bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S2 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Excel file, with all expression related data and its correlation with methylation
Figure S3 from Adaptive Protein Translation by the Integrated Stress Response Maintains the Proliferative and Migratory Capacity of Lung Adenocarcinoma Cells
Authors: Albert Alexandra E. , Adua Sally J. , Cai Wesley L. , Arnal-Estapé Anna , Cline Gary W. , Liu Zongzhi , Zhao Minghui , Cao Paul D. , Mariappan Malaiyalam , Nguyen Don X.
Published: April 2023

Thsi figure further describes the molecular effects of ATF4 inhibition and ISRIB during asparagine starvation.
Supplementary Table S1 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Excel file with all methylation related data
Figure S2 from Adaptive Protein Translation by the Integrated Stress Response Maintains the Proliferative and Migratory Capacity of Lung Adenocarcinoma Cells
Authors: Albert Alexandra E. , Adua Sally J. , Cai Wesley L. , Arnal-Estapé Anna , Cline Gary W. , Liu Zongzhi , Zhao Minghui , Cao Paul D. , Mariappan Malaiyalam , Nguyen Don X.
Published: April 2023

This figure describes the effects of ISRIB on the adaptive proliferation and motility of LUAD cells under amino acid stress.
Supplementary Figure legends from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Figure legends for Supplementary Figures
Supplementary Figure S6 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Methylation and gene expression changes in sensitive and resistant TNBC PDX tumors.
Supplementary Figure S5 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Clinical significance of methylation signatures of resistance
Supplementary Figure S4 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Clinical significance of methylation signatures of resistance
Supplemental Figure Legends from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

Supplemental Figure Legends 1-8
Figure S8 from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

mRNA level of PKD1 expression from stomach cancer TCGA data
Supplementary Figure S3 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Differential DNA methylation patterns between docetaxel sensitive, resistant or residual disease TNBC PDX models
Supplementary Figure S2 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

Global DNA methylation in docetaxel sensitive, resistant or residual disease TNBC PDX models
Figure S6 from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

mRNA level of PKD1 expression from prostate cancer TCGA data
Supplementary Figure S1 from The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models
Authors: Gómez-Miragaya Jorge , Morán Sebastián , Calleja-Cervantes Maria Eréndira , Collado-Sole Alejandro , Paré Laia , Gómez Antonio , Serra Violeta , Dobrolecki Lacey E. , Lewis Michael T. , Diaz-Lagares Angel , Eroles Pilar , Prat Aleix , Esteller Manel , González-Suárez Eva
Published: April 2023

DNA methylation signatures applied to breast cancer PDX models and comparasion with human normal mammary gland
Figure S5 from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

mRNA level of PKD1 expression from pancreatic cancer TCGA data
Figure S4 from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

mRNA level of PKD1 expression from lung adenocarcinoma (top) and lung squamous cell cancer (bottom) TCGA data
Supplementary table S2 from MST1 Suppresses Pancreatic Cancer Progression via ROS-Induced Pyroptosis
Authors: Cui Jiujie , Zhou Zhuqing , Yang Haiyan , Jiao Feng , Li Ning , Gao Yong , Wang Liwei , Chen Jingde , Quan Ming
Published: April 2023

Supplementary Table S2. Caspase-1 expression and clinicopathologic characteristics of TMA
Supplementary table S1 from MST1 Suppresses Pancreatic Cancer Progression via ROS-Induced Pyroptosis
Authors: Cui Jiujie , Zhou Zhuqing , Yang Haiyan , Jiao Feng , Li Ning , Gao Yong , Wang Liwei , Chen Jingde , Quan Ming
Published: April 2023

Supplementary Table S1.MST1 expression and clinicopathologic characteristics of TMA
Figure S2 from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

mRNA level of PKD1 expression from colorectal cancer (top) and kidney renal clear cell cancer (bottom) TCGA data
Figure S1 from Deciphering the Role of Protein Kinase D1 (PKD1) in Cellular Proliferation
Authors: Youssef Ilige , Ricort Jean-Marc
Published: April 2023

mRNA level of PKD1 expression from breast cancer TCGA data
Supplementary Figure S4 from MST1 Suppresses Pancreatic Cancer Progression via ROS-Induced Pyroptosis
Authors: Cui Jiujie , Zhou Zhuqing , Yang Haiyan , Jiao Feng , Li Ning , Gao Yong , Wang Liwei , Chen Jingde , Quan Ming
Published: April 2023

Supplementary Figure S4. ROS induces activation of caspase-1 in PDAC. BxPC-3 and FG cells were incubated with 0 mM, 15ï�­M and 30ï�­M H2O2 for 24hours. The levels of cl.caspase-1, mature-IL-1ï�¢ï€ andï€ mature-IL-18 were tested by western blot.
Supplementary Figure S3 from MST1 Suppresses Pancreatic Cancer Progression via ROS-Induced Pyroptosis
Authors: Cui Jiujie , Zhou Zhuqing , Yang Haiyan , Jiao Feng , Li Ning , Gao Yong , Wang Liwei , Chen Jingde , Quan Ming
Published: April 2023

Supplementary Figure S3. The expression of caspase-1 and its association with MST1 in PDAC tissues. TMA PDAC specimens were immunostained with a specific anti-caspase-1 antibody. A. Representative images of caspase-1 expression were shown (left panel represent normal tissue; middle panel represent cancer tissue with caspase-1 negative expression; right panel represent cancer tissue with caspase-1 strong expression). B. The expression of caspase-1 was significantly lower in tumors (TT) than in adjacent normal tissues (TN) and normal tissues (NN), while there was no difference between TN and NN. H and I, Positive correlation of MST1 with caspase-1 expression was assessed using Pearson correlation coefficient analysis (n=154; r=0.639, P<0.001).
Table S2 from Competitive Kinase Enrichment Proteomics Reveals that Abemaciclib Inhibits GSK3β and Activates WNT Signaling
Authors: Cousins Emily M. , Goldfarb Dennis , Yan Feng , Roques Jose , Darr David , Johnson Gary L. , Major Michael B.
Published: April 2023

comparison of abemaciclib targets
Supplementary Figure S2 from MST1 Suppresses Pancreatic Cancer Progression via ROS-Induced Pyroptosis
Authors: Cui Jiujie , Zhou Zhuqing , Yang Haiyan , Jiao Feng , Li Ning , Gao Yong , Wang Liwei , Chen Jingde , Quan Ming
Published: April 2023

Supplementary Figure S2. The correlated levels of MST1, Caspase-1 and ROS in PDAC cell lines. A, The expression of caspase-1 was tested by western blot (For better understand of the results, some of the data were duplicated with Fig. 1A). B and C, densitometry analysis of the protein levels of MST1 and caspase-1 of Western blot in Supplementary Fig. S2A. D, Relative levels of endogenous ROS in PDAC cell lines.
Table S1 from Competitive Kinase Enrichment Proteomics Reveals that Abemaciclib Inhibits GSK3β and Activates WNT Signaling
Authors: Cousins Emily M. , Goldfarb Dennis , Yan Feng , Roques Jose , Darr David , Johnson Gary L. , Major Michael B.
Published: April 2023

MIB/MS data
Supplementary Figure S1 from MST1 Suppresses Pancreatic Cancer Progression via ROS-Induced Pyroptosis
Authors: Cui Jiujie , Zhou Zhuqing , Yang Haiyan , Jiao Feng , Li Ning , Gao Yong , Wang Liwei , Chen Jingde , Quan Ming
Published: April 2023

Supplementary Figure S1. mRNA and protein levels of MST1 in PDAC tissues. The mRNA and protein of four paired PDAC tissues (TT) and its adjacent normal tissue (TN) were extracted. A, the protein levels of MST1 were tested by western blot. B, the mRNA levels of MST1 were tested by real-time PCR.
Supplementary Tables S1 - S4 from Overt Increase of Oxidative Stress and DNA Damage in Murine and Human Colitis and Colitis-Associated Neoplasia
Authors: Frick Adrian , Khare Vineeta , Paul Gregor , Lang Michaela , Ferk Franziska , Knasmüller Siegfried , Beer Andrea , Oberhuber Georg , Gasche Christoph
Published: April 2023

Supplementary Table 1. Antibodies used for Immunohistochemistry with working concentration. Supplementary Table 2. Primer pairs for LOH analysis. Supplementary Table 3. Markers used for MSI analysis. Supplementary Table 4. Total number of HGD and invasive carcinoma found in mice with corresponding percentage of affected animals.
Figure S1 from Competitive Kinase Enrichment Proteomics Reveals that Abemaciclib Inhibits GSK3β and Activates WNT Signaling
Authors: Cousins Emily M. , Goldfarb Dennis , Yan Feng , Roques Jose , Darr David , Johnson Gary L. , Major Michael B.
Published: April 2023

Dasatinib and BMS777607 competitive MIBMS
Supplemental Tables 1-2 from Clusterin, a Novel DEC1 Target, Modulates DNA Damage–Mediated Cell Death
Authors: Ming Xin , Bao Chenyi , Hong Tao , Yang Ying , Chen Xinbin , Jung Yong-Sam , Qian Yingjuan
Published: April 2023

Sequences of primers used for RT-PCR. Sequences of siRNA.
Supplemental Materials and Methods from Cholesterol Sulfotransferase SULT2B1b Modulates Sensitivity to Death Receptor Ligand TNFα in Castration-Resistant Prostate Cancer
Authors: Vickman Renee E. , Yang Jiang , Lanman Nadia A. , Cresswell Gregory M. , Zheng Faye , Zhang Chi , Doerge R. W. , Crist Scott A. , Mesecar Andrew D. , Hu Chang-Deng , Ratliff Timothy L.
Published: April 2023

The Supplemental Methods give additional details for methods in the main text.
Supplementary Table S1 from Cortactin Phosphorylation by Casein Kinase 2 Regulates Actin-Related Protein 2/3 Complex Activity, Invadopodia Function, and Tumor Cell Invasion
Authors: Markwell Steven M. , Ammer Amanda G. , Interval Erik T. , Allen Jessica L. , Papenberg Brenen W. , Hames River A. , Castaño Johnathan E. , Schafer Dorothy A. , Weed Scott A.
Published: April 2023

Predictive phospho site analysis software showing CK2 as likely cortactin T24 kinase.
Table S1 from AP-1 Signaling by Fra-1 Directly Regulates HMGA1 Oncogene Transcription in Triple-Negative Breast Cancers
Authors: Tolza Claire , Bejjani Fabienne , Evanno Emilie , Mahfoud Samantha , Moquet-Torcy Gabriel , Gostan Thierry , Maqbool Muhammad Ahmad , Kirsh Olivier , Piechaczyk Marc , Jariel-Encontre Isabelle
Published: April 2023

Primer and siRNA sequences
Figure S6 from AP-1 Signaling by Fra-1 Directly Regulates HMGA1 Oncogene Transcription in Triple-Negative Breast Cancers
Authors: Tolza Claire , Bejjani Fabienne , Evanno Emilie , Mahfoud Samantha , Moquet-Torcy Gabriel , Gostan Thierry , Maqbool Muhammad Ahmad , Kirsh Olivier , Piechaczyk Marc , Jariel-Encontre Isabelle
Published: April 2023

HMGA1 (A) and uPA/PLAU (B) mRNA levels upon depletion of p300 and/or CBP
Table S4 from High Prevalence of a Hotspot of Noncoding Somatic Mutations in Intron 6 of GPR126 in Bladder Cancer
Authors: Garinet Simon , Pignot Géraldine , Vacher Sophie , Le Goux Constance , Schnitzler Anne , Chemlali Walid , Sirab Nanor , Barry Delongchamps Nicolas , Zerbib Marc , Sibony Mathilde , Allory Yves , Damotte Diane , Bieche Ivan
Published: April 2023

Relationship between GPR126 transcript level and standard clinical pathological and biological parameters in bladder cancer
Figure S4 from AP-1 Signaling by Fra-1 Directly Regulates HMGA1 Oncogene Transcription in Triple-Negative Breast Cancers
Authors: Tolza Claire , Bejjani Fabienne , Evanno Emilie , Mahfoud Samantha , Moquet-Torcy Gabriel , Gostan Thierry , Maqbool Muhammad Ahmad , Kirsh Olivier , Piechaczyk Marc , Jariel-Encontre Isabelle
Published: April 2023

Contact matrices from Hi-C data from on the Chr6 33,724,700-34,948,488 region that contain the HMGA1 gene
Figure S3 from AP-1 Signaling by Fra-1 Directly Regulates HMGA1 Oncogene Transcription in Triple-Negative Breast Cancers
Authors: Tolza Claire , Bejjani Fabienne , Evanno Emilie , Mahfoud Samantha , Moquet-Torcy Gabriel , Gostan Thierry , Maqbool Muhammad Ahmad , Kirsh Olivier , Piechaczyk Marc , Jariel-Encontre Isabelle
Published: April 2023

Analysis of Fos and Jun family components binding at the HMGA1 locus according to Chip-seq data available in the ENCODE data base
Figure S1 from High Prevalence of a Hotspot of Noncoding Somatic Mutations in Intron 6 of GPR126 in Bladder Cancer
Authors: Garinet Simon , Pignot Géraldine , Vacher Sophie , Le Goux Constance , Schnitzler Anne , Chemlali Walid , Sirab Nanor , Barry Delongchamps Nicolas , Zerbib Marc , Sibony Mathilde , Allory Yves , Damotte Diane , Bieche Ivan
Published: April 2023

Survival curves of two patients groups according to GPR126 overexpression status in the series of 59 MIBC. x-axes represents the time (months). y-axes represents A : Recurrence-free-survival ; B: Overall survival. p=value is the result of log-rank test.
Table S1 from Differential Regulation of LET-7 by LIN28B Isoform–Specific Functions
Authors: Mizuno Rei , Chatterji Priya , Andres Sarah , Hamilton Kathryn , Simon Lauren , Foley Shawn W. , Jeganathan Arjun , Gregory Brian D. , Madison Blair , Rustgi Anil K.
Published: April 2023

qPCR primers
Figure S4 from Desmoglein 1 Regulates Invadopodia by Suppressing EGFR/Erk Signaling in an Erbin-Dependent Manner
Authors: Valenzuela-Iglesias Alejandra , Burks Hope E. , Arnette Christopher R. , Yalamanchili Amulya , Nekrasova Oxana , Godsel Lisa M. , Green Kathleen J.
Published: April 2023

Supplemental Figure 4: Expression levels of major proteinases secreted by invadopodia.
Figure S2 from Desmoglein 1 Regulates Invadopodia by Suppressing EGFR/Erk Signaling in an Erbin-Dependent Manner
Authors: Valenzuela-Iglesias Alejandra , Burks Hope E. , Arnette Christopher R. , Yalamanchili Amulya , Nekrasova Oxana , Godsel Lisa M. , Green Kathleen J.
Published: April 2023

Supplemental Figure 2: Western blot of Cal33 and Dsg1FL Cal33 expressing cells to analyze desmosomal cadherin expression.
Figure S1 from Desmoglein 1 Regulates Invadopodia by Suppressing EGFR/Erk Signaling in an Erbin-Dependent Manner
Authors: Valenzuela-Iglesias Alejandra , Burks Hope E. , Arnette Christopher R. , Yalamanchili Amulya , Nekrasova Oxana , Godsel Lisa M. , Green Kathleen J.
Published: April 2023

Supplemental Figure 1. Western blot of whole cell lysates from squamous cell carcinoma lines to look at cell-cell junction associated proteins.
Supplemental Figure 4 from TGFβ-Induced Lung Cancer Cell Migration Is NR4A1-Dependent
Authors: Hedrick Erik , Mohankumar Kumaravel , Safe Stephen
Published: April 2023

Interactions of NR4A1, SMAD7 and other proteasome complex proteins.
Supplemental Figure 1 from TGFβ-Induced Lung Cancer Cell Migration Is NR4A1-Dependent
Authors: Hedrick Erik , Mohankumar Kumaravel , Safe Stephen
Published: April 2023

Confocal microscopic analysis of TGFbeta-induced nuclear export of NR4A1.
Table S2 from Population-dependent Intron Retention and DNA Methylation in Breast Cancer
Authors: Kim Dongwook , Shivakumar Manu , Han Seonggyun , Sinclair Michael S. , Lee Young-Ji , Zheng Yonglan , Olopade Olufunmilayo I. , Kim Dokyoon , Lee Younghee
Published: April 2023

Summary of 44 retained introns
Supplemental Table 1 from Epigenetic Targeting of Adipocytes Inhibits High-Grade Serous Ovarian Cancer Cell Migration and Invasion
Authors: Tang Jessica , Pulliam Nicholas , Özeş Ali , Buechlein Aaron , Ding Ning , Keer Harold , Rusch Doug , O'Hagan Heather , Stack M. Sharon , Nephew Kenneth P.
Published: April 2023

Primer sequences and SUSD2 protein-protein interaction database
Supplementary Figures S1-S10 from D-2-Hydroxyglutarate Is Necessary and Sufficient for Isocitrate Dehydrogenase 1 Mutant–Induced MIR148A Promoter Methylation
Authors: Li Tie , Cox Christopher D. , Ozer Byram H. , Nguyen Nhung T. , Nguyen HuyTram N. , Lai Thomas J. , Li Sichen , Liu Fei , Kornblum Harley I. , Liau Linda M. , Nghiemphu Phioanh L. , Cloughesy Timothy F. , Lai Albert
Published: April 2023

Supplementary Figure S1: Treatment with octyl-D-2-HG-induces MIR148A methylation; Supplementary Figure S2: Octyl-D-2-HG-induced MIR148A methylation status remains constant at late passages; Supplementary Figure S3: Octyl-D-2-HG induces CpG island methylation of the RBP1 promoter in 293T cells; Supplementary Figure S4: Octyl-D-2-HG induces CpG island methylation of the MIR148A promoter in normal human astrocytes (NHA); Supplementary Figure S5: MIR148A promoter CpG methylation in IDH1MUT-transfected 293T cells; Supplementary Figure S6: C227 prevents IDH1 mutant-induced MIR148A promoter methylation; Supplementary Figure S7: C227 prevents IDH1 mutant-induced RBP1 promoter methylation; Supplementary Figure S8: Schematic graph of MIR148A genomic location, CpG island, and promoter-reporter construct; Supplementary Figure S9: MIR148a expression is unchanged by octyl-D-2-HG treatment in early passages in 293T and NHA cells; Supplementary Figure S10: Octyl-D-2-HG withdrawal restores MIR148A promoter to an unmethylated state
Supplementary Data File 4 from GSK2801, a BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer
Authors: Bevill Samantha M. , Olivares-Quintero Jose F. , Sciaky Noah , Golitz Brian T. , Singh Darshan , Beltran Adriana S. , Rashid Naim U. , Stuhlmiller Timothy J. , Hale Andrew , Moorman Nathaniel J. , Santos Charlene M. , Angus Steven P. , Zawistowski Jon S. , Johnson Gary L.
Published: April 2023

File includes drug synergy scores for 4 cell lines screened against CPI-637
Supplementary Data File 3 from GSK2801, a BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer
Authors: Bevill Samantha M. , Olivares-Quintero Jose F. , Sciaky Noah , Golitz Brian T. , Singh Darshan , Beltran Adriana S. , Rashid Naim U. , Stuhlmiller Timothy J. , Hale Andrew , Moorman Nathaniel J. , Santos Charlene M. , Angus Steven P. , Zawistowski Jon S. , Johnson Gary L.
Published: April 2023

File includes drug synergy scores for 1 cell line screened against OTX015
Supplementary Data_Legends from A Novel FGFR3 Splice Variant Preferentially Expressed in African American Prostate Cancer Drives Aggressive Phenotypes and Docetaxel Resistance
Authors: Olender Jacqueline , Wang Bi-Dar , Ching Travers , Garmire Lana X. , Garofano Kaitlin , Ji Youngmi , Knox Tessa , Latham Patricia , Nguyen Kenneth , Rhim Johng , Lee Norman H.
Published: April 2023

Figure and Table legends for supplemental data.
Supplementary Data from DNA Damage, Liver Injury, and Tumorigenesis: Consequences of DDX3X Loss
Authors: Chan Chieh-Hsiang , Chen Chun-Ming , Lee Yan-Hwa Wu , You Li-Ru
Published: April 2023

All Supplementary Data
Supplemental Files from Lipid Uptake Is an Androgen-Enhanced Lipid Supply Pathway Associated with Prostate Cancer Disease Progression and Bone Metastasis
Authors: Tousignant Kaylyn D. , Rockstroh Anja , Taherian Fard Atefeh , Lehman Melanie L. , Wang Chenwei , McPherson Stephen J. , Philp Lisa K. , Bartonicek Nenad , Dinger Marcel E. , Nelson Colleen C. , Sadowski Martin C.
Published: April 2023

Figure S1: LNCaP, VCaP and DuCaP cells were grown in charcoal-dextran stripped serum (CSS) for 48 h and treated with increasing concentrations of R1881 or DHT in the presence or absence of Enzalutamide (10 µM) or vehicle (Ctrl) for 48 h. Figure S2: Androgens increased lipid uptake of long-chain fatty acids. LAPC4 cells were grown in CSS for 48 h and treated with 1 nM R1881 or vehicle for 48 h. Figure S3: (A) LNCaP cells were synchronized in G0/G1 by androgen deprivation (CSS for 48 h) followed by treatment with Tunicamycin (1 mg/mL), Hydroxyurea (1 M), or Nocodazole (25 ug/mL) for another 24 h, placing cell cycle blocks in G0/G1, S phase and mitosis, respectively. Figure S4: Oncomine analysis of candidate lipid transporters in (A) Grasso [2], (B) Varambally [3] and (C) LaTulippe datasets [4] comparing gene expression of normal prostate gland versus localized, primary prostate cancer tumor samples. Figure S5: (A) DuCaP (top panel) and VCaP cells (bottom panel) were grown in CSS for 48 h and treated with 10 nM DHT in the absence or presence of Enz (10 µM) or vehicle (Ctrl) for 48 h. Table S1. Primer sequences
Figure S4 from CRISPR Editing of Mutant IDH1 R132H Induces a CpG Methylation-Low State in Patient-Derived Glioma Models of G-CIMP
Authors: Moure Casey J. , Diplas Bill H. , Chen Lee H. , Yang Rui , Pirozzi Christopher J. , Wang Zhaohui , Spasojevic Ivan , Waitkus Matthew S. , He Yiping , Yan Hai
Published: April 2023

Conummee Copy Number Calls
Figure S3 from CRISPR Editing of Mutant IDH1 R132H Induces a CpG Methylation-Low State in Patient-Derived Glioma Models of G-CIMP
Authors: Moure Casey J. , Diplas Bill H. , Chen Lee H. , Yang Rui , Pirozzi Christopher J. , Wang Zhaohui , Spasojevic Ivan , Waitkus Matthew S. , He Yiping , Yan Hai
Published: April 2023

Supplementary Methylation Analysis
Supplementary Materials and Methods from TANKYRASE Inhibition Enhances the Antiproliferative Effect of PI3K and EGFR Inhibition, Mutually Affecting β-CATENIN and AKT Signaling in Colorectal Cancer
Authors: Solberg Nina T. , Waaler Jo , Lund Kaja , Mygland Line , Olsen Petter A. , Krauss Stefan
Published: April 2023

Extensive descriptions of the materials and methods used in the study.
Figure S1 from CRISPR Editing of Mutant IDH1 R132H Induces a CpG Methylation-Low State in Patient-Derived Glioma Models of G-CIMP
Authors: Moure Casey J. , Diplas Bill H. , Chen Lee H. , Yang Rui , Pirozzi Christopher J. , Wang Zhaohui , Spasojevic Ivan , Waitkus Matthew S. , He Yiping , Yan Hai
Published: April 2023

IMA and 08-0537 Cloning Supplementary Data
Supplementary Figures S1 - S21 from TANKYRASE Inhibition Enhances the Antiproliferative Effect of PI3K and EGFR Inhibition, Mutually Affecting β-CATENIN and AKT Signaling in Colorectal Cancer
Authors: Solberg Nina T. , Waaler Jo , Lund Kaja , Mygland Line , Olsen Petter A. , Krauss Stefan
Published: April 2023

Supplementary Figures supporting the results and conclusions stated in the manuscript beyond what is shown in the main figures. This includes, inhibitor dose responses, growth response to alternative PI3K and EGFR inhibitors, molecular responses to combined tankyrase/MEK inhibition, C-terminal B-cat response, nuclear FOXO3a, as well as xenograft statistics and mouse body end weights. Additionally, similar data as was shown for COLO320DM and HCT-15 in the main figures are reported for the SW403 and SW480 CRC cell lines. The supplementary figures also show growth responses of HCT-8, WiDR, COLO205 and RKO CRC cell lines to inhibitor treatments. Growth responses of COLO320DM and HCT-15 cells to esiRNA mediated TP53 knock down is also shown, both with and without inhibitor treatments.
Supplementary Figure S1 from Effects of Oncogenic Gαq and Gα11 Inhibition by FR900359 in Uveal Melanoma
Authors: Lapadula Dominic , Farias Eduardo , Randolph Clinita E. , Purwin Timothy J. , McGrath Dougan , Charpentier Thomas H. , Zhang Lihong , Wu Shihua , Terai Mizue , Sato Takami , Tall Gregory G. , Zhou Naiming , Wedegaertner Philip B. , Aplin Andrew E. , Aguirre-Ghiso Julio , Benovic Jeffrey L.
Published: April 2023

GNAQ and GNA11 sequence analysis of UM002B cells.
Supplementary Figure 6 from Ovarian Tumor Cell Expression of Claudin-4 Reduces Apoptotic Response to Paclitaxel
Authors: Breed Christopher , Hicks Douglas A. , Webb Patricia G. , Galimanis Carly E. , Bitler Benjamin G. , Behbakht Kian , Baumgartner Heidi K.
Published: April 2023

Images of apoptotic response (claudin-4 overexpression).
All Supplementary Figures and Tables from The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients
Authors: Chatrath Ajay , Kiran Manjari , Kumar Pankaj , Ratan Aakrosh , Dutta Anindya
Published: April 2023

S1. A boxplot representing the percentage of variants called in the whole exome sequenced (WXS) tumor sample that is likely somatic mutations. S2. Correlation between the variant allele frequencies calculated from the four variant sets and the distribution of allele frequencies. S3. Principal components calculated from germline variants from the whole exome sequencing data from the non-tumor samples. S4. Kaplan-Meier plot for the germline variant rs28672782 in BRSK2. Table S1. Quality control checks reveal that somatic mutations and RNA editing did not affect the results of our analysis. Table S2. Correlation between the allele frequencies calculated in our four variant sets and the allele frequencies reported by gnomAD. Table S3. Variants genetically linked to rs61757955 in the European population, the population that is most similar to the TCGA lower grade glioma patient population. Table S4. Results from testing for an association between the germline variant rs34988193 and genomic and histological variables.
Figure S4 from HILPDA Regulates Lipid Metabolism, Lipid Droplet Abundance, and Response to Microenvironmental Stress in Solid Tumors
Authors: VandeKopple Matthew J. , Wu Jinghai , Auer Erich N. , Giaccia Amato J. , Denko Nicholas C. , Papandreou Ioanna
Published: April 2023

Impact of ATGL inhibition on LD accumulation
Figure S1 from HILPDA Regulates Lipid Metabolism, Lipid Droplet Abundance, and Response to Microenvironmental Stress in Solid Tumors
Authors: VandeKopple Matthew J. , Wu Jinghai , Auer Erich N. , Giaccia Amato J. , Denko Nicholas C. , Papandreou Ioanna
Published: April 2023

LD staining parameters in HILPDA WT and KO cells
Supplementary Table S2 from Nomogram Integrating Genomics with Clinicopathologic Features Improves Prognosis Prediction for Colorectal Cancer
Authors: Xiong Yongfu , You Wenxian , Hou Min , Peng Linglong , Zhou He , Fu Zhongxue
Published: April 2023

Eligible patient inclusion in this study
Supplementary Figure S1 from Nomogram Integrating Genomics with Clinicopathologic Features Improves Prognosis Prediction for Colorectal Cancer
Authors: Xiong Yongfu , You Wenxian , Hou Min , Peng Linglong , Zhou He , Fu Zhongxue
Published: April 2023

Supplementary Figure S1. Flowchart for developing and validating the clinicopathologic-genomic nomogram in a large-scale CRC cohort. Gene expression signatures concerning CRC prognosis were systematically retrieved from PubMed. CRC microarray datasets with clinically annotated information were retrieved from GEO. After excluding patients with incomplete clinical data and duplications, we combined these datasets into a large-scale CRC cohort, which was further analyzed by PCA and clustering. Then, the CRC cohort was randomly divided into a training set (n = 855) and a validation set (n = 855) to develop and validate the clinicopathologic-genomic nomogram, respectively. Based on the training set, we assessed the prognostic performances of signatures that met the inclusion criteria detailed in the flowchart. Next, a nomogram integrating well-performing signatures with clinical variables was constructed via a backward stepwise Cox proportional hazard model. Based on the validation set, we further evaluated the prognostic value of the clinicopathologic-genomic nomogram to determine whether it could robustly identify patients at high risk of recurrence.
Supplementary Figure S1 from ETV4 Facilitates Cell-Cycle Progression in Pancreatic Cells through Transcriptional Regulation of Cyclin D1
Authors: Tyagi Nikhil , Deshmukh Sachin K. , Srivastava Sanjeev K. , Azim Shafquat , Ahmad Aamir , AL-Ghadhban Ahmed , Singh Ajay P. , Carter James E. , Wang Bin , Singh Seema
Published: April 2023

Immunohistochemical Analyses of ETV4 expression in pancreatic cancer tissue specimens.
Figure S6 from BRD4 Regulates Metastatic Potential of Castration-Resistant Prostate Cancer through AHNAK
Authors: Shafran Jordan S. , Andrieu Guillaume P. , Györffy Balázs , Denis Gerald V.
Published: April 2023

BRD4 and AHNAK expression correlate in mCRPC patients
Figure S3 from BRD4 Regulates Metastatic Potential of Castration-Resistant Prostate Cancer through AHNAK
Authors: Shafran Jordan S. , Andrieu Guillaume P. , Györffy Balázs , Denis Gerald V.
Published: April 2023

BRD4 regulates AHNAK in PC-3 cells and interacts with the AHNAK promoter in DU 145 cells
Figure S2 from BRD4 Regulates Metastatic Potential of Castration-Resistant Prostate Cancer through AHNAK
Authors: Shafran Jordan S. , Andrieu Guillaume P. , Györffy Balázs , Denis Gerald V.
Published: April 2023

BRD4 regulates DU 145 cell invasion and PC-3 cell migration
Supplementary Figure 3 from Mitotically-Associated lncRNA (MANCR) Affects Genomic Stability and Cell Division in Aggressive Breast Cancer
Authors: Tracy Kirsten M. , Tye Coralee E. , Ghule Prachi N. , Malaby Heidi L.H. , Stumpff Jason , Stein Janet L. , Stein Gary S. , Lian Jane B.
Published: April 2023

MANCR-depleted MDA-MB-231 cells exhibit a more normal-like expression of genes related to cell cycle processes.
Supplementary Figure 1 from Mitotically-Associated lncRNA (MANCR) Affects Genomic Stability and Cell Division in Aggressive Breast Cancer
Authors: Tracy Kirsten M. , Tye Coralee E. , Ghule Prachi N. , Malaby Heidi L.H. , Stumpff Jason , Stein Janet L. , Stein Gary S. , Lian Jane B.
Published: April 2023

Robust ASO-mediated depletion of MANCR in MDA-MB-231 cells.
Supplementary Figure S1 from The Transcription Factor AP4 Promotes Oncogenic Phenotypes and Cisplatin Resistance by Regulating LAPTM4B Expression
Authors: Wang Lu , Meng Yue , Xu Jian-Jun , Zhang Qing-Yun
Published: April 2023

Supplementary Figure S1 shows the results of TF profiling plate arrays.
Supplementary Materials and Methods from Multiple Defects Sensitize p53-Deficient Head and Neck Cancer Cells to the WEE1 Kinase Inhibition
Authors: Diab Ahmed , Kao Michael , Kehrli Keffy , Kim Hee Yeon , Sidorova Julia , Mendez Eduardo
Published: April 2023

Materials used in Supplementary Data and additional Methods info
Supplementary Figures, Legends and Tables from Multiple Defects Sensitize p53-Deficient Head and Neck Cancer Cells to the WEE1 Kinase Inhibition
Authors: Diab Ahmed , Kao Michael , Kehrli Keffy , Kim Hee Yeon , Sidorova Julia , Mendez Eduardo
Published: April 2023

Figure S1. Severe DNA replication inhibition in UM-SCC-74a HNSCC line and untransformed primary cells. Figure S2. Efficiency of WEE1 inhibition by AZD1775. Figure S3. Cell cycle progression and ï�§H2AX response in the p53 mutant PCI-15B cells. Figure S4. Inactivation of p53 by expression of E6 protein of HPV16 reproduces AZD1775-dependent phenotypes of shRNA-mediated p53 depletion in UM-SCC-74a cells. Figure S5. Dynamics of ï�§H2AX++ and mitotic cells in p53kd and control UM-SCC-74a recovering from AZD1775. Figure S6. Validation of Sorted microfluidic-assisted Replication Track Analysis (SmaRTA). Table S1: Synergy analysis for AZD1775 and triapine combination in p53kd and control UM-SCC-74a cells. Table S2: Synergy analysis for AZD1775 and CDDP combination in p53kd and control UM-SCC-74a cells as described for Table S1.
Supplementary Figure S2 from Hyperphosphorylation of CDH1 in Glioblastoma Cancer Stem Cells Attenuates APC/CCDH1 Activity and Pharmacologic Inhibition of APC/CCDH1/CDC20 Compromises Viability
Authors: De Kuntal , Grubb Treg M. , Zalenski Abigail A. , Pfaff Kayla E. , Pal Debjani , Majumder Shubhra , Summers Matthew K. , Venere Monica
Published: April 2023

Nocodazole synchronization for GBM NSTCs
Supplementary figure from HuR Suppresses Fas Expression and Correlates with Patient Outcome in Liver Cancer
Authors: Zhu Haifeng , Berkova Zuzana , Mathur Rohit , Sehgal Lalit , Khashab Tamer , Tao Rong-Hua , Ao Xue , Feng Lei , Sabichi Anita L. , Blechacz Boris , Rashid Asif , Samaniego Felipe
Published: April 2023

Supplementary figure 1-2: Fig. S1. Fas mRNA in HCC cell lines and the effects of HuR knockdown on alternative Fas splicing. Fig S2. Effect of HuR knock-down on FasL-induced apoptosis in HepG2 cells.
Supplementary Figure Legend from Loss of Stromal IMP1 Promotes a Tumorigenic Microenvironment in the Colon
Authors: Hamilton Kathryn E. , Chatterji Priya , Lundsmith Emma T. , Andres Sarah F. , Giroux Veronique , Hicks Philip D. , Noubissi Felicite K. , Spiegelman Vladimir S. , Rustgi Anil K.
Published: April 2023

Supp. Fig. 1 legend
Supplementary Figure 1 from Loss of Stromal IMP1 Promotes a Tumorigenic Microenvironment in the Colon
Authors: Hamilton Kathryn E. , Chatterji Priya , Lundsmith Emma T. , Andres Sarah F. , Giroux Veronique , Hicks Philip D. , Noubissi Felicite K. , Spiegelman Vladimir S. , Rustgi Anil K.
Published: April 2023

Supplementary Figure 1. Dermo1Cre;Rosa-CAG-LSL-TdTomato mice.
Supplementary Figures 1 - 9 from mTOR/MYC Axis Regulates O-GlcNAc Transferase Expression and O-GlcNAcylation in Breast Cancer
Authors: Sodi Valerie L. , Khaku Sakina , Krutilina Raisa , Schwab Luciana P. , Vocadlo David J. , Seagroves Tiffany N. , Reginato Mauricio J.
Published: April 2023

Supplemental Figure 1: OGT expression in oncogene expressing MCF-10A cells. Supplemental Figure 2: Inhibition of PI3K and mTOR does not reduce OGT RNA levels in breast cancer cells. Supplemental Figure 3: OGA expression in breast cancer cells treated with inhibitors. Supplemental Figure 4: MEK/ERK pathway is not sufficient to regulate OGT and O-GlcNAcylation levels. Supplemental Figure 5: OGA expression is reduced in TSC2 -/- MEFs. Supplemental Figure 6: Myc does not regulate OGT RNA levels in cancer cells. Supplemental Figure 7: Proteasomal degradation regulates unfolded OGT. Supplemental Figure 8: MYC regulates OGT protein via transcriptional target HSP90. Supplemental Figure 9: MYC-driven breast cancers overexpress OGT.
Figure S3. SF3 Xcelligence data from Differential Effects of Clinically Relevant N- versus C-Terminal Truncating CDKN1A Mutations on Cisplatin Sensitivity in Bladder Cancer
Authors: Sikder Rahmat K. , Ellithi Moataz , Uzzo Robert N. , Weader David J. , Metz Alexander L. , Behbahani Ali , McKenzie Erica R. , El-Deiry Wafik S. , Abbosh Philip H.
Published: April 2023

Figure S3: SW780 and RT4 cells are sensitized to cisplatin after the loss of p21. SW780 sg12A clone is more sensitive to cisplatin than sg109A clone, whereas in RT4, the sg12A and sg109a clones have similar sensitivities to cisplatin.
Supplementary Figure 1 from Anti–miR-21 Suppresses Hepatocellular Carcinoma Growth via Broad Transcriptional Network Deregulation
Authors: Wagenaar Timothy R. , Zabludoff Sonya , Ahn Sung-Min , Allerson Charles , Arlt Heike , Baffa Raffaele , Cao Hui , Davis Scott , Garcia-Echeverria Carlos , Gaur Rajula , Huang Shih-Min A. , Jiang Lan , Kim Deokhoon , Metz-Weidmann Christiane , Pavlicek Adam , Pollard Jack , Reeves Jason , Rocnik Jennifer L. , Scheidler Sabine , Shi Chaomei , Sun Fangxian , Tolstykh Tatiana , Weber William , Winter Christopher , Yu Eunsil , Yu Qunyan , Zheng Gang , Wiederschain Dmitri
Published: April 2023

Supplementary Figure 1. miR-21 mimic suppresses expression of ANKRD46, DDAH1 and RECK. SKHep1 cells were transfected with miR-21 or negative mimic. RNA was isolated and expression of ANKRD46, DDAH1 and RECK was assessed by qPCR. (Mean, {plus minus} SD, n=3).
Data Supplement from The lncRNA PCAT29 Inhibits Oncogenic Phenotypes in Prostate Cancer
Authors: Malik Rohit , Patel Lalit , Prensner John R. , Shi Yang , Iyer Matthew K. , Subramaniyan Shruthi , Carley Alexander , Niknafs Yashar S. , Sahu Anirban , Han Sumin , Ma Teng , Liu Meilan , Asangani Irfan A. , Jing Xiaojun , Cao Xuhong , Dhanasekaran Saravana M. , Robinson Dan R. , Feng Felix Y. , Chinnaiyan Arul M.
Published: April 2023

Supplementary Table S1. shRNA and primer sequence table.
Supplementary Figure Legend from Salt-Inducible Kinase 2 Regulates Mitotic Progression and Transcription in Prostate Cancer
Authors: Bon Hélène , Wadhwa Karan , Schreiner Alexander , Osborne Michelle , Carroll Thomas , Ramos-Montoya Antonio , Ross-Adams Helen , Visser Matthieu , Hoffmann Ralf , Ahmed Ahmed Ashour , Neal David E. , Mills Ian G.
Published: April 2023

Supplementary Figure Legend
Supplementary Data, Supplementary Table 1, Supplementary Figures 1-9 from A New Pipeline to Predict and Confirm Tumor Neoantigens Predict Better Response to Immune Checkpoint Blockade
Authors: Lazdun Yelena , Si Han , Creasy Todd , Ranade Koustubh , Higgs Brandon W. , Streicher Katie , Durham Nicholas M.
Published: April 2023

Table S1. Twenty mutated peptides submitted for in vitro validation from five bladder cancer patients. Figure S1. Flow chart for in vitro pipeline for screening neoantigens. Figure S2. After 10 days of expansion, MART-1 cultures were analyzed for (A) MHC-I MART dextramer staining and (B) cytokine production to MART-1 peptide. Figure S3. MART-1-specific T cells were titrated and restimulated with T2 cells on IFNγ ELISpot plates to determine the level of detection for antigen-specific T cells. Figure S4. Corresponding data for Peptide 1 following deconvolution from two additional donors that were screened. Figure S5. Peptide-1 (P1)-specific MHC multimer staining. Figure S6. Antigen-specific T cell killing was measured via cell impedance over time by the xCelligence RTCA system. Figure S7. Additional donor that was used to screen top four peptides from five individual bladder patients. Figure S8. Probability of OS from the TCGA BLCA disease cohort stratified by median neoantigen load. Figure S9. CDR3 overlap between individual peptides and Pool1.
Figure S4 from DNA Methylome Analyses Implicate Fallopian Tube Epithelia as the Origin for High-Grade Serous Ovarian Cancer
Authors: Klinkebiel David , Zhang Wa , Akers Stacey N. , Odunsi Kunle , Karpf Adam R.
Published: April 2023

Methylation of HOX genes in HGSC, FTE, and OSE.
Supplementary Figure 2 from Decreased eIF3e Expression Can Mediate Epithelial-to-Mesenchymal Transition through Activation of the TGFβ Signaling Pathway
Authors: Desnoyers Guillaume , Frost Laura D. , Courteau Lynn , Wall Michael L. , Lewis Stephen M.
Published: April 2023

Supplementary Figure 2- Phosphorylation of eIF4E is decreased in A549 and MCF-10A cells that have decreased eIF3e expression. Whole cells lysates harvested from A549 and MCF-10A cells harboring a non-silencing control shRNA (scr) or the eIF3e-targeting shRNA (205) were examined for the expression of eIF4E, phospho-eIF4E and GAPDH by Western-blot analysis.
Supplemental Material and Methods from Tumor Suppressor NF2 Blocks Cellular Migration by Inhibiting Ectodomain Cleavage of CD44
Authors: Hartmann Monika , Parra Liseth M. , Ruschel Anne , Böhme Sandra , Li Yong , Morrison Helen , Herrlich Andreas , Herrlich Peter
Published: April 2023

Supplemental Material and Methods. Cell lines, Transfections, Precipitation of Proteins by TCA-DOC , Co-immunoprecipitation (Co-IP) from Cell Lysates, Preparation of Cell Lysates
Supplementary File 3 from Targeting NAD+ Biosynthesis Overcomes Panobinostat and Bortezomib-Induced Malignant Glioma Resistance
Authors: Jane Esther P. , Premkumar Daniel R. , Thambireddy Swetha , Golbourn Brian , Agnihotri Sameer , Bertrand Kelsey C. , Mack Stephen C. , Myers Max I. , Chattopadhyay Ansuman , Taylor D. Lansing , Schurdak Mark E. , Stern Andrew M. , Pollack Ian F.
Published: April 2023

Supplemental File 3: Gene-Ontology Analysis
Supplementary File 2 from Targeting NAD+ Biosynthesis Overcomes Panobinostat and Bortezomib-Induced Malignant Glioma Resistance
Authors: Jane Esther P. , Premkumar Daniel R. , Thambireddy Swetha , Golbourn Brian , Agnihotri Sameer , Bertrand Kelsey C. , Mack Stephen C. , Myers Max I. , Chattopadhyay Ansuman , Taylor D. Lansing , Schurdak Mark E. , Stern Andrew M. , Pollack Ian F.
Published: April 2023

Supplemental File 2: Genes common to all resistant U87 cell lines compared to drug naive control
Supplemental Figure Legends from Tumor Suppressor NF2 Blocks Cellular Migration by Inhibiting Ectodomain Cleavage of CD44
Authors: Hartmann Monika , Parra Liseth M. , Ruschel Anne , Böhme Sandra , Li Yong , Morrison Helen , Herrlich Andreas , Herrlich Peter
Published: April 2023

Supplemental Figure Legends S1-S7. Supplemental Figure Legends
Supplementary Table 2 from Bone Marrow Microenvironment Niche Regulates miR-221/222 in Acute Lymphoblastic Leukemia
Authors: Moses Blake S. , Evans Rebecca , Slone William L. , Piktel Debbie , Martinez Ivan , Craig Michael D. , Gibson Laura F.
Published: April 2023

Excel sheet showing mean signal intensities and p-values of SUP-B15 ALL cells cultured in media only or co-cultured with HOB. Statistics were done as follows: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
Supplementary Figure 2- Constitutive overexpression of p27 increases ALL cell chemoresistance from Bone Marrow Microenvironment Niche Regulates miR-221/222 in Acute Lymphoblastic Leukemia
Authors: Moses Blake S. , Evans Rebecca , Slone William L. , Piktel Debbie , Martinez Ivan , Craig Michael D. , Gibson Laura F.
Published: April 2023

S2A, REH leukemic cells have overexpressed p27 protein compared to empty vector control. S2B, an increase in viability was observed in REH cells overexpressing p27 compared to empty vector control.
Supplementary Figure 1- PTEN and p57 have increased abundance in ALL cells influenced by the BMM from Bone Marrow Microenvironment Niche Regulates miR-221/222 in Acute Lymphoblastic Leukemia
Authors: Moses Blake S. , Evans Rebecca , Slone William L. , Piktel Debbie , Martinez Ivan , Craig Michael D. , Gibson Laura F.
Published: April 2023

Consistent with p27 two other validated miR-221/222 target genes which have been previously shown to play a role in cellular quiescence and survival, PTEN and CDKN1C (p57), were assessed in leukemic cells under conditions mentioned above. S1A,B, both PTEN and p57 protein abundance was increased in leukemic cells co-cultured with BMSC or HOB compared to leukemic cells grown in media alone.
Supplementary Figures 1-14 from Palmitate-Induced IRE1–XBP1–ZEB Signaling Represses Desmoplakin Expression and Promotes Cancer Cell Migration
Authors: Nath Aritro , Oak Amrita , Chen Kevin Y. , Li Irene , Splichal R. Chauncey , Portis Jason , Foster Sean , Walton S. Patrick , Chan Christina
Published: April 2023

S1A. Plasmids containing single guide RNAs targeted against the IRE1 locus. B. XBP1 splicing assay to assay IRE1 endoribonuclease activity in Hep3B and MDA MB 231 cells. S2. CRISPR clones obtained for MDA-MB-231 cells. S3. CRISPR clones obtained for Hep3B cells. S4. CRISPR clones obtained for HepG2 cells. S5. Representative brightfield images of Boyden's chamber migration assay. S6. Representative brightfield images of Boyden's chamber migration assay. S7. Representative brightfield images of Boyden's chamber migration assay. S8. Heatmap of standardized DSP, ZEB1 or ZEB2 expression in the TCGA PANCAN dataset. S9. Scatter plots showing the correlation between DSP methylation and the expression of DSP, ZEB1 or ZEB2 in the TCGA. S10A. Western blots showing expression levels of DSP, ZEB1, and GAPDH in MDA-MB-231 cells treated with scramble, no treatment, or siZEB1 at 100 nM (ORIGENE, cat # SR321982) for 48 hrs. The plots represent the quantification of the western blots. B-C. Barplots displaying relative gene expression levels measured using qRT-PCR of (B) ZEB1 and DSP (normalized to scramble) in MDA-MB-231 cells treated with siZEB1 at 100 nM 24 hrs, and (C) ZEB2 and DSP (normalized to scramble) in MDA-MB-231 cells treated with siZEB2 at 80 nM for 24 hrs. S11. A. Western blots showing expression levels of DSP, ZEB1, and GAPDH in Hep3B cells treated with scramble, no treatment, or siZEB1 at 100 nM (ORIGENE, cat # SR321982) for 48 hrs. The plots represent the quantification of the western blots. B-C. Barplots displaying relative gene expression levels measured using qRT-PCR of (B) ZEB1 and DSP (normalized to scramble) in Hep3B cells treated with siZEB1 at 100 nM 24 hrs, and (C) ZEB2 and DSP (normalized to scramble) in Hep3B cells treated with siZEB2 at 80 nM for 24 hrs. S12. Positive ChIP control for ZEB1 binding in Hep3B, MDA-MB-231 and HepG2 cells in the CDH1 promoter. S13. Relative ZEB1 protein expression in PA or BSA treated (48 hr) WT- or IRE1-KO MDA-MB-231 cells. S14. Relative ZEB1 protein expression in PA or BSA treated (72 hrs) WT- or IRE1-KO Hep3B cells.
Supplementary Materials and Methods from Phosphoproteomics Reveals MAPK Inhibitors Enhance MET- and EGFR-Driven AKT Signaling in KRAS-Mutant Lung Cancer
Authors: Kim Jae-Young , Welsh Eric A. , Fang Bin , Bai Yun , Kinose Fumi , Eschrich Steven A. , Koomen John M. , Haura Eric B.
Published: April 2023

Supplementary Materials and Methods