bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 10-12 from DNA Methylation Signature Reveals Cell Ontogeny of Renal Cell Carcinomas
Authors: Malouf Gabriel G. , Su Xiaoping , Zhang Jianping , Creighton Chad J. , Ho Thai H. , Lu Yue , Raynal Noël J.-M. , Karam Jose A. , Tamboli Pheroze , Allanick Frederick , Mouawad Roger , Spano Jean-Philippe , Khayat David , Wood Christopher G. , Jelinek Jaroslav , Tannir Nizar M.
Published: April 2023

Supplementary Table 10: List of samples misclassified among the clear-cell renal cell carcinomas dataset with the corresponding new classification. Among those, many of them have been demonstrated to belong to the C4 cluster of long non-coding RNA classification. The first table reports the 5 misclassified TCGA clear-cell RCC (KIRC) using gene expression and which turned out to be chromophobe RCC (chRCC). The second table reports on misclassified TCGA KIRC cases with DNA methylation available. Supplementary Table 11: List of importance scores for genes used in the statistical model for predicting outcome of patients with clear-cell RCC. Supplementary Table 12: Associations (both training and validation datasets) between mutational load, TCGA clear-cell renal cell carcinomas transcriptomic subtypes classification and recurrent somatic mutations (VHL, PBRM1, BAP1 and KDM6A) identified in clear-cell renal cell carcinoma TCGA dataset with our 56 genes epi-signature. P-values less than 0.05 is considered as statistically significant.
Supplementary Figure 3 from Cisplatin-Induced Renal Injury Is Independently Mediated by OCT2 and p53
Authors: Sprowl Jason A. , Lancaster Cynthia S. , Pabla Navjotsingh , Hermann Edwin , Kosloske Ashley M. , Gibson Alice A. , Li Lie , Zeeh Dorothea , Schlatter Eberhard , Janke Laura J. , Ciarimboli Giuliano , Sparreboom Alex
Published: April 2023

PDF file - 479K, Comparative analysis of p53(-/-), Oct1/2(-/-), p53(-/-)/Oct1/2(-/-) and wildtype FVB mice.
Supplementary Figure 2 from Cisplatin-Induced Renal Injury Is Independently Mediated by OCT2 and p53
Authors: Sprowl Jason A. , Lancaster Cynthia S. , Pabla Navjotsingh , Hermann Edwin , Kosloske Ashley M. , Gibson Alice A. , Li Lie , Zeeh Dorothea , Schlatter Eberhard , Janke Laura J. , Ciarimboli Giuliano , Sparreboom Alex
Published: April 2023

PDF file - 339K, Comparative cisplatin-induced nephrotoxicity and urinary elimination of cisplatin in FVB and C57BL/6 mice.
Supplemental Figure 2 from CDK 4/6 Inhibitor Palbociclib (PD0332991) in Rb+ Advanced Breast Cancer: Phase II Activity, Safety, and Predictive Biomarker Assessment
Authors: DeMichele Angela , Clark Amy S. , Tan Kay See , Heitjan Daniel F. , Gramlich Kristi , Gallagher Maryann , Lal Priti , Feldman Michael , Zhang Paul , Colameco Christopher , Lewis David , Langer Melissa , Goodman Noah , Domchek Susan , Gogineni Keerthi , Rosen Mark , Fox Kevin , O'Dwyer Peter
Published: April 2023

Supplemental Figure 2. Representative biomarker staining
Supplemental Figure 1 from CDK 4/6 Inhibitor Palbociclib (PD0332991) in Rb+ Advanced Breast Cancer: Phase II Activity, Safety, and Predictive Biomarker Assessment
Authors: DeMichele Angela , Clark Amy S. , Tan Kay See , Heitjan Daniel F. , Gramlich Kristi , Gallagher Maryann , Lal Priti , Feldman Michael , Zhang Paul , Colameco Christopher , Lewis David , Langer Melissa , Goodman Noah , Domchek Susan , Gogineni Keerthi , Rosen Mark , Fox Kevin , O'Dwyer Peter
Published: April 2023

Supplemental Figure 1. Number of cycles received
Supplementary tables S1-6 from SIRT1/PGC1α-Dependent Increase in Oxidative Phosphorylation Supports Chemotherapy Resistance of Colon Cancer
Authors: Vellinga Thomas T. , Borovski Tijana , de Boer Vincent C.J. , Fatrai Szabolcs , van Schelven Susanne , Trumpi Kari , Verheem Andre , Snoeren Nikol , Emmink Benjamin L. , Koster Jan , Rinkes Inne H.M. Borel , Kranenburg Onno
Published: April 2023

Supplementary tables S1-6. Supplementary table S1 Primers used for RT-qPCR analyses. Supplementary table S2 Clinical variables associated with differences in gene expression among 119 resected liver metastases. Supplementary table S3 613 genes whose expression was significantly upregulated and 481 genes whose expression was significantly (p<0.05) down-regulated in chemotherapy-treated tumors compared to chemo-naive tumors. Supplementary table S4 KEGG pathway finder analysis and Ingenuity Pathway Analysis of upregulated genes in chemo-treated compared to chemo-naive tumors. Supplementary table S5 P-values of expression levels of genes involved in mitochondrial dysfunction, ubiquinone synthesis and mitochondrial biogenesis upregulated in chemo-treated compared to chemo-naive tumors. Supplementary table S6 (additional information regarding the calculation listed below) ATP synthesis rates through glycolysis and OXPHOS.
Supplementary Figures 1-6, Tables 1-4 from DUSP1 Expression Induced by HDAC1 Inhibition Mediates Gefitinib Sensitivity in Non–Small Cell Lung Cancers
Authors: Lin Yun-Chieh , Lin Yu-Chin , Shih Jin-Yuan , Huang Wei-Jan , Chao Shi-Wei , Chang Yih-Leong , Chen Ching-Chow
Published: April 2023

Figure S1. The effect of gefitinib on gefitinib-resistant NSCLC cells. Figure S2. Knockdown of HDAC1 in PC9/IR and HCC827/IR cells restored gefitinib sensitivity. Figure S3. Novel HDAC inhibitors WJ compounds inhibited cell growth and induced acetylation of histone-H3 and α-tubulin in various cancer cells. Figure S4. Synergistic effect of WJ-26210-2 in combination with gefitinib on cell viability and apoptotic markers in gefitinib-resistant NSCLC cells. Figure S5. DUSP1 was induced in gefitinib-resistant cells by combination treatment and knockdown of it conferred gefitinib resistance in gefitinib-sensitive cells. Figure S6. Combination of HDAC1 inhibition and gefitinib induced in vivo DUSP1 expression in H1975 cells and inhibited lung cancer growth. Table S1. IC50 value for the inhibition of HDACs by WJ compounds and SAHA. Table S2. IC50 and CI values for the antiproliferative effects of gefitinib, WJ-26210-2 and SAHA alone or combination on the growth of NSCLC cells. Table S3. Effect of combination of gefitinib and WJ-26210-2 on RT2 Profiler PCR-array in gefitinib-resistant cells. Table S4. The DUSP1/TBP ratio of malignant pleura effusions of NSCLC patients.
Supplemental methods from Profiling of 149 Salivary Duct Carcinomas, Carcinoma Ex Pleomorphic Adenomas, and Adenocarcinomas, Not Otherwise Specified Reveals Actionable Genomic Alterations
Authors: Wang Kai , Russell Jeffery S. , McDermott Jessica D. , Elvin Julia A. , Khaira Depinder , Johnson Adrienne , Jennings Timothy A. , Ali Siraj M. , Murray Molly , Marshall Carrie , Oldham Dwight S. , Washburn Donna , Wong Stuart J. , Chmielecki Juliann , Yelensky Roman , Lipson Doron , Miller Vincent A. , Stephens Philip J. , Serracino Hilary S. , Ross Jeffrey S. , Bowles Daniel W.
Published: April 2023

Expanded methods for the study.
supplemental figure legend and Materials and Methods from Cyclin D1 Loss Distinguishes Prostatic Small-Cell Carcinoma from Most Prostatic Adenocarcinomas
Authors: Tsai Harrison , Morais Carlos L. , Alshalalfa Mohammed , Tan Hsueh-Li , Haddad Zaid , Hicks Jessica , Gupta Nilesh , Epstein Jonathan I. , Netto George J. , Isaacs William B. , Luo Jun , Mehra Rohit , Vessella Robert L. , Karnes R. Jeffrey , Schaeffer Edward M. , Davicioni Elai , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

supplemental figure legend and Materials and Methods
Supplementary Figures Legends from Interactions between Ibrutinib and Anti-CD20 Antibodies: Competing Effects on the Outcome of Combination Therapy
Authors: Skarzynski Martin , Niemann Carsten U. , Lee Yuh Shan , Martyr Sabrina , Maric Irina , Salem Dalia , Stetler-Stevenson Maryalice , Marti Gerald E. , Calvo Katherine R. , Yuan Constance , Valdez Janet , Soto Susan , Farooqui Mohammed Z.H. , Herman Sarah E.M. , Wiestner Adrian
Published: April 2023

Supplementary Figures Legends from Interactions between Ibrutinib and Anti-CD20 Antibodies: Competing Effects on the Outcome of Combination Therapy
Supplemental Table S4 from The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs
Authors: Boi Michela , Gaudio Eugenio , Bonetti Paola , Kwee Ivo , Bernasconi Elena , Tarantelli Chiara , Rinaldi Andrea , Testoni Monica , Cascione Luciano , Ponzoni Maurilio , Mensah Afua Adjeiwaa , Stathis Anastasios , Stussi Georg , Riveiro María Eugenia , Herait Patrice , Inghirami Giorgio , Cvitkovic Esteban , Zucca Emanuele , Bertoni Francesco
Published: April 2023

Supplemental Table S4: List of gene-sets associated with the sensitivity to OTX015.
Supplemental Table S2-3 from The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs
Authors: Boi Michela , Gaudio Eugenio , Bonetti Paola , Kwee Ivo , Bernasconi Elena , Tarantelli Chiara , Rinaldi Andrea , Testoni Monica , Cascione Luciano , Ponzoni Maurilio , Mensah Afua Adjeiwaa , Stathis Anastasios , Stussi Georg , Riveiro María Eugenia , Herait Patrice , Inghirami Giorgio , Cvitkovic Esteban , Zucca Emanuele , Bertoni Francesco
Published: April 2023

Supplemental Table S2-3. Supplemental Table S2: List of genes affected by OTX015 in DLBCL cell lines exposed to OTX015. Supplemental Table S3: gene-sets affected by OTX015 in DLBCL cell lines exposed to OTX015.
Supplemental Figure S6 from Targeting Acidity in Pancreatic Adenocarcinoma: Multispectral Optoacoustic Tomography Detects pH-Low Insertion Peptide Probes In Vivo
Authors: Kimbrough Charles W. , Khanal Anil , Zeiderman Matthew , Khanal Bigya R. , Burton Neal C. , McMasters Kelly M. , Vickers Selwyn M. , Grizzle William E. , McNally Lacey R.
Published: April 2023

Supplemental Figure S6: Dosimetry analysis demonstrates accumulation of V7-750 and K7-750 ex vivo in the liver, kidney, and pancreas tumor from planar fluorescent images.
Supplemental Figure Legend from Targeting Acidity in Pancreatic Adenocarcinoma: Multispectral Optoacoustic Tomography Detects pH-Low Insertion Peptide Probes In Vivo
Authors: Kimbrough Charles W. , Khanal Anil , Zeiderman Matthew , Khanal Bigya R. , Burton Neal C. , McMasters Kelly M. , Vickers Selwyn M. , Grizzle William E. , McNally Lacey R.
Published: April 2023

Supplemental Figure Legend from Targeting Acidity in Pancreatic Adenocarcinoma: Multispectral Optoacoustic Tomography Detects pH-Low Insertion Peptide Probes In Vivo
Supplementary Figure S4 from pVHL/HIF-Regulated CD70 Expression Is Associated with Infiltration of CD27+ Lymphocytes and Increased Serum Levels of Soluble CD27 in Clear Cell Renal Cell Carcinoma
Authors: Ruf Melanie , Mittmann Christiane , Nowicka Anna M. , Hartmann Arndt , Hermanns Thomas , Poyet Cédric , van den Broek Maries , Sulser Tullio , Moch Holger , Schraml Peter
Published: April 2023

A) Concentrations of sCD27 in supernatants of 786-O cocultured with different numbers of PBMCs determined by ELISA. B) Western blot of CD70 in 786-O and C) A498 treated with siRNA targeting CD70 (siCD70#1-4) or treated with siRNA control (siScr).
Supplementary Figure S2 from pVHL/HIF-Regulated CD70 Expression Is Associated with Infiltration of CD27+ Lymphocytes and Increased Serum Levels of Soluble CD27 in Clear Cell Renal Cell Carcinoma
Authors: Ruf Melanie , Mittmann Christiane , Nowicka Anna M. , Hartmann Arndt , Hermanns Thomas , Poyet Cédric , van den Broek Maries , Sulser Tullio , Moch Holger , Schraml Peter
Published: April 2023

A) Western blot of HIF1α, HIF2α and CD70 in SLR22 after silencing of HIF1α, HIF2α or both together for 48 h and 72 h. B) Western blot of HIF2α and CD70 in SLR24 and C) SLR22 after transient overexpression of HIF2α and D) in A498 and E) SLR22 after transient overexpression of HIF2α and its DNA binding mutant.
Supplementary Figure Legends from Direct Serum Assay for Cell-Free Bmi-1 mRNA and Its Potential Diagnostic and Prognostic Value for Colorectal Cancer
Authors: Zhang Xin , Yang Xiaoyun , Zhang Yanli , Liu Xinfeng , Zheng Guixi , Yang Yongmei , Wang Lili , Du Lutao , Wang Chuanxin
Published: April 2023

Supplementary Figure Legends
Supplementary Figure 2 from Selective Toxicity of Investigational Ixazomib for Human Leukemia Cells Expressing Mutant Cytoplasmic NPM1: Role of Reactive Oxygen Species
Authors: Garcia Jacqueline S. , Huang Min , Medeiros Bruno C. , Mitchell Beverly S.
Published: April 2023

Evaluation of induction of (A) reactive oxygen species, (B) hydrogen peroxide (H2O2), and of the N-acetylcysteine (NAC) pre-treatment effect on ixazomib-induced (C) superoxide and (D) apoptosis in OCI-AML3 cells.
Supplementary Figure 4 from SH3BGRL3 Protein as a Potential Prognostic Biomarker for Urothelial Carcinoma: A Novel Binding Partner of Epidermal Growth Factor Receptor
Authors: Chiang Cheng-Yao , Pan Chin-Chen , Chang Hong-Yi , Lai Ming-Derg , Tzai Tzong-Shin , Tsai Yuh-Shyan , Ling Pin , Liu Hsiao-Sheng , Lee Bi-Fang , Cheng Hong-Ling , Ho Chung-Liang , Chen Shu-Hui , Chow Nan-Haw
Published: April 2023

Involvement of SH3BGRL3 in nuclear translocation of beta-catenin, phosphorylation status of Raf-1 after EGF treatment and sensitivity of gefitinib
Supplementary Figure 1 from SH3BGRL3 Protein as a Potential Prognostic Biomarker for Urothelial Carcinoma: A Novel Binding Partner of Epidermal Growth Factor Receptor
Authors: Chiang Cheng-Yao , Pan Chin-Chen , Chang Hong-Yi , Lai Ming-Derg , Tzai Tzong-Shin , Tsai Yuh-Shyan , Ling Pin , Liu Hsiao-Sheng , Lee Bi-Fang , Cheng Hong-Ling , Ho Chung-Liang , Chen Shu-Hui , Chow Nan-Haw
Published: April 2023

Verification of protein expression by western blotting and bioinformatics analysis of SH3BGRL3 online
Figure Legends - Supplementary Data from Progression-Free and Overall Survival in ALK-Positive NSCLC Patients Treated with Sequential Crizotinib and Ceritinib
Authors: Gainor Justin F. , Tan Daniel S.W. , De Pas Tomasso , Solomon Benjamin J. , Ahmad Aziah , Lazzari Chiara , de Marinis Filippo , Spitaleri Gianluca , Schultz Katherine , Friboulet Luc , Yeap Beow Y. , Engelman Jeffrey A. , Shaw Alice T.
Published: April 2023

Figure Legends - Supplementary Data
Supplementary Tables S1-S15 from Tankyrase Inhibition Blocks Wnt/β-Catenin Pathway and Reverts Resistance to PI3K and AKT Inhibitors in the Treatment of Colorectal Cancer
Authors: Arqués Oriol , Chicote Irene , Puig Isabel , Tenbaum Stephan P. , Argilés Guillem , Dienstmann Rodrigo , Fernández Natalia , Caratù Ginevra , Matito Judit , Silberschmidt Daniel , Rodon Jordi , Landolfi Stefania , Prat Aleix , Espín Eloy , Charco Ramón , Nuciforo Paolo , Vivancos Ana , Shao Wenlin , Tabernero Josep , Palmer Héctor G.
Published: April 2023

Supplementary Tables S1-S15. Table S1. Genes and positions analyzed by amplicon sequencing. Table S2. Genes sequenced by Haloplex Target Enrichment System. Table S3. Antibodies. Table S4. Treatment-induced apoptosis in 10 primary patient-derived sphere cell cultures. Table S5. Genotype of patient-derived colorectal cancer models. Table S6. Exome sequencing of colorectal cancer patient-derived models. Table S7. Genes regulated by NVP-TNKS656 in PDX-P2. Table S8. Genes regulated by NVP-TNKS656 in PDX-P30. Table S9. Genes regulated by NVP-TNKS656 in PDX-P5. Table S10. Intestinal β-catenin/TCF signature in human CRC. Table S11. Genes regulated by β-catenin/FOXO3A signaling in human CRC. Table S12. Molecular profiling of 130 CRC tumors. Table S13. Clinicopathological data of 40 CRC patients treated with PI3K/AKT/mTOR inhibitors and their corresponding baseline tumor samples analyzed for mutations and nuclear β-catenin content. Table S14. Nuclear β-catenin content but not relevant mutations or TNM stage determine response of CRC patients to PI3K/AKT/mTOR inhibitors. Table S15. Multivariate analysis of baseline tumors from patients treated with PI3K/AKT/mTOR inhibitors.
Data Supplement from Activating FGFR2–RAS–BRAF Mutations in Ameloblastoma
Authors: Brown Noah A. , Rolland Delphine , McHugh Jonathan B. , Weigelin Helmut C. , Zhao Lili , Lim Megan S. , Elenitoba-Johnson Kojo S.J. , Betz Bryan L.
Published: April 2023

Supplemental Table S1. Ameloblastoma genotypic and clinicopathologic data.
Data Supplement from Activating FGFR2–RAS–BRAF Mutations in Ameloblastoma
Authors: Brown Noah A. , Rolland Delphine , McHugh Jonathan B. , Weigelin Helmut C. , Zhao Lili , Lim Megan S. , Elenitoba-Johnson Kojo S.J. , Betz Bryan L.
Published: April 2023

Supplemental Methods. Immunohistochemistry staining procedure
Supplementary Figure S2 from DNMT1–MicroRNA126 Epigenetic Circuit Contributes to Esophageal Squamous Cell Carcinoma Growth via ADAM9–EGFR–AKT Signaling
Authors: Liu Ronghua , Gu Jie , Jiang Pei , Zheng Yijie , Liu Xiaoming , Jiang Xuechao , Huang Enyu , Xiong Shudao , Xu Fengkai , Liu Guangwei , Ge Di , Chu Yiwei
Published: April 2023

Supplementary Figure S2. MiR-126 promotes ECa-109 and KYSE-510 cell apoptosis, but has no effect on cell cycle.
Supplementary Table (S4) from HAGE in Triple-Negative Breast Cancer Is a Novel Prognostic, Predictive, and Actionable Biomarker: A Transcriptomic and Protein Expression Analysis
Authors: Abdel-Fatah Tarek M.A. , McArdle Stephanie E.B. , Agarwal Devika , Moseley Paul M. , Green Andrew R. , Ball Graham R. , Pockley A. Graham , Ellis Ian O. , Rees Robert C. , Chan Stephen Y.T.
Published: April 2023

Supplementary Table (S4). Antigens, primary antibodies, clone, source, optimal dilution and scoring system used for each immunohistochemical marker
Supplementary Figure S1 from DNMT1–MicroRNA126 Epigenetic Circuit Contributes to Esophageal Squamous Cell Carcinoma Growth via ADAM9–EGFR–AKT Signaling
Authors: Liu Ronghua , Gu Jie , Jiang Pei , Zheng Yijie , Liu Xiaoming , Jiang Xuechao , Huang Enyu , Xiong Shudao , Xu Fengkai , Liu Guangwei , Ge Di , Chu Yiwei
Published: April 2023

Supplementary Figure S1. Overexpression of DNMT1 suppresses ESCC cell proliferation and migration.
Supplementary Table (S2) from HAGE in Triple-Negative Breast Cancer Is a Novel Prognostic, Predictive, and Actionable Biomarker: A Transcriptomic and Protein Expression Analysis
Authors: Abdel-Fatah Tarek M.A. , McArdle Stephanie E.B. , Agarwal Devika , Moseley Paul M. , Green Andrew R. , Ball Graham R. , Pockley A. Graham , Ellis Ian O. , Rees Robert C. , Chan Stephen Y.T.
Published: April 2023

Supplementary Table (S2). Clinicopathological characteristics of triple negative breast cancer in the METABRIC cohort
Supplemental Figure 3 from The MET Inhibitor AZD6094 (Savolitinib, HMPL-504) Induces Regression in Papillary Renal Cell Carcinoma Patient–Derived Xenograft Models
Authors: Schuller Alwin G. , Barry Evan R. , Jones Rhys D.O. , Henry Ryan E. , Frigault Melanie M. , Beran Garry , Linsenmayer David , Hattersley Maureen , Smith Aaron , Wilson Joanne , Cairo Stefano , Déas Olivier , Nicolle Delphine , Adam Ammar , Zinda Michael , Reimer Corinne , Fawell Stephen E. , Clark Edwin A. , D'Cruz Celina M.
Published: April 2023

Supplemental Figure 3. HGF and HGFAC expression in RCC-43b and RCC-47
Supplementary Table 8 from Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer
Authors: Sanz-Pamplona Rebeca , Lopez-Doriga Adriana , Paré-Brunet Laia , Lázaro Kira , Bellido Fernando , Alonso M. Henar , Aussó Susanna , Guinó Elisabet , Beltrán Sergi , Castro-Giner Francesc , Gut Marta , Sanjuan Xavier , Closa Adria , Cordero David , Morón-Duran Francisco D. , Soriano Antonio , Salazar Ramón , Valle Laura , Moreno Victor
Published: April 2023

Mutations found in AMER1 gene across different datasets
Supplementary Table 7 from Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer
Authors: Sanz-Pamplona Rebeca , Lopez-Doriga Adriana , Paré-Brunet Laia , Lázaro Kira , Bellido Fernando , Alonso M. Henar , Aussó Susanna , Guinó Elisabet , Beltrán Sergi , Castro-Giner Francesc , Gut Marta , Sanjuan Xavier , Closa Adria , Cordero David , Morón-Duran Francisco D. , Soriano Antonio , Salazar Ramón , Valle Laura , Moreno Victor
Published: April 2023

List of statistically significant functions in which mutated genes are implicated.
Supplementary Table 6 from Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer
Authors: Sanz-Pamplona Rebeca , Lopez-Doriga Adriana , Paré-Brunet Laia , Lázaro Kira , Bellido Fernando , Alonso M. Henar , Aussó Susanna , Guinó Elisabet , Beltrán Sergi , Castro-Giner Francesc , Gut Marta , Sanjuan Xavier , Closa Adria , Cordero David , Morón-Duran Francisco D. , Soriano Antonio , Salazar Ramón , Valle Laura , Moreno Victor
Published: April 2023

List of recurrent mutated genes ranked by MutSig tool.
Supplementary Table 4 from Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer
Authors: Sanz-Pamplona Rebeca , Lopez-Doriga Adriana , Paré-Brunet Laia , Lázaro Kira , Bellido Fernando , Alonso M. Henar , Aussó Susanna , Guinó Elisabet , Beltrán Sergi , Castro-Giner Francesc , Gut Marta , Sanjuan Xavier , Closa Adria , Cordero David , Morón-Duran Francisco D. , Soriano Antonio , Salazar Ramón , Valle Laura , Moreno Victor
Published: April 2023

List of recurrent mutations
Supplementary Table 1 from Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer
Authors: Sanz-Pamplona Rebeca , Lopez-Doriga Adriana , Paré-Brunet Laia , Lázaro Kira , Bellido Fernando , Alonso M. Henar , Aussó Susanna , Guinó Elisabet , Beltrán Sergi , Castro-Giner Francesc , Gut Marta , Sanjuan Xavier , Closa Adria , Cordero David , Morón-Duran Francisco D. , Soriano Antonio , Salazar Ramón , Valle Laura , Moreno Victor
Published: April 2023

Baseline characteristics of CRC patients (discovery dataset, Sanger validation dataset and TCGA datasets).
Supplementary Materials and Methods from The Opposing Function of STAT3 as an Oncoprotein and Tumor Suppressor Is Dictated by the Expression Status of STAT3β in Esophageal Squamous Cell Carcinoma
Authors: Zhang Hai-Feng , Chen Ye , Wu Chengsheng , Wu Zhi-Yong , Tweardy David J. , Alshareef Abdulraheem , Liao Lian-Di , Xue Yu-Jie , Wu Jian-Yi , Chen Bo , Xu Xiu-E , Gopal Keshav , Gupta Nidhi , Li En-Min , Xu Li-Yan , Lai Raymond
Published: April 2023

Supplementary Materials and Methods
Supplementary Figure S1-5 from The Opposing Function of STAT3 as an Oncoprotein and Tumor Suppressor Is Dictated by the Expression Status of STAT3β in Esophageal Squamous Cell Carcinoma
Authors: Zhang Hai-Feng , Chen Ye , Wu Chengsheng , Wu Zhi-Yong , Tweardy David J. , Alshareef Abdulraheem , Liao Lian-Di , Xue Yu-Jie , Wu Jian-Yi , Chen Bo , Xu Xiu-E , Gopal Keshav , Gupta Nidhi , Li En-Min , Xu Li-Yan , Lai Raymond
Published: April 2023

Supplementary Figure S1. STAT3β suppresses ESCC chemoresistance in vitro. Supplementary Figure S2. STAT3β suppresses cancer stem-like cells in ESCC. Supplementary Figure S3. STAT3β antagonizes the oncogenic function of STAT3α in ESCC cells. Supplementary Figure S4. The complete Western blot data showing the expression of phospho-STAT3α/βTyr705 (pSTAT3α/β) and STAT3α/β in 94 cases of ESCC samples and adjacent non-tumorous tissues. Supplementary Figure S5. STAT3β suppresses STAT3 transcription activity in KYSE150 cells.
Supplementary figure 2 from The BRAF and MEK Inhibitors Dabrafenib and Trametinib: Effects on Immune Function and in Combination with Immunomodulatory Antibodies Targeting PD-1, PD-L1, and CTLA-4
Authors: Liu Li , Mayes Patrick A. , Eastman Stephen , Shi Hong , Yadavilli Sapna , Zhang Tianqian , Yang Jingsong , Seestaller-Wehr Laura , Zhang Shu-Yun , Hopson Chris , Tsvetkov Lyuben , Jing Junping , Zhang Shu , Smothers James , Hoos Axel
Published: April 2023

Supplementary figure 2. Tumor gene expression changes measured by RT-PCR from mice treated with trametinib (T) in combination with the immunomodulator-targeting PD1 in the CT26 murine syngeneic model.
Supplementary Methods from Safety, Pharmacokinetics, and Pharmacodynamics of a Humanized Anti-Semaphorin 4D Antibody, in a First-In-Human Study of Patients with Advanced Solid Tumors
Authors: Patnaik Amita , Weiss Glen J. , Leonard John E. , Rasco Drew Warren , Sachdev Jasgit C. , Fisher Terrence L. , Winter Laurie A. , Reilly Christine , Parker Robert B. , Mutz Danielle , Blaydorn Lisa , Tolcher Anthony W. , Zauderer Maurice , Ramanathan Ramesh K.
Published: April 2023

This Supplementary Methods section provides details for assays that allowed elucidation of the pharmacokinetic and pharmacodynamic results described in the Results and Discussion sections of the article. These supplemental methods descriptions are to be published with the manuscript
Supplementary Fig. S1. Total Soluble SEMA4D Levels as a Function of Weekly VX15/2503 Administration from Safety, Pharmacokinetics, and Pharmacodynamics of a Humanized Anti-Semaphorin 4D Antibody, in a First-In-Human Study of Patients with Advanced Solid Tumors
Authors: Patnaik Amita , Weiss Glen J. , Leonard John E. , Rasco Drew Warren , Sachdev Jasgit C. , Fisher Terrence L. , Winter Laurie A. , Reilly Christine , Parker Robert B. , Mutz Danielle , Blaydorn Lisa , Tolcher Anthony W. , Zauderer Maurice , Ramanathan Ramesh K.
Published: April 2023

Total sSEMA4D levels for subjects in the 9 mg/kg dose cohort were measured in sera by ELISA and the data plotted versus study day. The data shown are representative of sSEMA4D results obtained with samples from subjects in other dose cohorts completing at least cycle 1. These data are intended for publication with the manuscript.
Supplementary Figure S7 from Gas6/AXL Signaling Regulates Self-Renewal of Chronic Myelogenous Leukemia Stem Cells by Stabilizing β-Catenin
Authors: Jin Yanli , Nie Danian , Li Juan , Du Xin , Lu Yuhong , Li Yangqiu , Liu Chang , Zhou Jingfeng , Pan Jingxuan
Published: April 2023

Gas6/AXL paracrine regulation loop elevates self-renewal of human CML CD34+ cells.
Supplementary Table S4 from Mutational Analysis of Gene Fusions Predicts Novel MHC Class I–Restricted T-Cell Epitopes and Immune Signatures in a Subset of Prostate Cancer
Authors: Kalina Jennifer L. , Neilson David S. , Lin Yen-Yi , Hamilton Phineas T. , Comber Alexandra P. , Loy Emma M.H. , Sahinalp S. Cenk , Collins Colin C. , Hach Faraz , Lum Julian J.
Published: April 2023

List of patient epitopes
Supplementary Figure S4 from Gas6/AXL Signaling Regulates Self-Renewal of Chronic Myelogenous Leukemia Stem Cells by Stabilizing β-Catenin
Authors: Jin Yanli , Nie Danian , Li Juan , Du Xin , Lu Yuhong , Li Yangqiu , Liu Chang , Zhou Jingfeng , Pan Jingxuan
Published: April 2023

Pharmacological inhibition of AXL activity has minimal effect on survival and self-renewal of human NBM CD34+ cells.
Supplemental Figure Legends from Circulating Tumor DNA as an Early Indicator of Response to T-cell Transfer Immunotherapy in Metastatic Melanoma
Authors: Xi Liqiang , Pham Trinh Hoc-Tran , Payabyab Eden C. , Sherry Richard M. , Rosenberg Steven A. , Raffeld Mark
Published: April 2023

Fig. S1. castPCR{trade mark, serif} design, analytical sensitivity and specificity, and cfDNA measurements Fig. S2. Mutational analysis of tumor specimens from 93 NCI TIL patients Fig. S3. Cases excluded from pattern analysis
supplementary file 3 from Multilayered Omics-Based Analysis of a Head and Neck Cancer Model of Cisplatin Resistance Reveals Intratumoral Heterogeneity and Treatment-Induced Clonal Selection
Authors: Niehr Franziska , Eder Theresa , Pilz Tanja , Konschak Robert , Treue Denise , Klauschen Frederick , Bockmayr Michael , Türkmen Seval , Jöhrens Korinna , Budach Volker , Tinhofer Ingeborg
Published: April 2023

Differentially expressed phosphopeptides associated with a CDDP-resistant phenotype
Supplementary Figure S1-S6 from Therapeutic Activity of Anti-AXL Antibody against Triple-Negative Breast Cancer Patient-Derived Xenografts and Metastasis
Authors: Leconet Wilhem , Chentouf Myriam , du Manoir Stanislas , Chevalier Clément , Sirvent Audrey , Aït-Arsa Imade , Busson Muriel , Jarlier Marta , Radosevic-Robin Nina , Theillet Charles , Chalbos Dany , Pasquet Jean-Max , Pèlegrin André , Larbouret Christel , Robert Bruno
Published: April 2023

Supplementary Figure 1. AXL, MER and TYRO-3 expression in Triple Negative Breast Cancer (TNBC) cell lines and PDXs by Western blot analysis. Supplementary Figure 2. AXL mRNA expression in a large dataset of breast cancer tumors. Supplementary Figure 3. The 100 genes most correlated with AXL expression in 254 basal-like breast cancers. Supplementary Figure 4. Effect of the anti-AXL monoclonal antibody 20G7-D9 on matrix degradation by breast cancer cell lines. Supplementary Figure 5. GAS6 regulates expression of EMT markers in TNBC - Western Blot quantifications. Supplementary Figure 6. E-cadherin expression in TNBC cell lines
Supplementary Table S2: Clinical trials of ribociclib from Ribociclib (LEE011): Mechanism of Action and Clinical Impact of This Selective Cyclin-Dependent Kinase 4/6 Inhibitor in Various Solid Tumors
Authors: Tripathy Debu , Bardia Aditya , Sellers William R.
Published: April 2023

Ongoing and planned clinical trials of ribociclib.
Supplemental Table S3: Recurrent mutations and segmental copy losses or gains identified in 39 DAWTs from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
Authors: Ooms Ariadne H.A.G. , Gadd Samantha , Gerhard Daniela S. , Smith Malcolm A. , Guidry Auvil Jaime M. , Meerzaman Daoud , Chen Qing-Rong , Hsu Chih Hao , Yan Chunhua , Nguyen Cu , Hu Ying , Ma Yussanne , Zong Zusheng , Mungall Andrew J. , Moore Richard A. , Marra Marco A. , Huff Vicki , Dome Jeffrey S. , Chi Yueh-Yun , Tian Jing , Geller James I. , Mullighan Charles G. , Ma Jing , Wheeler David A. , Hampton Oliver A. , Walz Amy L. , van den Heuvel-Eibrink Marry M. , de Krijger Ronald R. , Ross Nicole , Gastier-Foster Julie M. , Perlman Elizabeth J.
Published: April 2023

This table shows the recurrent mutations that were identified as well as the gains/losses at previously reported chromosomal segments in the 39 DAWTs that were selected for in-depth analysis
Supplemental Table S2: Clinicopathological features of 118 DAWTs from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
Authors: Ooms Ariadne H.A.G. , Gadd Samantha , Gerhard Daniela S. , Smith Malcolm A. , Guidry Auvil Jaime M. , Meerzaman Daoud , Chen Qing-Rong , Hsu Chih Hao , Yan Chunhua , Nguyen Cu , Hu Ying , Ma Yussanne , Zong Zusheng , Mungall Andrew J. , Moore Richard A. , Marra Marco A. , Huff Vicki , Dome Jeffrey S. , Chi Yueh-Yun , Tian Jing , Geller James I. , Mullighan Charles G. , Ma Jing , Wheeler David A. , Hampton Oliver A. , Walz Amy L. , van den Heuvel-Eibrink Marry M. , de Krijger Ronald R. , Ross Nicole , Gastier-Foster Julie M. , Perlman Elizabeth J.
Published: April 2023

This table shows the clinical and pathological characteristics of all 118 DAWTs
Supplementary materials and methods untracked from A Synthetic Cell-Penetrating Dominant-Negative ATF5 Peptide Exerts Anticancer Activity against a Broad Spectrum of Treatment-Resistant Cancers
Authors: Karpel-Massler Georg , Horst Basil A. , Shu Chang , Chau Lily , Tsujiuchi Takashi , Bruce Jeffrey N. , Canoll Peter , Greene Lloyd A. , Angelastro James M. , Siegelin Markus D.
Published: April 2023

Supplementary materials and methods untracked
Supplementary Figure S4 from A Complex Network of Tumor Microenvironment in Human High-Grade Serous Ovarian Cancer
Authors: Kreuzinger Caroline , Geroldinger Angelika , Smeets Dominiek , Braicu Elena Ioana , Sehouli Jalid , Koller Julia , Wolf Andrea , Darb-Esfahani Silvia , Joehrens Korinna , Vergote Ignace , Vanderstichele Adriaan , Boeckx Bram , Lambrechts Diether , Gabra Hani , Wisman G. Bea A. , Trillsch Fabian , Heinze Georg , Horvat Reinhard , Polterauer Stephan , Berns Els , Theillet Charles , Cacsire Castillo-Tong Dan
Published: April 2023

Supervised clustering of primary HGSOC (n=80) from the data set of Patch et al using the 126 immune related genes
Supplementary figures 1-15 from A Synthetic Cell-Penetrating Dominant-Negative ATF5 Peptide Exerts Anticancer Activity against a Broad Spectrum of Treatment-Resistant Cancers
Authors: Karpel-Massler Georg , Horst Basil A. , Shu Chang , Chau Lily , Tsujiuchi Takashi , Bruce Jeffrey N. , Canoll Peter , Greene Lloyd A. , Angelastro James M. , Siegelin Markus D.
Published: April 2023

Suppl. fig. 1: Effect of CP-d/n-ATF5-S1 on ATF5 expression and stability Suppl. fig. 2: Effect of CP-d/n-ATF5-S1 on ASNS mRNA expression Suppl. fig. 3: Effect of CP-d/n-ATF5-S1 on cell viability in HL-60 cells Suppl. fig. 4: Pro-apoptotic activity of CP-d/n-ATF5-S1 in SF188 and GBM12 cells Suppl. fig. 5: Effect of CP-d/n-ATF5-S1 in HCT116 colorectal cancer Suppl. fig. 6: Effect of pan-caspase inhibition on CP-d/n-ATF5-S1 treatment Suppl. fig. 7: Effect of CP-d/n-ATF5-S1 on Bcl-2 family and Usp9X/Bag3 protein expression in A375 and PC3 Suppl. fig. 8: Effect of pan-caspase inhibition on CP-d/n-ATF5-S1-mediated down-regulation of Usp9X Suppl. fig. 9: Effect of Usp9X knock-down on apoptosis in LN229 Suppl. fig. 10: Isobologram for CP-d/n-ATF5-S1 and ABT263 Suppl. fig. 11: Effect of CP-d/n-ATF5-S1 and ABT263 on GBM12 cells Suppl. fig. 12: Knock-down of Mcl-1 sensitizes for ABT263-mediated apoptosis Suppl. fig. 13: Effects of CP-d/n-ATF5-S1 on U87MG xenograft model Suppl. fig. 14: Effects of CP-d/n-ATF5-S1 on PANC-1 and MDA-MB-231 xenograft model Suppl. fig. 15: Effect of CP-d/n-ATF5-S1 on organ toxicity
Supplementary Figure S1 from A Complex Network of Tumor Microenvironment in Human High-Grade Serous Ovarian Cancer
Authors: Kreuzinger Caroline , Geroldinger Angelika , Smeets Dominiek , Braicu Elena Ioana , Sehouli Jalid , Koller Julia , Wolf Andrea , Darb-Esfahani Silvia , Joehrens Korinna , Vergote Ignace , Vanderstichele Adriaan , Boeckx Bram , Lambrechts Diether , Gabra Hani , Wisman G. Bea A. , Trillsch Fabian , Heinze Georg , Horvat Reinhard , Polterauer Stephan , Berns Els , Theillet Charles , Cacsire Castillo-Tong Dan
Published: April 2023

Supervised clustering of primary and recurrent tumors
Supplemenatry figure 1 from Genomic Characterization of Vulvar (Pre)cancers Identifies Distinct Molecular Subtypes with Prognostic Significance
Authors: Nooij Linda S. , ter Haar Natalja T. , Ruano Dina , Rakislova Natalia , van Wezel Tom , Smit Vincent T.H.B.M. , Trimbos Baptist J.B.M.Z. , Ordi Jaume , van Poelgeest Mariette I.E. , Bosse Tjalling
Published: April 2023

Heatmap precursor and adjacent cancer
Figure S3 from Genomic Characterization of Vulvar (Pre)cancers Identifies Distinct Molecular Subtypes with Prognostic Significance
Authors: Nooij Linda S. , ter Haar Natalja T. , Ruano Dina , Rakislova Natalia , van Wezel Tom , Smit Vincent T.H.B.M. , Trimbos Baptist J.B.M.Z. , Ordi Jaume , van Poelgeest Mariette I.E. , Bosse Tjalling
Published: April 2023

Figure S3: Concordance p53 IHC and sequencing
Supplemental Table and Figures from Suppression of Lymphocyte Functions by Plasma Exosomes Correlates with Disease Activity in Patients with Head and Neck Cancer
Authors: Ludwig Sonja , Floros Theofanis , Theodoraki Marie-Nicole , Hong Chang-Sook , Jackson Edwin K. , Lang Stephan , Whiteside Theresa L.
Published: April 2023

'Supp. Table 1 shows clinicopathological characteristics of patients. Supp. Fig. 1 shows Densitometry measurements. Supp. Fig. 2 shows No correlation between FasL expression & Annexin V binding.'
Supplemental legend from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome
Authors: Derks Jules L. , Leblay Noémie , Thunnissen Erik , van Suylen Robert Jan , den Bakker Michael , Groen Harry J.M. , Smit Egbert F. , Damhuis Ronald , van den Broek Esther C. , Charbrier Amélie , Foll Matthieu , McKay James D. , Fernandez-Cuesta Lynnette , Speel Ernst-Jan M. , Dingemans Anne-Marie C.
Published: April 2023

Supplemental legend
Supplementary Figure Legends from Phase Ib Study of Immune Biomarker Modulation with Neoadjuvant Cetuximab and TLR8 Stimulation in Head and Neck Cancer to Overcome Suppressive Myeloid Signals
Authors: Shayan Gulidanna , Kansy Benjamin A. , Gibson Sandra P. , Srivastava Raghvendra M. , Bryan James Kyle , Bauman Julie E. , Ohr James , Kim Seungwon , Duvvuri Umamaheswar , Clump David A. , Heron Dwight E. , Johnson Jonas T. , Hershberg Robert M. , Ferris Robert L.
Published: April 2023

Supplementary figure S1 & supplementary table S1 legends
Supplementary Table S2 from Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma
Authors: Dong Zhong-Yi , Zhong Wen-Zhao , Zhang Xu-Chao , Su Jian , Xie Zhi , Liu Si-Yang , Tu Hai-Yan , Chen Hua-Jun , Sun Yue-Li , Zhou Qing , Yang Jin-Ji , Yang Xue-Ning , Lin Jia-Xin , Yan Hong-Hong , Zhai Hao-Ran , Yan Li-Xu , Liao Ri-Qiang , Wu Si-Pei , Wu Yi-Long
Published: April 2023

Clinicopathologic and molecular features of immunotherapeutic patients in MSKCC and GLCI cohorts.
Table S5 from Chemogenomic Landscape of RUNX1-mutated AML Reveals Importance of RUNX1 Allele Dosage in Genetics and Glucocorticoid Sensitivity
Authors: Simon Laura , Lavallée Vincent-Philippe , Bordeleau Marie-Eve , Krosl Jana , Baccelli Irène , Boucher Geneviève , Lehnertz Bernhard , Chagraoui Jalila , MacRae Tara , Ruel Réjean , Chantigny Yves , Lemieux Sébastien , Marinier Anne , Hébert Josée , Sauvageau Guy
Published: April 2023

Genes and positions investigated using km approach.
Supplementary Figure S1 from Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma
Authors: Dong Zhong-Yi , Zhong Wen-Zhao , Zhang Xu-Chao , Su Jian , Xie Zhi , Liu Si-Yang , Tu Hai-Yan , Chen Hua-Jun , Sun Yue-Li , Zhou Qing , Yang Jin-Ji , Yang Xue-Ning , Lin Jia-Xin , Yan Hong-Hong , Zhai Hao-Ran , Yan Li-Xu , Liao Ri-Qiang , Wu Si-Pei , Wu Yi-Long
Published: April 2023

(a) Quantitative analysis of PD-L1 mRNA and protein expression compared TP53 mutation with TP53 wild type tumor. (b) Quantitative analysis of PD-L1 mRNA and protein expression compared KRAS mutation with KRAS wild type tumor. (c) Immunohistochemistry (IHC) analysis of PD-L1 expression (strong: {greater than or equal to}50% vs. weak: 1-49% vs. negative: <1%) based on TP53 mutation status in a cohort of 93 lung adenocarcinoma. NS, no significant; mut, mutation; wt, wild type; *** P < 0.001, * P < 0.05
Table S3 from Chemogenomic Landscape of RUNX1-mutated AML Reveals Importance of RUNX1 Allele Dosage in Genetics and Glucocorticoid Sensitivity
Authors: Simon Laura , Lavallée Vincent-Philippe , Bordeleau Marie-Eve , Krosl Jana , Baccelli Irène , Boucher Geneviève , Lehnertz Bernhard , Chagraoui Jalila , MacRae Tara , Ruel Réjean , Chantigny Yves , Lemieux Sébastien , Marinier Anne , Hébert Josée , Sauvageau Guy
Published: April 2023

Additional mutations in RUNX1mut specimens. VAF: variant allele frequency, ITD: internal tandem duplication, PTD: partial tandem duplication.
Table S1 from Chemogenomic Landscape of RUNX1-mutated AML Reveals Importance of RUNX1 Allele Dosage in Genetics and Glucocorticoid Sensitivity
Authors: Simon Laura , Lavallée Vincent-Philippe , Bordeleau Marie-Eve , Krosl Jana , Baccelli Irène , Boucher Geneviève , Lehnertz Bernhard , Chagraoui Jalila , MacRae Tara , Ruel Réjean , Chantigny Yves , Lemieux Sébastien , Marinier Anne , Hébert Josée , Sauvageau Guy
Published: April 2023

List of 97 gene mutations and fusions systematically included in mutational analysis.
Supplementary Figure 1 from An miRNA–DNMT1 Axis Is Involved in Azacitidine Resistance and Predicts Survival in Higher-Risk Myelodysplastic Syndrome and Low Blast Count Acute Myeloid Leukemia
Authors: Solly Françoise , Koering Catherine , Mohamed Aminetou Mint , Maucort-Boulch Delphine , Robert Guillaume , Auberger Patrick , Flandrin-Gresta Pascale , Adès Lionel , Fenaux Pierre , Kosmider Olivier , Tavernier-Tardy Emmanuelle , Cornillon Jérôme , Guyotat Denis , Campos Lydia , Mortreux Franck , Wattel Eric
Published: April 2023

Pathway enrichment analysis. For ontology analysis, gene lists were analyzed using DAVID software (KEGG pathways). The complete set of genes featured in the microarrays was used as the reference background. The three numbers on the right represent the number of deregulated mRNAs, the overall number of genes within the pathway and the p value, respectively. Data are presented for genes targeted by at least one of the 7 miRNAs and that were found repressed in SKM1 AZA resistant cells.
Supplementary Figure S5 from Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer
Authors: Guedes Liana B. , Morais Carlos L. , Almutairi Fawaz , Haffner Michael C. , Zheng Qizhi , Isaacs John T. , Antonarakis Emmanuel S. , Lu Changxue , Tsai Harrison , Luo Jun , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

Correlation of AR protein by IHC and AR-E1 RISH labeling in high grade primary tumors and benign prostate epithelium sampled on needle biopsy (Figure 5). (A) AR IHC quantified as brown/(brown+blue) pixels vs AR-E1 quantification shows a weak but significant correlation among primary tumors. (B) Quantified AR-IHC from (A) is higher in tumor compared to paired benign epithelium. (C) AR-IHC quantified as a modified H-score (see Methods) shows an insignificant correlation with quantified AR-E1 in the same samples. (D) There is a significant trend towards increased AR IHC H-scores in tumor compared to paired benign epithelium.
Figure S6 from Degalactotigonin, a Natural Compound from Solanum nigrum L., Inhibits Growth and Metastasis of Osteosarcoma through GSK3β Inactivation–Mediated Repression of the Hedgehog/Gli1 Pathway
Authors: Zhao Zhiqiang , Jia Qiang , Wu Man-Si , Xie Xianbiao , Wang Yongqian , Song Guohui , Zou Chang-Ye , Tang Qinglian , Lu Jinchang , Huang Gang , Wang Jin , Lin De-Chen , Koeffler H. Phillip , Yin Jun-Qiang , Shen Jingnan
Published: April 2023

The mRNA changes in Gli1 target genes.
Supplementary Figure S3 from Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer
Authors: Guedes Liana B. , Morais Carlos L. , Almutairi Fawaz , Haffner Michael C. , Zheng Qizhi , Isaacs John T. , Antonarakis Emmanuel S. , Lu Changxue , Tsai Harrison , Luo Jun , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

Correlation of relative quantified AR-E1 and AR-CE3 RISH labeling with one another and with relative AR-FL and AR-V7 expression by RT-PCR in metastases from Figure 3. AR-E1 by RISH and AR-V7 by RT-PCR are significantly correlated (A), as are AR-FL vs AR-V7 by RT-PCR (B) and AR-E1 vs AR-CE3 by RISH (C).
Supplementary Figure S2 from Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer
Authors: Guedes Liana B. , Morais Carlos L. , Almutairi Fawaz , Haffner Michael C. , Zheng Qizhi , Isaacs John T. , Antonarakis Emmanuel S. , Lu Changxue , Tsai Harrison , Luo Jun , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

Supplementary Figure S2: AR-E1 RISH signals show greater nuclear localization compared to other genes and are decreased with RNase pre-treatment of slides prior to RISH assay. (A) AR-E1 RISH signal shows dramatic nuclear localization (arrows) with some cytoplasmic signal (arrowheads) across benign and malignant primary prostate tumors, including some that have been treated with androgen deprivation therapy. In contrast, other genes such as positive control gene PPIB (cyclophilin B) show only cytoplasmic signal. (B) Both intranuclear and cytoplasmic signals are markedly decreased and nearly undetectable after RNase, confirming both signals correspond to RNA. (C) qRT-PCR analysis of LNCaP and LAPC4 cells performed on nuclear and cytosolic fractions of RNA (accompanying immunoblot confirms appropriate laminin and GAPDH enrichment in each fraction) reveals abundance of unspliced AR RNA in the nuclear compartment of both cell lines, while spliced AR message is present in both compartments.
Supplemental Table S3 from GTL001, A Therapeutic Vaccine for Women Infected with Human Papillomavirus 16 or 18 and Normal Cervical Cytology: Results of a Phase I Clinical Trial
Authors: Van Damme Pierre , Bouillette-Marussig Myriam , Hens Annick , De Coster Ilse , Depuydt Christophe , Goubier Anne , Van Tendeloo Viggo , Cools Nathalie , Goossens Herman , Hercend Thierry , Timmerman Benedikt , Bissery Marie-Christine
Published: April 2023

ELISpot response rates
Figure S1 from Degalactotigonin, a Natural Compound from Solanum nigrum L., Inhibits Growth and Metastasis of Osteosarcoma through GSK3β Inactivation–Mediated Repression of the Hedgehog/Gli1 Pathway
Authors: Zhao Zhiqiang , Jia Qiang , Wu Man-Si , Xie Xianbiao , Wang Yongqian , Song Guohui , Zou Chang-Ye , Tang Qinglian , Lu Jinchang , Huang Gang , Wang Jin , Lin De-Chen , Koeffler H. Phillip , Yin Jun-Qiang , Shen Jingnan
Published: April 2023

The IC50 of DGT in hfob1.19 and MSC1#, MSC2# cells measured by MTT assay.
Supplementary Methods, Tables, and Figure Legends from Transmembrane and Coiled-Coil Domain 1 Impairs the AKT Signaling Pathway in Urinary Bladder Urothelial Carcinoma: A Characterization of a Tumor Suppressor
Authors: Li Chien-Feng , Wu Wen-Ren , Chan Ti-Chun , Wang Yu-Hui , Chen Lih-Ren , Wu Wen-Jeng , Yeh Bi-Wen , Liang Shih-Shin , Shiue Yow-Ling
Published: April 2023

The file includes Supplementary Methods, Tables, and Figure Legends. Table S1. TMCO1 is identified as a differentially expressed transcript with molecular function of growth factor activity (GO:0008083) and low expression levels shows positive correlations to cancer invasiveness and metastasis in the transcriptome of urothelial carcinoma of urinary bladder (GSE31684) Table S2. Correlations between the TMCO1 protein level and important clinicopathological parameters in urothelial carcinomas Table S3. TMCO1 promoter methylation detected by pyrosequencing in urothelial cancer cells and tissues
Supplementary Figure Legends from PD-L1 Expression and Immune Escape in Melanoma Resistance to MAPK Inhibitors
Authors: Kakavand Hojabr , Rawson Robert V. , Pupo Gulietta M. , Yang Jean Y. H. , Menzies Alexander M. , Carlino Matteo S. , Kefford Richard F. , Howle Julie R. , Saw Robyn P.M. , Thompson John F. , Wilmott James S. , Long Georgina V. , Scolyer Richard A. , Rizos Helen
Published: April 2023

Supplementary Figure Legends
Figure S1 from PD-L1 Expression and Immune Escape in Melanoma Resistance to MAPK Inhibitors
Authors: Kakavand Hojabr , Rawson Robert V. , Pupo Gulietta M. , Yang Jean Y. H. , Menzies Alexander M. , Carlino Matteo S. , Kefford Richard F. , Howle Julie R. , Saw Robyn P.M. , Thompson John F. , Wilmott James S. , Long Georgina V. , Scolyer Richard A. , Rizos Helen
Published: April 2023

Heat map of immunohistochemical (IHC) expression of tumor PD-L1, HLA-A and HLA-DPB1 (top panel) compared to the RNA expression for the HLA genes (bottom panel). A. Comparison of protein and RNA expression of patients' PRE tumors (n=17). B. Comparison of the change (Î") in protein expression from PRE to EDT to the change in RNA expression (n=8). C. Comparison of the change (Î") in protein expression from PRE to PROG to the change in RNA expression (n=13).
Table S3. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures
Authors: Zhang Yanxiao , Koneva Lada A. , Virani Shama , Arthur Anna E. , Virani Alisha , Hall Pelle B. , Warden Charles D. , Carey Thomas E. , Chepeha Douglas B. , Prince Mark E. , McHugh Jonathan B. , Wolf Gregory T. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

Enriched GO terms for genes differentially expressed between HPV-KRT and HPV-IMU subgroups in the UM cohort.
Supplementary Table S4 from A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non–Small Cell Lung Cancer and Serum DNA
Authors: Ooki Akira , Maleki Zahra , Tsay Jun-Chieh J. , Goparaju Chandra , Brait Mariana , Turaga Nitesh , Nam Hae-Seong , Rom William N. , Pass Harvey I. , Sidransky David , Guerrero-Preston Rafael , Hoque Mohammad Obaidul
Published: April 2023

Supplementary Table S4.The correlation between clinicopathological features and methylation in lung cancer.