figure S2 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance
Authors: Miller Miles A. , Oudin Madeleine J. , Sullivan Ryan J. , Wang Stephanie J. , Meyer Aaron S. , Im Hyungsoon , Frederick Dennie T. , Tadros Jenny , Griffith Linda G. , Lee Hakho , Weissleder Ralph , Flaherty Keith T. , Gertler Frank B. , Lauffenburger Douglas A.
Published: April 2023

Supplementary Figure S2. Correlation between plasma RTK changes with MAPKi, PFS, and initial tumor shrinkage (using RECIST) in melanoma patients.
Supplementary Figure 4 from Chronic Myelogenous Leukemia– Initiating Cells Require Polycomb Group Protein EZH2
Authors: Xie Huafeng , Peng Cong , Huang Jialiang , Li Bin E. , Kim Woojin , Smith Elenoe C. , Fujiwara Yuko , Qi Jun , Cheloni Giulia , Das Partha P. , Nguyen Minh , Li Shaoguang , Bradner James E. , Orkin Stuart H.
Published: April 2023

Gene expression analysis.
Supplementary Figure 1 from Chronic Myelogenous Leukemia– Initiating Cells Require Polycomb Group Protein EZH2
Authors: Xie Huafeng , Peng Cong , Huang Jialiang , Li Bin E. , Kim Woojin , Smith Elenoe C. , Fujiwara Yuko , Qi Jun , Cheloni Giulia , Das Partha P. , Nguyen Minh , Li Shaoguang , Bradner James E. , Orkin Stuart H.
Published: April 2023

Figure showing expression of EZH2 in CML and sensitivity of CML cells to EZH2 inhibition.
Supplementary Figure Legends, Tables 1 - 3 from High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial
Authors: Pearson Alex , Smyth Elizabeth , Babina Irina S. , Herrera-Abreu Maria Teresa , Tarazona Noelia , Peckitt Clare , Kilgour Elaine , Smith Neil R. , Geh Catherine , Rooney Claire , Cutts Ros , Campbell James , Ning Jian , Fenwick Kerry , Swain Amanda , Brown Gina , Chua Sue , Thomas Anne , Johnston Stephen R.D. , Ajaz Mazhar , Sumpter Katherine , Gillbanks Angela , Watkins David , Chau Ian , Popat Sanjay , Cunningham David , Turner Nicholas C.
Published: April 2023

Supplementary Table 1. Expression of estrogen receptor regulated genes in patient 207 was determined using Nanostring. Data was normalized as described in the Online Methods and is presented as the Log2 ratio. Supplementary Table 2. A list of cell lines including FGFR status. Supplementary Table 3. Copy Number Variation and Gene Expression Assays.
Supplementary Figure 3 from High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial
Authors: Pearson Alex , Smyth Elizabeth , Babina Irina S. , Herrera-Abreu Maria Teresa , Tarazona Noelia , Peckitt Clare , Kilgour Elaine , Smith Neil R. , Geh Catherine , Rooney Claire , Cutts Ros , Campbell James , Ning Jian , Fenwick Kerry , Swain Amanda , Brown Gina , Chua Sue , Thomas Anne , Johnston Stephen R.D. , Ajaz Mazhar , Sumpter Katherine , Gillbanks Angela , Watkins David , Chau Ian , Popat Sanjay , Cunningham David , Turner Nicholas C.
Published: April 2023

High-level FGFR2 amplified cell lines are highly sensitive to FGFR inhibition.
Supplementary Figure 2 from High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial
Authors: Pearson Alex , Smyth Elizabeth , Babina Irina S. , Herrera-Abreu Maria Teresa , Tarazona Noelia , Peckitt Clare , Kilgour Elaine , Smith Neil R. , Geh Catherine , Rooney Claire , Cutts Ros , Campbell James , Ning Jian , Fenwick Kerry , Swain Amanda , Brown Gina , Chua Sue , Thomas Anne , Johnston Stephen R.D. , Ajaz Mazhar , Sumpter Katherine , Gillbanks Angela , Watkins David , Chau Ian , Popat Sanjay , Cunningham David , Turner Nicholas C.
Published: April 2023

FGFR2 expression in cancers with high-level amplification of FGFR2.
Supplementary Figure Legends from Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma
Authors: Okada Tomoyo , Lee Ann Y. , Qin Li-Xuan , Agaram Narasimhan , Mimae Takahiro , Shen Yawei , O'Connor Rachael , López-Lago Miguel A. , Craig Amanda , Miller Martin L. , Agius Phaedra , Molinelli Evan , Socci Nicholas D. , Crago Aimee M. , Shima Fumi , Sander Chris , Singer Samuel
Published: April 2023

Supplementary Figure Legends
Supplementary Figure 1 from High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial
Authors: Pearson Alex , Smyth Elizabeth , Babina Irina S. , Herrera-Abreu Maria Teresa , Tarazona Noelia , Peckitt Clare , Kilgour Elaine , Smith Neil R. , Geh Catherine , Rooney Claire , Cutts Ros , Campbell James , Ning Jian , Fenwick Kerry , Swain Amanda , Brown Gina , Chua Sue , Thomas Anne , Johnston Stephen R.D. , Ajaz Mazhar , Sumpter Katherine , Gillbanks Angela , Watkins David , Chau Ian , Popat Sanjay , Cunningham David , Turner Nicholas C.
Published: April 2023

Clinical activity of FGFR inhibitor AZD4547 in FGFR amplified breast and gastric cancer.
Figures S1-S8 from BLIMP1 Induces Transient Metastatic Heterogeneity in Pancreatic Cancer
Authors: Chiou Shin-Heng , Risca Viviana I. , Wang Gordon X. , Yang Dian , Grüner Barbara M. , Kathiria Arwa S. , Ma Rosanna K. , Vaka Dedeepya , Chu Pauline , Kozak Margaret , Castellini Laura , Graves Edward E. , Kim Grace E. , Mourrain Philippe , Koong Albert C. , Giaccia Amato J. , Winslow Monte M.
Published: April 2023

Supplementary Figure S1. Isolation of the Hmga2-GFPpos PDAC sub-population from the KPCcolors mice and GFPpos PDAC cells are a highly metastatic state;Supplementary Figure S2. Highly metastatic PDAC cells have a gene signature that is not enriched for CSC markers and distal PDAC metastases reveal minor gene expression changes related to glucose metabolism;Supplementary Figure S3. Identification of top candidate pro-metastatic genes and interrogation of Blimp1 function in PDAC metastasis;Supplementary Figure S4. Hmga2positive PDAC areas overlap with hypoxic areas and Hmga2 protein is slightly induced by hypoxia but not critical to the expression of hypoxia-induced target genes;Supplementary Figure S5. Hypoxia-induced Blimp1 expression is linked to functional HRE motifs 240 kb upstream of its transcription start site;Supplementary Figure S6. Blimp1 may contribute to migratory and clonal growth ability and is critical for a subset of hypoxia-induced gene expression changes that are independent of changes in chromatin accessibility;Supplementary Figure S7. Blimp1 regulates a subset of hypoxia-induced genes; Supplementary Figure S8. Blimp1 is required for hypoxia-induced cell cycle arrest and the expression of metastasis modulators.
Supplementary Figure 1 from Response to MET Inhibitors in Patients with Stage IV Lung Adenocarcinomas Harboring MET Mutations Causing Exon 14 Skipping
Authors: Paik Paul K. , Drilon Alexander , Fan Pang-Dian , Yu Helena , Rekhtman Natasha , Ginsberg Michelle S. , Borsu Laetitia , Schultz Nikolaus , Berger Michael F. , Rudin Charles M. , Ladanyi Marc
Published: April 2023

Comparative mRNA expression of MET exons 2-3, 14, and 20-21 from 5 patients with MET exon 14 splicing variants. All tumor samples tested had significantly and markedly lower expression of exon 14 in keeping with the transcriptional effects of the splice site mutations.
Suppl Table 1 from The BTK Inhibitor ARQ 531 Targets Ibrutinib-Resistant CLL and Richter Transformation
Authors: Reiff Sean D. , Mantel Rose , Smith Lisa L. , Greene J.T. , Muhowski Elizabeth M. , Fabian Catherine A. , Goettl Virginia M. , Tran Minh , Harrington Bonnie K. , Rogers Kerry A. , Awan Farrukh T. , Maddocks Kami , Andritsos Leslie , Lehman Amy M. , Sampath Deepa , Lapalombella Rosa , Eathiraj Sudharshan , Abbadessa Giovanni , Schwartz Brian , Johnson Amy J. , Byrd John C. , Woyach Jennifer A.
Published: April 2023

Suppl Table 1 with legend
Supplementary Table S3 from Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Authors: Eckhardt Manon , Zhang Wei , Gross Andrew M. , Von Dollen John , Johnson Jeffrey R. , Franks-Skiba Kathleen E. , Swaney Danielle L. , Johnson Tasha L. , Jang Gwendolyn M. , Shah Priya S. , Brand Toni M. , Archambault Jacques , Kreisberg Jason F. , Grandis Jennifer R. , Ideker Trey , Krogan Nevan J.
Published: April 2023

Gene Ontology Terms. Related to Figure 1.
Suppl Figure 2 from The BTK Inhibitor ARQ 531 Targets Ibrutinib-Resistant CLL and Richter Transformation
Authors: Reiff Sean D. , Mantel Rose , Smith Lisa L. , Greene J.T. , Muhowski Elizabeth M. , Fabian Catherine A. , Goettl Virginia M. , Tran Minh , Harrington Bonnie K. , Rogers Kerry A. , Awan Farrukh T. , Maddocks Kami , Andritsos Leslie , Lehman Amy M. , Sampath Deepa , Lapalombella Rosa , Eathiraj Sudharshan , Abbadessa Giovanni , Schwartz Brian , Johnson Amy J. , Byrd John C. , Woyach Jennifer A.
Published: April 2023

Suppl Figure 2 with legend
Supplementary Table S1 from Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Authors: Eckhardt Manon , Zhang Wei , Gross Andrew M. , Von Dollen John , Johnson Jeffrey R. , Franks-Skiba Kathleen E. , Swaney Danielle L. , Johnson Tasha L. , Jang Gwendolyn M. , Shah Priya S. , Brand Toni M. , Archambault Jacques , Kreisberg Jason F. , Grandis Jennifer R. , Ideker Trey , Krogan Nevan J.
Published: April 2023

Previously Reported HPV-Human PPIs. Related to Figures 1 and 2.
Supplementary Document S1 from Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Authors: Eckhardt Manon , Zhang Wei , Gross Andrew M. , Von Dollen John , Johnson Jeffrey R. , Franks-Skiba Kathleen E. , Swaney Danielle L. , Johnson Tasha L. , Jang Gwendolyn M. , Shah Priya S. , Brand Toni M. , Archambault Jacques , Kreisberg Jason F. , Grandis Jennifer R. , Ideker Trey , Krogan Nevan J.
Published: April 2023

This combined Supplementary Document contains Supplementary Notes, Methods and References, Legends to Supplementary Tables S1-S6, and Supplementary Figures S1-S5.
Supplementary Tables 1 - 6 from Synthetic Lethality in ATM-Deficient RAD50-Mutant Tumors Underlies Outlier Response to Cancer Therapy
Authors: Al-Ahmadie Hikmat , Iyer Gopa , Hohl Marcel , Asthana Saurabh , Inagaki Akiko , Schultz Nikolaus , Hanrahan Aphrothiti J. , Scott Sasinya N. , Brannon A. Rose , McDermott Gregory C. , Pirun Mono , Ostrovnaya Irina , Kim Philip , Socci Nicholas D. , Viale Agnes , Schwartz Gary K. , Reuter Victor , Bochner Bernard H. , Rosenberg Jonathan E. , Bajorin Dean F. , Berger Michael F. , Petrini John H.J. , Solit David B. , Taylor Barry S.
Published: April 2023

PDF file - 2461KB, A complete listing of somatic mutations and rearrangements detected as well as targeted genes, sequences, MRN complex mutation frequency, and strains utilized.
Supplementary Figure 7 from Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies
Authors: Jordan Emmet J. , Kim Hyunjae R. , Arcila Maria E. , Barron David , Chakravarty Debyani , Gao JianJiong , Chang Matthew T. , Ni Andy , Kundra Ritika , Jonsson Philip , Jayakumaran Gowtham , Gao Sizhi Paul , Johnsen Hannah C. , Hanrahan Aphrothiti J. , Zehir Ahmet , Rekhtman Natasha , Ginsberg Michelle S. , Li Bob T. , Yu Helena A. , Paik Paul K. , Drilon Alexander , Hellmann Matthew D. , Reales Dalicia N. , Benayed Ryma , Rusch Valerie W. , Kris Mark G. , Chaft Jamie E. , Baselga José , Taylor Barry S. , Schultz Nikolaus , Rudin Charles M. , Hyman David M. , Berger Michael F. , Solit David B. , Ladanyi Marc , Riely Gregory J.
Published: April 2023

Median number of mutations in samples sequenced by MSK-IMPACT in patients with a Level 1-4 alteration or assigned to the unknown mitogenic driver cohort.
Supplementary Figure 5 from Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies
Authors: Jordan Emmet J. , Kim Hyunjae R. , Arcila Maria E. , Barron David , Chakravarty Debyani , Gao JianJiong , Chang Matthew T. , Ni Andy , Kundra Ritika , Jonsson Philip , Jayakumaran Gowtham , Gao Sizhi Paul , Johnsen Hannah C. , Hanrahan Aphrothiti J. , Zehir Ahmet , Rekhtman Natasha , Ginsberg Michelle S. , Li Bob T. , Yu Helena A. , Paik Paul K. , Drilon Alexander , Hellmann Matthew D. , Reales Dalicia N. , Benayed Ryma , Rusch Valerie W. , Kris Mark G. , Chaft Jamie E. , Baselga José , Taylor Barry S. , Schultz Nikolaus , Rudin Charles M. , Hyman David M. , Berger Michael F. , Solit David B. , Ladanyi Marc , Riely Gregory J.
Published: April 2023

Breakdown of MAP2K1, RAF1, ARAF, FGFR3-TACC3 fusion and CDKN2A loss patients
Supplementary Figure 4 from Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies
Authors: Jordan Emmet J. , Kim Hyunjae R. , Arcila Maria E. , Barron David , Chakravarty Debyani , Gao JianJiong , Chang Matthew T. , Ni Andy , Kundra Ritika , Jonsson Philip , Jayakumaran Gowtham , Gao Sizhi Paul , Johnsen Hannah C. , Hanrahan Aphrothiti J. , Zehir Ahmet , Rekhtman Natasha , Ginsberg Michelle S. , Li Bob T. , Yu Helena A. , Paik Paul K. , Drilon Alexander , Hellmann Matthew D. , Reales Dalicia N. , Benayed Ryma , Rusch Valerie W. , Kris Mark G. , Chaft Jamie E. , Baselga José , Taylor Barry S. , Schultz Nikolaus , Rudin Charles M. , Hyman David M. , Berger Michael F. , Solit David B. , Ladanyi Marc , Riely Gregory J.
Published: April 2023

Breakdown of RET and ROS1 fusion positive patients
Supplementary Figure 3 from Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies
Authors: Jordan Emmet J. , Kim Hyunjae R. , Arcila Maria E. , Barron David , Chakravarty Debyani , Gao JianJiong , Chang Matthew T. , Ni Andy , Kundra Ritika , Jonsson Philip , Jayakumaran Gowtham , Gao Sizhi Paul , Johnsen Hannah C. , Hanrahan Aphrothiti J. , Zehir Ahmet , Rekhtman Natasha , Ginsberg Michelle S. , Li Bob T. , Yu Helena A. , Paik Paul K. , Drilon Alexander , Hellmann Matthew D. , Reales Dalicia N. , Benayed Ryma , Rusch Valerie W. , Kris Mark G. , Chaft Jamie E. , Baselga José , Taylor Barry S. , Schultz Nikolaus , Rudin Charles M. , Hyman David M. , Berger Michael F. , Solit David B. , Ladanyi Marc , Riely Gregory J.
Published: April 2023

Patient 2 Concurrent EGFR and KRAS mutations in a patient identified by MSK-IMPACT
Supplementary Figure 2 from Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies
Authors: Jordan Emmet J. , Kim Hyunjae R. , Arcila Maria E. , Barron David , Chakravarty Debyani , Gao JianJiong , Chang Matthew T. , Ni Andy , Kundra Ritika , Jonsson Philip , Jayakumaran Gowtham , Gao Sizhi Paul , Johnsen Hannah C. , Hanrahan Aphrothiti J. , Zehir Ahmet , Rekhtman Natasha , Ginsberg Michelle S. , Li Bob T. , Yu Helena A. , Paik Paul K. , Drilon Alexander , Hellmann Matthew D. , Reales Dalicia N. , Benayed Ryma , Rusch Valerie W. , Kris Mark G. , Chaft Jamie E. , Baselga José , Taylor Barry S. , Schultz Nikolaus , Rudin Charles M. , Hyman David M. , Berger Michael F. , Solit David B. , Ladanyi Marc , Riely Gregory J.
Published: April 2023

Patient 1 Concurrent EGFR and KRAS mutations in a patient identified by MSK-IMPACT
Supplementary Figure 1 from Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies
Authors: Jordan Emmet J. , Kim Hyunjae R. , Arcila Maria E. , Barron David , Chakravarty Debyani , Gao JianJiong , Chang Matthew T. , Ni Andy , Kundra Ritika , Jonsson Philip , Jayakumaran Gowtham , Gao Sizhi Paul , Johnsen Hannah C. , Hanrahan Aphrothiti J. , Zehir Ahmet , Rekhtman Natasha , Ginsberg Michelle S. , Li Bob T. , Yu Helena A. , Paik Paul K. , Drilon Alexander , Hellmann Matthew D. , Reales Dalicia N. , Benayed Ryma , Rusch Valerie W. , Kris Mark G. , Chaft Jamie E. , Baselga José , Taylor Barry S. , Schultz Nikolaus , Rudin Charles M. , Hyman David M. , Berger Michael F. , Solit David B. , Ladanyi Marc , Riely Gregory J.
Published: April 2023

Co-occurring Level 1-3 alterations by MSK-IMPACT in 52 patients
Supplementary Tables 3, 7-8 from Targeting the MTF2–MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy
Authors: Maganti Harinad B. , Jrade Hani , Cafariello Christopher , Manias Rothberg Janet L. , Porter Christopher J. , Yockell-Lelièvre Julien , Battaion Hannah L. , Khan Safwat T. , Howard Joel P. , Li Yuefeng , Grzybowski Adrian T. , Sabri Elham , Ruthenburg Alexander J. , Dilworth F. Jeffrey , Perkins Theodore J. , Sabloff Mitchell , Ito Caryn Y. , Stanford William L.
Published: April 2023

Supplementary Tables 3, 7-8
Supplementary Table S3 from Cell-Cycle Reprogramming for PI3K Inhibition Overrides a Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma
Authors: Chiron David , Di Liberto Maurizio , Martin Peter , Huang Xiangao , Sharman Jeff , Blecua Pedro , Mathew Susan , Vijay Priyanka , Eng Ken , Ali Siraj , Johnson Amy , Chang Betty , Ely Scott , Elemento Olivier , Mason Christopher E. , Leonard John P. , Chen-Kiang Selina
Published: April 2023

Significant non-synonymous damaging SNVs detected in CDS by WTS in Pt 1 serial samples.
Supplementary Table S1 from Cell-Cycle Reprogramming for PI3K Inhibition Overrides a Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma
Authors: Chiron David , Di Liberto Maurizio , Martin Peter , Huang Xiangao , Sharman Jeff , Blecua Pedro , Mathew Susan , Vijay Priyanka , Eng Ken , Ali Siraj , Johnson Amy , Chang Betty , Ely Scott , Elemento Olivier , Mason Christopher E. , Leonard John P. , Chen-Kiang Selina
Published: April 2023

Integrative WTS and WES analysis of MCL cells from serial samples of Pt 1.
Supplemental Tables from PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability
Authors: Gryder Berkley E. , Yohe Marielle E. , Chou Hsien-Chao , Zhang Xiaohu , Marques Joana , Wachtel Marco , Schaefer Beat , Sen Nirmalya , Song Young , Gualtieri Alberto , Pomella Silvia , Rota Rossella , Cleveland Abigail , Wen Xinyu , Sindiri Sivasish , Wei Jun S. , Barr Frederic G. , Das Sudipto , Andresson Thorkell , Guha Rajarshi , Lal-Nag Madhu , Ferrer Marc , Shern Jack F. , Zhao Keji , Thomas Craig J. , Khan Javed
Published: April 2023

Supplemental Tables
Supplemental Methods and Legends from PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability
Authors: Gryder Berkley E. , Yohe Marielle E. , Chou Hsien-Chao , Zhang Xiaohu , Marques Joana , Wachtel Marco , Schaefer Beat , Sen Nirmalya , Song Young , Gualtieri Alberto , Pomella Silvia , Rota Rossella , Cleveland Abigail , Wen Xinyu , Sindiri Sivasish , Wei Jun S. , Barr Frederic G. , Das Sudipto , Andresson Thorkell , Guha Rajarshi , Lal-Nag Madhu , Ferrer Marc , Shern Jack F. , Zhao Keji , Thomas Craig J. , Khan Javed
Published: April 2023

Supplemental Methods and Legends
Supplementary_table_S5 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Authors: Yang Dian , Denny Sarah K. , Greenside Peyton G. , Chaikovsky Andrea C. , Brady Jennifer J. , Ouadah Youcef , Granja Jeffrey M. , Jahchan Nadine S. , Lim Jing Shan , Kwok Shirley , Kong Christina S. , Berghoff Anna S. , Schmitt Anna , Reinhardt H. Christian , Park Kwon-Sik , Preusser Matthias , Kundaje Anshul , Greenleaf William J. , Sage Julien , Winslow Monte M.
Published: April 2023

table_S5_ATACseq_sample_summary
Supplementary_table_S3 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Authors: Yang Dian , Denny Sarah K. , Greenside Peyton G. , Chaikovsky Andrea C. , Brady Jennifer J. , Ouadah Youcef , Granja Jeffrey M. , Jahchan Nadine S. , Lim Jing Shan , Kwok Shirley , Kong Christina S. , Berghoff Anna S. , Schmitt Anna , Reinhardt H. Christian , Park Kwon-Sik , Preusser Matthias , Kundaje Anshul , Greenleaf William J. , Sage Julien , Winslow Monte M.
Published: April 2023

table_S3_differential_genes
Supplementary_table_S1 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Authors: Yang Dian , Denny Sarah K. , Greenside Peyton G. , Chaikovsky Andrea C. , Brady Jennifer J. , Ouadah Youcef , Granja Jeffrey M. , Jahchan Nadine S. , Lim Jing Shan , Kwok Shirley , Kong Christina S. , Berghoff Anna S. , Schmitt Anna , Reinhardt H. Christian , Park Kwon-Sik , Preusser Matthias , Kundaje Anshul , Greenleaf William J. , Sage Julien , Winslow Monte M.
Published: April 2023

table_S1_SCLC_cre model_pathology
Supplementary Figure S1-S17 from Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin
Authors: Yang Dian , Denny Sarah K. , Greenside Peyton G. , Chaikovsky Andrea C. , Brady Jennifer J. , Ouadah Youcef , Granja Jeffrey M. , Jahchan Nadine S. , Lim Jing Shan , Kwok Shirley , Kong Christina S. , Berghoff Anna S. , Schmitt Anna , Reinhardt H. Christian , Park Kwon-Sik , Preusser Matthias , Kundaje Anshul , Greenleaf William J. , Sage Julien , Winslow Monte M.
Published: April 2023

All supplementary figures (S1-S17)
Table S4 from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Table S4
Supplementary Figures 1 through 4 from Overcoming the Immunosuppressive Tumor Microenvironment of Hodgkin Lymphoma Using Chimeric Antigen Receptor T Cells
Authors: Ruella Marco , Klichinsky Michael , Kenderian Saad S. , Shestova Olga , Ziober Amy , Kraft Daniel O. , Feldman Michael , Wasik Mariusz A. , June Carl H. , Gill Saar
Published: April 2023

Figure S1. CD123 and CD30 expression in Hodgkin lymphoma. Figure S2. Hodgkin Lymphoma polarizes normal macrophage to an immunosuppressive phenotype. Figure S3. Anti-lymphoma activity of CART123. Figure S4. CART123 efficiently kill macrophages.
Supplementary Data from TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia
Authors: Lobbardi Riadh , Pinder Jordan , Martinez-Pastor Barbara , Theodorou Marina , Blackburn Jessica S. , Abraham Brian J. , Namiki Yuka , Mansour Marc , Abdelfattah Nouran S. , Molodtsov Aleksey , Alexe Gabriela , Toiber Debra , de Waard Manon , Jain Esha , Boukhali Myriam , Lion Mattia , Bhere Deepak , Shah Khalid , Gutierrez Alejandro , Stegmaier Kimberly , Silverman Lewis B. , Sadreyev Ruslan I. , Asara John M. , Oettinger Marjorie A. , Haas Wilhelm , Look A. Thomas , Young Richard A. , Mostoslavsky Raul , Dellaire Graham , Langenau David M.
Published: April 2023

Supplementary Data
Supplementary Tables 1 through 3, Supplementary Figures 1 through 7, and Supplementary Methods from Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors
Authors: Quigley David , Alumkal Joshi J. , Wyatt Alexander W. , Kothari Vishal , Foye Adam , Lloyd Paul , Aggarwal Rahul , Kim Won , Lu Eric , Schwartzman Jacob , Beja Kevin , Annala Matti , Das Rajdeep , Diolaiti Morgan , Pritchard Colin , Thomas George , Tomlins Scott , Knudsen Karen , Lord Christopher J. , Ryan Charles , Youngren Jack , Beer Tomasz M. , Ashworth Alan , Small Eric J. , Feng Felix Y.
Published: April 2023

Supplementary Table S1: Patient 1 reversion alleles. Supplementary Table 2: DNA read identifiers supporting reversion alleles. Supplementary Table S3: Gene targets of the SeqCap library used for cfDNA sequencing. Supplementary Figure S1: Frequent loss of heterozygosity in Patient 1's tumor DNA. Supplementary Figure S2: A single copy of chromosome 13 at the BRCA2 locus is present in Patient 1's tumor DNA. Supplementary Figure S3: Mutation signature three is present in patient 1's solid tumor. Supplementary Figure S4: A single copy of chromosome 13 at the BRCA2 locus is present in Patient 2's tumor DNA. Supplementary Figure S5: Patient 2's DNA coverage depth at residue 259. Supplementary Figure S6: Nucleotide and inferred protein sequences for patient 2's reversion alleles. Supplementary Figure S7: Reversion indels were significantly longer than the background distribution of indels. Supplementary Methods.
Supplementary Table S4 from Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial
Authors: Khan Khurum H. , Cunningham David , Werner Benjamin , Vlachogiannis Georgios , Spiteri Inmaculada , Heide Timon , Mateos Javier Fernandez , Vatsiou Alexandra , Lampis Andrea , Damavandi Mahnaz Darvish , Lote Hazel , Huntingford Ian Said , Hedayat Somaieh , Chau Ian , Tunariu Nina , Mentrasti Giulia , Trevisani Francesco , Rao Sheela , Anandappa Gayathri , Watkins David , Starling Naureen , Thomas Janet , Peckitt Clare , Khan Nasir , Rugge Massimo , Begum Ruwaida , Hezelova Blanka , Bryant Annette , Jones Thomas , Proszek Paula , Fassan Matteo , Hahne Jens C. , Hubank Michael , Braconi Chiara , Sottoriva Andrea , Valeri Nicola
Published: April 2023

Supplementary Table S4
Supplementary Tables 1 - 2 from Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research
Authors: Hidalgo Manuel , Amant Frederic , Biankin Andrew V. , Budinská Eva , Byrne Annette T. , Caldas Carlos , Clarke Robert B. , de Jong Steven , Jonkers Jos , Mælandsmo Gunhild Mari , Roman-Roman Sergio , Seoane Joan , Trusolino Livio , Villanueva Alberto
Published: April 2023

Supplementary Table 1: Mouse Strains Used to Develop PDX Models. Supplementary Table 2: Collection of PDX Models Available by the EuroPDX Consortium.
Supplementary Figure and Table Legends from Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research
Authors: Hidalgo Manuel , Amant Frederic , Biankin Andrew V. , Budinská Eva , Byrne Annette T. , Caldas Carlos , Clarke Robert B. , de Jong Steven , Jonkers Jos , Mælandsmo Gunhild Mari , Roman-Roman Sergio , Seoane Joan , Trusolino Livio , Villanueva Alberto
Published: April 2023

Supplementary Figure and Tables Legends.
Supplementary Figures 1 - 16, Table 1, Database 1 from Primary Resistance to PD-1 Blockade Mediated by JAK1/2 Mutations
Authors: Shin Daniel Sanghoon , Zaretsky Jesse M. , Escuin-Ordinas Helena , Garcia-Diaz Angel , Hu-Lieskovan Siwen , Kalbasi Anusha , Grasso Catherine S. , Hugo Willy , Sandoval Salemiz , Torrejon Davis Y. , Palaskas Nicolaos , Rodriguez Gabriel Abril , Parisi Giulia , Azhdam Ariel , Chmielowski Bartosz , Cherry Grace , Seja Elizabeth , Berent-Maoz Beata , Shintaku I. Peter , Le Dung T. , Pardoll Drew M. , Diaz Luis A. , Tumeh Paul C. , Graeber Thomas G. , Lo Roger S. , Comin-Anduix Begoña , Ribas Antoni
Published: April 2023

Supplementary Figure 1. Exome sequencing and copy number changes in M431 and corresponding whole-tumor biopsy. Supplementary Figure 2. Mutations in antigen presentation machinery from anti-PD1 treated melanoma cohort. Supplementary Figure 3. Immunohistochemistry (IHC) analysis of biopsies from melanoma metastases with a JAK1 loss of function mutation. Supplementary Figure 4. Selection of PD-L1 flow cytometry antibody and impact of phosphatase inhibitor as well as temperature on measuring surface PD-L1 expression and pAKT. Supplementary Figure 5. Flow cytometry gating strategy and dose response curve of interferon alpha, beta and gamma to determine the optimal concentrations. Supplementary Figure 6. Time course of PD-L1 surface expression upon interferon alpha, beta and gamma treatment for selected cell lines to determine the optimal time point for the screening. Supplementary Figure 7. Time course of PD-L1 expression upon interferon alpha, beta or gamma treatment for the cell lines with poor or no up-regulation upon 18 hours exposure. Supplementary Figure 8. Interferon signaling pathway in good and poorly responding cell lines. Supplementary Figure 9. PD-L1 expression upon interferon alpha and beta exposure. Supplementary Figure 10. Predicted functional consequences of M368 JAK2 D313 splice site mutation. Supplementary Figure 11. Immunohistochemistry (IHC) analysis of biopsies from melanoma metastases with a JAK1 loss of function mutation. Supplementary Figure 12. JAK1 wild-type lentiviral vector transduction. Supplementary Figure 13. Mutations in antigen presentation machinery from anti-PD1 treated colorectal cohort. Supplementary Figure 14. DNA damage repair gene mutations in endometrial cancer cell lines with JAK1/2 mutations. Supplementary Figure 15. Frequency of JAK1 and JAK2 alterations and their association with overall survival in additional TCGA datasets. Supplementary Figure 16. Functional effect of genetic loss of reactive PD-L1 on responses to PD-1 blockade. Supplementary Database 1. Whole exome sequencing of 23 baseline biopsies from patients analyzed in Fig. 1, and whole exome sequencing of the M431 cell line (Accession code: SRP067938).
Supplementary Figure 1 from High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial
Authors: Massard Christophe , Michiels Stefan , Ferté Charles , Le Deley Marie-Cécile , Lacroix Ludovic , Hollebecque Antoine , Verlingue Loic , Ileana Ecaterina , Rosellini Silvia , Ammari Samy , Ngo-Camus Maud , Bahleda Rastislav , Gazzah Anas , Varga Andrea , Postel-Vinay Sophie , Loriot Yohann , Even Caroline , Breuskin Ingrid , Auger Nathalie , Job Bastien , De Baere Thierry , Deschamps Frederic , Vielh Philippe , Scoazec Jean-Yves , Lazar Vladimir , Richon Catherine , Ribrag Vincent , Deutsch Eric , Angevin Eric , Vassal Gilles , Eggermont Alexander , André Fabrice , Soria Jean-Charles
Published: April 2023

Genes that contain molecular alterations matched with therapies according to tumor type.
Supplementary Table S2 from Dual Inhibition of EGFR with Afatinib and Cetuximab in Kinase Inhibitor–Resistant EGFR-Mutant Lung Cancer with and without T790M Mutations
Authors: Janjigian Yelena Y. , Smit Egbert F. , Groen Harry J.M. , Horn Leora , Gettinger Scott , Camidge D. Ross , Riely Gregory J. , Wang Bushi , Fu Yali , Chand Vikram K. , Miller Vincent A. , Pao William
Published: April 2023

Adverse events of any grade.
Figure S5 from MYC Instructs and Maintains Pancreatic Adenocarcinoma Phenotype
Authors: Sodir Nicole M. , Kortlever Roderik M. , Barthet Valentin J.A. , Campos Tania , Pellegrinet Luca , Kupczak Steven , Anastasiou Panayiotis , Swigart Lamorna Brown , Soucek Laura , Arends Mark J. , Littlewood Trevor D. , Evan Gerard I.
Published: April 2023

Inhibition of the GAS6/AXL pathway selectively blocks a subset of Myc-induced stromal changes in KMp48 pancreatic tumors
Supplementary Table 1 from Targeting HER2 with Trastuzumab Deruxtecan: A Dose-Expansion, Phase I Study in Multiple Advanced Solid Tumors
Authors: Tsurutani Junji , Iwata Hiroji , Krop Ian , Jänne Pasi A. , Doi Toshihiko , Takahashi Shunji , Park Haeseong , Redfern Charles , Tamura Kenji , Wise-Draper Trisha M. , Saito Kaku , Sugihara Masahiro , Singh Jasmeet , Jikoh Takahiro , Gallant Gilles , Li Bob T.
Published: April 2023

Mutation type and confirmed response for 19 patients with HER2-mutated tumors
Supplementary Appendix A from Targeting HER2 with Trastuzumab Deruxtecan: A Dose-Expansion, Phase I Study in Multiple Advanced Solid Tumors
Authors: Tsurutani Junji , Iwata Hiroji , Krop Ian , Jänne Pasi A. , Doi Toshihiko , Takahashi Shunji , Park Haeseong , Redfern Charles , Tamura Kenji , Wise-Draper Trisha M. , Saito Kaku , Sugihara Masahiro , Singh Jasmeet , Jikoh Takahiro , Gallant Gilles , Li Bob T.
Published: April 2023

Interstitial lung disease monitoring and management
Supplementary Table 7 from Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities
Authors: Kelly Marcus R. , Kostyrko Kaja , Han Kyuho , Mooney Nancie A. , Jeng Edwin E. , Spees Kaitlyn , Dinh Phuong T. , Abbott Keene L. , Gwinn Dana M. , Sweet-Cordero E. Alejandro , Bassik Michael C. , Jackson Peter K.
Published: April 2023

Results from the "Paralog" sublibrary screen. Different metrics are reported on each of the three tabs of the spreadsheet as indicated. GI-T-Score : GIT Score; MWU Adj Pval: FDR of Mann-Whitney U Test p-value after Benjamini-Hochberg correction; Double KO Phenotype : phenotype Z-score (pZ) of double knockout pair. Columns correspond to individual replicates in the indicated cell line.
Supplementary Table 6 from Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities
Authors: Kelly Marcus R. , Kostyrko Kaja , Han Kyuho , Mooney Nancie A. , Jeng Edwin E. , Spees Kaitlyn , Dinh Phuong T. , Abbott Keene L. , Gwinn Dana M. , Sweet-Cordero E. Alejandro , Bassik Michael C. , Jackson Peter K.
Published: April 2023

Results from the "GI-Directed" sublibrary screen. Different metrics are reported on each of the three tabs of the spreadsheet as indicated. GI-T-Score : GIT Score; MWU Adj Pval: FDR of Mann-Whitney U Test p-value after Benjamini-Hochberg correction; Double KO Phenotype : phenotype Z-score (pZ) of double knockout pair. Columns correspond to individual replicates in the indicated cell line.
Supplementary Table 2 from Pan-Cancer Efficacy of Vemurafenib in BRAFV600-Mutant Non-Melanoma Cancers
Authors: Subbiah Vivek , Puzanov Igor , Blay Jean-Yves , Chau Ian , Lockhart A. Craig , Raje Noopur S. , Wolf Juergen , Baselga José , Meric-Bernstam Funda , Roszik Jason , Diamond Eli L. , Riely Gregory J. , Sherman Eric J. , Riehl Todd , Pitcher Bethany , Hyman David M.
Published: April 2023

Supplementary Table 2
Supplementary Table 5 from Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities
Authors: Kelly Marcus R. , Kostyrko Kaja , Han Kyuho , Mooney Nancie A. , Jeng Edwin E. , Spees Kaitlyn , Dinh Phuong T. , Abbott Keene L. , Gwinn Dana M. , Sweet-Cordero E. Alejandro , Bassik Michael C. , Jackson Peter K.
Published: April 2023

Results from the first pairwise sgRNA screen in A549-Cas9 and H23-Cas9 cells. Columns are as in the previous table, except that they refer to Gene A or Gene B as indicated, where the symbol for GeneA comes alphabetically before the symbol of Gene B. Test statistics reflect comparisons with inferred expected phenotypes from Gene A/safe or Gene B/safe sgRNA pairs (see Methods).
Supplementary Data from Pan-Cancer Efficacy of Vemurafenib in BRAFV600-Mutant Non-Melanoma Cancers
Authors: Subbiah Vivek , Puzanov Igor , Blay Jean-Yves , Chau Ian , Lockhart A. Craig , Raje Noopur S. , Wolf Juergen , Baselga José , Meric-Bernstam Funda , Roszik Jason , Diamond Eli L. , Riely Gregory J. , Sherman Eric J. , Riehl Todd , Pitcher Bethany , Hyman David M.
Published: April 2023

Supplementary figures 1 & 2