bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S3 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

Single nucleotide variants and indels.
Supplementary Methods, Figure Legends, Table Legends from A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics
Authors: Sadanandam Anguraj , Wullschleger Stephan , Lyssiotis Costas A. , Grötzinger Carsten , Barbi Stefano , Bersani Samantha , Körner Jan , Wafy Ismael , Mafficini Andrea , Lawlor Rita T. , Simbolo Michele , Asara John M. , Bläker Hendrik , Cantley Lewis C. , Wiedenmann Bertram , Scarpa Aldo , Hanahan Douglas
Published: April 2023

Supplementary information with descriptive methods and legends for supplementary tables and figures.
Supplementary Table S5 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

DNA repair pathway mutations found in the founding clone (Cluster 1). Gene list was derived from http://sciencepark.mdanderson.org/labs/wood/dna_repair_genes.html, and annotated with data from ClinVar (www.ncbi.nlm.nih.gov/clinvar/), COSMIC http://cancer.sanger.ac.uk/cosmic), the Foundation Medicine report provided to this patient, and SIFT/PolyPhen predictions from ExAC (http://exac.broadinstitute.org/).
Supplementary Table S4: Enhancer, mRNA, and SY-1425 EC50 in AML cell lines 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 Enhancer, mRNA, and SY-1425 EC50 values in AML cell lines
Supplementary Table S2 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

Segmented somatic copy number calls.
Supplementary Table S2: mRNA Cluster Signatures 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

RNA-seq derived signatures and per-cluster weights for TCGA clustering
Supplementary Table S1 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

Somatic SNVs and Indels with transcript annotation, population frequencies, and readcounts appended.
Supplementary Methods and Figure Legends 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 and expanded descriptions of methods and figure legends for supplementary data
Supplementary Table 2 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 lists.
Supplementary Figure 4 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

Results of parallel siRNA screens in FGFR driven cell lines with analysis of ERK and AKT phosphorylation in and panel of FGFR driven cancer cell lines.
Supplementary Figure 1 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

Migratory CD103+ DCs are the main mediators of cross-priming at the tumor-draining LNs.
Supplementary Figure Legends, Figures S1 - S7, Tables S1 - S8 from The CREBBP Acetyltransferase Is a Haploinsufficient Tumor Suppressor in B-cell Lymphoma
Authors: Zhang Jiyuan , Vlasevska Sofija , Wells Victoria A. , Nataraj Sarah , Holmes Antony B. , Duval Romain , Meyer Stefanie N. , Mo Tongwei , Basso Katia , Brindle Paul K. , Hussein Shafinaz , Dalla-Favera Riccardo , Pasqualucci Laura
Published: April 2023

Supplementary Figure S1. CREBBP binds to GC-specific super-enhancers. Supplementary Figure S2. Crebbp and EP300 expression in the B cell subsets development in Crebbpfl/flCγ1-Cre and Crebbpfl/flCD19-Cre mice. Supplementary Figure S3. GSEA analysis of Crebbpfl/fl vs Crebbp+/+ Cγ1-Cre GC B cells. Supplementary Figure S4. Analysis of GC B cell responses in the Cγ1-Cre and CD19-Cre cohorts. Supplementary Figure S5. Analysis of plasma cell differentiation in the Cγ1-Cre and CD19-Cre cohorts. Supplementary Figure S6. Distribution pattern of CREBBP mutations in FL and de novo DLBCL. Supplementary Figure S7. Analysis of Crebbp-conditional knockout cohorts. Supplementary Table S1. Overlap between CREBBP bound regions and predicted superenhancers in GC B cells. Supplementary Table S2. Genes differentially expressed in Crebbpfl/fl vs Crebbp+/+ GC B cells. Supplementary Table S3. List of CREBBP "core target" genes (bound by CREBBP in human GC B cells and downregulated in Crebbpfl/flCγ1-Cre GC B cells). Supplementary Table S4. Pathway enrichment analysis of CREBBP "core target" genes (bound by CREBBP in human GC B cells and downregulated in Cγ1-Cre Crebbpfl/fl GC B cells). Supplementary Table S5. Leading edge associated with GSEA of CREBBP core target genes in the rank of genes differentially expressed in DZ vs LZ GC B cells. Supplementary Table S6. Pathway enrichment analysis of genes co-bound by CREBBP and BCL6 in human GC B cells. Supplementary Table S7. V gene rearrangement analysis of B-cell lymphomas in the Crebbpfl/f/Cγ1-Cre /VavP-Bcl2 conditional knock-out mouse model. Supplementary Table S8. List of antibodies used in FACS analysis.
Supplementary Figures 1 - 2 from Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy
Authors: Sotillo Elena , Barrett David M. , Black Kathryn L. , Bagashev Asen , Oldridge Derek , Wu Glendon , Sussman Robyn , Lanauze Claudia , Ruella Marco , Gazzara Matthew R. , Martinez Nicole M. , Harrington Colleen T. , Chung Elaine Y. , Perazzelli Jessica , Hofmann Ted J. , Maude Shannon L. , Raman Pichai , Barrera Alejandro , Gill Saar , Lacey Simon F. , Melenhorst Jan J. , Allman David , Jacoby Elad , Fry Terry , Mackall Crystal , Barash Yoseph , Lynch Kristen W. , Maris John M. , Grupp Stephan A. , Thomas-Tikhonenko Andrei
Published: April 2023

Supplementary Figure 1. Enhanced skipping of exons 2 and 5-6 in post-CART-19 leukemias. Supplementary Figure 2. Analysis of splicing factors involved in alternative splicing of CD19-exon2.
Supplementary Table S4 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

Differentially Mutated Genes in HPV(-) vs. HPV(+) Samples. Related to Figure 3.
Suppl Figure 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 Figure 1 with legend
Supplementary Figures and Tables from Expressed Gene Fusions as Frequent Drivers of Poor Outcomes in Hormone Receptor–Positive Breast Cancer
Authors: Matissek Karina J. , Onozato Maristela L. , Sun Sheng , Zheng Zongli , Schultz Andrew , Lee Jesse , Patel Kristofer , Jerevall Piiha-Lotta , Saladi Srinivas Vinod , Macleay Allison , Tavallai Mehrad , Badovinac-Crnjevic Tanja , Barrios Carlos , Beşe Nuran , Chan Arlene , Chavarri-Guerra Yanin , Debiasi Marcio , Demirdögen Elif , Egeli Ünal , Gökgöz Sahsuvar , Gomez Henry , Liedke Pedro , Tasdelen Ismet , Tolunay Sahsine , Werutsky Gustavo , St. Louis Jessica , Horick Nora , Finkelstein Dianne M. , Le Long Phi , Bardia Aditya , Goss Paul E. , Sgroi Dennis C. , Iafrate A. John , Ellisen Leif W.
Published: April 2023

Supplementary Figure S1-S6 and Supplementary Tables S1-S8
Supplementary Table S4 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 - 116KB, Association between acquired mutations (P values of Fisher's exact test for independence) among the 168 patients cohort.
Supplementary Figure 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 - 136KB, Representative flow chart of the sorting procedure.
Supplementary Figure 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

PDF file - 126KB, Analyses of two patients with detectable SF3B1 mutations in CD19+, CD34+ and CD14+ fractions.
Supplementary Tables S1 - S2 from Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia
Authors: Shih Alan H. , Meydan Cem , Shank Kaitlyn , Garrett-Bakelman Francine E. , Ward Patrick S. , Intlekofer Andrew M. , Nazir Abbas , Stein Eytan M. , Knapp Kristina , Glass Jacob , Travins Jeremy , Straley Kim , Gliser Camelia , Mason Christopher E. , Yen Katharine , Thompson Craig B. , Melnick Ari , Levine Ross L.
Published: April 2023

Supplementary Table S1. List of Synergy Genes. Supplementary Table S2. A, Statistical testing of DMCs identified in combination therapy compared to single treatment. B, Differentially methylated CpGs in response to combination therapy.
Supplementary Methods, Figure Legends from Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia
Authors: Shih Alan H. , Meydan Cem , Shank Kaitlyn , Garrett-Bakelman Francine E. , Ward Patrick S. , Intlekofer Andrew M. , Nazir Abbas , Stein Eytan M. , Knapp Kristina , Glass Jacob , Travins Jeremy , Straley Kim , Gliser Camelia , Mason Christopher E. , Yen Katharine , Thompson Craig B. , Melnick Ari , Levine Ross L.
Published: April 2023

Supplementary Methods, Figure Legends
Supplementary Figures S1 - S9 from Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia
Authors: Shih Alan H. , Meydan Cem , Shank Kaitlyn , Garrett-Bakelman Francine E. , Ward Patrick S. , Intlekofer Andrew M. , Nazir Abbas , Stein Eytan M. , Knapp Kristina , Glass Jacob , Travins Jeremy , Straley Kim , Gliser Camelia , Mason Christopher E. , Yen Katharine , Thompson Craig B. , Melnick Ari , Levine Ross L.
Published: April 2023

Supplementary Figure S1. Response of Tet2-/- Flt3ITD leukemia model to 5-Aza therapy Tet2-/-Flt3ITD leukemia model treated with vehicle or 5-Aza (n=5). Supplementary Figure S2. Idh2R140QFlt3ITD leukemia model phenotype. Supplementary Figure S3. Idh2R140QFlt3ITD leukemia model treatment response to AG-221 Idh2R140QFlt3ITD leukemia model treated with vehicle or AG-221 (n=6). Supplementary Figure S4. Genomic methylation analysis of Idh2R140Q Flt3ITD leukemia model response to AG-221 therapy. Supplementary Figure S5. GSEA analysis of 5-Aza and AG-221 response. Supplementary Figure S6. Response of Tet2-/-Flt3ITD leukemia model to 5-Aza and AC220 therapy. Supplementary Figure S7. Idh2R140QFlt3ITD and Tet2-/-Flt3ITD leukemia model response to combination therapy. Supplementary Figure S8. Methylation and expression response of Tet2-/-Flt3ITD and Idh2R140QFlt3ITD leukemia model to combination therapy. Supplementary Figure S9. Response of Tet2-/- Flt3ITD and Idh2R140QFlt3ITD leukemia model to combination therapy.
Supplementary Table 4 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 4. Patient A Single and vorinostat COMBINATION High Throughput Drug Screen.
Supplementary Figures S1 - S4, Tables S1 - S8 from A First-in-Human Phase I Study of the ATP-Competitive AKT Inhibitor Ipatasertib Demonstrates Robust and Safe Targeting of AKT in Patients with Solid Tumors
Authors: Saura Cristina , Roda Desamparados , Roselló Susana , Oliveira Mafalda , Macarulla Teresa , Pérez-Fidalgo José Alejandro , Morales-Barrera Rafael , Sanchis-García Juan Manuel , Musib Luna , Budha Nageshwar , Zhu Jin , Nannini Michelle , Chan Wai Y. , Sanabria Bohórquez Sandra M. , Meng Raymond D. , Lin Kui , Yan Yibing , Patel Premal , Baselga José , Tabernero Josep , Cervantes Andrés
Published: April 2023

Supplementary Table S1. IC50 values of ipatasertib on cell viability in cell lines with or without alterations in PTEN or PIK3CA. Supplementary Table S2. Percent tumor growth inhibition (%TGI) in xenograft models with or without alterations in PTEN or PIK3CA. Supplementary Table S3. PI3K/Akt pathway status in archival tumors. Supplementary Table S4. Reasons for discontinuation of study. Supplementary Table S5. Common adverse events for ipatasertib in {greater than or equal to} 10% of patients in any presented group. Supplementary Table S6. All Grade {greater than or equal to} 3 adverse events related to ipatasertib. Supplementary Table S7. Hemoglobin A1C (HgbA1C) values for patients who had both pre-treatment and post-treatment values in Stages 1 and 2. Supplementary Table S8. Summary data for patients with best radiographic stable disease (SD) by RECIST version 1.0 criteria. Supplementary Figure S1. Exposure plots confirm that exposures achieved in patients in the dose-escalation stage (right side) correlated with exposures in preclinical models at TGI90 (left side). Supplementary Figure S2. Relationship between exposure of ipatasertib to the most common ipatasertib-related AEs of fatigue, diarrhea, nausea, and rash. Supplementary Figure S3. Suppression of pGSK3β in platelet-rich plasma versus ipatasertib concentrations. Supplementary Figure S4. Pharmacodynamic (PD) dose-dependent elevations in glucose and insulin following treatment with ipatasertib.
Supplementary Table 3 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 3. Patient A single and duparlisib combination high throughout drug screen.
Table S4 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 S4
Supplemental Tables 1-16 from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations
Authors: Huang Franklin W. , Mosquera Juan Miguel , Garofalo Andrea , Oh Coyin , Baco Maria , Amin-Mansour Ali , Rabasha Bokang , Bahl Samira , Mullane Stephanie A. , Robinson Brian D. , Aldubayan Saud , Khani Francesca , Karir Beerinder , Kim Eejung , Chimene-Weiss Jeremy , Hofree Matan , Romanel Alessandro , Osborne Joseph R. , Kim Jong Wook , Azabdaftari Gissou , Woloszynska-Read Anna , Sfanos Karen , De Marzo Angelo M. , Demichelis Francesca , Gabriel Stacey , Van Allen Eliezer M. , Mesirov Jill , Tamayo Pablo , Rubin Mark A. , Powell Isaac J. , Garraway Levi A.
Published: April 2023

Supplemental Table 1. Overall cohort characteristics of AAPC whole exome sequencing cohort (n=102) Supplemental Table 2. Clinical and pathological characteristics of AAPC WES discovery cohort (n=102) Supplemental Table 3. Comparison of numbers of tumors by Gleason grade between the TCGA and AAPC cohorts Supplemental Table 4. Germline pathogenic variants in genes in the DNA repair pathway and list of 20 DNA repair genes assessed in targeted analysis Supplemental Table 5. Alteration file of somatic variants detected in the AAPC WES discovery cohort (n=102) Supplemental Table 6. Focal deletion and amplification peaks and genes located within peaks by GISTIC2.0 analysis of AAPC WES cohort Supplemental Table 7. ERF deletions and mutations in prostate tumors of the Weill Cornell Precision Medicine cohort Supplemental Table 8. Clinical and pathological characteristics of AAPC targeted sequencing extension cohort Supplemental Table 9. List of genes and intronic regions targeted with hybrid capture bait set used for AAPC extension cohort Supplemental Table 10. Alteration file of somatic variants detected in the AAPC extension cohort (n=90) using the targeted sequencing panel Supplemental Table 11. ERF mutation frequencies across published prostate cancer cohorts Supplemental Table 12. Germline ERF variant detected in the AAPC WES cohort Supplemental Table 13. Mutations in cytochrome P450 genes in the AAPC exome discovery cohort Supplemental Table 14. ERF oligonucleotides used for RNA in situ hybridization Supplemental Table 15. Gene sets shERF_VCAP_UP_LnCAP_UP_overlap_UP and shERF_vs_CNTRL.LHSAR_UP Supplemental Table 16. Tumor purity estimates for AAPC exome discovery cohort
Supplementary Data from Cholinergic Signaling via Muscarinic Receptors Directly and Indirectly Suppresses Pancreatic Tumorigenesis and Cancer Stemness
Authors: Renz Bernhard W. , Tanaka Takayuki , Sunagawa Masaki , Takahashi Ryota , Jiang Zhengyu , Macchini Marina , Dantes Zahra , Valenti Giovanni , White Ruth A. , Middelhoff Moritz A. , Ilmer Matthias , Oberstein Paul E. , Angele Martin K. , Deng Huan , Hayakawa Yoku , Westphalen C. Benedikt , Werner Jens , Remotti Helen , Reichert Maximilian , Tailor Yagnesh H. , Nagar Karan , Friedman Richard A. , Iuga Alina C. , Olive Kenneth P. , Wang Timothy C.
Published: April 2023

Supplementary Figures, Legends and Methods
Supplementary figures from A Digital RNA Signature of Circulating Tumor Cells Predicting Early Therapeutic Response in Localized and Metastatic Breast Cancer
Authors: Kwan Tanya T. , Bardia Aditya , Spring Laura M. , Giobbie-Hurder Anita , Kalinich Mark , Dubash Taronish , Sundaresan Tilak , Hong Xin , LiCausi Joseph A. , Ho Uyen , Silva Erin J. , Wittner Ben S. , Sequist Lecia V. , Kapur Ravi , Miyamoto David T. , Toner Mehmet , Haber Daniel A. , Maheswaran Shyamala
Published: April 2023

All supplementary figures
Supplementary Tables from A Digital RNA Signature of Circulating Tumor Cells Predicting Early Therapeutic Response in Localized and Metastatic Breast Cancer
Authors: Kwan Tanya T. , Bardia Aditya , Spring Laura M. , Giobbie-Hurder Anita , Kalinich Mark , Dubash Taronish , Sundaresan Tilak , Hong Xin , LiCausi Joseph A. , Ho Uyen , Silva Erin J. , Wittner Ben S. , Sequist Lecia V. , Kapur Ravi , Miyamoto David T. , Toner Mehmet , Haber Daniel A. , Maheswaran Shyamala
Published: April 2023

All supplementary tables
Supplementary Figure S4 from Maturation Stage of T-cell Acute Lymphoblastic Leukemia Determines BCL-2 versus BCL-XL Dependence and Sensitivity to ABT-199
Authors: Chonghaile Triona Ni , Roderick Justine E. , Glenfield Cian , Ryan Jeremy , Sallan Stephen E. , Silverman Lewis B. , Loh Mignon L. , Hunger Stephen P. , Wood Brent , DeAngelo Daniel J. , Stone Richard , Harris Marian , Gutierrez Alejandro , Kelliher Michelle A. , Letai Anthony
Published: April 2023

The mean of the BAD and the HRK peptide responses are plotted for triplicate wells +/- SD of the pediatric and adult Dana-Farber patient samples (A). The BAD peptide minus the HRK peptide was used as a variable to measure BCL-2 dependence in both the typical T-ALL samples and the ETP-ALL samples (B).
Supplementary Figure S1 from Maturation Stage of T-cell Acute Lymphoblastic Leukemia Determines BCL-2 versus BCL-XL Dependence and Sensitivity to ABT-199
Authors: Chonghaile Triona Ni , Roderick Justine E. , Glenfield Cian , Ryan Jeremy , Sallan Stephen E. , Silverman Lewis B. , Loh Mignon L. , Hunger Stephen P. , Wood Brent , DeAngelo Daniel J. , Stone Richard , Harris Marian , Gutierrez Alejandro , Kelliher Michelle A. , Letai Anthony
Published: April 2023

T-cell ALL cell lines were treated for 48hr with five doses of ABT-199 and ABT-263. Apoptosis was assessed by Annexin V and Propidium Iodide (PI) staining. The mean % viability of three independent experiments is graphed +/- standard error. The calculated IC50 in μM for each of the BH3 mimetics is listed.
Supplementary Table 5 from The Rodent Liver Undergoes Weaning-Induced Involution and Supports Breast Cancer Metastasis
Authors: Goddard Erica T. , Hill Ryan C. , Nemkov Travis , D'Alessandro Angelo , Hansen Kirk C. , Maller Ori , Mongoue-Tchokote Solange , Mori Motomi , Partridge Ann H. , Borges Virginia F. , Schedin Pepper
Published: April 2023

University of Colorado and Dana-Farber Cancer Institute Combined Metastasis Cohort patient statistics.
Supplementary Table 3 from The Rodent Liver Undergoes Weaning-Induced Involution and Supports Breast Cancer Metastasis
Authors: Goddard Erica T. , Hill Ryan C. , Nemkov Travis , D'Alessandro Angelo , Hansen Kirk C. , Maller Ori , Mongoue-Tchokote Solange , Mori Motomi , Partridge Ann H. , Borges Virginia F. , Schedin Pepper
Published: April 2023

Summary of end-points analyzed for assessment of weaning-induced liver involution.
Supplementary Figure S6 from PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition
Authors: Mathur Deepti , Stratikopoulos Elias , Ozturk Sait , Steinbach Nicole , Pegno Sarah , Schoenfeld Sarah , Yong Raymund , Murty Vundavalli V. , Asara John M. , Cantley Lewis C. , Parsons Ramon
Published: April 2023

Supplementary Figure S6. ATR signaling defects contribute to synthetic lethality.
Supplementary Figure S5 from PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition
Authors: Mathur Deepti , Stratikopoulos Elias , Ozturk Sait , Steinbach Nicole , Pegno Sarah , Schoenfeld Sarah , Yong Raymund , Murty Vundavalli V. , Asara John M. , Cantley Lewis C. , Parsons Ramon
Published: April 2023

Supplementary Figure S5. Leflunomide inhibits PTEN mutant tumors.
Supplementary Figure Legends, Methods from PTEN Regulates Glutamine Flux to Pyrimidine Synthesis and Sensitivity to Dihydroorotate Dehydrogenase Inhibition
Authors: Mathur Deepti , Stratikopoulos Elias , Ozturk Sait , Steinbach Nicole , Pegno Sarah , Schoenfeld Sarah , Yong Raymund , Murty Vundavalli V. , Asara John M. , Cantley Lewis C. , Parsons Ramon
Published: April 2023

Supplementary Figure Legends, Methods
Supplementary Figure S6 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S6. Histopathology analysis of liver cancer.
Supplementary Figure S4 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S4. DCA and LTA promote obesity-associated HCC.
Supplementary Figure S1 from Gut Microbiota Promotes Obesity-Associated Liver Cancer through PGE2-Mediated Suppression of Antitumor Immunity
Authors: Loo Tze Mun , Kamachi Fumitaka , Watanabe Yoshihiro , Yoshimoto Shin , Kanda Hiroaki , Arai Yuriko , Nakajima-Takagi Yaeko , Iwama Atsushi , Koga Tomoaki , Sugimoto Yukihiko , Ozawa Takayuki , Nakamura Masaru , Kumagai Miho , Watashi Koichi , Taketo Makoto M. , Aoki Tomohiro , Narumiya Shuh , Oshima Masanobu , Arita Makoto , Hara Eiji , Ohtani Naoko
Published: April 2023

Supplementary Figure S1. Fecal bacterial analysis.
Supplementary Table S5 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

Detection of BTK C481S mutation in MCL patients at relapse from a durable but not transient ibrutinib response or no response.
Supplementary Table S4 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 targeted exome sequencing in Pt 2 relapse sample.
Supplementary Methods 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

This file provides supplementary methods for genomics, including TGS, CGH array, WES, RNAseq Analysis, IHC -MET.
Supplementary Figure 2 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

Individual PFS2 vs PFS1 profile plot. Each patient has been aligned at time 0 of PFS2 and sorted by the sum of PFS1 and PFS2.
Supplementary Figures S1 - S8 from In Vivo Genetic Screens of Patient-Derived Tumors Revealed Unexpected Frailty of the Transformed Phenotype
Authors: Bossi Daniela , Cicalese Angelo , Dellino Gaetano I. , Luzi Lucilla , Riva Laura , D'Alesio Carolina , Diaferia Giuseppe R. , Carugo Alessandro , Cavallaro Elena , Piccioni Rossana , Barberis Massimo , Mazzarol Giovanni , Testori Alessandro , Punzi Simona , Pallavicini Isabella , Tosti Giulio , Giacó Luciano , Melloni Giorgio , Heffernan Timothy P. , Natoli Gioacchino , Draetta Giulio F. , Minucci Saverio , Pelicci PierGiuseppe , Lanfrancone Luisa
Published: April 2023

Supplementary Figure S1 shows IHC analysis of metastatic melanoma tissues of MM13, MM16, and MM27 patients and their paired PDX1/PDX2. Supplementary Figure S2 shows exome sequencing analysis of human metastatic melanoma MM13, MM16, and MM27 and their paired PDX1/PDX2. Supplementary Figure S3 shows silencing efficiency of BAZ1B, SMARCA4, CHD4 and KMT2D shRNAs. Supplementary Figure S4 shows results of the in vitro proliferation and migration assays with SMARCA4- and CHD4-overexpressed MM16 PDX cells. Supplementary Figure S5 shows the functional analysis of KMT2-knockout- SK-MEL30 or A375 melanoma cell lines generated using the CRISPR/Cas9 system. Supplementary Figure S6 shows NRAS- and BRAS-mutant overexpression in shKMT2 or shLUC melanoma cell lines. Supplementary Figure S7 shows comparison of in vitro shRNA screens on melanoma cell lines with in vivo screens on PDX melanoma cells. Supplementary Figure S8 shows Mutation rate and clinical relevance of epigenetic hits identified in our melanoma screens.
Supplementary Table S1 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 and any causality.
Supplementary Table 1 from Defining Key Signaling Nodes and Therapeutic Biomarkers in NF1-Mutant Cancers
Authors: Malone Clare F. , Fromm Jody A. , Maertens Ophélia , DeRaedt Thomas , Ingraham Rachel , Cichowski Karen
Published: April 2023

PDF file - 75KB, Reported in vitro isoform specificities of PI3K inhibitors. The IC50 (nM) reported in the literature for each PI3K inhibitor against Class IA catalytic isoforms in in vitro binding assays is shown. The source for each data set is listed. A66-(S) is termed a p110alphaspecific inhibitor, AZD-6482 is classified as a p110beta-specific inhibitor, and CAL-101 shows selectivity for p110delta. GDC-0941 does not show significant isoform selectivity.
Table S7 from A Phase Ib Dose-Escalation and Expansion Study of the BCL2 Inhibitor Venetoclax Combined with Tamoxifen in ER and BCL2–Positive Metastatic Breast Cancer
Authors: Lok Sheau W. , Whittle James R. , Vaillant François , Teh Charis E. , Lo Louisa L. , Policheni Antonia N. , Bergin Alice R.T. , Desai Jayesh , Ftouni Sarah , Gandolfo Luke C. , Liew Danny , Liu He K. , Mann G. Bruce , Moodie Kate , Murugasu Anand , Pal Bhupinder , Roberts Andrew W. , Rosenthal Mark A. , Shackleton Kylie , Silva Maria João , Siow Zhen R. , Smyth Gordon K. , Taylor Leanne , Travers Avraham , Yeo Belinda , Yeung Miriam M. , Bujak Andjelija Zivanovic , Dawson Sarah-Jane , Gray Daniel H.D. , Visvader Jane E. , Lindeman Geoffrey J.
Published: April 2023

Supplementary Table S7
Supplementary Methods from A Stromal Lysolipid–Autotaxin Signaling Axis Promotes Pancreatic Tumor Progression
Authors: Auciello Francesca R. , Bulusu Vinay , Oon Chet , Tait-Mulder Jacqueline , Berry Mark , Bhattacharyya Sohinee , Tumanov Sergey , Allen-Petersen Brittany L. , Link Jason , Kendsersky Nicholas D. , Vringer Esmee , Schug Michelle , Novo David , Hwang Rosa F. , Evans Ronald M. , Nixon Colin , Dorrell Craig , Morton Jennifer P. , Norman Jim C. , Sears Rosalie C. , Kamphorst Jurre J. , Sherman Mara H.
Published: April 2023

Supplementary Methods
Supplemental Figures and Table from mTOR and HDAC Inhibitors Converge on the TXNIP/Thioredoxin Pathway to Cause Catastrophic Oxidative Stress and Regression of RAS-Driven Tumors
Authors: Malone Clare F. , Emerson Chloe , Ingraham Rachel , Barbosa William , Guerra Stephanie , Yoon Haejin , Liu Lin L. , Michor Franziska , Haigis Marcia , Macleod Kay F. , Maertens Ophélia , Cichowski Karen
Published: April 2023

Supplementary Figure S1. MPNSTs are sensitive to combined HDAC and mTOR inhibtion; Supplementary Figure S2. Change in animal weight while on combiniation treatment; Supplementary Figure S3. A) 90-8TL cells were treated with Nexturastat A at concentration indicated, with (black) or without (white) 100nM sapanisertib; Supplementary Figure S4. Combined HDAC and mTOR inhibition increases reactive oxygen species in MPNSTs;Supplementary Figure S5. TXNIP is required for combination induced MPNST cell death;Supplementary Table S1. Differentially expressed gene sets in MPNSTs treated with HDAC and mTOR inhibitors
Figures S1-S6 & Tables S1 & S2 from Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress
Authors: Port Jennifer , Muthalagu Nathiya , Raja Meera , Ceteci Fatih , Monteverde Tiziana , Kruspig Björn , Hedley Ann , Kalna Gabriela , Lilla Sergio , Neilson Lisa , Brucoli Martina , Gyuraszova Katarina , Tait-Mulder Jacqueline , Mezna Mokdad , Svambaryte Silvija , Bryson Amy , Sumpton David , McVie Allan , Nixon Colin , Drysdale Martin , Esumi Hiroyasu , Murray Graeme I. , Sansom Owen J. , Zanivan Sara R. , Murphy Daniel J.
Published: April 2023

Merged supplementary Figures & Figure legends and Tables & Table legends
Figure S4 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

A, Immunofluorescence images for CD20 (green), CD3 (red) and DAPI (blue) in R.304 before (pre, day -7) and following CD20 CAR T cell transfer (day 7 (d7)), in lymph node (LN) and brain (day 8 (d8)) and in normal RM brain. B, H&E CSF cytospin (day 8, R.304) shows marked lymphocytosis following CD20 CAR T cell transfer. C, Fraction (%) of EGFRt+ or EGFRt- CD4 an CD8 T cells expressing ï�¡4 and ï�¢1 integrins, in the blood of normal RM controls (n = 5), on day 0, pre-CD20 CAR infusion (d0, n = 4) and on day 7 or 8 (peak CD20 CAR expansion, (d7/8, n = 4)), in the CSF (on day 8 (R.304); d8, n = 1) and in the brain (on day 8 (R.304); d8, n = 1 ). * P < 0.05.
Figure S3 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

Serum levels of 24 cytokines and chemokines measured before and at indicated days after adoptive GFP or CD20 CAR T cell transfer in the blood.
Figure S1 from Chimeric Antigen Receptor T Cell–Mediated Neurotoxicity in Nonhuman Primates
Authors: Taraseviciute Agne , Tkachev Victor , Ponce Rafael , Turtle Cameron J. , Snyder Jessica M. , Liggitt H. Denny , Myerson David , Gonzalez-Cuyar Luis , Baldessari Audrey , English Chris , Yu Alison , Zheng Hengqi , Furlan Scott N. , Hunt Daniel J. , Hoglund Virginia , Finney Olivia , Brakke Hannah , Blazar Bruce R. , Berger Carolina , Riddell Stanley R. , Gardner Rebecca , Kean Leslie S. , Jensen Michael C.
Published: April 2023

A, Schema of the CD20 CAR construct. B, Cytolytic activity of human CD19 CAR T cells (solid lines) and mock (dashed lines) T cells against 51Cr-labeled human K562 and CD19-K562 and RM B-LCL1 and B-LCL2.
Figure S6 from Identification of Pik3ca Mutation as a Genetic Driver of Prostate Cancer That Cooperates with Pten Loss to Accelerate Progression and Castration-Resistant Growth
Authors: Pearson Helen B. , Li Jason , Meniel Valerie S. , Fennell Christina M. , Waring Paul , Montgomery Karen G. , Rebello Richard J. , Macpherson Arthi A. , Koushyar Sarah , Furic Luc , Cullinane Carleen , Clarkson Richard W. , Smalley Matthew J. , Simpson Kaylene J. , Phesse Toby J. , Shepherd Peter R. , Humbert Patrick O. , Sansom Owen J. , Phillips Wayne A.
Published: April 2023

Supplementary Figure 6: Pik3ca+/HR and Ptenfl/fl prostate cancers acquire CRPC, while Pik3ca+/HR;Ptenfl/fl mutants are resistant to castration. (A) Representative H&E images of Pik3ca+/HR, Ptenfl/fl and Pik3ca+/HR;Ptenfl/fl anterior (AP) and ventral (VP) prostate lobes post-castration (scale bar: 50 um, n = 3). (B) Representative IHC images of Pik3ca+/HR, Ptenfl/fl and Pik3ca+/HR;Ptenfl/fl prostate tissue stained to detect Androgen receptor (AR) 2 weeks post-castration compared to uncastrated, age-matched controls (scale bar: 50 um, n = 3). Mice were castrated when prostate carcinoma was prevalent; Pik3ca+/HR = 400 d old, Ptenfl/fl = 200 d old and Pik3ca+/HR;Ptenfl/fl = 100 d old. Insert displays positive AR nuclei (arrows) in Pik3ca+/HR;Ptenfl/fl compound mutants (scale bar: 5 um). (C) Bar chart displaying total prostate weight normalised to body weight for Pik3ca+/HR mice 0, 2 and 42 weeks post-castration (n = 8, 7 and 7, respectively). Error bars: SEM, *P <0.05 compared to 0 weeks post-castration, or as indicated, one-way ANOVA with Tukey's multiple comparison test. (D) Representative H&E images of Pik3ca+/HR mice 0, 2 and 42 weeks post-castration (scale bar: 100 um). Mice were castrated at 100 d of age.
Supplementary Tables S1-S2 from Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts
Authors: Drapkin Benjamin J. , George Julie , Christensen Camilla L. , Mino-Kenudson Mari , Dries Ruben , Sundaresan Tilak , Phat Sarah , Myers David T. , Zhong Jun , Igo Peter , Hazar-Rethinam Mehlika H. , Licausi Joseph A. , Gomez-Caraballo Maria , Kem Marina , Jani Kandarp N. , Azimi Roxana , Abedpour Nima , Menon Roopika , Lakis Sotirios , Heist Rebecca S. , Büttner Reinhard , Haas Stefan , Sequist Lecia V. , Shaw Alice T. , Wong Kwok-Kin , Hata Aaron N. , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A. , Peifer Martin , Dyson Nicholas , Thomas Roman K. , Farago Anna F.
Published: April 2023

Supplementary Tables S1-S2
Supplementary Figures 1-11 from Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts
Authors: Drapkin Benjamin J. , George Julie , Christensen Camilla L. , Mino-Kenudson Mari , Dries Ruben , Sundaresan Tilak , Phat Sarah , Myers David T. , Zhong Jun , Igo Peter , Hazar-Rethinam Mehlika H. , Licausi Joseph A. , Gomez-Caraballo Maria , Kem Marina , Jani Kandarp N. , Azimi Roxana , Abedpour Nima , Menon Roopika , Lakis Sotirios , Heist Rebecca S. , Büttner Reinhard , Haas Stefan , Sequist Lecia V. , Shaw Alice T. , Wong Kwok-Kin , Hata Aaron N. , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A. , Peifer Martin , Dyson Nicholas , Thomas Roman K. , Farago Anna F.
Published: April 2023

Supplementary Figures 1-11
Supplementary Data from BCL6 Evolved to Enable Stress Tolerance in Vertebrates and Is Broadly Required by Cancer Cells to Adapt to Stress
Authors: Fernando Tharu M. , Marullo Rossella , Pera Gresely Benet , Phillip Jude M. , Yang Shao Ning , Lundell-Smith Geoffrey , Torregroza Ingrid , Ahn Haelee , Evans Todd , Győrffy Balázs , Privé Gilbert G. , Hirano Masayuki , Melnick Ari M. , Cerchietti Leandro
Published: April 2023

Supplementary Figures 1-8 Supplementary Tables 1-2 Supplementary Materials and Methods
Supplementary Table S6 from Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival
Authors: Oser Matthew G. , Fonseca Raquel , Chakraborty Abhishek A. , Brough Rachel , Spektor Alexander , Jennings Rebecca B. , Flaifel Abdallah , Novak Jesse S. , Gulati Aditi , Buss Elizabeth , Younger Scott T. , McBrayer Samuel K. , Cowley Glenn S. , Bonal Dennis M. , Nguyen Quang-De , Brulle-Soumare Laura , Taylor Paula , Cairo Stefano , Ryan Colm J. , Pease Elizabeth J. , Maratea Kim , Travers Jon , Root David E. , Signoretti Sabina , Pellman David , Ashton Susan , Lord Christopher J. , Barry Simon T. , Kaelin William G.
Published: April 2023

Supplementary Table S6 shows mutational status of RB1 and TP53 and amplification status of MYC in cell line xenograft and PDX SCLC mouse models.
Supplementary Table S5 from Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival
Authors: Oser Matthew G. , Fonseca Raquel , Chakraborty Abhishek A. , Brough Rachel , Spektor Alexander , Jennings Rebecca B. , Flaifel Abdallah , Novak Jesse S. , Gulati Aditi , Buss Elizabeth , Younger Scott T. , McBrayer Samuel K. , Cowley Glenn S. , Bonal Dennis M. , Nguyen Quang-De , Brulle-Soumare Laura , Taylor Paula , Cairo Stefano , Ryan Colm J. , Pease Elizabeth J. , Maratea Kim , Travers Jon , Root David E. , Signoretti Sabina , Pellman David , Ashton Susan , Lord Christopher J. , Barry Simon T. , Kaelin William G.
Published: April 2023

Supplementary Table S5 shows RNA sequencing data and gene set enrichment analysis of NCI-H82 cells Dox-On pRB cells grown in the presence or absence of DOX and then treated with DMSO or AZD2811.
Supplementary Table S1 from Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival
Authors: Oser Matthew G. , Fonseca Raquel , Chakraborty Abhishek A. , Brough Rachel , Spektor Alexander , Jennings Rebecca B. , Flaifel Abdallah , Novak Jesse S. , Gulati Aditi , Buss Elizabeth , Younger Scott T. , McBrayer Samuel K. , Cowley Glenn S. , Bonal Dennis M. , Nguyen Quang-De , Brulle-Soumare Laura , Taylor Paula , Cairo Stefano , Ryan Colm J. , Pease Elizabeth J. , Maratea Kim , Travers Jon , Root David E. , Signoretti Sabina , Pellman David , Ashton Susan , Lord Christopher J. , Barry Simon T. , Kaelin William G.
Published: April 2023

Supplementary Table S1 shows complete list of genes targeted by our custom sgRNA library and sgRNA sequences.