bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from Bortezomib Stabilizes and Activates p53 in Proliferative Compartments of Both Normal and Tumor Tissues In Vivo
Authors: Xue Yuezhen , Barker Nick , Hoon Shawn , He Pingping , Thakur Teena , Abdeen Shifana Raja , Maruthappan Priadarsini , Ghadessy Farid J. , Lane David P.
Published: March 2023

Supplementary information contains "Supplementary Materials and Methods" and "Supplementary figure legends".
Supplementary Data from IL12 Abrogates Calcineurin-Dependent Immune Evasion during Leukemia Progression
Authors: Rabe Jennifer L. , Gardner Lori , Hunter Rae , Fonseca Jairo A. , Dougan Jodi , Gearheart Christy M. , Leibowitz Michael S. , Lee-Miller Cathy , Baturin Dmitry , Fosmire Susan P. , Zelasko Susan E. , Jones Courtney L. , Slansky Jill E. , Rupji Manali , Dwivedi Bhakti , Henry Curtis J. , Porter Christopher C.
Published: March 2023

Supplemental Table 1: Gene expression analysis by RNA-seq from shNS and shCnB leukemia cells. Data are normalized as Reads per Kilobase per Million.
Figure S6 from Bortezomib Stabilizes and Activates p53 in Proliferative Compartments of Both Normal and Tumor Tissues In Vivo
Authors: Xue Yuezhen , Barker Nick , Hoon Shawn , He Pingping , Thakur Teena , Abdeen Shifana Raja , Maruthappan Priadarsini , Ghadessy Farid J. , Lane David P.
Published: March 2023

Upregulation of p53 target genes in response to irradiation in intestinal adenomas.
Figure S3 from Bortezomib Stabilizes and Activates p53 in Proliferative Compartments of Both Normal and Tumor Tissues In Vivo
Authors: Xue Yuezhen , Barker Nick , Hoon Shawn , He Pingping , Thakur Teena , Abdeen Shifana Raja , Maruthappan Priadarsini , Ghadessy Farid J. , Lane David P.
Published: March 2023

p53 is stabilized in the transit amplifying zone of the stomach corpus.
Supplementary Movie 1 from Gene Editing of α6 Integrin Inhibits Muscle Invasive Networks and Increases Cell–Cell Biophysical Properties in Prostate Cancer
Authors: Rubenstein Cynthia S. , Gard Jaime M.C. , Wang Mengdie , McGrath Julie E. , Ingabire Nadia , Hinton James P. , Marr Kendra D. , Simpson Skyler J. , Nagle Raymond B. , Miranti Cindy K. , Warfel Noel A. , Garcia Joe G.N. , Arif-Tiwari Hina , Cress Anne E.
Published: March 2023

Invasive Network formation in DU145 α6WT cells
Figure S2 from Bortezomib Stabilizes and Activates p53 in Proliferative Compartments of Both Normal and Tumor Tissues In Vivo
Authors: Xue Yuezhen , Barker Nick , Hoon Shawn , He Pingping , Thakur Teena , Abdeen Shifana Raja , Maruthappan Priadarsini , Ghadessy Farid J. , Lane David P.
Published: March 2023

p53 mRNA was not stabilized by bortezomib treatment.
Figure S1 from Bortezomib Stabilizes and Activates p53 in Proliferative Compartments of Both Normal and Tumor Tissues In Vivo
Authors: Xue Yuezhen , Barker Nick , Hoon Shawn , He Pingping , Thakur Teena , Abdeen Shifana Raja , Maruthappan Priadarsini , Ghadessy Farid J. , Lane David P.
Published: March 2023

Longer p53 stabilization in the small intestine by higher dose of bortezomib.
Supplementary Figure 4 from Gene Editing of α6 Integrin Inhibits Muscle Invasive Networks and Increases Cell–Cell Biophysical Properties in Prostate Cancer
Authors: Rubenstein Cynthia S. , Gard Jaime M.C. , Wang Mengdie , McGrath Julie E. , Ingabire Nadia , Hinton James P. , Marr Kendra D. , Simpson Skyler J. , Nagle Raymond B. , Miranti Cindy K. , Warfel Noel A. , Garcia Joe G.N. , Arif-Tiwari Hina , Cress Anne E.
Published: March 2023

Specific guide RNAs and positions used for genomic editing of α6 integrin using CRISPR/Cas9 in DU145 cells injected into mice and resulting tumor growth kinetics
Supplementary Table 2 from WWOX Inhibits Metastasis of Triple-Negative Breast Cancer Cells via Modulation of miRNAs
Authors: Khawaled Saleh , Suh Sung Suk , Abdeen Suhaib K. , Monin Jonathan , Distefano Rosario , Nigita Giovanni , Croce Carlo M. , Aqeilan Rami I.
Published: March 2023

Nanostring microRNAs data
Supplementary Table 1 from WWOX Inhibits Metastasis of Triple-Negative Breast Cancer Cells via Modulation of miRNAs
Authors: Khawaled Saleh , Suh Sung Suk , Abdeen Suhaib K. , Monin Jonathan , Distefano Rosario , Nigita Giovanni , Croce Carlo M. , Aqeilan Rami I.
Published: March 2023

TCGA TNBC samples
Supplementary Figures from WWOX Inhibits Metastasis of Triple-Negative Breast Cancer Cells via Modulation of miRNAs
Authors: Khawaled Saleh , Suh Sung Suk , Abdeen Suhaib K. , Monin Jonathan , Distefano Rosario , Nigita Giovanni , Croce Carlo M. , Aqeilan Rami I.
Published: March 2023

Figure S1 Figure S2 Figure S3 Figure S4 Figure S5 Figure S6 Figure S7 Figure S8 Figure S9 Figure S10 Figure S11 Figure S12 Figure S13
Supplementary Figure Legends from WWOX Inhibits Metastasis of Triple-Negative Breast Cancer Cells via Modulation of miRNAs
Authors: Khawaled Saleh , Suh Sung Suk , Abdeen Suhaib K. , Monin Jonathan , Distefano Rosario , Nigita Giovanni , Croce Carlo M. , Aqeilan Rami I.
Published: March 2023

Supplementary Figure 1: Relapse-free survival (RFS) analysis for WWOX in KM plotter. Supplementary Figure 2: Relapse-free survival (RFS) analysis for the WWOX gene in TCGA dataset. Supplementary Figure 3: Boxplots for each comparison of the expression of the specific gene between WWOX+ (>75th percentile) and WWOX- (<25th percentile) samples. Supplementary Figure 4: WWOX restoration reduces proliferation and Matrigel invasion in vitro. Supplementary Figure 5: WWOX restoration attenuates mammary tumor growth and inhibits metastasis formation in vivo. Supplementary Figure 6: WWOX restoration inhibits metastasis formation and colonization in vivo. Supplementary figure 7: Effect of WWOX manipulation in TNBC cells. Supplementary figure 8: WWOX negatively regulates Fibronectin expression in vivo. Supplementary figure 9: WWOX overexpression modulates microRNAs expression. Supplementary figure 10: Inverse correlation between Fibronectin and miR-146a in TNBC samples. Supplementary Figure 11: miR-146a expression predicts improved survival in triple-negative breast cancer patients. Supplementary Figure 12: WWOX overexpression inhibits MYC activity. Supplementary figure 13: Densitometric quantification of all western blots.
Supplemental Materials and Methods from Stearoyl-CoA Desaturase 1 Protects Ovarian Cancer Cells from Ferroptotic Cell Death
Authors: Tesfay Lia , Paul Bibbin T. , Konstorum Anna , Deng Zhiyong , Cox Anderson O. , Lee Jingyun , Furdui Cristina M. , Hegde Poornima , Torti Frank M. , Torti Suzy V.
Published: March 2023

Supplemental Materials and Methods
Supplemental Figure 6 from Stearoyl-CoA Desaturase 1 Protects Ovarian Cancer Cells from Ferroptotic Cell Death
Authors: Tesfay Lia , Paul Bibbin T. , Konstorum Anna , Deng Zhiyong , Cox Anderson O. , Lee Jingyun , Furdui Cristina M. , Hegde Poornima , Torti Frank M. , Torti Suzy V.
Published: March 2023

Combined treatment with an SCD1 inhibitor and ferroptosis inducer potentiates cell death in ovarian cancer cells with a mesenchymal phenotype and reduces tumor number and mass in mice with established tumors
Supplemental Figure 3 from Stearoyl-CoA Desaturase 1 Protects Ovarian Cancer Cells from Ferroptotic Cell Death
Authors: Tesfay Lia , Paul Bibbin T. , Konstorum Anna , Deng Zhiyong , Cox Anderson O. , Lee Jingyun , Furdui Cristina M. , Hegde Poornima , Torti Frank M. , Torti Suzy V.
Published: March 2023

Knockdown of SCD1 and effect of an SCD1 inhibitor on sensitivity to erastin
Supplementary Figure S4 from Chromosome 12p Amplification in Triple-Negative/BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity
Authors: Gómez-Miragaya Jorge , Díaz-Navarro Ander , Tonda Raul , Beltran Sergi , Palomero Luis , Palafox Marta , Dobrolecki Lacey E. , Huang Chen , Vasaikar Suhas , Zhang Bing , Wulf Gerburg M. , Collado-Sole Alejandro , Trinidad Eva M. , Muñoz Purificación , Paré Laia , Prat Aleix , Bruna Alejandra , Caldas Carlos , Arribas Joaquín , Soler-Monso María Teresa , Petit Anna , Balmaña Judith , Cruz Cristina , Serra Violeta , Pujana Miguel Angel , Lewis Michael T. , Puente Xose S. , González-Suárez Eva
Published: March 2023

Integrative genomic analysis using cBioPortal and METABRIC samples
Supplementary Table S3 from SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes
Authors: Song Xiao , Wan Xuechao , Huang Tianzhi , Zeng Chang , Sastry Namratha , Wu Bingli , James C. David , Horbinski Craig , Nakano Ichiro , Zhang Wei , Hu Bo , Cheng Shi-Yuan
Published: March 2023

List of differentially expressed genes after SRSF3-KO in GSCs
Supplementary Figure S2 from Chromosome 12p Amplification in Triple-Negative/BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity
Authors: Gómez-Miragaya Jorge , Díaz-Navarro Ander , Tonda Raul , Beltran Sergi , Palomero Luis , Palafox Marta , Dobrolecki Lacey E. , Huang Chen , Vasaikar Suhas , Zhang Bing , Wulf Gerburg M. , Collado-Sole Alejandro , Trinidad Eva M. , Muñoz Purificación , Paré Laia , Prat Aleix , Bruna Alejandra , Caldas Carlos , Arribas Joaquín , Soler-Monso María Teresa , Petit Anna , Balmaña Judith , Cruz Cristina , Serra Violeta , Pujana Miguel Angel , Lewis Michael T. , Puente Xose S. , González-Suárez Eva
Published: March 2023

Supplementary Figure S2
Supplementary Figure S1 from Chromosome 12p Amplification in Triple-Negative/BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity
Authors: Gómez-Miragaya Jorge , Díaz-Navarro Ander , Tonda Raul , Beltran Sergi , Palomero Luis , Palafox Marta , Dobrolecki Lacey E. , Huang Chen , Vasaikar Suhas , Zhang Bing , Wulf Gerburg M. , Collado-Sole Alejandro , Trinidad Eva M. , Muñoz Purificación , Paré Laia , Prat Aleix , Bruna Alejandra , Caldas Carlos , Arribas Joaquín , Soler-Monso María Teresa , Petit Anna , Balmaña Judith , Cruz Cristina , Serra Violeta , Pujana Miguel Angel , Lewis Michael T. , Puente Xose S. , González-Suárez Eva
Published: March 2023

Point mutations or small INDELs are not associated to docetaxel chemoresistance acquisition in TNBC PDX
Supplementary Data from SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes
Authors: Song Xiao , Wan Xuechao , Huang Tianzhi , Zeng Chang , Sastry Namratha , Wu Bingli , James C. David , Horbinski Craig , Nakano Ichiro , Zhang Wei , Hu Bo , Cheng Shi-Yuan
Published: March 2023

This files contains supplemental figures related to Figures 1-3, 4, and 6, and four supplemental tables, and supplemental materials and methods.
Supplementary figures and tables from PPARδ Mediates the Effect of Dietary Fat in Promoting Colorectal Cancer Metastasis
Authors: Wang Dingzhi , Fu Lingchen , Wei Jie , Xiong Ying , DuBois Raymond N.
Published: March 2023

Activation of PPARdelta induces colonic CSC via Nanog
Supplementary Data from Targeting Myeloperoxidase Disrupts Mitochondrial Redox Balance and Overcomes Cytarabine Resistance in Human Acute Myeloid Leukemia
Authors: Hosseini Mohsen , Rezvani Hamid Reza , Aroua Nesrine , Bosc Claudie , Farge Thomas , Saland Estelle , Guyonnet-Dupérat Véronique , Zaghdoudi Sonia , Jarrou Latifa , Larrue Clément , Sabatier Marie , Mouchel Pierre Luc , Gotanègre Mathilde , Piechaczyk Marc , Bossis Guillaume , Récher Christian , Sarry Jean-Emmanuel
Published: March 2023

Supplementary Table 2 Gene signatures used in this study
Supplementary Data from Serine-Phosphorylated STAT3 Promotes Tumorigenesis via Modulation of RNA Polymerase Transcriptional Activity
Authors: Balic Jesse J. , Garama Daniel J. , Saad Mohamed I. , Yu Liang , West Alison C. , West Alice J. , Livis Thaleia , Bhathal Prithi S. , Gough Daniel J. , Jenkins Brendan J.
Published: March 2023

File containing essential supplementary figures (7) and tables (3) comprising pre-clinical mouse model and clinical data supporting the role of constitutive pS-STAT3 in gastric cancer. This file also contains additional supplementary methods.
Supplementary Table 2 from Antitumor Effects of Anti-Semaphorin 4D Antibody Unravel a Novel Proinvasive Mechanism of Vascular-Targeting Agents
Authors: Zuazo-Gaztelu Iratxe , Pàez-Ribes Marta , Carrasco Patricia , Martín Laura , Soler Adriana , Martínez-Lozano Mar , Pons Roser , Llena Judith , Palomero Luis , Graupera Mariona , Casanovas Oriol
Published: March 2023

Ranked list of proteins present in anti-Sema4D treated macrophage conditioned media obtained in the GSEA analysis of the proteomic data
Supplementary Table 1 from Antitumor Effects of Anti-Semaphorin 4D Antibody Unravel a Novel Proinvasive Mechanism of Vascular-Targeting Agents
Authors: Zuazo-Gaztelu Iratxe , Pàez-Ribes Marta , Carrasco Patricia , Martín Laura , Soler Adriana , Martínez-Lozano Mar , Pons Roser , Llena Judith , Palomero Luis , Graupera Mariona , Casanovas Oriol
Published: March 2023

Expression of some angiogenesis related genes in response to anti-Sema4D and anti-VEGFR2 treatment
Supplementary Materials and Methods from Antitumor Effects of Anti-Semaphorin 4D Antibody Unravel a Novel Proinvasive Mechanism of Vascular-Targeting Agents
Authors: Zuazo-Gaztelu Iratxe , Pàez-Ribes Marta , Carrasco Patricia , Martín Laura , Soler Adriana , Martínez-Lozano Mar , Pons Roser , Llena Judith , Palomero Luis , Graupera Mariona , Casanovas Oriol
Published: March 2023

Supplementary Materials and Methods
Supplementary Figure 6 from Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies
Authors: Triska Petr , Kaneva Kristiyana , Merkurjev Daria , Sohail Noor , Falk Marni J. , Triche Timothy J. , Biegel Jaclyn A. , Gai Xiaowu
Published: March 2023

Supplementary Figure 6 show the distributions of the heteroplasmy levels of mtDNA mutations, depending on the gene and the location affected.
Supplementary Figure 5 from Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies
Authors: Triska Petr , Kaneva Kristiyana , Merkurjev Daria , Sohail Noor , Falk Marni J. , Triche Timothy J. , Biegel Jaclyn A. , Gai Xiaowu
Published: March 2023

Supplementary Figure 5 illustrates that mtDNA mutations in the mtDNA hypermutated pediatric tumor samples tend to occur at low heteroplasmy levels and are more likely to be benign in nature.
Supplementary Table S1 from A Model System for Studying the DNMT3A Hotspot Mutation (DNMT3AR882) Demonstrates a Causal Relationship between Its Dominant-Negative Effect and Leukemogenesis
Authors: Lu Rui , Wang Jun , Ren Zhihong , Yin Jiekai , Wang Yinsheng , Cai Ling , Wang Gang Greg
Published: March 2023

This supplementary table lists the differentially methylated CpG probes (DMPs) induced by DNMT3A_R882H in TF-1 cells.
Supplementary Figure 1 from Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies
Authors: Triska Petr , Kaneva Kristiyana , Merkurjev Daria , Sohail Noor , Falk Marni J. , Triche Timothy J. , Biegel Jaclyn A. , Gai Xiaowu
Published: March 2023

Supplementary Figure 1 illustrates single-cell ATAC-seq data contains sufficient mtDNA reads for interrogating mtDNA variants.
Supplementary Figure S5 from A Model System for Studying the DNMT3A Hotspot Mutation (DNMT3AR882) Demonstrates a Causal Relationship between Its Dominant-Negative Effect and Leukemogenesis
Authors: Lu Rui , Wang Jun , Ren Zhihong , Yin Jiekai , Wang Yinsheng , Cai Ling , Wang Gang Greg
Published: March 2023

This Supplementary Figure S5 shows that DNMT3A hotspot mutation is associated to CpG hypomethylation of LMO2.
Supplementary Figure S4 from A Model System for Studying the DNMT3A Hotspot Mutation (DNMT3AR882) Demonstrates a Causal Relationship between Its Dominant-Negative Effect and Leukemogenesis
Authors: Lu Rui , Wang Jun , Ren Zhihong , Yin Jiekai , Wang Yinsheng , Cai Ling , Wang Gang Greg
Published: March 2023

This Supplementary Figure S4 shows that DNMT3A hotspot mutation does not prefer flanking sequences for CpG methylation and that a heterodimerization interface is critical for the R882 mutant to induce transformation and CpG hypomethylation.
Supplementary Data from Dysfunction of Poly (ADP-Ribose) Glycohydrolase Induces a Synthetic Lethal Effect in Dual Specificity Phosphatase 22-Deficient Lung Cancer Cells
Authors: Sasaki Yuka , Fujimori Hiroaki , Hozumi Miyuki , Onodera Takae , Nozaki Tadashige , Murakami Yasufumi , Ashizawa Kazuto , Inoue Kengo , Koizumi Fumiaki , Masutani Mitsuko
Published: March 2023

Figure S1 shows cleavage of caspase 3 and PARP1 increased by DUSP22 and PARG double knockdown in A549.
Supplementary Data from Dysfunction of Poly (ADP-Ribose) Glycohydrolase Induces a Synthetic Lethal Effect in Dual Specificity Phosphatase 22-Deficient Lung Cancer Cells
Authors: Sasaki Yuka , Fujimori Hiroaki , Hozumi Miyuki , Onodera Takae , Nozaki Tadashige , Murakami Yasufumi , Ashizawa Kazuto , Inoue Kengo , Koizumi Fumiaki , Masutani Mitsuko
Published: March 2023

Figure S2 shows that cell growth inhibition by knockdown of both DUSP22 and PARG was recovered by the treatment with p38 MAPK inhibitor.
Supplementary Data from Tomoelastography Distinguishes Noninvasively between Benign and Malignant Liver Lesions
Authors: Shahryari Mehrgan , Tzschätzsch Heiko , Guo Jing , Marticorena Garcia Stephan R. , Böning Georg , Fehrenbach Uli , Stencel Lisa , Asbach Patrick , Hamm Bernd , Käs Joseph A. , Braun Jürgen , Denecke Timm , Sack Ingolf
Published: March 2023

More tumor cases and details of patient inclusion, tomoelastography setup, mechanical parameters, and ROC analysis.
Table S5 from Tie2–FGFR1 Interaction Induces Adaptive PI3K Inhibitor Resistance by Upregulating Aurora A/PLK1/CDK1 Signaling in Glioblastoma
Authors: Li Xiaolong , Martinez-Ledesma Emmanuel , Zhang Chen , Gao Feng , Zheng Siyuan , Ding Jie , Wu Shaofang , Nguyen Nghi , Clifford Stephan C. , Wen Patrick Y. , Ligon Keith L. , Yung W.K. Alfred , Koul Dimpy
Published: March 2023

Full drug names and the abbreviations
Table S2 from Tie2–FGFR1 Interaction Induces Adaptive PI3K Inhibitor Resistance by Upregulating Aurora A/PLK1/CDK1 Signaling in Glioblastoma
Authors: Li Xiaolong , Martinez-Ledesma Emmanuel , Zhang Chen , Gao Feng , Zheng Siyuan , Ding Jie , Wu Shaofang , Nguyen Nghi , Clifford Stephan C. , Wen Patrick Y. , Ligon Keith L. , Yung W.K. Alfred , Koul Dimpy
Published: March 2023

Compounds map of high-throughput drug screening
Supplementary Data from Cleaved Caspase-3 Transcriptionally Regulates Angiogenesis-Promoting Chemotherapy Resistance
Authors: Bernard Antoine , Chevrier Sandy , Beltjens Françoise , Dosset Magalie , Viltard Etienne , Lagrange Anaïs , Derangère Valentin , Oudot Alexandra , Ghiringhelli François , Collin Bertrand , Apetoh Lionel , Feron Olivier , Chen Suzie , Arnould Laurent , Végran Frédérique , Boidot Romain
Published: March 2023

This file contains all supplementary figures with their legends, supplementary tables and supplementary methods
Table S1 from Tie2–FGFR1 Interaction Induces Adaptive PI3K Inhibitor Resistance by Upregulating Aurora A/PLK1/CDK1 Signaling in Glioblastoma
Authors: Li Xiaolong , Martinez-Ledesma Emmanuel , Zhang Chen , Gao Feng , Zheng Siyuan , Ding Jie , Wu Shaofang , Nguyen Nghi , Clifford Stephan C. , Wen Patrick Y. , Ligon Keith L. , Yung W.K. Alfred , Koul Dimpy
Published: March 2023

RPPA antibody list
Supplementary Data Figure S1 to S6, and Table S3 and S4. from Tie2–FGFR1 Interaction Induces Adaptive PI3K Inhibitor Resistance by Upregulating Aurora A/PLK1/CDK1 Signaling in Glioblastoma
Authors: Li Xiaolong , Martinez-Ledesma Emmanuel , Zhang Chen , Gao Feng , Zheng Siyuan , Ding Jie , Wu Shaofang , Nguyen Nghi , Clifford Stephan C. , Wen Patrick Y. , Ligon Keith L. , Yung W.K. Alfred , Koul Dimpy
Published: March 2023

This file contains supplementary Figure S1 to S6, and Table S3 and S4.
Supplementary data (Figures S1 to S12) from CML Hematopoietic Stem Cells Expressing IL1RAP Can Be Targeted by Chimeric Antigen Receptor–Engineered T Cells
Authors: Warda Walid , Larosa Fabrice , Neto Da Rocha Mathieu , Trad Rim , Deconinck Eric , Fajloun Ziad , Faure Cyril , Caillot Denis , Moldovan Marius , Valmary-Degano Severine , Biichle Sabeha , Daguindau Etienne , Garnache-Ottou Francine , Tabruyn Sebastien , Adotevi Olivier , Deschamps Marina , Ferrand Christophe
Published: March 2023

Figure S1. In vitro detection (using #A3C3) of recombinant IL-1RAP protein by ELISA Figure S2. Procedure for generating IL-1RAP CART cells and CD4/CD8 ratio at the end of the process Figure S3. Staining of IL-1RAP CAR at the cell surface of T cell line or primary T -lymphocytes Figure S4. Impact of the IL-1RAP soluble form on IL-1RAP CART-cells toxicity Figure S5. Tissue macroarray (TMA) using #A3C3 monoclonal antibody Figure S6. Experimental immunosafety human CD34+ engrafted NOG murine model Figure S7. Colony Forming Unit (CFU-GM) experiment after coculture of autologous CART-cells with CD34+ HSC. Figure S8. In-vitro and in-vivo iCASP/AP1903 suicide gene safety switch Figure S9. Production and characterization of IL-1RAP (soluble and membrane) transfected cell line Figure S10. Cytokine secretion profiling of IL-1RAP CART-cells after co-culturing with targets Figure S11. Tumoral xenograft murine model Figure S12. Autologous cytotoxicity of IL-1RAP CART-cells directed against initial CML disease
Supplementary Data. Figure Legends S1-S12 & Tables S1-S4 from CML Hematopoietic Stem Cells Expressing IL1RAP Can Be Targeted by Chimeric Antigen Receptor–Engineered T Cells
Authors: Warda Walid , Larosa Fabrice , Neto Da Rocha Mathieu , Trad Rim , Deconinck Eric , Fajloun Ziad , Faure Cyril , Caillot Denis , Moldovan Marius , Valmary-Degano Severine , Biichle Sabeha , Daguindau Etienne , Garnache-Ottou Francine , Tabruyn Sebastien , Adotevi Olivier , Deschamps Marina , Ferrand Christophe
Published: March 2023

Figure S1. In vitro detection (using #A3C3) of recombinant IL-1RAP protein by ELISA Figure S2. Procedure for generating IL-1RAP CART cells and CD4/CD8 ratio at the end of the process Figure S3. Staining of IL-1RAP CAR at the cell surface of T cell line or primary T -lymphocytes Figure S4. Impact of the IL-1RAP soluble form on IL-1RAP CART-cells toxicity Figure S5. Tissue macroarray (TMA) using #A3C3 monoclonal antibody Figure S6. Experimental immunosafety human CD34+ engrafted NOG murine model Figure S7. Colony Forming Unit (CFU-GM) experiment after coculture of autologous CART-cells with CD34+ HSC. Figure S8. In-vitro and in-vivo iCASP/AP1903 suicide gene safety switch Figure S9. Production and characterization of IL-1RAP (soluble and membrane) transfected cell line Figure S10. Cytokine secretion profiling of IL-1RAP CART-cells after co-culturing with targets Figure S11. Tumoral xenograft murine model Figure S12. Autologous cytotoxicity of IL-1RAP CART-cells directed against initial CML disease Table S1: Antibodies and kits Table S2: IL-1RAP (mAb#A3C3) immunostaining of normal tissues Table S3: Percentage of alive cells in different subpopulations according co-culture with different ratio of E (MockT-cells or IL-1RAP CART-cells) :T. Table S4: CML patient's characteristics with available PBSC cryopreserved autografts
Figure S6 from SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program
Authors: Oliphant Michael U.J. , Vincent Melanie Y. , Galbraith Matthew D. , Pandey Ahwan , Zaberezhnyy Vadym , Rudra Pratyaydipta , Johnson Katherine R. , Costello James C. , Ghosh Debashis , DeGregori James , Espinosa Joaquin M. , Ford Heide L.
Published: March 2023

Six2 is more highly expressed in the fetal mammary stem cell population compared to adult mouse mammary cells.
Figure S4 from SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program
Authors: Oliphant Michael U.J. , Vincent Melanie Y. , Galbraith Matthew D. , Pandey Ahwan , Zaberezhnyy Vadym , Rudra Pratyaydipta , Johnson Katherine R. , Costello James C. , Ghosh Debashis , DeGregori James , Espinosa Joaquin M. , Ford Heide L.
Published: March 2023

Six2 regulates Sox2 in multiple human TNBC models.
Figure S6 from Chemotherapy-Induced Extracellular Vesicle miRNAs Promote Breast Cancer Stemness by Targeting ONECUT2
Authors: Shen Meng , Dong Chuan , Ruan Xianhui , Yan Wei , Cao Minghui , Pizzo Donald , Wu Xiwei , Yang Lin , Liu Liang , Ren Xiubao , Wang Shizhen Emily
Published: March 2023

Figure S6 showing histological staining of tumor tissues
Figure S5 from Chemotherapy-Induced Extracellular Vesicle miRNAs Promote Breast Cancer Stemness by Targeting ONECUT2
Authors: Shen Meng , Dong Chuan , Ruan Xianhui , Yan Wei , Cao Minghui , Pizzo Donald , Wu Xiwei , Yang Lin , Liu Liang , Ren Xiubao , Wang Shizhen Emily
Published: March 2023

Figure S5 showing direct effect of chemotherapy on cell lines used in this study
Supplementary Table S3 from YES1 Is a Targetable Oncogene in Cancers Harboring YES1 Gene Amplification
Authors: Hamanaka Natsuki , Nakanishi Yoshito , Mizuno Takakazu , Horiguchi-Takei Kana , Akiyama Nukinori , Tanimura Hiromi , Hasegawa Masami , Satoh Yasuko , Tachibana Yukako , Fujii Toshihiko , Sakata Kiyoaki , Ogasawara Kiyomoto , Ebiike Hirosato , Koyano Hiroshi , Sato Haruhiko , Ishii Nobuya , Mio Toshiyuki
Published: March 2023

Anti-proliferative activity of various MTAs against 66 cancer cell lines.
Figure S3 from Chemotherapy-Induced Extracellular Vesicle miRNAs Promote Breast Cancer Stemness by Targeting ONECUT2
Authors: Shen Meng , Dong Chuan , Ruan Xianhui , Yan Wei , Cao Minghui , Pizzo Donald , Wu Xiwei , Yang Lin , Liu Liang , Ren Xiubao , Wang Shizhen Emily
Published: March 2023

Figure S3 showing dose-dependent regulation of selected miRNAs by chemotherapy
Supplementary FigureS1, S2, S3, S4, S5, S6, S7, S8, S9 from YES1 Is a Targetable Oncogene in Cancers Harboring YES1 Gene Amplification
Authors: Hamanaka Natsuki , Nakanishi Yoshito , Mizuno Takakazu , Horiguchi-Takei Kana , Akiyama Nukinori , Tanimura Hiromi , Hasegawa Masami , Satoh Yasuko , Tachibana Yukako , Fujii Toshihiko , Sakata Kiyoaki , Ogasawara Kiyomoto , Ebiike Hirosato , Koyano Hiroshi , Sato Haruhiko , Ishii Nobuya , Mio Toshiyuki
Published: March 2023

Supplementary Figure S1. YES1 gene is amplified and YES1 expression is related to poor prognosis in esophageal cancer and lung cancer in clinical. Supplementary Figure S2. YES1 gene amplification including the upregulation of YES1 expression. Supplementary Figure S3. Cell growth inhibition profile of various molecular targeted agents. Supplementary Figure S4. Antiproliferative activity of dasatinib against cancer cell lines expressing YES1-WT or YES1-GK. Supplementary Figure S5. The contribution of SFK other than YES1 in YES1-amplified cancer cell lines. Supplementary Figure S6. The antitumor activity of dasatinib against YES1-amplified xenograft tumor. Supplementary Figure S7. Dasatinib inhibited YAP1 downstream signal via YES1 kinase inhibition against YES1-amplified cancer cell. Supplementary Figure S8. YAP1 and DAPI staining in treatment with CH6953755. Supplementary Figure S9. YAP1 localization change in xenograft tumor tissue by CH6953755 treatment.
Supplementary Methods and Material from The Open Chromatin Landscape of Non–Small Cell Lung Carcinoma
Authors: Wang Zhoufeng , Tu Kailing , Xia Lin , Luo Kai , Luo Wenxin , Tang Jie , Lu Keying , Hu Xinlei , He Yijing , Qiao Wenliang , Zhou Yongzhao , Zhang Jun , Cao Feng , Dai Shuiping , Tian Panwen , Wang Ye , Liu Lunxu , Che Guowei , Zhou Qinghua , Xie Dan , Li Weimin
Published: March 2023

Supplementary Methods and Material
Supplementary Data from Constant Degradation of the Androgen Receptor by MDM2 Conserves Prostate Cancer Stem Cell Integrity
Authors: Vummidi Giridhar Premkumar , Williams Karin , VonHandorf Andrew P. , Deford Paul L. , Kasper Susan
Published: March 2023

The file contains 4 supplementary tables. Table S1 lists the primary antibodies used in the study. Table S2 provides the primers used to characterize AR-V expression. Table S3 provides the primers used to characterize epithelial and stem cell marker expression. Table S4 summarizes and compares the characteristics of CSC-like AR(-) HPET and HuSLCs with that of the standard AR(+) PCa cell line, LNCaP.
Table S2 from Identification of Coding and Long Noncoding RNAs Differentially Expressed in Tumors and Preferentially Expressed in Healthy Tissues
Authors: Unfried Juan P. , Serrano Guillermo , Suárez Beatriz , Sangro Paloma , Ferretti Valeria , Prior Celia , Boix Loreto , Bruix Jordi , Sangro Bruno , Segura Víctor , Fortes Puri
Published: March 2023

Deregulated coding and long non-coding transcripts in the 13 tumor-types examined. LncRNAs upregulated or downregulated in more than 5 tumors. Clinical associations of genes deregulated in LIHC. Molecular classifications (Hoshida's and iCluster), clinical parameters (vascular invasion, macrotrabecular massive (MTM) histologic subtype, alpha fetoprotein levels (AFP< or >300 IU/mL), pathological stage (stage I to IV according to the TNM staging system) and histological grade (G1-good differentiation to G3-poor differentiation)) and genetic features (TERT expression, TP53 and CTNNB1 wild-type or mutant). P-values are indicated.
Table S1 from Identification of Coding and Long Noncoding RNAs Differentially Expressed in Tumors and Preferentially Expressed in Healthy Tissues
Authors: Unfried Juan P. , Serrano Guillermo , Suárez Beatriz , Sangro Paloma , Ferretti Valeria , Prior Celia , Boix Loreto , Bruix Jordi , Sangro Bruno , Segura Víctor , Fortes Puri
Published: March 2023

Patient and primer data. Patient data. Clinical and histological features of patients from the TCGA and from the Clínica Universidad de Navarra and Hospital Clinic (BCL-CUN). All results are expressed in frequencies and percentages except specified. SD: Standard Deviation. IQR: Interquartile range. NASH: Non-Alcoholic Steatohepatitis. Primer data: Sequence of the primers used to quantify gene expression by RT-PCR.
Figure S4 from Identification of Coding and Long Noncoding RNAs Differentially Expressed in Tumors and Preferentially Expressed in Healthy Tissues
Authors: Unfried Juan P. , Serrano Guillermo , Suárez Beatriz , Sangro Paloma , Ferretti Valeria , Prior Celia , Boix Loreto , Bruix Jordi , Sangro Bruno , Segura Víctor , Fortes Puri
Published: March 2023

Relative expression of several lncRNAs deregulated in LIHC in cell lines and liver tumors. A. Expression in cancer cells and fibroblasts. RNA was isolated from the indicated cells and the expression of the indicated lncRNAs was quantified by qRT-PCR. As a reference, the average expression of each lncRNA in all the liver cells evaluated is indicated as "average". The levels of RPLP0 mRNA were also evaluated and used as a reference to calculate the relative expression. The values indicate the average of 3 different experiments. Error bars denote standard deviations. A relative expression of 0.01 marks the lower detection limit. B. Expression in LIHC. The relative expression of each lncRNA was evaluated in paired peritumoral (PT) and tumor (T) samples from the TCGA RNA-Seq data. The result of the statistical analysis with paired t-tests is indicated in each graph. C. Analysis of RP11-242J7.1 expression in patients with different prognosis. Relative expression of RP11-242J7.1 in tumor and peritumoral samples of patients from the BCL-CUN cohort with best prognosis (Best; left) and worse prognosis (Worse, right). The result of the statistical analysis with Wilcoxon matched pairs signed rank tests is indicated in each graph. D. Analysis of lncRNAs associated with tumor differentiation (well versus poorly differentiated), tumor size (small versus large tumors) and with the number of tumor nodules (one versus multiple nodules) using data from the BCL-CUN cohort. The result of the statistical analysis (two-tailed unpaired t-test in B and U-Mann Whitney in C) is indicated in each graph.
Supplementary Tables from Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker
Authors: Dong Shihua , Li Wei , Wang Lin , Hu Jie , Song Yuanlin , Zhang Baolong , Ren Xiaoguang , Ji Shimeng , Li Jin , Xu Peng , Liang Ying , Chen Gang , Lou Jia-Tao , Yu Wenqiang
Published: March 2023

Supplementary Tables 1~14
Supplementary Data from CDK4 Regulates Lysosomal Function and mTORC1 Activation to Promote Cancer Cell Survival
Authors: Martínez-Carreres Laia , Puyal Julien , Leal-Esteban Lucía C. , Orpinell Meritxell , Castillo-Armengol Judit , Giralt Albert , Dergai Oleksandr , Moret Catherine , Barquissau Valentin , Nasrallah Anita , Pabois Angélique , Zhang Lianjun , Romero Pedro , Lopez-Mejia Isabel C. , Fajas Lluis
Published: March 2023

Supplementary Methods.
Supplementary Materials from Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker
Authors: Dong Shihua , Li Wei , Wang Lin , Hu Jie , Song Yuanlin , Zhang Baolong , Ren Xiaoguang , Ji Shimeng , Li Jin , Xu Peng , Liang Ying , Chen Gang , Lou Jia-Tao , Yu Wenqiang
Published: March 2023

Supplementary Materials
Tables S2 and S3 from Diminished AHR Signaling Drives Human Acute Myeloid Leukemia Stem Cell Maintenance
Authors: Ly Michelle , Rentas Stefan , Vujovic Ana , Wong Nicholas , Moreira Steven , Xu Joshua , Holzapfel Nicholas , Bhatia Sonam , Tran Damian , Minden Mark D. , Draper Jonathan S. , Hope Kristin J.
Published: March 2023

These tables display the lists of up and down regulated AHR targets in various leukemic subpopulations and across diverse AML subtypes
Table S4 from Diminished AHR Signaling Drives Human Acute Myeloid Leukemia Stem Cell Maintenance
Authors: Ly Michelle , Rentas Stefan , Vujovic Ana , Wong Nicholas , Moreira Steven , Xu Joshua , Holzapfel Nicholas , Bhatia Sonam , Tran Damian , Minden Mark D. , Draper Jonathan S. , Hope Kristin J.
Published: March 2023

This table displays the clinical characteristics of all primary AML patient samples used in the study
Table S1 from Diminished AHR Signaling Drives Human Acute Myeloid Leukemia Stem Cell Maintenance
Authors: Ly Michelle , Rentas Stefan , Vujovic Ana , Wong Nicholas , Moreira Steven , Xu Joshua , Holzapfel Nicholas , Bhatia Sonam , Tran Damian , Minden Mark D. , Draper Jonathan S. , Hope Kristin J.
Published: March 2023

This table displays the sequences for PCR probes and primers used throughout the paper
Figure S3 from A Microbial Siderophore-Inspired Self-Gelling Hydrogel for Noninvasive Anticancer Phototherapy
Authors: Ko Seungbeom , Park Joo Yeon , Oh Yu-Kyoung
Published: March 2023

Stability of hydrogel
Supplementary Tables S11-S14 from Isoflavone ME-344 Disrupts Redox Homeostasis and Mitochondrial Function by Targeting Heme Oxygenase 1
Authors: Zhang Leilei , Zhang Jie , Ye Zhiwei , Manevich Yefim , Ball Lauren E. , Bethard Jennifer R. , Jiang Yu-Lin , Broome Ann-Marie , Dalton Annamarie C. , Wang Gavin Y. , Townsend Danyelle M. , Tew Kenneth D.
Published: March 2023

Supplementary Table S11. All Proteins Identified. Supplementary Table S12. The Protein Groups text file from MaxQuant was processed using Perseus. Common contaminants, reversed database hits, and proteins identified by modified peptides were removed. LFQ normalized protein intensities were log2 transformed. Proteins were filtered to retain proteins identified by MS/MS (not matching between runs) in all three ME-344 pull down experiments with at least 2 peptides. Missing values in the control pull downs were imputed in Perseus with a width of 0.6 and downshift of 1.8. The difference in mean log2 protein intensities (ME344 bait - control) and fold change in abundance are provided. Supplementary Table S13. The Protein Groups text file from MaxQuant was processed using Perseus. Common contaminants, reversed database hits, and proteins identified by modified peptides were removed. LFQ normalized protein intensities were log2 transformed. Proteins were filtered to retain proteins identified by MS/MS (not matching between runs) in all three ME-344 pull down experiments with at least 2 peptides. Missing values in the control pull downs were imputed in Perseus with a width of 0.6 and downshift of 1.8. The difference in mean log2 protein intensities (ME344 bait - control) and fold change in abundance are provided. Proteins enriched with ME-344 (Difference in Log2 Protein Intensities >0). Supplementary Table S14. Proteins with at least 2 peptides identified by MS/MS in all three ME-344 pull down experiments that were not identified in the control affinity enrichment.
Supplementary Tables S1-S18 from Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer
Authors: Anagnostou Valsamo , Forde Patrick M. , White James R. , Niknafs Noushin , Hruban Carolyn , Naidoo Jarushka , Marrone Kristen , Sivakumar I.K. Ashok , Bruhm Daniel C. , Rosner Samuel , Phallen Jillian , Leal Alessandro , Adleff Vilmos , Smith Kellie N. , Cottrell Tricia R. , Rhymee Lamia , Palsgrove Doreen N. , Hann Christine L. , Levy Benjamin , Feliciano Josephine , Georgiades Christos , Verde Franco , Illei Peter , Li Qing Kay , Gabrielson Edward , Brock Malcolm V. , Isbell James M. , Sauter Jennifer L. , Taube Janis , Scharpf Robert B. , Karchin Rachel , Pardoll Drew M. , Chaft Jamie E. , Hellmann Matthew D. , Brahmer Julie R. , Velculescu Victor E.
Published: March 2023

Supplementary Table S1. Summary of patient characteristics Supplementary Table S2. Summary of plasma samples analyzed Supplementary Table S3. Summary of peripheral blood lymphocytes and tumor infiltrating lymphocytes samples analyzed Supplementary Table S4. Genes analyzed by TEC-Seq Supplementary Table S5. Summary of TEC-Seq Characteristics Supplementary Table S6. Somatic sequence alterations detected in cfDNA Supplementary Table S7. Mutation Cellularity Analysis for tumor-specific cfDNA variants Supplementary Table S8. TCR-beta sequencing analysis Supplementary Table S9. Differentially abundant clones for CGLU111 Supplementary Table S10. Differentially abundant clones for CGLU117 Supplementary Table S11. Differentially abundant clones for CGLU127 Supplementary Table S12. Differentially abundant clones for CGLU212 Supplementary Table S13. Differentially abundant clones for CGLU135 Supplementary Table S14. Differentially abundant clones for CGLU161 Supplementary Table S15. Differentially abundant clones for CGLU159 Supplementary Table S16. Differentially abundant clones for CGLU162 Supplementary Table S17. Differentially abundant clones for CGLU203 Supplementary Table S18. Differentially abundant clones for CGLU243
Supplementary Figures S1-S14 from Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer
Authors: Anagnostou Valsamo , Forde Patrick M. , White James R. , Niknafs Noushin , Hruban Carolyn , Naidoo Jarushka , Marrone Kristen , Sivakumar I.K. Ashok , Bruhm Daniel C. , Rosner Samuel , Phallen Jillian , Leal Alessandro , Adleff Vilmos , Smith Kellie N. , Cottrell Tricia R. , Rhymee Lamia , Palsgrove Doreen N. , Hann Christine L. , Levy Benjamin , Feliciano Josephine , Georgiades Christos , Verde Franco , Illei Peter , Li Qing Kay , Gabrielson Edward , Brock Malcolm V. , Isbell James M. , Sauter Jennifer L. , Taube Janis , Scharpf Robert B. , Karchin Rachel , Pardoll Drew M. , Chaft Jamie E. , Hellmann Matthew D. , Brahmer Julie R. , Velculescu Victor E.
Published: March 2023

Supplementary Figure S1. ctDNA clonal dynamics during anti-PD1 for patients with a clinical response. Supplementary Figure S2. ctDNA clonal dynamics during anti-PD1 for patients with molecular primary resistance. Supplementary Figure S3. ctDNA molecular responses precede radiologic responses. Supplementary Figure S4. Molecular responses correlate with a favorable prognosis. Supplementary Figure S5. Duration of molecular response correlates with progression-free and overall survival. Supplementary Figure S6. Disease prognostication by radiologic imaging at first assessment. Supplementary Figure S7. Differential clinical outcome by molecular responses in patients with radiologically stable disease. Supplementary Figure S8. Disease prognostication by tumor mutation burden. Supplementary Figure S9. ctDNA molecular response more accurately distinguish clinical responders from non-responders compared to clonal tumor mutation burden. Supplementary Figure S10. Molecular responses mirror pathologic responses to anti-PD1 therapy in early stage operable NSCLC. Supplementary Figure S11. TCR clonal dynamics during response and acquired resistance to anti-PD1. Supplementary Figure S12. TCR clonal dynamics for patients with clinical primary resistance. Supplementary Figure S13. Differential VJ gene usage for a patient with clinical response compared to a patient with clinical primary resistance. Supplementary Figure S14. Dynamic changes in pro-inflammatory and immunosuppressive cytokines in early stage NSCLC patients with differential responses to anti-PD1 therapy.
Supplementary Data S2 from Oncogenic KRAS Sensitizes Lung Adenocarcinoma to GSK-J4–Induced Metabolic and Oxidative Stress
Authors: Hong Beom-Jin , Park Woo-Yong , Kim Hwa-Ryeon , Moon Jin Woo , Lee Ho Yeon , Park Jun Hyung , Kim Seon-Kyu , Oh Youngbin , Roe Jae-Seok , Kim Mi-Young
Published: March 2023

GO analysis of GSK-J4 downregulated genes
Supplementary Figure Legends and Methods from The Highly Recurrent PP2A Aα-Subunit Mutation P179R Alters Protein Structure and Impairs PP2A Enzyme Function to Promote Endometrial Tumorigenesis
Authors: Taylor Sarah E. , O'Connor Caitlin M. , Wang Zhizhi , Shen Guobo , Song Haichi , Leonard Daniel , Sangodkar Jaya , LaVasseur Corinne , Avril Stefanie , Waggoner Steven , Zanotti Kristine , Armstrong Amy J. , Nagel Christa , Resnick Kimberly , Singh Sareena , Jackson Mark W. , Xu Wenqing , Haider Shozeb , DiFeo Analisa , Narla Goutham
Published: March 2023

Supplementary Figure Legends and Methods
Supplementary Data from Mitochondrial miRNA Determines Chemoresistance by Reprogramming Metabolism and Regulating Mitochondrial Transcription
Authors: Fan Song , Tian Tian , Chen Weixiong , Lv Xiaobin , Lei Xinyuan , Zhang Hanqing , Sun Sheng , Cai Lei , Pan Guokai , He Lile , Ou Zhanpeng , Lin Xinyu , Wang Xinhui , Perez Matthew Francis , Tu Zhiming , Ferrone Soldano , Tannous Bakhos A. , Li Jinsong
Published: March 2023

Supplementary Data: Supplementary Materials and Methods, Supplementary Figures and Supplementary Tables.
Figure S2 from Metformin Inhibits Progression of Head and Neck Squamous Cell Carcinoma by Acting Directly on Carcinoma-Initiating Cells
Authors: Wu Xingyu , Yeerna Huwate , Goto Yusuke , Ando Toshinori , Wu Victoria H. , Zhang Xuefeng , Wang Zhiyong , Amornphimoltham Panomwat , Murphy Anne N. , Tamayo Pablo , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: March 2023

Impact of metformin on sphere-formation in CAL27 and SCC47 HNSCC cells.
Supplementary Data from MK5 Regulates YAP Stability and Is a Molecular Target in YAP-Driven Cancers
Authors: Seo Jimyung , Kim Min Hwan , Hong Hyowon , Cho Hyunsoo , Park Seongyeol , Kim Sang Kyum , Kim Joon
Published: March 2023

Supplementary Figures, Supplementary materials and methods, and supplementary tables.
Supplementary Data from Drak/STK17A Drives Neoplastic Glial Proliferation through Modulation of MRLC Signaling
Authors: Chen Alexander S. , Wardwell-Ozgo Joanna , Shah Nilang N. , Wright Deidre , Appin Christina L. , Vigneswaran Krishanthan , Brat Daniel J. , Kornblum Harley I. , Read Renee D.
Published: March 2023

This file contains all supplementary figures, including Supplementary Table 1 and Table 2 that list the Drosophila reagents used for genetic tests described in the manuscript. This file also contains Supplementary Figures S1, S2, S3, S4, and S5, which includes additional Drosophila phenotypic analysis, protein expression data and shRNA results from human cells, and TCGA data analysis.
Supplementary Data from The Promoter-Associated Noncoding RNA pncCCND1_B Assembles a Protein–RNA Complex to Regulate Cyclin D1 Transcription in Ewing Sarcoma
Authors: Palombo Ramona , Frisone Paola , Fidaleo Marco , Mercatelli Neri , Sette Claudio , Paronetto Maria Paola
Published: March 2023

Supplementary Experimental Procedures: Patient Datasets; Computational tools; SDS-PAGE and Western blot analyses; RTâ^'PCR analysis and Real-time quantitative PCR analyses; Immunoprecipitation; Chromatin immunoprecipitation; In vivo crosslinking and immunoprecipitation (CLIP); Sub-cellular Fractionation; Clonogenic Assay and Immunofluorescence analysis. Supplementary Figure Legends Supplementary Figures (1-8): SF1: Statistical analysis of CCND1 expression among Sarcoma samples; SF2: EWS-FLI1 regulates CCND1 expression; SF3: pncCCND1_B expression in 24 Ewing sarcoma patients;SF4: Identification of pncCCND1_B sequence; SF5: RT-qPCR analysis of CCND1 expression in Ewing sarcoma cells displaying different chromosomal translocation; SF6: Sam68 negatively affects CCND1 expression; SF7: YK-4-279 inhibits the interaction between EWS-FLI1 and DHX9, and trigger the formation of DHX9-Sam68 interaction; SF8: IGF-1 promotes Sam68 phosphorylation thus affecting its binding to pncCCND1_B RNA. Supplementary Table 1: List of oligonucleotides.
Supplementary Figure Legends from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Authors: Coggins Grace E. , Farrel Alvin , Rathi Komal S. , Hayes Colin M. , Scolaro Laura , Rokita Jo Lynne , Maris John M.
Published: March 2023

This file includes figure legends corresponding to Supplementary Figures S1-6.
Video 4 from MAP4K3/GLK Promotes Lung Cancer Metastasis by Phosphorylating and Activating IQGAP1
Authors: Chuang Huai-Chia , Chang Chih-Chi , Teng Chiao-Fang , Hsueh Chia-Hsin , Chiu Li-Li , Hsu Pu-Ming , Lee Ming-Ching , Hsu Chung-Ping , Chen Yi-Rong , Liu Yi-Chung , Lyu Ping-Chiang , Tan Tse-Hua
Published: March 2023

Video4.avi GLK co-localizes with IQGAP1 at the leading edge of a migrating cell (Cell #4)
Supplemental Tables S1-5 from YAP1 Mediates Resistance to MEK1/2 Inhibition in Neuroblastomas with Hyperactivated RAS Signaling
Authors: Coggins Grace E. , Farrel Alvin , Rathi Komal S. , Hayes Colin M. , Scolaro Laura , Rokita Jo Lynne , Maris John M.
Published: March 2023

Table S1 includes MYCN amplification and chromosome 11q status across a panel of 16 neuroblastoma cell lines. Table S2-4 include differentially-expressed genes identified in each of the three differential expression analyses. Table S5 includes unique differentially expressed genes between NLF sgCon + DMSO and NLF YAP1-/- #4 + Tram.
Video 3 from MAP4K3/GLK Promotes Lung Cancer Metastasis by Phosphorylating and Activating IQGAP1
Authors: Chuang Huai-Chia , Chang Chih-Chi , Teng Chiao-Fang , Hsueh Chia-Hsin , Chiu Li-Li , Hsu Pu-Ming , Lee Ming-Ching , Hsu Chung-Ping , Chen Yi-Rong , Liu Yi-Chung , Lyu Ping-Chiang , Tan Tse-Hua
Published: March 2023

Video.avi GLK co-localizes with IQGAP1 at filopodia and lamellipodia of a cell (Cell #3).
Video 2 from MAP4K3/GLK Promotes Lung Cancer Metastasis by Phosphorylating and Activating IQGAP1
Authors: Chuang Huai-Chia , Chang Chih-Chi , Teng Chiao-Fang , Hsueh Chia-Hsin , Chiu Li-Li , Hsu Pu-Ming , Lee Ming-Ching , Hsu Chung-Ping , Chen Yi-Rong , Liu Yi-Chung , Lyu Ping-Chiang , Tan Tse-Hua
Published: March 2023

Cell tracking in time-lapse microscopy images from of lung epithelial cells from littermate wild-type (WT), GLK transgenic (Polâ…¡-GLK), GLK transgenic/IQGAP1-heterozygous (Polâ…¡-GLK;IQGAP1+/- ), and GLK transgenic/IQGAP1 knockout (Polâ…¡-GLK;IQGAP1-/- ) mice. The tracked path of the migration cell is shown as the line.
Supplementary Tables S1-4 from ERBB3 and IGF1R Signaling Are Required for Nrf2-Dependent Growth in KEAP1-Mutant Lung Cancer
Authors: Vartanian Steffan , Lee James , Klijn Christiaan , Gnad Florian , Bagniewska Maria , Schaefer Gabriele , Zhang Donglu , Tan Jenille , Watson Sara A. , Liu Liling , Chen Honglin , Liang Yuxin , Watanabe Colin , Cuellar Trinna , Kan David , Hartmaier Ryan J. , Lau Ted , Costa Michael R. , Martin Scott E. , Merchant Mark , Haley Benjamin , Stokoe David
Published: March 2023

S1. Sequences of RNAi reagents S2. Data from siRNA screens S3. Genes decreased following Nrf2 KD and increased in KEAP1 mutant lung cancer cells S4. Data from CRISPR screens