bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from In Silico Evaluation of Pharmacokinetic Optimization for Antimitogram-Based Clinical Trials
Authors: Haviari Skerdi , You Benoît , Tod Michel
Published: March 2023

Pseudocode for statistical computations.
Figures S4 S5 S6 from In Silico Evaluation of Pharmacokinetic Optimization for Antimitogram-Based Clinical Trials
Authors: Haviari Skerdi , You Benoît , Tod Michel
Published: March 2023

Figures S4, S5 and S6, in that order : survival and power for (respectively) low, medium and high PK variability.
Fig. S5 from Reciprocal Regulation of DUSP9 and DUSP16 Expression by HIF1 Controls ERK and p38 MAP Kinase Activity and Mediates Chemotherapy-Induced Breast Cancer Stem Cell Enrichment
Authors: Lu Haiquan , Tran Linh , Park Youngrok , Chen Ivan , Lan Jie , Xie Yangyiran , Semenza Gregg L.
Published: March 2023

p38 MAPK regulates stability of pluripotency factor mRNAs.
Figure S8 from In Silico Evaluation of Pharmacokinetic Optimization for Antimitogram-Based Clinical Trials
Authors: Haviari Skerdi , You Benoît , Tod Michel
Published: March 2023

Post-hoc sensitivity analyses.
Figure S7 from In Silico Evaluation of Pharmacokinetic Optimization for Antimitogram-Based Clinical Trials
Authors: Haviari Skerdi , You Benoît , Tod Michel
Published: March 2023

Pre-planned sensitivity analyses.
Figure S2 from In Silico Evaluation of Pharmacokinetic Optimization for Antimitogram-Based Clinical Trials
Authors: Haviari Skerdi , You Benoît , Tod Michel
Published: March 2023

Model behavior during the first four cycles in the PKO and NO arms.
Figure S1 from In Silico Evaluation of Pharmacokinetic Optimization for Antimitogram-Based Clinical Trials
Authors: Haviari Skerdi , You Benoît , Tod Michel
Published: March 2023

Detailed model equations
Supplementary Data from Solid Tumor–Induced Immune Regulation Alters the GvHD/GvT Paradigm after Allogenic Bone Marrow Transplantation
Authors: Dang Nana , Lin Yuan , Rutgeerts Omer , Sagaert Xavier , Billiau An D. , Waer Mark , Sprangers Ben
Published: March 2023

Figure S1. Treg cells accumulate at multiple organs in tumor-bearing mice. Figure S2. allo-BMT leads to aGVHD. Figure S3. Treg cells accumulate at multiple organs post-BMT. Figure S4. Efficiency of Treg depletion. Figure S5. Efficiency of thymectomy of B6 mice. Figure S6. T cell add-back abrogates the GVT effect of the TCD transplant. Figure S7. Macrophage loss abrogates the impact of TCD on GVT. Figure S8. M1 polarization disrupts Treg cells expansion.
Supplementary Data from LPA4-Mediated Vascular Network Formation Increases the Efficacy of Anti–PD-1 Therapy against Brain Tumors
Authors: Eino Daisuke , Tsukada Yohei , Naito Hisamichi , Kanemura Yonehiro , Iba Tomohiro , Wakabayashi Taku , Muramatsu Fumitaka , Kidoya Hiroyasu , Arita Hideyuki , Kagawa Naoki , Fujimoto Yasunori , Takara Kazuhiro , Kishima Haruhiko , Takakura Nobuyuki
Published: March 2023

Supplementary Figure 1. Coverage of pericyte and the basal membrane by LPA. Expression of LPA4 in several tumors. Supplementary Figure 2. Survival of wild-type and LPA4-KO mice harboring LLC brain tumors treated with or without LPA in the presence or absence of 5-FU. Supplementary Figure 3. Junctional protein expressioon in vascular endothelial cells by LPA. Supplementary Figure 4. LPA induces ICAM-1 expression but doesn't alter the expression of an HEV marker protein on endothelial cells Supplementary Figure 5. Investigation of LPA mediated VCAM-1 expression in MS-1 cells by using several inhibitors. Supplementary Figure 6. PD-L1 expression in GL261 brain tumors and LLC subcutaneous tumors. HE staining of the brain after anti-PD-1 antibody and LPA treatment.
Supplementary Figures 1-16 from Pyruvate Dehydrogenase PDH-E1β Controls Tumor Progression by Altering the Metabolic Status of Cancer Cells
Authors: Yonashiro Ryo , Eguchi Kayoko , Wake Masaki , Takeda Norihiko , Nakayama Koh
Published: March 2023

Supplementary Figure 1: Viability assay for the breast cancer cell lines pre-treated with normoxia or hypoxia. Supplementary Figure 2: Decrease of PDH-E1β expression in different cell types. Supplementary Figure 3: PDH-E1β expression increases upon HIF-1α depletion by siRNA. Supplementary Figure 4: Effect of HIF-1 knockdown on PDH-E1β expression in HeLa cells. Supplementary Figure 5: Effect of HIF-1 knockdown on PDH-E1β expression in MB231 cells. Supplementary Figure 6: Induction of transcriptional repressors in hypoxia. Supplementary Figure 7: Expression of PDH-E1α and PDH-E1β in PDH-E1α and PDH-E1β-KD MB231 cells. Supplementary Figure 8: Protein degradation of PDH-E1β is not mediated by proteasome or lysosome. Supplementary Figure 9: Depletion of mitochondria matrix proteases by siRNA. Supplementary Figure 10: Metabolic state of PDH-E1α and PDH-E1β-depleted MB231 and MCF7 cells. Supplementary Figure 11: Metabolic state of PDH-E1α and PDH-E1β-depleted MCF7 cells. Supplementary Figure 12: Depletion of PDH-E1α and PDH-E1β in tumors. Supplementary Figure 13: Expression of PDH-E1α and PDH-E1β in MCF7 cells ectopically expressing PDH-E1β (MCF7+E1β). Supplementary Figure 14: Formation of PDH complex in MCF7 cells ectopically expressing PDH-E1β (MCF7+E1β). Supplementary Figure 15: Tumor formation of breast cancer cells pre-treated with normoxia or hypoxia. Supplementary Figure 16: ChIP assay for the PDH-E1β promoter region in MCF7 cells.
Supplementary movie S2 from Phosphatase 1 Nuclear Targeting Subunit Mediates Recruitment and Function of Poly (ADP-Ribose) Polymerase 1 in DNA Repair
Authors: Wang Feifei , Zhu Songli , Fisher Laura A. , Wang Ling , Eurek Nicholas J. , Wahl James K. , Lan Li , Peng Aimin
Published: March 2023

Movie S2. The recruitment of GFP-PNUTS after laser microirradiation, in the presence of olaparib is shown in a 10 min period.
Supplementary movie S1 from Phosphatase 1 Nuclear Targeting Subunit Mediates Recruitment and Function of Poly (ADP-Ribose) Polymerase 1 in DNA Repair
Authors: Wang Feifei , Zhu Songli , Fisher Laura A. , Wang Ling , Eurek Nicholas J. , Wahl James K. , Lan Li , Peng Aimin
Published: March 2023

Movie S1. The recruitment of GFP-PNUTS after laser microirradiation is shown in a 10 min period.
Supplementary Tables from MetaLnc9 Facilitates Lung Cancer Metastasis via a PGK1-Activated AKT/mTOR Pathway
Authors: Yu Tao , Zhao Yingjun , Hu Zhixiang , Li Jing , Chu Dandan , Zhang Jiwei , Li Zhe , Chen Bing , Zhang Xiao , Pan Hongyu , Li Shengli , Lin Hechun , Liu Lei , Yan Mingxia , He Xianghuo , Yao Ming
Published: March 2023

Several tables contain the nucleotide sequences, antibodies information, LncRNA expression profiles, LncRNA screening, the correlation between MetaLnc9 and clinicopathological features, the mass spectrometric analysis results, RNA-seq analysis, KEGG and GSEA analysis.
Supplementary Figures S1-S9 from Phosphatase 1 Nuclear Targeting Subunit Mediates Recruitment and Function of Poly (ADP-Ribose) Polymerase 1 in DNA Repair
Authors: Wang Feifei , Zhu Songli , Fisher Laura A. , Wang Ling , Eurek Nicholas J. , Wahl James K. , Lan Li , Peng Aimin
Published: March 2023

Figure S1. PNUTS depletion causes endogenous DNA damage. Figure S2. PNUTS depletion leads to DNA damage hypersensitivity. Figure S3. The recruitment of PNUTS to DNA damage sites is dependent on PARP1. Figure S4. PNUTS is required for the efficient induction of PARylation after DNA damage. Figure S5. PNUTS binds the middle segment of PARP1, and promotes its recruitment to laser-induced DNA damage sites. Figure S6. PNUTS knockdown impairs the recruitment of GFP-PARP1 to laser-induced DNA damage sites. Figure S7. PNUTS knockdown disrupts the recruitment of PARP1 to laser-induced DNA damage sites. Figure S8. PNUTS targeting sensitizes SCC38 cells to PARP inhibition. Figure S9. PNUTS targeting sensitizes HeLa cells to PARP inhibition.
Supplementary Figures and Figure Legends from MetaLnc9 Facilitates Lung Cancer Metastasis via a PGK1-Activated AKT/mTOR Pathway
Authors: Yu Tao , Zhao Yingjun , Hu Zhixiang , Li Jing , Chu Dandan , Zhang Jiwei , Li Zhe , Chen Bing , Zhang Xiao , Pan Hongyu , Li Shengli , Lin Hechun , Liu Lei , Yan Mingxia , He Xianghuo , Yao Ming
Published: March 2023

Supplementary Figures and Figure legends that contain the information of the characteristics of MetaLnc9 in NSCLC, Non-coding RNA analysis, the efficiency for MetaLnc9 overexpression and Knockdown, the molecular mechanism of PGK1 and NONO.
Table S1 from Combined Mutation of Apc, Kras, and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer
Authors: Sakai Eri , Nakayama Mizuho , Oshima Hiroko , Kouyama Yuta , Niida Atsushi , Fujii Satoshi , Ochiai Atsushi , Nakayama Keiichi I. , Mimori Koshi , Suzuki Yutaka , Hong Chang Pyo , Ock Chan-Young , Kim Seong-Jin , Oshima Masanobu
Published: March 2023

Histological diagnosis of the primary tumors
Figure S4 from Combined Mutation of Apc, Kras, and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer
Authors: Sakai Eri , Nakayama Mizuho , Oshima Hiroko , Kouyama Yuta , Niida Atsushi , Fujii Satoshi , Ochiai Atsushi , Nakayama Keiichi I. , Mimori Koshi , Suzuki Yutaka , Hong Chang Pyo , Ock Chan-Young , Kim Seong-Jin , Oshima Masanobu
Published: March 2023

Villous-type morphology of intestinal tumors by AKF combination
Figure S1 from Combined Mutation of Apc, Kras, and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer
Authors: Sakai Eri , Nakayama Mizuho , Oshima Hiroko , Kouyama Yuta , Niida Atsushi , Fujii Satoshi , Ochiai Atsushi , Nakayama Keiichi I. , Mimori Koshi , Suzuki Yutaka , Hong Chang Pyo , Ock Chan-Young , Kim Seong-Jin , Oshima Masanobu
Published: March 2023

Genomic PCR results for confirmation of organoid genotypes
Table S1 from Licofelone Enhances the Efficacy of Paclitaxel in Ovarian Cancer by Reversing Drug Resistance and Tumor Stem-like Properties
Authors: Hirst Jeff , Pathak Harsh B. , Hyter Stephen , Pessetto Ziyan Y. , Ly Thuc , Graw Stefan , Koestler Devin C. , Krieg Adam J. , Roby Katherine F. , Godwin Andrew K.
Published: March 2023

Expression of ABC transporter genes in 2D and in 3D cultures.
Supplemental Figures from Licofelone Enhances the Efficacy of Paclitaxel in Ovarian Cancer by Reversing Drug Resistance and Tumor Stem-like Properties
Authors: Hirst Jeff , Pathak Harsh B. , Hyter Stephen , Pessetto Ziyan Y. , Ly Thuc , Graw Stefan , Koestler Devin C. , Krieg Adam J. , Roby Katherine F. , Godwin Andrew K.
Published: March 2023

This document contains supplemental figures 1-17. Figure legends corresponding to each SF are on the subsequent page. Supplemental Figure 1. MCTS formation across a panel of ovarian cancer cell lines. Supplemental Figure 2. The number of proliferating cells is universally reduced in ovarian cancer cells grown as spheroids. Supplemental Figure 3. HIO cell lines form small spheroids which lack stem-like properties. Supplemental Figure 4. JMJD1A protein expression is enhanced in ovarian cancer cells when grown in 3D. Supplemental Figure 5. Targeted therapies used in ovarian cancer clinical trials induce a variable pattern of expression of stem-like associated genes. Supplemental Figure 6. CellTiter-Glo measured cell viability and drug response in MCTS. Supplemental Figure 7. 3D drug screening in non-tumorigenic cell lines did not identify 3D Hits. Supplemental Figure 8. Secondary screening validated 3D hits across multiple cell lines. Supplemental Figure 9. Dosage response validation of a 2D hit and 2D and 3D hit. Supplemental Figure 10. Licofelone showed enhanced activity in paclitaxel resistant 2D cells. Supplemental Figure 11. Licofelone had more activity against ovarian cancer cell-derived MCTS than the COX-2 specific inhibitor celecoxib. Supplemental Figure 12. Combination index values show strong synergy between with paclitaxel following licofelone pretreatment. Supplemental Figure 13. Pretreatment of ovarian cancer cell-derived MCTS with paclitaxel synergistically enhances licofelone activity. Supplemental Figure 14. Combination of licofelone and paclitaxel leads to increases in apoptosis in ovarian cancer cell-derived MCTS. Supplemental Figure 15. Licofelone can also sensitize ovarian cancer cells grown as spheroids to carboplatin. Supplemental Figure 16. Licofelone treatment decreases mitochondrial metabolism in OVCAR8 spheroids. Supplemental Figure 17. Changes in Cell Proliferation in Tumor Cells Isolated from Recurrent PDX Ascites Fluid.
Supplementary Video S1 from TCIApathfinder: An R Client for the Cancer Imaging Archive REST API
Authors: Russell Pamela , Fountain Kelly , Wolverton Dulcy , Ghosh Debashis
Published: March 2023

Instructional video for TCIApathfinder
Table S2 from Expression of Adipocyte/Macrophage Fatty Acid–Binding Protein in Tumor-Associated Macrophages Promotes Breast Cancer Progression
Authors: Hao Jiaqing , Yan Fei , Zhang Yuwen , Triplett Ashley , Zhang Ying , Schultz Debra A. , Sun Yanwen , Zeng Jun , Silverstein Kevin A.T. , Zheng Qi , Bernlohr David A. , Cleary Margot P. , Egilmez Nejat K. , Sauter Edward , Liu Shujun , Suttles Jill , Li Bing
Published: March 2023

Table S2 analyzes the association of A-FABP levels with breast cancer survival using TCGA dataset.
Suppl Figure 5 from FSTL1 Promotes Metastasis and Chemoresistance in Esophageal Squamous Cell Carcinoma through NFκB–BMP Signaling Cross-talk
Authors: Lau Marco Chi-Chung , Ng Kai Yu , Wong Tin Lok , Tong Man , Lee Terence K. , Ming Xiao-Yan , Law Simon , Lee Nikki P. , Cheung Annie L. , Qin Yan-Ru , Chan Kwok Wah , Ning Wen , Guan Xin-Yuan , Ma Stephanie
Published: March 2023

Quantification of number of cells that migrated through a membrane, invaded through a Matrigel-coated membrane, formed spheroids or formed colonies in (A) KYSE150-Luc cells co-cultured with conditioned medium collected from EV or FSTL1 OE cells; or (B) KYSE150-Luc cells treated with control or recombinant FSTL1, in the presence or absence of C34.
Figure S3-S4 from Expression of Adipocyte/Macrophage Fatty Acid–Binding Protein in Tumor-Associated Macrophages Promotes Breast Cancer Progression
Authors: Hao Jiaqing , Yan Fei , Zhang Yuwen , Triplett Ashley , Zhang Ying , Schultz Debra A. , Sun Yanwen , Zeng Jun , Silverstein Kevin A.T. , Zheng Qi , Bernlohr David A. , Cleary Margot P. , Egilmez Nejat K. , Sauter Edward , Liu Shujun , Suttles Jill , Li Bing
Published: March 2023

Figure S3 shows A-FABP expression in TAM of human breast tissues. Figure S4 analyzes macrophage depletion in spleen of WT and A-FABP-/- mice.
Suppl Figure 2 from FSTL1 Promotes Metastasis and Chemoresistance in Esophageal Squamous Cell Carcinoma through NFκB–BMP Signaling Cross-talk
Authors: Lau Marco Chi-Chung , Ng Kai Yu , Wong Tin Lok , Tong Man , Lee Terence K. , Ming Xiao-Yan , Law Simon , Lee Nikki P. , Cheung Annie L. , Qin Yan-Ru , Chan Kwok Wah , Ning Wen , Guan Xin-Yuan , Ma Stephanie
Published: March 2023

Representative images and quantification of number of cells that migrated or invaded in EC109 cells with or without FSTL1 suppressed and KYSE150-Luc cells with or without FSTL1 overexpressed, in the presence of mitomycin C.
Supplemental table 1 from Nedd4-Binding Protein 1 and TNFAIP3-Interacting Protein 1 Control MHC-1 Display in Neuroblastoma
Authors: Spel Lotte , Nieuwenhuis Joppe , Haarsma Rianne , Stickel Elmer , Bleijerveld Onno B. , Altelaar Maarten , Boelens Jaap Jan , Brummelkamp Thijn R. , Nierkens Stefan , Boes Marianne
Published: March 2023

Basemean and fold change scores per indivudual gRNA used in the CRISPR screen resulting in a significant TRUE of FALSE hit in the screen.
Figure S1-S7 from Loss of XIST in Breast Cancer Activates MSN-c-Met and Reprograms Microglia via Exosomal miRNA to Promote Brain Metastasis
Authors: Xing Fei , Liu Yin , Wu Shih-Ying , Wu Kerui , Sharma Sambad , Mo Yin-Yuan , Feng Jiamei , Sanders Stephanie , Jin Guangxu , Singh Ravi , Vidi Pierre-Alexandre , Tyagi Abhishek , Chan Michael D. , Ruiz Jimmy , Debinski Waldemar , Pasche Boris C. , Lo Hui-Wen , Metheny-Barlow Linda J. , D'Agostino Ralph B , Watabe Kounosuke
Published: March 2023

The supplementary infomation containing Figure legends, seven supplemental figures and one supplemental table. Figure S1 XIST expression is preferentially correlated with brain metastasis in breast cancer. Figure S2 Knockout of XIST preferentially promotes brain metastases. Figure S3 Knockout of XIST enhances tumor growth and distant metastases. Figure S4 Knockdown of XIST promotes EMT and stemness. Figure S5 c-Met is regulated by X-chromosome gene, MSN. Figure S6 miR-503 promotes the conversion of M1 to M2 phenotype of microglia. Figure S7 Fludarabine selectively suppresses the growth of XISTlow cells. Table S1 reagent and resource.
Figure S6 from NFAT1-Mediated Regulation of NDEL1 Promotes Growth and Invasion of Glioma Stem-like Cells
Authors: Jiang Yang , Song Yifu , Wang Run , Hu Tianhao , Zhang Di , Wang Zixun , Tie Xinxin , Wang Minghao , Han Sheng
Published: March 2023

EGFR silencing does not affect NFAT1-induced growth and invasion in T98G-GSCs.
Figure S4 from Discovery of Human-Similar Gene Fusions in Canine Cancers
Authors: Ulvé Ronan , Rault Mélanie , Bahin Mathieu , Lagoutte Laetitia , Abadie Jérôme , De Brito Clotilde , Coindre Jean-Michel , Botherel Nadine , Rousseau Audrey , Wucher Valentin , Cadieu Edouard , Thieblemont Catherine , Hitte Christophe , Cornevin Laurence , Cabillic Florian , Bachelot Laura , Gilot David , Hennuy Benoit , Guillaudeux Thierry , Le Goff Arnaud , Derrien Thomas , Hédan Benoît , André Catherine
Published: March 2023

Alignment of the human and canine BRAF proteins.
Figure S2 from Discovery of Human-Similar Gene Fusions in Canine Cancers
Authors: Ulvé Ronan , Rault Mélanie , Bahin Mathieu , Lagoutte Laetitia , Abadie Jérôme , De Brito Clotilde , Coindre Jean-Michel , Botherel Nadine , Rousseau Audrey , Wucher Valentin , Cadieu Edouard , Thieblemont Catherine , Hitte Christophe , Cornevin Laurence , Cabillic Florian , Bachelot Laura , Gilot David , Hennuy Benoit , Guillaudeux Thierry , Le Goff Arnaud , Derrien Thomas , Hédan Benoît , André Catherine
Published: March 2023

Alignment of the human and canine PDGFB proteins.
Figure S3 from NFAT1-Mediated Regulation of NDEL1 Promotes Growth and Invasion of Glioma Stem-like Cells
Authors: Jiang Yang , Song Yifu , Wang Run , Hu Tianhao , Zhang Di , Wang Zixun , Tie Xinxin , Wang Minghao , Han Sheng
Published: March 2023

NDEL1 expression is correlated with malignant subtypes in gliomas.
Supplementary Data 5 from Inhibition of EphB4–Ephrin-B2 Signaling Reprograms the Tumor Immune Microenvironment in Head and Neck Cancers
Authors: Bhatia Shilpa , Oweida Ayman , Lennon Shelby , Darragh Laurel B. , Milner Dallin , Phan Andy V. , Mueller Adam C. , Van Court Benjamin , Raben David , Serkova Natalie J. , Wang Xiao-Jing , Jimeno Antonio , Clambey Eric T. , Pasquale Elena B. , Karam Sana D.
Published: March 2023

Systemic depletion of CD8+ T cells results in increased tumor growth in Ly2 tumors treated with TNYL-RAW-Fc (A). Confirmation of CD8+ T cell depletion by flow cytometry (B). Student's t-test or one-way ANOVA was used to calculate the significance of the differences between the groups.
Supplementary Data 4 from Inhibition of EphB4–Ephrin-B2 Signaling Reprograms the Tumor Immune Microenvironment in Head and Neck Cancers
Authors: Bhatia Shilpa , Oweida Ayman , Lennon Shelby , Darragh Laurel B. , Milner Dallin , Phan Andy V. , Mueller Adam C. , Van Court Benjamin , Raben David , Serkova Natalie J. , Wang Xiao-Jing , Jimeno Antonio , Clambey Eric T. , Pasquale Elena B. , Karam Sana D.
Published: March 2023

(A) ELISA assay measuring the concentration of TNYL-RAW-Fc protein in plasma 7 days after hydrodynamic injection of the TNYL-RAW-Fc plasmid. Data represent mean {plus minus} SD from measurements using different mice (n=2). (B) Inhibition of EphB4-ephrin-B2 signaling by TNYL-RAW-Fc does not affect immune cell populations in the circulation of Ly2 tumor-bearing mice.
Supplementary Data 3 from Inhibition of EphB4–Ephrin-B2 Signaling Reprograms the Tumor Immune Microenvironment in Head and Neck Cancers
Authors: Bhatia Shilpa , Oweida Ayman , Lennon Shelby , Darragh Laurel B. , Milner Dallin , Phan Andy V. , Mueller Adam C. , Van Court Benjamin , Raben David , Serkova Natalie J. , Wang Xiao-Jing , Jimeno Antonio , Clambey Eric T. , Pasquale Elena B. , Karam Sana D.
Published: March 2023

qPCR analysis shows elevated expression of EphB4 on intratumoral macrophages harvested from Ly2 tumors compared to ephrin-B2.
Supplemental Figure 2 from Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer
Authors: Brand Toni M. , Hartmann Stefan , Bhola Neil E. , Li Hua , Zeng Yan , O'Keefe Rachel A. , Ranall Max V. , Bandyopadhyay Sourav , Soucheray Margaret , Krogan Nevan J. , Kemp Carolyn , Duvvuri Umamaheswar , LaVallee Theresa , Johnson Daniel E. , Ozbun Michelle A. , Bauman Julie E. , Grandis Jennifer R.
Published: March 2023

Pan-phospho-RTK profiling identifies HER3 to be hyper-phosphorylated after BYL719 treatment in HPV(+) cell lines
Supplemental Figure 1 from Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer
Authors: Brand Toni M. , Hartmann Stefan , Bhola Neil E. , Li Hua , Zeng Yan , O'Keefe Rachel A. , Ranall Max V. , Bandyopadhyay Sourav , Soucheray Margaret , Krogan Nevan J. , Kemp Carolyn , Duvvuri Umamaheswar , LaVallee Theresa , Johnson Daniel E. , Ozbun Michelle A. , Bauman Julie E. , Grandis Jennifer R.
Published: March 2023

HPV(+) cell lines are less responsive to BKM120 and BEZ235 than HPV(-) cell lines
Supplementary Table 3 from Temozolomide Treatment Induces lncRNA MALAT1 in an NF-κB and p53 Codependent Manner in Glioblastoma
Authors: Voce David J. , Bernal Giovanna M. , Wu Longtao , Crawley Clayton D. , Zhang Wei , Mansour Nassir M. , Cahill Kirk E. , Szymura Szymon J. , Uppal Abhineet , Raleigh David R. , Spretz Ruben , Nunez Luis , Larsen Gustavo , Khodarev Nikolai N. , Weichselbaum Ralph R. , Yamini Bakhtiar
Published: March 2023

Genome-wide expression analysis of sh-p105 vs. sh-p105 with TMZ
Supplementary Table 2 from Temozolomide Treatment Induces lncRNA MALAT1 in an NF-κB and p53 Codependent Manner in Glioblastoma
Authors: Voce David J. , Bernal Giovanna M. , Wu Longtao , Crawley Clayton D. , Zhang Wei , Mansour Nassir M. , Cahill Kirk E. , Szymura Szymon J. , Uppal Abhineet , Raleigh David R. , Spretz Ruben , Nunez Luis , Larsen Gustavo , Khodarev Nikolai N. , Weichselbaum Ralph R. , Yamini Bakhtiar
Published: March 2023

Genome-wide expression analysis of sh-control vs. sh-control with TMZ
Supplementary Figures from Pharmacological Inhibition of PARP6 Triggers Multipolar Spindle Formation and Elicits Therapeutic Effects in Breast Cancer
Authors: Wang Zebin , Grosskurth Shaun E. , Cheung Tony , Petteruti Philip , Zhang Jingwen , Wang Xin , Wang Wenxian , Gharahdaghi Farzin , Wu Jiaquan , Su Nancy , Howard Ryan T. , Mayo Michele , Widzowski Dan , Scott David A. , Johannes Jeffrey W. , Lamb Michelle L. , Lawson Deborah , Dry Jonathan R. , Lyne Paul D. , Tate Edward W. , Zinda Michael , Mikule Keith , Fawell Stephen E. , Reimer Corinne , Chen Huawei
Published: March 2023

Supplemental Fig S1- S6
Supplementary Figures S1-S9 from KIT Suppresses BRAFV600E-Mutant Melanoma by Attenuating Oncogenic RAS/MAPK Signaling
Authors: Neiswender James V. , Kortum Robert L. , Bourque Caitlin , Kasheta Melissa , Zon Leonard I. , Morrison Deborah K. , Ceol Craig J.
Published: March 2023

This file contains Supplementary Figures S1-S9 with accompanying legends. Supplementary Fig. S1 examines the relationship between KIT expression and BRAFV600E mutations in TCGA human melanoma samples. Supplementary Fig. S2 shows the rescue of melanocytes in kit(lf)-mutant zebrafish by BRAFV600E. Supplementary Fig. S3 shows tumor onset for an additional kit loss-of-function allele as well as tumor invasion images representative of a mosaic analysis. Supplementary Fig. S4 portrays the levels of Mitfa and pAkt in zebrafish melanomas. Supplementary Fig. S5 shows RAF dimerization and signaling experiments performed with V-BRAFV600E stimulated by NRASQ61K. Supplementary Fig. S6 shows RAF dimerization and signaling experiments performed with V-BRAFWT stimulated by KIT and SCF. Supplemental Fig. S7 shows results of experiments overexpressing KIT in A375 and UACC257 human melanoma cells with accompanying growth and signaling changes. Supplementary Fig. S8 shows survival curves for TCGA patients with melanomas expressing high or low KIT. Lastly, Supplementary Fig. S9 displays a measurement of BRAFV600E levels in zebrafish melanomas overexpressing BRAFWT.
Figure S1-4, TABLES1, S2 from ATG5 Mediates a Positive Feedback Loop between Wnt Signaling and Autophagy in Melanoma
Authors: Ndoye Abibatou , Budina-Kolomets Anna , Kugel Curtis H. , Webster Marie R. , Kaur Amanpreet , Behera Reeti , Rebecca Vito W. , Li Ling , Brafford Patricia A. , Liu Qin , Gopal Y.N. Vashisht , Davies Michael A. , Mills Gordon B. , Xu Xiaowei , Wu Hong , Herlyn Meenhard , Nicastri Michael C. , Winkler Jeffrey D. , Soengas Maria S. , Amaravadi Ravi K. , Murphy Maureen E. , Weeraratna Ashani T.
Published: March 2023

Figure S1: Wnt5A expression correlates with high autophagy in melanoma. Figure S2: Wnt5A increases autophagy in melanoma Figure S3: ATG5 affects Wnt signaling in melanoma Figure S4: β-catenin increases the sensitivity of melanoma cells to autophagy inhibition Supplemental Figure Legends SUPPLEMENTAL TABLE 1: DENSITOMETRY FOR ALL WESTERNS Supplemental Table 2. Tissue microarrays (TMA) H scores
Table S5 from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

Cell surface genes as candidate drug targets.
Table S4 from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

Drug target disease associations for curated drug associations.
Table S3 from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

Analysis of targets of drugs in clinical use and in clinical trials.
Table S2 from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

Summary of data
Table S1 from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

Annotation table
Supplementary Material 1 from Cross-Talk between Receptor Tyrosine Kinases AXL and ERBB3 Regulates Invadopodia Formation in Melanoma Cells
Authors: Revach Or-Yam , Sandler Oded , Samuels Yardena , Geiger Benjamin
Published: March 2023

A list of primers and siRNA sequences utilized in the study.
Figure S1-S5, Table S1 from Cross-Talk between Receptor Tyrosine Kinases AXL and ERBB3 Regulates Invadopodia Formation in Melanoma Cells
Authors: Revach Or-Yam , Sandler Oded , Samuels Yardena , Geiger Benjamin
Published: March 2023

In the file an additional information on the screen workflow and characterization of the effects of the genes that were found in the screen on invadopodia formation. Further there is Supplementary Table 1 (screen results for 63T cells). In addition, there are supplementary experiments supporting the role of AXL as a regulator of invadopodia in melanoma, as well as breast cancer cells.
Supplementary Materials, Methods and Figures from MCT1 Inhibitor AZD3965 Increases Mitochondrial Metabolism, Facilitating Combination Therapy and Noninvasive Magnetic Resonance Spectroscopy
Authors: Beloueche-Babari Mounia , Wantuch Slawomir , Casals Galobart Teresa , Koniordou Markella , Parkes Harold G. , Arunan Vaitha , Chung Yuen-Li , Eykyn Thomas R. , Smith Paul D. , Leach Martin O.
Published: March 2023

This file contains Supplementary Materials, Methods and Figures relating to the manuscript as follows: Supplementary Materials: Antibodies for western blotting, Supplementary Methods: LDH activity assay, ATP measurements, confocal microscopy, histopathology analysis of tumors, high resolution NMR data acquisition and processing. Supplementary Figures S1-S7: Figure S1 shows time series spectra of changes in hyperpolarized 13C-lactate signal over time following addition of hyperpolarized 13C-pyruvate in control and AZD3965-treated Raji human lymphoma cells. Figure S2 shows that AZD3965 has no effect on LDH activity in Raji cells. Figure S3 shows confirmation of increased ATP levels with AZD3965 treatment in Raji and Hut78 human lymphoma cells as shown by a bioluminescent assay. Figure S4 shows that AZD3965 treatment has no effect on functioning mitochondrial density as revealed by confocal microscopy images of Mito Tracker Red staining n Raji cells. Figure S5 shows increased potency of AZD3965 (cell counts and % cell death) following co-treatment with the mitochondrial complex I inhibitor metformin in Kelly and IMR-32 human neuroblastoma cells (harbouring different levels of MCT4 expression) that is associated with increased mitochondrial metabolism (at least in Kelly cells). Figure S6 shows increased potency of AZD3965 (cell counts and % cell death) in Hut78 human lymphoma cells following co-treatment with either metformin or the mitochondrial pyruvate carrier UK5099. Figure S7 shows histopathology data of tumor necrosis and perfusion indicating that these parameters were comparable in the two tumor size groups used in the in vivo spectroscopy and growth inhibition experiments.
Table S4 from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

Differentially Expressed miRNAs in Ceritinib Resistant Cells
Supplementary Data from Activation of MAPK Signaling by CXCR7 Leads to Enzalutamide Resistance in Prostate Cancer
Authors: Li Shangze , Fong Ka-wing , Gritsina Galina , Zhang Ali , Zhao Jonathan C. , Kim Jung , Sharp Adam , Yuan Wei , Aversa Caterina , Yang Ximing J. , Nelson Peter S. , Feng Felix Y. , Chinnaiyan Arul M. , de Bono Johann S. , Morrissey Colm , Rettig Matthew B. , Yu Jindan
Published: March 2023

Supplementary Figure 1. Generation of Enz-resistant prostate cancer cell lines. Supplementary Figure 2. AR directly represses CXCR7 gene expression. Supplementary Figure 3. CXCR7 expression is required for C4-2B Enz-resistant prostate cancer cell survival and invasiveness. Supplementary Figure 4. CXCR7 activates MAPK pathway independently of CXCR4 and CXCL12. Supplementary Figure 5. ARRB2 expression is required for Enz-resistant prostate cancer cell growth and invasion. Supplementary Figure 6. CXCR7 is upregulated in metastatic prostate cancer. Supplementary Figure 7. MEK inhibitor trametinib suppresses Enz-resistant prostate cancer growth in vitro and in vivo. Supplementary Table S1: Oligonucleotides that were utilized in this study.
Table S2 from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

Gene set enrichment analysis of previously published EMT gene signatures in LR cells compared with parental cells
Supplementary Table S2 from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Table S2 provides lists of TE UP genes that are WNT pathway components, TE UP genes and TE UP WNT pathway components with the (CGG)4 motif, and TE UP WNT pathway components with the 6-nt polypurine sequences at the 5' UTR.
Supplementary figures S7, S8, S9, S10, S11, S12 from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

Supplementary Figure S7. Supplementary Figure S8. Transfection efficiency of miR-34a and miR-449a mimics and inhibitors in cell lines, related to Fig. 3. Supplementary Figure S9. The effects of miR-34a and miR-449a inhibitors on the viability of parental H3122 cells. Supplementary Figure S10. Genes with H3K27ac gain or loss in their promoters induced by the panobinostat treatment, related to Fig. 4. Supplementary Figure S11. H3122 and H3122-LR cells treated with ceritinib alone (1 Ã,ÂµM), panobinostat alone (100 nM), or the combination, related to Fig. 5. Supplementary Figure S12.
Supplementary figure legends from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

Supplementary figure legends S1 to S12
Supplementary Figure S4 from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Figure S4 shows validation of TE UP and TE DOWN genes with polysome analysis.
Supplemental figure S1, S2, S3, S4, S5, S6 from Enhancer Remodeling and MicroRNA Alterations Are Associated with Acquired Resistance to ALK Inhibitors
Authors: Yun Mi Ran , Lim Sun Min , Kim Seon-Kyu , Choi Hun Mi , Pyo Kyoung-Ho , Kim Seong Keun , Lee Ji Min , Lee You Won , Choi Jae Woo , Kim Hye Ryun , Hong Min Hee , Haam Keeok , Huh Nanhyung , Kim Jong-Hwan , Kim Yong Sung , Shim Hyo Sup , Soo Ross Andrew , Shih Jin-Yuan , Yang James Chih-Hsin , Kim Mirang , Cho Byoung Chul
Published: March 2023

Supplementary Figure S1. Viability of H3122-LR and H2228-LR cells Supplementary Figure S2. Gene set enrichment analysis and western blot Supplementary Figure S3. Effects of AXL inhibition on EMT gene expression in LR cells, related to Fig. 1E. Supplementary Figure S4. Mice with established H3122-derived tumors were treated with four doses (50, 75, 87.5, or 100 mg/kg) of ceritinib to derive ceritinib-resistant tumors Supplementary Figure S5. Enhancer remodeling during ceritinib resistance, related to Fig. 2. Supplementary Figure S6. Genes with H3K27ac loss or gain in their promoters during ceritinib resistance, related to Fig.2.
Supplementary Figure S3 from FGFR1-Activated Translation of WNT Pathway Components with Structured 5′ UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation
Authors: Nguyen Tuan M. , Kabotyanski Elena B. , Dou Yongchao , Reineke Lucas C. , Zhang Peng , Zhang Xiang H.-F. , Malovannaya Anna , Jung Sung Yun , Mo Qianxing , Roarty Kevin P. , Chen Yiwen , Zhang Bing , Neilson Joel R. , Lloyd Richard E. , Perou Charles M. , Ellis Matthew J. , Rosen Jeffrey M.
Published: March 2023

Supplementary Figure S3 shows comprehensive multi-omics correlation analysis and assessment of the magnitude of improvement in inter-omic correlations as the cells switched from a steady state to a dynamic state induced by iFGFR1 activation.
Supplementary Figure 8 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S8
Supplementary Figure 7 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S7
Supplementary Figure 6 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S6
Supplementary Figure 5 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S5
Supplementary Figure 4 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S4
Supplemental Materials and Methods from An HK2 Antisense Oligonucleotide Induces Synthetic Lethality in HK1−HK2+ Multiple Myeloma
Authors: Xu Shili , Zhou Tianyuan , Doh Hanna M. , Trinh K Ryan , Catapang Art , Lee Jason T. , Braas Daniel , Bayley Nicholas A. , Yamada Reiko E. , Vasuthasawat Alex , Sasine Joshua P. , Timmerman John M. , Larson Sarah M. , Kim Youngsoo , MacLeod A. Robert , Morrison Sherie L. , Herschman Harvey R.
Published: March 2023

This file contains supplemental materials and methods used in the study.
Supplementary Figure 1 from Pomalidomide Inhibits PD-L1 Induction to Promote Antitumor Immunity
Authors: Fujiwara Yuki , Sun Yi , Torphy Robert J. , He Jiadai , Yanaga Katsuhiko , Edil Barish H. , Schulick Richard D. , Zhu Yuwen
Published: March 2023

Figure S1
Supplementary Figures S1 to S7 from Peli1 Modulates the Subcellular Localization and Activity of Mdmx
Authors: Li Dawei , Tavana Omid , Sun Shao-Cong , Gu Wei
Published: March 2023

These extra data provide additional evidence indicating the crucial role of Peli1 in modulating the activities of Mdmx and p53.
Compiled supplemental data from Radiotherapy and CD40 Activation Separately Augment Immunity to Checkpoint Blockade in Cancer
Authors: Rech Andrew J. , Dada Hannah , Kotzin Jonathan J. , Henao-Mejia Jorge , Minn Andy J. , Twyman-Saint Victor Christina , Vonderheide Robert H.
Published: March 2023

Supplemental Methods: Mouse strains and flow cytometry antibodies Supplemental Figure 1: Individual tumor kinetics of the unirradiated tumor in the PDA model. Tumor kinetics (mean and individual) of the irradiated tumor and survival in the B16-F10 melanoma model. Supplemental Figure 2: Individual tumor kinetics of the unirradiated tumor in antibody depleted mice (Cd4, CD8 and Ly6c) and knockout mice (Morrbid, Batf3, IFN gamma, CD40.) Mean tumor kinetics of the unirradiated tumor and survival in uMT and B220 knockout mice. Supplemental Figure 3: Mean tumor kinetics of the unirradiated tumor and survival in antibody depleted mice (IFNAR) and knockout mice (MyD88, TLR4, IFNAR, Sting.) Supplemental Figure 4: Flow cytometry plots for the top RF variables for the effect of RT Supplemental Figure 5: As for Supplemental figure 4, but for CD40 Supplemental Figure 6: As for supplemental Figure 4, but for the peak response Supplemental Figure 7: Heat map of the RF variables that predict response in irradiated and unirradiated tumors at 24 and 72 hours. Supplemental Figure 8: Histological samples of CD8 T cell infiltrate and SMA expression. Supplemental Figure 9: Graphical representation
Data Supplement from Macrophage-Derived Granulin Drives Resistance to Immune Checkpoint Inhibition in Metastatic Pancreatic Cancer
Authors: Quaranta Valeria , Rainer Carolyn , Nielsen Sebastian R. , Raymant Meirion L. , Ahmed Muhammad S. , Engle Dannielle D. , Taylor Arthur , Murray Trish , Campbell Fiona , Palmer Daniel H. , Tuveson David A. , Mielgo Ainhoa , Schmid Michael C.
Published: March 2023

Files in this Data Supplement: - Supplementary Figures. Figure S1: Loss of CD8+ T cell numbers during metastatic progression in PDAC patients and genetically engineered mouse model of pancreatic cancer. Figure S2: Colony stimulating factor 1 (CSF-1) is expressed by disseminated PDAC cells, and its cognate receptor CSF-1R is expressed by metastasis associated macrophages. Figure S3: Pharmacological blockade of CSF-1R using BLZ945 reprograms MAMs, restores T cell infiltration, and reduces metastasis. Figure S4: CSF-1 inhibition reduces desmoplasia, enhances CD8+ T cell infiltration and sensitizes metastatic PDAC to αPD-1 treatment. Figure S5: Administration of Digoxin, a transcriptional inhibitor of HIF-1α, promotes M1-like MAM reprogramming and reduces Granulin level in vivo. Figure S6: αPD-1 therapy dramatically reduces metastatic tumor burden in the absence of granulin, an effect which depends on a high abundance of immune stimulatory MAMs. Figure S7: Reduction in liver fibrosis improves CD8+ T cell infiltration and enhances αPD-1 therapy in metastatic pancreatic cancer. Figure S8: Macrophage-derived granulin drives resistance to immune checkpoint inhibition in metastatic pancreatic cancer.
Supplemental Figures from Demethylation-Induced Overexpression of Shc3 Drives c-Raf–Independent Activation of MEK/ERK in HCC
Authors: Liu Yun , Zhang Xinran , Yang Baicai , Zhuang Hao , Guo Hua , Wei Wen , Li Yuan , Chen Ruibing , Li Yongmei , Zhang Ning
Published: March 2023

This file contains all Supplemental figures and Legends for Supplemental figures. Figure S1: Increased Shc3 expression is associated with HCC metastasis. Figure S2: Shc3 interacts with MVP. Figure S3: Shc3/MVP complex activates the MEK and ERK pathway. Figure S4: Shc3 promotes HCC proliferation and invasion in vitro. Figure S5: Shc3 induces EMT by interacting with MVP. Figure S6: MVP rescues Shc3-induced proliferation and migration. Figure S7: DNA methylation affects Shc3 transcription. Figure S8: Shc3 promotes tumor growth and intrahepatic metastasis in vivo. Figure S9: Shc3 promotes tumor growth and intrahepatic metastasis through MVP in vivo.
Figure S7 from Anti-CD137 Suppresses Tumor Growth by Blocking Reverse Signaling by CD137 Ligand
Authors: Kang Sang W. , Lee Sang C. , Park So H. , Kim Juyang , Kim Hyeon H. , Lee Hyeon-Woo , Seo Su K. , Kwon Byoung S. , Cho Hong R. , Kwon Byungsuk
Published: March 2023

A. Expression of CD137 in intratumoral microphages. Intratumoral macrophages were stained with FITC-conjugated anti-CD45, PE-conjugated anti-CD137, PercpCy5-conjugated anti-Gr-1, APC-conjugated anti-F4/80, and APCCy7-conjugated anti-CD11b antibodies. CD137 expression in CD45+Gr-1-CD11b+F4/80+ cells is shown by FACS histograms. Filled: isotype control; unfilled, CD137 staining. B. Expression of CD137 or CD137L in CT26 tumor cells isolated from tumor masses.
Tables S1-S3 from Lysyl Oxidase–like Protein LOXL2 Promotes Lung Metastasis of Breast Cancer
Authors: Salvador Fernando , Martin Alberto , López-Menéndez Celia , Moreno-Bueno Gema , Santos Vanesa , Vázquez-Naharro Alberto , Santamaría Patricia G. , Morales Saleta , Dubus Pierre R. , Muinelo-Romay Laura , López-López Rafael , Tung Jason C. , Weaver Valerie M. , Portillo Francisco , Cano Amparo
Published: March 2023

Primers used for genotyping (Table S1) and RT-PCR (Table S2), and list of antibodies (Table S3)
Table S4 from Lysyl Oxidase–like Protein LOXL2 Promotes Lung Metastasis of Breast Cancer
Authors: Salvador Fernando , Martin Alberto , López-Menéndez Celia , Moreno-Bueno Gema , Santos Vanesa , Vázquez-Naharro Alberto , Santamaría Patricia G. , Morales Saleta , Dubus Pierre R. , Muinelo-Romay Laura , López-López Rafael , Tung Jason C. , Weaver Valerie M. , Portillo Francisco , Cano Amparo
Published: March 2023

E-cadherin expression in PyMT tumors with deleted (KO) and overexpressed Loxl2
Figure S6 from Anti-CD137 Suppresses Tumor Growth by Blocking Reverse Signaling by CD137 Ligand
Authors: Kang Sang W. , Lee Sang C. , Park So H. , Kim Juyang , Kim Hyeon H. , Lee Hyeon-Woo , Seo Su K. , Kwon Byoung S. , Cho Hong R. , Kwon Byungsuk
Published: March 2023

Figure S6. Depletion of NK cells does not affect tumor growth, intratumoral macrophage differentiation and generation of Tc1 cells within tumors.
Figure S5 from Anti-CD137 Suppresses Tumor Growth by Blocking Reverse Signaling by CD137 Ligand
Authors: Kang Sang W. , Lee Sang C. , Park So H. , Kim Juyang , Kim Hyeon H. , Lee Hyeon-Woo , Seo Su K. , Kwon Byoung S. , Cho Hong R. , Kwon Byungsuk
Published: March 2023

Figure S5. CD137L-/- and anti-CD137L-injected mice show lower antitumor immunity than CD137-/- or anti-CD137-injected mice.
Figures S6 & S7 from Lysyl Oxidase–like Protein LOXL2 Promotes Lung Metastasis of Breast Cancer
Authors: Salvador Fernando , Martin Alberto , López-Menéndez Celia , Moreno-Bueno Gema , Santos Vanesa , Vázquez-Naharro Alberto , Santamaría Patricia G. , Morales Saleta , Dubus Pierre R. , Muinelo-Romay Laura , López-López Rafael , Tung Jason C. , Weaver Valerie M. , Portillo Francisco , Cano Amparo
Published: March 2023

Collagen organization in metastatic lungs (Fig. S6) and Tenascin-C and fibronectin expression in primary tumors and lungs from PyMT mice with deregulated Loxl2
Figure S3 from Anti-CD137 Suppresses Tumor Growth by Blocking Reverse Signaling by CD137 Ligand
Authors: Kang Sang W. , Lee Sang C. , Park So H. , Kim Juyang , Kim Hyeon H. , Lee Hyeon-Woo , Seo Su K. , Kwon Byoung S. , Cho Hong R. , Kwon Byungsuk
Published: March 2023

Figure S3. Increase in intratumoral CD103+ DCs and Tc1 cells in CD137-/- and anti-CD137-injected mice challenged with Renca tumor cells.
Figure S2 from Anti-CD137 Suppresses Tumor Growth by Blocking Reverse Signaling by CD137 Ligand
Authors: Kang Sang W. , Lee Sang C. , Park So H. , Kim Juyang , Kim Hyeon H. , Lee Hyeon-Woo , Seo Su K. , Kwon Byoung S. , Cho Hong R. , Kwon Byungsuk
Published: March 2023

Figure S2. CD137-/- and anti-CD137-injected mice show enhanced antitumor immunity to EL-4 lymphoma and Renca renal carcinoma.