bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Fig. 2 from Biomarker-Based PET Imaging of Diffuse Intrinsic Pontine Glioma in Mouse Models
Authors: Kossatz Susanne , Carney Brandon , Schweitzer Melanie , Carlucci Giuseppe , Miloushev Vesselin Z. , Maachani Uday B. , Rajappa Prajwal , Keshari Kayvan R. , Pisapia David , Weber Wolfgang A. , Souweidane Mark M. , Reiner Thomas
Published: March 2023

Chemical structures of PARPi-FL and [18F]PARPi. We developed a fluorescent ("PARPi-FL") (a) and 18F-labelled ("[18F]PARPi") (b) version of a PARP1 targeted small molecule, based on the structure of Olaparib23, 26, 27. Mouse and human PARP1 are orthologs, therefore PARP1 inhibitors bind to both with the same affinity.
Supplementary tables 2,3 and 4 from Sunitinib Treatment Enhances Metastasis of Innately Drug-Resistant Breast Tumors
Authors: Wragg Joseph W. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary table 2. Expression change of genes on which sunitinib has a known or predicted effect, in tumour bulk harvested at each time-point. Log2 fold change in gene expression shown. Supplementary table 3. Expression change of genes on which sunitinib has a predicted effect, in EC isolates from tumours harvested at 1300 mm3. Log2 fold change in gene expression shown. Supplementary table 4. Expression change of genes that enhance metastasis in tumour bulk harvested at each time-point. Log2 fold change in gene expression shown.
Supplementary figure 1 from Aspirin Suppresses Growth in PI3K-Mutant Breast Cancer by Activating AMPK and Inhibiting mTORC1 Signaling
Authors: Henry Whitney S. , Laszewski Tyler , Tsang Tiffany , Beca Francisco , Beck Andrew H. , McAllister Sandra S. , Toker Alex
Published: March 2023

Supplementary figure 1. Expression of mutant PIK3CA increases COX-2 expression and IKKbeta/NF-KB signaling.
Supplementary table 5 and 6 from Sunitinib Treatment Enhances Metastasis of Innately Drug-Resistant Breast Tumors
Authors: Wragg Joseph W. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary table 5. Expression change of genes that enhance metastasis in tumour bulk harvested at 1300 mm3. Log2 fold change in gene expression shown. Supplementary table 6. Expression change of genes that enhance endothelial migration in tumour bulk harvested at each time-point. Log2 fold change in gene expression shown.
Supplementary table 1 from Sunitinib Treatment Enhances Metastasis of Innately Drug-Resistant Breast Tumors
Authors: Wragg Joseph W. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Murine RTqPCR primers used for the research detailed in this paper.
Supplementary Table 1 and 2 from Cetuximab Resistance in Head and Neck Cancer Is Mediated by EGFR-K521 Polymorphism
Authors: Braig Friederike , Kriegs Malte , Voigtlaender Minna , Habel Beate , Grob Tobias , Biskup Karina , Blanchard Veronique , Sack Markus , Thalhammer Anja , Ben Batalla Isabel , Braren Ingke , Laban Simon , Danielczyk Antje , Goletz Steffen , Jakubowicz Elzbieta , Märkl Bruno , Trepel Martin , Knecht Rainald , Riecken Kristoffer , Fehse Boris , Loges Sonja , Bokemeyer Carsten , Binder Mascha
Published: March 2023

Supplementary Table 1 Patient characteristics including EGFRK521 allele frequency. Supplementary Table 2 Characteristics and sequencing data of squamous cell carcinoma cell lines.
Supplementary Figure Legends from Cetuximab Resistance in Head and Neck Cancer Is Mediated by EGFR-K521 Polymorphism
Authors: Braig Friederike , Kriegs Malte , Voigtlaender Minna , Habel Beate , Grob Tobias , Biskup Karina , Blanchard Veronique , Sack Markus , Thalhammer Anja , Ben Batalla Isabel , Braren Ingke , Laban Simon , Danielczyk Antje , Goletz Steffen , Jakubowicz Elzbieta , Märkl Bruno , Trepel Martin , Knecht Rainald , Riecken Kristoffer , Fehse Boris , Loges Sonja , Bokemeyer Carsten , Binder Mascha
Published: March 2023

Supplementary Figure 1. Inhibitory effect of Cetuximab determined by western blot analysis of 12 HNSCC cell line lysates. Supplementary Figure 2. Time course of EGFR phosphorylation in HNSCC cell line UT-SCC 8. Supplementary Figure 3. Correlation of total and membrane exposed EGFR in HNSCC cell lines. Supplementary Figure 4. IL-3 dependent Ba/F3 cells can be transformed to EGF dependence by stable transduction with EGFR and EGFRK521 genes. Supplementary Figure 5. Far-UV CD spectra of Fc-EGFR and Fc-EGFRK521. Supplementary Figure 6. ADCC induction in EGFR-transduced Ba/F3 cells by Cetuximab and CetuGEX{trade mark, serif}.
Supplementary figure 2 from Sunitinib Treatment Enhances Metastasis of Innately Drug-Resistant Breast Tumors
Authors: Wragg Joseph W. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Endothelial isolation from murine breast tumours. A, workflow of the main steps involved in the murine endothelial cell isolation procedure. B, RTqPCR for markers of leukocytes (CD11b), macrophages (CD68), epithelium (EPCAM), smooth muscle (PDGFRA) and endothelium (PECAM) in the endothelial isolates (EC) from responsive, untreated and non-responsive tumours (n=4,4,4) standardised to beta-actin (a house keeping gene) and normalised for marker expression to matched bulk tissue. Mean fold change of marker expression between the endothelial and bulk fraction is shown {plus minus} SEM.
Supplementary Tables from TET-Mediated Sequestration of miR-26 Drives EZH2 Expression and Gastric Carcinogenesis
Authors: Deng Min , Zhang Ruixin , He Zhengxi , Qiu Qinwei , Lu Xihong , Yin Jiang , Liu Hao , Jia Xiaoting , He Zhimin
Published: March 2023

Supplementary Tables S1-3. Supplementary Table S1. Clinicopathological characteristics of GC patients; Supplementary Table S2. Primers used for qRT-PCR; Supplementary Table S3. Correlation between clinicopathological parameters and TET transcriptional levels in GC patients.
Supplementary Table S5 from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

Differential response to irradiation between Grade 3 and Grade 0 patients for the probesets part of the NHEJ/BEJ geneset.
Supplementary Methods from TET-Mediated Sequestration of miR-26 Drives EZH2 Expression and Gastric Carcinogenesis
Authors: Deng Min , Zhang Ruixin , He Zhengxi , Qiu Qinwei , Lu Xihong , Yin Jiang , Liu Hao , Jia Xiaoting , He Zhimin
Published: March 2023

Description of additional experimental methods including vector construction, absolute quantification of mRNA and miRNA, RNA ï¬,uorescence in situ hybridization, and dot blotting.
Supplementary Figures from TET-Mediated Sequestration of miR-26 Drives EZH2 Expression and Gastric Carcinogenesis
Authors: Deng Min , Zhang Ruixin , He Zhengxi , Qiu Qinwei , Lu Xihong , Yin Jiang , Liu Hao , Jia Xiaoting , He Zhimin
Published: March 2023

Supplementary Figures S1-7. Supplementary Figure S1. Analysis of TET1/2/3 expression and 5-hmC levels in GC specimens and cell lines; Supplementary Figure S2. Effect of TETs on GC cell cycle, apoptosis and invasion; Supplementary Figure S3. Diagram of different recombinant expression vectors containing the TET1/2 5''UTR, the TET1/2/3 CDS, the TET1/2/3 3''UTR and the TET1/2/3 3''UTR with mutation of miR-26 binding sites as well as the TET1/2/3 full-length cDNA; Supplementary Figure S4. The expression levels of TET1, TET2 and TET3 in MKN-28 cells transfected with TET1/2/3 5''UTR, CDS, 3''UTR and full-length cDNA plasmids or empty vector; Supplementary Figure S5. TETs are direct targets of miR-26 in GC cells; Supplementary Figure S6. The regulatory role of TETs in the expression of EZH2; Supplementary Figure S7. TETs co-localize with miR-26 and EZH2 in the cytoplasm of GC cells.
Supplementary Table and Figure Legends from Ex Vivo Explant Cultures of Non–Small Cell Lung Carcinoma Enable Evaluation of Primary Tumor Responses to Anticancer Therapy
Authors: Karekla Ellie , Liao Wen-Jing , Sharp Barry , Pugh John , Reid Helen , Quesne John Le , Moore David , Pritchard Catrin , MacFarlane Marion , Pringle James Howard
Published: March 2023

Supplementary Table and Figure Legends
Supplementary Table S1 from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

Top-25 probesets differentially expressed between irradiated (2Gy) and control (0Gy) lymphocytes.
Supplementary Table 1 and Supplementary Figures 1 through 5 from Ex Vivo Explant Cultures of Non–Small Cell Lung Carcinoma Enable Evaluation of Primary Tumor Responses to Anticancer Therapy
Authors: Karekla Ellie , Liao Wen-Jing , Sharp Barry , Pugh John , Reid Helen , Quesne John Le , Moore David , Pritchard Catrin , MacFarlane Marion , Pringle James Howard
Published: March 2023

Table S1. Summary of patient, tumour and explant characteristics. Figure S1. LA-ICP-MS analysis of FFPE sections to determine Pt ion distribution. Figure S2. Characteristics of viable and nonâ€�viable tumours. Figure S3. Individual explant responses to cisplatin. Figure S4. Identification of cisplatin sensitive/resistant samples. Figure S5. LA-ICP-MS analysis of cisplatin sensitive and resistant explants.
Supplementary Methods and References from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplementary Figures S1-S5 from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

Receiver operating characteristic (ROC) curve and foci decay ratios from our retrospective study ; Induction of gene expression upon irradiation calculated within each individual patient (indicated by the index on the x-axis) for three selected radiation-sensitive genes ; Enrichment of the set of 439 probesets included in the HALLMARK P53 PATHWAY geneset that was strongly induced upon irradiation ; Volcano plots for the comparison of response to irradiation between Grade 3, 2, 1 and Grade 0 patients ; Receiver operating characteristic curve for the mean log2 fold inductions of the HR geneset .
Table S1 from Subtype-Specific Tumor-Associated Fibroblasts Contribute to the Pathogenesis of Uterine Leiomyoma
Authors: Wu Xin , Serna Vanida A. , Thomas Justin , Qiang Wenan , Blumenfeld Michael L. , Kurita Takeshi
Published: March 2023

Mutations and SMC concentrations of MED12-LM cases in Figure 1D.
Figure S4 from Subtype-Specific Tumor-Associated Fibroblasts Contribute to the Pathogenesis of Uterine Leiomyoma
Authors: Wu Xin , Serna Vanida A. , Thomas Justin , Qiang Wenan , Blumenfeld Michael L. , Kurita Takeshi
Published: March 2023

IF assay for endothelial cells in MED12-LMs. Distribution of endothelial cells in MED12-LMs was assessed by IF for PECAM1 and VWF. The concentration of endothelial cells varied between LMs.
Supplemental Table S4 from Advances in the Classification and Treatment of Mastocytosis: Current Status and Outlook toward the Future
Authors: Valent Peter , Akin Cem , Hartmann Karin , Nilsson Gunnar , Reiter Andreas , Hermine Olivier , Sotlar Karl , Sperr Wolfgang R. , Escribano Luis , George Tracy I. , Kluin-Nelemans Hanneke C. , Ustun Celalettin , Triggiani Massimo , Brockow Knut , Gotlib Jason , Orfao Alberto , Schwartz Lawrence B. , Broesby-Olsen Sigurd , Bindslev-Jensen Carsten , Kovanen Petri T. , Galli Stephen J. , Austen K. Frank , Arber Daniel A. , Horny Hans-Peter , Arock Michel , Metcalfe Dean D.
Published: March 2023

Supplemental Table S4
Supplemental Table S3 from Advances in the Classification and Treatment of Mastocytosis: Current Status and Outlook toward the Future
Authors: Valent Peter , Akin Cem , Hartmann Karin , Nilsson Gunnar , Reiter Andreas , Hermine Olivier , Sotlar Karl , Sperr Wolfgang R. , Escribano Luis , George Tracy I. , Kluin-Nelemans Hanneke C. , Ustun Celalettin , Triggiani Massimo , Brockow Knut , Gotlib Jason , Orfao Alberto , Schwartz Lawrence B. , Broesby-Olsen Sigurd , Bindslev-Jensen Carsten , Kovanen Petri T. , Galli Stephen J. , Austen K. Frank , Arber Daniel A. , Horny Hans-Peter , Arock Michel , Metcalfe Dean D.
Published: March 2023

Supplemental Table S3
Figure S3 from Subtype-Specific Tumor-Associated Fibroblasts Contribute to the Pathogenesis of Uterine Leiomyoma
Authors: Wu Xin , Serna Vanida A. , Thomas Justin , Qiang Wenan , Blumenfeld Michael L. , Kurita Takeshi
Published: March 2023

IF assay for MAC387 in MED12-LMs. Distribution of MAC387-positive cells in MED12-LMs. The concentration of MAC387-positive cells varied between samples. The positive cells were relatively rare and concentrated in perivascular areas. The blood vessels were outlined by dotted lines.
Supplemental Table S2 from Advances in the Classification and Treatment of Mastocytosis: Current Status and Outlook toward the Future
Authors: Valent Peter , Akin Cem , Hartmann Karin , Nilsson Gunnar , Reiter Andreas , Hermine Olivier , Sotlar Karl , Sperr Wolfgang R. , Escribano Luis , George Tracy I. , Kluin-Nelemans Hanneke C. , Ustun Celalettin , Triggiani Massimo , Brockow Knut , Gotlib Jason , Orfao Alberto , Schwartz Lawrence B. , Broesby-Olsen Sigurd , Bindslev-Jensen Carsten , Kovanen Petri T. , Galli Stephen J. , Austen K. Frank , Arber Daniel A. , Horny Hans-Peter , Arock Michel , Metcalfe Dean D.
Published: March 2023

Supplemental Table S2
Figure S1 from Subtype-Specific Tumor-Associated Fibroblasts Contribute to the Pathogenesis of Uterine Leiomyoma
Authors: Wu Xin , Serna Vanida A. , Thomas Justin , Qiang Wenan , Blumenfeld Michael L. , Kurita Takeshi
Published: March 2023

IHC screening for HMGA2 in LM cases. Representative HMGA2 IHC images of LMs. In a MED12-LM, a moderate signal for HMGA2 was detected in a subpopulation of SMCs. Other MED12-LMs were totally negative for HMGA2.
Table S3 from R-Spondin1/LGR5 Activates TGFβ Signaling and Suppresses Colon Cancer Metastasis
Authors: Zhou Xiaolin , Geng Liying , Wang Degeng , Yi Haowei , Talmon Geoffrey , Wang Jing
Published: March 2023

TGFbeta1 regulated genes
Table S2 from R-Spondin1/LGR5 Activates TGFβ Signaling and Suppresses Colon Cancer Metastasis
Authors: Zhou Xiaolin , Geng Liying , Wang Degeng , Yi Haowei , Talmon Geoffrey , Wang Jing
Published: March 2023

RSPO1 regulated genes
Figure S5 from A Synthetic CD8α:MyD88 Coreceptor Enhances CD8+ T-cell Responses to Weakly Immunogenic and Lowly Expressed Tumor Antigens
Authors: Kaczanowska Sabina , Joseph Ann Mary , Guo Jitao , Tsai Alexander K , Lasola Jackline Joy , Younger Kenisha , Zhang Yuji , Gonzales Cruz Velasco , Davila Eduardo
Published: March 2023

These data demonstrate that a single injection of CD8a:MyD88 T cells delay tumor progression and can prolong mouse survival.
Supplementary Figures from R-Spondin1/LGR5 Activates TGFβ Signaling and Suppresses Colon Cancer Metastasis
Authors: Zhou Xiaolin , Geng Liying , Wang Degeng , Yi Haowei , Talmon Geoffrey , Wang Jing
Published: March 2023

Fig. S1: Validation of colon cancer cell lines, LGR5 mRNA expression in normal colon, adenomas and carcinomas and evaluation of the specificity of the anti-LGR5 antibody in IHC Staining. Fig. S2: Primary tumor weight of CBS control and LGR5 knockdown cells and RT-PCR analysis of human GAPDH in the lung and liver of each mouse. Fig. S3: RSPO1 activates Wnt signaling in HEK293T cells but not in FET cells. Fig. S4: RSPO1 activates TGFbeta signaling in a dose-dependent manner and in HT29 cells. Fig. S5: Knockdown of beta-catenin or expression of a dnTCF has no effect on RSPO1-mediated activation of TGFbeta signaling Fig. S6: RSPO1 and TGFbeta1 increase the aggregation of LGR5 and TGFbeta RI, WNT5A does not activate TGFbeta signaling in FET cells and expression of LGR5 homologues in colon cancer cells. Knockdown of beta-catenin or expression of a dnTCF has no effect on upregulation of RASA4 and TSPAN2 expression.
Figure S4 from A Synthetic CD8α:MyD88 Coreceptor Enhances CD8+ T-cell Responses to Weakly Immunogenic and Lowly Expressed Tumor Antigens
Authors: Kaczanowska Sabina , Joseph Ann Mary , Guo Jitao , Tsai Alexander K , Lasola Jackline Joy , Younger Kenisha , Zhang Yuji , Gonzales Cruz Velasco , Davila Eduardo
Published: March 2023

These data show changes in the levels of cytokines and chemokines in tumors induced by CD8a:MyD88-expressing T cells.
Figure S3 from A Synthetic CD8α:MyD88 Coreceptor Enhances CD8+ T-cell Responses to Weakly Immunogenic and Lowly Expressed Tumor Antigens
Authors: Kaczanowska Sabina , Joseph Ann Mary , Guo Jitao , Tsai Alexander K , Lasola Jackline Joy , Younger Kenisha , Zhang Yuji , Gonzales Cruz Velasco , Davila Eduardo
Published: March 2023

These data show changes in the levels of cytokines and chemokines induced by CD8a:MyD88 expression in T cells.
Supplementary Table S1-S6 from Tim-3 Expression on Tumor-Infiltrating PD-1+CD8+ T Cells Correlates with Poor Clinical Outcome in Renal Cell Carcinoma
Authors: Granier Clémence , Dariane Charles , Combe Pierre , Verkarre Virginie , Urien Saïk , Badoual Cécile , Roussel Hélène , Mandavit Marion , Ravel Patrice , Sibony Mathilde , Biard Lucie , Radulescu Camélia , Vinatier Emeline , Benhamouda Nadine , Peyromaure Michael , Oudard Stéphane , Méjean Arnaud , Timsit Marc-Olivier , Gey Alain , Tartour Eric
Published: March 2023

Table S1: Baseline clinical characteristics of the 87 primary clear cell RCC patient selected for multiparametric immunofluorescence in situ analysis Table S2: Baseline clinical characteristics of the 42 primary RCC patient with analysis of fresh tumor TIL Table S3 : List of antibodies used for cytometry and in situ immunofluorescence Table S4: Correlation between the total number (Nb) of CD8+T cells and those expressing Tim-3 and/or PD-1 and the Fuhrman grade and UISS. Table S5 : RCC patients characteristics in the prospective cohorts Table S6 : RCC patients characteristics in the retrospective cohorts
Figure S1 from A Synthetic CD8α:MyD88 Coreceptor Enhances CD8+ T-cell Responses to Weakly Immunogenic and Lowly Expressed Tumor Antigens
Authors: Kaczanowska Sabina , Joseph Ann Mary , Guo Jitao , Tsai Alexander K , Lasola Jackline Joy , Younger Kenisha , Zhang Yuji , Gonzales Cruz Velasco , Davila Eduardo
Published: March 2023

These data show the vector constructs verify expression of the intended protein.
Supplementary Table S1 and S2 from Proliferating EpCAM-Positive Ductal Cells in the Inflamed Liver Give Rise to Hepatocellular Carcinoma
Authors: Matsumoto Tomonori , Takai Atsushi , Eso Yuji , Kinoshita Kazuo , Manabe Toshiaki , Seno Hiroshi , Chiba Tsutomu , Marusawa Hiroyuki
Published: March 2023

Supplementary Table S1 shows genes differentially expressed among PDC-derived HCCs with or without CLC components and Alb-derived HCCs. Supplementary Table S2 shows KEGG pathways which were enriched in gene clusters identified by microarray analyses.
Figures S1-S6 from Proliferating EpCAM-Positive Ductal Cells in the Inflamed Liver Give Rise to Hepatocellular Carcinoma
Authors: Matsumoto Tomonori , Takai Atsushi , Eso Yuji , Kinoshita Kazuo , Manabe Toshiaki , Seno Hiroshi , Chiba Tsutomu , Marusawa Hiroyuki
Published: March 2023

Supplementary Figure S1 shows BAC construction for generating EpcamCreERT2 mice. Supplementary Figure S2 shows microscopic images of the liver of DDC-fed wild-type mice. Supplementary Figure S3 shows immunostaining images indicating cell behaviors in DDC-damaged liver. Supplementary Figure S4 shows immunostaining images demonstrating AID induction in DDC-damaged liver. Supplementary Figure S5 shows H&E, and immunostaining images of PDC-derived and Alb-derived HCCs. Supplementary Figure S6 shows tumorigenicity of PDC-derived HCCs.
Supplemental Table 2 from RB Loss Promotes Prostate Cancer Metastasis
Authors: Thangavel Chellappagounder , Boopathi Ettickan , Liu Yi , Haber Alex , Ertel Adam , Bhardwaj Anshul , Addya Sankar , Williams Noelle , Ciment Stephen J. , Cotzia Paolo , Dean Jeffry L. , Snook Adam , McNair Chris , Price Matt , Hernandez James R. , Zhao Shuang G. , Birbe Ruth , McCarthy James B. , Turley Eva A. , Pienta Kenneth J. , Feng Felix Y. , Dicker Adam P. , Knudsen Karen E. , Den Robert B.
Published: March 2023

in silico docking information
Supplemental Table 1 from RB Loss Promotes Prostate Cancer Metastasis
Authors: Thangavel Chellappagounder , Boopathi Ettickan , Liu Yi , Haber Alex , Ertel Adam , Bhardwaj Anshul , Addya Sankar , Williams Noelle , Ciment Stephen J. , Cotzia Paolo , Dean Jeffry L. , Snook Adam , McNair Chris , Price Matt , Hernandez James R. , Zhao Shuang G. , Birbe Ruth , McCarthy James B. , Turley Eva A. , Pienta Kenneth J. , Feng Felix Y. , Dicker Adam P. , Knudsen Karen E. , Den Robert B.
Published: March 2023

nucleotide sequence
Supplementary Figure 4 from MYC Mediates Large Oncosome-Induced Fibroblast Reprogramming in Prostate Cancer
Authors: Minciacchi Valentina R. , Spinelli Cristiana , Reis-Sobreiro Mariana , Cavallini Lorenzo , You Sungyong , Zandian Mandana , Li Xiaohong , Mishra Rajeev , Chiarugi Paola , Adam Rosalyn M. , Posadas Edwin M. , Viglietto Giuseppe , Freeman Michael R. , Cocucci Emanuele , Bhowmick Neil A. , Di Vizio Dolores
Published: March 2023

Additional data on Akt1 activation by LO
Supplementary Figure 3 from MYC Mediates Large Oncosome-Induced Fibroblast Reprogramming in Prostate Cancer
Authors: Minciacchi Valentina R. , Spinelli Cristiana , Reis-Sobreiro Mariana , Cavallini Lorenzo , You Sungyong , Zandian Mandana , Li Xiaohong , Mishra Rajeev , Chiarugi Paola , Adam Rosalyn M. , Posadas Edwin M. , Viglietto Giuseppe , Freeman Michael R. , Cocucci Emanuele , Bhowmick Neil A. , Di Vizio Dolores
Published: March 2023

Additional data on MYC activation by LO
Supplementary Figures from Radiation-Induced Enhancement of Antitumor T-cell Immunity by VEGF-Targeted 4-1BB Costimulation
Authors: Schrand Brett , Verma Bhavna , Levay Agata , Patel Shradha , Castro Iris , Benaduce Ana Paula , Brenneman Randall , Umland Oliver , Yagita Hideo , Gilboa Eli , Ishkanian Adrian
Published: March 2023

Biodistribution of VEGF-4-1BB conjugate. Survival assay in MCA induced fibrosarcoma model. Cytokine levels in treated animals. Tumor volume studies with combinatorial therapy in Balb/c model. Histology and morphology for toxicity profiles.
Supplementary Figure 2 from MYC Mediates Large Oncosome-Induced Fibroblast Reprogramming in Prostate Cancer
Authors: Minciacchi Valentina R. , Spinelli Cristiana , Reis-Sobreiro Mariana , Cavallini Lorenzo , You Sungyong , Zandian Mandana , Li Xiaohong , Mishra Rajeev , Chiarugi Paola , Adam Rosalyn M. , Posadas Edwin M. , Viglietto Giuseppe , Freeman Michael R. , Cocucci Emanuele , Bhowmick Neil A. , Di Vizio Dolores
Published: March 2023

Additional data on LO internalization
Supplementary Figure 1 from MYC Mediates Large Oncosome-Induced Fibroblast Reprogramming in Prostate Cancer
Authors: Minciacchi Valentina R. , Spinelli Cristiana , Reis-Sobreiro Mariana , Cavallini Lorenzo , You Sungyong , Zandian Mandana , Li Xiaohong , Mishra Rajeev , Chiarugi Paola , Adam Rosalyn M. , Posadas Edwin M. , Viglietto Giuseppe , Freeman Michael R. , Cocucci Emanuele , Bhowmick Neil A. , Di Vizio Dolores
Published: March 2023

Additional data on Akt1 in circulating EVs
Supplementary Table S1: Primer sequences for RFLP sites and Her2 transgene from Mitochondrial Haplotype Alters Mammary Cancer Tumorigenicity and Metastasis in an Oncogenic Driver–Dependent Manner
Authors: Brinker Amanda E. , Vivian Carolyn J. , Koestler Devin C. , Tsue Trevor T. , Jensen Roy A. , Welch Danny R.
Published: March 2023

Supplementary Table S1: Primer sequences for RFLP sites and Her2 transgene
Supplemental Figure 8 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

The effects of Poly-IC and poly-IC in combination with nutlin-3a on immune cell infiltration to the B16 TME.
Supplementary Dataset 6 from Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis
Authors: Rokavec Matjaz , Horst David , Hermeking Heiko
Published: March 2023

lncRNA signatures
Supplemental Figure 7 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Nutlin-3a induces immunogenic cell death of B16 tumors.
Supplemental Figure 3 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Nutlin-3a induces localized p53 upregulation in the EL4 TME associated with similar tumor death in WT and immune deficient Rag1null mice.
Supplemental Figure 2 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Intratumoral nutlin-3a injection did not impose systemic toxicity to host lymphoid tissues.
Supplementary Dataset 1 from Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis
Authors: Rokavec Matjaz , Horst David , Hermeking Heiko
Published: March 2023

mRNA signatures
Supplemental Figure 1 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Nutlin-3a induces activation of the p53 pathway and p53-dependent cell death of EL4 and B16 tumors in a dose-dependent manner.
Supplemental figures, tables, material and methods from Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis
Authors: Rokavec Matjaz , Horst David , Hermeking Heiko
Published: March 2023

Supplemental methods: RNA isolation and quantitative real-time PCR (qPCR), Immunofluorescence and confocal laser-scanning microscopy, Boyden-chamber cell invasion assay, Wound healing cell migration assay, TOP/FOP Wnt activity assay, Analyzes of signal transduction pathway activity, Metastases formation in a xenograft mouse model, RNA expression profiling by RNA-Seq, miRNA expression profiling using arrays, DNA methylation profiling by 450k arrays, Analyzes of histone modifications by ChIP-seq, Hierarchical clustering and principal component analysis, Analysis of expression and DNA methylation data from online databases, suppl. References Supplemental Figures: Figure S1 is related to Figure 1: Establishment of a cellular model that recapitulates the EMT/MET switching during colon cancer metastasis. Figure S2 is related to Figure 2: mRNA profiling of DLD1 cell derivatives. Figure S3 is related to Figure 3: miRNA alterations in DLD1 cell derivatives. Figure S4 is related to Figure 4: DNA Methylation profiling of DLD1 cell derivatives. Figure S5 is related to Figure 5: H3K4me3, H3K79me3, and H3K27me3 histone modifications are associated with expression in DLD1 derivatives. Figure S6 is related to Figure 6: Analyzes of lncRNA signatures and the H19 lncRNA. Figure S7: Pathway analysis in DLD1 cell derivatives. Figure S8 is related to Figure 7: DNA methylation of gene regulatory regions of axon guidance-associated genes. Figure S9 is related to Figure 7: Elevated expression and hypomethylation of SEMA4A is associated with colon cancer metastasis. Supplemental Tables: Table S1. Predicted DM miRNA targets among MES mRNAs Table S2. Predicted MES miRNA targets among DM mRNAs Table S3. Top genes exhibiting altered expression and DNA methylation between DLD1 and SA/SPH derivatives Table S4. Top genes exhibiting altered expression and DNA methylation between SA/SPH and METS derivatives Table S5. Top genes exhibiting altered expression and DNA methylation between DLD1 and METS derivatives
Supplementary Tables from MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia
Authors: Saba Nakhle S. , Wong Deanna H. , Tanios Georges , Iyer Jessica R. , Lobelle-Rich Patricia , Dadashian Eman L. , Liu Delong , Fontan Lorena , Flemington Erik K. , Nichols Cydney M. , Underbayev Chingiz , Safah Hana , Melnick Ari , Wiestner Adrian , Herman Sarah E. M.
Published: March 2023

Supplementary Table S1. Patient characteristics. Supplementary Table S2. Characteristics of patients treated with ibrutinib. Supplementary Table S3. Primers and probes used for digital PCR. Supplementary Table S4. List of genes up- or down-regulated genes by MI-2 in CLL. Supplementary Table S5. Gene sets identified by GSEA that are affected by MI-2.
Supplementary Table Descritptions from MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia
Authors: Saba Nakhle S. , Wong Deanna H. , Tanios Georges , Iyer Jessica R. , Lobelle-Rich Patricia , Dadashian Eman L. , Liu Delong , Fontan Lorena , Flemington Erik K. , Nichols Cydney M. , Underbayev Chingiz , Safah Hana , Melnick Ari , Wiestner Adrian , Herman Sarah E. M.
Published: March 2023

Description and Legends for Supplementary Tables S1-5
Supplementary Figure Legends from MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia
Authors: Saba Nakhle S. , Wong Deanna H. , Tanios Georges , Iyer Jessica R. , Lobelle-Rich Patricia , Dadashian Eman L. , Liu Delong , Fontan Lorena , Flemington Erik K. , Nichols Cydney M. , Underbayev Chingiz , Safah Hana , Melnick Ari , Wiestner Adrian , Herman Sarah E. M.
Published: March 2023

Supplementary Figure Legends S1-3
Supplementary Tables and Legends from Circulating Tumor Cells with Aberrant ALK Copy Number Predict Progression-Free Survival during Crizotinib Treatment in ALK-Rearranged Non–Small Cell Lung Cancer Patients
Authors: Pailler Emma , Oulhen Marianne , Borget Isabelle , Remon Jordi , Ross Kirsty , Auger Nathalie , Billiot Fanny , Ngo Camus Maud , Commo Frédéric , Lindsay Colin R. , Planchard David , Soria Jean-Charles , Besse Benjamin , Farace Françoise
Published: March 2023

Supplementary data including: the legend for Supplementary Figure 1 the Supplementary Table 1 entitled detection of ALK-rearrangement and ALK copy number gain in tumors and CTC of ALK-rearranged patients the Supplementary Table 2 entitled descriptive statistics of numbers of CTC in ALK-rearranged patients at baseline and under crizotinib therapy the Supplementary Table 3 entitled levels of significant association between CTC subsets and clinical parameters at baseline the Supplementary Table 4 entitled successive treatment lines received post-crizotinib
Supplementary Figure S8 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

Network hotspot analysis.
Supplementary Figure 1 from Circulating Tumor Cells with Aberrant ALK Copy Number Predict Progression-Free Survival during Crizotinib Treatment in ALK-Rearranged Non–Small Cell Lung Cancer Patients
Authors: Pailler Emma , Oulhen Marianne , Borget Isabelle , Remon Jordi , Ross Kirsty , Auger Nathalie , Billiot Fanny , Ngo Camus Maud , Commo Frédéric , Lindsay Colin R. , Planchard David , Soria Jean-Charles , Besse Benjamin , Farace Françoise
Published: March 2023

Supplementary Figure 1 entitled example of combined immunofluorescent staining and a three-color FA-FISH experiment using filtration enriched-H2228 cell line spiked into peripheral blood samples from a healthy donor and ALK break-apart probes coupled to the chromosome 2-specific centromeric probe.
Supplementary Figure S7 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

Principal component and GSEA analyses of microarray data.
Supplementary figures legend from Paxillin Binding to the Cytoplasmic Domain of CD103 Promotes Cell Adhesion and Effector Functions for CD8+ Resident Memory T Cells in Tumors
Authors: Gauthier Ludiane , Corgnac Stéphanie , Boutet Marie , Gros Gwendoline , Validire Pierre , Bismuth Georges , Mami-Chouaib Fathia
Published: March 2023

S. Figure 1. Involvement of Pxn in CD103-mediated adhesion and spreading of CD8+/CD103+ TRM cells. S. Figure 2. T-cell treatment with saracatinib or infection with shRNA targeting Pxn does not alter cell viability and cell surface protein expression levels. S. Figure 3. Transfection of the JTag T-cell clone with CD103-GFP constructs. S. Figure 4. The alphaE cytoplasmic tail is required for Pxn-dependent CD103 polarization and CD103-mediated early T-cell signaling.
Supplementary Figure S5 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

T cells of host and HSCT origin do not participate to tumor recognition.
Figure S3 from Paxillin Binding to the Cytoplasmic Domain of CD103 Promotes Cell Adhesion and Effector Functions for CD8+ Resident Memory T Cells in Tumors
Authors: Gauthier Ludiane , Corgnac Stéphanie , Boutet Marie , Gros Gwendoline , Validire Pierre , Bismuth Georges , Mami-Chouaib Fathia
Published: March 2023

Transfection of the JTag T-cell clone with CD103-GFP constructs.
Supplementary Figure S3 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

Combined Tumor+Allo/Y ACT prolong survival of mice with autochthonous adenocarcinomas of the pancreas.
Supplementary Figure S2 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

Assessing Disease State in ACT treated TRAMP mice.
Figure S1 from Paxillin Binding to the Cytoplasmic Domain of CD103 Promotes Cell Adhesion and Effector Functions for CD8+ Resident Memory T Cells in Tumors
Authors: Gauthier Ludiane , Corgnac Stéphanie , Boutet Marie , Gros Gwendoline , Validire Pierre , Bismuth Georges , Mami-Chouaib Fathia
Published: March 2023

Involvement of Pxn in CD103-mediated adhesion and spreading of CD8+/CD103+ TRM cells
Supplementary Figure S1 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

Phenotype of TCR-redirected T cells.
Supplementary information from Soluble IL6R Expressed by Myeloid Cells Reduces Tumor-Specific Th1 Differentiation and Drives Tumor Progression
Authors: Tsukamoto Hirotake , Fujieda Koji , Hirayama Masatoshi , Ikeda Tokunori , Yuno Akira , Matsumura Keiko , Fukuma Daiki , Araki Kimi , Mizuta Hiroshi , Nakayama Hideki , Senju Satoru , Nishimura Yasuharu
Published: March 2023

This file includes "Supplementary Materials and Methods" and figure legends for "Supplementary Figures 1 to 4"
Supplementary Tables S1-S5 from DDB2 Is a Novel Regulator of Wnt Signaling in Colon Cancer
Authors: Huang Shuo , Fantini Damiano , Merrill Bradley J. , Bagchi Srilata , Guzman Grace , Raychaudhuri Pradip
Published: March 2023

Table S1: Sequences of DsiRNA; Table S2: Primers for ChIP assays; Table S3: Primers for gene expression assays; Table S4: Correlation analysis of DDB2 and RNF43 expression in patient colonic samples; Table S5:Primers and probes for 3C assay
Supplementary Methods from DDB2 Is a Novel Regulator of Wnt Signaling in Colon Cancer
Authors: Huang Shuo , Fantini Damiano , Merrill Bradley J. , Bagchi Srilata , Guzman Grace , Raychaudhuri Pradip
Published: March 2023

Supplementary methods of Protein Extraction, Immunoblotting and Co-immunoprecipitations, Chromatin Conformation Capture Assay, Immunofluorescent Staining and Whole Exome Sequencing (WES)
Supplementary Figure 4 from Soluble IL6R Expressed by Myeloid Cells Reduces Tumor-Specific Th1 Differentiation and Drives Tumor Progression
Authors: Tsukamoto Hirotake , Fujieda Koji , Hirayama Masatoshi , Ikeda Tokunori , Yuno Akira , Matsumura Keiko , Fukuma Daiki , Araki Kimi , Mizuta Hiroshi , Nakayama Hideki , Senju Satoru , Nishimura Yasuharu
Published: March 2023

Comparative analysis in immunological parameters from cancer patients and healthy donors.
Supplementary Figure 2 from Soluble IL6R Expressed by Myeloid Cells Reduces Tumor-Specific Th1 Differentiation and Drives Tumor Progression
Authors: Tsukamoto Hirotake , Fujieda Koji , Hirayama Masatoshi , Ikeda Tokunori , Yuno Akira , Matsumura Keiko , Fukuma Daiki , Araki Kimi , Mizuta Hiroshi , Nakayama Hideki , Senju Satoru , Nishimura Yasuharu
Published: March 2023

Tumor cell-derived sIL-6R does not play a major role in attenuating Th1 differentiation in tumor-bearing mice.
Supplementary Figure 1 from Soluble IL6R Expressed by Myeloid Cells Reduces Tumor-Specific Th1 Differentiation and Drives Tumor Progression
Authors: Tsukamoto Hirotake , Fujieda Koji , Hirayama Masatoshi , Ikeda Tokunori , Yuno Akira , Matsumura Keiko , Fukuma Daiki , Araki Kimi , Mizuta Hiroshi , Nakayama Hideki , Senju Satoru , Nishimura Yasuharu
Published: March 2023

Macrophages and MDSC produce sIL-6R in tumor-bearing mice.
Table S3 from Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA–MUF Interaction with ANXA2 and miR-34a
Authors: Yan Xinlong , Zhang Dongdong , Wu Wei , Wu Shuheng , Qian Jingfeng , Hao Yajing , Yan Fang , Zhu Pingping , Wu Jiayi , Huang Guanling , Huang Yinghui , Luo Jianjun , Liu Xinhui , Liu Benyu , Chen Xiaomin , Du Ying , Chen Runsheng , Fan Zusen
Published: March 2023

RNA pulldown assays followed by mass spectrum indicated that lncRNA-MUF can bind with ANXA2.
Table S2 from Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA–MUF Interaction with ANXA2 and miR-34a
Authors: Yan Xinlong , Zhang Dongdong , Wu Wei , Wu Shuheng , Qian Jingfeng , Hao Yajing , Yan Fang , Zhu Pingping , Wu Jiayi , Huang Guanling , Huang Yinghui , Luo Jianjun , Liu Xinhui , Liu Benyu , Chen Xiaomin , Du Ying , Chen Runsheng , Fan Zusen
Published: March 2023

Human lncRNA-MUF sequence has no coding potentiality.
Supplementary Information Method from Macrophage-Secreted TNFα and TGFβ1 Influence Migration Speed and Persistence of Cancer Cells in 3D Tissue Culture via Independent Pathways
Authors: Li Ran , Hebert Jess D. , Lee Tara A. , Xing Hao , Boussommier-Calleja Alexandra , Hynes Richard O. , Lauffenburger Douglas A. , Kamm Roger D.
Published: March 2023

This files contains detailed methods on procedures used in this study, which complements the method described in the main paper. It also expands on the methods described in the main paper. Specifically, it contains method on Microfluidic 3D cell migration assay; 2D Cell Migration Assay; Immunofluorescent staining, confocal microscopy, and DQ-Collagen I Release Assay; ELISA; Cancer cell-macrophage co-culture for western blot analysis; Treatment of cancer cells for western blot analysis; Protein isolation and western blot analysis; Total RNA extraction and mRNA detection; In vivo metastasis assay
Supplementary figure legends and materials from Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA–MUF Interaction with ANXA2 and miR-34a
Authors: Yan Xinlong , Zhang Dongdong , Wu Wei , Wu Shuheng , Qian Jingfeng , Hao Yajing , Yan Fang , Zhu Pingping , Wu Jiayi , Huang Guanling , Huang Yinghui , Luo Jianjun , Liu Xinhui , Liu Benyu , Chen Xiaomin , Du Ying , Chen Runsheng , Fan Zusen
Published: March 2023

HCC-MSCs induced EMT and upregulated lncRNA-MUF,ANXA2 interacted with GSK3 beta,lncRNA-MUF acted as a ceRNA of miR34a and other detailed methods
Supplementary Information Figure Captions from Macrophage-Secreted TNFα and TGFβ1 Influence Migration Speed and Persistence of Cancer Cells in 3D Tissue Culture via Independent Pathways
Authors: Li Ran , Hebert Jess D. , Lee Tara A. , Xing Hao , Boussommier-Calleja Alexandra , Hynes Richard O. , Lauffenburger Douglas A. , Kamm Roger D.
Published: March 2023

This file contains the figure captions for the supplementary information figures. Again, Fig. S1 and S2 is related to Fig. 1; Fig. S3 and S4 is related to Fig. 2; Fig. S5, S6, S7 is related to Fig. 3; Fig. S8-11 is related to Fig. 4; Fig. S12 is related to Fig. 6. Each figure caption describes its corresponding figure, summarize the results, and describes the statistics of the data.
Figure S3 from Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA–MUF Interaction with ANXA2 and miR-34a
Authors: Yan Xinlong , Zhang Dongdong , Wu Wei , Wu Shuheng , Qian Jingfeng , Hao Yajing , Yan Fang , Zhu Pingping , Wu Jiayi , Huang Guanling , Huang Yinghui , Luo Jianjun , Liu Xinhui , Liu Benyu , Chen Xiaomin , Du Ying , Chen Runsheng , Fan Zusen
Published: March 2023

ANXA2 modulates beta-catenin-target genes and can interact with GSK3beta.
Figure S2 from Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA–MUF Interaction with ANXA2 and miR-34a
Authors: Yan Xinlong , Zhang Dongdong , Wu Wei , Wu Shuheng , Qian Jingfeng , Hao Yajing , Yan Fang , Zhu Pingping , Wu Jiayi , Huang Guanling , Huang Yinghui , Luo Jianjun , Liu Xinhui , Liu Benyu , Chen Xiaomin , Du Ying , Chen Runsheng , Fan Zusen
Published: March 2023

LncRNA-MUF is upregulated in HCC cells by HCC-MSCs
Supplementary Table S7 from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

SILAC secretome data
Supplementary Table S6 from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

IP-MS (SWATH) data
Supplemental Figure 1 from IL10 Release upon PD-1 Blockade Sustains Immunosuppression in Ovarian Cancer
Authors: Lamichhane Purushottam , Karyampudi Lavakumar , Shreeder Barath , Krempski James , Bahr Deborah , Daum Joshua , Kalli Kimberly R. , Goode Ellen L. , Block Matthew S. , Cannon Martin J. , Knutson Keith L.
Published: March 2023

Expression of PD-1 on BMDCs and T cells after exposure to IL-6 and IL-10
Supplementary Table S5 from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

miRNA alignment results
Table S2 from MUC1-C Induces PD-L1 and Immune Evasion in Triple-Negative Breast Cancer
Authors: Maeda Takahiro , Hiraki Masayuki , Jin Caining , Rajabi Hasan , Tagde Ashujit , Alam Maroof , Bouillez Audrey , Hu Xiufeng , Suzuki Yozo , Miyo Masaaki , Hata Tsuyoshi , Hinohara Kunihiko , Kufe Donald
Published: March 2023

This file contains ChIP qPCR primer pairs for the GAPDH and PD-L1 promoters.
Supplementary Materials and Figure Legends from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

Supplementary material and methods relating to cell culture, cell treatments and transfections, proliferation assays, Western blot analysis etc. and Supplementary Figure Legends for Supplementary Figures 1-8
Figure S6 and Legend from MUC1-C Induces PD-L1 and Immune Evasion in Triple-Negative Breast Cancer
Authors: Maeda Takahiro , Hiraki Masayuki , Jin Caining , Rajabi Hasan , Tagde Ashujit , Alam Maroof , Bouillez Audrey , Hu Xiufeng , Suzuki Yozo , Miyo Masaaki , Hata Tsuyoshi , Hinohara Kunihiko , Kufe Donald
Published: March 2023

This file contains results showing that treatment of Eo771/MUC1-C tumors with GO-203/NPs activates tumor infiltrating CD8+ T-cells as evidenced by increases in IFN-γ (S6A), CD107α (S6B) and granzyme B (S6C).
Supplementary Figures S3-S8 from PACE4 Undergoes an Oncogenic Alternative Splicing Switch in Cancer
Authors: Couture Frédéric , Sabbagh Robert , Kwiatkowska Anna , Desjardins Roxane , Guay Simon-Pierre , Bouchard Luigi , Day Robert
Published: March 2023

Supplementary data and material regarding the alternative splicing detailed analysis by PCR and IHC, decitabine efficacy, supplementary cell line testing by overexpression and silencing and substrate screening by western blots
Figure S3 and Legend from MUC1-C Induces PD-L1 and Immune Evasion in Triple-Negative Breast Cancer
Authors: Maeda Takahiro , Hiraki Masayuki , Jin Caining , Rajabi Hasan , Tagde Ashujit , Alam Maroof , Bouillez Audrey , Hu Xiufeng , Suzuki Yozo , Miyo Masaaki , Hata Tsuyoshi , Hinohara Kunihiko , Kufe Donald
Published: March 2023

This file contains the results of studies with DOX-treated BT-549/tet-MUC1shRNA and MDA-MB-231/tet-MUC1shRNA cells, demonstrating that targeting MUC1-C decreases activation of NF-κB p65 (S3A and S3B). The studies also show that targeting NF-κB p65 with a p65shRNA (S3C and S3D) or the BAY-11-7085 inhibitor (S3E and S3F) decreases PD-L1 expression.
Figure S2 and Legend from MUC1-C Induces PD-L1 and Immune Evasion in Triple-Negative Breast Cancer
Authors: Maeda Takahiro , Hiraki Masayuki , Jin Caining , Rajabi Hasan , Tagde Ashujit , Alam Maroof , Bouillez Audrey , Hu Xiufeng , Suzuki Yozo , Miyo Masaaki , Hata Tsuyoshi , Hinohara Kunihiko , Kufe Donald
Published: March 2023

This file contains the results obtained from JQ1 treatment of BT-549 (S2A) and BT-20/MUC1-C (S2B), which demonstrate that JQ1 decreases MYC and PD-L1 expression.