bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental figure 3 from An Imbalance in TAZ and YAP Expression in Hepatocellular Carcinoma Confers Cancer Stem Cell–like Behaviors Contributing to Disease Progression
Authors: Hayashi Hiromitsu , Higashi Takaaki , Yokoyama Naomi , Kaida Takayoshi , Sakamoto Keita , Fukushima Yukiko , Ishimoto Takatsugu , Kuroki Hideyuki , Nitta Hidetoshi , Hashimoto Daisuke , Chikamoto Akira , Oki Eiji , Beppu Toru , Baba Hideo
Published: March 2023

Effects of YAP overexpression on phosphorylation of Erk1/2 in HuH1 cells.
Suppl. Figure 7 from HSP70 Inhibition Limits FAK-Dependent Invasion and Enhances the Response to Melanoma Treatment with BRAF Inhibitors
Authors: Budina-Kolomets Anna , Webster Marie R. , Leu Julia I-Ju , Jennis Matthew , Krepler Clemens , Guerrini Anastasia , Kossenkov Andrew V. , Xu Wei , Karakousis Giorgos , Schuchter Lynn , Amaravadi Ravi K. , Wu Hong , Yin Xiangfan , Liu Qin , Lu Yiling , Mills Gordon B. , Xu Xiaowei , George Donna L. , Weeraratna Ashani T. , Murphy Maureen E.
Published: March 2023

Impact of PET-16 on the level of HSP70 client proteins in vivo A. Immunofluorescence analysis for phospho-FAK (pTyr-397) in the tumors from mice described in (6G). Scale bar = 15 μm B
Suppl. Figure 6 from HSP70 Inhibition Limits FAK-Dependent Invasion and Enhances the Response to Melanoma Treatment with BRAF Inhibitors
Authors: Budina-Kolomets Anna , Webster Marie R. , Leu Julia I-Ju , Jennis Matthew , Krepler Clemens , Guerrini Anastasia , Kossenkov Andrew V. , Xu Wei , Karakousis Giorgos , Schuchter Lynn , Amaravadi Ravi K. , Wu Hong , Yin Xiangfan , Liu Qin , Lu Yiling , Mills Gordon B. , Xu Xiaowei , George Donna L. , Weeraratna Ashani T. , Murphy Maureen E.
Published: March 2023

Impact of PET-16 on ER stress Melanoma cell lines 1205Lu and WM852 were treated with DMSO or 1 μM PET-16 for 0, 8 and 24 hours.
Supplementary Figure 2 from Low-Dose Paclitaxel Reduces S100A4 Nuclear Import to Inhibit Invasion and Hematogenous Metastasis of Cholangiocarcinoma
Authors: Cadamuro Massimiliano , Spagnuolo Gaia , Sambado Luisa , Indraccolo Stefano , Nardo Giorgia , Rosato Antonio , Brivio Simone , Caslini Chiara , Stecca Tommaso , Massani Marco , Bassi Nicolò , Novelli Eugenio , Spirli Carlo , Fabris Luca , Strazzabosco Mario
Published: March 2023

Supplementary Figure 2. Low dose PTX reduced motility and invasiveness of CCA-TV3 cells.
Supplementary Information from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine
Authors: Leadem Benjamin R. , Kagiampakis Ioannis , Wilson Catherine , Cheung Tommy K. , Arnott David , Trojer Patrick , Classon Marie , Easwaran Hariharan , Baylin Stephen B.
Published: March 2023

Legends for Supplementary Figures and Tables
Supplementary Materials and Methods from Tumor Suppressor HIPK2 Regulates Malignant Growth via Phosphorylation of Notch1
Authors: Ann Eun-Jung , Kim Mi-Yeon , Yoon Ji-Hye , Ahn Ji-Seon , Jo Eun-Hye , Lee Hye-Jin , Lee Hyun-Woo , Kang Hyeok-Gu , Choi Dong Wook , Chun Kyung-Hee , Lee Ji Shin , Choi Cheol Yong , Ferrando Adolfo A. , Lee Keesook , Park Hee-Sae
Published: March 2023

Description of additional methods and procedures used in the study.
Figure S2 from A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine
Authors: Leadem Benjamin R. , Kagiampakis Ioannis , Wilson Catherine , Cheung Tommy K. , Arnott David , Trojer Patrick , Classon Marie , Easwaran Hariharan , Baylin Stephen B.
Published: March 2023

DAC & KDM5i induced expression changes
Supplementary Table 11 from MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome
Authors: Wragg Joseph W. , Finnity Jonathan P. , Anderson Jane A. , Ferguson Henry J.M. , Porfiri Emilio , Bhatt Rupesh I. , Murray Paul G. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary Table 11: Key clinical data for the CRC cohort showing overall survival (OS)
Supplementary Table 10 from MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome
Authors: Wragg Joseph W. , Finnity Jonathan P. , Anderson Jane A. , Ferguson Henry J.M. , Porfiri Emilio , Bhatt Rupesh I. , Murray Paul G. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Supplementary Table 10: Key clinical data for clear cell RCC cohort 3 showing overall survival (OS).
Table S3 and S4 from Molecular Pathology of Patient Tumors, Patient-Derived Xenografts, and Cancer Cell Lines
Authors: Guo Sheng , Qian Wubin , Cai Jie , Zhang Likun , Wery Jean-Pierre , Li Qi-Xiang
Published: March 2023

Table S3. Biomarkers for lung origin and colon origins. Table S4. IHC analysis of the outlier models
Supplemental figure 4 from CCR2 Influences T Regulatory Cell Migration to Tumors and Serves as a Biomarker of Cyclophosphamide Sensitivity
Authors: Loyher Pierre-Louis , Rochefort Juliette , Baudesson de Chanville Camille , Hamon Pauline , Lescaille Géraldine , Bertolus Chloé , Guillot-Delost Maude , Krummel Matthew F. , Lemoine François M. , Combadière Christophe , Boissonnas Alexandre
Published: March 2023

Non-cycling Treg accumulate in the dLN of Ccr2-/- mice compare to WT mice
Supplemental Methods from mTORC2 Signaling Drives the Development and Progression of Pancreatic Cancer
Authors: Driscoll David R. , Karim Saadia A , Sano Makoto , Gay David M. , Jacob Wright , Yu Jun , Mizukami Yusuke , Gopinathan Aarthi , Jodrell Duncan I. , Evans T.R. Jeffry , Bardeesy Nabeel , Hall Michael N. , Quattrochi Brian J. , Klimstra David S. , Barry Simon T. , Sansom Owen J. , Lewis Brian C. , Morton Jennifer P.
Published: March 2023

Supplementary materials and methods
Supplementary movie S2 from Pharmacological Inhibition of Centrosome Clustering by Slingshot-Mediated Cofilin Activation and Actin Cortex Destabilization
Authors: Konotop Gleb , Bausch Elena , Nagai Tomoaki , Turchinovich Andrey , Becker Natalia , Benner Axel , Boutros Michael , Mizuno Kensaku , Krämer Alwin , Raab Marc Steffen
Published: March 2023

Representative fluorescence time-lapse microscopy comparing mitotic events of H2B-mCherry-ÃŽÂ±-tubulin-EGFP- HeLa cells treated with 1 Ã,ÂµM CP-673451.
Supplementary Figure S1 from Kv1.3 Channels Mark Functionally Competent CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Cancer
Authors: Chimote Ameet A. , Hajdu Peter , Sfyris Alexandros M. , Gleich Brittany N. , Wise-Draper Trisha , Casper Keith A. , Conforti Laura
Published: March 2023

Specificity of Kv1.3 antibodies
Supplementary Table S1 from Glucose Metabolism Reprogrammed by Overexpression of IKKϵ Promotes Pancreatic Tumor Growth
Authors: Zubair Haseeb , Azim Shafquat , Srivastava Sanjeev Kumar , Ahmad Aamir , Bhardwaj Arun , Khan Mohammad Aslam , Patel Girijesh Kumar , Arora Sumit , Carter James Elliot , Singh Seema , Singh Ajay Pratap
Published: March 2023

List of primers used.
Supplementary Methods from Glucose Metabolism Reprogrammed by Overexpression of IKKϵ Promotes Pancreatic Tumor Growth
Authors: Zubair Haseeb , Azim Shafquat , Srivastava Sanjeev Kumar , Ahmad Aamir , Bhardwaj Arun , Khan Mohammad Aslam , Patel Girijesh Kumar , Arora Sumit , Carter James Elliot , Singh Seema , Singh Ajay Pratap
Published: March 2023

Description of additional methods and procedures used in the study.
Supplemental Figure Legends from TLR Adaptor Protein MYD88 Mediates Sensitivity to HDAC Inhibitors via a Cytokine-Dependent Mechanism
Authors: New Maria , Sheikh Semira , Bekheet Mina , Olzscha Heidi , Thezenas Marie-Laetitia , Care Matthew A. , Fotheringham Susan , Tooze Reuben M. , Kessler Benedikt , La Thangue Nicholas B.
Published: March 2023

Supplemental figures 1-5 legends
Supplementary Figures S1-S7 from Glucose Metabolism Reprogrammed by Overexpression of IKKϵ Promotes Pancreatic Tumor Growth
Authors: Zubair Haseeb , Azim Shafquat , Srivastava Sanjeev Kumar , Ahmad Aamir , Bhardwaj Arun , Khan Mohammad Aslam , Patel Girijesh Kumar , Arora Sumit , Carter James Elliot , Singh Seema , Singh Ajay Pratap
Published: March 2023

IKKepsilon expression in pancreatic tumor samples and PDAC cell lines (S1); Ectopic expression of IKKepsilon enhances growth of pancreatic cancer cells (S2); Transient knockdown of IKKepsilon in MiaPaCa and Colo357 cells by siRNA (S3); Forced expression of IKKepsilon in BxPC3 cells enhances glucose-uptake and consumption (S4); Overexpression of IKKepsilon in BxPC3 enhanced the expression and nuclear translocation of c-MYC (S5); IKKepsilon knockdown decreases half-life of c-MYC in MiaPaCa and Colo357 cells (S6); Ectopic expression of IKKepsilon in pancreatic cancer cell line BxPC3 activates Akt (S7).
Supplementary table, figures, and figure legends from Endosialin-Expressing Pericytes Promote Metastatic Dissemination
Authors: Viski Carmen , König Courtney , Kijewska Magdalena , Mogler Carolin , Isacke Clare M. , Augustin Hellmut G.
Published: March 2023

Table S1. Listed antibodies in this table were used for immunohistochemistry and immunofluorescence stainings S1. Endosialin localization and expression in mouse tumors S2. Quantification of metastatic burden in wild-type and endosialin-knockout mice S3. Characterization of tumor vessels in wild-type and endosialin-knockout mice S4. Characterization of vessel functionality in wild-type and endosialin-knockout mice S5. Diagram outlying in vitro tumor cell transmigration assays S6. Characterization of pericyte populations S7. Tumor cell transmigration and adhesion assays S8. Correlation of endosialin expression and metastasis in human patient samples
SI Figure 4 from TLR Adaptor Protein MYD88 Mediates Sensitivity to HDAC Inhibitors via a Cytokine-Dependent Mechanism
Authors: New Maria , Sheikh Semira , Bekheet Mina , Olzscha Heidi , Thezenas Marie-Laetitia , Care Matthew A. , Fotheringham Susan , Tooze Reuben M. , Kessler Benedikt , La Thangue Nicholas B.
Published: March 2023

MYD88 expression coincides with an acetylation signature at ABC subgroup-specific GO gene clusters
SI Figure 3 from TLR Adaptor Protein MYD88 Mediates Sensitivity to HDAC Inhibitors via a Cytokine-Dependent Mechanism
Authors: New Maria , Sheikh Semira , Bekheet Mina , Olzscha Heidi , Thezenas Marie-Laetitia , Care Matthew A. , Fotheringham Susan , Tooze Reuben M. , Kessler Benedikt , La Thangue Nicholas B.
Published: March 2023

High levels of MYD88 are apparent in tissue microarray biopsies from patients with DLBCL, but not prostate and colorectal cancer.
Supplementary Figures S1-S5 from Stimulation of Natural Killer Cell–Mediated Tumor Immunity by an IL15/TGFβ–Neutralizing Fusion Protein
Authors: Ng Spencer , Deng Jiusheng , Chinnadurai Raghavan , Yuan Shala , Pennati Andrea , Galipeau Jacques
Published: March 2023

FIST15 treatment increases the proportion of CD8+ T cells NK cells without inducing proliferation of CD4+ T cells or B cells in vitro (S1); MHC-I Expression on B16 and MC-38 tumor cell lines (S2); FIST15 treatment promotes CD8+ memory phenotype cell expansion (S3); NK cell response to FIST15 treatment (S4); FIST15 augments CD8+ T cell cytotoxic effector molecule production (S5).
Supplementary Figure Legends from Stimulation of Natural Killer Cell–Mediated Tumor Immunity by an IL15/TGFβ–Neutralizing Fusion Protein
Authors: Ng Spencer , Deng Jiusheng , Chinnadurai Raghavan , Yuan Shala , Pennati Andrea , Galipeau Jacques
Published: March 2023

Legends for Supplementary Figures S1-S5.
SI Figure 2 from TLR Adaptor Protein MYD88 Mediates Sensitivity to HDAC Inhibitors via a Cytokine-Dependent Mechanism
Authors: New Maria , Sheikh Semira , Bekheet Mina , Olzscha Heidi , Thezenas Marie-Laetitia , Care Matthew A. , Fotheringham Susan , Tooze Reuben M. , Kessler Benedikt , La Thangue Nicholas B.
Published: March 2023

HDAC6 is a key regulator of MYD88 acetylation and somatic mutation in MYD88 influences HDI sensitivity.
Table S4 from Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes
Authors: Marusyk Andriy , Tabassum Doris P. , Janiszewska Michalina , Place Andrew E. , Trinh Anne , Rozhok Andrii I. , Pyne Saumyadipta , Guerriero Jennifer L. , Shu Shaokun , Ekram Muhammad , Ishkin Alexander , Cahill Daniel P. , Nikolsky Yuri , Chan Timothy A. , Rimawi Mothaffar F. , Hilsenbeck Susan , Schiff Rachel , Osborne Kent C. , Letai Antony , Polyak Kornelia
Published: March 2023

List of the inhibitors tested for the ability to overcome CAF mediated resistance to lapatinib.
Supplementary Table S1 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Table S1. List of somatic mutations detected by whole exome sequencing.
Table S2 from Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes
Authors: Marusyk Andriy , Tabassum Doris P. , Janiszewska Michalina , Place Andrew E. , Trinh Anne , Rozhok Andrii I. , Pyne Saumyadipta , Guerriero Jennifer L. , Shu Shaokun , Ekram Muhammad , Ishkin Alexander , Cahill Daniel P. , Nikolsky Yuri , Chan Timothy A. , Rimawi Mothaffar F. , Hilsenbeck Susan , Schiff Rachel , Osborne Kent C. , Letai Antony , Polyak Kornelia
Published: March 2023

Classification of METABRIC cohort into prognostic groups. The file has three worksheets. Patient Grouping and Scores: Summary of patient classification and stromal and immune scores from ESTIMATE. Gene Signatures: list of genes in each gene signature. Multivariate Analysis models: contributions of each clinical covariate to multivariate cox proportional hazards models.
Table S1 from Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes
Authors: Marusyk Andriy , Tabassum Doris P. , Janiszewska Michalina , Place Andrew E. , Trinh Anne , Rozhok Andrii I. , Pyne Saumyadipta , Guerriero Jennifer L. , Shu Shaokun , Ekram Muhammad , Ishkin Alexander , Cahill Daniel P. , Nikolsky Yuri , Chan Timothy A. , Rimawi Mothaffar F. , Hilsenbeck Susan , Schiff Rachel , Osborne Kent C. , Letai Antony , Polyak Kornelia
Published: March 2023

List of differentially expressed genes. The table lists values of fold changes in gene expression for the genes, up or down regulated in the indicated breast cancer cell lines cultured in the presence of CAFs compared to breast cancer cells cultured separately.
Supplementary Data from Spatial Proximity to Fibroblasts Impacts Molecular Features and Therapeutic Sensitivity of Breast Cancer Cells Influencing Clinical Outcomes
Authors: Marusyk Andriy , Tabassum Doris P. , Janiszewska Michalina , Place Andrew E. , Trinh Anne , Rozhok Andrii I. , Pyne Saumyadipta , Guerriero Jennifer L. , Shu Shaokun , Ekram Muhammad , Ishkin Alexander , Cahill Daniel P. , Nikolsky Yuri , Chan Timothy A. , Rimawi Mothaffar F. , Hilsenbeck Susan , Schiff Rachel , Osborne Kent C. , Letai Antony , Polyak Kornelia
Published: March 2023

Supplementary Figures, Detailed Methods, and Supplementary References
Supplementary Figure S3 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Figure S3. The genomic and transcriptomic differences between multiple lymph nodes of patients TH2, TH3, TH4 and TH6. The density plots of cancer cell fraction (CCF) between the primary site and lymph node metastases are shown in upper panels. The scatter plots for similarity of gene expression profiles between the primary site and lymph node metastases are shown in lower panels. Differentially expressed cancer related-genes (>2-fold change) are highlighted in red and green colors.
Supplementary Figure S2 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Figure S2. EML4-ALK fusion gene detected from TH2 and TH5. (A) The break point region is located within intron 19 of ALK and intron 6 of EML4. (B-D) The IGV visualization of EML4-ALK fusion in TH1 from RNA-seq data, in TH1 from panel-sequencing data and in TH4 from RNA-seq data.
Supplementary Figure S1 from Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer
Authors: Um Sang-Won , Joung Je-Gun , Lee Hyun , Kim Hojoong , Kim Kyu-Tae , Park Jinha , Hayes D. Neil , Park Woong-Yang
Published: March 2023

Figure S1. Somatic mutations of each tumor. Missense, nonsense and splicing identified by whole-exome sequencing analysis
Supplementary Table 1 from JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2–Targeted Therapies
Authors: Manole Simin , Richards Edward J. , Meyer Aaron S.
Published: March 2023

Cell line data used to generate Figure 1G.
Supplementary Figure S4 from LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1
Authors: Sun Ming , Nie Fengqi , Wang Yunfei , Zhang Zhihong , Hou Jiakai , He Dandan , Xie Min , Xu Lin , De Wei , Wang Zhaoxia , Wang Jun
Published: March 2023

HOXA11-AS interacts with EZH2 and LSD1 et al. RNA binding proteins in GC cells.
Supplementary Figure 5 from JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2–Targeted Therapies
Authors: Manole Simin , Richards Edward J. , Meyer Aaron S.
Published: March 2023

Quantification of cJun abundance.
Supplementary Figure 4 from JNK Pathway Activation Modulates Acquired Resistance to EGFR/HER2–Targeted Therapies
Authors: Manole Simin , Richards Edward J. , Meyer Aaron S.
Published: March 2023

JNK pathway activation modulates bypass resistance.
Table S5 from Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations
Authors: Lu Songjian , Cai Chunhui , Yan Gonghong , Zhou Zhuan , Wan Yong , Chen Vicky , Chen Lujia , Cooper Gregory F. , Obeid Lina M. , Hannun Yusuf A. , Lee Adrian V. , Lu Xinghua
Published: March 2023

An MS Word file containing the genes in a perturbation module that regulate the expression of a response module annotated with GO:001251 (programmed cell death) and the literature associated with the genes.
Supplementary Figure S5 from Splenic Marginal Zone Granulocytes Acquire an Accentuated Neutrophil B-Cell Helper Phenotype in Chronic Lymphocytic Leukemia
Authors: Gätjen Marcel , Brand Franziska , Grau Michael , Gerlach Kerstin , Kettritz Ralph , Westermann Jörg , Anagnostopoulos Ioannis , Lenz Peter , Lenz Georg , Höpken Uta E. , Rehm Armin
Published: March 2023

Eμ-Tcl1 leukemia-associated splenic neutrophils exhibit a unique gene expression profile.
Supplementary Figure S2 from Splenic Marginal Zone Granulocytes Acquire an Accentuated Neutrophil B-Cell Helper Phenotype in Chronic Lymphocytic Leukemia
Authors: Gätjen Marcel , Brand Franziska , Grau Michael , Gerlach Kerstin , Kettritz Ralph , Westermann Jörg , Anagnostopoulos Ioannis , Lenz Peter , Lenz Georg , Höpken Uta E. , Rehm Armin
Published: March 2023

Polarization of leukemia-associated macrophages in spleen.
Supplemental Table S1 from CIC-DUX4 Induces Small Round Cell Sarcomas Distinct from Ewing Sarcoma
Authors: Yoshimoto Toyoki , Tanaka Miwa , Homme Mizuki , Yamazaki Yukari , Takazawa Yutaka , Antonescu Cristina R. , Nakamura Takuro
Published: March 2023

The list of PCR primers
Table S7 from MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy
Authors: Reinhardt Julia , Landsberg Jennifer , Schmid-Burgk Jonathan L. , Ramis Bartomeu Bibiloni , Bald Tobias , Glodde Nicole , Lopez-Ramos Dorys , Young Arabella , Ngiow Shin Foong , Nettersheim Daniel , Schorle Hubert , Quast Thomas , Kolanus Waldemar , Schadendorf Dirk , Long Georgina V. , Madore Jason , Scolyer Richard A. , Ribas Antoni , Smyth Mark J. , Tumeh Paul C. , Tüting Thomas , Hölzel Michael
Published: March 2023

Supplemental Table S7. Hallmark gene sets up in ACT-treated relapse (R) HCmel3 melanomas versus early during treatment (EDT) HCmel3 melanomas (GSEA results).
Table S4 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

List of p53 interaction network proteins affected by selinexor
Table S1 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Nuclear proteins
Table S1 from Methods of Academic Course Planning for Cancer Biology PhD Students to Enhance Knowledge of Clinical Oncology
Authors: Mattes Malcolm D. , Swart Elizabeth , Markwell Steven M. , Wen Sijin , Vona-Davis Linda C.
Published: March 2023

Survey questions for faculty
Figure S4 from Therapeutic Rationale to Target Highly Expressed CDK7 Conferring Poor Outcomes in Triple-Negative Breast Cancer
Authors: Li Bo , Ni Chonghaile Triona , Fan Yue , Madden Stephen F. , Klinger Rut , O'Connor Aisling E. , Walsh Louise , O'Hurley Gillian , Mallya Udupi Girish , Joseph Jesuchristopher , Tarrant Finbarr , Conroy Emer , Gaber Alexander , Chin Suet-Feung , Bardwell Helen A. , Provenzano Elena , Crown John , Dubois Thierry , Linn Sabine , Jirstrom Karin , Caldas Carlos , O'Connor Darran P. , Gallagher William M.
Published: March 2023

CDK7 and MYC mRNA expression in subsets of breast cancer
Supplementary Materials and Methods from Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA
Authors: Jdey Wael , Thierry Sylvain , Popova Tatiana , Stern Marc-Henri , Dutreix Marie
Published: March 2023

Supplementary Materials and Methods used to generate data represented in Figure S2.
Figure S1 from Therapeutic Rationale to Target Highly Expressed CDK7 Conferring Poor Outcomes in Triple-Negative Breast Cancer
Authors: Li Bo , Ni Chonghaile Triona , Fan Yue , Madden Stephen F. , Klinger Rut , O'Connor Aisling E. , Walsh Louise , O'Hurley Gillian , Mallya Udupi Girish , Joseph Jesuchristopher , Tarrant Finbarr , Conroy Emer , Gaber Alexander , Chin Suet-Feung , Bardwell Helen A. , Provenzano Elena , Crown John , Dubois Thierry , Linn Sabine , Jirstrom Karin , Caldas Carlos , O'Connor Darran P. , Gallagher William M.
Published: March 2023

High CDK7 mRNA expression is associated with poor prognosis in TNBC transcriptomic datasets
Supplementary Figure 3 from T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia
Authors: Jing Weiqing , Gershan Jill A. , Holzhauer Sandra , Weber James , Palen Katie , McOlash Laura , Pulakanti Kirthi , Wesley Erin , Rao Sridhar , Johnson Bryon D. , Riese Matthew J.
Published: March 2023

Presence of donor T cells at various time points after ACT
Supplementary Figure Legends from An Immunosuppressive Dendritic Cell Subset Accumulates at Secondary Sites and Promotes Metastasis in Pancreatic Cancer
Authors: Kenkel Justin A. , Tseng William W. , Davidson Matthew G. , Tolentino Lorna L. , Choi Okmi , Bhattacharya Nupur , Seeley E. Scott , Winer Daniel A. , Reticker-Flynn Nathan E. , Engleman Edgar G.
Published: March 2023

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

Cell surface phenotype of adoptively transferred T cells
Figure S7 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

Expression of PD-L1 on MDA-MB-231, BxPC-3 and NCI-M87, as determined by flow cytometry.
Figure S6 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

T cells purified from thawed. cryopreserved PBMCs (lot 032417) induced killing of HT-29 (A) or LS 174T (B) spheroids in the presence of (14)-3s (100 pM).
Supplementary Table 3 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Primer sequences of the primers utilized in Sanger sequencing.
Figure S10 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

Flow cytometric dot plots showing PD-1 expression on CD3+ T cells in PBMCs (left) or CD3+ T cells purified from PBMCs
Supplementary Table 2 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Additional information about the mutations in sets A, B and C.
Supplementary Table S2 from Fructose-1,6-bisphosphatase Inhibits ERK Activation and Bypasses Gemcitabine Resistance in Pancreatic Cancer by Blocking IQGAP1–MAPK Interaction
Authors: Jin Xin , Pan Yunqian , Wang Liguo , Ma Tao , Zhang Lizhi , Tang Amy H. , Billadeau Daniel D. , Wu Heshui , Huang Haojie
Published: March 2023

FBP1-associated proteins identified by tandem affinity purification and mass spectrometry
Supplementary Materials and Methods from Fructose-1,6-bisphosphatase Inhibits ERK Activation and Bypasses Gemcitabine Resistance in Pancreatic Cancer by Blocking IQGAP1–MAPK Interaction
Authors: Jin Xin , Pan Yunqian , Wang Liguo , Ma Tao , Zhang Lizhi , Tang Amy H. , Billadeau Daniel D. , Wu Heshui , Huang Haojie
Published: March 2023

Supplementary Materials and Methods
Supplementary Figure 1 from Fructose-1,6-bisphosphatase Inhibits ERK Activation and Bypasses Gemcitabine Resistance in Pancreatic Cancer by Blocking IQGAP1–MAPK Interaction
Authors: Jin Xin , Pan Yunqian , Wang Liguo , Ma Tao , Zhang Lizhi , Tang Amy H. , Billadeau Daniel D. , Wu Heshui , Huang Haojie
Published: March 2023

Assessment of the effectiveness of IQGAP1 depletion and the effect of gemcitabine on the pERK1/2 levels in the PDAC patient samples.
Figure S1 from Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer
Authors: Gulbahce Natali , Magbanua Mark Jesus M. , Chin Robert , Agarwal Misha R. , Luo Xuhao , Liu Jia , Hayden Daniel M. , Mao Qing , Ciotlos Serban , Li Zhenyu , Chen Yanxiang , Chen Xingpeng , Li Yuxiang , Zhang Rebecca Yu , Lee Katharine , Tearle Rick , Park Emily , Drmanac Snezana , Rugo Hope S. , Park John W. , Drmanac Radoje , Peters Brock A.
Published: March 2023

Distribution of allele fraction of inherited and somatic variants before and after filtering. This figure is similar to Fig. 4a, but includes a plotting of all somatic variants before filtering (black), which contains a large number of false positive errors.
Figure S4 from Plk1 Phosphorylation of Mre11 Antagonizes the DNA Damage Response
Authors: Li Zhiguo , Li Jie , Kong Yifan , Yan Shan , Ahmad Nihal , Liu Xiaoqi
Published: March 2023

Figure S4 shows that Mre11 phosphorylation at S649/S688 has no impact on the MRN complex stability.
Figure S5 from Glutamine Addiction in Kidney Cancer Suppresses Oxidative Stress and Can Be Exploited for Real-Time Imaging
Authors: Abu Aboud Omran , Habib Samy L. , Trott Josephine , Stewart Benjamin , Liang Sitai , Chaudhari Abhijit J. , Sutcliffe Julie , Weiss Robert H.
Published: March 2023

Coronal PET MIP images overlaid with CT images.
Figure S1 from SOCS1 Gene Therapy Improves Radiosensitivity and Enhances Irradiation-Induced DNA Damage in Esophageal Squamous Cell Carcinoma
Authors: Sugase Takahito , Takahashi Tsuyoshi , Serada Satoshi , Fujimoto Minoru , Hiramatsu Kosuke , Ohkawara Tomoharu , Tanaka Koji , Miyazaki Yasuhiro , Makino Tomoki , Kurokawa Yukinori , Yamasaki Makoto , Nakajima Kiyokazu , Kishimoto Tadamitsu , Mori Masaki , Doki Yuichiro , Naka Tetsuji
Published: March 2023

This figure shows the association between STAT3 activation and chemotherapy. There were no differences of p-STAT3 and Mcl-1 expression after irradiation.
Figure S2 from Plk1 Phosphorylation of Mre11 Antagonizes the DNA Damage Response
Authors: Li Zhiguo , Li Jie , Kong Yifan , Yan Shan , Ahmad Nihal , Liu Xiaoqi
Published: March 2023

Figure S2 shows that Plk1 phosphorylation of Mre11 is required for inactivation of the ATM-Chk2 pathway.
Table S1 from A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220
Authors: Hou Panpan , Wu Chao , Wang Yuchen , Qi Rui , Bhavanasi Dheeraj , Zuo Zhixiang , Dos Santos Cedric , Chen Shuliang , Chen Yu , Zheng Hong , Wang Hong , Perl Alexander , Guo Deyin , Huang Jian
Published: March 2023

Supplementary Table 1. The summary of the top hits identified in the screen (recovered sgRNA>3). The number of sgRNAs recovered and the average copy number of sgRNAs for each gene are shown in the table.
Figure S3 from A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220
Authors: Hou Panpan , Wu Chao , Wang Yuchen , Qi Rui , Bhavanasi Dheeraj , Zuo Zhixiang , Dos Santos Cedric , Chen Shuliang , Chen Yu , Zheng Hong , Wang Hong , Perl Alexander , Guo Deyin , Huang Jian
Published: March 2023

Supplementary Figure 3. AC220 inhibits FLT3-ITD downstream signaling pathways and SPRY3 or GSK3 deletions reactivate RAS/ERK and Wnt signaling pathways in the presence of AC220 in Ba/F3 cells. (A) Ba/F3 and Ba/F3 FLT3-ITD cells were treated with FLT3-ligand or IL-3 and collected and lysed. Western blots analysis was carried out. (B) 0.3 X 106 cells were starved overnight and treated with DMSO or 10nM AC220 in combination with 3uM Chiron. The cells were harvested at indicated times and lysed. The western blots analysis was performed. (C) 0.3 X 106 MV4-11 cells were starved overnight and treated with FGF-1 (100ng/ml) and heparin (10ug/ml) in combination with 10 nM AC220. The cells were harvested at indicated times and lysed. Western blots analysis was performed. (D) 0.3 X 106 cells were starved overnight and treated with DMSO or 10nM AC220 in combination with 3uM Chiron. Western blots analysis was carried out.
Supplemental Figure S1 from Sunitinib Stimulates Expression of VEGFC by Tumor Cells and Promotes Lymphangiogenesis in Clear Cell Renal Cell Carcinomas
Authors: Dufies Maeva , Giuliano Sandy , Ambrosetti Damien , Claren Audrey , Ndiaye Papa Diogop , Mastri Michalis , Moghrabi Walid , Cooley Lindsay S. , Ettaiche Marc , Chamorey Emmanuel , Parola Julien , Vial Valerie , Lupu-Plesu Marilena , Bernhard Jean Christophe , Ravaud Alain , Borchiellini Delphine , Ferrero Jean-Marc , Bikfalvi Andréas , Ebos John M. , Khabar Khalid Saad , Grépin Renaud , Pagès Gilles
Published: March 2023

Supplementary Figure S1. Tyrosine kinase Inhibitor stimulated VEGFC expression. Tyrosine kinase inhibitors stimulate VEGFC expression in RCC cell lines and primary RCC cells but not in normal cells.
Table S5 from Correlates of Prenatal and Early-Life Tobacco Smoke Exposure and Frequency of Common Gene Deletions in Childhood Acute Lymphoblastic Leukemia
Authors: de Smith Adam J. , Kaur Maneet , Gonseth Semira , Endicott Alyson , Selvin Steve , Zhang Luoping , Roy Ritu , Shao Xiaorong , Hansen Helen M. , Kang Alice Y. , Walsh Kyle M. , Dahl Gary V. , McKean-Cowdin Roberta , Metayer Catherine , Wiemels Joseph L.
Published: March 2023

Correlation matrix for the parental reported tobacco smoke exposure variables. P-values and correlation coefficients were calculated using the Spearman's rank correlation coefficient test.
Supplementary Tables from S100A4 Elevation Empowers Expression of Metastasis Effector Molecules in Human Breast Cancer
Authors: Ismail Thamir M. , Bennett Daimark , Platt-Higgins Angela M. , Al-Medhity Morteta , Barraclough Roger , Rudland Philip S.
Published: March 2023

Table S1 MMPs/ S100A4, Table 2 Survival Times, Table S3 Cox Results, Table S4 2x2 Tables, Table S5 Logistic Association , Table S6 Same Area Staining.
Supplemental Table S1 from Correlates of Prenatal and Early-Life Tobacco Smoke Exposure and Frequency of Common Gene Deletions in Childhood Acute Lymphoblastic Leukemia
Authors: de Smith Adam J. , Kaur Maneet , Gonseth Semira , Endicott Alyson , Selvin Steve , Zhang Luoping , Roy Ritu , Shao Xiaorong , Hansen Helen M. , Kang Alice Y. , Walsh Kyle M. , Dahl Gary V. , McKean-Cowdin Roberta , Metayer Catherine , Wiemels Joseph L.
Published: March 2023

Number of deletions in each gene tested amongst 559 ALL cases from the CCLS, assessed by MLPA.
Supplementary Table S3 from Extracellular Matrix Receptor Expression in Subtypes of Lung Adenocarcinoma Potentiates Outgrowth of Micrometastases
Authors: Stevens Laura E. , Cheung William K.C. , Adua Sally J. , Arnal-Estapé Anna , Zhao Minghui , Liu Zongzhi , Brewer Kelly , Herbst Roy S. , Nguyen Don X.
Published: March 2023

Correlation between MIR34A methylation with mir-34a or HMMR expression in concordant LUAD samples from TCGA.
Supplementary Figures 2-5 from Mathematical Modeling of Tumor–Tumor Distant Interactions Supports a Systemic Control of Tumor Growth
Authors: Benzekry Sebastien , Lamont Clare , Barbolosi Dominique , Hlatky Lynn , Hahnfeldt Philip
Published: March 2023

Single tumor model fits (exponential, Gompertz and power law) and delay analysis
Supplementary Table 4 from Plk4 Promotes Cancer Invasion and Metastasis through Arp2/3 Complex Regulation of the Actin Cytoskeleton
Authors: Kazazian Karineh , Go Christopher , Wu Hannah , Brashavitskaya Olga , Xu Roland , Dennis James W. , Gingras Anne-Claude , Swallow Carol J.
Published: March 2023

List of high confidence preys of PLK4.
Supplementary Table 3 from Plk4 Promotes Cancer Invasion and Metastasis through Arp2/3 Complex Regulation of the Actin Cytoskeleton
Authors: Kazazian Karineh , Go Christopher , Wu Hannah , Brashavitskaya Olga , Xu Roland , Dennis James W. , Gingras Anne-Claude , Swallow Carol J.
Published: March 2023

Summary of effect of Plk4 manipulation on change in centriole number, and on migration in wound healing assays.
Supplementary Figures 4-6 from Plk4 Promotes Cancer Invasion and Metastasis through Arp2/3 Complex Regulation of the Actin Cytoskeleton
Authors: Kazazian Karineh , Go Christopher , Wu Hannah , Brashavitskaya Olga , Xu Roland , Dennis James W. , Gingras Anne-Claude , Swallow Carol J.
Published: March 2023

Fig S4. Plk4 overexpression increases U2OS migration. Fig S5. Plk4 regulates HeLa invasion and spreading. Fig S6. Persistent Plk4 knockdown in MDA-MB-231 cells using a lentiviral shRNA system.
Figure S4. The effect of blocking type I IFN on tumor cells and tumor-infiltrating lymphocytes. from Suppression of Type I IFN Signaling in Tumors Mediates Resistance to Anti-PD-1 Treatment That Can Be Overcome by Radiotherapy
Authors: Wang Xiaohong , Schoenhals Jonathan E. , Li Ailin , Valdecanas David R. , Ye Huiping , Zang Fenglin , Tang Chad , Tang Ming , Liu Chang-Gong , Liu Xiuping , Krishnan Sunil , Allison James P. , Sharma Padmanee , Hwu Patrick , Komaki Ritsuko , Overwijk Willem W. , Gomez Daniel R. , Chang Joe Y. , Hahn Stephen M. , Cortez Maria Angelica , Welsh James W.
Published: March 2023

This figure addresses the reviewer's questions about the effect of blocking type I IFN on tumor cells and tumor-infiltrating lymphocytes.
Supplemental Table S3 from Modeling Alveolar Soft Part Sarcoma Unveils Novel Mechanisms of Metastasis
Authors: Tanaka Miwa , Homme Mizuki , Yamazaki Yukari , Shimizu Rikuka , Takazawa Yutaka , Nakamura Takuro
Published: March 2023

Genes upregulated in mouse ASPS tumors.
Supplemental Material from Cellular and Molecular Identity of Tumor-Associated Macrophages in Glioblastoma
Authors: Chen Zhihong , Feng Xi , Herting Cameron J. , Garcia Virginia Alvarez , Nie Kai , Pong Winnie W. , Rasmussen Rikke , Dwivedi Bhakti , Seby Sandra , Wolf Susanne A. , Gutmann David H. , Hambardzumyan Dolores
Published: March 2023

Figure S1. Circulating Ly6CHi inflammatory monocytes diminish at terminal illness. Figure S2. Enhanced BM-derived cell infiltration in Cx3cr1GFP/GFP;Ccr2RFP/WT mice. Figure S3. RFP+ cells are only observed in the meninges in healthy naïve Cx3cr1GFP/WT;Ccr2RFP/WT mice. Figure S4. Bone marrow reconstitution efficiency as examined by flow cytometry. Figure S5. Significant up-regulated (red) and down-regulated (green) genes based on the pairwise comparisons. Figure S6. Loss of Ccl2 in stroma does not prolong survival of tumor-bearing mice. Figure S7. Immunohistochemistry staining and quantification of phosphor-histone 3 proliferating cells. Figure S8. Immunohistochemistry staining and quantification of Ki67+ proliferating cells. Figure S9. TUNEL staining of apoptotic cells. Figure S10. Survival curve of PDGF-driven tumor in WT, Ccl2+/- and Ccl2-/- mice. Supplementary Table S1. Combined Cx3cr1 and Ccr2 heterozygous knockout does not affect tumor development or survival. Supp. Table S2. Significantly enriched functional pathways in tumor-associated microglia. Supp. Table S3. Significantly enriched functional pathways in tumor-associated microglia and tumor-associate macrophages. Supp. Table S4. Significantly enriched functional pathways in tumor-associated macrophages.
Supplementary Figure 1 through 7 and Supplementary Tables 1 through 6 and 8 through 14, and Supplementary Materials and Methods from Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer
Authors: Mathot Lucy , Kundu Snehangshu , Ljungström Viktor , Svedlund Jessica , Moens Lotte , Adlerteg Tom , Falk-Sörqvist Elin , Rendo Verónica , Bellomo Claudia , Mayrhofer Markus , Cortina Carme , Sundström Magnus , Micke Patrick , Botling Johan , Isaksson Anders , Moustakas Aristidis , Batlle Eduard , Birgisson Helgi , Glimelius Bengt , Nilsson Mats , Sjöblom Tobias
Published: March 2023

Supplementary Fig. 1. Luciferase reporter assay reveals downregulation of BMP pathway activity upon overexpression of mutant BMPR2 Supplementary Fig. 2. Genes found in the largest number of significant outcomes when comparing mutation rate between metastatic and non-metastatic patients Supplementary Fig. 3. In situ mutation detection in FF colon tumour sections Supplementary Fig. 4. Expression levels of EPHB1 in DLD-1 cell lines overexpressing EPHB1 and its four mutant versions Supplementary Fig. 5. EPHB2 interacts with ephrinB1 ligand used as a positive control for the compartmentalisation experiment Supplementary Fig. 6. Detections of four non-synonymous mutations at the transcript level by Sanger sequencing and real time growth analysis of cell lines used in the compartmentalisation experiment Supplementary Fig. 7. The EPHB1 kinase inhibitor dasatinib abrogates the compartmentalisation phenotype of EPHB1 cells co-cultured with ephrinB1 ligand expressing cells Supplementary Table 1. Probe sequences for in situ mutation detection Supplementary Table 2. Probe performance for in situ mutation detection Supplementary Table 3. LNA primers for reverse transcription in situ Supplementary Table 4. Fluorescently labelled detection probes for RCPs Supplementary Table 5. Genes and corresponding length of the coding regions included in this study Supplementary Table 6. Patient-matched tumour and normal samples Supplementary Table 8. Comparison of pathway mutation rates in metastatic vs non-metastatic samples Supplementary Table 9. Functional annotation of mutated genes unique to metastatic patients Supplementary Table 10. Somatic mutations in Ephrin receptor genes Supplementary Table 11. Mean read depth of Eph receptor tyrosine kinases Supplementary Table 12. Prediction scores for amino acid conservation and effect of point mutations Supplementary Table 13. Mutation counts for Eph receptor mutations in situ Supplementary Table 14. Primer sequences for Sanger sequencing mutant constructs. Supplementary Materials and Methods
Supplementary Figures S1-S10, Materials and Methods from Mechano-Signal Transduction in Mesenchymal Stem Cells Induces Prosaposin Secretion to Drive the Proliferation of Breast Cancer Cells
Authors: Ishihara Seiichiro , Inman David R. , Li Wan-Ju , Ponik Suzanne M. , Keely Patricia J.
Published: March 2023

This file contains supplementary figures S1-S10 and supplementary materials and methods. Figure S1 shows experimental design of mesenchymal stem cells in this article. Figure S2 shows differentiation of transgenic mesenchymal stem cells. Figure S3 shows differentiation and gel contraction of mesenchymal stem cells. Figure S4 shows YAP activity in mesenchymal stem cells on a stiff matrix. Figure S5 shows expression and activation of YAP-related signaling molecules in mesenchymal stem cells. Figure S6 shows contribution of mesenchymal stem cells to tumor progression. Figure S7 shows prosaposin detection in mammary tumors. Figure S8 shows the role of prosaposin for ERK and caspase 3. Figure S9 shows contribution of prosaposin to late tumor growth and progression. Figure S10 shows the role of stiff matrix for mesenchymal stem cells from B6 mice.
Supplementary Figures and Tables from SDHD Promoter Mutations Ablate GABP Transcription Factor Binding in Melanoma
Authors: Zhang Tongwu , Xu Mai , Makowski Matthew M. , Lee Christine , Kovacs Michael , Fang Jun , Willems Esther , Trent Jeffrey M. , Hayward Nicholas K. , Vermeulen Michiel , Brown Kevin M.
Published: March 2023

Supplementary Figure 1. Confirmation of the recurrent C524, C541 and C544 SDHD promoter mutations in melanoma cell lines via Sanger sequencing. Supplementary Figure 2. Expression of SDHD in melanomas harboring promoter mutations compared to SDHD wild-type samples across TCGA samples. Supplementary Figure 3. Luciferase reporter assays for the C541T and C544T SDHD hotspot promoter mutations in multiple melanoma cell lines. Supplementary Figure 4. Prediction of the consequences of the C541T and C544T SDHD promoter mutations on transcription factor binding. Supplementary Figure 5. mRNA expression correlation between SDHD and multiple ETS transcription factors in TCGA SKCM samples harboring the SDHD C523T promoter mutation. Supplementary Figure 6. Band-shift analysis of recombinant human ELF1 binding to wild-type and C523T, C524T, C541T, and C544T SDHD promoter sequences. Supplementary Figure 7. Effect of siRNA-mediated knockdown of ELF1 on SDHD expression in melanoma cells. Supplementary Figure 8. Effect of siRNA-mediated knockdown of PRDM1 or IRF4 on SDHD expression and SDHD promoter activity in melanoma cells. Supplementary Table 1. SDHD promoter mutations identified in melanoma tumors datasets (TCGA, Broad and Yale) and melanoma cell lines. Supplementary Table 2. MotifBreakR results predicting the effects of recurrent SDHD promoter mutations (C523T, C524T, C541T, C544T, and C548T) on transcription factor binding sites. Supplementary Table 3. Oligonucleotide design for quantitative mass spectrometry.
Supplementary figure-5 from Mutant IDH1 Cooperates with ATRX Loss to Drive the Alternative Lengthening of Telomere Phenotype in Glioma
Authors: Mukherjee Joydeep , Johannessen Tor-Christian , Ohba Shigeo , Chow Tracy T. , Jones Lindsey , Pandita Ajay , Pieper Russell O.
Published: March 2023

Multiple telomere signals, change in cell viability and chromosome fusion in IDH1mut, ATRX-KO ALT astrocytes with and without XRCC1 overexpression.
Figure S5 from Proinflammatory CXCL12–CXCR4/CXCR7 Signaling Axis Drives Myc-Induced Prostate Cancer in Obese Mice
Authors: Saha Achinto , Ahn Songyeon , Blando Jorge , Su Fei , Kolonin Mikhail G. , DiGiovanni John
Published: March 2023

CXCR4 and CXCR7 knockdown decreases migration and invasion in HMVP2 cells
Supplementary Materials and Methods from Mouse Models of Pediatric Supratentorial High-grade Glioma Reveal How Cell-of-Origin Influences Tumor Development and Phenotype
Authors: Sreedharan Smitha , Maturi Naga Prathyusha , Xie Yuan , Sundström Anders , Jarvius Malin , Libard Sylwia , Alafuzoff Irina , Weishaupt Holger , Fryknäs Mårten , Larsson Rolf , Swartling Fredrik J. , Uhrbom Lene
Published: March 2023

Supplementary Materials and Methods
Figure S1 from Loss of FOXO1 Cooperates with TMPRSS2–ERG Overexpression to Promote Prostate Tumorigenesis and Cell Invasion
Authors: Yang Yinhui , Blee Alexandra M. , Wang Dejie , An Jian , Pan Yunqian , Yan Yuqian , Ma Tao , He Yundong , Dugdale Joseph , Hou Xiaonan , Zhang Jun , Weroha S. John , Zhu Wei-Guo , Wang Y. Alan , DePinho Ronald A. , Xu Wanhai , Huang Haojie
Published: March 2023

Supplementary Figure S1. In panel A, ERG pull-down in HUVEC cells showing no interaction between FOXO1 and ERG. In contrast, AR binding with ERG is detected as expected. In panel B, bioinformatic analysis of 492 prostate cancer cases from TCGA to show the profiles of FOXO1, PTEN and ERG alterations. PTEN and FOXO1 deletions largely do not overlap.
Supplementary Materials and Methods from ERβ-Mediated Alteration of circATP2B1 and miR-204-3p Signaling Promotes Invasion of Clear Cell Renal Cell Carcinoma
Authors: Han Zhenwei , Zhang Yong , Sun Yin , Chen Jiaqi , Chang Chawnshang , Wang Xiaolu , Yeh Shuyuan
Published: March 2023

Supplementary Material and Methods include information for performing/preparing (1) lentivirus particle production and transduction of RCC cells, (2) qPCR, (3) western blot analysis, (4) IHC staining and quantification, and (5) the shRNA#1 and #2 targeting sequences for circATP2B1 and ERβ.
Supplementary Figure Legends from ERβ-Mediated Alteration of circATP2B1 and miR-204-3p Signaling Promotes Invasion of Clear Cell Renal Cell Carcinoma
Authors: Han Zhenwei , Zhang Yong , Sun Yin , Chen Jiaqi , Chang Chawnshang , Wang Xiaolu , Yeh Shuyuan
Published: March 2023

Figure Legends for the Supplementary Figures
Supplementary Table S3 from Circadian Clock Gene Bmal1 Inhibits Tumorigenesis and Increases Paclitaxel Sensitivity in Tongue Squamous Cell Carcinoma
Authors: Tang Qingming , Cheng Bo , Xie Mengru , Chen Yatao , Zhao Jiajia , Zhou Xin , Chen Lili
Published: March 2023

Differentially expressed genes between SCC9/Bmal1 cells and SCC9/vehicle cells
Supplementary Video S8 from Mitosis-Mediated Intravasation in a Tissue-Engineered Tumor–Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

Mitosis-mediated intravasation of an MDA-MB-231 breast cancer cell (BCC) where one daughter cell intravasates and the other returns into the ECM-vessel interface.
Supplementary Figure S1 from Circadian Clock Gene Bmal1 Inhibits Tumorigenesis and Increases Paclitaxel Sensitivity in Tongue Squamous Cell Carcinoma
Authors: Tang Qingming , Cheng Bo , Xie Mengru , Chen Yatao , Zhao Jiajia , Zhou Xin , Chen Lili
Published: March 2023

Bmal1 overexpression increases paclitaxel sensitivity in SCC25 and CAL27 cells