bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data Fig. 6 from Negative Regulation of p53-Induced Senescence by N-WASP Is Crucial for DMBA/TPA-Induced Skin Tumor Formation
Authors: Li Hui , Petersen Simon , Garcia Mariscal Alberto , Brakebusch Cord
Published: April 2023

Senescence of N-WASP ko keratinocytes is dependent on p16Ink4a and p21
Supplementary Data Fig. 1 from Negative Regulation of p53-Induced Senescence by N-WASP Is Crucial for DMBA/TPA-Induced Skin Tumor Formation
Authors: Li Hui , Petersen Simon , Garcia Mariscal Alberto , Brakebusch Cord
Published: April 2023

Skin tumors and effects of IL-23 on senescence development
Supplementary Data 7 from Blockade of a Laminin-411–Notch Axis with CRISPR/Cas9 or a Nanobioconjugate Inhibits Glioblastoma Growth through Tumor-Microenvironment Cross-talk
Authors: Sun Tao , Patil Rameshwar , Galstyan Anna , Klymyshyn Dmytro , Ding Hui , Chesnokova Alexandra , Cavenee Webster K. , Furnari Frank B. , Ljubimov Vladimir A. , Shatalova Ekaterina S. , Wagner Shawn , Li Debiao , Mamelak Adam N. , Bannykh Serguei I. , Patil Chirag G. , Rudnick Jeremy D. , Hu Jethro , Grodzinski Zachary B. , Rekechenetskiy Arthur , Falahatian Vida , Lyubimov Alexander V. , Chen Yongmei L. , Leoh Lai S. , Daniels-Wells Tracy R. , Penichet Manuel L. , Holler Eggehard , Ljubimov Alexander V. , Black Keith L. , Ljubimova Julia Y.
Published: April 2023

Figures S8 and S9. Quantification of expression of laminin-411 β1 chain, its binding β1 integrin, Notch family members and other stem cell markers after nanobioconjugate treatment. All markers were significantly suppressed in treated tumors.
Supplementary Data from Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor Cells In Vivo
Authors: Bushnell Grace G. , Hardas Tejaswini P. , Hartfield Rachel M. , Zhang Yining , Oakes Robert S. , Ronquist Scott , Chen Haiming , Rajapakse Indika , Wicha Max S. , Jeruss Jacqueline S. , Shea Lonnie D.
Published: April 2023

1. Fig S1: Gating strategy for flow cytometric assays 2. Fig S2: Metastatic lung tumor burden for LUNG and LUNG2 lines developed from mice with and without scaffolds 3. Fig S3: Mutational analysis of cell lines by whole exome sequencing 4. Table S1: Table of unique mutations identified for each cell line by whole exome sequencing 5. Table S2: Table of Gene ontology terms significantly altered in genes with mutations in SCAF, PT and LUNG cell lines 6. Fig S4: RNAseq supplemental information 7. Fig S5: Schematic of multiscale Hi-C analysis 8. Fig S6: Hi-C does not reveal additional copy number variations, translocations, or breakpoint mutations between SCAF and PT cell line. 9. Table S3: Table of KEGG pathways investigated for structure/function changes
Figure S1 from Selective EGLN Inhibition Enables Ablative Radiotherapy and Improves Survival in Unresectable Pancreatic Cancer
Authors: Fujimoto Tara N. , Colbert Lauren E. , Huang Yanqing , Molkentine Jessica M. , Deorukhkar Amit , Baseler Laura , de la Cruz Bonilla Marimar , Yu Meifang , Lin Daniel , Gupta Sonal , Cabeceiras Peter K. , Kingsley Charles V. , Tailor Ramesh C. , Sawakuchi Gabriel O. , Koay Eugene J. , Piwnica-Worms Helen , Maitra Anirban , Taniguchi Cullen M.
Published: April 2023

Raw Western blots for all figures
Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Authors: Buckley Melissa A. , Woods Nicholas T. , Tyrer Jonathan P. , Mendoza-Fandiño Gustavo , Lawrenson Kate , Hazelett Dennis J. , Najafabadi Hamed S. , Gjyshi Anxhela , Carvalho Renato S. , Lyra Paulo C. , Coetzee Simon G. , Shen Howard C. , Yang Ally W. , Earp Madalene A. , Yoder Sean J. , Risch Harvey , Chenevix-Trench Georgia , Ramus Susan J. , Phelan Catherine M. , Coetzee Gerhard A. , Noushmehr Houtan , Hughes Timothy R. , Sellers Thomas A. , Goode Ellen L. , Pharoah Paul D. , Gayther Simon A. , Monteiro Alvaro N.A.
Published: April 2023

List of 134 SNPs in linkage disequilibrium (r2 {greater than or equal to} 0.3) with rs3814113 (based on 1000GP v3), selected for functional analysis.
Supplementary Figure S8. WEE1 inhibitor in combination with IR inhibits cellular proliferation of normal and tumor cells. from STING Promotes Homeostasis via Regulation of Cell Proliferation and Chromosomal Stability
Authors: Ranoa Diana Rose E. , Widau Ryan C. , Mallon Stephen , Parekh Akash D. , Nicolae Claudia M. , Huang Xiaona , Bolt Michael J. , Arina Ainhoa , Parry Renate , Kron Stephen J. , Moldovan George-Lucian , Khodarev Nikolai N. , Weichselbaum Ralph R.
Published: April 2023

(A) Quantification of bands from Western gel shown in Main Figure 5D using Image J. The pixel units obtained for each protein band was normalized to the pixel units calculated from their respective b-Actin loading control. (B-E) Kinetic analysis of WT MEFs (B) as well as shScrambled D54 (C), HCT116 (D), and SCC61 (E) proliferation in vitro were measured over time in response to WEE1 inhibitor MK1775 {plus minus} IR (6 Gy) using the IncuCyte live cell imaging system. In vitro growth curve data are representative of at least three experiments, each with n = 3 per group. P-values were determined using unpaired Student's t-test. Error bars are SEM. *P < 0.05, **P < 0.01, ***P < 0.005.
Supplementary Information from Antibody-Mediated Endocytosis of Polysialic Acid Enables Intracellular Delivery and Cytotoxicity of a Glycan-Directed Antibody–Drug Conjugate
Authors: Cox Emily C. , Thornlow Dana N. , Jones Michaela A. , Fuller Jordan L. , Merritt Judith H. , Paszek Matthew J. , Alabi Christopher A. , DeLisa Matthew P.
Published: April 2023

This is a single pdf file that contains: (1) supplementary methods; (2) supplementary table 1 (microarray glycans), supplementary table 2 (ADCs), and supplementary table 3 (primers); (3) supplementary figure 1 (ch735 Ab expression/purification), supplementary figure 2 (mo735 mAb ELISA), supplementary figure 3 (mo735 glycan microarray profiling), supplementary figure 4 (binding affinity data), supplementary figure 5 (histograms of Ab-stained cell lines), supplementary figure 6 (cell surface binding of cancer cell lines), supplementary figure 7 (CRISPR-Cas knockout cell lines), supplementary figure 8 (internalization of mo735), supplementary figure 9 (colocalization of mo735), and supplementary figure 10 (synthesis of ADC).
Supplementary Figure S3. STING confers radiosensitivity in a variety of human and mice cell lines. from STING Promotes Homeostasis via Regulation of Cell Proliferation and Chromosomal Stability
Authors: Ranoa Diana Rose E. , Widau Ryan C. , Mallon Stephen , Parekh Akash D. , Nicolae Claudia M. , Huang Xiaona , Bolt Michael J. , Arina Ainhoa , Parry Renate , Kron Stephen J. , Moldovan George-Lucian , Khodarev Nikolai N. , Weichselbaum Ralph R.
Published: April 2023

(A) Quantification of bands from Western gel shown in Main Figure 3A using Image J. The pixel units obtained for each protein band was normalized to the pixel units calculated from their respective b-Actin loading control. (B-G) Clonogenic survival of various human and mice tumor cell lines with stable shSTING knockdown in response to increasing dose of IR. (H-I) Cell viability assays of primary and immortalized MEFs isolated from WT and STING-/- mice in response to increasing IR dose. Data are representative of at least three experiments. P-values were determined using unpaired Student's t-test. Error bars are SEM. *P < 0.05, **P < 0.01, ***P < 0.005.
Table S4 from Spatiotemporal Regulation of ΔNp63 by TGFβ-Regulated miRNAs Is Essential for Cancer Metastasis
Authors: Bui Ngoc H.B. , Napoli Marco , Davis Andrew John , Abbas Hussein A. , Rajapakshe Kimal , Coarfa Cristian , Flores Elsa R.
Published: April 2023

Table S4. PCA scores for each patient in the four COCA molecular subtypes from TCGA.
Supplementary Data 2 from Inhibition of NF-κB–Dependent Signaling Enhances Sensitivity and Overcomes Resistance to BET Inhibition in Uveal Melanoma
Authors: Ambrosini Grazia , Do Catherine , Tycko Benjamin , Realubit Ronald B. , Karan Charles , Musi Elgilda , Carvajal Richard D. , Chua Vivian , Aplin Andrew E. , Schwartz Gary K.
Published: April 2023

PTL inhibits NF-kB activity and induces apoptosis in combination with PLX51107 in Omm1.3 cells
Figure S4 from Spatiotemporal Regulation of ΔNp63 by TGFβ-Regulated miRNAs Is Essential for Cancer Metastasis
Authors: Bui Ngoc H.B. , Napoli Marco , Davis Andrew John , Abbas Hussein A. , Rajapakshe Kimal , Coarfa Cristian , Flores Elsa R.
Published: April 2023

Figure S4. TGFÃŽÂ² inhibits expression of ÃŽÂ€�Np63 via canonical Smad-dependent signaling in breast cancer.
Supplementary Figure 1-11 from Overexpression of RUNX3 Represses RUNX1 to Drive Transformation of Myelodysplastic Syndrome
Authors: Yokomizo-Nakano Takako , Kubota Sho , Bai Jie , Hamashima Ai , Morii Mariko , Sun Yuqi , Katagiri Seiichiro , Iimori Mihoko , Kanai Akinori , Tanaka Daiki , Oshima Motohiko , Harada Yuka , Ohyashiki Kazuma , Iwama Atsushi , Harada Hironori , Osato Motomi , Sashida Goro
Published: April 2023

Supplementary Figure 1-11
Supplementary Data 3 from Overexpression of RUNX3 Represses RUNX1 to Drive Transformation of Myelodysplastic Syndrome
Authors: Yokomizo-Nakano Takako , Kubota Sho , Bai Jie , Hamashima Ai , Morii Mariko , Sun Yuqi , Katagiri Seiichiro , Iimori Mihoko , Kanai Akinori , Tanaka Daiki , Oshima Motohiko , Harada Yuka , Ohyashiki Kazuma , Iwama Atsushi , Harada Hironori , Osato Motomi , Sashida Goro
Published: April 2023

Runx1 target genes
Supplementary Data 1 from Overexpression of RUNX3 Represses RUNX1 to Drive Transformation of Myelodysplastic Syndrome
Authors: Yokomizo-Nakano Takako , Kubota Sho , Bai Jie , Hamashima Ai , Morii Mariko , Sun Yuqi , Katagiri Seiichiro , Iimori Mihoko , Kanai Akinori , Tanaka Daiki , Oshima Motohiko , Harada Yuka , Ohyashiki Kazuma , Iwama Atsushi , Harada Hironori , Osato Motomi , Sashida Goro
Published: April 2023

Up- and down-regulated genes
Supplementary Materials and Methods from Nicotinamide Phosphoribosyltransferase Acts as a Metabolic Gate for Mobilization of Myeloid-Derived Suppressor Cells
Authors: Travelli Cristina , Consonni Francesca Maria , Sangaletti Sabina , Storto Mariangela , Morlacchi Sara , Grolla Ambra A. , Galli Ubaldina , Tron Gian Cesare , Portararo Paola , Rimassa Lorenza , Pressiani Tiziana , Mazzone Massimiliano , Trovato Rosalinda , Ugel Stefano , Bronte Vincenzo , Tripodo Claudio , Colombo Mario P. , Genazzani Armando A. , Sica Antonio
Published: April 2023

Supplementary methods and list of materials
Figure S6 from Nicotinamide Phosphoribosyltransferase Acts as a Metabolic Gate for Mobilization of Myeloid-Derived Suppressor Cells
Authors: Travelli Cristina , Consonni Francesca Maria , Sangaletti Sabina , Storto Mariangela , Morlacchi Sara , Grolla Ambra A. , Galli Ubaldina , Tron Gian Cesare , Portararo Paola , Rimassa Lorenza , Pressiani Tiziana , Mazzone Massimiliano , Trovato Rosalinda , Ugel Stefano , Bronte Vincenzo , Tripodo Claudio , Colombo Mario P. , Genazzani Armando A. , Sica Antonio
Published: April 2023

G-CSF and M-CSF control NAMPT-dependent regulation of CXCR4
Supplementary Data from Retrodifferentiation of Human Tumor Hepatocytes to Stem Cells Leads to Metabolic Reprogramming and Chemoresistance
Authors: Fekir Karim , Dubois-Pot-Schneider Hélène , Désert Romain , Daniel Yoann , Glaise Denise , Rauch Claudine , Morel Fabrice , Fromenty Bernard , Musso Orlando , Cabillic Florian , Corlu Anne
Published: April 2023

Supplemental Table 3 provides the lists of genes significantly deregulated between HepaRG-Spheres and HepaRG-D10 cells and between HepaRG-SP and HepaRG-D10 cells.
Movie S1 from Targeting Novel Sodium Iodide Symporter Interactors ADP-Ribosylation Factor 4 and Valosin-Containing Protein Enhances Radioiodine Uptake
Authors: Fletcher Alice , Read Martin L. , Thornton Caitlin E.M. , Larner Dean P. , Poole Vikki L. , Brookes Katie , Nieto Hannah R. , Alshahrani Mohammed , Thompson Rebecca J. , Lavery Gareth G. , Landa Iñigo , Fagin James A. , Campbell Moray J. , Boelaert Kristien , Turnell Andrew S. , Smith Vicki E. , McCabe Christopher J.
Published: April 2023

Significant co-localization and trafficking of ARF4-dsRED and NIS-GFP proteins in co-incident vesicles at the plasma membrane in HeLa cells
Supplementary Table S3 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Table S3 summaries primer sequences and probe for quantitative PCR or Northern blotting
Supplementary Table S1 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Table S1 shows clinicopathologic characteristics of 50 CRC patients
Supplementary Data from Smarcal1 and Zranb3 Protect Replication Forks from Myc-Induced DNA Replication Stress
Authors: Puccetti Matthew V. , Adams Clare M. , Kushinsky Saul , Eischen Christine M.
Published: April 2023

There are 7 Supplemental figures with figure legends. Figure S1. Generation of Zranb3 knockout mice; Figure S2. Loss of Smarcal1 alone does not affect replication fork stability; Figure S3. Zranb3 is not required for fork stability in the absence of Myc overexpression; Figure S4. Loss of Smarcal1 or Zranb3 does not alter B cell development in the bone marrow; Figure S5. Loss of Smarcal1 or Zranb3 does not affect the ability of bone marrow cells to differentiate into pro-B cells ex vivo; Figure S6. Overexpression of Myc combined with loss of Smarcal1 or Zranb3 does not alter B cell development in the bone marrow; Figure S7. Loss of Smarcal1 or Zranb3 does not affect pro-B cell growth.
Supplementary Table 6 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Table S6 indicates that PNO1 mRNA expression is significantly up-regulated in various types of malignancies, including CRC, lung cancer, and breast cancer.
Supplementary Table 5 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Table S5 shows 16 up-regulated genes and 10 predicted potential transcript factors in the global expression analysis
Table S1 from The Frequency of Ras Mutations in Cancer
Authors: Prior Ian A. , Hood Fiona E. , Hartley James L.
Published: April 2023

Comparison of KRAS mutation frequencies in each database. Significant variability in sampling depth and mutation frequency is evident between each database. Summary statistics from databases with tissue type classification are included together with disease-specific values when available.
Figure S2 from GARP Dampens Cancer Immunity by Sustaining Function and Accumulation of Regulatory T Cells in the Colon
Authors: Salem Mohammad , Wallace Caroline , Velegraki Maria , Li Anqi , Ansa-Addo Ephraim , Metelli Alessandra , Kwon Hyunwoo , Riesenberg Brian , Wu Bill , Zhang Yongliang , Guglietta Silvia , Sun Shaoli , Liu Bei , Li Zihai
Published: April 2023

Mild Systemic Autoimmunity in Mice with GARP-/- Treg Cells
Supplementary Table 1 and Fig 1-8 including legends from Platelet-Specific PDGFB Ablation Impairs Tumor Vessel Integrity and Promotes Metastasis
Authors: Zhang Yanyu , Cedervall Jessica , Hamidi Anahita , Herre Melanie , Viitaniemi Kati , D'Amico Gabriela , Miao Zuoxiu , Unnithan Ragaseema Valsala Madhavan , Vaccaro Alessandra , van Hooren Luuk , Georganaki Maria , Thulin Åsa , Qiao Qi , Andrae Johanna , Siegbahn Agneta , Heldin Carl-Henrik , Alitalo Kari , Betsholtz Christer , Dimberg Anna , Olsson Anna-Karin
Published: April 2023

Supplementary Table 1 and Fig 1-8 including legends. Table S1: Observed and expected numbers of Pf4-Cre;Pdgfbfl/fl embryos at different developmental stages. Figure S1: Platelet-specific PDGFB knockout embryos display no obvious abnormalities. Figure S2: Platelet counts and proportion in peripheral blood from WT and pl-PDGFB KO mice. Figure S3: Generation of RIP1-Tag2 mice lacking PDGFB in platelets. Figure S4: Lack of platelet PDGFB does not affect the angiogenic switch or tumor growth in RT2 mice. Figure S5: Tumor vessels in MC38 colon carcinoma in mice with platelet-specific PDGFB ablation have impaired function and decreased pericyte coverage. Figure S6: Increased spontaneous lung metastasis in mice with platelet-specific PDGFB ablation in the HCmel12 melanoma model. Figure S7: Reduced pericyte coverage already in pre-tumorigenic tissue in mice lacking PDGFB in platelets. Figure S8: Expression of Cxcl3, Cxcl5, Cxcl7 and Cxcl15 in tumor tissue from Pf4-Cre- and Pf4-Cre+ mice.
Antibodies from Platelet-Specific PDGFB Ablation Impairs Tumor Vessel Integrity and Promotes Metastasis
Authors: Zhang Yanyu , Cedervall Jessica , Hamidi Anahita , Herre Melanie , Viitaniemi Kati , D'Amico Gabriela , Miao Zuoxiu , Unnithan Ragaseema Valsala Madhavan , Vaccaro Alessandra , van Hooren Luuk , Georganaki Maria , Thulin Åsa , Qiao Qi , Andrae Johanna , Siegbahn Agneta , Heldin Carl-Henrik , Alitalo Kari , Betsholtz Christer , Dimberg Anna , Olsson Anna-Karin
Published: April 2023

Antibody concentration and blocking conditions
Supplementary Table 1 from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

Supplementary Table 1
Supplementary Figure 5 from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

a. Immunohistochemistry for E-cadherin in six patients who have germline CDH1 mutations. Red long arrows denote cancer cells, short green arrows denote normal stomach glands. P: patient. For P16, normal stomach and cancer cells are shown in two separate panels. Scale bar = 50 μm. b. Amount of DNA in which the CDH1 promoter is methylated.
Fig. S9 from Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes
Authors: Oakes Robert S. , Bushnell Grace G. , Orbach Sophia M. , Kandagatla Pridvi , Zhang Yining , Morris Aaron H. , Hall Matthew S. , LaFaire Petrina , Decker Joseph T. , Hartfield Rachel M. , Brooks Michael D. , Wicha Max S. , Jeruss Jacqueline S. , Shea Lonnie D.
Published: April 2023

Additional data from post-excision model demonstrating the cohort survival curve and gene expression trajectories. (a) Kaplan-Meier survival analysis comparing TFC and TB mice that received mammary gland excisions. (b-k) Time course analysis for 10 gene panel. Error bars in line plots for gene expression and signature trajectory indicate SEM. The cohort size for each group is decreased by one at Day 21 due recurrence and animal censorship. For longitudinal data, statistics were performed via a linear mixed model. Post hoc simple effects analysis indicates significant differences (p<0.05) between (*) TFC and resistant, (â€¡) TFC and responsive, (&) resistant and responsive, (#) responsive and responsive Day 0 (pre-excision), and ($) resistant and resistant Day 0 (pre-excision) following significant (p<0.05) or trending (p<0.1) interactions in a two-way ANOVA (see Data File 4 for descriptive statistics, exact F and p values).
Supplementary Figures from Transcription Factors Involved in Tumorigenesis Are Over-Represented in Mutated Active DNA-Binding Sites in Neuroblastoma
Authors: Capasso Mario , Lasorsa Vito Alessandro , Cimmino Flora , Avitabile Marianna , Cantalupo Sueva , Montella Annalaura , De Angelis Biagio , Morini Martina , de Torres Carmen , Castellano Aurora , Locatelli Franco , Iolascon Achille
Published: April 2023

Supplementary Figures. Figure S1: Percentage of DHS regions shared by NB cell lines and other Encode cell lines; Figure S2: Descriptive statistics of Whole Genome Sequencing (WGS) of 14 normal-primary NB sample pairs; Figure S3: Somatic variants filtering summary; Figure S4: Results from mutational enrichment analysis; Figure S5: K-means clustering of NB samples; Figure S6: ADPRHL1 and MCFL1 genomic interactions with the mutated TFBS; Figure S7: TH deregulation by somatic regulatory variants.
Table S4 from An Integrative Gene Expression and Mathematical Flux Balance Analysis Identifies Targetable Redox Vulnerabilities in Melanoma Cells
Authors: Paudel B. Bishal , Lewis Joshua E. , Hardeman Keisha N. , Hayford Corey E. , Robbins Charles J. , Stauffer Philip E. , Codreanu Simona G. , Sherrod Stacy D. , McLean John A. , Kemp Melissa L. , Quaranta Vito
Published: April 2023

Table S4
Figure S1 from Loss of a Negative Feedback Loop between IRF8 and AR Promotes Prostate Cancer Growth and Enzalutamide Resistance
Authors: Wu Hongxi , You Linjun , Li Yan , Zhao Zhili , Shi Guangjiang , Chen Zhen , Wang Zhuo , Li Xianjing , Du Shijia , Ye Wanli , Gao Xiaofang , Duan Jingjing , Cheng Yan , Tao Weiyan , Bian Jinsong , Zhou Jin-Rong , Zhu Qingyi , Yang Yong
Published: April 2023

IRF8 protein is expressed in human PCa cells and not methylated.
Supplementary Data from HPV16 E5 Mediates Resistance to PD-L1 Blockade and Can Be Targeted with Rimantadine in Head and Neck Cancer
Authors: Miyauchi Sayuri , Sanders P. Dominick , Guram Kripa , Kim Sangwoo S. , Paolini Francesca , Venuti Aldo , Cohen Ezra E.W. , Gutkind J. Silvio , Califano Joseph A. , Sharabi Andrew B.
Published: April 2023

SF 1: Radiation combined with anti-PD-L1 immunotherapy activates CD8+ T-cells, but decreases regulatory T cell population in a head and neck cancer model. SF 2: N-FLAG E5 localized in Golgi apparatus and promoted lung metastasis. SF 3: Patients with high expression of HPV16 E5 have low HLA expression SF 4: Rimantadine enhances MHC expression and antigen-presentation on tumor cells. SF 5: Rimantadine inhibits cell proliferation in head and neck cancer cell lines and downregulates microtubule-associated molecules. ST 1: Clinical data of HNSCC Johns Hopkins University cohort ST 2: HPV status and HLA mRNA expression level
Supplementary Figure S2 from Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition
Authors: Liang Junbo , Zhao Hong , Diplas Bill H. , Liu Song , Liu Jianmei , Wang Dingding , Lu Yan , Zhu Qing , Wu Jiayu , Wang Wenjia , Yan Hai , Zeng Yi-Xin , Wang Xiaoyue , Jiao Yuchen
Published: April 2023

Figure S2. MAGeCK mle beta scores for all genes in ATRX WT and ATRX KO PLC/PRF/5 cells.
Supplementary Information from Localized Metabolomic Gradients in Patient-Derived Xenograft Models of Glioblastoma
Authors: Randall Elizabeth C. , Lopez Begoña G.C. , Peng Sen , Regan Michael S. , Abdelmoula Walid M. , Basu Sankha S. , Santagata Sandro , Yoon Haejin , Haigis Marcia C. , Agar Jeffrey N. , Tran Nhan L. , Elmquist William F. , White Forest M. , Sarkaria Jann N. , Agar Nathalie Y.R.
Published: April 2023

Supplementary results, Supplementary figures S1-S9 and Supplementary methods.
Supplementary Data File 1 from Localized Metabolomic Gradients in Patient-Derived Xenograft Models of Glioblastoma
Authors: Randall Elizabeth C. , Lopez Begoña G.C. , Peng Sen , Regan Michael S. , Abdelmoula Walid M. , Basu Sankha S. , Santagata Sandro , Yoon Haejin , Haigis Marcia C. , Agar Jeffrey N. , Tran Nhan L. , Elmquist William F. , White Forest M. , Sarkaria Jann N. , Agar Nathalie Y.R.
Published: April 2023

Annotated peaklists from MALDI FT ICR MSI data, including measured m/z, possible identification according to Lipid Maps database and associated Δppm.
Figure S3 from Oxygen-Enhanced Optoacoustic Tomography Reveals the Effectiveness of Targeting Heme and Oxidative Phosphorylation at Normalizing Tumor Vascular Oxygenation
Authors: Ghosh Poorva , Guo Yihang , Ashrafi Adnin , Chen Jingyu , Dey Sanchareeka , Zhong Shigen , Liu Jie , Campbell James , Konduri Purna Chaitanya , Gerberich Jeni , Garrossian Massoud , Mason Ralph P. , Zhang Li , Liu Li
Published: April 2023

Fig. S3. Treatment with HSP2 or CycT does not affect mitochondrial structural proteins in tumor tissues. (A) Representative IHC images of H1299 NSCLC tumor tissue sections and graphs showing the levels of the mitochondria marker TOMM20 in control, HSP2, and CycT-treated tumors. (B) Representative IHC images of H1299 tumor tissue sections and graphs showing the levels of the mitochondria marker VDAC1 in control, HSP2, and CycT-treated tumors. Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in treated mice were compared to the levels in untreated mice with a Welch 2-sample t-test. No statistical significance was detected in any group.
Supplementary Figures and Tables from ETV4 Is Necessary for Estrogen Signaling and Growth in Endometrial Cancer Cells
Authors: Rodriguez Adriana C. , Vahrenkamp Jeffery M. , Berrett Kristofer C. , Clark Kathleen A. , Guillen Katrin P. , Scherer Sandra D. , Yang Chieh-Hsiang , Welm Bryan E. , Janát-Amsbury Margit M. , Graves Barbara J. , Gertz Jason
Published: April 2023

SF1: ETV4 expression levels in endometrial cancer. SF2: Expression levels of ETV4 in candidate knockout clones. SF3: Short-term knockdown of ETV4 reduces ER genomic binding. SF4: Validation of rescue and overexpression of ETV4. SF5: Estrogen induced fold changes are higher in wildtype cells than ETV4 knockout cells and genes that lose estrogen induction are closer to ETV4 bound sites. SF6: Global chromatin accessibility is similar between wildtype and ETV4 knockout lines. SF7: Introduction of ETV4 in T-47D breast cancer cell line. SF8: GR localization does not change due to ETV4 loss. SF9: Growth phenotype observed in 2D growth of ETV4 knockout lines. SF10: ETV4 knockouts increase expression of cytokeratins, a marker of normal endometrium.
Table S9 from Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology
Authors: Failmezger Henrik , Muralidhar Sathya , Rullan Antonio , de Andrea Carlos E. , Sahai Erik , Yuan Yinyin
Published: April 2023

Comparison of pathways enriched for genes correlated with stromal barrier, as identified by CNx and lol
Figure S5 from Cancer Cell–Derived Matrisome Proteins Promote Metastasis in Pancreatic Ductal Adenocarcinoma
Authors: Tian Chenxi , Öhlund Daniel , Rickelt Steffen , Lidström Tommy , Huang Ying , Hao Liangliang , Zhao Renee T. , Franklin Oskar , Bhatia Sangeeta N. , Tuveson David A. , Hynes Richard O.
Published: April 2023

Example images for lungs after tail-vein injection and cells with TKS5 immunofluorescence staining.
Figure S4 from Cancer Cell–Derived Matrisome Proteins Promote Metastasis in Pancreatic Ductal Adenocarcinoma
Authors: Tian Chenxi , Öhlund Daniel , Rickelt Steffen , Lidström Tommy , Huang Ying , Hao Liangliang , Zhao Renee T. , Franklin Oskar , Bhatia Sangeeta N. , Tuveson David A. , Hynes Richard O.
Published: April 2023

QPCR with human-specific primers shows that AGRN promotes EMT in primary tumors.
Ingenuity Pathway Analysis from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches
Authors: Hebert Jess D. , Myers Samuel A. , Naba Alexandra , Abbruzzese Genevieve , Lamar John M. , Carr Steven A. , Hynes Richard O.
Published: April 2023

IPA predictions of potential upstream regulators
GSEA gene sets from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches
Authors: Hebert Jess D. , Myers Samuel A. , Naba Alexandra , Abbruzzese Genevieve , Lamar John M. , Carr Steven A. , Hynes Richard O.
Published: April 2023

Gene sets used to perform GSEA
Figure S2 from Cancer Cell–Derived Matrisome Proteins Promote Metastasis in Pancreatic Ductal Adenocarcinoma
Authors: Tian Chenxi , Öhlund Daniel , Rickelt Steffen , Lidström Tommy , Huang Ying , Hao Liangliang , Zhao Renee T. , Franklin Oskar , Bhatia Sangeeta N. , Tuveson David A. , Hynes Richard O.
Published: April 2023

In vitro proliferation assay for the overexpression and knockdown sets of cells.
Figure S5 from PET Reporter Gene Imaging and Ganciclovir-Mediated Ablation of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Murty Surya , Labanieh Louai , Murty Tara , Gowrishankar Gayatri , Haywood Tom , Alam Israt S. , Beinat Corinne , Robinson Elise , Aalipour Amin , Klysz Dorota D. , Cochran Jennifer R. , Majzner Robbie G. , Mackall Crystal L. , Gambhir Sanjiv S.
Published: April 2023

Figure S5 shows flow cytometry of spleens at 9 days following the final GCV treatment
Figure S4 from PET Reporter Gene Imaging and Ganciclovir-Mediated Ablation of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Murty Surya , Labanieh Louai , Murty Tara , Gowrishankar Gayatri , Haywood Tom , Alam Israt S. , Beinat Corinne , Robinson Elise , Aalipour Amin , Klysz Dorota D. , Cochran Jennifer R. , Majzner Robbie G. , Mackall Crystal L. , Gambhir Sanjiv S.
Published: April 2023

Figure S4 shows long-term monitoring of mice following GCV treatment, confirming persistent T-cell ablation
Figure S3 from PET Reporter Gene Imaging and Ganciclovir-Mediated Ablation of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Murty Surya , Labanieh Louai , Murty Tara , Gowrishankar Gayatri , Haywood Tom , Alam Israt S. , Beinat Corinne , Robinson Elise , Aalipour Amin , Klysz Dorota D. , Cochran Jennifer R. , Majzner Robbie G. , Mackall Crystal L. , Gambhir Sanjiv S.
Published: April 2023

FIgure S3 shows B7H3 CAR expression of remaining viable B7H3-sr39tk CAR T-cells after GCV treatment
Figure S3 from The PET-Tracer 89Zr-Df-IAB22M2C Enables Monitoring of Intratumoral CD8 T-cell Infiltrates in Tumor-Bearing Humanized Mice after T-cell Bispecific Antibody Treatment
Authors: Griessinger Christoph M. , Olafsen Tove , Mascioni Alessandro , Jiang Ziyue Karen , Zamilpa Charles , Jia Fang , Torgov Michael , Romero Jason M. , Marchioni Filippo , Satpayev Daulet , Lee Chenyu , Zhang Green , Nayak Tapan K. , Pincha Mudita , Amann Maria , Mohan Preethi L.B. , Richard Marine , Nicolini Valeria G. , Sam Johannes , Claus Christina , Ferrara Claudia , Brünker Peter , Bacac Marina , Umana Pablo , Rüttinger Dominik , Wilson Ian A. , Gudas Jean , Klein Christian , Tessier Jean J.L.
Published: April 2023

Figure S3 shows autoradiography slides after CEA-4-1BBL/CEA-TCB single or combo treatment.
Table S5 & 6 from ARRB1-Promoted NOTCH1 Degradation Is Suppressed by OncomiR miR-223 in T-cell Acute Lymphoblastic Leukemia
Authors: Shu Yi , Wang Yi , Lv Wen-Qiong , Peng Dan-Yi , Li Juan , Zhang Hang , Jiang Guang-Jie , Yang Bi-Jie , Liu Shan , Zhang Jia , Chen Yan-Hua , Tang Shi , Wan Ke-Xing , Yuan Jun-Tao , Guo Wei , Fu Guo , Qi Xin-Kun , Liu Zhi-Dai , Liu Hai-Yan , Yang Chao , Zhang Ling-Huan , Liu Fang-Jie , Yu Jie , Zhang Peng-Hui , Qu Bin , Zhao Hui , He Tong-Chuan , Zou Lin
Published: April 2023

Table S5 & 6. Supplementary Table 5. Oligocleotide List; Supplementary Table 6. Antibody List
Table S2 from ARRB1-Promoted NOTCH1 Degradation Is Suppressed by OncomiR miR-223 in T-cell Acute Lymphoblastic Leukemia
Authors: Shu Yi , Wang Yi , Lv Wen-Qiong , Peng Dan-Yi , Li Juan , Zhang Hang , Jiang Guang-Jie , Yang Bi-Jie , Liu Shan , Zhang Jia , Chen Yan-Hua , Tang Shi , Wan Ke-Xing , Yuan Jun-Tao , Guo Wei , Fu Guo , Qi Xin-Kun , Liu Zhi-Dai , Liu Hai-Yan , Yang Chao , Zhang Ling-Huan , Liu Fang-Jie , Yu Jie , Zhang Peng-Hui , Qu Bin , Zhao Hui , He Tong-Chuan , Zou Lin
Published: April 2023

Table S2, Supplementary Table2. The characteristics of T-ALL cases
Supplementary Data from ERK-Mediated Loss of miR-199a-3p and Induction of EGR1 Act as a “Toggle Switch” of GBM Cell Dedifferentiation into NANOG- and OCT4-Positive Cells
Authors: Almairac Fabien , Turchi Laurent , Sakakini Nathalie , Debruyne David Nicolas , Elkeurti Sarah , Gjernes Elisabet , Polo Beatrice , Bianchini Laurence , Fontaine Denys , Paquis Philippe , Chneiweiss Herve , Junier Marie-Pierre , Verrando Patrick , Burel-Vandenbos Fanny , Virolle Thierry
Published: April 2023

These figures describe that : dedifferentiation restores stem-like and tumorigenic properties (sup fig 5); EGFR and ERK inhibitions on the dedifferentiation process (sup fig 6 and 7).
Supplementary Data from ERK-Mediated Loss of miR-199a-3p and Induction of EGR1 Act as a “Toggle Switch” of GBM Cell Dedifferentiation into NANOG- and OCT4-Positive Cells
Authors: Almairac Fabien , Turchi Laurent , Sakakini Nathalie , Debruyne David Nicolas , Elkeurti Sarah , Gjernes Elisabet , Polo Beatrice , Bianchini Laurence , Fontaine Denys , Paquis Philippe , Chneiweiss Herve , Junier Marie-Pierre , Verrando Patrick , Burel-Vandenbos Fanny , Virolle Thierry
Published: April 2023

The supplemental figure 10 describes the acquisition of pluripotency markers by tumor cells freshly dissociated from tumors at a single cell level. The supplemental figure 11 shows the ability of EGF, PDGF, bFGF to induce or not the dedifferentiation process.
Supplementary Data 1 from Gain-of-Function Mutant p53 R273H Interacts with Replicating DNA and PARP1 in Breast Cancer
Authors: Xiao Gu , Lundine Devon , Annor George K. , Canar Jorge , Ellison Viola , Polotskaia Alla , Donabedian Patrick L. , Reiner Thomas , Khramtsova Galina F. , Olopade Olufunmilayo I. , Mazo Alexander , Bargonetti Jill
Published: April 2023

S1 Chromatin protein levels of mtp53, H2B and Lamin A were compared by Western blot analysis.
Table S1 from Integrin β4–Targeted Cancer Immunotherapies Inhibit Tumor Growth and Decrease Metastasis
Authors: Ruan Shasha , Lin Ming , Zhu Yong , Lum Lawrence , Thakur Archana , Jin Runming , Shao Wenlong , Zhang Yalei , Hu Yangyang , Huang Shiang , Hurt Elaine M. , Chang Alfred E. , Wicha Max S. , Li Qiao
Published: April 2023

Table S1 demonstrated that ITGB4-targeted immunotherapies with or without anti-PD-L1 did not significantly affect hematopoiesis.
Supplementary Material from Epigenetic SMAD3 Repression in Tumor-Associated Fibroblasts Impairs Fibrosis and Response to the Antifibrotic Drug Nintedanib in Lung Squamous Cell Carcinoma
Authors: Ikemori Rafael , Gabasa Marta , Duch Paula , Vizoso Miguel , Bragado Paloma , Arshakyan Marselina , Luis Iuliana-Cristiana , Marín Albert , Morán Sebastian , Castro Manuel , Fuster Gemma , Gea-Sorli Sabrina , Jauset Toni , Soucek Laura , Montuenga Luis M. , Esteller Manel , Monsó Eduard , Peinado Victor Ivo , Gascon Pere , Fillat Cristina , Hilberg Frank , Reguart Noemí , Alcaraz Jordi
Published: April 2023

Supplementary Material
Supplemental Legends from Rb and p53 Execute Distinct Roles in the Development of Pancreatic Neuroendocrine Tumors
Authors: Yamauchi Yuki , Kodama Yuzo , Shiokawa Masahiro , Kakiuchi Nobuyuki , Marui Saiko , Kuwada Takeshi , Sogabe Yuko , Tomono Teruko , Mima Atsushi , Morita Toshihiro , Matsumori Tomoaki , Ueda Tatsuki , Tsuda Motoyuki , Nishikawa Yoshihiro , Kuriyama Katsutoshi , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Masuda Atsuhiro , Tatsuoka Hisato , Yabe Daisuke , Minamiguchi Sachiko , Masui Toshihiko , Inagaki Nobuya , Uemoto Shinji , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Supplemental Figure legends and Table Legend
Legends of Supplementary Tables, and Supplementary References from Hybrid Epithelial–Mesenchymal Phenotypes Are Controlled by Microenvironmental Factors
Authors: Selvaggio Gianluca , Canato Sara , Pawar Archana , Monteiro Pedro T. , Guerreiro Patrícia S. , Brás M. Manuela , Janody Florence , Chaouiya Claudine
Published: April 2023

Legends of Supplementary Tables, and Supplementary References
Table S2 from Epigenetic CRISPR Screens Identify Npm1 as a Therapeutic Vulnerability in Non–Small Cell Lung Cancer
Authors: Li Fei , Ng Wai-Lung , Luster Troy A. , Hu Hai , Sviderskiy Vladislav O. , Dowling Catríona M. , Hollinshead Kate E.R. , Zouitine Paula , Zhang Hua , Huang Qingyuan , Ranieri Michela , Wang Wei , Fang Zhaoyuan , Chen Ting , Deng Jiehui , Zhao Kai , So Hon-Cheong , Khodadadi-Jamayran Alireza , Xu Mousheng , Karatza Angeliki , Pyon Val , Li Shuai , Pan Yuanwang , Labbe Kristen , Almonte Christina , Poirier John T. , Miller George , Possemato Richard , Qi Jun , Wong Kwok-Kin
Published: April 2023

Candidate lists for CRISPR screens
Supplementary Figure S3 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

The effects of BACH1 silencing on cellular migration in wild type KRAS cells. Details are described in methods and legends file (Supplementary_methods_and_legends).
Supplementary Tables from A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma
Authors: Wu Siqi , Zhang Liyuan , Deng Jieqiong , Guo Binbin , Li Fang , Wang Yirong , Wu Rui , Zhang Shenghua , Lu Jiachun , Zhou Yifeng
Published: April 2023

Supplementary Tables. Table S1. Distributions of characteristics among male ESCC patients in Chinese populations used for study. Table S2. Used Primers and shRNAs/siRNAs in this study. Table S3. Characteristics of cell lines used in this study.
Supplementary Figure S5 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure S5 shows the characterization of MCF7 cultures involving dispersed cells.
Supplementary methods from Transcriptionally Active Androgen Receptor Splice Variants Promote Hepatocellular Carcinoma Progression
Authors: Dauki Anees M. , Blachly James S. , Kautto Esko A. , Ezzat Sameera , Abdel-Rahman Mohamed H. , Coss Christopher C.
Published: April 2023

Supplementary methods and materials
Supplementary Table S2 from Intake of Dietary Fruit, Vegetables, and Fiber and Risk of Colorectal Cancer According to Molecular Subtypes: A Pooled Analysis of 9 Studies
Authors: Hidaka Akihisa , Harrison Tabitha A. , Cao Yin , Sakoda Lori C. , Barfield Richard , Giannakis Marios , Song Mingyang , Phipps Amanda I. , Figueiredo Jane C. , Zaidi Syed H. , Toland Amanda E. , Amitay Efrat L. , Berndt Sonja I. , Borozan Ivan , Chan Andrew T. , Gallinger Steven , Gunter Marc J. , Guinter Mark A. , Harlid Sophia , Hampel Heather , Jenkins Mark A. , Lin Yi , Moreno Victor , Newcomb Polly A. , Nishihara Reiko , Ogino Shuji , Obón-Santacana Mireia , Parfrey Patrick S. , Potter John D. , Slattery Martha L. , Steinfelder Robert S. , Um Caroline Y. , Wang Xiaoliang , Woods Michael O. , Van Guelpen Bethany , Thibodeau Stephen N. , Hoffmeister Michael , Sun Wei , Hsu Li , Buchanan Daniel D. , Campbell Peter T. , Peters Ulrike
Published: April 2023

Supplementary Table S2
Supplementary Data from ALPPL2 Is a Highly Specific and Targetable Tumor Cell Surface Antigen
Authors: Su Yang , Zhang Xin , Bidlingmaier Scott , Behrens Christopher R. , Lee Nam-Kyung , Liu Bin
Published: April 2023

Supplementary Tables and Figures
Figure S5 from Microenvironmental Cues Determine Tumor Cell Susceptibility to Neutrophil Cytotoxicity
Authors: Gershkovitz Maya , Fainsod-Levi Tanya , Khawaled Saleh , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Fridlender Zvi G. , Granot Zvi
Published: April 2023

Supplemental Figure S5. Metastatic seeding of BMP7 treated cells is not enhanced by neutrophil depletion in tumor baring mice. Representative images of lung associated GFP+ BMP7 treated cells in control (BMP7) and neutrophil depleted (BMP7 depletion) mice, 48 hrs following tail-vein injection.
Supplementary Figure S1 from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: April 2023

CD8/CD68 ratio is predictive of recurrence. Receiver Operating Characteristic (ROC) curve analysis for visceral recurrence (n=52, AUC=0.684, p=0.0350 by Mann-Whitney U test).
Supplementary FRET Methods from High PD-1/PD-L1 Checkpoint Interaction Infers Tumor Selection and Therapeutic Sensitivity to Anti-PD-1/PD-L1 Treatment
Authors: Sánchez-Magraner Lissete , Miles James , Baker Claire L. , Applebee Christopher J. , Lee Dae-Jin , Elsheikh Somaia , Lashin Shaimaa , Withers Katriona , Watts Andrew G. , Parry Richard , Edmead Christine , Lopez Jose Ignacio , Mehta Raj , Italiano Antoine , Ward Stephen G. , Parker Peter J. , Larijani Banafshé
Published: April 2023

Supplementary FRET Methods
Figure S7 from Normal Breast-Derived Epithelial Cells with Luminal and Intrinsic Subtype-Enriched Gene Expression Document Interindividual Differences in Their Differentiation Cascade
Authors: Kumar Brijesh , Prasad Mayuri , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Kalra Maitri , Marino Natascia , Storniolo Anna Maria , Rao Xi , Liu Sheng , Wan Jun , Liu Yunlong , Nakshatri Harikrishna
Published: April 2023

The effect of TGFβ1 on stem/differentiated cell associated cell surface marker expression.
Figure S6 from Normal Breast-Derived Epithelial Cells with Luminal and Intrinsic Subtype-Enriched Gene Expression Document Interindividual Differences in Their Differentiation Cascade
Authors: Kumar Brijesh , Prasad Mayuri , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Kalra Maitri , Marino Natascia , Storniolo Anna Maria , Rao Xi , Liu Sheng , Wan Jun , Liu Yunlong , Nakshatri Harikrishna
Published: April 2023

KTB cell lines show differences in basal activity of several signaling molecules.
Figure S4 from Obesity/Type 2 Diabetes-Associated Liver Tumors Are Sensitive to Cyclin D1 Deficiency
Authors: Luo Chi , Liang Jiaxin , Sharabi Kfir , Hatting Maximilian , Perry Elizabeth A. , Tavares Clint D.J. , Goyal Lipika , Srivastava Amitabh , Bilodeau Marc , Zhu Andrew X. , Sicinski Piotr , Puigserver Pere
Published: April 2023

Cyclin D1 dependency positively correlates with palbociclib sensitivity in liver cancer cells
Figures S1, S2, S3 from The D2 and D3 Sublineages of Human Papilloma Virus 16–Positive Cervical Cancer in Guatemala Differ in Integration Rate and Age of Diagnosis
Authors: Lou Hong , Boland Joseph F. , Torres-Gonzalez Edmundo , Albanez Anaseidy , Zhou Weiyin , Steinberg Mia K. , Diaw Lena , Mitchell Jason , Roberson David , Cullen Michael , Garland Lisa , Bass Sara , Burk Robert D. , Yeager Meredith , Wentzensen Nicolas , Schiffman Mark , Freites Enrique Alvirez , Gharzouzi Eduardo , Mirabello Lisa , Dean Michael
Published: April 2023

Supplementary Figures and legends
Supplementary Data Tables S1-S8 from A Wnt-Induced Phenotypic Switch in Cancer-Associated Fibroblasts Inhibits EMT in Colorectal Cancer
Authors: Mosa Mohammed H. , Michels Birgitta E. , Menche Constantin , Nicolas Adele M. , Darvishi Tahmineh , Greten Florian R. , Farin Henner F.
Published: April 2023

Supplementary Data Tables S1-S8 - Table S1. Details of all antibodies (A) and primer sequences (B) used in this study, Table S2. Differentially expressed genes of tumor organoids cultured in vitro, Table S3. Differentially expressed genes of FACS-purified tumor cells after organoid transplantation, Table S4. Differentially expressed genes of FACS-purified CAFs after organoid transplantation, Table S5. Differentially expressed genes of mouse fibroblasts cultured in vitro, Table S6. Summary of GSEA results, Table S7. iCAF and myCAF signatures, Table S8. Differentially expressed mouse genes identified in human CRC organoids upon xenotransplantation.
Supplementary Data Figures S1-S11 from A Wnt-Induced Phenotypic Switch in Cancer-Associated Fibroblasts Inhibits EMT in Colorectal Cancer
Authors: Mosa Mohammed H. , Michels Birgitta E. , Menche Constantin , Nicolas Adele M. , Darvishi Tahmineh , Greten Florian R. , Farin Henner F.
Published: April 2023

Figure S1. Generation of engineered tumor organoids, Figure S2. Characterization of Sfrp1-expressing organoids in vitro and upon transplantation, Figure S3. Characterization of APTK organoids upon transplantation, Figure S4. Characterization of Dkk1-expressing organoids in vitro and upon transplantation, Figure S5. Immunohistology of tumors after transplantation of organoids in NSG and Bl/6 mice, Figure S6. Study of tumor growth upon xenotransplantation of human CRC organoids, Figure S7. Analysis of stromal gene expression in tumors after xenotransplantation, Figure S8. Co-culture model to study the influence of fibroblast differentiation on tumor organoids, Figure S9. 'NicheNet' analysis for identification of candidate mediators of the stromal crosstalk, Figure S10. Phenotypic analysis of mice after fibroblast-specific deletion of β-catenin, Figure S11. Histologic characterization of tumor cell invasion after stromal Wnt inhibition.
Supplementary Figure 2 from Radiomic Detection of EGFR Mutations in NSCLC
Authors: Rossi Giovanni , Barabino Emanuele , Fedeli Alessandro , Ficarra Gianluca , Coco Simona , Russo Alessandro , Adamo Vincenzo , Buemi Francesco , Zullo Lodovica , Dono Mariella , De Luca Giuseppa , Longo Luca , Dal Bello Maria Giovanna , Tagliamento Marco , Alama Angela , Cittadini Giuseppe , Pronzato Paolo , Genova Carlo
Published: April 2023

Supplementary Figure 2
Supplementary Materials & Methods from YAP Orchestrates Heterotypic Endothelial Cell Communication via HGF/c-MET Signaling in Liver Tumorigenesis
Authors: Thomann Stefan , Weiler Sofia M.E. , Marquard Simone , Rose Fabian , Ball Claudia R. , Tóth Marcell , Wei Teng , Sticht Carsten , Fritzsche Sarah , Roessler Stephanie , De La Torre Carolina , Ryschich Eduard , Ermakova Olga , Mogler Carolin , Kazdal Daniel , Gretz Norbert , Glimm Hanno , Rempel Eugen , Schirmacher Peter , Breuhahn Kai
Published: April 2023

Supplementary Materials & Methods
Supplementary Data from A Very Long-Acting PARP Inhibitor Suppresses Cancer Cell Growth in DNA Repair-Deficient Tumor Models
Authors: Fontaine Shaun D. , Ashley Gary W. , Houghton Peter J. , Kurmasheva Raushan T. , Diolaiti Morgan , Ashworth Alan , Peer Cody J. , Nguyen Ryan , Figg William D. , Beckford-Vera Denis R. , Santi Daniel V.
Published: April 2023

Supplemental methods, data, and figures