bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S1-S10 from Targeting RICTOR Sensitizes SMAD4-Negative Colon Cancer to Irinotecan
Authors: Wong Chen Khuan , Lambert Arthur W. , Ozturk Sait , Papageorgis Panagiotis , Lopez Delia , Shen Ning , Sen Zaina , Abdolmaleky Hamid M. , Győrffy Balázs , Feng Hui , Thiagalingam Sam
Published: April 2023

S1: SMAD4+/+ and SMAD4-/- colon cancer cells were serum-starved and seeded on transwells and allowed to cross the membrane for 24 hours (transwell migration; RFU, relative fluorescence unit; mean {plus minus} SD, n = 3 biological replicates; **P < 0.01). S2: RICTOR depletion in SMAD4-negative colon cancer cells using shRNA#2 was measured by RT-qPCR (RT-qPCR; mean {plus minus} SD, n = 3 technical replicates; ***P < 0.001). B, Western blotting shows the relative levels of RICTOR, p-AKTS473, and cleaved-caspase 3 upon knockdown of RICTOR and in response to irinotecan. C, The indicated cell lines were treated with irinotecan (10μM) for 72 hours. S3: Cells depleted of RICTOR were serum starved and seeded on transwells and allowed to cross the membrane for 24 hours (transwell migration; RFU, relative fluorescence unit; mean {plus minus} SD, n = 6 biological replicates; ***P < 0.001). S4: A, Western blot shows the relative levels of RICTOR and p-AKTS47 in SW403 cells upon transfection with the indicated siRNAs. B, siRNA-transfected SW403 cells were treated with irinotecan (10μM) for 120 hours. Viability of cells was normalized to DMSO-treated controls (cell viability assay; mean {plus minus} SD, n = 3 biological replicates; **P < 0.01). S5: High RICTOR/AKT1 expression correlates with worse survival in colon cancer. S6: Targeting AKT with MK2206 sensitizes SMAD4-negative SW403 colon cancer cells to irinotecan. S7: Targeting AKT with either AKTi-1/2 or MK2206 sensitizes SMAD4-negative colon cancer cells to irinotecan. S8: No toxicity observed in mice exposed to MK2206 and irinotecan. S9: Targeting AKT with MK2206 sensitizes SMAD4-negative ASPC1 and CFPAC1 pancreatic cancer cells to irinotecan. S10: In silico Kaplan-Meier analyses showing the correlation between SMAD4, RICTOR, or AKT1 expression and overall survival (OS) in pancreatic cancer patients.
Supplemental Table 1 from Aberrant LPL Expression, Driven by STAT3, Mediates Free Fatty Acid Metabolism in CLL Cells
Authors: Rozovski Uri , Grgurevic Srdana , Bueso-Ramos Carlos , Harris David M. , Li Ping , Liu Zhiming , Wu Ji Yuan , Jain Preetesh , Wierda William , Burger Jan , O'Brien Susan , Jain Nitin , Ferrajoli Alessandra , Keating Michael J. , Estrov Zeev
Published: April 2023

Supplemental Table 1. Patient Characteristics
Supplementary Data from αvβ3 Integrin Mediates Radioresistance of Prostate Cancer Cells through Regulation of Survivin
Authors: Wang Tao , Huang Jiayi , Vue Mai , Alavian Michael R. , Goel Hira Lal , Altieri Dario C. , Languino Lucia R. , FitzGerald Thomas J.
Published: April 2023

SF legend
Figure S5 from αvβ3 Integrin Mediates Radioresistance of Prostate Cancer Cells through Regulation of Survivin
Authors: Wang Tao , Huang Jiayi , Vue Mai , Alavian Michael R. , Goel Hira Lal , Altieri Dario C. , Languino Lucia R. , FitzGerald Thomas J.
Published: April 2023

siRNA doses
Figure S2 from αvβ3 Integrin Mediates Radioresistance of Prostate Cancer Cells through Regulation of Survivin
Authors: Wang Tao , Huang Jiayi , Vue Mai , Alavian Michael R. , Goel Hira Lal , Altieri Dario C. , Languino Lucia R. , FitzGerald Thomas J.
Published: April 2023

alphaV and beta1 in PC-3 beta3 shRNA
Supplementary Figure Legends from Defective Myb Function Ablates Cyclin E1 Expression and Perturbs Intestinal Carcinogenesis
Authors: Cheasley Dane , Pereira Lloyd , Sampurno Shienny , Sieber Oliver , Jorissen Robert , Xu Huiling , Germann Markus , Yuqian Yan , Ramsay Robert G. , Malaterre Jordane
Published: April 2023

Supplementary Figure Legends
Figure S1 from αvβ3 Integrin Mediates Radioresistance of Prostate Cancer Cells through Regulation of Survivin
Authors: Wang Tao , Huang Jiayi , Vue Mai , Alavian Michael R. , Goel Hira Lal , Altieri Dario C. , Languino Lucia R. , FitzGerald Thomas J.
Published: April 2023

alphaV and beta1 in LNCaP transfectants
Supplementary Table S2 from Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value
Authors: Cheng Chao , Lou Shaoke , Andrews Erik H. , Ung Matthew H. , Varn Frederick S.
Published: April 2023

Regulatory programs associated with three subtypes of liposarcoma
Supplementary Table S1 from Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value
Authors: Cheng Chao , Lou Shaoke , Andrews Erik H. , Ung Matthew H. , Varn Frederick S.
Published: April 2023

Regulatory programs associated with liposcarcoma
Supplementary Figures S1-S3 from Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value
Authors: Cheng Chao , Lou Shaoke , Andrews Erik H. , Ung Matthew H. , Varn Frederick S.
Published: April 2023

Supplementary Figures S1-S3
Supplementary Information from The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus
Authors: Sakurai Kouhei , Reon Brian J. , Anaya Jordan , Dutta Anindya
Published: April 2023

Supplementary Information. Supplementary material and method, figure legend and references
Supplementary Material from Colorectal Carcinogenesis: Connecting K-RAS–Induced Transformation and CREB Activity In Vitro and In Vivo
Authors: Steven André , Heiduk Max , Recktenwald Christian V. , Hiebl Bernhard , Wickenhauser Claudia , Massa Chiara , Seliger Barbara
Published: April 2023

Supplementary Methods, Figure Legends and Tables Supplementary Table I: Inhibitors used in this study Supplementary Table II: Summary of primers used for murine (m) and human (h) samples Supplementary Table III: Primer for murine promoter constructs and mutagenesis primer
Supplemental Figure S2 from The Histone Demethylase Jumonji Coordinates Cellular Senescence Including Secretion of Neural Stem Cell–Attracting Cytokines
Authors: Perrigue Patrick M. , Silva Michael E. , Warden Charles D. , Feng Nathan L. , Reid Michael A. , Mota Daniel J. , Joseph Lauren P. , Tian Yangzi Isabel , Glackin Carlotta A. , Gutova Margarita , Najbauer Joseph , Aboody Karen S. , Barish Michael E.
Published: April 2023

Figure S2. (A) U251.JMJD3wt cells lack γH2AX foci. U251.JMJD3wt cells immunostained for γH2AX foci (red) and counterstained with DAPI (blue). As a positive control for γH2AX foci formation, U251.JMJD3wt cells were irradiated (Cs137 source) with 10 Gy γ-radiation and examined after 24 hr. Note the absence of γH2AX foci in untreated U251.JMJD3wt cells. Scale bar = 10 µm. (B) Western blot for γH2AX in U251.JMJD3 cells showing the relative deficit of γH2AX in non-irradiated cells.
Supplementary Table from PPARδ Interacts with the Hippo Coactivator YAP1 to Promote SOX9 Expression and Gastric Cancer Progression
Authors: Song Shumei , Wang Zhenning , Li Yuan , Ma Lang , Jin Jiankang , Scott Ailing W. , Xu Yan , Estrella Jeannelyn Santiano , Song Yongxi , Liu Bin , Johnson Randy L. , Ajani Jaffer A.
Published: April 2023

Supplementary Table 1
Supplemental Table 1 from Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome
Authors: Fu Leiping , Minton Denise R. , Zhang Tuo , Nanus David M. , Gudas Lorraine J.
Published: April 2023

Supplemental Table 1. Summary of number of reads for each sample.
Supplemental Figure 1 from Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome
Authors: Fu Leiping , Minton Denise R. , Zhang Tuo , Nanus David M. , Gudas Lorraine J.
Published: April 2023

Supplemental Figure 1. Validation of some metabolic genes by semi-quantitative PCR.
Supplementary Tables 1-11 from Clinical Characteristics and Exploratory Genomic Analyses of Germline BRCA1 or BRCA2 Mutations in Breast Cancer
Authors: Park Sehhoon , Lee Eunjin , Park Seri , Lee Sohee , Nam Seok Jin , Kim Seok Won , Lee Jeong Eon , Yu Jong-Han , Kim Ji-Yeon , Ahn Jin Seok , Im Young-Hyuck , Park Woong-Yang , Park Kyunghee , Park Yeon Hee
Published: April 2023

Table S1. List of 381 genes from CancerSCANTM Table S2. gBRCA1/2 mutation profile of study population. Table S3. Raw data for differentially expressed genes found by comparing gBRCA1 and gBRCA2 mutants. Table S4. Raw GSVA data derived by comparing gBRCA1 and gBRCA2 mutants. Table S5. Raw data for differentially expressed genes found by comparing patients with mutated and wild-type gBRCA1/2. Table S6. Raw GSVA data derived by comparing patients with mutated and wild-type gBRCA1/2. Table S7. Raw data for differentially expressed genes found by comparing mutated and wild-type gBRCA1 in triple negative patients. Table S8. Raw GSVA data derived by comparing mutated and wild-type gBRCA1 in triple negative patients. Table S9. Raw data for differentially expressed genes found by comparing mutated and wild-type gBRCA2 in estrogen receptor-positive patients. Table S10. Raw GSVA data derived by comparing mutated and wild-type gBRCA2 in estrogen receptor-positive patients. Table S11. Loss of heterozygosity status and the allele frequency of samples available for the target sequencing.
Supplementary Movie 1 from Structure, Dynamics, and Functionality of Tankyrase Inhibitor-Induced Degradasomes
Authors: Thorvaldsen Tor Espen , Pedersen Nina Marie , Wenzel Eva M. , Schultz Sebastian W. , Brech Andreas , Liestøl Knut , Waaler Jo , Krauss Stefan , Stenmark Harald
Published: April 2023

GFP-TNKS1 puncta are rapidly induced upon G007-LK-treatment of SW480 cells.
Supplementary Figure 7 from Structure, Dynamics, and Functionality of Tankyrase Inhibitor-Induced Degradasomes
Authors: Thorvaldsen Tor Espen , Pedersen Nina Marie , Wenzel Eva M. , Schultz Sebastian W. , Brech Andreas , Liestøl Knut , Waaler Jo , Krauss Stefan , Stenmark Harald
Published: April 2023

Fluorescence recovery after photobleaching (FRAP) reveals different dynamic properties of Î²-catenin and TNKS in G007-LK-induced degradasomes.
Supplementary Figure S5 from UBE2C Is Upregulated by Estrogen and Promotes Epithelial–Mesenchymal Transition via p53 in Endometrial Cancer
Authors: Liu Yan , Zhao Rong , Chi Shuqi , Zhang Wei , Xiao Chengyu , Zhou Xing , Zhao Yingchao , Wang Hongbo
Published: April 2023

UBE2C mRNA expression is induced by E2 stimulation in EC cell lines.
Supplementary Figure 5 from Structure, Dynamics, and Functionality of Tankyrase Inhibitor-Induced Degradasomes
Authors: Thorvaldsen Tor Espen , Pedersen Nina Marie , Wenzel Eva M. , Schultz Sebastian W. , Brech Andreas , Liestøl Knut , Waaler Jo , Krauss Stefan , Stenmark Harald
Published: April 2023

Degradasomes target Î²-catenin for proteasomal degradation.
Supplementary Figure 4 from Structure, Dynamics, and Functionality of Tankyrase Inhibitor-Induced Degradasomes
Authors: Thorvaldsen Tor Espen , Pedersen Nina Marie , Wenzel Eva M. , Schultz Sebastian W. , Brech Andreas , Liestøl Knut , Waaler Jo , Krauss Stefan , Stenmark Harald
Published: April 2023

Degradasomes are highly dynamic complexes in terms of assembly and disassembly.
Supplementary Figure 1 from Structure, Dynamics, and Functionality of Tankyrase Inhibitor-Induced Degradasomes
Authors: Thorvaldsen Tor Espen , Pedersen Nina Marie , Wenzel Eva M. , Schultz Sebastian W. , Brech Andreas , Liestøl Knut , Waaler Jo , Krauss Stefan , Stenmark Harald
Published: April 2023

Stably expressed GFP-TNKS1 localizes to TNKSi-induced degradasomes in SW480 cells.
Supplementary tables from High-Fat Diet-Induced Complement Activation Mediates Intestinal Inflammation and Neoplasia, Independent of Obesity
Authors: Doerner Stephanie K. , Reis Edimara S. , Leung Elaine S. , Ko Justine S. , Heaney Jason D. , Berger Nathan A. , Lambris John D. , Nadeau Joseph H.
Published: April 2023

Supplemental Table 1. Composition of hydrogenated coconut, corn and olive oil diets. Supplemental Table 2. Supplementary Table 2. Primers for testing expression levels of metabolic marker genes. Supplementary Table 3. B6 and CSS strains after 60 days on the coconut diet: Final body weight (FBW), epididymal fat pad mass (EFPM), body mass index (BMI), fasting insulin, fasting glucose, HOMA-IR and total polyp number. Supplementary Table 4. B6.Apc+/+ and B6.ApcMin/+ after 30 or 60 days on the coconut, corn or olive oil diets: Final body weight (FBW), epididymal fat pad mass (EFPM), body mass index (BMI), fasting insulin, fasting glucose, and total polyp number. Supplementary Table 5. Complement C5aR-deficient and mice treated with the C5aR inhibitor after 30 days on the coconut diet: Final body weight (FBW), epididymal fat pad mass (EFPM), body mass index (BMI), fasting insulin, fasting glucose, and total polyp number.
Supplementary figure 3 from High-Fat Diet-Induced Complement Activation Mediates Intestinal Inflammation and Neoplasia, Independent of Obesity
Authors: Doerner Stephanie K. , Reis Edimara S. , Leung Elaine S. , Ko Justine S. , Heaney Jason D. , Berger Nathan A. , Lambris John D. , Nadeau Joseph H.
Published: April 2023

S3. HFD induces generation of C5a independent of obesity status.
Supplemental figure S2 from Detection of Tumor Suppressor Genes in Cancer Development by a Novel shRNA-Based Method
Authors: von Burstin Johannes , Diersch Sandra , Schneider Günter , Reichert Maximilian , Rustgi Anil K. , Schmid Roland M.
Published: April 2023

Supplemental Figure S2: shRNA mediated loss of tumor suppressor genes results in liver metastasis. Histology shows microscopic liver metastasis that developed in animals that received Kras-shRNAp16Ink4a #2-PDCs or Kras-shRNATrp53-PDCs. Of note animals that were implanted with Kras-shRNAp16Ink4a #1-PDCs did not develop liver metastasis.
Data Supplement from Nonamplified FGFR1 Is a Growth Driver in Malignant Pleural Mesothelioma
Authors: Marek Lindsay A. , Hinz Trista K. , von Mässenhausen Anne , Olszewski Kyle A. , Kleczko Emily K. , Boehm Diana , Weiser-Evans Mary C. , Nemenoff Raphael A. , Hoffmann Hans , Warth Arne , Gozgit Joseph M. , Perner Sven , Heasley Lynn E.
Published: April 2023

Figure S1. Fluorescence in situ hybridization (FISH) analysis of FGFR1 gene copy number status in mesothelioma cell lines. Figure S2. Bioluminescence imaging of orthotopically implanted H226 tumors treated with or without ponatinib. Supplementary Tables S1 through S3.
table S1 from Treatment Efficacy and Resistance Mechanisms Using the Second-Generation ALK Inhibitor AP26113 in Human NPM-ALK–Positive Anaplastic Large Cell Lymphoma
Authors: Ceccon M. , Mologni L. , Giudici G. , Piazza R. , Pirola A. , Fontana D. , Gambacorti-Passerini C.
Published: April 2023

Table S1. IC50 values obtained for all Ba/F3 NPM-ALK and KARPAS-derived cell lines are shown. ) RR index corresponding to each IC50 value is reported. Green: RR < 2. Yellow: RR = 2.1-4. Orange: RR = 4.1 - 10 Red: RR > 10. Data are the average from at least 2 independent experiments.
figure supplementary 6 from Treatment Efficacy and Resistance Mechanisms Using the Second-Generation ALK Inhibitor AP26113 in Human NPM-ALK–Positive Anaplastic Large Cell Lymphoma
Authors: Ceccon M. , Mologni L. , Giudici G. , Piazza R. , Pirola A. , Fontana D. , Gambacorti-Passerini C.
Published: April 2023

Supplementary Figure 6. ALK kinase domain (PDB code 3LCS) is depicted. Residues mutated in AP26113 resistant SUP-M2 derived cell lines are highlighted. The aC helix is shown in purple. The short helix following aDFG motif and activation -loop (A-loop) are in green.
Figure S2 from Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin–Independent Targets by Proteomics
Authors: Popow Olesja , Paulo João A. , Tatham Michael H. , Volk Melanie S. , Rojas-Fernandez Alejandro , Loyer Nicolas , Newton Ian P. , Januschke Jens , Haigis Kevin M. , Näthke Inke
Published: April 2023

Validation of APC interactors identified by AE-MS
Data Supplement from Targeting TBK1 Inhibits Migration and Resistance to MEK Inhibitors in Mutant NRAS Melanoma
Authors: Vu Ha Linh , Aplin Andrew E.
Published: April 2023

Supplementary Table 1. Mutant NRAS cell lines used.
Supporting Information Figure Legends from Estrogen Drives Cellular Transformation and Mutagenesis in Cells Expressing the Breast Cancer–Associated R438W DNA Polymerase Lambda Protein
Authors: Nemec Antonia A. , Bush Korie B. , Towle-Weicksel Jamie B. , Taylor B. Frazier , Schulz Vincent , Weidhaas Joanne B. , Tuck David P. , Sweasy Joann B.
Published: April 2023

Supporting Information Figure Legends from Estrogen Drives Cellular Transformation and Mutagenesis in Cells Expressing the Breast Cancer–Associated R438W DNA Polymerase Lambda Protein
Supplementary Table 1 from MELK and EZH2 Cooperate to Regulate Medulloblastoma Cancer Stem-like Cell Proliferation and Differentiation
Authors: Liu Hailong , Sun Qianwen , Sun Youliang , Zhang Junping , Yuan Hongyu , Pang Shuhuan , Qi Xueling , Wang Haoran , Zhang Mingshan , Zhang Hongwei , Yu Chunjiang , Gu Chunyu
Published: April 2023

Table S1. Univariate and multivariate analysis by Cox proportional model.
Supplementary Figure 5 from MELK and EZH2 Cooperate to Regulate Medulloblastoma Cancer Stem-like Cell Proliferation and Differentiation
Authors: Liu Hailong , Sun Qianwen , Sun Youliang , Zhang Junping , Yuan Hongyu , Pang Shuhuan , Qi Xueling , Wang Haoran , Zhang Mingshan , Zhang Hongwei , Yu Chunjiang , Gu Chunyu
Published: April 2023

Daoy CSCs were treated with the indicated concentration of OTSSP167, DZNep and combination of both inhibitors for 42 h and proliferation was measured by MTT. No significant differences existed in the three therapeutic groups (p = 0.31).
Supplementary Figure Legends from G-Protein-Coupled Estrogen Receptor 1 Promotes Gender Disparities in Hepatocellular Carcinoma via Modulation of SIN1 and mTOR Complex 2 Activity
Authors: Feng Guanying , Cai Jingshu , Huang Yunchuanxiang , Zhu Xianjun , Gong Bo , Yang Zhenglin , Yan Chunhong , Hu Zhuowei , Yang Lu , Wang Ziyan
Published: April 2023

Supplementary Figure Legends 1-8
Supplementary Figure 3 from MELK and EZH2 Cooperate to Regulate Medulloblastoma Cancer Stem-like Cell Proliferation and Differentiation
Authors: Liu Hailong , Sun Qianwen , Sun Youliang , Zhang Junping , Yuan Hongyu , Pang Shuhuan , Qi Xueling , Wang Haoran , Zhang Mingshan , Zhang Hongwei , Yu Chunjiang , Gu Chunyu
Published: April 2023

MELK and EZH2 profiles in SHH-MB.
Supplementary Figure 1 from MELK and EZH2 Cooperate to Regulate Medulloblastoma Cancer Stem-like Cell Proliferation and Differentiation
Authors: Liu Hailong , Sun Qianwen , Sun Youliang , Zhang Junping , Yuan Hongyu , Pang Shuhuan , Qi Xueling , Wang Haoran , Zhang Mingshan , Zhang Hongwei , Yu Chunjiang , Gu Chunyu
Published: April 2023

A-B, Expression of MELK and EZH2 in pan-cancers from TCGA database. C, Correlation between MELK and EZH2 in SHH associated MB from GSE50765 dataset. D, Correlation between MELK and EZH2 mRNA relative expression in GBM from TCGA database.
Figure S4 from G-Protein-Coupled Estrogen Receptor 1 Promotes Gender Disparities in Hepatocellular Carcinoma via Modulation of SIN1 and mTOR Complex 2 Activity
Authors: Feng Guanying , Cai Jingshu , Huang Yunchuanxiang , Zhu Xianjun , Gong Bo , Yang Zhenglin , Yan Chunhong , Hu Zhuowei , Yang Lu , Wang Ziyan
Published: April 2023

Figure S4 reveals tha estrogen promotes the nuclear accumulation of Sin1.
Supplemental Figure S6 from Disruption of Proline Synthesis in Melanoma Inhibits Protein Production Mediated by the GCN2 Pathway
Authors: Kardos Gregory R. , Wastyk Hannah C. , Robertson Gavin P.
Published: April 2023

Supplemental Figure S6. P5CS protein knockdown did not consistently affect hydrogen peroxide or ROS levels.
Supplementary Table S4 from The ERG-Regulated LINC00920 Promotes Prostate Cancer Cell Survival via the 14-3-3ϵ–FOXO Pathway
Authors: Angeles Arlou Kristina , Heckmann Doreen , Flosdorf Niclas , Duensing Stefan , Sültmann Holger
Published: April 2023

Sequences of biotinylated antisense ssDNA 20-mers used in chromatin isolation by RNA precipitation (ChIRP).
Figure S1 from R-spondin2 Suppresses the Progression of Hepatocellular Carcinoma via MAPK Signaling Pathway
Authors: Zheng Chang , Zhou Fan , Shi Liang Liang , Xu Gui Fang , Zhang Bin , Wang Lei , Zhuge Yuzheng , Zou Xiao Ping , Wang Yi
Published: April 2023

Figure S1. (A) Representative IHC images of negative control and normal liver tissues from 10 patients with hepatic hemangioma (100X, 200X). (B) Western blot assay of R-spondin1, R-spondin3 and β-actin in PLC/PRF/5, Hep-3B, Hep-C2, Huh-7, MHCC-97L and HCCL-M3 cells. (C) Western blot assay of R-spondin2 in Huh-7 and HCCL-M3 treated with an brefeldin A (0, 10, 50, 100 ng/ml). (D) Coomassie Blue Staining assay of total protein and western blot assay of R-spondin1, R-spondin2, R-spondin3 in cell culture supernatant of these six HCC cell lines. (C) R-spondin2 protein expression levels were not significantly down-regulated in Hep-3B and PLC/PRF/5 cells by sh2 according to western blot assay. (D) Western blot assay of R-spondin1, R-spondin2, R-spondin3 and β-actin in PLC/PRF/5-NC, PLC/PRF/5-sh1, Hep-3B-NC and Hep-3B-sh1.
Supplementary Figure S3 from Metabolic Profiling of Formalin-Fixed Paraffin-Embedded Tissues Discriminates Normal Colon from Colorectal Cancer
Authors: Arima Kota , Lau Mai Chan , Zhao Melissa , Haruki Koichiro , Kosumi Keisuke , Mima Kosuke , Gu Mancang , Väyrynen Juha P. , Twombly Tyler S. , Baba Yoshifumi , Fujiyoshi Kenji , Kishikawa Junko , Guo Chunguang , Baba Hideo , Richards William G. , Chan Andrew T. , Nishihara Reiko , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giannakis Marios , Fuchs Charles S. , Ogino Shuji
Published: April 2023

Supplementary Figure S3. (A, B): Principal component (PC) analysis plot showing the distribution of the tumor and normal tissues in FFPE samples in the top two PC space before (A) and after (B) removal of 2 FFPE samples. (C, D): PC analysis plot showing the distribution of the tumor and normal tissues in fresh frozen samples in first and second PC (C) as well as first and third PC (D); whereby the analysis was conducted using the Spearman correlation between the tumor and normal samples on the 200 (A, B) and 536 (C, D) detected metabolites. FFPE, formalin-fixed paraffin-embedded; PC, principal component.
Supplementary Data from Prostate Epithelial RON Signaling Promotes M2 Macrophage Activation to Drive Prostate Tumor Growth and Progression
Authors: Sullivan Camille , Brown Nicholas E. , Vasiliauskas Juozas , Pathrose Peterson , Starnes Sandra L. , Waltz Susan E.
Published: April 2023

Supplementary Methods
Supplementary Figure S2 from Metabolic Profiling of Formalin-Fixed Paraffin-Embedded Tissues Discriminates Normal Colon from Colorectal Cancer
Authors: Arima Kota , Lau Mai Chan , Zhao Melissa , Haruki Koichiro , Kosumi Keisuke , Mima Kosuke , Gu Mancang , Väyrynen Juha P. , Twombly Tyler S. , Baba Yoshifumi , Fujiyoshi Kenji , Kishikawa Junko , Guo Chunguang , Baba Hideo , Richards William G. , Chan Andrew T. , Nishihara Reiko , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giannakis Marios , Fuchs Charles S. , Ogino Shuji
Published: April 2023

Supplementary Figure S2. Distribution of carbohydrates, xenobiotics, cofactors and vitamins, and energy in tumor and normal. (A-D): Heatmap of 8 carbohydrates (A), 7 xenobiotics (B), 7 cofactors and vitamins (C), and 7 energy metabolites (D) sorted by sample types and then tissue types. Heat-map colors represent z-score values of raw detection amount. FFPE, formalin-fixed paraffin-embedded; N, normal; T, tumor.
Supplemental Figure 2 from Prostate Epithelial RON Signaling Promotes M2 Macrophage Activation to Drive Prostate Tumor Growth and Progression
Authors: Sullivan Camille , Brown Nicholas E. , Vasiliauskas Juozas , Pathrose Peterson , Starnes Sandra L. , Waltz Susan E.
Published: April 2023

Supplemental Figure 2. Prostate weights from mice used to evaluate metastasis.
Supplementary Tables 1-3 from Cooperative Dynamics of AR and ER Activity in Breast Cancer
Authors: D'Amato Nicholas C. , Gordon Michael A. , Babbs Beatrice , Spoelstra Nicole S. , Carson Butterfield Kiel T. , Torkko Kathleen C. , Phan Vernon T. , Barton Valerie N. , Rogers Thomas J. , Sartorius Carol A. , Elias Anthony , Gertz Jason , Jacobsen Britta M. , Richer Jennifer K.
Published: April 2023

S1. E2 induces AR binding at sites that overlap with ER binding. S2. Enza alters expression of E2-regulated genes in PT12 xenograft tumors. S3. Pathway analysis of Enza-regulated genes in PT12 xenograft tumors.
Supplementary Methods from Cooperative Dynamics of AR and ER Activity in Breast Cancer
Authors: D'Amato Nicholas C. , Gordon Michael A. , Babbs Beatrice , Spoelstra Nicole S. , Carson Butterfield Kiel T. , Torkko Kathleen C. , Phan Vernon T. , Barton Valerie N. , Rogers Thomas J. , Sartorius Carol A. , Elias Anthony , Gertz Jason , Jacobsen Britta M. , Richer Jennifer K.
Published: April 2023

Supplementary Methods
Supplemental Table 2 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma
Authors: Walline Heather M. , Komarck Christine M. , McHugh Jonathan B. , Bellile Emily L. , Brenner J. Chad , Prince Mark E. , McKean Erin L. , Chepeha Douglas B. , Wolf Gregory T. , Worden Francis P. , Bradford Carol R. , Carey Thomas E.
Published: April 2023

TaqMan quantitative RT-PCR assay primer and probe sequences.
Supplementary Movie 1 from Relocation of CLIC1 Promotes Tumor Cell Invasion and Colonization of Fibrin
Authors: Gurski Lisa A. , Knowles Lynn M. , Basse Per H. , Maranchie Jodi K. , Watkins Simon C. , Pilch Jan
Published: April 2023

Live cell imaging of fibrin-embedded shSCR 786-O cells.
Supplemental Figure 2 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma
Authors: Walline Heather M. , Komarck Christine M. , McHugh Jonathan B. , Bellile Emily L. , Brenner J. Chad , Prince Mark E. , McKean Erin L. , Chepeha Douglas B. , Wolf Gregory T. , Worden Francis P. , Bradford Carol R. , Carey Thomas E.
Published: April 2023

Differential mRNA expression of genes with copy number alterations. The relative mRNA expression of amplified genes was assessed across the all publically available next generation sequencing data where matched genome or exome-sequencing and transcriptome sequencing were available using the Oncomine database. Three plots were generated for each gene with copy number alterations, the respective gene is indicated on top of the plot. RNA expression was not evaluable for TCGA-CN-A49A, which harbored a SMOC1 amplification. DNA copy number calculated from exome or whole genome sequencing data is shown along the x-axis and absolute fragments per kilobase million are shown along the y-axis (Values are presented as Log base 2). Samples within the plots have either do not have genomic alterations or have mutations, gene fusions or copy number alterations as indicated in the inset legend. Blue dashed line indicates the limit for calling genomic deletions and the pink line for genomic amplifications. The black line indicates best fit for correlation between DNA copy number and gene expression.
Supplementary Figure Legends from Adapting a Drug Screening Platform to Discover Associations of Molecular Targeted Radiosensitizers with Genomic Biomarkers
Authors: Liu Qi , Wang Meng , Kern Ashley M. , Khaled Saman , Han Jing , Yeap Beow Y. , Hong Theodore S. , Settleman Jeff , Benes Cyril H. , Held Kathryn D. , Efstathiou Jason A. , Willers Henning
Published: April 2023

Legends for Suppl. Fig. 1-6
Suppl. Table 1 from Adapting a Drug Screening Platform to Discover Associations of Molecular Targeted Radiosensitizers with Genomic Biomarkers
Authors: Liu Qi , Wang Meng , Kern Ashley M. , Khaled Saman , Han Jing , Yeap Beow Y. , Hong Theodore S. , Settleman Jeff , Benes Cyril H. , Held Kathryn D. , Efstathiou Jason A. , Willers Henning
Published: April 2023

Suppl. Table 1. Excel table containing all drug/cell line combination data
Supplemental Method from p53 and ΔNp63α Coregulate the Transcriptional and Cellular Response to TGFβ and BMP Signals
Authors: Balboni Amanda L. , Cherukuri Pratima , Ung Matthew , DeCastro Andrew J. , Cheng Chao , DiRenzo James
Published: April 2023

Supplemental Method. Oligonucleotide sequences used to amplify regions of the ID2 regulatory region in ChIP and ChIP-reChIP studies
Supplemental Figure S4 from p53 and ΔNp63α Coregulate the Transcriptional and Cellular Response to TGFβ and BMP Signals
Authors: Balboni Amanda L. , Cherukuri Pratima , Ung Matthew , DeCastro Andrew J. , Cheng Chao , DiRenzo James
Published: April 2023

Supplemental Figure S4. Shared genes among p63 and BMP gene sets. Overlap between p63 target genes (PEREZ_TP63_TARGETS) and BMP pathway genes (PID_BMPPATHWAY) from the MSigDB database.
Supplemental Figure S3 from p53 and ΔNp63α Coregulate the Transcriptional and Cellular Response to TGFβ and BMP Signals
Authors: Balboni Amanda L. , Cherukuri Pratima , Ung Matthew , DeCastro Andrew J. , Cheng Chao , DiRenzo James
Published: April 2023

Supplemental Figure S3. Shared P63 and Smad3 target genes enriched during TGFβ induced EMT. Analysis of shared p63 and Smad3 target genes enriched during a time course of TGFβ induced EMT. Each time point following TGFβ treatment is compared to time t=0. P63 and Smad3 targets were downloaded from the CHEA data base (PMID: TP63-17297297 and SMAD3-18955504).
Supplemental Table 1 from Calcipotriol Targets LRP6 to Inhibit Wnt Signaling in Pancreatic Cancer
Authors: Arensman Michael D. , Nguyen Phillip , Kershaw Kathleen M. , Lay Anna R. , Ostertag-Hill Claire A. , Sherman Mara H. , Downes Michael , Liddle Christopher , Evans Ronald M. , Dawson David W.
Published: April 2023

Supplemental Table 1. QPCR PRIMERS
Supplemental Figure 2 from Calcipotriol Targets LRP6 to Inhibit Wnt Signaling in Pancreatic Cancer
Authors: Arensman Michael D. , Nguyen Phillip , Kershaw Kathleen M. , Lay Anna R. , Ostertag-Hill Claire A. , Sherman Mara H. , Downes Michael , Liddle Christopher , Evans Ronald M. , Dawson David W.
Published: April 2023

Supplemental Figure 2. Calcipotriol does not alter LRP6 expression in Low-BAR/Low-VDR cell lines. (A) Western blot for LRP6 or tubulin (loading control) following treatment with vehicle or 10 μM calcipotriol. Representative experiments from 2-3 biologic replicates are shown.
Figure S2 from NF-κB–Activated miR-574 Promotes Multiple Malignant and Metastatic Phenotypes by Targeting BNIP3 in Thyroid Carcinoma
Authors: Zhang Zhe-Jia , Xiao Qian , Li Xin-Ying
Published: April 2023

Figure S2. The miR-574/BNIP3 axis in TC cells regulated cell apoptosis and tube formation of HUVECs.
Supplementary Figure S7 from Integration of Downstream Signals of Insulin-like Growth Factor-1 Receptor by Endoplasmic Reticulum Stress for Estrogen-Induced Growth or Apoptosis in Breast Cancer Cells
Authors: Fan Ping , Cunliffe Heather E. , Maximov Philipp Y. , Agboke Fadeke A. , McDaniel Russell E. , Zou Xiaojun , Ramos Pilar , Russell Megan L. , Jordan V. Craig
Published: April 2023

(A) Activation of p38 by E2. MCF-7:5C cells were treated with E2 (10-9 mol/L), 4-OHT (10-6 mol/L), and E2 (10-9 mol/L) plus 4-OHT (10-6 mol/L) for the time points indicated. p-p38 was examined by Western blot. Total p38 was measured as loading control. (B) The p38 inhibitor could not block E2-induced apoptosis. MCF-7:5C cells were treated with vehicle (0.1% DMSO; con), E2 (10-9 mol/L), SB203580 (10-5 mol/L), and E2 (10-9 mol/L) plus SB203580 (10-5 mol/L) for 72 hours. Annexin V binding assay was used to detect apoptosis. p<0.001, ** compared with control.
Figure S4 from AKT1E17K Activates Focal Adhesion Kinase and Promotes Melanoma Brain Metastasis
Authors: Kircher David A. , Trombetti Kirby A. , Silvis Mark R. , Parkman Gennie L. , Fischer Grant M. , Angel Stephanie N. , Stehn Christopher M. , Strain Sean C. , Grossmann Allie H. , Duffy Keith L. , Boucher Kenneth M. , McMahon Martin , Davies Michael A. , Mendoza Michelle C. , VanBrocklin Matthew W. , Holmen Sheri L.
Published: April 2023

Supplementary Figure 4. P-FAK and P-paxillin are elevated in tumors that express AKT1E17K.
Supplementary Figure S3 from Integration of Downstream Signals of Insulin-like Growth Factor-1 Receptor by Endoplasmic Reticulum Stress for Estrogen-Induced Growth or Apoptosis in Breast Cancer Cells
Authors: Fan Ping , Cunliffe Heather E. , Maximov Philipp Y. , Agboke Fadeke A. , McDaniel Russell E. , Zou Xiaojun , Ramos Pilar , Russell Megan L. , Jordan V. Craig
Published: April 2023

MCF-7:5C cells were treated with vehicle (0.1% DMSO; con), E2 (10-9 mol/L), SP600125 (10-5 mol/L), and E2 (10-9 mol/L) plus SP600125 (10-5 mol/L) for 72 hours. Cells were harvested in TRIzol. Genes were quantitated by real-time RT-PCR. (A) PMAIP1, (B) PPP1R15A. p<0.001, ** compared with control.
Supplementary Figure S2 from Integration of Downstream Signals of Insulin-like Growth Factor-1 Receptor by Endoplasmic Reticulum Stress for Estrogen-Induced Growth or Apoptosis in Breast Cancer Cells
Authors: Fan Ping , Cunliffe Heather E. , Maximov Philipp Y. , Agboke Fadeke A. , McDaniel Russell E. , Zou Xiaojun , Ramos Pilar , Russell Megan L. , Jordan V. Craig
Published: April 2023

(A) The JNK inhibitor effectively blocked phosphorylation of JNK. MCF-7:2A cells were treated with vehicle (0.1% DMSO) or SP600125 (10-5 mol/L) for 24 hours. p-JNK was examined by Western blot. Total JNK was measured as loading control. (B) The JNK inhibitor could not block E2-induced apoptosis in MCF-7:2A cells. MCF-7:2A cells were treated with vehicle (0.1% DMSO; con), E2 (10-9 mol/L), SP600125 (10-5 mol/L), and E2 (10-9 mol/L) plus SP600125 (10-5 mol/L) for 6 days. Annexin V binding assay was used to detect apoptosis. p<0.001, ** compared with control. (C) Cell viability after E2 combination with the JNK inhibitor. MCF-7:2A cells were treated with vehicle (0.1% DMSO), E2 (10-9 mol/L), SP600125 (10-5 mol/L), and E2 (10-9 mol/L) plus SP600125 (10-5 mol/L). Cells were harvested after 7 days treatment and cell viability was quantitated by determination of total DNA. p<0.001, ** compared with control.
Table S1 from A Noncanonical Role of Fructose-1, 6-Bisphosphatase 1 Is Essential for Inhibition of Notch1 in Breast Cancer
Authors: Lu Chao , Ren Chune , Yang Tingting , Sun Yonghong , Qiao Pengyun , Wang Dan , Lv Shijun , Yu Zhenhai
Published: April 2023

The novel binding partners of FBP1
Supplementary Figure S2 from PTK6 Potentiates Gemcitabine-Induced Apoptosis by Prolonging S-phase and Enhancing DNA Damage in Pancreatic Cancer
Authors: Ono Hiroaki , Basson Marc D. , Ito Hiromichi
Published: April 2023

Supplementary Figure S2. Effect of Caspase-8 gene silencing on PTK6 mediated apoptosis. Apoptotic markers at 96 hours after gemcitabine treatment were decreased by gene-silencing of Caspase-8 in Panc1PTK6.
Supplementary Figure S2 from A PSCA/PGRN–NF-κB–Integrin–α4 Axis Promotes Prostate Cancer Cell Adhesion to Bone Marrow Endothelium and Enhances Metastatic Potential
Authors: Zhao Zhigang , Li Ermao , Luo Lianmin , Zhao Shankun , Liu Luhao , Wang Jiamin , Kang Ran , Luo Jintai
Published: April 2023

PSCA had no effect on the expression levels of integrin αv (ITGAV), integrin β1 (ITGB1) and integrin β3 (ITGB3) in PCa cells. A. Western blot analyses. B. qRT-PCR analyses.
Supplementary Methods from Targeting Nodal in Conjunction with Dacarbazine Induces Synergistic Anticancer Effects in Metastatic Melanoma
Authors: Hardy Katharine M. , Strizzi Luigi , Margaryan Naira V. , Gupta Kanika , Murphy George F. , Scolyer Richard A. , Hendrix Mary J.C.
Published: April 2023

Additional methods for supplementary data
Supplementary Figure S1 from A PSCA/PGRN–NF-κB–Integrin–α4 Axis Promotes Prostate Cancer Cell Adhesion to Bone Marrow Endothelium and Enhances Metastatic Potential
Authors: Zhao Zhigang , Li Ermao , Luo Lianmin , Zhao Shankun , Liu Luhao , Wang Jiamin , Kang Ran , Luo Jintai
Published: April 2023

PSCA expression had no effect on the adhesion of PCa cells to extracellular matrix proteins-fibronectin, laminin and vitronectin.
Supplementary Figure 5 from Targeting Nodal in Conjunction with Dacarbazine Induces Synergistic Anticancer Effects in Metastatic Melanoma
Authors: Hardy Katharine M. , Strizzi Luigi , Margaryan Naira V. , Gupta Kanika , Murphy George F. , Scolyer Richard A. , Hendrix Mary J.C.
Published: April 2023

Nodal in SK-MEL-28 cells surviving treatment with the B-RAF inhibitor, RG7204.
Supplementary Fig. S3 from Dynamic Epigenetic Regulation by Menin During Pancreatic Islet Tumor Formation
Authors: Lin Wenchu , Watanabe Hideo , Peng Shouyong , Francis Joshua M. , Kaplan Nathan , Pedamallu Chandra Sekhar , Ramachandran Aruna , Agoston Agoston , Bass Adam J. , Meyerson Matthew
Published: April 2023

Supplementary Fig. S3. Histone mark profiles in Hox genes
Supplemental Table S2 from HDAC6 Deacetylates HMGN2 to Regulate Stat5a Activity and Breast Cancer Growth
Authors: Medler Terry R. , Craig Justin M. , Fiorillo Alyson A. , Feeney Yvonne B. , Harrell J. Chuck , Clevenger Charles V.
Published: April 2023

Supplemental Table S2. Primers used for qPCR.
Supplemental Figure S5 from HDAC6 Deacetylates HMGN2 to Regulate Stat5a Activity and Breast Cancer Growth
Authors: Medler Terry R. , Craig Justin M. , Fiorillo Alyson A. , Feeney Yvonne B. , Harrell J. Chuck , Clevenger Charles V.
Published: April 2023

S5. Bufexamac treatment impairs the viability of triple-negative WHIM2 PDX cells.
Supplemental Figure 2 from Development of a Novel c-MET–Based CTC Detection Platform
Authors: Zhang Tian , Boominathan Rengasamy , Foulk Brad , Rao Chandra , Kemeny Gabor , Strickler John H. , Abbruzzese James L. , Harrison Michael R. , Hsu David S. , Healy Patrick , Li Jing , Pi Cinthia , Prendergast Katherine M. , Hobbs Carey , Gemberling Sarah , George Daniel J. , Hurwitz Herbert I. , Connelly Mark , Garcia-Blanco Mariano A. , Armstrong Andrew J.
Published: April 2023

CD45+/CK+ cells captured with c-MET separated by disease site (2A). Boxplot of all samples from cancer patients versus healthy controls (2B). Representative sample of dual positive cells (2C).
Supplementary Figure 6 from VDR Activity Is Differentially Affected by Hic-5 in Prostate Cancer and Stromal Cells
Authors: Solomon Joshua D. , Heitzer Marjet D. , Liu Teresa T. , Beumer Jan H. , Parise Robert A. , Normolle Daniel P. , Leach Damien A. , Buchanan Grant , DeFranco Donald B.
Published: April 2023

PDF file - 12K, RT-qPCR and Confidence Intervals serum free.
Supp. Fig. 4 from SOCS3 Modulates the Response to Enzalutamide and Is Regulated by Androgen Receptor Signaling and CpG Methylation in Prostate Cancer Cells
Authors: Handle Florian , Erb Holger H.H. , Luef Birgit , Hoefer Julia , Dietrich Dimo , Parson Walther , Kristiansen Glen , Santer Frédéric R. , Culig Zoran
Published: April 2023

AR binding to DNA occurs in close proximity of several important components of the IL6 pathway. Publicly available ChIP-Seq data sets were analyzed to visualize AR binding sites, displayed as black rectangles. A, no AR binding sites could be found in close proximity of SOCS3, whereas a positive control, PSA/KLK3, displayed abundand AR binding. B, AR binding sites could be identified in close proximity of several genes (IL6, IL6R, IL6ST and JAK1) of the IL6 signaling pathway. Detailed analysis of the identified regions demonstrated only low basal AR binding in absence of ligand. Treatment with R1881 induced AR binding to the DNA in these regions and enzalutamide was able to revert this effect.
Figure S5 from Ercc1 Deficiency Promotes Tumorigenesis and Increases Cisplatin Sensitivity in a Tp53 Context-Specific Manner
Authors: Jokić Mladen , Vlašić Ignacija , Rinneburger Miriam , Klümper Niklas , Spiro Judith , Vogel Wenzel , Offermann Anne , Kümpers Christiane , Fritz Christian , Schmitt Anna , Riabinska Arina , Wittersheim Maike , Michels Sebastian , Ozretić Luka , Florin Alexandra , Welcker Daniela , Akyuz Mehmet Deniz , Nowak Michael , Erkel Martin , Wolf Jürgen , Büttner Reinhard , Schumacher Björn , Thomale Jürgen , Persigehl Thorsten , Maintz David , Perner Sven , Reinhardt Hans Christian
Published: April 2023

S5. (a-e) µCT-based monitoring of KPE and KPE post cis allograft tumor response in KPE syngeneic mice (n = 4) prior to and after etoposide treatment (Mice 2-5 shown). Allograft tumors are marked with "T".
Supplementary Table 1 from Homologous Mutation to Human BRAF V600E Is Common in Naturally Occurring Canine Bladder Cancer—Evidence for a Relevant Model System and Urine-Based Diagnostic Test
Authors: Decker Brennan , Parker Heidi G. , Dhawan Deepika , Kwon Erika M. , Karlins Eric , Davis Brian W. , Ramos-Vara José A. , Bonney Patty L. , McNiel Elizabeth A. , Knapp Deborah W. , Ostrander Elaine A.
Published: April 2023

Supplementary Table 1. This is a table of all mutations found the four InvTCC tumors, there positions, and genotype quality scores.
Supplemental Figure 2 from PRAS40 Phosphorylation Correlates with Insulin-Like Growth Factor-1 Receptor-Induced Resistance to Epidermal Growth Factor Receptor Inhibition in Head and Neck Cancer Cells
Authors: Dougherty Michael I. , Lehman Christine E. , Spencer Adam , Mendez Rolando E. , David Abel P. , Taniguchi Linnea E. , Wulfkuhle Julie , Petricoin Emanuel F. , Gioeli Daniel , Jameson Mark J.
Published: April 2023

Supplemental Figure 2: Knockdown of PRAS40 is insufficient to alter downstream signaling and therefore sensitivity to gefitinib or desIGF1. OSC19 cells were transfected with siRNA specific to PRAS40 (siRNA #1 and siRNA #2) or a scramble siRNA followed by treatment with desIGF1, gefitinib or the combination of both. (A) Immunoblot representation and quantification of PRAS40, phospho-S6 and S6 48 hours after siRNA transfection. (B) OSC19 cell viability as measured by CyQUANT 72 h following transfection and drug treatment. (C) Relative expression of TRAIL (left panel) and PINK (right panel) 48 hours after transfection and 6 hours post drug treatment as quantified by qPCR. Data represents results from at least 3 biological replicates. Asterisks represent significant changes with p<0.05 as determined by Tukey test.
Supplementary Table 6 from A YAP/TAZ-Regulated Molecular Signature Is Associated with Oral Squamous Cell Carcinoma
Authors: Hiemer Samantha E. , Zhang Liye , Kartha Vinay K. , Packer Trevor S. , Almershed Munirah , Noonan Vikki , Kukuruzinska Maria , Bais Manish V. , Monti Stefano , Varelas Xaralabos
Published: April 2023

Supplementary Table 6. Hyper-enrichment analysis of YAP/TAZ-regulated molecular signature.
Supplementary Data from O-GlcNAc Transferase Regulates Cancer Stem–like Potential of Breast Cancer Cells
Authors: Akella Neha M. , Le Minh Giang , Ciraku Lorela , Mukherjee Ayonika , Bacigalupa Zachary A. , Mukhopadhyay Dimpi , Sodi Valerie L. , Reginato Mauricio J.
Published: April 2023

S1. OGT and O-GlcNAc not regulated by loss of cell adhesion in cancer cells. S2. OGT inhibition attenuates mammosphere formation and CD44HCD24L TIC population. S3. OGT inhibition attenuates mammosphere formation and CD44HCD24L TIC population. S4. Elevated OGT and O-GlcNAc ameliorate mammosphere formation and CD44HCD24L TIC population. S5. OGT/O-GlcNAc modulation affects NANOG-GFP+ and ALDH+ TIC population. S6. OGT/O-GlcNAc modulation affects NANOG-GFP+ TIC population. S7. OGT regulates EMT and stem cell markers. S8. OGT regulates EMT and stem cell markers. S9. KLF8 is a critical regulator of mammosphere formation and required for OGT-mediated mammosphere growth.
Supplementary material from Hypoxic Cancer-Secreted Exosomal miR-182-5p Promotes Glioblastoma Angiogenesis by Targeting Kruppel-like Factor 2 and 4
Authors: Li Junjun , Yuan Hongliang , Xu Hao , Zhao Hongyang , Xiong Nanxiang
Published: April 2023

Supplementary figure 1: Exosomes derived from GBM cells promote angiogenesis and increase permeability in HUVECs. Supplementary figure 2: The proangiogenic effect of hypoxic U-251MG and U-87MG-derived exosomes on HUVECs under normoxic conditions. Supplementary figure 3: MiR-182-5p is secreted by hypoxic GBM cells and transferred to endothelial cells by exosome secretion. Supplementary figure 4: Exosomal miR-182-5p derived from hypoxic GBM cells targets KLF2 and KLF4. Supplementary figure 5: Hypoxic GBM-secreted miR-182-5p silenced KLF2 and KLF4 in HUVECs. Supplementary figure 6: Detection of human- and mouse-related indicators. Supplementary Table 1: Sequences of synthetic miRNA mimics. Supplementary Table 2: Sequences of synthetic miRNA inhibitor. Supplementary Table 3: Primer sequences for qPCR Supplementary Table 4: Antibody description. Supplementary Table 5: Probes used in In situ hybridization (ISH).
Supplementary Figure S2 from Combined Src/EGFR Inhibition Targets STAT3 Signaling and Induces Stromal Remodeling to Improve Survival in Pancreatic Cancer
Authors: Dosch Austin R. , Dai Xizi , Reyzer Michelle L. , Mehra Siddharth , Srinivasan Supriya , Willobee Brent A. , Kwon Deukwoo , Kashikar Nilesh , Caprioli Richard , Merchant Nipun B. , Nagathihalli Nagaraj S.
Published: April 2023

MALDI-IMS analysis of treated xenograft tissues.
Supplementary Figure 1 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT
Authors: Yang-Hartwich Yang , Tedja Roslyn , Roberts Cai M. , Goodner-Bingham Jamie , Cardenas Carlos , Gurea Marta , Sumi Natalia J. , Alvero Ayesha B. , Glackin Carlotta A. , Mor Gil
Published: April 2023

The protein levels of Twist1 (A) and p53 (B) in tumor samples. Protein levels were determined by the quantification of western blot band intensity comparing to GAPDH bands as loading control.
Supplemental Figures 1-6 from Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes
Authors: Ye I. Chae , Fertig Elana J. , DiGiacomo Josh W. , Considine Michael , Godet Inês , Gilkes Daniele M.
Published: April 2023

S1. RNA sequencing of 31 cells line exposed to 20% O2 and 1% O2 . Heat map of the top 1000 genes that are differentially expressed across all samples. S2. Basal breast cancer cells express higher endogenous levels of the 42-gene hypoxia signature. S3. The 42-gene hypoxia signature is prognostic in basal breast cancer. S4. The mRNA expression of HIF-1α and HIF-2α do not change under hypoxic conditions. S5. Gene Set Enrichment analysis shows HIF-regulated genes are enriched under 1% O2. S6. Novel hypoxia regulated genes identified in the HIF-signature require HIF-1α expression.
Supplemental Tables S1-3, Supplemental Figures S1-8 from Characterization and Evidence of the miR-888 Cluster as a Novel Cancer Network in Prostate
Authors: Hasegawa Tsuyoshi , Glavich Garrison J. , Pahuski Mary , Short Aleena , Semmes O. John , Yang Lifang , Galkin Vitold , Drake Richard , Esquela-Kerscher Aurora
Published: April 2023

This supplemental data file consists of 3 supplemental tables and 8 supplemental figures. Suppl. Tables 1-2 lists specific miRNA mimics, inhibitors, TaqMan and PCR primers used in the in vitro functional assays depicted in Figs. 1-4, 6-7. Suppl. Table 3 provides a phenotypic summary of the in vitro assays in Figs. 2-4. Suppl. Fig. 1 shows characterization of exosomes secreted from PC3-derived cell lines profiled in Fig. 1C. Suppl. Figs. 2-4 confirms miR-888 and miR-891a misexpression using miRNA mimics, miRNA inhibitors, and lentiviral miRNA mimic reagents in human prostate cells analyzed in Figs. 2-7. Suppl. Fig. 5 represents predicted miR-888 and miR-891a binding sites found in the 3'UTR regions of RBL1, SMAD4, KLF5, and TIMP2 transcripts validated in Fig. 6A using luciferase reporter assays. Suppl. Fig. 6 indicates that miR-888 targets RBL1, SMAD4, KLF5, and TIMP2 possess cell type specific expression in LNCaP when compared to PC3-N cells in Fig. 6B-C. Suppl. Fig. 7 shows functional evidence that miR-888 targets RBL1 and TIMP2 to control proliferation and invasion activities assayed in Figs. 2-3. Suppl. Fig. 8 implicates that miR-888 and miR-891a act synergistically to regulate prostate cell proliferation depicted in Fig. 2 and provides a model of how the miR-888 cluster regulates prostate cancer progression.
Supplemental Figure Legend from IGFBP3 Modulates Lung Tumorigenesis and Cell Growth through IGF1 Signaling
Authors: Wang Yong Antican , Sun Yunguang , Palmer Joshua , Solomides Charalambos , Huang Li-Ching , Shyr Yu , Dicker Adam P. , Lu Bo
Published: April 2023

Supplemental Figure 1