bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Tables S1-10 from Genetic and Epigenetic Characterization of Growth Hormone–Secreting Pituitary Tumors
Authors: Välimäki Niko , Schalin-Jäntti Camilla , Karppinen Atte , Paetau Anders , Kivipelto Leena , Aaltonen Lauri A. , Karhu Auli
Published: April 2023

Supplementary Tables S1-S10 shows: 1) All the coding region variants (missense, premature stop codon, frameshift) of 21 sequenced somatotropinomas that passed the somatic filtering. 2) Results of correlation tests between genetic instability (GI%) and clinical variables. 3) Differentially expressed transcripts (FDR {less than or equal to} 5%, FC -2 {greater than or equal to} x {greater than or equal to} 2) in CA- and CS-tumors. 4) Significantly enriched canonical pathways carried out from differentially expressed genes (FDR < 5% and |FC|>2; CA- vs CS-tumors). 5) Immunostaining intensities of total- and phosphorylated-RB1 in CA- and CS-tumors. 6) CpG quality statistics. 7) Replication timing and CpG methylation. 8) Differentially methylated regions (DMRs) between Gsp+ versus Gsp- tumors, and nearby genes. 9) Integration of DMRs with matched transcriptomes by expression quantitative trait methylation (eQTM) analysis (at 5% FDR). 10) The complete list of significantly (p< 0.05) enriched cis-eQTM pathways.
Supplementary Figures S7-S11 from Genetic and Epigenetic Characterization of Growth Hormone–Secreting Pituitary Tumors
Authors: Välimäki Niko , Schalin-Jäntti Camilla , Karppinen Atte , Paetau Anders , Kivipelto Leena , Aaltonen Lauri A. , Karhu Auli
Published: April 2023

Supplementary Figures S7-11 show 7) Principal component analysis of CpG methylation estimates. 8) DNMT1 and genome-wide methylation. 9) Replication timing and CpG methylation. 10) Context-specific characteristics of CpG methylation estimates. 11) Unsupervised analysis of expression quantitative trait methylation (eQTM).
Figure S5 from Loss of Fas Expression and Function Is Coupled with Colon Cancer Resistance to Immune Checkpoint Inhibitor Immunotherapy
Authors: Xiao Wei , Ibrahim Mohammed L. , Redd Priscilla S. , Klement John D. , Lu Chunwan , Yang Dafeng , Savage Natasha M. , Liu Kebin
Published: April 2023

Overexpression of Fas does not alter sphere formation.
Supplementary Figures S4- S5 from Genetic and Epigenetic Characterization of Growth Hormone–Secreting Pituitary Tumors
Authors: Välimäki Niko , Schalin-Jäntti Camilla , Karppinen Atte , Paetau Anders , Kivipelto Leena , Aaltonen Lauri A. , Karhu Auli
Published: April 2023

Supplementary Figures S4-5 show 4) Total- and phsoporylated-RB1 inmmunohostochemistry in CA- and CS-tumors. 5) PTPR and PTPRK immunohistochemistry in CA- and CS-tumors.
Supplementary Figures S1-S3 from Genetic and Epigenetic Characterization of Growth Hormone–Secreting Pituitary Tumors
Authors: Välimäki Niko , Schalin-Jäntti Camilla , Karppinen Atte , Paetau Anders , Kivipelto Leena , Aaltonen Lauri A. , Karhu Auli
Published: April 2023

Supplementary Figures S1-3 show 1) Overview of the somatic copy-number aberrations. 2) Enrichment of whole-chromosome deletions and amplifications. 3) Principal component analysis of expression array data.
Figure S2 from Loss of Fas Expression and Function Is Coupled with Colon Cancer Resistance to Immune Checkpoint Inhibitor Immunotherapy
Authors: Xiao Wei , Ibrahim Mohammed L. , Redd Priscilla S. , Klement John D. , Lu Chunwan , Yang Dafeng , Savage Natasha M. , Liu Kebin
Published: April 2023

Loss of Fas function leads to resistance to FasL-induced apoptosis.
Supplementary Video. NIR-PIT effect for PC3pip cells. from Near-Infrared Photoimmunotherapy Targeting Prostate Cancer with Prostate-Specific Membrane Antigen (PSMA) Antibody
Authors: Nagaya Tadanobu , Nakamura Yuko , Okuyama Shuhei , Ogata Fusa , Maruoka Yasuhiro , Choyke Peter L. , Kobayashi Hisataka
Published: April 2023

Supplementary Video. NIR-PIT effect for PC3pip cells. Immediately after exposure to excitation light cellular swelling, bleb formation, and rupture of vesicles representing necrotic cell death were observed.
Supplementary tables from Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-Based Subtypes
Authors: Zhang Li , MacIsaac Kenzie D. , Zhou Ting , Huang Pei-Yu , Xin Chunlin , Dobson Jason R. , Yu Kun , Chiang Derek Y. , Fan Yue , Pelletier Marc , Wang Yan , Jaeger Savina , Krishnamurthy Radhakrishnan Viveksagar , JeBailey Lellean , Skewes-Cox Peter , Zhang Jing , Fang Wenfeng , Huang Yan , Zhao Hongyun , Zhao Yuanyuan , Li En , Peng Bin , Huang Alan , Dranoff Glenn , Hammerman Peter S. , Engelman Jeffrey , Bitter Hans , Zeng Yi-Xin , Yao Yao
Published: April 2023

Supplementary tables Table S1: Patient characteristics. Table S2: Non-synonymous mutations for paired cohort. Table S3: Non-synonymous mutations for unpaired cohort. Table S4: Copy number variants. Table S5: Correlation of principal components with gene expression. Table S6: Pathway enrichment analysis by principal component. Table S7: Gene signature evaluated in this study. Table S8: Tumor genes correlated with EBV genes. Table S9: Pathway enrichment of EBV-correlated genes.
Supplementary Table S3 from HBx-K130M/V131I Promotes Liver Cancer in Transgenic Mice via AKT/FOXO1 Signaling Pathway and Arachidonic Acid Metabolism
Authors: Chiu Amy P. , Tschida Barbara R. , Sham Tung-Ting , Lo Lilian H. , Moriarity Branden S. , Li Xiao-Xiao , Lo Regina C. , Hinton David E. , Rowlands Dewi K. , Chan Chi-On , Mok Daniel K.W. , Largaespada David A. , Warner Nadia , Keng Vincent W.
Published: April 2023

Supplementary Table S3. Up-stream regulator of IGF2.
Supplementary Table S1 from HBx-K130M/V131I Promotes Liver Cancer in Transgenic Mice via AKT/FOXO1 Signaling Pathway and Arachidonic Acid Metabolism
Authors: Chiu Amy P. , Tschida Barbara R. , Sham Tung-Ting , Lo Lilian H. , Moriarity Branden S. , Li Xiao-Xiao , Lo Regina C. , Hinton David E. , Rowlands Dewi K. , Chan Chi-On , Mok Daniel K.W. , Largaespada David A. , Warner Nadia , Keng Vincent W.
Published: April 2023

Supplementary Table S1. Differentially expressed genes identified in HBx-B Mut tumours against peripheral normal tissues.
Supplementary Materials and Methods from Identification of TP53RK-Binding Protein (TPRKB) Dependency in TP53-Deficient Cancers
Authors: Goswami Moloy T. , VanDenBerg Kelly R. , Han Sumin , Wang Lei Lucy , Singh Bhavneet , Weiss Travis , Barlow Myles , Kamberov Steven , Wilder-Romans Kari , Rhodes Daniel R. , Feng Felix Y. , Tomlins Scott A.
Published: April 2023

Materials and Methods for Supplemental experiments
Supplementary Figures 1-5 from Identification of TP53RK-Binding Protein (TPRKB) Dependency in TP53-Deficient Cancers
Authors: Goswami Moloy T. , VanDenBerg Kelly R. , Han Sumin , Wang Lei Lucy , Singh Bhavneet , Weiss Travis , Barlow Myles , Kamberov Steven , Wilder-Romans Kari , Rhodes Daniel R. , Feng Felix Y. , Tomlins Scott A.
Published: April 2023

Figure S1. Validation of Project Achilles data, evaluation of TPRKB expression profile across human tissues and ability to knock down TPRKB across cell lines. Figure S2. Cell lines with different types of TP53 alterations show dramatic reductions in cell proliferation upon TPRKB knockdown. Figure S3. Cell lines harboring mutant TP53 show reduced proliferation with TPRKB knockdown. Figure S4. Knockdown of EKC/KEOPS members PRPK, OSGEP and LAGE3 have variable effects across cell lines not related to TP53 status. Figure S5. PRPK specifically stabilizes TPRKB expression.
Supplementary Data Figure 1 from Atorvastatin Decreases HBx-Induced Phospho-Akt in Hepatocytes via P2X Receptors
Authors: Ghalali Aram , Martin-Renedo Javier , Högberg Johan , Stenius Ulla
Published: April 2023

Overexpression of HBx protein increases pAkt level in Huh7 cells.
Supplemental Legends from Atorvastatin Decreases HBx-Induced Phospho-Akt in Hepatocytes via P2X Receptors
Authors: Ghalali Aram , Martin-Renedo Javier , Högberg Johan , Stenius Ulla
Published: April 2023

Supplemental Legends
Table S4 from Establishment and Genetic Landscape of Precancer Cell Model Systems from the Head and Neck Mucosal Lining
Authors: de Boer D. Vicky , Brink Arjen , Buijze Marijke , Stigter-van Walsum Marijke , Hunter Keith D. , Ylstra Bauke , Bloemena Elisabeth , Leemans C. René , Brakenhoff Ruud H.
Published: April 2023

Overview of all detected genetic alterations. (A) Overview of the locations of all detected CNAs in the cultured margin samples generated in our lab. (B). Overview of the mutations detected in the precancerous samples that were assessed. Validation revealed that some mutations appeared to be germline, those were excluded from further analysis.
Table S3 from Establishment and Genetic Landscape of Precancer Cell Model Systems from the Head and Neck Mucosal Lining
Authors: de Boer D. Vicky , Brink Arjen , Buijze Marijke , Stigter-van Walsum Marijke , Hunter Keith D. , Ylstra Bauke , Bloemena Elisabeth , Leemans C. René , Brakenhoff Ruud H.
Published: April 2023

Genetic characterization of the five established tumor cultures. The five tumor cultures we generated contained multiple CNAs, three samples showed a loss of CDKN2A and all contained a mutation in TP53.
Figure S7 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis
Authors: Shen He , Yang Nuo , Truskinovsky Alexander , Chen Yanmin , Mussell Ashley L. , Nowak Norma J. , Kobzik Lester , Frangou Costa , Zhang Jianmin
Published: April 2023

Knockdown of SKP2 inhibits breast cancer cell proliferation and tumor formation.
Supplementary Spreadsheet S2 from p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes
Authors: Pappas Kyrie , Xu Jia , Zairis Sakellarios , Resnick-Silverman Lois , Abate Francesco , Steinbach Nicole , Ozturk Sait , Saal Lao H. , Su Tao , Cheung Pamela , Schmidt Hank , Aaronson Stuart , Hibshoosh Hanina , Manfredi James , Rabadan Raul , Parsons Ramon
Published: April 2023

Basal p53 ChIP-seq peaks in U2OS cells (after raw data analysis described in Materials in Methods section) ordered by significance of the peak call. Spreadsheet includes (columns left to right) peak locus (Chromosome, start, end), MACS2 significance, closest relevant gene (genes discussed in paper in red type), and original HOMER gene call (if relevant gene differs from called gene).
Figure S3 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis
Authors: Shen He , Yang Nuo , Truskinovsky Alexander , Chen Yanmin , Mussell Ashley L. , Nowak Norma J. , Kobzik Lester , Frangou Costa , Zhang Jianmin
Published: April 2023

Efficient knockdown of TAZ by siRNA in breast cancer cells.
Supplementary Information from Therapeutic Targeting of PTK7 is Cytotoxic in Atypical Teratoid Rhabdoid Tumors
Authors: Messerli Shanta M. , Hoffman Mariah M. , Gnimpieba Etienne Z. , Bhardwaj Ratan D.
Published: April 2023

Supplementary Fig. S4. PTK7 is structurally similar to receptors that bind Vatalanib. A) Stitch 5.0 network centered around Vatalanib (5) shows proteins that have been identified to interact with Vatalanib. Supplementary Table 1. The GenesLikeMe function of the Gene Card Suite (8) was used to search for similar genes to PTK7 with all of the search weight given to the â€œdomainsâ€� parameter.
Figure S1 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis
Authors: Shen He , Yang Nuo , Truskinovsky Alexander , Chen Yanmin , Mussell Ashley L. , Nowak Norma J. , Kobzik Lester , Frangou Costa , Zhang Jianmin
Published: April 2023

Activation of TAZ induced EMT, increase cell migration and colony formation in soft-agar in response to Dox treatment.
Supplementary Figures from Hypoxia-Associated Factor (HAF) Mediates Neurofibromin Ubiquitination and Degradation Leading to Ras–ERK Pathway Activation in Hypoxia
Authors: Green Yangsook Song , Sargis Timothy , Reichert Ethan Conrad , Rudasi Eleanor , Fuja Daniel , Jonasch Eric , Koh Mei Yee
Published: April 2023

Supplementary Figures 1-7
Supplementary Figure Legends from Hypoxia-Associated Factor (HAF) Mediates Neurofibromin Ubiquitination and Degradation Leading to Ras–ERK Pathway Activation in Hypoxia
Authors: Green Yangsook Song , Sargis Timothy , Reichert Ethan Conrad , Rudasi Eleanor , Fuja Daniel , Jonasch Eric , Koh Mei Yee
Published: April 2023

S1: A) Agarose gels showing PCR amplification of a region within HIF-2α exon 2 from genomic DNA from 786-0 HIF-2α deletion mutants, EPAS1-/- #4 and EPAS1-/-#11 compared to 786-0 cells transfected with Nickase control (NicCon). Clone #4 and #11 were generated using separate pairs of guide strands targeting different regions within exon 2. B) PCR primers used for amplification. C) Western blot showing HIF-2α protein levels in 786-0 Crispr clones compared to Nickase Control. D) Luciferase assay showing luciferase activity of a transiently transfected hypoxia-responsive element (HRE) - luciferase reporter normalized to a co-transfected beta-actin Renilla luciferase reporter in 786-0 Crispr clones compared to parental 786-0 cells. E) Genetic characterization of EPAS1-/-#4 aligned to EPAS1 NCBI RefSeq NG_016000.1. Clone #4 is a clonal population of cells with a 70bp deletion within one EPAS1 (HIF-2α) allele, and multiple indels within the corresponding region of the second allele: 5 insertions (underlined), 8 mutations (caps). F) Genetic characterization of EPAS-/- #11 aligned to EPAS1 NCBI RefSeq NG_016000.1. Clone #11 is a polyclonal cell population containing at least three variants of EPAS1 (HIF-2α), each with multiple mutations/indels within the targeted region. No wild-type allele was detected. S2: A) Growth curves of 786-0 Vec and HAF overexpressing CCRCC cells in normoxia. B) Normalized densitometry values of Western blots shown in Fig. 5A S3: Western blot showing expression levels of total PDGFR in ACHN, 786-0 and Caki-1 cells. S4: Western blot showing dose-dependent effect of SCH772984 on levels of phosphorylated and total p42/p44 ERK, and their downstream targets, the p90 ribosomal S6 kinases (RSK1/2/3) in 786-0 cells in normoxia. S5: Quantitation of HAF nuclear positivity in CCRCC tumor microarray comprising tumor cores of patients treated with sorafenib. Representative tumor cores image with low and high HAF levels with Aperio quantitation of HAF staining (given by % positivity) are shown. S6: HAF (SART1) expression data from TCGA-KIRC with associated survival data and HAF expression level group stratification. To show survival in months (in Figure 7), survival in days was divided by an average of 30 days per month. S7: A) Western blot showing levels of phosphorylated and total p70 ribosomal S6 protein (S6 ribosomal protein) in 786-0 cells stably expressing HAF or HAF DM after 24 hours' exposure to normoxia or hypoxia. B) Impact of 24 hours' rapamycin treatment on levels of phospho- and total mTOR, S6RP and ERK in 786-0 cells stably expressing empty vector or HAF.
Supplementary Figure Legends 1-3 from Inhibition of Aurora-A Promotes CD8+ T-Cell Infiltration by Mediating IL10 Production in Cancer Cells
Authors: Han Jing , Jiang Zhen , Wang Chennan , Chen Xin , Li Rongqing , Sun Na , Liu Xiangye , Wang Hui , Hong Li , Zheng Kuiyang , Yang Jing , Ikezoe Takayuki
Published: April 2023

Supplementary Figure S1. Alisertib suppressed tumor growth in association with an increase in the percentage of infiltrated intratumoral CD8+ T cells. Supplementary Figure S2. IL-10 induced the expression of IL-10Ralpha mRNA. Supplementary Figure S3. Alisertib decreased the percentage of macrophages and B cells.
Supplementary Table 1 from Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models
Authors: Khandelwal Garima , Girotti María Romina , Smowton Christopher , Taylor Sam , Wirth Christopher , Dynowski Marek , Frese Kristopher K. , Brady Ged , Dive Caroline , Marais Richard , Miller Crispin
Published: April 2023

Mapping percentages for RNA-sequencing datasets.
Supplementary Table 1 from IKKβ-Mediated Resistance to Skin Cancer Development Is Ink4a/Arf-Dependent
Authors: Page Angustias , Bravo Ana , Suarez-Cabrera Cristian , Alameda Josefa P. , Casanova M. Llanos , Lorz Corina , Segrelles Carmen , Segovia José C. , Paramio Jesús M. , Navarro Manuel , Ramirez Angel
Published: April 2023

Primer sequences.
Figure S3 from AHNAK Loss in Mice Promotes Type II Pneumocyte Hyperplasia and Lung Tumor Development
Authors: Park Jun Won , Kim Il Yong , Choi Ji Won , Lim Hee Jung , Shin Jae Hoon , Kim Yo Na , Lee Seo Hyun , Son Yeri , Sohn Mira , Woo Jong Kyu , Jeong Joseph H. , Lee Cheolju , Bae Yun Soo , Seong Je Kyung
Published: April 2023

Representative H&E images of Ahnak-/- and WT lungs in embryonic day 18.5 and postnatal day 1.
Table S3 from Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation
Authors: Kumar Pankaj , Dillon Laura W. , Shibata Yoshiyuki , Jazaeri Amir A. , Jones David R. , Dutta Anindya
Published: April 2023

Table S3: Summary of microDNA sequencing and mapping to human genomes in lung cancer patients.
Table S2 from Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation
Authors: Kumar Pankaj , Dillon Laura W. , Shibata Yoshiyuki , Jazaeri Amir A. , Jones David R. , Dutta Anindya
Published: April 2023

Table S2: Summary of microDNA sequencing and mapping to human genomes in lung cancer patients.
Figure S5 from E-Cadherin Represses Anchorage-Independent Growth in Sarcomas through Both Signaling and Mechanical Mechanisms
Authors: Jolly Mohit Kumar , Ware Kathryn E. , Xu Shengnan , Gilja Shivee , Shetler Samantha , Yang Yanjun , Wang Xueyang , Austin R. Garland , Runyambo Daniella , Hish Alexander J. , Bartholf DeWitt Suzanne , George Jason T. , Kreulen R. Timothy , Boss Mary-Keara , Lazarides Alexander L. , Kerr David L. , Gerber Drew G. , Sivaraj Dharshan , Armstrong Andrew J. , Dewhirst Mark W. , Eward William C. , Levine Herbert , Somarelli Jason A.
Published: April 2023

S5. Revised E-cad/TBX2 signaling model.
Figure S4 from E-Cadherin Represses Anchorage-Independent Growth in Sarcomas through Both Signaling and Mechanical Mechanisms
Authors: Jolly Mohit Kumar , Ware Kathryn E. , Xu Shengnan , Gilja Shivee , Shetler Samantha , Yang Yanjun , Wang Xueyang , Austin R. Garland , Runyambo Daniella , Hish Alexander J. , Bartholf DeWitt Suzanne , George Jason T. , Kreulen R. Timothy , Boss Mary-Keara , Lazarides Alexander L. , Kerr David L. , Gerber Drew G. , Sivaraj Dharshan , Armstrong Andrew J. , Dewhirst Mark W. , Eward William C. , Levine Herbert , Somarelli Jason A.
Published: April 2023

S4. E-cadherin induces E- to N-cadherin switching in sarcoma cells.
Figure S1 & Figure S2 from Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation
Authors: Kumar Pankaj , Dillon Laura W. , Shibata Yoshiyuki , Jazaeri Amir A. , Jones David R. , Dutta Anindya
Published: April 2023

Properties of mouse-derived microDNA in the serum of SKOV3 xenograft mice & Properties of microDNA in human matched tumor and normal lung tissues
Figure S1 from E-Cadherin Represses Anchorage-Independent Growth in Sarcomas through Both Signaling and Mechanical Mechanisms
Authors: Jolly Mohit Kumar , Ware Kathryn E. , Xu Shengnan , Gilja Shivee , Shetler Samantha , Yang Yanjun , Wang Xueyang , Austin R. Garland , Runyambo Daniella , Hish Alexander J. , Bartholf DeWitt Suzanne , George Jason T. , Kreulen R. Timothy , Boss Mary-Keara , Lazarides Alexander L. , Kerr David L. , Gerber Drew G. , Sivaraj Dharshan , Armstrong Andrew J. , Dewhirst Mark W. , Eward William C. , Levine Herbert , Somarelli Jason A.
Published: April 2023

S1. E-cadherin over-expression does not alter sarcoma cell growth in monolayer culture.
Supplementary Figure S3 from Potent EMT and CSC Phenotypes Are Induced By Oncostatin-M in Pancreatic Cancer
Authors: Smigiel Jacob M. , Parameswaran Neetha , Jackson Mark W.
Published: April 2023

Sorted CD24HI/CD44LOW populations retain phenotype in culture
Supplementary Data 1 from Abemaciclib Is Effective Against Pancreatic Cancer Cells and Synergizes with HuR and YAP1 Inhibition
Authors: Dhir Teena , Schultz Christopher W. , Jain Aditi , Brown Samantha Z. , Haber Alex , Goetz Austin , Xi Chunhua , Su Gloria H. , Xu Liang , Posey James , Jiang Wei , Yeo Charles J. , Golan Talia , Pishvaian Michael J. , Brody Jonathan R.
Published: April 2023

Supplemental figure 1: (A) RT-PCR of human genomic DNA probed for CDKN2A in Mia PaCa2, Panc-1, HS 766T, HPNE and PDXs, compared to positive control cells PA-1[54]. Subsequent RT-PCR of mouse genomic DNA probed for CDKN2A in KPC (KRAS mutant, p53 null) and KTC (KRAS mutant, HuR null) mouse organoids to validate CDKN2A status. (B) Pico green cell viability assay on PDX cell lines treated with palbociclib, abemaciclib or gemcitabine for 5 days, with IC50 tabulated below. (C) Cell titer glow cell viability assay to calculate IC50 for abemaciclib in KPC (IC50 4.9µM) and CDKN2A null organoids (IC50 4.0µM). (D) Top: Pico green assays to assess short-term abemaciclib drug response in Mia PaCa2, which has a deletion of CDKN2A gene, compared to HPNE, which has a preserved CDKN2A gene. IC50 for both cell lines are shown in the parenthesis. Bottom: Drug curves for HPNE cells treated with abemaciclib, gemcitabine or oxaliplatin are graphed with IC50 shown in parenthesis. (E) Crystal violet colony formation images for cells treated with palbociclib or abemaciclib at respective concentrations. (F) PCR primer sequences used for RT-PCR reactions.
Figure S6 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate
Authors: Elfandy Habiba , Armenia Joshua , Pederzoli Filippo , Pullman Eli , Pertega-Gomes Nelma , Schultz Nikolaus , Viswanathan Kartik , Vosoughi Aram , Blattner Mirjam , Stopsack Konrad H. , Zadra Giorgia , Penney Kathryn L. , Mosquera Juan Miguel , Tyekucheva Svitlana , Mucci Lorelei A. , Barbieri Christopher , Loda Massimo
Published: April 2023

Cribriform Morphology in PTENloss and SPOPmut Transgenic Mouse Prostate Model
Figure S4 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate
Authors: Elfandy Habiba , Armenia Joshua , Pederzoli Filippo , Pullman Eli , Pertega-Gomes Nelma , Schultz Nikolaus , Viswanathan Kartik , Vosoughi Aram , Blattner Mirjam , Stopsack Konrad H. , Zadra Giorgia , Penney Kathryn L. , Mosquera Juan Miguel , Tyekucheva Svitlana , Mucci Lorelei A. , Barbieri Christopher , Loda Massimo
Published: April 2023

Invasive Cribriform Carcinoma is Associated with High Gleason Score and Tumor Stage.
Supplementary Figures 1-7 from Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type–Specific Differences
Authors: Kaymaz Yasin , Oduor Cliff I. , Yu Hongbo , Otieno Juliana A. , Ong'echa John Michael , Moormann Ann M. , Bailey Jeffrey A.
Published: April 2023

S1. Assessment of putative tumor purity levels using IRIS signature genes from Abbas et al. S2. Epstein-barr virus transcription and lytic activity level measurements within primary eBL biopsies. S3. Dimension reduction with principal component analysis (PCA) on gene expression profiles. S4. All expressed human gene expression comparison between eBL tumors carrying EBV type 1 and eBL tumors with type 2 in log2 scale. S5. Sample to sample correlation heatmap of eBL, sBL tumors, and long-term BL cultures after removing all unwanted covariates except tumor origins. Gene expression profiles group into two clusters based on endemic and sporadic origins. S6. A) Common SNP counts detected in each sample after variant calling with RNAseq data by subsampling to balance the detection power (dbSNP v146). B) Rare non-synonymous variant fractions detected in each sample. S7. Lollipop plot for the non-synonymous mutations detected in BL tumors. -
Supplementary Figures 1-2 from IEX-1 Deficiency Protects against Colonic Cancer
Authors: Ustyugova Irina V. , Zhi Liang , Abramowitz Joel , Birnbaumer Lutz , Wu Mei X.
Published: April 2023

PDF file - 154K, Generation of Galphai2flx/flx-CD4-Cre mice and confirmation of Galphai2 deletion in T cells
Supplementary Material, Supplementary Figures 1-6, Supplementary Tables 1 and 2 from Aberrant Induction of a Mesenchymal/Stem Cell Program Engages Senescence in Normal Mammary Epithelial Cells
Authors: Bryson Benjamin L. , Tamagno Ilaria , Taylor Sarah E. , Parameswaran Neetha , Chernosky Noah M. , Balasubramaniam Nikhila , Jackson Mark W.
Published: April 2023

Supplemental Information to: Aberrant induction of a mesenchymal/stem-cell program engages senescence in normal mammary epithelial cells S1. Cytokine-induced senescence induces EMT and SC-associated gene expression changes. S2. OSM-mediated Snail induction drives an aberrant EMT that induces senescence. S3. OSM-induced EMT requires STAT3- and TGF-β/SMAD3-mediated signaling. S4. Senescence-escape generates transformed CSC which are highly sensitive to palbociclib. S5. Proposed mechanisms of OSM induced senescence, EMT, and stemness in normal human epithelial cells versus transformed cells. S6. Uncropped images of all western blots presented in the current study (continued). Supplementary Table 1. List of primary antibodies used in this study Supplementary Table 2. qRT-PCR primer sequences (listed 5'-to-3') used in this study.
Supplementary Figure Legends 1-7 from Expression of Wnt3 Activates Wnt/β-Catenin Pathway and Promotes EMT-like Phenotype in Trastuzumab-Resistant HER2-Overexpressing Breast Cancer Cells
Authors: Wu Yanyuan , Ginther Charles , Kim Juri , Mosher Nicole , Chung Seyung , Slamon Dennis , Vadgama Jaydutt V.
Published: April 2023

PDF file - 73K
Supplementary Figure 4 from Vasohibin-2 Expressed in Human Serous Ovarian Adenocarcinoma Accelerates Tumor Growth by Promoting Angiogenesis
Authors: Takahashi Yoshifumi , Koyanagi Takahiro , Suzuki Yasuhiro , Saga Yasushi , Kanomata Naoki , Moriya Takuya , Suzuki Mitsuaki , Sato Yasufumi
Published: April 2023

PDF file - 84K, RT-PCR analysis of VASH2 and SVBP in human ovarian cancer cells and EL-4
Supplementary Figure 2 from Vasohibin-2 Expressed in Human Serous Ovarian Adenocarcinoma Accelerates Tumor Growth by Promoting Angiogenesis
Authors: Takahashi Yoshifumi , Koyanagi Takahiro , Suzuki Yasuhiro , Saga Yasushi , Kanomata Naoki , Moriya Takuya , Suzuki Mitsuaki , Sato Yasufumi
Published: April 2023

PDF file - 32K, Proliferation and apoptosis of cancer cells in vivo
Supplementary Figure 2 from Expression of Wnt3 Activates Wnt/β-Catenin Pathway and Promotes EMT-like Phenotype in Trastuzumab-Resistant HER2-Overexpressing Breast Cancer Cells
Authors: Wu Yanyuan , Ginther Charles , Kim Juri , Mosher Nicole , Chung Seyung , Slamon Dennis , Vadgama Jaydutt V.
Published: April 2023

PDF file - 1MB, Pathway signaling differentially expressed in SKBR3/100-8 compared to SKBR3 revealed by IPA
Supplementary Figure 1 from Expression of Wnt3 Activates Wnt/β-Catenin Pathway and Promotes EMT-like Phenotype in Trastuzumab-Resistant HER2-Overexpressing Breast Cancer Cells
Authors: Wu Yanyuan , Ginther Charles , Kim Juri , Mosher Nicole , Chung Seyung , Slamon Dennis , Vadgama Jaydutt V.
Published: April 2023

PDF file - 67K, Increased dimerization of HER2/HER3 in SKBR3/100-8 cells
Supplemental Figures-Legends from DNA-Directed Polymerase Subunits Play a Vital Role in Human Telomeric Overhang Processing
Authors: Diotti Raffaella , Kalan Sampada , Matveyenko Anastasiya , Loayza Diego
Published: April 2023

Figure legends to supplemental figures 1-6
Supplemental Figure 5 from DNA-Directed Polymerase Subunits Play a Vital Role in Human Telomeric Overhang Processing
Authors: Diotti Raffaella , Kalan Sampada , Matveyenko Anastasiya , Loayza Diego
Published: April 2023

Supplemental Figure 5. A. Western blot for HeLaII expressing stable p68 shRNA B. In-gel hybridization for HeLaII treated with shRNA for p68 after ten passages. B. Overhang intensity for shRNA samples, processed as described in Fig.5B. C. Quantitation of the overhangs detected as in panel B, with values from three independent experiments. The p-value (two-tailed t-test) is shown for sh644.
Supplementary Figure 3 from The ATM Substrate KAP1 Controls DNA Repair in Heterochromatin: Regulation by HP1 Proteins and Serine 473/824 Phosphorylation
Authors: White David , Rafalska-Metcalf Ilona U. , Ivanov Alexey V. , Corsinotti Andrea , Peng Hongzhuang , Lee Sheng-Chung , Trono Didier , Janicki Susan M. , Rauscher Frank J.
Published: April 2023

PDF file - 295K
Supplementary Figure 2 from RhoC Is an Unexpected Target of RhoGDI2 in Prevention of Lung Colonization of Bladder Cancer
Authors: Griner Erin M. , Dancik Garrett M. , Costello James C. , Owens Charles , Guin Sunny , Edwards Michael G. , Brautigan David L. , Theodorescu Dan
Published: April 2023

Supplementary Figure 2. Effect of RhoC knock down in LuL2 bladder cancer cells A. Expression of RhoA and RhoC in LuL2 cells following stable knock down of RhoC by shRNA. Representative western blots shown. B. Invasion of LuL2 cells expressing shCont or shRhoC-1 through matrigel was determined using a transwell assay. Results expressed as number of invaded cells per well presented as the mean{plus minus} S.E. *P<0.05. Independent experiments (n=3) were performed in triplicate. C. Colony formation in soft agar was assessed in LuL2 cells expressing shCont or shRhoC-1. Bargraph indicates the number of colonies formed and is presented as the mean{plus minus} S.E. *P<0.05. Independent experiments (n=3) were performed in triplicate.
Supplementary Figure 1 from RhoC Is an Unexpected Target of RhoGDI2 in Prevention of Lung Colonization of Bladder Cancer
Authors: Griner Erin M. , Dancik Garrett M. , Costello James C. , Owens Charles , Guin Sunny , Edwards Michael G. , Brautigan David L. , Theodorescu Dan
Published: April 2023

Supplementary Figure 1. Co-immuoprecipitation of RhoGDI2 with RhoC in non-bladder cell types Endogenous RhoGDI2 from MDA-MB-231 breast cancer cells (Left), Jurkat lymphocyte cells (Center), or OVCAR-4 ovarian cancer cells (Right) was immunoprecipitated and analyzed by western blot for co-immunoprecipitation of Rac1 and RhoC. Representative western blots of 3 independent experiments shown.
Supplementary Figure 3 from Yes-Associated Protein 1 Is Activated and Functions as an Oncogene in Meningiomas
Authors: Baia Gilson S. , Caballero Otavia L. , Orr Brent A. , Lal Anita , Ho Janelle S. Y. , Cowdrey Cynthia , Tihan Tarik , Mawrin Christian , Riggins Gregory J.
Published: April 2023

PDF file - 154K, YAP1 protein expression and nuclear localization in meningioma cells
Supplementary Figure 1 from Fibroblast Growth Factor-2 Is an Important Factor that Maintains Cellular Immaturity and Contributes to Aggressiveness of Osteosarcoma
Authors: Shimizu Takatsune , Ishikawa Tomoki , Iwai Sayaka , Ueki Arisa , Sugihara Eiji , Onishi Nobuyuki , Kuninaka Shinji , Miyamoto Takeshi , Toyama Yoshiaki , Ijiri Hiroshi , Mori Hajime , Matsuzaki Yumi , Yaguchi Tomonori , Nishio Hiroshi , Kawakami Yutaka , Ikeda Yasuo , Saya Hideyuki
Published: April 2023

PDF file - 96K
Supplementary Figure Legend from The Role of Versican in Modulating Breast Cancer Cell Self-renewal
Authors: Du William Weidong , Fang Ling , Yang Xiangling , Sheng Wang , Yang Bing L. , Seth Arun , Zhang Yaou , Yang Burton B. , Yee Albert J.
Published: April 2023

PDF file - 85K
Supplementary Figure Legend from PRSS3/Mesotrypsin Is a Therapeutic Target for Metastatic Prostate Cancer
Authors: Hockla Alexandra , Miller Erin , Salameh Moh'd A. , Copland John A. , Radisky Derek C. , Radisky Evette S.
Published: April 2023

PDF file - 74K
Supplementary Tables 1 - 3 from Synergistic Effect of Olaparib with Combination of Cisplatin on PTEN-Deficient Lung Cancer Cells
Authors: Minami Daisuke , Takigawa Nagio , Takeda Hiromasa , Takata Minoru , Ochi Nobuaki , Ichihara Eiki , Hisamoto Akiko , Hotta Katsuyuki , Tanimoto Mitsune , Kiura Katsuyuki
Published: April 2023

PDF file - Combination index (CI) according to various concentration ratios of cisplatin and olaparib in each cell line was described; Drug sensitivity; Concentration ratio (molar) of cisplatin to olaparib.
Supplementary Figure 2 from PRSS3/Mesotrypsin Is a Therapeutic Target for Metastatic Prostate Cancer
Authors: Hockla Alexandra , Miller Erin , Salameh Moh'd A. , Copland John A. , Radisky Derek C. , Radisky Evette S.
Published: April 2023

PDF file - 1767K, Figure demonstrating that active mesotrypsin protein reconstituted the invasive morphology of prostate cancer cells in which PRSS3 was silenced
Supplementary Figure 2 from Synergistic Effect of Olaparib with Combination of Cisplatin on PTEN-Deficient Lung Cancer Cells
Authors: Minami Daisuke , Takigawa Nagio , Takeda Hiromasa , Takata Minoru , Ochi Nobuaki , Ichihara Eiki , Hisamoto Akiko , Hotta Katsuyuki , Tanimoto Mitsune , Kiura Katsuyuki
Published: April 2023

PDF file - 49K, Western blot showing Mre11 expression in H1650 and Mre11-transfected H1650 cells.
Supplementary Figure 2 from Group I p21-Activated Kinases (PAKs) Promote Tumor Cell Proliferation and Survival through the AKT1 and Raf–MAPK Pathways
Authors: Menges Craig W. , Sementino Eleonora , Talarchek Jacqueline , Xu Jinfei , Chernoff Jonathan , Peterson Jeffrey R. , Testa Joseph R.
Published: April 2023

PDF file - 187K, Immunoblot analysis of MM cells (Me12) treated with siRNA against PAK1 and PAK2 revealing that the slower migrating band is PAK1 and the faster migrating band is PAK2
Supplementary Figures 1-4 from Molecular Hierarchy of Heparin-Binding EGF-like Growth Factor–Regulated Angiogenesis in Triple-Negative Breast Cancer
Authors: Yotsumoto Fusanori , Tokunaga Eriko , Oki Eiji , Maehara Yoshihiko , Yamada Hiromi , Nakajima Kyoko , Nam Sung Ouk , Miyata Kohei , Koyanagi Midori , Doi Keiko , Shirasawa Senji , Kuroki Masahide , Miyamoto Shingo
Published: April 2023

PDF - 752K, Screening of genes involved in TNBC tumorigenesis.
Figure S4 from Mitochondria Participate in Chemoresistance to Cisplatin in Human Ovarian Cancer Cells
Authors: Zampieri Luca X. , Grasso Debora , Bouzin Caroline , Brusa Davide , Rossignol Rodrigue , Sonveaux Pierre
Published: April 2023

Figure S4 shows that inhibiting autophagy better preserves mtDNA in SKOV-3-R versus SKOV-3 cells.
Supplementary Figures S1-S5, Tables 1-3 from Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53
Authors: Quigley David , Silwal-Pandit Laxmi , Dannenfelser Ruth , Langerød Anita , Vollan Hans Kristian Moen , Vaske Charles , Siegel Josie Ursini , Troyanskaya Olga , Chin Suet-Feung , Caldas Carlos , Balmain Allan , Børresen-Dale Anne-Lise , Kristensen Vessela
Published: April 2023

Supplementary Figures S1-S5, Tables 1-3. S1: Distributions of P values from interaction analysis of Discovery (a) and Validation (c) cohorts. Comparison of Permutation P values and parametric P values for interaction analysis in Discovery (b) and Validation (d) cohorts. S2: Plots of estimated fold-change distributions comparing TP53-WT to TP53-mutant tumors separated by ER status, PAM50 subtype, and Integrative Cluster (as in Figure 3). Gene lists were derived from (Gu-Trantien JCI 2013, reference 30), with probes listed in Supplementary Table 3. S3: Effect plots of CTL expression score grouped by Integrative Cluster and TP53 mutation status (as in Figure 1b). TP53-WT plotted in black, TP53-mutant plotted in blue. Points indicate mean, error bars indicate 95% confidence intervals calculated from twice the standard error. S4: Box plots of TP53 expression levels in tumors with no mutation or LOH (AB), LOH but no mutation (BB), or both mutation and LOH (B). S5: Plots of CTL pathway expression gene expression divided by TP53 mutation and LOH status in (left) HER2-enriched, ER-negative tumors and (right) HER2-enriched, ER-positive tumors. Supplemental Table 1: This table lists probes with significant interactions in both the Discovery and Validation cohort. Uncorrected P values are listed first, next to P values correct with Holm's multiple testing correction. Fold-change for each intrinsic subtype is listed. Supplemental Table 2: Gene symbols for TH1, TH2, and CTL pathways identified by Nanodissect analysis, along with microarray probe IDs assigned by manual review. NA for probe ID indicates no appropriate probe was found or was expressed above background on that platform. Supplementary Table 3: Gene symbols for TH1, TH2, TREG, and TH17 and CTL pathways identified by FACS sorting of individual cell populations followed by microarray analysis, along with Illumina microarray probe IDs assigned by manual review. NA for probe ID indicates no appropriate probe was found or was expressed above background on that platform.
Supplementary Table 2 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas
Authors: Cheng Yingduan , Liang Pei , Geng Hua , Wang Zhaohui , Li Lili , Cheng Suk Hang , Ying Jianming , Su Xianwei , Ng Ka Man , Ng Margaret H.L. , Mok Tony S.K. , Chan Anthony T.C. , Tao Qian
Published: April 2023

PDF file - 28K, RT-PCR, MSP, BGS and cloning primers used for ZNF545
Supplementary Figures S1-S6 from Histone Modifications at the ABCG2 Promoter following Treatment with Histone Deacetylase Inhibitor Mirror Those in Multidrug-Resistant Cells
Authors: To Kenneth K.W. , Polgar Orsolya , Huff Lyn M. , Morisaki Kuniaki , Bates Susan E.
Published: April 2023

Supplementary Figures S1-S6 from Histone Modifications at the ABCG2 Promoter following Treatment with Histone Deacetylase Inhibitor Mirror Those in Multidrug-Resistant Cells
Supplementary Table S2 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment
Authors: Schwartz Donald R. , Moin Kamiar , Yao Bin , Matrisian Lynn M. , Coussens Lisa M. , Bugge Thomas H. , Fingleton Barbara , Acuff Heath B. , Sinnamon Mark , Nassar Hind , Platts Adrian E. , Krawetz Stephen A. , Linebaugh Bruce E. , Sloane Bonnie F.
Published: April 2023

Supplementary Table S2 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment
Supplementary Table S1 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment
Authors: Schwartz Donald R. , Moin Kamiar , Yao Bin , Matrisian Lynn M. , Coussens Lisa M. , Bugge Thomas H. , Fingleton Barbara , Acuff Heath B. , Sinnamon Mark , Nassar Hind , Platts Adrian E. , Krawetz Stephen A. , Linebaugh Bruce E. , Sloane Bonnie F.
Published: April 2023

Supplementary Table S1 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment
Supplementary Figure S1 from Protein Expression Profiling Identifies Cyclophilin A as a Molecular Target in Fhit-Mediated Tumor Suppression
Authors: Semba Shuho , Huebner Kay
Published: April 2023

Supplementary Figure S1 from Protein Expression Profiling Identifies Cyclophilin A as a Molecular Target in Fhit-Mediated Tumor Suppression
Supplementary Table S1 from Meta-Analysis and Systematic Review of the Genomics of Mucosal Melanoma
Authors: Broit Natasa , Johansson Peter A. , Rodgers Chloe B. , Walpole Sebastian T. , Newell Felicity , Hayward Nicholas K. , Pritchard Antonia L.
Published: April 2023

Study, Sample and Sequencing Panel Information
Supplementary Table 2 from SPANX Control of Lamin A/C Modulates Nuclear Architecture and Promotes Melanoma Growth
Authors: Lazar Ikrame , Fabre Bertrand , Feng Yongmei , Khateb Ali , Turko Patrick , Martinez Gomez Julia M. , Frederick Dennie T. , Levesque Mitchell P. , Feld Lea , Zhang Gao , Zhang Tongwu , James Brian , Shklover Jeny , Avitan-Hersh Emily , Livneh Ido , Scortegagna Marzia , Brown Kevin , Larsson Ola , Topisirovic Ivan , Wolfenson Haguy , Herlyn Meenhard , Flaherty Keith , Dummer Reinhard , Ronai Ze'ev A.
Published: April 2023

Supplementary Table S2: List of SPANX-interacting proteins identified by LC-MS/MS
Supplemental Figure S2 from RAF-Mutant Melanomas Differentially Depend on ERK2 Over ERK1 to Support Aberrant MAPK Pathway Activation and Cell Proliferation
Authors: Crowe Matthew S. , Zavorotinskaya Tatiana , Voliva Charles F. , Shirley Matthew D. , Wang Yanqun , Ruddy David A. , Rakiec Daniel P. , Engelman Jeffery A. , Stuart Darrin D. , Freeman Alyson K.
Published: April 2023

Supplementary Figure S2 shows Western blot analysis of A375, WM266-4 and NHEM-TCB cells, colony formation assays for A375 and NHEM-TCB cells, and the effects of ERK1 or ERK2 suppression immediately before or immediately after BRAF-V600E transformation of NHEM-TCB cells.
Supplementary Data from SPANX Control of Lamin A/C Modulates Nuclear Architecture and Promotes Melanoma Growth
Authors: Lazar Ikrame , Fabre Bertrand , Feng Yongmei , Khateb Ali , Turko Patrick , Martinez Gomez Julia M. , Frederick Dennie T. , Levesque Mitchell P. , Feld Lea , Zhang Gao , Zhang Tongwu , James Brian , Shklover Jeny , Avitan-Hersh Emily , Livneh Ido , Scortegagna Marzia , Brown Kevin , Larsson Ola , Topisirovic Ivan , Wolfenson Haguy , Herlyn Meenhard , Flaherty Keith , Dummer Reinhard , Ronai Ze'ev A.
Published: April 2023

Supplemental Methods, Figures, Figure legends, Table and Movie Legends
Supplemental Figure S1 from RAF-Mutant Melanomas Differentially Depend on ERK2 Over ERK1 to Support Aberrant MAPK Pathway Activation and Cell Proliferation
Authors: Crowe Matthew S. , Zavorotinskaya Tatiana , Voliva Charles F. , Shirley Matthew D. , Wang Yanqun , Ruddy David A. , Rakiec Daniel P. , Engelman Jeffery A. , Stuart Darrin D. , Freeman Alyson K.
Published: April 2023

Supplementary Figure S1 shows genetic dependency profiles for BRAF, MAPK1 (ERK2), and MAPK3 (ERK1) by BRAFV600 mutation status from three independent screens: DRIVE, ACHILLES, and AVANA.
Figure S3: Potential clustering solutions for defining groups of dynamic methylation clusters. from 5-Azacytidine Transiently Restores Dysregulated Erythroid Differentiation Gene Expression in TET2-Deficient Erythroleukemia Cells
Authors: Reilly Brian M. , Luger Timothy , Park Soo , Lio Chan-Wang Jerry , González-Avalos Edahí , Wheeler Emily C. , Lee Minjung , Williamson Laura , Tanaka Tiffany , Diep Dinh , Zhang Kun , Huang Yun , Rao Anjana , Bejar Rafael
Published: April 2023

Line plots in grid: each colored line represents a single CpG locus over time after 5-Aza treatment. Black line indicates mean value for that cluster group. Dotted black line indicates mean +/- 1 standard deviation. From left to right: clustering solutions with K=2 to K=9 clusters (derived from cutting the hierarchical cluster tree at different levels); top to bottom: the patterns of methylation in each cluster for that cluster solution. Mean silhouette width plot shows the mean silhouette width of all clusters for each individual clustering solution. K=4 clusters produced the most well-defined clusters as indicated by the peak in silhouette width.
Supplementary Table 1 from Proteomic Analysis of Src Family Kinase Phosphorylation States in Cancer Cells Suggests Deregulation of the Unique Domain
Authors: Ruiz-Saenz Ana , Zahedi Farima , Peterson Elliott , Yoo Ashley , Dreyer Courtney A. , Spassov Danislav S. , Oses-Prieto Juan , Burlingame Alma , Moasser Mark M.
Published: April 2023

Sources of the cell lines
Table S3 from Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment
Authors: Shiota Hitoshi , Alekseyenko Artyom A. , Wang Zhipeng A. , Filic Ivona , Knox Tatiana M. , Luong Nhi M. , Huang Yeying , Scott David A. , Jones Kristen L. , Gokhale Prafulla C. , Lemieux Madeleine E. , Cole Philip A. , Kuroda Mitzi I. , French Christopher A.
Published: April 2023

Supplemental Table
Table S1 from Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment
Authors: Shiota Hitoshi , Alekseyenko Artyom A. , Wang Zhipeng A. , Filic Ivona , Knox Tatiana M. , Luong Nhi M. , Huang Yeying , Scott David A. , Jones Kristen L. , Gokhale Prafulla C. , Lemieux Madeleine E. , Cole Philip A. , Kuroda Mitzi I. , French Christopher A.
Published: April 2023

Supplemental Table
Figure S4 from NF-κB Blockade with Oral Administration of Dimethylaminoparthenolide (DMAPT), Delays Prostate Cancer Resistance to Androgen Receptor (AR) Inhibition and Inhibits AR Variants
Authors: Morel Katherine L. , Hamid Anis A. , Clohessy John G. , Pandell Nicole , Ellis Leigh , Sweeney Christopher J.
Published: April 2023

Representative images of cell death staining in 22Rv1 empty vector control and p65 overexpressing tumoroids treated +/- DMAPT and/or enzalutamide.
Figure S2 from NF-κB Blockade with Oral Administration of Dimethylaminoparthenolide (DMAPT), Delays Prostate Cancer Resistance to Androgen Receptor (AR) Inhibition and Inhibits AR Variants
Authors: Morel Katherine L. , Hamid Anis A. , Clohessy John G. , Pandell Nicole , Ellis Leigh , Sweeney Christopher J.
Published: April 2023

Cleaved caspase-3 IHC staining and quantification in VCaP-CR tumors.
Figure S1 from NF-κB Blockade with Oral Administration of Dimethylaminoparthenolide (DMAPT), Delays Prostate Cancer Resistance to Androgen Receptor (AR) Inhibition and Inhibits AR Variants
Authors: Morel Katherine L. , Hamid Anis A. , Clohessy John G. , Pandell Nicole , Ellis Leigh , Sweeney Christopher J.
Published: April 2023

Individual VCaP-CR tumor growth curves in mice treated with vehicle, DMAPT, castration or DMAPT plus castration.
Supplementary Figure Legends from Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment
Authors: Shiota Hitoshi , Alekseyenko Artyom A. , Wang Zhipeng A. , Filic Ivona , Knox Tatiana M. , Luong Nhi M. , Huang Yeying , Scott David A. , Jones Kristen L. , Gokhale Prafulla C. , Lemieux Madeleine E. , Cole Philip A. , Kuroda Mitzi I. , French Christopher A.
Published: April 2023

Supplementary Figure Legends 1-4
Table S3 from The Epithelial–Stromal Microenvironment in Early Colonic Neoplasia
Authors: Ideta Takayasu , Li Boyang , Flynn Christopher , Igarashi Yuichi , Lowman Geoffrey , Looney Tim , Devers Thomas J. , Birk John , Forouhar Faripour , Giardina Charles , Rosenberg Daniel W.
Published: April 2023

Supplemental Table S3: CD8 cell infiltration into normal crypts and ACF. The percent area of epithelium and stroma occupied by CD8+ infiltrating lymphocytes was determined as described by Hendry et al., Adv Anat Pathol. 2017; 24(5): 235-251. The area occupied by CD8+ cells was determined through visual inspection by a pathologist.
Table S1 from The Epithelial–Stromal Microenvironment in Early Colonic Neoplasia
Authors: Ideta Takayasu , Li Boyang , Flynn Christopher , Igarashi Yuichi , Lowman Geoffrey , Looney Tim , Devers Thomas J. , Birk John , Forouhar Faripour , Giardina Charles , Rosenberg Daniel W.
Published: April 2023

Demographics of Participants with Proximal ACF
Figure S4 from The Epithelial–Stromal Microenvironment in Early Colonic Neoplasia
Authors: Ideta Takayasu , Li Boyang , Flynn Christopher , Igarashi Yuichi , Lowman Geoffrey , Looney Tim , Devers Thomas J. , Birk John , Forouhar Faripour , Giardina Charles , Rosenberg Daniel W.
Published: April 2023

Supplemental Figure S4. Expression of differentially expressed genes identified in stromal samples. (A) 32 up-regulated genes. (B) 50 down-regulated genes
Supplementary data from Opposing Effects of Granulocyte Colony-Stimulating Factor on the Initiation and Progression of Breast Cancer Bone Metastases
Authors: Hiraga Toru , Ito Susumu , Mizoguchi Toshihide
Published: April 2023

Supplementary data from Opposing Effects of Granulocyte Colony-Stimulating Factor on the Initiation and Progression of Breast Cancer Bone Metastases