bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Periodontal Disease, Tooth Loss, and Risk of Serrated Polyps and Conventional Adenomas
Authors: Lo Chun-Han , Nguyen Long H. , Wu Kana , Ogino Shuji , Chan Andrew T. , Giovannucci Edward L. , Song Mingyang
Published: April 2023

Abstract
Growing data indicate an association between periodontal disease and the development of cancer. However, the evidence for colorectal cancer has been inconsistent and longitudinal study examining its precursor lesions is lacking. We prospectively collected information on periodontal disease and number of tooth loss in the Nurses' Health Study (1992–2002) and the Health Professionals Follow-up Study (1992–2010). Polyp diagnosis was acquired via self-reported questionnaires and confirmed through review of medical records. We used logistic regression to calculate the multivariate-adjusted ORs and 95% confidence intervals (CI) with adjustment for smoking and other known risk factors for periodontal disease and colorectal cancer. In this study, we included 17,904 women and 24,582 men. We documented 2,336 cases of serrated polyps and 4,102 cases of conventional adenomas among 84,714 person-endoscopies throughout follow-up. The ORs of serrated polyps and conventional adenomas comparing individuals with and without periodontal disease were 1.17 (95% CI, 1.06–1.29) and 1.11 (95% CI, 1.02–1.19), respectively. Compared with participants without tooth loss, those who lost ≥4 teeth had 20% (OR, 1.20; 95% CI, 1.03–1.39) greater risk of serrated polyps (Ptrend 0.01). Among never smokers, similar associations with periodontal disease were observed for both serrated polyps (OR, 1.20; 95% CI, 1.02–1.41) and conventional adenomas (OR, 1.12; 95% CI, 1.00–1.26). History of periodontal disease and possibly higher number of tooth loss may modestly increase the risk of developing colorectal precursor lesions. Our findings advance our understanding of the interplay between oral health, microbiome, and early colorectal carcinogenesis.
Supplementary Table S1 from Modulation of Activation-Loop Phosphorylation by JAK Inhibitors Is Binding Mode Dependent
Authors: Andraos Rita , Qian Zhiyan , Bonenfant Débora , Rubert Joëlle , Vangrevelinghe Eric , Scheufler Clemens , Marque Fanny , Régnier Catherine H. , De Pover Alain , Ryckelynck Hugues , Bhagwat Neha , Koppikar Priya , Goel Aviva , Wyder Lorenza , Tavares Gisele , Baffert Fabienne , Pissot-Soldermann Carole , Manley Paul W. , Gaul Christoph , Voshol Hans , Levine Ross L. , Sellers William R. , Hofmann Francesco , Radimerski Thomas
Published: April 2023

PDF file - 11K, Activity of NVP-BBT594 in biochemical and cell-based assays. The IC50 (mean of two experiments) of NVP-BBT594 on the JAK2 kinase was determined in a biochemical kinase assay with the active enzyme. Half-maximal growth inhibition (GI50,) of NVP-BBT594 was determined in SET-2, CMK and K-562 cell lines (mean � SD, n = 4).
Supplementary Figure 1 from A Molecularly Annotated Platform of Patient-Derived Xenografts (“Xenopatients”) Identifies HER2 as an Effective Therapeutic Target in Cetuximab-Resistant Colorectal Cancer
Authors: Bertotti Andrea , Migliardi Giorgia , Galimi Francesco , Sassi Francesco , Torti Davide , Isella Claudio , Corà Davide , Di Nicolantonio Federica , Buscarino Michela , Petti Consalvo , Ribero Dario , Russolillo Nadia , Muratore Andrea , Massucco Paolo , Pisacane Alberto , Molinaro Luca , Valtorta Emanuele , Sartore-Bianchi Andrea , Risio Mauro , Capussotti Lorenzo , Gambacorta Marcello , Siena Salvatore , Medico Enzo , Sapino Anna , Marsoni Silvia , Comoglio Paolo M. , Bardelli Alberto , Trusolino Livio
Published: April 2023

PDF file - 431K
Supplementary Methods, Figures 1-5, Tables 1-3 from Functional Characterization of an Isoform-Selective Inhibitor of PI3K-p110β as a Potential Anticancer Agent
Authors: Ni Jing , Liu Qingsong , Xie Shaozhen , Carlson Coby , Von Thanh , Vogel Kurt , Riddle Steve , Benes Cyril , Eck Michael , Roberts Thomas , Gray Nathanael , Zhao Jean
Published: April 2023

PDF file - 1MB
Supplementary Figure 1 from PI3Kδ Inhibitors in Cancer: Rationale and Serendipity Merge in the Clinic
Authors: Fruman David A. , Rommel Christian
Published: April 2023

PDF file - 122K
Supplementary Table 2 from A Central Role for RAF→MEK→ERK Signaling in the Genesis of Pancreatic Ductal Adenocarcinoma
Authors: Collisson Eric A. , Trejo Christy L. , Silva Jillian M. , Gu Shenda , Korkola James E. , Heiser Laura M. , Charles Roch-Philippe , Rabinovich Brian A. , Hann Byron , Dankort David , Spellman Paul T. , Phillips Wayne A. , Gray Joe W. , McMahon Martin
Published: April 2023

XLS file - 65K, Interaction indicies of MEK inhibitor GSK1120212, AKT inhibitor GSK690693 in PDA cell lines
Supplementary Materials and Methods from A Central Role for RAF→MEK→ERK Signaling in the Genesis of Pancreatic Ductal Adenocarcinoma
Authors: Collisson Eric A. , Trejo Christy L. , Silva Jillian M. , Gu Shenda , Korkola James E. , Heiser Laura M. , Charles Roch-Philippe , Rabinovich Brian A. , Hann Byron , Dankort David , Spellman Paul T. , Phillips Wayne A. , Gray Joe W. , McMahon Martin
Published: April 2023

PDF file - 65K
Supplementary Figure 4 from Functional Metabolic Screen Identifies 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 as an Important Regulator of Prostate Cancer Cell Survival
Authors: Ros Susana , Santos Claudio R. , Moco Sofia , Baenke Franziska , Kelly Gavin , Howell Michael , Zamboni Nicola , Schulze Almut
Published: April 2023

PDF file - 542K
Supplementary Figure 5 from HER2 Amplification: A Potential Mechanism of Acquired Resistance to EGFR Inhibition in EGFR-Mutant Lung Cancers That Lack the Second-Site EGFRT790M Mutation
Authors: Takezawa Ken , Pirazzoli Valentina , Arcila Maria E. , Nebhan Caroline A. , Song Xiaoling , de Stanchina Elisa , Ohashi Kadoaki , Janjigian Yelena Y. , Spitzler Paula J. , Melnick Mary Ann , Riely Greg J. , Kris Mark G. , Miller Vincent A. , Ladanyi Marc , Politi Katerina , Pao William
Published: April 2023

PDF file - 92K, Effects of HER2 overexpression on the sensitivity of HCC827 cells to EGFR TKIs
Supplementary Figure 8 from A Hormone–DNA Repair Circuit Governs the Response to Genotoxic Insult
Authors: Goodwin Jonathan F. , Schiewer Matthew J. , Dean Jeffry L. , Schrecengost Randy S. , de Leeuw Renée , Han Sumin , Ma Teng , Den Robert B. , Dicker Adam P. , Feng Felix Y. , Knudsen Karen E.
Published: April 2023

Supplementary Figure 8 - PDF file 140K, Supplemental data demonstrating that DNAPKcs is required for DNA repair in the presence of androgen
Supplementary Figure S1 from Inhibiting EGF Receptor or SRC Family Kinase Signaling Overcomes BRAF Inhibitor Resistance in Melanoma
Authors: Girotti Maria R. , Pedersen Malin , Sanchez-Laorden Berta , Viros Amaya , Turajlic Samra , Niculescu-Duvaz Dan , Zambon Alfonso , Sinclair John , Hayes Andrew , Gore Martin , Lorigan Paul , Springer Caroline , Larkin James , Jorgensen Claus , Marais Richard
Published: April 2023

PDF file - 64K, Western blotting for phospho-EGFR in tumour xenografts
Supplementary Figure 5 from Preexisting MEK1 Exon 3 Mutations in V600E/KBRAF Melanomas Do Not Confer Resistance to BRAF Inhibitors
Authors: Shi Hubing , Moriceau Gatien , Kong Xiangju , Koya Richard C. , Nazarian Ramin , Pupo Gulietta M. , Bacchiocchi Antonella , Dahlman Kimberly B. , Chmielowski Bartosz , Sosman Jeffrey A. , Halaban Ruth , Kefford Richard F. , Long Georgina V. , Ribas Antoni , Lo Roger S.
Published: April 2023

PDF file - 144K, Long-term effects of P124SMEK1 expression on population doubling and p-ERK levels. (A) Impact of regulated expression of P124SMEK1 on long-term growth of M238. Stable lines expressing empty vector, FLAG-MEK1 WT or FLAG-MEK1 P124S were cultured with different levels of doxycycline, enabling low (0.1 ng/ml) or high (0 ng/ml) expression levels of exogenous MEK1. Equal number of cells were serially plated every 4 days and fold growth calculated by dividing the number of viable cells (trypan-blue negative) at the end of each four day period over the starting seeding number. (B) Long-term, regulated expression of WTMEK or P124SMEK and corresponding levels of ERK activation in a clonogenic assay (Fig. 2G). Doxycycline-controlled expression of vector (control), FLAG-MEK1 WT, vs. FLAG-MEK1 P124S in the V600EB-RAF melanoma cell line, M238. Protein lysates (192 h post seeding at 0, 0.1, and 100 ng/ml doxycycline) were probed by Western blotting for the indicated phospho- and total protein levels. Tubulin, loading control.
Supplementary Figure 3 from Preexisting MEK1 Exon 3 Mutations in V600E/KBRAF Melanomas Do Not Confer Resistance to BRAF Inhibitors
Authors: Shi Hubing , Moriceau Gatien , Kong Xiangju , Koya Richard C. , Nazarian Ramin , Pupo Gulietta M. , Bacchiocchi Antonella , Dahlman Kimberly B. , Chmielowski Bartosz , Sosman Jeffrey A. , Halaban Ruth , Kefford Richard F. , Long Georgina V. , Ribas Antoni , Lo Roger S.
Published: April 2023

PDF file - 188K, Effects of MEK1 P124S co-expression with B-RAF V600K on cellular p-ERK levels and growth inhibitory sensitivities to B-RAFi and MEKi. (A) The YULAC V600KB-RAF melanoma cell line was stably introduced with the doxycycline-repressible tetracycline transactivator (tTA) and subsequently with vector, FLAG-MEK1, or FLAG-MEK1 P124S expression constructs. Stable cell lines incubated with doxycycline (100 ng/ml) or washed from doxycycline for 2 days were lysed, and the lysates probed for levels of indicated proteins by Western blotting. Tubulin, loading controls. (B) Survival curves for indicated YULAC stable cell lines treated with the indicated PLX4032 or AZD6244 for 72 h in the presence of doxycycline (top) or its absence (bottom). Data represent percent surviving cells relative to DMSO-treated controls (mean +/- SEM, n = 5). The dashed line corresponds to 50% cell killing.
Supplementary Figures 1-7 from Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents
Authors: Birkbak Nicolai J. , Wang Zhigang C. , Kim Ji-Young , Eklund Aron C. , Li Qiyuan , Tian Ruiyang , Bowman-Colin Christian , Li Yang , Greene-Colozzi April , Iglehart J. Dirk , Tung Nadine , Ryan Paula D. , Garber Judy E. , Silver Daniel P. , Szallasi Zoltan , Richardson Andrea L.
Published: April 2023

PDF file - 325K
Supplementary Figures 1-7 from Genotype-Selective Combination Therapies for Melanoma Identified by High-Throughput Drug Screening
Authors: Held Matthew A. , Langdon Casey G. , Platt James T. , Graham-Steed Tisheeka , Liu Zongzhi , Chakraborty Ashok , Bacchiocchi Antonella , Koo Andrew , Haskins Jonathan W. , Bosenberg Marcus W. , Stern David F.
Published: April 2023

PDF file - 1.1MB, Figure S1. Single agent concentration-effect curves, related to Figure 1; Figure S2. Drug class and concentration choices for combinatorial drug screening, related to Figure 2; Figure S3, Mutant BRAF and mutant RAS selective drug pairs, related to Figure 3; Figure S4. Analysis of drug combinations by target class, related to Figure 4D; Figure S5. Sensitization of mutant BRAF lines with lapatinib and MK-2206, related to Figure 5; Figure S6. Immunoblot analyses of vemurafenib-resistant lines after drug treatments, related to Figure 5; Figure S7. Signaling and biological effects of simvastatin and flavopiridol in vitro and in vivo, related to Figure 6
Supplementary Methods from From Differences in Means between Cases and Controls to Risk Stratification: A Business Plan for Biomarker Development
Authors: Wentzensen Nicolas , Wacholder Sholom
Published: April 2023

PDF file - 124K, 1. From biomarker levels in cases and controls to risk stratification: The algebra 2. From difference in Means to Risk Stratification: A spreadsheet
Supplementary Tables 1-4 from A High-Throughput Functional Complementation Assay for Classification of BRCA1 Missense Variants
Authors: Bouwman Peter , van der Gulden Hanneke , van der Heijden Ingrid , Drost Rinske , Klijn Christiaan N. , Prasetyanti Pramudita , Pieterse Mark , Wientjens Ellen , Seibler Jost , Hogervorst Frans B.L. , Jonkers Jos
Published: April 2023

Supplementary Tables 1-4 - PDF 99K, Information on BRCA1 mutants used to validate the functional complementation assays (Table S1), BRCA1 VUS showing low protein levels (Table S2), the results of all proliferation and cisplatin sensitivity assays (Table S3), and predictions of functional consequences from literature and in silico analyses together with a summary of the results of the functional complementation assays for all BRCA1 variants analyzed (Table S4)
Supplementary Movie 5 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: <1 MB.
Supplementary Table 5 from The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
Authors: Littlepage Laurie E. , Adler Adam S. , Kouros-Mehr Hosein , Huang Guiqing , Chou Jonathan , Krig Sheryl R. , Griffith Obi L. , Korkola James E. , Qu Kun , Lawson Devon A. , Xue Qing , Sternlicht Mark D. , Dijkgraaf Gerrit J.P. , Yaswen Paul , Rugo Hope S. , Sweeney Colleen A. , Collins Colin C. , Gray Joe W. , Chang Howard Y. , Werb Zena
Published: April 2023

PDF file - 37K, Drug list identified in silico. List of drugs identified in silico to inhibit breast cancer cell lines that overexpress ZNF217. Correlation of ZNF217 expression in the cell line panel with the drug panel of ~50,000 drugs generated by the NCI Developmental Therapeutics Program (dtp.nci.nih.gov) identified several drugs that selectively inhibited growth of cells, assessed by GI50, expressing high levels of ZNF217 with a low drug concentration
Supplementary Table 4 from The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
Authors: Littlepage Laurie E. , Adler Adam S. , Kouros-Mehr Hosein , Huang Guiqing , Chou Jonathan , Krig Sheryl R. , Griffith Obi L. , Korkola James E. , Qu Kun , Lawson Devon A. , Xue Qing , Sternlicht Mark D. , Dijkgraaf Gerrit J.P. , Yaswen Paul , Rugo Hope S. , Sweeney Colleen A. , Collins Colin C. , Gray Joe W. , Chang Howard Y. , Werb Zena
Published: April 2023

PDF file - 29K, Overlapping adult stem cell signature genes. List of overlapping genes between our dataset (this study) and our adult stem cell signature, which is downregulated in many epithelial cancers relative to normal tissue. Primary MECs overexpressing Znf217 significantly repressed genes of the adult stem cell signature (P=1.89x10-10)
Supplementary Movie 2 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: 3 MB.
Supplementary Movie 12 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: 6 MB.
Supplementary Table 1 from The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
Authors: Littlepage Laurie E. , Adler Adam S. , Kouros-Mehr Hosein , Huang Guiqing , Chou Jonathan , Krig Sheryl R. , Griffith Obi L. , Korkola James E. , Qu Kun , Lawson Devon A. , Xue Qing , Sternlicht Mark D. , Dijkgraaf Gerrit J.P. , Yaswen Paul , Rugo Hope S. , Sweeney Colleen A. , Collins Colin C. , Gray Joe W. , Chang Howard Y. , Werb Zena
Published: April 2023

PDF file - 50K, Human microarray summary. Summary of correlations between ZNF217 and selected genes from ChIP-chip and gene expression microarray datasets. ZNF217 expression levels correlated with expression of K19 and K8/18, genes that have ZNF217 enriched at their promoters, in human breast cancer cell lines, tumors, and after knockdown in MCF7 cells
Supplementary Figures 1-3 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

Supplementary Figures 1-3 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Supplementary Materials and Methods from The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
Authors: Littlepage Laurie E. , Adler Adam S. , Kouros-Mehr Hosein , Huang Guiqing , Chou Jonathan , Krig Sheryl R. , Griffith Obi L. , Korkola James E. , Qu Kun , Lawson Devon A. , Xue Qing , Sternlicht Mark D. , Dijkgraaf Gerrit J.P. , Yaswen Paul , Rugo Hope S. , Sweeney Colleen A. , Collins Colin C. , Gray Joe W. , Chang Howard Y. , Werb Zena
Published: April 2023

PDF file - 233K, This file contains supplemental materials and methods, including cell lines, antibodies and staining procedures used in this study
Supplementary Figure 4 from TGF-β Receptor II Loss Promotes Mammary Carcinoma Progression by Th17-Dependent Mechanisms
Authors: Novitskiy Sergey V. , Pickup Michael W. , Gorska Agnieszka E. , Owens Philip , Chytil Anna , Aakre Mary , Wu Huiyun , Shyr Yu , Moses Harold L.
Published: April 2023

PDF file - 266K
Supplementary Table 2 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia
Authors: Sanda Takaomi , Tyner Jeffrey W. , Gutierrez Alejandro , Ngo Vu N. , Glover Jason , Chang Bill H. , Yost Arla , Ma Wenxue , Fleischman Angela G. , Zhou Wenjun , Yang Yandan , Kleppe Maria , Ahn Yebin , Tatarek Jessica , Kelliher Michelle A. , Neuberg Donna S. , Levine Ross L. , Moriggl Richard , Müller Mathias , Gray Nathanael S. , Jamieson Catriona H.M. , Weng Andrew P. , Staudt Louis M. , Druker Brian J. , Look A. Thomas
Published: April 2023

XLSX file - 525K, Summary of inducible shRNA screen on three T-ALL cell lines.
Supplementary Figure 4 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia
Authors: Sanda Takaomi , Tyner Jeffrey W. , Gutierrez Alejandro , Ngo Vu N. , Glover Jason , Chang Bill H. , Yost Arla , Ma Wenxue , Fleischman Angela G. , Zhou Wenjun , Yang Yandan , Kleppe Maria , Ahn Yebin , Tatarek Jessica , Kelliher Michelle A. , Neuberg Donna S. , Levine Ross L. , Moriggl Richard , Müller Mathias , Gray Nathanael S. , Jamieson Catriona H.M. , Weng Andrew P. , Staudt Louis M. , Druker Brian J. , Look A. Thomas
Published: April 2023

PDF file - 74K, Knockdown efficiency and BCL2 expression in JURKAT cells.
Supplementary Figure 3 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia
Authors: Sanda Takaomi , Tyner Jeffrey W. , Gutierrez Alejandro , Ngo Vu N. , Glover Jason , Chang Bill H. , Yost Arla , Ma Wenxue , Fleischman Angela G. , Zhou Wenjun , Yang Yandan , Kleppe Maria , Ahn Yebin , Tatarek Jessica , Kelliher Michelle A. , Neuberg Donna S. , Levine Ross L. , Moriggl Richard , Müller Mathias , Gray Nathanael S. , Jamieson Catriona H.M. , Weng Andrew P. , Staudt Louis M. , Druker Brian J. , Look A. Thomas
Published: April 2023

PDF file - 400K, Protein expression levels and phosphorylation of candidate signaling molecules in T-ALL cell lines.
Supplementary Figures 6-8 from Metabolomics Strategy Reveals Subpopulation of Liposarcomas Sensitive to Gemcitabine Treatment
Authors: Braas Daniel , Ahler Ethan , Tam Brenna , Nathanson David , Riedinger Mirielle , Benz Matthias R. , Smith Kathleen B. , Eilber Fritz C. , Witte Owen N. , Tap William D. , Wu Hong , Christofk Heather R.
Published: April 2023

PDF file - 85K, Gemcitabine has a cytotoxic effect on three liposarcoma cell lines. Supplemental Figure 7: Gemcitabine is cytotoxic to liposarcoma cell lines and xenograft tumors in mice. Supplemental Figure 8: Gemcitabine decreases tumor growth in serially passaged LPS2 xenografts
Supplementary Figures 1-4 from Metabolomics Strategy Reveals Subpopulation of Liposarcomas Sensitive to Gemcitabine Treatment
Authors: Braas Daniel , Ahler Ethan , Tam Brenna , Nathanson David , Riedinger Mirielle , Benz Matthias R. , Smith Kathleen B. , Eilber Fritz C. , Witte Owen N. , Tap William D. , Wu Hong , Christofk Heather R.
Published: April 2023

PDF file - 163, Supplemental Figure 1: Serially passaged liposarcoma xenograft tumors derived from primary tumors and xenograft tumors derived from liposarcoma cell lines both exhibit similar 18F-FDG uptake by PET. Supplemental Figure 2: High grade liposarcomas exhibit variable FDG uptake by PET. Supplemental Figure 3: Nutrient concentrations in medium and metabolites consumed by liposarcoma cell lines. Supplemental Figure 4: Glucose and glutamine consumption rates and lactate production rates are similar in three liposarcoma cell lines
Supplementary Appendix from High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing
Authors: Wagle Nikhil , Berger Michael F. , Davis Matthew J. , Blumenstiel Brendan , DeFelice Matthew , Pochanard Panisa , Ducar Matthew , Van Hummelen Paul , MacConaill Laura E. , Hahn William C. , Meyerson Matthew , Gabriel Stacey B. , Garraway Levi A.
Published: April 2023

XLS file - 3.7MB
Supplementary Figure 1 from Increased Levels of COX-2 and Prostaglandin E2 Contribute to Elevated Aromatase Expression in Inflamed Breast Tissue of Obese Women
Authors: Subbaramaiah Kotha , Morris Patrick G. , Zhou Xi Kathy , Morrow Monica , Du Baoheng , Giri Dilip , Kopelovich Levy , Hudis Clifford A. , Dannenberg Andrew J.
Published: April 2023

PDF file - 41K
Supplementary Table 1 from Molecular Ontogeny of Donor-Derived Follicular Lymphomas Occurring after Hematopoietic Cell Transplantation
Authors: Weigert Oliver , Kopp Nadja , Lane Andrew A. , Yoda Akinori , Dahlberg Suzanne E. , Neuberg Donna , Bahar Anita Y. , Chapuy Bjoern , Kutok Jeffery L. , Longtine Janina A. , Kuo Frank C. , Haley Terry , Salois Maura , Sullivan Timothy J. , Fisher David C. , Fox Edward A. , Rodig Scott J. , Antin Joseph H. , Weinstock David M.
Published: April 2023

PDF file - 133K
Supplementary Figures S4 - S7 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figures S4, S5, S6, S7 - PDF file 1832K, Figure S4:Pyrvinium effect on beta-catenin in SYT-SSX2 expressing C2C12 and synovial sarcoma cells Figure S5:Phosphorylated �-catenin and full-length APC in HS-SY-II and SYO-1 SS cells Figure S6:SSTC-104 effects on growth and beta-catenin in HS-SY-II synovial sarcoma cells Figure S7: LRP6 depletion in HS-SY-II synovial sarcoma cells induces �-catenin nuclear exit
Supplementary Figure S9 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figure S9 - PDF file 867K,Figure S9: The SYT-SSX2 domain SSXRD executes �-catenin activation and myogenic differentiation
Supplementary Tables 1-2 from Androgen Receptor Signaling in Circulating Tumor Cells as a Marker of Hormonally Responsive Prostate Cancer
Authors: Miyamoto David T. , Lee Richard J. , Stott Shannon L. , Ting David T. , Wittner Ben S. , Ulman Matthew , Smas Malgorzata E. , Lord Jenna B. , Brannigan Brian W. , Trautwein Julie , Bander Neil H. , Wu Chin-Lee , Sequist Lecia V. , Smith Matthew R. , Ramaswamy Sridhar , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

PDF file - 110K, Supplemental Tables. (S1) Clinical characteristics and CTC data for metastatic prostate cancer patients treated with hormonal therapy. (S2) Time course data for metastatic prostate cancer patients treated with hormonal therapy and analyzed for AR signaling in CTCs.
Supplementary Figure S11 and Tables S1-S3 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figure S11 and Tables S1-S3 - PDF file 460K, Figure S11: Regulation of an embryonic Wnt-interactive network by SYT-SSX2 and in human synovial sarcomas Table S1: Differentially regulated Wnt components in mesenchymal precursor cells expressing SYT-SSX2 and in synovial sarcoma tumors Table S2: Differentially regulated Wnt targets in mesenchymal precursor cells expressing SYT-SSX2 and in synovial sarcoma tumors Table S3: The embryonic Wnt interactive network in mesenchymal precursor cells expressing SYTSSX2 and in synovial sarcoma tumors
Supplementary Figures 1-6 from Androgen Receptor Signaling in Circulating Tumor Cells as a Marker of Hormonally Responsive Prostate Cancer
Authors: Miyamoto David T. , Lee Richard J. , Stott Shannon L. , Ting David T. , Wittner Ben S. , Ulman Matthew , Smas Malgorzata E. , Lord Jenna B. , Brannigan Brian W. , Trautwein Julie , Bander Neil H. , Wu Chin-Lee , Sequist Lecia V. , Smith Matthew R. , Ramaswamy Sridhar , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

PDF file - 3.8MB, Supplemental Figures. (S1) AR transcriptional signature derivation and validation. (S2) Time course for immunofluorescence assay for AR signaling. (S3) Time course for multiparameter single cell immunofluorescence assay for AR signaling applied to VCaP prostate cancer cells. (S4) Immunofluorescence images of LNCaP cells treated with R1881 or bicalutamide and captured on HB CTC-chip. (S5) Enumeration of CTCs in healthy donor controls, male patients without cancer, and metastatic prostate cancer patients. (S6) Kaplan-Meier survival curves for overall survival in patients treated with abiraterone acetate according to increase in % AR-on CTCs and PSA response.
Supplementary Table 6 from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

XLS file - 75K
Supplementary Table 1 from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

XLS file - 15.2MB
Supplementary Table 2 from DDX5 Regulates DNA Replication and Is Required for Cell Proliferation in a Subset of Breast Cancer Cells
Authors: Mazurek Anthony , Luo Weijun , Krasnitz Alexander , Hicks James , Powers R. Scott , Stillman Bruce
Published: April 2023

PDF file - 47K, This file contains supplementary Table 2 that has a list of genes identified in the screen that scored for the plasmid stability assay.
Supporting Information from A Functional Cancer Genomics Screen Identifies a Druggable Synthetic Lethal Interaction between MSH3 and PRKDC
Authors: Dietlein Felix , Thelen Lisa , Jokic Mladen , Jachimowicz Ron D. , Ivan Laura , Knittel Gero , Leeser Uschi , van Oers Johanna , Edelmann Winfried , Heukamp Lukas C. , Reinhardt H. Christian
Published: April 2023

PDF file 129K, Supplementary Methods provide additional information on experimental techniques and data analysis. Supplementary Legends describe supplementary figures S1-S10 and supplementary table S1
Supplementary Figure 1 from Elucidating Distinct Roles for NF1 in Melanomagenesis
Authors: Maertens Ophélia , Johnson Bryan , Hollstein Pablo , Frederick Dennie T. , Cooper Zachary A. , Messiaen Ludwine , Bronson Roderick T. , McMahon Martin , Granter Scott , Flaherty Keith , Wargo Jennifer A. , Marais Richard , Cichowski Karen
Published: April 2023

PDF file - 96K, Schwann cells (RT4) expressing an inducible RAF construct (∆RAF:ER) were treated with the indicated concentrations of hydroxy-tamoxifen (4-OHT) in the absence and presence of a short hairpin RNA (shRNA) specific for NF1. RAS-GTP levels were assessed using a RAS pulldown assay. Immunoblots on total cell lysates are shown.
Supplementary Tables S1 - S8 from Discovery of Biomarkers Predictive of GSI Response in Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma
Authors: Stoeck Alexander , Lejnine Serguei , Truong Andrew , Pan Li , Wang Hongfang , Zang Chongzhi , Yuan Jing , Ware Chris , MacLean John , Garrett-Engele Philip W. , Kluk Michael , Laskey Jason , Haines Brian B. , Moskaluk Christopher , Zawel Leigh , Fawell Stephen , Gilliland Gary , Zhang Theresa , Kremer Brandon E. , Knoechel Birgit , Bernstein Bradley E. , Pear Warren S. , Liu X. Shirley , Aster Jon C. , Sathyanarayanan Sriram
Published: April 2023

Table S1: Analysis of Notch gene rearrangements in triple negative breast cancer subtypes. Table S2: Genes whose expression correlates with Notch gene-rearrangement status in cancer cell lines. Table S3: Genes whose expression correlates with Notch gene-rearrangement in triple negative breast cancer. Table S4. Novel mutations identified in the NRR and PEST domains of NOTCH1 in solid tumors. Table S5: Notch NRR and PEST domain mutation frequency. Table S6: NOTCH1 mutational status, N1-ICD levels, MYC expression in Adenoid Cystic Carcinoma models. Table S7: Primary antibodies. Table S8: RT-PCR Primers.
Supplementary Table S3 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map
Authors: Martins Maria M. , Zhou Alicia Y. , Corella Alexandra , Horiuchi Dai , Yau Christina , Rakhshandehroo Taha , Gordan John D. , Levin Rebecca S. , Johnson Jeff , Jascur John , Shales Mike , Sorrentino Antonio , Cheah Jaime , Clemons Paul A. , Shamji Alykhan F. , Schreiber Stuart L. , Krogan Nevan J. , Shokat Kevan M. , McCormick Frank , Goga Andrei , Bandyopadhyay Sourav
Published: April 2023

Supplementary Table S3. Chemical-genetic interaction scores derived in this study
Supplementary Figures S1 - S7 from Discovery of Biomarkers Predictive of GSI Response in Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma
Authors: Stoeck Alexander , Lejnine Serguei , Truong Andrew , Pan Li , Wang Hongfang , Zang Chongzhi , Yuan Jing , Ware Chris , MacLean John , Garrett-Engele Philip W. , Kluk Michael , Laskey Jason , Haines Brian B. , Moskaluk Christopher , Zawel Leigh , Fawell Stephen , Gilliland Gary , Zhang Theresa , Kremer Brandon E. , Knoechel Birgit , Bernstein Bradley E. , Pear Warren S. , Liu X. Shirley , Aster Jon C. , Sathyanarayanan Sriram
Published: April 2023

S1: NOTCH gene rearrangement in breast cancer cell lines and human breast tumors. S2: NOTCH gene rearrangement and sensitivity to MRK-003. S3: HES4 expression is associated with NOTCH gene-rearrangement or activating mutation in NOTCH. S4: HES4 expression is a poor prognostic marker in TNBC. S5: Proliferation inhibition by combination therapy with MRK-003 and ERK inhibitor (SCH772984). S6: Effect of MRK-003 treatment on CD44+/CD24 high stem-like cell population. S7: N1ICD level correlates with mutation status and is predictive of MRK-003 response in xenograft models.
Supplementary File 3 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Authors: Brastianos Priscilla K. , Carter Scott L. , Santagata Sandro , Cahill Daniel P. , Taylor-Weiner Amaro , Jones Robert T. , Van Allen Eliezer M. , Lawrence Michael S. , Horowitz Peleg M. , Cibulskis Kristian , Ligon Keith L. , Tabernero Josep , Seoane Joan , Martinez-Saez Elena , Curry William T. , Dunn Ian F. , Paek Sun Ha , Park Sung-Hye , McKenna Aaron , Chevalier Aaron , Rosenberg Mara , Barker Frederick G. , Gill Corey M. , Van Hummelen Paul , Thorner Aaron R. , Johnson Bruce E. , Hoang Mai P. , Choueiri Toni K. , Signoretti Sabina , Sougnez Carrie , Rabin Michael S. , Lin Nancy U. , Winer Eric P. , Stemmer-Rachamimov Anat , Meyerson Matthew , Garraway Levi , Gabriel Stacey , Lander Eric S. , Beroukhim Rameen , Batchelor Tracy T. , Baselga José , Louis David N. , Getz Gad , Hahn William C.
Published: April 2023

Supplementary File 3. Detailed plots of the data used for phylogenetic inference in each case. The description for the plots in Supplementary File 3 can be found in the Legend of Supplementary Figure S13-S17.
Supplementary Movie C from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

MOV file 697K, Cell undergoing a segregation error followed by cell death in the daughter cell (see Supplementary Figure 4 for movie stills)
Supplementary Table from Inhibition of KRAS-Driven Tumorigenicity by Interruption of an Autocrine Cytokine Circuit
Authors: Zhu Zehua , Aref Amir R. , Cohoon Travis J. , Barbie Thanh U. , Imamura Yu , Yang Shenghong , Moody Susan E. , Shen Rhine R. , Schinzel Anna C. , Thai Tran C. , Reibel Jacob B. , Tamayo Pablo , Godfrey Jason T. , Qian Zhi Rong , Page Asher N. , Maciag Karolina , Chan Edmond M. , Silkworth Whitney , Labowsky Mary T. , Rozhansky Lior , Mesirov Jill P. , Gillanders William E. , Ogino Shuji , Hacohen Nir , Gaudet Suzanne , Eck Michael J. , Engelman Jeffrey A. , Corcoran Ryan B. , Wong Kwok-Kin , Hahn William C. , Barbie David A.
Published: April 2023

S1 XLSX file 63K, This Supplementary Table contains the results of ORF screen to identify genes that can rescue the suppression of TBK1 in a KRAS-dependent cell line
Supplementary Table 2 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Authors: Wagle Nikhil , Van Allen Eliezer M. , Treacy Daniel J. , Frederick Dennie T. , Cooper Zachary A. , Taylor-Weiner Amaro , Rosenberg Mara , Goetz Eva M. , Sullivan Ryan J. , Farlow Deborah N. , Friedrich Dennis C. , Anderka Kristin , Perrin Danielle , Johannessen Cory M. , McKenna Aaron , Cibulskis Kristian , Kryukov Gregory , Hodis Eran , Lawrence Donald P. , Fisher Sheila , Getz Gad , Gabriel Stacey B. , Carter Scott L. , Flaherty Keith T. , Wargo Jennifer A. , Garraway Levi A.
Published: April 2023

XLSX file 3569K, Change in Cancer Cell Fraction for all SNVs and Indels in All Samples
Supplementary Figure S4 from The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints
Authors: Llosa Nicolas J. , Cruise Michael , Tam Ada , Wicks Elizabeth C. , Hechenbleikner Elizabeth M. , Taube Janis M. , Blosser Richard L. , Fan Hongni , Wang Hao , Luber Brandon S. , Zhang Ming , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Sears Cynthia L. , Anders Robert A. , Pardoll Drew M. , Housseau Franck
Published: April 2023

Supplementary Figure S4. PD-L1 induction on human CRC cell lines.
Supplementary Table and Figure Legends from Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations
Authors: Tirode Franck , Surdez Didier , Ma Xiaotu , Parker Matthew , Le Deley Marie Cécile , Bahrami Armita , Zhang Zhaojie , Lapouble Eve , Grossetête-Lalami Sandrine , Rusch Michael , Reynaud Stéphanie , Rio-Frio Thomas , Hedlund Erin , Wu Gang , Chen Xiang , Pierron Gaelle , Oberlin Odile , Zaidi Sakina , Lemmon Gordon , Gupta Pankaj , Vadodaria Bhavin , Easton John , Gut Marta , Ding Li , Mardis Elaine R. , Wilson Richard K. , Shurtleff Sheila , Laurence Valérie , Michon Jean , Marec-Bérard Perrine , Gut Ivo , Downing James , Dyer Michael , Zhang Jinghui , Delattre Olivier
Published: April 2023

List of supplementary tables and figures.
Supplementary Table 1 from Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia
Authors: Ye Jiangbin , Fan Jing , Venneti Sriram , Wan Ying-Wooi , Pawel Bruce R. , Zhang Ji , Finley Lydia W.S. , Lu Chao , Lindsten Tullia , Cross Justin R. , Qing Guoliang , Liu Zhandong , Simon M. Celeste , Rabinowitz Joshua D. , Thompson Craig B.
Published: April 2023

Knockdown of SHMT2 reduces xenograft growth in vivo.
Supplementary Figure S2 from Rapid Induction of Apoptosis by PI3K Inhibitors Is Dependent upon Their Transient Inhibition of RAS–ERK Signaling
Authors: Will Marie , Qin Alice Can Ran , Toy Weiyi , Yao Zhan , Rodrik-Outmezguine Vanessa , Schneider Claudia , Huang Xiaodong , Monian Prashant , Jiang Xuejun , de Stanchina Elisa , Baselga José , Liu Ningshu , Chandarlapaty Sarat , Rosen Neal
Published: April 2023

PDF file 2251K, Supplementary Figure S2. PI3K, but not AKT or mTOR, is upstream of the ERK signaling pathway. Related to main Figure 2
Supplementary Figure 2 from Discovery of a Mutant-Selective Covalent Inhibitor of EGFR that Overcomes T790M-Mediated Resistance in NSCLC
Authors: Walter Annette O. , Sjin Robert Tjin Tham , Haringsma Henry J. , Ohashi Kadoaki , Sun Jing , Lee Kwangho , Dubrovskiy Aleksandr , Labenski Matthew , Zhu Zhendong , Wang Zhigang , Sheets Michael , St Martin Thia , Karp Russell , van Kalken Dan , Chaturvedi Prasoon , Niu Deqiang , Nacht Mariana , Petter Russell C. , Westlin William , Lin Kevin , Jaw-Tsai Sarah , Raponi Mitch , Van Dyke Terry , Etter Jeff , Weaver Zoe , Pao William , Singh Juswinder , Simmons Andrew D. , Harding Thomas C. , Allen Andrew
Published: April 2023

Supplementary Figure 2 - PDF file 111K, CO-1686 inhibits cell growth in EGFR-mutant erlotinib-resistant cell lines
Supplementary Tables S1-S10 from NUP98–PHF23 Is a Chromatin-Modifying Oncoprotein That Causes a Wide Array of Leukemias Sensitive to Inhibition of PHD Histone Reader Function
Authors: Gough Sheryl M. , Lee Fan , Yang Fan , Walker Robert L. , Zhu Yeulin J. , Pineda Marbin , Onozawa Masahiro , Chung Yang Jo , Bilke Sven , Wagner Elise K. , Denu John M. , Ning Yi , Xu Bowen , Wang Gang Greg , Meltzer Paul S. , Aplan Peter D.
Published: April 2023

XLSX file 368K, Table S1. NP23 Diagnoses. Table S2. Notch1 mutations. Table S3. Leukemic fold change (gene expression). Table S4. Leukemic unions, upregulated genes. Table S5. Leukemic unions, downregulated genes. Table S6. NP23 fold change, gene expression. Table S7. T-cell line ChIP-seq. Table S8. 961C cell line ChIP-seq. Table S9. NP23+H3K4me3 loci versus upregulated genes. Table S10. PCR primers
Supplementary Figures 1 - 9 from Loss of MIG6 Accelerates Initiation and Progression of Mutant Epidermal Growth Factor Receptor–Driven Lung Adenocarcinoma
Authors: Maity Tapan K. , Venugopalan Abhilash , Linnoila Ilona , Cultraro Constance M. , Giannakou Andreas , Nemati Roxanne , Zhang Xu , Webster Joshua D. , Ritt Daniel , Ghosal Sarani , Hoschuetzky Heinz , Simpson R. Mark , Biswas Romi , Politi Katerina , Morrison Deborah K. , Varmus Harold E. , Guha Udayan
Published: April 2023

Supplementary Figure S1. Serial MRI imaging and lung histopathology analyses show rapid tumor progression of mutant EGFR-driven tumorigenesis in Mig6-/- background. Supplementary Figure S2. Representative photomicrographs of CC10rtTA/EGFRL858R/Mig6+/- mouse lungs at early stages of doxycycline treatment show variability of tumor progression. Supplementary Figure S3. Rapid progression of tumorigenesis 7 days after doxycycline induction of mutant EGFR in Mig6-/- mice. Supplementary Figure S4. No loss of heterozygosity (LOH) in lung tumors of Mig6+/- mice. Supplementary Figure S5. QPCR analysis of mRNA expression in lung tumor samples from Mig6+/+, Mig6+/-, and Mig6-/- mice. Supplementary Figure S6. QPCR analysis of mRNA expression in lung samples from Mig6+/+, Mig6+/-, and Mig6-/- mice at early stages of doxycycline treatment. Supplementary Figure S7. MS and MS/MS spectra of Y394/395 containing tryptic peptide identified in MIG6 (gene symbol ERRFI1). Supplementary Figure S8. Specificity of monoclonal antibodies made against wild type and mutant EGFRs. Supplementary Figure S9. Co-localization of (A-B) MIG6 and EEA1, a marker of early endosomes with both WT EGFR and EGFRL858R and (C-D) LAMP1, a late endosomal marker with WT EGFR, but not EGFRL858R.
Supplementary Figures S1 - S5 from Heterogeneity Underlies the Emergence of EGFRT790 Wild-Type Clones Following Treatment of T790M-Positive Cancers with a Third-Generation EGFR Inhibitor
Authors: Piotrowska Zofia , Niederst Matthew J. , Karlovich Chris A. , Wakelee Heather A. , Neal Joel W. , Mino-Kenudson Mari , Fulton Linnea , Hata Aaron N. , Lockerman Elizabeth L. , Kalsy Anuj , Digumarthy Subba , Muzikansky Alona , Raponi Mitch , Garcia Angel R. , Mulvey Hillary E. , Parks Melissa K. , DiCecca Richard H. , Dias-Santagata Dora , Iafrate A. John , Shaw Alice T. , Allen Andrew R. , Engelman Jeffrey A. , Sequist Lecia V.
Published: April 2023

Supplementary Figure S1. CONSORT diagram. Supplementary Figure S2. Histologic analysis of the pre-rociletinib biopsy from patient 12 (H&E 400x, left panel) demonstrates characteristic adenocarcinoma with an open chromatin pattern, ample cytoplasm and variable cell density. Supplementary Figure S3. Panel A. The nucleotide sequences of single-cell cloning analysis for six additional clones isolated from the afatinib-resistant cell line MGH176 are shown (see also figure 2B). Panel B. Summary of single-clone analyses performed on two additional patient-derived cell lines. Supplementary Figure S4. Longitudinal quantitative analyses of EGFR mutations in the ctDNA are shown for patients 8 (panel A), 6 (panel B) and 3 (panel C). Supplementary Figure S5. Scatterplot showing the relationship between the allelic fraction of T790M (calculated as the percent of T790M alleles/percent of EGFR activating mutation alleles as quantified by allele-specific PCR or NGS) in the pre-rociletinib tumor biopsy (y-axis) and in the pre-rociletinib plasma (as quantified by BEAMing) (x-axis).
Supplementary Tables from First-in-Humans Trial of an RNA Interference Therapeutic Targeting VEGF and KSP in Cancer Patients with Liver Involvement
Authors: Tabernero Josep , Shapiro Geoffrey I. , LoRusso Patricia M. , Cervantes Andres , Schwartz Gary K. , Weiss Glen J. , Paz-Ares Luis , Cho Daniel C. , Infante Jeffrey R. , Alsina Maria , Gounder Mrinal M. , Falzone Rick , Harrop Jamie , White Amy C. Seila , Toudjarska Iva , Bumcrot David , Meyers Rachel E. , Hinkle Gregory , Svrzikapa Nenad , Hutabarat Renta M. , Clausen Valerie A. , Cehelsky Jeffrey , Nochur Saraswathy V. , Gamba-Vitalo Christina , Vaishnaw Akshay K. , Sah Dinah W.Y. , Gollob Jared A. , Burris Howard A.
Published: April 2023

Supplementary Tables PDF file - 67K, Includes data showing effect of ALN-VSP on spleen in non-human primates, tumor response data from the Phase I trial, and safety data (including adverse events and dose-limiting toxicities) from the Phase I trial
Supplementary Table 2 from Brain Tumor Cells in Circulation Are Enriched for Mesenchymal Gene Expression
Authors: Sullivan James P. , Nahed Brian V. , Madden Marissa W. , Oliveira Samantha M. , Springer Simeon , Bhere Deepak , Chi Andrew S. , Wakimoto Hiroaki , Rothenberg S. Michael , Sequist Lecia V. , Kapur Ravi , Shah Khalid , Iafrate A. John , Curry William T. , Loeffler Jay S. , Batchelor Tracy T. , Louis David N. , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

Tumor genotypes and CTC frequency
Supplementary Figure 1 from Efficacy of Intermittent Combined RAF and MEK Inhibition in a Patient with Concurrent BRAF- and NRAS-Mutant Malignancies
Authors: Abdel-Wahab Omar , Klimek Virginia M. , Gaskell Alisa A. , Viale Agnes , Cheng Donavan , Kim Eunhee , Rampal Raajit , Bluth Mark , Harding James J. , Callahan Margaret K. , Merghoub Taha , Berger Michael F. , Solit David B. , Rosen Neal , Levine Ross L. , Chapman Paul B.
Published: April 2023

PDF file 88K, Spleen length size
Supplementary Table S6 from Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma
Authors: Saha Supriya K. , Gordan John D. , Kleinstiver Benjamin P. , Vu Phuong , Najem Mortada S. , Yeo Jia-Chi , Shi Lei , Kato Yasutaka , Levin Rebecca S. , Webber James T. , Damon Leah J. , Egan Regina K. , Greninger Patricia , McDermott Ultan , Garnett Mathew J. , Jenkins Roger L. , Rieger-Christ Kimberly M. , Sullivan Travis B. , Hezel Aram F. , Liss Andrew S. , Mizukami Yusuke , Goyal Lipika , Ferrone Cristina R. , Zhu Andrew X. , Joung J. Keith , Shokat Kevan M. , Benes Cyril H. , Bardeesy Nabeel
Published: April 2023

Cas9 and sgRNA expression plasmids.
Supplementary Table 2 from A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma
Authors: Mirabello Lisa , Koster Roelof , Moriarity Branden S. , Spector Logan G. , Meltzer Paul S. , Gary Joy , Machiela Mitchell J. , Pankratz Nathan , Panagiotou Orestis A. , Largaespada David , Wang Zhaoming , Gastier-Foster Julie M. , Gorlick Richard , Khanna Chand , de Toledo Silvia Regina Caminada , Petrilli Antonio S. , Patiño-Garcia Ana , Sierrasesúmaga Luis , Lecanda Fernando , Andrulis Irene L. , Wunder Jay S. , Gokgoz Nalan , Serra Massimo , Hattinger Claudia , Picci Piero , Scotlandi Katia , Flanagan Adrienne M. , Tirabosco Roberto , Amary Maria Fernanda , Halai Dina , Ballinger Mandy L. , Thomas David M. , Davis Sean , Barkauskas Donald A. , Marina Neyssa , Helman Lee , Otto George M. , Becklin Kelsie L. , Wolf Natalie K. , Weg Madison T. , Tucker Margaret , Wacholder Sholom , Fraumeni Joseph F. , Caporaso Neil E. , Boland Joseph F. , Hicks Belynda D. , Vogt Aurelie , Burdett Laurie , Yeager Meredith , Hoover Robert N. , Chanock Stephen J. , Savage Sharon A.
Published: April 2023

Relationship of variables to metastasis at diagnosis in the discovery set.
Supplementary Figure S1. Copy Number Alteration analysis of human prostate cancer confirms loss of PTEN and TP53 genes as a genetic hallmark of metastatic prostate cancer. from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure S1. Copy Number Alteration analysis of human prostate cancer confirms loss of PTEN and TP53 genes as a genetic hallmark of metastatic prostate cancer. (A) Co-deletion frequency for PTEN and TP53 in metastatic and primary prostate cancer samples. (B) Co-deletion frequency for PTEN and TP53 in metastatic and primary prostate cancer samples. (C) Co-deletion frequency for PTEN and TP53 in metastatic prostate cancer samples . (D) Gene maps of the conditional alleles used for ablation of Pten/ Trp53 genes and activation of tdTomato. Cre leads to recombination of loxP sites in the Pten/Trp53 genes and excision of a STOP cassette that leads to activation of the fluorescence protein tdTomato. (E) Analysis of tdTomato-positive cells using Guava flow cytometry system show that AdCre leads to activation of tdTomato in over 95% percent of cells without the need for selection. (F) Activation of tdTomato can be easily visualized using fluorescence microscopy.