bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data Fig. S2 from Lymphoma Angiogenesis Is Orchestrated by Noncanonical Signaling Pathways
Authors: Gloger Marleen , Menzel Lutz , Grau Michael , Vion Anne-Clemence , Anagnostopoulos Ioannis , Zapukhlyak Myroslav , Gerlach Kerstin , Kammertöns Thomas , Hehlgans Thomas , Zschummel Maria , Lenz Georg , Gerhardt Holger , Höpken Uta E. , Rehm Armin
Published: March 2023

Lack of inflammatory gene signatures
Supplementary Table S1 from Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance
Authors: Chandra Ankush , Jahangiri Arman , Chen William , Nguyen Alan T. , Yagnik Garima , Pereira Matheus P. , Jain Saket , Garcia Joseph H. , Shah Sumedh S. , Wadhwa Harsh , Joshi Rushikesh S. , Weiss Jacob , Wolf Kayla J. , Lin Jung-Ming G. , Müller Sören , Rick Jonathan W. , Diaz Aaron A. , Gilbert Luke A. , Kumar Sanjay , Aghi Manish K.
Published: March 2023

Supplementary Table S1 describes all of the patient xenografts and samples used in this manuscript
Supplementary Methods from Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance
Authors: Chandra Ankush , Jahangiri Arman , Chen William , Nguyen Alan T. , Yagnik Garima , Pereira Matheus P. , Jain Saket , Garcia Joseph H. , Shah Sumedh S. , Wadhwa Harsh , Joshi Rushikesh S. , Weiss Jacob , Wolf Kayla J. , Lin Jung-Ming G. , Müller Sören , Rick Jonathan W. , Diaz Aaron A. , Gilbert Luke A. , Kumar Sanjay , Aghi Manish K.
Published: March 2023

Supplementary Methods describes details about methods including animal work, microarray analysis, neurosphere assays, and hyaluronic acid assays that could not fit in the main methods.
Supplementary Figures S1-S23 from Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance
Authors: Chandra Ankush , Jahangiri Arman , Chen William , Nguyen Alan T. , Yagnik Garima , Pereira Matheus P. , Jain Saket , Garcia Joseph H. , Shah Sumedh S. , Wadhwa Harsh , Joshi Rushikesh S. , Weiss Jacob , Wolf Kayla J. , Lin Jung-Ming G. , Müller Sören , Rick Jonathan W. , Diaz Aaron A. , Gilbert Luke A. , Kumar Sanjay , Aghi Manish K.
Published: March 2023

Supplementary Figures S1-S23 show some extra data including immunohistochemical stains and bar graphs that could not fit in the main text.
Supplementary Data from Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers
Authors: Andersson Natalie , Bakker Bjorn , Karlsson Jenny , Valind Anders , Holmquist Mengelbier Linda , Spierings Diana C.J. , Foijer Floris , Gisselsson David
Published: March 2023

Supplementary Materials and Methods, Supplementary Figures S1-S4, Supplementary Tables S1-S4
Supplementary Data from Cdkn2a Loss in a Model of Neurofibroma Demonstrates Stepwise Tumor Progression to Atypical Neurofibroma and MPNST
Authors: Chaney Katherine E. , Perrino Melissa R. , Kershner Leah J. , Patel Ami V. , Wu Jianqiang , Choi Kwangmin , Rizvi Tilat A. , Dombi Eva , Szabo Sara , Largaespada David A. , Ratner Nancy
Published: March 2023

Figure S1
Supplementary Table 3 from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Ovarian PDX response category by therapy.
Supplementary Table 2 from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Ovarian PDX raw growth and sequencing data.
Supplementary Table 1 from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Compound dose, dosing schedule, administration route, target and drug type.
Supplementary Materials from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Supplementary Material PDF, including supplementary methods and supplementary figures 1-4
Supplementary Figure S4 from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Most ovarian tumors respond to one of four biomarker-guided treatments.
Full Western Blot Images from Twist1-Induced Epithelial Dissemination Requires Prkd1 Signaling
Authors: Georgess Dan , Padmanaban Veena , Sirka Orit Katarina , Coutinho Kester , Choi Alex , Frid Gabriela , Neumann Neil M. , Inoue Takanari , Ewald Andrew J.
Published: March 2023

This file contains the full blot images of all Western blots.
Supplementary Figure S1 from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Ovarian cancer cell lines do not reproduce the clinical association between BRCA loss of function and sensitivity to olaparib, but patient-derived ovarian tumor xenografts do.
Supplementary Spread Sheet 2 from Peritoneal Spread of Ovarian Cancer Harbors Therapeutic Vulnerabilities Regulated by FOXM1 and EGFR/ERBB2 Signaling
Authors: Parashar Deepak , Nair Bindu , Geethadevi Anjali , George Jasmine , Nair Ajay , Tsaih Shirng-Wern , Kadamberi Ishaque P. , Gopinadhan Nair Gopa Kumar , Lu Yiling , Ramchandran Ramani , Uyar Denise S. , Rader Janet S. , Ram Prahlad T. , Mills Gordon B. , Pradeep Sunila , Chaluvally-Raghavan Pradeep
Published: March 2023

Supplementary Spread Sheet 2
Supplementary Spread Sheet 1 from Peritoneal Spread of Ovarian Cancer Harbors Therapeutic Vulnerabilities Regulated by FOXM1 and EGFR/ERBB2 Signaling
Authors: Parashar Deepak , Nair Bindu , Geethadevi Anjali , George Jasmine , Nair Ajay , Tsaih Shirng-Wern , Kadamberi Ishaque P. , Gopinadhan Nair Gopa Kumar , Lu Yiling , Ramchandran Ramani , Uyar Denise S. , Rader Janet S. , Ram Prahlad T. , Mills Gordon B. , Pradeep Sunila , Chaluvally-Raghavan Pradeep
Published: March 2023

Supplementary Spread Sheet 1
Supplementary Data from Rare BRIP1 Missense Alleles Confer Risk for Ovarian and Breast Cancer
Authors: Moyer Cassandra L. , Ivanovich Jennifer , Gillespie Jessica L. , Doberstein Rachel , Radke Marc R. , Richardson Marcy E. , Kaufmann Scott H. , Swisher Elizabeth M. , Goodfellow Paul J.
Published: March 2023

Supplementary methods; FS1: BRIP1 nonsense and frameshift mutations; FS2: BRIP1 expression in CRISPR cell lines; FS3: hydroxyurea and TMPyP4 challenge; FS4: HEK293TN CRISPR cell lines; FS5: HeLa stable clone rescues; FS6: Transient rescue screening assay; FS7: Degradation of missense mutant proteins; TS1: List of BRIP1 missense variants identified in cohorts;
Combined Supplementary Materials from Peritoneal Spread of Ovarian Cancer Harbors Therapeutic Vulnerabilities Regulated by FOXM1 and EGFR/ERBB2 Signaling
Authors: Parashar Deepak , Nair Bindu , Geethadevi Anjali , George Jasmine , Nair Ajay , Tsaih Shirng-Wern , Kadamberi Ishaque P. , Gopinadhan Nair Gopa Kumar , Lu Yiling , Ramchandran Ramani , Uyar Denise S. , Rader Janet S. , Ram Prahlad T. , Mills Gordon B. , Pradeep Sunila , Chaluvally-Raghavan Pradeep
Published: March 2023

Supplementary Figures, Legends to Supplementary materials,and Supplementary Tables
Table S2 from A Premalignant Cell-Based Model for Functionalization and Classification of PTEN Variants
Authors: Chao Jesse T. , Hollman Rocio , Meyers Warren M. , Meili Fabian , Matreyek Kenneth A. , Dean Pamela , Fowler Douglas M. , Haas Kurt , Roskelley Calvin D. , Loewen Christopher J.R.
Published: March 2023

Table S2
Table S1 from A Premalignant Cell-Based Model for Functionalization and Classification of PTEN Variants
Authors: Chao Jesse T. , Hollman Rocio , Meyers Warren M. , Meili Fabian , Matreyek Kenneth A. , Dean Pamela , Fowler Douglas M. , Haas Kurt , Roskelley Calvin D. , Loewen Christopher J.R.
Published: March 2023

Table S1
Supplementary Table 1 from CD44 Promotes PD-L1 Expression and Its Tumor-Intrinsic Function in Breast and Lung Cancers
Authors: Kong Tim , Ahn Ryuhjin , Yang Kangning , Zhu Xianbing , Fu Zheng , Morin Geneviève , Bramley Rachel , Cliffe Nikki C. , Xue Yibo , Kuasne Hellen , Li Qinghao , Jung Sungmi , Gonzalez Anne V. , Camilleri-Broet Sophie , Guiot Marie-Christine , Park Morag , Ursini-Siegel Josie , Huang Sidong
Published: March 2023

List of candidate genes identified from the shRNA screens in both MDA-MB-231 and BT-549 cells
Figure S1 from A Premalignant Cell-Based Model for Functionalization and Classification of PTEN Variants
Authors: Chao Jesse T. , Hollman Rocio , Meyers Warren M. , Meili Fabian , Matreyek Kenneth A. , Dean Pamela , Fowler Douglas M. , Haas Kurt , Roskelley Calvin D. , Loewen Christopher J.R.
Published: March 2023

Supplemental Figure 1
Supplementary Data from CD44 Promotes PD-L1 Expression and Its Tumor-Intrinsic Function in Breast and Lung Cancers
Authors: Kong Tim , Ahn Ryuhjin , Yang Kangning , Zhu Xianbing , Fu Zheng , Morin Geneviève , Bramley Rachel , Cliffe Nikki C. , Xue Yibo , Kuasne Hellen , Li Qinghao , Jung Sungmi , Gonzalez Anne V. , Camilleri-Broet Sophie , Guiot Marie-Christine , Park Morag , Ursini-Siegel Josie , Huang Sidong
Published: March 2023

This Supplementary Data file contains Supplementary Figures 1-18.
Supplementary Data from IL6/STAT3 Signaling Orchestrates Premetastatic Niche Formation and Immunosuppressive Traits in Lung
Authors: Jing Bo , Wang Tong , Sun Beibei , Xu Jianhua , Xu Dongliang , Liao Yueling , Song Hongyong , Guo Wenzheng , Li Kaimi , Hu Min , Zhang Siwei , Ling Jing , Kuang Yanbin , Zhang Tuo , Zhou Binhua P. , Yao Feng , Deng Jiong
Published: March 2023

Supplementary Fig. S1-S6, supplementary methods, supplementary table S1-S2. Supplementary Table S1. Primers used in the study; Supplementary Table S2. Antibodies information for flow cytometry analysis; Figure S1. IL6/ Gp130 pathway is involved in maintenance of stemness and in suppression of host immunity for lung metastasis; Figure S2. IL6 signaling is essential for lung metastasis in Gprc5a-ko mice lung tissues; Figure S3. IL6 signaling is essential for Lewis lung carcinoma cells in lung metastasis in Gprc5a-ko mice lung tissues; Figure S4. IL-6 signaling mediates the inhibition on innate immunity in Gprc5a-ko mouse lungs; Figure S5. IL-6 signaling orchestrates the inhibition on innate and adaptive immunity in Gprc5a-ko mouse lungs; Figure S6. Proposed model of IL-6/STAT3 signaling in lung metastasis
Supplementary Table S3 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Metabolic Pathway Enrichment in PDAC Patients Treated with Gemcitabine (Data Pooled from TCGA)
Supplementary Table Legends from Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer
Authors: Dai Chen , Charlestin Verodia , Wang Man , Walker Zachary T. , Miranda-Vergara Maria Cristina , Facchine Beth A. , Wu Junmin , Kaliney William J. , Dovichi Norman J. , Li Jun , Littlepage Laurie E.
Published: March 2023

Supplementary Table Legends
Supplementary Figure S8 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Effects of glutamine deprivation on cell viability and NRF2 expression
Supplementary Figure S5 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Cell cycle analysis of PDAC cells upon NRF2 activation
Supplementary Figure S2 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Isotype control for NRF2 in IHC and survival measure for NRF2
Supplementary Table S1-9 from Across-Site Differences in the Mechanism of Alcohol-Induced Digestive Tract Carcinogenesis: An Evaluation by Mediation Analysis
Authors: Koyanagi Yuriko N. , Suzuki Etsuji , Imoto Issei , Kasugai Yumiko , Oze Isao , Ugai Tomotaka , Iwase Madoka , Usui Yoshiaki , Kawakatsu Yukino , Sawabe Michi , Hirayama Yutaka , Tanaka Tsutomu , Abe Tetsuya , Ito Seiji , Komori Koji , Hanai Nobuhiro , Tajika Masahiro , Shimizu Yasuhiro , Niwa Yasumasa , Ito Hidemi , Matsuo Keitaro
Published: March 2023

Supplementary Table S1 shows the first-visit hospital unit among controls in each study. Supplementary Table S2 shows the baseline characteristics of case and control subjects. Supplementary Table S3 contains the frequencies of never/ever drinkers and median (IQR) values of alcohol intake (g/day) among ever drinkers across ALDH2 genotypes in control subjects. Supplementary Table S4 presents the sample size (n cases/n controls) for each group for both the exposure and mediator association, and the mediator and outcome association. Supplementary Table S5 shows the total-effect odds ratios (ORs) of ALDH2 Lys allele in each cancer risk. Supplementary Table S6 shows the direct- and indirect-effect odds ratios (ORs) in stomach cancer for ALDH2 Lys allele with further adjustment for Helicobacter pylori [H.pylori] infection and atrophic gastritis statuses. Supplementary Table S7 shows the direct- and indirect-effect odds ratios (ORs) on each cancer for ALDH2 Glu/Lys and Lys/Lys. Supplementary Table S8 presents the results for smoking-drinking interaction analyses on each cancer risk. Supplementary Table S9 shows the direct- and indirect-effect odds ratios (ORs) on each cancer for ALDH2 Lys allele in strata of cumulative smoking exposure (pack-years).
Supplementary Table 2 from Cancer Cell–Derived Matrisome Proteins Promote Metastasis in Pancreatic Ductal Adenocarcinoma
Authors: Tian Chenxi , Öhlund Daniel , Rickelt Steffen , Lidström Tommy , Huang Ying , Hao Liangliang , Zhao Renee T. , Franklin Oskar , Bhatia Sangeeta N. , Tuveson David A. , Hynes Richard O.
Published: March 2023

List of published results of the identified proteins.
Supplementary Figures from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches
Authors: Hebert Jess D. , Myers Samuel A. , Naba Alexandra , Abbruzzese Genevieve , Lamar John M. , Carr Steven A. , Hynes Richard O.
Published: March 2023

Supplementary Figures S1 to S10. Supplementary Figure S1. Quality control western blots; Supplementary Figure S2. Label-free matrisome protein abundance; Supplementary Figure S3. Label-free percentage protein abundance; Supplementary Figure S4. Proteins identified in only one TMT 10-plex; Supplementary Figure S5. Tumor-cell-only proteins; Supplementary Figure S6. Abundance of tumor-cell-derived and stroma-derived matrisome proteins in metastases to different tissues; Supplementary Figure S7. Stromal proteins elevated in metastases relative to normal tissue; Supplementary Figure S8. Alterations in SERPINB1 are associated with lower progression-free survival; Supplementary Figure S9. Additional proteins evaluated for altered metastatic tropism; Supplementary figure S10. Gene Set Enrichment Analysis of ECM proteins and predicted upstream regulators in brain metastases.
Supplementary Figure S3 from Resolution of Spatial and Temporal Heterogeneity in Bevacizumab-Treated Breast Tumors by Eigenspectra Multispectral Optoacoustic Tomography
Authors: Liapis Evangelos , Klemm Uwe , Karlas Angelos , Reber Josefine , Ntziachristos Vasilis
Published: March 2023

Supplementary Figure S3
Supplementary Figure S1 from Resolution of Spatial and Temporal Heterogeneity in Bevacizumab-Treated Breast Tumors by Eigenspectra Multispectral Optoacoustic Tomography
Authors: Liapis Evangelos , Klemm Uwe , Karlas Angelos , Reber Josefine , Ntziachristos Vasilis
Published: March 2023

Supplementary Figure S1
Table S1 from Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma
Authors: Mitra Sanhita , Muralidharan Somsundar Veppil , Di Marco Mirco , Juvvuna Prasanna Kumar , Kosalai Subazini Thankaswamy , Reischl Silke , Jachimowicz Daniel , Subhash Santhilal , Raimondi Ivan , Kurian Leo , Huarte Maite , Kogner Per , Fischer Matthias , Johnsen John Inge , Mondal Tanmoy , Kanduri Chandrasekhar
Published: March 2023

Primers used in the current investigation.
Supplementary information from Allosteric SHP2 Inhibitor, IACS-13909, Overcomes EGFR-Dependent and EGFR-Independent Resistance Mechanisms toward Osimertinib
Authors: Sun Yuting , Meyers Brooke A. , Czako Barbara , Leonard Paul , Mseeh Faika , Harris Angela L. , Wu Qi , Johnson Sarah , Parker Connor A. , Cross Jason B. , Di Francesco Maria Emilia , Bivona Benjamin J. , Bristow Christopher A. , Burke Jason P. , Carrillo Caroline C. , Carroll Christopher L. , Chang Qing , Feng Ningping , Gao Guang , Gera Sonal , Giuliani Virginia , Huang Justin K. , Jiang Yongying , Kang Zhijun , Kovacs Jeffrey J. , Liu Chiu-Yi , Lopez Anastasia M. , Ma Xiaoyan , Mandal Pijus K. , McAfoos Timothy , Miller Meredith A. , Mullinax Robert A. , Peoples Michael , Ramamoorthy Vandhana , Seth Sahil , Spencer Nakia D. , Suzuki Erika , Williams Christopher C. , Yu Simon S. , Zuniga Andy M. , Draetta Giulio F. , Marszalek Joseph R. , Heffernan Timothy P. , Kohl Nancy E. , Jones Philip
Published: March 2023

Supplementary Materials and Methods Supplementary References Tables S1 to S3 and legends Figures S1 to S4 and legends
Table S4 from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

The percentage of reconstructed genome covered by the assembly, the mean coverage depth, the number of contigs obtained and the best-predicted haplogroup are reported for each sample.
Table S3 from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

Identified metabolites in chRCC and kidney tissues and MRM instrument settings.
Table S2 from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

MaxQuant output file, protein ratios, and pathway enrichment analysis (GSEA) of all up-regulated and down-regulated pathways between chRCC and kidney tissues.
Figure S3 from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

Correlation between mtDNA content, ETC protein and transcript levels, and GSH level in 786-O and HK2 cells
Supplemental Movie 5 from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Movie over 12 hours of a whole zebrafish embryo injected with YAP-AA over-expressing A375 cells
Figure S1 from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

Exome-based copy number variation analysis in chRCC
Supplemental Movie 2 from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Movie over 12 hours of the head of a zebrafish embryo injected with EV control A375 cells.
Figure S6. from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Expression of YAP mutants.
Figure S5. from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Tumor cell transit times do not vary between EV and YAP-AA cells
Figure S3. from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

YAP-AA does not enhance entry into circulation from the injection site by 10HPI.
Supplementary Data from Senescent Stromal Cells Promote Cancer Resistance through SIRT1 Loss-Potentiated Overproduction of Small Extracellular Vesicles
Authors: Han Liu , Long Qilai , Li Shenjun , Xu Qixia , Zhang Boyi , Dou Xuefeng , Qian Min , Jiramongkol Yannasittha , Guo Jianming , Cao Liu , Chin Y. Eugene , Lam Eric W.-F. , Jiang Jing , Sun Yu
Published: March 2023

Figure S1. Cellular senescence, expression profiling and the SASP development in human stromal cells upon genotoxic treatment. Figure S2. SIRT1 decline is not related with single strand breaks, proteasome degradation or autophagy deficiency upon cellular senescence. Figure S3. Senescent stromal sEVs enhance the malignancy of prostate cancer cells. Figure S4. Transcriptomic profiling of prostate cancer cells upon exposure to senescent stromal sEVs and establishment of protein-protein interaction network involving ABCB4. Figure S5. Senescent stromal sEV-conferred malignancy is diminished upon elimination of ABCB4 from cancer cells. Figure S6. Pharmacological targeting SIRT1 minimizes senescent stromal sEV production and prevents ABCB4 upregulation in prostate cancer cells.
Supplementary Data from Senescent Stromal Cells Promote Cancer Resistance through SIRT1 Loss-Potentiated Overproduction of Small Extracellular Vesicles
Authors: Han Liu , Long Qilai , Li Shenjun , Xu Qixia , Zhang Boyi , Dou Xuefeng , Qian Min , Jiramongkol Yannasittha , Guo Jianming , Cao Liu , Chin Y. Eugene , Lam Eric W.-F. , Jiang Jing , Sun Yu
Published: March 2023

Primer information summary.
Supplementary Data from Senescent Stromal Cells Promote Cancer Resistance through SIRT1 Loss-Potentiated Overproduction of Small Extracellular Vesicles
Authors: Han Liu , Long Qilai , Li Shenjun , Xu Qixia , Zhang Boyi , Dou Xuefeng , Qian Min , Jiramongkol Yannasittha , Guo Jianming , Cao Liu , Chin Y. Eugene , Lam Eric W.-F. , Jiang Jing , Sun Yu
Published: March 2023

Functional enrichments in PPT network.
Supplementary Table S4 from Integrated Genomic Characterization of the Human Immunome in Cancer
Authors: Li Yongsheng , Burgman Brandon , McGrail Daniel J. , Sun Ming , Qi Dan , Shukla Sachet A. , Wu Erxi , Capasso Anna , Lin Shiaw-Yih , Wu Catherine J. , Eckhardt S. Gail , Mills Gordon B. , Li Bo , Sahni Nidhi , Yi S. Stephen
Published: March 2023

Table S4. Gene mutations that perturb binding of HLAs.
Table S1-4 from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Supplementary Table S1-4
Supplementary Data from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Supplementary materials and methods
Figure S7 from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Supplementary Figure S7
Figure S6 from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Figure S6
Table S1 from Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer
Authors: Stevens Payton D. , Wen Yang-An , Xiong Xiaopeng , Zaytseva Yekaterina Y. , Li Austin T. , Wang Chi , Stevens Ashley T. , Farmer Trevor N. , Gan Tong , Weiss Heidi L. , Inagaki Masaki , Marchetto Sylvie , Borg Jean-Paul , Gao Tianyan
Published: March 2023

Table S1. The mutation status of cancer genes in CRC cell lines used in this study. Data were obtained from reference (25) and COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk).
Figure S6 from Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer
Authors: Stevens Payton D. , Wen Yang-An , Xiong Xiaopeng , Zaytseva Yekaterina Y. , Li Austin T. , Wang Chi , Stevens Ashley T. , Farmer Trevor N. , Gan Tong , Weiss Heidi L. , Inagaki Masaki , Marchetto Sylvie , Borg Jean-Paul , Gao Tianyan
Published: March 2023

Figure S6. Mutations identified in ERBIN gene in CRC patients. Total 38 missense and 12 truncating mutations were identified in ERBIN gene as documented by cBioPortal in available CRC patient datasets. Erbin contains a number of LRR domains at the N-terminus and a PDZ domain at the C-terminus of the protein.
Figure S2 from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Supplementary Figure S2
Figure S5 from Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer
Authors: Stevens Payton D. , Wen Yang-An , Xiong Xiaopeng , Zaytseva Yekaterina Y. , Li Austin T. , Wang Chi , Stevens Ashley T. , Farmer Trevor N. , Gan Tong , Weiss Heidi L. , Inagaki Masaki , Marchetto Sylvie , Borg Jean-Paul , Gao Tianyan
Published: March 2023

Figure S5. Loss of Erbin deletion promotes tumorigenesis and the expression of genes associated with cancer stem cells. (A) Histology analysis of intestine adenomas in age-matched Apc/WT and Apc/Het mice (at 4.5 months) as well as Apc/WT mice at 6 months. Scale bar, 200μm. Note that the tumor burden in the Apc/Het mouse at 4.5 month is similar as that Apc/WT mice at 6 month. (B) Tumor organoids derived from three cohorts of mice (Apc/WT, Apc/Het and Apc/KO) were grown in 3D culture for 72 hours, collected, and analyzed using qRT-PCR for the expression of genes associated with cancer stem cells (Lgr5 and Axin2), cell proliferation (Ccnd1, Ki67) and intestinal cell differentiation (Fabp2). Data represents mean {plus minus} SEM (n = 4, * p<0.05 and # p<0.0001).
Supplementary Materials from Epigenetic Control of Cdkn2a.Arf Protects Tumor-Infiltrating Lymphocytes from Metabolic Exhaustion
Authors: Koss Brian , Shields Bradley D. , Taylor Erin M. , Storey Aaron J. , Byrum Stephanie D. , Gies Allen J. , Washam Charity L. , Choudhury Samrat Roy , Hyun Ahn Jeong , Uryu Hidetaka , Williams Jason B. , Krager Kimberly J. , Chiang Tung-Chin , Mackintosh Samuel G. , Edmondson Rick D. , Aykin-Burns Nukhet , Gajewski Thomas F. , Wang Gang Greg , Tackett Alan J.
Published: March 2023

Figure S1-7. Figure S1: Assessing the effect of EZH2i on in vitro T cell cytotoxic function. Figure S2: Systems approach uncovers drivers of T cell exhaustion resulting from EZH2-inhibtion. Figure S3: Loss of EZH2 function leads to metabolic exhaustion of T cells. Figure S4: Histone epigenetic landscape post EZH2 inhibition. Figure S5: EZH2 inhibition leads to histone epigenetic reprogramming. Figure S6: Arf contributes metabolic exhaustion independent of p53. Figure S7: Exogenous expression of EZH2Y641F in lymphocytes. Extended methods, table of key reagents and resources
Supplementary figures and tables from A Global and Integrated Analysis of CINSARC-Associated Genetic Defects
Authors: Lesluyes Tom , Chibon Frédéric
Published: March 2023

Supplementary figures 1-3 and tables 1-5. Supplementary figure 1. Survival analysis of the 77 cases using the FNCLCC grading system (grade 1 and 2 versus grade 3). Supplementary figure 2. WGD refers to whole genome doubling; CNA refers to copy-number alteration; ITH refers to intra-tumour heterogeneity. Supplementary figure 3. WGD refers to whole genome doubling; CNA refers to copy-number alteration; Meth refers to methylation; ITH refers to intra-tumour heterogeneity. Supplementary table 1. Clinical information for the 77 cases. Supplementary table 2. Genomic coordinates of the 13 differentially (adjusted P < 0.05 and absolute M-value difference > 1) methylated probes with distances from nearest CpG islands and transcription start site. Supplementary table 3. Enrichment for CINSARC genes in top anti-correlated genes to each miRNA of interest. Supplementary table 4. Top 20 Gene Ontologies (GO) enriched in genes having validated interactions with miRNA. Supplementary table 5. Cancer Gene Census information for genes significantly anti-correlated with miRNAs of interest.
Figure legends for supplementary figures from BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency
Authors: Gupta Manav , Concepcion Carla P. , Fahey Caroline G. , Keshishian Hasmik , Bhutkar Arjun , Brainson Christine F. , Sanchez-Rivera Francisco J. , Pessina Patrizia , Kim Jonathan Y. , Simoneau Antoine , Paschini Margherita , Beytagh Mary C. , Stanclift Caroline R. , Schenone Monica , Mani D.R. , Li Chendi , Oh Audris , Li Fei , Hu Hai , Karatza Angeliki , Bronson Roderick T. , Shaw Alice T. , Hata Aaron N. , Wong Kwok-Kin , Zou Lee , Carr Steven A. , Jacks Tyler , Kim Carla F.
Published: March 2023

All figure legends for supplementary figures included here.
Supplementary Table 1 from Identification of a Small-Molecule Inhibitor That Disrupts the SIX1/EYA2 Complex, EMT, and Metastasis
Authors: Zhou Hengbo , Blevins Melanie A. , Hsu Jessica Y. , Kong Deguang , Galbraith Matthew D. , Goodspeed Andrew , Culp-Hill Rachel , Oliphant Michael U.J. , Ramirez Dominique , Zhang Lingdi , Trinidad-Pineiro Jennyvette , Mathews Griner Lesley , King Rebecca , Barnaeva Elena , Hu Xin , Southall Noel T. , Ferrer Marc , Gustafson Daniel L. , Regan Daniel P. , D'Alessandro Angelo , Costello James C. , Patnaik Samarjit , Marugan Juan , Zhao Rui , Ford Heide L.
Published: March 2023

Detailed information (source and working dilution) of antibodies have been used for WB, ICC and IHC.
Figure S4 from Tumor Cell–Derived IL1β Promotes Desmoplasia and Immune Suppression in Pancreatic Cancer
Authors: Das Shipra , Shapiro Beny , Vucic Emily A. , Vogt Sandra , Bar-Sagi Dafna
Published: March 2023

IL-1b neutralization sensitizes PDA tumors to PD-1 checkpoint blockade.
Table S2 from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: March 2023

List of protein-coding (pc) and non_coding (nc) genes differentially expressed (UP or DOWN) following induction of WT and MUT FOXL2 in polyA and ribodepleted RNA-seq datasets.
Supplemental Table S1. from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: March 2023

Notch1 mutations detected by exome sequencing from Brca1L1363P/ L1363P; p53+/+ thymic tumor
Supplementary Methods from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: March 2023

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

Brca1L1363P mutant protein is capable of interacting with Bach1
Supplementary Data from CD122-Selective IL2 Complexes Reduce Immunosuppression, Promote Treg Fragility, and Sensitize Tumor Response to PD-L1 Blockade
Authors: Drerup Justin M. , Deng Yilun , Pandeswara Sri Lakshmi , Padrón Álvaro S. , Reyes Ryan M. , Zhang Xinyue , Mendez Jenny , Liu Aijie , Clark Curtis A. , Chen Wanjiao , Conejo-Garcia José R. , Hurez Vincent , Gupta Harshita , Curiel Tyler J.
Published: March 2023

Supplementary figures 1-10. Figure S1. IL-2c increases conventional CD4 T cell in ascites three weeks after final IL-2c, but does not affect ascites Treg and effector T cell numbers at one week after final IL-2c administration. Figure S2. IL-2c treatment increases CD8+ central and effector memory T cells in the ascites, and central memory T cells in TDLN. Fig S3. Additional Treg phenotype in ascites and TDLN after IL-2c treatment. Fig S4. IL-2c directly inhibits Treg suppression specifically in the tumor microenvironment. Fig S5. IL-2 signaling is not impaired in TDLN after IL-2c treatment. Figure S6. Specific Treg depletion is highly effective against ID8agg. Figure S7. αCD25 attenuates IL-2c-induced tumor rejection and T cell function in ID8agg OC. Figure S8. IL-2c promotes intratumoral T cell infiltration. Figure S9. IL-2c reduces intratumoral Treg activation and functional molecules in B16 melanoma. Figure S10. IL-2c increases TIGIT+LAG-3+PD-1+ CD8+ T cells in B16 tumors.
Supplementary Data 3 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: March 2023

Results of IHC on SCLC lines-derived xenograft TMA and resected primary SCLC TMA, and IHC protocols.
Supplementary Data Figures S1-S14 from State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia
Authors: Rockne Russell C. , Branciamore Sergio , Qi Jing , Frankhouser David E. , O'Meally Denis , Hua Wei-Kai , Cook Guerry , Carnahan Emily , Zhang Lianjun , Marom Ayelet , Wu Herman , Maestrini Davide , Wu Xiwei , Yuan Yate-Ching , Liu Zheng , Wang Leo D. , Forman Stephen , Carlesso Nadia , Kuo Ya-Huei , Marcucci Guido
Published: March 2023

Figure S1. Details of animal model and fusion gene CM, Figure S2. Ex vivo flow cytometry analysis of bone marrow, Figure S3. Details of principal component analysis, Figure S4. Comparison of state-space construction with different dimension reduction methods, Figure S5. Hierarchical clustering of time-series RNA-seq data and relation to state-space, Figure S6. Details of critical point estimation, construction of quasi-potential, and state-space dynamics, Figure S7. Correlation of state-space geometry with Kit and CM gene expression. Sensitivity of state-space geometry to inclusion of Kit and CM, Figure S8. Volcano plots of critical-point based differential gene expression analysis, Figure S9. Heatmaps of selected GO pathways in early, transition, persistent, and leukemic events, Figure S10. Computation of eigengene angle in state-space, Figure S11. Details of principal component analysis of validation cohorts and state-space dynamics, Figure S12. Mean-squared displacement analysis of particle trajectories in state-space and calibration of Fokker-Planck diffusion coefficient with training cohort, Figure S13. Sensitivity analysis of state-space construction to sample and normalization thresholds, Figure S14. Bootstrap cross validation of state-space construction.
Supplementary Data 1 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: March 2023

List of differentially expressed genes between control and FGFR1-expressing preSC
Supplementary Data from ATF3 Coordinates Antitumor Synergy between Epigenetic Drugs and Protein Disulfide Isomerase Inhibitors
Authors: Duncan Ravyn M. , Reyes Leticia , Moats Katelyn , Robinson Reeder M. , Murphy Sara A. , Kaur Balveen , Stessman Holly A.F. , Dolloff Nathan G.
Published: March 2023

The supplementary figures provide data supporting the combination drug screening process that uncovered synergy between PDI and HDAC inhibitors, and further supplements the findings in the main figures demonstrating the genomic, biochemical, and cellular characterization of the molecular mechanisms responsible for that synergy.
Supplementary Data from Circulating Proteoglycan Endocan Mediates EGFR-Driven Progression of Non–Small Cell Lung Cancer
Authors: Yang Yi-Chieh , Pan Ke-Fan , Lee Wei-Jiunn , Chang Jer-Hwa , Tan Peng , Gu Chia-Chi , Chang Wei-Min , Yang Shun-Fa , Hsiao Michael , Hua Kuo-Tai , Chien Ming-Hsien
Published: March 2023

SUPPLEMENTARY INFORMATION Supplementary material and methods, Table S1, and Figure S1-S7 - This file contains Supplementary material and methods; Table S1. The Cox univariate and multivariate analyses of endocan and clinicopathological factors in overall survival of patients in NSCLC patients.; Supplementary Figure S1. The clinical value of endocan in lung adenocarcinoma.; Supplementary Figure S2. Correlation of endocan and EGFR expression in lung cancer patients.; Supplementary Figure S3. Endocan enhances EGFâ€�induced activation of EGFR in a concentration-dependent manner.; Supplementary Figure S4. The JAK/STAT3 and ERK/ELK signaling regulates endocan promoter activity.; Supplementary Figure S5. The interaction of endocan and EGF/EGFR complex.; Supplementary Figure S6. Endocan peptide treatment inhibits the PC9 tumor growth in vivo.; Supplementary Figure S7. Endocan peptide treatment suppresses the activation of EGFR harboring L858R/T790M/C797S triple mutations.
Supplementary Table S1 from Genetic Variants Implicate Dual Oxidase-2 in Familial and Sporadic Nonmedullary Thyroid Cancer
Authors: Bann Darrin V. , Jin Qunyan , Sheldon Kathryn E. , Houser Kenneth R. , Nguyen Lan , Warrick Joshua I. , Baker Maria J. , Broach James R. , Gerhard Glenn S. , Goldenberg David
Published: March 2023

Supplemental Table 1. PCR and sequencing primers
Figure S2 from Microenvironmental Cues Determine Tumor Cell Susceptibility to Neutrophil Cytotoxicity
Authors: Gershkovitz Maya , Fainsod-Levi Tanya , Khawaled Saleh , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Fridlender Zvi G. , Granot Zvi
Published: March 2023

Supplemental Figure S2. Circulating tumor cells express higher levels of TRPM2 compared with primary tumor cells in pancreatic cancer patients. A. Transcriptome analysis of mesenchymal genes, epithelial genes and TRPM2 on primary 4T1 tumor cells and circulating 4T1 tumor cells. The analysis was performed on dataset (GSE37244) published by LeBlue et al. (28). B. Microarray study for gene expression (GSE18670) changes in 6 samples from pancreatic cancer primary tumor (Primary) and circulating tumor cells (CTC) was described previously by Sergeant at al. (29). Here the same dataset was reanalyzed for the log2 expression ratio of TRMP2 in these samples. Data show TRPM2 expression in primary tumor cells (blue) and CTC (Red). *p<0.05 (2-tailed paired t-test).
Supplementary Data from Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non–Muscle-Invasive Bladder Cancer
Authors: Bellmunt Joaquim , Kim Jaegil , Reardon Brendan , Perera-Bel Júlia , Orsola Anna , Rodriguez-Vida Alejo , Wankowicz Stephanie A. , Bowden Michaela , Barletta Justine A. , Morote Juan , de Torres Inés , Juanpere Nuria , Lloreta-Trull Josep , Hernandez Silvia , Mouw Kent W. , Taplin Mary-Ellen , Cejas Paloma , Long Henry W. , Van Allen Eliezer M. , Getz Gad , Kwiatkowski David J.
Published: March 2023

Supplementary figures, tables, material & methods and results
Supplementary Materials and Methods from Gain of HIF1 Activity and Loss of miRNA let-7d Promote Breast Cancer Metastasis to the Brain via the PDGF/PDGFR Axis
Authors: Wyss Christof B. , Duffey Nathalie , Peyvandi Sanam , Barras David , Martinez Usatorre Amaïa , Coquoz Oriana , Romero Pedro , Delorenzi Mauro , Lorusso Girieca , Rüegg Curzio
Published: March 2023

This file contains all the materials and methods that were not included in the main text.
Video S2 from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: March 2023

Live imaging of the inset region of clustered spheroids containing SUM159T-dox:Î"Np63 cells {plus minus} doxycycline (H2B:GFP, green, nuclei) showing cell motility.
Supplementary Data from ΔNp63-Regulated Epithelial-to-Mesenchymal Transition State Heterogeneity Confers a Leader–Follower Relationship That Drives Collective Invasion
Authors: Westcott Jill M. , Camacho Sharon , Nasir Apsra , Huysman Molly E. , Rahhal Raneen , Dang Tuyen T. , Riegel Anna T. , Brekken Rolf A. , Pearson Gray W.
Published: March 2023

Supplemental Figures S1-S5 and Supplemental Legends
Supplementary Data from A Transcriptome-Wide Association Study Identifies Candidate Susceptibility Genes for Pancreatic Cancer Risk
Authors: Liu Duo , Zhou Dan , Sun Yanfa , Zhu Jingjing , Ghoneim Dalia , Wu Chong , Yao Qizhi , Gamazon Eric R. , Cox Nancy J. , Wu Lang
Published: March 2023

Five supplementary tables and one supplementary figure. Supplementary Table 1. Performance of gene expression prediction models built. Supplementary Table 2. Twenty-five lambda pairs and the corresponding prediction performance in the tuning set for prediction models of the 13 associated genes. Supplementary Table 3. Associations of age, sex, top principle components, and assessed pancreatic cancer risk variants with pancreatic cancer risk in conditional analyses of 13 associated genes. Supplementary Table 4. The functions of RCCD1, and CFDP1 and their reported links with human cancers. Supplementary Table 5. Associations of genes identified in Zhong et al. with pancreatic cancer risk in the present study. Supplementary Figure 1. The flowchart of quality control and prediction model training in the reference dataset.
Supplementary Data from The Alternative Splicing Factor, MBNL1, Inhibits Glioblastoma Tumor Initiation and Progression by Reducing Hypoxia-Induced Stemness
Authors: Voss Dillon M. , Sloan Anthony , Spina Raffaella , Ames Heather M. , Bar Eli E.
Published: March 2023

Supplementary Figures 1-8 S1. MBNL1 expression in Glioblastoma by subtype S2. MBNL1 target gene splicing S3. MBNL1 expression in cultured GSCs S4. MBNL1 activity is monitored with RG6 splicing reporter minigene S5. Effect of induced MBNL1 expression on GSC proliferation S6. Self-renewal assays in 622 and 08-387 neurospheres S7. Self-renewal assays in 913-luciferase neurospheres S8. Survival analysis for RTTA control cells
Supplemental Table ST1 from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: March 2023

Patient characteristics of the Macrophage Survey sub-cohort.
Supplemental Figure Legends from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: March 2023

Supplemental Figure Legends