bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental figures from Spi-B–Mediated Silencing of Claudin-2 Promotes Early Dissemination of Lung Cancer Cells from Primary Tumors
Authors: Du Wei , Xu Xing , Niu Qing , Zhang Xuexi , Wei Yiliang , Wang Ziqiao , Zhang Wei , Yan Jun , Ru Yongxin , Fu Zheng , Li Xiaobo , Jiang Yuan , Ma Zhenyi , Zhang Zhenfa , Yao Zhi , Liu Zhe
Published: March 2023

Figure S1, related to Figure 3. Effect of Spi-B on EMT. (A) Phase-contrast micrographs of HBECs expressing vector or Spi-B. Scale bars are 100μm; (B) western blot showed expression of Spi-B, E-cadherin, Vimentin and Actin; (C) Quantitative RT-PCR assay for Spi-B, Snail1, Snail2, Twist1 and ZEB1. Figure S2, related to Figure 3. (A) Phase-contrast micrographs of H526 cells expressing control or Spi-B shRNAs. Scale bars are 50μm; (B) BrdU in corporation assay of A549 expressing vector or Spi-B; (C) vector or Spi-B-expressing A549 cells were plated on fibronectin-coated plates. After 15 min, attached cells were counted. Scale bars represent 200 mm. Bar graph below shows number of adherent cells. Mean {plus minus} SD of three duplications is shown. Figure S3, related to Figure 5. Expression of claudin-2 in tumor-adjacent tissues. (A) IHC showed expression of claudin-2 in bronchial epithelial cells; (B) IHC showed expression of claudin-2 in alveolar epithelial cells (arrows). Scale bars are 50μm. Figure S4, related to Figure 6. Other Spi-B downregulated tight junction proteins, Claudin-14 and Crumbs3, are not able to rescue Spi-B induced cellular behavior. (A) A549 cells were transduced with Spi-B or Spi-B and Claudin-14 or Spi-B and Crumbs3 as indicated. Representative images of the clones in soft agar were shown in left panels. The bar chart shows the percentage of mass (blue), and loose colonies (red). Error bars indicate means {plus minus} SD for a representative experiment performed in triplicate. Scale bars represent 100 μm. (B) A549 cells were transduced with Spi-B or Spi-B and Claudin-14 or Spi-B and Crumbs3 as indicated. Phase contrast of acini were shown in left panel and quantified in right panel. The bar chart shows the percentage of mass (blue) and grape-like (red). Error bars indicate means {plus minus} SD for a representative experiment performed in triplicate. Scale bars represent 25 μm. (C) A549 cells were transduced with Spi-B or Spi-B and Claudin-14 or Spi-B and Crumbs3 as indicated and subjected to an invasion assay. Error bars indicate means{plus minus} SD for a representative experiment performed in triplicate. Scale bars represent 100 μm. Figure S5. (A) A549 cells were transduced with Spi-B or Spi-B and shRNA of MMP9 as indicated and subjected to an invasion assay. (B) A549 cells were transduced with Spi-B or Spi-B and MMP9 inhibitor (TIMP1) as indicated and subjected to an invasion assay. Error bars indicate means{plus minus} SD for a representative experiment performed in triplicate. Scale bars represent 100 μm.
Table S2 from TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
Authors: Cooper Jonathan M. , Ou Yi-Hung , McMillan Elizabeth A. , Vaden Rachel M. , Zaman Aubhishek , Bodemann Brian O. , Makkar Gurbani , Posner Bruce A. , White Michael A.
Published: March 2023

Table S2 contains the data for the comparisons between TBK1 inhibitors (BX795 and Compound II) and published chemical breadth of efficacy screens in NSCLC lines
Table S1 from TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
Authors: Cooper Jonathan M. , Ou Yi-Hung , McMillan Elizabeth A. , Vaden Rachel M. , Zaman Aubhishek , Bodemann Brian O. , Makkar Gurbani , Posner Bruce A. , White Michael A.
Published: March 2023

Table S1 contains the summary of the TBK1 inhibitor (BX795 and Compound II) screen in NSCLC lines
Table S8 from Correlates of Prenatal and Early-Life Tobacco Smoke Exposure and Frequency of Common Gene Deletions in Childhood Acute Lymphoblastic Leukemia
Authors: de Smith Adam J. , Kaur Maneet , Gonseth Semira , Endicott Alyson , Selvin Steve , Zhang Luoping , Roy Ritu , Shao Xiaorong , Hansen Helen M. , Kang Alice Y. , Walsh Kyle M. , Dahl Gary V. , McKean-Cowdin Roberta , Metayer Catherine , Wiemels Joseph L.
Published: March 2023

Association analyses stratified by sex between tobacco smoke exposures and the number of deletions in the child's leukemia using multivariable Poisson regressions, the California Childhood Leukemia Study, 1995-2015.
Table S6 from Correlates of Prenatal and Early-Life Tobacco Smoke Exposure and Frequency of Common Gene Deletions in Childhood Acute Lymphoblastic Leukemia
Authors: de Smith Adam J. , Kaur Maneet , Gonseth Semira , Endicott Alyson , Selvin Steve , Zhang Luoping , Roy Ritu , Shao Xiaorong , Hansen Helen M. , Kang Alice Y. , Walsh Kyle M. , Dahl Gary V. , McKean-Cowdin Roberta , Metayer Catherine , Wiemels Joseph L.
Published: March 2023

Association analyses between tobacco smoke exposures and the number of deletions in the child's leukemia using multivariable Poisson regressions, with maternal smoking adjusted for paternal smoking and vice-versa.
Table S4 from Correlates of Prenatal and Early-Life Tobacco Smoke Exposure and Frequency of Common Gene Deletions in Childhood Acute Lymphoblastic Leukemia
Authors: de Smith Adam J. , Kaur Maneet , Gonseth Semira , Endicott Alyson , Selvin Steve , Zhang Luoping , Roy Ritu , Shao Xiaorong , Hansen Helen M. , Kang Alice Y. , Walsh Kyle M. , Dahl Gary V. , McKean-Cowdin Roberta , Metayer Catherine , Wiemels Joseph L.
Published: March 2023

Number of cases with 0, 1, or {greater than or equal to}2 deletions in relation to the binary tobacco exposure variables.
Suplementary Figures from S100A4 Elevation Empowers Expression of Metastasis Effector Molecules in Human Breast Cancer
Authors: Ismail Thamir M. , Bennett Daimark , Platt-Higgins Angela M. , Al-Medhity Morteta , Barraclough Roger , Rudland Philip S.
Published: March 2023

Fig S1 Whole Mounts, Fig S2 Westerns, Fig S3 Male/Female Bsk, Fig S4 Inhibitors, Fig S5 Breast Tumors, Fig S6 MMP2 + Other, Fig S7 MMP2/S100A4, Supp Methods, Figure 5 Legend.
Supplementary figures and legends from Extracellular Matrix Receptor Expression in Subtypes of Lung Adenocarcinoma Potentiates Outgrowth of Micrometastases
Authors: Stevens Laura E. , Cheung William K.C. , Adua Sally J. , Arnal-Estapé Anna , Zhao Minghui , Liu Zongzhi , Brewer Kelly , Herbst Roy S. , Nguyen Don X.
Published: March 2023

Supplementary Figures 1-7. Supplementary Fig. S1: Expression of ECM related genes across LUAD subtypes, related to Fig.1. Supplementary Fig. S2: Expression of HMMR, regulation by miR-34A, and correlation with poor prognosis, related to Fig. 2 and 3. Supplementary Fig. S3: Effect of HMMR/Hmmr on lung tumorigenesis, related to Fig. 3. Supplementary Fig. S4: Effect of HMMR on metastasis, related to Fig. 4. Supplementary Fig. S5: Effect of HMMR on seeding and outgrowth in vivo, related to Fig. 5. Supplementary Fig. S6: HA in the lung and brain TME, related to Fig. 6. Supplementary Fig. S7: Mechanism of HMMR mediated outgrowth, related to Fig. 7. Supplementary Fig. S8: un-cropped versions of all western blots.
Table S1-S5 from Skp2-Mediated Stabilization of MTH1 Promotes Survival of Melanoma Cells upon Oxidative Stress
Authors: Wang Jia Yu , Liu Guang Zhi , Wilmott James S. , La Ting , Feng Yu Chen , Yari Hamed , Yan Xu Guang , Thorne Rick F. , Scolyer Richard A. , Zhang Xu Dong , Jin Lei
Published: March 2023

Table S1 shows the list of antibodies. Table S2 shows the list of reagents. Table S3 shows shRNA sequences. Table S4 shows the list of primers. Table S5 shows the list of proteins identified by mass spectrometry.
Supplementary Materials and Methods from Plk4 Promotes Cancer Invasion and Metastasis through Arp2/3 Complex Regulation of the Actin Cytoskeleton
Authors: Kazazian Karineh , Go Christopher , Wu Hannah , Brashavitskaya Olga , Xu Roland , Dennis James W. , Gingras Anne-Claude , Swallow Carol J.
Published: March 2023

Supplementary Materials and Methods
Supplementary Figure 2 from Role of Megakaryocytes in Breast Cancer Metastasis to Bone
Authors: Jackson Walter , Sosnoski Donna M. , Ohanessian Sara E. , Chandler Paige , Mobley Adam , Meisel Kacey D. , Mastro Andrea M.
Published: March 2023

The tumor volumes of mice injected with 4T1.2 or 67NR cells.
Supplementary Figure Legends from Plk4 Promotes Cancer Invasion and Metastasis through Arp2/3 Complex Regulation of the Actin Cytoskeleton
Authors: Kazazian Karineh , Go Christopher , Wu Hannah , Brashavitskaya Olga , Xu Roland , Dennis James W. , Gingras Anne-Claude , Swallow Carol J.
Published: March 2023

Supplementary Figure Legends
Figure S1. PD-L1 expression is not quantitatively altered on the anti-PD-1 resistant tumor cells. from Suppression of Type I IFN Signaling in Tumors Mediates Resistance to Anti-PD-1 Treatment That Can Be Overcome by Radiotherapy
Authors: Wang Xiaohong , Schoenhals Jonathan E. , Li Ailin , Valdecanas David R. , Ye Huiping , Zang Fenglin , Tang Chad , Tang Ming , Liu Chang-Gong , Liu Xiuping , Krishnan Sunil , Allison James P. , Sharma Padmanee , Hwu Patrick , Komaki Ritsuko , Overwijk Willem W. , Gomez Daniel R. , Chang Joe Y. , Hahn Stephen M. , Cortez Maria Angelica , Welsh James W.
Published: March 2023

This figure shows that PD-L1 expression is not quantitatively altered on the anti-PD-1 resistant tumor cells, compared to parental tumor cells.
Supplemental Table 1 from CD40 Signaling Drives Potent Cellular Immune Responses in Heterologous Cancer Vaccinations
Authors: Nimanong Supot , Ostroumov Dmitrij , Wingerath Jessica , Knocke Sarah , Woller Norman , Gürlevik Engin , Falk Christine S. , Manns Michael P. , Kühnel Florian , Wirth Thomas C.
Published: March 2023

This table contains the sequences of the used neoantigen peptides, their affinity according to MHC-NET and the magnitude of the induced CD8 T cell immune responses
Supplementary Tables and Figures from Combined CDK4/6 and PI3Kα Inhibition Is Synergistic and Immunogenic in Triple-Negative Breast Cancer
Authors: Teo Zhi Ling , Versaci Stephanie , Dushyanthen Sathana , Caramia Franco , Savas Peter , Mintoff Chris P. , Zethoven Magnus , Virassamy Balaji , Luen Stephen J. , McArthur Grant A. , Phillips Wayne A. , Darcy Phillip K. , Loi Sherene
Published: March 2023

Supplementary Table S1 and Supplementary Figures S1-S3 - Supplementary Table S1: Characteristics of human triple-negative breast cancer cell lines. Supplementary Figure S1: Quantitation of protein expression in HC1806 and MDAMB231 cells following 72 hours of treatment in vitro. Supplementary Figure S2: Combined BYL719 and LEE011 induces anti-tumor immunity in AT3OVA mouse model of triple-negative breast cancer in vivo. Supplementary Figure S3: Immune checkpoint blockade in combination with BYL719 and LEE011 results in durable tumor regression in vivo.
Table S1 from A Potent, Metabolically Stable Tubulin Inhibitor Targets the Colchicine Binding Site and Overcomes Taxane Resistance
Authors: Arnst Kinsie E. , Wang Yuxi , Hwang Dong-Jin , Xue Yi , Costello Terry , Hamilton David , Chen Qiang , Yang Jinliang , Park Frank , Dalton James T. , Miller Duane D. , Li Wei
Published: March 2023

Raw data from pharmacological profile screening for DJ101 performed by DicoverX using its Safety47 panel.
Supplementary Figures 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

Figure S1: Mutation burden in atypical adenomatous hyperplasia and lung adenocarcinoma; Figure S2: Mutation burden in atypical adenomatous hyperplasia and lung adenocarcinoma based on tobacco history; Figure S3: Mutations in cancer driver genes in atypical adenomatous hyperplasia and lung adenocarcinoma; Figure S4: Representative validation of somatic mutations by digital PCR.
Supplementary table-1 from Mutant IDH1 Cooperates with ATRX Loss to Drive the Alternative Lengthening of Telomere Phenotype in Glioma
Authors: Mukherjee Joydeep , Johannessen Tor-Christian , Ohba Shigeo , Chow Tracy T. , Jones Lindsey , Pandita Ajay , Pieper Russell O.
Published: March 2023

Primers used for quantitative PCR analysis in this study.
Supplementary figure-4 from Mutant IDH1 Cooperates with ATRX Loss to Drive the Alternative Lengthening of Telomere Phenotype in Glioma
Authors: Mukherjee Joydeep , Johannessen Tor-Christian , Ohba Shigeo , Chow Tracy T. , Jones Lindsey , Pandita Ajay , Pieper Russell O.
Published: March 2023

siRNA-mediated suppression of RAP1 and/or XRCC1 substitutes for mutant IDH1 in driving the ALT phenotype.
Supplementary figure-3 from Mutant IDH1 Cooperates with ATRX Loss to Drive the Alternative Lengthening of Telomere Phenotype in Glioma
Authors: Mukherjee Joydeep , Johannessen Tor-Christian , Ohba Shigeo , Chow Tracy T. , Jones Lindsey , Pandita Ajay , Pieper Russell O.
Published: March 2023

Forced overexpression of RAP1 and/or XRCC1 suppresses mutant IDH1-mediated ALT phenotype in genetically modified human astrocytes.
Figure S6 from Proinflammatory CXCL12–CXCR4/CXCR7 Signaling Axis Drives Myc-Induced Prostate Cancer in Obese Mice
Authors: Saha Achinto , Ahn Songyeon , Blando Jorge , Su Fei , Kolonin Mikhail G. , DiGiovanni John
Published: March 2023

Reduction of CXCL12 induced activation of NFκB, STAT3 and MAPK signaling by AMD3100 in HMVP2 cells
Figure S3 from Proinflammatory CXCL12–CXCR4/CXCR7 Signaling Axis Drives Myc-Induced Prostate Cancer in Obese Mice
Authors: Saha Achinto , Ahn Songyeon , Blando Jorge , Su Fei , Kolonin Mikhail G. , DiGiovanni John
Published: March 2023

CXCL12 induced invasion of mouse PCa cells but not normal mouse (NMVP) prostate epithelial cells
Supplementary Figure 5 from Mouse Models of Pediatric Supratentorial High-grade Glioma Reveal How Cell-of-Origin Influences Tumor Development and Phenotype
Authors: Sreedharan Smitha , Maturi Naga Prathyusha , Xie Yuan , Sundström Anders , Jarvius Malin , Libard Sylwia , Alafuzoff Irina , Weishaupt Holger , Fryknäs Mårten , Larsson Rolf , Swartling Fredrik J. , Uhrbom Lene
Published: March 2023

Figure S5, related to Figure 5. Comparisons of drug response between GCs and control cells.
Figure S3 from Loss of FOXO1 Cooperates with TMPRSS2–ERG Overexpression to Promote Prostate Tumorigenesis and Cell Invasion
Authors: Yang Yinhui , Blee Alexandra M. , Wang Dejie , An Jian , Pan Yunqian , Yan Yuqian , Ma Tao , He Yundong , Dugdale Joseph , Hou Xiaonan , Zhang Jun , Weroha S. John , Zhu Wei-Guo , Wang Y. Alan , DePinho Ronald A. , Xu Wanhai , Huang Haojie
Published: March 2023

Supplementary Figure S3. Immunohistochemistry for Cleaved Caspase 3 (CC3) in wild-type, Foxo1pc-/-, Pb-ERG and Foxo1pc-/-; Pb-ERG, and Ptenpc-/-;castration mouse prostates. Only Ptenpc-/-;castration mouse prostates displayed an increase in CC3-positive cells compared to wild-type, as expected.
Suppl.Tables and Figures from In Silico Modeling of Immunotherapy and Stroma-Targeting Therapies in Human Colorectal Cancer
Authors: Kather Jakob Nikolas , Poleszczuk Jan , Suarez-Carmona Meggy , Krisam Johannes , Charoentong Pornpimol , Valous Nektarios A. , Weis Cleo-Aron , Tavernar Luca , Leiss Florian , Herpel Esther , Klupp Fee , Ulrich Alexis , Schneider Martin , Marx Alexander , Jäger Dirk , Halama Niels
Published: March 2023

This file contains all supplementary Tables and Figures. Supplementary Tables show detailed information on the model parameters and on the patient samples that were used in this study. Supplementary Figures show additional details on the model calibration process and on the model behavior and resulting phenotypes.
Supplementary Figure 1 from Mouse Models of Pediatric Supratentorial High-grade Glioma Reveal How Cell-of-Origin Influences Tumor Development and Phenotype
Authors: Sreedharan Smitha , Maturi Naga Prathyusha , Xie Yuan , Sundström Anders , Jarvius Malin , Libard Sylwia , Alafuzoff Irina , Weishaupt Holger , Fryknäs Mårten , Larsson Rolf , Swartling Fredrik J. , Uhrbom Lene
Published: March 2023

Figure S1, related to Figure 1. Double immunofluorescence stainings for GFP and chicken vimentin of neonatal G/tv-a and C/tv-a mouse brains infected with RCAS-eGFP.
Supplementary Figure S2 from Circadian Clock Gene Bmal1 Inhibits Tumorigenesis and Increases Paclitaxel Sensitivity in Tongue Squamous Cell Carcinoma
Authors: Tang Qingming , Cheng Bo , Xie Mengru , Chen Yatao , Zhao Jiajia , Zhou Xin , Chen Lili
Published: March 2023

Bmal1 knockdown decreases paclitaxel sensitivity in SCC9 cells
Supplementary Figure Legends from Circadian Clock Gene Bmal1 Inhibits Tumorigenesis and Increases Paclitaxel Sensitivity in Tongue Squamous Cell Carcinoma
Authors: Tang Qingming , Cheng Bo , Xie Mengru , Chen Yatao , Zhao Jiajia , Zhou Xin , Chen Lili
Published: March 2023

Supplementary Figure Legends
Supplementary Video S4 from Mitosis-Mediated Intravasation in a Tissue-Engineered Tumor–Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

Mitosis-mediated intravasation.
Supplementary Video S13 from Mitosis-Mediated Intravasation in a Tissue-Engineered Tumor–Microvessel Platform
Authors: Wong Andrew D. , Searson Peter C.
Published: March 2023

Perivascular space reduces deflection from dividing MDA-MB-231 breast cancer cells (BCC) at the ECM-vessel interface.
Supplementary Figure S2 from Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma
Authors: Wei Xiaomu , Calvo-Vidal M. Nieves , Chen Siwei , Wu Gang , Revuelta Maria V. , Sun Jian , Zhang Jinghui , Walsh Michael F. , Nichols Kim E. , Joseph Vijai , Snyder Carrie , Vachon Celine M. , McKay James D. , Wang Shu-Ping , Jayabalan David S. , Jacobs Lauren M. , Becirovic Dina , Waller Rosalie G. , Artomov Mykyta , Viale Agnes , Patel Jayeshkumar , Phillip Jude , Chen-Kiang Selina , Curtin Karen , Salama Mohamed , Atanackovic Djordje , Niesvizky Ruben , Landgren Ola , Slager Susan L. , Godley Lucy A. , Churpek Jane , Garber Judy E. , Anderson Kenneth C. , Daly Mark J. , Roeder Robert G. , Dumontet Charles , Lynch Henry T. , Mullighan Charles G. , Camp Nicola J. , Offit Kenneth , Klein Robert J. , Yu Haiyuan , Cerchietti Leandro , Lipkin Steven M.
Published: March 2023

KDM1A mutation promotes enrichment of LSK and HoxA9 leukemia stem cell signatures in near haploid hypodiploid acute lymphoblastic leukemia.
Supplemental Figure Legends from Secretory Autophagy in Cancer-Associated Fibroblasts Promotes Head and Neck Cancer Progression and Offers a Novel Therapeutic Target
Authors: New Jacob , Arnold Levi , Ananth Megha , Alvi Sameer , Thornton Mackenzie , Werner Lauryn , Tawfik Ossama , Dai Hongying , Shnayder Yelizaveta , Kakarala Kiran , Tsue Terance T. , Girod Douglas A. , Ding Wen-Xing , Anant Shrikant , Thomas Sufi Mary
Published: March 2023

Includes legends for all supplementary figures. S1: CAFs exhibit increased LC3 puncta per cell compared to NF. S2: CAF autophagy inhibition significantly decreases HNSCC in vitro progression. S3: IL-6 and IL-8 induce fibroblast autophagy. S4: bFGF treatment increases autophagy regulated secreted factors. S5: Autophagy inhibition reduces HNSCC in combination therapy, and does not affect CAF proliferation.
Supplemental Figure Legend from Bone Pain Induced by Multiple Myeloma Is Reduced by Targeting V-ATPase and ASIC3
Authors: Hiasa Masahiro , Okui Tatsuo , Allette Yohance M. , Ripsch Matthew S. , Sun-Wada Ge-Hong , Wakabayashi Hiroki , Roodman G. David , White Fletcher A. , Yoneda Toshiyuki
Published: March 2023

Legend for Supplementary Figures S1-S2.
Supplementary materials and methods from CD155T/TIGIT Signaling Regulates CD8+ T-cell Metabolism and Promotes Tumor Progression in Human Gastric Cancer
Authors: He Weiling , Zhang Hui , Han Fei , Chen Xinlin , Lin Run , Wang Wei , Qiu Haibo , Zhuang Zhenhong , Liao Qi , Zhang Weijing , Cai Qinbo , Cui Yongmei , Jiang Wenting , Wang Han , Ke Zunfu
Published: March 2023

This file includes supplementary methods that describe the details of transwell assay, RT-PCR, western blotting, immunohistochemistry and CTC enrichment by NanoVelcro system.
Supplementary Table 2 from CD155T/TIGIT Signaling Regulates CD8+ T-cell Metabolism and Promotes Tumor Progression in Human Gastric Cancer
Authors: He Weiling , Zhang Hui , Han Fei , Chen Xinlin , Lin Run , Wang Wei , Qiu Haibo , Zhuang Zhenhong , Liao Qi , Zhang Weijing , Cai Qinbo , Cui Yongmei , Jiang Wenting , Wang Han , Ke Zunfu
Published: March 2023

Supplementary Table 2 includes the primers for RT-PCR.
Supplementary Table S5 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

TCGA tumor purity correlations.
Figure S2 from miR-519d Promotes Melanoma Progression by Downregulating EphA4
Authors: Hua Kuo-Tai , Hong Jin-Bong , Sheen Yi-Shuan , Huang Hsin-Yi , Huang Yi-Ling , Chen Jau-Shiuh , Liao Yi-Hua
Published: March 2023

Suppl. Figure 2. After miR-519d overexpression, no significant decrease of protein expression levels of PTEN, PPAR1, p21, the predicted targets of miR-519d by miRanda and TargetScan algorithms.
Supplementary Table S2 from Anti-Folate Receptor-α IgE but not IgG Recruits Macrophages to Attack Tumors via TNFα/MCP-1 Signaling
Authors: Josephs Debra H. , Bax Heather J. , Dodev Tihomir , Georgouli Mirella , Nakamura Mano , Pellizzari Giulia , Saul Louise , Karagiannis Panagiotis , Cheung Anthony , Herraiz Cecilia , Ilieva Kristina M. , Correa Isabel , Fittall Matthew , Crescioli Silvia , Gazinska Patrycja , Woodman Natalie , Mele Silvia , Chiaruttini Giulia , Gilbert Amy E. , Koers Alexander , Bracher Marguerite , Selkirk Christopher , Lentfer Heike , Barton Claire , Lever Elliott , Muirhead Gareth , Tsoka Sophia , Canevari Silvana , Figini Mariangela , Montes Ana , Downes Noel , Dombrowicz David , Corrigan Christopher J. , Beavil Andrew J. , Nestle Frank O. , Jones Paul S. , Gould Hannah J. , Sanz-Moreno Victoria , Blower Philip J. , Spicer James F. , Karagiannis Sophia N.
Published: March 2023

Table of Healthy Volunteer Characteristics
Supplementary Figure S4 from Anti-Folate Receptor-α IgE but not IgG Recruits Macrophages to Attack Tumors via TNFα/MCP-1 Signaling
Authors: Josephs Debra H. , Bax Heather J. , Dodev Tihomir , Georgouli Mirella , Nakamura Mano , Pellizzari Giulia , Saul Louise , Karagiannis Panagiotis , Cheung Anthony , Herraiz Cecilia , Ilieva Kristina M. , Correa Isabel , Fittall Matthew , Crescioli Silvia , Gazinska Patrycja , Woodman Natalie , Mele Silvia , Chiaruttini Giulia , Gilbert Amy E. , Koers Alexander , Bracher Marguerite , Selkirk Christopher , Lentfer Heike , Barton Claire , Lever Elliott , Muirhead Gareth , Tsoka Sophia , Canevari Silvana , Figini Mariangela , Montes Ana , Downes Noel , Dombrowicz David , Corrigan Christopher J. , Beavil Andrew J. , Nestle Frank O. , Jones Paul S. , Gould Hannah J. , Sanz-Moreno Victoria , Blower Philip J. , Spicer James F. , Karagiannis Sophia N.
Published: March 2023

Evaluation of FRalpha expression by tumor cell lines
Figure S6 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

Effects of STAT3-Y705F mutants on miR-520d-5p.
Supplemental Figure 3 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 3. Integrative analysis of methylation and gene expression. The methylation level for the five most differentially expressed genes (listed at the top of each page), for which also methylation data was available, is shown in Panels A-E for each gene. Chromosomal position of the corresponding gene is shown on the x-axis, and the methylation in percentage is shown on the y-axis. Each star represents one CpG. CpG''s for BB are shown in green, while CpG''s for FB are shown in orange. For both types a LOWESS (Locally Weighted Scatterplot Smoothing) smoother was used to create a "regression line". The boxplot in panel F for each gene presents the normalized gene expression for both samples (BB and FB) for the five previously picked genes. Again, green indicates a BB-sample and orange indicates a FB-sample. Each box visualizes two normalized gene expressions (two replicates).
Supplemental Figure 2 from Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression
Authors: Vivian Carolyn J. , Brinker Amanda E. , Graw Stefan , Koestler Devin C. , Legendre Christophe , Gooden Gerald C. , Salhia Bodour , Welch Danny R.
Published: March 2023

Supplemental Figure 2. Deduplication and alignment statistics. a. Bismark v0.10.1 was used for alignment and deduplication. Duplicates were discarded using deduplicate_bismark perl script. With total number of alignments analyzed (red), total number of duplicated alignments removed (green) and total count of de-duplicated sequences (blue). b. Total sequence pairs analyzed (yellow), number of paired-end alignments with a unique hit (green), sequence pairs with no alignment (light blue), sequence pairs that did not map (blue), sequence pairs that were discarded due to no genomic sequence extracted (pink)
Supplemental Figure Legends from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

Supplemental Figure Legends
Supplementary Legends from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

Legends describing each of the supplementary figures and tables
Supplemental Figure 5 from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

PD-L1 mini-body is expressed at tumor site 10 days post-injection of HER2.CAR T-cells, but minimally impacts CD4+ T-cell phenotype long-term.
Supplemental Figure 3 from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

Anti-PD-L1 antibody and PD-L1 mini-body enhance HER2.CAR T-cell proliferation in vitro.
Supplementary Figure Legend from EZH2 Modifies Sunitinib Resistance in Renal Cell Carcinoma by Kinome Reprogramming
Authors: Adelaiye-Ogala Remi , Budka Justin , Damayanti Nur P. , Arrington Justine , Ferris Mary , Hsu Chuan-Chih , Chintala Sreenivasulu , Orillion Ashley , Miles Kiersten Marie , Shen Li , Elbanna May , Ciamporcero Eric , Arisa Sreevani , Pettazzoni Piergiorgio , Draetta Giulio F. , Seshadri Mukund , Hancock Bradley , Radovich Milan , Kota Janaiah , Buck Michael , Keilhack Heike , McCarthy Brian P. , Persohn Scott A. , Territo Paul R. , Zang Yong , Irudayaraj Joseph , Tao W. Andy , Hollenhorst Peter , Pili Roberto
Published: March 2023

Supplementary Figure Legend
Supplemental Figures from EZH2 Modifies Sunitinib Resistance in Renal Cell Carcinoma by Kinome Reprogramming
Authors: Adelaiye-Ogala Remi , Budka Justin , Damayanti Nur P. , Arrington Justine , Ferris Mary , Hsu Chuan-Chih , Chintala Sreenivasulu , Orillion Ashley , Miles Kiersten Marie , Shen Li , Elbanna May , Ciamporcero Eric , Arisa Sreevani , Pettazzoni Piergiorgio , Draetta Giulio F. , Seshadri Mukund , Hancock Bradley , Radovich Milan , Kota Janaiah , Buck Michael , Keilhack Heike , McCarthy Brian P. , Persohn Scott A. , Territo Paul R. , Zang Yong , Irudayaraj Joseph , Tao W. Andy , Hollenhorst Peter , Pili Roberto
Published: March 2023

Supplemental data on additional models to support the role of EZH2 in RTKi resistance
Supplementary File 3 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

Pharmacodynamic markers
Supplementary File 2 from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

Pharmacodynamic changes (pathways)
Extended Methods from Mass Spectrometry–Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Authors: Mundt Filip , Rajput Sandeep , Li Shunqiang , Ruggles Kelly V. , Mooradian Arshag D. , Mertins Philipp , Gillette Michael A. , Krug Karsten , Guo Zhanfang , Hoog Jeremy , Erdmann-Gilmore Petra , Primeau Tina , Huang Shixia , Edwards Dean P. , Wang Xiaowei , Wang Xuya , Kawaler Emily , Mani D.R. , Clauser Karl R. , Gao Feng , Luo Jingqin , Davies Sherri R. , Johnson Gary L. , Huang Kuan-lin , Yoon Christopher J. , Ding Li , Fenyö David , Ellis Matthew J. , Townsend R. Reid , Held Jason M. , Carr Steven A. , Ma Cynthia X.
Published: March 2023

Extended Materials and Methods with in depth details about experimental procedures and protocols
Supplementary Information from Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma
Authors: Lin De-Chen , Mayakonda Anand , Dinh Huy Q. , Huang Pinbo , Lin Lehang , Liu Xiaoping , Ding Ling-wen , Wang Jie , Berman Benjamin P. , Song Er-Wei , Yin Dong , Koeffler H. Phillip
Published: March 2023

File containing Supplementary methods and figure legends
Supplementary Figure S5 from ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer
Authors: Shukla Vivek , Rao Mahadev , Zhang Hongen , Beers Jeanette , Wangsa Darawalee , Wangsa Danny , Buishand Floryne O. , Wang Yonghong , Yu Zhiya , Stevenson Holly S. , Reardon Emily S. , McLoughlin Kaitlin C. , Kaufman Andrew S. , Payabyab Eden C. , Hong Julie A. , Zhang Mary , Davis Sean , Edelman Daniel , Chen Guokai , Miettinen Markku M. , Restifo Nicholas P. , Ried Thomas , Meltzer Paul A. , Schrump David S.
Published: March 2023

Overexpression of ASXL3 is independent of DNA methylation status in the ASXL3 promoter
Supplementary Figure S1 from ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer
Authors: Shukla Vivek , Rao Mahadev , Zhang Hongen , Beers Jeanette , Wangsa Darawalee , Wangsa Danny , Buishand Floryne O. , Wang Yonghong , Yu Zhiya , Stevenson Holly S. , Reardon Emily S. , McLoughlin Kaitlin C. , Kaufman Andrew S. , Payabyab Eden C. , Hong Julie A. , Zhang Mary , Davis Sean , Edelman Daniel , Chen Guokai , Miettinen Markku M. , Restifo Nicholas P. , Ried Thomas , Meltzer Paul A. , Schrump David S.
Published: March 2023

Characterization of iPSCs
Supplementary information from The STAT3-miRNA-92-Wnt Signaling Pathway Regulates Spheroid Formation and Malignant Progression in Ovarian Cancer
Authors: Chen Min-Wei , Yang Shu-Ting , Chien Ming-Hsien , Hua Kuo-Tai , Wu Chin-Jui , Hsiao S.M. , Lin Hao , Hsiao Michael , Su Jen-Liang , Wei Lin-Hung
Published: March 2023

Table S1. Target sequence of STAT3 shRNAs Table S2. Primers sequence of miR-92a and pre-miR-92a QPCR Table S3, Clinicopathologic characteristics of patients with epithelial ovarian cancer Fig.S1. STAT3 silencing by shRNA in EOC cell lines inhibits the cell viability in 3-dimensional cultures. Fig.S2. Immunoblot analysis of SKOV3/SKOV3 STAT3-KD cells for the expression of cleaved-PARP, Bcl-xL, and xIAP. b-actin was used as a loading control. Fig.S3. Top, representative spheroids formed by ES2 scramble/ES2 STAT3-KD cells treated with or without paclitaxel (PTX). Bottom, plot of the number of spheroids formed per 1000 cells in selected cells. Error bars represent the SD from triplicate cultures.
Supplementary Figure Legends from PP2A Inactivation Mediated by PPP2R4 Haploinsufficiency Promotes Cancer Development
Authors: Sents Ward , Meeusen Bob , Kalev Petar , Radaelli Enrico , Sagaert Xavier , Miermans Eline , Haesen Dorien , Lambrecht Caroline , Dewerchin Mieke , Carmeliet Peter , Westermarck Jukka , Sablina Anna , Janssens Veerle
Published: March 2023

Supplementary Figure legends
Figure S4 from PP2A Inactivation Mediated by PPP2R4 Haploinsufficiency Promotes Cancer Development
Authors: Sents Ward , Meeusen Bob , Kalev Petar , Radaelli Enrico , Sagaert Xavier , Miermans Eline , Haesen Dorien , Lambrecht Caroline , Dewerchin Mieke , Carmeliet Peter , Westermarck Jukka , Sablina Anna , Janssens Veerle
Published: March 2023

PTPA and PP2A subunit expression in WT, Ptpa +/gt and Ptpa gt/gt healthy and neoplastic spleens.
Supplementary Fig. 7 from Biomarker-Based PET Imaging of Diffuse Intrinsic Pontine Glioma in Mouse Models
Authors: Kossatz Susanne , Carney Brandon , Schweitzer Melanie , Carlucci Giuseppe , Miloushev Vesselin Z. , Maachani Uday B. , Rajappa Prajwal , Keshari Kayvan R. , Pisapia David , Weber Wolfgang A. , Souweidane Mark M. , Reiner Thomas
Published: March 2023

Monitoring tumor growth using [18F]PARPi. Display of weekly imaging of tumor development in adult ntv-a;p53fl/fl mice at the indicated time after DF1 cell injection. PET/CT imaging was always conducted 2 h p.i. of [18F]PARPi. Animals were sacrificed after week 6 and tumor presence was confirmed histologically. (b) One animal showed no increase in [18F]PARPi uptake over the weeks and we confirmed histologically that tumor development was absent in this case.
Supplementary figure 3 from Aspirin Suppresses Growth in PI3K-Mutant Breast Cancer by Activating AMPK and Inhibiting mTORC1 Signaling
Authors: Henry Whitney S. , Laszewski Tyler , Tsang Tiffany , Beca Francisco , Beck Andrew H. , McAllister Sandra S. , Toker Alex
Published: March 2023

Supplementary figure 3. Sulforhodamine assay, MCF10A cells expressing JP1520-GFP, PIK3CA-WT and PIK3CA H1047R respectively were treated with increasing concentrations of aspirin and 0.5microM BYL719 for 48 hrs.
Supplementary figure 2 from Aspirin Suppresses Growth in PI3K-Mutant Breast Cancer by Activating AMPK and Inhibiting mTORC1 Signaling
Authors: Henry Whitney S. , Laszewski Tyler , Tsang Tiffany , Beca Francisco , Beck Andrew H. , McAllister Sandra S. , Toker Alex
Published: March 2023

Supplementary figure 2. Aspirin treatment results in activation of AMPK and decrease in mTORC1 signaling.
Supplementary figure 3 from Sunitinib Treatment Enhances Metastasis of Innately Drug-Resistant Breast Tumors
Authors: Wragg Joseph W. , Heath Victoria L. , Bicknell Roy
Published: March 2023

Representative tumours from the non-responsive (square), responsive (circle) and untreated (cross) group at each time period, were subjected to microarray transcriptomic analysis. Graphs showing individual tumour growth data points and mean tumour size of the selected tumours over the period of the experiment. N-numbers for each experiment are shown.
Supplementary Table S6 from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

Grade ≥ 3 adverse events (28 patients)
Supplementary Table S3 from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

Top-10 probesets with a different response to irradiation between the four patient groups.
Supplementary Table S2 from Prostate Cancer Patients with Late Radiation Toxicity Exhibit Reduced Expression of Genes Involved in DNA Double-Strand Break Repair and Homologous Recombination
Authors: van Oorschot Bregje , Uitterhoeve Lon , Oomen Ilja , ten Cate Rosemarie , Medema Jan Paul , Vrieling Harry , Stalpers Lukas J.A. , Moerland Perry D. , Franken Nicolaas A.P.
Published: March 2023

A CAMERA geneset test was performed to identify sets consisting of genes that are highly ranked in terms of differential expression upon irradiation relative to genes not in the set.
Supplementary Figures 1 through 8 from Basophils Promote Tumor Rejection via Chemotaxis and Infiltration of CD8+ T Cells
Authors: Sektioglu Ibrahim M. , Carretero Rafael , Bulbuc Nadja , Bald Tobias , Tüting Thomas , Rudensky Alexander Y. , Hämmerling Günter J.
Published: March 2023

Supplementary Figure 1 shows that DT application in Foxp3DTR and Foxp3.LuciDTR4 mice resulted in different degree of Treg depletion not only in tumor but also in blood, spleen and lymph nodes. Supplementary Figure 2 demonstrates Treg depletion in Foxp3DTR mice, but not Treg depletion in Foxp3.LuciDTR4 mice, induced complete rejection of established B16 tumors, similarly to what we observed with HCmel12 tumors. Supplementary Figure 3 shows that Adoptive cell reconstitution of Treg-depleted Foxp3DTR mice with increasing numbers of purified CD4+ CD25+ Tregs isolated from wild-type mice impaired rejection of HCmel12 tumors, indicating that relatively small number of Treg were able prevent immune-mediated tumor rejection. Supplementary Figure 4 demonstrates that Basophil depletion impaired infiltration of T cells into Treg-depleted B16 tumors and rejection of B16 tumors observed after Treg depletion in Foxp3DTR mice, which confirms our findings in HCmel12 setting. Supplementary Figure 5 shows that FcεRI was expressed only by basophils in HCmel12 tumors after Treg depletion in Foxp3DTR mice, showing that tumoral basophils can be selectively targeted by MAR-1 antibody, and basophil depletion resulted in reduced intratumoral expression of CCL3 and CCL4, indicating that basophils are the major source of intratumoral CCL3 and CCL4. Supplementary Figure 6 shows that Eosinophil depletion had no impact on rejection of HCmel12 tumors observed after Treg depletion in Foxp3DTR mice. Supplementary Figure 7 demonstrates that IL-3/anti-IL-3 antibody complex injection induced basophilia in not only in tumor but also in other organs in B16-OVA-bearing mice and this was associated with increased specific chemokines (CCL3 and CCL4) and cytokines (IL-4 and IL-13) in the tumor microenvironment. Supplementary Figure 8 shows that combination of adoptive transfer of tumor-specific CD8+ T cells with IL-3/anti-IL-3 antibody complex induces strong leukocyte subpopulation infiltration into B16-OVA tumors, in addition to OT-I CD8 T cells.
Supplementary Fig S1-S8 from Tim-3 Expression on Tumor-Infiltrating PD-1+CD8+ T Cells Correlates with Poor Clinical Outcome in Renal Cell Carcinoma
Authors: Granier Clémence , Dariane Charles , Combe Pierre , Verkarre Virginie , Urien Saïk , Badoual Cécile , Roussel Hélène , Mandavit Marion , Ravel Patrice , Sibony Mathilde , Biard Lucie , Radulescu Camélia , Vinatier Emeline , Benhamouda Nadine , Peyromaure Michael , Oudard Stéphane , Méjean Arnaud , Timsit Marc-Olivier , Gey Alain , Tartour Eric
Published: March 2023

Figure S1 : Heterogeneous distribution of various subpopulations of intratumor CD8+T cells defined by the differential expression of PD1 and Tim-3 using an in situ multiparametric immunofluorescence technique. Figure S2: PD-1 and Tim-3 co-expression on CD8+T cells (in situ IF analyzis) correlates with clinical parameters of RCC aggressiveness Figure S3 : Relationships between the total number of intratumor T cells and subpopulations of CD8+T cells and Progression Free Survival Figure S4: Heterogeneous distribution of various subpopulations of tumor-infiltrating CD8+T cells defined by the differential expression of PD1 and Tim-3 analyzed by cytometry Figure S5: Patients who co-expressed PD-1 and Tim-3 on CD8+T cells more often exhibited clear cell RCC histology Figure S6: Tim-3 expression was decreased on PD-1+CD8+T cells after treatment with collagenase Figure S7 : PD-1 and Tim-3 expression on renal cell carcinoma by in situ immunofluorescence analysis Figure S8 : Blockade experiments with anti-PD-1 and anti-Tim-3 on bulk TIL
Supplementary Material and Methods from RB Loss Promotes Prostate Cancer Metastasis
Authors: Thangavel Chellappagounder , Boopathi Ettickan , Liu Yi , Haber Alex , Ertel Adam , Bhardwaj Anshul , Addya Sankar , Williams Noelle , Ciment Stephen J. , Cotzia Paolo , Dean Jeffry L. , Snook Adam , McNair Chris , Price Matt , Hernandez James R. , Zhao Shuang G. , Birbe Ruth , McCarthy James B. , Turley Eva A. , Pienta Kenneth J. , Feng Felix Y. , Dicker Adam P. , Knudsen Karen E. , Den Robert B.
Published: March 2023

Supplemental Methods and Material
Supplementary Table 1 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 1: RT-qPCR primers sequences.
Supplemental Methods 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

Additional Experimental Procedure Information
Supplementary Dataset 5 from Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis
Authors: Rokavec Matjaz , Horst David , Hermeking Heiko
Published: March 2023

Expression and H3K27me3 changes
Supplemental Figure 6 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Intratumoral injection of nutlin-3a in the EL4 TME results in marked reduction of MDSCs in the TME and TDLNs.
Supplemental Figure 5 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Nutlin-3a induces p53-dependent cell death of WT lymphocytes and myeloid cells with different potency.
Supplemental Figure 4 from Local Activation of p53 in the Tumor Microenvironment Overcomes Immune Suppression and Enhances Antitumor Immunity
Authors: Guo Gang , Yu Miao , Xiao Wei , Celis Esteban , Cui Yan
Published: March 2023

Nutlin-3a induces immunogenic cell death of EL4 tumors.
Supplementary Dataset 2 from Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis
Authors: Rokavec Matjaz , Horst David , Hermeking Heiko
Published: March 2023

Expression and methylation changes
Supplementary Tables S1-S4, Figures S1-S4 from Biallelic Dicer1 Loss Mediated by aP2-Cre Drives Angiosarcoma
Authors: Hanna Jason A. , Drummond Catherine J. , Garcia Matthew R. , Go Jonathan C. , Finkelstein David , Rehg Jerold E. , Hatley Mark E.
Published: March 2023

This file contains four supplementary tables and four supplementary figures pertinent to the submitted manuscript as follows: Table S1 lists the Enrichr analysis of miRNA targets in angiosarcoma. Table S2 lists the antibodies used for immunohistochemistry. Table S3 lists the SYBR primers and Taqman probes used for qRT-PCR. Table S4 lists the antibodies used for immunoblots. Figure S1 shows Dicer1 deletion in adipose tissue. Figure S2 displays angiosarcomas in the lungs of aP2-Cre;Dicer1Flox/- mice. Figure S3 compares mouse and human angiosarcomas. Figure S4 illustrates the interaction of the miR~23~27~24 cluster with gene targets in angiosarcoma.
Supplementary Figure S6 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

H&E analyses of CD3+ tumor-infiltrating cells.
Supplementary Figure S4 from T Cells Redirected to a Minor Histocompatibility Antigen Instruct Intratumoral TNFα Expression and Empower Adoptive Cell Therapy for Solid Tumors
Authors: Manzo Teresa , Sturmheit Tabea , Basso Veronica , Petrozziello Elisabetta , Hess Michelini Rodrigo , Riba Michela , Freschi Massimo , Elia Angela R. , Grioni Matteo , Curnis Flavio , Protti Maria Pia , Schumacher Ton N. , Debets Reno , Swartz Melody A. , Corti Angelo , Bellone Matteo , Mondino Anna
Published: March 2023

In vitro responsiveness of Tumor and Allo/Y-redirected T cells.
Supplementary Figures S6 -S11 from DDB2 Is a Novel Regulator of Wnt Signaling in Colon Cancer
Authors: Huang Shuo , Fantini Damiano , Merrill Bradley J. , Bagchi Srilata , Guzman Grace , Raychaudhuri Pradip
Published: March 2023

Figure S6: Association of DDB2, TCF4 and β-catenin on Rnf43 upstream region and intron regions.Figure S7: EZH2 and PAF are required for Rnf43 expression.Figure S8: DDB2 is required for the RNF43-mediated sequestration of TCF4 to the nuclear membrane.Figure S9: WES showed missense mutation in Ctnnb1 gene.Figure S10: DDB2 regulates RNF43 and Wnt target gene expression in normal colonic tissues.Figure S11: Model of how DDB2 regulates Wnt pathway and colon cancer development through RNF43.