bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1 from Restraining Network Response to Targeted Cancer Therapies Improves Efficacy and Reduces Cellular Resistance
Authors: Das Tirtha K. , Esernio Jessica , Cagan Ross L.
Published: March 2023

Figure S1 shows fly drug screening assay and list of compounds screened
Figure S2 from Tissue Stiffness and Hypoxia Modulate the Integrin-Linked Kinase ILK to Control Breast Cancer Stem-like Cells
Authors: Pang Mei-Fong , Siedlik Michael J. , Han Siyang , Stallings-Mann Melody , Radisky Derek C. , Nelson Celeste M.
Published: March 2023

ILK is required for CSC development in human breast cancer cells. (A) qRT-PCR and immunoblotting analysis for ILK in MDA-MB-231cells stably expressing shRNA against ILK (shILK) or scrambled sequence control (shctrl). Transcript levels of (B) ITGB1, (C) ILK, (D) CD44, (E) Nanog, and (F) CD49f in MDA-MB-231-shctrl or MDA-MB-231-shILK cells cultured on soft or stiff substrata under normoxia or hypoxia. Phase contrast images and quantification of (G) secondary mammospheres and (H) colonies formed in soft agar by MDA-MB-231-shctrl and MDA-MB-231-shILK cells. Scale bars, 50 µm. Shown are mean (plus minus) s.e.m. *, P<0.05; **, P<0.01; ***, P<0.001.
Supplementary methods from Bidirectional Notch Signaling and Osteocyte-Derived Factors in the Bone Marrow Microenvironment Promote Tumor Cell Proliferation and Bone Destruction in Multiple Myeloma
Authors: Delgado-Calle Jesus , Anderson Judith , Cregor Meloney D. , Hiasa Masahiro , Chirgwin John M. , Carlesso Nadia , Yoneda Toshiyuki , Mohammad Khalid S. , Plotkin Lilian I. , Roodman G. David , Bellido Teresita
Published: March 2023

Supplementary methods
Supplementary figure legends from Bidirectional Notch Signaling and Osteocyte-Derived Factors in the Bone Marrow Microenvironment Promote Tumor Cell Proliferation and Bone Destruction in Multiple Myeloma
Authors: Delgado-Calle Jesus , Anderson Judith , Cregor Meloney D. , Hiasa Masahiro , Chirgwin John M. , Carlesso Nadia , Yoneda Toshiyuki , Mohammad Khalid S. , Plotkin Lilian I. , Roodman G. David , Bellido Teresita
Published: March 2023

Supplementary figure legends
Supplementary table 1 from Abscopal Effects of Radiotherapy Are Enhanced by Combined Immunostimulatory mAbs and Are Dependent on CD8 T Cells and Crosspriming
Authors: Rodriguez-Ruiz María E. , Rodriguez Inmaculada , Garasa Saray , Barbes Benigno , Solorzano Jose Luis , Perez-Gracia Jose Luis , Labiano Sara , Sanmamed Miguel F. , Azpilikueta Arantza , Bolaños Elixabet , Sanchez-Paulete Alfonso R. , Aznar M. Angela , Rouzaut Ana , Schalper Kurt A. , Jure-Kunkel Maria , Melero Ignacio
Published: March 2023

Statistical comparisons for figures 1, 2, 4 and supplementary figure 1.
Supplementary Figure S5 from Germinal Centers Determine the Prognostic Relevance of Tertiary Lymphoid Structures and Are Impaired by Corticosteroids in Lung Squamous Cell Carcinoma
Authors: Siliņa Karīna , Soltermann Alex , Attar Farkhondeh Movahedian , Casanova Ruben , Uckeley Zina M. , Thut Helen , Wandres Muriel , Isajevs Sergejs , Cheng Phil , Curioni-Fontecedro Alessandra , Foukas Periklis , Levesque Mitchell P. , Moch Holger , Linē Aija , van den Broek Maries
Published: March 2023

Analysis of the correlation between TLS maturation stage and tumor stage or patients survival.
Supplementary Table S1 from A Heritable Missense Polymorphism in CDKN2A Confers Strong Risk of Childhood Acute Lymphoblastic Leukemia and Is Preferentially Selected during Clonal Evolution
Authors: Walsh Kyle M. , de Smith Adam J. , Hansen Helen M. , Smirnov Ivan V. , Gonseth Semira , Endicott Alyson A. , Xiao Jianqiao , Rice Terri , Fu Cecilia H. , McCoy Lucie S. , Lachance Daniel H. , Eckel-Passow Jeanette E. , Wiencke John K. , Jenkins Robert B. , Wrensch Margaret R. , Ma Xiaomei , Metayer Catherine , Wiemels Joseph L.
Published: March 2023

Subject characteristics of cases and controls undergoing genetic association analyses from the California Childhood Leukemia Study, The Children's Oncology Group, The Wellcome Trust Consortium, the GENEVA Melanoma Study, The University of California, San Francisco Adult Glioma Study, The Mayo Clinic glioma study, and the CGEMS PanScan pancreatic cancer case-control study.
Supplementary Materials and Methods from Endothelial Side Population Cells Contribute to Tumor Angiogenesis and Antiangiogenic Drug Resistance
Authors: Naito Hisamichi , Wakabayashi Taku , Kidoya Hiroyasu , Muramatsu Fumitaka , Takara Kazuhiro , Eino Daisuke , Yamane Keitaro , Iba Tomohiro , Takakura Nobuyuki
Published: March 2023

Supplementary Materials and Methods
Supplementary Figure 1 from The Small Molecule IMR-1 Inhibits the Notch Transcriptional Activation Complex to Suppress Tumorigenesis
Authors: Astudillo Luisana , Da Silva Thiago G. , Wang Zhiqiang , Han Xiaoqing , Jin Ke , VanWye Jeffrey , Zhu Xiaoxia , Weaver Kelly , Oashi Taiji , Lopes Pedro E.M. , Orton Darren , Neitzel Leif R. , Lee Ethan , Landgraf Ralf , Robbins David J. , MacKerell Alexander D. , Capobianco Anthony J.
Published: March 2023

Primary screen of CADD-derived compounds.
Figure S2 from Nkx2.8 Inhibits Epithelial–Mesenchymal Transition in Bladder Urothelial Carcinoma via Transcriptional Repression of Twist1
Authors: Yu Chunping , Liu Zhuowei , Chen Qiuhong , Li Yonghong , Jiang Lijuan , Zhang Zhiling , Zhou Fangjian
Published: March 2023

Representative images of orthotopic xenograft bladder cancer model with T24/vector and T24/Nkx2.8 cells
Figure S1 from Nkx2.8 Inhibits Epithelial–Mesenchymal Transition in Bladder Urothelial Carcinoma via Transcriptional Repression of Twist1
Authors: Yu Chunping , Liu Zhuowei , Chen Qiuhong , Li Yonghong , Jiang Lijuan , Zhang Zhiling , Zhou Fangjian
Published: March 2023

Silencing endogenous Nkx2.8 induces EMT of UC cells
Legends for supplementary Figures from RASSF1A Directly Antagonizes RhoA Activity through the Assembly of a Smurf1-Mediated Destruction Complex to Suppress Tumorigenesis
Authors: Lee Min-Goo , Jeong Seong-In , Ko Kyung-Phil , Park Soon-Ki , Ryu Byung-Kyu , Kim Ick-Young , Kim Jeong-Kook , Chi Sung-Gil
Published: March 2023

Experimental methods and materials and brief summary of the results for Supplementary data (Figures S1-S7)
Figure S1 from Myc Expression Drives Aberrant Lipid Metabolism in Lung Cancer
Authors: Hall Zoe , Ament Zsuzsanna , Wilson Catherine H. , Burkhart Deborah L. , Ashmore Tom , Koulman Albert , Littlewood Trevor , Evan Gerard I. , Griffin Julian L.
Published: March 2023

Clustering of MALDI imaging dataset for a lung section.
Figure S4 from RASSF1A Directly Antagonizes RhoA Activity through the Assembly of a Smurf1-Mediated Destruction Complex to Suppress Tumorigenesis
Authors: Lee Min-Goo , Jeong Seong-In , Ko Kyung-Phil , Park Soon-Ki , Ryu Byung-Kyu , Kim Ick-Young , Kim Jeong-Kook , Chi Sung-Gil
Published: March 2023

Figure S4. RASSF1A blocks Rhotekin interaction with and activation of RhoA. A, Enhanced RhoA-Rhotekin interaction in RASSF1A-depeletd cells. HeLa cells transfected with siControl or siRASSF1A (20 nM) were maintained in the absence of serum for 24 h. At 12 h after serum addition, immunoprecipitation and immunoblot were performed as indicated. B, Rhotekin suppression of RASSF1A-induced RhoA ubiquitination. A549 cells were co-transfected with WT-RASSF1A and Myc-Rhotekin and immunoprecipitation assays were performed to measure ubiquitinated RhoA level. C, RASSF1A inhibition of Rhotekin's protective effect on RhoA ubiquitination. D, No effect of RASSF1A-R269F on RhoA ubiquitination. E, IP assay showing RhoA interaction with Rhotekin and S100A4. F, No effect of RASSF1A on S100A4 protein level. G, RASSF1A suppression of S100A4 activation of RhoA signaling.
Supplemental Figure 3 from Cyclin A1 and P450 Aromatase Promote Metastatic Homing and Growth of Stem-like Prostate Cancer Cells in the Bone Marrow
Authors: Miftakhova Regina , Hedblom Andreas , Semenas Julius , Robinson Brian , Simoulis Athanasios , Malm Johan , Rizvanov Albert , Heery David M. , Mongan Nigel P. , Maitland Norman J. , Allegrucci Cinzia , Persson Jenny L.
Published: March 2023

Evaluate bone marrow metastasis initiated by PC3M cells via intracardiac injection of tumor cells into mice.
Supplemental Figure Legends from Notch4 Signaling Induces a Mesenchymal–Epithelial–like Transition in Melanoma Cells to Suppress Malignant Behaviors
Authors: Bonyadi Rad Ehsan , Hammerlindl Heinz , Wels Christian , Popper Ulrich , Ravindran Menon Dinoop , Breiteneder Heimo , Kitzwoegerer Melitta , Hafner Christine , Herlyn Meenhard , Bergler Helmut , Schaider Helmut
Published: March 2023

Supplemental Figure Legends for Supplemental Figures 1 to 5
Supplemental Figures from PINK1 Is a Negative Regulator of Growth and the Warburg Effect in Glioblastoma
Authors: Agnihotri Sameer , Golbourn Brian , Huang Xi , Remke Marc , Younger Susan , Cairns Rob A. , Chalil Alan , Smith Christian A. , Krumholtz Stacey-Lynn , Mackenzie Danielle , Rakopoulos Patricia , Ramaswamy Vijay , Taccone Michael S. , Mischel Paul S. , Fuller Gregory N. , Hawkins Cynthia , Stanford William L. , Taylor Michael D. , Zadeh Gelareh , Rutka James T.
Published: March 2023

Supplemental Figure 1: Related to Figure 1: Characterization of Gene-Trapped Clones Supplemental Figure 2 Related to Figure 2: PINK1 alters normal astrocyte metabolism Supplemental Figure 3 Related to Figure 2: PINK1 alters normal astrocyte metabolism Supplemental Figure 4: Related to Figure 3: PINK1 alters normal astrocyte metabolism and stabilizes HIF1a Supplemental Figure 5: Related to Figure 3: PINK1 overexpression stops GBM cell growth and inhibits glycolysis. Supplemental Figure 6: Related to Figure 3: PINK1 overexpression inhibits glycolysis. Supplemental Figure 7: Related to Figure 3: PINK1 overexpression inhibits glycolysis. Supplemental Figure 8: Related to Figure 4: Selective targeting in PINK1 expressing GBM cells leads to reduced viability Supplemental Figure 9: Related to Figure 4: Targeting of PINK1 in GBM cells leads to reduced colony formation and caspase activity Supplemental Figure 10: Related to Figure 5 and 6. PINK1 expression in vivo. Supplemental Table 1: Genes identified from gene-trap screen.
Supplemental Figure 1 from JPO2/CDCA7L and LEDGF/p75 Are Novel Mediators of PI3K/AKT Signaling and Aggressive Phenotypes in Medulloblastoma
Authors: Chan Tiffany Sin Yu , Hawkins Cynthia , Krieger Jonathan R. , McGlade C. Jane , Huang Annie
Published: March 2023

JPO2 has limited effects on MB cell proliferation
Supplemental tables 1-3 from HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis
Authors: Lang Michaela , Berry David , Passecker Katharina , Mesteri Ildiko , Bhuju Sabin , Ebner Florian , Sedlyarov Vitaly , Evstatiev Rayko , Dammann Kyle , Loy Alexander , Kuzyk Orest , Kovarik Pavel , Khare Vineeta , Beibel Martin , Roma Guglielmo , Meisner-Kober Nicole , Gasche Christoph
Published: March 2023

Antibody list, organoid culture medium reagents and primer sequences
Supplemental figure 4 from An Imbalance in TAZ and YAP Expression in Hepatocellular Carcinoma Confers Cancer Stem Cell–like Behaviors Contributing to Disease Progression
Authors: Hayashi Hiromitsu , Higashi Takaaki , Yokoyama Naomi , Kaida Takayoshi , Sakamoto Keita , Fukushima Yukiko , Ishimoto Takatsugu , Kuroki Hideyuki , Nitta Hidetoshi , Hashimoto Daisuke , Chikamoto Akira , Oki Eiji , Beppu Toru , Baba Hideo
Published: March 2023

YAP knockdown in other gastrointestinal cancer cells (SW620 and TE-1 cells) with high YAP expression.
Supplementary Methods and figure legends from CCR2 Influences T Regulatory Cell Migration to Tumors and Serves as a Biomarker of Cyclophosphamide Sensitivity
Authors: Loyher Pierre-Louis , Rochefort Juliette , Baudesson de Chanville Camille , Hamon Pauline , Lescaille Géraldine , Bertolus Chloé , Guillot-Delost Maude , Krummel Matthew F. , Lemoine François M. , Combadière Christophe , Boissonnas Alexandre
Published: March 2023

Includes mat and methods and legends relative to supplementary figures
Supplemental Tables 1 through 3 from mTORC2 Signaling Drives the Development and Progression of Pancreatic Cancer
Authors: Driscoll David R. , Karim Saadia A , Sano Makoto , Gay David M. , Jacob Wright , Yu Jun , Mizukami Yusuke , Gopinathan Aarthi , Jodrell Duncan I. , Evans T.R. Jeffry , Bardeesy Nabeel , Hall Michael N. , Quattrochi Brian J. , Klimstra David S. , Barry Simon T. , Sansom Owen J. , Lewis Brian C. , Morton Jennifer P.
Published: March 2023

Table S1: Antibodies for immunohistochemistry. Table S2: shRNA sequences. Table S3: Antibodies for western blotting.
Supplemental figure 2 from CCR2 Influences T Regulatory Cell Migration to Tumors and Serves as a Biomarker of Cyclophosphamide Sensitivity
Authors: Loyher Pierre-Louis , Rochefort Juliette , Baudesson de Chanville Camille , Hamon Pauline , Lescaille Géraldine , Bertolus Chloé , Guillot-Delost Maude , Krummel Matthew F. , Lemoine François M. , Combadière Christophe , Boissonnas Alexandre
Published: March 2023

The dynamic of Tregs is reduced in the dLN of Ccr2-/- mice compared to WT mice
Supplementary Methods, Figures, and Tables from Persistent Immune Stimulation Exacerbates Genetically Driven Myeloproliferative Disorders via Stromal Remodeling
Authors: Tripodo Claudio , Burocchi Alessia , Piccaluga Pier Paolo , Chiodoni Claudia , Portararo Paola , Cappetti Barbara , Botti Laura , Gulino Alessandro , Isidori Alessandro , Liso Arcangelo , Visani Giuseppe , Martelli Maria Paola , Falini Brunangelo , Pandolfi Pier Paolo , Colombo Mario P. , Sangaletti Sabina
Published: March 2023

The file includes supplementary methods for histopathology and gene expression profile analysis and 8 supplementary Figures. In detail Figure S1 shows kidney and lung histopathology of naive and DC-NET immunized mice
Supplementary Figure S3 from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
Authors: Tech Katherine , Tikunov Andrey P. , Farooq Hamza , Morrissy A. Sorana , Meidinger Jessica , Fish Taylor , Green Sarah C. , Liu Hedi , Li Yisu , Mungall Andrew J. , Moore Richard A. , Ma Yussanne , Jones Steven J.M. , Marra Marco A. , Vander Heiden Matthew G. , Taylor Michael D. , Macdonald Jeffrey M. , Gershon Timothy R.
Published: March 2023

Schematic diagram showing the patterns of incorporation of 13C atoms from [1,6-13C] glucose into the products of the Krebs Cycle.
Supplementary Materials and Methods from Androgen and Estrogen Receptors in Breast Cancer Coregulate Human UDP-Glucuronosyltransferases 2B15 and 2B17
Authors: Hu Dong G. , Selth Luke A. , Tarulli Gerard A. , Meech Robyn , Wijayakumara Dhilushi , Chanawong Apichaya , Russell Roslin , Caldas Carlos , Robinson Jessica L.L. , Carroll Jason S. , Tilley Wayne D. , Mackenzie Peter I. , Hickey Theresa E.
Published: March 2023

Word document containing additional details of materials and methods
Supplementary Figure S1 from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
Authors: Tech Katherine , Tikunov Andrey P. , Farooq Hamza , Morrissy A. Sorana , Meidinger Jessica , Fish Taylor , Green Sarah C. , Liu Hedi , Li Yisu , Mungall Andrew J. , Moore Richard A. , Ma Yussanne , Jones Steven J.M. , Marra Marco A. , Vander Heiden Matthew G. , Taylor Michael D. , Macdonald Jeffrey M. , Gershon Timothy R.
Published: March 2023

Western blot showing explanted CGNP expresssion of pAKT, PKM1, PKM2 and cleaved caspse-3, comparing Pkm2-deleted and control genotypes.
Supplementary Table 3 from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: March 2023

Relationship of expression of nuclear p65, E-cadherin, and vimentin with lymph node metastasis in surgical PDAC specimens
Supplementary Figure S4 from The p53/p21 Complex Regulates Cancer Cell Invasion and Apoptosis by Targeting Bcl-2 Family Proteins
Authors: Kim Eun Mi , Jung Chan-Hun , Kim Jongdoo , Hwang Sang-Gu , Park Jong Kuk , Um Hong-Duck
Published: March 2023

p53-p21 cooperation in HCT116 conlon cancer cells
SUPPLEMENTARY figure 6 from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: March 2023

Quantification of western blotting from main Figure 6 and the mRNA levels of PTEN.
Supplemental Figure Legends from T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia
Authors: Jing Weiqing , Gershan Jill A. , Holzhauer Sandra , Weber James , Palen Katie , McOlash Laura , Pulakanti Kirthi , Wesley Erin , Rao Sridhar , Johnson Bryon D. , Riese Matthew J.
Published: March 2023

Supplemental Figure Legends
Table S1 from Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers
Authors: Yau Edwin H. , Kummetha Indrasena Reddy , Lichinchi Gianluigi , Tang Rachel , Zhang Yunlin , Rana Tariq M.
Published: March 2023

Table with Gene level analysis of transduction replicates in the genome-wide xenograft screen using RIGER
Supplemental Figures from Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers
Authors: Yau Edwin H. , Kummetha Indrasena Reddy , Lichinchi Gianluigi , Tang Rachel , Zhang Yunlin , Rana Tariq M.
Published: March 2023

This file contains supplemental figures S1-S4. Figure S1 - library abundance and replicate correlation of genome-wide CRISPR screen. Figure S2 - Validation experiments for candidate metabolic synthetic lethal candidates. Figure S3 - Venn diagram for the generation of a candidate gene list for the secondary library screen and replicate correlation of secondary screen. Figure S4 - Validation of INO80C as a candidate tumor suppressor gene.
Supplementary Table 7 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Mutation significance and sequencing information on the MiSeq sequenced microsatellites.
Table S1, Table S2, table S3, and Table S4 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

Combined file of Table S1 thru S4. Table S1. Blockade of PD-1 binding to PD-L1 on MDA-MB-231 by anti-PD-1. Table S2. Surface expression of CEACAM5 and Trop-2 on selective cell lines. Table S3. Expression of Trop-2 and PD-L1 on MDA-MB-231 and its Trop-2-transfected sublines, including the IC50 of (E1)-3s determined with T cells purified from PBMCs of the same donor. Table S4. Effect of cPD-1 on IC50/EC50 of (E1)-3s to kill MDA-MB-231 or MDA-MB-231-S120 with redirected T cells.
Figure S8 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

Upregulation of PD-L1on HCC1954 cells by IFN-gamma.
Supplementary Table 3 from PD-1 Expression in Head and Neck Squamous Cell Carcinomas Derives Primarily from Functionally Anergic CD4+ TILs in the Presence of PD-L1+ TAMs
Authors: Mattox Austin K. , Lee Jina , Westra William H. , Pierce Robert H. , Ghossein Ronald , Faquin William C. , Diefenbach Thomas J. , Morris Luc G. , Lin Derrick T. , Wirth Lori J. , Lefranc-Torres Armida , Ishida Eiichi , Chakravarty Patrick D. , Johnson Lauren , Zeng Yang C. , Chen Huabiao , Poznansky Mark C. , Iyengar Neil M. , Pai Sara I.
Published: March 2023

This file contains Supplementary Table 3. Supplementary Table 3 shows the clinicopathological characteristics of the patient cohort.
Supplementary Figures 1-8 from GUCY2C Signaling Opposes the Acute Radiation-Induced GI Syndrome
Authors: Li Peng , Wuthrick Evan , Rappaport Jeff A. , Kraft Crystal , Lin Jieru E. , Marszalowicz Glen , Snook Adam E. , Zhan Tingting , Hyslop Terry M. , Waldman Scott A.
Published: March 2023

Supplementary Figure 1. Silencing p53 expression in intestine of p53int-/- mice eliminates phospho-p53 responses to DNA damage induced by radiation. Supplementary Figure 2. Silencing p53 expression in intestine of p53int-/- mice amplifies RIGS-related toxicity. Supplementary Figure 3. Littermates are utilized to minimize the effect of genetic backgrounds in transgenic mice. Supplementary Figure 4. HCT116 cells do not exhibit GUCY2C ligand binding. Supplementary Figure 5. Total body irradiation induces gastrointestinal injury. Supplementary Figure 6. Hormone expression is preserved in RIGS in Gucy2c-/- mice. Supplementary Figure 7. Oral ST fails to oppose RIGS in the absence of GUCY2C. Supplementary Figure 8. Silencing p53 expression in intestine of p53int-/- mice does not affect apoptosis in RIGS.
Supplementary Figure Legends from GUCY2C Signaling Opposes the Acute Radiation-Induced GI Syndrome
Authors: Li Peng , Wuthrick Evan , Rappaport Jeff A. , Kraft Crystal , Lin Jieru E. , Marszalowicz Glen , Snook Adam E. , Zhan Tingting , Hyslop Terry M. , Waldman Scott A.
Published: March 2023

Supplementary Figure Legends
Supplemental Figure Legend from WEE1 Kinase Inhibitor AZD1775 Has Preclinical Efficacy in LKB1-Deficient Non–Small Cell Lung Cancer
Authors: Richer Amanda L. , Cala Jacqueline M. , O'Brien Kelley , Carson Vashti M. , Inge Landon J. , Whitsett Timothy G.
Published: March 2023

Figure legends for supplemental figures 1 and 2
Supplemental Figure 1 from WEE1 Kinase Inhibitor AZD1775 Has Preclinical Efficacy in LKB1-Deficient Non–Small Cell Lung Cancer
Authors: Richer Amanda L. , Cala Jacqueline M. , O'Brien Kelley , Carson Vashti M. , Inge Landon J. , Whitsett Timothy G.
Published: March 2023

Treatment scheme for the in vivo experiments along with representative bioluminescent imaging.
Figure S1-S6, Table S1-S2 from Targeting Histone Demethylases in MYC-Driven Neuroblastomas with Ciclopirox
Authors: Yang Jun , Milasta Sandra , Hu Dongli , AlTahan Alaa M. , Interiano Rodrigo B. , Zhou Junfang , Davidson Jesse , Low Jonathan , Lin Wenwei , Bao Ju , Goh Pollyanna , Nathwani Amit C. , Wang Ruoning , Wang Yingdi , Ong Su Sien , Boyd Vincent A. , Young Brandon , Das Sourav , Shelat Anang , Wu Yinan , Li Zhenmei , Zheng Jie J. , Mishra Ashutosh , Cheng Yong , Qu Chunxu , Peng Junmin , Green Douglas R. , White Stephen , Guy R. Kiplin , Chen Taosheng , Davidoff Andrew M.
Published: March 2023

Figure S1 shows siRNA screening in neuroblastoma cells. Figure S2 shows the dentification of ciclopirox that targets KDM4B. Figure S3 shows the CPX effect on other histone methyl marks. Figure S4 shows that CPX targets the Myc pathway. Figure S5 shows that CPX inhibits oxidative phosphorylation. Figure S6 shows the CPX effect on BE2C xenografts with KDM4B knockdown. Table S1 shows the sequences of the focused KDM siRNA library. Table S2 shows the primers for real time PCR.
Supplementary Tables from Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer
Authors: Gulbahce Natali , Magbanua Mark Jesus M. , Chin Robert , Agarwal Misha R. , Luo Xuhao , Liu Jia , Hayden Daniel M. , Mao Qing , Ciotlos Serban , Li Zhenyu , Chen Yanxiang , Chen Xingpeng , Li Yuxiang , Zhang Rebecca Yu , Lee Katharine , Tearle Rick , Park Emily , Drmanac Snezana , Rugo Hope S. , Park John W. , Drmanac Radoje , Peters Brock A.
Published: March 2023

The following file contains Tables S1-12. The contents of these tables are referenced through the manuscript and contain the basis for the results summarized in the paper. The list of tables is as follows: S1. CNV. This table contains all the copy number gains and losses identified in the CTCs. S2. SNV. This table contains all of the somatic SNVs identified in the CTCs. S3. Indel. This table contains all of the somatic insertions and deletions identified in the CTCs. S4. NA12877 somatic. This table contains all of the somatic SNVs identified in NA12877. S5. Allele fraction. This table contains allele fraction calculations and compartment number filtering calculations. S6. Sanger and Miseq. This table contains all of the Sanger sequencing and Miseq validation for the 77 somatic SNVs validated in this study. S7. Mutational spectrum. This table contains the mutation spectrum analysis and the comparison of the CTC mutation spectrum to other tumor types. S8. Non-coding annotation. This table contains a list of potentially important somatic noncoding variants. S9. Splicing. This table contains somatic splicing variants. S10. MHC-II. This table contains the potential somatic coding changes which would result in MHC-II binding antigens. S11. Two hit. This table contains genes with two potential inactivating variants, this can include inherited and somatic variants. S12. Phasing. This table contains phased somatic and/or inherited variants that potentially inactivate a gene through a compound heterozygous mechanism.
Supplementary Methods from Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer
Authors: Gulbahce Natali , Magbanua Mark Jesus M. , Chin Robert , Agarwal Misha R. , Luo Xuhao , Liu Jia , Hayden Daniel M. , Mao Qing , Ciotlos Serban , Li Zhenyu , Chen Yanxiang , Chen Xingpeng , Li Yuxiang , Zhang Rebecca Yu , Lee Katharine , Tearle Rick , Park Emily , Drmanac Snezana , Rugo Hope S. , Park John W. , Drmanac Radoje , Peters Brock A.
Published: March 2023

This file contains descriptions of all of the bioinformatic analyses used in the paper.
Supplementary Figures from PRC2-Mediated Transcriptomic Alterations at the Embryonic Stage Govern Tumorigenesis and Clinical Outcome in MYCN-Driven Neuroblastoma
Authors: Tsubota Shoma , Kishida Satoshi , Shimamura Teppei , Ohira Miki , Yamashita Satoshi , Cao Dongliang , Kiyonari Shinichi , Ushijima Toshikazu , Kadomatsu Kenji
Published: March 2023

This file contains Supplementary Fig. S1 to S8. Figure S1: RA (+) and RA (-) medium comparison. Figure S2: Transcriptomic differences in SMG and spheres from 3-week-old WT and TH-MYCN mice. Figure S3: Expression pattern of human MYCN mRNA and H&E staining of subcutaneous tumors derived from TH-MYCN spheres. Figure S4: Validation of microarray analysis including the expression of PRC2 components in WT and TH-MYCN spheres. Figure S5: DNA-methylation analysis and its association with mRNA expression and H3K27me3 mark in E13.5 WT and TH-MYCN spheres. Figure S6: Growth IC50 values of EPZ-6438 for TH-MYCN spheres. Figure S7: Effects of Ezh2 inhibition by EPZ-6438 on in situ tumor formation in TH-MYCN mice. Figure S8: Associations between the expression of PRC2 components and several clinical statuses in human neuroblastoma.
An array CGH of TH-MYCN spheres and tumor tissues from PRC2-Mediated Transcriptomic Alterations at the Embryonic Stage Govern Tumorigenesis and Clinical Outcome in MYCN-Driven Neuroblastoma
Authors: Tsubota Shoma , Kishida Satoshi , Shimamura Teppei , Ohira Miki , Yamashita Satoshi , Cao Dongliang , Kiyonari Shinichi , Ushijima Toshikazu , Kadomatsu Kenji
Published: March 2023

The table contains the results of array comparative genomic hybridization (array CGH) of TH-MYCN spheres and tumor tissues.
Supplementary Table S5 from Cic Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation
Authors: Yang Rui , Chen Lee H. , Hansen Landon J. , Carpenter Austin B. , Moure Casey J. , Liu Heng , Pirozzi Christopher J. , Diplas Bill H. , Waitkus Matthew S. , Greer Paula K. , Zhu Huishan , McLendon Roger E. , Bigner Darell D. , He Yiping , Yan Hai
Published: March 2023

Anti-CIC Chip assay of HOG isogenic cell lines.
Supplementary Tables from Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma
Authors: Sivakumar Smruthy , Lucas F. Anthony San , McDowell Tina L. , Lang Wenhua , Xu Li , Fujimoto Junya , Zhang Jianjun , Futreal P. Andrew , Fukuoka Junya , Yatabe Yasushi , Dubinett Steven M. , Spira Avrum E. , Fowler Jerry , Hawk Ernest T. , Wistuba Ignacio I. , Scheet Paul , Kadara Humam
Published: March 2023

Table S1: Samples analyzed by DNA and RNA sequencing; Table S2: DNA (n=67) and RNA (n=48) sequencing quality metrics for each sample; Table S3: Exonic mutations in known lung adenocarcinoma drivers and other cancer associated genes; Table S4: Genes mutated in atypical adenomatous hyperplasias and lung adenocarcinomas; Table S5: Validation of specific BRAF, KRAS and EGFR mutations using digital PCR; Table S6: Genes differentially expressed among normal lung tissues, atypical adenomatous hyperplasias and lung adenocarcinomas; Table S7: Genes differentially expressed between BRAF-mutant, KRAS-mutant and BRAF/KRAS wild type atypical adenomatous hyperplasias; Table S8: Markers of immune signaling that are aberrantly expressed between normal lung tissues, atypical adenomatous hyperplasias and lung adenocarcinomas.
Figure S1 to S10 from Clonality, Heterogeneity, and Evolution of Synchronous Bilateral Ovarian Cancer
Authors: Yin Xia , Jing Ying , Cai Mei-Chun , Ma Pengfei , Zhang Yi , Xu Cong , Zhang Meiying , Di Wen , Zhuang Guanglei
Published: March 2023

Supplementary Figure S1. Representative images of hematoxylin and eosin (H&E) staining and computed tomography from each patients.Supplementary Figure S2. Distribution of cancer-predisposition genes in each patient. Blue: splice site; dark gray: single nucleotide variations; light gray: absent. Supplementary Figure S3. SciClone analysis of sequenced tumor samples from RJOC12. Supplementary Figure S4. Circos plot displays the copy number variations and inter- and intra-chromosal translocations. Supplementary Figure S5. Heat maps display the Cancer Cell Fraction (CCF) of all mutations in both ovarian lesions of RJOC1-11 (up). Phylogenetic tree of both ovarian tumors were constructed from all somatic mutations. Supplementary Figure S6. Mutation signatures of SNVs in early and late stages. Supplementary Figure S7. Mutational signatures of SBOCs. Supplementary Figure S8. SciClone analysis of 11 SBOC patients. Supplementary Figure S9. Pyclone analysis of 11 SBOC patients.Supplementary Figure S10. Germline and somatic alterations of DNA repair genes.
Figure S2 from Subtype-Specific Tumor-Associated Fibroblasts Contribute to the Pathogenesis of Uterine Leiomyoma
Authors: Wu Xin , Serna Vanida A. , Thomas Justin , Qiang Wenan , Blumenfeld Michael L. , Kurita Takeshi
Published: March 2023

Anti-Calponin IgG dilution test for FACS analysis. CLP antibody was titrated for FACS analysis of LMs. The shift of the peak for CLP-negative cells indicates the presence of non-specific binding of the antibody. Based on this result, the anti-CLP antibody was used at 1:25 dilution.
Supplemental Figure Legends from R-Spondin1/LGR5 Activates TGFβ Signaling and Suppresses Colon Cancer Metastasis
Authors: Zhou Xiaolin , Geng Liying , Wang Degeng , Yi Haowei , Talmon Geoffrey , Wang Jing
Published: March 2023

Supplemental Figure Legends
Supplementary Table 2 from MYC Mediates Large Oncosome-Induced Fibroblast Reprogramming in Prostate Cancer
Authors: Minciacchi Valentina R. , Spinelli Cristiana , Reis-Sobreiro Mariana , Cavallini Lorenzo , You Sungyong , Zandian Mandana , Li Xiaohong , Mishra Rajeev , Chiarugi Paola , Adam Rosalyn M. , Posadas Edwin M. , Viglietto Giuseppe , Freeman Michael R. , Cocucci Emanuele , Bhowmick Neil A. , Di Vizio Dolores
Published: March 2023

Supplementary Table 2: Master regulator analysis (MRA), using TF-target interaction information collected from public databases, including the Biomolecular Interaction Network database (BIND), EdgeExpress database (EEDB), Transcriptional Regulatory Element database (TRED), ChIP Enrichment Analysis (ChEA), ChIPBase, and hmChIP, of 274 TF, was performed on 207 differentially expressed genes (DEG) (FDR < 0.1 and fold change {greater than or equal to} 1.5)
Supplementary Information Figures from Macrophage-Secreted TNFα and TGFβ1 Influence Migration Speed and Persistence of Cancer Cells in 3D Tissue Culture via Independent Pathways
Authors: Li Ran , Hebert Jess D. , Lee Tara A. , Xing Hao , Boussommier-Calleja Alexandra , Hynes Richard O. , Lauffenburger Douglas A. , Kamm Roger D.
Published: March 2023

This file contains figures in the supplementary information. These data complements data in the main figures. It contains: Figure S1: Microfluidic Assay for cell migration in 3D ECM; Figure S2: Macrophages increase cancer cell invasion rate in 3D ECM; macrophages increase cancer cell migration total speed but decrease directedness on 2D substrates; Figure S3: MMP activity is crucial for cancer cell migration, and macrophages enhance cancer cell MMP expression; Figure S4: The abilities of macrophages to enhance cancer cell migration dynamics and the expression of MMPs are due primarily to the paracrine factors secreted by macrophages; Figure S5: Neutralizing antibody blocking is specific to factors released by macrophages; Figure S6: Blocking TNFalpha and TGFbeta1 secreted by macrophages significantly reduced macrophage-induced MMP expression and macrophage-enhanced cancer cell invasion rate; Figure S7: TNFalpha and TGFbeta1 secreted by macrophages mostly accounts for macrophage-enhanced cancer cell migration total speed and directedness; Figure S8: TGFbeta1 has a larger effect on cancer cell migration total speed than TNFalpha. TNFalpha and TGFbeta1 synergistically increase cancer cell migration directedness; Figure S9: Cancer cell migration total speed is correlated with cancer cell expression of MT1-MMP, while cancer cell migration directedness is correlated with cancer cell expression of MMP1; Figure S10: Inhibiting both TNFalpha and TGFbeta1 in a mice model of breast tumor effectively reduces lung metastasis; Figure S11: TNFalpha and TGFbeta1 co-treatment synergistically up-regulate cancer cell MMP1 protein production and secretion. TGFbeta1 is mainly responsible for the increase in MT1-MMP protein production; Figure S12: TNFalpha and TGFbeta1 co-treatment synergistically enhance NF-κB nuclear localization in MDA-MB-435S cells. Fig. S1 and S2 is related to Fig. 1; Fig. S3 and S4 is related to Fig. 2; Fig. S5, S6, S7 is related to Fig. 3; Fig. S8-11 is related to Fig. 4; Fig. S12 is related to Fig. 6
Supplementary figure 2-3 from Prominent Oncogenic Roles of EVI1 in Breast Carcinoma
Authors: Wang Hui , Schaefer Thorsten , Konantz Martina , Braun Martin , Varga Zsuzsanna , Paczulla Anna M. , Reich Selina , Jacob Francis , Perner Sven , Moch Holger , Fehm Tanja N. , Kanz Lothar , Schulze-Osthoff Klaus , Lengerke Claudia
Published: March 2023

Validation of effects using an alternative EVI1 shRNA and an additional cell line (Hs578T).
Figure S6 from Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma
Authors: Sadahiro Hirokazu , Kang Kyung-Don , Gibson Justin T. , Minata Mutsuko , Yu Hai , Shi Junfeng , Chhipa Rishi , Chen Zhihong , Lu Songjian , Simoni Yannick , Furuta Takuya , Sabit Hemragul , Zhang Suojun , Bastola Soniya , Yamaguchi Shinobu , Alsheikh Hebaallah , Komarova Svetlana , Wang Jun , Kim Sung-Hak , Hambardzumyan Dolores , Lu Xinghua , Newell Evan W. , DasGupta Biplab , Nakada Mitsutoshi , Lee L. James , Nabors Burt , Norian Lyse A. , Nakano Ichiro
Published: March 2023

Supplementary Figure S6. BGB324 inhibits mouse tumor cells.
Supplemental Material from Cellular Hierarchy as a Determinant of Tumor Sensitivity to Chemotherapy
Authors: Rodriguez-Brenes Ignacio A. , Kurtova Antonina V. , Lin Christopher , Lee Yu-Cheng , Xiao Jing , Mims Martha , Chan Keith Syson , Wodarz Dominik
Published: March 2023

This file contains additional details regarding the models and methodologies.
Figure S1 from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Schematic showing experimental strategy to identify altered proteins in PEAK1-depleted PDAC cells
Figure S5 from A Subpopulation of Stromal Cells Controls Cancer Cell Homing to the Bone Marrow
Authors: Rossnagl Stephanie , Ghura Hiba , Groth Christopher , Altrock Eva , Jakob Franz , Schott Sarah , Wimberger Pauline , Link Theresa , Kuhlmann Jan Dominik , Stenzl Arnulf , Hennenlotter Jörg , Todenhöfer Tilmann , Rojewski Markus , Bieback Karen , Nakchbandi Inaam A.
Published: March 2023

Supplementary-Figure 5 Flow cytometry of MSC markers in human bone marrow biopsies Bone marrow aspirates from patients with prostate cancer (A) and breast cancer (B) who had an evaluation of their bone marrows for the presence of cytokeratin-stained cells to detect disseminated cancer cells (DTCs) were stained for the various MSC markers and analyzed by flow cytometry. The expression of the following markers was not different between cytokeratin negative or positive biopsies: MSCA1, Stro1, CD146, FAP, CD44, CD144, CD73, CD349, CD56 and CD140b in prostate cancer biopsies, n=15/21 (A) and MSCA1, Stro1, CD146, FAP, CD44, CD73 and CD349 in breast cancer biopsies, n=30/30 (B). (C) To exclude any effect of neoadjuvant chemotherapy on the MSC population, the breast cancer patient samples were divided into samples from patients with or without neoadjuvant chemotherapy. Both groups showed an increase in the MSC subpopulation in samples without evidence of cytokeratin-stained cells in bone marrow, n= 10/11/20/19.
Figure S3 from Mutational Mechanisms That Activate Wnt Signaling and Predict Outcomes in Colorectal Cancer Patients
Authors: Hankey William , McIlhatton Michael A. , Ebede Kenechi , Kennedy Brian , Hancioglu Baris , Zhang Jie , Brock Guy N. , Huang Kun , Groden Joanna
Published: March 2023

Increased expression of SERPINE2 in human colorectal tumors of advanced stage is validated in a second dataset.
Supplementary Table S2 from Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer
Authors: Alexander Joan , Kendall Jude , McIndoo Jean , Rodgers Linda , Aboukhalil Robert , Levy Dan , Stepansky Asya , Sun Guoli , Chobardjiev Lubomir , Riggs Michael , Cox Hilary , Hakker Inessa , Nowak Dawid G. , Laze Juliana , Llukani Elton , Srivastava Abhishek , Gruschow Siobhan , Yadav Shalini S. , Robinson Brian , Atwal Gurinder , Trotman Lloyd C. , Lepor Herbert , Hicks James , Wigler Michael , Krasnitz Alexander
Published: March 2023

Comparison of genomic and pathological assessments
Figure S3 from Cancer-Associated Fibroblasts Drive Glycolysis in a Targetable Signaling Loop Implicated in Head and Neck Squamous Cell Carcinoma Progression
Authors: Kumar Dhruv , New Jacob , Vishwakarma Vikalp , Joshi Radhika , Enders Jonathan , Lin Fangchen , Dasari Sumana , Gutierrez Wade R. , Leef George , Ponnurangam Sivapriya , Chavan Hemantkumar , Ganaden Lydia , Thornton Mackenzie M. , Dai Hongying , Tawfik Ossama , Straub Jeffrey , Shnayder Yelizaveta , Kakarala Kiran , Tsue Terance Ted , Girod Douglas A. , Van Houten Bennett , Anant Shrikant , Krishnamurthy Partha , Thomas Sufi Mary
Published: March 2023

Endogenous expression of bFGF in HNSCC and FGFR in CAFs.
Supplementary Figures S1-S7 from Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs
Authors: Varn Frederick S. , Schaafsma Evelien , Wang Yue , Cheng Chao
Published: March 2023

Supplementary Figure S1: Differences in immune signature enrichment scores between virus-infected and non-infected samples. Supplementary Figure S2: Differences in the expression of HLA genes between HBV-positive and HBV-negative LIHC patients. Supplementary Figure S3: Differences in non-silent mutation burden between virus-infected and non-infected samples. Supplementary Figure S4: Differences in TCR read abundance between virus-infected and non-infected cancer patients. Supplementary Figure S5: Performance of the virus infection gene expression signature in four HNSC datasets. Supplementary Figure S6: Survival meta-analysis of the virus infection gene expression signature in six cancer types. Supplementary Figure S7: Differences in MKI67 gene expression and ESTIMATE immune scores between HPV-positive and HPV-negative HNSC patients.
Figure S6 from SETD2 Haploinsufficiency for Microtubule Methylation Is an Early Driver of Genomic Instability in Renal Cell Carcinoma
Authors: Chiang Yun-Chen , Park In-Young , Terzo Esteban A. , Tripathi Durga Nand , Mason Frank M. , Fahey Catherine C. , Karki Menuka , Shuster Charles B. , Sohn Bo-Hwa , Chowdhury Pratim , Powell Reid T. , Ohi Ryoma , Tsai Yihsuan S. , de Cubas Aguirre A. , Khan Abid , Davis Ian J. , Strahl Brian D. , Parker Joel S. , Dere Ruhee , Walker Cheryl L. , Rathmell W. Kimryn
Published: March 2023

Human tumor analysis
Supplementary Data from Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs
Authors: Varn Frederick S. , Schaafsma Evelien , Wang Yue , Cheng Chao
Published: March 2023

Supplementary Table S5: Differences in MiTCR statistics between virus-infected and non-infected samples
Supplemental Figures and Tables from Inhibition of Casein Kinase 2 Disrupts Differentiation of Myeloid Cells in Cancer and Enhances the Efficacy of Immunotherapy in Mice
Authors: Hashimoto Ayumi , Gao Chan , Mastio Jerome , Kossenkov Andrew , Abrams Scott I. , Purandare Ashok V. , Desilva Heshani , Wee Susan , Hunt John , Jure-Kunkel Maria , Gabrilovich Dmitry I.
Published: March 2023

This file contains Table with the description of antibodies used in the study and the Table listing sequence of primers used in the study. Supplemental Figure 1 shows antitumor effect of CK2 inhibitor, Figure 2 - effect CK2 inhibitors on tumor cells in vitro, Figure 3 - suppressive activity of MDSC in CK2 inhibitor treated mice, and Figure 4 effect of CK2 inhibitors on Notch signaling related genes.
Supplementary Figure S7 from HER2/EGFR–AKT Signaling Switches TGFβ from Inhibiting Cell Proliferation to Promoting Cell Migration in Breast Cancer
Authors: Huang Fei , Shi Qiaoni , Li Yuzhen , Xu Linlin , Xu Chi , Chen Fenfang , Wang Hai , Liao Hongwei , Chang Zai , Liu Fang , Zhang Xiang H.-F. , Feng Xin-Hua , Han Jing-Dong J. , Luo Shiwen , Chen Ye-Guang
Published: March 2023

Knockdown of Smad3 and Smad2 attenuates TGF-ÃŽÂ²-induced anti-proliferation of MDA-MB-231 cells in the presence of Lapatinib; Smad3(S208) phosphorylation is positively correlated with HER2 activation and AKT activity in human breast cancer tissues.
Extended supplementary procedures from CDKN2A/p16 Deletion in Head and Neck Cancer Cells Is Associated with CDK2 Activation, Replication Stress, and Vulnerability to CHK1 Inhibition
Authors: Gadhikar Mayur A. , Zhang Jiexin , Shen Li , Rao Xiayu , Wang Jing , Zhao Mei , Kalu Nene N. , Johnson Faye M. , Byers Lauren A. , Heymach John , Hittelman Walter N. , Udayakumar Durga , Pandita Raj K. , Pandita Tej K. , Pickering Curtis R. , Redwood Abena B. , Piwnica-Worms Helen , Schlacher Katharina , Frederick Mitchell J. , Myers Jeffrey N.
Published: March 2023

This file contains detailed experimental procedures on immunoblotting, DNA fiber assay, exome sequencing and mutation calling
Supplementary Tables S1 - S6 from Downregulation of Dipeptidyl Peptidase 4 Accelerates Progression to Castration-Resistant Prostate Cancer
Authors: Russo Joshua W. , Gao Ce , Bhasin Swati S. , Voznesensky Olga S. , Calagua Carla , Arai Seiji , Nelson Peter S. , Montgomery Bruce , Mostaghel Elahe A. , Corey Eva , Taplin Mary-Ellen , Ye Huihui , Bhasin Manoj , Balk Steven P.
Published: March 2023

Table S1: Differentially expressed genes in serial biopsies of VCaP xenografts, AER vs. Pre-Cx. Table S2: Differentially expressed genes in serial biopsies of VCaP xenografts, CRPC vs. Pre-Cx. Table S3: Differentially expressed genes in serial biopsies of VCaP xenografts, AER vs. CRPC. Table S4: Differentially expressed genes (DEGs) in AER vs. Pre-Cx using stringent statistical cutoff and the levels of the same differentially expressed genes in CRPC vs Pre-Cx. Table S5: Differentially expressed AR target genes in serial biopsies of VCaP xenografts, AER vs. Pre-Cx. Table S6: Differentially expressed AR target genes in serial biopsies of VCaP xenografts, CRPC vs. Pre-Cx.
Supplementary Tables from Induction of Paracrine Signaling in Metastatic Melanoma Cells by PPARγ Agonist Rosiglitazone Activates Stromal Cells and Enhances Tumor Growth
Authors: Pich Christine , Meylan Patrick , Mastelic-Gavillet Beatris , Nguyen Thanh Nhan , Loyon Romain , Trang Bao Khanh , Moser Hélène , Moret Catherine , Goepfert Christine , Hafner Jürg , Levesque Mitchell P. , Romero Pedro , Jandus Camilla , Michalik Liliane
Published: March 2023

Three supplementary tables showing: - Characteristics of the melanoma cell lines - Top 10 of significantly upregulated and downregulated genes upon PPARγ specific activation in A375 cells, as quantified by RNA-sequencing - Top 20 of deregulated pathways in RGZ vs Ctrl A375-Media, after an in-depth MS analysis, analyzed with Reactome
Supplementary Data from Induction of Paracrine Signaling in Metastatic Melanoma Cells by PPARγ Agonist Rosiglitazone Activates Stromal Cells and Enhances Tumor Growth
Authors: Pich Christine , Meylan Patrick , Mastelic-Gavillet Beatris , Nguyen Thanh Nhan , Loyon Romain , Trang Bao Khanh , Moser Hélène , Moret Catherine , Goepfert Christine , Hafner Jürg , Levesque Mitchell P. , Romero Pedro , Jandus Camilla , Michalik Liliane
Published: March 2023

Supplementary Materials and methods