bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 2 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 PI3Kγ inhibition on immune cell populations.
Supplementary Tables 1 - 3 from Long-Range Chromatin Interactions Drive Mutant TERT Promoter Activation
Authors: Akıncılar Semih Can , Khattar Ekta , Boon Priscilla Li Shan , Unal Bilal , Fullwood Melissa Jane , Tergaonkar Vinay
Published: April 2023

Supplementary Table 1. Differential gene expression data list of BLM6 and BLM14 cells (-146C>T vs. -146C) for the genes that were predicted to be off-targets of the guide RNA that has been used for the CRISPR/Cas9 genome engineering. Supplementary Table 2. Table showing list of interacting regions obtained from 4C analysis. 4C was performed in BLM6 and BLM14 cells. Differential interactions were obtained from 4C analysis. List shows the genomic coordinates (column 1-3) and their Refseq identities (column 4) of regions interacting with mutant Tert promoter. Column 5 shows whether the regions were tested by 3C-qPCR assay. Y = Yes, N=No. Column 6 shows whether the region was removed by CRISPR/Cas9 editing in the later part of the study. * mark is named as T-INT1 region. Supplementary Table 3. Primer sequences for ChIP-qPCR, 4C and 3C and RT-qPCR experiments.
Supplementary Figures 1 - 6 from Long-Range Chromatin Interactions Drive Mutant TERT Promoter Activation
Authors: Akıncılar Semih Can , Khattar Ekta , Boon Priscilla Li Shan , Unal Bilal , Fullwood Melissa Jane , Tergaonkar Vinay
Published: April 2023

Supplementary figures and legends.
Supplementary Figure 1 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 1. Generation of Pten+/-Inpp4b+/- and Pten+/-Inpp4b-/- mice.
Supplementary Table S2 from DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia
Authors: Meyer Sara E. , Qin Tingting , Muench David E. , Masuda Kohei , Venkatasubramanian Meenakshi , Orr Emily , Suarez Lauren , Gore Steven D. , Delwel Ruud , Paietta Elisabeth , Tallman Martin S. , Fernandez Hugo , Melnick Ari , Le Beau Michelle M. , Kogan Scott , Salomonis Nathan , Figueroa Maria E. , Grimes H. Leighton
Published: April 2023

Frequencies of monocyte and myelomonocytic populations in the bone marrow and spleen of Flt3ITD/ITD;Dnmt3afl/fl MxCre mice and age-matched Flt3ITD/ITD;Dnmt3afl/fl and wild-type control mice by flow cytometric analyses.
Supplementary Table S7 from Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube
Authors: Eckert Mark A. , Pan Shawn , Hernandez Kyle M. , Loth Rachel M. , Andrade Jorge , Volchenboum Samuel L. , Faber Pieter , Montag Anthony , Lastra Ricardo , Peter Marcus E. , Yamada S. Diane , Lengyel Ernst
Published: April 2023

Newick trees and cophenetic correlation coefficients.
Supplementary Figure Legends, Table Legends, Figures S1 - S4 from DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia
Authors: Meyer Sara E. , Qin Tingting , Muench David E. , Masuda Kohei , Venkatasubramanian Meenakshi , Orr Emily , Suarez Lauren , Gore Steven D. , Delwel Ruud , Paietta Elisabeth , Tallman Martin S. , Fernandez Hugo , Melnick Ari , Le Beau Michelle M. , Kogan Scott , Salomonis Nathan , Figueroa Maria E. , Grimes H. Leighton
Published: April 2023

Supplementary Figure S1. Dnmt3a haploinsufficiency transforms Flt3ITD MPN into an AML with clonogenic c-Kit+ leukemic stem and progenitors in the spleen. Supplementary Figure S2. Comparative patterns of differential global DNA methylation in DNMT3A-mutant human and murine AML. Supplementary Figure S3. Hematopoietic stem cells/progenitor and c-Myc signatures are upregulated in murine AML. Supplementary Figure S4. DNMT3A rescued murine Flt3ITD/ITD;Dnmt3afl/fl MxCre AML hypermethylated regions correspond to HSPC-like populations.
Supplementary Table S5 from Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube
Authors: Eckert Mark A. , Pan Shawn , Hernandez Kyle M. , Loth Rachel M. , Andrade Jorge , Volchenboum Samuel L. , Faber Pieter , Montag Anthony , Lastra Ricardo , Peter Marcus E. , Yamada S. Diane , Lengyel Ernst
Published: April 2023

Copy number variation segments.
Supplementary Table S4 from Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube
Authors: Eckert Mark A. , Pan Shawn , Hernandez Kyle M. , Loth Rachel M. , Andrade Jorge , Volchenboum Samuel L. , Faber Pieter , Montag Anthony , Lastra Ricardo , Peter Marcus E. , Yamada S. Diane , Lengyel Ernst
Published: April 2023

TP53 mutations in the patient cohort.
Supplementary Table S2 from Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube
Authors: Eckert Mark A. , Pan Shawn , Hernandez Kyle M. , Loth Rachel M. , Andrade Jorge , Volchenboum Samuel L. , Faber Pieter , Montag Anthony , Lastra Ricardo , Peter Marcus E. , Yamada S. Diane , Lengyel Ernst
Published: April 2023

Exome sequencing quality metrics.
Supplementary Table S1 from Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube
Authors: Eckert Mark A. , Pan Shawn , Hernandez Kyle M. , Loth Rachel M. , Andrade Jorge , Volchenboum Samuel L. , Faber Pieter , Montag Anthony , Lastra Ricardo , Peter Marcus E. , Yamada S. Diane , Lengyel Ernst
Published: April 2023

Clinicopathologic features of high grade serous ovarian cancer (HGSOC) cohort.
Supplementary Table Legends, Figures S1 - S6 from Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube
Authors: Eckert Mark A. , Pan Shawn , Hernandez Kyle M. , Loth Rachel M. , Andrade Jorge , Volchenboum Samuel L. , Faber Pieter , Montag Anthony , Lastra Ricardo , Peter Marcus E. , Yamada S. Diane , Lengyel Ernst
Published: April 2023

Supplementary Figure S1. Sequencing of HGSOC reveals conserved mutational signatures and TP53 mutations. Supplementary Figure S2. Distribution of mutations and mutational signatures in HGSOC. Supplementary Figure S3. Genomic instability is a core feature of ovarian cancer that frequently involves DNA-damage repair genes. Supplementary Figure S4. Annotated dendrograms of HGSOC metastatic trajectories. Supplementary Figure S5. Ex vivo model of metastasis to the fallopian tube. Supplementary Figure S6. In vitro model of HGSOC-fallopian tube adhesion.
Supplementary Table S7: GREAT analysis 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

GREAT analysis of genes near H3K27ac peaks up-regulated by SY-1425 in RARA-high cell lines in perturbation gene sets
Supplementary Table S5 & 6: GSEA of SY-1425 response 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

GSEA of transcriptional response to SY-1425 in RARA-high cell lines in perturbation gene sets & GSEA of transcriptional response to SY-1425 in RARA-high cell lines in hallmark/pathways and perturbation gene sets
Supplementary Table S4 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 Expression from RNA-sequencing in each of the three tumors.
Supplementary Table S3: Median Survival By Cluster 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

Table of median survival in TCGA data by predicted clusters
Supplementary Methods, Figures S1 - S4 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

Supplementary Figure S1. Mutation Spectra of each subclonal population. Supplementary Figure S2. Somatic Copy Number calls. Top: Primary, Middle: C7-T2 Metastasis, Bottom: T7-8 Metastasis. Supplementary Figure S3. Mutation signatures derived for each subclone independently. Supplementary Figure S4: Expression of immune-related genes.
Supplementary Tables 1 - 11 from Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade
Authors: Chen Pei-Ling , Roh Whijae , Reuben Alexandre , Cooper Zachary A. , Spencer Christine N. , Prieto Peter A. , Miller John P. , Bassett Roland L. , Gopalakrishnan Vancheswaran , Wani Khalida , De Macedo Mariana Petaccia , Austin-Breneman Jacob L. , Jiang Hong , Chang Qing , Reddy Sangeetha M. , Chen Wei-Shen , Tetzlaff Michael T. , Broaddus Russell J. , Davies Michael A. , Gershenwald Jeffrey E. , Haydu Lauren , Lazar Alexander J. , Patel Sapna P. , Hwu Patrick , Hwu Wen-Jen , Diab Adi , Glitza Isabella C. , Woodman Scott E. , Vence Luis M. , Wistuba Ignacio I. , Amaria Rodabe N. , Kwong Lawrence N. , Prieto Victor , Davis R. Eric , Ma Wencai , Overwijk Willem W. , Sharpe Arlene H. , Hu Jianhua , Futreal P. Andrew , Blando Jorge , Sharma Padmanee , Allison James P. , Chin Lynda , Wargo Jennifer A.
Published: April 2023

Supplementary Table S1a. Patient Cohort Clinical Summary. Supplementary Table S1b. Patient clinical characteristics. Supplementary Table S1c. Immune profiling by IHC sample log. Supplementary Table S1d. Nanostring 54 sample log. Supplementary Table S2. Summary of immune profiling by immunohistochemistry. Supplementary Table S3. Summary of immune profiling by 4 additional myeloid markers. Supplementary Table S4. Summary of immune profiling by IHC of additional CTLA-4 blockade-naïve samples. Supplementary Table S5. Nanostring Gene List. Supplementary Table S6a. Nanostring summary 54 samples. Supplementary Table S6b. Differentially upregulated and downregulated genes in pre-treatment anti-CTLA-4 samples. Supplementary Table S6c. Differentially upregulated and downregulated genes in on-treatment anti-CTLA-4 samples. Supplementary Table S6d. Differentially upregulated and downregulated genes in pre-treatment anti-PD-1 samples. Supplementary Table S6e. Differentially upregulated and downregulated genes in on-treatment anti-PD-1 samples. Supplementary Table S7. Differentially upregulated and downregulated genes from pre- to on-treatment anti-CTLA-4. Supplementary Table S8. Differentially upregulated and downregulated genes from pre- to on-treatment anti-PD-1. Supplementary Table S9a. Nanostring gene list - chip used for comparison of CTLA-4 blockade-experienced vs -naive anti-PD1 samples (28 samples). Supplementary Table S9b. NanoString additional 28 samples to compare CTLA-4 blockade-experienced vs -naive anti-PD1 samples. Supplementary Table S9c. NanoString normalized data of additional 28 samples to compare CTLA-4 blockade-experienced vs -naive anti-PD1 samples. Supplementary Table S10. Commonly differentially regulated genes between pre- to on-treatment CTLA-4 blockade and PD-1 blockade. Supplementary Table S11a. Fold changes of significant change by anti-PD-1 therapy for paired samples. Supplementary Table S11b. Frequency of significant change by anti-PD1 therapy for paired samples.
Supplementary Methods, Figure Legends 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 Methods, Figure Legends
Supplementary Figure S5 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 S5. AXL association with MET and HER2 increases following 2h MEKi or MPi treatment in MDA-MB231, determined by s-EGS crosslinking and a bead-based co-I.P.
Supplementary Figure S4 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 S4. Corresponding to Ab-microarray results (Fig. 4A), the enrichment score trace for the bottom-ranked gene-set in the GSEA shows an increase in secreted (not shed) cytokines with MEKi.
Supplementary Figure S1 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 S1. U0126 treatment reduces p-Erk1/2 while increasing p-cJUN in a panel of cell lines, measured by bead-based immunoassay.
Supplementary Figure 6 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Figure S6. Resistance to W+T combination treatment. (A) Individual tumor volume beyond 20 weeks of WZ4002 + trametinib co-treatment. (B) Representative MRI image of tumor rebound. (C) Immunohistochemical analysis of WZ4002 + trametinib combination resistant tumors demonstrating positive staining for phospho-EGFR, ERK1/2, S6 and 4EBP1 at 50 nM (left panel) and 100 nM (right panel). (D) Immunoblot analysis of EGFR pathway reactivation in WZ4002 + trametinib resistant LT GEMMs. Phospho-EGFR, AKT, ERK1/2, S6 and 4EBP1 were assessed. Lysates from LT GEMMs were treated with vehicle or with WZ4002 for 24 hours were included as positive and negative controls for EGFR pathway activation.
Supplementary Figure Legends from Cancer Immunotherapy with Immunomodulatory Anti-CD137 and Anti–PD-1 Monoclonal Antibodies Requires BATF3-Dependent Dendritic Cells
Authors: Sánchez-Paulete Alfonso R. , Cueto Francisco J. , Martínez-López María , Labiano Sara , Morales-Kastresana Aizea , Rodríguez-Ruiz María E. , Jure-Kunkel Maria , Azpilikueta Arantza , Aznar M. Angela , Quetglas José I. , Sancho David , Melero Ignacio
Published: April 2023

Supplementary Figure Legends
Supplementary Figure 5 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Figure S5. Response to W+T treatment in the L858R/T790M EGFR genetically engineered mouse model (LT GEMM). (A) Immunohistochemical analysis LT GEMMs treated with two doses of WZ4002, trametinib or a combination thereof assessing phosphorylation of EGFR, AKT and ERK1/2 at 100 nM. (B) TUNEL staining analysis of LT GEMMs treated with two doses of WZ4002, trametinib or a combination thereof at the 50 and 100 nM. (C) Tumor volume of individual LT GEMMs treated with 50 mg/kg WZ4002, 2.5 mg/kg trametinib and the combination up to 20 weeks (13). (D) Representative MRI images from each treatment.
Supplementary Figure 4 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Figure S4. PC9 GR4 xenograft response to W+T treatment. Mice were treated with two doses (A) or four doses (B) of WZ4002, trametinib or a combination thereof. Tumors were lysed, subjected to immunoblot and phosphorylation of EGFR, AKT, ERK1/2 and S6 were assessed. Hsp90 was used as a loading control. (C) Mice were photographed 31 days following cessation of drug treatment.
Supplementary Figure 3 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Figure S3. Biochemical analysis of WZ4002 + trametinib (W+T) resistant and sensitive cell lines. Each cell line was treated with 100 nM WZ4002 (W) or 30 nM trametinib (T) or a combination (C) thereof for 8 hours and total or phospho-EGFR, ERK1/2, AKT and S6 were assessed by western blot. Sensitivity to six week W+T treatment is indicated below the image. Hsp90 was used as a loading control.
Supplementary Figure 2 from Cancer Immunotherapy with Immunomodulatory Anti-CD137 and Anti–PD-1 Monoclonal Antibodies Requires BATF3-Dependent Dendritic Cells
Authors: Sánchez-Paulete Alfonso R. , Cueto Francisco J. , Martínez-López María , Labiano Sara , Morales-Kastresana Aizea , Rodríguez-Ruiz María E. , Jure-Kunkel Maria , Azpilikueta Arantza , Aznar M. Angela , Quetglas José I. , Sancho David , Melero Ignacio
Published: April 2023

CTLs against the Adpgk neoantigen of MC38 are induced by anti-CD137 and anti-PD-1 mAbs in a fraction of WT mice, but not in Batf3-/- mice.
Supplementary Methods, Tables S1 - S3 and S5 - S6, Figures S1 - S12 from Selective Inhibition of Oncogenic KRAS Output with Small Molecules Targeting the Inactive State
Authors: Patricelli Matthew P. , Janes Matthew R. , Li Lian-Sheng , Hansen Rasmus , Peters Ulf , Kessler Linda V. , Chen Yuching , Kucharski Jeff M. , Feng Jun , Ely Tess , Chen Jeffrey H. , Firdaus Sarah J. , Babbar Anjali , Ren Pingda , Liu Yi
Published: April 2023

Supplementary Table 1. Biochemical and Cell engagement SAR. Supplementary Table 2. Data collection and refinement statistics (Molecular replacement). Supplementary Table 3. Selectivity of ARS-853 across KRAS isoforms and GTP vs. GDP states. Supplementary Table 5. Kinetics of intrinsic KRAS-G12C GTP hydrolysis/exchange at 37 oC. Supplementary Table 6. LC-MS/MS Target and standard peptide information. Supplementary Figure 1. Additional structural details from the ARS-853 bound KRAS-G12C crystal structure. Supplementary Figure 2. KRAS-G12C inhibitors block SOS and EDTA mediated nucleotide exchange. Supplementary Figure 3. Global cysteine reactivity profiling of ARS-853. Supplementary Figure 4. Effects of ARS-853 on long-term signaling and cell cycle. Supplementary Figure 5. Effects of ARS-853 on KRAS-mediated NIH-3T3 transformation. Supplementary Figure 6. Proliferation structure activity relationship across ARS-853 analogs. Supplementary Figure 7. Assessment of KRAS dependence and ARS-853 in 2D versus 3D assay formats. Supplementary Figure 8. Comparison of KRAS-G12C and off-target Reticulon-4 (RTN4) cell engagement profiles. Supplementary Figure 9. Schematic of the methods workflow for the RBD-MS assay and determination of percent RAS-GTP in cells and percent RAS abundance on RAF-RBD. Supplementary Figure 10. Time dependent reduction in GTP-bound KRAS-G12C following erlotinib treatment. Supplementary Figure 11. EGFR combinations augment the efficacy of ARS-853. Supplementary Figure 12. A, synthesis of ARS-107. B, synthesis of ARS-853.
Supplementary Table 5 from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Table 5. Proteins in the two distict bands specific to GClnc1 identified by Liquid Chromatography-Mass Spectrometry.
Suppl Table 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 Table 2 with legend
Supplementary Materials 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 - 321KB, A detailed description of additional methods utilized (and associated references) for sequencing and analysis as well as an explanatory note regarding the TM pathway in yeast.
Supplementary tables S1-4 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

Supplementary Table S1: List of actionable genes and potential matched therapy Supplementary Table S2: List of co-occurring Level 1-4 mutations Supplementary Table S3: EGFR mutations identified and associated therapy Supplementary Table S4: List of 410 genes in MSK-IMPACT assay
Supplementary Figures 1 - 10 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 - 470KB, All supplementary figures including tumor histology, RAD50 immunohistochemistry, candidate mutations and their clonality, and supporting yeast and MEF experimental data.
Supplementary Figure 6 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

Types of Clinical trials patients enrolled to according to level 1-4 and UMD assigned samples
Supplementary figures and legends 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 figures and legends
Supplementary Tables 1-2, 4-6, 9-11 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 1-2, 4-6, 9-11
Extended Material and Methods 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

Extended Material and Methods
Supplementary Text, Supplementary Figures 1 through 13, Supplementary Methods from Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma
Authors: Qamra Aditi , Xing Manjie , Padmanabhan Nisha , Kwok Jeffrey Jun Ting , Zhang Shenli , Xu Chang , Leong Yan Shan , Lee Lim Ai Ping , Tang Qianqao , Ooi Wen Fong , Suling Lin Joyce , Nandi Tannistha , Yao Xiaosai , Ong Xuewen , Lee Minghui , Tay Su Ting , Keng Angie Tan Lay , Gondo Santoso Erna , Ng Cedric Chuan Young , Ng Alvin , Jusakul Apinya , Smoot Duane , Ashktorab Hassan , Rha Sun Young , Yeoh Khay Guan , Peng Yong Wei , Chow Pierce K.H. , Chan Weng Hoong , Ong Hock Soo , Soo Khee Chee , Kim Kyoung-Mee , Wong Wai Keong , Rozen Steven G. , Teh Bin Tean , Kappei Dennis , Lee Jeeyun , Connolly John , Tan Patrick
Published: April 2023

Supplementary text S1. Supplementary Figure 1: Chromatin Profiles of Primary GC. Supplementary Figure 2: Epithelial features of GC promoters. Supplementary Figure 3: GC Somatic Promoter Features. Supplementary Figure 4: Association of Somatic Promoters with Gene Expression in GC and Other Tumor Types. Supplementary Figure 5: Changes in DNA methylation at CpG island containing promoters. Supplementary Figure 6: Expression distribution of alternative and canonical isoforms. Supplementary Figure 7: Characterization of RASA3 Isoform. Supplementary Figure 8: Characterization of MET Isoforms. Supplementary Figure 9: Immunogenicity of N-terminal peptides. Supplementary Figure 10: Immunogenicity Assay and Nanostring Profiling. Supplementary Figure 11: Functional Assessment of Peptide Immunogenicity. Supplementary Figure 12: EZH2 Inhibition. Supplementary Figure 13: Unannotated somatic promoters.
Supplementary Table S5 from Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients
Authors: Damm Frederik , Mylonas Elena , Cosson Adrien , Yoshida Kenichi , Della Valle Véronique , Mouly Enguerran , Diop M'boyba , Scourzic Laurianne , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Miyano Satoru , Kikushige Yoshikane , Davi Frederick , Lambert Jérôme , Gautheret Daniel , Merle-Béral Hélène , Sutton Laurent , Dessen Philippe , Solary Eric , Akashi Koichi , Vainchenker William , Mercher Thomas , Droin Nathalie , Ogawa Seishi , Nguyen-Khac Florence , Bernard Olivier A.
Published: April 2023

XLS file - 75KB, Details of signature and expression analyses.
Supplementary Table S3 from Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients
Authors: Damm Frederik , Mylonas Elena , Cosson Adrien , Yoshida Kenichi , Della Valle Véronique , Mouly Enguerran , Diop M'boyba , Scourzic Laurianne , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Miyano Satoru , Kikushige Yoshikane , Davi Frederick , Lambert Jérôme , Gautheret Daniel , Merle-Béral Hélène , Sutton Laurent , Dessen Philippe , Solary Eric , Akashi Koichi , Vainchenker William , Mercher Thomas , Droin Nathalie , Ogawa Seishi , Nguyen-Khac Florence , Bernard Olivier A.
Published: April 2023

PDF file - 98KB, Biological and clinical features of the 168 CLL patients according to EGR2, NFKBIE and BRAF mutations.
Supplementary Table S2 from Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients
Authors: Damm Frederik , Mylonas Elena , Cosson Adrien , Yoshida Kenichi , Della Valle Véronique , Mouly Enguerran , Diop M'boyba , Scourzic Laurianne , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Miyano Satoru , Kikushige Yoshikane , Davi Frederick , Lambert Jérôme , Gautheret Daniel , Merle-Béral Hélène , Sutton Laurent , Dessen Philippe , Solary Eric , Akashi Koichi , Vainchenker William , Mercher Thomas , Droin Nathalie , Ogawa Seishi , Nguyen-Khac Florence , Bernard Olivier A.
Published: April 2023

PDF file - 211KB, Biological and clinical features of the 24 patients included in the whole-exome study.
Supplementary Table S1 from Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients
Authors: Damm Frederik , Mylonas Elena , Cosson Adrien , Yoshida Kenichi , Della Valle Véronique , Mouly Enguerran , Diop M'boyba , Scourzic Laurianne , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Miyano Satoru , Kikushige Yoshikane , Davi Frederick , Lambert Jérôme , Gautheret Daniel , Merle-Béral Hélène , Sutton Laurent , Dessen Philippe , Solary Eric , Akashi Koichi , Vainchenker William , Mercher Thomas , Droin Nathalie , Ogawa Seishi , Nguyen-Khac Florence , Bernard Olivier A.
Published: April 2023

XLS file - 336KB, Biological and clinical features of the 24 patients included in the whole-exome study.
Supplementary Tables S1-S3, Figures S1-S5 from SD-101 in Combination with Pembrolizumab in Advanced Melanoma: Results of a Phase Ib, Multicenter Study
Authors: Ribas Antoni , Medina Theresa , Kummar Shivaani , Amin Asim , Kalbasi Anusha , Drabick Joseph J. , Barve Minal , Daniels Gregory A. , Wong Deborah J. , Schmidt Emmett V. , Candia Albert F. , Coffman Robert L. , Leung Abraham C.F. , Janssen Robert S.
Published: April 2023

Supplementary Table S1. Anti-PD-1/L1 treatment experience by SD-101 dose group. Supplementary Table S2. Overview of safety. Supplementary Table S3. Treatment-related events in 20% or more of patients in the total treatment cohort are presented. Supplementary Figure S1.Percent change from baseline over time in tumors in patients who were naïve to anti-PD-1/L1 therapy. Supplementary Figure S2. IFN gene signature in Blood Cells. Supplementary Figure S3. RNA gene expression profiling. Supplementary Figure S4. A subset of patient biopsies that were assessed by RNA expression profiling, were assessed by fluorescent immunohistochemistry for infiltration of CD4 (A) and CD8 (B) T cells. Supplementary Figure S5. Correlation between fluorescent immunohistochemistry (IHC) and RNA expression profiling by Nanostring.
Supplementary Figure S2 from Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients
Authors: Damm Frederik , Mylonas Elena , Cosson Adrien , Yoshida Kenichi , Della Valle Véronique , Mouly Enguerran , Diop M'boyba , Scourzic Laurianne , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Miyano Satoru , Kikushige Yoshikane , Davi Frederick , Lambert Jérôme , Gautheret Daniel , Merle-Béral Hélène , Sutton Laurent , Dessen Philippe , Solary Eric , Akashi Koichi , Vainchenker William , Mercher Thomas , Droin Nathalie , Ogawa Seishi , Nguyen-Khac Florence , Bernard Olivier A.
Published: April 2023

PDF file - 170KB, Early mutations affect genes mutated in various human cancers (addition to the main text).
Supplementary Table S4 from SD-101 in Combination with Pembrolizumab in Advanced Melanoma: Results of a Phase Ib, Multicenter Study
Authors: Ribas Antoni , Medina Theresa , Kummar Shivaani , Amin Asim , Kalbasi Anusha , Drabick Joseph J. , Barve Minal , Daniels Gregory A. , Wong Deborah J. , Schmidt Emmett V. , Candia Albert F. , Coffman Robert L. , Leung Abraham C.F. , Janssen Robert S.
Published: April 2023

Nanostring data from tumor biopsies.
Tables S1-S5 from Crebbp Loss Drives Small Cell Lung Cancer and Increases Sensitivity to HDAC Inhibition
Authors: Jia Deshui , Augert Arnaud , Kim Dong-Wook , Eastwood Emily , Wu Nan , Ibrahim Ali H. , Kim Kee-Beom , Dunn Colin T. , Pillai Smitha P.S. , Gazdar Adi F. , Bolouri Hamid , Park Kwon-Sik , MacPherson David
Published: April 2023

Supplementary tables S1 to S5
Supplementary Tables 1, 2, 4, 5, 8, 10, 13, 14, 15 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

Supplementary Tables 1, 2, 4, 5, 8, 10, 13, 14, 15
Table S1 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

MC38 MDOTS correlation statistics
Supplementary Movies 1-3 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

In vitro killing assay movies. Co-culture of 12T melanoma cells with autologous 12TILs
Supp. Movie 2 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

PDOTS Movie 2
Supplementary Figure S2 from Circulating Cell-Free DNA to Guide Prostate Cancer Treatment with PARP Inhibition
Authors: Goodall Jane , Mateo Joaquin , Yuan Wei , Mossop Helen , Porta Nuria , Miranda Susana , Perez-Lopez Raquel , Dolling David , Robinson Dan R. , Sandhu Shahneen , Fowler Gemma , Ebbs Berni , Flohr Penny , Seed George , Rodrigues Daniel Nava , Boysen Gunther , Bertan Claudia , Atkin Mark , Clarke Matthew , Crespo Mateus , Figueiredo Ines , Riisnaes Ruth , Sumanasuriya Semini , Rescigno Pasquale , Zafeiriou Zafeiris , Sharp Adam , Tunariu Nina , Bianchini Diletta , Gillman Alexa , Lord Christopher J. , Hall Emma , Chinnaiyan Arul M. , Carreira Suzanne , de Bono Johann S.
Published: April 2023

Plots showing percentage changes in total cfDNA concentration for each patient at weeks 4 and 8 of treatment, compared to same-patient baseline value. The left plot includes non-responding patients and the right plot includes patients who responded to olaparib in the clinical trial. Below, Mann-Whitney test comparing these changes at each time point for responders and non-responder patients.
Supplementary Table Legends from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Table Legends
Supplementary Table 7 from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Table 7. Patient D SINGLE and afatinib COMBINATION High Throughput Drug Screen.
Supplementary Table 6 from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Table 6. Patient C Single and trametinib Combination High Throughput Drug Screen.
Supplementary Figure S4 from Loss of RasGAP Tumor Suppressors Underlies the Aggressive Nature of Luminal B Breast Cancers
Authors: Olsen Sarah Naomi , Wronski Ania , Castaño Zafira , Dake Benjamin , Malone Clare , De Raedt Thomas , Enos Miriam , DeRose Yoko S. , Zhou Wenhui , Guerra Stephanie , Loda Massimo , Welm Alana , Partridge Ann H. , McAllister Sandra S. , Kuperwasser Charlotte , Cichowski Karen
Published: April 2023

Ras Pathway Activation upon Rescue with wild-type or GAP-mutant DAB2IP and RASAL2.
Supplementary Table 2 from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Table 2. Drug Library Concentrations.
Supplementary Table 1 from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Table 1. Genomic analysis of 15 patients.
Table S3 from AACR Project GENIE: Powering Precision Medicine through an International Consortium
Authors: André Fabrice , Arnedos Monica , Baras Alexander S. , Baselga José , Bedard Philippe L. , Berger Michael F. , Bierkens Mariska , Calvo Fabien , Cerami Ethan , Chakravarty Debyani , Dang Kristen K. , Davidson Nancy E. , Del Vecchio Fitz Catherine , Dogan Semih , DuBois Raymond N. , Ducar Matthew D. , Futreal P. Andrew , Gao Jianjiong , Garcia Francisco , Gardos Stu , Gocke Christopher D. , Gross Benjamin E. , Guinney Justin , Heins Zachary J. , Hintzen Stephanie , Horlings Hugo , Hudeček Jan , Hyman David M. , Kamel-Reid Suzanne , Kandoth Cyriac , Kinyua Walter , Kumari Priti , Kundra Ritika , Ladanyi Marc , Lefebvre Céline , LeNoue-Newton Michele L. , Lepisto Eva M. , Levy Mia A. , Lindeman Neal I. , Lindsay James , Liu David , Lu Zhibin , MacConaill Laura E. , Maurer Ian , Maxwell David S. , Meijer Gerrit A. , Meric-Bernstam Funda , Micheel Christine M. , Miller Clinton , Mills Gordon , Moore Nathanael D. , Nederlof Petra M. , Omberg Larsson , Orechia John A. , Park Ben Ho , Pugh Trevor J. , Reardon Brendan , Rollins Barrett J. , Routbort Mark J. , Sawyers Charles L. , Schrag Deborah , Schultz Nikolaus , Shaw Kenna R Mills , Shivdasani Priyanka , Siu Lillian L. , Solit David B. , Sonke Gabe S. , Soria Jean Charles , Sripakdeevong Parin , Stickle Natalie H. , Stricker Thomas P. , Sweeney Shawn M. , Taylor Barry S. , ten Hoeve Jelle J. , Thomas Stacy B. , Van Allen Eliezer M. , Van 'T Veer Laura J. , van de Velde Tony , van Tinteren Harm , Velculescu Victor E. , Virtanen Carl , Voest Emile E. , Wang Lucy L. , Wathoo Chetna , Watt Stuart , Yu Celeste , Yu Thomas V. , Yu Emily , Zehir Ahmet , Zhang Hongxin
Published: April 2023

Table S3
Supplementary Figure Legends from Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Antitumor Innate Immunity
Authors: Patnaik Akash , Swanson Kenneth D. , Csizmadia Eva , Solanki Aniruddh , Landon-Brace Natalie , Gehring Marina P. , Helenius Katja , Olson Brian M. , Pyzer Athalia R. , Wang Lily C. , Elemento Olivier , Novak Jesse , Thornley Thomas B. , Asara John M. , Montaser Laleh , Timmons Joshua J. , Morgan Todd M. , Wang Yugang , Levantini Elena , Clohessy John G. , Kelly Kathleen , Pandolfi Pier Paolo , Rosenblatt Jacalyn M. , Avigan David E. , Ye Huihui , Karp Jeffrey M. , Signoretti Sabina , Balk Steven P. , Cantley Lewis C.
Published: April 2023

Supplementary Figure Legends