bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S6 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. S6. Biodistribution of Cy3-conjugated 3DNA +/- conjugation to folic acid (FA). Following systemic delivery of FA-targeted Cy3-3DNA to ovarian tumor bearing mice, significant Cy3 fluorescence was observed in ovarian tumors, lesser amount in normal ovaries of tumor-bearing mice, very low amounts in brain, liver, spleen, and lung (white arrows), and no fluorescence was observed in heart. No fluorescence was observed in the ovary of non-tumor bearing mouse.
Supplemenatary Methods and References from Nrf2 Activation Promotes Keratinocyte Survival during Early Skin Carcinogenesis via Metabolic Alterations
Authors: Rolfs Frank , Huber Marcel , Kuehne Andreas , Kramer Stefan , Haertel Eric , Muzumdar Sukalp , Wagner Johanna , Tanner Yasmine , Böhm Friederike , Smola Sigrun , Zamboni Nicola , Levesque Mitchell P. , Dummer Reinhard , Beer Hans-Dietmar , Hohl Daniel , Werner Sabine , Schäfer Matthias
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Tables S1-S3 from Histone Deacetylase Inhibition in Prostate Cancer Triggers miR-320–Mediated Suppression of the Androgen Receptor
Authors: Sato Shinya , Katsushima Keisuke , Shinjo Keiko , Hatanaka Akira , Ohka Fumiharu , Suzuki Shugo , Naiki-Ito Aya , Soga Norihito , Takahashi Satoru , Kondo Yutaka
Published: March 2023

Supplementary Table S1. Background of Prostate Cancer Patients. Supplementary Table S2. List of the primers. Supplementary Table S3. 91 miRNAs upregulated in at least 1 of 3 cell lines.
Supplementary Materials and Methods from Histone Deacetylase Inhibition in Prostate Cancer Triggers miR-320–Mediated Suppression of the Androgen Receptor
Authors: Sato Shinya , Katsushima Keisuke , Shinjo Keiko , Hatanaka Akira , Ohka Fumiharu , Suzuki Shugo , Naiki-Ito Aya , Soga Norihito , Takahashi Satoru , Kondo Yutaka
Published: March 2023

Additional information of Materials and Methods.
Supplemental Methods and Supplemental Table 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

Equations to calculate sample size in a homozygous discordant design. Supplemental Table: Sample size requirements (n in each group)
Supplementary Data from Urokinase Receptor Promotes Skin Tumor Formation by Preventing Epithelial Cell Activation of Notch1
Authors: Mazzieri Roberta , Pietrogrande Giovanni , Gerasi Laura , Gandelli Alessandro , Colombo Piergiuseppe , Moi Davide , Brombin Chiara , Ambrosi Alessandro , Danese Silvio , Mignatti Paolo , Blasi Francesco , D'Alessio Silvia
Published: March 2023

This file include more detailed Material and Methods
Figure S7 from Nkx2.8 Inhibits Epithelial–Mesenchymal Transition in Bladder Urothelial Carcinoma via Transcriptional Repression of Twist1
Authors: Yu Chunping , Liu Zhuowei , Chen Qiuhong , Li Yonghong , Jiang Lijuan , Zhang Zhiling , Zhou Fangjian
Published: March 2023

Survival significance of Twist1 in human UC
Figure S4 from Nkx2.8 Inhibits Epithelial–Mesenchymal Transition in Bladder Urothelial Carcinoma via Transcriptional Repression of Twist1
Authors: Yu Chunping , Liu Zhuowei , Chen Qiuhong , Li Yonghong , Jiang Lijuan , Zhang Zhiling , Zhou Fangjian
Published: March 2023

Ablation of Twist1 restores the inhibitory effect of Nkx2.8 on the invasiveness of Nkx2.8-silenced UC cells
Figure S1 from RASSF1A Directly Antagonizes RhoA Activity through the Assembly of a Smurf1-Mediated Destruction Complex to Suppress Tumorigenesis
Authors: Lee Min-Goo , Jeong Seong-In , Ko Kyung-Phil , Park Soon-Ki , Ryu Byung-Kyu , Kim Ick-Young , Kim Jeong-Kook , Chi Sung-Gil
Published: March 2023

Figure S1. RASSF1A stimulates GTP-RhoA degradation. A, RASSF1A inhibition of RhoA-induced membrane ruffling and protrusion. GFP-expressing cells were transfected with RASSF1A and/or RhoA-G14V. B, RASSF1A suppression of RhoA-mediated FAK, MLC, and LIMK1/2 phosphorylation. C, No effect of RASSF1A on Ras activation of Raf-Mek-Erk signaling. A549 cells were co-transfected with RASSF1A-V5 and either HA-tagged H-Ras-G14V, K-Ras-G14V, or N-Ras-Q61R. Immunoblots were performed at 48 h after transfection. D. Effect of RASSF1A depletion on EGF (10 ng/ml) induction of GTP-RhoA. E. RASSF1A suppression of serum- or LPA-mediated GTP-RhoA induction. Cells transfected with either RASSF1A or RASSF1C were maintained in the absence of serum for 24 h and then exposed to serum or LPA. GTP-RhoA level was determined by GTPase pull-down assay. F, No effect of RASSF1A on Rho-GAP and Rho-GEF levels. G, A CHX assay showing reduction of the RhoA protein half-life by RASSF1A. RhoA intensities were measured by densitometric scanning of the immunoblot gels (Fig. 1H) and adjusted for Tubulin.
Supplemental Figure 8 from JPO2/CDCA7L and LEDGF/p75 Are Novel Mediators of PI3K/AKT Signaling and Aggressive Phenotypes in Medulloblastoma
Authors: Chan Tiffany Sin Yu , Hawkins Cynthia , Krieger Jonathan R. , McGlade C. Jane , Huang Annie
Published: March 2023

Correlation of JPO2 and LEDGF/p75 transcript levels in MB subtypes
Supplemental Materials and Mehods from Notch4 Signaling Induces a Mesenchymal–Epithelial–like Transition in Melanoma Cells to Suppress Malignant Behaviors
Authors: Bonyadi Rad Ehsan , Hammerlindl Heinz , Wels Christian , Popper Ulrich , Ravindran Menon Dinoop , Breiteneder Heimo , Kitzwoegerer Melitta , Hafner Christine , Herlyn Meenhard , Bergler Helmut , Schaider Helmut
Published: March 2023

Supplemental Materials and Methods used to create Supplemental Figures only in addition to Materials and Methods listed in the main manuscript
Supplemental Figure 5 from JPO2/CDCA7L and LEDGF/p75 Are Novel Mediators of PI3K/AKT Signaling and Aggressive Phenotypes in Medulloblastoma
Authors: Chan Tiffany Sin Yu , Hawkins Cynthia , Krieger Jonathan R. , McGlade C. Jane , Huang Annie
Published: March 2023

LEDGF increases JPO2 protein levels
Supplemental Figure 8: Chao1 and Shannon richness estimates and indicator OTUs for AOM/DSS mice. from HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis
Authors: Lang Michaela , Berry David , Passecker Katharina , Mesteri Ildiko , Bhuju Sabin , Ebner Florian , Sedlyarov Vitaly , Evstatiev Rayko , Dammann Kyle , Loy Alexander , Kuzyk Orest , Kovarik Pavel , Khare Vineeta , Beibel Martin , Roma Guglielmo , Meisner-Kober Nicole , Gasche Christoph
Published: March 2023

Phylum and family levels of APCMin and AOM/DSS mouse feces upon MS-444 treatment.
Supplemental table 1 from An Imbalance in TAZ and YAP Expression in Hepatocellular Carcinoma Confers Cancer Stem Cell–like Behaviors Contributing to Disease Progression
Authors: Hayashi Hiromitsu , Higashi Takaaki , Yokoyama Naomi , Kaida Takayoshi , Sakamoto Keita , Fukushima Yukiko , Ishimoto Takatsugu , Kuroki Hideyuki , Nitta Hidetoshi , Hashimoto Daisuke , Chikamoto Akira , Oki Eiji , Beppu Toru , Baba Hideo
Published: March 2023

Characteristics of 110 patients with hepatocellular carcinoma
Supplemental Figure 5: Immune cell infiltration in intestinal tumors and cytokine expression in small intestinal organoids upon MS-444. from HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis
Authors: Lang Michaela , Berry David , Passecker Katharina , Mesteri Ildiko , Bhuju Sabin , Ebner Florian , Sedlyarov Vitaly , Evstatiev Rayko , Dammann Kyle , Loy Alexander , Kuzyk Orest , Kovarik Pavel , Khare Vineeta , Beibel Martin , Roma Guglielmo , Meisner-Kober Nicole , Gasche Christoph
Published: March 2023

CD8+ cytotoxic T-lymphocytes, NKp46+ natural killer cells and F4/80+ macrophages in tumors of AOM/DSS and APCMin mice. Analysis of cytokines secreted by small intestinal organoids upon MS-444 treatment.
Supplemental Figure 3: High MS-444 concentrations impede intestinal epithelial re-epithelialization and induce HuR nucleocytoplasmic shuttling in an acute colitis model. from HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis
Authors: Lang Michaela , Berry David , Passecker Katharina , Mesteri Ildiko , Bhuju Sabin , Ebner Florian , Sedlyarov Vitaly , Evstatiev Rayko , Dammann Kyle , Loy Alexander , Kuzyk Orest , Kovarik Pavel , Khare Vineeta , Beibel Martin , Roma Guglielmo , Meisner-Kober Nicole , Gasche Christoph
Published: March 2023

HuR nucleocytoplasmic shuttling is increased with increasing MS-444 concentrationsin an acute colitis model.
Supplementary methods from Low-Dose Paclitaxel Reduces S100A4 Nuclear Import to Inhibit Invasion and Hematogenous Metastasis of Cholangiocarcinoma
Authors: Cadamuro Massimiliano , Spagnuolo Gaia , Sambado Luisa , Indraccolo Stefano , Nardo Giorgia , Rosato Antonio , Brivio Simone , Caslini Chiara , Stecca Tommaso , Massani Marco , Bassi Nicolò , Novelli Eugenio , Spirli Carlo , Fabris Luca , Strazzabosco Mario
Published: March 2023

Supplementary file containing the supplementary methods
Supplementary Figure 5. from Low-Dose Paclitaxel Reduces S100A4 Nuclear Import to Inhibit Invasion and Hematogenous Metastasis of Cholangiocarcinoma
Authors: Cadamuro Massimiliano , Spagnuolo Gaia , Sambado Luisa , Indraccolo Stefano , Nardo Giorgia , Rosato Antonio , Brivio Simone , Caslini Chiara , Stecca Tommaso , Massani Marco , Bassi Nicolò , Novelli Eugenio , Spirli Carlo , Fabris Luca , Strazzabosco Mario
Published: March 2023

Supplementary Figure 5. Low dose PTX did not affect cytoskeletal integrity of EGI-1 cells.
Supplementary Figure 4. from Low-Dose Paclitaxel Reduces S100A4 Nuclear Import to Inhibit Invasion and Hematogenous Metastasis of Cholangiocarcinoma
Authors: Cadamuro Massimiliano , Spagnuolo Gaia , Sambado Luisa , Indraccolo Stefano , Nardo Giorgia , Rosato Antonio , Brivio Simone , Caslini Chiara , Stecca Tommaso , Massani Marco , Bassi Nicolò , Novelli Eugenio , Spirli Carlo , Fabris Luca , Strazzabosco Mario
Published: March 2023

Supplementary Figure 4. Low dose PTX did not affect Rac-1 GTP levels, while it reduced the MT1-MMP membrane expression.
Suppl. Figure 1 from HSP70 Inhibition Limits FAK-Dependent Invasion and Enhances the Response to Melanoma Treatment with BRAF Inhibitors
Authors: Budina-Kolomets Anna , Webster Marie R. , Leu Julia I-Ju , Jennis Matthew , Krepler Clemens , Guerrini Anastasia , Kossenkov Andrew V. , Xu Wei , Karakousis Giorgos , Schuchter Lynn , Amaravadi Ravi K. , Wu Hong , Yin Xiangfan , Liu Qin , Lu Yiling , Mills Gordon B. , Xu Xiaowei , George Donna L. , Weeraratna Ashani T. , Murphy Maureen E.
Published: March 2023

Chemical structures of the HSP70 inhibitors used in this study
Supplementary Figure 1 from Low-Dose Paclitaxel Reduces S100A4 Nuclear Import to Inhibit Invasion and Hematogenous Metastasis of Cholangiocarcinoma
Authors: Cadamuro Massimiliano , Spagnuolo Gaia , Sambado Luisa , Indraccolo Stefano , Nardo Giorgia , Rosato Antonio , Brivio Simone , Caslini Chiara , Stecca Tommaso , Massani Marco , Bassi Nicolò , Novelli Eugenio , Spirli Carlo , Fabris Luca , Strazzabosco Mario
Published: March 2023

Supplementary Figure 1. Schedule of treatment with low dose metronomic PTX and assessment by bioluminescence analysis in SCID mice xenografted with EGI-1 cells.
Supplementary figures from DNMT1 Inhibition Reprograms Pancreatic Cancer Stem Cells via Upregulation of the miR-17-92 Cluster
Authors: Zagorac Sladjana , Alcala Sonia , Fernandez Bayon Gustavo , Bou Kheir Tony , Schoenhals Matthieu , González-Neira Anna , Fernandez Fraga Mario , Aicher Alexandra , Heeschen Christopher , Sainz Bruno
Published: March 2023

Supplementary figures and tables: Supplementary Figure S1. Autofluoresecnce as a biomarker for the isolation of pancreatic cancer stem cells. Results related to Figure 1. Supplementary Figure S2. PDAC CSCs over-express DNMT1 and bear higher 5mC levels. Results related to Figure 1 and Figure 2. Supplementary Figure S3. The DNMT1 inhibitor Zebularine decreases CSC phenotypes. Related to Figure 3. Supplementary Figure S4. The DNMT1 inhibitor Decitabine decreases CSC phenotypes. Related to Figure 3. Supplementary Figure S5. DNMT1 inhibitor Zebularine promotes CSC differentiation. Related to Figure 5. Supplementary Figure S6. DNMT1 inhibition modulates expression of miR-203, miR-205, and the miR-17-92 cluster. Related to Figure 6. Table S1. Table showing decreased DNA methylation for miRs following Zebularine treatment, represented as fold changes. Table S2. Table showing decreased DNA methylation of genes upon Zebularine treatment, represented as fold changes. Table S3. Table showing decreased DNA methylation of genes upon Zebularine treatment, represented as fold changes.
Supplemental Figures S1-S9 from Immunoregulatory Protein B7-H3 Reprograms Glucose Metabolism in Cancer Cells by ROS-Mediated Stabilization of HIF1α
Authors: Lim Sangbin , Liu Hao , da Silva Luciana Madeira , Arora Ritu , Liu Zixing , Phillips Joshua B. , Schmitt David C. , Vu Tung , McClellan Steven , Lin Yifeng , Lin Wensheng , Piazza Gary A. , Fodstad Oystein , Tan Ming
Published: March 2023

Fig. S1: Glucose uptake and lactate production in B7-H3 knockdown Fig. S2: Growth inhibition W/O B7-H3 Fig S3: Proliferation assay in glucose deprivation. Fig. S4: Expression in B7-H3 knockdown w/o CoCl2. Fig. S5: mRNA levels. Fig. S6: Reduction of ROS by ROS scavenger in B7-H3 overexpression. Fig. S7: G6PD and SOD activity. Fig. S8: Growth Inhibition by ROS scavenger. Fig. S9: Immunohistochemistry analysis of xenograft tumors.
Supplementary Materials & Methods from DNMT1 Inhibition Reprograms Pancreatic Cancer Stem Cells via Upregulation of the miR-17-92 Cluster
Authors: Zagorac Sladjana , Alcala Sonia , Fernandez Bayon Gustavo , Bou Kheir Tony , Schoenhals Matthieu , González-Neira Anna , Fernandez Fraga Mario , Aicher Alexandra , Heeschen Christopher , Sainz Bruno
Published: March 2023

Supplementary Materials & Methods: Additional methods and materials not detailed in the main manuscript. Includes, details of the Illumina methylation array, differential methylation, genomic region and CGI analyses, as well as additional methods and details regarding antagomiRs, treatments, cell viability and apoptosis assays, cell cycle analysis, WB and RTqPCR, 5mC quantification, CRISPR/Cas9, and immunofluorescence and immunohistochemistry.
Figure S6 from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine
Authors: Leadem Benjamin R. , Kagiampakis Ioannis , Wilson Catherine , Cheung Tommy K. , Arnott David , Trojer Patrick , Classon Marie , Easwaran Hariharan , Baylin Stephen B.
Published: March 2023

KDM5i and DAC do not synergize in MCF10A, nor alter cell cycle in MCF-7
Figure S3 from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine
Authors: Leadem Benjamin R. , Kagiampakis Ioannis , Wilson Catherine , Cheung Tommy K. , Arnott David , Trojer Patrick , Classon Marie , Easwaran Hariharan , Baylin Stephen B.
Published: March 2023

KDM5i alone and in combination with DAC upregulates cancer hallmark & immunomodulatory pathways
Supplementary Table and Figure 1 from MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome
Authors: Wragg Joseph W. , Finnity Jonathan P. , Anderson Jane A. , Ferguson Henry J.M. , Porfiri Emilio , Bhatt Rupesh I. , Murray Paul G. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary Table 1: Primer sequences for RTqPCR using the Roche Exiqon probe library system. Supplementary Figure 1. Representative images demonstrative of scoring for staining intensity. Images are of MCAM staining in RCC at a weak (i-ii) or strong (iii-iv) level with associated H&E images (v,vi,vii,viii) . Scale bar = 50 μm.
Supplementary Table 7 from MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome
Authors: Wragg Joseph W. , Finnity Jonathan P. , Anderson Jane A. , Ferguson Henry J.M. , Porfiri Emilio , Bhatt Rupesh I. , Murray Paul G. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary Table 7: Key clinical data for different types of kidney cancer and metastasis
Supplementary Table S2 from Measurement of Endogenous versus Exogenous Formaldehyde–Induced DNA–Protein Crosslinks in Animal Tissues by Stable Isotope Labeling and Ultrasensitive Mass Spectrometry
Authors: Lai Yongquan , Yu Rui , Hartwell Hadley J. , Moeller Benjamin C. , Bodnar Wanda M. , Swenberg James A.
Published: March 2023

2 ppm Rat Exposure Results.
Supplementary Methods and Reference from Measurement of Endogenous versus Exogenous Formaldehyde–Induced DNA–Protein Crosslinks in Animal Tissues by Stable Isotope Labeling and Ultrasensitive Mass Spectrometry
Authors: Lai Yongquan , Yu Rui , Hartwell Hadley J. , Moeller Benjamin C. , Bodnar Wanda M. , Swenberg James A.
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary Reference.
Supplementary Figures S1-S3 from Measurement of Endogenous versus Exogenous Formaldehyde–Induced DNA–Protein Crosslinks in Animal Tissues by Stable Isotope Labeling and Ultrasensitive Mass Spectrometry
Authors: Lai Yongquan , Yu Rui , Hartwell Hadley J. , Moeller Benjamin C. , Bodnar Wanda M. , Swenberg James A.
Published: March 2023

Typical calibration curve used for the quantification of dG-Me-Cys with the linearity from 0.15 to 6.0 fmol (S1); Schematic of rat nose only inhalation chamber (S2); Schematic of primate whole-body inhalation chamber (S3).
Supplemental figure legends from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: March 2023

legends for supplemental figures.
Supplementary Methods from T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia
Authors: Jing Weiqing , Gershan Jill A. , Holzhauer Sandra , Weber James , Palen Katie , McOlash Laura , Pulakanti Kirthi , Wesley Erin , Rao Sridhar , Johnson Bryon D. , Riese Matthew J.
Published: March 2023

A description of additional methods used in manuscript
Table S1 from Venetoclax Synergizes with Radiotherapy for Treatment of B-cell Lymphomas
Authors: O'Steen Shyril , Green Damian J. , Gopal Ajay K. , Orozco Johnnie J. , Kenoyer Aimee L. , Lin Yukang , Wilbur D. Scott , Hamlin Donald K. , Fisher Darrell R. , Hylarides Mark D. , Gooley Theodore A. , Waltman Amelia , Till Brian G. , Press Oliver W.
Published: March 2023

Table S1 presents mouse survival data for in vivo experiments
Supplementary Figures 1-13 from The SWI/SNF Complex Protein Snr1 Is a Tumor Suppressor in Drosophila Imaginal Tissues
Authors: Xie Gengqiang , Chen Hanqing , Jia Dongyu , Shu Zhiqiang , Palmer William Hunt , Huang Yi-Chun , Zeng Xiankun , Hou Steven X. , Jiao Renjie , Deng Wu-Min
Published: March 2023

Supplementary figure 1: Snr1 is required for cell survival in Drosophila wing imaginal disc. Supplementary figure 2: Tumorigenic overgrowth in wing discs carrying snr1-depletion by tissue-specific Gal4 drivers. Supplementary figure 3: Coexpression of rpr and p35 does not induce neoplastic tumorigenic overgrowth in the wing disc. Supplementary figure 4: Wing discs with snr1 loss shows neoplastic overgrowth. Supplementary figure 5: Tumorigenic overgrowth in the wing disc with mosaic clones of snr1 mutation. Supplementary figure 6: Depletion of brm or osa causes apoptotic phenotype in wing pouch region. Supplementary figure 7: Subcellular localization in salivary gland cells. Supplementary figure 8: Knockdown of other components of the SWI/SNF complex does not affect trafficking signaling. Supplementary figure 9: Transmembrane proteins are not accumulated in brm- or osa-depleted cells. Supplementary figure 10: Notch signaling is not upregulated in brm- or osa-RNAi cells. Supplementary figure 11: Depletion of brm or osa does not change JAK-STAT signaling activity. Supplementary figure 12: JNK signaling is barely affected in brm- or osa-depleted cells. Supplementary figure 13: Knockdown of dilp8 or mmp1 does not suppress snr1 depletion-induced tumorigenic overgrowth.
Supplementary Table 6 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Summary of all the genes included in the MiSeq validation (Sets A and B); mutation frequency and significance in exome and MiSeq data (per microsatellite and per gene) as well as the NAFs in the MiSeq data. repeats. microsatellite classes
Supplementary Table 5 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

The median coverage at different genes in the MiSeq data. frequency and significance in exome and MiSeq data (per microsatellite and per gene) as well as the NAFs in the MiSeq data.
Figure S1, Figure S2, Figure S3, Figure S4, and Figure S5 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

Combined file of Fig.S1 thru Fig.S5 - Fig. S1. Biochemical characterization of 5G9.G1.B11. Fig. S2. Binding of 5G9.G1.B11 to native PD-1. Fig. S3. Blocking activities of 5G9.G1.B11. Fig. S4. Biochemical characterization of cPD-1. Fig. S5. Binding of cPD-1 to SpESF-X10-2D1 cells transfected to overexpress human PD-1.
Supplementary Table 1 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Clinical and sequencing related information about the 24 exome and 93 MiSeq sequenced tumors.
Supplementary Figure 2 from Fructose-1,6-bisphosphatase Inhibits ERK Activation and Bypasses Gemcitabine Resistance in Pancreatic Cancer by Blocking IQGAP1–MAPK Interaction
Authors: Jin Xin , Pan Yunqian , Wang Liguo , Ma Tao , Zhang Lizhi , Tang Amy H. , Billadeau Daniel D. , Wu Heshui , Huang Haojie
Published: March 2023

Assessment of the effect of gemcitabine treatment on the cell cycle and interaction of IQGAP1 and ERK1/2 in PANC-1 cells.
Supplementary method from PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer
Authors: Hsu Jessie Hao-Ru , Hubbell-Engler Benjamin , Adelmant Guillaume , Huang Jialiang , Joyce Cailin E. , Vazquez Francisca , Weir Barbara A. , Montgomery Philip , Tsherniak Aviad , Giacomelli Andrew O. , Perry Jennifer A. , Trowbridge Jennifer , Fujiwara Yuko , Cowley Glenn S. , Xie Huafeng , Kim Woojin , Novina Carl D. , Hahn William C. , Marto Jarrod A. , Orkin Stuart H.
Published: March 2023

Supplementary proteomics method
Supplementary Table 4 from PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer
Authors: Hsu Jessie Hao-Ru , Hubbell-Engler Benjamin , Adelmant Guillaume , Huang Jialiang , Joyce Cailin E. , Vazquez Francisca , Weir Barbara A. , Montgomery Philip , Tsherniak Aviad , Giacomelli Andrew O. , Perry Jennifer A. , Trowbridge Jennifer , Fujiwara Yuko , Cowley Glenn S. , Xie Huafeng , Kim Woojin , Novina Carl D. , Hahn William C. , Marto Jarrod A. , Orkin Stuart H.
Published: March 2023

Function enrichment of down regulated genes upon Prmt1 depletion at the translation level using DAVID functional annotation tool (GO BP_direct).
Supplementary Data from Aurora A and NF-κB Survival Pathway Drive Chemoresistance in Acute Myeloid Leukemia via the TRAF-Interacting Protein TIFA
Authors: Wei Tong-You Wade , Wu Pei-Yu , Wu Ting-Jung , Hou Hsin-An , Chou Wen-Chien , Teng Chieh-Lin Jerry , Lin Chih-Ru , Chen Jo-Mei Maureen , Lin Ting-Yang , Su Hsiang-Chun , Huang Chia-Chi Flora , Yu Chang-Tze Ricky , Hsu Shih-Lan , Tien Hwei-Fang , Tsai Ming-Daw
Published: March 2023

Supplementary Methods - construction of plasmids, synthesis of siRNA, and methods for RT-qPCR. Supplementary Figure Legends - legends for supplementary figures. Supplementary References - references for supplementary methods. Supplementary Figures (S1-S7) - S1 shows control experiments for TIFA phosphorylation by Aurora A (A-C), and TIFA interaction with Aurora A (D-E). S2 shows western blot analysis of PBMCs from AML patients and normal donors (A-B), and Pearson's correlation coefficient among TIFA, Aurora A, and NF-κB signaling factors (C). S3 shows that TIFA silencing (A) attenuated cell viabilities (B-C) and enhanced chemotoxicities (D-I) of leukemic lines. S4 shows that TIFA silencing enhanced chemotoxicities of AML PBMCs (A-C) via promotion of apoptosis (D-F). S5 shows that TIFA is a therapeutic target to enhance chemotherapeutic drug treatments. S6 shows that anti-inflammatory drugs enhanced effects of cytarabine treatment in vitro and in vivo (A-B and D), and the control experiments for figure 6D and 6E in the main text (C and E, respectively). S7 shows the schematic model of the functional role of TIFA in supporting leukemic cell growth and chemoresistance. Supplementary Tables (S1-S7) - S1 shows clinical manifestations of AML patients with higher and lower BM TIFA expression. S2 shows comparison of immune phenotypes of leukemia cells between AML patients with higher and lower BM TIFA expression. S3-5 show IC50 values of drugs for AML lines (S3), ALL and CML lines (S4), and AML patient PBMCs (S5) upon silencing of TIFA. S6-7 show IC50 values of drugs for AML
Supplementary Table 1 from PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer
Authors: Hsu Jessie Hao-Ru , Hubbell-Engler Benjamin , Adelmant Guillaume , Huang Jialiang , Joyce Cailin E. , Vazquez Francisca , Weir Barbara A. , Montgomery Philip , Tsherniak Aviad , Giacomelli Andrew O. , Perry Jennifer A. , Trowbridge Jennifer , Fujiwara Yuko , Cowley Glenn S. , Xie Huafeng , Kim Woojin , Novina Carl D. , Hahn William C. , Marto Jarrod A. , Orkin Stuart H.
Published: March 2023

Arginine methylated peptides identified by SILAC-proteomics
Supplementary Tables 1-3, 5-9,Supplementary Figures 1-5 from Infection Exposure Promotes ETV6-RUNX1 Precursor B-cell Leukemia via Impaired H3K4 Demethylases
Authors: Rodríguez-Hernández Guillermo , Hauer Julia , Martín-Lorenzo Alberto , Schäfer Daniel , Bartenhagen Christoph , García-Ramírez Idoia , Auer Franziska , González-Herrero Inés , Ruiz-Roca Lucia , Gombert Michael , Okpanyi Vera , Fischer Ute , Chen Cai , Dugas Martin , Bhatia Sanil , Linka René Martin , Garcia-Suquia Marta , Rascón-Trincado María Victoria , Garcia-Sanchez Angel , Blanco Oscar , García-Cenador Maria Begoña , García-Criado Francisco Javier , Cobaleda César , Alonso-López Diego , De Las Rivas Javier , Müschen Markus , Vicente-Dueñas Carolina , Sánchez-García Isidro , Borkhardt Arndt
Published: March 2023

Contents: Supplementary Table 1: Characteristics of the pediatric patients enrolled in whole-genome- and whole-exome-sequencing. Supplementary Table 2: Conventional Facility Health Monitoring Report. Supplementary Table 3: Percentage of hematopoietic subsets in young ETV6-RUNX1 and wild type mice housed in conventional facility. Supplementary Table 5: Differential regulation of histonemodifying genes in ETV6-RUNX1 mice compared to human ETV6-RUNX1 pB-ALL. Supplementary Table 6: Alterations in genes related to histone modification in pB-ALL human samples Supplementary Table 7: Summary of whole genome sequencing statistics. Supplementary Table 8: Summary of exome sequencing statistics. Supplementary Table 9: Validated SNVs in the patient cohort. Supplementary Fig. 1: Distribution of genomic ETV6-RUNX1 breakpoints amongst patients. Supplementary Fig. 2: Development of Sca1-ETV6-RUNX1 mice. Supplementary Fig. 3: pB-ALL development in Sca1-ETV6-RUNX1 mice and B cell development in young Sca1-ETV6-RUNX1 mice housed in SPF facility. Supplementary Fig. 4: Tumor exome sequencing data identify genes mutated in mouse and human. Supplementary Fig. 5: Study of proB cells in young Sca1-ETV6-RUNX1 mice.
Table S5 from S100A4 Is a Biomarker and Regulator of Glioma Stem Cells That Is Critical for Mesenchymal Transition in Glioblastoma
Authors: Chow Kin-Hoe , Park Hee Jung , George Joshy , Yamamoto Keiko , Gallup Andrew D. , Graber Joel H. , Chen Yuanxin , Jiang Wen , Steindler Dennis A. , Neilson Eric G. , Kim Betty Y.S. , Yun Kyuson
Published: March 2023

Supplementary Table 5 showing IPA prediction of upstream regulators for up-regulated genes in S100A4 knockdown cells
Supplementary Materials and Methods.docx from SPINK6 Promotes Metastasis of Nasopharyngeal Carcinoma via Binding and Activation of Epithelial Growth Factor Receptor
Authors: Zheng Li-Sheng , Yang Jun-Ping , Cao Yun , Peng Li-Xia , Sun Rui , Xie Ping , Wang Meng-Yao , Meng Dong-Fang , Luo Dong-Hua , Zou Xiong , Chen Ming-Yuan , Mai Hai-Qiang , Guo Ling , Guo Xiang , Shao Jian-Yong , Huang Bi-Jun , Zhang Wei , Qian Chao-Nan
Published: March 2023

Supplementary Materials and Methods
Table S4 from S100A4 Is a Biomarker and Regulator of Glioma Stem Cells That Is Critical for Mesenchymal Transition in Glioblastoma
Authors: Chow Kin-Hoe , Park Hee Jung , George Joshy , Yamamoto Keiko , Gallup Andrew D. , Graber Joel H. , Chen Yuanxin , Jiang Wen , Steindler Dennis A. , Neilson Eric G. , Kim Betty Y.S. , Yun Kyuson
Published: March 2023

Supplementary Table 4 showing IPA prediction of upstream regulators for downregulated genes in S100A4 knockdown cells
Table S1 from S100A4 Is a Biomarker and Regulator of Glioma Stem Cells That Is Critical for Mesenchymal Transition in Glioblastoma
Authors: Chow Kin-Hoe , Park Hee Jung , George Joshy , Yamamoto Keiko , Gallup Andrew D. , Graber Joel H. , Chen Yuanxin , Jiang Wen , Steindler Dennis A. , Neilson Eric G. , Kim Betty Y.S. , Yun Kyuson
Published: March 2023

Supplementary Table 1 showing expression correlation between S100A4 and markers of MES and PRO GBM subtypes using the TCGA GBM dataset.
Supplementary Figures 1 and 2 and Supplementary Tables 1 and 2 from MIF-Induced Stromal PKCβ/IL8 Is Essential in Human Acute Myeloid Leukemia
Authors: Abdul-Aziz Amina M. , Shafat Manar S. , Mehta Tarang K. , Di Palma Federica , Lawes Matthew J. , Rushworth Stuart A. , Bowles Kristian M.
Published: March 2023

This file contains Supplementary Figures and Tables. Supplementary Figure 1 shows long term survival of AML on BM-MSC. Supplementary Figure 2 shows the combinations of AML and BM-MSC co-cultures. Supplementary Table 1 shows AML patient information and Supplementary table 2 shows BM-MSC patient information.
Supplementary Table S1 from A Conference of New Ideas in Cancer—Challenging Dogmas
Authors: Gandhi Varsha , Jalali Rakesh
Published: March 2023

List of speakers at the TMC Platinum Jubilee Conference entitled "A Conference of New Ideas in Cancer - Challenging Dogmas" held in Mumbai from 26th - 28th February 2016.
Supplementary Figures 9-10 from Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors
Authors: Tschida Barbara R. , Temiz Nuri A. , Kuka Timothy P. , Lee Lindsey A. , Riordan Jesse D. , Tierrablanca Carlos A. , Hullsiek Robert , Wagner Sandra , Hudson Wendy A. , Linden Michael A. , Amin Khalid , Beckmann Pauline J. , Heuer Rachel A. , Sarver Aaron L. , Yang Ju Dong , Roberts Lewis R. , Nadeau Joseph H. , Dupuy Adam J. , Keng Vincent W. , Largaespada David A.
Published: March 2023

Schematic of transposon insertions in Nat10(S9) and transgene expression in livers of Fah-deficient mice after hydrodynamic injection with Nat10/shp53(S10)
Supplementary Table 2 from Transcriptional Selectivity of Epigenetic Therapy in Cancer
Authors: Sato Takahiro , Cesaroni Matteo , Chung Woonbok , Panjarian Shoghag , Tran Anthony , Madzo Jozef , Okamoto Yasuyuki , Zhang Hanghang , Chen Xiaowei , Jelinek Jaroslav , Issa Jean-Pierre J.
Published: March 2023

An excel file containing a list of tumor suppressor genes that are 2 fold decreased in YB5 compared to normal colon (277 genes out of 716 total tumor suppressor genes from TSGene), and are significantly upregulated (> 2FC and < 0.1 FDR) by each inhibitor in YB5 cells.
Figure S2 from Glutamine Addiction in Kidney Cancer Suppresses Oxidative Stress and Can Be Exploited for Real-Time Imaging
Authors: Abu Aboud Omran , Habib Samy L. , Trott Josephine , Stewart Benjamin , Liang Sitai , Chaudhari Abhijit J. , Sutcliffe Julie , Weiss Robert H.
Published: March 2023

Glucose (Glu), glutamine (Gln), glutathione (GSH), and cell viability in RCC cells
Figure S1 from Glutamine Addiction in Kidney Cancer Suppresses Oxidative Stress and Can Be Exploited for Real-Time Imaging
Authors: Abu Aboud Omran , Habib Samy L. , Trott Josephine , Stewart Benjamin , Liang Sitai , Chaudhari Abhijit J. , Sutcliffe Julie , Weiss Robert H.
Published: March 2023

Further representative sections of normal right kidney (RK) and tumor tissues were subjected to immunohistochemical analysis for NRF2
Supplementary Table 3 from Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
Authors: Davies Helen , Morganella Sandro , Purdie Colin A. , Jang Se Jin , Borgen Elin , Russnes Hege , Glodzik Dominik , Zou Xueqing , Viari Alain , Richardson Andrea L. , Børresen-Dale Anne-Lise , Thompson Alastair , Eyfjord Jorunn E. , Kong Gu , Stratton Michael R. , Nik-Zainal Serena
Published: March 2023

Mutations in MMR genes
Supplementary Table 1 from Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
Authors: Davies Helen , Morganella Sandro , Purdie Colin A. , Jang Se Jin , Borgen Elin , Russnes Hege , Glodzik Dominik , Zou Xueqing , Viari Alain , Richardson Andrea L. , Børresen-Dale Anne-Lise , Thompson Alastair , Eyfjord Jorunn E. , Kong Gu , Stratton Michael R. , Nik-Zainal Serena
Published: March 2023

Substitution signature exposures estimated in 640 breast cancer WGS and the ovarian sample (AOCS-166).
Supplementary Data from An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia
Authors: Viswanathan Vignesh , Damle Shirish , Zhang Tao , Opdenaker Lynn , Modarai Shirin , Accerbi Monica , Schmidt Skye , Green Pamela , Galileo Deni , Palazzo Juan , Fields Jeremy , Haghighat Sepehr , Rigoutsos Isidore , Gonye Greg , Boman Bruce M.
Published: March 2023

'Fig S1. Validation of miRNA chip results by quantitative PCR analysis. Fig S2. Analysis of differentially expressed miRNAs using target predictions. Fig S3. The relative abundance of the common predicted targets in relation to miRNA levels in CRC cell lines. Fig S4. The effect of miRNAs on mRNA expression levels of their predicted targets. Fig S5. Relative expression of four candidate microRNAs in HT29 ALDH+ cells as compared to ALDH- cells. Fig S6. miRNA23b targets 3' UTR of LGR5 and LRIG1 mRNA. Fig S7: miRNA23b affects cell proliferation. Fig S8: CaCo2 data on miRNA23b precursor and antimer effect on sphere forming ability as well as 5FU response.'
'Supplementary Figure Legends' from An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia
Authors: Viswanathan Vignesh , Damle Shirish , Zhang Tao , Opdenaker Lynn , Modarai Shirin , Accerbi Monica , Schmidt Skye , Green Pamela , Galileo Deni , Palazzo Juan , Fields Jeremy , Haghighat Sepehr , Rigoutsos Isidore , Gonye Greg , Boman Bruce M.
Published: March 2023

'Legends for Supplementary Figures'
Supplementary information, methods, and figures from Identification of Interacting Stromal Axes in Triple-Negative Breast Cancer
Authors: Saleh Sadiq M.I. , Bertos Nicholas , Gruosso Tina , Gigoux Mathieu , Souleimanova Margarita , Zhao Hong , Omeroglu Atilla , Hallett Michael T. , Park Morag
Published: March 2023

Supplementary information and materials and methods. Supplemental Figure 1: Laser capture microdissection (LCM) successfully isolates normal vs. tumor-associated stromal compartments. Supplemental Figure 2: Identifying differentially expressed genes based on stroma-defined axes. Supplemental Figure 3: Survival curves for T, B, and E axis scores when first stratified by D axis score. Supplemental Figure 4: Survival curves for T, B, and E axis scores among patients not treated with chemotherapy when first stratified by D axis score. Supplemental Figure 5: Survival curves for T, B, and E axis scores among patients treated with chemotherapy when first stratified by D axis score. Supplemental Figure 6: Full heatmap depicting the subtype-specific performance of predictors. Supplemental Figure 7: Naive Bayes classifier predictions agree with ROI95 assignments
TCR Sequencing data from Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8+ T-cell Recognition of a Retroviral Antigen
Authors: Probst Philipp , Kopp Janine , Oxenius Annette , Colombo Mario P. , Ritz Danilo , Fugmann Tim , Neri Dario
Published: March 2023

Sequences of AH1-specific TCRs identified by TCR-beta sequencing
Supplementary Figures 1 -9 from Glycerol-3-phosphate Acyltransferase 1 Promotes Tumor Cell Migration and Poor Survival in Ovarian Carcinoma
Authors: Marchan Rosemarie , Büttner Bettina , Lambert Jörg , Edlund Karolina , Glaeser Iris , Blaszkewicz Meinolf , Leonhardt Gregor , Marienhoff Lisa , Kaszta Darius , Anft Moritz , Watzl Carsten , Madjar Katrin , Grinberg Marianna , Rempel Eugen , Hergenröder Roland , Selinski Silvia , Rahnenführer Jörg , Lesjak Michaela S. , Stewart Joanna D. , Cadenas Cristina , Hengstler Jan G.
Published: March 2023

Supplementary Fig. S1: Confirmation of the effect of GPAM and EDI3 on migration in HeLa cells, related to Fig.1. Supplementary Fig. S2: Confirmation that CHKA has no effect on viability and migration, related to Fig. 2. Supplementary Fig. S3: No decreased viability or off-target effect after GPAM silencing, related to Fig. 3. Supplementary Fig. S4: Confirmation of GPAM effect on migration with multiple siRNA oligos (HeLa cells), related to Fig. 3. Supplementary Fig. S5: Confirmation of GPAM effect on migration with two siRNA oligos (MDA-MB-231 cells), related to Fig. 3. Supplementary Fig. S6: Evidence that transfection accelerates the uptake of fluorescently-labeled LPA in cells, related to Fig. 5. Supplementary Fig. S7: Common gene expression changes after EDI3 and GPAM KD, related to Fig. 4 and 5. Supplementary Fig. S8: GPAM expression in ovarian cancer cohorts - 2nd probeset and dichotomizations, related to Fig. 6. Supplementary Fig. S9: GPAM silencing decreases migration and tumor growth - 2nd set of oligos and images of xenograft tumors, related to Fig. 7.
Marchan_Supplementary Table 6 from Glycerol-3-phosphate Acyltransferase 1 Promotes Tumor Cell Migration and Poor Survival in Ovarian Carcinoma
Authors: Marchan Rosemarie , Büttner Bettina , Lambert Jörg , Edlund Karolina , Glaeser Iris , Blaszkewicz Meinolf , Leonhardt Gregor , Marienhoff Lisa , Kaszta Darius , Anft Moritz , Watzl Carsten , Madjar Katrin , Grinberg Marianna , Rempel Eugen , Hergenröder Roland , Selinski Silvia , Rahnenführer Jörg , Lesjak Michaela S. , Stewart Joanna D. , Cadenas Cristina , Hengstler Jan G.
Published: March 2023

Differential gene expression (adj. p<0.01, FC>1.5) for GPAM-1 and GPAM-2 siRNA oligos with lists for up- and downregulated probe sets and genes for the individual oligos, as well as the overlapping probe sets and genes.
Supplementary Material, Supplementary Tables 2 through 4, 6 and 7, and Supplementary Figures 1 through 6, 8 through 12, and 14 from Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer
Authors: Jaeger Samira , Igea Ana , Arroyo Rodrigo , Alcalde Victor , Canovas Begoña , Orozco Modesto , Nebreda Angel R. , Aloy Patrick
Published: March 2023

The Supplementary Material File contains specific methodological information as well as additional results related (and cited) in the main manuscript. In particular, it contains six sections providing information on: S1) Experimental validation of drug combinations in human cancer cell lines, S2) Impact of the Residual Standard Error, S3) In vivo xenograf model, S4) Functional relationships among KEGG pathways, S5) Efficacy of clinically relevant drug combinations with respect to the PCI and S6) Enrichment of synergistic combinations in comparison with high-throughput experimental screens.
Supplementary Table S1-S3 from NEMO, a Transcriptional Target of Estrogen and Progesterone, Is Linked to Tumor Suppressor PML in Breast Cancer
Authors: Elsarraj Hanan S. , Valdez Kelli E. , Hong Yan , Grimm Sandra L. , Ricci Lawrence R. , Fan Fang , Tawfik Ossama , May Lisa , Cusick Therese , Inciardi Marc , Redick Mark , Gatewood Jason , Winblad Onalisa , Hilsenbeck Susan , Edwards Dean P. , Hagan Christy R. , Godwin Andrew K. , Fabian Carol , Behbod Fariba
Published: March 2023

S1:Differences in response to E+P were not correlated with any available patient data, including biomarker expression, age, or nuclear grade. S2:ER target genes with a role in NFkB pathway.S3:Relapse-free survival (RFS), distant metastasis-free survival (DMFS) and overall survival (OS) in all breast cancer patients or luminal A or B subtypes based on their expression levels of IKBKG and PML
Figure S5 from Astrocytes Promote Medulloblastoma Progression through Hedgehog Secretion
Authors: Liu Yongqiang , Yuelling Larra W. , Wang Yuan , Du Fang , Gordon Renata E. , O'Brien Jenny A. , Ng Jessica M.Y. , Robins Shannon , Lee Eric H. , Liu Hailong , Curran Tom , Yang Zeng-Jie
Published: March 2023

GCV treatment did not affect MB cell survival
Figure S6 from Secretory Autophagy in Cancer-Associated Fibroblasts Promotes Head and Neck Cancer Progression and Offers a Novel Therapeutic Target
Authors: New Jacob , Arnold Levi , Ananth Megha , Alvi Sameer , Thornton Mackenzie , Werner Lauryn , Tawfik Ossama , Dai Hongying , Shnayder Yelizaveta , Kakarala Kiran , Tsue Terance T. , Girod Douglas A. , Ding Wen-Xing , Anant Shrikant , Thomas Sufi Mary
Published: March 2023

Examples of Electron Microscopy Autophagosomes
Figure S2 from Secretory Autophagy in Cancer-Associated Fibroblasts Promotes Head and Neck Cancer Progression and Offers a Novel Therapeutic Target
Authors: New Jacob , Arnold Levi , Ananth Megha , Alvi Sameer , Thornton Mackenzie , Werner Lauryn , Tawfik Ossama , Dai Hongying , Shnayder Yelizaveta , Kakarala Kiran , Tsue Terance T. , Girod Douglas A. , Ding Wen-Xing , Anant Shrikant , Thomas Sufi Mary
Published: March 2023

CAF autophagy inhibition significantly decreases HNSCC in vitro progression.
Supplementary Figures from CD155T/TIGIT Signaling Regulates CD8+ T-cell Metabolism and Promotes Tumor Progression in Human Gastric Cancer
Authors: He Weiling , Zhang Hui , Han Fei , Chen Xinlin , Lin Run , Wang Wei , Qiu Haibo , Zhuang Zhenhong , Liao Qi , Zhang Weijing , Cai Qinbo , Cui Yongmei , Jiang Wenting , Wang Han , Ke Zunfu
Published: March 2023

This file includes supplementary data about cell isolation; characteristics of TIGIT+ T cells, T cell glucose metabolism.
Figure S3 from miR-519d Promotes Melanoma Progression by Downregulating EphA4
Authors: Hua Kuo-Tai , Hong Jin-Bong , Sheen Yi-Shuan , Huang Hsin-Yi , Huang Yi-Ling , Chen Jau-Shiuh , Liao Yi-Hua
Published: March 2023

Suppl. Figure 3. Immunofluorescence study showed loss of EphA4 membranous and juxtanuclear staining in cells with miR-519d overexpression.
Supplementary Figures S1-S9 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

S1: Characterization of M1/M2 and MDSC nature of macrophage profile. S2: Mutation burden and infiltration from B cells, NK cells, and macrophages. S3: Conservation of correlation structure between TCGA and PRECOG datasets. S4: Stratification thresholds for CD8+ T cell Kaplan-Meier analysis. S5: Survival meta-analysis for infiltration from B cells, NK cells, and macrophages. S6: Stratification thresholds for CD8+ T cells in CD8+ T cell/macrophage multiclass Kaplan-Meier analysis. S7: Stratification thresholds for macrophages in CD8+ T cell/macrophage multiclass Kaplan-Meier analysis. S8: Effect of CD8+ T cell infiltration and macrophage infiltration on patient survival in three additional datasets. S9: Stratification thresholds for CD8+ T cell/macrophage Kaplan-Meier analysis in three additional datasets.
Supplementary Figure S2 from CXCL-8/IL8 Produced by Diffuse Large B-cell Lymphomas Recruits Neutrophils Expressing a Proliferation-Inducing Ligand APRIL
Authors: Manfroi Benoit , McKee Thomas , Mayol Jean Francois , Tabruyn Sebastien , Moret Sebastien , Villiers Christian , Righini Christian , Dyer Martin , Callanan Mary , Schneider Pascal , Tzankov Alexandar , Matthes Thomas , Sturm Nathalie , Huard Bertrand
Published: March 2023

APRIL-producing neutrophils infiltrate the tumor nest.
Supplementary Figures 1 through 8 from A Multifunctional Role for Adjuvant Anti-4-1BB Therapy in Augmenting Antitumor Response by Chimeric Antigen Receptor T Cells
Authors: Mardiana Sherly , John Liza B. , Henderson Melissa A. , Slaney Clare Y. , von Scheidt Bianca , Giuffrida Lauren , Davenport Alexander J. , Trapani Joseph A. , Neeson Paul J. , Loi Sherene , Haynes Nicole M. , Kershaw Michael H. , Beavis Paul A. , Darcy Phillip K.
Published: March 2023

Supplementary Figure S1. Expression of activation and memory markers on transduced mouse T cells. Supplementary Figure S2. CAR T cell cytotoxic responses are not modulated by anti-4-1BB mAb therapy. Supplementary Figure S3. Her2 expression level on the mouse breast cancer cell line e0771-Her2 is comparable to the Her2-overexpressing human breast cancer cell line SKBR3. Supplementary Figure S4. Tumor weight is significantly reduced following CAR T cell and alpha-4-1BB therapy. Supplementary Figure S5. Anti-4-1BB therapy does not modulate the frequency of transferred or endogenous CD8+ tumor-infiltrating T cells. Supplementary Figure S6. Anti-4-1BB therapy modulates the frequency of mature dendritic cells in tumors and draining lymph nodes. Supplementary Figure S7. Anti-4-1BB does not modulate the frequency of MDSCs and DCs in RAG -/- mice. Supplementary Figure S8. Anti-4-1BB therapy drives maturation of NK cells.