bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S1-S10 and Table S1 from Replication Stress Leading to Apoptosis within the S-phase Contributes to Synergism between Vorinostat and AZD1775 in HNSCC Harboring High-Risk TP53 Mutation
Authors: Tanaka Noriaki , Patel Ameeta A. , Tang Lin , Silver Natalie L. , Lindemann Antje , Takahashi Hideaki , Jaksik Roman , Rao Xiayu , Kalu Nene N. , Chen Tseng-Cheng , Wang Jiping , Frederick Mitchell J. , Johnson Faye , Gleber-Netto Frederico O. , Fu Siqing , Kimmel Marek , Wang Jing , Hittelman Walter N. , Pickering Curtis R. , Myers Jeffrey N. , Osman Abdullah A.
Published: April 2023

Supplementary Figure S1. Synergistic effects of vorinostat and AZD1775 in vitro in established isogenic pair HNSCC cell lines with known TP53 mutational status. Supplementary Figure S2. Synergistic effects of vorinostat and AZD1775 in vitro in various established HNSCC cell lines with known TP53 mutational status. Supplementary Figure S3. Laser scanning confocal microscopy showing stress-induced membrane blebbing prior to apoptosis in selected populations of PCI13-G245D cells. Supplementary Figure S4. Combination of vorinostat and AZD1775 is associated with subsequent accumulation of cells in G2/M phase in HNSCC mutp53 cells. Supplementary Figure S5. Vorinostat interacts synergistically with AZD1775 in HNSCC to induce markers of DNA damge, replication stress and apoptosis. Supplementary Figure S6. Correlation between overall survival and expression levels of genes regulated by vorinostat alone or in combination with AZD1775 in HNSCC TCGA dataset. Supplementary Figure S7. Proteomic profiling of HNSCC mutant p53 cells treated with vorinostat and AZD1775 identifies proteins involved in cell cycle regulation. Supplementary Figure S8. Tumor volume growth curves for individual mice in each treatment group. Supplementary Figure S9. Immunostaining of p21, PCNA, RRM2 and survivin in tumor of HNSCC oral xenografts mice. Supplementary Figure S10. Combination of vorinostat and AZD1775 is well tolerated in an orthotopic mouse model of oral cancer. Supplementary Table S1. Combination index of vorinostat in combination with AZD1775 in various HNSCC cell lines.
Table S1 from Neurotensin Receptor 1 Antagonist SR48692 Improves Response to Carboplatin by Enhancing Apoptosis and Inhibiting Drug Efflux in Ovarian Cancer
Authors: Liu Jin , Agopiantz Mikaël , Poupon Joël , Wu Zherui , Just Pierre-Alexandre , Borghese Bruno , Ségal-Bendirdjian Evelyne , Gauchotte Guillaume , Gompel Anne , Forgez Patricia
Published: April 2023

Clinical and histological characteristics of the patients included in our article.
Figure S2 from Dichotomous ALK-IHC Is a Better Predictor for ALK Inhibition Outcome than Traditional ALK-FISH in Advanced Non–Small Cell Lung Cancer
Authors: van der Wekken A.J. , Pelgrim R. , 't Hart N. , Werner N. , Mastik M.F. , Hendriks L. , van der Heijden E.H.F.M. , Looijen-Salamon M. , de Langen A.J. , Staal-van den Brekel J. , Riemersma S. , van den Borne B.E. , Speel E.J.M. , Dingemans A-M.C. , Hiltermann T.J.N. , van den Berg A. , Timens W. , Schuuring E. , Groen H.J.M.
Published: April 2023

Percentage of nuclei considered as ALK positive based on ALK-FISH in the screening cohort.
Supplementary Table 3 from A Phase 2/3 Multicenter, Randomized, Open-Label Study to Compare the Efficacy and Safety of Lenalidomide Versus Investigator's Choice in Patients with Relapsed or Refractory Diffuse Large B-Cell Lymphoma
Authors: Czuczman Myron S. , Trněný Marek , Davies Andrew , Rule Simon , Linton Kim M. , Wagner-Johnston Nina , Gascoyne Randy D. , Slack Graham W. , Brousset Pierre , Eberhard David A. , Hernandez-Ilizaliturri Francisco J. , Salles Gilles , Witzig Thomas E. , Zinzani Pier Luigi , Wright George W. , Staudt Louis M. , Yang Yandan , Williams P. Mickey , Lih Chih-Jian , Russo Jacqueline , Thakurta Anjan , Hagner Patrick , Fustier Pierre , Song Dale , Lewis Ian D.
Published: April 2023

Grade 3/4 Treatment-Emergent Adverse Events Reported in {greater than or equal to}5% of Patients (Safety Population)
Supplementary Figure 1 from A Phase 2/3 Multicenter, Randomized, Open-Label Study to Compare the Efficacy and Safety of Lenalidomide Versus Investigator's Choice in Patients with Relapsed or Refractory Diffuse Large B-Cell Lymphoma
Authors: Czuczman Myron S. , Trněný Marek , Davies Andrew , Rule Simon , Linton Kim M. , Wagner-Johnston Nina , Gascoyne Randy D. , Slack Graham W. , Brousset Pierre , Eberhard David A. , Hernandez-Ilizaliturri Francisco J. , Salles Gilles , Witzig Thomas E. , Zinzani Pier Luigi , Wright George W. , Staudt Louis M. , Yang Yandan , Williams P. Mickey , Lih Chih-Jian , Russo Jacqueline , Thakurta Anjan , Hagner Patrick , Fustier Pierre , Song Dale , Lewis Ian D.
Published: April 2023

DLC-001 Study Design (CONSORT diagram)
Supplemental Figure Legends from Fractionated Radiation Therapy Stimulates Antitumor Immunity Mediated by Both Resident and Infiltrating Polyclonal T-cell Populations when Combined with PD-1 Blockade
Authors: Dovedi Simon J. , Cheadle Eleanor J. , Popple Amy L. , Poon Edmund , Morrow Michelle , Stewart Ross , Yusko Erik C. , Sanders Catherine M. , Vignali Marissa , Emerson Ryan O. , Robins Harlan S. , Wilkinson Robert W. , Honeychurch Jamie , Illidge Timothy M.
Published: April 2023

Figure legends for Supplemental Figures 1-6
Supplementary Data from Plasma HER2 (ERBB2) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer
Authors: Siravegna Giulia , Sartore-Bianchi Andrea , Nagy Rebecca J. , Raghav Kanwal , Odegaard Justin I. , Lanman Richard B. , Trusolino Livio , Marsoni Silvia , Siena Salvatore , Bardelli Alberto
Published: April 2023

Supp. Table 2 ROC analysis to determine adjusted plasma copy number cutoff
Figure S3 from Cross-talk between T Cells and Hematopoietic Stem Cells during Adoptive Cellular Therapy for Malignant Glioma
Authors: Wildes Tyler J. , Grippin Adam , Dyson Kyle A. , Wummer Brandon M. , Damiani David J. , Abraham Rebecca S. , Flores Catherine T. , Mitchell Duane A.
Published: April 2023

HSPCs proliferate and differentiate into antigen-presenting cells in the presence of T cell-released soluble factors.
Supplemental Data from A Phase II Study of Dovitinib in Patients with Recurrent or Metastatic Adenoid Cystic Carcinoma
Authors: Dillon Patrick M. , Petroni Gina R. , Horton Bethany J. , Moskaluk Christopher A. , Fracasso Paula M. , Douvas Michael G. , Varhegyi Nikole , Zaja-Milatovic Snjezana , Thomas Christopher Y.
Published: April 2023

Methodology and results for exploratory aims, FISH, IHC and quality of life. SUPPLEMENTAL FIGURE 1: Change point analysis including a second inflection point in calculation of average slope of 34 evaluable patients. Supplemental Figure 2: First, last, and difference between first and last measurements for Fact-G and its components. Supplemental Figure 3: QOL trajectory for each patient by FACT-G analysis. Supplemental table 1: Mutation analysis as provided by Foundation Medicine for a subset of patients with residual tissue available for targeted mutation profiling. Table 2: Basic statistics for first, last, and difference between first and last measurements of Fact-G and its components Supplemental Figure 3: QOL trajectory for each patient by FACT-G analysis. Supplemental Table 3: Summary of adverse event counts for all consented patients. Supplemental Table 4: PET response at day 12 PET scan compared with baseline PET scans.
Supplementary Table S1 from Inhibition of BUB1 Kinase by BAY 1816032 Sensitizes Tumor Cells toward Taxanes, ATR, and PARP Inhibitors In Vitro and In Vivo
Authors: Siemeister Gerhard , Mengel Anne , Fernández-Montalván Amaury E. , Bone Wilhelm , Schröder Jens , Zitzmann-Kolbe Sabine , Briem Hans , Prechtl Stefan , Holton Simon J. , Mönning Ursula , von Ahsen Oliver , Johanssen Sandra , Cleve Arwed , Pütter Vera , Hitchcock Marion , von Nussbaum Franz , Brands Michael , Ziegelbauer Karl , Mumberg Dominik
Published: April 2023

BAY 1816032 kinase selectivity profile
Supplementary Table S2 from Homeobox B9 Mediates Resistance to Anti-VEGF Therapy in Colorectal Cancer Patients
Authors: Carbone Carmine , Piro Geny , Simionato Francesca , Ligorio Francesca , Cremolini Chiara , Loupakis Fotios , Alì Greta , Rossini Daniele , Merz Valeria , Santoro Raffaela , Zecchetto Camilla , Zanotto Marco , Di Nicolantonio Federica , Bardelli Alberto , Fontanini Gabriella , Tortora Giampaolo , Melisi Davide
Published: April 2023

Supplementary Table S2. Compliance with REMARK guidelines
Supplementary Table S1 from Homeobox B9 Mediates Resistance to Anti-VEGF Therapy in Colorectal Cancer Patients
Authors: Carbone Carmine , Piro Geny , Simionato Francesca , Ligorio Francesca , Cremolini Chiara , Loupakis Fotios , Alì Greta , Rossini Daniele , Merz Valeria , Santoro Raffaela , Zecchetto Camilla , Zanotto Marco , Di Nicolantonio Federica , Bardelli Alberto , Fontanini Gabriella , Tortora Giampaolo , Melisi Davide
Published: April 2023

Supplementary Table S1. Patient characteristics
Supplementary Materials and Methods from Homeobox B9 Mediates Resistance to Anti-VEGF Therapy in Colorectal Cancer Patients
Authors: Carbone Carmine , Piro Geny , Simionato Francesca , Ligorio Francesca , Cremolini Chiara , Loupakis Fotios , Alì Greta , Rossini Daniele , Merz Valeria , Santoro Raffaela , Zecchetto Camilla , Zanotto Marco , Di Nicolantonio Federica , Bardelli Alberto , Fontanini Gabriella , Tortora Giampaolo , Melisi Davide
Published: April 2023

Supplementary Materials and Methods
Supplementary Dataset 2 from Matrix Screen Identifies Synergistic Combination of PARP Inhibitors and Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibitors in Ewing Sarcoma
Authors: Heske Christine M. , Davis Mindy I. , Baumgart Joshua T. , Wilson Kelli , Gormally Michael V. , Chen Lu , Zhang Xiaohu , Ceribelli Michele , Duveau Damien Y. , Guha Rajarshi , Ferrer Marc , Arnaldez Fernanda I. , Ji Jiuping , Tran Huong-Lan , Zhang Yiping , Mendoza Arnulfo , Helman Lee J. , Thomas Craig J.
Published: April 2023

Metabolic outcomes
Supplementary Figure S4 from PD-L1 Is a Therapeutic Target of the Bromodomain Inhibitor JQ1 and, Combined with HLA Class I, a Promising Prognostic Biomarker in Neuroblastoma
Authors: Melaiu Ombretta , Mina Marco , Chierici Marco , Boldrini Renata , Jurman Giuseppe , Romania Paolo , D'Alicandro Valerio , Benedetti Maria C. , Castellano Aurora , Liu Tao , Furlanello Cesare , Locatelli Franco , Fruci Doriana
Published: April 2023

This figure includes distribution of PD-1+ and LAG-3+ lymphocytes in lymphoid aggregates (A). B-D Kaplan-Meier curves of OS according to the density of PD-1+ or LAG-3+ lymphocytes alone (B), or in combination with PD-L1+ tumor cells (C), or HLA-I+ tumor cells (D). E-H, Kaplan-Meier curves of RFS (E and G) and EFS (F and H) according to the combined PD-L1+ and HLA-I+ tumor-cell densities with tumor infiltrating PD-1+ lymphocytes (E and F) or LAG-3+ lymphocytes (G and H).
Supplementary Figure S3 from PD-L1 Is a Therapeutic Target of the Bromodomain Inhibitor JQ1 and, Combined with HLA Class I, a Promising Prognostic Biomarker in Neuroblastoma
Authors: Melaiu Ombretta , Mina Marco , Chierici Marco , Boldrini Renata , Jurman Giuseppe , Romania Paolo , D'Alicandro Valerio , Benedetti Maria C. , Castellano Aurora , Liu Tao , Furlanello Cesare , Locatelli Franco , Fruci Doriana
Published: April 2023

This figure includes Kaplan-Meier curves of RFS (A, C and E) and EFS (B, D and F) according to the density of the combined PD-L1+ and HLA-I+ tumor-cell densities with tumor infiltrating CD3+ T cells (A and B), tumor infiltrating CD4+ T cells (C and D), and tumor infiltrating CD8+ T cells (E and F).
Supplementary Figure S1 from PD-L1 Is a Therapeutic Target of the Bromodomain Inhibitor JQ1 and, Combined with HLA Class I, a Promising Prognostic Biomarker in Neuroblastoma
Authors: Melaiu Ombretta , Mina Marco , Chierici Marco , Boldrini Renata , Jurman Giuseppe , Romania Paolo , D'Alicandro Valerio , Benedetti Maria C. , Castellano Aurora , Liu Tao , Furlanello Cesare , Locatelli Franco , Fruci Doriana
Published: April 2023

This figures includes (A-D) representative examples of PD-L1+ (A), HLA-I+ (B), PD-1+ (C) and LAG3+ (D) cell staining in human tonsil sections; E and F, Kaplan-Meier curves show the duration of RFS (E) and EFS (F) according to the PD-L1+ and HLA-I+ tumor-cell densities; G and H, Kaplan-Meier curves of RFS (G) and EFS (H) according to the combined PD-L1+ and HLA-I+ tumor-cell densities. (I), density plot of PD-L1+ tumor cells in neuroblastoma samples.
Supplemental Table 1 from A Combination CDK4/6 and IGF1R Inhibitor Strategy for Ewing Sarcoma
Authors: Guenther Lillian M. , Dharia Neekesh V. , Ross Linda , Conway Amy , Robichaud Amanda L. , Catlett Jerrel L. , Wechsler Caroline S. , Frank Elizabeth S. , Goodale Amy , Church Alanna J. , Tseng Yuen-Yi , Guha Rajarshi , McKnight Crystal G. , Janeway Katherine A. , Boehm Jesse S. , Mora Jaume , Davis Mindy I. , Alexe Gabriela , Piccioni Federica , Stegmaier Kimberly
Published: April 2023

Related to Figure 1
Supplemental Methods from A Combination CDK4/6 and IGF1R Inhibitor Strategy for Ewing Sarcoma
Authors: Guenther Lillian M. , Dharia Neekesh V. , Ross Linda , Conway Amy , Robichaud Amanda L. , Catlett Jerrel L. , Wechsler Caroline S. , Frank Elizabeth S. , Goodale Amy , Church Alanna J. , Tseng Yuen-Yi , Guha Rajarshi , McKnight Crystal G. , Janeway Katherine A. , Boehm Jesse S. , Mora Jaume , Davis Mindy I. , Alexe Gabriela , Piccioni Federica , Stegmaier Kimberly
Published: April 2023

Supplemental Experimental Methods
Supplemental Figure Legends from A Combination CDK4/6 and IGF1R Inhibitor Strategy for Ewing Sarcoma
Authors: Guenther Lillian M. , Dharia Neekesh V. , Ross Linda , Conway Amy , Robichaud Amanda L. , Catlett Jerrel L. , Wechsler Caroline S. , Frank Elizabeth S. , Goodale Amy , Church Alanna J. , Tseng Yuen-Yi , Guha Rajarshi , McKnight Crystal G. , Janeway Katherine A. , Boehm Jesse S. , Mora Jaume , Davis Mindy I. , Alexe Gabriela , Piccioni Federica , Stegmaier Kimberly
Published: April 2023

Legends for Supplemental Figures 1-5
Movie S3 from Rare but Recurrent ROS1 Fusions Resulting From Chromosome 6q22 Microdeletions are Targetable Oncogenes in Glioma
Authors: Davare Monika A. , Henderson Jacob J. , Agarwal Anupriya , Wagner Jacob P. , Iyer Sudarshan R. , Shah Nameeta , Woltjer Randy , Somwar Romel , Gilheeney Stephen W. , DeCarvalo Ana , Mikkelson Tom , Van Meir Erwin G. , Ladanyi Marc , Druker Brian J.
Published: April 2023

U118MG spheroid treated with 50nM lorlatinib for 72 hrs
Movie S1 from Rare but Recurrent ROS1 Fusions Resulting From Chromosome 6q22 Microdeletions are Targetable Oncogenes in Glioma
Authors: Davare Monika A. , Henderson Jacob J. , Agarwal Anupriya , Wagner Jacob P. , Iyer Sudarshan R. , Shah Nameeta , Woltjer Randy , Somwar Romel , Gilheeney Stephen W. , DeCarvalo Ana , Mikkelson Tom , Van Meir Erwin G. , Ladanyi Marc , Druker Brian J.
Published: April 2023

Vehicle Treated U118MG Spheroid (72 hrs)
Supplementary Tables S1-S7 from Novel MYBL1 Gene Rearrangements with Recurrent MYBL1–NFIB Fusions in Salivary Adenoid Cystic Carcinomas Lacking t(6;9) Translocations
Authors: Mitani Yoshitsugu , Liu Bin , Rao Pulivarthi H. , Borra Vishnupriya J. , Zafereo Mark , Weber Randal S. , Kies Merrill , Lozano Guillermina , Futreal P. Andrew , Caulin Carlos , El-Naggar Adel K.
Published: April 2023

Supplementary Table S1. Sample description of Adenoid cystic carcinoma in this study. Supplementary Table S2. Somatic mutations identified in 21 Adenoid cystic carcinomas by WGS. Supplementary Table S3. Identification of fusion genes by whole genome sequencing in ACCs. Supplementary Table S4. PCR Primer information. Supplementary Table S5. MYB or MYBL1 fusion information in expression array set. Supplementary Table S6. Gene set enrichment analysis (GSEA) of MYB/MYBL1-NFIB fusions in ACC. Supplementary Table S7. Clinicopathologic and MYB/MYBL1 alterations in salivary adenoid cystic carcinoma.
Figure S1-3, Table S1-4 from Large-scale Circulating microRNA Profiling for the Liquid Biopsy of Prostate Cancer
Authors: Urabe Fumihiko , Matsuzaki Juntaro , Yamamoto Yusuke , Kimura Takahiro , Hara Tomohiko , Ichikawa Makiko , Takizawa Satoko , Aoki Yoshiaki , Niida Shumpei , Sakamoto Hiromi , Kato Ken , Egawa Shin , Fujimoto Hiroyuki , Ochiya Takahiro
Published: April 2023

Figure S1-3, Table S1-4
Table S2 from Lymphotoxin-β Interacts with Methylated EGFR to Mediate Acquired Resistance to Cetuximab in Head and Neck Cancer
Authors: Hsu Dennis Shin-Shian , Hwang Wei-Lun , Yuh Chiou-Hwa , Chu Chen-Hsi , Ho Yang-Hui , Chen Pon-Bo , Lin Han-Syuan , Lin Hua-Kuo , Wu Shih-Pei , Lin Chih-Yi , Hsu Wen-Hao , Lan Hsin-Yi , Wang Hsiao-Jung , Tai Shyh-Kuan , Hung Mien-Chie , Yang Muh-Hwa
Published: April 2023

S2A: Sequence of primers used in real-time PCR, ChIP and sequencing; S2B: List of proteins tested by antibodies and characteristics of the corresponding antibodies
Supplementary Figure Legends from The PARP Inhibitor Veliparib Can Be Safely Added to Bendamustine and Rituximab and Has Preliminary Evidence of Activity in B-Cell Lymphoma
Authors: Soumerai Jacob D. , Zelenetz Andrew D. , Moskowitz Craig H. , Palomba M. Lia , Hamlin Paul A. , Noy Ariela , Straus David J. , Moskowitz Alison J. , Younes Anas , Matasar Matthew J. , Horwitz Steven M. , Portlock Carol S. , Konner Jason A. , Gounder Mrinal M. , Hyman David M. , Voss Martin H. , Fury Matthew G. , Gajria Devika , Carvajal Richard D. , Ho Alan L. , Beumer Jan H. , Kiesel Brian , Zhang Zhigang , Chen Alice , Little Richard F. , Jarjies Christine , Dang Thu O. , France Fallon , Mishra Nishant , Gerecitano John F.
Published: April 2023

Supplementary Figure Legends
Figure S1 from Lymphotoxin-β Interacts with Methylated EGFR to Mediate Acquired Resistance to Cetuximab in Head and Neck Cancer
Authors: Hsu Dennis Shin-Shian , Hwang Wei-Lun , Yuh Chiou-Hwa , Chu Chen-Hsi , Ho Yang-Hui , Chen Pon-Bo , Lin Han-Syuan , Lin Hua-Kuo , Wu Shih-Pei , Lin Chih-Yi , Hsu Wen-Hao , Lan Hsin-Yi , Wang Hsiao-Jung , Tai Shyh-Kuan , Hung Mien-Chie , Yang Muh-Hwa
Published: April 2023

Generation and characterization of the cetuximab-resistant head and neck cancer cells
Supplemental Figure 2 from A Phase I/Ib Study of Enzalutamide Alone and in Combination with Endocrine Therapies in Women with Advanced Breast Cancer
Authors: Schwartzberg Lee S. , Yardley Denise A. , Elias Anthony D. , Patel Manish , LoRusso Patricia , Burris Howard A. , Gucalp Ayca , Peterson Amy C. , Blaney Martha E. , Steinberg Joyce L. , Gibbons Jacqueline A. , Traina Tiffany A.
Published: April 2023

Relationships between aromatase inhibitor plasma exposures (AUCtau) and concentrations of (A, B) estradiol and (C, D) estrone in individual patients. Red lines indicate expected estrogen levels with anastrozole or exemestane use
Supplementary Tables 1-6 from MET-Oncogenic and JAK2-Inactivating Alterations Are Independent Factors That Affect Regulation of PD-L1 Expression in Lung Cancer
Authors: Saigi Maria , Alburquerque-Bejar Juan J. , Mc Leer-Florin Anne , Pereira Carolina , Pros Eva , Romero Octavio A. , Baixeras Nuria , Esteve-Codina Anna , Nadal Ernest , Brambilla Elisabeth , Sanchez-Cespedes Montse
Published: April 2023

Supplementary Table 1. Characteristics of tumors and patients included in the analysis; Supplementary Table 2. List of antibodies and treatments used; Supplementary Table 3. Sequence of primers used for real-time quantitative PCR and size of amplified; Supplementary Table 4. Alterations at the indicated genes in lung cancer cell lines. cell carcinomas; SCLC, small Supplementary Table S5: RNA-sequencing report; Supplementary Table S6: List of genes from the MET-Activated (MET-Sign) and Interferon Treatment (IFN-
Table S6 from PDK1 Mediates NOTCH1-Mutated Head and Neck Squamous Carcinoma Vulnerability to Therapeutic PI3K/mTOR Inhibition
Authors: Sambandam Vaishnavi , Frederick Mitchell J. , Shen Li , Tong Pan , Rao Xiayu , Peng Shaohua , Singh Ratnakar , Mazumdar Tuhina , Huang Chenfei , Li Qiuli , Pickering Curtis R. , Myers Jeffery N. , Wang Jing , Johnson Faye M.
Published: April 2023

Table S6. Combination index (CI) values for the combination of GSK2126458 and γ-secretase inhibitors at the corresponding fraction affected (Fa) from the experimental values for four NOTCH1WT cell lines
Table S5 from PDK1 Mediates NOTCH1-Mutated Head and Neck Squamous Carcinoma Vulnerability to Therapeutic PI3K/mTOR Inhibition
Authors: Sambandam Vaishnavi , Frederick Mitchell J. , Shen Li , Tong Pan , Rao Xiayu , Peng Shaohua , Singh Ratnakar , Mazumdar Tuhina , Huang Chenfei , Li Qiuli , Pickering Curtis R. , Myers Jeffery N. , Wang Jing , Johnson Faye M.
Published: April 2023

Table S5. Proteins that were differentially expressed between drug-resistant and -sensitive groups based on 70% inhibitory concentration values
Table S4 from PDK1 Mediates NOTCH1-Mutated Head and Neck Squamous Carcinoma Vulnerability to Therapeutic PI3K/mTOR Inhibition
Authors: Sambandam Vaishnavi , Frederick Mitchell J. , Shen Li , Tong Pan , Rao Xiayu , Peng Shaohua , Singh Ratnakar , Mazumdar Tuhina , Huang Chenfei , Li Qiuli , Pickering Curtis R. , Myers Jeffery N. , Wang Jing , Johnson Faye M.
Published: April 2023

Table S4. Genes that were differentially expressed between drug-resistant and -sensitive groups based on 70% inhibitory concentration values
Table S3 from PDK1 Mediates NOTCH1-Mutated Head and Neck Squamous Carcinoma Vulnerability to Therapeutic PI3K/mTOR Inhibition
Authors: Sambandam Vaishnavi , Frederick Mitchell J. , Shen Li , Tong Pan , Rao Xiayu , Peng Shaohua , Singh Ratnakar , Mazumdar Tuhina , Huang Chenfei , Li Qiuli , Pickering Curtis R. , Myers Jeffery N. , Wang Jing , Johnson Faye M.
Published: April 2023

Table S3. Spearman correlation of protein expression to drug sensitivity based on 70% inhibitory concentration (IC70) or area under the curve (AUC)
Figure S7 from PDK1 Mediates NOTCH1-Mutated Head and Neck Squamous Carcinoma Vulnerability to Therapeutic PI3K/mTOR Inhibition
Authors: Sambandam Vaishnavi , Frederick Mitchell J. , Shen Li , Tong Pan , Rao Xiayu , Peng Shaohua , Singh Ratnakar , Mazumdar Tuhina , Huang Chenfei , Li Qiuli , Pickering Curtis R. , Myers Jeffery N. , Wang Jing , Johnson Faye M.
Published: April 2023

Figure S7. Effects of the combined inhibition of the PI3K/mTOR and NOTCH1 pathways in NOTCH1WT head and neck squamous cell carcinoma (HNSCC). A. Four NOTCH1WT HNSCC cell lines were treated with the indicated concentrations of GSK2126458 (GSK212) and 20 µM N-[N-(3,5-difluorophenacetyl-L-alanyl)]-S-phenylglycine t-butyl ester (DAPT) or 20 µM dibenzazepine (DBZ) for 72 hours, and cell viability was assessed with the CellTiter-Glo assay. Representative dose-response curves are shown. B. The combination index (CI) for each fraction affected (Fa) was calculated using the Chou-Talalay method. C. Western blotting for apoptosis markers after treatment with 50 nM GSK212 and 20 µM DAPT for 48 hours. D and E. NOTCH1WT cells were treated with 50 nM GSK212 and 20 µM DBZ or DAPT for 48 hours, and apoptosis was measured using an Annexin V/propidium iodide assay. The percentages of apoptotic cells are expressed as the means {plus minus} standard deviations of three independent experiments. *p<0.001, **p<0.05, two-way ANOVA corrected for multiple comparisons by the Tukey test; ns, not significant.
Figure S1 from PDK1 Mediates NOTCH1-Mutated Head and Neck Squamous Carcinoma Vulnerability to Therapeutic PI3K/mTOR Inhibition
Authors: Sambandam Vaishnavi , Frederick Mitchell J. , Shen Li , Tong Pan , Rao Xiayu , Peng Shaohua , Singh Ratnakar , Mazumdar Tuhina , Huang Chenfei , Li Qiuli , Pickering Curtis R. , Myers Jeffery N. , Wang Jing , Johnson Faye M.
Published: April 2023

Figure S1:Landscape of sensitivity to PI3K/mTOR pathway inhibitors in head and neck squamous cell carcinoma (HNSCC) cell lines. A. HNSCC cell lines (n=59) were incubated with seven PI3K/mTOR pathway inhibitors. B. The 70% inhibitory concentration (IC70) values for each drug were plotted. Each data point represents one cell line. C. Spearman correlation analysis was used to assess the association of each drug's IC70 value with those of the other drugs. The drugs included seven PI3K/mTOR pathway inhibitors (red text) and three cell cycle kinase inhibitors (blue text). The heat map shows the Spearman correlation values for each drug combination; unsupervised clustering showed that all PI3K/mTOR pathway inhibitors exhibited similar sensitivity patterns.
Figure S7 from Radium-223 Dichloride in Combination with Vascular Endothelial Growth Factor–Targeting Therapy in Advanced Renal Cell Carcinoma with Bone Metastases
Authors: McKay Rana R. , Bossé Dominick , Gray Kathryn P. , Michaelson M. Dror , Krajewski Katherine , Jacene Heather A. , Walsh Meghara , Bellmunt Joaquim , Pomerantz Mark , Harshman Lauren C. , Choueiri Toni K.
Published: April 2023

Figure for online supplement
Table S3 from Prevalence and Cellular Distribution of Novel Immune Checkpoint Targets Across Longitudinal Specimens in Treatment-naïve Melanoma Patients: Implications for Clinical Trials
Authors: Edwards Jarem , Tasker Annie , Pires da Silva Inês , Quek Camelia , Batten Marcel , Ferguson Angela , Allen Ruth , Allanson Benjamin , Saw Robyn P.M. , Thompson John F. , Menzies Alexander M. , Palendira Umaimainthan , Wilmott James S. , Long Georgina V. , Scolyer Richard A.
Published: April 2023

Clinical characteristics of melanoma biopsies used in CYTOF
Figure S6 from Radium-223 Dichloride in Combination with Vascular Endothelial Growth Factor–Targeting Therapy in Advanced Renal Cell Carcinoma with Bone Metastases
Authors: McKay Rana R. , Bossé Dominick , Gray Kathryn P. , Michaelson M. Dror , Krajewski Katherine , Jacene Heather A. , Walsh Meghara , Bellmunt Joaquim , Pomerantz Mark , Harshman Lauren C. , Choueiri Toni K.
Published: April 2023

Figure for online supplement
Table S2 from Prevalence and Cellular Distribution of Novel Immune Checkpoint Targets Across Longitudinal Specimens in Treatment-naïve Melanoma Patients: Implications for Clinical Trials
Authors: Edwards Jarem , Tasker Annie , Pires da Silva Inês , Quek Camelia , Batten Marcel , Ferguson Angela , Allen Ruth , Allanson Benjamin , Saw Robyn P.M. , Thompson John F. , Menzies Alexander M. , Palendira Umaimainthan , Wilmott James S. , Long Georgina V. , Scolyer Richard A.
Published: April 2023

Correlation between CD3 and checkpoint receptors from IHC data
Supplementary Figure 2 from Phase I Study of CC-486 Alone and in Combination with Carboplatin or nab-Paclitaxel in Patients with Relapsed or Refractory Solid Tumors
Authors: Von Hoff Daniel D. , Rasco Drew W. , Heath Elisabeth I. , Munster Pamela N. , Schellens Jan H.M. , Isambert Nicolas , Tourneau Christophe Le , O'Neil Bert , Mathijssen Ron H.J. , Lopez-Martin Jose A. , Edenfield W. Jeff , Martin Miguel , LoRusso Patricia M. , Bray Gordon L. , DiMartino Jorge , Nguyen Aaron , Liu Kejian , Laille Eric , Bendell Johanna C.
Published: April 2023

Mean paclitaxel plasma concentrations following nab-paclitaxel administration alone or with CC-486 in part 1 arm B
Figures S1-S5 from The Anticancer Activity of a First-in-class Small-molecule Targeting PCNA
Authors: Gu Long , Lingeman Robert , Yakushijin Fumiko , Sun Emily , Cui Qi , Chao Jianfei , Hu Weidong , Li Hongzhi , Hickey Robert J. , Stark Jeremy M. , Yuan Yate-Ching , Chen Yuan , Vonderfecht Steven L. , Synold Timothy W. , Shi Yanhong , Reckamp Karen L. , Horne David , Malkas Linda H.
Published: April 2023

Supplementary Figures Supplemental figure legend: Figure S1. A diagram illustrating the process of virtual screen and follow-up cellular assays used in compound triage. The virtual screen by the computer modeling programs, MOE and Glide, is based on the known crystal structures of the PCNA/FEN1 complex that are available from the RCSB protein database. The cellular assays that led to the identification of AOH39 is described in Figure S3. Figure S2. The chemical structures of the 57 hits (AOH compounds) identified by the virtual screen. Compounds sharing structural similarities are organized on the same rows. Compounds that showed inhibitory activities on cancer cells are highlighted. Figure S3. Effect of AOH compounds on cell growth. The SK-N-AS and SK-N-DZ NB cells and human PBMCs were incubated in the presence of various concentrations of the indicated AOH compounds for 72 hours. The cell growth was measured by a CellTiter-Glo assay (Promega, Madison, WI). The relative cell abundance was graphed by Prism. Figure S4. Effect of AOH1160 on NCI60 cancer cells. AOH1160 was submitted to the Developmental Therapeutics Program (DTP) of the National Cancer Institute (NCI). The compound was tested in the NCI60 cell lines in the standard 5-dose assay as described (https://dtp.cancer.gov/discovery_development/nci-60/methodology.htm). Briefly, cells were incubated in the presence of various concentrations of AOH1160 for 48 hours. Cells growth was analyzed by a Sulforhodamine B (SRB) assay after cells were fixed by ice-cold 10% trichloroacetic acid (TCA). The GI50 in molar for each cell line was calculated by DTP. Shown in the graph are the LogGI50. Figure S5. Enhanced sensitivity to cisplatin by AOH1160. Human SK-N-AS NB cells were treated with or without 1 ï�­M of cisplatin (CPT) in the presence or absence of 500 nM of AOH1160 for 18 h. Cells were washed with growth medium and were cultured in fresh media for 3 weeks to allow colony formation. The normalized colony counts under each treatment condition in triplicates were averaged and graphed plus/minus standard deviations. Based on Bliss independence model (see Methods), the combination index (Cl) for 1 ï�­M of CPT and 500 nM of AOH1160 is about 0.74.
Figure Legends (S1-S5) from The Anticancer Activity of a First-in-class Small-molecule Targeting PCNA
Authors: Gu Long , Lingeman Robert , Yakushijin Fumiko , Sun Emily , Cui Qi , Chao Jianfei , Hu Weidong , Li Hongzhi , Hickey Robert J. , Stark Jeremy M. , Yuan Yate-Ching , Chen Yuan , Vonderfecht Steven L. , Synold Timothy W. , Shi Yanhong , Reckamp Karen L. , Horne David , Malkas Linda H.
Published: April 2023

Figure Legends Supplemental figure legend: Figure S1. A diagram illustrating the process of virtual screen and follow-up cellular assays used in compound triage. The virtual screen by the computer modeling programs, MOE and Glide, is based on the known crystal structures of the PCNA/FEN1 complex that are available from the RCSB protein database. The cellular assays that led to the identification of AOH39 is described in Figure S3. Figure S2. The chemical structures of the 57 hits (AOH compounds) identified by the virtual screen. Compounds sharing structural similarities are organized on the same rows. Compounds that showed inhibitory activities on cancer cells are highlighted. Figure S3. Effect of AOH compounds on cell growth. The SK-N-AS and SK-N-DZ NB cells and human PBMCs were incubated in the presence of various concentrations of the indicated AOH compounds for 72 hours. The cell growth was measured by a CellTiter-Glo assay (Promega, Madison, WI). The relative cell abundance was graphed by Prism. Figure S4. Effect of AOH1160 on NCI60 cancer cells. AOH1160 was submitted to the Developmental Therapeutics Program (DTP) of the National Cancer Institute (NCI). The compound was tested in the NCI60 cell lines in the standard 5-dose assay as described (https://dtp.cancer.gov/discovery_development/nci-60/methodology.htm). Briefly, cells were incubated in the presence of various concentrations of AOH1160 for 48 hours. Cells growth was analyzed by a Sulforhodamine B (SRB) assay after cells were fixed by ice-cold 10% trichloroacetic acid (TCA). The GI50 in molar for each cell line was calculated by DTP. Shown in the graph are the LogGI50. Figure S5. Enhanced sensitivity to cisplatin by AOH1160. Human SK-N-AS NB cells were treated with or without 1 ï�­M of cisplatin (CPT) in the presence or absence of 500 nM of AOH1160 for 18 h. Cells were washed with growth medium and were cultured in fresh media for 3 weeks to allow colony formation. The normalized colony counts under each treatment condition in triplicates were averaged and graphed plus/minus standard deviations. Based on Bliss independence model (see Methods), the combination index (Cl) for 1 ï�­M of CPT and 500 nM of AOH1160 is about 0.74.
Supplementary Fig. 2 from Therapeutic Targeting of TFE3/IRS-1/PI3K/mTOR Axis in Translocation Renal Cell Carcinoma
Authors: Damayanti Nur P. , Budka Justin A. , Khella Heba W.Z , Ferris Mary W. , Ku Sheng Yu , Kauffman Eric , Wood Anthony C. , Ahmed Khunsha , Chintala Venkata Nithinsai , Adelaiye-Ogala Remi , Elbanna May , Orillion Ashley , Chintala Sreenivasulu , Kao Chinghai , Linehan W. Marston , Yousef George M. , Hollenhorst Peter C. , Pili Roberto
Published: April 2023

ChiP-seq for TFE3 in UOK-146
Figure S4 from Capecitabine Efficacy Is Correlated with TYMP and RB1 Expression in PDX Established from Triple-Negative Breast Cancers
Authors: Marangoni Elisabetta , Laurent Cécile , Coussy Florence , El-Botty Rania , Château-Joubert Sophie , Servely Jean-Luc , de Plater Ludmilla , Assayag Franck , Dahmani Ahmed , Montaudon Elodie , Nemati Fariba , Fleury Justine , Vacher Sophie , Gentien David , Rapinat Audrey , Foidart Pierre , Sounni Nor Eddine , Noel Agnès , Vincent-Salomon Anne , Lae Marick , Decaudin Didier , Roman-Roman Sergio , Bièche Ivan , Piccart Martine , Reyal Fabien
Published: April 2023

A) Immunohistochemistry analysis of HER2, Rb and TYMP (20X) in the HBCx-73 PDX B) response to trastuzumab and capecitabine in the HBCx-73 PDX
Supplementary Fig. 1 from Therapeutic Targeting of TFE3/IRS-1/PI3K/mTOR Axis in Translocation Renal Cell Carcinoma
Authors: Damayanti Nur P. , Budka Justin A. , Khella Heba W.Z , Ferris Mary W. , Ku Sheng Yu , Kauffman Eric , Wood Anthony C. , Ahmed Khunsha , Chintala Venkata Nithinsai , Adelaiye-Ogala Remi , Elbanna May , Orillion Ashley , Chintala Sreenivasulu , Kao Chinghai , Linehan W. Marston , Yousef George M. , Hollenhorst Peter C. , Pili Roberto
Published: April 2023

Specificity of TFE3 antibody across TFE3 oncoproteins
Figure S3 from Capecitabine Efficacy Is Correlated with TYMP and RB1 Expression in PDX Established from Triple-Negative Breast Cancers
Authors: Marangoni Elisabetta , Laurent Cécile , Coussy Florence , El-Botty Rania , Château-Joubert Sophie , Servely Jean-Luc , de Plater Ludmilla , Assayag Franck , Dahmani Ahmed , Montaudon Elodie , Nemati Fariba , Fleury Justine , Vacher Sophie , Gentien David , Rapinat Audrey , Foidart Pierre , Sounni Nor Eddine , Noel Agnès , Vincent-Salomon Anne , Lae Marick , Decaudin Didier , Roman-Roman Sergio , Bièche Ivan , Piccart Martine , Reyal Fabien
Published: April 2023

Boxplot of the expression of genes encoding proteins involved in capecitabine metabolism (TYMP, TYMS, TK1, DPYD) and cell-cycle control (RB1, CDKN2A, CCND1).
Supplementary Data from Efficacy of Combined VEGFR1-3, PDGFα/β, and FGFR1-3 Blockade Using Nintedanib for Esophagogastric Cancer
Authors: Won Elizabeth , Basunia Azfar , Chatila Walid K. , Hechtman Jaclyn F. , Chou Joanne F. , Ku Geoffrey Y. , Chalasani Sree B. , Boyar Michelle S. , Goldberg Zoe , Desai Avni M. , Tuvy Yaelle , Berger Michael F. , Tang Laura , Kelsen David P. , Schattner Mark , Ilson David H. , Capanu Marinela , Solit David B. , Schultz Nikolaus , Janjigian Yelena Y.
Published: April 2023

Supplementary Table 1
Supplementary Data from Efficacy of Combined VEGFR1-3, PDGFα/β, and FGFR1-3 Blockade Using Nintedanib for Esophagogastric Cancer
Authors: Won Elizabeth , Basunia Azfar , Chatila Walid K. , Hechtman Jaclyn F. , Chou Joanne F. , Ku Geoffrey Y. , Chalasani Sree B. , Boyar Michelle S. , Goldberg Zoe , Desai Avni M. , Tuvy Yaelle , Berger Michael F. , Tang Laura , Kelsen David P. , Schattner Mark , Ilson David H. , Capanu Marinela , Solit David B. , Schultz Nikolaus , Janjigian Yelena Y.
Published: April 2023

Supplementary Table 2
Supplementary Data from Hyperspectral Imaging for Resection Margin Assessment during Cancer Surgery
Authors: Kho Esther , de Boer Lisanne L. , Van de Vijver Koen K. , van Duijnhoven Frederieke , Vrancken Peeters Marie-Jeanne T.F.D. , Sterenborg Henricus J.C.M. , Ruers Theo J.M.
Published: April 2023

H&E sections, and the corresponding hyperspectral analysis of the resection side.
Supplementary Table S4. from Phase II Study of Taselisib (GDC-0032) in Combination with Fulvestrant in Patients with HER2-Negative, Hormone Receptor–Positive Advanced Breast Cancer
Authors: Dickler Maura N. , Saura Cristina , Richards Donald A. , Krop Ian E. , Cervantes Andrés , Bedard Philippe L. , Patel Manish R. , Pusztai Lajos , Oliveira Mafalda , Cardenas Alison K. , Cui Na , Wilson Timothy R. , Stout Thomas J. , Wei Michael C. , Hsu Jerry Y. , Baselga José
Published: April 2023

Exposure to taselisib
Supplementary Figure S4: Minimal Correlation of Gene Expression and subclonal CNV events. from Genomic Heterogeneity and the Small Renal Mass
Authors: Ueno Daiki , Xie Zuoquan , Boeke Marta , Syed Jamil , Nguyen Kevin A. , McGillivray Patrick , Adeniran Adebowale , Humphrey Peter , Dancik Garrett M. , Kluger Yuval , Liu Zongzhi , Kluger Harriet , Shuch Brian
Published: April 2023

Minimal correlation of gene expression was decreasing with increasing in subclonal CNV events. (R2=0.431, p<0.001)
Supplementary Table S3. from Phase II Study of Taselisib (GDC-0032) in Combination with Fulvestrant in Patients with HER2-Negative, Hormone Receptor–Positive Advanced Breast Cancer
Authors: Dickler Maura N. , Saura Cristina , Richards Donald A. , Krop Ian E. , Cervantes Andrés , Bedard Philippe L. , Patel Manish R. , Pusztai Lajos , Oliveira Mafalda , Cardenas Alison K. , Cui Na , Wilson Timothy R. , Stout Thomas J. , Wei Michael C. , Hsu Jerry Y. , Baselga José
Published: April 2023

Adverse events (AEs) of special interest in the safety population
Supplementary Figure S1. from Phase II Study of Taselisib (GDC-0032) in Combination with Fulvestrant in Patients with HER2-Negative, Hormone Receptor–Positive Advanced Breast Cancer
Authors: Dickler Maura N. , Saura Cristina , Richards Donald A. , Krop Ian E. , Cervantes Andrés , Bedard Philippe L. , Patel Manish R. , Pusztai Lajos , Oliveira Mafalda , Cardenas Alison K. , Cui Na , Wilson Timothy R. , Stout Thomas J. , Wei Michael C. , Hsu Jerry Y. , Baselga José
Published: April 2023

Participant PIK3CA-mutation central testing results
Supplementary Figure S2 from Validation of the 16-Gene Recurrence Score in Patients with Locoregional, High-Risk Renal Cell Carcinoma from a Phase III Trial of Adjuvant Sunitinib
Authors: Rini Brian I. , Escudier Bernard , Martini Jean-Francois , Magheli Ahmed , Svedman Christer , Lopatin Margarita , Knezevic Dejan , Goddard Audrey D. , Febbo Phillip G. , Li Rachel , Lin Xun , Valota Olga , Staehler Michael , Motzer Robert J. , Ravaud Alain
Published: April 2023

Distribution of RS results in T3 patients in the gene signature cohort. Abbreviations: RS, recurrence score; T3, stage III tumor.
Suppl.Mat., Suppl. Table, Suppl. Figs Legends from Phenformin-Induced Mitochondrial Dysfunction Sensitizes Hepatocellular Carcinoma for Dual Inhibition of mTOR
Authors: Veiga Sónia R. , Ge Xuemei , Mercer Carol A. , Hernández-Álvarez María I. , Thomas Hala Elnakat , Hernandez-Losa Javier , Ramón y Cajal Santiago , Zorzano Antonio , Thomas George , Kozma Sara C.
Published: April 2023

Supplementary data and supplementary table and figures Legends
Supplementary Tables from A Coclinical Radiogenomic Validation Study: Conserved Magnetic Resonance Radiomic Appearance of Periostin-Expressing Glioblastoma in Patients and Xenograft Models
Authors: Zinn Pascal O. , Singh Sanjay K. , Kotrotsou Aikaterini , Hassan Islam , Thomas Ginu , Luedi Markus M. , Elakkad Ahmed , Elshafeey Nabil , Idris Tagwa , Mosley Jennifer , Gumin Joy , Fuller Gregory N. , de Groot John F. , Baladandayuthapani Veera , Sulman Erik P. , Kumar Ashok J. , Sawaya Raymond , Lang Frederick F. , Piwnica-Worms David , Colen Rivka R.
Published: April 2023

Supplementary Tables
Supplementary Figure Legends and Methods from A Coclinical Radiogenomic Validation Study: Conserved Magnetic Resonance Radiomic Appearance of Periostin-Expressing Glioblastoma in Patients and Xenograft Models
Authors: Zinn Pascal O. , Singh Sanjay K. , Kotrotsou Aikaterini , Hassan Islam , Thomas Ginu , Luedi Markus M. , Elakkad Ahmed , Elshafeey Nabil , Idris Tagwa , Mosley Jennifer , Gumin Joy , Fuller Gregory N. , de Groot John F. , Baladandayuthapani Veera , Sulman Erik P. , Kumar Ashok J. , Sawaya Raymond , Lang Frederick F. , Piwnica-Worms David , Colen Rivka R.
Published: April 2023

Supplementary Figure Legends and Methods
Figure S3 from SMAD4 Gene Mutation Renders Pancreatic Cancer Resistance to Radiotherapy through Promotion of Autophagy
Authors: Wang Feng , Xia Xiaojun , Yang Chunying , Shen Jianliang , Mai Junhua , Kim Han-Cheon , Kirui Dickson , Kang Ya'an , Fleming Jason B. , Koay Eugene J. , Mitra Sankar , Ferrari Mauro , Shen Haifa
Published: April 2023

Figure S3. SMAD4 depletion increased reactive oxygen species generation in Panc-1 cells using shRNA lentiviral vector. The flow cytometry measure the basal level of ROS in Panc-1 cells. (A) Immunoblot of SMAD4 was measured using antibody against SMAD4 in Panc-1-CTL, Panc-1-sh-SMAD4-#2 Cells. (B) Panc-1-CTL, Panc-1-sh-SMAD4-#2 Cells were treated with γ-irradiation (6 Gy), and then incubated with ROS indicator (CM-H2DCFDA), and fluorescence intensity was assessed by flow cytometry at indicated time points. Labeled tert-butyl hydrogen peroxide (TBHP, 50µM) serve as a positive control. * , P < .05, **, P < .001.
Supplementary Data from Radiomics of Multiparametric MRI for Pretreatment Prediction of Pathologic Complete Response to Neoadjuvant Chemotherapy in Breast Cancer: A Multicenter Study
Authors: Liu Zhenyu , Li Zhuolin , Qu Jinrong , Zhang Renzhi , Zhou Xuezhi , Li Longfei , Sun Kai , Tang Zhenchao , Jiang Hui , Li Hailiang , Xiong Qianqian , Ding Yingying , Zhao Xinming , Wang Kun , Liu Zaiyi , Tian Jie
Published: April 2023

supporting information
Supplementary Tables and Figures from A Visually Apparent and Quantifiable CT Imaging Feature Identifies Biophysical Subtypes of Pancreatic Ductal Adenocarcinoma
Authors: Koay Eugene J. , Lee Yeonju , Cristini Vittorio , Lowengrub John S. , Kang Ya'an , Lucas F. Anthony San , Hobbs Brian P. , Ye Rong , Elganainy Dalia , Almahariq Muayad , Amer Ahmed M. , Chatterjee Deyali , Yan Huaming , Park Peter C. , Rios Perez Mayrim V. , Li Dali , Garg Naveen , Reiss Kim A. , Yu Shun , Chauhan Anil , Zaid Mohamed , Nikzad Newsha , Wolff Robert A. , Javle Milind , Varadhachary Gauri R. , Shroff Rachna T. , Das Prajnan , Lee Jeffrey E. , Ferrari Mauro , Maitra Anirban , Taniguchi Cullen M. , Kim Michael P. , Crane Christopher H. , Katz Matthew H. , Wang Huamin , Bhosale Priya , Tamm Eric P. , Fleming Jason B.
Published: April 2023

Includes Supplementary Tables S1 through S9, and Supplementary Figures S1 through S12
Supplementary Methods from A Visually Apparent and Quantifiable CT Imaging Feature Identifies Biophysical Subtypes of Pancreatic Ductal Adenocarcinoma
Authors: Koay Eugene J. , Lee Yeonju , Cristini Vittorio , Lowengrub John S. , Kang Ya'an , Lucas F. Anthony San , Hobbs Brian P. , Ye Rong , Elganainy Dalia , Almahariq Muayad , Amer Ahmed M. , Chatterjee Deyali , Yan Huaming , Park Peter C. , Rios Perez Mayrim V. , Li Dali , Garg Naveen , Reiss Kim A. , Yu Shun , Chauhan Anil , Zaid Mohamed , Nikzad Newsha , Wolff Robert A. , Javle Milind , Varadhachary Gauri R. , Shroff Rachna T. , Das Prajnan , Lee Jeffrey E. , Ferrari Mauro , Maitra Anirban , Taniguchi Cullen M. , Kim Michael P. , Crane Christopher H. , Katz Matthew H. , Wang Huamin , Bhosale Priya , Tamm Eric P. , Fleming Jason B.
Published: April 2023

Additional methods
Supplementary Material from Development and External Validation of Prediction Models for 10-Year Survival of Invasive Breast Cancer. Comparison with PREDICT and CancerMath
Authors: Karapanagiotis Solon , Pharoah Paul D.P. , Jackson Christopher H. , Newcombe Paul J.
Published: April 2023

Supplementary methods, figures and tables Table S3: Fractional polynomial functions for age at diagnosis (years), tumour size (mm), number of positive nodes, tumour grade (I, II, III) and mode of detection (screening vs clinical) by ER status (positive, negative). Table S4: Results, for the fixed effects and interaction terms from RJMCMC Logistic model for ER-positive tumours. Table S5: Results, for the fixed effects and interaction terms from RJMCMC Weibull model for ER-positive tumours. Table S6: Results, for the fixed effects and interaction terms from RJMCMC Logistic model for ER-negative tumours. Table S7: Results, for the fixed effects and interaction terms from RJMCMC Weibull model for ER-negative tumours. Figure S1: Marginal Posterior Probability of inclusion in the model for each interaction term, i.e. the relative frequency a covariate was included in the model for (A) ER positive and (B) ER negative tumours. It can be interpreted as the posterior probability an association exists with survival, adjusted for all other covariates in the model. Figure S2: Individual calibration plots of the four models in the validation set with ;7% CI for (A) ER positive and (B) ER negative tumours. Figure S3: Individual net benefit plots of the four models in the validation set for (A) ER positive and (B) ER negative tumours. Shaded area represents ;7% confidence intervals based on 1000 bootstrap replicates.
Figure S2 from Magnetic Resonance Imaging of Tumor-Associated Macrophages: Clinical Translation
Authors: Aghighi Maryam , Theruvath Ashok J. , Pareek Anuj , Pisani Laura L. , Alford Raphael , Muehe Anne M. , Sethi Tarsheen K. , Holdsworth Samantha J. , Hazard Florette K. , Gratzinger Dita , Luna-Fineman Sandra , Advani Ranjana , Spunt Sheri L. , Daldrup-Link Heike E.
Published: April 2023

In Figure S2 iron oxide nanoparticle distribution corresponds with TAM distribution on histopathology. (A) Prussian blue stain (blue) of a bone sarcoma shows similar iron distribution and co-localization with (B) CD68 and (C) CD163 macrophage stains (brown), indicating intracytoplasmatic iron within macrophages. Scale bars, 100µm.
Figure S1 from Parallel Accumulation of Tumor Hyaluronan, Collagen, and Other Drivers of Tumor Progression
Authors: Li Xiaoming , Shepard H. Michael , Cowell Jessica A. , Zhao Chunmei , Osgood Ryan J. , Rosengren Sanna , Blouw Barbara , Garrovillo Sheryl A. , Pagel Mark D. , Whatcott Clifford J. , Han Haiyong , Von Hoff Daniel D. , Taverna Darin M. , LaBarre Michael J. , Maneval Daniel C. , Thompson Curtis B.
Published: April 2023

In HA-accumulating AsPC-1/HAS3 tumors, low-dose PEGPH20 decreased tumor HA levels by >64%; whereas the level of tumor HA in the already very HA-low parental AsPC-1 (AsPC-1-P) tumors remained statistically unchanged (n = 10/group).
Supplemental Figure S4 from Multimodality Treatment of Desmoplastic Small Round Cell Tumor: Chemotherapy and Complete Cytoreductive Surgery Improve Patient Survival
Authors: Subbiah Vivek , Lamhamedi-Cherradi Salah-Eddine , Cuglievan Branko , Menegaz Brian A. , Camacho Pamela , Huh Winston , Ramamoorthy Vandhana , Anderson Pete M. , Pollock Raphael E. , Lev Dina C. , Qiao Wei , McAleer Mary Frances , Benjamin Robert S. , Patel Shreyaskumar , Herzog Cynthia E. , Daw Najat C. , Feig Barry W. , Lazar Alexander J. , Hayes-Jordan Andrea , Ludwig Joseph A.
Published: April 2023

Overall Survival Probability of Bimodality vs. Trimodality Therapy
Supplementary Figure S3 from High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients
Authors: Chen Justin , Haanpää Maria K. , Gruber Joshua J. , Jäger Natalie , Ford James M. , Snyder Michael P.
Published: April 2023

Figure S3. Average methylation at the promoters of 24 known breast cancer genes. Boxplots showing the distribution of average methylation ratios between cohort subgroups in windows spanning the transcriptional start sites (TSS) in 24 genes. Windows were approximately 2kb, beginning 1.5kb upstream of the distal TSS and extending 500bp beyond any other proximal TSS. Statistically significant methylation differences are indicated by asterisks (***p < 0.001, ****p < 0.0001).