bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental figure legends from Dynamic Patterns of Clonal Evolution in Tumor Vasculature Underlie Alterations in Lymphocyte–Endothelial Recognition to Foster Tumor Immune Escape
Authors: Corey Daniel M. , Rinkevich Yuval , Weissman Irving L.
Published: March 2023

Supplemental figure legends
Supplementary Figure Legends from Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients
Authors: Osman Abdullah A. , Neskey David M. , Katsonis Panagiotis , Patel Ameeta A. , Ward Alexandra M. , Hsu Teng-Kuei , Hicks Stephanie C. , McDonald Thomas O. , Ow Thomas J. , Alves Marcus Ortega , Pickering Curtis R. , Skinner Heath D. , Zhao Mei , Sturgis Eric M. , Kies Merrill S. , El-Naggar Adel , Perrone Federica , Licitra Lisa , Bossi Paolo , Kimmel Marek , Frederick Mitchell J. , Lichtarge Olivier , Myers Jeffrey N.
Published: March 2023

Supplementary Figure Legends. Expression of p53 target genes is impaired following cisplatin treatment in HNSCC harboring mutant TP53; TP53 knockdown illustrates both loss and gain of function in vitro in HNSCC cells;Effect of cisplatin therapy on tumor growth and survival in an orthotopic nude mouse model of oral tongue cancer harboring TP53 mutations presented as area under the growth curve (AUC).
Supplementary Methods and References from A CDK4/6-Dependent Epigenetic Mechanism Protects Cancer Cells from PML-induced Senescence
Authors: Acevedo Mariana , Vernier Mathieu , Mignacca Lian , Lessard Frédéric , Huot Geneviève , Moiseeva Olga , Bourdeau Véronique , Ferbeyre Gerardo
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Figure 3 from Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients
Authors: Osman Abdullah A. , Neskey David M. , Katsonis Panagiotis , Patel Ameeta A. , Ward Alexandra M. , Hsu Teng-Kuei , Hicks Stephanie C. , McDonald Thomas O. , Ow Thomas J. , Alves Marcus Ortega , Pickering Curtis R. , Skinner Heath D. , Zhao Mei , Sturgis Eric M. , Kies Merrill S. , El-Naggar Adel , Perrone Federica , Licitra Lisa , Bossi Paolo , Kimmel Marek , Frederick Mitchell J. , Lichtarge Olivier , Myers Jeffrey N.
Published: March 2023

Supplementary Figure 3: Effect of cisplatin therapy on tumor growth and survival in an orthotopic nude mouse model of oral tongue cancer harboring TP53 mutations presented as area under the growth curve (AUC).
Supplemental Table 4 from Jak1–STAT3 Signals Are Essential Effectors of the USP6/TRE17 Oncogene in Tumorigenesis
Authors: Quick Laura , Young Robert , Henrich Ian C. , Wang Xiaoke , Asmann Yan W. , Oliveira Andre M. , Chou Margaret M.
Published: March 2023

Entire NF dataset
Supplementary table 1 from S-nitrosylation of the Mitochondrial Chaperone TRAP1 Sensitizes Hepatocellular Carcinoma Cells to Inhibitors of Succinate Dehydrogenase
Authors: Rizza Salvatore , Montagna Costanza , Cardaci Simone , Maiani Emiliano , Di Giacomo Giuseppina , Sanchez-Quiles Virginia , Blagoev Blagoy , Rasola Andrea , De Zio Daniela , Stamler Jonathan S. , Cecconi Francesco , Filomeni Giuseppe
Published: March 2023

WB densitometry and statistical analyses
Supplementary Figures S1-S10 from Downregulation of the TGFβ Pseudoreceptor BAMBI in Non–Small Cell Lung Cancer Enhances TGFβ Signaling and Invasion
Authors: Marwitz Sebastian , Depner Sofia , Dvornikov Dmytro , Merkle Ruth , Szczygieł Magdalena , Müller-Decker Karin , Lucarelli Philippe , Wäsch Marvin , Mairbäurl Heimo , Rabe Klaus F. , Kugler Christian , Vollmer Ekkehard , Reck Martin , Scheufele Swetlana , Kröger Maren , Ammerpohl Ole , Siebert Reiner , Goldmann Torsten , Klingmüller Ursula
Published: March 2023

Activity of the TGF-beta pathway in tumor-free lung and lung cancer (S1); Validation of the microarray data for individual targets with qRT-PCR assay (S2); Expression of EMT-related proteins in human lung tumor tissues and tumor-free lung (S3); Secretion of TGF-beta and expression of the pathway components in NSCLC cell lines (S4); Activation of TGF-beta pathway members and expression of EMT markers in lung cancer cells with BAMBI reconstitution (S5); Verification of DNA methylation values determined by HumanMethylation450K BeadChip analysis by performing bisulfite pyrosequencing (S6); siRNA-mediated knockdown of BAMBI expression in A549 cell line enhances TGF-beta-induced signaling (S7); siRNA-mediated knockdown of BAMBI expression in the squamous cell carcinoma cell line SK-MES1 enhances TGF-beta-induced signaling (S8); Human alveolar epithelial cells type II (AECII) cells express low amount of SMAD3 (S9); GFP- and BAMBI-GFP-positive A549 cells are present in the mice lungs at the time of sacrifice (S10).
Supplementary tables from Myeloid-Derived Suppressor Cells Endow Stem-like Qualities to Breast Cancer Cells through IL6/STAT3 and NO/NOTCH Cross-talk Signaling
Authors: Peng Dongjun , Tanikawa Takashi , Li Wei , Zhao Lili , Vatan Linda , Szeliga Wojciech , Wan Shanshan , Wei Shuang , Wang Yin , Liu Yan , Staroslawska Elzbieta , Szubstarski Franciszek , Rolinski Jacek , Grywalska Ewelina , Stanisławek Andrzej , Polkowski Wojciech , Kurylcio Andrzej , Kleer Celina , Chang Alfred E. , Wicha Max , Sabel Michael , Zou Weiping , Kryczek Ilona
Published: March 2023

Supplementary tables: Supplementary Table 1. Patient characteristics (All 3 cohorts) Supplementary Table 2. shRNA Sequences and Real-time PCR primers Supplementary Table 3. Multivariate analysis of overall survival (All 3 cohorts) Supplementary Table 4. Multivariate analysis of overall survival (Cohort 1, HER2+ patients) Supplementary Table 5. Multivariate analysis of overall survival (Cohorts 2 and 3, random patients)
Supplementary Material from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
Authors: Lohse Stefan , Meyer Saskia , Meulenbroek Laura A.P.M. , Jansen J.H. Marco , Nederend Maaike , Kretschmer Anna , Klausz Katja , Möginger Uwe , Derer Stefanie , Rösner Thies , Kellner Christian , Schewe Denis , Sondermann Peter , Tiwari Sanjay , Kolarich Daniel , Peipp Matthias , Leusen Jeanette H.W. , Valerius Thomas
Published: March 2023

Material and Methods Glycoprofiling
Supplementary Figure 1 from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
Authors: Lohse Stefan , Meyer Saskia , Meulenbroek Laura A.P.M. , Jansen J.H. Marco , Nederend Maaike , Kretschmer Anna , Klausz Katja , Möginger Uwe , Derer Stefanie , Rösner Thies , Kellner Christian , Schewe Denis , Sondermann Peter , Tiwari Sanjay , Kolarich Daniel , Peipp Matthias , Leusen Jeanette H.W. , Valerius Thomas
Published: March 2023

SDS-PAGE separated and electroblotted IgA Proteins after staining with direct blue 71. The red boxes indicate the bands cut out for subsequent N-glycan Analysis.
Supplemental Figure Legends from In Situ Tumor Vaccination by Combining Local Radiation and Tumor-Specific Antibody or Immunocytokine Treatments
Authors: Morris Zachary S. , Guy Emily I. , Francis David M. , Gressett Monica M. , Werner Lauryn R. , Carmichael Lakeesha L. , Yang Richard K. , Armstrong Eric A. , Huang Shyhmin , Navid Fariba , Gillies Stephen D. , Korman Alan , Hank Jacquelyn A. , Rakhmilevich Alexander L. , Harari Paul M. , Sondel Paul M.
Published: March 2023

Supplemental Figure Legends
Supplementary Figure Legends from Chemotherapy-Induced miRNA-29c/Catenin-δ Signaling Suppresses Metastasis in Gastric Cancer
Authors: Wang Yuxuan , Liu Changzheng , Luo Min , Zhang Zhengyi , Gong Jianan , Li Jingjing , You Lei , Dong Lei , Su Rui , Lin Haishuang , Ma Yanni , Wang Fang , Wang Yi , Chen Jie , Zhang Junwu , Jia Hongyan , Kong Yan , Yu Jia
Published: March 2023

Legends for Supplementary Figures S1-S10.
Supplementary Figures 1-6 from Treatment of Triple-Negative Breast Cancer with TORC1/2 Inhibitors Sustains a Drug-Resistant and Notch-Dependent Cancer Stem Cell Population
Authors: Bhola Neil E. , Jansen Valerie M. , Koch James P. , Li Hua , Formisano Luigi , Williams Janice A. , Grandis Jennifer R. , Arteaga Carlos L.
Published: March 2023

Figure S1. Inhibition of TORC1/2 promotes a CSC-like phenotype in TNBC cells. Figure S2. TORC1/2 inhibition increases expression of Notch1, FGF1 and Notch1 activity. Figure S3. TORC1/2 inhibition and paclitaxel sustains Notch1 activity and a CSC-like phenotype. Figure S4. Inhibiting Notch1 decreases the CSC-like population induced by inhibition of TORC1/2. Figure S5. TORC1/2 inhibition induces mitochondrial metabolism. Figure S6. Induction of NICD and CSCs upon TORC1/2 inhibition is FGFR-dependent.
Supplementary Figures 1 and 2 from Cyclin D1 Promotes Androgen-Dependent DNA Damage Repair in Prostate Cancer Cells
Authors: Casimiro Mathew C. , Di Sante Gabriele , Ju Xiaoming , Li Zhiping , Chen Ke , Crosariol Marco , Yaman Ismail , Gormley Michael , Meng Hui , Lisanti Michael P. , Pestell Richard G.
Published: March 2023

Endogenous cyclin D1 promotes LNCaP cell proliferation and DNA synthesis (S1); The epithelial population in Cyclin D1+/+ PECs is predominantly composed of luminal CK8+ cells (S2).
Supplementary Figure Legends from Cyclin D1 Promotes Androgen-Dependent DNA Damage Repair in Prostate Cancer Cells
Authors: Casimiro Mathew C. , Di Sante Gabriele , Ju Xiaoming , Li Zhiping , Chen Ke , Crosariol Marco , Yaman Ismail , Gormley Michael , Meng Hui , Lisanti Michael P. , Pestell Richard G.
Published: March 2023

Legends for supplementary figures.
Supplementary Figures S1-S8 from Improved Treatment of Breast Cancer with Anti-HER2 Therapy Requires Interleukin-21 Signaling in CD8+ T Cells
Authors: Mittal Deepak , Caramia Franco , Michiels Stefan , Joensuu Heikki , Kellokumpu-Lehtinen Pirkko-Liisa , Sotiriou Christos , Loi Sherene , Smyth Mark J.
Published: March 2023

IL-21R expression on splenocytes and TILs from H2N100 tumor-bearing mice (S1); ErbB-2 positive tumor cell lines do not express IL-21R (S2); CD8+ T cells and NK cells after ACT in Balb/c.Rag2-/- γc-/- mice (S3); B-cells and NKT cells are not likely to be required for anti-ErbB-2 mAb therapy (S4); Tfh cells are not likely to be required for anti-ErbB-2 mAb therapy (S5); Myeloid cell infiltrates in ErbB-2+ tumors (S6); Recombinant IL-21 improves therapeutic efficacy of anti-ErbB-2 mAb therapy (S7); Spearmans' correlations are shown between genes of interest, TILs as previously described and selected genes representing CD8+ T cell phenotype using patient's samples from the FinHER clinical trial (S8).
Supplementary Table S9 from Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers
Authors: Kaczkowski Bogumil , Tanaka Yuji , Kawaji Hideya , Sandelin Albin , Andersson Robin , Itoh Masayoshi , Lassmann Timo , Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R.R.
Published: March 2023

Gene level overlap between differentially expressed, protein-coding genes from the FANTOM5 analysis, the TCGA in-house analysis and the TCGA analysis by Cabanski at al. and Zhang at al.
Supplemental data from YAP Mediates Tumorigenesis in Neurofibromatosis Type 2 by Promoting Cell Survival and Proliferation through a COX-2–EGFR Signaling Axis
Authors: Guerrant William , Kota Smitha , Troutman Scott , Mandati Vinay , Fallahi Mohammad , Stemmer-Rachamimov Anat , Kissil Joseph L.
Published: March 2023

Supplemental figures, methods and tables. Figure S1 (related to Figure 1): YAP activity is required for NF2-null Schwann cell proliferation. Figure S2 (related to Figure 2): YAP is required for colony formation in vitro and tumor growth in vivo. Figure S3 (related to Figure 4): COX-2 activity is required for NF2-null Schwann cell growth. Figure S4 (related to Figure 5): SU6656 treatment suppresses EGFR activation. (A&B) Figure S5 (related to Figure 6): YAP activity increases the expression of COX-2 and AREG. Figure S6: Schematic model for the proposed role of YAP in NF2-null schwannoma cells. Table S1: Sequences of siRNAs Table S2: Primer Sequences for RT-PCR
Supplementary Table S7 from Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers
Authors: Kaczkowski Bogumil , Tanaka Yuji , Kawaji Hideya , Sandelin Albin , Andersson Robin , Itoh Masayoshi , Lassmann Timo , Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R.R.
Published: March 2023

Genes located within 100kb from the promoters of differentially expressed long non-coding RNAs.
Supplementary Table S3 from Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers
Authors: Kaczkowski Bogumil , Tanaka Yuji , Kawaji Hideya , Sandelin Albin , Andersson Robin , Itoh Masayoshi , Lassmann Timo , Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R.R.
Published: March 2023

Differentially expressed promoters.
Supplementary Table S13 from Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers
Authors: Kaczkowski Bogumil , Tanaka Yuji , Kawaji Hideya , Sandelin Albin , Andersson Robin , Itoh Masayoshi , Lassmann Timo , Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R.R.
Published: March 2023

The genomic overlap of differentially expressed promoters and repetitive elements from RepeatMasker.
Supplementary Table S10 from Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers
Authors: Kaczkowski Bogumil , Tanaka Yuji , Kawaji Hideya , Sandelin Albin , Andersson Robin , Itoh Masayoshi , Lassmann Timo , Hayashizaki Yoshihide , Carninci Piero , Forrest Alistair R.R.
Published: March 2023

Gene level overlap between differentially expressed lncRNAs from the FANTOM5 analysis and the miTranscriptome study.
Supplementary Methods from Modeling Spontaneous Metastasis following Surgery: An In Vivo-In Silico Approach
Authors: Benzekry Sebastien , Tracz Amanda , Mastri Michalis , Corbelli Ryan , Barbolosi Dominique , Ebos John M.L.
Published: March 2023

Description of additional methods and procedures used in the study.
Supplementary Figures S1-S11 from Modeling Spontaneous Metastasis following Surgery: An In Vivo-In Silico Approach
Authors: Benzekry Sebastien , Tracz Amanda , Mastri Michalis , Corbelli Ryan , Barbolosi Dominique , Ebos John M.L.
Published: March 2023

In vitro fit and direct statistical analysis of the xenograft breast data (S1); Population fit of the tumor growth data that were measured by BL, under the Gomp-Exp model and initial volume Vi fixed by the conversion rule inferred from the correlation between volume and BL (S2); Population fits of the breast xenograft data under different growth theories (S3); Population fits of the kidney isograft data under different growth theories (S4); Second kidney data set used for fitting the data (S5); Individual fits of primary tumor and metastatic burden kinetics Breast animal model (S6); Individual fits of primary tumor and metastatic burden kinetics. Kidney animal model (S7); Link between experimental and model survival (S8); Surgery benefit on survival and metastatic burden reduction as a function of resection size, for varying values of metastatic potential (S9); Population fits of the ortho-surgical metastasis animal models for a dissemination coefficient d(Vp) = ??Vyp and various values of y (S10); Population fits of the ortho-surgical metastasis animal models for various values of the signal-to-cell ratio V0 (S11).
Fig.S8 from Dual Roles for CXCL4 Chemokines and CXCR3 in Angiogenesis and Invasion of Pancreatic Cancer
Authors: Quemener Cathy , Baud Jessica , Boyé Kevin , Dubrac Alexandre , Billottet Clotilde , Soulet Fabienne , Darlot Florence , Dumartin Laurent , Sire Marie , Grepin Renaud , Daubon Thomas , Rayne Fabienne , Wodrich Harald , Couvelard Anne , Pineau Raphael , Schilling Martin , Castronovo Vincent , Sue Shih-Che , Clarke Kim , Lomri Abderrahim , Khatib Abdel-Majid , Hagedorn Martin , Prats Hervé , Bikfalvi Andreas
Published: March 2023

Characterization of CXCR3 overexpression in MIA PaCa-2 cells in vitro
Supplementary Movie 3 from Metabolic Stress-Induced Phosphorylation of KAP1 Ser473 Blocks Mitochondrial Fusion in Breast Cancer Cells
Authors: Cheng Chun-Ting , Kuo Ching-Ying , Ouyang Ching , Li Chien-Feng , Chung Yiyin , Chan David C. , Kung Hsing-Jien , Ann David K.
Published: March 2023

Movie 3. Time-lapse imaging of MDA-MB-231/shKAP1/S473A-KAP1 cells in glucose-depleted medium.
Supplementary Materials from Metabolic Stress-Induced Phosphorylation of KAP1 Ser473 Blocks Mitochondrial Fusion in Breast Cancer Cells
Authors: Cheng Chun-Ting , Kuo Ching-Ying , Ouyang Ching , Li Chien-Feng , Chung Yiyin , Chan David C. , Kung Hsing-Jien , Ann David K.
Published: March 2023

This file includes supplementary figure legends and movie legends.
Supplementary Figure S5 from Mutational Landscape and Antiproliferative Functions of ELF Transcription Factors in Human Cancer
Authors: Ando Mizuo , Kawazu Masahito , Ueno Toshihide , Koinuma Daizo , Ando Koji , Koya Junji , Kataoka Keisuke , Yasuda Takahiko , Yamaguchi Hiroyuki , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Sai Eirin , Yamashita Yoshihiro , Asakage Takahiro , Miyazaki Yasushi , Kurokawa Mineo , Miyazono Kohei , Nimer Stephen D. , Yamasoba Tatsuya , Mano Hiroyuki
Published: March 2023

Anti-proliferation activity of ELF4, but not ELF4(L211M)
Supplementary Figure S3 from Mutational Landscape and Antiproliferative Functions of ELF Transcription Factors in Human Cancer
Authors: Ando Mizuo , Kawazu Masahito , Ueno Toshihide , Koinuma Daizo , Ando Koji , Koya Junji , Kataoka Keisuke , Yasuda Takahiko , Yamaguchi Hiroyuki , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Sai Eirin , Yamashita Yoshihiro , Asakage Takahiro , Miyazaki Yasushi , Kurokawa Mineo , Miyazono Kohei , Nimer Stephen D. , Yamasoba Tatsuya , Mano Hiroyuki
Published: March 2023

Transactivation activity of FLAG-tagged ELF4
Supplementary Figure S2 from Mutational Landscape and Antiproliferative Functions of ELF Transcription Factors in Human Cancer
Authors: Ando Mizuo , Kawazu Masahito , Ueno Toshihide , Koinuma Daizo , Ando Koji , Koya Junji , Kataoka Keisuke , Yasuda Takahiko , Yamaguchi Hiroyuki , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Sai Eirin , Yamashita Yoshihiro , Asakage Takahiro , Miyazaki Yasushi , Kurokawa Mineo , Miyazono Kohei , Nimer Stephen D. , Yamasoba Tatsuya , Mano Hiroyuki
Published: March 2023

Expression level of ELF4 in stably transduced T3M-1 Cl-10 cells
Supplementary Figure S5 from STAT3/IRF1 Pathway Activation Sensitizes Cervical Cancer Cells to Chemotherapeutic Drugs
Authors: Walch-Rückheim Barbara , Pahne-Zeppenfeld Jennifer , Fischbach Jil , Wickenhauser Claudia , Horn Lars Christian , Tharun Lars , Büttner Reinhard , Mallmann Peter , Stern Peter , Kim Yoo-Jin , Bohle Rainer Maria , Rübe Christian , Ströder Russalina , Juhasz-Böss Ingolf , Solomayer Erich-Franz , Smola Sigrun
Published: March 2023

HeLa cells were co-transfected with 1.85 µg pEFBos-STAT3F or pEFBos control vector and 0.35 µg EGFP expression vector.
Figure S6-8 from FIH Is an Oxygen Sensor in Ovarian Cancer for G9a/GLP-Driven Epigenetic Regulation of Metastasis-Related Genes
Authors: Kang Jengmin , Shin Seung-Hyun , Yoon Haejin , Huh June , Shin Hyun-Woo , Chun Yang-Sook , Park Jong-Wan
Published: March 2023

The FIH-G9a/GLP axis regulates invasive potential of OvCa cells in an oxygen dependent manner. This file is related to Fig. 4.
Supplemental Table 1 from miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis
Authors: Tellez Carmen S. , Juri Daniel E. , Do Kieu , Picchi Maria A. , Wang Teresa , Liu Gang , Spira Avrum , Belinsky Steven A.
Published: March 2023

Established In Vitro Model of Pre-Malignant Lung Cancer.
Table S1 from Secondary Tumors Arising in Patients Undergoing BRAF Inhibitor Therapy Exhibit Increased BRAF–CRAF Heterodimerization
Authors: Boussemart Lise , Girault Isabelle , Malka-Mahieu Hélène , Mateus Christine , Routier Emilie , Rubington Margot , Kamsu-Kom Nyam , Thomas Marina , Tomasic Gorana , Agoussi Sandrine , Breckler Marie , Laporte Mélanie , Lacroix Ludovic , Eggermont Alexander M. , Cavalcanti Andrea , Grange Florent , Adam Julien , Vagner Stéphan , Robert Caroline
Published: March 2023

Tumoral biospies from patients treated with BRAF inhibitors: Mutational status, pERK level and BRAF-CRAF PLA score.
Supplementary Figure S4 from Delivery of Therapeutics Targeting the mRNA-Binding Protein HuR Using 3DNA Nanocarriers Suppresses Ovarian Tumor Growth
Authors: Huang Yu-Hung , Peng Weidan , Furuuchi Narumi , Gerhart Jacquelyn , Rhodes Kelly , Mukherjee Neelanjan , Jimbo Masaya , Gonye Gregory E. , Brody Jonathan R. , Getts Robert C. , Sawicki Janet A.
Published: March 2023

Supplementary Fig. S4. TUNEL and Ki67 staining for detection of proliferating and apoptotic cells, respectively. A. TUNEL and Ki67 stained sections of four OVCAR5-shHuR and four OVCAR5-shCtrl ovarian xenografts. Areas of Ki67- cells are delineated with a white dotted line. B. In vitro staining of parental OVCAR5 cells, OVCAR5-shCtrl cells and OVCAR5-shHuR cells. Ki67+ cells and DAPI-stained cells were counted in three 1.4mm2 fields to determine % Ki67+ cells. * indicates p = 0.003 between parental and shHuR cells. DAPI stains nuclei in panels A and B. White bar = 50 mm.
Supplementary figure 5 from Abscopal Effects of Radiotherapy Are Enhanced by Combined Immunostimulatory mAbs and Are Dependent on CD8 T Cells and Crosspriming
Authors: Rodriguez-Ruiz María E. , Rodriguez Inmaculada , Garasa Saray , Barbes Benigno , Solorzano Jose Luis , Perez-Gracia Jose Luis , Labiano Sara , Sanmamed Miguel F. , Azpilikueta Arantza , Bolaños Elixabet , Sanchez-Paulete Alfonso R. , Aznar M. Angela , Rouzaut Ana , Schalper Kurt A. , Jure-Kunkel Maria , Melero Ignacio
Published: March 2023

single dose radiotherapy and hypofractionated doses increase the level of CD137 and PD-1 expression on the surface of tumor-infiltrating T cells.
Supplementary figure 4 from Abscopal Effects of Radiotherapy Are Enhanced by Combined Immunostimulatory mAbs and Are Dependent on CD8 T Cells and Crosspriming
Authors: Rodriguez-Ruiz María E. , Rodriguez Inmaculada , Garasa Saray , Barbes Benigno , Solorzano Jose Luis , Perez-Gracia Jose Luis , Labiano Sara , Sanmamed Miguel F. , Azpilikueta Arantza , Bolaños Elixabet , Sanchez-Paulete Alfonso R. , Aznar M. Angela , Rouzaut Ana , Schalper Kurt A. , Jure-Kunkel Maria , Melero Ignacio
Published: March 2023

A course of radiotherapy plus immunostimulatory monoclonal antibodies anti-CD137 and anti-PD-1 mAb increases CD4 and CD8 T cells in the tumor infiltrate as well as the number of tumor antigen-specific CD8 T cells.
Supplementary figure 1 from Abscopal Effects of Radiotherapy Are Enhanced by Combined Immunostimulatory mAbs and Are Dependent on CD8 T Cells and Crosspriming
Authors: Rodriguez-Ruiz María E. , Rodriguez Inmaculada , Garasa Saray , Barbes Benigno , Solorzano Jose Luis , Perez-Gracia Jose Luis , Labiano Sara , Sanmamed Miguel F. , Azpilikueta Arantza , Bolaños Elixabet , Sanchez-Paulete Alfonso R. , Aznar M. Angela , Rouzaut Ana , Schalper Kurt A. , Jure-Kunkel Maria , Melero Ignacio
Published: March 2023

Mouse external beam irradiation setting and combinations of radiotherapy and anti-CD137 and/or anti-PD1 immunostimulatory monoclonal antibodies are safe and effective to treat MC38-derived bilateral tumors of which only one of the tumor sites is irradiated.
Supplemental Figure from Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus
Authors: Camp Nicola J. , Lin Wei-Yu , Bigelow Alex , Burghel George J. , Mosbruger Timothy L. , Parry Marina A. , Waller Rosalie G. , Rigas Sushilaben H. , Tai Pei-Yi , Berrett Kristofer , Rajamanickam Venkatesh , Cosby Rachel , Brock Ian W. , Jones Brandt , Connley Dan , Sargent Robert , Wang Guoying , Factor Rachel E. , Bernard Philip S. , Cannon-Albright Lisa , Knight Stacey , Abo Ryan , Werner Theresa L. , Reed Malcolm W.R. , Gertz Jason , Cox Angela
Published: March 2023

Supplemental Figure: Description of sample sets for the DNAseq and RNAseq experiments.
Supplementary Methods from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma
Authors: Siliņa Karīna , Soltermann Alex , Attar Farkhondeh Movahedian , Casanova Ruben , Uckeley Zina M. , Thut Helen , Wandres Muriel , Isajevs Sergejs , Cheng Phil , Curioni-Fontecedro Alessandra , Foukas Periklis , Levesque Mitchell P. , Moch Holger , Linē Aija , van den Broek Maries
Published: March 2023

Contains additional information about the histological, immunostaining, gene expression analysis and animal experiments.
Supplementary Figure Legends from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma
Authors: Siliņa Karīna , Soltermann Alex , Attar Farkhondeh Movahedian , Casanova Ruben , Uckeley Zina M. , Thut Helen , Wandres Muriel , Isajevs Sergejs , Cheng Phil , Curioni-Fontecedro Alessandra , Foukas Periklis , Levesque Mitchell P. , Moch Holger , Linē Aija , van den Broek Maries
Published: March 2023

Contains descriptions of Supplementary Figures S1-S5.
Supplementary Figure 3 from Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability
Authors: Li Xiangchun , Wu William K.K. , Xing Rui , Wong Sunny H. , Liu Yuexin , Fang Xiaodong , Zhang Yanlin , Wang Mengyao , Wang Jiaqian , Li Lin , Zhou Yong , Tang Senwei , Peng Shaoliang , Qiu Kunlong , Chen Longyun , Chen Kexin , Yang Huanming , Zhang Wei , Chan Matthew T.V. , Lu Youyong , Sung Joseph J.Y. , Yu Jun
Published: March 2023

Fig. S3: Prognostic significance of CDH1 mutation.
Supplemental Table S2 from Osteogenic Potential of Mesenchymal Stromal Cells Contributes to Primary Myelofibrosis
Authors: Martinaud Christophe , Desterke Christophe , Konopacki Johanna , Pieri Lisa , Torossian Frédéric , Golub Rachel , Schmutz Sandrine , Anginot Adrienne , Guerton Bernadette , Rochet Nathalie , Albanese Patricia , Henault Emilie , Pierre-Louis Olivier , Souraud Jean-Baptiste , de Revel Thierry , Dupriez Brigitte , Ianotto Jean-Christophe , Bourgeade Marie-Françoise , Vannucchi Alessandro M. , Lataillade Jean-Jacques , Le Bousse-Kerdilès Marie-Caroline
Published: March 2023

Hematopoiesis support by MSCs in LTBMC BFU-E, CFU-G, CFU-M and CFU-GM by PMF (n=3) and healthy donors (HD, n=3) expressed as number of colonies for 104 bone marrow mononuclear cells.
Supplementary Figures S1-7 from GON4L Drives Cancer Growth through a YY1–Androgen Receptor–CD24 Axis
Authors: Agarwal Neeraj , Dancik Garrett M. , Goodspeed Andrew , Costello James C. , Owens Charles , Duex Jason E. , Theodorescu Dan
Published: March 2023

Figure S1 - Expression pattern of CD24 in different cell lines used and effect of candidate gene depletion on CD24 protein levels. Figure S2 - siRNA dose-dependent GON4L knockdown and STRING analysis for GON4L interactions. Figure S3 - Effect of YY1 knockdown on GON4L mRNA levels. Figure S4 - Effect of GON4L and YY1 knockdown on tumor growth in vivo and their expression in bladder cancer. Figure S5 - Luciferase reporter assays in control plasmids, endogenous CO-IP for AR and YY1 interaction, and effect of GON4L and YY1 knockdown on AR expression. Figure S6 - AR expression levels in different cancer cell lines, and GON4L and YY1 knockdown as measured by qRT-PCR. Figure S7 - GON4L and YY1 knockdown in AR- cancer cell lines.
Table S5 from Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes
Authors: Marusyk Andriy , Tabassum Doris P. , Janiszewska Michalina , Place Andrew E. , Trinh Anne , Rozhok Andrii I. , Pyne Saumyadipta , Guerriero Jennifer L. , Shu Shaokun , Ekram Muhammad , Ishkin Alexander , Cahill Daniel P. , Nikolsky Yuri , Chan Timothy A. , Rimawi Mothaffar F. , Hilsenbeck Susan , Schiff Rachel , Osborne Kent C. , Letai Antony , Polyak Kornelia
Published: March 2023

Associations between molecular features and clinical outcome. Patient outcome and changes in pSTAT3+, SMA+, Ki67+ cells and distance between Ki67+&SMA+ cells are indicated. Initial values from Day 0 where possible, otherwise Day 1. For continuous data, increase or decrease of at least 5% of initial value used as a threshold. Changes computed as Time0 - mean (Time 2,4,6 weeks). Outcome is percentage shrinkage of tumor at week 6.
Table S3 from MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy
Authors: Reinhardt Julia , Landsberg Jennifer , Schmid-Burgk Jonathan L. , Ramis Bartomeu Bibiloni , Bald Tobias , Glodde Nicole , Lopez-Ramos Dorys , Young Arabella , Ngiow Shin Foong , Nettersheim Daniel , Schorle Hubert , Quast Thomas , Kolanus Waldemar , Schadendorf Dirk , Long Georgina V. , Madore Jason , Scolyer Richard A. , Ribas Antoni , Smyth Mark J. , Tumeh Paul C. , Tüting Thomas , Hölzel Michael
Published: March 2023

Supplemental Table S3. Gene sets correlating with NT5E (CD73) expression in MITFhigh melanoma cell lines from the Broad melanoma cell line panel (GSEA results).
Figure S3 from YAP/TAZ Initiates Gastric Tumorigenesis via Upregulation of MYC
Authors: Choi Wonyoung , Kim Jeongsik , Park Jaeoh , Lee Da-Hye , Hwang Daehee , Kim Jeong-Hwan , Ashktorab Hassan , Smoot Duane , Kim Seon-Young , Choi Chan , Koh Gou Young , Lim Dae-Sik
Published: March 2023

YAP/TAZ overexpression causes transformation of normal gastric epithelial cells
Table S2 from Inhibition of the Wnt/β-Catenin Pathway Overcomes Resistance to Enzalutamide in Castration-Resistant Prostate Cancer
Authors: Zhang Zhuangzhuang , Cheng Lijun , Li Jie , Farah Elia , Atallah Nadia M. , Pascuzzi Pete E. , Gupta Sanjay , Liu Xiaoqi
Published: March 2023

DEGs analysis in high (Gleason grade score{greater than or equal to}8) and low (Gleason grade score<8) grade PCa tumors
Supplementary Figure S4 from HER2/EGFR–AKT Signaling Switches TGFβ from Inhibiting Cell Proliferation to Promoting Cell Migration in Breast Cancer
Authors: Huang Fei , Shi Qiaoni , Li Yuzhen , Xu Linlin , Xu Chi , Chen Fenfang , Wang Hai , Liao Hongwei , Chang Zai , Liu Fang , Zhang Xiang H.-F. , Feng Xin-Hua , Han Jing-Dong J. , Luo Shiwen , Chen Ye-Guang
Published: March 2023

HER2/EGFR signaling stimulates Smad3 S208 phosphorylation
Figures S1-S5 from Mechanistic Distinctions between CHK1 and WEE1 Inhibition Guide the Scheduling of Triple Therapy with Gemcitabine
Authors: Koh Siang-Boon , Wallez Yann , Dunlop Charles R. , Bernaldo de Quirós Fernández Sandra , Bapiro Tashinga E. , Richards Frances M. , Jodrell Duncan I.
Published: March 2023

Fig. S1 (related to Fig. 1) shows in vitro effects of treatment. Fig. S2 (related to Fig. 2) shows live single-cell FastFUCCI analyses. Fig. S3 (related to Fig. 3) shows spatiotemporal effects of treatment. Fig. S4 (related to Fig. 4) shows CHK1/WEE1 expression analyses and in vitro effects of treatment. Fig. S5 (related to Fig. 5) shows in vivo effects of treatment.
Figure S5 from The miR-371∼373 Cluster Represses Colon Cancer Initiation and Metastatic Colonization by Inhibiting the TGFBR2/ID1 Signaling Axis
Authors: Ullmann Pit , Rodriguez Fabien , Schmitz Martine , Meurer Steffen K. , Qureshi-Baig Komal , Felten Paul , Ginolhac Aurélien , Antunes Laurent , Frasquilho Sonia , Zügel Nikolaus , Weiskirchen Ralf , Haan Serge , Letellier Elisabeth
Published: March 2023

miR-371~373 cluster expression in extracted xenografts and its effect on metastatic outgrowth capacity in SW620 SCs
Figure S5 from CDKN2A/p16 Deletion in Head and Neck Cancer Cells Is Associated with CDK2 Activation, Replication Stress, and Vulnerability to CHK1 Inhibition
Authors: Gadhikar Mayur A. , Zhang Jiexin , Shen Li , Rao Xiayu , Wang Jing , Zhao Mei , Kalu Nene N. , Johnson Faye M. , Byers Lauren A. , Heymach John , Hittelman Walter N. , Udayakumar Durga , Pandita Raj K. , Pandita Tej K. , Pickering Curtis R. , Redwood Abena B. , Piwnica-Worms Helen , Schlacher Katharina , Frederick Mitchell J. , Myers Jeffrey N.
Published: March 2023

This file contains data showing impact of roscovitine co-treatment on the cell cycle responses of hypersensitive cells following Chk1 inhibition and a theoretical model explaining basis for prexasertib sensitivity in HNSCC cells. This file is linked to main figure 6.
FigureS5 from Inhibition of Nr4a Receptors Enhances Antitumor Immunity by Breaking Treg-Mediated Immune Tolerance
Authors: Hibino Sana , Chikuma Shunsuke , Kondo Taisuke , Ito Minako , Nakatsukasa Hiroko , Omata-Mise Setsuko , Yoshimura Akihiko
Published: March 2023

Validation of the chemotherapeutic agent Camptothecin as a functional Nr4a inhibitor
Supplementary Figures from Induction of Paracrine Signaling in Metastatic Melanoma Cells by PPARγ Agonist Rosiglitazone Activates Stromal Cells and Enhances Tumor Growth
Authors: Pich Christine , Meylan Patrick , Mastelic-Gavillet Beatris , Nguyen Thanh Nhan , Loyon Romain , Trang Bao Khanh , Moser Hélène , Moret Catherine , Goepfert Christine , Hafner Jürg , Levesque Mitchell P. , Romero Pedro , Jandus Camilla , Michalik Liliane
Published: March 2023

Four supplementary figures showing - PPARg activation regulates pro-inflammatory cytokine expression in A375 melanoma cells - Impact of RGZ exposure on the expression of PPARg-target genes and of pro-inflammatory cytokines in a variety of cancer cell lines - Impact of direct exposure to RGZ or T0070907 on interleukin receptor expression, proliferation, cell cycle, apoptosis and senescence of A375 cells, and on human fibroblasts, endothelial cells and monocytes - Impact of the exposure to RGZ or to RGZ-conditioned media collected from different human melanoma cells on human endothelial cells, human fibroblasts, murine fibroblasts and murine endothelial cells
Figure S5 from Oncogenic Kinase–Induced PKM2 Tyrosine 105 Phosphorylation Converts Nononcogenic PKM2 to a Tumor Promoter and Induces Cancer Stem–like Cells
Authors: Zhou Zhifen , Li Min , Zhang Lin , Zhao Hong , Şahin Özgür , Chen Jing , Zhao Jean J. , Songyang Zhou , Yu Dihua
Published: March 2023

Correlation between pY105-PKM2, pY1221/1222-ErbB2, nuclear YAP, and CD44 in FVB WT mice MFP and PTEN-/-/NIC mice mammary tumors
Additional methods for putative drive genes discovery and oaCGH results from SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma
Authors: Sakthikumar Sharadha , Elvers Ingegerd , Kim Jaegil , Arendt Maja L. , Thomas Rachael , Turner-Maier Jason , Swofford Ross , Johnson Jeremy , Schumacher Steven E. , Alföldi Jessica , Axelsson Erik , Couto C. Guillermo , Kisseberth William C. , Pettersson Mats E. , Getz Gad , Meadows Jennifer R.S. , Modiano Jaime F. , Breen Matthew , Kierczak Marcin , Forsberg-Nilsson Karin , Marinescu Voichita D. , Lindblad-Toh Kerstin
Published: March 2023

File contains additional information regarding methods for identifying putative driver genes with MutSigCV and high-impact mutations based analysis. Also methods for predicting impacts of TP53 and SETD2 genes. And further information about the oaCGH analysis for somatic copy number aberrations across a subset of 22 dogs.
Supplementary table S3 from Matrix Stiffening and EGFR Cooperate to Promote the Collective Invasion of Cancer Cells
Authors: Grasset Eloise M. , Bertero Thomas , Bozec Alexandre , Friard Jonas , Bourget Isabelle , Pisano Sabrina , Lecacheur Margaux , Maiel Majdi , Bailleux Caroline , Emelyanov Alexander , Ilie Marius , Hofman Paul , Meneguzzi Guerrino , Duranton Christophe , Bulavin Dmitry V. , Gaggioli Cedric
Published: March 2023

Quantification of relative matrix remodeling by CAF in presence of selective inhibitors.
Supplemental materials and methods from Matrix Stiffening and EGFR Cooperate to Promote the Collective Invasion of Cancer Cells
Authors: Grasset Eloise M. , Bertero Thomas , Bozec Alexandre , Friard Jonas , Bourget Isabelle , Pisano Sabrina , Lecacheur Margaux , Maiel Majdi , Bailleux Caroline , Emelyanov Alexander , Ilie Marius , Hofman Paul , Meneguzzi Guerrino , Duranton Christophe , Bulavin Dmitry V. , Gaggioli Cedric
Published: March 2023

Supplemental files
Table S4 from RNF6 Promotes Colorectal Cancer by Activating the Wnt/β-Catenin Pathway via Ubiquitination of TLE3
Authors: Liu Lei , Zhang Yanquan , Wong Chi Chun , Zhang Jingwan , Dong Yujuan , Li Xiangchun , Kang Wei , Chan Francis K.L. , Sung Joseph J.Y. , Yu Jun
Published: March 2023

Cox regression analysis of potential prognostic predictors for patients in the colorectal cancer cohort (HongKong cohort 1 and BeiJing cohort 1, n=160)
Supplementary Video 2 from A Direct Podocalyxin–Dynamin-2 Interaction Regulates Cytoskeletal Dynamics to Promote Migration and Metastasis in Pancreatic Cancer Cells
Authors: Wong Bin Sheng , Shea Daniel J. , Mistriotis Panagiotis , Tuntithavornwat Soontorn , Law Robert A. , Bieber Jake M. , Zheng Lei , Konstantopoulos Konstantinos
Published: March 2023

PODXL knockdown suppresses chemotactic migration of pancreatic cancer cells inside PDMS-based microchannels of prescribed widths. Representative scramble control (top) and PODXL-KD (bottom) cells migrating inside microchannels of 200 µm in length, 10µm in height, and either 6, 10, 20 or 50 µm in width. Scale bar represents 50µm. Related to Fig. 1E.
Figure S1 from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: March 2023

Tumor growth in 4T1 and 4T1/HAS3 tumors
Figure S2 from Glutamate Decarboxylase 65 Signals through the Androgen Receptor to Promote Castration Resistance in Prostate Cancer
Authors: Gao Yi , Chen Lu , Du ZunGuo , Gao WenChao , Wu ZhengMing , Liu XiuJuan , Huang Hai , Xu DanFeng , Li QingQuan
Published: March 2023

Figure S2 shows increased GAD65 enzymatic activity caused by phosphorylation at serine 6
Supplementary Methods and Materials from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: March 2023

SNP selection criteria, imputation and bioinformatic analyses
Figure S4 from Genetic Variants of VEGFA and FLT4 Are Determinants of Survival in Renal Cell Carcinoma Patients Treated with Sorafenib
Authors: Crona Daniel J. , Skol Andrew D. , Leppänen Veli-Matti , Glubb Dylan M. , Etheridge Amy S. , Hilliard Eleanor , Peña Carol E. , Peterson Yuri K. , Klauber-DeMore Nancy , Alitalo Kari K. , Innocenti Federico
Published: March 2023

T494A is located in the 5th Ig-like domain of VEGFR-3.
Figure S3 from Arming Tumor-Associated Macrophages to Reverse Epithelial Cancer Progression
Authors: Wettersten Hiromi I. , Weis Sara M. , Pathria Paulina , Von Schalscha Tami , Minami Toshiyuki , Varner Judith A. , Cheresh David A.
Published: March 2023

Figure shows tumor growth and integrin avb3 expression for HCC827 lung tumors with in vivo acquired resistance to erlotinib.
Figure S4 from Chemotherapy-Induced Extracellular Vesicle miRNAs Promote Breast Cancer Stemness by Targeting ONECUT2
Authors: Shen Meng , Dong Chuan , Ruan Xianhui , Yan Wei , Cao Minghui , Pizzo Donald , Wu Xiwei , Yang Lin , Liu Liang , Ren Xiubao , Wang Shizhen Emily
Published: March 2023

Figure S4 showing effect of chemo-EVs on other ONECUT family members and ONECUT2 target genes
Supplementary Figures from The Open Chromatin Landscape of Non–Small Cell Lung Carcinoma
Authors: Wang Zhoufeng , Tu Kailing , Xia Lin , Luo Kai , Luo Wenxin , Tang Jie , Lu Keying , Hu Xinlei , He Yijing , Qiao Wenliang , Zhou Yongzhao , Zhang Jun , Cao Feng , Dai Shuiping , Tian Panwen , Wang Ye , Liu Lunxu , Che Guowei , Zhou Qinghua , Xie Dan , Li Weimin
Published: March 2023

SF1:Supplementary Fig. S1, Somatic mutations of NSCLC patients related to Fig. 1; SF2:Supplementary Fig. S2, Data quality and subtyping of NSCLC, Related to Figure 2; SF3:Supplementary Fig. S3, Delineation of single cell open chromatin signature of patient LWQC; SF4:Supplementary Fig. S4, Distribution and function of broad open regions, Related to Figure 4; SF5:Supplementary Fig. S5, The relationship between somatic CNV, open chromatin peaks and gene expression, Related to Fig. 5; SF6:Supplementary Fig. S6, Characteristics of eQTLs and ATAC-QTLs, Related to Fig. 6 and Fig. 7; SF7:Supplementary Fig. S7, Validation of genomic regulation in NSCLC cell line
Figure S5 from Identification of Coding and Long Noncoding RNAs Differentially Expressed in Tumors and Preferentially Expressed in Healthy Tissues
Authors: Unfried Juan P. , Serrano Guillermo , Suárez Beatriz , Sangro Paloma , Ferretti Valeria , Prior Celia , Boix Loreto , Bruix Jordi , Sangro Bruno , Segura Víctor , Fortes Puri
Published: March 2023

Functional analysis with GSEA. A. Enrichment plots of cell cycle genes for each lncRNA. B. Specific enrichment plots for the indicated lncRNAs. FDR q-value = 0. NES indicates the normalized enrichment score. C. Expression correlation of LINC00665 with ZNF gene clusters of chr 19. Pearson correlation of the expression of the indicated genes with the levels of LINC00665. All genes have been ordered by location at chr19 p12, q13.41 or q13.12, where LINC00665 gene is located.
Figure S3 from Diminished AHR Signaling Drives Human Acute Myeloid Leukemia Stem Cell Maintenance
Authors: Ly Michelle , Rentas Stefan , Vujovic Ana , Wong Nicholas , Moreira Steven , Xu Joshua , Holzapfel Nicholas , Bhatia Sonam , Tran Damian , Minden Mark D. , Draper Jonathan S. , Hope Kristin J.
Published: March 2023

This figure shows shows intersections between significantly down regulated AHR-target genes in AML-subtypes compared to healthy bone marrow and LSCs compared non-LSCs.
Supplementary Tables S1 and S2, supplementary figures S1-S7, legends, and methods from Oncogenic KRAS Sensitizes Lung Adenocarcinoma to GSK-J4–Induced Metabolic and Oxidative Stress
Authors: Hong Beom-Jin , Park Woo-Yong , Kim Hwa-Ryeon , Moon Jin Woo , Lee Ho Yeon , Park Jun Hyung , Kim Seon-Kyu , Oh Youngbin , Roe Jae-Seok , Kim Mi-Young
Published: March 2023

Supplementary Table S1. Protein-protein interaction enrichment analysis of GSK-J4-induced genes in sensitive lines; Supplementary Table S2. Mutation status of several oncogenes and tumor suppressor genes in GSK-J4-sensitive and resistant lines. Supplementary Figure S1. GSK-J4 segregates LuAC cell lines into the "sensitive" and "resistant" groups via targeting KDM6B; Supplementary Figure S2. Effects of GSK-J4 on cell cycle and apoptosis of the GSK-J4-sensitive and resistant LuAC lines; Supplementary Figure S3. GSK-J4 affects expression of specific gene sets in sensitive LuAC cell lines; Supplementary Figure S4. Chromatin and gene expression analysis of GSK-J4-regulated genes in various LuAC; Supplementary Figure S5. GSK-J4 induces the ATF4 pathway in sensitive LuAC lines but ATF4 knockdown does not affect GSK-J4 sensitivity; Supplementary Figure S6. GSK-J4 induces oxidative and metabolic stress in the sensitive LuAC lines; Supplementary Figure S7. Oncogenic KRAS sensitizes LuAC and PDAC cell lines to GSK-J4. Supplementary materials and methods include materials, colony formation assay, animal studies, RNA extraction from subcutaneous tumor samples, quantification of ROS upon KRAS knockdown, generation of overexpression cell lines, motif analysis, genome-wide ChIP-seq analysis, qRT-PCR, western blotting, apoptosis analysis, cell viability assay, genome-wide RNA-seq analysis, overexpression constructs, oligo sequences for siRNAs.
Figure S2 from The Highly Recurrent PP2A Aα-Subunit Mutation P179R Alters Protein Structure and Impairs PP2A Enzyme Function to Promote Endometrial Tumorigenesis
Authors: Taylor Sarah E. , O'Connor Caitlin M. , Wang Zhizhi , Shen Guobo , Song Haichi , Leonard Daniel , Sangodkar Jaya , LaVasseur Corinne , Avril Stefanie , Waggoner Steven , Zanotti Kristine , Armstrong Amy J. , Nagel Christa , Resnick Kimberly , Singh Sareena , Jackson Mark W. , Xu Wenqing , Haider Shozeb , DiFeo Analisa , Narla Goutham
Published: March 2023

Sequencing outcomes and PPP2R1A hotspot mutation frequency for the Case Comprehensive Cancer Center Gynecologic Tumor Biobank
Figure S3 from Metformin Inhibits Progression of Head and Neck Squamous Cell Carcinoma by Acting Directly on Carcinoma-Initiating Cells
Authors: Wu Xingyu , Yeerna Huwate , Goto Yusuke , Ando Toshinori , Wu Victoria H. , Zhang Xuefeng , Wang Zhiyong , Amornphimoltham Panomwat , Murphy Anne N. , Tamayo Pablo , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: March 2023

GSEA analysis of metformin-induced gene expression programs in NDI1 expressing tumor samples
Supplementary Figure S5 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Authors: Coggins Grace E. , Farrel Alvin , Rathi Komal S. , Hayes Colin M. , Scolaro Laura , Rokita Jo Lynne , Maris John M.
Published: March 2023

Figure S5 shows the confirmation of differential gene expression between RNA seq samples.
Supplementary Material S2 from A Tumor-in-Host DEB-Based Approach for Modeling Cachexia and Bevacizumab Resistance
Authors: Tosca Elena M. , Rocchetti Maurizio , Pesenti Enrico , Magni Paolo
Published: March 2023

Figure of simulated plasma concentration profiles in the experiments from a to g
Suppl. Video 1 from A Pygopus 2-Histone Interaction Is Critical for Cancer Cell Dedifferentiation and Progression in Malignant Breast Cancer
Authors: Saxena Meera , Kalathur Ravi K.R. , Rubinstein Natalia , Vettiger Andrea , Sugiyama Nami , Neutzner Melanie , Coto-Llerena Mairene , Kancherla Venkatesh , Ercan Caner , Piscuoglio Salvatore , Fischer Jonas , Fagiani Ernesta , Cantù Claudio , Basler Konrad , Christofori Gerhard
Published: March 2023

Suppl. Video 1: Confocal analysis of a Pygo2+/+ tumor spheroid stained for b-catenin. (Related to Figure S2C).
Supplementary Video 3 from Pattern of Invasion in Human Pancreatic Cancer Organoids Is Associated with Loss of SMAD4 and Clinical Outcome
Authors: Huang Wenjie , Navarro-Serer Bernat , Jeong Yea Ji , Chianchiano Peter , Xia Limin , Luchini Claudio , Veronese Nicola , Dowiak Cameron , Ng Tammy , Trujillo Maria A. , Huang Bo , Pflüger Michael J. , Macgregor-Das Anne M. , Lionheart Gemma , Jones Danielle , Fujikura Kohei , Nguyen-Ngoc Kim-Vy , Neumann Neil M. , Groot Vincent P. , Hasanain Alina , van Oosten A. Floortje , Fischer Sandra E. , Gallinger Steven , Singhi Aatur D. , Zureikat Amer H. , Brand Randall E. , Gaida Matthias M. , Heinrich Stefan , Burkhart Richard A. , He Jin , Wolfgang Christopher L. , Goggins Michael G. , Thompson Elizabeth D. , Roberts Nicholas J. , Ewald Andrew J. , Wood Laura D.
Published: March 2023

Supplementary Video 3. Amoeboid invasion in PDAC organoid cultured in collagen I.
Supplementary Materials from Pattern of Invasion in Human Pancreatic Cancer Organoids Is Associated with Loss of SMAD4 and Clinical Outcome
Authors: Huang Wenjie , Navarro-Serer Bernat , Jeong Yea Ji , Chianchiano Peter , Xia Limin , Luchini Claudio , Veronese Nicola , Dowiak Cameron , Ng Tammy , Trujillo Maria A. , Huang Bo , Pflüger Michael J. , Macgregor-Das Anne M. , Lionheart Gemma , Jones Danielle , Fujikura Kohei , Nguyen-Ngoc Kim-Vy , Neumann Neil M. , Groot Vincent P. , Hasanain Alina , van Oosten A. Floortje , Fischer Sandra E. , Gallinger Steven , Singhi Aatur D. , Zureikat Amer H. , Brand Randall E. , Gaida Matthias M. , Heinrich Stefan , Burkhart Richard A. , He Jin , Wolfgang Christopher L. , Goggins Michael G. , Thompson Elizabeth D. , Roberts Nicholas J. , Ewald Andrew J. , Wood Laura D.
Published: March 2023

List of Supplementary Materials
Supplementary Table 1 from P2X7 Receptor Activity Limits Accumulation of T Cells within Tumors
Authors: Romagnani Andrea , Rottoli Elsa , Mazza Emilia Maria Cristina , Rezzonico-Jost Tanja , De Ponte Conti Benedetta , Proietti Michele , Perotti Michela , Civanelli Elisa , Perruzza Lisa , Catapano Alberico L. , Baragetti Andrea , Tenedini Elena , Tagliafico Enrico , Falzoni Simonetta , Di Virgilio Francesco , Norata Giuseppe Danilo , Bicciato Silvio , Grassi Fabio
Published: March 2023

Supplementary Table 1