bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures from RAD51 Mediates Resistance of Cancer Stem Cells to PARP Inhibition in Triple-Negative Breast Cancer
Authors: Liu Yajing , Burness Monika L. , Martin-Trevino Rachel , Guy Joey , Bai Shoumin , Harouaka Ramdane , Brooks Michael D. , Shang Li , Fox Alex , Luther Tahra K. , Davis April , Baker Trenton L. , Colacino Justin , Clouthier Shawn G. , Shao Zhi-ming , Wicha Max S. , Liu Suling
Published: April 2023

Supplementary Figure S1. BRCA1 mutation confirmation and RAD51 gene expression in SUM149 cells. Supplementary Figure S2. RAD51 foci is associated with CSC population of BRCA1-mutant TNBC cells and effect of long-term PARP inhibition on RAD51. Supplementary Figure S3: Knockdown of RAD51 prevents foci formation in SUM149 and SUM159 cells. Supplementary Figure S4. The effect of RAD51 KD on TNBC viable cell count, CSCs, and cell cycle. Supplementary Figure S5. RAD51 KD sensitizes TNBC CSCs to PARPi. Supplementary Figure S6. Efficiency of RAD51 shRNA knockdown with additional shRNA vectors. Supplementary Figure S7. Knocking down RAD51 with two additional shRNA vectors also sensitizes CSCs to PARPi. Supplementary Figure S8. "Physiologic" RAD51 knockdown decreases cancer stem cells in SUM149 cells.
Table S3 from Global Promoter Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes in Natural Killer Cell Lymphoma
Authors: Küçük Can , Hu Xiaozhou , Jiang Bei , Klinkebiel David , Geng Huimin , Gong Qiang , Bouska Alyssa , Iqbal Javeed , Gaulard Philippe , McKeithan Timothy W. , Chan Wing C.
Published: April 2023

Table S3. This table(Supplementary Table 3)shows the genes with the best evidence for being silenced by promoter methylation.
Supplementary Information from Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients
Authors: de Jong Monique C. , ten Hoeve Jelle J. , Grénman Reidar , Wessels Lodewyk F. , Kerkhoven Ron , te Riele Hein , van den Brekel Michiel W.M. , Verheij Marcel , Begg Adrian C.
Published: April 2023

Supplementary Information. This file contains a text file with the interactions between miRs and mRNAs used for the analyses
Table S1 from Global Promoter Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes in Natural Killer Cell Lymphoma
Authors: Küçük Can , Hu Xiaozhou , Jiang Bei , Klinkebiel David , Geng Huimin , Gong Qiang , Bouska Alyssa , Iqbal Javeed , Gaulard Philippe , McKeithan Timothy W. , Chan Wing C.
Published: April 2023

Table S1. Pathological characteristics and available data of NK-cell lymphoma cases (A) and NK cell lines (B).
Supplemental Figures 1-12 from Global Promoter Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes in Natural Killer Cell Lymphoma
Authors: Küçük Can , Hu Xiaozhou , Jiang Bei , Klinkebiel David , Geng Huimin , Gong Qiang , Bouska Alyssa , Iqbal Javeed , Gaulard Philippe , McKeithan Timothy W. , Chan Wing C.
Published: April 2023

Supplemental Figures 1-12. Fig.1: The distribution of mappable HpaII sites(MSCC cut sites) and the distribution of MSCC reads in normal NK cells; Fig.2: Mean log2 cut counts per site for promoters and bodies of genes with differing normal NK expression levels; Fig.3: Correlation of promoter hypermethylation and gene expression of candidate genes in malignant NK samples; Fig.4: Genome-wide comparisons of MSCC and RRBS methodologies on detection of promoter methylation levels; Fig.5: Hypermethylated candidate tumor suppressor genes have low expression in malignant NK-cell lines.; Fig.6: BIM protein is silenced in NK-cell lines; Fig.7: Comparison of MSCC with locus-specific pyrosequencing; Fig.8: Pyrosequencing analysis of BIM, ASNS and DAPK1 promoters in NK-cell lines and normal NK-cells cross-validates MSCC results; Fig.9: Validation of BIM and ASNS promoter methylation with locus-specific q-MSP in malignant NK samples; Fig.10: BIM protein is induced after Decitabine treatment; Fig.11: Ectopic expression of BIM in NKYS cells 2 days post-transduction; Fig.12: Ectopic expression of SOCS6 in NK-cell lines
Data Supplement from Phase II Study of Cetuximab in Combination with Cisplatin and Radiation in Unresectable, Locally Advanced Head and Neck Squamous Cell Carcinoma: Eastern Cooperative Oncology Group Trial E3303
Authors: Egloff Ann Marie , Lee Ju-Whei , Langer Corey J. , Quon Harry , Vaezi Alec , Grandis Jennifer R. , Seethala Raja R. , Wang Lin , Shin Dong M. , Argiris Athanassios , Yang Donghua , Mehra Ranee , Ridge John Andrew , Patel Urjeet A. , Burtness Barbara A. , Forastiere Arlene A.
Published: April 2023

List of Supplemental Materials: Supplemental Table 1. Criteria for Unresectable Disease Supplemental Table 2. Modified RECIST Criteria for Head and Neck Cancer. Supplemental Table 3. Summary of Serum Analyte Levels. Supplemental Figure 1. Study Schematic Supplemental Figure 2. Time to locoregional failure for all eligible and treated patients (a) and by tumor HPV status (b). Log rank test comparing time to failure for HPV+ versus HPV- p value provided. Supplemental Figure 3. Representative tissue cores with high or low expression levels of XPF or ERCC1 as assessed by AQUA. Tumors were stained for cytokeratin (CK) to create a tumor mask and with DAPI to define the nuclear compartment. Supplemental Figure 4. Representative tumor IHC molecular correlates ERCC1, XPF and MET.
Supplementary Figures and Tables, clean version from Clinical Utility of a STAT3-Regulated miRNA-200 Family Signature with Prognostic Potential in Early Gastric Cancer
Authors: Yu Liang , Wu Di , Gao Hugh , Balic Jesse J. , Tsykin Anna , Han Tae-Su , Liu You Dong , Kennedy Catherine L. , Li Ji Kun , Mao Jie Qi , Tan Patrick , Oshima Masanobu , Goodall Gregory J. , Jenkins Brendan J.
Published: April 2023

These figures and tables contain supporting (and essential) data to confirm the clinical utility of the miR-200 family and signature in early gastric cancer, as well as its regulation by STAT3. Supplementary Figure S1. The association of WHO intestinal-type GC sub-classes and individual TNM stage with the expression of miR-200 family members and miR-21 in TCGA GC patients. Supplementary Figure S2. The association between patient survival and expression of miR- 200s and a complete network map of GSEA results generated from TCGA GC patients. Supplementary Figure S3. miR-429 promotes AGS cells proliferation and clonigenicity. Supplementary Figure S4. The association between patient survival and expression of individual genes from the miR-200 family-associated 15-gene signature. Supplementary Figure S5. STAT3 activation correlates with miR-429 and other miR-200 members in mouse and human gastric epithelial cells. Supplementary Figure S6. Generation of STAT3 knockout human GC lines, and STAT3- independent transcriptional regulation of miR-200 family members. Supplementary Table S1. Clinicopathological features and demographics of GC patients from TCGA cohort used for expression profiling of hsa-miR-429. Supplementary Table S2. Chi-square analysis between the miR-200 family 15-gene signature and conventional key prognostic factors using two independent cohorts. 2 Supplementary Table S3. Multivariate analysis of overall survival comparing the miR-200 family 15-gene signature and other conventional clinical parameters including histology and tumor grade (differentiation) using updated TCGA data.
Supplementary Table S2 from Failures in Phase III: Causes and Consequences
Authors: Seruga Bostjan , Ocana Alberto , Amir Eitan , Tannock Ian F.
Published: April 2023

RCTs with positive primary outcome
Supplementary table S2 from Patient-Derived Xenografts from Non–Small Cell Lung Cancer Brain Metastases Are Valuable Translational Platforms for the Development of Personalized Targeted Therapy
Authors: Lee Hye Won , Lee Jung-il , Lee Se Jeong , Cho Hyun Jung , Song Hye Jin , Jeong Da Eun , Seo Yun Jee , Shin Sang , Joung Je-Gun , Kwon Yong-Jun , Choi Yoon-La , Park Woong-Yang , Lee Hyun Moo , Seol Ho Jun , Shim Young Mog , Joo Kyeung Min , Nam Do-Hyun
Published: April 2023

Supplementary table S2. In vivo passagability and time to tumor formation of patient-derived xenografts
Supplementary Figure S3 from The Stat3/5 Signaling Biosignature in Hematopoietic Stem/Progenitor Cells Predicts Response and Outcome in Myelodysplastic Syndrome Patients Treated with Azacitidine
Authors: Miltiades Paraskevi , Lamprianidou Eleftheria , Vassilakopoulos Theodoros P. , Papageorgiou Sotirios G. , Galanopoulos Athanasios G. , Kontos Christos K. , Adamopoulos Panagiotis G. , Nakou Evangelia , Vakalopoulou Sofia , Garypidou Vassilia , Papaioannou Maria , Hatjiharissi Evdoxia , Papadaki Helen A. , Spanoudakis Emmanuil , Pappa Vassiliki , Scorilas Andreas , Tsatalas Constantinos , Kotsianidis Ioannis
Published: April 2023

Flow cytometric analyses of cellular hierarchy in Lin-CD34+ selected cells.
Supplementary Figure S1 from The Stat3/5 Signaling Biosignature in Hematopoietic Stem/Progenitor Cells Predicts Response and Outcome in Myelodysplastic Syndrome Patients Treated with Azacitidine
Authors: Miltiades Paraskevi , Lamprianidou Eleftheria , Vassilakopoulos Theodoros P. , Papageorgiou Sotirios G. , Galanopoulos Athanasios G. , Kontos Christos K. , Adamopoulos Panagiotis G. , Nakou Evangelia , Vakalopoulou Sofia , Garypidou Vassilia , Papaioannou Maria , Hatjiharissi Evdoxia , Papadaki Helen A. , Spanoudakis Emmanuil , Pappa Vassiliki , Scorilas Andreas , Tsatalas Constantinos , Kotsianidis Ioannis
Published: April 2023

Application of the GFM prognostic score on the patient cohort of the study (n=72).
Supplementary Tables 1-3 from Cellular Mechanisms Underlying Complete Hematological Response of Chronic Myeloid Leukemia to BRAF and MEK1/2 Inhibition in a Patient with Concomitant Metastatic Melanoma
Authors: Andrews Miles C. , Turner Natalie , Boyd Janis , Roberts Andrew W. , Grigg Andrew P. , Behren Andreas , Cebon Jonathan
Published: April 2023

Supplementary Tables 1-3. Supplementary Table 1: Changes in manual differential white cell counts over time under treatment with BRAF/MEK inhibitor combination therapy for melanoma. Supplementary Table 2. BCR-ABL monitoring during treatment. Supplementary Table 3. Leukocyte sub-populations as defined by flow cytometry.
Supplementary Figure S1 from Biomarker Associations with Efficacy of Abiraterone Acetate and Exemestane in Postmenopausal Patients with Estrogen Receptor–Positive Metastatic Breast Cancer
Authors: Li Weimin , O'Shaughnessy Joyce , Hayes Daniel , Campone Mario , Bondarenko Igor , Zbarskaya Irina , Brain Etienne , Stenina Marina , Ivanova Olga , Graas Marie-Pascale , Neven Patrick , Ricci Deborah , Griffin Thomas , Kheoh Thian , Yu Margaret , Gormley Michael , Martin Jason , Schaffer Michael , Zelinsky Kathy , De Porre Peter , Johnston Stephen R.D.
Published: April 2023

Supplementary Figure S1. Comparison of associations of the negative expression of androgen receptor (AR) (< 10%) with progression-free survival (PFS).
Supplementary Figure 3 from Cellular Mechanisms Underlying Complete Hematological Response of Chronic Myeloid Leukemia to BRAF and MEK1/2 Inhibition in a Patient with Concomitant Metastatic Melanoma
Authors: Andrews Miles C. , Turner Natalie , Boyd Janis , Roberts Andrew W. , Grigg Andrew P. , Behren Andreas , Cebon Jonathan
Published: April 2023

Supplementary Figure 3. Effects of kinase inhibitor treatment on expression of the pro-apoptotic molecule BIM.
Supplementary Data from Biomarker Associations with Efficacy of Abiraterone Acetate and Exemestane in Postmenopausal Patients with Estrogen Receptor–Positive Metastatic Breast Cancer
Authors: Li Weimin , O'Shaughnessy Joyce , Hayes Daniel , Campone Mario , Bondarenko Igor , Zbarskaya Irina , Brain Etienne , Stenina Marina , Ivanova Olga , Graas Marie-Pascale , Neven Patrick , Ricci Deborah , Griffin Thomas , Kheoh Thian , Yu Margaret , Gormley Michael , Martin Jason , Schaffer Michael , Zelinsky Kathy , De Porre Peter , Johnston Stephen R.D.
Published: April 2023

Supplementary Table S1. Biomarkers evaluated Supplementary Table S2. Additional biomarker associations with PFS by treatment
Supplementary Figure 1 from Cellular Mechanisms Underlying Complete Hematological Response of Chronic Myeloid Leukemia to BRAF and MEK1/2 Inhibition in a Patient with Concomitant Metastatic Melanoma
Authors: Andrews Miles C. , Turner Natalie , Boyd Janis , Roberts Andrew W. , Grigg Andrew P. , Behren Andreas , Cebon Jonathan
Published: April 2023

Supplementary Figure 1. Representative flow cytometry plots and gates.
Supplementary Tables 1 - 7 from BRAF Inhibitor Resistance Mechanisms in Metastatic Melanoma: Spectrum and Clinical Impact
Authors: Rizos Helen , Menzies Alexander M. , Pupo Gulietta M. , Carlino Matteo S. , Fung Carina , Hyman Jessica , Haydu Lauren E. , Mijatov Branka , Becker Therese M. , Boyd Suzanah C. , Howle Julie , Saw Robyn , Thompson John F. , Kefford Richard F. , Scolyer Richard A. , Long Georgina V.
Published: April 2023

PDF file - 197KB, Table S1 Exome sequencing data summary. Table S2 Candidate resistant variants identified in Prog melanomas. Table S3 Median MAPK activity scores of Pre-treatment versus Prog melanoma metastases and associated P-value. Table S4 Gene Set Enrichment Analysis of MAPK-inhibited Prog tumors (n=6) vs. MAPK-re-activated Prog tumors (n=15). Table S5 Inter-tumoral heterogeneity of BRAF inhibitor resistance mechanisms and MAPK activity. Table S6 BRAF inhibitor resistance mechanism and response to subsequent MAPK inhibitors. Table S7 Amplification and Sequencing Primers.
Supplemental Materials from Clinical Relevance of KRAS-Mutated Subclones Detected with Picodroplet Digital PCR in Advanced Colorectal Cancer Treated with Anti-EGFR Therapy
Authors: Laurent-Puig Pierre , Pekin Deniz , Normand Corinne , Kotsopoulos Steve K. , Nizard Philippe , Perez-Toralla Karla , Rowell Rachel , Olson Jeff , Srinivasan Preethi , Le Corre Delphine , Hor Thevy , El Harrak Zakaria , Li Xinyu , Link Darren R. , Bouché Olivier , Emile Jean-François , Landi Bruno , Boige Valérie , Hutchison J. Brian , Taly Valerie
Published: April 2023

Supplemental Materials. Supplemental Table 1: Patient mutational status and agreement between qPCR, dPCR and sequencing results. Supplemental Table 2: Analysis of different tissue samples coming from the same patient. Supplemental Figure 1: Fraction of mutated alleles (including multiple subclones) in the patients detected by both conventional and droplet-digital PCR procedures. Supplemental Figure 2: Fraction of mutated DNA observed for the different tested mutations of KRAS and BRAF.
Supplementary Table 1 from The IL-15-Based ALT-803 Complex Enhances FcγRIIIa-Triggered NK Cell Responses and In Vivo Clearance of B Cell Lymphomas
Authors: Rosario Maximillian , Liu Bai , Kong Lin , Collins Lynne I. , Schneider Stephanie E. , Chen Xiaoyue , Han Kaiping , Jeng Emily K. , Rhode Peter R. , Leong Jeffrey W. , Schappe Timothy , Jewell Brea A. , Keppel Catherine R. , Shah Keval , Hess Brian , Romee Rizwan , Piwnica-Worms David R. , Cashen Amanda F. , Bartlett Nancy L. , Wong Hing C. , Fehniger Todd A.
Published: April 2023

Characteristics of primary iNHL patient samples used in this study.
Supplementary Figure 1 from The IL-15-Based ALT-803 Complex Enhances FcγRIIIa-Triggered NK Cell Responses and In Vivo Clearance of B Cell Lymphomas
Authors: Rosario Maximillian , Liu Bai , Kong Lin , Collins Lynne I. , Schneider Stephanie E. , Chen Xiaoyue , Han Kaiping , Jeng Emily K. , Rhode Peter R. , Leong Jeffrey W. , Schappe Timothy , Jewell Brea A. , Keppel Catherine R. , Shah Keval , Hess Brian , Romee Rizwan , Piwnica-Worms David R. , Cashen Amanda F. , Bartlett Nancy L. , Wong Hing C. , Fehniger Todd A.
Published: April 2023

Spleen NK cell numbers and percentages in SCID mice analyzed in Figures 4E/F.
Supplementary Figures S1-S5, Tables S1-S5 from Cytotoxicity of Human Endogenous Retrovirus K–Specific T Cells toward Autologous Ovarian Cancer Cells
Authors: Rycaj Kiera , Plummer Joshua B. , Yin Bingnan , Li Ming , Garza Jeremy , Radvanyi Laszlo , Ramondetta Lois M. , Lin Kevin , Johanning Gary L. , Tang Dean G. , Wang-Johanning Feng
Published: April 2023

Figure S1. Schematic for patient sample preparation and IVS procedure; S2. Schematic representation of HERV transcripts; S3. Ovarian (cancer) patient characteristics; S4. OC cells in the ascites express cancer stem cell markers and both epithelial and mesenchymal cell markers; S5. Characterizations of OC cells and expression HERV-K transcripts and protein; Supplementary Table S1. Clinicopathologic characteristics and use of patient samples; S2. Normal Samples* S3. Marker analysis in primary cells from normal, benign, and malignant ovarian tissues; S4. Primers used in semi-quantitative RT-PCR analysis of various HERV-K transcripts; S5: Characterization of patient PBMCs and IVS cells.
Supplementary Figure and Method from Lenalidomide Enhances Immune Checkpoint Blockade-Induced Immune Response in Multiple Myeloma
Authors: Görgün Güllü , Samur Mehmet K. , Cowens Kristen B. , Paula Steven , Bianchi Giada , Anderson Julie E. , White Randie E. , Singh Ahaana , Ohguchi Hiroto , Suzuki Rikio , Kikuchi Shohei , Harada Takeshi , Hideshima Teru , Tai Yu-Tzu , Laubach Jacob P. , Raje Noopur , Magrangeas Florence , Minvielle Stephane , Avet-Loiseau Herve , Munshi Nikhil C. , Dorfman David M. , Richardson Paul G. , Anderson Kenneth C.
Published: April 2023

Supplementary Figure and Method. Supplementary Figure: PD-L1 gene expression in MM cells from patients with ND-MM compared to normal plasma cells by Exon Array Analysis. Supplementary Method: Exon Array Dataset and Gene Expression Analysis.
Supplemental Table S1 from The Prostate Cancer Susceptibility Variant rs2735839 Near KLK3 Gene Is Associated with Aggressive Prostate Cancer and Can Stratify Gleason Score 7 Patients
Authors: He Yonggang , Gu Jian , Strom Sara , Logothetis Christopher J. , Kim Jeri , Wu Xifeng
Published: April 2023

Supplementary table S1. Prostate cancer susceptibility variants genotyped in the study.
Supplementary Figures from ICAM-1–Related Noncoding RNA in Cancer Stem Cells Maintains ICAM-1 Expression in Hepatocellular Carcinoma
Authors: Guo Weixing , Liu Shupeng , Cheng Yuqiang , Lu Lei , Shi Jie , Xu Guixia , Li Nan , Cheng Kai , Wu Mengchao , Cheng Shuqun , Liu Shanrong
Published: April 2023

Supplementary Fig. S1-11. Supplementary Fig. S1. Differentially expressed lncRNAs and mRNAs between CSQT-2 and Hep3B. Supplementary Fig. S2. Potential relationship between ICR and ICAM-1 mRNA. Supplementary Fig. S3. Coding potential assessment tool analysis of ICR. Supplementary Fig. S4. In situ analysis of ICAM-1 and ICR expression in HCC tumor and PVTT tissues. Supplementary Fig. S5. ICR and ICAM-1 expression assessed by Real-time PCR and western blot. Supplementary Fig. S6. Melt curve from real-time PCR in RNase protection assay (RPA) analysis. Supplementary Fig. S7. Migration analysis of tumor cells with ICR modulation. Supplementary Fig. S8. ICAM-1 expression in cell line/tumors with modulated ICR and tumor growth in mice. Supplementary Fig. S9. ICAM-1 expression in mouse tumors assessed by IF. Supplementary Fig. S10. Representative image of ChIP assays with Nanog antibody. Supplementary Fig. S11. Nanog and ICR Expression in HCC cell lines with Nanog modulation.
Supplementary Figure Legend from ICAM-1–Related Noncoding RNA in Cancer Stem Cells Maintains ICAM-1 Expression in Hepatocellular Carcinoma
Authors: Guo Weixing , Liu Shupeng , Cheng Yuqiang , Lu Lei , Shi Jie , Xu Guixia , Li Nan , Cheng Kai , Wu Mengchao , Cheng Shuqun , Liu Shanrong
Published: April 2023

Detailed description of Supplementary Figures such as genes expression in cell lines/tumor tissues, high magnification images and so on.
Supplementary Table 3 from Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor
Authors: Karpathakis Anna , Dibra Harpreet , Pipinikas Chistodoulos , Feber Andrew , Morris Tiffany , Francis Joshua , Oukrif Dahmane , Mandair Dalvinder , Pericleous Marinos , Mohmaduvesh Mullan , Serra Stefano , Ogunbiyi Olagunju , Novelli Marco , Luong TuVinh , Asa Sylvia L. , Kulke Matthew , Toumpanakis Christos , Meyer Tim , Caplin Martyn , Meyerson Matthew , Beck Stephan , Thirlwell Christina
Published: April 2023

Supplementary Table S3. Chromosome 18 probes demonstrating differential methylation between SI NET within 18LOH group and normal small intestine.
Supplementary Table 1 from Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor
Authors: Karpathakis Anna , Dibra Harpreet , Pipinikas Chistodoulos , Feber Andrew , Morris Tiffany , Francis Joshua , Oukrif Dahmane , Mandair Dalvinder , Pericleous Marinos , Mohmaduvesh Mullan , Serra Stefano , Ogunbiyi Olagunju , Novelli Marco , Luong TuVinh , Asa Sylvia L. , Kulke Matthew , Toumpanakis Christos , Meyer Tim , Caplin Martyn , Meyerson Matthew , Beck Stephan , Thirlwell Christina
Published: April 2023

Supplementary Table S1. Supervised comparison of three subgroups of SI NET identifies methylation variable positions (MVPs) distinguishing the groups.
Supplementary Figures 1-3 from Loss of SOD3 (EcSOD) Expression Promotes an Aggressive Phenotype in Human Pancreatic Ductal Adenocarcinoma
Authors: O'Leary Brianne R. , Fath Melissa A. , Bellizzi Andrew M. , Hrabe Jennifer E. , Button Anna M. , Allen Bryan G. , Case Adam J. , Altekruse Sean , Wagner Brett A. , Buettner Garry R. , Lynch Charles F. , Hernandez Brenda Y. , Cozen Wendy , Beardsley Robert A. , Keene Jeffery , Henry Michael D. , Domann Frederick E. , Spitz Douglas R. , Mezhir James J.
Published: April 2023

Supplementary Figures 1-3. S1: Creation and characterization of EcSOD stably expressing PDA cell lines.; S2: Activity of EcSOD activity from stably expression PDA cell lines; S3: L-NNA decreases NOS activity in PDA cells.
Supplementary figure 1 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 1. Tumor growth kinetics in individual mice treated with trametinib (T) in combination with the immunomodulator-targeting PD1 in the CT26 murine syngeneic model.
Supplementary Figure S3 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

AXL knockdown eliminated LSCs in BCR-ABL-driven CML mice.
Supplementary Figure S2 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

AXL knockdown has minimal effect on self-renewal capacity of human NBM CD34+ cells.
Supplementary Table S1 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

Patient Identification
supplementary information 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

supplementary information
Supplementary Table S1 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

Suppl.Table 1: Analysis of the cellular localization, pathways and gene expression modification of the 100 genes most correlated with AXL expression in 254 basal-like breast cancers.
Supplementary Figures 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

supplementary figures S1-S7
Supplementary Table S2: A hypothetical example of an updated DTP for Cohorts 4 to 6 in the Viola trial from Dose Transition Pathways: The Missing Link Between Complex Dose-Finding Designs and Simple Decision-Making
Authors: Yap Christina , Billingham Lucinda J. , Cheung Ying Kuen , Craddock Charlie , O'Quigley John
Published: April 2023

A hypothetical example of an updated DTP for Cohorts 4 to 6 in the Viola trial after observing 0/3 DLT at Dose 0, 1/3 DLT at Dose 1 and 0/3 DLT at Dose 1 for Cohorts 1 to 3 respectively (i.e. pathway 5 in Table 2). This table presents all 64 pathways for Cohorts 4-6 (with Dose 2 for Cohort 4) as recommended by the modified tailored CRM model.
Supplementary table 3c from Pan-Cancer Immunogenomic Perspective on the Tumor Microenvironment Based on PD-L1 and CD8 T-Cell Infiltration
Authors: Ock Chan-Young , Keam Bhumsuk , Kim Sehui , Lee Ju-Seog , Kim Miso , Kim Tae Min , Jeon Yoon Kyung , Kim Dong-Wan , Chung Doo Hyun , Heo Dae Seog
Published: April 2023

Supplementary table 3c. Specific deletion of cancer driver genes to predict tumor microenvironment immune types
Supplementary Table S3 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

Functional assignment of the 113 genes with the highest expression difference in the two clusters revealed by unsupervised clustering of primary samples
Table S1 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

Overview of somatic mutations
Supplementary data file 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

Pathology review data and next-generation sequencing datafile.
Figure S3 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

Original magnification overview x10 and insert x40 in panel-consensus diagnosed LCNECs. A) No nuclear staining for RB1 (13A10) in LCNEC mutated for RB1 and TP53 genes. B) Nuclear and cytoplasmatic staining for P16. C) Nuclear staining for RB1 protein staining (13A10) in LCNEC with RB1 and TP53 wild-type genes (10x); the arrow indicates a positive internal control. D) In the same case as C, no staining for P16 protein (J8C)
Figure S1 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

A) Overall survival according to the original established diagnosis in patients included in the panel-consensus revision (n=232). B) Overall survival according to the panel-consensus diagnoses. Abbreviations: NSCLC NED, non-small cell lung carcinoma with neuroendocrine differentiation; NEC, neuroendocrine carcinoma; dd, differential diagnosis; NET NOS, neuroendocrine tumor not otherwise specified.
Supplementary Table S4 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

Multivariate linear regression analysis of mutation count in patients stratified by smoking status on the base of validation set (GLCI).
Table S4 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 100 genes most differentially expressed genes in RUNX1mut AML (n=47) compared to RUNX1wt AML (n=368).
Figure S1-S8 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

Supplementary Figure 1. Additional examples of genes most correlated (> 0.50 or <-0.50) to RUNX1 mutation type and VAF, as described in Figure 2C. Supplementary Figure 2. (a) Waterfall plot showing Pearson correlation coefficients calculated between all compounds tested in viability screen (n=5,068) and Dexamethasone. Supplementary Figure 3. Dose response curves for Flumethasone (Flu), representative of the Glucocorticoid cluster, for RUNX1mut and RUNX1wt specimens. Supplementary Figure 4. Heat map showing response profile of 32 AML cell lines to compounds of the GC cluster (n=24) and 6-thioguanine. Supplementary Figure 5. Response to GC Mometasone Furoate (MF) observed in Kasumi-1 and OCI-AML3 cells in the presence of increasing concentrations of GR full antagonist RU486. Supplementary Figure 6. (a) Infection of OCI-AML3 cells with shRNAs targeting NR3C1 (sh1 to sh4) and assessment of GR knockdown efficiency in GFP+ sorted cells by western blotting. Supplementary Figure 7. (a) Top. Expression profile of lymphoid markers and of the NR3C1 gene (encoding the GR) in AML specimens of the Leucegene cohort. Supplementary Figure 8. (a) Dose response curves and associated IC50s for Flumethasone (Flu) and Budesonide (Bude) upon RUNX1 knockdown in OCI-AML5 cells.
Supplementary Figure Legends from The Novel KLF4/MSI2 Signaling Pathway Regulates Growth and Metastasis of Pancreatic Cancer
Authors: Guo Kun , Cui Jiujie , Quan Ming , Xie Dacheng , Jia Zhiliang , Wei Daoyan , Wang Liang , Gao Yong , Ma Qingyong , Xie Keping
Published: April 2023

Supplementary Figure S1. Expression of MSI2 in PDAC specimens. Supplementary Figure S2. Localization of MSI2 in PDAC cells. Supplementary Figure S3. Co-expression of MSI2 and KLF4 in colon and gastric cancer cells.
Table S1 and S2 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

Table S1: Primers for real-time PCR. Table S2: Patient characteristics at initial diagnosis.
Figure S5 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

Clinical relevance of Gli1 expression in human osteosarcoma specimens.
Supplementary Figure S1 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 S1: AR-E1 and AR-CE3 RISH assays are specific. (A) AR-E1 is undetectable in AR-negative, untransfected M12 cells. Transfection with AR-FL construct is detectable by AR_E1, but not by AR_CE3 RISH as expected in M12 cells. (B) Untransfected HeLa cells have low to undetectable levels of AR-E1. Transfection with AR-E1-containing construct leads to highly detectable AR_E1 by RISH. (C) RISH with probes detected human AR_E1 sequence is negative in murine prostate. As a positive control for RNA quality, RISH for c-myc is positive in these transgenic mice which express the c-myc transgene.
Supplemental Table S2 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

Worst Cervical cytology during the study
Supplemental Methods 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

Supplemental Methods
Table S2 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

Gene sets Differentially expressed (q<0.1) from Pre to Prog tumors
Table 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

Genes Differentially expressed (q<0.1) from Pre to EDT tumors
Figure S2 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 S4. 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

Neoplasm-associated genes on chr3q and chr16q (identified by gene2Mesh). - The 'logFC', 'p-value' and 'q-value' columns are from testing the expression difference between HPV-KRT and HPV-IMU tumors (UM and TCGA combined).
Supplementary Tables from Low Tumor Mitochondrial DNA Content Is Associated with Better Outcome in Breast Cancer Patients Receiving Anthracycline-Based Chemotherapy
Authors: Weerts Marjolein J.A. , Hollestelle Antoinette , Sieuwerts Anieta M. , Foekens John A. , Sleijfer Stefan , Martens John W.M.
Published: April 2023

Supplementary Table 1: Clinicopathological variables of node-positive patients receiving adjuvant chemotherapy (FAC/FEC or CMF) (complete adjuvant cohort). Supplementary Table 2: Clinicopathological variables of the patients with recurrent disease receiving first-line chemotherapy (FAC/FEC or CMF) (complete advanced cohort). Supplementary Table 3: Patient response to first-line FAC/FEC or CMF chemotherapy after disease recurrence (advanced cohort). Supplementary Table 4: Performance of the calibration curves taken along in each plate for the used qPCR assays. Supplementary Table 5: Association between mtDNA content and chemotherapy given, either adjuvant in the adjuvant cohort, or as first-line for disease recurrence in the advanced cohort. Supplementary Table 6: Association between adjuvant chemotherapy given and clinicopathological variables of node-positive patients (adjuvant cohort). Supplementary Table 7: Association between first-line chemotherapy given and clinicopathological variables of patients with recurrent disease (advanced cohort). Supplementary Table 8: Cox regression analysis for DMFS of node-positive patients receiving FAC/FEC adjuvant chemotherapy (adjuvant cohort) limited to the 86 patients with no missing values. Supplementary Table 9: Cox regression analysis for PFS of patients receiving FAC/FEC first-line chemotherapy for their recurrent disease (advanced cohort) limited to the 70 patients with no missing values. Supplementary Table 10: Univariable Cox regression analysis of postulated markers for anthracycline sensitivity. Supplementary Table 11: Association between mtDNA content and postulated markers for anthracycline sensitivity.
Supplementary Figure 1 from Low Tumor Mitochondrial DNA Content Is Associated with Better Outcome in Breast Cancer Patients Receiving Anthracycline-Based Chemotherapy
Authors: Weerts Marjolein J.A. , Hollestelle Antoinette , Sieuwerts Anieta M. , Foekens John A. , Sleijfer Stefan , Martens John W.M.
Published: April 2023

Study design (REMARK diagram) for the adjuvant (left) and advanced cohort (right).
Table S1. 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

Differentially expressed neoplasm-associated genes between HPV(+) and HPV(-) HNC tumors in the UM cohort.
Supplemental Table 2 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma
Authors: Chicard Mathieu , Boyault Sandrine , Colmet Daage Leo , Richer Wilfrid , Gentien David , Pierron Gaelle , Lapouble Eve , Bellini Angela , Clement Nathalie , Iacono Isabelle , Bréjon Stéphanie , Carrere Marjorie , Reyes Cécile , Hocking Toby , Bernard Virginie , Peuchmaur Michel , Corradini Nadège , Faure-Conter Cécile , Coze Carole , Plantaz Dominique , Defachelles Anne Sophie , Thebaud Estelle , Gambart Marion , Millot Frédéric , Valteau-Couanet Dominique , Michon Jean , Puisieux Alain , Delattre Olivier , Combaret Valérie , Schleiermacher Gudrun
Published: April 2023

Tumour aCGH-specific and cfDNA- specific breakpoints
Supplementary information 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 information includes Supplementary Figure S1-S6 and Supplementary Materials and Methods.Figure S1 shows DMR scatterplots and bisulfite sequencing chromatrograms of 6 genes (CDO1, HOXA9, AJAP1, PTGDR, UNCX, and MARCH11). Figure S2 shows the correlation between methylation and the expression status of CDO1, PTGDR, AJAP1, and HOXA9 in the LUAD TCGA dataset. Figure S3 shows the Kaplan-Meier curves of overall survival according to the methylation status (positive or negative for hypermethylation) of tested genes in early stage disease (n=53). Figure S4 shows the methylation status of the 6 genes in serum samples from 43 stage IA LUAD, 40 stage IA LUSC, and 42 population-matched control subjects. Figure S5 shows promoter methylation levels for the 6 markers in pleural effusion and asities. Figure S6 shows the clinical significance of HOX paralogue group 9 genes (HOXA9, HOXB9, HOXC9, and HOXD9) in the TCGA dataset.
Supplemental Figure 3 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma
Authors: Chicard Mathieu , Boyault Sandrine , Colmet Daage Leo , Richer Wilfrid , Gentien David , Pierron Gaelle , Lapouble Eve , Bellini Angela , Clement Nathalie , Iacono Isabelle , Bréjon Stéphanie , Carrere Marjorie , Reyes Cécile , Hocking Toby , Bernard Virginie , Peuchmaur Michel , Corradini Nadège , Faure-Conter Cécile , Coze Carole , Plantaz Dominique , Defachelles Anne Sophie , Thebaud Estelle , Gambart Marion , Millot Frédéric , Valteau-Couanet Dominique , Michon Jean , Puisieux Alain , Delattre Olivier , Combaret Valérie , Schleiermacher Gudrun
Published: April 2023

Correlation of genomic profiles determined by tumor aCGH and cfDNA analysis
Figure S3 from In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The ϕ-Index
Authors: Bakas Spyridon , Akbari Hamed , Pisapia Jared , Martinez-Lage Maria , Rozycki Martin , Rathore Saima , Dahmane Nadia , O'Rourke Donald M. , Davatzikos Christos
Published: April 2023

Single slices from an EGFRvIII+ and an EGFRvIII- example patient from the T1-CE and the T2-FLAIR volumes.
Supplementary Table 4 from Interleukin-17–Producing Neutrophils Link Inflammatory Stimuli to Disease Progression by Promoting Angiogenesis in Gastric Cancer
Authors: Li Tuan-Jie , Jiang Yu-Ming , Hu Yan-Feng , Huang Lei , Yu Jiang , Zhao Li-Ying , Deng Hai-Jun , Mou Ting-Yu , Liu Hao , Yang Yang , Zhang Qi , Li Guo-Xin
Published: April 2023

Univariate and Multivariate Analyses of Factors Associated with Overall Survival (OS) and Progression-free Survival (PFS).
Supplementary Table 5 from Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer
Authors: Zhao Eric Y. , Shen Yaoqing , Pleasance Erin , Kasaian Katayoon , Leelakumari Sreeja , Jones Martin , Bose Pinaki , Ch'ng Carolyn , Reisle Caralyn , Eirew Peter , Corbett Richard , Mungall Karen L. , Thiessen Nina , Ma Yussanne , Schein Jacqueline E. , Mungall Andrew J. , Zhao Yongjun , Moore Richard A. , Den Brok Wendie , Wilson Sheridan , Villa Diego , Shenkier Tamara , Lohrisch Caroline , Chia Stephen , Yip Stephen , Gelmon Karen , Lim Howard , Renouf Daniel , Sun Sophie , Schrader Kasmintan A. , Young Sean , Bosdet Ian , Karsan Aly , Laskin Janessa , Marra Marco A. , Jones Steven J.M.
Published: April 2023

Table S5: Data from this study have been submitted to the European Genome-Phenome Archive (EGA) (www.ebi.ac.uk/ega/home) under the study accession number EGAS00001001159. This table provides the accession numbers for each dataset included in this study.
Supplementary Information from Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer
Authors: Zhao Eric Y. , Shen Yaoqing , Pleasance Erin , Kasaian Katayoon , Leelakumari Sreeja , Jones Martin , Bose Pinaki , Ch'ng Carolyn , Reisle Caralyn , Eirew Peter , Corbett Richard , Mungall Karen L. , Thiessen Nina , Ma Yussanne , Schein Jacqueline E. , Mungall Andrew J. , Zhao Yongjun , Moore Richard A. , Den Brok Wendie , Wilson Sheridan , Villa Diego , Shenkier Tamara , Lohrisch Caroline , Chia Stephen , Yip Stephen , Gelmon Karen , Lim Howard , Renouf Daniel , Sun Sophie , Schrader Kasmintan A. , Young Sean , Bosdet Ian , Karsan Aly , Laskin Janessa , Marra Marco A. , Jones Steven J.M.
Published: April 2023

Supplementary Figures S1-S5. Supplementary Tables S1-S5. Figure S1. Comparison of SNV mutation signatures across histological and molecular subtypes. Figure S2. Treatment timelines and radiographic outcomes. Figure S3. Mutation signature stability metrics and comparisons to known signatures. Figure S4. Structural variant mutation sigantures. Figure S5. Comparison of mutation burden between aging-driven and non-aging-driven breast tumours. Table S1. Kruskal-Wallis tests. Table S2. HRDetect prediction test metrics. Table S3. Area under the curve of HRD signatures in platinum response prediction. Table S4. Logistic regression model odds ratios of clinical improvement on platinum. Table S5. Accession IDs of genome datasets submitted to the European Genome-Phenome Archive.
Supplementary Figure 3 from Interleukin-17–Producing Neutrophils Link Inflammatory Stimuli to Disease Progression by Promoting Angiogenesis in Gastric Cancer
Authors: Li Tuan-Jie , Jiang Yu-Ming , Hu Yan-Feng , Huang Lei , Yu Jiang , Zhao Li-Ying , Deng Hai-Jun , Mou Ting-Yu , Liu Hao , Yang Yang , Zhang Qi , Li Guo-Xin
Published: April 2023

Culture supernatants from GC cells inhibit neutrophil apoptosis in vitro. Neutrophils were untreated or stimulated with 20% culture supernatants from GC cells (AGS) for the indicated times. The rate of apoptosis of the cells was analyzed by staining with FITC-conjugated Annexin V and propidium iodide and determined by flow cytometry. The values represent the mean {plus minus} SE of four separate experiments: (A) representative image; (B) statistical results.