bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S6 from Macrophage-Derived Neuropilin-2 Exhibits Novel Tumor-Promoting Functions
Authors: Roy Sohini , Bag Arup K. , Dutta Samikshan , Polavaram Navatha Shree , Islam Ridwan , Schellenburg Samuel , Banwait Jasjit , Guda Chittibabu , Ran Sophia , Hollingsworth Michael A. , Singh Rakesh K. , Talmadge James E. , Muders Michael H. , Batra Surinder K. , Datta Kaustubh
Published: March 2023

Weight of harvested tumors following NRP2 deletion in macrophages
Figure S5 from Macrophage-Derived Neuropilin-2 Exhibits Novel Tumor-Promoting Functions
Authors: Roy Sohini , Bag Arup K. , Dutta Samikshan , Polavaram Navatha Shree , Islam Ridwan , Schellenburg Samuel , Banwait Jasjit , Guda Chittibabu , Ran Sophia , Hollingsworth Michael A. , Singh Rakesh K. , Talmadge James E. , Muders Michael H. , Batra Surinder K. , Datta Kaustubh
Published: March 2023

Expression of NRP2 in mouse TAMs
Figure S3 from Macrophage-Derived Neuropilin-2 Exhibits Novel Tumor-Promoting Functions
Authors: Roy Sohini , Bag Arup K. , Dutta Samikshan , Polavaram Navatha Shree , Islam Ridwan , Schellenburg Samuel , Banwait Jasjit , Guda Chittibabu , Ran Sophia , Hollingsworth Michael A. , Singh Rakesh K. , Talmadge James E. , Muders Michael H. , Batra Surinder K. , Datta Kaustubh
Published: March 2023

Effect of NRP2 or NRP1 on phagocytic uptake and maturation
Figure S2 from Macrophage-Derived Neuropilin-2 Exhibits Novel Tumor-Promoting Functions
Authors: Roy Sohini , Bag Arup K. , Dutta Samikshan , Polavaram Navatha Shree , Islam Ridwan , Schellenburg Samuel , Banwait Jasjit , Guda Chittibabu , Ran Sophia , Hollingsworth Michael A. , Singh Rakesh K. , Talmadge James E. , Muders Michael H. , Batra Surinder K. , Datta Kaustubh
Published: March 2023

M-CSF or cancer cell CM drives macrophages towards alternative phenotype
Supplementary Figure S5 from The MDA-9/Syntenin/IGF1R/STAT3 Axis Directs Prostate Cancer Invasion
Authors: Das Swadesh K. , Pradhan Anjan K. , Bhoopathi Praveen , Talukdar Sarmistha , Shen Xue-Ning , Sarkar Devanand , Emdad Luni , Fisher Paul B.
Published: March 2023

MDA-9/Syntenin-mediated STAT3 activation is IGFBP-2-dependent
Supplementary Figure S3 from The MDA-9/Syntenin/IGF1R/STAT3 Axis Directs Prostate Cancer Invasion
Authors: Das Swadesh K. , Pradhan Anjan K. , Bhoopathi Praveen , Talukdar Sarmistha , Shen Xue-Ning , Sarkar Devanand , Emdad Luni , Fisher Paul B.
Published: March 2023

MDA-9/Syntenin activates STAT3.
Supplementary Figure S2 from The MDA-9/Syntenin/IGF1R/STAT3 Axis Directs Prostate Cancer Invasion
Authors: Das Swadesh K. , Pradhan Anjan K. , Bhoopathi Praveen , Talukdar Sarmistha , Shen Xue-Ning , Sarkar Devanand , Emdad Luni , Fisher Paul B.
Published: March 2023

Manipulation of MDA-9/Syntenin expression.
Supplementary Figure S1 from The MDA-9/Syntenin/IGF1R/STAT3 Axis Directs Prostate Cancer Invasion
Authors: Das Swadesh K. , Pradhan Anjan K. , Bhoopathi Praveen , Talukdar Sarmistha , Shen Xue-Ning , Sarkar Devanand , Emdad Luni , Fisher Paul B.
Published: March 2023

MDA-9/Syntenin is upregulated in prostate cancer cells
Supplementary data from A Polysome-Based microRNA Screen Identifies miR-24-3p as a Novel Promigratory miRNA in Mesothelioma
Authors: Oliveto Stefania , Alfieri Roberta , Miluzio Annarita , Scagliola Alessandra , Secli Raissa S. , Gasparini Pierluigi , Grosso Stefano , Cascione Luciano , Mutti Luciano , Biffo Stefano
Published: March 2023

Supplementary Figure S1. Most ribosome-associated miRNAs show medium occupancy and may share common biological functions. Supplementary Figure S2. miR-24-3p is expressed in lung and breast cancer cells. Supplementary Figure S3. miR-24-3p knockdown mildly affects cell proliferation and does not influence the apoptotic rate of MPM cell lines. Supplementary Figure S4. miR-24-3p fosters cells migration capability. Supplementary Figure S5. RNA-seq analysis on miR-24-3p knockdown REN and MM98 cells. Supplementary Figure S6. CXADR and BCAM mRNA distribution in REN polysomes. Supplementary Table S1. Autopsies of NOD-SCID mice 30 days after I .P. REN injection.
Supplementary data from FBXO22 Possesses Both Protumorigenic and Antimetastatic Roles in Breast Cancer Progression
Authors: Sun Rui , Xie Hong-Yan , Qian Jin-Xian , Huang Yan-Ni , Yang Fan , Zhang Fang-Lin , Shao Zhi-Min , Li Da-Qiang
Published: March 2023

The Supplementary Information includes: Figure S1. The effects of FBXO22 on breast cancer cell proliferation and anchorage-independent 3D growth. Figure S2. FBXO22 promotes xenograft tumor growth of MDA-MB-231 cells in vivo. Figure S3. FBXO22 suppresses cell migration and invasion. Figure S4. The effects of FBXO22 on the expression levels of EMT markers. Figure S5. The effects of FBXO22 on the mRNA levels of SNAIL. Figure S6. Schematic diagram of the structural domains of FBXO22 and SNAIL proteins. Figure S7. Phosphorylation of SNAIL by GSK3β affects its stability and subcellular localization. Figure S8. The mutation pattern of FBXO22 in breast cancer. Figure S9. The effects of deletion of F-box domain or W52R mutation on subcellular localization of FBXO22 and protein stability of SNAIL. Figure S10. The proposed working model. Table S1. Characterization of clincopathological features of 164 primary breast cancer patients. Table S2. siRNA target sequences for GSK3β. Tables S3. Primers used for molecular cloning of expression vectors. Tables S4. Information of expression vectors used in this study. Tables S5. Information for primary antibodies used in this study. Tables S6. Primers used for qPCR analysis. Table S7. Correlation between FBXO22 expression and clincopathological factors in 164 primary breast cancer patients. Table S8. Multivariate analysis of clincopathological factors for OS and DFS in 164 primary breast cancer patients.
Supplementary Table S2 from A Polysome-Based microRNA Screen Identifies miR-24-3p as a Novel Promigratory miRNA in Mesothelioma
Authors: Oliveto Stefania , Alfieri Roberta , Miluzio Annarita , Scagliola Alessandra , Secli Raissa S. , Gasparini Pierluigi , Grosso Stefano , Cascione Luciano , Mutti Luciano , Biffo Stefano
Published: March 2023

miR-24-3p regulated genes in both REN and MM98 cells. List of genes regulated by miR-24-3p in REN and MM98 cells.
Supplementary Table 1 from Targeting the SUMO Pathway Primes All-trans Retinoic Acid–Induced Differentiation of Nonpromyelocytic Acute Myeloid Leukemias
Authors: Baik Hayeon , Boulanger Mathias , Hosseini Mohsen , Kowalczyk Julie , Zaghdoudi Sonia , Salem Tamara , Sarry Jean-Emmanuel , Hicheri Yosr , Cartron Guillaume , Piechaczyk Marc , Bossis Guillaume
Published: March 2023

Supplementary Table 1: Characteristics of all patients used in Figure 7 or Supplementary Figure 4. D: diagnosis, R:relapse. For the molecular characteristics, only those routinely clinically tested are indicated.
Supplementary Figures from Targeting the SUMO Pathway Primes All-trans Retinoic Acid–Induced Differentiation of Nonpromyelocytic Acute Myeloid Leukemias
Authors: Baik Hayeon , Boulanger Mathias , Hosseini Mohsen , Kowalczyk Julie , Zaghdoudi Sonia , Salem Tamara , Sarry Jean-Emmanuel , Hicheri Yosr , Cartron Guillaume , Piechaczyk Marc , Bossis Guillaume
Published: March 2023

Supplementary Figure 1: Inhibition of SUMOylation increases morphological changes associated with ATRA-induced differentiation. Supplementary Figure 2: Effect of SENP overexpression on total and chromatin bound proteins. Supplementary Figure 3: Inhibition of the SUMO pathway increases the differentiation of primary AML cells. Supplementary Figure 4: Inhibition of the SUMO pathway induces the differentiation of primary non-APL AML cells.Supplementary Figure 5: Inhibition of the SUMO pathway increases the death of primary AML cells.
Supplementary Materials and Methods from Transcription Factor YY1 Promotes Cell Proliferation by Directly Activating the Pentose Phosphate Pathway
Authors: Wu Shourong , Wang Huimin , Li Yanjun , Xie Yudan , Huang Can , Zhao Hezhao , Miyagishi Makoto , Kasim Vivi
Published: March 2023

Supplementary Materials and Methods - RNA extraction and quantitative PCR analysis; Western blotting; Immunohistochemical analysis; Nile Red Staining; Luciferase assay; 5-ethynyl-2â€²-deoxyuridine (EdU) incorporation assay and colony formation assay; Chromatin immunoprecipitation (ChIP) assay; Cell counting assay and antioxidant defense.
Table S1 from Epigenetic Regulation of CXCL12 Plays a Critical Role in Mediating Tumor Progression and the Immune Response In Osteosarcoma
Authors: Li Binghao , Wang Zhan , Wu Hao , Xue Mingfeng , Lin Peng , Wang Shengdong , Lin Nong , Huang Xin , Pan Weibo , Liu Meng , Yan Xiaobo , Qu Hao , Sun Lingling , Li Hengyuan , Wu Yan , Teng Wangsiyuan , Wang Zenan , Zhou Xingzhi , Chen Huabiao , Poznansky Mark C. , Ye Zhaoming
Published: March 2023

Supplementary Table S1. Primers for qRT-PCR and MSP
Fig s1-s8 from Aberrant FGFR Tyrosine Kinase Signaling Enhances the Warburg Effect by Reprogramming LDH Isoform Expression and Activity in Prostate Cancer
Authors: Liu Junchen , Chen Guo , Liu Zezhen , Liu Shaoyou , Cai Zhiduan , You Pan , Ke Yuepeng , Lai Li , Huang Yun , Gao Hongchang , Zhao Liangcai , Pelicano Helene , Huang Peng , McKeehan Wallace L. , Wu Chin-Lee , Wang Cong , Zhong Weide , Wang Fen
Published: March 2023

This file containing all the supplemental data supporting the statements indicated in the manuscripts.
Figure S4 from Epigenetic Regulation of CXCL12 Plays a Critical Role in Mediating Tumor Progression and the Immune Response In Osteosarcoma
Authors: Li Binghao , Wang Zhan , Wu Hao , Xue Mingfeng , Lin Peng , Wang Shengdong , Lin Nong , Huang Xin , Pan Weibo , Liu Meng , Yan Xiaobo , Qu Hao , Sun Lingling , Li Hengyuan , Wu Yan , Teng Wangsiyuan , Wang Zenan , Zhou Xingzhi , Chen Huabiao , Poznansky Mark C. , Ye Zhaoming
Published: March 2023

Supplementary figure S4. Immunofluorescence on intratumoral lymphocytes and qRT-PCR assays on TH1-type chemokine expression
Figure S1 from YAP/TAZ Initiates Gastric Tumorigenesis via Upregulation of MYC
Authors: Choi Wonyoung , Kim Jeongsik , Park Jaeoh , Lee Da-Hye , Hwang Daehee , Kim Jeong-Hwan , Ashktorab Hassan , Smoot Duane , Kim Seon-Young , Choi Chan , Koh Gou Young , Lim Dae-Sik
Published: March 2023

Knockout of Lats1 and Lats2 in Lgr5+ stem cells causes dysplasia in the pyloric stomach
Supplementary Tables from HER2/EGFR–AKT Signaling Switches TGFβ from Inhibiting Cell Proliferation to Promoting Cell Migration in Breast Cancer
Authors: Huang Fei , Shi Qiaoni , Li Yuzhen , Xu Linlin , Xu Chi , Chen Fenfang , Wang Hai , Liao Hongwei , Chang Zai , Liu Fang , Zhang Xiang H.-F. , Feng Xin-Hua , Han Jing-Dong J. , Luo Shiwen , Chen Ye-Guang
Published: March 2023

Table S1 lists shRNA sequences from Sigma. Table S2 lists antibodies used in this study. Table S3 lists chemical inhibitors used in this study. Table S4 lists cell lines used in this study. Table S5 lists RT-qPCR primers and ChIP-qPCR primers used in this study
Table S4, S5 and S6 from Inhibition of the Wnt/β-Catenin Pathway Overcomes Resistance to Enzalutamide in Castration-Resistant Prostate Cancer
Authors: Zhang Zhuangzhuang , Cheng Lijun , Li Jie , Farah Elia , Atallah Nadia M. , Pascuzzi Pete E. , Gupta Sanjay , Liu Xiaoqi
Published: March 2023

Table S4: Genomic pathways enrichment analysis. Table S5: Tumor formation with gradient dilution of GFP+ and GFP- C4-2 cells in nude mice. Table S6: Multinomial logistic regression analysis in clinical specimens.
Supplementary Figure S6 from HER2/EGFR–AKT Signaling Switches TGFβ from Inhibiting Cell Proliferation to Promoting Cell Migration in Breast Cancer
Authors: Huang Fei , Shi Qiaoni , Li Yuzhen , Xu Linlin , Xu Chi , Chen Fenfang , Wang Hai , Liao Hongwei , Chang Zai , Liu Fang , Zhang Xiang H.-F. , Feng Xin-Hua , Han Jing-Dong J. , Luo Shiwen , Chen Ye-Guang
Published: March 2023

S208 phosphorylation is important for Smad3 nuclear accumulation
Table S3 from Inhibition of the Wnt/β-Catenin Pathway Overcomes Resistance to Enzalutamide in Castration-Resistant Prostate Cancer
Authors: Zhang Zhuangzhuang , Cheng Lijun , Li Jie , Farah Elia , Atallah Nadia M. , Pascuzzi Pete E. , Gupta Sanjay , Liu Xiaoqi
Published: March 2023

GSEA of altered pathways upon enzalutamide resistance in both PCa cells and tumors.
Supplementary Figure S5 from HER2/EGFR–AKT Signaling Switches TGFβ from Inhibiting Cell Proliferation to Promoting Cell Migration in Breast Cancer
Authors: Huang Fei , Shi Qiaoni , Li Yuzhen , Xu Linlin , Xu Chi , Chen Fenfang , Wang Hai , Liao Hongwei , Chang Zai , Liu Fang , Zhang Xiang H.-F. , Feng Xin-Hua , Han Jing-Dong J. , Luo Shiwen , Chen Ye-Guang
Published: March 2023

HER2/EGFR signaling induces Smad3 S208 phosphorylation through AKT
Supplementary Materials and Methods from Inhibition of the Wnt/β-Catenin Pathway Overcomes Resistance to Enzalutamide in Castration-Resistant Prostate Cancer
Authors: Zhang Zhuangzhuang , Cheng Lijun , Li Jie , Farah Elia , Atallah Nadia M. , Pascuzzi Pete E. , Gupta Sanjay , Liu Xiaoqi
Published: March 2023

Supplementary Materials and Methods and Figure legends.
Supplementary Tables from Interleukin-30/IL27p28 Shapes Prostate Cancer Stem-like Cell Behavior and Is Critical for Tumor Onset and Metastasization
Authors: Sorrentino Carlo , Ciummo Stefania L. , Cipollone Giuseppe , Caputo Sara , Bellone Matteo , Di Carlo Emma
Published: March 2023

Supplementary Table S1. Sequences of IL-30 shRNAs designed to target mIL-30 gene. Supplementary Table S2. Sequences of gRNA used for CRISPR/Cas9-mediated IL-30 gene knockout. Supplementary Table S3. Antibodies used in immunostaining.
Supplementary Materials and Methods from Interleukin-30/IL27p28 Shapes Prostate Cancer Stem-like Cell Behavior and Is Critical for Tumor Onset and Metastasization
Authors: Sorrentino Carlo , Ciummo Stefania L. , Cipollone Giuseppe , Caputo Sara , Bellone Matteo , Di Carlo Emma
Published: March 2023

More detailed Materials and Methods
Supplementary Figure S6 from Interleukin-30/IL27p28 Shapes Prostate Cancer Stem-like Cell Behavior and Is Critical for Tumor Onset and Metastasization
Authors: Sorrentino Carlo , Ciummo Stefania L. , Cipollone Giuseppe , Caputo Sara , Bellone Matteo , Di Carlo Emma
Published: March 2023

WB analyses of pSTAT1 and pSTAT3 protein expression.
Supplementary Figure S4 from Interleukin-30/IL27p28 Shapes Prostate Cancer Stem-like Cell Behavior and Is Critical for Tumor Onset and Metastasization
Authors: Sorrentino Carlo , Ciummo Stefania L. , Cipollone Giuseppe , Caputo Sara , Bellone Matteo , Di Carlo Emma
Published: March 2023

Immunohistochemical analyses of Sca-1 expression in subcutaneously developed EV-IL-30PIN-SC and IL-30PIN-SC tumors compared with EV-IL-30PIN-SC and IL-30PIN-SC orthotopic tumors.*p<0.05 by Student's t test compared with EV-IL-30PIN-SC Sc. **p<0.05 by Student's t test compared with IL-30PIN-SC Sc. and EV-IL-30PIN-SC Ortho.
Supplementary Figure S3 from Interleukin-30/IL27p28 Shapes Prostate Cancer Stem-like Cell Behavior and Is Critical for Tumor Onset and Metastasization
Authors: Sorrentino Carlo , Ciummo Stefania L. , Cipollone Giuseppe , Caputo Sara , Bellone Matteo , Di Carlo Emma
Published: March 2023

WB analyses of IL-30 protein expression and ELISA assay after IL-30 gene deletion with two gRNA sequences in wild type PIN-SCs.
Tables S1-S4 from The miR-371∼373 Cluster Represses Colon Cancer Initiation and Metastatic Colonization by Inhibiting the TGFBR2/ID1 Signaling Axis
Authors: Ullmann Pit , Rodriguez Fabien , Schmitz Martine , Meurer Steffen K. , Qureshi-Baig Komal , Felten Paul , Ginolhac Aurélien , Antunes Laurent , Frasquilho Sonia , Zügel Nikolaus , Weiskirchen Ralf , Haan Serge , Letellier Elisabeth
Published: March 2023

Antibodies, primers, and lentiviral particles (S1); in vivo tumorigenicity for SW480 vs. SW620 (S2); top 20 differentially expressed miRNAs (S3); peritoneal cancer index scores (S4)
Figure S7 from The miR-371∼373 Cluster Represses Colon Cancer Initiation and Metastatic Colonization by Inhibiting the TGFBR2/ID1 Signaling Axis
Authors: Ullmann Pit , Rodriguez Fabien , Schmitz Martine , Meurer Steffen K. , Qureshi-Baig Komal , Felten Paul , Ginolhac Aurélien , Antunes Laurent , Frasquilho Sonia , Zügel Nikolaus , Weiskirchen Ralf , Haan Serge , Letellier Elisabeth
Published: March 2023

The miR-371~373/TGFBR2 downstream target ID1 regulates tumor growth and metastatic dissemination potential
Supplementary Figure S1 from Interleukin-30/IL27p28 Shapes Prostate Cancer Stem-like Cell Behavior and Is Critical for Tumor Onset and Metastasization
Authors: Sorrentino Carlo , Ciummo Stefania L. , Cipollone Giuseppe , Caputo Sara , Bellone Matteo , Di Carlo Emma
Published: March 2023

WB analyses of EBI3 protein expression and ELISA assay (THP-1 cells were uses as positive control) to detect EBI3 in wild type PIN-SC supernatant.
Supplementary:Figure Legend from A Novel Mechanism for Activation of GLI1 by Nuclear SMO That Escapes Anti-SMO Inhibitors
Authors: Rahman Muhammad M. , Hazan Allon , Selway Joanne L. , Herath Dimalee S. , Harwood Catherine A. , Pirzado Muhammad S. , Atkar Ravinder , Kelsell David P. , Linton Kenneth J. , Philpott Mike P. , Neill Graham W.
Published: March 2023

[A] Various exon 24 clones generated from heterogeneous populations of PTCH1 suppressed NEB1 cells show reduced PTCH1 and increased GLI1 mRNA expression. [B] Both human and mouse SMO protein sequences contain predicted nuclear and nucleolar localisation signals located within the C-terminal region, non-matching amino acids are highlighted in red. Site directed mutagenesis was employed to alter the N(o)LS by changing each amino acid to alanine for the mNLS construct, mNLS2 was used for Figures 2B and 2C. [C] NEB1-shCON cells and to a greater extent NEB1-shPTCH1 cells transfected with EGFP-SMO and EGFP-SMO-M2 show upregulation of GLI1 mRNA expression that is then reduced to below basal levels upon mutation of N(o)LS sequences, particularly mNLS2. qPCR analysis for GLI1 expression in [D] NEB1 and [E] N/Tert exon 3 and exon 24 shPTCH1 clones treated with both KAAD-Cyc and SANT-1 show all shPTCH1 clones are unresponsive to SMO pharmacological inhibitors. [F] qPCR on NEB1-shPTCH1 exon 3 clone and N/Tert-shPTCH1 cells to validate the results for cancer related genes obtained from the microarray analysis. [G] Immunofluorescence staining of NEB1 cells with three different SMO antibodies. [Table 1] List of differentially expressed zinc-finger protein genes. *P{less than or equal to}0.05 and **P{less than or equal to}0.01 (as calculated by Student's t test), error bars represent standard deviation, n=6.
Table S2 from Metabolic and Physiologic Imaging Biomarkers of the Tumor Microenvironment Predict Treatment Outcome with Radiation or a Hypoxia-Activated Prodrug in Mice
Authors: Matsumoto Shingo , Kishimoto Shun , Saito Keita , Takakusagi Yoichi , Munasinghe Jeeva P. , Devasahayam Nallathamby , Hart Charles P. , Gillies Robert J. , Mitchell James B. , Krishna Murali C.
Published: March 2023

Lactate to pyruvate ratio and kpyr-lac of individual PDAC tumors in hyperpolarized 13C MRI study.
Table S1 from Metabolic and Physiologic Imaging Biomarkers of the Tumor Microenvironment Predict Treatment Outcome with Radiation or a Hypoxia-Activated Prodrug in Mice
Authors: Matsumoto Shingo , Kishimoto Shun , Saito Keita , Takakusagi Yoichi , Munasinghe Jeeva P. , Devasahayam Nallathamby , Hart Charles P. , Gillies Robert J. , Mitchell James B. , Krishna Murali C.
Published: March 2023

Median pO2 and HF10 of individual PDAC tumors in EPR oxygen imaging study.
Figure S1 from NFATc1 Promotes Antitumoral Effector Functions and Memory CD8+ T-cell Differentiation during Non–Small Cell Lung Cancer Development
Authors: Heim Lisanne , Friedrich Juliane , Engelhardt Marina , Trufa Denis I. , Geppert Carol I. , Rieker Ralf J. , Sirbu Horia , Finotto Susetta
Published: March 2023

Supplementary Figure 1: Decreased NFATc1 in T cells in the tumoural region of NSCLC patients with advanced disease stages.
Figure S1 from Metabolic and Physiologic Imaging Biomarkers of the Tumor Microenvironment Predict Treatment Outcome with Radiation or a Hypoxia-Activated Prodrug in Mice
Authors: Matsumoto Shingo , Kishimoto Shun , Saito Keita , Takakusagi Yoichi , Munasinghe Jeeva P. , Devasahayam Nallathamby , Hart Charles P. , Gillies Robert J. , Mitchell James B. , Krishna Murali C.
Published: March 2023

Immunoblotting of SDHA and SDHB expression in three pancreatic tumors.
Supplementary Data from Inhibition of Nr4a Receptors Enhances Antitumor Immunity by Breaking Treg-Mediated Immune Tolerance
Authors: Hibino Sana , Chikuma Shunsuke , Kondo Taisuke , Ito Minako , Nakatsukasa Hiroko , Omata-Mise Setsuko , Yoshimura Akihiko
Published: March 2023

Supplementary methods and legends
FigureS4 from Inhibition of Nr4a Receptors Enhances Antitumor Immunity by Breaking Treg-Mediated Immune Tolerance
Authors: Hibino Sana , Chikuma Shunsuke , Kondo Taisuke , Ito Minako , Nakatsukasa Hiroko , Omata-Mise Setsuko , Yoshimura Akihiko
Published: March 2023

Screening of drugs that inhibit transcriptional activity of Nr4a
Figure S3 from CDKN2A/p16 Deletion in Head and Neck Cancer Cells Is Associated with CDK2 Activation, Replication Stress, and Vulnerability to CHK1 Inhibition
Authors: Gadhikar Mayur A. , Zhang Jiexin , Shen Li , Rao Xiayu , Wang Jing , Zhao Mei , Kalu Nene N. , Johnson Faye M. , Byers Lauren A. , Heymach John , Hittelman Walter N. , Udayakumar Durga , Pandita Raj K. , Pandita Tej K. , Pickering Curtis R. , Redwood Abena B. , Piwnica-Worms Helen , Schlacher Katharina , Frederick Mitchell J. , Myers Jeffrey N.
Published: March 2023

This file contains data showing lack of association between IMMP2L RNA expression and prexasertib sensitivity, dose dependent effect of p16 induction on the proliferation of UMSCC22A-p16 cells and also p16-induced alteration of cell cycle responses in UMSCC22A-p16 cells following Chk1 inhibition. This file is linked to main figure 4.
Supplementary Figures S1-S10 from Downregulation of Dipeptidyl Peptidase 4 Accelerates Progression to Castration-Resistant Prostate Cancer
Authors: Russo Joshua W. , Gao Ce , Bhasin Swati S. , Voznesensky Olga S. , Calagua Carla , Arai Seiji , Nelson Peter S. , Montgomery Bruce , Mostaghel Elahe A. , Corey Eva , Taplin Mary-Ellen , Ye Huihui , Bhasin Manoj , Balk Steven P.
Published: March 2023

Figure S1. Targeted siRNA knockdown of DPP4 decreases DPP4 antibody positivity in western blots and IHC; Figure S2. Immunoscoring of AR, AR-V7, P-AR(S81), and PSA protein expression in serially biopsied VCaP xenografts; Figure S3. Ingenuity Pathway, Hierarchical Clustering, and Principal Component analysis of Pre-Cx, CRPC, and AER, serial biopsies; Figure S4. DPP4 is an AR-stimulated gene; Figure S5. DPP4 expression is decreased in Post-ADT therapy samples in several clinical and one preclinical data set compared to Pre-Cx; Figure S6. DPP4 expression is decreased in clinical CRPC sections, despite normal levels of PSA; Figure S7. CpG islands in the DPP4 promoter and exon 1 are unmethylated; Figure S8. lncRNA-OIS1 is expressed at similar levels in Pre-Cx and AER VCaP tumors; Figure S9. Androgen treatment of VCaP CRPC xenografts restores DPP4 expression; Figure S10. The volume ratio (End Volume/Starting Volume) of VCaP tumors shows a trend toward positive correlation with tumor DPP4 protein levels.
Supplementary Tables 1-14 from SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma
Authors: Sakthikumar Sharadha , Elvers Ingegerd , Kim Jaegil , Arendt Maja L. , Thomas Rachael , Turner-Maier Jason , Swofford Ross , Johnson Jeremy , Schumacher Steven E. , Alföldi Jessica , Axelsson Erik , Couto C. Guillermo , Kisseberth William C. , Pettersson Mats E. , Getz Gad , Meadows Jennifer R.S. , Modiano Jaime F. , Breen Matthew , Kierczak Marcin , Forsberg-Nilsson Karin , Marinescu Voichita D. , Lindblad-Toh Kerstin
Published: March 2023

File contains supplementary tables and figures for the main article. Supplementary Table 1 - Source for tools and databases used in the methods for analysis. Supplementary Table 2 - Summary of Somatic Point and Indel Mutation across the three breeds. Supplementary Table 3 - Summary of GISTIC-defined recurrent large-scale SCNAs and gene frequency. Supplementary Table 4 - List of GISTIC classified amplification genes. See attached excel spreadsheet. Supplementary Table 5 - List of GISTIC classified deletion genes. See attached excel spreadsheet. Supplementary Table 6 - List of GISTIC genes and their predicted roles in cancer. Supplementary Table 7 - Significantly over-represented pathways for GISTIC- and MuSiC-defined genes. Supplementary Table 8 - Significantly mutated genes as identified by MuSiC and the proportion of samples per breed that show mutation in them. Supplementary Table 9 - Putative driver genes as detected by MutSigCV algorithm Supplementary Table 10 - Putative driver genes assessed by VEP high-impact mutations and their variant allele frequency. Supplementary Table 11 - Mutations and their effects on p53 protein. Supplementary Table 12 - Mutations and their effects on SETD2 protein. Supplementary Table 13 - Count of non-silent mutations per breed/per germline for OSA susceptibility genes Supplementary Table 14 - Overlap of GISTIC-defined recurrent SCNA genes between humans and dogs. See attached excel spreadsheet.
Figure S3 from Oncogenic Kinase–Induced PKM2 Tyrosine 105 Phosphorylation Converts Nononcogenic PKM2 to a Tumor Promoter and Induces Cancer Stem–like Cells
Authors: Zhou Zhifen , Li Min , Zhang Lin , Zhao Hong , Şahin Özgür , Chen Jing , Zhao Jean J. , Songyang Zhou , Yu Dihua
Published: March 2023

Phosphorylation of PKM2-Y105 promotes nuclear translocation of YAP.
Supplementary table S4 from Matrix Stiffening and EGFR Cooperate to Promote the Collective Invasion of Cancer Cells
Authors: Grasset Eloise M. , Bertero Thomas , Bozec Alexandre , Friard Jonas , Bourget Isabelle , Pisano Sabrina , Lecacheur Margaux , Maiel Majdi , Bailleux Caroline , Emelyanov Alexander , Ilie Marius , Hofman Paul , Meneguzzi Guerrino , Duranton Christophe , Bulavin Dmitry V. , Gaggioli Cedric
Published: March 2023

Selected SCC12 invasion inhibitors and their corresponding targeted genes.
Figure S1 from Oncogenic Kinase–Induced PKM2 Tyrosine 105 Phosphorylation Converts Nononcogenic PKM2 to a Tumor Promoter and Induces Cancer Stem–like Cells
Authors: Zhou Zhifen , Li Min , Zhang Lin , Zhao Hong , Şahin Özgür , Chen Jing , Zhao Jean J. , Songyang Zhou , Yu Dihua
Published: March 2023

PKM2 is important for breast cancer cell growth but has no discernible effect on non-transformed cells.
Figure S4 from High USP6NL Levels in Breast Cancer Sustain Chronic AKT Phosphorylation and GLUT1 Stability Fueling Aerobic Glycolysis
Authors: Avanzato Daniele , Pupo Emanuela , Ducano Nadia , Isella Claudio , Bertalot Giovanni , Luise Chiara , Pece Salvatore , Bruna Alejandra , Rueda Oscar M. , Caldas Carlos , Di Fiore Pier Paolo , Sapino Anna , Lanzetti Letizia
Published: March 2023

USP6NL silencing does not affect the USP6NL-low H1299 cell line
Figure S2 from RNF6 Promotes Colorectal Cancer by Activating the Wnt/β-Catenin Pathway via Ubiquitination of TLE3
Authors: Liu Lei , Zhang Yanquan , Wong Chi Chun , Zhang Jingwan , Dong Yujuan , Li Xiangchun , Kang Wei , Chan Francis K.L. , Sung Joseph J.Y. , Yu Jun
Published: March 2023

Knockdown of RNF6 inhibits tumor growth.
Figure S6 from The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State
Authors: Yoo Jae Hyuk , Brady Samuel W. , Acosta-Alvarez Lehi , Rogers Aaron , Peng Jingfu , Sorensen Lise K. , Wolff Roger K. , Mleynek Tara , Shin Donghan , Rich Coulson P. , Kircher David A. , Bild Andrea , Odelberg Shannon J. , Li Dean Y. , Holmen Sheri L. , Grossmann Allie H.
Published: March 2023

Figure S6. ARF6-GDP inhibits PI3K-AKT activation and is necessary for AKT activation. (a-b) Quantification of western blots shown in Figure 5c-d. Reproducible reduction in pAKT by Myc-ARF6T27N over expression in A375 cells (n=4), A2058 cells (n=4), and HEY-T30 cells (n=5). Reduced pAKT with siRNA knockdown of ARF6 in SK-MEL-147 (n=5), A2058 (n=4), and CACL (n=4) and HEY-T30 (n=6). Graphs show individual data points normalized to control along with geometric means, 95% CI, ratio paired t test. (c) Phosphokinase array images (left) and quantification of signal by densitometry (right, histogram), n=1. Expression of ARF6T27N in A2058 cells preferentially reduced pAKT and the AKT substrate PRAS40 over most other proteins in the array.
Supplementary Table & Figures from A Chemo-enzymatically Linked Bispecific Antibody Retargets T Cells to a Sialylated Epitope on CD43 in Acute Myeloid Leukemia
Authors: Bartels Lina , de Jong Greta , Gillissen Marijn A. , Yasuda Etsuko , Kattler Veronika , Bru Camille , Fatmawati Christien , van Hal-van Veen Susan E. , Cercel Madalina G. , Moiset Gemma , Bakker Arjen Q. , van Helden Pauline M. , Villaudy Julien , Hazenberg Mette D. , Spits Hergen , Wagner Koen
Published: March 2023

Overview lysis primary AML samples; Quality control during bTCE preparation; Supportive data on T-cell induced AML cell lysis and T-cell activation
Figure S5 from The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State
Authors: Yoo Jae Hyuk , Brady Samuel W. , Acosta-Alvarez Lehi , Rogers Aaron , Peng Jingfu , Sorensen Lise K. , Wolff Roger K. , Mleynek Tara , Shin Donghan , Rich Coulson P. , Kircher David A. , Bild Andrea , Odelberg Shannon J. , Li Dean Y. , Holmen Sheri L. , Grossmann Allie H.
Published: March 2023

Figure S5: ARF6-GTP induces morphologic changes in mouse melanoma cells. Bright field images (100x magnification) of primary mouse melanoma cell lines derived from control BrafCA;Cdkn2af/f (5588) or BrafCA;Cdkn2af/f + Arf6Q67L (6431, 6455) mice. ARF6-GTP induces elongation/spindling of tumor cells relative to the more polygonal-shaped controls. Scale bars = 400um.
Figure S3 from The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State
Authors: Yoo Jae Hyuk , Brady Samuel W. , Acosta-Alvarez Lehi , Rogers Aaron , Peng Jingfu , Sorensen Lise K. , Wolff Roger K. , Mleynek Tara , Shin Donghan , Rich Coulson P. , Kircher David A. , Bild Andrea , Odelberg Shannon J. , Li Dean Y. , Holmen Sheri L. , Grossmann Allie H.
Published: March 2023

Figure S3. Arf6Q67L-HA expression in tumors from BrafCA;Cdkn2af/f;Ptenf/f mice. qRT-PCR detection of Arf6 Q67L-HA from fresh, frozen primary tumor fragments. Bars represent the absolute difference in crossing threshold (Ct) between Arf6 Q67L-HA and Gapdh. The Ct threshold that defines detection was established above the background signal for controls in both the BrafCA;Cdkn2af/f and the BrafCA;Cdkn2af/f ;Ptenf/f cohorts (see also Figure S1). All mouse tumor negative by qRT-PCR showed detectable HA-tagged ARF6Q67L by immunohistochemistry (not shown, see Figure S1 for example).
Supplementary Table S2 from SATB2-AS1 Suppresses Colorectal Carcinoma Aggressiveness by Inhibiting SATB2-Dependent Snail Transcription and Epithelial–Mesenchymal Transition
Authors: Wang Yi-Qing , Jiang Dong-Mei , Hu Sha-Sha , Zhao Li , Wang Lan , Yang Min-Hui , Ai Mei-Ling , Jiang Hui-Juan , Han Yue , Ding Yan-Qing , Wang Shuang
Published: March 2023

Supplementary Table S2 lists the target sequences for siRNAs.
Supplementary Table S1 from SATB2-AS1 Suppresses Colorectal Carcinoma Aggressiveness by Inhibiting SATB2-Dependent Snail Transcription and Epithelial–Mesenchymal Transition
Authors: Wang Yi-Qing , Jiang Dong-Mei , Hu Sha-Sha , Zhao Li , Wang Lan , Yang Min-Hui , Ai Mei-Ling , Jiang Hui-Juan , Han Yue , Ding Yan-Qing , Wang Shuang
Published: March 2023

Supplementary Table S1 lists the primer sequences used for PCR.
Supplementary Material and Methods from SATB2-AS1 Suppresses Colorectal Carcinoma Aggressiveness by Inhibiting SATB2-Dependent Snail Transcription and Epithelial–Mesenchymal Transition
Authors: Wang Yi-Qing , Jiang Dong-Mei , Hu Sha-Sha , Zhao Li , Wang Lan , Yang Min-Hui , Ai Mei-Ling , Jiang Hui-Juan , Han Yue , Ding Yan-Qing , Wang Shuang
Published: March 2023

Supplementary material and methods described the details, including cell culture, in situ hybridization, cell proliferation and colony formation assay, wound healing assay, cell invasion assays, western blot, RIP and ChIP assays, co-immunoprecipitation, and luciferase reporter assay.
Supplemental Figures and Tables from A Soft Microenvironment Protects from Failure of Midbody Abscission and Multinucleation Downstream of the EMT-Promoting Transcription Factor Snail
Authors: Simi Allison K. , Anlaş Alişya A. , Stallings-Mann Melody , Zhang Sherry , Hsia Tiffaney , Cichon Magdalena , Radisky Derek C. , Nelson Celeste M.
Published: March 2023

Figures S1-S5 show how stiffness-mediated signaling downstream of Snail is affected by proliferation and expression of septin-6. Tables S1-S2 list primers for qPCR and binding sites in the septin-6 promoter. Legends for Movies S1-S2, which show abscission failure, are also included.
Movie S2 from A Soft Microenvironment Protects from Failure of Midbody Abscission and Multinucleation Downstream of the EMT-Promoting Transcription Factor Snail
Authors: Simi Allison K. , Anlaş Alişya A. , Stallings-Mann Melody , Zhang Sherry , Hsia Tiffaney , Cichon Magdalena , Radisky Derek C. , Nelson Celeste M.
Published: March 2023

Movie S2 shows timelapse of cells undergoing failure of abscission and becoming multinucleated. Midbodies are visible as prominent spots between daughter cells.
Supplementary Data from miR-146a Controls Immune Response in the Melanoma Microenvironment
Authors: Mastroianni Justin , Stickel Natalie , Andrlova Hana , Hanke Kathrin , Melchinger Wolfgang , Duquesne Sandra , Schmidt Dominik , Falk Martina , Andrieux Geoffroy , Pfeifer Dietmar , Dierbach Heide , Schmitt-Graeff Annette , Meiss Frank , Boerries Melanie , Zeiser Robert
Published: March 2023

(S1) Supplemental Figure S1 shows the flow cytometry based analysis of B16 cells transformed with a lentiviral vector with Luc-GFP-neo (S2-S7) Supplemental Figures S2-S7 show complete western blot images (S8) Supplemental Figure S8 shows the impact of IFN gamma on melanoma cells with respect to gene expression, OCR and ROS production (S9) Supplemental Figure S9 shows the effect of prolonging combination therapy regimen in melanoma bearing mice (S10) Supplemental Figure S10 shows the combined effects of IFN-γ and miR-146a inhibition on melanoma cells in vitro (S11) Supplemental Figure S11 shows the proposed mechanism of action.
Table S1 from Targeting the Chromosomal Passenger Complex Subunit INCENP Induces Polyploidization, Apoptosis, and Senescence in Neuroblastoma
Authors: Sun Ming , Veschi Veronica , Bagchi Sukriti , Xu Man , Mendoza Arnulfo , Liu Zhihui , Thiele Carol J.
Published: March 2023

Related to Fig.S6. List of differentially expressed genes identified by RNA-Seq (p <= 0.05 and fold change >= 1.5)
Supplementary Table 7 from Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer–Associated Genetic Variant rs4415084
Authors: Zhang Yi , Manjunath Mohith , Zhang Shilu , Chasman Deborah , Roy Sushmita , Song Jun S.
Published: March 2023

Differential chromatin interaction analysis between MCF-7 and T-47D based on Hi-C data.
Supplementary Information containing supplementary methods, figures and tables with their legends from Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer–Associated Genetic Variant rs4415084
Authors: Zhang Yi , Manjunath Mohith , Zhang Shilu , Chasman Deborah , Roy Sushmita , Song Jun S.
Published: March 2023

Supplementary Information containing supplementary methods, figures and tables with their legends. This file includes: Supplementary Materials and Methods; Supplementary Table 1 - Breast cancer cell line DNase-seq data used for SNP prioritization; Supplementary Table 2 - Breast cancer cell line ChIP-seq data used in this study; Supplementary Table 3 - Transcription factor motif databases used in this study; Supplementary Table 4 - A comparison of eQTL genes for all three 5p12 breast cancer GWAS SNPs; Supplementary Table 5 - eQTL results of rs4415084 for genes within TAD; Supplementary Table 6 - Significant isoform-QTL results of rs4415084; Supplementary Table 7 - Differential chromatin interaction analysis between MCF-7 and T-47D based on Hi-C data; Supplementary Figure 1 - A schematic representation of the phasing certainty measure in local chromosome allele-specific expression (LCASE) analysis; Supplementary Figure 2 - A schematic representation of TF prioritization based on TF-gene expression correlation analyses; Supplementary Figure 3 - Transcription elongation downstream of MRPS30; Supplementary Figure 4 - eQTL results for rs4415084 based on normal breast tissue data from GTEx; Supplementary Figure 5 - LCASE SNPs in MRPS30 processed transcripts; Supplementary Figure 6 - LCASE SNPs in RP11-53O19.3; Supplementary Figure 7 - LCASE SNPs in RP11-53O19.1; Supplementary Figure 8 - Other candidate causative SNPs and TFs.
Supplementary File from The Cancer Editome Atlas: A Resource for Exploratory Analysis of the Adenosine-to-Inosine RNA Editome in Cancer
Authors: Lin Chui-Hsien , Chen Sean Chun-Chang
Published: March 2023

Comparison with other resources, cohort information, impacts of hyper edited reads, and clustering of editing patterns.
Supplementary Figures from Retinoblastoma Inactivation Induces a Protumoral Microenvironment via Enhanced CCL2 Secretion
Authors: Li Fengkai , Kitajima Shunsuke , Kohno Susumu , Yoshida Akiyo , Tange Shoichiro , Sasaki Soichiro , Okada Nobuhiro , Nishimoto Yuuki , Muranaka Hayato , Nagatani Naoko , Suzuki Misa , Masuda Sayuri , Thai Tran C. , Nishiuchi Takumi , Tanaka Tomoaki , Barbie David A. , Mukaida Naofumi , Takahashi Chiaki
Published: March 2023

This file contains additional data to further support the conclusions in the main manuscript. Supplementary figure S1 shows the data related to figure 1,2,3. Supplementary figure S2 shows the data related to figure 4,5,6.
Supplementary Table 7 from Methylation of C/EBPα by PRMT1 Inhibits Its Tumor-Suppressive Function in Breast Cancer
Authors: Liu Li-Ming , Sun Wen-Zheng , Fan Xue-Zhe , Xu Ya-Li , Cheng Mo-Bin , Zhang Ye
Published: March 2023

CEBPA interactors from MASS
Supplementary Table 6 from Methylation of C/EBPα by PRMT1 Inhibits Its Tumor-Suppressive Function in Breast Cancer
Authors: Liu Li-Ming , Sun Wen-Zheng , Fan Xue-Zhe , Xu Ya-Li , Cheng Mo-Bin , Zhang Ye
Published: March 2023

Differential gene expression from RNA-seq
Supplementary Figures S1-12 from Activation of B-1 Cells Promotes Tumor Cell Killing in the Peritoneal Cavity
Authors: Haro Marcela A. , Dyevoich Allison M. , Phipps James P. , Haas Karen M.
Published: March 2023

Supplementary Figures 1-12. Figure S1-S2 demonstrates survival in TA3-Ha-challenged mice treated with cyclophosphamide + MPL/TDCM (S1) or TDB and MPL individually (S2). Figures S3-S4 demonstrate B cell purification strategies. Figures S5-S6 demonstrate the effect of memory B-1a cells (S5) and IL-10 deficiency (S6) on survival following TA3-Ha challenge. Figures S8-S10 demonstrate MPL/TDCM treatment induces the production of TA3-Ha- and GD2-reactive IgM both in vivo (S8, S10) and TA3-Ha reactive IgM in vitro (S9). Figure S11 shows MPL/TDCM treatment following primary EL4 challenge generates memory that provides protection during rechallenge. Figure S12 shows the effect of passive transfer of serum from MPL/TDCM-treated mice into naïve mice on survival following TA3-Ha challenge.
Supplementary Table 5 from Methylation of C/EBPα by PRMT1 Inhibits Its Tumor-Suppressive Function in Breast Cancer
Authors: Liu Li-Ming , Sun Wen-Zheng , Fan Xue-Zhe , Xu Ya-Li , Cheng Mo-Bin , Zhang Ye
Published: March 2023

Description of 103 samples
Supplementary Table 1-4 from Methylation of C/EBPα by PRMT1 Inhibits Its Tumor-Suppressive Function in Breast Cancer
Authors: Liu Li-Ming , Sun Wen-Zheng , Fan Xue-Zhe , Xu Ya-Li , Cheng Mo-Bin , Zhang Ye
Published: March 2023

Primers for Cyclin D1 promotre, truncated CEBPA, shRNA, RT-PCR, and ChIP
Supplementary Data from MDM2-Recruiting PROTAC Offers Superior, Synergistic Antiproliferative Activity via Simultaneous Degradation of BRD4 and Stabilization of p53
Authors: Hines John , Lartigue Schan , Dong Hanqing , Qian Yimin , Crews Craig M.
Published: March 2023

Table S1 shows a synergistic antiproliferative effect of the two biologically-active components of PROTAC A1874 against A375 melanoma cells according to the Bliss-Independence Model of drug interactions.
Figure S3 from Methylation of C/EBPα by PRMT1 Inhibits Its Tumor-Suppressive Function in Breast Cancer
Authors: Liu Li-Ming , Sun Wen-Zheng , Fan Xue-Zhe , Xu Ya-Li , Cheng Mo-Bin , Zhang Ye
Published: March 2023

The effects of HDAC3 on Cyclin D1
Figure S2 from Methylation of C/EBPα by PRMT1 Inhibits Its Tumor-Suppressive Function in Breast Cancer
Authors: Liu Li-Ming , Sun Wen-Zheng , Fan Xue-Zhe , Xu Ya-Li , Cheng Mo-Bin , Zhang Ye
Published: March 2023

PRMT1 methylated C/EBPα
Supplementary Data from RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Elloumi Fathi , Ofori-Atta Kwabena , Lee Sunmin , Trepel Jane B. , Meltzer Paul S. , Doroshow James H. , Pommier Yves
Published: March 2023

Supplemental Figure 1. Density plot comparisons of RNA-Seq to microarray transcript data and comparison of both to DNA copy, DNA methylation and protein expression data. Supplemental Figure 2. Scatter plots for 9 selected genes for transcript expression as measured by microarray versus RNA-seq in the NCI-60. "r" is Pearson's correlation.
Supplemental Table 2 from RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Elloumi Fathi , Ofori-Atta Kwabena , Lee Sunmin , Trepel Jane B. , Meltzer Paul S. , Doroshow James H. , Pommier Yves
Published: March 2023

Transcript levels for 46,834 isoforms (fragments per kilobase per million reads, FPKM)
Supplemental Figures and Tables from Discovery of Potent and Selective MRCK Inhibitors with Therapeutic Effect on Skin Cancer
Authors: Unbekandt Mathieu , Belshaw Simone , Bower Justin , Clarke Maeve , Cordes Jacqueline , Crighton Diane , Croft Daniel R. , Drysdale Martin J. , Garnett Mathew J. , Gill Kathryn , Gray Christopher , Greenhalgh David A. , Hall James A.M. , Konczal Jennifer , Lilla Sergio , McArthur Duncan , McConnell Patricia , McDonald Laura , McGarry Lynn , McKinnon Heather , McMenemy Carol , Mezna Mokdad , Morrice Nicolas A. , Munro June , Naylor Gregory , Rath Nicola , Schüttelkopf Alexander W. , Sime Mairi , Olson Michael F.
Published: March 2023

Supplemental Figure 1. Kinome selectivity profiles for BDP8900 and BDP9066. Supplemental Figure 2. Cancer cell line sensitivity to BDP8900 and BDP9066. Supplemental Figure 3. MRCKα phosphorylations compared with MRCKβ. Supplemental Figure 4. MRCKα, MRCKβ and MRCKα pS1003 antibody validation. Supplemental Figure 5. MRCK and DMPK expression in MDA MB 231 D3H2 LN human breast cancer cells, SCC12 human squamous cell carcinoma cells, and human skeletal muscle. Supplemental Table 1. Crystallographic data and model statistics. Supplemental Table 2: BDP8900 and BDP9066 selectivity in vitro (in-house determinations). Supplemental Table 3. Kinase selectivity screen for BDP8900 and BDP9066. Supplemental Table 4. BDP8900 selectivity in vitro (out-sourced determinations). Supplemental Table 5. BDP9066 selectivity in vitro (out-sourced determinations). Supplemental Table 6. Cancer cell line EC50 values for BDP8900 and BDP9066. Supplemental Table 7. MRCKα phosphorylation sites. Supplemental Table 8. MRCKα phosphorylation on S1003.
Table S3 from A Gene Expression Classifier from Whole Blood Distinguishes Benign from Malignant Lung Nodules Detected by Low-Dose CT
Authors: Kossenkov Andrew V. , Qureshi Rehman , Dawany Noor B. , Wickramasinghe Jayamanna , Liu Qin , Majumdar R. Sonali , Chang Celia , Widura Sandy , Kumar Trisha , Horng Wen-Hwai , Konnisto Eric , Criner Gerard , Tsay Jun-Chieh J. , Pass Harvey , Yendamuri Sai , Vachani Anil , Bauer Thomas , Nam Brian , Rom William N. , Showe Michael K. , Showe Louise C.
Published: March 2023

Numbers of genes selected and designed based on different criteria
Supplementary Data from Long Noncoding RNA MIR17HG Promotes Colorectal Cancer Progression via miR-17-5p
Authors: Xu Jie , Meng Qingtao , Li Xiaobo , Yang Hongbao , Xu Jin , Gao Na , Sun Hao , Wu Shenshen , Familiari Giuseppe , Relucenti Michela , Zhu Haitao , Wu Jiong , Chen Rui
Published: March 2023

This file contains supplemental materials and methods, supplemental tables: ST1 Demographic characteristics of CRC patients recruited for microarray assay, ST2: Distributions of demographic and clinicopathologic characteristics of patients recruited for TMA; ST3: Demographic information of colorectal adenoma (ADE) patients for PCR analysis; ST4:Demographic information of colorectal cancer (CRC) patients for PCR analysis; supplemental figures SF1:Construction of an immunity-associated network involved in CRC progression; SF2:Roles of RELA and MIR17HG in murine AOM-DSS models and CRC cohorts; SF3:miR-17-5p promotes CRC tumorigenesis; SF4: MIR17HG promotes CRC tumorigenesis through suppressing BLNK; SF5: MIR17HG promotes CRC tumorigenesis through binding to miR-17-3p in vitro and in vivo; SF6: Regulation of MALT1, NFKBIE, PPP3R1 and MAP3K7 by miR-17-3p in CRC; SF7: Expression levels of PD-L1 mRNA in cells; SF8: Expression levels of PD-L1 protein in tumor tissues
Supplementary Data Figure 7 from Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor–Positive Breast Cancer
Authors: Buchta Rosean Claire , Bostic Raegan R. , Ferey Joshua C.M. , Feng Tzu-Yu , Azar Francesca N. , Tung Kenneth S. , Dozmorov Mikhail G. , Smirnova Ekaterina , Bos Paula D. , Rutkowski Melanie R.
Published: March 2023

Mice receiving a FMT with a dysbiotic microbiome do not have differences in tumor growth (A) but do have enhanced dissemination of GFP+ tumor cells within the blood (B), Lungs (C) and distal axillary lymph nodes (D)
Supplementary Data Figure 6 from Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor–Positive Breast Cancer
Authors: Buchta Rosean Claire , Bostic Raegan R. , Ferey Joshua C.M. , Feng Tzu-Yu , Azar Francesca N. , Tung Kenneth S. , Dozmorov Mikhail G. , Smirnova Ekaterina , Bos Paula D. , Rutkowski Melanie R.
Published: March 2023

Representative plots quantitating disseminated GFP+ tumor cells in mice treated with absorbable vs non absorbable antibiotics. A is blood CTCs, and B is the lungs.
Supplementary Data Figure 5 from Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor–Positive Breast Cancer
Authors: Buchta Rosean Claire , Bostic Raegan R. , Ferey Joshua C.M. , Feng Tzu-Yu , Azar Francesca N. , Tung Kenneth S. , Dozmorov Mikhail G. , Smirnova Ekaterina , Bos Paula D. , Rutkowski Melanie R.
Published: March 2023

Commensal dysbiosis enhances breast tumor cell dissemination in an autochthonous model. A is tumor growth rates, B represents gating strategy, C is quantitation of GFP+ tumor cells in lungs and D is quantitation of GFP+ tumor cells in lymph nodes, numbers are percentages of live.
Supplementary Data Figure 4 from Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor–Positive Breast Cancer
Authors: Buchta Rosean Claire , Bostic Raegan R. , Ferey Joshua C.M. , Feng Tzu-Yu , Azar Francesca N. , Tung Kenneth S. , Dozmorov Mikhail G. , Smirnova Ekaterina , Bos Paula D. , Rutkowski Melanie R.
Published: March 2023

Commensal dysbiosis does not alter estrus cycles (A) or proportions of mice cycling (B)
Supplementary Data Figure 3 from Preexisting Commensal Dysbiosis Is a Host-Intrinsic Regulator of Tissue Inflammation and Tumor Cell Dissemination in Hormone Receptor–Positive Breast Cancer
Authors: Buchta Rosean Claire , Bostic Raegan R. , Ferey Joshua C.M. , Feng Tzu-Yu , Azar Francesca N. , Tung Kenneth S. , Dozmorov Mikhail G. , Smirnova Ekaterina , Bos Paula D. , Rutkowski Melanie R.
Published: March 2023

Flow cytometry gating strategies to detect GFP+ disseminated tumor cells (A) within the blood (B) and distal lymph node (C).