bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 1 from COX-2 Elevates Oncogenic miR-526b in Breast Cancer by EP4 Activation
Authors: Majumder Mousumi , Landman Erin , Liu Ling , Hess David , Lala Peeyush K.
Published: April 2023

Supplementary Figure 1. Validation of Transfection/COX-2 mRNA in breast cancer cell lines/ miR-526b expression levels in a panel of breast cancer cell lines
Figure S6 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs
Authors: Javaid Sarah , Zhang Jianmin , Smolen Gromoslaw A. , Yu Min , Wittner Ben S. , Singh Anurag , Arora Kshitij S. , Madden Marissa W. , Desai Rushil , Zubrowski Matthew J. , Schott Benjamin J. , Ting David T. , Stott Shannon L. , Toner Mehmet , Maheswaran Shyamala , Shioda Toshi , Ramaswamy Sridhar , Haber Daniel A.
Published: April 2023

Figure S6. Knockdown of MAPK7 does not increase proliferation rate in primary tumor or lung metastasis.
Figure S2 from ERK/MAPK Signaling Drives Overexpression of the Rac-GEF, PREX1, in BRAF- and NRAS-Mutant Melanoma
Authors: Ryan Meagan B. , Finn Alexander J. , Pedone Katherine H. , Thomas Nancy E. , Der Channing J. , Cox Adrienne D.
Published: April 2023

Copy number analysis for PREX1 in breast cancer, prostate cancer, and melanoma
Figure S1 from ERK/MAPK Signaling Drives Overexpression of the Rac-GEF, PREX1, in BRAF- and NRAS-Mutant Melanoma
Authors: Ryan Meagan B. , Finn Alexander J. , Pedone Katherine H. , Thomas Nancy E. , Der Channing J. , Cox Adrienne D.
Published: April 2023

PREX1 and PREX1 expression and mutation profiles in breast cancer, prostate cancer, and melanoma
Figure S3 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs
Authors: Javaid Sarah , Zhang Jianmin , Smolen Gromoslaw A. , Yu Min , Wittner Ben S. , Singh Anurag , Arora Kshitij S. , Madden Marissa W. , Desai Rushil , Zubrowski Matthew J. , Schott Benjamin J. , Ting David T. , Stott Shannon L. , Toner Mehmet , Maheswaran Shyamala , Shioda Toshi , Ramaswamy Sridhar , Haber Daniel A.
Published: April 2023

Figure S3. Illustration of modeling and correcting for dependence of each marker through the expression level of housekeeping genes.
Supplemental Figure Legend from Combined Exosomal GPC1, CD82, and Serum CA19-9 as Multiplex Targets: A Specific, Sensitive, and Reproducible Detection Panel for the Diagnosis of Pancreatic Cancer
Authors: Xiao Dong , Dong Zhanjun , Zhen Linqing , Xia Guanggai , Huang Xinyu , Wang Tiezhong , Guo Huaibin , Yang Binhui , Xu Cheng , Wu Weiwei , Zhao Xiaoyu , Xu Hong
Published: April 2023

Supplemental Figure Legend 1
Figure S1 from Combined Exosomal GPC1, CD82, and Serum CA19-9 as Multiplex Targets: A Specific, Sensitive, and Reproducible Detection Panel for the Diagnosis of Pancreatic Cancer
Authors: Xiao Dong , Dong Zhanjun , Zhen Linqing , Xia Guanggai , Huang Xinyu , Wang Tiezhong , Guo Huaibin , Yang Binhui , Xu Cheng , Wu Weiwei , Zhao Xiaoyu , Xu Hong
Published: April 2023

Intra-and inter-assay stability analysis of GPC1 and CD82 expression
Supplementary Figure S5 from AMPK-Independent LKB1 Activity Is Required for Efficient Epithelial Ovarian Cancer Metastasis
Authors: Buensuceso Adrian , Ramos-Valdes Yudith , DiMattia Gabriel E. , Shepherd Trevor G.
Published: April 2023

LKB1 loss does not alter MAPK phosphorylation in EOC cells and spheroids.
Supplementary Figure S4 from AMPK-Independent LKB1 Activity Is Required for Efficient Epithelial Ovarian Cancer Metastasis
Authors: Buensuceso Adrian , Ramos-Valdes Yudith , DiMattia Gabriel E. , Shepherd Trevor G.
Published: April 2023

Loss of LKB1 does not alter sensitivity of OVCAR8 cells to several metabolic stresses.
Supplementary Figure S1 from AMPK-Independent LKB1 Activity Is Required for Efficient Epithelial Ovarian Cancer Metastasis
Authors: Buensuceso Adrian , Ramos-Valdes Yudith , DiMattia Gabriel E. , Shepherd Trevor G.
Published: April 2023

Morphology of STK11KO cell lines in adherent culture.
OVCAR8-STK11KO spheroid from AMPK-Independent LKB1 Activity Is Required for Efficient Epithelial Ovarian Cancer Metastasis
Authors: Buensuceso Adrian , Ramos-Valdes Yudith , DiMattia Gabriel E. , Shepherd Trevor G.
Published: April 2023

Single OVCAR8-STK11KO spheroid formation and growth over time as imaged by IncuCyte ZOOM
S2 from Augmented TME O-GlcNAcylation Promotes Tumor Proliferation through the Inhibition of p38 MAPK
Authors: Moriwaki Kazumasa , Asahi Michio
Published: April 2023

Supplemental Figure 2. Spontaneous apoptosis in tumor tissues does not differ significantly between WT and Ogt-Tg/+ mice.
HeyA8 spheroid from AMPK-Independent LKB1 Activity Is Required for Efficient Epithelial Ovarian Cancer Metastasis
Authors: Buensuceso Adrian , Ramos-Valdes Yudith , DiMattia Gabriel E. , Shepherd Trevor G.
Published: April 2023

Single HeyA8 spheroid formation and growth over time as imaged by IncuCyte ZOOM
Supplementary Figure 7 from TGFβ and Hippo Pathways Cooperate to Enhance Sarcomagenesis and Metastasis through the Hyaluronan-Mediated Motility Receptor (HMMR)
Authors: Ye Shuai , Liu Ying , Fuller Ashley M. , Katti Rohan , Ciotti Gabrielle E. , Chor Susan , Alam Md. Zahidul , Devalaraja Samir , Lorent Kristin , Weber Kristy , Haldar Malay , Pack Michael A. , Eisinger-Mathason T.S. Karin
Published: April 2023

S7. Modeling UPS extravasation with zebrafish xenografts
Figure S5 from Circadian Oscillations Persist in Cervical and Esophageal Cancer Cells Displaying Decreased Expression of Tumor-Suppressing Circadian Clock Genes
Authors: van der Watt Pauline J. , Roden Laura C. , Davis Kate T. , Parker M. Iqbal , Leaner Virna D.
Published: April 2023

CpG island prediction software, MethPrimer (www.urogene.org), identifies CpG islands in the 5' regulatory sequences of circadian clock genes, CLOCK, RORα, CRY1 and PER2. The regions from -2000 to +2000 were analysed, relative to the transcription start site of +1. In the linear scale depicted, 0 refers to 2000 bases upstream and 4000 refers to 2000 bases downstream of the transcription start site.
Figure S4 from Circadian Oscillations Persist in Cervical and Esophageal Cancer Cells Displaying Decreased Expression of Tumor-Suppressing Circadian Clock Genes
Authors: van der Watt Pauline J. , Roden Laura C. , Davis Kate T. , Parker M. Iqbal , Leaner Virna D.
Published: April 2023

Relative differences in expression of circadian clock genes between cell lines remains the same at different time points after synchronisation. A. Western blot analysis showing similarly downregulated CLOCK and CRY1 protein levels in HeLa cells compared to ARPE19 cells, as well as upregulated PER2 protein levels, at 0, 12 and 24 hours post-synchronisation with Dexamethasone. Numbers represent quantified band intensities relative to p38, as determined using Image J software. B. Real-time RT-PCR analysis showing similarly downregulated PER2 mRNA expression in SVWI38 cells compared to WI38 cells, at 0, 12 and 24 hours post-synchronisation with Dexamethasone.
Supplementary Table 1 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

Table S1: List of 182 SMAD4-interacting candidates subjected to IPA for direct protein-protein interaction analysis.
Figure S4 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

cRGD PC-3
Figure S3 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

cRGD LNCaP beta3
Supplementary Table 1 from Loss of SWI/SNF Chromatin Remodeling Alters NRF2 Signaling in Non–Small Cell Lung Carcinoma
Authors: Song Shujie , Nguyen Vinh , Schrank Travis , Mulvaney Kathleen , Walter Vonn , Wei Darmood , Orvis Tess , Desai Nisarg , Zhang Jiren , Hayes D. Neil , Zheng Yanfang , Major Michael B. , Weissman Bernard E.
Published: April 2023

Table shows genes with significantly altered expression by RNA-seq after BRG1 or BRM knockout.
Supplementary Figure 1 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 1. Myb, TCF-4, and E2F-1 binding sites identified within the murine Cyclin E1 promoter region.
Supplementary Figures 1-7 from Targeting TSLP-Induced Tyrosine Kinase Signaling Pathways in CRLF2-Rearranged Ph-like ALL
Authors: Sia Keith C.S. , Zhong Ling , Mayoh Chelsea , Norris Murray D. , Haber Michelle , Marshall Glenn M. , Raftery Mark J. , Lock Richard B.
Published: April 2023

S1. In vitro effects of TSLP on target cells as assessed by Alamar Blue assay. S2. Demographics of phosphosites identified from MHH-CALL-4 and MUTZ-5 cells in global P-Tyr profiling. S3. In vitro single agent efficacy of BMS-754807 and ponatinib against CRLF2r cell lines and PDXs. S4. siRNA knockdown of IGF1R and FGFR1 in MHH-CALL-4 and MUTZ-5 cell lines. S5. Tolerability testing of ponatinib in combination with BMS754807 in naïve NSG mice as assessed by percentage of body weight change. S6. Ex vivo combination effect of BMS-754807 and ponatinib over time against CRLF2r Ph-like ALL PDXs. S7. Plasma concentrations of BMS-754807 and ponatinib at specific timepoints.
Data Supplement from Snail Cooperates with KrasG12D In Vivo to Increase Stem Cell Factor and Enhance Mast Cell Infiltration
Authors: Knab Lawrence M. , Ebine Kazumi , Chow Christina R. , Raza Sania S. , Sahai Vaibhav , Patel Akash P. , Kumar Krishan , Bentrem David J. , Grippo Paul J. , Munshi Hidayatullah G.
Published: April 2023

Supplementary Figure S1 - Effect of pancreatitis on mast cell infiltration. Supplementary Figure S2 - Snail expression in CD18 cells. Supplementary Figure S3 - Slug expression in AsPC1 cells.
Supplementary Figures 1-3, Table 1 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 Figures 1-3, Table 1. Supplementary Figure 1: Cellular localization of DRAIC and 3'RACE of DRAIC gene Supplementary Figure 2: Transcriptional variants of DRAIC gene Supplementary Figure 3: AR, FOXA1 and NKX3-1 binding sequences at DRAIC locus Supplementary Table 1: Primer, siRNA and shRNA sequences
Supplementary Figure 6 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 Figure 6: Histology, immunohistochemistry and morphology of murine tumors
Supplementary Figure Legends 1-5 from NRF2-Driven KEAP1 Transcription in Human Lung Cancer
Authors: Tian Yijun , Liu Qian , Yu Shengnan , Chu Qian , Chen Yuan , Wu Kongming , Wang Liang
Published: April 2023

Supplementary Figure S1. Evidence for selecting TXN as KEAP1 transcription footprint. Supplementary Figure S2. Cut-off finding and enrichment performance for gene ratio strategy. Supplementary Figure S3. Survival analysis using gene ratio in other SQC cohorts. Supplementary Figure S4. Crucial NRF2 pathway gene alterations including SQSTM1 Supplementary Figure S5. A. KEAP1 protein change in H520 cells during 24-hour 60 μM tBHQ treatment.
Figure S5 from NRF2-Driven KEAP1 Transcription in Human Lung Cancer
Authors: Tian Yijun , Liu Qian , Yu Shengnan , Chu Qian , Chen Yuan , Wu Kongming , Wang Liang
Published: April 2023

Western blotting bands quantification
Supplementary Figure 3 from The Chemokine (CCL2–CCR2) Signaling Axis Mediates Perineural Invasion
Authors: He Shizhi , He Shuangba , Chen Chun-Hao , Deborde Sylvie , Bakst Richard L. , Chernichenko Natalya , McNamara William F. , Lee Sei Young , Barajas Fernando , Yu Zhenkun , Al-Ahmadie Hikmat A. , Wong Richard J.
Published: April 2023

A. A schematic of the DRG and cancer cell co-culture model depicts that cancer cells initially attach to DRG neurites. Over time, the cancer cells migrate along the neurites towards the DRG and also proliferate. B. Close up views of the photomicrographs from Figure 3 show an association between the shControl PC-3 cells and the DRG neurites (Figure 3A), but fewer associations between the shCCR-2 PC-3 cells and DRG neurites (Figure 3B).
Supplementary Figure 2 from The Chemokine (CCL2–CCR2) Signaling Axis Mediates Perineural Invasion
Authors: He Shizhi , He Shuangba , Chen Chun-Hao , Deborde Sylvie , Bakst Richard L. , Chernichenko Natalya , McNamara William F. , Lee Sei Young , Barajas Fernando , Yu Zhenkun , Al-Ahmadie Hikmat A. , Wong Richard J.
Published: April 2023

PC-3 migration towards DRG as the attractant is reduced by the addition of anti-CCL2 neutralizing antibody at 10 μg/ml to the DRG. In contrast, the addition of non-specific rat IgG at 10 μg/ml shows no inhibitory effects (* p<0.05 for comparisons to to both rat IgG control and anti-CCL2 antibody at 1µg/ml).
Supplementary Data from Histone Demethylase JMJD1A Promotes Tumor Progression via Activating Snail in Prostate Cancer
Authors: Tang Dong-E , Dai Yong , Xu Song-Hui
Published: April 2023

Supplementary Data from Histone Demethylase JMJD1A Promotes Tumor Progression via Activating Snail in Prostate Cancer
Supplementary Figure 2 from Hypoxia Promotes Dissemination and Colonization in New Bone Marrow Niches in Waldenström Macroglobulinemia
Authors: Muz Barbara , de la Puente Pilar , Azab Feda , Ghobrial Irene M. , Azab Abdel Kareem
Published: April 2023

Supplementary Figure 2. Re-oxygenation induces WM cell clump-formation. The effect of hypoxia (1% O2, 48hrs) and re-oxygenation (hypoxia for 24hrs followed by normoxia for 24hrs) on BCWM.1 size of colonies normalized to hypoxic cells (A), and on the creation of clumps monitored and captured using light microscopy (scale bar represents 1 micrometer) (B).
Supplemental Table 2 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 2. All 98 GO biological process ontologies that are over-represented in the differentially expressed (DE) genes.
Supplemental Methods, Figure Legends 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 Methods, Figure Legends from Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome
Supplementary Figures 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 Figures 1-7
FigureS8 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

Figure S8. Volcano plot of GSVA analyses showing the difference between (A) merged gBRCA1/2 mutation vs. wild type (WT), (B) gBRCA mutations vs. WT in triple negative patients, (C) gBRCA2 mutations vs. WT in estrogen receptor-positive patients.
Supplementary Movie 3 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

TNKS and Î²-catenin display similar kinetics upon washout of G007-LK.
Supplementary Movie 2 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

G007-LK-induced degradasomes are rapidly dissolved upon washout of inhibitor.
Supplementary Figure S4 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 positively correlates with ERα expression in endometrial cancer tissue samples and cell lines.
Supplementary Figure S3 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 negatively regulates the p53 tumor suppressor in RL95-2 cells.
Supplementary figures 1-4, Supplementary tables 1-4 from Galectin-3 Interacts with C/EBPβ and Upregulates Hyaluronan-Mediated Motility Receptor Expression in Gastric Cancer
Authors: Kang Hyeon-Gu , Kim Won-Jin , Kang Hyeok-Gu , Chun Kyung-Hee , Kim Seok-Jun
Published: April 2023

Figure S1. The basal mRNA expression level of HMMR in the gastric cancer cell line. Figure S2. Indirect regulation of transcription activity with galectin-3. Figure S3. Detection of mRNA and protein expression level of C/EBP family with galectin-3. Figure S4. Detection of mRNA and protein expression of HMMR with C/EBPβ overexpression. Supplementary Table 1. List of gene ontology significantly upregulated by galectin-3 silencing in AGS cells Supplementary Table 2. List of gene ontology significantly downregulated by galectin-3 silencing in AGS cells Supplementary Table 3. List of upregulated genes related to cell progression and cell motility with galectin-3 silencing in AGS cells Supplementary Table 4. List of downregulated genes related to cell progression and cell motility with galectin-3 silencing in AGS cells
Table S1 from Activation of AXL as a Preclinical Acquired Resistance Mechanism Against Osimertinib Treatment in EGFR-Mutant Non–Small Cell Lung Cancer Cells
Authors: Namba Kei , Shien Kazuhiko , Takahashi Yuta , Torigoe Hidejiro , Sato Hiroki , Yoshioka Takahiro , Takeda Tatsuaki , Kurihara Eisuke , Ogoshi Yusuke , Yamamoto Hiromasa , Soh Junichi , Tomida Shuta , Toyooka Shinichi
Published: April 2023

Table S1. ClearSeq Cancer Panel Gene List
Figure S1-S7 from Activation of AXL as a Preclinical Acquired Resistance Mechanism Against Osimertinib Treatment in EGFR-Mutant Non–Small Cell Lung Cancer Cells
Authors: Namba Kei , Shien Kazuhiko , Takahashi Yuta , Torigoe Hidejiro , Sato Hiroki , Yoshioka Takahiro , Takeda Tatsuaki , Kurihara Eisuke , Ogoshi Yusuke , Yamamoto Hiromasa , Soh Junichi , Tomida Shuta , Toyooka Shinichi
Published: April 2023

Figure S1. Copy numbers of YES1 in osimertinib-resistant cell lines. Figure S2. PARP and MET expressions in MET-amplified osimertinib-resistant cell lines. Figure S3. Relative ALDH1A1 and ABCB1 expression levels using qRT-PCR in NSCLC EGFR-mutant cell lines and their corresponding osimertinib-resistant cell lines. Figure S4. Expressions of AXL protein in NSCLC EGFR-mutant cell lines and their corresponding osimertinib-resistant cell lines. Figure S5. Copy numbers of AXL in osimertinib-resistant cell lines. Figure S6. siRNA and combined drug treatment studies in HCC4006 and HCC4006 resistant cells. Figure S7. Combined treatment with AXL knockdown and osimertinib in H1975 and H1975 resistant cells.
SUPPLEMENTARY DATA from TGFβ1 Protects Cells from γ-IR by Enhancing the Activity of the NHEJ Repair Pathway
Authors: Kim Mi-Ra , Lee Jeeyong , An You Sun , Jin Yeung Bae , Park In-Chul , Chung Eunkyung , Shin Incheol , Barcellos-Hoff Mary Helen , Yi Jae Youn
Published: April 2023

SUPPLEMENTARY DATA. 7 figures, figure legends and supplementary methods Suppl. Fig. 1. TGF-ÃŸ1 pretreatment induces G1 arrest. Suppl. Fig. 2. TGF-ÃŸ1 pretreatment protects cells from low dose IR-induced apoptosis, regardless of p21. Suppl. Fig. 3. Smad2 and Smad3 are required for TGF-ÃŸ1-mediated suppression of low dose IR-induced apoptosis. Suppl. Fig. 4. TGF-ÃŸ1-mediated suppression of IR-induced DSBs is not observed immediately after ?-irradiation. Suppl. Fig. 5. TGF-ÃŸ1 pretreatment reduces chromosome breakage. Suppl. Fig. 6. Vectors used for in vivo NHEJ assay. Suppl. Fig. 7. TGF-ÃŸ1 pretreatment promotes the nuclear retention of NHEJ proteins.
Supplemental Figure S1 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 S1: Lentiviral transduction of Kras-PDCs in vitro induces sustained loss of target gene protein expression in vivo. Primary tumors derived from Kras-shRNAp16Ink4a-PDCs or Kras-shRNATrp53-PDCs stained negative for P16INK4a and TRP53, respectively. Tissues containing PanINs derived form Ptf1a-Cre;LSL-KrasG12D served as positive controls.
Figure S5 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

MINK1 binds to and is negatively regulated by APC
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 Materials and Methods and Supplementary Figure Legends
Figure S2 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

Representative western of Pol lambda expression in HME1 cells.
Figure S6: Proliferation of shFAK-expressing 8505C orthotopic tumors is not significantly inhibited. from FAK Expression, Not Kinase Activity, Is a Key Mediator of Thyroid Tumorigenesis and Protumorigenic Processes
Authors: Kessler Brittelle E. , Sharma Vibha , Zhou Qiong , Jing Xia , Pike Laura A. , Kerege Anna A. , Sams Sharon B. , Schweppe Rebecca E.
Published: April 2023

Ki67 staining of 8505C shFAK and Scrambled orthotopic thyroid tumors was performed. Proliferation was measured by the percent of Ki67 positive cells scored by a pathologist. Results are % Ki67 {plus minus} SEM.
Figure S2: Sensitivity to FAK inhibition under anchorage-independent conditions in a panel of thyroid cancer cells. from FAK Expression, Not Kinase Activity, Is a Key Mediator of Thyroid Tumorigenesis and Protumorigenic Processes
Authors: Kessler Brittelle E. , Sharma Vibha , Zhou Qiong , Jing Xia , Pike Laura A. , Kerege Anna A. , Sams Sharon B. , Schweppe Rebecca E.
Published: April 2023

Viability of thyroid cancer cells treated with 1µM PF-573,228 for 6 days was normalized to DMSO-treated cells, set to 100%. Results are % viable cells per mL {plus minus} SD of at least 2 experiments performed in triplicate (t-test: C643, K1, THJ11T: p{less than or equal to}0.05; TPC1 PF-573: p{less than or equal to}0.01; all others p=n.s.). (B) Colonies of thyroid cancer cells treated with 1µM PF-573,228 in soft agar were allowed to form for 20 days and normalized to DMSO-treated cells, set to 100%. Results shown are percent of colony formation {plus minus} SD of 2 independent experiments performed in duplicate (t-test: TPC-1 PF-573: p{less than or equal to}0.001; C643 PF-573: p{less than or equal to}0.001; K1 PF-573: p{less than or equal to}0.001).
Figure S8 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 S8 shows the model of GPER1-mediated Sin1 in regulation of cell proliferation via mTORC2-AKT signaling in HCC.
Figure S3 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 S3 tells that GPER1-E2 signaling does not affect apoptosis of HCC cells.
Supplementary Figure 1 from PARP1 Trapping by PARP Inhibitors Drives Cytotoxicity in Both Cancer Cells and Healthy Bone Marrow
Authors: Hopkins Todd A. , Ainsworth William B. , Ellis Paul A. , Donawho Cherrie K. , DiGiammarino Enrico L. , Panchal Sanjay C. , Abraham Vivek C. , Algire Mikkel A. , Shi Yan , Olson Amanda M. , Johnson Eric F. , Wilsbacher Julie L. , Maag David
Published: April 2023

Association of PARP1 and H2A.X detected by Proximity Ligation Assay (PLA).
Figure S2 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 S2 demonstrates that Sin1 is specifically induced by estrogen, but not by androgen, in HCC cells.
Supplemental materials and methods 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 materials and methods for supplemental experiments.
Supplemental Figure S8 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 S8. Proline supplementation did not restore protein synthesis in 1205 Lu cells by day 5.
Supplemental Figure S7 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 S7. P5CS protein knockdown did not cause cell cycle arrest but decreased glycolytic activity in UACC 903 cells.
Supplementary Table S5 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

LINC00920-deregulated genes (n=315) analyzed with Ingenuity Pathway Analysis (IPA).
Supplementary Figure S1 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 S1. Distribution of lipids, amino acids, and nucleotides in tumor and normal. (A-C): Heat-map of 97 lipids (A), 53 amino acids (B), and 18 nucleotides (C) 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.
Supplementary Figures 1 - 3 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

Supplementary Fig. S1 (A-B), western blotting for CLIC1 to demonstrate knockdown in shCLIC1 786-0 and HT1080 clones compared to shSCR control (A) as well as in HUVEC cells compared to non-targeted control siRNA (B). For both cell types, clones shCLIC1-2 and shCLIC1-4 were selected for further experiments. (C), fluorescence microscopy images of fibrin clots were analyzed for percent propidium iodide-positive 786-0 per optical field after CLIC1 silencing with two CLIC1 shRNA vectors (shCLIC1-2 and 4) compared to scrambled shRNA (shSCR). Not significant (ns), p > 0.05. Supplementary Fig. 2 (A), CLIC1 fluorescence intensity is depicted as a ratio of peripheral to interior CLIC1 in shβ3-786-0 cells compared to shSCR-786-0 cells to assess CLIC1 redistribtion to invadopodia at indicated times. ***P < 0.001, *P <0.05. (B-C), western blotting for β3 integrin expression in shSCR-786-0 compared to shβ3 (B) and shCLIC1 (C). Ponceau S staining shows equal loading. Supplementary Fig. S3 (A), western blotting for RhoA-GTP in shSCR and shCLIC1 786-0 cells following rhotekin-RBD pull-down using the RhoA activation assay biochem kit (Cytoskeleton). (B), 786-0 cells transformed with shSCR (left) or shCLIC1 (right) cultured in 3D fibrin for 48 hours were fixed in 4% PFA, then washed in PBS, blocked in 2% BSA and probed for fibronectin (green) prior to confocal microscopy. Nuclei are stained with draq5 (blue).
Supplemental Figure S2 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 S2. Analysis of transcription factor target gene enrichment during TGFβ induced EMT. Target genes were identified from available human ChIP-CHIP, ChIP-Seq, or ChIP-PET data in the CHEA database. Graphs represent enrichment of target genes for the indicated transcription factor in genes differentially expressed during EMT (GSE17708) . The number in each chart title is the PMID for the publication the ChIP-X data was generated.
Supplemental Figure S1 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 S1. TGFβ induces full EMT in MCF10As. A. Quantitative PCR analysis of EMT-related genes in MCF10A cells treated with vehicle or 500pM TGFβ for 72 hours.
Supplemental Table S3 from Inhibition of S-Adenosylmethionine-Dependent Methyltransferase Attenuates TGFβ1-Induced EMT and Metastasis in Pancreatic Cancer: Putative Roles of miR-663a and miR-4787-5p
Authors: Mody Hardik R. , Hung Sau Wai , AlSaggar Mohammad , Griffin Jazmine , Govindarajan Rajgopal
Published: April 2023

Table S3. List of miRNAs downregulated (fold difference {greater than or equal to} 1.5 in MIA PaCa-2.
Figure S6 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 6. Expression of AKT1E17K promotes the dysregulation of integrins.
Figure S3 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 3. Phospho-FAK (P-FAK) and paxillin are candidate factors in tumor progression.
Supplementary Figure S3 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 S3. A cell growth assay of stable transfectants of MIAPaCa2 and Panc1 cells. MIAPaCa2PTK6 and Panc1PTK6 demonstrated the similar growth rates when they were cultured without chemotherapeutic agent compared to their control counterparts, MIAPaCa2mock and Panc1mock.
Supplementary Table 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

Primer sets used in the study, related to the PCR and qRT-PCR
Supplementary Table 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

Primer sequences for the knockdown of PSCA and ITGA4 genes and the control
Supplementary Figure 4 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

DTIC and anti-Nodal antibody combination treatment promotes cell death in SK-MEL-28 cells.
Supplementary Figure 3 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

Effects of anti-Nodal antibody treatment on SK-MEL-28 cells.
Supplementary Figure 2 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 expression in DTIC-treated melanoma cell lines.
Supplementary Figure S2 from Let-7e Suppresses DNA Damage Repair and Sensitizes Ovarian Cancer to Cisplatin through Targeting PARP1
Authors: Xiao Man , Guo Jianfeng , Xie Lisha , Yang Chun , Gong Lanqing , Wang Zehua , Cai Jing
Published: April 2023

Supplementary Figure S2 shows the cellular viability of A2780, SKOV3 and Caov3 cell lines treated with cisplatin and/or olaparib for indicated duration.
Table S4 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

Table S4. Biological annotation for the top 25 genes
Supplementary Figure S1 from Let-7e Suppresses DNA Damage Repair and Sensitizes Ovarian Cancer to Cisplatin through Targeting PARP1
Authors: Xiao Man , Guo Jianfeng , Xie Lisha , Yang Chun , Gong Lanqing , Wang Zehua , Cai Jing
Published: April 2023

Supplementary Figure S1 shows the expression of IGF1R and p-Akt in let-7e-inhibited xenograft tumors.
Table 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

Table S3. Differential H3k4me3 signal in Men1 KO pancreatic islet compared with RIP-Cre control
Supplementary Figures from Phosphorylation of PLCγ1 by EphA2 Receptor Tyrosine Kinase Promotes Tumor Growth in Lung Cancer
Authors: Song Wenqiang , Kim Laura C. , Han Wei , Hou Yuan , Edwards Deanna N. , Wang Shan , Blackwell Timothy S. , Cheng Feixiong , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

Supplemental Figure 1. Densitometry analysis of p-PLCγ1and p-EphA2 inhibition by ALWand human lung TMA analysis. Supplemental Figure 2. sgPLCG1 mismatch detection.
Supplementary Fig. S4 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. S4. Relationship between H3K4me3 and H3K27me3 levels in Men1 target genes
Supplementary Figure Legend from Cdc42 Mediates Cancer Cell Chemotaxis in Perineural Invasion
Authors: Chernichenko Natalya , Omelchenko Tatiana , Deborde Sylvie , Bakst Richard L. , He Shizhi , Chen Chun-Hao , Gusain Laxmi , Vakiani Efsevia , Katabi Nora , Hall Alan , Wong Richard J.
Published: April 2023

A.Immunofluorescence microscopy was performed on control or shCdc42 MiaPaCa2 murine sciatic nerve tumors. Slides were stained with DAPI (blue) nuclear staining and primary antibodies (green) targeting total Cdc42, ï�¢-Pix, RET, and phospho-RET. B. Hematoxylin and eosin staining and GTP-Cdc42 immunohistochemistry of a control MiaPaCa2 murine sciatic nerve tumor.
Supplementary Fig. S2 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. S2. Histone mark profiles in known menin targets
Supplementary Fig. S1 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. S1. Intersection of genes showing enhanced H3K4me3 with upregulated genes, in Men1 KO islets
Supplemental Figure S4 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

S4. Bufexamac inhibits MDA-MB-231 tumor growth in vivo.
Supplementary Figure 2 from Autocrine VEGF/VEGFR1 Signaling in a Subpopulation of Cells Associates with Aggressive Osteosarcoma
Authors: Ohba Tetsuro , Cates Justin M.M. , Cole Heather A. , Slosky David A. , Haro Hirotaka , Ando Takashi , Schwartz Herbert S. , Schoenecker Jonathan G.
Published: April 2023

S2. (A) K7M3 cells (1x105 cell/well) treated with anti-VEGF164 antibody or VEGFR1 kinase inhibitor were seeded in the upper layer of a tranwell incubation chamber with or without 10% FBS added to the lower chamber and incubated for 24 hours. Non-migrating cells were removed from the upper chamber and the filter was fixed and stained with crystal violet (magnification x100, scale bar indicates 500 microm). (B) Absorbance was quantified at 590nm (OD 590). Data represent the mean (plus or minus) SD from two independent experiments (*, P < 0.01).
Supplemental Figure 1 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

Immunofluorescence characterization of EpCAM and c-MET in cell lines. Immunofluorescence of SNU5, HeLa and SIHA cell lines, with (clockwise from top left of each panel) external c-MET, EpCAM, DAPI from EpCAM slide, and DAPI from c-MET slide.
Supplementary Figure Legends 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 - 583K
Supplementary Figure 5 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 - 52K, Confidence Intervals for RT-qPCR.
Supplementary Figure 3 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 - 8K, RT-qPCR and Confidence Intervals for Jag1.
Supp. Fig. Legends 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

Supplementary Fig. S1 Epigenetic regulation of SOCS3 in cell lines. A, SOCS3 mRNA was measured in AR positive prostate cancer cell lines after treatement with 10 mM 5-Aza-2'deoxycytidine for 72 hours. B, publicly available Bisulfite-Seq. data for the SOCS3 CpG island was analyzed using the UCSC genome browser (hg19) and the ENCODE HAIB Methyl RRBS data track. A region of the SOCS3 promoter that is found to be differentially methylated in cell lines and tissue samples was selected for further methylation specific qPCR analysis. Supplementary Fig. S2 AR positive cell lines do not express IL6 mRNA. IL6 mRNA expression was measured by qPCR during cultivation under normal growth conditions. Supplementary Fig. S3 Knock-down and overexpression efficiency of SOCS3 in LNCaP. SOCS3 expression in LNCaP was modulated by stable over-expression and knock-down with lentiviral vectors and the effect on SOCS3 mRNA was determined by qPCR after 72 hours of reatment with 5 ng/ml IL6. Supplementary Fig. S4 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. Supplementary Fig. S5 SOCS3 is not regulated on post-transcriptional level by R1881. A luciferase reporter vector containing the coding sequence (CDS) and the 3'UTR of SOCS3 in the untranslated region after the luciferase stop codon was transfected into LNCaP cells. Treatment with 1 nM R1881 did not influence the reported expression, whereas, as a positive control, co-transfection with a shRNA targeting SOCS3 reduced the luciferase activity by more than 50 %. The firefly luc2 luciferase activity was normalized to a co-transfected renilla luciferase control vector. Supplementary Fig. S6 Knock-down and overexpression of SOCS3 is sustained after 3 weeks of combined IL6 and Enzalutamide treatment. SOCS3 expression in LNCaP was modulated by lentiviral over-expression and knock-down with a pool of 3 individual shRNAs targeting SOCS3 and the effect on SOCS3 mRNA was determined by qPCR after 3 weeks of combined IL6 and enzalutamide treatment.
Supplementary File 1 - Detailed methods from AXL Is a Putative Tumor Suppressor and Dormancy Regulator in Prostate Cancer
Authors: Axelrod Haley D. , Valkenburg Kenneth C. , Amend Sarah R. , Hicks Jessica L. , Parsana Princy , Torga Gonzalo , DeMarzo Angelo M. , Pienta Kenneth J.
Published: April 2023

Detailed methods
Supp. Fig. 2 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 positive cell lines do not express IL6 mRNA. IL6 mRNA expression was measured by qPCR during cultivation under normal growth conditions.
Figure S2 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

S2.(a) µCT-based monitoring of tumor response in K and KE mice prior to and after cisplatin treatment (left). Quantification of tumor volume in K and KE mice prior to and after cisplatin treatment (right). P values were calculated using two-tailed t-test. (b) Representative immunostaining of Pt-(GpG) adducts in tumor lung sections of KP and KPE mice after single cisplatin treatment (left). Quantification of Pt-(GpG) adduct staining in of KP (n = 3) and KPE mice (n = 4) after single cisplatin treatment (right). P values were calculated using two-tailed t-test. (c) Survival of chemo-naive vs. cisplatin-treated KrasLSL.G12D/wt (K) mice (top left), chemo-naive vs. cisplatin-treated KrasLSL.G12D/wt;Ercc1fl/fl (KE) mice (top right) and comparison of cisplatin-treated KrasLSL.G12D/wt (K) and cisplatin-treated KrasLSL.G12D/wt;Ercc1fl/fl (KE) mice (bottom). P values were calculated using log-rank test.
Figure S1 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

S1.(a) Distribution of tumor vs. normal lung tissue in K, KE, KP and KPE mice at 4 weeks post tumor induction (top). Distribution of murine lung adenocarcinoma grades (G1, G2, G3) in corresponding K, KE, KP and KPE mice at 4 weeks post tumor induction (bottom). (b) Anti-Ercc1 immunostaining of lung sections of KE mice (n = 2) at 4 weeks post tumor induction (mouse KE.1 shown at two magnifications, mouse KE.2 shown at two magnifications) (top). Anti-Ercc1 immunostaining of lung sections of KE mice (n = 2) at 12 weeks post tumor induction (mouse KE.3 shown at two magnifications, mouse KE.4 shown at two magnifications) (bottom). (c) Anti-Ercc1 immunostaining of lung sections of KPE mice (n = 5) at 4 weeks post tumor induction (shown at different magnifications) and of KPE mice (n = 5) at 12 weeks post tumor induction (shown at different magnifications).