bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 1 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S1 shows that NAMPT inhibition suppresses the SASP in OVCAR5 cell line.
Supplementary Data from β-Galactosylceramidase Promotes Melanoma Growth via Modulation of Ceramide Metabolism
Authors: Belleri Mirella , Paganini Giuseppe , Coltrini Daniela , Ronca Roberto , Zizioli Daniela , Corsini Michela , Barbieri Andrea , Grillo Elisabetta , Calza Stefano , Bresciani Roberto , Maiorano Eugenio , Mastropasqua Mauro G. , Annese Tiziana , Giacomini Arianna , Ribatti Domenico , Casas Josefina , Levade Thierry , Fabrias Gemma , Presta Marco
Published: April 2023

Supplementary Data - Single file with supplemental methods, tables, figures, legends. Supplemental Materials and Methods; Table S1: Primers used for RT-qPCR analysis; Table S2: GALC downregulation affects the lipid profile of murine B16-F10 melanoma cells; Table S3: Expression levels of enzymes involved in sphingolipid metabolism in B16-F10 cells; Table S4: RT-qPCR analysis of the expression of tumor infiltrate markers and immune checkpoints in B16-F10 tumor grafts; Figure S1: Galca does not affect melanocyte differentiation in zebrafish; Figure S2: Galc downregulation does not affect cell cycle distribution and cell death in B16-F10 cells; Figure S3: The neutral sphingomyelinase inhibitor GW4869 increases the tumorigenic activity of shGALC-B16-F10 cells; Figure S4: Inhibition of the tumorigenic activity in shGALC-bis-B16-F10 cells; Figure S5: Public data mining of GALC expression in human melanoma; Figure S6: Public data mining of SMPD3 expression in human melanoma.
Supplementary File 1 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

Excel file- RNA seq results
Supplementary Figure 6 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

Expression of lipogenic enzymes in human TSC2-deficient and TSC2 add-back cells treated with GLPG1690
Supplementary Figure 5 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

Human P-Kinase array reveals changes in Akt and Erk signaling in human TSC2-deficient cells treated with GLPG1690
Supplementary Table S2 from Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma
Authors: Tamura Naoka , Shaikh Nadeem , Muliaditan Daniel , Soliman Tanya N. , McGuinness Jennifer R. , Maniati Eleni , Moralli Daniela , Durin Mary-Anne , Green Catherine M. , Balkwill Frances R. , Wang Jun , Curtius Kit , McClelland Sarah E.
Published: April 2023

Genetic mutations in HGSC cell lines
Supplementary Movie 1 from Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma
Authors: Tamura Naoka , Shaikh Nadeem , Muliaditan Daniel , Soliman Tanya N. , McGuinness Jennifer R. , Maniati Eleni , Moralli Daniela , Durin Mary-Anne , Green Catherine M. , Balkwill Frances R. , Wang Jun , Curtius Kit , McClelland Sarah E.
Published: April 2023

Movie of MT assembly rate assay
Supplementary Material from Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma
Authors: Tamura Naoka , Shaikh Nadeem , Muliaditan Daniel , Soliman Tanya N. , McGuinness Jennifer R. , Maniati Eleni , Moralli Daniela , Durin Mary-Anne , Green Catherine M. , Balkwill Frances R. , Wang Jun , Curtius Kit , McClelland Sarah E.
Published: April 2023

One supplemental movie, four supplemental tables, six supplemental figures, supplemental methods
Supplementary Figure 2 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

GLPG1690 treatment inhibits the proliferation of Tsc2-/- MEFs in vitro
Supplementary Data from Adipocyte-Induced FABP4 Expression in Ovarian Cancer Cells Promotes Metastasis and Mediates Carboplatin Resistance
Authors: Mukherjee Abir , Chiang Chun-Yi , Daifotis Helen A. , Nieman Kristin M. , Fahrmann Johannes F. , Lastra Ricardo R. , Romero Iris L. , Fiehn Oliver , Lengyel Ernst
Published: April 2023

Supplementary methods, figures and tables
Supplementary Data from A Novel Bioengineered miR-127 Prodrug Suppresses the Growth and Metastatic Potential of Triple-Negative Breast Cancer Cells
Authors: Umeh-Garcia Maxine , Simion Catalina , Ho Pui-Yan , Batra Neelu , Berg Anastasia L. , Carraway Kermit L. , Yu Aiming , Sweeney Colleen
Published: April 2023

Supplemental Tables 1, 2, 3 and 4, Supplemental Figures 1 through 7 and Supplemental Figure legends
Supplemental RNAseq File 2 from A Novel Bioengineered miR-127 Prodrug Suppresses the Growth and Metastatic Potential of Triple-Negative Breast Cancer Cells
Authors: Umeh-Garcia Maxine , Simion Catalina , Ho Pui-Yan , Batra Neelu , Berg Anastasia L. , Carraway Kermit L. , Yu Aiming , Sweeney Colleen
Published: April 2023

mRNA Sequencing Data Matrix Table
Supplementary Table S2 from The Fire Within: NF-κB Involvement in Non–Small Cell Lung Cancer
Authors: Dimitrakopoulos Foteinos-Ioannis D. , Kottorou Anastasia E. , Kalofonou Melpomeni , Kalofonos Haralabos P.
Published: April 2023

Supplementary Table S2. Published studies on genetic variations of NF-κB family members and their clinical significance in NSCLC.
Supplemental RNAseq File 1 from A Novel Bioengineered miR-127 Prodrug Suppresses the Growth and Metastatic Potential of Triple-Negative Breast Cancer Cells
Authors: Umeh-Garcia Maxine , Simion Catalina , Ho Pui-Yan , Batra Neelu , Berg Anastasia L. , Carraway Kermit L. , Yu Aiming , Sweeney Colleen
Published: April 2023

sRNA Sequencing Data Matrix Table
Supplementary Tables from Penetrance Estimates Over Time to First and Second Primary Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single Institution Perspective
Authors: Shin Seung Jun , Dodd-Eaton Elissa B. , Gao Fan , Bojadzieva Jasmina , Chen Jingxiao , Kong Xianhua , Amos Christopher I. , Ning Jing , Strong Louise C. , Wang Wenyi
Published: April 2023

This supplementary tables file contains information in the TP53 germline mutations that were sequenced in each MDA cohort.
Supplementary Figures from Penetrance Estimates Over Time to First and Second Primary Cancer Diagnosis in Families with Li-Fraumeni Syndrome: A Single Institution Perspective
Authors: Shin Seung Jun , Dodd-Eaton Elissa B. , Gao Fan , Bojadzieva Jasmina , Chen Jingxiao , Kong Xianhua , Amos Christopher I. , Ning Jing , Strong Louise C. , Wang Wenyi
Published: April 2023

The supplementary figures included in this file describe the distribution of gap time from first to second primary by proband status(Fig 1), by cancer type (Fig 2) and by sex (Fig 3).
Supplementary Data from Modeling Tumor Evolutionary Dynamics to Predict Clinical Outcomes for Patients with Metastatic Colorectal Cancer: A Retrospective Analysis
Authors: Zhou Jiawei , Liu Yutong , Zhang Yubo , Li Quefeng , Cao Yanguang
Published: April 2023

Supplementary Text S1. Mathematical model and parameter estimation; Supplementary Table 1. Cohen's d point estimate and 95% confidence interval in effect size tests among patients with PD (Progressive Disease), SD (Stable Disease) or PR (Partial Response) responses; Supplementary Figure 1. The individual tumor growth profiles for all 599 individuals; Supplementary Figure 2. Kaplan-Meier curves of the overall survival starting from last tumor observation for each individual patient. The curves were categorized by evolutionary parameters and the number of cell subclones at diagnosis derived from the evolutionary model.
Figure S2 from Remission of Spontaneous Canine Tumors after Systemic Cellular Viroimmunotherapy
Authors: Cejalvo Teresa , Perisé-Barrios Ana Judith , del Portillo Isabel , Laborda Eduardo , Rodriguez-Milla Miguel A. , Cubillo Isabel , Vázquez Fernando , Sardón David , Ramirez Manuel , Alemany Ramon , del Castillo Noemí , García-Castro Javier
Published: April 2023

Clinical and anatomo-pathological results in canine patients treated with dCelyvir.
Supplementary Table S3 from Intake of Dietary Fruit, Vegetables, and Fiber and Risk of Colorectal Cancer According to Molecular Subtypes: A Pooled Analysis of 9 Studies
Authors: Hidaka Akihisa , Harrison Tabitha A. , Cao Yin , Sakoda Lori C. , Barfield Richard , Giannakis Marios , Song Mingyang , Phipps Amanda I. , Figueiredo Jane C. , Zaidi Syed H. , Toland Amanda E. , Amitay Efrat L. , Berndt Sonja I. , Borozan Ivan , Chan Andrew T. , Gallinger Steven , Gunter Marc J. , Guinter Mark A. , Harlid Sophia , Hampel Heather , Jenkins Mark A. , Lin Yi , Moreno Victor , Newcomb Polly A. , Nishihara Reiko , Ogino Shuji , Obón-Santacana Mireia , Parfrey Patrick S. , Potter John D. , Slattery Martha L. , Steinfelder Robert S. , Um Caroline Y. , Wang Xiaoliang , Woods Michael O. , Van Guelpen Bethany , Thibodeau Stephen N. , Hoffmeister Michael , Sun Wei , Hsu Li , Buchanan Daniel D. , Campbell Peter T. , Peters Ulrike
Published: April 2023

Supplementary Table S3
Supplementary Note from Physical Activity Does Not Lower the Risk of Lung Cancer
Authors: Baumeister Sebastian-Edgar , Leitzmann Michael F. , Bahls Martin , Meisinger Christa , Amos Christopher I. , Hung Rayjean J. , Teumer Alexander , Baurecht Hansjörg
Published: April 2023

Collaborators of the TRICL-ILCCO and LC3 consortium
Supplementary Methods from High-Throughput Screening of Combinatorial Immunotherapies with Patient-Specific In Silico Models of Metastatic Colorectal Cancer
Authors: Kather Jakob Nikolas , Charoentong Pornpimol , Suarez-Carmona Meggy , Herpel Esther , Klupp Fee , Ulrich Alexis , Schneider Martin , Zoernig Inka , Luedde Tom , Jaeger Dirk , Poleszczuk Jan , Halama Niels
Published: April 2023

Extensive description of the model implementation and the specifics of treatment simulation.
Supplementary Video S7 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Table S2 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Chemokines upregulated in human macrophages with M1 or M1-like phenotypes in inflammatory and tumor microenvironments and their relative receptors expressed on leukemia cells
Supplementary Video S5 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Table S1 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Primers used in real-time RT-PCR
Supplementary Video S4 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Figure S6 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Supplemental materials to study the role of the CCL8-CCR1/CCR2 and CCL9/10-CCR1 axes.
Supplementary Video S2 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Figure S4 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Supplemental materials from experiments testing the migration potential and non-specific phagocytic activity of SP LAM subsets as well as the T-ALL model in CCR2-/- mice.
Figure S2 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Cell cycle analysis of SP LAM subsets and phenotypic evolution of MOMF in the liver of T-ALL mice.
Supplemental Table S1 from A Bis-Indole–Derived NR4A1 Antagonist Induces PD-L1 Degradation and Enhances Antitumor Immunity
Authors: Karki Keshav , Wright Gus A. , Mohankumar Kumaravel , Jin Un-Ho , Zhang Xing-Han , Safe Stephen
Published: April 2023

Supplemental Table S1. Summary of reagents, antibodies, immune staining sources, oligonucleotides and primers
Supplemental Figure S5 from A Bis-Indole–Derived NR4A1 Antagonist Induces PD-L1 Degradation and Enhances Antitumor Immunity
Authors: Karki Keshav , Wright Gus A. , Mohankumar Kumaravel , Jin Un-Ho , Zhang Xing-Han , Safe Stephen
Published: April 2023

Supplemental Figure S5. A-F. Gating Strategy for Teff (CD3+/CD8+) and Treg (CD3+/CD4+/CD25+/FoxP3+) cells. In panel A, cells are selected within the "cells" gate from the Forward Scatter versus Side Scatter dot plot. In panel B, cells from within the "cells" gate are plotted on a dot plot showing Side Scatter Area versus Side Scatter Height in which the single cells are selected within the "singlets" gate. In panel C, single cells from within the "cells" and "singlets" gates are plotted on a dot plot depicting Side Scatter versus Live/Dead Near IR dye. Viable, single cells are selected within the "viable" gate. In panel D, viable, single cells are shown on a dot plot depicting Side Scatter versus CD3 PE-Cy5.5 in which the CD3+ cells are selected within the "CD3+" gate. In panel E, CD3+, live, single cells are visualized on a dot plot with CD8 PE-eFluor 610 on the x-axis and CD4 Alexa Fluor 488 on the y-axis. The CD4+ cells are selected within "CD4+" gate and the CD8+ cells are selected within the "CD8+" gate. In panel E, the CD4+, CD3+, viable, single cells are plotted on a dot plot showing FoxP3 BV 421 versus CD25 Alexa Fluor 647. The regulatory T cells are selected within the "T reg cells" gate. G/H. GraphPad PRISM software was used to calculate Effective concentration (EC50) of PD-L1 mRNA (G) and PD-L1 protein (H) after treatment with different concentrations of CDIM-8 and Cl-OCH3 and the values were calculated by regression analysis using the dose-response curves generated from the experimental data.
Supplementary Data from CHD4 Promotes Breast Cancer Progression as a Coactivator of Hypoxia-Inducible Factors
Authors: Wang Yijie , Chen Yan , Bao Lei , Zhang Bo , Wang Jennifer E. , Kumar Ashwani , Xing Chao , Wang Yingfei , Luo Weibo
Published: April 2023

Supplementary Table S1-S3 and Figure S1-S3
Figure S3 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Absence of ectopic crypts in the single mutants
Supplemental Methods from Nitrogen Trapping as a Therapeutic Strategy in Tumors with Mitochondrial Dysfunction
Authors: Madala Hanumantha Rao , Helenius Iiro Taneli , Zhou Wen , Mills Evanna , Zhang Yiyun , Liu Yan , Metelo Ana M. , Kelley Michelle L. , Punganuru Surendra , Kim Kyung Bo , Olenchock Benjamin , Rhee Eugene , Intlekofer Andrew M. , Iliopoulos Othon , Chouchani Edward , Yeh Jing-Ruey Joanna
Published: April 2023

Supplemental Methods
Supplementary Data from Skipping Nonsense to Maintain Function: The Paradigm of BRCA2 Exon 12
Authors: Meulemans Laëtitia , Mesman Romy L.S. , Caputo Sandrine M. , Krieger Sophie , Guillaud-Bataille Marine , Caux-Moncoutier Virginie , Léone Mélanie , Boutry-Kryza Nadia , Sokolowska Johanna , Révillion Françoise , Delnatte Capucine , Tubeuf Hélène , Soukarieh Omar , Bonnet-Dorion Françoise , Guibert Virginie , Bronner Myriam , Bourdon Violaine , Lizard Sarab , Vilquin Paul , Privat Maud , Drouet Aurélie , Grout Charlotte , Calléja Fabienne M.G.R. , Golmard Lisa , Vrieling Harry , Stoppa-Lyonnet Dominique , Houdayer Claude , Frebourg Thierry , Vreeswijk Maaike P.G. , Martins Alexandra , Gaildrat Pascaline
Published: April 2023

Fig. S1 to S10. Figure S1. Variant selection from human variation databases; Figure S2. Capillary electrophoresis analyses of BRCA2 exon 12 splicing patterns in minigene assays of presumed LoF variants; Figure S3. Bioinformatics predictions of 3'/5' ss alterations for variants located at position IVS{plus minus}1/2 of BRCA2 exon 12; Figure S4. Bioinformatics analysis of variants predicted to alter 3'/5' ss of BRCA2 exon 12 (â^†MES {less than or equal to} -15%); Figure S5. Capillary electrophoresis analyses of BRCA2 exon 12 splicing patterns in minigene assays of variants predicted to alter 3'/5' ss (A) or ESR (B); Figure S6. Capillary electrophoresis analyses of BRCA2 exon 12 splicing patterns in control and patient lymphoblastoid cell lines; Figure S7. RT-PCR analysis of BRCA2 exon 12 splicing patterns in puromycin- or mock-treated lymphoblastoid cell lines of control individuals and patients carrying the c.6844G>T or c.6901G>T nonsense variants; Figure S8. Capillary electrophoresis analyses of BRCA2 exon 12 splicing patterns in variant-expressing mESC; Figure S9. Quantitation of BRCA2 protein expression in mESC; Figure S10. Sensitivity of BRCA2 variants to cisplatin and PARP inhibitors.
Supplementary Data Tables S1-S4 from Skipping Nonsense to Maintain Function: The Paradigm of BRCA2 Exon 12
Authors: Meulemans Laëtitia , Mesman Romy L.S. , Caputo Sandrine M. , Krieger Sophie , Guillaud-Bataille Marine , Caux-Moncoutier Virginie , Léone Mélanie , Boutry-Kryza Nadia , Sokolowska Johanna , Révillion Françoise , Delnatte Capucine , Tubeuf Hélène , Soukarieh Omar , Bonnet-Dorion Françoise , Guibert Virginie , Bronner Myriam , Bourdon Violaine , Lizard Sarab , Vilquin Paul , Privat Maud , Drouet Aurélie , Grout Charlotte , Calléja Fabienne M.G.R. , Golmard Lisa , Vrieling Harry , Stoppa-Lyonnet Dominique , Houdayer Claude , Frebourg Thierry , Vreeswijk Maaike P.G. , Martins Alexandra , Gaildrat Pascaline
Published: April 2023

Supplementary Tables S1-S4. Table S1. Description of primers used in this study. Table S2. Variants selected in BRCA2 exon 12 and its flanking intronic regions. Table S3. Overview of bioinformatics predictions and experimental data obtained for the 40 selected BRCA2 exon 12 variants. Table S4. Clinical and family data of patients carrying BRCA2 exon 12 spliceogenic variants.
Supplementary Figures 1-6 from UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
Authors: Qiao Xi , Liu Ying , Prada Maria Llamazares , Mohan Aravind K. , Gupta Abhishekh , Jaiswal Alok , Sharma Mukund , Merisaari Joni , Haikala Heidi M. , Talvinen Kati , Yetukuri Laxman , Pylvänäinen Joanna W. , Klefström Juha , Kronqvist Pauliina , Meinander Annika , Aittokallio Tero , Hietakangas Ville , Eilers Martin , Westermarck Jukka
Published: April 2023

Supplementary Figures 1-6. Figure S1: UBR5 and MYC interaction assays and WB controls for RNA-seq. experiment. Fig. S2: MYC and NMYC stability regulation by UBR5 and ubiquitin assays in denaturating conditions. Fig. S3: Additional Drosophila phenotype data. Fig. S4: Colony growth and apoptosis assays in UBR5 depleted control and drug-treated cells. Fig. S5: Role of UBR5 in basal-like breast cancer cells and Kaplan-Meier analyses. Fig. S6: IF and IHC analysis of MYC and UBR5 expression in basal-like TNBC.
Supplementary Tables from Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System
Authors: Tubeuf Hélène , Caputo Sandrine M. , Sullivan Teresa , Rondeaux Julie , Krieger Sophie , Caux-Moncoutier Virginie , Hauchard Julie , Castelain Gaia , Fiévet Alice , Meulemans Laëtitia , Révillion Françoise , Léoné Mélanie , Boutry-Kryza Nadia , Delnatte Capucine , Guillaud-Bataille Marine , Cleveland Linda , Reid Susan , Southon Eileen , Soukarieh Omar , Drouet Aurélie , Di Giacomo Daniela , Vezain Myriam , Bonnet-Dorion Françoise , Bourdon Violaine , Larbre Hélène , Muller Danièle , Pujol Pascal , Vaz Fátima , Audebert-Bellanger Séverine , Colas Chrystelle , Venat-Bouvet Laurence , Solano Angela R. , Stoppa-Lyonnet Dominique , Houdayer Claude , Frebourg Thierry , Gaildrat Pascaline , Sharan Shyam K. , Martins Alexandra
Published: April 2023

Supp Tables S1-S6 (including variant classification, bioinformatics predictions versus experimental data, primer sequences, summary of biological, clinical, tumoral, familial and multifactorial data, and description of statistical analysis approaches)
Supplementary Data from Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System
Authors: Tubeuf Hélène , Caputo Sandrine M. , Sullivan Teresa , Rondeaux Julie , Krieger Sophie , Caux-Moncoutier Virginie , Hauchard Julie , Castelain Gaia , Fiévet Alice , Meulemans Laëtitia , Révillion Françoise , Léoné Mélanie , Boutry-Kryza Nadia , Delnatte Capucine , Guillaud-Bataille Marine , Cleveland Linda , Reid Susan , Southon Eileen , Soukarieh Omar , Drouet Aurélie , Di Giacomo Daniela , Vezain Myriam , Bonnet-Dorion Françoise , Bourdon Violaine , Larbre Hélène , Muller Danièle , Pujol Pascal , Vaz Fátima , Audebert-Bellanger Séverine , Colas Chrystelle , Venat-Bouvet Laurence , Solano Angela R. , Stoppa-Lyonnet Dominique , Houdayer Claude , Frebourg Thierry , Gaildrat Pascaline , Sharan Shyam K. , Martins Alexandra
Published: April 2023

Word doc, marked changes. Supp Table of contents, Supp Materials and Methods, Supp Figures S1-S17 (including description of BRCA2 mRNA and protein domains, selection of BRCA2 variants, minigene structure, RNA splicing data versus bioinformatics predictions, minigene results versus patients' RNA and mESC's data, and results from mESC complementation assays), Supp Note and Supp Reference
Table S1 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Table 1
Figure S5 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Data 5
Supplementary Information from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Information
Supplementary Figure S6 A-F from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S6. PA2G4 increases neuroblastoma tumorigenicity. A, Representative images of athymic nude mice inoculated with neuroblastoma (SH-EP) cells stably transfected with either EV control or a PA2G4 expression vector at 10 weeks post-injection. B, Images of tumor formation after mice were culled 12 weeks post-injection. C, Real-time PCR analysis of PA2G4 mRNA expression level in tumors from mice injected with either SH-EP cells overexpressing PA2G4, or SH-EP EV control cells. β2-microglobulin was used as a reference gene for total RNA loading. D, Protein was extracted from SH-EP tumor xenografts overexpressing PA2G4 and control vectors, then analysed for PA2G4-Flag and MYCN expression by immunoblotting using anti-MYCN and anti-PA2G4 antibodies, using a Vinculin loading control. E, Immunoblots of three tumor samples from each siRNA-treated cohort showing the levels of PA2G4 and MYCN protein expression, using a Vinculin loading control. F, Real-time PCR analysis of PA2G4 and MYCN mRNA expression in tumor samples taken from tumour-bearing mice xenografted with BE(2)-C neuroblastoma cells, which had been treated with either nano-particle encapsulated siRNA control, PA2G4 siRNA or PA2G4-p48 siRNA. Data are shown as means and SD derived from 6 mice per group, P-values were calculated by t-test.
Supplementary Figure from Inhaled TLR9 Agonist Renders Lung Tumors Permissive to PD-1 Blockade by Promoting Optimal CD4+ and CD8+ T-cell Interplay
Authors: Gallotta Marilena , Assi Hikmat , Degagné Émilie , Kannan Shravan Kumar , Coffman Robert L. , Guiducci Cristiana
Published: April 2023

The supplementary figure contains four figures. The first figure shows that the 4T1 tumors when growing in the lung tissue have an excluded phenotype, with T cells and PDL-1 positive cells surrounding the perimeter of the tumor. The second Figure shows the characterization of the CD11b myeloid population in 4T1 bearing animals treated with Saline or SD-10, by FACS analysis. The third figures shows that CD4 T cells depletion results in a significant decrease of SD-101 induced IL-21 protein, detected in tumor bearing lung BAL. The fourth Figure demonstrates that there is no expansion of CD8 T cells in untreated tumor bearing mice depleted of CD4 T cells.
Supplementary Figure S3 F-G from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S3 F-G F, Left panel: Histopathologic and immunohistochemical analyses of MYCN;GFP tumors treated with vehicle (left) or WS6 (right). Left Panel, Top to Bottom: Neuroblastoma tumour sections immunohistochemically stained for Haematoxylin & Eosin (H&E), Proliferating Cell Nuclear Antigen (pCNA), Neural Hu protein C (Hu-C), MYCN, PA2G4 and Tyrosine Hydroxylase. Scale bar, 50 μm. Right Panel: Histograms illustrating the staining intensity of cells of vehicle (left) or WS6 treated neuroblastoma tumours expressing either MYCN, PA2G4 or Tyrosine Hydroxylase as measured by Image J software. Sample means (horizontal bars) were compared by students t-test (two-tailed). *** represents p-value <0.0001. ns represents p-value of no significance. error bars represent SEM. G, IC50 value of WS6, compared to other MYCN oncogenic signal inhibitors, after treatment of MYCN amplified Kelly neuroblastoma cells. IC50 value for CD532 is the average IC50 values for 169 cancer cell lines.
Supplementary materials from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary materials and methods, figure legends, and tables.
Supplementary Figure S3 A-E from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S3. Competitive chemical inhibition of MYCN-PA2G4 binding. A, Chemical structure of WS6. B, Cycloheximide chase assay measuring the half-life of MYCN protein in BE(2)-C and Kelly cells following 0.8 µM WS6 treatment for 24 hours, then treatment with 100 µg/µl CHX for up to 60 minutes. C, BE(2)-C and Kelly cells treated with 0.2 µM or 0.4 µM WS6, followed by colony formation assessment, compared to untreated cells. D, Immunoblotting with an anti-MYC-Tag antibody to quantify PA2G4 protein expression from SH-SY5Y and Kelly cells transfected with the MYC-tagged PA2G4 vector. E, Densitometric quantification of MYCN and PA2G4 protein levels of immunoblots using tumor tissues of TH-MYCN mice treated with either DMSO (n=5) or WS6 (n=5), and quantified by Image J software. Sample means were compared by students t-test. * Represents p-value <0. 05. Error bars represent SEM.
Supplementary Figure 4 from CTGF Mediates Tumor–Stroma Interactions between Hepatoma Cells and Hepatic Stellate Cells to Accelerate HCC Progression
Authors: Makino Yuki , Hikita Hayato , Kodama Takahiro , Shigekawa Minoru , Yamada Ryoko , Sakamori Ryotaro , Eguchi Hidetoshi , Morii Eiichi , Yokoi Hideki , Mukoyama Masashi , Hiroshi Suemizu , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplementary Fig. 4. CTGF knock-down in HepG2 cells abolishes the growth-promoting effect by the co-existence of LX-2 cells. HepG2 cell growth was evaluated using a WST-8 assay in vitro or in xenograft models at the indicated time points. In the cell culture experiments, HepG2 cells were incubated under monoculture or Transwell-co-culture with the same number of LX-2 cells. (A) The CTGF protein expression and the growth of HepG2 cells transfected with CTGF siRNAs (#1 and #2) or control siRNA under monoculture or Transwell co-culture with LX-2 cells. Total protein was collected 72 hours after siRNA transfection. Cells were re-plated 72 hours after siRNA transfection and incubated under monoculture or Transwell co-culture with LX-2 cells. (B) CTGF protein expression and in vitro growth of HepG2 cells transfected with CTGF shRNAs or control shRNA. Total protein was collected 24 hours after plating. (C) Xenograft models of HepG2 cells transfected with CTGF shRNAs or control shRNA co-injected with or without the same number of LX-2 cells. HepG2 cells were injected alone or co-injected with the same number of LX-2 cells into the left and right flanks of the mice, respectively. The mice were sacrificed, and the xenograft tumors were enucleated 22 days after inoculation. Representative images of enucleated tumors and sequential tumor volumes are presented as N = 4 (A, B) or 9-10 (C) per group. In the line graphs, plots with whiskers represent mean values {plus minus} standard deviations. *p < 0.05 vs the control.
Supplementary Figure S1 A-E from Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface
Authors: Koach Jessica , Holien Jessica K. , Massudi Hassina , Carter Daniel R. , Ciampa Olivia C. , Herath Mika , Lim Taylor , Seneviratne Janith A. , Milazzo Giorgio , Murray Jayne E. , McCarroll Joshua A. , Liu Bing , Mayoh Chelsea , Keenan Bryce , Stevenson Brendan W. , Gorman Michael A. , Bell Jessica L. , Doughty Larissa , Hüttelmaier Stefan , Oberthuer Andre , Fischer Matthias , Gifford Andrew J. , Liu Tao , Zhang Xiaoling , Zhu Shizhen , Gustafson W. Clay , Haber Michelle , Norris Murray D. , Fletcher Jamie I. , Perini Giovanni , Parker Michael W. , Cheung Belamy B. , Marshall Glenn M.
Published: April 2023

Supplementary Figure S1. PA2G4 is a MYCN transactivation target gene. A, Quantification of protein expression using anti-PA2G4 and anti-MYCN antibodies against whole cell protein lysates from BE(2)-C and Kelly cells, following MYCN siRNA knockdown for 48 hours. B, mRNA expression of PA2G4 and MYCN in SH-EP MYCN3 overexpression cells treated with 1µg/ml doxycycline for 24-96 hr. C, The effect of doxycycline-induced MYCN overexpression in SHEP-TRE-MYCN cells on c-MYC and PA2G4 protein expression. D, Chromatin immunoprecipitation (ChIP) assay in Kelly cells using an anti-MYCN antibody, and real-time PCR analysis with primers identifying the MYCN DNA binding sites in the PA2G4 gene promoter (500bP upstream of transcription start site [TSS]) or Intron 1a & 1b regions of the PA2G4 gene, with and without MYCN siRNA knockdown. ChIP and real-time PCR analysis using primers against a region 1200bp upstream of TSS was used as a negative control for MYCN chromatin binding. ChIP and real-time PCR analysis using primers against the ornithine decarboxylase (ODC1) gene promoter region was used as a positive control for MYCN chromatin binding. E, Immunoblot analysis of PA2G4, MYCN and MYC protein levels in a panel of human MYCN amplified and non-amplified neuroblastoma, and normal fibroblast, cell lines using antibodies recognising PA2G4, MYCN and MYC.
Supplementary Data File from Autofluorescence Imaging of 3D Tumor–Macrophage Microscale Cultures Resolves Spatial and Temporal Dynamics of Macrophage Metabolism
Authors: Heaster Tiffany M. , Humayun Mouhita , Yu Jiaquan , Beebe David J. , Skala Melissa C.
Published: April 2023

Supplementary figures 1-5 and supplementary tables 1-3. Supplementary Figure 1: Fluorescence lifetimes of NAD(P)H and FAD exhibit differences between macrophage polarization states. Supplementary Figure 2: Validation of two-photon wavelength mixing for evaluating autofluorescence and migration effects in 2D cultures and the 3D Stacks microfluidic platform. Supplementary Figure 3: Prolonged co-culture of mouse breast cancer and macrophages yields heterogeneous NAD(P)H and FAD fluorescence lifetime and migration compared to monoculture. Supplementary Figure 4: Primary human tumor cells stimulate changes in NAD(P)H and FAD fluorescence lifetime and cell migration in co-cultured human monocyte-derived macrophages. Supplementary Figure 5: Metabolic changes in human THP-1s following co-culture with MDA-MB-231 human breast carcinoma. Supplementary Table 1: Mouse and Human Macrophage Polarization Gene Panels. Supplementary Table 2: Significance of redox ratio fold change in inhibitor-treated 2D cytokine-stimulated mouse macrophages. Supplementary Table 3: Coefficients of variation (CV) and significance of CV equality for optical redox ratio in 2D cytokine-stimulated mouse macrophages and 3D mouse monocultures and co-cultures.
Supplemental0530.pdf from Deletion of Glutathione S-Transferase Omega 1 Activates Type I Interferon Genes and Downregulates Tissue Factor
Authors: Xu Yibin , Bankhead Armand , Tian Xiaoli , Tang Jianming , Ljungman Mats , Neamati Nouri
Published: April 2023

Supplemental Figures 1-15 and Supplemental Tables 1-32
Supplementary Data from Noninvasive MRI Native T1 Mapping Detects Response to MYCN-targeted Therapies in the Th-MYCN Model of Neuroblastoma
Authors: Zormpas-Petridis Konstantinos , Poon Evon , Clarke Matthew , Jerome Neil P. , Boult Jessica K.R. , Blackledge Matthew D. , Carceller Fernando , Koers Alexander , Barone Giuseppe , Pearson Andrew D.J. , Moreno Lucas , Anderson John , Sebire Neil , McHugh Kieran , Koh Dow-Mu , Chesler Louis , Yuan Yinyin , Robinson Simon P. , Jamin Yann
Published: April 2023

Table S1: MRI acquisition parameters, Supplementary results including Table S2 summarising the subregional analysis, Table S3: confusion matrix for cell classification, Figure S1 showing tumor volumes at the time of enrolment, Figure S2 showing individual therapy-induced changes in volume, Figure S3 showing the validation of our algorithm for the automatic classification of apoptotic cells from HE-stained slides digitised images with cleaved caspase-3 imunohistochemistry, Figure S4 showing cleaved caspase-3 imunohistochemistry.
Table S3 from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: April 2023

Known transcription factor motifs enriched in shared and FOXL2 mutant-specific peaks predicted by Homer motif analysis.
Table S2 from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: April 2023

List of protein-coding (pc) and non_coding (nc) genes differentially expressed (UP or DOWN) following induction of WT and MUT FOXL2 in polyA and ribodepleted RNA-seq datasets.
Table S1 from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: April 2023

RNA-seq (polyA and ribodepleted) RPKM matrix for protein coding genes from primary AGCT and SVOG3e derived isogenic cell lines.
Supplementary Methods from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: April 2023

Detailed supplemental methods of cell lines and cell culture, cell cycle synchronization and inducible expression of FOXL2, quantitative mass spectrometry analysis of induced FOXL2 expression, FOXL2 ChIP-seq analysis, RNA-seq analysis, and electrophoretic mobility shift assay.
Figure S5 from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Brca1L1363P mutant protein is capable of interacting with Bach1
Figure S4 from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Brca1L1363P mutation induces premature senescent phenotype in pMEFs
Figure S2 from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: April 2023

Spermatogonial germ cells failed to proliferate in Brca1L1363P/L1363P animals
Supplementary Data from Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression
Authors: Midorikawa Yutaka , Yamamoto Shogo , Tatsuno Kenji , Renard-Guillet Claire , Tsuji Shingo , Hayashi Akimasa , Ueda Hiroki , Fukuda Shiro , Fujita Takanori , Katoh Hiroto , Ishikawa Shumpei , Covington Kyle R. , Creighton Chad J. , Sugitani Masahiko , Wheeler David A. , Shibata Tatsuhiro , Nagae Genta , Takayama Tadatoshi , Aburatani Hiroyuki
Published: April 2023

Supplementary Figure legends
Table S3 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Chromosome regions significantly enriched for chromothriptic events and breast cancer drivers statistically overrepresented in such regions
Figure S1, Figure S2 from Upregulation of E3 Ubiquitin Ligase CBLC Enhances EGFR Dysregulation and Signaling in Lung Adenocarcinoma
Authors: Hong Shiao-Ya , Kao Yu-Rung , Lee Te-Chang , Wu Cheng-Wen
Published: April 2023

Figure S1- CBLC expression is upregulated in NSCLC cell lines and clinical patients. Figure S2- Negative correlation between CBLC promoter methylation and mRNA expression in TCGA LUAD and LUSC studies.
Table S1 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Description of the patient cohorts and available data
Supplementary Figure Legends from HDAC6 Inhibition Synergizes with Anti-PD-L1 Therapy in ARID1A-Inactivated Ovarian Cancer
Authors: Fukumoto Takeshi , Fatkhutdinov Nail , Zundell Joseph A. , Tcyganov Evgenii N. , Nacarelli Timothy , Karakashev Sergey , Wu Shuai , Liu Qin , Gabrilovich Dmitry I. , Zhang Rugang
Published: April 2023

Supplementary Figure Legends
Supplementary Files Legends from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Legends of Supplementary Figures and Tables
Figure S3 from HDAC6 Inhibition Synergizes with Anti-PD-L1 Therapy in ARID1A-Inactivated Ovarian Cancer
Authors: Fukumoto Takeshi , Fatkhutdinov Nail , Zundell Joseph A. , Tcyganov Evgenii N. , Nacarelli Timothy , Karakashev Sergey , Wu Shuai , Liu Qin , Gabrilovich Dmitry I. , Zhang Rugang
Published: April 2023

Figure S3 shows that the effects of HDAC6 inhibitor ACY1215 alone or in combination with anti-PD-L1 on tumor immune microenvironment and that the combination of HDAC6 inhibitor ACY1215 and anti-PD-L1 does not affect the body weight of the treated mice.
Supplementary Figure 6 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Timed copy number changes and chromothriptic events in sample pairs
Figure S2 from HDAC6 Inhibition Synergizes with Anti-PD-L1 Therapy in ARID1A-Inactivated Ovarian Cancer
Authors: Fukumoto Takeshi , Fatkhutdinov Nail , Zundell Joseph A. , Tcyganov Evgenii N. , Nacarelli Timothy , Karakashev Sergey , Wu Shuai , Liu Qin , Gabrilovich Dmitry I. , Zhang Rugang
Published: April 2023

Figure S2 shows ARID1A suppresses PD-L1 expression.
Supplementary Figure 5 from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: April 2023

Copy-number plots and rainfall plots for the 11 patients with two tumors from the DKFZ-HIPO17 cohort
Supplementary Data from E74-Like Factor 3 Is a Key Regulator of Epithelial Integrity and Immune Response Genes in Biliary Tract Cancer
Authors: Suzuki Masami , Saito-Adachi Mihoko , Arai Yasuhito , Fujiwara Yuko , Takai Erina , Shibata Shinsuke , Seki Masahide , Rokutan Hirofumi , Maeda Daichi , Horie Masafumi , Suzuki Yutaka , Shibata Tatsuhiro , Kiyono Tohru , Yachida Shinichi
Published: April 2023

Supplemental experimental procedures, Figure S1-S16, Table S5