bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S6 from Twist1 Regulates Vimentin through Cul2 Circular RNA to Promote EMT in Hepatocellular Carcinoma
Authors: Meng Jing , Chen Shuang , Han Jing-Xia , Qian Baoxin , Wang Xiao-Rui , Zhong Wei-Long , Qin Yuan , Zhang Heng , Gao Wan-Feng , Lei Yue-Yang , Yang Wei , Yang Lan , Zhang Chao , Liu Hui-Juan , Liu Yan-Rong , Zhou Hong-Gang , Sun Tao , Yang Cheng
Published: April 2023

Figure S6. The Twist1 and Vimentin expression in HCC. (A) Twist1 was positive correlated with Vimentin. (B) The co-expression of Twist1 and Vimentin presented a shorter survival time. The median survival times were 12.5 month and 62.5 month in Twist1/Vimentin positive and negative groups, respectively.
Figure S5 from Twist1 Regulates Vimentin through Cul2 Circular RNA to Promote EMT in Hepatocellular Carcinoma
Authors: Meng Jing , Chen Shuang , Han Jing-Xia , Qian Baoxin , Wang Xiao-Rui , Zhong Wei-Long , Qin Yuan , Zhang Heng , Gao Wan-Feng , Lei Yue-Yang , Yang Wei , Yang Lan , Zhang Chao , Liu Hui-Juan , Liu Yan-Rong , Zhou Hong-Gang , Sun Tao , Yang Cheng
Published: April 2023

Figure S5. Proteomic analysis by GSEA and GO analysis assay established the differential expression under circ-10720 overexpression. (A) GSEA plots for the gene sets in PLC-PRF-5 cells overexpressed circ-10720 or control vectors. (B) Statistical analysis of the up-regulated biological processes, molecular function and cellular component of PLC-PRF-5 cells after circ-10720 overexpression. (C) Up-regulated genes associated with intracellular transport, invadopodia proteins, TGF-Î² receptor signaling pathways and so on in circ-10720 overexpressed PLC-PRF-5 cells was analyzed.
Figure S3 from Twist1 Regulates Vimentin through Cul2 Circular RNA to Promote EMT in Hepatocellular Carcinoma
Authors: Meng Jing , Chen Shuang , Han Jing-Xia , Qian Baoxin , Wang Xiao-Rui , Zhong Wei-Long , Qin Yuan , Zhang Heng , Gao Wan-Feng , Lei Yue-Yang , Yang Wei , Yang Lan , Zhang Chao , Liu Hui-Juan , Liu Yan-Rong , Zhou Hong-Gang , Sun Tao , Yang Cheng
Published: April 2023

Figure S3. The bioinformatic prediction of circ-10720-miRNAs, miRNA-Vimentin binding site. (A)The bioinformatic prediction (circInteractome datebase) of the putative binding sites of circ-10720 with miRNAs and mutated each miRNA target site of the circ-10720 sequence. (B)The bioinformatic prediction (microRNA datebase) of the putative binding sites of Vimentin 3'-UTR with miR-1246, miR-578, miR-490-5p and mutated miRNA sequence. (C) Expression level of miR-1246, miR-578, and miR-490-5p in human normal tissues and hepatocellular carcinoma tissues.
Supplementary Materials and Methods from IL-6 Mediates Cross-Talk between Tumor Cells and Activated Fibroblasts in the Tumor Microenvironment
Authors: Karakasheva Tatiana A. , Lin Eric W. , Tang Qiaosi , Qiao Edmund , Waldron Todd J. , Soni Monica , Klein-Szanto Andres J. , Sahu Varun , Basu Devraj , Ohashi Shinya , Baba Kiichiro , Giaccone Zachary T. , Walker Sarah R. , Frank David A. , Wileyto E. Paul , Long Qi , Dunagin Margaret C. , Raj Arjun , Diehl J. Alan , Wong K.K. , Bass Adam J. , Rustgi Anil K.
Published: April 2023

Supplementary Materials and Methods with expanded description of cell lines, 2D co-culture of ESCC cells and CAFs, 3D tumoroid and organotypic cultures, xenograft tumors, generation of CRISPR knockout cell lines, real-time qPCR, histology and RNA in situ hybridization
Figure S1 from Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC
Authors: Sun Haoyu , Xu Jing , Huang Qiang , Huang Mei , Li Kun , Qu Kun , Wen Hao , Lin Renyong , Zheng Meijuan , Wei Haiming , Xiao Weihua , Sun Rui , Tian Zhigang , Sun Cheng
Published: April 2023

Figure S1 shows (A) Cumulative percentage of CD160 or BTLA on CD8+ T cells from representative normal liver, PT and IT of HCC patient; (B) Cumulative percentage of CD160+ or BTLA+ CD8+ T cells in healthy liver, IT and PT of HCC patients; (C) Absolute count of CD160+ or BTLA+ CD8+ T cells in healthy liver, IT and PT of HCC patients; and (D) The strategy for gating liver-infiltrating leukocytes and NK cells via flow cytometry.
Supplementary Tables from Inflammatory Breast Cancer Promotes Development of M2 Tumor-Associated Macrophages and Cancer Mesenchymal Cells through a Complex Chemokine Network
Authors: Valeta-Magara Amanda , Gadi Abhilash , Volta Viviana , Walters Beth , Arju Rezina , Giashuddin Shah , Zhong Hua , Schneider Robert J.
Published: April 2023

TS1 describes the characteristics of the cell lines used in this study, including hormone receptor status and type of breast cancer. TS2 lists the antibodies used and the method by which immunohistochemistry stained breast cancer specimens were scored. TS3 describes the levels of IL8, Jak2, P-Ja2, STAT3, P-STAT3 and monocyte macrophages (CD68, CD163) in normal breast tissue and IBC specimens. TS4 lists the expression levels of 80 cytokines, chemokines and growth factors in the conditioned media from SUM149 cells. Data were obtained from at least three independent studies. TS5 lists the sequences of siRNAs that were used for gene silencing in this study. TS6 lists the primer sequences and the genes targeted for qPCR studies carried out.
Supplementary Figures 1-4 from Inflammatory Breast Cancer Promotes Development of M2 Tumor-Associated Macrophages and Cancer Mesenchymal Cells through a Complex Chemokine Network
Authors: Valeta-Magara Amanda , Gadi Abhilash , Volta Viviana , Walters Beth , Arju Rezina , Giashuddin Shah , Zhong Hua , Schneider Robert J.
Published: April 2023

FS1: Four panels (A-D) demonstrating that SUM190 cells are enriched in cancer stem-like cells, shown by immunoblot analysis, cell flow cytometry and by increased cell invasion. FS2: Three panels (A-C) showing that co-culture of IBC cells with monocytes-macrophages increases IBC cell mesenchymal characteristics, shown by immunoblot analysis and invasion assays. FS3: Three immunoblot panels showing that addition of IL8 and GRO cytokines to the media of IBC cells promotes phosphorylation of STAT3 and cancer stem cell-like and mesenchymal characteristics. FS4: Four panels showing that IBC cells secrete attracting and type II polarization factors for monocytes and macrophages. Shown by function assays, cytokine sandwich blot assays, flow cytometry and immunohistochemistry.
Supplementary Figure Legends from Inflammatory Breast Cancer Promotes Development of M2 Tumor-Associated Macrophages and Cancer Mesenchymal Cells through a Complex Chemokine Network
Authors: Valeta-Magara Amanda , Gadi Abhilash , Volta Viviana , Walters Beth , Arju Rezina , Giashuddin Shah , Zhong Hua , Schneider Robert J.
Published: April 2023

Figure legends for supplementary figures 1-4
SV-3: Horizontal reconstruction of P1 cells from A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity
Authors: Díaz-Carballo David , Saka Sahitya , Klein Jacqueline , Rennkamp Tobias , Acikelli Ali H. , Malak Sascha , Jastrow Holger , Wennemuth Gunther , Tempfer Clemens , Schmitz Inge , Tannapfel Andrea , Strumberg Dirk
Published: April 2023

P1 reconstruction in 3D horizontal projection from TEM sections superposed. The inner structure of G1-containing cells is shown.
Supplementary Tables from Retinoic Acid–Related Orphan Receptor C Regulates Proliferation, Glycolysis, and Chemoresistance via the PD-L1/ITGB6/STAT3 Signaling Axis in Bladder Cancer
Authors: Cao Dalong , Qi Zihao , Pang Yangyang , Li Haoran , Xie Huyang , Wu Junlong , Huang Yongqiang , Zhu Yao , Shen Yijun , Zhu Yiping , Dai Bo , Hu Xin , Ye Dingwei , Wang Ziliang
Published: April 2023

Supplementary Tables include Table S1 (The correlation of clinicopathological characteristics and overall survival in bladder cancer patients), Table S2 (The primer sequences of qRT-PCR assay), Table S3 (Acronyms and abbreviations), and Table S4 (The association of clinicopathological characteristics with RORC, PD-L1, ITGB6, STAT3 and p-STAT3 expression in bladder cancer patients).
Supplementary Figure Legends from Retinoic Acid–Related Orphan Receptor C Regulates Proliferation, Glycolysis, and Chemoresistance via the PD-L1/ITGB6/STAT3 Signaling Axis in Bladder Cancer
Authors: Cao Dalong , Qi Zihao , Pang Yangyang , Li Haoran , Xie Huyang , Wu Junlong , Huang Yongqiang , Zhu Yao , Shen Yijun , Zhu Yiping , Dai Bo , Hu Xin , Ye Dingwei , Wang Ziliang
Published: April 2023

Supplementary Figure Legends
Figure S6 from Retinoic Acid–Related Orphan Receptor C Regulates Proliferation, Glycolysis, and Chemoresistance via the PD-L1/ITGB6/STAT3 Signaling Axis in Bladder Cancer
Authors: Cao Dalong , Qi Zihao , Pang Yangyang , Li Haoran , Xie Huyang , Wu Junlong , Huang Yongqiang , Zhu Yao , Shen Yijun , Zhu Yiping , Dai Bo , Hu Xin , Ye Dingwei , Wang Ziliang
Published: April 2023

The associations among the expression of PD-L1, ITGB6, STAT3 and p-STAT3 and survival of Bladder Urothelial Cancer Patients
Supplemental Materials and Methods from Truncated Glioma-Associated Oncogene Homolog 1 (tGLI1) Mediates Mesenchymal Glioblastoma via Transcriptional Activation of CD44
Authors: Rimkus Tadas K. , Carpenter Richard L. , Sirkisoon Sherona , Zhu Dongqin , Pasche Boris C. , Chan Michael D. , Lesser Glenn J. , Tatter Stephen B. , Watabe Kounosuke , Debinski Waldemar , Lo Hui-Wen
Published: April 2023

This file contains supplemental materials and methods
Figure S5 from SWI/SNF-Compromised Cancers Are Susceptible to Bromodomain Inhibitors
Authors: Shorstova Tatiana , Marques Maud , Su Jie , Johnston Jake , Kleinman Claudia L. , Hamel Nancy , Huang Sidong , Alaoui-Jamali Moulay A. , Foulkes William D. , Witcher Michael
Published: April 2023

c-MYC expression in response to BETi treatment in ovarian cancer cells. BRD4 knockdown represses HER3 expression and downstream signaling.
Figure S4 from SWI/SNF-Compromised Cancers Are Susceptible to Bromodomain Inhibitors
Authors: Shorstova Tatiana , Marques Maud , Su Jie , Johnston Jake , Kleinman Claudia L. , Hamel Nancy , Huang Sidong , Alaoui-Jamali Moulay A. , Foulkes William D. , Witcher Michael
Published: April 2023

OTX015 transcriptionally regulates a network of genes involved in cell signaling
Figure S3 from KDM4 Inhibition Targets Breast Cancer Stem–like Cells
Authors: Metzger Eric , Stepputtis Stella S. , Strietz Juliane , Preca Bogdan-Tiberius , Urban Sylvia , Willmann Dominica , Allen Anita , Zenk Fides , Iovino Nicola , Bronsert Peter , Proske Amelie , Follo Marie , Boerries Melanie , Stickeler Elmar , Xu Jiangchun , Wallace Michael B. , Stafford Jeffrey A. , Kanouni Toufike , Maurer Jochen , Schüle Roland
Published: April 2023

QC6352 strongly decreases proliferation and sphere formation of a second breast cancer stem cell line (BCSC2). Other breast cancer-targeting agents like QC6688 and paclitaxel are unable to abolish secondary sphere formation in BCSC1 or BCSC2.
Figure S3 from Extracellular Matrix Protein Tenascin C Increases Phagocytosis Mediated by CD47 Loss of Function in Glioblastoma
Authors: Ma Ding , Liu Senquan , Lal Bachchu , Wei Shuang , Wang Shuyan , Zhan Daqian , Zhang Hao , Lee Richard S. , Gao Peisong , Lopez-Bertoni Hernando , Ying Mingyao , Li Jian Jian , Laterra John , Wilson Mary Ann , Xia Shuli
Published: April 2023

Figure S3 shows INOS and TGM2 staining and quantification in CD47 WT and CD47 KO xenografts.
Figure S2 from Extracellular Matrix Protein Tenascin C Increases Phagocytosis Mediated by CD47 Loss of Function in Glioblastoma
Authors: Ma Ding , Liu Senquan , Lal Bachchu , Wei Shuang , Wang Shuyan , Zhan Daqian , Zhang Hao , Lee Richard S. , Gao Peisong , Lopez-Bertoni Hernando , Ying Mingyao , Li Jian Jian , Laterra John , Wilson Mary Ann , Xia Shuli
Published: April 2023

Figure S2 shows Iba-1 staining in CD47 WT and CD47 KO xenografts.
Supplemental Figure (4) from Upregulation of Cystathionine-β-Synthase in Colonic Epithelia Reprograms Metabolism and Promotes Carcinogenesis
Authors: Phillips Ches'Nique M. , Zatarain John R. , Nicholls Michael E. , Porter Craig , Widen Steve G. , Thanki Ketan , Johnson Paul , Jawad Muhammad U. , Moyer Mary P. , Randall James W. , Hellmich Judith L. , Maskey Manjit , Qiu Suimin , Wood Thomas G. , Druzhyna Nadiya , Szczesny Bartosz , Módis Katalin , Szabo Csaba , Chao Celia , Hellmich Mark R.
Published: April 2023

CBS overexpression and an H2S donor (GYY4137) enhanced NCM356 cell growth in soft agar.
Supplementary Figure 1 from Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer
Authors: D'Costa Zenobia , Jones Keaton , Azad Abul , van Stiphout Ruud , Lim Su Y. , Gomes Ana L. , Kinchesh Paul , Smart Sean C. , Gillies McKenna W. , Buffa Francesca M. , Sansom Owen J. , Muschel Ruth J. , O'Neill Eric , Fokas Emmanouil
Published: April 2023

Supplementary Figure describing TIMP-1 expression and its effect in clonogenic survival in-vitro.
Supplementary FIgure 2 from Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer
Authors: D'Costa Zenobia , Jones Keaton , Azad Abul , van Stiphout Ruud , Lim Su Y. , Gomes Ana L. , Kinchesh Paul , Smart Sean C. , Gillies McKenna W. , Buffa Francesca M. , Sansom Owen J. , Muschel Ruth J. , O'Neill Eric , Fokas Emmanouil
Published: April 2023

Supplementary Figure describing the effect of TIMP-1 in PDAC cells in-vitro.
Figure S8 from Elevated Heme Synthesis and Uptake Underpin Intensified Oxidative Metabolism and Tumorigenic Functions in Non–Small Cell Lung Cancer Cells
Authors: Sohoni Sagar , Ghosh Poorva , Wang Tianyuan , Kalainayakan Sarada Preeta , Vidal Chantal , Dey Sanchareeka , Konduri Purna Chaitanya , Zhang Li
Published: April 2023

Fig. S8 The effect of HSP2 on the growth and progression of H1299 NSCLC lung tumor xenografts and on blood and liver functions in mice. (A) The quantified luminescence signals representing tumor volumes. Treatment started at week 3 when tumors have grown significantly and BLI signals were about 5x107 photons/seconds. Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in treated tumors were compared to the levels in untreated tumors with a Welch 2-sample t-test. *, p-value < 0.05. (B) Representative H&E images of control tumors and tumors treated with HSP2 or control saline. Tumors are marked with light blue outlines. Scale bar: 2 mm. (C) Average red blood cell count in mice bearing orthotopic lung tumor xenografts treated with or without HSP2. (D) Average hemoglobin levels in mice bearing orthotopic lung tumor xenografts treated with or without HSP2. (E) Average serum ALT (alanine transaminase) levels in mice bearing orthotopic lung tumor xenografts treated with or without HSP2. (F) Western blots showing the levels of ALAS1 in H1299 cells bearing the control or overexpression vector for ALAS1. (G) Western blots showing the levels of SLC48A1 in H1299 cells bearing the control or overexpression vector for ALAS1. (H) Oxygen consumption rates are increased in cells overexpressing ALAS1 or SLC48A1. (I) overexpression of ALAS1 or SLC48A1 promotes colony formation by H1299 NSCLC cells. For statistical analysis, the levels in cells overexpressing ALAS1 or SLC48A1 were compared to the levels in control cells with a Welch 2-sample t-test. **, p-value < 0.005. (J) The levels of heme synthesis in H1299 cells cultured in normal medium and heme-depleted medium (H dep), respectively. The level of heme synthesis in heme-depleted medium presumably represents the total cellular heme levels needed for the cells. The data show that de novo heme synthesis accounts for approximately 68% of total cellular heme levels in H1299 cells, indicating that heme uptake accounts for 32%. Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in heme-depleted medium were compared to the levels in normal medium with a Welch 2-sample t-test.*, p-value, 0.05, **, p-value < 0.005.
Video 1 from Optical Coherence Tomography Detects Necrotic Regions and Volumetrically Quantifies Multicellular Tumor Spheroids
Authors: Huang Yongyang , Wang Shunqiang , Guo Qiongyu , Kessel Sarah , Rubinoff Ian , Chan Leo Li-Ying , Li Peter , Liu Yaling , Qiu Jean , Zhou Chao
Published: April 2023

3D rendering of an U-87 MG tumor spheroid over 21 days.
Figure S7 from Elevated Heme Synthesis and Uptake Underpin Intensified Oxidative Metabolism and Tumorigenic Functions in Non–Small Cell Lung Cancer Cells
Authors: Sohoni Sagar , Ghosh Poorva , Wang Tianyuan , Kalainayakan Sarada Preeta , Vidal Chantal , Dey Sanchareeka , Konduri Purna Chaitanya , Zhang Li
Published: April 2023

Fig. S7 HSPs inhibit tumorigenic functions in A549 NSCLC cells. (A) HSPs inhibit migration in A549 NSCLC cells. (B) HSPs inhibit invasion in A549 NSCLC cells. The potent inhibitor of heme synthesis, succinyl acetone (SA), is shown for comparison. Addition of 10 μM heme largely reversed the effects of SA and HSPs. The images shown are cells that had migrated across Transwell inserts (in A) or had crossed invasion chambers coated with Corning Matrigel matrix and also passed Transwell inserts (in B). Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in treated cells were compared to the levels in untreated cells with a Welch 2-sample t-test.*, p-value, 0.05, **, p-value < 0.005. For heme add-back experiments, the levels in cells treated with heme and SA or HSPs were compared to the levels in cells treated with only SA or HSPs. [**], p-value < 0.005. The effects SA, HSPs, heme oxygenase inhibitors, and iron chelator DFX on NSCLC cell colony formation are shown in C-G. (C) The effect of SA on colony formation in A549 cells. (D) The effect of HSP1 on colony formation in A549 cells. (E) The effect of HSP2 on colony formation in A549 cells. (F) The effects of heme oxygenase inhibitor SnPP and ZnPP on colony formation in A549 cells. (G) The effect of DFX on colony formation in A549 cells. (H) Comparison of the effects of HSP2 and DFX treatments on the levels of transferrin receptor TFRC. (I) Comparison of the effects of HSP2 and DFX treatments on the levels of ferroportin SLC40A1. In H & I, data from Western blotting analysis of proteins prepared from NSCLC cells treated with HSP2 or DFX for 6 days were shown. For statistical analysis, the levels in treated cells were compared to the levels in untreated cells (Control) with a Welch 2-sample t-test. **, p-value < 0.005.
Table S1-3 from Downregulation of Membrane Trafficking Proteins and Lactate Conditioning Determine Loss of Dendritic Cell Function in Lung Cancer
Authors: Caronni Nicoletta , Simoncello Francesca , Stafetta Francesca , Guarnaccia Corrado , Ruiz-Moreno Juan Sebastian , Opitz Bastian , Galli Thierry , Proux-Gillardeaux Veronique , Benvenuti Federica
Published: April 2023

Primers and DQ-BSA/pHRodo MFI
Figure S1 from Downregulation of Membrane Trafficking Proteins and Lactate Conditioning Determine Loss of Dendritic Cell Function in Lung Cancer
Authors: Caronni Nicoletta , Simoncello Francesca , Stafetta Francesca , Guarnaccia Corrado , Ruiz-Moreno Juan Sebastian , Opitz Bastian , Galli Thierry , Proux-Gillardeaux Veronique , Benvenuti Federica
Published: April 2023

Characterization of VAMP3 null DCs
Table S2 from Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Boguslawski Elissa A. , Grit Jamie , Dodd Rebecca D. , Khachaturov Vadim , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: April 2023

Copy number analysis of Met and Hgf in murine MPNST models.
Figure S6 from Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Boguslawski Elissa A. , Grit Jamie , Dodd Rebecca D. , Khachaturov Vadim , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: April 2023

Mean percent reduction in growth ratesof A) NF1-MET, B) NF1-P53, and C) NF1 mice treated with each treatment arm versus vehicle.
Figure S5 from Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Boguslawski Elissa A. , Grit Jamie , Dodd Rebecca D. , Khachaturov Vadim , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: April 2023

Tumorgrafts are differentially sensitive to MET inhibition with capmatinib.
Table S2 from NK Cells Mediate Synergistic Antitumor Effects of Combined Inhibition of HDAC6 and BET in a SCLC Preclinical Model
Authors: Liu Yan , Li Yuyang , Liu Shengwu , Adeegbe Dennis O. , Christensen Camilla L. , Quinn Max M. , Dries Ruben , Han Shiwei , Buczkowski Kevin , Wang Xiaoen , Chen Ting , Gao Peng , Zhang Hua , Li Fei , Hammerman Peter S. , Bradner James E. , Quayle Steven N. , Wong Kwok-Kin
Published: April 2023

Characteristics of SCLC cell lines
Supplementary video 6 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Ex vivo migration assay in the presence of BDP-9066.
Supplementary Materials and Methods from HERC2 Facilitates BLM and WRN Helicase Complex Interaction with RPA to Suppress G-Quadruplex DNA
Authors: Wu Wenwen , Rokutanda Nana , Takeuchi Jun , Lai Yongqiang , Maruyama Reo , Togashi Yukiko , Nishikawa Hiroyuki , Arai Naoko , Miyoshi Yasuo , Suzuki Nao , Saeki Yasushi , Tanaka Keiji , Ohta Tomohiko
Published: April 2023

Affinity purification of HERC2 complex and Mass Spectrometry; Sister chromatid exchange (SCE) assays.
Supplementary video 5 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Subconfluent migration assays in the presence of 1000nM BDP-9066
Supplementary Figures S1-S11 from HERC2 Facilitates BLM and WRN Helicase Complex Interaction with RPA to Suppress G-Quadruplex DNA
Authors: Wu Wenwen , Rokutanda Nana , Takeuchi Jun , Lai Yongqiang , Maruyama Reo , Togashi Yukiko , Nishikawa Hiroyuki , Arai Naoko , Miyoshi Yasuo , Suzuki Nao , Saeki Yasushi , Tanaka Keiji , Ohta Tomohiko
Published: April 2023

S1. Analyses of HERC2 complex immunoprecipitated with a newly generated antibody; S2. HERC2 regulates BLM-RPA complex formation; S3. Effect of HERC2 depletion on BLM-RPA and WRN-RPA complex formation was reproduced with a different shRNA; S4. Detection of nuclear G4 foci in cells in different conditions; S5. HERC2 suppresses SCE; S6. Specificity of the HERC2 antibody for the immunostain; S7. Analyses of HERC2 interacting proteins in HERC2Î"E3/Î"E3 HCT116 cells; S8. Inhibition of HERC2 E3 activity increases SCE; S9. Proliferation of HERC-perturbed cell lines; S10. HERC2 is downregulated in various human cancers; S11. Possible model for the role of HERC2 on G4 unwinding.
Supplementary video 4 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Subconfluent migration assays in the presence of 100nM BDP-9066
Supplementary Table S2 from Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures
Authors: Tasdemir Nilgun , Bossart Emily A. , Li Zheqi , Zhu Li , Sikora Matthew J. , Levine Kevin M. , Jacobsen Britta M. , Tseng George C. , Davidson Nancy E. , Oesterreich Steffi
Published: April 2023

Lists of upregulated and downregulated genes in ILC versus IDC cell lines, tumors and organoids.
Supplementary table 2 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Summary of the properties of BDP-9066
Supplementary Table 1 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

Antibodies used for western blotting
Supplemental Figures from Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy
Authors: Saito Ryoichi , Smith Christof C. , Utsumi Takanobu , Bixby Lisa M. , Kardos Jordan , Wobker Sara E. , Stewart Kyle G. , Chai Shengjie , Manocha Ujjawal , Byrd Kevin M. , Damrauer Jeffrey S. , Williams Scott E. , Vincent Benjamin G. , Kim William Y.
Published: April 2023

Supplemental Figure 1: Inactivation of Pten and Trp53 in Keratin 5 expressing cells does not result in bladder cancer. Supplemental Figure 2: Histologic features of BBN induced tumors. Supplemental Figure 3: Generation of KT normal urothelial cells and comparison to MB49 and 3T3 cells. Supplemental Figure 4: Hierarchical clustering of MB49, BBN963, and UPPL1541 cell lines and cell line derived tumors. Supplemental Figure 5: IPA Pathways enriched in BBN963 versus UPPL1541 cell line derived tumors. Supplemental Figure 6: MB49 cell line derived tumors are more mesenchymal than BBN963 and UPPL1541 cell line derived tumors. Supplemental Figure 7: Immune Gene Signatures and correlation between tumor-infiltrating lymphocyte phenotype and tumor size. Supplemental Figure 8: TCR clonotype in anti-PD-1 treated BBN963 tumors. Supplemental Figure 9: Memory T cell gene signature expression in TCGA BLCA tumors. Supplemental Figure 10: Oncoprint of whole exome sequencing of UPPL1541, BBN963, and MB49 cell line derived tumors.
Supplemental Figure Legends from Molecular Subtype-Specific Immunocompetent Models of High-Grade Urothelial Carcinoma Reveal Differential Neoantigen Expression and Response to Immunotherapy
Authors: Saito Ryoichi , Smith Christof C. , Utsumi Takanobu , Bixby Lisa M. , Kardos Jordan , Wobker Sara E. , Stewart Kyle G. , Chai Shengjie , Manocha Ujjawal , Byrd Kevin M. , Damrauer Jeffrey S. , Williams Scott E. , Vincent Benjamin G. , Kim William Y.
Published: April 2023

Supplemental Figure Legends
Figure S3 from TRPM2 Mediates Neutrophil Killing of Disseminated Tumor Cells
Authors: Gershkovitz Maya , Caspi Yaki , Fainsod-Levi Tanya , Katz Ben , Michaeli Janna , Khawaled Saleh , Lev Shaya , Polyansky Lola , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Mori Yasuo , Karni Rotem , Fridlender Zvi G. , Binshtok Alexander M. , Granot Zvi
Published: April 2023

Supplemental Figure S3. TRPM2 expression is associated with prolonged progression free survival in breast cancer patients. Kaplan-Meyer analysis of recurrence free survival (RFS, upper panels) and distant metastasis free survival (DMFS, lower panels) of breast cancer patients (all subtypes and subset specific), stratified by TRPM2 expression using 3 different probe sets. Gene expression data obtained from the open-source KM Plotter (39).
Supplementary Figires S1 to S3 from Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape
Authors: Cubuk Cankut , Hidalgo Marta R. , Amadoz Alicia , Pujana Miguel A. , Mateo Francesca , Herranz Carmen , Carbonell-Caballero Jose , Dopazo Joaquin
Published: April 2023

Figure S1: The metabolic module Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate module (M00010). Figure S2: PCA plots for detecting batch effects. Figure S3: Detailed description of changes in pairwise module correlation.
Supplementary Figure S7 from mTOR Inhibition via Displacement of Phosphatidic Acid Induces Enhanced Cytotoxicity Specifically in Cancer Cells
Authors: Nguyen Tra-Ly , Nokin Marie-Julie , Egorov Maxim , Tomé Mercedes , Bodineau Clément , Di Primo Carmelo , Minder Lætitia , Wdzieczak-Bakala Joanna , Garcia-Alvarez Maria Concepcion , Bignon Jérôme , Thoison Odile , Delpech Bernard , Surpateanu Georgiana , Frapart Yves-Michel , Peyrot Fabienne , Abbas Kahina , Terés Silvia , Evrard Serge , Khatib Abdel-Majid , Soubeyran Pierre , Iorga Bogdan I. , Durán Raúl V. , Collin Pascal
Published: April 2023

The file contains supplementary results showing that ICSN3250 specifically targets cancer cells both in vitro and ex vivo.
Supplementary Figure legends from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets
Authors: Cortazar Ana R. , Torrano Veronica , Martín-Martín Natalia , Caro-Maldonado Alfredo , Camacho Laura , Hermanova Ivana , Guruceaga Elizabeth , Lorenzo-Martín Luis F. , Caloto Ruben , Gomis Roger R. , Apaolaza Iñigo , Quesada Victor , Trka Jan , Gomez-Muñoz Antonio , Vincent Silvestre , Bustelo Xose R. , Planes Francisco J. , Aransay Ana M. , Carracedo Arkaitz
Published: April 2023

Supplementary Figure legends
Figure S1, Figure S2, Figure S3, Figure S4 from Long Noncoding RNA CRYBG3 Blocks Cytokinesis by Directly Binding G-Actin
Authors: Pei Hailong , Hu Wentao , Guo Ziyang , Chen Huaiyuan , Ma Ji , Mao Weidong , Li Bingyan , Wang Aiqing , Wan Jianmei , Zhang Jian , Nie Jing , Zhou Guangming , Hei Tom K.
Published: April 2023

Supplement Figure 1: Cell cycle synchronization validation and cell cycle results. Supplement Figure 2: LNC CRYBG3 localization and proportion of binucleated cells in different cell lines. Supplement Figure 3: Western blot and immunofluorescence analysis determined the actin expression and microfilaments morphology. Supplement Figure 4: LNC CRYBG3 expression after overexpressed K-ras G12V and EGFR T790M / L858R .
Figure S4 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

RNA splicing perturbation by pharmacologic compounds induce R loop and ATR-mediated RPA32 phosphorylation.
Figure S3 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

Expression of wild type or different mutants of U2AF1.
Supplemental Figure S6 from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers
Authors: Elion David L. , Jacobson Max E. , Hicks Donna J. , Rahman Bushra , Sanchez Violeta , Gonzales-Ericsson Paula I. , Fedorova Olga , Pyle Anna M. , Wilson John T. , Cook Rebecca S.
Published: April 2023

4T1 mouse mammary tumors were grown orthotopically in athymic Balb/C (nu/nu) female mice. Tumor-bearing mice were randomized into treatment groups for intratumoral delivery of SLR20 (or OH-SLR20, or saline) on treatment days 1, 5, and 9. Tumors were measured throughout treatment (days 1-10) and for 5 days after treatment ceased (days 10-15). N = 7 per group.
Figure S2 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

Protein expression levels of R loop regulators in U2AF1(WT)- or U2AF1(S34F)-expressing cells.
Supplemental Figure S3 from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers
Authors: Elion David L. , Jacobson Max E. , Hicks Donna J. , Rahman Bushra , Sanchez Violeta , Gonzales-Ericsson Paula I. , Fedorova Olga , Pyle Anna M. , Wilson John T. , Cook Rebecca S.
Published: April 2023

A. Schematic of treatment strategy for intra-tumoral nanoparticle delivery of SLR20 (or OH-SLR20) to WT Balb/C mice harboring 4T1 mammary tumors. Saline was delivered intratumorally as a control. Tumors were measured throughout treatment . B. Tumor volume was measured beginning at treatment day 0. N = 7-8 per group.
Supplement material descriptions and Figure S1-S7 and Table S1-S3 from GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma
Authors: Zhang Weiruo , Bouchard Gina , Yu Alice , Shafiq Majid , Jamali Mehran , Shrager Joseph B. , Ayers Kelsey , Bakr Shaimaa , Gentles Andrew J. , Diehn Maximilian , Quon Andrew , West Robert B. , Nair Viswam , van de Rijn Matt , Napel Sandy , Plevritis Sylvia K.
Published: April 2023

This supplement file provides additional information and analysis descriptions to the main manuscript ordered as in which they appear in the main text. This supplement file also provides general descriptions and overview to all the supplement materials included. This supplement file also includes Figure S1-S7 and Table S1-S3.
Supplemental Figure S2 from Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers
Authors: Elion David L. , Jacobson Max E. , Hicks Donna J. , Rahman Bushra , Sanchez Violeta , Gonzales-Ericsson Paula I. , Fedorova Olga , Pyle Anna M. , Wilson John T. , Cook Rebecca S.
Published: April 2023

Western analysis of whole cel lysates harvested from BT474, MCF7, and MDA-MB-361 cells using antibodies indicated at the left of each panel. Western analysis of whole cell lysates harvested from MDA-MB-361 cells tranfected with SLR20 or OH-SLR20 at 12 hours after transfection. Immunohistochemistry was used to measure RIG-I and P-STAT1 in tumors harvested at day 5. Representative Images are shown. N = 5.
De-identified ID of the patients included in the RG cohort from GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma
Authors: Zhang Weiruo , Bouchard Gina , Yu Alice , Shafiq Majid , Jamali Mehran , Shrager Joseph B. , Ayers Kelsey , Bakr Shaimaa , Gentles Andrew J. , Diehn Maximilian , Quon Andrew , West Robert B. , Nair Viswam , van de Rijn Matt , Napel Sandy , Plevritis Sylvia K.
Published: April 2023

This supplement file contains a list of de-identified IDs of the patients included in the RG cohort data available online.
Supplementary Information from Plk1-Mediated Phosphorylation of TSC1 Enhances the Efficacy of Rapamycin
Authors: Li Zhiguo , Kong Yifan , Song Longzhen , Luo Qian , Liu Jinghui , Shao Chen , Hou Xianzeng , Liu Xiaoqi
Published: April 2023

Supplementary Materials and Methods and Figure legends
Figure S5 from YAP1-Mediated Suppression of USP31 Enhances NFκB Activity to Promote Sarcomagenesis
Authors: Ye Shuai , Lawlor Matthew A. , Rivera-Reyes Adrian , Egolf Shaun , Chor Susan , Pak Koreana , Ciotti Gabrielle E. , Lee Avery C. , Marino Gloria E. , Shah Jennifer , Niedzwicki David , Weber Kristy , Park Paul M.C. , Alam Md. Zahidul , Grazioli Alison , Haldar Malay , Xu Mousheng , Perry Jennifer A. , Qi Jun , Eisinger-Mathason T.S. Karin
Published: April 2023

The effects of SAHA/JQ1 on phospho-YAP1
Figure S3 from YAP1-Mediated Suppression of USP31 Enhances NFκB Activity to Promote Sarcomagenesis
Authors: Ye Shuai , Lawlor Matthew A. , Rivera-Reyes Adrian , Egolf Shaun , Chor Susan , Pak Koreana , Ciotti Gabrielle E. , Lee Avery C. , Marino Gloria E. , Shah Jennifer , Niedzwicki David , Weber Kristy , Park Paul M.C. , Alam Md. Zahidul , Grazioli Alison , Haldar Malay , Xu Mousheng , Perry Jennifer A. , Qi Jun , Eisinger-Mathason T.S. Karin
Published: April 2023

Supplemental in vitro rescue assays and qRT-PCR of SAHA/JQ1 treated cells
Figure S1 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism
Authors: Lopes-Ramos Camila M. , Kuijjer Marieke L. , Ogino Shuji , Fuchs Charles S. , DeMeo Dawn L. , Glass Kimberly , Quackenbush John
Published: April 2023

Pathways differentially targeted between healthy and colon cancer tissues.
Table S1 from The Canonical Wnt Pathway Drives Macropinocytosis in Cancer
Authors: Redelman-Sidi Gil , Binyamin Anna , Gaeta Isabella , Palm Wilhelm , Thompson Craig B. , Romesser Paul B. , Lowe Scott W. , Bagul Mukta , Doench John G. , Root David E. , Glickman Michael S.
Published: April 2023

Table S1: A Whole-genome shRNA screen for inhibitors of macropinocytosis
Supplementary Figure S2 from Targeting PARP1 in XRCC1-Deficient Sporadic Invasive Breast Cancer or Preinvasive Ductal Carcinoma In Situ Induces Synthetic Lethality and Chemoprevention
Authors: Ali Reem , Al-Kawaz Abdulbaqi , Toss Michael S. , Green Andrew R. , Miligy Islam M. , Mesquita Katia A. , Seedhouse Claire , Mirza Sameer , Band Vimla , Rakha Emad A , Madhusudan Srinivasan
Published: April 2023

Western blots, FACS and clonogenic assays
Supplementary Figure S1 from Targeting PARP1 in XRCC1-Deficient Sporadic Invasive Breast Cancer or Preinvasive Ductal Carcinoma In Situ Induces Synthetic Lethality and Chemoprevention
Authors: Ali Reem , Al-Kawaz Abdulbaqi , Toss Michael S. , Green Andrew R. , Miligy Islam M. , Mesquita Katia A. , Seedhouse Claire , Mirza Sameer , Band Vimla , Rakha Emad A , Madhusudan Srinivasan
Published: April 2023

Kaplan-Meier curve for BCSS
Figure legends from Targeting PARP1 in XRCC1-Deficient Sporadic Invasive Breast Cancer or Preinvasive Ductal Carcinoma In Situ Induces Synthetic Lethality and Chemoprevention
Authors: Ali Reem , Al-Kawaz Abdulbaqi , Toss Michael S. , Green Andrew R. , Miligy Islam M. , Mesquita Katia A. , Seedhouse Claire , Mirza Sameer , Band Vimla , Rakha Emad A , Madhusudan Srinivasan
Published: April 2023

Legends for Supplementary Figure S1 & Supplementary Figure S2
Data Supplement 1 from Differential Burden of Rare and Common Variants on Tumor Characteristics, Survival, and Mode of Detection in Breast Cancer
Authors: Li Jingmei , Ugalde-Morales Emilio , Wen Wei Xiong , Decker Brennan , Eriksson Mikael , Torstensson Astrid , Christensen Helene Nordahl , Dunning Alison M. , Allen Jamie , Luccarini Craig , Pooley Karen A. , Simard Jacques , Dorling Leila , Easton Douglas F. , Teo Soo Hwang , Hall Per , Czene Kamila
Published: April 2023

eMethods describes additional details on the targeted sequencing and data processing methodology. Table S7 shows the associations between breast cancer genetic loci and breast cancer tumor characteristics diagnosed with breast cancer at below age 50. Table S8 shows the associations between breast cancer genetic loci and breast cancer tumor characteristics diagnosed with breast cancer at age 50 years and above. Figure S1 illustrates a flowchart summarizing the data processing work flow. Figure S2 shows a visual summary of the different rare variants called. Figure 3 shows the relationship between polygenic risk score (PRS) and protein-truncating variant carriership illustrated by boxplots. Figures S4-S6 show the results obtained by considering a subset of HBOC genes for the analyses on tumor characteristics, survival and mode of detection, respectively.
Supplementary Figure 4 from Extracorporeal Photochemotherapy Drives Monocyte-to-Dendritic Cell Maturation to Induce Anticancer Immunity
Authors: Ventura Alessandra , Vassall Aaron , Robinson Eve , Filler Renata , Hanlon Douglas , Meeth Katrina , Ezaldein Harib , Girardi Michael , Sobolev Olga , Bosenberg Marcus W. , Edelson Richard L.
Published: April 2023

Additional data for Figure 2B, showing representative tumor growth volumes, for review and publication
Supplementary Data from ZNF677 Suppresses Akt Phosphorylation and Tumorigenesis in Thyroid Cancer
Authors: Li Yujun , Yang Qi , Guan Haixia , Shi Bingyin , Ji Meiju , Hou Peng
Published: April 2023

1. Supplementary tables include: the relationship between promoter methylation of ZNF677 and clinical characteristics in PTCs, STR DNA profiling of cell lines, primers for PCR, qPCR, pyrosequencing and plasmid construction, the sequences of siRNAs and shRNAs, and informations of antibodies. 2. Supplementary figures include: methylation and expression of ZNF677; the inhibitory effect of ZNF677 on migration and invasion; the effect of ZNF677 on the activity of the MAPK/Erk signaling; the effect of CDKN3 or HSPB1 knockdown on tumor promoting role of ZNF677 depletion in thyroid cancer cells; dual-luciferase reporter assay in HEK293T cells, the effect of CDKN3 or HSPB1 overexpression on tumor inhibitory role of ZNF677 in lung, gastric and breast cancers; Ki-67 staining of xenograft tumors; quantitative illustration of the proteins in figures 3, 5 and 6. 3. Supplementary figure legends.
Table S3 from Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma
Authors: Luoto Suvi , Hermelo Ismaïl , Vuorinen Elisa M. , Hannus Paavo , Kesseli Juha , Nykter Matti , Granberg Kirsi J.
Published: April 2023

Tables contain immune system related Gene ontology and KEGG pathway enrichments for identified immune response related gene clusters.
Supp Tables T1-T4 from Lorlatinib Treatment Elicits Multiple On- and Off-Target Mechanisms of Resistance in ALK-Driven Cancer
Authors: Redaelli Sara , Ceccon Monica , Zappa Marina , Sharma Geeta G. , Mastini Cristina , Mauri Mario , Nigoghossian Marion , Massimino Luca , Cordani Nicoletta , Farina Francesca , Piazza Rocco , Gambacorti-Passerini Carlo , Mologni Luca
Published: April 2023

Primers used and mutations identified by WES
Figure S1-S12 from Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma
Authors: Luoto Suvi , Hermelo Ismaïl , Vuorinen Elisa M. , Hannus Paavo , Kesseli Juha , Nykter Matti , Granberg Kirsi J.
Published: April 2023

File contains supplementary figures S1-S12. Figures include the concept, results and validation of the regression analysis, estimated cell proportions for all the non-malignant reference cells and tissues, validation of immune subgroups in separate GBM cohort, and different associations between GBM subgroups, genetic aberrations, relative cell proportions or cluster. Furthermore, figures showing gene expression of HLA genes in immune subgroups as well as HLA protein levels in glioma cell lines and patient-derived GBM cultures are included.
Supp Figures S7-S9 from Lorlatinib Treatment Elicits Multiple On- and Off-Target Mechanisms of Resistance in ALK-Driven Cancer
Authors: Redaelli Sara , Ceccon Monica , Zappa Marina , Sharma Geeta G. , Mastini Cristina , Mauri Mario , Nigoghossian Marion , Massimino Luca , Cordani Nicoletta , Farina Francesca , Piazza Rocco , Gambacorti-Passerini Carlo , Mologni Luca
Published: April 2023

PCR analyses; models of drug resistance
Supplementary Materials and Methods from An ATM/TRIM37/NEMO Axis Counteracts Genotoxicity by Activating Nuclear-to-Cytoplasmic NF-κB Signaling
Authors: Wu Geyan , Song Libing , Zhu Jinrong , Hu Yameng , Cao Lixue , Tan Zhanyao , Zhang Shuxia , Li Ziwen , Li Jun
Published: April 2023

Supplementary information to support primary data.
Table S1 from Loss of MED12 Induces Tumor Dormancy in Human Epithelial Ovarian Cancer via Downregulation of EGFR
Authors: Luo Xiao-Lin , Deng Cheng-Cheng , Su Xiao-Dong , Wang Fang , Chen Zhen , Wu Xing-Ping , Liang Shao-Bo , Liu Ji-Hong , Fu Li-Wu
Published: April 2023

Effect of MED12 KO on tumorigenicity in HO8910 and SKOV3.
Figure S4 from Loss of MED12 Induces Tumor Dormancy in Human Epithelial Ovarian Cancer via Downregulation of EGFR
Authors: Luo Xiao-Lin , Deng Cheng-Cheng , Su Xiao-Dong , Wang Fang , Chen Zhen , Wu Xing-Ping , Liang Shao-Bo , Liu Ji-Hong , Fu Li-Wu
Published: April 2023

No obvious change of Wnt/β-catenin signaling was found after MED12 knocked-out.
Supplementary Fig S5 from Mucosal HPV E6/E7 Peptide Vaccination in Combination with Immune Checkpoint Modulation Induces Regression of HPV+ Oral Cancers
Authors: Dorta-Estremera Stephanie , Chin Renee L. , Sierra Gloria , Nicholas Courtney , Yanamandra Ananta V. , Nookala Sita M.K. , Yang Guojun , Singh Shail , Curran Michael A. , Sastry K. Jagannadha
Published: April 2023

Induction of systemic antigen-specific CD8+ T cell responses after vaccine immunotherapy.
Supplementary Fig S4 from Mucosal HPV E6/E7 Peptide Vaccination in Combination with Immune Checkpoint Modulation Induces Regression of HPV+ Oral Cancers
Authors: Dorta-Estremera Stephanie , Chin Renee L. , Sierra Gloria , Nicholas Courtney , Yanamandra Ananta V. , Nookala Sita M.K. , Yang Guojun , Singh Shail , Curran Michael A. , Sastry K. Jagannadha
Published: April 2023

Therapeutic efficacy of the combination of a4-1BB and aCD40 with and without HPV peptide vaccine is CD8+ T cell dependent
Supplementary Fig S3 from Mucosal HPV E6/E7 Peptide Vaccination in Combination with Immune Checkpoint Modulation Induces Regression of HPV+ Oral Cancers
Authors: Dorta-Estremera Stephanie , Chin Renee L. , Sierra Gloria , Nicholas Courtney , Yanamandra Ananta V. , Nookala Sita M.K. , Yang Guojun , Singh Shail , Curran Michael A. , Sastry K. Jagannadha
Published: April 2023

Therapeutic efficacy of immunotherapy combinations correlates with the presence of TcEO cells in the tumors
Table S2 from Reduced Expression of PROX1 Transitions Glioblastoma Cells into a Mesenchymal Gene Expression Subtype
Authors: Goudarzi Kaveh M. , Espinoza Jaime A. , Guo Min , Bartek Jiri , Nistér Monica , Lindström Mikael S. , Hägerstrand Daniel
Published: April 2023

Table containing qRT-PCR primer sequences
Figure S1 from Cyclophilin A Function in Mammary Epithelium Impacts Jak2/Stat5 Signaling, Morphogenesis, Differentiation, and Tumorigenesis in the Mammary Gland
Authors: Volker Sonja E. , Hedrick Shannon E. , Feeney Yvonne B. , Clevenger Charles V.
Published: April 2023

Loss of CypA is associated delayed mammary development.
Figure S5 from Paclitaxel Reduces Tumor Growth by Reprogramming Tumor-Associated Macrophages to an M1 Profile in a TLR4-Dependent Manner
Authors: Wanderley Carlos W. , Colón David F. , Luiz João Paulo M. , Oliveira Francisco F. , Viacava Paula R. , Leite Caio A. , Pereira Janaina A. , Silva Camila M. , Silva Cassia R. , Silva Rangel L. , Speck-Hernandez Cesar A. , Mota José M. , Alves-Filho José C. , Lima-Junior Roberto C. , Cunha Thiago M. , Cunha Fernando Q.
Published: April 2023

Generation of myeloid cell-specific TLR4 knockout mice