bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures 1 - 5 from Noninvasive Detection of Response and Resistance in EGFR-Mutant Lung Cancer Using Quantitative Next-Generation Genotyping of Cell-Free Plasma DNA
Authors: Oxnard Geoffrey R. , Paweletz Cloud P. , Kuang Yanan , Mach Stacy L. , O'Connell Allison , Messineo Melissa M. , Luke Jason J. , Butaney Mohit , Kirschmeier Paul , Jackman David M. , Jänne Pasi A.
Published: April 2023

PDF file - 365K, Supplemental Figure 1: Assay optimization. For each TaqMan probe, the optimal annealing temperature was determined by testing each assay across a temperature gradient of 55.0 - 65{degree sign}C. Typical FAM plots for EGFR L858R (A) and EGFR exon 19 deletion (B) are shown. Supplemental Figure 2: Assay characteristics. As the sample input increases, the copies/μL output increases in a linear fashion across a wide dynamic range for both the L858R assay (A) and the exon 19 deletion assay (B). Testing for 10 and 50 copies of mutant EGFR in a background of 1000 and 50,000 genome equivalents (GE), the L858R assay demonstrates more consistent sensitivity (C) than the exon 19 deletion assay (D). Supplemental Figure 3: Detection of BRAF V600E in cfDNA from patients with advanced melanoma. Supplemental Figure 4: Correlation of LINE-1 quantitative PCR (QPCR) levels with DNA concentration as measured with PicoGreen across 69 plasma specimens (R2 = 0.94, p<0.0001). Supplemental Figure 5: Inter- and intra-day variation of the ddPCR assay. (A) Identical serial dilutions ranging from 10-10,000 T790M mutation copies per reaction were assayed in triplicates on three nonconsecutive days. Percent coefficients of variation ranged between 12.2- 21.4% within days and 15.9-32.2% between days. (B) Technical replicates of samples containing either 1, 2, 10, or 20 copies of mutant T790M were assayed 32 times on the same day. Results show that ddPCR exhibits Poisson-distributed single molecule detection.
Supplementary Figure Legends from Noninvasive Detection of Response and Resistance in EGFR-Mutant Lung Cancer Using Quantitative Next-Generation Genotyping of Cell-Free Plasma DNA
Authors: Oxnard Geoffrey R. , Paweletz Cloud P. , Kuang Yanan , Mach Stacy L. , O'Connell Allison , Messineo Melissa M. , Luke Jason J. , Butaney Mohit , Kirschmeier Paul , Jackman David M. , Jänne Pasi A.
Published: April 2023

PDF file - 71K
Supplementary Figure 2 from EASL- and mRECIST-Evaluated Responses to Combination Therapy of Sorafenib with Transarterial Chemoembolization Predict Survival in Patients with Hepatocellular Carcinoma
Authors: Liu Lei , Wang Weijuan , Chen Hui , Zhao Yan , Bai Wei , Yin Zhanxin , He Chuangye , Jia Jia , Yang Man , Xia Jielai , Fan Daiming , Han Guohong
Published: April 2023

PDF file - 2971K, Supplementary Fig. 2: Kaplan-Meier curves comparing survival between responders and non-responders according (D) RECIST, (E) EASL, and (F) mRECIST assessed at second follow-up after treatment. Abbreviations: EASL, European Association for the Study of the Liver; mRECIST, modified RECIST; RECIST, response evaluation criteria in solid tumors.
Supplementary Tables 3 - 5 from Network Analysis Identifies an HSP90-Central Hub Susceptible in Ovarian Cancer
Authors: Liu Hanqing , Xiao Fang , Serebriiskii Ilya G. , O'Brien Shane W. , Maglaty Marisa A. , Astsaturov Igor , Litwin Samuel , Martin Lainie P. , Proia David A. , Golemis Erica A. , Connolly Denise C.
Published: April 2023

PDF file - 100KB, Supplementary Table 3. Coefficient of interaction (CI) values for ganetespib combined with other drugs (dasatinib, erlotinib, cisplatin and paclitaxel) in ovarian cancer cell lines A1847 and OVCAR-5, based on Chou-Talalay analysis. Supplementary Table 4. Fold changes in proteins levels detected by reverse phase protein array following treatment with ganetespib, paclitaxel or ganetespib + paclitaxel. Supplementary Table 5. HSP90-interacting proteins sensitize EOC cells to ganetespib.
Supplementary Figure 1 from EASL- and mRECIST-Evaluated Responses to Combination Therapy of Sorafenib with Transarterial Chemoembolization Predict Survival in Patients with Hepatocellular Carcinoma
Authors: Liu Lei , Wang Weijuan , Chen Hui , Zhao Yan , Bai Wei , Yin Zhanxin , He Chuangye , Jia Jia , Yang Man , Xia Jielai , Fan Daiming , Han Guohong
Published: April 2023

PDF file - 2489K, Supplementary Fig. 1: Kaplan-Meier curves comparing survival between responders and non-responders according (A) RECIST, (B) EASL, and (C) mRECIST assessed at first follow-up after treatment. Abbreviations: EASL, European Association for the Study of the Liver; mRECIST, modified RECIST; RECIST, response evaluation criteria in solid tumors.
Supplementary Table 2 from Network Analysis Identifies an HSP90-Central Hub Susceptible in Ovarian Cancer
Authors: Liu Hanqing , Xiao Fang , Serebriiskii Ilya G. , O'Brien Shane W. , Maglaty Marisa A. , Astsaturov Igor , Litwin Samuel , Martin Lainie P. , Proia David A. , Golemis Erica A. , Connolly Denise C.
Published: April 2023

XLSX file - 22KB, Table of 130 proteins in expanded sensitization network with reported drug inhibitors, based on data reported in DrugBank and Ingenuity.
Supplementary Table 1 from Network Analysis Identifies an HSP90-Central Hub Susceptible in Ovarian Cancer
Authors: Liu Hanqing , Xiao Fang , Serebriiskii Ilya G. , O'Brien Shane W. , Maglaty Marisa A. , Astsaturov Igor , Litwin Samuel , Martin Lainie P. , Proia David A. , Golemis Erica A. , Connolly Denise C.
Published: April 2023

XLSX file - 55KB, Sensitization ranking across five independent drug sensitization screens.
Supplementary Methods, Table Legends from Network Analysis Identifies an HSP90-Central Hub Susceptible in Ovarian Cancer
Authors: Liu Hanqing , Xiao Fang , Serebriiskii Ilya G. , O'Brien Shane W. , Maglaty Marisa A. , Astsaturov Igor , Litwin Samuel , Martin Lainie P. , Proia David A. , Golemis Erica A. , Connolly Denise C.
Published: April 2023

PDF file - 86KB
Supplementary Figure 4 from Network Analysis Identifies an HSP90-Central Hub Susceptible in Ovarian Cancer
Authors: Liu Hanqing , Xiao Fang , Serebriiskii Ilya G. , O'Brien Shane W. , Maglaty Marisa A. , Astsaturov Igor , Litwin Samuel , Martin Lainie P. , Proia David A. , Golemis Erica A. , Connolly Denise C.
Published: April 2023

PDF file - 203KB, Ganetespib and paclitaxel inhibit ovarian cancer growth in vivo.
Supplementary Figure Legend from Topical TLR7 Agonist Imiquimod Can Induce Immune-Mediated Rejection of Skin Metastases in Patients with Breast Cancer
Authors: Adams Sylvia , Kozhaya Lina , Martiniuk Frank , Meng Tze-Chiang , Chiriboga Luis , Liebes Leonard , Hochman Tsivia , Shuman Nicholas , Axelrod Deborah , Speyer James , Novik Yelena , Tiersten Amy , Goldberg Judith D. , Formenti Silvia C. , Bhardwaj Nina , Unutmaz Derya , Demaria Sandra
Published: April 2023

PDF file, 73K.
Supplementary Figure 1 from Topical TLR7 Agonist Imiquimod Can Induce Immune-Mediated Rejection of Skin Metastases in Patients with Breast Cancer
Authors: Adams Sylvia , Kozhaya Lina , Martiniuk Frank , Meng Tze-Chiang , Chiriboga Luis , Liebes Leonard , Hochman Tsivia , Shuman Nicholas , Axelrod Deborah , Speyer James , Novik Yelena , Tiersten Amy , Goldberg Judith D. , Formenti Silvia C. , Bhardwaj Nina , Unutmaz Derya , Demaria Sandra
Published: April 2023

PDF file, 282K, A (non-responder 1): In situ TILs analysis by IHC in a patient with minimal T cell infiltrate before treatment (H&E stain and IHC for CD3, CD4, CD8 and FoxP3, 200x). B: (non-responder 2): In situ TILs analysis by IHC in a patient with moderate T cell infiltrate before imiquimod treatment. (H&E stain and IHC for CD3, CD4, CD8 and FoxP3, 200x).
Supplementary Methods and Figures and Tables from The Role of Aberrant VHL/HIF Pathway Elements in Predicting Clinical Outcome to Pazopanib Therapy in Patients with Metastatic Clear-Cell Renal Cell Carcinoma
Authors: Choueiri Toni K. , Fay André P. , Gagnon Robert , Lin Ying , Bahamon Brittany , Brown Victoria , Rosenberg Jonathan E. , Hutson Thomas E. , Baker-Neblett Katherine L. , Carpenter Christopher , Liu Yuan , Pandite Lini , Signoretti Sabina
Published: April 2023

PDF file, 296K, The role of aberrant VHL/HIF pathway elements in predicting clinical outcome to pazopanib therapy in patients with metastatic clear-cell renal cell carcinoma. Figure S1: Study design. Figure S2: Heatmap showing 4 potential gene expression patterns. Figure S3: Percentage of HIF2-alpha-positive nuclei compared between paraffin-dipped and non-paraffin-dipped tissue slides; p=0.0004.
Supplementary Video 2 from Rab25 Regulates Invasion and Metastasis in Head and Neck Cancer
Authors: Amornphimoltham Panomwat , Rechache Kamil , Thompson Jamie , Masedunskas Andrius , Leelahavanichkul Kantima , Patel Vyomesh , Molinolo Alfredo , Gutkind J. Silvio , Weigert Roberto
Published: April 2023

MOV file - 9371K, Intravital imaging of tongue cancer using 930 nm as excitation wavelength.
Supplementary Video 1 from Rab25 Regulates Invasion and Metastasis in Head and Neck Cancer
Authors: Amornphimoltham Panomwat , Rechache Kamil , Thompson Jamie , Masedunskas Andrius , Leelahavanichkul Kantima , Patel Vyomesh , Molinolo Alfredo , Gutkind J. Silvio , Weigert Roberto
Published: April 2023

MOV file - 8754K, Intravital imaging of tongue cancer using 750 nm as excitation wavelength.
Supplementary Figure Legend from Rab25 Regulates Invasion and Metastasis in Head and Neck Cancer
Authors: Amornphimoltham Panomwat , Rechache Kamil , Thompson Jamie , Masedunskas Andrius , Leelahavanichkul Kantima , Patel Vyomesh , Molinolo Alfredo , Gutkind J. Silvio , Weigert Roberto
Published: April 2023

PDF file - 82K
Supplementary Figure 1B from Phase II Trial of MEK Inhibitor Selumetinib (AZD6244, ARRY-142886) in Patients with BRAFV600E/K-Mutated Melanoma
Authors: Catalanotti Federica , Solit David B. , Pulitzer Melissa P. , Berger Michael F. , Scott Sasinya N. , Iyriboz Tunc , Lacouture Mario E. , Panageas Katherine S. , Wolchok Jedd D. , Carvajal Richard D. , Schwartz Gary K. , Rosen Neal , Chapman Paul B.
Published: April 2023

PDF file - 2703K, Immunohistochemical (IHC) staining of low pAKT tumors
Supplementary Figure 2 from Rab25 Regulates Invasion and Metastasis in Head and Neck Cancer
Authors: Amornphimoltham Panomwat , Rechache Kamil , Thompson Jamie , Masedunskas Andrius , Leelahavanichkul Kantima , Patel Vyomesh , Molinolo Alfredo , Gutkind J. Silvio , Weigert Roberto
Published: April 2023

PDF file - 79K, A. Tongue tumor weight and volume from HeLa-O3 expressing venus and venus Rab25 tumors were measured at the samples collection date. B. Lymphatic (Lyve1 staining) and blood vessels (CD31 staining) density from HeLa-O3 expressing venus and venus Rab25 tumors are depicted in arbitrary unit. C. Apoptotic cells and proliferating cells from HeLa-O3 expressing venus and venus Rab25 tumors were detected by cleaved caspase3 (green) and Ki67 (red) antibody, respectively. The percentage of positive cells is shown in the lower panel graphs. ns= not statistically significant ; t-test ; p values > 0.05.
Supplementary Figure 1 from Platinum-Based Chemotherapy for Variant Castrate-Resistant Prostate Cancer
Authors: Aparicio Ana M. , Harzstark Andrea L. , Corn Paul G. , Wen Sijin , Araujo John C. , Tu Shi-Ming , Pagliaro Lance C. , Kim Jeri , Millikan Randall E. , Ryan Charles , Tannir Nizar M. , Zurita Amado J. , Mathew Paul , Arap Wadih , Troncoso Patricia , Thall Peter F. , Logothetis Christopher J.
Published: April 2023

Supplementary Figure 1 - PDF file 90K, A heat-map based on a matrix with patient characteristics and C1-C7 as columns and patients as rows. The clustering of columns and rows are based on the Euclidean distances (root sum-of-squares of difference)
Supplementary Methods, Tables 1 - 3, Figures 1 - 7 from HDAC Inhibitors Augmented Cell Migration and Metastasis through Induction of PKCs Leading to Identification of Low Toxicity Modalities for Combination Cancer Therapy
Authors: Lin Kuen-Tyng , Wang Yi-Wei , Chen Chiung-Tong , Ho Chun-Ming , Su Wen-Hui , Jou Yuh-Shan
Published: April 2023

PDF file, 2015K, Table S1. MMPs and PKCs primer pairs and PCR conditions for RT-PCR. Table S2. MMPs and PKCs primer pairs and PCR conditions for ChIP assay. Table S3. Antibodies for Western blot analysis. Figure S1. The remaining subset of human cancer cell lines without enhancement of cell migration activity after TSA treatment. Figure S2. Validation of HDACi-enhanced cell migration with treatments of 6 different HDACi. Figure S3. HDACi treatments of HCC and lung cancer cells enhance in vivo experimental metastasis. Figure S4. Treatment of HDACi modulated MMPs and PKCs expressions. Figure S5. The combination treatments of HDACi with MMPi or PKCi repress HDACi-enhanced migration activity. Figure S6. The effects of HDACi and PKCi on tumorigenesis, toxicity and tumor-progressive protein expressions in vivo. Figure S7. Suppressive effects of tumorigenesis and metastasis in liver metastasis model of TSA/Tam and TSA/Cur treated mice.
Supplementary Figure 2 from Myeloid-Derived Suppressor Cells Predict Survival of Patients with Advanced Melanoma: Comparison with Regulatory T Cells and NY-ESO-1- or Melan-A–Specific T Cells
Authors: Weide Benjamin , Martens Alexander , Zelba Henning , Stutz Christina , Derhovanessian Evelyna , Di Giacomo Anna Maria , Maio Michele , Sucker Antje , Schilling Bastian , Schadendorf Dirk , Büttner Petra , Garbe Claus , Pawelec Graham
Published: April 2023

PDF file - 67K, Kaplan-Meier survival curves of the combined cohort of non-resectable stage IV patients.
Supplementary Figure 1 from Myeloid-Derived Suppressor Cells Predict Survival of Patients with Advanced Melanoma: Comparison with Regulatory T Cells and NY-ESO-1- or Melan-A–Specific T Cells
Authors: Weide Benjamin , Martens Alexander , Zelba Henning , Stutz Christina , Derhovanessian Evelyna , Di Giacomo Anna Maria , Maio Michele , Sucker Antje , Schilling Bastian , Schadendorf Dirk , Büttner Petra , Garbe Claus , Pawelec Graham
Published: April 2023

PDF file - 506K, Detailed gating strategy for each analyzed immune cell subset.
Supplementary Figure 2 from Hedgehog–GLI Signaling Inhibition Suppresses Tumor Growth in Squamous Lung Cancer
Authors: Huang Lingling , Walter Vonn , Hayes D. Neil , Onaitis Mark
Published: April 2023

PDF file - 43K, Microarray analysis of human LSCC cell lines.
Supplementary Methods and Tables 1 - 15, 19 from Nonequivalent Gene Expression and Copy Number Alterations in High-Grade Serous Ovarian Cancers with BRCA1 and BRCA2 Mutations
Authors: George Joshy , Alsop Kathryn , Etemadmoghadam Dariush , Hondow Heather , Mikeska Thomas , Dobrovic Alexander , deFazio Anna , Smyth Gordon K. , Levine Douglas A. , Mitchell Gillian , Bowtell David D.
Published: April 2023

PDF file - 338K
Supplementary Table 2 from HER2-Associated Radioresistance of Breast Cancer Stem Cells Isolated from HER2-Negative Breast Cancer Cells
Authors: Duru Nadire , Fan Ming , Candas Demet , Menaa Cheikh , Liu Hsin-Chen , Nantajit Danupon , Wen Yunfei , Xiao Kai , Eldridge Angela , Chromy Brett A. , Li Shiyong , Spitz Douglas R. , Lam Kit S. , Wicha Max S. , Li Jian Jian
Published: April 2023

PDF file - 79K, Peptide and protein HPLC-MS/MS identification data for all proteins included in Table S1
Supplementary Figure 6 from HER2-Associated Radioresistance of Breast Cancer Stem Cells Isolated from HER2-Negative Breast Cancer Cells
Authors: Duru Nadire , Fan Ming , Candas Demet , Menaa Cheikh , Liu Hsin-Chen , Nantajit Danupon , Wen Yunfei , Xiao Kai , Eldridge Angela , Chromy Brett A. , Li Shiyong , Spitz Douglas R. , Lam Kit S. , Wicha Max S. , Li Jian Jian
Published: April 2023

PDF file - 540K, Protein profiling analysis of HER2+ versus HER2- BCSCs
Supplementary Figure 4 from HER2-Associated Radioresistance of Breast Cancer Stem Cells Isolated from HER2-Negative Breast Cancer Cells
Authors: Duru Nadire , Fan Ming , Candas Demet , Menaa Cheikh , Liu Hsin-Chen , Nantajit Danupon , Wen Yunfei , Xiao Kai , Eldridge Angela , Chromy Brett A. , Li Shiyong , Spitz Douglas R. , Lam Kit S. , Wicha Max S. , Li Jian Jian
Published: April 2023

PDF file - 89K, Enhanced gap filling rates in HER2+ versus HER2- BCSCs
Supplementary Figure 2 from HER2-Associated Radioresistance of Breast Cancer Stem Cells Isolated from HER2-Negative Breast Cancer Cells
Authors: Duru Nadire , Fan Ming , Candas Demet , Menaa Cheikh , Liu Hsin-Chen , Nantajit Danupon , Wen Yunfei , Xiao Kai , Eldridge Angela , Chromy Brett A. , Li Shiyong , Spitz Douglas R. , Lam Kit S. , Wicha Max S. , Li Jian Jian
Published: April 2023

PDF file - 36K, Mitochondrial membrane potential in HER2 siRNA treated cells
Supplementary Material from Ligand-Dependent Activation of EGFR in Follicular Dendritic Cells Sarcoma is Sustained by Local Production of Cognate Ligands
Authors: Vermi William , Giurisato Emanuele , Lonardi Silvia , Balzarini Piera , Rossi Elisa , Medicina Daniela , Bosisio Daniela , Sozzani Silvano , Pellegrini Wilma , Doglioni Claudio , Marchetti Antonio , Rossi Giulio , Pileri Stefano , Facchetti Fabio
Published: April 2023

Technical details of the Material and Methods section and legend to Supplementary Figures
Supplementary Figure S4 from Ligand-Dependent Activation of EGFR in Follicular Dendritic Cells Sarcoma is Sustained by Local Production of Cognate Ligands
Authors: Vermi William , Giurisato Emanuele , Lonardi Silvia , Balzarini Piera , Rossi Elisa , Medicina Daniela , Bosisio Daniela , Sozzani Silvano , Pellegrini Wilma , Doglioni Claudio , Marchetti Antonio , Rossi Giulio , Pileri Stefano , Facchetti Fabio
Published: April 2023

Expression of betacellulin (BTC) in pancreatic alpha cells
Supplementary Figure 1 from Inactivation of the CDKN2A Tumor-Suppressor Gene by Deletion or Methylation Is Common at Diagnosis in Follicular Lymphoma and Associated with Poor Clinical Outcome
Authors: Alhejaily Abdulmohsen , Day Andrew G. , Feilotter Harriet E. , Baetz Tara , LeBrun David P.
Published: April 2023

PDF file - 68K, (A) Laser capture microdissection of neoplastic lymphoid follicles. A histological section immunostained for CD20 is shown before and (B) after laser capture microdissection of 4 neoplastic lymphoid follicles.
Supplementary Figure Legends 1-7 from Differential Protein Stability and ALK Inhibitor Sensitivity of EML4-ALK Fusion Variants
Authors: Heuckmann Johannes M. , Balke-Want Hyatt , Malchers Florian , Peifer Martin , Sos Martin L. , Koker Mirjam , Meder Lydia , Lovly Christine M. , Heukamp Lukas C. , Pao William , Küppers Ralf , Thomas Roman K.
Published: April 2023

PDF file - 96K
CCR Translation for This Article from Differential Protein Stability and ALK Inhibitor Sensitivity of EML4-ALK Fusion Variants
Authors: Heuckmann Johannes M. , Balke-Want Hyatt , Malchers Florian , Peifer Martin , Sos Martin L. , Koker Mirjam , Meder Lydia , Lovly Christine M. , Heukamp Lukas C. , Pao William , Küppers Ralf , Thomas Roman K.
Published: April 2023

CCR Translation for This Article from Differential Protein Stability and ALK Inhibitor Sensitivity of EML4-ALK Fusion Variants
Supplementary Table 2 from Next-Generation Sequencing of Translocation Renal Cell Carcinoma Reveals Novel RNA Splicing Partners and Frequent Mutations of Chromatin-Remodeling Genes
Authors: Malouf Gabriel G. , Su Xiaoping , Yao Hui , Gao Jianjun , Xiong Liangwen , He Qiuming , Compérat Eva , Couturier Jérôme , Molinié Vincent , Escudier Bernard , Camparo Philippe , Doss Denaha J. , Thompson Erika J. , Khayat David , Wood Christopher G. , Yu Willie , Teh Bin T. , Weinstein John , Tannir Nizar M.
Published: April 2023

XLSX file - 12K, List of fusion transcripts identified in our dataset with validation accuracy.
Supplementary Figure 1 from Next-Generation Sequencing of Translocation Renal Cell Carcinoma Reveals Novel RNA Splicing Partners and Frequent Mutations of Chromatin-Remodeling Genes
Authors: Malouf Gabriel G. , Su Xiaoping , Yao Hui , Gao Jianjun , Xiong Liangwen , He Qiuming , Compérat Eva , Couturier Jérôme , Molinié Vincent , Escudier Bernard , Camparo Philippe , Doss Denaha J. , Thompson Erika J. , Khayat David , Wood Christopher G. , Yu Willie , Teh Bin T. , Weinstein John , Tannir Nizar M.
Published: April 2023

PDF file - 498K, Coordinate of the exonic breakpoint of the novel KHSRP/TFE3 translocation.
Supplementary Table 1 from PD-L1 Expression Is Characteristic of a Subset of Aggressive B-cell Lymphomas and Virus-Associated Malignancies
Authors: Chen Benjamin J. , Chapuy Bjoern , Ouyang Jing , Sun Heather H. , Roemer Margaretha G.M. , Xu Mina L. , Yu Hongbo , Fletcher Christopher D.M. , Freeman Gordon J. , Shipp Margaret A. , Rodig Scott J.
Published: April 2023

PDF file - 75K, Supplemental Table 1. Pathological Characteristics and PD-L1 Expression in Hodgkin Lymphomas and Related Cases.
Supplementary Table 2 from Identification of KIF5B-RET and GOPC-ROS1 Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions
Authors: Suehara Yoshiyuki , Arcila Maria , Wang Lu , Hasanovic Adnan , Ang Daphne , Ito Tatsuo , Kimura Yuki , Drilon Alexander , Guha Udayan , Rusch Valerie , Kris Mark G. , Zakowski Maureen F. , Rizvi Naiyer , Khanin Raya , Ladanyi Marc
Published: April 2023

PDF file - 308K, Complete list of target sequences for NanoString probes
Supplementary Table 1 from Identification of KIF5B-RET and GOPC-ROS1 Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions
Authors: Suehara Yoshiyuki , Arcila Maria , Wang Lu , Hasanovic Adnan , Ang Daphne , Ito Tatsuo , Kimura Yuki , Drilon Alexander , Guha Udayan , Rusch Valerie , Kris Mark G. , Zakowski Maureen F. , Rizvi Naiyer , Khanin Raya , Ladanyi Marc
Published: April 2023

PDF file - 32K, Clinicopathological characteristics of study cohort
Supplementary Figure 1 from Japonicone A Suppresses Growth of Burkitt Lymphoma Cells through Its Effect on NF-κB
Authors: Li Xiaoguang , Yang Xinying , Liu Yanling , Gong Nuoxi , Yao Wenbo , Chen Peizhan , Qin Jiangjiang , Jin Huizi , Li Jingquan , Chu Ruiai , Shan Lei , Zhang Ruiwen , Zhang Weidong , Wang Hui
Published: April 2023

JA selectively decreases cell growth and viability of various human cancer cells.
Supplementary Figure 1 from Identification of KIF5B-RET and GOPC-ROS1 Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions
Authors: Suehara Yoshiyuki , Arcila Maria , Wang Lu , Hasanovic Adnan , Ang Daphne , Ito Tatsuo , Kimura Yuki , Drilon Alexander , Guha Udayan , Rusch Valerie , Kris Mark G. , Zakowski Maureen F. , Rizvi Naiyer , Khanin Raya , Ladanyi Marc
Published: April 2023

PDF file - 76K, Examples of negative results with the NanoString assay for kinase fusions.
Supplementary Methods from NMS-E973, a Novel Synthetic Inhibitor of Hsp90 with Activity against Multiple Models of Drug Resistance to Targeted Agents, Including Intracranial Metastases
Authors: Fogliatto Gianpaolo , Gianellini Laura , Brasca Maria G. , Casale Elena , Ballinari Dario , Ciomei Marina , Degrassi Anna , De Ponti Anna , Germani Massimiliano , Guanci Marco , Paolucci Mauro , Polucci Paolo , Russo Micaela , Sola Francesco , Valsasina Barbara , Visco Carlo , Zuccotto Fabio , Donati Daniele , Felder Eduard , Pesenti Enrico , Galvani Arturo , Mantegani Sergio , Isacchi Antonella
Published: April 2023

Supplementary Methods - PDF file 56K, Time-lapse imaging of A375 cells
Supplementary Figure S2 from NMS-E973, a Novel Synthetic Inhibitor of Hsp90 with Activity against Multiple Models of Drug Resistance to Targeted Agents, Including Intracranial Metastases
Authors: Fogliatto Gianpaolo , Gianellini Laura , Brasca Maria G. , Casale Elena , Ballinari Dario , Ciomei Marina , Degrassi Anna , De Ponti Anna , Germani Massimiliano , Guanci Marco , Paolucci Mauro , Polucci Paolo , Russo Micaela , Sola Francesco , Valsasina Barbara , Visco Carlo , Zuccotto Fabio , Donati Daniele , Felder Eduard , Pesenti Enrico , Galvani Arturo , Mantegani Sergio , Isacchi Antonella
Published: April 2023

Supplementary Figure S2 - PDF file 456K, Time-lapse imaging of A375 cells treated with NMS-E973
Table S3 from MicroRNA Array Analysis Finds Elevated Serum miR-1290 Accurately Distinguishes Patients with Low-Stage Pancreatic Cancer from Healthy and Disease Controls
Authors: Li Ang , Yu Jun , Kim Haeryoung , Wolfgang Christopher L. , Canto Marcia Irene , Hruban Ralph H. , Goggins Michael
Published: April 2023

Table S3 - XLSX file 152K, Supplemental Table S3. MicroRNAs elevated in serum of pancreatic cancer patients relative to patients with chronic pancreatitis by microarray analysis
Supplementary Figure S1 from NMS-E973, a Novel Synthetic Inhibitor of Hsp90 with Activity against Multiple Models of Drug Resistance to Targeted Agents, Including Intracranial Metastases
Authors: Fogliatto Gianpaolo , Gianellini Laura , Brasca Maria G. , Casale Elena , Ballinari Dario , Ciomei Marina , Degrassi Anna , De Ponti Anna , Germani Massimiliano , Guanci Marco , Paolucci Mauro , Polucci Paolo , Russo Micaela , Sola Francesco , Valsasina Barbara , Visco Carlo , Zuccotto Fabio , Donati Daniele , Felder Eduard , Pesenti Enrico , Galvani Arturo , Mantegani Sergio , Isacchi Antonella
Published: April 2023

Supplementary Figure S1 - PDF file 32K, Chemical structure of NMS-E973
Table S2 from MicroRNA Array Analysis Finds Elevated Serum miR-1290 Accurately Distinguishes Patients with Low-Stage Pancreatic Cancer from Healthy and Disease Controls
Authors: Li Ang , Yu Jun , Kim Haeryoung , Wolfgang Christopher L. , Canto Marcia Irene , Hruban Ralph H. , Goggins Michael
Published: April 2023

Table S2 - XLSX file 12K, Supplemental Table S2. MicroRNAs elevated in serum of pancreatic cancer patients relative to patients with pancreatic neuroendocrine tumors by microarray analysis
Supplementary Legend from MicroRNA Array Analysis Finds Elevated Serum miR-1290 Accurately Distinguishes Patients with Low-Stage Pancreatic Cancer from Healthy and Disease Controls
Authors: Li Ang , Yu Jun , Kim Haeryoung , Wolfgang Christopher L. , Canto Marcia Irene , Hruban Ralph H. , Goggins Michael
Published: April 2023

Supplementary Legend - PDF file 87K Supplementary legend
Supplementary Patient Data from Emergence of Constitutively Active Estrogen Receptor-α Mutations in Pretreated Advanced Estrogen Receptor–Positive Breast Cancer
Authors: Jeselsohn Rinath , Yelensky Roman , Buchwalter Gilles , Frampton Garrett , Meric-Bernstam Funda , Gonzalez-Angulo Ana Maria , Ferrer-Lozano Jaime , Perez-Fidalgo Jose A. , Cristofanilli Massimo , Gómez Henry , Arteaga Carlos L. , Giltnane Jennifer , Balko Justin M. , Cronin Maureen T. , Jarosz Mirna , Sun James , Hawryluk Matthew , Lipson Doron , Otto Geoff , Ross Jeffrey S. , Dvir Addie , Soussan-Gutman Lior , Wolf Ido , Rubinek Tamar , Gilmore Lauren , Schnitt Stuart , Come Steven E. , Pusztai Lajos , Stephens Philip , Brown Myles , Miller Vincent A.
Published: April 2023

XLSX file - 122K
Supplementary Figure 5 from Role of Hedgehog Signaling in Malignant Pleural Mesothelioma
Authors: Shi Yandong , Moura Ubiratan , Opitz Isabelle , Soltermann Alex , Rehrauer Hubert , Thies Svenja , Weder Walter , Stahel Rolf A. , Felley-Bosco Emanuela
Published: April 2023

PDF file, 50K, GLI1 transfection (GLI1) leads to increased expression of GLI1 target HHIP compared to control vector (V) transfected ZL55SPT cells.
Supplementary Materials from Isocitrate Dehydrogenase 1 Is a Novel Plasma Biomarker for the Diagnosis of Non–Small Cell Lung Cancer
Authors: Sun Nan , Chen Zhaoli , Tan Fengwei , Zhang Baihua , Yao Ran , Zhou Chengcheng , Li Jiagen , Gao Yibo , Liu Ziyuan , Tan Xiaogang , Zhou Fang , He Max Y.F , Shao Kang , Li Ning , Qiu Bin , Sun Jian , Yu Yue , Wang Suya , Zhao Yuda , Shi Xuejiao , He Jie
Published: April 2023

Statistical process of grouping and modeling
Supplementary Methods, Figures 1 - 11, Tables 1 - 6 from hERG1 Channels Regulate VEGF-A Secretion in Human Gastric Cancer: Clinicopathological Correlations and Therapeutical Implications
Authors: Crociani Olivia , Lastraioli Elena , Boni Luca , Pillozzi Serena , Romoli Maria Raffaella , D'Amico Massimo , Stefanini Matteo , Crescioli Silvia , Taddei Antonio , Bencini Lapo , Bernini Marco , Farsi Marco , Beghelli Stefania , Scarpa Aldo , Messerini Luca , Tomezzoli Anna , Vindigni Carla , Morgagni Paolo , Saragoni Luca , Giommoni Elisa , Gasperoni Silvia , Di Costanzo Francesco , Roviello Franco , De Manzoni Giovanni , Bechi Paolo , Arcangeli Annarosa
Published: April 2023

PDF file - 738K, ADDITIONAL MATERIALS AND METHODS, FIGURES AND TABLES Fig S1- Immunohistochemical detection of hERG1 protein in GC specimens. Fig S2- hERG1 protein expression in GC primary samples. Figure S3- hERG1b characterization in primary GC. Fig S4- hERG1 protein expression in GC cell lines. Fig S5- hERG1USO protein expression in GC cell lines. Fig S6- Effects of the PI3K/Akt inhibition on VEGF-A secretion in AKG cells under normoxic conditions. Fig S7- Immunohistochemical detection of hERG1 protein in GC specimens. Fig S8- Immunohistochemical detection of hERG1 protein in GC specimens. Fig S9- VEGF-A and hERG1 expression in GC samples. Fig S10. Interaction analyses on OS between hERG1 and other clinical and pathological parameters (Forest Plot). Fig S11- Comparison between herg1a mRNA and hERG1A protein expression in GC samples. Table S1- Antibodies used for IHC experiments described in the main text. Table S2- Primer Sequences. Primers were used for methylation analysis and RQ-PCR. Table S3- Cell lines used in the experiments described in the main text. Table S4- hERG1 expression in AKG cells treated with alpha-hERG1 siRNAs and WAY hERG1 blocker. Table S5- VEGF-A and Kv 1.3 expression in AKG cells treated with alpha-hERG1 siRNAs, WAY hERG1 blocker and alpha-vegf-a siRNA. Table S6- Characteristics of patients excluded and included into the statistical analyses and distributions of clinical and pathological variables after multiple imputation of missing values.
Supplementary Tables 1-4 from Phase I Study of Pazopanib in Patients with Advanced Solid Tumors and Hepatic Dysfunction: A National Cancer Institute Organ Dysfunction Working Group Study
Authors: Shibata Stephen I. , Chung Vincent , Synold Timothy W. , Longmate Jeffrey A. , Suttle A. Benjamin , Ottesen Lone H. , Lenz Heinz-Josef , Kummar Shivaani , Harvey R. Donald , Hamilton Anne L. , O'Neil Bert H. , Sarantopoulos John , LoRusso Patricia , Rudek Michelle A. , Dowlati Afshin , Mulkerin Daniel L. , Belani Chandra P. , Gandhi Leena , Lau S. Cecilia , Ivy S. Percy , Newman Edward M.
Published: April 2023

PDF - 90K, Supplemental Table 1: Most Frequently Reported Adverse Events at Least Possibly Related to Pazopanib Supplemental Table 2: Steady-State Pazopanib Metabolite Pharmacokinetics Measured in All Patients at Week 3 (medians and ranges) Supplemental Table 3: Ratio of Metabolite AUC(0-6) to Pazopanib AUC(0-6) Measured at Steady-State in All Patients at Week 3 (medians and ranges) Supplemental Table 4: First-dose Pazopanib Metabolite Pharmacokinetics in Expanded Cohorts and the Maximum Tolerated Dose (medians and ranges)
Supplementary Figures 1 - 7 from A New Approach to Simultaneously Quantify Both TCR α- and β-Chain Diversity after Adoptive Immunotherapy
Authors: Zhang Minying , Maiti Sourindra , Bernatchez Chantale , Huls Helen , Rabinovich Brian , Champlin Richard E. , Vence Luis M. , Hwu Patrick , Radvanyi Laszlo , Cooper Laurence J.N.
Published: April 2023

PDF file, 264K, Supplementary Fig. S1. TCR Va and Vb gene expression in total RNA from TILs patient 303 and patient 232. Supplementary Fig S2. Global measurement of TCR Va (A-C) and TCR Vb (D-F) gene expression in patient 231 including in vitro rapid expanded TIL (A and D) and PBMC (B-C and E-F) collected after TIL infusion. Supplementary Fig S3. Global measurement of TCR Va (A-D) and TCR Vb (E-H) gene expression in patient 228 including in vitro rapid expanded TIL (A and E) and PBMC (B-D) and (F-H) collected after TIL infusion. Supplementary Fig S4. Global measurement of TCR Va (A-D) and TCR Vb (E-H) gene expression in patient 106 including in vitro rapid expanded TIL (A and E) and PBMC (B-D) and (F-H) collected after TIL infusion. Supplementary Fig S5. Global measurement of TCR Va (A-D) and TCR Vb (E-H) gene expression in patient 172 including in vitro rapid expanded TIL (A and E) and PBMC (B-D) and (F-H) collected after TIL infusion. Supplementary Fig S6. Global measurement of TCR Va (A-D) and TCR Vb (E-H) gene expression in patient 152 including in vitro rapid expanded TIL (A and E) and PBMC (B-D) and (F-H) collected after TIL infusion. Supplementary Fig S7. Global measurement of TCR Va (A-D) and TCR Vb (E-H) gene expression in patient 188 including in vitro rapid expanded TIL (A and E) and PBMC (B-D) and (F-H) collected after TIL infusion.
Supplementary Table 2 from PD-L1 on Tumor Cells Is Induced in Ascites and Promotes Peritoneal Dissemination of Ovarian Cancer through CTL Dysfunction
Authors: Abiko Kaoru , Mandai Masaki , Hamanishi Junzo , Yoshioka Yumiko , Matsumura Noriomi , Baba Tsukasa , Yamaguchi Ken , Murakami Ryusuke , Yamamoto Ayaka , Kharma Budiman , Kosaka Kenzo , Konishi Ikuo
Published: April 2023

XLSX file - 115K, Table S2 shows GO terms enriched in cytoloty-positive cases in KOV-MA-64. Terms colored yellow are terms related to immune system.
Supplementary Figure 2 from PD-L1 on Tumor Cells Is Induced in Ascites and Promotes Peritoneal Dissemination of Ovarian Cancer through CTL Dysfunction
Authors: Abiko Kaoru , Mandai Masaki , Hamanishi Junzo , Yoshioka Yumiko , Matsumura Noriomi , Baba Tsukasa , Yamaguchi Ken , Murakami Ryusuke , Yamamoto Ayaka , Kharma Budiman , Kosaka Kenzo , Konishi Ikuo
Published: April 2023

PDF file - 94K, A list of IFN-γ-up-regulated 57 genes plotted as black vertical bars in Figure 1A is shown. Gene expression levels in cytology-positive and cytology-negative cases in KOV-MA-64 are represented in heat map. Underlined gene name CD274 refers to PD-L1.
Supplementary Methods from Clinical Activity and Safety of Combination Therapy with Temsirolimus and Bevacizumab for Advanced Melanoma: A Phase II Trial (CTEP 7190/Mel47)
Authors: Slingluff Craig L. , Petroni Gina R. , Molhoek Kerrington R. , Brautigan David L. , Chianese-Bullock Kimberly A. , Shada Amber L. , Smolkin Mark E. , Olson Walter C. , Gaucher Alison , Chase Cheryl Murphy , Grosh William W. , Weiss Geoffrey R. , Wagenseller Aubrey G. , Olszanski Anthony J. , Martin Lainie , Shea Sofia M. , Erdag Gulsun , Ram Prahlad , Gershenwald Jeffrey E. , Weber Michael J.
Published: April 2023

PDF file - 155K
Supplementary Table 4 from A 12-Gene Set Predicts Survival Benefits from Adjuvant Chemotherapy in Non–Small Cell Lung Cancer Patients
Authors: Tang Hao , Xiao Guanghua , Behrens Carmen , Schiller Joan , Allen Jeffrey , Chow Chi-Wan , Suraokar Milind , Corvalan Alejandro , Mao Jianhua , White Michael A. , Wistuba Ignacio I. , Minna John D. , Xie Yang
Published: April 2023

PDF file - 104K, Members of the 18-hub gene signature have been included in MSigDB database C2 signature catalogues.
Supplemental Figure 1 from Direct Evidence of Target Inhibition with Anti-VEGF, EGFR, and mTOR Therapies in a Clinical Model of Wound Healing
Authors: Jia Jingquan , Dellinger Andrew E. , Weiss Eric S. , Bulusu Anuradha , Rushing Christel , Li Haiyan , Howard Leigh A. , Kaplan Neal , Pang Herbert , Hurwitz Herbert I. , Nixon Andrew B.
Published: April 2023

Supplemental Figure 1. Changes in average vascular score (AVS) from baseline.
Data Supplement from Efficient Identification of Mutated Cancer Antigens Recognized by T Cells Associated with Durable Tumor Regressions
Authors: Lu Yong-Chen , Yao Xin , Crystal Jessica S. , Li Yong F. , El-Gamil Mona , Gross Colin , Davis Lindy , Dudley Mark E. , Yang James C. , Samuels Yardena , Rosenberg Steven A. , Robbins Paul F.
Published: April 2023

Supplementary Fig. S1. Identification of dominant HLA-restriction element. Supplementary Fig. S2. TIL 2591 T cells recognize multiple known antigens. Supplementary Fig. S3. Gene structure of SERPINE2, DUSP12 and SLC24A5. Supplementary Fig. S4. SLC24A5 WT expression in normal tissue. Supplementary Fig. S5. Gene structure and DNA sequence chromatogram results of KIF2C and POLA2. Supplementary Table S1. Tandem minigene constructs for Mel 2359. Supplementary Table S2. Candidate binding peptides for mutated KIF2C. Supplementary Table S3. Tandem minigene constructs for Mel 2591. Supplementary Table S4. Candidate binding peptides for mutated POLA2.
Data Supplement from T-box Transcription Factor Brachyury Is Associated with Prostate Cancer Progression and Aggressiveness
Authors: Pinto Filipe , Pértega-Gomes Nelma , Pereira Márcia S. , Vizcaíno José R. , Monteiro Pedro , Henrique Rui M. , Baltazar Fátima , Andrade Raquel P. , Reis Rui M.
Published: April 2023

Supplementary Table S1. List of primers used in the present study.
Table S1 from Phosphoinositide 3-Kinase Inhibitors Combined with Imatinib in Patient-Derived Xenograft Models of Gastrointestinal Stromal Tumors: Rationale and Efficacy
Authors: Van Looy Thomas , Wozniak Agnieszka , Floris Giuseppe , Sciot Raf , Li Haifu , Wellens Jasmien , Vanleeuw Ulla , Fletcher Jonathan A. , Manley Paul W. , Debiec-Rychter Maria , Schöffski Patrick
Published: April 2023

Table S1. Study design
Supplementary Figure 5 from BRAF Inhibition Increases Tumor Infiltration by T cells and Enhances the Antitumor Activity of Adoptive Immunotherapy in Mice
Authors: Liu Chengwen , Peng Weiyi , Xu Chunyu , Lou Yanyan , Zhang Minying , Wargo Jennifer A. , Chen Jie Qing , Li Haiyan S. , Watowich Stephanie S. , Yang Yan , Frederick Dennie Tompers , Cooper Zachary A. , Mbofung Rina M. , Whittington Mayra , Flaherty Keith T. , Woodman Scott E. , Davies Michael A. , Radvanyi Laszlo G. , Overwijk Willem W. , Lizée Gregory , Hwu Patrick
Published: April 2023

PDF file - 95K, Tumor antigen expression is important for PLX4720-induced T cell infiltration into tumors
Supplementary Table 2 from Evidence for Efficacy of New Hsp90 Inhibitors Revealed by Ex Vivo Culture of Human Prostate Tumors
Authors: Centenera Margaret M. , Gillis Joanna L. , Hanson Adrienne R. , Jindal Shalini , Taylor Renea A. , Risbridger Gail P. , Sutherland Peter D. , Scher Howard I. , Raj Ganesh V. , Knudsen Karen E. , Yeadon Trina , Tilley Wayne D. , Butler Lisa M.
Published: April 2023

PDF file, 66KB, Immunohistochemistry methodology.
Supplementary Figure 4 from Evidence for Efficacy of New Hsp90 Inhibitors Revealed by Ex Vivo Culture of Human Prostate Tumors
Authors: Centenera Margaret M. , Gillis Joanna L. , Hanson Adrienne R. , Jindal Shalini , Taylor Renea A. , Risbridger Gail P. , Sutherland Peter D. , Scher Howard I. , Raj Ganesh V. , Knudsen Karen E. , Yeadon Trina , Tilley Wayne D. , Butler Lisa M.
Published: April 2023

PDF file, 581KB, Representative (A) Ki67 and (B) cleaved caspase-3 immunostaining in tumors cultured for 48 hours with vehicle control or increasing doses of Hsp90 inhibitors as indicated. Bar = 50�m.
Supplementary Figure 1 from Evidence for Efficacy of New Hsp90 Inhibitors Revealed by Ex Vivo Culture of Human Prostate Tumors
Authors: Centenera Margaret M. , Gillis Joanna L. , Hanson Adrienne R. , Jindal Shalini , Taylor Renea A. , Risbridger Gail P. , Sutherland Peter D. , Scher Howard I. , Raj Ganesh V. , Knudsen Karen E. , Yeadon Trina , Tilley Wayne D. , Butler Lisa M.
Published: April 2023

PDF file, 158KB, Hsp90 inhibitors cause dose dependent inhibition of growth and induction of death in LNCaP prostate cancer cells. LNCaP cells were cultured in medium containing the indicated doses of (A&B) AUY922, (C&D) HSP990 or (E&F) 17-AAG. Cell proliferation (upper panel) and percentage cell death (lower panel) were assessed by trypan blue exclusion. Results are representative of 3 independent experiments and represent the mean � SE of triplicate wells. ANOVA with Tukey's post hoc test: *p<0.01, **p<0.001 treatment versus control.
Figure S5 from Molecular Characterization of Choroid Plexus Tumors Reveals Novel Clinically Relevant Subgroups
Authors: Merino Diana M. , Shlien Adam , Villani Anita , Pienkowska Malgorzata , Mack Stephen , Ramaswamy Vijay , Shih David , Tatevossian Ruth , Novokmet Ana , Choufani Sanaa , Dvir Rina , Ben-Arush Myran , Harris Brent T. , Hwang Eugene I. , Lulla Rishi , Pfister Stefan M. , Achatz Maria Isabel , Jabado Nada , Finlay Jonathan L. , Weksberg Rosanna , Bouffet Eric , Hawkins Cynthia , Taylor Michael D. , Tabori Uri , Ellison David W. , Gilbertson Richard J. , Malkin David
Published: April 2023

Figure S5. Kaplan-Meier curves depicting (A) overall survival and (B) event-free survival estimates of CPCs by ploidy (hyperdiploid: green, hypodiploid: blue). Statistical values were obtained with the Log-rank (Mantel-Cox) test.
Figure S4 from Molecular Characterization of Choroid Plexus Tumors Reveals Novel Clinically Relevant Subgroups
Authors: Merino Diana M. , Shlien Adam , Villani Anita , Pienkowska Malgorzata , Mack Stephen , Ramaswamy Vijay , Shih David , Tatevossian Ruth , Novokmet Ana , Choufani Sanaa , Dvir Rina , Ben-Arush Myran , Harris Brent T. , Hwang Eugene I. , Lulla Rishi , Pfister Stefan M. , Achatz Maria Isabel , Jabado Nada , Finlay Jonathan L. , Weksberg Rosanna , Bouffet Eric , Hawkins Cynthia , Taylor Michael D. , Tabori Uri , Ellison David W. , Gilbertson Richard J. , Malkin David
Published: April 2023

Figure S4. Gene set enrichment analysis (GSEA) comparing the expression of different biological pathways and processes between hypodiploid (red) and hyperdiploid (blue) CPCs. (5% FDR, p<0·05). Visualization was obtained by Cytoscape and Enrichment Map, where each colored circle represents a node, and each line an edge. Nodes represent enriched gene sets annotated by similarity in biological pathway or process. Node size varies according to the number of genes within each gene set. This network has been curated to group similar sub-networks into larger and related networks, and to remove uninformative sub-networks.
Supplementary Table S1 from Development and Validation of Urine-based Peptide Biomarker Panels for Detecting Bladder Cancer in a Multi-center Study
Authors: Frantzi Maria , van Kessel Kim E. , Zwarthoff Ellen C. , Marquez Mirari , Rava Marta , Malats Núria , Merseburger Axel S. , Katafigiotis Ioannis , Stravodimos Konstantinos , Mullen William , Zoidakis Jerome , Makridakis Manousos , Pejchinovski Martin , Critselis Elena , Lichtinghagen Ralph , Brand Korbinian , Dakna Mohammed , Roubelakis Maria G. , Theodorescu Dan , Vlahou Antonia , Mischak Harald , Anagnou Nicholas P.
Published: April 2023

Supplementary Table S1. Clinical and demographical data for the full list of 721 samples from patients with primary UBC, separated in 451 urine samples to be included in the discovery phase and 270 urine samples to be included in the validation phase.
Supplemental Material and Methods from Glycodelin: A New Biomarker with Immunomodulatory Functions in Non–Small Cell Lung Cancer
Authors: Schneider Marc A. , Granzow Martin , Warth Arne , Schnabel Philipp A. , Thomas Michael , Herth Felix J.F. , Dienemann Hendrik , Muley Thomas , Meister Michael
Published: April 2023

Supplemental Material and Methods. More detailed Material and Methods.
Supplementary Figure 2 from Dysregulation of the Repressive H3K27 Trimethylation Mark in Head and Neck Squamous Cell Carcinoma Contributes to Dysregulated Squamous Differentiation
Authors: Gannon Orla M. , Merida de Long Lilia , Endo-Munoz Liliana , Hazar-Rethinam Mehlika , Saunders Nicholas A.
Published: April 2023

PDF file - 1290K, Supplementary Figure 2. siRNA against EZH2 does not induce apoptosis. Detroit 562 cells and primary keratinocytes (HEK) were treated with siRNA against EZH2 for 48 hours or 96 hours and stained with Annexin V/7 aminoactinomycin D and subjected to FACS analysis to determine the proportion of apoptotic cells. a) The ability of siRNA to inhibit EZH2 was determined in the HEKs. β-actin is a loading control. b) EZH2 siRNA did not induce apoptosis after 48 hours or c) 96 hours. Data is mean � SEM, n=2
Supplementary Figure 1 from Dysregulation of the Repressive H3K27 Trimethylation Mark in Head and Neck Squamous Cell Carcinoma Contributes to Dysregulated Squamous Differentiation
Authors: Gannon Orla M. , Merida de Long Lilia , Endo-Munoz Liliana , Hazar-Rethinam Mehlika , Saunders Nicholas A.
Published: April 2023

PDF file - 79K, Supplementary Figure 1. EZH2 expression in HNSCC cell lines. EZH2 expression in Cal27, SCC25 and Detroit 562 cell lines relative to normal keratinocytes was determined in three independent experiments and quantified using Image J. Data is mean � SEM, n=3.
Supplemental Figure 1 from Manipulating the Tumor Microenvironment Ex Vivo for Enhanced Expansion of Tumor-Infiltrating Lymphocytes for Adoptive Cell Therapy
Authors: Chacon Jessica Ann , Sarnaik Amod A. , Chen Jie Qing , Creasy Caitlin , Kale Charuta , Robinson John , Weber Jeffrey , Hwu Patrick , Pilon-Thomas Shari , Radvanyi Laszlo
Published: April 2023

Supplemental Figure 1. Detection of 4-1BB on CD8+ T cells within fresh melanoma tumor fragments and in early tumor fragment cultures.
Supplemental Table 2 from MHC Class I Loss Is a Frequent Mechanism of Immune Escape in Papillary Thyroid Cancer That Is Reversed by Interferon and Selumetinib Treatment In Vitro
Authors: Angell Trevor E. , Lechner Melissa G. , Jang Julie K. , LoPresti Jonathan S. , Epstein Alan L.
Published: April 2023

Supplemental Table 2. Clinical and pathologic data for 33 subjects with papillary thyroid cancer.
Supplemental Figure 4 from MHC Class I Loss Is a Frequent Mechanism of Immune Escape in Papillary Thyroid Cancer That Is Reversed by Interferon and Selumetinib Treatment In Vitro
Authors: Angell Trevor E. , Lechner Melissa G. , Jang Julie K. , LoPresti Jonathan S. , Epstein Alan L.
Published: April 2023

Supplemental Figure 4. Effect of Selumetinib treatment on expression of antigen processing machinery (APM), cytokines, signal transducer of activation and transcription (STAT), and MHC class I molecule genes in thyroid cancer cell lines. Mean fold change in gene expression in papillary thyroid cancer cell lines (A) BCPAP, (B) K-1, or (C) TPC-1 following selumetinib (10μM) treatment relative to vehicle control is shown (statistical significant difference from 1 is indicated by an asterix, p<0.05). All cell lines showed up-regulation of TAP1, STAT1, STAT6, and LMP2 with selumetinib, though these differences did not meet statistical significance. Notably, increases in expression of APM genes were greatest in K-1, the cell line showing greatest phenotypic response to selumetinib treatment. In addition, the expression of IFNγ, IFNα1A, and IFNα2A was down-regulated in BCPAP and TPC-1 and of IFNα2A in K-1, supporting the additive effect of interferon and selumetinib therapy seen in these cell lines. Mean fold change increases in the gene expression of HLA-A, B, C and beta-2 microglobulin (β2m) for each cell line are shown for illustration purposes and paralleled phenotypic changes observed by flow cytometry for these cell lines.
Supplementary Tables 5 - 10 from High-Throughput Detection of Clinically Relevant Mutations in Archived Tumor Samples by Multiplexed PCR and Next-Generation Sequencing
Authors: Bourgon Richard , Lu Shan , Yan Yibing , Lackner Mark R. , Wang Weiru , Weigman Victor , Wang David , Guan Yinghui , Ryner Lisa , Koeppen Hartmut , Patel Rajesh , Hampton Garret M. , Amler Lukas C. , Wang Yulei
Published: April 2023

XLSX file - 602KB, Supplementary Table 5. Cancer cell lines analyzed in this study. Supplementary Table 6. Tumor tissues analyzed in this study. Supplementary Table 7. List of 340 well characterized hotspot mutations interrogated by the amplicon libraries in this study. Variants also assayed by asPCR are indicated. Supplementary Table 8. Variants detected in 66 cancer cell lines, after applying post-processing filters. Note that indels and predicted deleterious SNVs are reported for all interrogated genes and transcripts. Supplementary Table 9. Variants detected in 73 FFPE endometrial tumor tissues, after applying post-processing filters. Note that indels and predicted deleterious SNVs are reported for all interrogated genes and transcripts. Supplementary Table 10. For cell line data, concordance with COSMIC somatic mutation annotation.