bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from EGFR and c-MET Cooperate to Enhance Resistance to PARP Inhibitors in Hepatocellular Carcinoma
Authors: Dong Qiongzhu , Du Yi , Li Hui , Liu Chunxiao , Wei Yongkun , Chen Mei-Kuang , Zhao Xixi , Chu Yu-Yi , Qiu Yufan , Qin Lunxiu , Yamaguchi Hirohito , Hung Mien-Chie
Published: April 2023

Supplementary Figures
Supplementary Data from MNK1/NODAL Signaling Promotes Invasive Progression of Breast Ductal Carcinoma In Situ
Authors: Guo Qianyu , Li Vivian Z. , Nichol Jessica N. , Huang Fan , Yang William , Preston Samuel E.J. , Talat Zahra , Lefrère Hanne , Yu Henry , Zhang Guihua , Basik Mark , Gonçalves Christophe , Zhan Yao , Plourde Dany , Su Jie , Torres Jose , Marques Maud , Habyan Sara Al , Bijian Krikor , Amant Frédéric , Witcher Michael , Behbod Fariba , McCaffrey Luke , Alaoui-Jamali Moulay , Giannakopoulos Nadia V. , Brackstone Muriel , Postovit Lynne-Marie , del Rincón Sonia V. , Miller Wilson H.
Published: April 2023

The supplementary material file provides extended data to further support that the MNK1/NODAL pathway plays a critical role in the DCIS to IDC transition, as well as information about the antibodies and statistical analyses used in this study.
Supplementary Figure 4 from Exosomes from Nischarin-Expressing Cells Reduce Breast Cancer Cell Motility and Tumor Growth
Authors: Maziveyi Mazvita , Dong Shengli , Baranwal Somesh , Mehrnezhad Ali , Rathinam Rajamani , Huckaba Thomas M. , Mercante Donald E. , Park Kidong , Alahari Suresh K.
Published: April 2023

Caspase 3 Staining of Mouse Tumors From Exosome Studies
Supplementary figure and legend from Spatiotemporal Regulation of Tumor Angiogenesis by Circulating Chromogranin A Cleavage and Neuropilin-1 Engagement
Authors: Dallatomasina Alice , Gasparri Anna Maria , Colombo Barbara , Sacchi Angelina , Bianco Mimma , Daniele Tiziana , Esposito Antonio , Pastorino Fabio , Ponzoni Mirco , Marcucci Fabrizio , Curnis Flavio , Corti Angelo
Published: April 2023

Sup Fig 1: Characterization of mAb 9D1 and its effects on tumor growth and NRP1/CgA1-373 interaction; Sup Fig 2: Effect of aprotinin treatment on tumor growth and CgA cleavage; Sup Fig 3: Anti-PGPQLR monoclonal and polyclonal antibodies inhibit tumor growth in various murine models; Sup Fig 4: Effect of anti-PQLR IgGs (highly specific for CgA1-373) and anti-QALRRG (C-terminal region of CgA1-439) on tumor growth; Sup Fig 5: Effect of anti-PGPQLR on WEHI-164 fibrosarcoma tumor vasculature; Sup Fig 6: Effect of CgA1-373 and FGF2 on HUVEC proliferation; Sup Fig 7: NRP1, but not NRP2, binds CgA1-373; the binding is blocked by anti-PGPQLR or anti-PQLR antibodies; Sup Fig 8: Effects of CgA1-373 and VEGF on VEGF-R2 phosphorylation at tyrosine (Y) residues 951, 996 or 1175 in HUVEC.
Supplementary Data from Absence of HIF1A Leads to Glycogen Accumulation and an Inflammatory Response That Enables Pancreatic Tumor Growth
Authors: Maruggi Marco , Layng Fabiana Izidro , Lemos Robert , Garcia Guillermina , James Brian P. , Sevilla Monica , Soldevilla Ferran , Baaten Bas J. , de Jong Petrus R. , Koh Mei Yee , Powis Garth
Published: April 2023

Supplementary Methods 1. Tumor Dissociation and Single Cell RNA Sequencing. Supplementary Figure S1. Sequences of shRNAs used to inhibit tumor HIF1A and GYS1. Supplementary Figure S2. Validation of HIF1A knockdown and inhibition of HIF1A target gene expression. Supplementary Figure S3. Pimonidazole staining for hypoxia and Oil Red O for lipid in shHIF1A tumors. Supplementary Figure S4. Characteristics of shGYS1 and shHIF1A cells and tumors. Supplementary Figure S5. IL-1B expression is maintained in second generation growth of shHIF1A xenografts. Supplementary Table 1. shHIF1A IL1B and NF-κB activation signatures Supplementary Table S2. Flow cytometry characterization of TIL in EV and shHIF1A tumors. Supplementary Table S3. Transcripts used to characterize mouse scRNAseq clusters cDC1 and cDC2.
Supplementary Data from Exosomes from Nischarin-Expressing Cells Reduce Breast Cancer Cell Motility and Tumor Growth
Authors: Maziveyi Mazvita , Dong Shengli , Baranwal Somesh , Mehrnezhad Ali , Rathinam Rajamani , Huckaba Thomas M. , Mercante Donald E. , Park Kidong , Alahari Suresh K.
Published: April 2023

Supplementary Figure legends
Supplementary Data from Investigating the Contribution of Collagen to the Tumor Biomechanical Phenotype with Noninvasive Magnetic Resonance Elastography
Authors: Li Jin , Zormpas-Petridis Konstantinos , Boult Jessica K.R. , Reeves Emma L. , Heindl Andreas , Vinci Maria , Lopes Filipa , Cummings Craig , Springer Caroline J. , Chesler Louis , Jones Chris , Bamber Jeffrey C. , Yuan Yinyin , Sinkus Ralph , Jamin Yann , Robinson Simon P.
Published: April 2023

Contains Supplementary Methods and Table S1 and S2 which summarize the origin, characteristics, provenance and culture conditions of the cell lines used in this study
Supplementary Information from Inhibitor of Differentiation-1 Sustains Mutant KRAS-Driven Progression, Maintenance, and Metastasis of Lung Adenocarcinoma via Regulation of a FOSL1 Network
Authors: Román Marta , López Inés , Guruceaga Elisabeth , Baraibar Iosune , Ecay Margarita , Collantes María , Nadal Ernest , Vallejo Adrián , Cadenas Silvia , Miguel Marta Echavarri-de , Jang Jae Hwi , Martin-Uriz Patxi San , Castro-Labrador Laura , Vilas-Zornoza Amaia , Lara-Astiaso David , Ponz-Sarvise Mariano , Rolfo Christian , Santos Edgardo S. , Raez Luis E. , Taverna Simona , Behrens Carmen , Weder Walter , Wistuba Ignacio I. , Vicent Silvestre , Gil-Bazo Ignacio
Published: April 2023

Supplementary tables and figure's headings
Supplementary Figure 4 from Inhibitor of Differentiation-1 Sustains Mutant KRAS-Driven Progression, Maintenance, and Metastasis of Lung Adenocarcinoma via Regulation of a FOSL1 Network
Authors: Román Marta , López Inés , Guruceaga Elisabeth , Baraibar Iosune , Ecay Margarita , Collantes María , Nadal Ernest , Vallejo Adrián , Cadenas Silvia , Miguel Marta Echavarri-de , Jang Jae Hwi , Martin-Uriz Patxi San , Castro-Labrador Laura , Vilas-Zornoza Amaia , Lara-Astiaso David , Ponz-Sarvise Mariano , Rolfo Christian , Santos Edgardo S. , Raez Luis E. , Taverna Simona , Behrens Carmen , Weder Walter , Wistuba Ignacio I. , Vicent Silvestre , Gil-Bazo Ignacio
Published: April 2023

Regulation of kinases by Id1 expression
Table S2 from Low-Dose IFNγ Induces Tumor Cell Stemness in Tumor Microenvironment of Non–Small Cell Lung Cancer
Authors: Song Mengjia , Ping Yu , Zhang Kai , Yang Li , Li Feng , Zhang Chaoqi , Cheng Shaoyan , Yue Dongli , Maimela Nomathamsanqa Resegofetse , Qu Jiao , Liu Shasha , Sun Ting , Li Zihai , Xia Jianchuan , Zhang Bin , Wang Liping , Zhang Yi
Published: April 2023

Multivariate Cox regression analysis of clinicopathologic factors for progression free survival in patients with NSCLC.
Table S1 from Low-Dose IFNγ Induces Tumor Cell Stemness in Tumor Microenvironment of Non–Small Cell Lung Cancer
Authors: Song Mengjia , Ping Yu , Zhang Kai , Yang Li , Li Feng , Zhang Chaoqi , Cheng Shaoyan , Yue Dongli , Maimela Nomathamsanqa Resegofetse , Qu Jiao , Liu Shasha , Sun Ting , Li Zihai , Xia Jianchuan , Zhang Bin , Wang Liping , Zhang Yi
Published: April 2023

Association of IFN-γ expression with clinicopathological features in patients with NSCLC.
Supplementary materials and methods from Low-Dose IFNγ Induces Tumor Cell Stemness in Tumor Microenvironment of Non–Small Cell Lung Cancer
Authors: Song Mengjia , Ping Yu , Zhang Kai , Yang Li , Li Feng , Zhang Chaoqi , Cheng Shaoyan , Yue Dongli , Maimela Nomathamsanqa Resegofetse , Qu Jiao , Liu Shasha , Sun Ting , Li Zihai , Xia Jianchuan , Zhang Bin , Wang Liping , Zhang Yi
Published: April 2023

Detailed information about transfected cell lines, sphere-formation assay, animal xenograft models, RNA extraction and quantitative RT-PCR, flow cytometry, IHC and IF staining, western blotting and TCGA database.
Supplementary File 2 from Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy
Authors: Manem Venkata SK. , Lambie Meghan , Smith Ian , Smirnov Petr , Kofia Victor , Freeman Mark , Koritzinsky Marianne , Abazeed Mohamed E. , Haibe-Kains Benjamin , Bratman Scott V.
Published: April 2023

Supplementary File 2 shows transcriptional pathways associated with alpha or beta from the linear-quadratic formalism.
Supplementary Data from Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy
Authors: Manem Venkata SK. , Lambie Meghan , Smith Ian , Smirnov Petr , Kofia Victor , Freeman Mark , Koritzinsky Marianne , Abazeed Mohamed E. , Haibe-Kains Benjamin , Bratman Scott V.
Published: April 2023

The Supplementary Data file contains 10 supplementary figures and 3 supplementary tables.
Fig S5 from Frizzled-7 Is Required for Wnt Signaling in Gastric Tumors with and Without Apc Mutations
Authors: Flanagan Dustin J. , Barker Nick , Costanzo Natasha S. Di , Mason Elizabeth A. , Gurney Austin , Meniel Valerie S. , Koushyar Sarah , Austin Chloe R. , Ernst Matthias , Pearson Helen B. , Boussioutas Alex , Clevers Hans , Phesse Toby J. , Vincan Elizabeth
Published: April 2023

Figure S5. Frequency of WNT pathway mutations in gastric cancer patients (TCGA).
Supplementary Data from Activation of the VEGFC/VEGFR3 Pathway Induces Tumor Immune Escape in Colorectal Cancer
Authors: Tacconi Carlotta , Ungaro Federica , Correale Carmen , Arena Vincenzo , Massimino Luca , Detmar Michael , Spinelli Antonino , Carvello Michele , Mazzone Massimiliano , Oliveira Ana I. , Rubbino Federica , Garlatti Valentina , Spanò Salvatore , Lugli Enrico , Colombo Federico S. , Malesci Alberto , Peyrin-Biroulet Laurent , Vetrano Stefania , Danese Silvio , D’Alessio Silvia
Published: April 2023

Supplementary Material and Methods
Supplementary Data Legends from AMPK Alpha-1 Intrinsically Regulates the Function and Differentiation of Tumor Myeloid-Derived Suppressor Cells
Authors: Trillo-Tinoco Jimena , Sierra Rosa A. , Mohamed Eslam , Cao Yu , de Mingo-Pulido Álvaro , Gilvary Danielle L. , Anadon Carmen M. , Costich Tara Lee , Wei Sheng , Flores Elsa R. , Ruffell Brian , Conejo-Garcia José R. , Rodriguez Paulo C.
Published: April 2023

This file contains the Supplementary legends describing the Supplementary Figures 1-5.
Figure S1 from Activation of the VEGFC/VEGFR3 Pathway Induces Tumor Immune Escape in Colorectal Cancer
Authors: Tacconi Carlotta , Ungaro Federica , Correale Carmen , Arena Vincenzo , Massimino Luca , Detmar Michael , Spinelli Antonino , Carvello Michele , Mazzone Massimiliano , Oliveira Ana I. , Rubbino Federica , Garlatti Valentina , Spanò Salvatore , Lugli Enrico , Colombo Federico S. , Malesci Alberto , Peyrin-Biroulet Laurent , Vetrano Stefania , Danese Silvio , D’Alessio Silvia
Published: April 2023

VEGFR3 is expressed on LVs and macrophages in non-metastatic colorectal cancer. Related to Figure 1
Table S1, Table S2 from miR-192-5p Silencing by Genetic Aberrations Is a Key Event in Hepatocellular Carcinomas with Cancer Stem Cell Features
Authors: Gu Yuanzhuo , Wei Xiyang , Sun Yulin , Gao Hongjun , Zheng Xin , Wong Linda L. , Jin Ling , Liu Niya , Hernandez Brenda , Peplowska Karolina , Zhao Xiaohang , Zhan Qi-Min , Feng Xin-Hua , Tang Zhao-You , Ji Junfang
Published: April 2023

Table S1-Summary of HCC clinical cohorts and their omics datasets. Table S2-Primers and oligoes used in this study
Fig S3. from miR-192-5p Silencing by Genetic Aberrations Is a Key Event in Hepatocellular Carcinomas with Cancer Stem Cell Features
Authors: Gu Yuanzhuo , Wei Xiyang , Sun Yulin , Gao Hongjun , Zheng Xin , Wong Linda L. , Jin Ling , Liu Niya , Hernandez Brenda , Peplowska Karolina , Zhao Xiaohang , Zhan Qi-Min , Feng Xin-Hua , Tang Zhao-You , Ji Junfang
Published: April 2023

Expression analysis of mature and precursor of miR-192-5p in HCC patients with different levels of multiple stem cell-related biomarkers, and miRNA sequence alignment analysis.
Supplementary Table S5 from EN1 Is a Transcriptional Dependency in Triple-Negative Breast Cancer Associated with Brain Metastasis
Authors: Peluffo Guillermo , Subedee Ashim , Harper Nicholas W. , Kingston Natalie , Jovanović Bojana , Flores Felipe , Stevens Laura E. , Beca Francisco , Trinh Anne , Chilamakuri Chandra Sekhar Reddy , Papachristou Evangelia K. , Murphy Katherine , Su Ying , Marusyk Andriy , D'Santos Clive S. , Rueda Oscar M. , Beck Andrew H. , Caldas Carlos , Carroll Jason S. , Polyak Kornelia
Published: April 2023

List of TLE3 and beta-catenin peaks in SUM149 and SUM159 cells.
Supplementary Table S2 from EN1 Is a Transcriptional Dependency in Triple-Negative Breast Cancer Associated with Brain Metastasis
Authors: Peluffo Guillermo , Subedee Ashim , Harper Nicholas W. , Kingston Natalie , Jovanović Bojana , Flores Felipe , Stevens Laura E. , Beca Francisco , Trinh Anne , Chilamakuri Chandra Sekhar Reddy , Papachristou Evangelia K. , Murphy Katherine , Su Ying , Marusyk Andriy , D'Santos Clive S. , Rueda Oscar M. , Beck Andrew H. , Caldas Carlos , Carroll Jason S. , Polyak Kornelia
Published: April 2023

EN1 targets in breast cancer cell lines.
Supplementary Table S1 from EN1 Is a Transcriptional Dependency in Triple-Negative Breast Cancer Associated with Brain Metastasis
Authors: Peluffo Guillermo , Subedee Ashim , Harper Nicholas W. , Kingston Natalie , Jovanović Bojana , Flores Felipe , Stevens Laura E. , Beca Francisco , Trinh Anne , Chilamakuri Chandra Sekhar Reddy , Papachristou Evangelia K. , Murphy Katherine , Su Ying , Marusyk Andriy , D'Santos Clive S. , Rueda Oscar M. , Beck Andrew H. , Caldas Carlos , Carroll Jason S. , Polyak Kornelia
Published: April 2023

List of genes differentially expressed and in SUM149 and SUM159 cells expressing shEN1.
Supplementary Data from Clonal Mutations Activate the NF-κB Pathway to Promote Recurrence of Nasopharyngeal Carcinoma
Authors: You Rui , Liu You-Ping , Lin De-Chen , Li Qing , Yu Tao , Zou Xiong , Lin Mei , Zhang Xiao-Long , He Gui-Ping , Yang Qi , Zhang Yi-Nuan , Xie Yu-Long , Jiang Rou , Wu Chen-Yan , Zhang Chao , Cui Cheng , Wang Jing-Qi , Wang Yue , Zhuang Ai-Hua , Guo Gui-Fang , Hua Yi-Jun , Sun Rui , Yun Jing-Ping , Zuo Zhi-Xiang , Liu Ze-Xian , Zhu Xiao-Feng , Kang Tie-Bang , Qian Chao-Nan , Mai Hai-Qiang , Sun Ying , Zeng Mu-Sheng , Feng Lin , Zeng Yi-Xin , Chen Ming-Yuan
Published: April 2023

Materials and Methods 1.Genomic DNA preparation and whole-genome or whole-exome sequencing. 2.Reads mapping and somatic genetic alteration detection. 3. PCR and Sanger sequencing. 4.Immunohistochemistry Supplementary Figure 1. GISTIC analysis of rNPC and pNPC samples. Supplementary Figure 2. Recurrent somatic mutations in rNPC and pNPC. Supplementary Figure 3. Western blot (WB) assay with the indicated antibodies in 293T cell line and SUNE2 cell line. Supplementary Figure 4. Immunohistochemical (IHC) staining to examine the expression of specific SMGs in 148 rNPC samples and 122 pNPC samples.
Supplementary Tables S1-S3 from Hepatic Endothelial Notch Activation Protects against Liver Metastasis by Regulating Endothelial-Tumor Cell Adhesion Independent of Angiocrine Signaling
Authors: Wohlfeil Sebastian A. , Häfele Verena , Dietsch Bianca , Schledzewski Kai , Winkler Manuel , Zierow Johanna , Leibing Thomas , Mohammadi Mona Malek , Heineke Joerg , Sticht Carsten , Olsavszky Victor , Koch Philipp-Sebastian , Géraud Cyrill , Goerdt Sergij
Published: April 2023

These Tables provide primer sequences for qRT-PCR, show original data of immunofluorescence quantifications and extend the information about metastasis of WT31 melanoma cells to other organs than the liver.
Supplementary Figures from Hepatic Endothelial Notch Activation Protects against Liver Metastasis by Regulating Endothelial-Tumor Cell Adhesion Independent of Angiocrine Signaling
Authors: Wohlfeil Sebastian A. , Häfele Verena , Dietsch Bianca , Schledzewski Kai , Winkler Manuel , Zierow Johanna , Leibing Thomas , Mohammadi Mona Malek , Heineke Joerg , Sticht Carsten , Olsavszky Victor , Koch Philipp-Sebastian , Géraud Cyrill , Goerdt Sergij
Published: April 2023

These Figures contain an expression analysis of Clec4g in the mouse, detailed characterization of Clec4g eYFP reporter mice, detailed analysis of nEGFP expression in livers of NICDOE-HEC mice, further characterization of NICDOE-HEC mice and additional immunofluorescence stainings as well as additional experimental data of tumor metastasis experiments.
Supplemental Figure 1 from Deletion of Atm in Tumor but not Endothelial Cells Improves Radiation Response in a Primary Mouse Model of Lung Adenocarcinoma
Authors: Torok Jordan A. , Oh Patrick , Castle Katherine D. , Reinsvold Michael , Ma Yan , Luo Lixia , Lee Chang-Lung , Kirsch David G.
Published: April 2023

Supplemental figure
Supplementary Figure Legends from Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance
Authors: Dalin Simona , Sullivan Mark R. , Lau Allison N. , Grauman-Boss Beatrice , Mueller Helen S. , Kreidl Emanuel , Fenoglio Silvia , Luengo Alba , Lees Jacqueline A. , Vander Heiden Matthew G. , Lauffenburger Douglas A. , Hemann Michael T.
Published: April 2023

Supplementary Figure Legends
Supplementary Appendix from miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells
Authors: Mukohyama Junko , Isobe Taichi , Hu Qingjiang , Hayashi Takanori , Watanabe Takashi , Maeda Masao , Yanagi Hisano , Qian Xin , Yamashita Kimihiro , Minami Hironobu , Mimori Koshi , Sahoo Debashis , Kakeji Yoshihiro , Suzuki Akira , Dalerba Piero , Shimono Yohei
Published: April 2023

Detailed description of materials and methods, together with Table S1 which shows a list of the oligonucleotide primers used.
Figure S3 from miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells
Authors: Mukohyama Junko , Isobe Taichi , Hu Qingjiang , Hayashi Takanori , Watanabe Takashi , Maeda Masao , Yanagi Hisano , Qian Xin , Yamashita Kimihiro , Minami Hironobu , Mimori Koshi , Sahoo Debashis , Kakeji Yoshihiro , Suzuki Akira , Dalerba Piero , Shimono Yohei
Published: April 2023

Clinical and pathological characteristics of the primary tumors and PDX tumors.
Figure S1 from Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance
Authors: Dalin Simona , Sullivan Mark R. , Lau Allison N. , Grauman-Boss Beatrice , Mueller Helen S. , Kreidl Emanuel , Fenoglio Silvia , Luengo Alba , Lees Jacqueline A. , Vander Heiden Matthew G. , Lauffenburger Douglas A. , Hemann Michael T.
Published: April 2023

Fig. S1. Conditioned media does not affect growth of PDAC cells except at 100% supplementation but does protect human PDAC cell lines regardless of P53 status. (A-E) Arbitrary units of resazurin fluorescence representing growth of PDAC cells after 3 days in culture are shown for cells cultured with the indicated supplement of media conditioned for the indicated number of days. Data show three biological replicates +/- SEM. ***, P {less than or equal to} 0.001, ns, not significant (one-way ANOVA with Bonferroni post-tests). (G) Viability of PDAC organoids after the indicated treatment with 0.05 uM gemcitabine, 20% CM, and/or 20 uM dC. Data show three biological replicates +/- SEM. Mean and SEM are indicated on the plot. One-way ANOVA with Bonferroni post-tests reveals no significant difference between gemcitabine treatment and gemcitabine + CM treatment, or gemcitabine + dC treatment. (F) Viability of the indicated cell lines at the indicated doses of gemcitabine with or without CM supplementation. Data show three biological replicates +/- SEM. *, P {less than or equal to} 0.05, **, P {less than or equal to} 0.01, ns, not significant (two-tailed one sample t-test).
Supplementary Figure 1 from Novel Third-Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance in Lung Cancer
Authors: Murtuza Ayesha , Bulbul Ajaz , Shen John Paul , Keshavarzian Parissa , Woodward Brian D. , Lopez-Diaz Fernando J. , Lippman Scott M. , Husain Hatim
Published: April 2023

EGFR Receptor Signaling and Bypass Pathways
Supplemental Table 1 from Targeting Glycolysis through Inhibition of Lactate Dehydrogenase Impairs Tumor Growth in Preclinical Models of Ewing Sarcoma
Authors: Yeung Choh , Gibson Anna E. , Issaq Sameer H. , Oshima Nobu , Baumgart Joshua T. , Edessa Leah D. , Rai Ganesha , Urban Daniel J. , Johnson Michelle S. , Benavides Gloria A. , Squadrito Giuseppe L. , Yohe Marielle E. , Lei Haiyan , Eldridge Sandy , Hamre John , Dowdy Tyrone , Ruiz-Rodado Victor , Lita Adrian , Mendoza Arnulfo , Shern Jack F. , Larion Mioara , Helman Lee J. , Stott Gordon M. , Krishna Murali C. , Hall Matthew D. , Darley-Usmar Victor , Neckers Leonard M. , Heske Christine M.
Published: April 2023

Table S1. List of all 94 Oncolead cell lines tested with corresponding IC50 values for NCI-737 and NCI-006.
Supplemental Figures 1-14 from Targeting Glycolysis through Inhibition of Lactate Dehydrogenase Impairs Tumor Growth in Preclinical Models of Ewing Sarcoma
Authors: Yeung Choh , Gibson Anna E. , Issaq Sameer H. , Oshima Nobu , Baumgart Joshua T. , Edessa Leah D. , Rai Ganesha , Urban Daniel J. , Johnson Michelle S. , Benavides Gloria A. , Squadrito Giuseppe L. , Yohe Marielle E. , Lei Haiyan , Eldridge Sandy , Hamre John , Dowdy Tyrone , Ruiz-Rodado Victor , Lita Adrian , Mendoza Arnulfo , Shern Jack F. , Larion Mioara , Helman Lee J. , Stott Gordon M. , Krishna Murali C. , Hall Matthew D. , Darley-Usmar Victor , Neckers Leonard M. , Heske Christine M.
Published: April 2023

Combined Supplementary Data file containing: Figure S1. Proliferation assays using NCI-737 and NCI-006 in an expanded panel of EWS cell lines. Figure S2. Effects of additional siRNA sequences against LDHA and LDHB in an expanded panel of EWS cell lines. Figure S3. Effects of additional siRNA sequences against EWS-FLI1 on LDHA and LDHB and additional ChIP-seq data. Figure S4. LDH expression, basal activity and in vitro early time course inhibition in EWS cell lines. Figure S5. Steady state levels of pyruvate and lactate and 13C-tracing experiments from 13C-U-glucose. Figure S6. Effects of NCI-737 and NCI-006 on ECAR measurements. Figure S7. Effects of NCI-737 on OCR measurements. Figure S8. Effects of NCI-737 on ECAR measurements of expanded panel of EWS cell lines. Figure S9. Results of oral dosing of LDH inhibitors in EWS xenograft models. Figure S10. Results of IV pilot studies of LDH inhibitors in EWS xenograft models. Figure S11. Additional growth rate and pharmacokinetic data for EWS xenograft models. Figure S12. Additional growth rate and necrosis data for EWS xenograft models. Figure S13. Depiction of of changes in lactate and pyruvate peaks and lactate/pyruvate ratio by hyperpolarized 13C-MR spectroscopy in EWS xenograft models. Figure S14. Measurements of toxicity in animals treated with NCI-737.
Supplementary Data from Phosphorylation of HSF1 by PIM2 Induces PD-L1 Expression and Promotes Tumor Growth in Breast Cancer
Authors: Yang Tingting , Ren Chune , Lu Chao , Qiao Pengyun , Han Xue , Wang Li , Wang Dan , Lv Shijun , Sun Yonghong , Yu Zhenhai
Published: April 2023

Supplementary Data. Supplementary Figures: SF1, MS spectra of representative HSF1 peptide; SF2, Validation of the anti-pThr120-HSF1 antibody by IHC; SF3, Cell proliferation in (T120D)-rescued shPIM2 MCF-7 cells; SF4, Combination of SMI-4a and KRIBB1 to treatment of breast cancer is efficacious in vivo; SF5, TCGA validates the association between PIM2/HSF1/PD-L1 in human clinical samples of breast cancer; Table S1-siRNA sequences used in our research; Table S2-Primary antibodies and inhibitors used in this study; Table S3- shRNA sequences used in our research; Table S4-The primers used for real-time PCR in our research; Table S5-The primers used for CHIP in our research; Table S6-Analysis of correlation between PIM2, pT120-HSF1 and PD-L1 protein levels and clinicopathological parameters of breast cancer patients.
Table S2 from Epidemiologic and Clinical Analysis of Cervical Cancer Using Data from the Population-Based Osaka Cancer Registry
Authors: Yagi Asami , Ueda Yutaka , Kakuda Mamoru , Tanaka Yusuke , Ikeda Sayaka , Matsuzaki Shinya , Kobayashi Eiji , Morishima Toshitaka , Miyashiro Isao , Fukui Keisuke , Ito Yuri , Nakayama Tomio , Kimura Tadashi
Published: April 2023

Difference of tumor stage of cervical cancer, by age group (1976-2012)
Table S1 from Epidemiologic and Clinical Analysis of Cervical Cancer Using Data from the Population-Based Osaka Cancer Registry
Authors: Yagi Asami , Ueda Yutaka , Kakuda Mamoru , Tanaka Yusuke , Ikeda Sayaka , Matsuzaki Shinya , Kobayashi Eiji , Morishima Toshitaka , Miyashiro Isao , Fukui Keisuke , Ito Yuri , Nakayama Tomio , Kimura Tadashi
Published: April 2023

Changes in number of cervical cancer cases, by treatment procedure
Supplementary Data from Pleiotropic Effects of PPARD Accelerate Colorectal Tumorigenesis, Progression, and Invasion
Authors: Liu Yi , Deguchi Yasunori , Tian Rui , Wei Daoyan , Wu Ling , Chen Weidong , Xu Weiguo , Xu Min , Liu Fuyao , Gao Shen , Jaoude Jonathan C. , Chrieki Sarah P. , Moussalli Micheline J. , Gagea Mihai , Morris Jeffrey , Broaddus Russell R. , Zuo Xiangsheng , Shureiqi Imad
Published: April 2023

This supplementary file includes additional methods details with tables list of antibodies and TaqMan probes.
Supplementary Data from Pleiotropic Effects of PPARD Accelerate Colorectal Tumorigenesis, Progression, and Invasion
Authors: Liu Yi , Deguchi Yasunori , Tian Rui , Wei Daoyan , Wu Ling , Chen Weidong , Xu Weiguo , Xu Min , Liu Fuyao , Gao Shen , Jaoude Jonathan C. , Chrieki Sarah P. , Moussalli Micheline J. , Gagea Mihai , Morris Jeffrey , Broaddus Russell R. , Zuo Xiangsheng , Shureiqi Imad
Published: April 2023

Supplementary Figures S1-S7 - This file includes supplementary figures S1-S7: Figure S1. PPARD increased active Î²-catenin and its target gene (e.g. c-Myc and cyclin D1) expression levels in mouse IECs and human HCT116 colorectal cancer cells by western blot and qRT-PCR. Figure S2. PPARD and its ligand GW501516 promoted intestinal tumorigenesis in multiple APC mutant mouse models, shown by intestinal photographs and tumor number counts. Figure S3. Western blot and IHCs showing that PPARD increased BMP7/TAK1/active Î²-catenin expression levels in mouse IECs. Figure S4. IHC microphotographs and score results showing active Î²-catenin expression levels in 41 human paired colorectal adenomas (Adenoma), CRC tumor centers (Tumor center), and cancer invasive fronts (Invasive front). Figure S5. Western blot and IHC results showing that PPARD upregulated AKT1 but not AKT2 to increase p-rpS6 levels in mouse IECs and human HCT116 colorectal cancer cells. Figure S6. Immunofluorescence staining of rRNA, IHC microphotographs and IHC score results of CDK1 showing rRNA expression levels in mouse intestinal tissues from PD and ApcÎ"580-PD mice and their corresponding control littermates, and nuclear CDK1 expression levels in 41 human paired colorectal adenomas (Adenoma), CRC tumor centers (Tumor center), and cancer invasive fronts (Invasive front). Figure S7. Multiple human public database analyses showing PPARD and BMP7 genetic alterations in colon cancer patients, and comparison of the survival probability for the colon cancer patients with low and high expression of BMP7.
Figure S1 from Epidemiologic and Clinical Analysis of Cervical Cancer Using Data from the Population-Based Osaka Cancer Registry
Authors: Yagi Asami , Ueda Yutaka , Kakuda Mamoru , Tanaka Yusuke , Ikeda Sayaka , Matsuzaki Shinya , Kobayashi Eiji , Morishima Toshitaka , Miyashiro Isao , Fukui Keisuke , Ito Yuri , Nakayama Tomio , Kimura Tadashi
Published: April 2023

10-years relative survival rate, by period and by stage (1976-2010, invasive cervical cancer)
Figure S from Precise Spatiotemporal Interruption of Regulatory T-cell–Mediated CD8+ T-cell Suppression Leads to Tumor Immunity
Authors: Zhou Xiaoyu , Zhao Shushu , He Yue , Geng Shuang , Shi Yan , Wang Bin
Published: April 2023

Supplementary data and legends
Supplementary Materials and Methods from The Pro-Oncogenic Adaptor CIN85 Acts as an Inhibitory Binding Partner of Hypoxia-Inducible Factor Prolyl Hydroxylase 2
Authors: Kozlova Nina , Mennerich Daniela , Samoylenko Anatoly , Dimova Elitsa Y. , Koivunen Peppi , Biterova Ekaterina , Richter Kati , Hassinen Antti , Kellokumpu Sakari , Manninen Aki , Miinalainen Ilkka , Glumoff Virpi , Ruddock Lloyd , Drobot Lyudmyla Borysivna , Kietzmann Thomas
Published: April 2023

Plasmids and site directed mutagenesis, GST-pull down, Fluorescence microscopy, CRISPR/Cas9-mediated EGLN1 gene editing, Lentivirus-mediated expression of sgRNAs and Cas9, Genomic DNA extraction and genotyping, RNA extraction and qRT-PCR, Scanning electron microscopy, Monolayer colony formation assay, Live Cell Imaging Assays Surface plasmon resonance (SPR)
Supplementary Table 3 from MEK Inhibition Modulates Cytokine Response to Mediate Therapeutic Efficacy in Lung Cancer
Authors: Xie Mengyu , Zheng Hong , Madan-Lala Ranjna , Dai Wenjie , Gimbrone Nicholas T. , Chen Zhihua , Kinose Fumi , Blackstone Sarah A. , Smalley Keiran S.M. , Cress W. Douglas , Haura Eric B. , Rix Uwe , Beg Amer A.
Published: April 2023

Table showing frequency distribution of cell cycle phases (G1, S, G2) from 3 biological replicates in indicated cell lines (A549, LKR, PC-9, HCC44, H23).
Supplementary Table 2 from MEK Inhibition Modulates Cytokine Response to Mediate Therapeutic Efficacy in Lung Cancer
Authors: Xie Mengyu , Zheng Hong , Madan-Lala Ranjna , Dai Wenjie , Gimbrone Nicholas T. , Chen Zhihua , Kinose Fumi , Blackstone Sarah A. , Smalley Keiran S.M. , Cress W. Douglas , Haura Eric B. , Rix Uwe , Beg Amer A.
Published: April 2023

Drug screening data used in Figure 2 are shown, including drug names, cell viability and expression levels of chemokines.
Supplementary Figures from MEK Inhibition Modulates Cytokine Response to Mediate Therapeutic Efficacy in Lung Cancer
Authors: Xie Mengyu , Zheng Hong , Madan-Lala Ranjna , Dai Wenjie , Gimbrone Nicholas T. , Chen Zhihua , Kinose Fumi , Blackstone Sarah A. , Smalley Keiran S.M. , Cress W. Douglas , Haura Eric B. , Rix Uwe , Beg Amer A.
Published: April 2023

Supplementary Figures for Xie et al, MEK inhibition modulates cytokine response to mediate therapeutic efficacy in lung cancer
Figure S1 - S14 from Super-Enhancer–Associated Long Noncoding RNA HCCL5 Is Activated by ZEB1 and Promotes the Malignancy of Hepatocellular Carcinoma
Authors: Peng Li , Jiang Binyuan , Yuan Xiaoqing , Qiu Yuntan , Peng Jiangyun , Huang Yongsheng , Zhang Chaoyang , Zhang Yin , Lin Zhaoyu , Li Jinsong , Yao Weicheng , Deng Weixi , Zhang Yaqin , Meng Meng , Pan Xi , Li Chunquan , Yin Dong , Bi Xinyu , Li Guancheng , Lin De-Chen
Published: April 2023

Supplementary Figure 1. Screening and Cloning of lncRNA HCCL5 in hepatocellular carcinoma. Supplementary Figure 2. Subcellular localization of HCCL5 in SMMC-7721 cells. Supplementary Figure 3. The mRNA expression of HCCL5 was measured across different HCC and nonmalignant cell lines. Supplementary Figure 4. The expression of HCCL5 was measured by qRT-PCR upon either over-expression or knockdown of HCCL5. Supplementary Figure 5. HCCL5 accelerated cell proliferation of HCC cells in vitro. Supplementary Figure 6. HCCL5 accelerated cell cycle in HCC cells. Supplementary Figure 7. HCCL5 overexpression had no effect on cell death of HCC cells. Supplementary Figure 8. HCCL5 interference had no effect on cell death of HCC cells. Supplementary Figure 9. HCCL5 deteriorated cell migration and invasion of HCC cells in vitro. Supplementary Figure 10. HCCL5 promotes xenogeneic growth while inhibits apoptosis of HCC cells in vivo. Supplementary Figure 11. The protein levels of EMT markers in HCC cells stably expressing HCCL5 overexpression or shRNA vectors. Supplementary Figure 12. Survival analysis of E-cadherin and Vimentin expression in TCGA HCC patients. Supplementary Figure 13. The protein level of Twist in HCC cells stably expressing HCCL5 shRNA vectors. Supplementary Figure 14. The luciferase activities of five constituent enhancers (E1-E5) within the super-enhancer of HCCL5 in 293T cells.
Table S3-4 from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

Mutational detail in EBV (S3) and host samples(S4). Full legend is provided in Supplementary methods.
Table S1 from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

A, detail information on all 1342 cancer samples used in this study. B, parts per million (P.P.M.) values for each cancer along with the number of reads that mapped to the EBV genome and the library size after removing low-quality reads and PCR duplicates. C, 56 EBV-integrated loci in the human genome. For each integration (rows), shown are the integration location, the nearest gene and its hg19 coordinates, the number of samples with the integration in each tissue type, and the coordinates of overlapping SEs from genesets shown in Fig. 1E. The total number of EBV+ samples analyzed in each tumor type is indicated in the header row. D, for each sample (rows), shown are the EBV integration location. E, expression (transcripts per million; T.P.M.) of all EBV genes (rows) in each sample (columns).
Figure S5-6 from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

Shown are information on host mutational pattern and host response networks to EBV infection. These are additional supporting information for Figure 5-6.
Figure S1-4 from Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host–Virus Interactions
Authors: Chakravorty Srishti , Yan Bingyu , Wang Chong , Wang Luopin , Quaid Joseph Taylor , Lin Chin Fang , Briggs Scott D. , Majumder Joydeb , Canaria D. Alejandro , Chauss Daniel , Chopra Gaurav , Olson Matthew R. , Zhao Bo , Afzali Behdad , Kazemian Majid
Published: April 2023

Shown are information related to EBV integration, EBV gene manipulation, and EBV mutational patterns. These are additional supporting information for Figure 1-4.
Supplementary Data from Randomly Distributed K14+ Breast Tumor Cells Polarize to the Leading Edge and Guide Collective Migration in Response to Chemical and Mechanical Environmental Cues
Authors: Hwang Priscilla Y. , Brenot Audrey , King Ashley C. , Longmore Gregory D. , George Steven C.
Published: April 2023

These are the movie legends and supplemental methods
Movie 3 from Randomly Distributed K14+ Breast Tumor Cells Polarize to the Leading Edge and Guide Collective Migration in Response to Chemical and Mechanical Environmental Cues
Authors: Hwang Priscilla Y. , Brenot Audrey , King Ashley C. , Longmore Gregory D. , George Steven C.
Published: April 2023

Movie demonstrating DDR2-/- cells migration
Table S1 from Anti–PD-L1 Treatment Results in Functional Remodeling of the Macrophage Compartment
Authors: Xiong Huizhong , Mittman Stephanie , Rodriguez Ryan , Moskalenko Marina , Pacheco-Sanchez Patricia , Yang Yagai , Nickles Dorothee , Cubas Rafael
Published: April 2023

Table S1
Figure S3 from Anti–PD-L1 Treatment Results in Functional Remodeling of the Macrophage Compartment
Authors: Xiong Huizhong , Mittman Stephanie , Rodriguez Ryan , Moskalenko Marina , Pacheco-Sanchez Patricia , Yang Yagai , Nickles Dorothee , Cubas Rafael
Published: April 2023

aPDL1 mediated anti-tumor activity is IFNγ dependent
Supplementary Data from RNF168-Mediated Ubiquitin Signaling Inhibits the Viability of BRCA1-Null Cancers
Authors: Krais John J. , Wang Yifan , Bernhardy Andrea J. , Clausen Emma , Miller Jessica A. , Cai Kathy Q. , Scott Clare L. , Johnson Neil
Published: April 2023

Supplemental figures 1-6. Figure S1. Cell line panel IRIF images; Figure S2. Assessment of RNF168 in tumors; Figure S3. BRCA1 add back rescues RAD51 foci but not RNF168 expression; Figure S4. Generation of dox-inducible GFP, ub-H2AX, and RNF168 expressing cells; Figure S5. RPA32 and RAD51 foci in RNF168-expressing cells; Figure S6. Effects of ectopic RNF8 on proliferation and IRIF
Figure S3 from EZH2 Inhibitor GSK126 Suppresses Antitumor Immunity by Driving Production of Myeloid-Derived Suppressor Cells
Authors: Huang Shuo , Wang Zhongyu , Zhou Jie , Huang Jiani , Zhou Li , Luo Jing , Wan Yisong Y. , Long Haixia , Zhu Bo
Published: April 2023

Effect of GSK126 on immune cells in the tumor
Supplementary Table S3 from Collagen Remodeling in the Hypoxic Tumor-Mesothelial Niche Promotes Ovarian Cancer Metastasis
Authors: Natarajan Suchitra , Foreman Kaitlyn M. , Soriano Michaela I. , Rossen Ninna S. , Shehade Hussein , Fregoso Daniel R. , Eggold Joshua T. , Krishnan Venkatesh , Dorigo Oliver , Krieg Adam J. , Heilshorn Sarah C. , Sinha Subarna , Fuh Katherine C. , Rankin Erinn B.
Published: April 2023

Supplementary Table S3 shows the list of primer sequences of forward and reverse human primer sets used for real time qPCR in the study. Suppl. to Materials and Methods
Supplementary Table 2 from Targeting Hippo-Dependent and Hippo-Independent YAP1 Signaling for the Treatment of Childhood Rhabdomyosarcoma
Authors: Slemmons Katherine K. , Yeung Choh , Baumgart Joshua T. , Juarez Jhazeel O. Martinez , McCalla Amy , Helman Lee J.
Published: April 2023

Ingenuity Pathway Analysis of RNAseq data.
Figure S4 from Oncogenic Properties of the Antisense lncRNA COMET in BRAF- and RET-Driven Papillary Thyroid Carcinomas
Authors: Esposito Roberta , Esposito Daniela , Pallante Pierlorenzo , Fusco Alfredo , Ciccodicola Alfredo , Costa Valerio
Published: April 2023

FOSL2 expression in papillary thyroid carcinoma
Figure S3 from Oncogenic Properties of the Antisense lncRNA COMET in BRAF- and RET-Driven Papillary Thyroid Carcinomas
Authors: Esposito Roberta , Esposito Daniela , Pallante Pierlorenzo , Fusco Alfredo , Ciccodicola Alfredo , Costa Valerio
Published: April 2023

COMET expression in TCGA data.
Figure S2 from Oncogenic Properties of the Antisense lncRNA COMET in BRAF- and RET-Driven Papillary Thyroid Carcinomas
Authors: Esposito Roberta , Esposito Daniela , Pallante Pierlorenzo , Fusco Alfredo , Ciccodicola Alfredo , Costa Valerio
Published: April 2023

Subtype-specific signature of protein coding genes in papillary thyroid carcinoma.
Supplementary Files from A Single-Step, High-Dose Selection Scheme Reveals Distinct Mechanisms of Acquired Resistance to Oncogenic Kinase Inhibition in Cancer Cells
Authors: Finn Kenneth J. , Martin Scott E. , Settleman Jeff
Published: April 2023

Full plasmid sequences and maps for BRAF expression constructs used in this study.
Supplementary Data 3 from A DNA Repair and Cell-Cycle Gene Expression Signature in Primary and Recurrent Glioblastoma: Prognostic Value and Clinical Implications
Authors: Gobin Matthieu , Nazarov Petr V. , Warta Rolf , Timmer Marco , Reifenberger Guido , Felsberg Joerg , Vallar Laurent , Chalmers Anthony J. , Herold-Mende Christel C. , Goldbrunner Roland , Niclou Simone P. , Van Dyck Eric
Published: April 2023

This document contains Supplementary Table S1, which provides the expression data pertaining to the 27-gene signature and relevant clinical data of the Heidelberg cohort.
Supplementary Data 2 from A DNA Repair and Cell-Cycle Gene Expression Signature in Primary and Recurrent Glioblastoma: Prognostic Value and Clinical Implications
Authors: Gobin Matthieu , Nazarov Petr V. , Warta Rolf , Timmer Marco , Reifenberger Guido , Felsberg Joerg , Vallar Laurent , Chalmers Anthony J. , Herold-Mende Christel C. , Goldbrunner Roland , Niclou Simone P. , Van Dyck Eric
Published: April 2023

This document contains Supplementary Figures S1-S6 as well as their Legends. Specifically, Fig. S1: characterization of the 52 gene signature; Fig. S2: Validation of the 27 DNA repair and cell cycle gene signature; Fig. S3: Analysis of the Murat cohort; Fig. S4: Analysis of the TCGA dataset; Fig. S5: Identification of differentially expressed genes and gene ontology analysis of the G1 and G3 groups; Fig. S6: DNA repair and cell-cycle-based strategies for personalized management of GBM".
Supplementary Data 1 from A DNA Repair and Cell-Cycle Gene Expression Signature in Primary and Recurrent Glioblastoma: Prognostic Value and Clinical Implications
Authors: Gobin Matthieu , Nazarov Petr V. , Warta Rolf , Timmer Marco , Reifenberger Guido , Felsberg Joerg , Vallar Laurent , Chalmers Anthony J. , Herold-Mende Christel C. , Goldbrunner Roland , Niclou Simone P. , Van Dyck Eric
Published: April 2023

This document details the preliminary differential gene expression analysis carried out using the Köln dataset
Supplementary Figure S6 from 4E-BP1 Is a Tumor Suppressor Protein Reactivated by mTOR Inhibition in Head and Neck Cancer
Authors: Wang Zhiyong , Feng Xiaodong , Molinolo Alfredo A. , Martin Daniel , Vitale-Cross Lynn , Nohata Nijiro , Ando Mizuo , Wahba Amy , Amornphimoltham Panomwat , Wu Xingyu , Gilardi Mara , Allevato Michael , Wu Victoria , Steffen Dana J. , Tofilon Philip , Sonenberg Nahum , Califano Joseph , Chen Qianming , Lippman Scott M. , Gutkind J. Silvio
Published: April 2023

Supplementary Figure S6 shows (A) Western blot analysis, (B) m7GTP pull down, (C) eIF4G co-IP analyzing the regulation of the translation initiation complex formation by mTOR inhibition; and D, densitometry analysis of western blots in Figure S6B.
Table S4 from Tumor-Derived Prostaglandin E2 Promotes p50 NF-κB-Dependent Differentiation of Monocytic MDSCs
Authors: Porta Chiara , Consonni Francesca Maria , Morlacchi Sara , Sangaletti Sabina , Bleve Augusto , Totaro Maria Grazia , Larghi Paola , Rimoldi Monica , Tripodo Claudio , Strauss Laura , Banfi Stefania , Storto Mariangela , Pressiani Tiziana , Rimassa Lorenza , Tartari Silvia , Ippolito Alessandro , Doni Andrea , Soldà Giulia , Duga Stefano , Piccolo Viviana , Ostuni Renato , Natoli Gioacchino , Bronte Vincenzo , Balzac Fiorella , Turco Emilia , Hirsch Emilio , Colombo Mario P. , Sica Antonio
Published: April 2023

Association of each induced gene to the nearest STAT1 peak according to the distance between the TSS (Transcription Start Site) of each gene and the summit of STAT1 induced peaks.
Supplementary Data from ZNF143-Mediated H3K9 Trimethylation Upregulates CDC6 by Activating MDIG in Hepatocellular Carcinoma
Authors: Zhang Lili , Huo Qi , Ge Chao , Zhao Fangyu , Zhou Qingqing , Chen Xiaoxia , Tian Hua , Chen Taoyang , Xie Haiyang , Cui Ying , Yao Ming , Li Hong , Li Jinjun
Published: April 2023

Supplementary Figures includes 8 supplementary figures and Legends. Supplementary Figure 1 shows the expression of ZNF143 in different cancers in HCCDB database. Supplementary Figure 2 mainly shows the relationship between ZNF143 and cell cycle transition in HCC cells. Supplementary Figure 3 shows the role of CDC6 in HCC cells. Supplementary Figure 4 mainly shows the enrichment of H3K4me3 or H3K27me3 in different promoter regions of CDC6 after overexpressing ZNF143. Supplementary Figure 5 shows the relationship between MDIG and cell cycle transition in HCC cells. Supplementary Figure 6 shows the role of CBX3, CBX5 on mediating the recruitment MDIG to CDC6 promoter. Supplementary Figure 7 shows MDIG is required for ZNF143 mediated HCC cell proliferation. Supplementary Figure 8 mainly shows the clinical significance of MDIG and CDC6 in HCC.
Supplementary Tables from Early Noninvasive Detection of Response to Targeted Therapy in Non–Small Cell Lung Cancer
Authors: Phallen Jillian , Leal Alessandro , Woodward Brian D. , Forde Patrick M. , Naidoo Jarushka , Marrone Kristen A. , Brahmer Julie R. , Fiksel Jacob , Medina Jamie E. , Cristiano Stephen , Palsgrove Doreen N. , Gocke Christopher D. , Bruhm Daniel C. , Keshavarzian Parissa , Adleff Vilmos , Weihe Elizabeth , Anagnostou Valsamo , Scharpf Robert B. , Velculescu Victor E. , Husain Hatim
Published: April 2023

The supplementary tables for "Early noninvasive detection of response to targeted therapy in non-small cell lung cancer" report clinical characteristics of patients analyzed (1), serial timepoints analyzed (2), genes analyzed (3), a summary of genomic analyses (4), somatic sequence alterations detected in cfDNA (5), somatic structural alterations detected in cfDNA (6), and blood cell proliferation alterations detected in cfDNA (7).
Supplementary Data from ZNF143-Mediated H3K9 Trimethylation Upregulates CDC6 by Activating MDIG in Hepatocellular Carcinoma
Authors: Zhang Lili , Huo Qi , Ge Chao , Zhao Fangyu , Zhou Qingqing , Chen Xiaoxia , Tian Hua , Chen Taoyang , Xie Haiyang , Cui Ying , Yao Ming , Li Hong , Li Jinjun
Published: April 2023

Supplementary Tables includes 4 supplementary tables. Supplementary table 1-3 shows primers and target sequences of siRNA/ shRNA used in this study. Supplementary table 4 shows upregulated or downregulated genes both in MHCC-97H and Huh7 cells after MDIG knockdown.
Supplementary Figure legends from Bcl-2 Is a Therapeutic Target for Hypodiploid B-Lineage Acute Lymphoblastic Leukemia
Authors: Diaz-Flores Ernesto , Comeaux Evan Q. , Kim Kailyn L. , Melnik Ella , Beckman Kyle , Davis Kara L. , Wu Kevin , Akutagawa Jon , Bridges Olga , Marino Roberta , Wohlfeil Margo , Braun Benjamin S. , Mullighan Charles G. , Loh Mignon L.
Published: April 2023

Legends for each supplementary figure
Figure S1-7 and Suppl. Tables from Bcl-2 Is a Therapeutic Target for Hypodiploid B-Lineage Acute Lymphoblastic Leukemia
Authors: Diaz-Flores Ernesto , Comeaux Evan Q. , Kim Kailyn L. , Melnik Ella , Beckman Kyle , Davis Kara L. , Wu Kevin , Akutagawa Jon , Bridges Olga , Marino Roberta , Wohlfeil Margo , Braun Benjamin S. , Mullighan Charles G. , Loh Mignon L.
Published: April 2023

Supplemental Figure 1. Protein and gene expression profiling of hypodiploid ALL. Supplemental Figure 2. Pairing biochemical characterization with viability/survival assays in hypodiploid B-ALL. Supplemental Figure 3. Primagraft samples used for ex vivo and in vivo experiments. Supplemental Figure 4. In vivo engraftment of hypodiploid ALL xenografts and response to ABT-199 during trial. Supplemental Figure 5. Clonal characterization of hypodiploid tumors at the beginning and end of trial. Supplemental Figure 6. Genome editing assays. Supplemental Figure 7. Genomic, karyotypic characterization and mechanistic experiments on Beck-1732 cells. Supplementary Tables of samples used in the in vivo studies.
Supplementary Tables from Epstein–Barr Virus miRNA BART2-5p Promotes Metastasis of Nasopharyngeal Carcinoma by Suppressing RND3
Authors: Jiang Chen , Li Lei , Xiang Yan-Qun , Lung Maria Li , Zeng Tingting , Lu Jiabin , Tsao Sai Wah , Zeng Mu-Sheng , Yun Jing-Ping , Kwong Dora L.W. , Guan Xin-Yuan
Published: April 2023

Supplementary tables include: Table.S1 Primers Table.S2 Clinical data of NPC patients Table.S3 Antibody list Table.S4 Multivariate analysis of Progression Free Time in nasopharyngeal carcinoma patients Table.S5 Association of expression level of Bart 2-5p with patients' clinical features in nasopharyngeal carcinoma Table.S6 Summary of metastatic status in spleen injection model
Supplementary Figure Legends from Epstein–Barr Virus miRNA BART2-5p Promotes Metastasis of Nasopharyngeal Carcinoma by Suppressing RND3
Authors: Jiang Chen , Li Lei , Xiang Yan-Qun , Lung Maria Li , Zeng Tingting , Lu Jiabin , Tsao Sai Wah , Zeng Mu-Sheng , Yun Jing-Ping , Kwong Dora L.W. , Guan Xin-Yuan
Published: April 2023

Supplementary Figure Legends