bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from Dopamine Signaling Promotes Tissue-Resident Memory Differentiation of CD8+ T Cells and Antitumor Immunity
Authors: Chen Yingshi , Yan Shu-Mei , Pu Zeyu , Feng Jinzhu , Tan Likai , Li Yuzhuang , Hu Hongrong , Huang Wenjing , Lin Yingtong , Peng Zhilin , He Xin , Huang Feng , Zhang Hui , Zhang Yiwen
Published: March 2023

Supplementary Data from Dopamine Signaling Promotes Tissue-Resident Memory Differentiation of CD8+ T Cells and Antitumor Immunity
Supplementary Data from Activity and Resistance of a Brain-Permeable Paradox Breaker BRAF Inhibitor in Melanoma Brain Metastasis
Authors: Bonfill-Teixidor Ester , Iurlaro Raffaella , Handl Cornelia , Wichmann Jürgen , Arias Alexandra , Cuartas Isabel , Emmenegger Jasmin , Romagnani Andrea , Mangano Luca , Lorber Thomas , Berrera Marco , Godfried Sie Christina , Köchl Fabian , Eckmann Jan , Feddersen Romi , Kornacker Martin , Schnetzler Gabriel , Cicuendez Marta , Cordero Esteban , Topczewski Thomaz E. , Ferres-Pijoan Abel , González Josep , Martínez-Ricarte Francisco , Muñoz-Couselo Eva , Tabernero Josep , Bischoff James R. , Pettazzoni Piergiorgio , Seoane Joan
Published: March 2023

Supplementary Data from Activity and Resistance of a Brain-Permeable Paradox Breaker BRAF Inhibitor in Melanoma Brain Metastasis
Supplementary Data from The X-Linked Helicase DDX3X Is Required for Lymphoid Differentiation and MYC-Driven Lymphomagenesis
Authors: Lacroix Marion , Beauchemin Hugues , Fraszczak Jennifer , Ross Julie , Shooshtarizadeh Peiman , Chen Riyan , Möröy Tarik
Published: March 2023

Supplementary Data from The X-Linked Helicase DDX3X Is Required for Lymphoid Differentiation and MYC-Driven Lymphomagenesis
Supplementary Data from The cAMP/PKA/CREB and TGFβ/SMAD4 Pathways Regulate Stemness and Metastatic Potential in Colorectal Cancer Cells
Authors: Fujishita Teruaki , Kojima Yasushi , Kajino-Sakamoto Rie , Mishiro-Sato Emi , Shimizu Yasuhiro , Hosoda Waki , Yamaguchi Rui , Taketo Makoto Mark , Aoki Masahiro
Published: March 2023

Supplementary Data from The cAMP/PKA/CREB and TGFβ/SMAD4 Pathways Regulate Stemness and Metastatic Potential in Colorectal Cancer Cells
Supplementary Figure S2 from Therapy-Induced Senescence Enhances the Efficacy of HER2-Targeted Antibody–Drug Conjugates in Breast Cancer
Authors: Duro-Sánchez Santiago , Nadal-Serrano Mercedes , Lalinde-Gutiérrez Marta , Arenas Enrique Javier , Bernadó Morales Cristina , Morancho Beatriz , Escorihuela Marta , Pérez-Ramos Sandra , Escrivá-de-Romaní Santiago , Gandullo-Sánchez Lucía , Pandiella Atanasio , Esteve-Codina Anna , Rodilla Verónica , Dijcks Fred A. , Dokter Wim H.A. , Cortés Javier , Saura Cristina , Arribas Joaquín
Published: March 2023

Effect of doxorubicin and Cdk4/6i on cells expressing different levels of HER2.
Supplementary Table from High-Resolution Profiling of Lung Adenocarcinoma Identifies Expression Subtypes with Specific Biomarkers and Clinically Relevant Vulnerabilities
Authors: Roh Whijae , Geffen Yifat , Cha Hongui , Miller Mendy , Anand Shankara , Kim Jaegil , Heiman David I. , Gainor Justin F. , Laird Peter W. , Cherniack Andrew D. , Ock Chan-Young , Lee Se-Hoon , Getz Gad
Published: March 2023

Supplementary Table from High-Resolution Profiling of Lung Adenocarcinoma Identifies Expression Subtypes with Specific Biomarkers and Clinically Relevant Vulnerabilities
Supplementary Figures and Legends from ATM Regulates Differentiation of Myofibroblastic Cancer-Associated Fibroblasts and Can Be Targeted to Overcome Immunotherapy Resistance
Authors: Mellone Massimiliano , Piotrowska Klaudia , Venturi Giulia , James Lija , Bzura Aleksandra , Lopez Maria A. , James Sonya , Wang Chuan , Ellis Matthew J. , Hanley Christopher J. , Buckingham Josephine F. , Cox Kerry L. , Hughes Gareth , Valge-Archer Viia , King Emma V. , Beers Stephen A. , Jaquet Vincent , Jones George D.D. , Savelyeva Natalia , Sayan Emre , Parsons Jason L. , Durant Stephen , Thomas Gareth J.
Published: March 2023

supplementary figures and legends
Supplementary Figure from High-Resolution Profiling of Lung Adenocarcinoma Identifies Expression Subtypes with Specific Biomarkers and Clinically Relevant Vulnerabilities
Authors: Roh Whijae , Geffen Yifat , Cha Hongui , Miller Mendy , Anand Shankara , Kim Jaegil , Heiman David I. , Gainor Justin F. , Laird Peter W. , Cherniack Andrew D. , Ock Chan-Young , Lee Se-Hoon , Getz Gad
Published: March 2023

Supplementary Figure from High-Resolution Profiling of Lung Adenocarcinoma Identifies Expression Subtypes with Specific Biomarkers and Clinically Relevant Vulnerabilities
Supplementary Data 5 from ATM Regulates Differentiation of Myofibroblastic Cancer-Associated Fibroblasts and Can Be Targeted to Overcome Immunotherapy Resistance
Authors: Mellone Massimiliano , Piotrowska Klaudia , Venturi Giulia , James Lija , Bzura Aleksandra , Lopez Maria A. , James Sonya , Wang Chuan , Ellis Matthew J. , Hanley Christopher J. , Buckingham Josephine F. , Cox Kerry L. , Hughes Gareth , Valge-Archer Viia , King Emma V. , Beers Stephen A. , Jaquet Vincent , Jones George D.D. , Savelyeva Natalia , Sayan Emre , Parsons Jason L. , Durant Stephen , Thomas Gareth J.
Published: March 2023

Non-redundant list of the leading-edge genes and ToppFun pathway analysis from the genesets in Suppl. File 4 used to make the DDR-TGFB_signature geneset
Supplementary Data 2 from ATM Regulates Differentiation of Myofibroblastic Cancer-Associated Fibroblasts and Can Be Targeted to Overcome Immunotherapy Resistance
Authors: Mellone Massimiliano , Piotrowska Klaudia , Venturi Giulia , James Lija , Bzura Aleksandra , Lopez Maria A. , James Sonya , Wang Chuan , Ellis Matthew J. , Hanley Christopher J. , Buckingham Josephine F. , Cox Kerry L. , Hughes Gareth , Valge-Archer Viia , King Emma V. , Beers Stephen A. , Jaquet Vincent , Jones George D.D. , Savelyeva Natalia , Sayan Emre , Parsons Jason L. , Durant Stephen , Thomas Gareth J.
Published: March 2023

list of primer sequences, antibody details and primary fibroblasts used
Macros for image quantification from ATM Regulates Differentiation of Myofibroblastic Cancer-Associated Fibroblasts and Can Be Targeted to Overcome Immunotherapy Resistance
Authors: Mellone Massimiliano , Piotrowska Klaudia , Venturi Giulia , James Lija , Bzura Aleksandra , Lopez Maria A. , James Sonya , Wang Chuan , Ellis Matthew J. , Hanley Christopher J. , Buckingham Josephine F. , Cox Kerry L. , Hughes Gareth , Valge-Archer Viia , King Emma V. , Beers Stephen A. , Jaquet Vincent , Jones George D.D. , Savelyeva Natalia , Sayan Emre , Parsons Jason L. , Durant Stephen , Thomas Gareth J.
Published: March 2023

macros for image quantifications
Supplementary Data from MEX3C-Mediated Decay of SOCS3 mRNA Promotes JAK2/STAT3 Signaling to Facilitate Metastasis in Hepatocellular Carcinoma
Authors: Xiao Yunyun , Li Yue , Shi Dongni , Wang Xiaoqing , Dai Shuqin , Yang Muwen , Kong Lingzhi , Chen Boyu , Huang Xinjian , Lin Chuyong , Liao Wenting , Xu Benke , Chen Xin , Wang Lishuai , Chen Xiangfu , Ouyang Ying , Liu Guozhen , Li Heping , Song Libing
Published: March 2023

Supplementary Data from MEX3C-Mediated Decay of SOCS3 mRNA Promotes JAK2/STAT3 Signaling to Facilitate Metastasis in Hepatocellular Carcinoma
Supplementary table S5 from HDAC5 Loss Enhances Phospholipid-Derived Arachidonic Acid Generation and Confers Sensitivity to cPLA2 Inhibition in Pancreatic Cancer
Authors: Pan Penglin , Qin Gengdu , Wang Bo , Yu Haixin , Chen Jie , Liu Jiaying , Bing Kaijian , Shen Jian , Ren Dianyun , Zhao Yuhan , Xia Wentao , Li Hui , Wu Heshui , Zhou Yingke
Published: March 2023

Result of HDAC5 mass spectra
Supplementary Data from Meta-Analysis of Human Cancer Single-Cell RNA-Seq Datasets Using the IMMUcan Database
Authors: Camps Jordi , Noël Floriane , Liechti Robin , Massenet-Regad Lucile , Rigade Sidwell , Götz Lou , Hoffmann Caroline , Amblard Elise , Saichi Melissa , Ibrahim Mahmoud M. , Pollard Jack , Medvedovic Jasna , Roider Helge G. , Soumelis Vassili
Published: March 2023

Supplementary Figure S1-4 and Supplementary Table S1-3
Supplementary file from Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy
Authors: Ran Xue-Bin , Ding Ling-Wen , Sun Qiao-Yang , Yang Henry , Said Jonathan W. , Zhentang Lao , Madan Vikas , Dakle Pushkar , Xiao Jin-Fen , Loh Xinyi , Li Ying , Xu Liang , Xiang Xiao-Qiang , Wang Ling-Zhi , Goh Boon Cher , Lin De-Chen , Chng Wee Joo , Tan Soo-Yong , Jha Sudhakar , Koeffler H. Phillip
Published: March 2023

This file contains supplementary methods, Figs. S1 to S6 and Tables S1 to S5.
Supplementary Data from ATF3 Reprograms the Bone Marrow Niche in Response to Early Breast Cancer Transformation
Authors: Perrone Milena , Chiodoni Claudia , Lecchi Mara , Botti Laura , Bassani Barbara , Piva Annamaria , Jachetti Elena , Milani Matteo , Lecis Daniele , Tagliabue Elda , Verderio Paolo , Sangaletti Sabina , Colombo Mario P.
Published: March 2023

Supplementary Material and Methods including a key resource Table
Supplementary Data from ATF3 Reprograms the Bone Marrow Niche in Response to Early Breast Cancer Transformation
Authors: Perrone Milena , Chiodoni Claudia , Lecchi Mara , Botti Laura , Bassani Barbara , Piva Annamaria , Jachetti Elena , Milani Matteo , Lecis Daniele , Tagliabue Elda , Verderio Paolo , Sangaletti Sabina , Colombo Mario P.
Published: March 2023

This file include the Supplementary Table S1A and S1B
Supplementary Table from Characterization of Immune-Related Alternative Polyadenylation Events in Cancer Immunotherapy
Authors: Wang Gaoyang , Xie Zuozhong , Su Juan , Chen Meishan , Du Yanhua , Gao Qian , Zhang Guanxiong , Zhang Hailun , Chen Xiang , Liu Hong , Han Leng , Ye Youqiong
Published: March 2023

Supplementary Table from Characterization of Immune-Related Alternative Polyadenylation Events in Cancer Immunotherapy
Supplementary Data from Characterization of Immune-Related Alternative Polyadenylation Events in Cancer Immunotherapy
Authors: Wang Gaoyang , Xie Zuozhong , Su Juan , Chen Meishan , Du Yanhua , Gao Qian , Zhang Guanxiong , Zhang Hailun , Chen Xiang , Liu Hong , Han Leng , Ye Youqiong
Published: March 2023

Supplementary Data from Characterization of Immune-Related Alternative Polyadenylation Events in Cancer Immunotherapy
Supplementary Data from Endometriosis-Associated Mesenchymal Stem Cells Support Ovarian Clear Cell Carcinoma through Iron Regulation
Authors: Atiya Huda I. , Frisbie Leonard , Goldfeld Ester , Orellana Taylor , Donnellan Nicole , Modugno Francesmary , Calderon Michael , Watkins Simon , Zhang Rugang , Elishaev Esther , Soong Thing Rinda , Vlad Anda , Coffman Lan
Published: March 2023

Supplementary figures and table
Supplementary Data from Loss of MLL Induces Epigenetic Dysregulation of Rasgrf1 to Attenuate Kras-Driven Lung Tumorigenesis
Authors: Zhu Ling-Yu , Yuan Jun-Bo , Zhang Li , He Chun-Xiao , Lin Xiao , Xu Bin , Jin Guang-Hui
Published: March 2023

Supplementary Data from Loss of MLL Induces Epigenetic Dysregulation of Rasgrf1 to Attenuate Kras-Driven Lung Tumorigenesis
Supplementary Figure 8 from Monounsaturated and Diunsaturated Fatty Acids Sensitize Cervical Cancer to Radiation Therapy
Authors: Muhammad Naoshad , Ruiz Fiona , Stanley Jennifer , Rashmi Ramachandran , Cho Kevin , Jayachandran Kay , Zahner Michael C. , Huang Yi , Zhang Jin , Markovina Stephanie , Patti Gary J. , Schwarz Julie K.
Published: March 2023

Individual mouse data for in vivo experiments.
Supplementary Material from Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms
Authors: Belleau Pascal , Deschênes Astrid , Chambwe Nyasha , Tuveson David A. , Krasnitz Alexander
Published: March 2023

Supplementary methods; supplementary figures; supplementary tables 1 - 18
Supplementary Figure 5 from Monounsaturated and Diunsaturated Fatty Acids Sensitize Cervical Cancer to Radiation Therapy
Authors: Muhammad Naoshad , Ruiz Fiona , Stanley Jennifer , Rashmi Ramachandran , Cho Kevin , Jayachandran Kay , Zahner Michael C. , Huang Yi , Zhang Jin , Markovina Stephanie , Patti Gary J. , Schwarz Julie K.
Published: March 2023

Radiation enhances lipid droplet formation through intracellular uptake of fatty acids
Supplementary Data from N-myc–Mediated Translation Control Is a Therapeutic Vulnerability in Medulloblastoma
Authors: Kuzuoglu-Ozturk Duygu , Aksoy Ozlem , Schmidt Christin , Lea Robin , Larson Jon D. , Phelps Ryan R.L. , Nasholm Nicole , Holt Megan , Contreras Adrian , Huang Miller , Wong-Michalak Shannon , Shao Hao , Wechsler-Reya Robert , Phillips Joanna J. , Gestwicki Jason E. , Ruggero Davide , Weiss William A.
Published: March 2023

7 Supplementary Figures and Legends
Supplementary Figures from Loss of NF1 in Melanoma Confers Sensitivity to SYK Kinase Inhibition
Authors: Abecunas Cara , Whitehead Christopher E. , Ziemke Elizabeth K. , Baumann Douglas G. , Frankowski-McGregor Christy L. , Sebolt-Leopold Judith S. , Fallahi-Sichani Mohammad
Published: March 2023

Supplementary Figures
Supplementary Data from Stress-Mediated Attenuation of Translation Undermines T-cell Activity in Cancer
Authors: Riesenberg Brian P. , Hunt Elizabeth G. , Tennant Megan D. , Hurst Katie E. , Andrews Alex M. , Leddy Lee R. , Neskey David M. , Hill Elizabeth G. , Rivera Guillermo O. Rangel , Paulos Chrystal M. , Gao Peng , Thaxton Jessica E.
Published: March 2023

Supplemental Figures S1-S11
Supplementary Dataset S6 from Loss of NF1 in Melanoma Confers Sensitivity to SYK Kinase Inhibition
Authors: Abecunas Cara , Whitehead Christopher E. , Ziemke Elizabeth K. , Baumann Douglas G. , Frankowski-McGregor Christy L. , Sebolt-Leopold Judith S. , Fallahi-Sichani Mohammad
Published: March 2023

Supplementary Dataset S6
Table S1, S2, S4 from Integrative Single-Cell Analysis Reveals Transcriptional and Epigenetic Regulatory Features of Clear Cell Renal Cell Carcinoma
Authors: Yu Zhenyuan , Lv Yufang , Su Cheng , Lu Wenhao , Zhang RuiRui , Li Jiaping , Guo Bingqian , Yan Haibiao , Liu Deyun , Yang Zhanbin , Mi Hua , Mo Linjian , Guo Yi , Feng Wenyu , Xu Haotian , Peng Wenyi , Cheng Jiwen , Nan Aruo , Mo Zengnan
Published: March 2023

Details of each sample
Supplementary MovieS2b from Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer
Authors: Chou Jonathan , Egusa Emily A. , Wang Sinan , Badura Michelle L. , Lee Fei , Bidkar Anil P. , Zhu Jun , Shenoy Tanushree , Trepka Kai , Robinson Troy M. , Steri Veronica , Huang Jiaoti , Wang Yuzhuo , Small Eric J. , Chan Emily , Stohr Bradley A. , Ashworth Alan , Delafontaine Brant , Rottey Sylvie , Cooke Keegan S. , Hashemi Sadraei Nooshin , Yu Brian , Salvati Mark , Bailis Julie M. , Feng Felix Y. , Flavell Robert R. , Aggarwal Rahul
Published: March 2023

Supplemental Movies 2a-2c: 22Rv1-NuclightGreen and SHP-77-NuclightRed mixed population co-cultures. Time-lapse movies of 22Rv1 cells (labeled with NuclightGreen) and SHP-77 cells (labeled with NuclightRed) co-cultured with T cells. Both the 22Rv1 and SHP-77 cells were plated at equal densities and treated with either NT control BiTE®, AMG 757, or the PSMA-targeting HLE BiTE, AMG 160. T cells were added to each well at an E:T ratio of 10:1. Images were captured every 4 hours at 4x magnification for 5 days.
a. 22Rv1, SHP-77, and T cells co-cultured with NT control BiTE®.
b. 22Rv1, SHP-77, and T cells co-cultured with AMG 757.
c. 22Rv1, SHP-77, and T cells co-cultured with AMG 160.
Figure S1-16 from Integrative Single-Cell Analysis Reveals Transcriptional and Epigenetic Regulatory Features of Clear Cell Renal Cell Carcinoma
Authors: Yu Zhenyuan , Lv Yufang , Su Cheng , Lu Wenhao , Zhang RuiRui , Li Jiaping , Guo Bingqian , Yan Haibiao , Liu Deyun , Yang Zhanbin , Mi Hua , Mo Linjian , Guo Yi , Feng Wenyu , Xu Haotian , Peng Wenyi , Cheng Jiwen , Nan Aruo , Mo Zengnan
Published: March 2023

Figure S1-16
Supplementary MovieS1d from Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer
Authors: Chou Jonathan , Egusa Emily A. , Wang Sinan , Badura Michelle L. , Lee Fei , Bidkar Anil P. , Zhu Jun , Shenoy Tanushree , Trepka Kai , Robinson Troy M. , Steri Veronica , Huang Jiaoti , Wang Yuzhuo , Small Eric J. , Chan Emily , Stohr Bradley A. , Ashworth Alan , Delafontaine Brant , Rottey Sylvie , Cooke Keegan S. , Hashemi Sadraei Nooshin , Yu Brian , Salvati Mark , Bailis Julie M. , Feng Felix Y. , Flavell Robert R. , Aggarwal Rahul
Published: March 2023

Supplemental Movies 1a-1d: 22Rv1-LacZ and 22Rv1-DLL3 cells co-cultures. Time-lapse movies of 22Rv1-LacZ and 22Rv1-DLL3 cells (labeled with NuclightRed) co-cultured with T cells and either NT control BiTE® or AMG 757. T cells were plated at an E:T ratio of 5:1. Images were captured every 6 hours at 10x magnification.
a. 22Rv1-LacZ cells and T cells treated with NT control BiTE®.
b. 22Rv1-DLL3 cells and T cells treated with NT control BiTE®.
c. 22Rv1-LacZ cells and T cells treated with AMG 757.
d. 22Rv1-DLL3 cells and T cells treated with AMG 757.
Supplementary MovieS1c from Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer
Authors: Chou Jonathan , Egusa Emily A. , Wang Sinan , Badura Michelle L. , Lee Fei , Bidkar Anil P. , Zhu Jun , Shenoy Tanushree , Trepka Kai , Robinson Troy M. , Steri Veronica , Huang Jiaoti , Wang Yuzhuo , Small Eric J. , Chan Emily , Stohr Bradley A. , Ashworth Alan , Delafontaine Brant , Rottey Sylvie , Cooke Keegan S. , Hashemi Sadraei Nooshin , Yu Brian , Salvati Mark , Bailis Julie M. , Feng Felix Y. , Flavell Robert R. , Aggarwal Rahul
Published: March 2023

Supplemental Movies 1a-1d: 22Rv1-LacZ and 22Rv1-DLL3 cells co-cultures. Time-lapse movies of 22Rv1-LacZ and 22Rv1-DLL3 cells (labeled with NuclightRed) co-cultured with T cells and either NT control BiTE® or AMG 757. T cells were plated at an E:T ratio of 5:1. Images were captured every 6 hours at 10x magnification.
a. 22Rv1-LacZ cells and T cells treated with NT control BiTE®.
b. 22Rv1-DLL3 cells and T cells treated with NT control BiTE®.
c. 22Rv1-LacZ cells and T cells treated with AMG 757.
d. 22Rv1-DLL3 cells and T cells treated with AMG 757.
Supplementary Data from Pharmacological Targeting of Androgen Receptor Elicits Context-Specific Effects in Estrogen Receptor–Positive Breast Cancer
Authors: Wei Lixuan , Gao Huanyao , Yu Jia , Zhang Huan , Nguyen Thanh Thanh L. , Gu Yayun , Passow Marie R. , Carter Jodi M. , Qin Bo , Boughey Judy C. , Goetz Matthew P. , Weinshilboum Richard M. , Ingle James N. , Wang Liewei
Published: March 2023

Figure S1-9
FigureS9 from Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer
Authors: Chou Jonathan , Egusa Emily A. , Wang Sinan , Badura Michelle L. , Lee Fei , Bidkar Anil P. , Zhu Jun , Shenoy Tanushree , Trepka Kai , Robinson Troy M. , Steri Veronica , Huang Jiaoti , Wang Yuzhuo , Small Eric J. , Chan Emily , Stohr Bradley A. , Ashworth Alan , Delafontaine Brant , Rottey Sylvie , Cooke Keegan S. , Hashemi Sadraei Nooshin , Yu Brian , Salvati Mark , Bailis Julie M. , Feng Felix Y. , Flavell Robert R. , Aggarwal Rahul
Published: March 2023

FigureS9
Supplementary Data from Pharmacological Targeting of Androgen Receptor Elicits Context-Specific Effects in Estrogen Receptor–Positive Breast Cancer
Authors: Wei Lixuan , Gao Huanyao , Yu Jia , Zhang Huan , Nguyen Thanh Thanh L. , Gu Yayun , Passow Marie R. , Carter Jodi M. , Qin Bo , Boughey Judy C. , Goetz Matthew P. , Weinshilboum Richard M. , Ingle James N. , Wang Liewei
Published: March 2023

Table S1-6
FigureS4 from Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer
Authors: Chou Jonathan , Egusa Emily A. , Wang Sinan , Badura Michelle L. , Lee Fei , Bidkar Anil P. , Zhu Jun , Shenoy Tanushree , Trepka Kai , Robinson Troy M. , Steri Veronica , Huang Jiaoti , Wang Yuzhuo , Small Eric J. , Chan Emily , Stohr Bradley A. , Ashworth Alan , Delafontaine Brant , Rottey Sylvie , Cooke Keegan S. , Hashemi Sadraei Nooshin , Yu Brian , Salvati Mark , Bailis Julie M. , Feng Felix Y. , Flavell Robert R. , Aggarwal Rahul
Published: March 2023

FigureS4
Figure S8 from Stromal Reprogramming through Dual PDGFRα/β Blockade Boosts the Efficacy of Anti–PD-1 Immunotherapy in Fibrotic Tumors
Authors: Akiyama Takahiko , Yasuda Tadahito , Uchihara Tomoyuki , Yasuda-Yoshihara Noriko , Tan Benjy J.Y. , Yonemura Atsuko , Semba Takashi , Yamasaki Juntaro , Komohara Yoshihiro , Ohnishi Koji , Wei Feng , Fu Lingfeng , Zhang Jun , Kitamura Fumimasa , Yamashita Kohei , Eto Kojiro , Iwagami Shiro , Tsukamoto Hirotake , Umemoto Terumasa , Masuda Mari , Nagano Osamu , Satou Yorifumi , Saya Hideyuki , Tan Patrick , Baba Hideo , Ishimoto Takatsugu
Published: March 2023

Supplementary Figure8
Figure S6 from Stromal Reprogramming through Dual PDGFRα/β Blockade Boosts the Efficacy of Anti–PD-1 Immunotherapy in Fibrotic Tumors
Authors: Akiyama Takahiko , Yasuda Tadahito , Uchihara Tomoyuki , Yasuda-Yoshihara Noriko , Tan Benjy J.Y. , Yonemura Atsuko , Semba Takashi , Yamasaki Juntaro , Komohara Yoshihiro , Ohnishi Koji , Wei Feng , Fu Lingfeng , Zhang Jun , Kitamura Fumimasa , Yamashita Kohei , Eto Kojiro , Iwagami Shiro , Tsukamoto Hirotake , Umemoto Terumasa , Masuda Mari , Nagano Osamu , Satou Yorifumi , Saya Hideyuki , Tan Patrick , Baba Hideo , Ishimoto Takatsugu
Published: March 2023

Supplementary Figure6
Table S7 from Shared Cancer Dataset Analysis Identifies and Predicts the Quantitative Effects of Pan-Cancer Somatic Driver Variants
Authors: Landau Jakob , Tsaban Linoy , Yaacov Adar , Ben Cohen Gil , Rosenberg Shai
Published: March 2023

Table S7 - Drivers Table
Figure S2 from Stromal Reprogramming through Dual PDGFRα/β Blockade Boosts the Efficacy of Anti–PD-1 Immunotherapy in Fibrotic Tumors
Authors: Akiyama Takahiko , Yasuda Tadahito , Uchihara Tomoyuki , Yasuda-Yoshihara Noriko , Tan Benjy J.Y. , Yonemura Atsuko , Semba Takashi , Yamasaki Juntaro , Komohara Yoshihiro , Ohnishi Koji , Wei Feng , Fu Lingfeng , Zhang Jun , Kitamura Fumimasa , Yamashita Kohei , Eto Kojiro , Iwagami Shiro , Tsukamoto Hirotake , Umemoto Terumasa , Masuda Mari , Nagano Osamu , Satou Yorifumi , Saya Hideyuki , Tan Patrick , Baba Hideo , Ishimoto Takatsugu
Published: March 2023

Supplementary Figure2
Supplementary Data from Shared Cancer Dataset Analysis Identifies and Predicts the Quantitative Effects of Pan-Cancer Somatic Driver Variants
Authors: Landau Jakob , Tsaban Linoy , Yaacov Adar , Ben Cohen Gil , Rosenberg Shai
Published: March 2023

Tables S1-S6
Figures S1-S5
Figure S10 from Stromal Reprogramming through Dual PDGFRα/β Blockade Boosts the Efficacy of Anti–PD-1 Immunotherapy in Fibrotic Tumors
Authors: Akiyama Takahiko , Yasuda Tadahito , Uchihara Tomoyuki , Yasuda-Yoshihara Noriko , Tan Benjy J.Y. , Yonemura Atsuko , Semba Takashi , Yamasaki Juntaro , Komohara Yoshihiro , Ohnishi Koji , Wei Feng , Fu Lingfeng , Zhang Jun , Kitamura Fumimasa , Yamashita Kohei , Eto Kojiro , Iwagami Shiro , Tsukamoto Hirotake , Umemoto Terumasa , Masuda Mari , Nagano Osamu , Satou Yorifumi , Saya Hideyuki , Tan Patrick , Baba Hideo , Ishimoto Takatsugu
Published: March 2023

Supplementary Figure10
Figure S1 from Stromal Reprogramming through Dual PDGFRα/β Blockade Boosts the Efficacy of Anti–PD-1 Immunotherapy in Fibrotic Tumors
Authors: Akiyama Takahiko , Yasuda Tadahito , Uchihara Tomoyuki , Yasuda-Yoshihara Noriko , Tan Benjy J.Y. , Yonemura Atsuko , Semba Takashi , Yamasaki Juntaro , Komohara Yoshihiro , Ohnishi Koji , Wei Feng , Fu Lingfeng , Zhang Jun , Kitamura Fumimasa , Yamashita Kohei , Eto Kojiro , Iwagami Shiro , Tsukamoto Hirotake , Umemoto Terumasa , Masuda Mari , Nagano Osamu , Satou Yorifumi , Saya Hideyuki , Tan Patrick , Baba Hideo , Ishimoto Takatsugu
Published: March 2023

Supplementary Figure1
Figure S1 from Breast Cancer Metastatic Dormancy and Relapse: An Enigma of Microenvironment(s)
Authors: Elkholi Islam E. , Lalonde Andréane , Park Morag , Côté Jean-François
Published: March 2023

Figure S1. Current experimental models to study breast cancer metastatic dormancy. (a) Different pairs of cell lines are used to study breast cancer dormancy in vitro. Both 4T07 and D2OR cells remain dormant in the secondary site after spontaneous metastasis. In contrast, 4T1 and D2A1, their corresponding counterparts, form overt metastases. (b) A simplistic representation of the in vitro 3D culture systems’ components as described in different studies. ECM-like components such as collagen and laminin among other factors (fibronectin, heparin, TGFB and others) have been included in different culture systems to recapitulate the native microenvironments. In addition, these culture systems include various cell types to be co-cultured with the cancer cells such as stromal and endothelial cells. These culture systems allowed studying the dormancy phase and the consequent switch to a proliferative state. (c) The transgenic MMTV-Neu mouse model has been leveraged to study breast cancer dormancy in vivo. This HER2+ subtype model develops spontaneous mammary tumors, and early DTCs can be detected in the lungs and the bone marrow during the early stages of tumorigenesis such as ADH and DCIS, around 9 weeks of age, hence before the invasive stage onset which is typically seen around 23-30 weeks of age. The endpoint stage is characterized by the detection of macrometastases. However, whether metastases originate from early or late DTCs or both is still an open question.
Supplementary Table S5 from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

Resource Table
Supplementary Table S4 from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

Results of differential gene expression analysis between pre-GTS1 tumor cells treated for 48 hours with DMSO or Dox.
Supplementary Table S2 from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

Results of differential gene expression analysis between GTML tumours and GTS tumours.
Supplementary video 3 from Depletion of Conventional Type-1 Dendritic Cells in Established Tumors Suppresses Immunotherapy Efficacy
Authors: Teijeira Alvaro , Garasa Saray , Luri-Rey Carlos , de Andrea Carlos , Gato Maria , Molina Carmen , Kaisho Tsuneyasu , Cirella Assunta , Azpilikueta Arantza , Wculek Steffanie K. , Egea Josune , Olivera Irene , Rodriguez Inmaculada , Rouzaut Ana , Verkhusha Vladislav , Valencia Karmele , Sancho David , Berraondo Pedro , Melero Ignacio
Published: March 2023

Video S3
Supplementary Table S1 from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

List of genes that are part of a quiescent cell signature and display regions of differentially opened chromatin.
Supplementary Figure Legends from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

Supplementary Figure Legends
Supplementary figures and methods from Depletion of Conventional Type-1 Dendritic Cells in Established Tumors Suppresses Immunotherapy Efficacy
Authors: Teijeira Alvaro , Garasa Saray , Luri-Rey Carlos , de Andrea Carlos , Gato Maria , Molina Carmen , Kaisho Tsuneyasu , Cirella Assunta , Azpilikueta Arantza , Wculek Steffanie K. , Egea Josune , Olivera Irene , Rodriguez Inmaculada , Rouzaut Ana , Verkhusha Vladislav , Valencia Karmele , Sancho David , Berraondo Pedro , Melero Ignacio
Published: March 2023

Supplementary figures 1-5
Supplementary methods
Supplementary Data from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

Supplementary figure 2
Supplementary Data from Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma
Authors: Borgenvik Anna , Holmberg Karl O. , Bolin Sara , Zhao Miao , Savov Vasil , Rosén Gabriela , Hutter Sonja , Garancher Alexandra , Rahmanto Aldwin Suryo , Bergström Tobias , Olsen Thale Kristin , Mainwaring Oliver J. , Sattanino Damiana , Verbaan Annemieke D. , Rusert Jessica M. , Sundström Anders , Bravo Mar Ballester , Dang Yonglong , Wenz Amelie S. , Richardson Stacey , Fotaki Grammatiki , Hill Rebecca M. , Dubuc Adrian M. , Kalushkova Antonia , Remke Marc , Čančer Matko , Jernberg-Wiklund Helena , Giraud Géraldine , Chen Xingqi , Taylor Michael D. , Sangfelt Olle , Clifford Steven C. , Schüller Ulrich , Wechsler-Reya Robert J. , Weishaupt Holger , Swartling Fredrik J.
Published: March 2023

Supplementary figure 4
Supplementary Data from Elevated Methionine Flux Drives Pyroptosis Evasion in Persister Cancer Cells
Authors: El-Kenawi Asmaa , Berglund Anders , Estrella Veronica , Zhang Yonghong , Liu Min , Putney Ryan M. , Yoder Sean J. , Johnson Joseph , Brown Joel , Gatenby Robert
Published: March 2023

Supplementary Table 1
Supplementary Data from Elevated Methionine Flux Drives Pyroptosis Evasion in Persister Cancer Cells
Authors: El-Kenawi Asmaa , Berglund Anders , Estrella Veronica , Zhang Yonghong , Liu Min , Putney Ryan M. , Yoder Sean J. , Johnson Joseph , Brown Joel , Gatenby Robert
Published: March 2023

Supplemental Materials Methods with additional references.
Supplementary Movie S9 from Plk1 Inhibitors and Abiraterone Synergistically Disrupt Mitosis and Kill Cancer Cells of Disparate Origin Independently of Androgen Receptor Signaling
Authors: Patterson Jesse C. , Varkaris Andreas , Croucher Peter J.P. , Ridinger Maya , Dalrymple Susan , Nouri Mannan , Xie Fang , Varmeh Shohreh , Jonas Oliver , Whitman Matthew A. , Chen Sen , Rashed Saleh , Makusha Lovemore , Luo Jun , Isaacs John T. , Erlander Mark G. , Einstein David J. , Balk Steven P. , Yaffe Michael B.
Published: March 2023

Entosis of mitotic C4-2 cells
Supplementary Movie S5 from Plk1 Inhibitors and Abiraterone Synergistically Disrupt Mitosis and Kill Cancer Cells of Disparate Origin Independently of Androgen Receptor Signaling
Authors: Patterson Jesse C. , Varkaris Andreas , Croucher Peter J.P. , Ridinger Maya , Dalrymple Susan , Nouri Mannan , Xie Fang , Varmeh Shohreh , Jonas Oliver , Whitman Matthew A. , Chen Sen , Rashed Saleh , Makusha Lovemore , Luo Jun , Isaacs John T. , Erlander Mark G. , Einstein David J. , Balk Steven P. , Yaffe Michael B.
Published: March 2023

Video montage comparing mitosis of vehicle control with abiraterone treated C4-2 cells
Supplementary Data from CSN6 Mediates Nucleotide Metabolism to Promote Tumor Development and Chemoresistance in Colorectal Cancer
Authors: Zou Shaomin , Qin Baifu , Yang Ziqing , Wang Wencong , Zhang Jieping , Zhang Yijing , Meng Manqi , Feng Junyan , Xie Yunling , Fang Ling , Xiao Lishi , Zhang Peng , Meng Xiangqi , Choi Hyun Ho , Wen Weijie , Pan Qihao , Ghesquière Bart , Lan Ping , Lee Mong-Hong , Fang Lekun
Published: March 2023

Table S1
Supplementary Data from CSN6 Mediates Nucleotide Metabolism to Promote Tumor Development and Chemoresistance in Colorectal Cancer
Authors: Zou Shaomin , Qin Baifu , Yang Ziqing , Wang Wencong , Zhang Jieping , Zhang Yijing , Meng Manqi , Feng Junyan , Xie Yunling , Fang Ling , Xiao Lishi , Zhang Peng , Meng Xiangqi , Choi Hyun Ho , Wen Weijie , Pan Qihao , Ghesquière Bart , Lan Ping , Lee Mong-Hong , Fang Lekun
Published: March 2023

Table S2
Table S3 from Phagocytosis of Glioma Cells Enhances the Immunosuppressive Phenotype of Bone Marrow–Derived Macrophages
Authors: Wu Min , Wu Lingxiang , Wu Wei , Zhu Mengyan , Li Jianyu , Wang Ziyu , Li Jie , Ding Rong , Liang Yuan , Li Liangyu , Zhang Tingting , Huang Bin , Cai Yun , Li Kening , Li Lu , Zhang Rui , Hu Baoli , Lin Fan , Wang Xiuxing , Zheng Siyuan , Chen Jian , You Yongping , Jiang Tao , Zhang Junxia , Chen Hongshan , Wang Qianghu
Published: March 2023

Information of TAMs harboring tumor-derived mutations
Table S1 from Hydrogen Sulfide Creates a Favorable Immune Microenvironment for Colon Cancer
Authors: Yue Taohua , Li Jichang , Zhu Jing , Zuo Shuai , Wang Xin , Liu Yucun , Liu Jia , Liu Xiaoyun , Wang Pengyuan , Chen Shanwen
Published: March 2023

Supplementary Table 1
Figure S3 from Hydrogen Sulfide Creates a Favorable Immune Microenvironment for Colon Cancer
Authors: Yue Taohua , Li Jichang , Zhu Jing , Zuo Shuai , Wang Xin , Liu Yucun , Liu Jia , Liu Xiaoyun , Wang Pengyuan , Chen Shanwen
Published: March 2023

Supplementary Figure 3
Figure S1 from Hydrogen Sulfide Creates a Favorable Immune Microenvironment for Colon Cancer
Authors: Yue Taohua , Li Jichang , Zhu Jing , Zuo Shuai , Wang Xin , Liu Yucun , Liu Jia , Liu Xiaoyun , Wang Pengyuan , Chen Shanwen
Published: March 2023

Supplementary Figure 1
Supplementary Figure Legends from KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer
Authors: Qiu Hong , Makarov Vladimir , Bolzenius Jennifer K. , Halstead Angela , Parker Yvonne , Wang Allen , Iyer Gopakumar V. , Wise Hannah , Kim Daniel , Thayaparan Varna , Lindner Daniel J. , Haber Georges-Pascal , Ting Angela H. , Ren Bing , Chan Timothy A. , Arora Vivek , Solit David B. , Lee Byron H.
Published: March 2023

Supplementary Figure Legends
Supplementary File 1 from Spatial Transcriptomic Analysis of a Diverse Patient Cohort Reveals a Conserved Architecture in Triple-Negative Breast Cancer
Authors: Bassiouni Rania , Idowu Michael O. , Gibbs Lee D. , Robila Valentina , Grizzard Pamela J. , Webb Michelle G. , Song Jiarong , Noriega Ashley , Craig David W. , Carpten John D.
Published: March 2023

Case Demographics and Clinical Annotation
Supplementary Figure 4 from KDM6A Loss Triggers an Epigenetic Switch That Disrupts Urothelial Differentiation and Drives Cell Proliferation in Bladder Cancer
Authors: Qiu Hong , Makarov Vladimir , Bolzenius Jennifer K. , Halstead Angela , Parker Yvonne , Wang Allen , Iyer Gopakumar V. , Wise Hannah , Kim Daniel , Thayaparan Varna , Lindner Daniel J. , Haber Georges-Pascal , Ting Angela H. , Ren Bing , Chan Timothy A. , Arora Vivek , Solit David B. , Lee Byron H.
Published: March 2023

Supplementary Figure 4
table s1 from The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors
Authors: Llano Elena , Todeschini Anne Laure , Felipe-Medina Natalia , Corte-Torres María D. , Condezo Yazmine B. , Sanchez-Martin Manuel , López-Tamargo Sara , Astudillo Aurora , Puente Xose S. , Pendas Alberto M. , Veitia Reiner A.
Published: March 2023

table S1
Table S2 from The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors
Authors: Llano Elena , Todeschini Anne Laure , Felipe-Medina Natalia , Corte-Torres María D. , Condezo Yazmine B. , Sanchez-Martin Manuel , López-Tamargo Sara , Astudillo Aurora , Puente Xose S. , Pendas Alberto M. , Veitia Reiner A.
Published: March 2023

Table S2
Supplementary Data from The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors
Authors: Llano Elena , Todeschini Anne Laure , Felipe-Medina Natalia , Corte-Torres María D. , Condezo Yazmine B. , Sanchez-Martin Manuel , López-Tamargo Sara , Astudillo Aurora , Puente Xose S. , Pendas Alberto M. , Veitia Reiner A.
Published: March 2023

supplementary figures S1-S4
Supplementary Data from HAND2 Assists MYCN Enhancer Invasion to Regulate a Noradrenergic Neuroblastoma Phenotype
Authors: Xu Man , Sun Ming , Zhang Xiyuan , Nguyen Rosa , Lei Haiyan , Shern Jack F. , Thiele Carol J. , Liu Zhihui
Published: March 2023

Table S4 shows genes regulated by HAND2 or MYCN in IMR32 cells.
Supplementary Data from Sphingosine Kinase 2 in Stromal Fibroblasts Creates a Hospitable Tumor Microenvironment in Breast Cancer
Authors: Weigel Cynthia , Maczis Melissa A. , Palladino Elisa N.D. , Green Christopher D. , Maceyka Michael , Guo Chunqing , Wang Xiang-Yang , Dozmorov Mikhail G. , Milstien Sheldon , Spiegel Sarah
Published: March 2023

Supplementary Table 2
Supplementary Data from Sphingosine Kinase 2 in Stromal Fibroblasts Creates a Hospitable Tumor Microenvironment in Breast Cancer
Authors: Weigel Cynthia , Maczis Melissa A. , Palladino Elisa N.D. , Green Christopher D. , Maceyka Michael , Guo Chunqing , Wang Xiang-Yang , Dozmorov Mikhail G. , Milstien Sheldon , Spiegel Sarah
Published: March 2023

Supplementary Dataset Table 3
Table S4 from Systematic Interrogation of Tumor Cell Resistance to Chimeric Antigen Receptor T-cell Therapy in Pancreatic Cancer
Authors: Hagel Kimberly R. , Arafeh Rand , Gang Sydney , Arnoff Taylor E. , Larson Rebecca C. , Doench John G. , Mathewson Nathan D. , Wucherpfennig Kai W. , Maus Marcela V. , Hahn William C.
Published: March 2023

enriched gene sets in HupT3 cells following TFAP4 knockout and overexpression, generated by the Enrichr search engine
Table S2 from Systematic Interrogation of Tumor Cell Resistance to Chimeric Antigen Receptor T-cell Therapy in Pancreatic Cancer
Authors: Hagel Kimberly R. , Arafeh Rand , Gang Sydney , Arnoff Taylor E. , Larson Rebecca C. , Doench John G. , Mathewson Nathan D. , Wucherpfennig Kai W. , Maus Marcela V. , Hahn William C.
Published: March 2023

differential gene expression in HupT3 cells following TFAP4 knockout and overexpression
Supplementary Data from Genome-Wide Analysis of Rare Haplotypes Associated with Breast Cancer Risk
Authors: Wang Fan , Moon Wonjong , Letsou William , Sapkota Yadav , Wang Zhaoming , Im Cindy , Baedke Jessica L. , Robison Leslie , Yasui Yutaka
Published: March 2023

This file contains figures S1-5 and Tables S1, 3-9, 12, and 13
Supplementary Data from Genome-Wide Analysis of Rare Haplotypes Associated with Breast Cancer Risk
Authors: Wang Fan , Moon Wonjong , Letsou William , Sapkota Yadav , Wang Zhaoming , Im Cindy , Baedke Jessica L. , Robison Leslie , Yasui Yutaka
Published: March 2023

This file contains Tables S2, S10, and S11.
Supplementary Data S2 from A Cell-Fate Reprogramming Strategy Reverses Epithelial-to-Mesenchymal Transition of Lung Cancer Cells While Avoiding Hybrid States
Authors: Kim Namhee , Hwang Chae Young , Kim Taeyoung , Kim Hyunjin , Cho Kwang-Hyun
Published: March 2023

Simulation results using our EMT network model.
Supplementary Data S1 from A Cell-Fate Reprogramming Strategy Reverses Epithelial-to-Mesenchymal Transition of Lung Cancer Cells While Avoiding Hybrid States
Authors: Kim Namhee , Hwang Chae Young , Kim Taeyoung , Kim Hyunjin , Cho Kwang-Hyun
Published: March 2023

Detailed information of the EMT network model.
Supplementary Data from Olig1/2-Expressing Intermediate Lineage Progenitors Are Predisposed to PTEN/p53-Loss–Induced Gliomagenesis and Harbor Specific Therapeutic Vulnerabilities
Authors: Verma Ravinder , Chen Xiameng , Xin Dazhuan , Luo Zaili , Ogurek Sean , Xin Mei , Rao Rohit , Berry Kalen , Lu Q. Richard
Published: March 2023

Supplementary figure with legends and supplementary methods
Figure S4 from YAP-Activated SATB2 Is a Coactivator of NRF2 That Amplifies Antioxidative Capacity and Promotes Tumor Progression in Renal Cell Carcinoma
Authors: Jin Juan , Chen Fen , He Wenfang , Zhao Li , Lin Bo , Zheng Danna , Chen Li , He Hongchao , He Qiang
Published: March 2023

Figure S4
Figure S3 from YAP-Activated SATB2 Is a Coactivator of NRF2 That Amplifies Antioxidative Capacity and Promotes Tumor Progression in Renal Cell Carcinoma
Authors: Jin Juan , Chen Fen , He Wenfang , Zhao Li , Lin Bo , Zheng Danna , Chen Li , He Hongchao , He Qiang
Published: March 2023

Figure S3
Figure S5 from PARP Inhibition Induces Synthetic Lethality and Adaptive Immunity in LKB1-Mutant Lung Cancer
Authors: Long Li-Li , Ma Si-Cong , Guo Ze-Qin , Zhang Yan-Pei , Fan Zhenzhen , Liu Li-Juan , Liu Li , Han Duan-Duan , Leng Meng-Xin , Wang Jian , Guo Xue-Jun , Tan Jia-Le , Cai Xiao-Ting , Lin Yan , Pan Xinghua , Wu De-Hua , Bai Xue , Dong Zhong-Yi
Published: March 2023

Olaparib-derived dual effects sensitize LKB1-deficient tumors to anti-PD-1 immunotherapy in preclinical models. (a) Mice-bearing orthotopic lung tumors were treated with different therapies. Bioluminescent images were shown. (b) Immunofluorescence staining of PD-L1 and CD8+T cells in resected lung tumors of mice bearing orthotopic tumors (n= 6 fields from independent tumors). Scale bar, 100 μm. (c). Quantification of tumor-infiltrating CD8+ T cells in immunofluorescence staining. (d, e) IHC statistical analysis of PAR and PD-L1 expression in resected lung tumors of mice bearing orthotopic tumors (n=5 fields from independent tumors). (f) Quantification of tumor-infiltrating CD8+ T cells in IHC staining in resected lung tumors of mice bearing orthotopic tumors (n= 5 fields from independent tumors). Data are represented as mean ± SD; Student's t-tests; * P < 0.05; ** P < 0.01; ***P<0.001; ****P<0.0001; ns, not significant. (g) Mean growth curve and individual growth curves of mice treated with different therapies (n=5~7 mice/group) in the first batch. Individual mice were injected with 1 × 106 LLC1 cells and the tumor volumes were monitored for 24 days. Results are presented as mean ± SEM; ****P < 0.0001; *** P < 0.001; ** P < 0.01; * P < 0.05, two-way ANOVA.
Supplementary Figure Legends from Androgen Signaling Contributes to Sex Differences in Cancer by Inhibiting NF-κB Activation in T Cells and Suppressing Antitumor Immunity
Authors: Zhang Xiaomin , Cheng Limin , Gao Chengqi , Chen Jing , Liao Shuangye , Zheng Yongqiang , Xu Liping , He Jingjing , Wang Danyang , Fang Ziqian , Zhang Jianeng , Yan Min , Luan Yi , Chen Siyu , Chen Likun , Xia Xiaojun , Deng Chunhao , Chen Guokai , Li Wende , Liu Zexian , Zhou Penghui
Published: March 2023

Supplementary Figure 1 and 2 Legends
Figure S2 from PARP Inhibition Induces Synthetic Lethality and Adaptive Immunity in LKB1-Mutant Lung Cancer
Authors: Long Li-Li , Ma Si-Cong , Guo Ze-Qin , Zhang Yan-Pei , Fan Zhenzhen , Liu Li-Juan , Liu Li , Han Duan-Duan , Leng Meng-Xin , Wang Jian , Guo Xue-Jun , Tan Jia-Le , Cai Xiao-Ting , Lin Yan , Pan Xinghua , Wu De-Hua , Bai Xue , Dong Zhong-Yi
Published: March 2023

Mechanistic link between LKB1 and PARP1. (a) A bioinformatics tool (Pepsite) was utilized to predict the possibility of PARP1 docking on the di-Arg ER retention motif of LKB1 (PRR). (b) Localization of PARP1 (green) relative to LKB1 (red) in LKB1-WT A549 cells and H1299 cells. Scale bar = 20 μm. (c) Lysates from H1299 cells were subjected to IP with anti-PARP1 and anti-LKB1 antibodies and western blot analysis with the indicated antibodies. (d) IHC statistical analysis of PAR expression in LLC-shCtrl and LLC-shLkb1 tumors. n=5 fields from independent tumors. Data are represented as mean ± SD; Student's t-tests; **, P < 0.01.
Supplementary Figure 2 from Androgen Signaling Contributes to Sex Differences in Cancer by Inhibiting NF-κB Activation in T Cells and Suppressing Antitumor Immunity
Authors: Zhang Xiaomin , Cheng Limin , Gao Chengqi , Chen Jing , Liao Shuangye , Zheng Yongqiang , Xu Liping , He Jingjing , Wang Danyang , Fang Ziqian , Zhang Jianeng , Yan Min , Luan Yi , Chen Siyu , Chen Likun , Xia Xiaojun , Deng Chunhao , Chen Guokai , Li Wende , Liu Zexian , Zhou Penghui
Published: March 2023

Supplementary Figure 2
Supplementary Figures and Tables from Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis
Authors: Chan Tracey W. , Dodson Jack P. , Arbet Jaron , Boutros Paul C. , Xiao Xinshu
Published: March 2023

Supplementary Figures S1-11 and Tables S1-2 are included in this file
Supplementary Table S1-S8 from CircPDIA4 Induces Gastric Cancer Progression by Promoting ERK1/2 Activation and Enhancing Biogenesis of Oncogenic circRNAs
Authors: Shen Yue , Zhang Nasha , Chai Jie , Wang Teng , Ma Chi , Han Linyu , Yang Ming
Published: March 2023

Table S1 shows primers for RT-qPCR. Table S2 shows sequences of shRNAs and siRNAs. Table S3 shows antibodies used in the study. Table S4 shows the sequence of the biotin-labeled probes for circPDIA4 and controls. Table S5 shows the overlap circRNAs of the three gastric cancer cell lines. Table S6 shows the relevant clinic-pathological characteristics of gastric cancer cases stratified by circPDIA4 levels in Combined cohort. Table S7 shows the relevant clinic-pathological characteristics of gastric cancer cases stratified by QKI levels in Combined cohort. Table S8 shows Mass Spectrometry of proteins pulled-down by circPDIA4 in HGC-27 cells.
Supplemental Table S4 from Spatial Transcriptomic Analysis of Ovarian Cancer Precursors Reveals Reactivation of IGFBP2 during Pathogenesis
Authors: Wang Yeh , Huang Peng , Wang Brant G. , Murdock Tricia , Cope Leslie , Hsu Fang-Chi , Wang Tian-Li , Shih Ie-Ming
Published: March 2023

Differentially expressed genes between different comparisons