bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S3 from Epstein–Barr Virus miRNA BART2-5p Promotes Metastasis of Nasopharyngeal Carcinoma by Suppressing RND3
Authors: Jiang Chen , Li Lei , Xiang Yan-Qun , Lung Maria Li , Zeng Tingting , Lu Jiabin , Tsao Sai Wah , Zeng Mu-Sheng , Yun Jing-Ping , Kwong Dora L.W. , Guan Xin-Yuan
Published: April 2023

Supplementary Figure 3 (a) CNE2 were transiently transfected with control mimic (Cel- 39), BART2-5p mimic, BART2-5p mimic + pcDNA3.1Vec, BART2-5p mimic + RND3 or BART2-5p and Y-27632 treatment. For control cells and BART2-5p transfected cells, F-Actin staining was performed to visualize stress fiber formation at 6 h after transfection. For cells transfected by BART2-5p and pcDNA3.1Vec or RND3 expressing vector, vector or RND3 was transfected 24 h earlier than transfection of BART2-5p to allow gene expression in cells. Pictures were taken at 6 h after transfection of BART2-5p. 1Î¼M ROCK inhibitor Y-27632 was added to culture medium for a 15min incubation at 6 h after transfection of BART2-5p before fixation. (b) CNE2 cells with BART2 expression or RND3 knock down were lysed for Western Blot. Either BART2 overexpression or RND3 knock down led to increased phosphorylated MLC2 and MYPT1. (c) Western Blot shows induced activation of ROCK signaling by BART2 in CNE2 cells could be abolished by reinstatement of RND3 or Y-27632 treatment. (d) Images of Western Blot show alteration of key components in ROCK signaling pathway in siBART2-5p transfected or RND3 overexpressed HONE-1 EBV (+/-) cells.
Supplementary Table and Supplementary Figures S1-S7 from Pomalidomide Alters Pancreatic Macrophage Populations to Generate an Immune-Responsive Environment at Precancerous and Cancerous Lesions
Authors: Bastea Ligia I. , Liou Geou-Yarh , Pandey Veethika , Fleming Alicia K. , von Roemeling Christina A. , Doeppler Heike , Li Zhimin , Qiu Yushi , Edenfield Brandy , Copland John A. , Tun Han W. , Storz Peter
Published: April 2023

Supplementary Table 1: Table with antibodies and dilutions used Supplementary Figure S1: Treatment scheme and analyses of stroma Supplementary Figure S2: Additional analyses of cell death and cell proliferation Supplementary Figure S3: Presence of Ym1+ macrophage and IL-13 in PanIN areas Supplementary Figure S4: Additional data on the role of IRF4 in macrophage polarization Supplementary Figure S5: Presence of macrophage-secreted factors and T cells Supplementary Figure S6: Treatment scheme and analyses of presence of immune cells Supplementary Figure S7: Blood counts and coagulation profile
Figure S2 from Epstein–Barr Virus miRNA BART2-5p Promotes Metastasis of Nasopharyngeal Carcinoma by Suppressing RND3
Authors: Jiang Chen , Li Lei , Xiang Yan-Qun , Lung Maria Li , Zeng Tingting , Lu Jiabin , Tsao Sai Wah , Zeng Mu-Sheng , Yun Jing-Ping , Kwong Dora L.W. , Guan Xin-Yuan
Published: April 2023

Supplementary Figure 2 (a) The four potential binding sites (position 931,1497,1522,1635) on the 3'UTR were predicted by the PITA analysis. Bases labeled blue were the mutated nucleotides of potential binding sites. (b) Downregulated RND3 expression in BART2 expressing CNE2 cells was revealed by western blot. (c) RIP assay was performed with CNE2 cells with Vector or BART2 expression. The RT-PCR revealed that RND3 3'UTR was enriched on the RISC complex in BART2 expressing cells, but not in cells carrying vector. Input: cell lysate before immunoprecipitation. NC: precipitates pulled down by isotype control mouse IgG. Ago2: precipitates pulled down by anti-Ago2 antibody. Ago2 is core component of RISC. (d) Quality control of RIP assay. Western Blot confirmed that Ago2 was successfully and specifically pulled down by anti-Ago2 antibody. Light and heavy chains of primary antibody were also detected. (e) RND3 expression was inhibited in lung metastatic lesions formed by BART2 expressing cells. (f) Knock down efficiency of RND3 by shRNA was determined by western blot. (Left) Migration and invasion assays were performed to evaluate cell motility after knock down RND3. Migrated or invaded cells were counted and statistically compared in the bar chart. (Middle and Right) (g) Successful reconstitution of RND3 was confirmed by western blot. (Left) Cell migration and invasion was evaluated by transwell assay. Migrated or invaded cells were counted and statistically compared in the bar chart. (Middle and Right) (h) HONE-1 EBVï¼^+ï¼‰and HONE-1 cells were transfected with Control mimic/siRNA targeting BART2-5p or infected by lentivirus to establish stable cell lines with Vector/RND3 expression. Migration assays were performed 8h after transient transfection or once Blasticidin selection finished. Migrated cells were counted under microscope for following statistical analysis. (i) HONE-1 EBVï¼^+ï¼‰and HONE-1 cells were transfected with Control mimic/siRNA targeting BART2-5p or infected by lentivirus to establish stable cell lines with Vector/RND3 expression. Cell invasiveness was evaluated 8h after transient transfection or once Blasticidin selection finished. Invaded cells were counted under microscope for subsequent statistical analysis.
Supplementary Figures and Methods from HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-Family GTPases
Authors: Kogler Melanie , Tortola Luigi , Negri Gian Luca , Leopoldi Alexandra , El-Naggar Amal M. , Mereiter Stefan , Gomez-Diaz Carlos , Nitsch Roberto , Tortora Davide , Kavirayani Anoop M. , Gapp Bianca V. , Rao Shuan , Uribesalgo Iris , Hoffmann David , Cikes Domagoj , Novatchkova Maria , Williams David A. , Trent Jeffrey M. , Ikeda Fumiyo , Daugaard Mads , Hagelkruys Astrid , Sorensen Poul H. , Penninger Josef M.
Published: April 2023

Supplementary Figures (Fig.S1-S4) and Supplementary Materials and Methods. Supplementary Figure S1. Loss of Hace1 results in increased lung tumorigenesis independent of RIPK3. Supplementary Figure S2. Analysis of RAC, NRF2 and 4HNE expression. Supplementary Figure S3. Analysis of tumor microenvironment. Supplementary Figure S4. Treatment of KRasG12D;Hace1-/- mice with a ROS scavenger diminishes lung tumorigenesis and Hace1-deficient cells are sensitive to exogenous induction of oxidative stress.
Supplementary Tables 1-9 from Sleeping Beauty Insertional Mutagenesis Reveals Important Genetic Drivers of Central Nervous System Embryonal Tumors
Authors: Beckmann Pauline J. , Larson Jon D. , Larsson Alex T. , Ostergaard Jason P. , Wagner Sandra , Rahrmann Eric P. , Shamsan Ghaidan A. , Otto George M. , Williams Rory L. , Wang Jun , Lee Catherine , Tschida Barbara R. , Das Paramita , Dubuc Adrian M. , Moriarity Branden S. , Picard Daniel , Wu Xiaochong , Rodriguez Fausto J. , Rosemarie Quincy , Krebs Ryan D. , Molan Amy M. , Demer Addison M. , Frees Michelle M. , Rizzardi Anthony E. , Schmechel Stephen C. , Eberhart Charles G. , Jenkins Robert B. , Wechsler-Reya Robert J. , Odde David J. , Huang Annie , Taylor Michael D. , Sarver Aaron L. , Largaespada David A.
Published: April 2023

Table S1 - Primers and Probes Table S2 - Antibodies Table S3 - Cell line information Table S4 - SB-induced medulloblastoma and CNS-PNET characteristics Table S5 - gene lists in mouse and human medulloblastoma Table S6 - gene lists in mouse and human CNS-PNET Table S7 - CIS genes for medulloblastoma and CNS-PNET Table S8 - CIS comparison between this and previous SB studies in medulloblastoma Table S9 - CIS comparison in this SB screen and a previous screen in osteosarcoma
Supplemental Figures S1 and S2 from Myeloid Cell–Derived TGFβ Signaling Regulates ECM Deposition in Mammary Carcinoma via Adenosine-Dependent Mechanisms
Authors: Vasiukov Georgii , Novitskaya Tatiana , Zijlstra Andries , Owens Philip , Ye Fei , Zhao Zhiguo , Moses Harold L. , Blackwell Timothy , Feoktistov Igor , Novitskiy Sergey V.
Published: April 2023

Analysis all available cancer types in TCGA data sets. Correlation analysis of METABRIC data between stages or aggressiveness of cancer vs. ECM proteins expression.
Figure S7 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

Quantitation of the expressions of the viral genes and Prox1
Figure S6 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

Productive KSHV Lytic Replication Is Necessary for Sustained Infection in LECs
Table S1 and Table S2 from A Protease-Activated Fluorescent Probe Allows Rapid Visualization of Keratinocyte Carcinoma during Excision
Authors: Walker Ethan , Liu Yiqiao , Kim InYoung , Biro Mark , Iyer Sukanya Raj , Ezaldein Harib , Scott Jeffrey , Merati Miesha , Mistur Rachel , Zhou Bo , Straight Brian , Yim Joshua J. , Bogyo Matthew , Mann Margaret , Wilson David L. , Basilion James P. , Popkin Daniel L.
Published: April 2023

Table S1 shows cancer type and histologic detection status following excision; Table S2 characterizes patients and specimens
Figure S1 from The Lymphatic Cell Environment Promotes Kaposi Sarcoma Development by Prox1-Enhanced Productive Lytic Replication of Kaposi Sarcoma Herpes Virus
Authors: Choi Dongwon , Park Eunkyung , Kim Kyu Eui , Jung Eunson , Seong Young Jin , Zhao Luping , Madhavan Shrimika , Daghlian George , Lee Hansuh H. , Daghlian Patill T. , Daghlian Saren , Bui Khoa , Koh Chester J. , Wong Alex K. , Cho Il-Taeg , Hong Young-Kwon
Published: April 2023

Sustained KSHV maintenance and massive cell death in KSHV-infected LECs
Figure S3D from A Protease-Activated Fluorescent Probe Allows Rapid Visualization of Keratinocyte Carcinoma during Excision
Authors: Walker Ethan , Liu Yiqiao , Kim InYoung , Biro Mark , Iyer Sukanya Raj , Ezaldein Harib , Scott Jeffrey , Merati Miesha , Mistur Rachel , Zhou Bo , Straight Brian , Yim Joshua J. , Bogyo Matthew , Mann Margaret , Wilson David L. , Basilion James P. , Popkin Daniel L.
Published: April 2023

Figure S3D shows histology of false positive (FP) skin samples with presence of healing area and inflammation.
Figure S1 from A Protease-Activated Fluorescent Probe Allows Rapid Visualization of Keratinocyte Carcinoma during Excision
Authors: Walker Ethan , Liu Yiqiao , Kim InYoung , Biro Mark , Iyer Sukanya Raj , Ezaldein Harib , Scott Jeffrey , Merati Miesha , Mistur Rachel , Zhou Bo , Straight Brian , Yim Joshua J. , Bogyo Matthew , Mann Margaret , Wilson David L. , Basilion James P. , Popkin Daniel L.
Published: April 2023

Figure S1 shows fluorescence that correlates with the presence of benign lesions
Supplementary Fig 5 from Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma
Authors: Wang Jun , Merino Diana M. , Light Nicholas , Murphy Brian L. , Wang Yong-Dong , Guo Xiaohui , Hodges Andrew P. , Chau Lianne Q. , Liu Kun-Wei , Dhall Girish , Asgharzadeh Shahab , Kiehna Erin N. , Shirey Ryan J. , Janda Kim D. , Taylor Michael D. , Malkin David , Ellison David W. , VandenBerg Scott R. , Eberhart Charles G. , Sears Rosalie C. , Roussel Martine F. , Gilbertson Richard J. , Wechsler-Reya Robert J.
Published: April 2023

Figure S5 shows reduced expression of genes on mouse chomosomes 8, 12 and 19 due to decreased DNA copy number.
Supplementary Fig 4 from Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma
Authors: Wang Jun , Merino Diana M. , Light Nicholas , Murphy Brian L. , Wang Yong-Dong , Guo Xiaohui , Hodges Andrew P. , Chau Lianne Q. , Liu Kun-Wei , Dhall Girish , Asgharzadeh Shahab , Kiehna Erin N. , Shirey Ryan J. , Janda Kim D. , Taylor Michael D. , Malkin David , Ellison David W. , VandenBerg Scott R. , Eberhart Charles G. , Sears Rosalie C. , Roussel Martine F. , Gilbertson Richard J. , Wechsler-Reya Robert J.
Published: April 2023

Figure S4 shows the expression of MYC and Ki67 by immunohistochemistry in human choroid plexus carcinoma patient specimens.
Table S3 from A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa
Authors: Harlemon Maxine , Ajayi Olabode , Kachambwa Paidamoyo , Kim Michelle S. , Simonti Corinne N. , Quiver Melanie H. , Petersen Desiree C. , Mittal Anuradha , Fernandez Pedro W. , Hsing Ann W. , Baichoo Shakuntala , Agalliu Ilir , Jalloh Mohamed , Gueye Serigne M. , Snyper Nana Yaa F. , Adusei Ben , Mensah James E. , Abrahams Afua O.D. , Adebiyi Akindele O. , Orunmuyi Akin T. , Aisuodionoe-Shadrach Oseremen I. , Nwegbu Maxwell M. , Joffe Maureen , Chen Wenlong C. , Irusen Hayley , Neugut Alfred I. , Quintana Yuri , Seutloali Moleboheng , Fadipe Mayowa B. , Warren Christopher , Woehrmann Marcos H. , Zhang Peng , Ongaco Chrissie M. , Mawhinney Michelle , McBride Jo , Andrews Caroline V. , Adams Marcia , Pugh Elizabeth , Rebbeck Timothy R. , Petersen Lindsay N. , Lachance Joseph
Published: April 2023

Markers used in PRS calculations. This list includes all markers from the Schumacher et al. 2018 CaP PRS (10) as well as proxy markers that are found on the MADCaP Array. Chromosome and positions (build hg38) listed here are for MADCaP markers used in PRS calculations. Allele frequencies and PBS scores are also included for the 139 CaP markers used in MADCaP PRS calculations. Numbers of markers on each genotyping array within 50kb of CaP-associated loci from Schumacher et al. 2018 are also included here.
Supplementary Figure. S1 from Disruption of Endolysosomal RAB5/7 Efficiently Eliminates Colorectal Cancer Stem Cells
Authors: Takeda Mitsunobu , Koseki Jun , Takahashi Hidekazu , Miyoshi Norikatsu , Nishida Naohiro , Nishimura Junichi , Hata Taishi , Matsuda Chu , Mizushima Tsunekazu , Yamamoto Hirofumi , Ishii Hideshi , Doki Yuichiro , Mori Masaki , Haraguchi Naotsugu
Published: April 2023

The status of acridine orange staining and BrDU retaining assay.
Table S2 from A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa
Authors: Harlemon Maxine , Ajayi Olabode , Kachambwa Paidamoyo , Kim Michelle S. , Simonti Corinne N. , Quiver Melanie H. , Petersen Desiree C. , Mittal Anuradha , Fernandez Pedro W. , Hsing Ann W. , Baichoo Shakuntala , Agalliu Ilir , Jalloh Mohamed , Gueye Serigne M. , Snyper Nana Yaa F. , Adusei Ben , Mensah James E. , Abrahams Afua O.D. , Adebiyi Akindele O. , Orunmuyi Akin T. , Aisuodionoe-Shadrach Oseremen I. , Nwegbu Maxwell M. , Joffe Maureen , Chen Wenlong C. , Irusen Hayley , Neugut Alfred I. , Quintana Yuri , Seutloali Moleboheng , Fadipe Mayowa B. , Warren Christopher , Woehrmann Marcos H. , Zhang Peng , Ongaco Chrissie M. , Mawhinney Michelle , McBride Jo , Andrews Caroline V. , Adams Marcia , Pugh Elizabeth , Rebbeck Timothy R. , Petersen Lindsay N. , Lachance Joseph
Published: April 2023

This .xlsx file lists Axiom genotyping solution QC thresholds. Genotyping metrics for both pegs of the MADCaP Array are listed here. This file also includes Benjamini-Hochberg adjusted p-values (FDR = 5%) for pairwise comparisons of derived allele frequencies, ancestry proportions of cases and controls, cumulative runs of homozygosity, and PRS distributions.
Supplementary Data Fig. 2 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

No SA-β-gal activity in N-WASP ko primary keratinocytes
Table S1 from H2A Monoubiquitination Links Glucose Availability to Epigenetic Regulation of the Endoplasmic Reticulum Stress Response and Cancer Cell Death
Authors: Zhang Yilei , Shi Jiejun , Liu Xiaoguang , Xiao Zhenna , Lei Guang , Lee Hyemin , Koppula Pranavi , Cheng Weijie , Mao Chao , Zhuang Li , Ma Li , Li Wei , Gan Boyi
Published: April 2023

List of Oligonucleotides
Supplementary Data 4 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 S2, S3 and S4. Morphometric analysis of laminin-411 β1 chain (S2) and cancer stem cell markers (Notch-1, Notch-3, CD133, Nestin, and c-Myc; S3 and S4) on frozen sections of patient brain tumors. The expression of all markers significantly correlated with glioma grade
Table S2 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

GSEA results
Supplementary Data 3 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

Table S5. Nanobioconjugate toxicity test in human blood by cytokine release. No significant cytokine release was observed, compatible with lack of drug toxicity
Supplementary Data 2 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

Table S4. Physico-chemical characterization of used control and treatment nanobioconjugates
Table S2 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

Table S2. Annotated survival and cause of death data for every mouse analyzed
Figure S5 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

Figure S5. Representative images from continuous longitudinal H&E sections of the proximal duodenum (Proximal) through the first part of the jejunum (distal), running left to right, then top to bottom. Each new row is a continuation of the end of the previous row. Portions of the villi blunting and crypt hypertrophy were observed in 2/5 mice in the VEH+RT group (middle, red blocks), but not in the VEH or FG+RT groups. These data provide an overview of a large continuous section of the intestine, which is important since only a portion of the GI tract is radiating in our focused fields. Scale bars=100 microns
Table S1 from TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression
Authors: Bonvin Elise , Radaelli Enrico , Bizet Martin , Luciani Flavie , Calonne Emilie , Putmans Pascale , Nittner David , Singh Nitesh Kumar , Santagostino Sara Francesca , Petit Valérie , Larue Lionel , Marine Jean Christophe , Fuks François
Published: April 2023

DhmR and gene expression related to Fig1
Figure S2 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

Figure S2. C57BL/6 mice after 67/5Gy administered in 15 fractions over 19 days. Survival analysis begins the day after RT is completed. No observable toxicity was seen in the first ten days and the first death was at Day 29 in the VEH + RT group. No differences were observed between the two survival curves (Log rank P=0.54.)
Suppl Table S4 from TET2-Dependent Hydroxymethylome Plasticity Reduces Melanoma Initiation and Progression
Authors: Bonvin Elise , Radaelli Enrico , Bizet Martin , Luciani Flavie , Calonne Emilie , Putmans Pascale , Nittner David , Singh Nitesh Kumar , Santagostino Sara Francesca , Petit Valérie , Larue Lionel , Marine Jean Christophe , Fuks François
Published: April 2023

Diff gene expression between melanoma tet2+/+ and tet2lox/lox
Supplementary Data from Long Noncoding RNA MRPL23-AS1 Promotes Adenoid Cystic Carcinoma Lung Metastasis
Authors: Chen Chu-Wen , Fu Min , Du Zhi-Hao , Zhao Fei , Yang Wen-Wen , Xu Li-Hua , Li Sheng-Lin , Ge Xi-Yuan
Published: April 2023

Supplementary Data
Figure S3 from Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes
Authors: Rohani Nazanin , Hao Liangliang , Alexis Maria S. , Joughin Brian A. , Krismer Konstantin , Moufarrej Mira N. , Soltis Anthony R. , Lauffenburger Douglas A. , Yaffe Michael B. , Burge Christopher B. , Bhatia Sangeeta N. , Gertler Frank B.
Published: April 2023

Figure S3 shows CA9 localization relative to markers for cell invasion and proliferation in human IDC
Figure S2 from Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes
Authors: Rohani Nazanin , Hao Liangliang , Alexis Maria S. , Joughin Brian A. , Krismer Konstantin , Moufarrej Mira N. , Soltis Anthony R. , Lauffenburger Douglas A. , Yaffe Michael B. , Burge Christopher B. , Bhatia Sangeeta N. , Gertler Frank B.
Published: April 2023

Figure S2 shows PM-LAMP2 co-localization with pHLIP in mouse and CA9 in human and pHLIP distribution relative to CD31 positivity.
Supplementary Table 5 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

eQTL Associations from GTEx (Release V7 (dbGaP Accession phs000424.v7.p2). Contains single gene eQTLs for BNC2, CNTLN, c9orf92 and SH3GL2 in all tissues and single SNP eQTL for all 40 SNPs in the credible candidate set.
Supplementary Table 1 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

Primers used in this study.
Supplementary Figure S4. STING is upstream of CDKN1A signaling, but only has partial control of CDKN1A. 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-D) Quantification of bands from Western gels shown in Main Figures 3H (A), 3I (B), 3J (C), and 3K (D) 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. (E) Western analysis of lysates harvested from HEK293 cells that were transiently transfected with either an empty vector of recombinant STING at 48 hours following exposure to 3Gy IR show that the protein levels of p21 and cyclin D1 were restored following overexpression of STING in HEK293 cells. (F) Western analysis of lysates harvested from siCDKN1A HCT116 cells at 48 hours following exposure to increasing dose of IR demonstrate that depletion of p21 did not affect STING expression, and only affected proteins that it regulates downstream of the pathway. (G) Western analysis of lysates harvested from MEFs that were transiently transfected with siRNA targeting STING and/or p21 at 48 hours reveal that depletion of STING led to down-regulation of p21, but not vice versa. Quantified bands are shown right next to each Western blot panels. (H-J) Kinetic analysis of STING-depleted human tumor cell lines D54 (H), HCT116 (I), and SCC61 (J) that were transiently transfected with siRNA targeting p21. Proliferation of nuclei-stained cells were measured in vitro over time using the IncuCyte live cell imaging system. The number of nuclei-stained cells were calculated using the Incucyte software and data are representative of 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.
Table S1-S7, Figure S1-S11, Supplementary Experimental Procedures from PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2
Authors: Mitobe Yuichi , Iino Kaori , Takayama Ken-ichi , Ikeda Kazuhiro , Suzuki Takashi , Aogi Kenjiro , Kawabata Hidetaka , Suzuki Yutaka , Horie-Inoue Kuniko , Inoue Satoshi
Published: April 2023

This file contains Supplementary Figure S1. High PSF expression is positively associated with poor prognosis of breast cancer patients.; Supplementary Figure S2. ESR1 expression is elevated in endocrine resistance model hydroxytamoxifen-resistant OHTR cells and ESR1 knockdown represses OHTR cell proliferation.; Supplementary Figure S3. PSF knockdown represses the proliferation and cell cycle progression of ER-positive T47D breast cancer cells.; Supplementary Figure S4. PSF correlates with estrogen signaling pathway and regulates the expression of estrogen target genes without altering its own mRNA expression.; Supplementary Figure S5. PSF regulates ESR1 expression at the posttranscriptional level.; Supplementary Figure S6. PSF overexpression enhances ESR1 expression and overcomes OHT-dependent cell proliferation inhibition.; Supplementary Figure S7. Mapping of PSF-immunoprecipitated RNAs in the vicinity of known PSF-associated genes or PSF-nonassociated gene and identification of PSF-binding RNAs with RIP-seq.; Supplementary Figure S8. PSF regulates SCFD2, TRA2B and ASPM expression at posttranscriptional level in ER-positive breast cancer cells.; Supplementary Figure S9. PSF knockdown promotes nuclear accumulation of SCFD2 and TRA2B but not ASPM in ER-positive breast cancer cells, whereas high expression of TRA2B and ASPM is significantly associated with shorter survivals of breast cancer patients.; Supplementary Figure S10. High expression of PSF-targeted SCFD2 is associated with shorter relapse-free survival of ER-positive breast cancer patients and SCFD2 knockdown represses T47D cell proliferation.; Supplementary Figure S11. PSF siRNA injection downregulates ER+ expression in xenograft tumors inoculated with tamoxifen-resistant cancer cells without altering mouse body weight and pre-mRNA expression of ESR1 and SCFD2.; Supplementary Table S1. Primers used in this study.; Supplementary Table S2. Association between PSF status and clinicopathological parameters in Shikoku Cancer Center cohort including 73 cases of human ER-positive breast cancers.; Supplementary Table S3. Clinicopathological parameters associated with distant disease-free or overall survival in univariate and multivariate analyses in Shikoku Cancer Center cohort (n = 73).; Supplementary Table S4. Association between PSF status and clinicopathological parameters in Toranomon Hospital cohort including 114 breast cancer cases.; Supplementary Table S5. Clinicopathological parameters associated with overall survival in univariate and multivariate analyses in Toranomon Hospital cohort (n = 114).; and Supplementary Experimental Procedures.
Supplementary Table S1 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

List of RNAs used in this study
Supplementary Data 4 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

UM cells resistant to PLX51107 show cross-resistance to other BET inhibitors, and a slower rate of growth
Figure S2 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 S2. ÃŽâ€�Np63 expression is essential for breast cancer lung colonization.
Table S3 : GSEA on KEGG collection results from Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5+ Intestinal Stem Cells
Authors: Bruschi Marco , Garnier Laure , Cleroux Elouan , Giordano Alicia , Dumas Michael , Bardet Anaïs F. , Kergrohen Thomas , Quesada Stanislas , Cesses Pierre , Weber Michael , Gerbe François , Jay Philippe
Published: April 2023

This file contains GSEA results from ApcWT- and ApcKO-Lgr5 cells for collections of signatures related to KEGG functional pathways.
Table S1 : RNA-seq data from Lgr5-GFP+ cells from Loss of Apc Rapidly Impairs DNA Methylation Programs and Cell Fate Decisions in Lgr5+ Intestinal Stem Cells
Authors: Bruschi Marco , Garnier Laure , Cleroux Elouan , Giordano Alicia , Dumas Michael , Bardet Anaïs F. , Kergrohen Thomas , Quesada Stanislas , Cesses Pierre , Weber Michael , Gerbe François , Jay Philippe
Published: April 2023

This file contains all RNAseq results for gene expression comparisons between FACS sorted ApcWT-, ApcHET-, and ApcKO-Lgr5-GFP profiles.
Video 3 from esiCancer: Evolutionary In Silico Cancer Simulator
Authors: Minussi Darlan Conterno , Henz Bernardo , dos Santos Oliveira Mariana , Filippi-Chiela Eduardo C. , Oliveira Manuel M. , Lenz Guido
Published: April 2023

This video presents example applications of esiCancer.
Supplementary Table 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

Primers for q-RT-PCR
Video 1 from esiCancer: Evolutionary In Silico Cancer Simulator
Authors: Minussi Darlan Conterno , Henz Bernardo , dos Santos Oliveira Mariana , Filippi-Chiela Eduardo C. , Oliveira Manuel M. , Lenz Guido
Published: April 2023

This video describes the basics of esiCancer.
Supplementary File 3 from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
Authors: Hoffman Mary , Gillmor Aaron H. , Kunz Daniel J. , Johnston Michael J. , Nikolic Ana , Narta Kiran , Zarrei Mehdi , King Jennifer , Ellestad Katrina , Dang Ngoc Ha , Cavalli Florence M.G. , Kushida Michelle M. , Coutinho Fiona J. , Zhu Yuankun , Luu Betty , Ma Yussanne , Mungall Andrew J. , Moore Richard , Marra Marco A. , Taylor Michael D. , Pugh Trevor J. , Dirks Peter B. , Strother Douglas , Lafay-Cousin Lucie , Resnick Adam C. , Scherer Stephen , Senger Donna L. , Simons Benjamin D. , Chan Jennifer A. , Morrissy A. Sorana , Gallo Marco
Published: April 2023

Summary of somatic and de novo germline events.
Supplementary File 2 from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
Authors: Hoffman Mary , Gillmor Aaron H. , Kunz Daniel J. , Johnston Michael J. , Nikolic Ana , Narta Kiran , Zarrei Mehdi , King Jennifer , Ellestad Katrina , Dang Ngoc Ha , Cavalli Florence M.G. , Kushida Michelle M. , Coutinho Fiona J. , Zhu Yuankun , Luu Betty , Ma Yussanne , Mungall Andrew J. , Moore Richard , Marra Marco A. , Taylor Michael D. , Pugh Trevor J. , Dirks Peter B. , Strother Douglas , Lafay-Cousin Lucie , Resnick Adam C. , Scherer Stephen , Senger Donna L. , Simons Benjamin D. , Chan Jennifer A. , Morrissy A. Sorana , Gallo Marco
Published: April 2023

Summary of genomic variants.
Supplementary Data from MET Inhibition Elicits PGC1α-Dependent Metabolic Reprogramming in Glioblastoma
Authors: Zhang Yiru , Nguyen Trang T.T. , Shang Enyuan , Mela Angeliki , Humala Nelson , Mahajan Aayushi , Zhao Junfei , Shu Chang , Torrini Consuelo , Sanchez-Quintero Maria J. , Kleiner Giulio , Bianchetti Elena , Westhoff Mike-Andrew , Quinzii Catarina M. , Karpel-Massler Georg , Bruce Jeffrey N. , Canoll Peter , Siegelin Markus D.
Published: April 2023

Figure S1. Crizotinib resistant cells reveal a reprogrammed tumor metabolism. Figure S2. Crizotinib modulates fatty acid metabolism and mitochondrial parameters. Figure S3. Tracing analysis reveals distinct modulation of metabolism by MET inhibition. Figure S4. Acute and chronic MET inhibition drives oxygen consumption rate and ECAR. Figure S5. Specific silencing of MET enhances oxidative metabolism in patient-derived xenograft cells. Figure S6. Inhibition of complex I and complex V of the electron transport chain and MET synergistically reduce viability of glioblastoma cells. Figure S7. Gamitrinib and etomoxir synergize with crizotinib to reduce cellular viability in glioblastoma model systems. Figure S8. Combined Met inhibition and Gamitrinib treatment elicits cleavage of caspases and modulate the expression of Bcl2 family members. Figure S9. Crizotinib and gamitrinib elicit cell death with features of apoptosis. Figure S10. Gamitrinib and crizotinib is superior over kinase inhibitor combination treatments to elicit apoptosis. Figure S11. The combination treatment of etomoxir and crizotinib elicits a reduction in tumor proliferation without induction of organ toxicity. Supplementary Table 1. Primer sequences for real time PCR and chromatin immunoprecipitation qPCR
Supplemental Methods from Combined Menin and EGFR Inhibitors Synergize to Suppress Colorectal Cancer via EGFR-Independent and Calcium-Mediated Repression of SKP2 Transcription
Authors: Katona Bryson W. , Glynn Rebecca A. , Paulosky Kayla E. , Feng Zijie , Davis Caroline I. , Ma Jian , Berry Corbett T. , Szigety Katherine M. , Matkar Smita , Liu Yuanyuan , Wang Haoren , Wu Yuan , He Xin , Freedman Bruce D. , Brady Donita C. , Hua Xianxin
Published: April 2023

This supplementary file contains methods for menin immunohistochemistry, reagents, cell culture, proliferation assays, western blotting, plasmids and transfections, RT-PCR, cell visualization assays including clonogenicity, H&E staining, and live cell imaging, ChIP assays, and calcium resin competition assays.
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 Figure 1 groups all supporting results
Supplementary Data from The EMT Transcription Factor ZEB2 Promotes Proliferation of Primary and Metastatic Melanoma While Suppressing an Invasive, Mesenchymal-Like Phenotype
Authors: Vandamme Niels , Denecker Geertrui , Bruneel Kenneth , Blancke Gillian , Akay Özden , Taminau Joachim , De Coninck Jordy , De Smedt Eva , Skrypek Nicolas , Van Loocke Wouter , Wouters Jasper , Nittner David , Köhler Corinna , Darling Douglas S. , Cheng Phil F. , Raaijmakers Marieke I.G. , Levesque Mitchell P. , Mallya Udupi Girish , Rafferty Mairin , Balint Balazs , Gallagher William M. , Brochez Lieve , Huylebroeck Danny , Haigh Jody J. , Andries Vanessa , Rambow Florian , Van Vlierberghe Pieter , Goossens Steven , van den Oord Joost J. , Marine Jean-Christophe , Berx Geert
Published: April 2023

Supplementary Figures. Supplementary Figure S1: Zeb2-wildtype cells outcompete Zeb2-negative cells in terms of expansion and differentiation. Supplementary Figure S2: Zeb2 does not accelerate melanoma development on a p53-wildtype background. Supplementary Figure S3: ZEB2 affects the phenotypical switch between proliferation and invasion in mouse and human melanoma cells. Supplementary Figure S4: ZEB2 affects the phenotypical switch between proliferation and invasion in human melanoma. Supplementary Figure S5: TGF-ÃŸ treatment mediates the switch from ZEB2 to ZEB1 and induces an invasive gene signature.
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

Supporting Table 6 provides the list and Gene Set Enrichment Analysis of common genes significantly deregulated in HepaRG-SP and HepaRG-Spheres.
Supplementary Data from USP10 Promotes Proliferation of Hepatocellular Carcinoma by Deubiquitinating and Stabilizing YAP/TAZ
Authors: Zhu Hong , Yan Fangjie , Yuan Tao , Qian Meijia , Zhou Tianyi , Dai Xiaoyang , Cao Ji , Ying Meidan , Dong Xiaowu , He Qiaojun , Yang Bo
Published: April 2023

Supplementary Figures, legends and tables
Supplementary Table 1 from Suppression of LIM Kinase 1 and LIM Kinase 2 Limits Glioblastoma Invasion
Authors: Chen Joseph , Ananthanarayanan Badriprasad , Springer Kelsey S. , Wolf Kayla J. , Sheyman Sharon M. , Tran Vivien D. , Kumar Sanjay
Published: April 2023

Sequences of shRNAs expressed by LIMK1/2 knockdown cells.
Supplementary Table 2 from Phosphorylation of RAB7 by TBK1/IKKϵ Regulates Innate Immune Signaling in Triple-Negative Breast Cancer
Authors: Ritter Jessica L. , Zhu Zehua , Thai Tran C. , Mahadevan Navin R. , Mertins Philipp , Knelson Erik H. , Piel Brandon P. , Han Saemi , Jaffe Jacob D. , Carr Steven A. , Barbie David A. , Barbie Thanh U.
Published: April 2023

Phosphopeptides from in vitro kinase screen
Supplementary Figure S3 from Suppression of LIM Kinase 1 and LIM Kinase 2 Limits Glioblastoma Invasion
Authors: Chen Joseph , Ananthanarayanan Badriprasad , Springer Kelsey S. , Wolf Kayla J. , Sheyman Sharon M. , Tran Vivien D. , Kumar Sanjay
Published: April 2023

Single Knockdown of LIMK1 and LIMK2 does not significantly influence 1D motility.
Supplementary Data from Phosphorylation of RAB7 by TBK1/IKKϵ Regulates Innate Immune Signaling in Triple-Negative Breast Cancer
Authors: Ritter Jessica L. , Zhu Zehua , Thai Tran C. , Mahadevan Navin R. , Mertins Philipp , Knelson Erik H. , Piel Brandon P. , Han Saemi , Jaffe Jacob D. , Carr Steven A. , Barbie David A. , Barbie Thanh U.
Published: April 2023

SF1: Unaltered immunoblots for Fig 4E. SF2: Unaltered immunoblots for Fig 4F. SF3: Unaltered immunoblots for Fig 4G. SF4: Additional phosphopeptide analysis for cell based and in vitro SILAC screen. SF5: Lower magnification (40X) of basal expression of V5 and Rab7 in mutants, to correspond with Fig 4A. SF6: EGFR and STING localization following TBK1/IKKE inhibition. SF7: Schematic for Rab7S72 role in regulating STING/TBK1/IKKE signaling in TNBCs. STableS3: Primer sequence for qRT-PCR. STableS4: List of antibodies. STableS5: PTEN/STING Staining of a TNBC TMA.
Supplementary Figure S1 from Suppression of LIM Kinase 1 and LIM Kinase 2 Limits Glioblastoma Invasion
Authors: Chen Joseph , Ananthanarayanan Badriprasad , Springer Kelsey S. , Wolf Kayla J. , Sheyman Sharon M. , Tran Vivien D. , Kumar Sanjay
Published: April 2023

PDMS device parameters
Figures SF1 to SF4 and Tables TS1 to TS4 from Label-Free Raman Spectroscopy Reveals Signatures of Radiation Resistance in the Tumor Microenvironment
Authors: Paidi Santosh K. , Diaz Paola Monterroso , Dadgar Sina , Jenkins Samir V. , Quick Charles M. , Griffin Robert J. , Dings Ruud P.M. , Rajaram Narasimhan , Barman Ishan
Published: April 2023

SF1: Tumor growth assays for lung and HN tumors. SF2: The complete set of MCR-derived pure component spectra and tables listing their peak assignments. SF3: Representative MCR score maps for lung and HN tumor datasets. SF4: Histologic images for HN tumor dataset. TS1-4: Results of binary leave-one-mouse-out SVM analyses.
Related Manuscript File 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

Fletcher A et al Data Source File
Supplementary Methods from CD38-Driven Mitochondrial Trafficking Promotes Bioenergetic Plasticity in Multiple Myeloma
Authors: Marlein Christopher R. , Piddock Rachel E. , Mistry Jayna J. , Zaitseva Lyubov , Hellmich Charlotte , Horton Rebecca H. , Zhou Zhigang , Auger Martin J. , Bowles Kristian M. , Rushworth Stuart A.
Published: April 2023

Supplementary methods. Contains sections on generation of rho0 stromal cells, co-culture of primary BMSC and MM cells and extended Seahorse extracellular flux assay methods,
Movie S2 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

Lack of co-trafficking for VCP-dsRED and NIS-GFP suggests that the site of functional interaction between VCP and NIS is distant to the plasma membrane in HeLa cells
Table S2 from The Frequency of Ras Mutations in Cancer
Authors: Prior Ian A. , Hood Fiona E. , Hartley James L.
Published: April 2023

Mutation statistics in major cancer genetics databases. Ras isoform mutation data (Table 1a) and copy number variance (CNV) analysis (Table 1b) are included together with details on how data was collated from COSMIC v85, cBioPortal v2.2.0, ICGC release 27 and TCGA release 12.0.
Supplementary Table 4 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 S4 summaries the characteristics of antibodies for analyses of Western-bloting, immunofluorescence, immunohistochemistry and co-immunoprecipitation.
Supplementary Data from CD317 Activates EGFR by Regulating Its Association with Lipid Rafts
Authors: Zhang Guizhong , Li Xin , Chen Qian , Li Junxin , Ruan Qingguo , Chen Youhai H. , Yang Xiaolu , Wan Xiaochun
Published: April 2023

Supplementary Figures with legends - Supplementary Figures S1 through S4. (1) Supplementary Figure S1 shows that upregulation of CD317 expression correlates with tumorigenesis (supplementary to fig. 1). (2) Supplementary Figure S2 shows CD317 promotes xenograft growth in vivo (Supplementary to Fig. 1). (3) Supplementary Figure S3 shows the effects of CD317 and its artificial mutants in cell cycle regulation (Supplementary to Fig. 2). (4) Supplementary Figure S4 shows that CD317 promotes cell cycle transition through lipid raft-dependent EGFR regulation (Supplementary to Figs 3 and 4). Supplementary Table S1 - Supplementary Table S1 lists the sequences of shRNAs and siRNAs. Supplementary Table S2 - Supplementary Table S2 lists primers of PCR and RT-PCR.
Figure S3 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

Altered Mild Systemic Autoimmunity in Mice with GARP-/- Treg Cells
Supplementary Material from An Orally Active Galectin-3 Antagonist Inhibits Lung Adenocarcinoma Growth and Augments Response to PD-L1 Blockade
Authors: Vuong Lynda , Kouverianou Eleni , Rooney Claire M. , McHugh Brian J. , Howie Sarah E.M. , Gregory Christopher D. , Forbes Stuart J. , Henderson Neil C. , Zetterberg Fredrik R. , Nilsson Ulf J. , Leffler Hakon , Ford Paul , Pedersen Anders , Gravelle Lise , Tantawi Susan , Schambye Hans , Sethi Tariq , MacKinnon Alison C.
Published: April 2023

Supplementary methods and figure legends
Supplementary Figures 3 and 4 from An Orally Active Galectin-3 Antagonist Inhibits Lung Adenocarcinoma Growth and Augments Response to PD-L1 Blockade
Authors: Vuong Lynda , Kouverianou Eleni , Rooney Claire M. , McHugh Brian J. , Howie Sarah E.M. , Gregory Christopher D. , Forbes Stuart J. , Henderson Neil C. , Zetterberg Fredrik R. , Nilsson Ulf J. , Leffler Hakon , Ford Paul , Pedersen Anders , Gravelle Lise , Tantawi Susan , Schambye Hans , Sethi Tariq , MacKinnon Alison C.
Published: April 2023

Figure S3 Galectin-3 knockdown impairs LLC1 cell proliferation in vitro but not in vivo. Figure S4 GB1107 has good oral bioavailability in mice.