bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 5 from Engineering the Human Fc Region Enables Direct Cell Killing by Cancer Glycan–Targeting Antibodies without the Need for Immune Effector Cells or Complement
Authors: Vankemmelbeke Mireille , McIntosh Richard S. , Chua Jia Xin , Kirk Thomas , Daniels Ian , Patsalidou Marilena , Moss Robert , Parsons Tina , Scott David , Harris Gemma , Ramage Judith M. , Spendlove Ian , Durrant Lindy G.
Published: April 2023

Individual tumor growth curves from mice included in the in vivo COLO205 xenograft model
Supplementary Data from HER2 CAR-T Cells Eradicate Uveal Melanoma and T-cell Therapy–Resistant Human Melanoma in IL2 Transgenic NOD/SCID IL2 Receptor Knockout Mice
Authors: Forsberg Elin M.V. , Lindberg Mattias F. , Jespersen Henrik , Alsén Samuel , Bagge Roger Olofsson , Donia Marco , Svane Inge Marie , Nilsson Ola , Ny Lars , Nilsson Lisa M. , Nilsson Jonas A.
Published: April 2023

Figure legends for Supplemental Figures
Figure S2 from HER2 CAR-T Cells Eradicate Uveal Melanoma and T-cell Therapy–Resistant Human Melanoma in IL2 Transgenic NOD/SCID IL2 Receptor Knockout Mice
Authors: Forsberg Elin M.V. , Lindberg Mattias F. , Jespersen Henrik , Alsén Samuel , Bagge Roger Olofsson , Donia Marco , Svane Inge Marie , Nilsson Ola , Ny Lars , Nilsson Lisa M. , Nilsson Jonas A.
Published: April 2023

Confirmation of CRISPR/Cas9 gene inactivation of HER2 by flow cytometry
Table S1 from Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer
Authors: Wang Shidan , Rong Ruichen , Yang Donghan M. , Fujimoto Junya , Yan Shirley , Cai Ling , Yang Lin , Luo Danni , Behrens Carmen , Parra Edwin R. , Yao Bo , Xu Lin , Wang Tao , Zhan Xiaowei , Wistuba Ignacio I. , Minna John , Xie Yang , Xiao Guanghua
Published: April 2023

Supplemental Table S1 Patient characteristics for the National Lung Screening Trial (NLST) and The Cancer Genome Atlas (TCGA) datasets.
Figure S2 from p38γ MAPK Is Essential for Aerobic Glycolysis and Pancreatic Tumorigenesis
Authors: Wang Fang , Qi Xiao-Mei , Wertz Ryan , Mortensen Matthew , Hagen Catherine , Evans John , Sheinin Yuri , James Michael , Liu Pengyuan , Tsai Susan , Thomas James , Mackinnon Alexander , Dwinell Michael , Myers Charles R. , Bartrons Bach Ramon , Fu Liwu , Chen Guan
Published: April 2023

Figure S2. p38ÃƒÅ½Ã,Â³ knockout (KO) decreases p-Rb and CDK6 protein levels, slows G1/S transition, and inhibits cell growth, migration, and invasion in KPC cells, but lacks significant effects in PanIN lesions in KC mice.
Figure S1 from p38γ MAPK Is Essential for Aerobic Glycolysis and Pancreatic Tumorigenesis
Authors: Wang Fang , Qi Xiao-Mei , Wertz Ryan , Mortensen Matthew , Hagen Catherine , Evans John , Sheinin Yuri , James Michael , Liu Pengyuan , Tsai Susan , Thomas James , Mackinnon Alexander , Dwinell Michael , Myers Charles R. , Bartrons Bach Ramon , Fu Liwu , Chen Guan
Published: April 2023

Figure S1. p38ÃƒÅ½Ã,Â³ is overexpressed in Pdac tissues and interacts with p-PFKFB3, PFKFB3, and GLUT2 in Pdac cells.
Figure S5 from Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer
Authors: Wang Shidan , Rong Ruichen , Yang Donghan M. , Fujimoto Junya , Yan Shirley , Cai Ling , Yang Lin , Luo Danni , Behrens Carmen , Parra Edwin R. , Yao Bo , Xu Lin , Wang Tao , Zhan Xiaowei , Wistuba Ignacio I. , Minna John , Xie Yang , Xiao Guanghua
Published: April 2023

Supplemental Figure S5 Validation of lymphocyte detection results in whole-slide image nuclei segmentation and classification by HD-Staining model.
Supplementary Methods from IL33 Is a Key Driver of Treatment Resistance of Cancer
Authors: Kudo-Saito Chie , Miyamoto Takahiro , Imazeki Hiroshi , Shoji Hirokazu , Aoki Kazunori , Boku Narikazu
Published: April 2023

Detailed methods to establish B16-F10 subclones and IL33 transfectants, and materials for RT-PCR, gene knockdown, and flow cytometry
Supplementary Figures S1 - S5 from IL33 Is a Key Driver of Treatment Resistance of Cancer
Authors: Kudo-Saito Chie , Miyamoto Takahiro , Imazeki Hiroshi , Shoji Hirokazu , Aoki Kazunori , Boku Narikazu
Published: April 2023

Figure S1: Gating strategy for flow cytometric analysis, Figure S2: IL33 knockdown in human cancer cells, Figure S3: Establishment of IL33 transfectants using human cancer cells, Figure S4: The roles of IL17RB+ ILC2s in the IL33+ tumor progression, and Figure S5: Validation of polyploidy of murine cancer cells
Figure S7 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

ZBC260 does not apparently decrease mouse body weights in both animal studies with lung cancer xenografts and PDXs and effectively modulates the levels of several protein markers in lung cancer PDXs
Figure S3 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

Basal levels of SPOP, Bim and Mcl-1 proteins in NSCLC cell lines with varied sensitivities to BET degraders and correlation between BRD4 and Mcl-1 or between Mcl-1 and cell response to ZBC260.
Figure S1 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

Effects of ZBC260, dBET and JQ-1 on the growth of 20 NSCLC and 7 SCLC cell lines and basal expression level of c-Myc in SCLC cell lines.
Supplementary Materials and Figure Legends from Genome-Wide Screening and Functional Analysis Identifies Tumor Suppressor Long Noncoding RNAs Epigenetically Silenced in Hepatocellular Carcinoma
Authors: Xu Feiyue , Li Chi Han , Wong Chi Hin , Chen George G. , Lai Paul Bo San , Shao Shengwen , Chan Stephen L. , Chen Yangchao
Published: April 2023

Supplementary Materials and Figure Legends
Figure S6 from GPD1 Enhances the Anticancer Effects of Metformin by Synergistically Increasing Total Cellular Glycerol-3-Phosphate
Authors: Xie Jianjiang , Ye Jianheng , Cai Zhiduan , Luo Yong , Zhu Xuejin , Deng Yulin , Feng Yuanfa , Liang Yingke , Liu Ren , Han Zhaodong , Liang Yuxiang , Zheng Yu , Mo Rujun , Zhuo Yangjia , Wu Yongding , Jiang Funeng , Zhu Jianguo , Wu Chin-Lee , Zhong Weide
Published: April 2023

Figure S6 showed that metformin induced AMPK phosphorylation and inhibited mTOR pathway, which were not affected by GPD1 overexpression.
Figure S5 from GPD1 Enhances the Anticancer Effects of Metformin by Synergistically Increasing Total Cellular Glycerol-3-Phosphate
Authors: Xie Jianjiang , Ye Jianheng , Cai Zhiduan , Luo Yong , Zhu Xuejin , Deng Yulin , Feng Yuanfa , Liang Yingke , Liu Ren , Han Zhaodong , Liang Yuxiang , Zheng Yu , Mo Rujun , Zhuo Yangjia , Wu Yongding , Jiang Funeng , Zhu Jianguo , Wu Chin-Lee , Zhong Weide
Published: April 2023

Figure S5 showed that metformin can suppress OCR through inhibiting GPD2 expression.
Figure S5 from A Versatile ES Cell–Based Melanoma Mouse Modeling Platform
Authors: Bok Ilah , Vera Olga , Xu Xiaonan , Jasani Neel , Nakamura Koji , Reff Jordan , Nenci Arianna , Gonzalez Jose G. , Karreth Florian A.
Published: April 2023

This Figure shows the percent of melanomas expressing ectopic Pten or GFP, and the expression of rtTA3 in Pten-restored tumors.
Supplementary Data from Therapeutic Potential of the miRNA–ATM Axis in the Management of Tumor Radioresistance
Authors: Rezaeian Abdol-Hossein , Khanbabaei Hashem , Calin George A.
Published: April 2023

S Fig 2
Supplementary Materials from LIN9 and NEK2 Are Core Regulators of Mitotic Fidelity That Can Be Therapeutically Targeted to Overcome Taxane Resistance
Authors: Roberts Melyssa S. , Sahni Jennifer M. , Schrock Morgan S. , Piemonte Katrina M. , Weber-Bonk Kristen L. , Seachrist Darcie D. , Avril Stefanie , Anstine Lindsey J. , Singh Salendra , Sizemore Steven T. , Varadan Vinay , Summers Matthew K. , Keri Ruth A.
Published: April 2023

Supplemental figure legends and additional methods
Supplementary Data from The Deubiquitinase USP38 Promotes NHEJ Repair through Regulation of HDAC1 Activity and Regulates Cancer Cell Response to Genotoxic Insults
Authors: Yang Yongfeng , Yang Chuanzhen , Li Tingting , Yu Shuyu , Gan Tingting , Hu Jiazhi , Cui Jun , Zheng Xiaofeng
Published: April 2023

Supplementary methods, Table S1,Figure S1-8 and legends
Supplementary Data from Stromal SNAI2 Is Required for ERBB2 Breast Cancer Progression
Authors: Blanco-Gómez Adrián , Hontecillas-Prieto Lourdes , Corchado-Cobos Roberto , García-Sancha Natalia , Salvador Nélida , Castellanos-Martín Andrés , Sáez-Freire María del Mar , Mendiburu-Eliçabe Marina , Alonso-López Diego , De Las Rivas Javier , Lorente Mar , García-Casas Ana , Del Carmen Sofía , Abad-Hernández María del Mar , Cruz-Hernández Juan Jesús , Rodríguez-Sánchez César Augusto , Claros-Ampuero Juncal , García-Cenador Begoña , García-Criado Javier , Orimo Akira , Gridley Thomas , Pérez-Losada Jesús , Castillo-Lluva Sonia
Published: April 2023

Supplementary material and methods; Supplementary figures S1-S6; supplementary tables S1-S9
Table S2: List of YAP-differential and TAZ-differential drugs from A Division of Labor between YAP and TAZ in Non–Small Cell Lung Cancer
Authors: Shreberk-Shaked Michal , Dassa Bareket , Sinha Sanju , Di Agostino Silvia , Azuri Ido , Mukherjee Saptaparna , Aylon Yael , Blandino Giovanni , Ruppin Eytan , Oren Moshe
Published: April 2023

List of 142 YAP-differential drugs and 38 TAZ-differential drugs in LUAD cells. Each row is a drug, and each column specifies additional information, including dose used in the screen, drug targets, indication, clinical phase and the p-value of the comparison.
Supplementary Dataset S6 from Therapeutic Targeting of the Premetastatic Stage in Human Lung-to-Brain Metastasis
Authors: Singh Mohini , Venugopal Chitra , Tokar Tomas , McFarlane Nicole , Subapanditha Minomi K. , Qazi Maleeha , Bakhshinyan David , Vora Parvez , Murty Naresh K. , Jurisica Igor , Singh Sheila K.
Published: April 2023

List of therapeutics targeting dysregulated BMIT genes
Supplementary Dataset S4 from Therapeutic Targeting of the Premetastatic Stage in Human Lung-to-Brain Metastasis
Authors: Singh Mohini , Venugopal Chitra , Tokar Tomas , McFarlane Nicole , Subapanditha Minomi K. , Qazi Maleeha , Bakhshinyan David , Vora Parvez , Murty Naresh K. , Jurisica Igor , Singh Sheila K.
Published: April 2023

GSEA of dysregulated BMIT genes within GO gene sets
Supplementary Dataset S1 from Therapeutic Targeting of the Premetastatic Stage in Human Lung-to-Brain Metastasis
Authors: Singh Mohini , Venugopal Chitra , Tokar Tomas , McFarlane Nicole , Subapanditha Minomi K. , Qazi Maleeha , Bakhshinyan David , Vora Parvez , Murty Naresh K. , Jurisica Igor , Singh Sheila K.
Published: April 2023

List of dysregulated BMIT genes as identified through RNA sequencing
Supplementary Material from Circulating Insulin-like Growth Factor-I Concentrations and Risk of 30 Cancers: Prospective Analyses in UK Biobank
Authors: Knuppel Anika , Fensom Georgina K. , Watts Eleanor L. , Gunter Marc J. , Murphy Neil , Papier Keren , Perez-Cornago Aurora , Schmidt Julie A. , Smith Byrne Karl , Travis Ruth C. , Key Timothy J.
Published: April 2023

Supplementary Tables S1-3 and Figures S1-3. Table S1: Median, interquartile range (IQR), minimum (Min.) and maximum (max.) of follow-up time by cancer site. Table S2: Hazard ratios (HRs) and 95% confidence intervals (CIs) of cancer risk according to circulating insulin-like growth factor-I concentrations. Table S3: Hazard ratios (HRs) and 95% confidence intervals (CIs) of cancer risk according to circulating insulin-like growth factor-I concentrations stratified by follow-up time, sex and age-group. Figure S1: Flow diagram for reaching the analytical sample. Figure S2: Hazard ratios (HRs) and 95% confidence intervals (CIs) for cancer risk per 5 nmol/l higher insulin-like growth factor-I concentration by cancer site and sex. Figure S3: Hazard ratios (HRs) and 95% confidence intervals (CIs) for cancer risk per 5 nmol/l higher insulin-like growth factor-I concentration by cancer site and age (<55, {greater than or equal to}55 years) at biomarker assessment.
Table S4 from A Circle RNA Regulatory Axis Promotes Lung Squamous Metastasis via CDR1-Mediated Regulation of Golgi Trafficking
Authors: Harrison Emily B. , Porrello Alessandro , Bowman Brittany M. , Belanger Adam R. , Yacovone Gabriella , Azam Salma H. , Windham Ian A. , Ghosh Subrata K. , Wang Menglin , Mckenzie Nicholas , Waugh Trent A. , Van Swearingen Amanda E.D. , Cohen Stephanie M. , Allen Devon G. , Goodwin Tyler J. , Mascenik Teresa , Bear James E. , Cohen Sarah , Randell Scott H. , Massion Pierre P. , Major Michael B. , Huang Leaf , Pecot Chad V.
Published: April 2023

Candidate target genes for miR-671-5p, values based on median expression of miR-671-5p and candidate genes.
Table S3 from A Circle RNA Regulatory Axis Promotes Lung Squamous Metastasis via CDR1-Mediated Regulation of Golgi Trafficking
Authors: Harrison Emily B. , Porrello Alessandro , Bowman Brittany M. , Belanger Adam R. , Yacovone Gabriella , Azam Salma H. , Windham Ian A. , Ghosh Subrata K. , Wang Menglin , Mckenzie Nicholas , Waugh Trent A. , Van Swearingen Amanda E.D. , Cohen Stephanie M. , Allen Devon G. , Goodwin Tyler J. , Mascenik Teresa , Bear James E. , Cohen Sarah , Randell Scott H. , Massion Pierre P. , Major Michael B. , Huang Leaf , Pecot Chad V.
Published: April 2023

Expression of miRs in SK-MES-1 and LN1 measured by Nanostring with normalized counts greater than 5 in at least one of the two compared samples.
Supplementary Video 1 from A Circle RNA Regulatory Axis Promotes Lung Squamous Metastasis via CDR1-Mediated Regulation of Golgi Trafficking
Authors: Harrison Emily B. , Porrello Alessandro , Bowman Brittany M. , Belanger Adam R. , Yacovone Gabriella , Azam Salma H. , Windham Ian A. , Ghosh Subrata K. , Wang Menglin , Mckenzie Nicholas , Waugh Trent A. , Van Swearingen Amanda E.D. , Cohen Stephanie M. , Allen Devon G. , Goodwin Tyler J. , Mascenik Teresa , Bear James E. , Cohen Sarah , Randell Scott H. , Massion Pierre P. , Major Michael B. , Huang Leaf , Pecot Chad V.
Published: April 2023

Time lapse imaging of RUSH assay in SK-MES-1-EV cells transfected with Ii-Str_ssSBP-EGFP (green) and Golgi marker mApple-SiT (magenta) beginning 5 min after biotin addition.
Supplementary Figure 5 from A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier
Authors: Hilfenhaus Georg , Mompeón Ana , Freshman Jonathan , Prajapati Divya P. , Hernandez Gloria , Freitas Vanessa M. , Ma Feiyang , Langenbacher Adam D. , Mirkov Snezana , Song Dana , Cho Byoung-Kyu , Goo Young Ah , Pellegrini Matteo , Chen Jau-Nian , Damoiseaux Robert , Iruela-Arispe M. Luisa
Published: April 2023

Work flow to assess effects of drug hits in vivo
Supplementary Figure 1 from A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier
Authors: Hilfenhaus Georg , Mompeón Ana , Freshman Jonathan , Prajapati Divya P. , Hernandez Gloria , Freitas Vanessa M. , Ma Feiyang , Langenbacher Adam D. , Mirkov Snezana , Song Dana , Cho Byoung-Kyu , Goo Young Ah , Pellegrini Matteo , Chen Jau-Nian , Damoiseaux Robert , Iruela-Arispe M. Luisa
Published: April 2023

Phenotypes of the human pancreatic cell Ines and effects on endothelium
Supplementary Figure S4 from Resolution of Spatial and Temporal Heterogeneity in Bevacizumab-Treated Breast Tumors by Eigenspectra Multispectral Optoacoustic Tomography
Authors: Liapis Evangelos , Klemm Uwe , Karlas Angelos , Reber Josefine , Ntziachristos Vasilis
Published: April 2023

Supplementary Figure S4
Table S2 from A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing
Published: April 2023

The 422,314 simple somatic mutations that could be associated with protein coding genes. Their respective genomic locations and DEEP scores are also annotated.
Supplementary Table 1 from Local Targeting of NAD+ Salvage Pathway Alters the Immune Tumor Microenvironment and Enhances Checkpoint Immunotherapy in Glioblastoma
Authors: Li Ming , Kirtane Ameya R. , Kiyokawa Juri , Nagashima Hiroaki , Lopes Aaron , Tirmizi Zain A. , Lee Christine K. , Traverso Giovanni , Cahill Daniel P. , Wakimoto Hiroaki
Published: April 2023

Table S1 - List of antibodies used
Supplementary Table 1 from ARC Is a Critical Protector against Inflammatory Bowel Disease (IBD) and IBD-Associated Colorectal Tumorigenesis
Authors: Wang Qiushi , Zhang Tianshun , Chang Xiaoyu , Lim Do Young , Wang Keke , Bai Ruihua , Wang Ting , Ryu Joohyun , Chen Hanyong , Yao Ke , Ma Wei-Ya , Boardman Lisa A. , Bode Ann M. , Dong Zigang
Published: April 2023

Supplementary Table 1
Figure S1, Figure S2, Figure S3 from YAP-Mediated Repression of HRK Regulates Tumor Growth, Therapy Response, and Survival Under Tumor Environmental Stress in Neuroblastoma
Authors: Shim Jenny , Lee Jasmine Y. , Jonus Hunter C. , Arnold Amanda , Schnepp Robert W. , Janssen Kaitlyn M. , Maximov Victor , Goldsmith Kelly C.
Published: April 2023

YAP protein expression in paired isogenic cell line; NGP pGAMA-YAP model; GSEA of stemness pathway genes
Figure S5 from Remission of Spontaneous Canine Tumors after Systemic Cellular Viroimmunotherapy
Authors: Cejalvo Teresa , Perisé-Barrios Ana Judith , del Portillo Isabel , Laborda Eduardo , Rodriguez-Milla Miguel A. , Cubillo Isabel , Vázquez Fernando , Sardón David , Ramirez Manuel , Alemany Ramon , del Castillo Noemí , García-Castro Javier
Published: April 2023

Hematological and biochemical analysis in canine patients during dCelyvir treatment.
Supplementary Table S5 from Intake of Dietary Fruit, Vegetables, and Fiber and Risk of Colorectal Cancer According to Molecular Subtypes: A Pooled Analysis of 9 Studies
Authors: Hidaka Akihisa , Harrison Tabitha A. , Cao Yin , Sakoda Lori C. , Barfield Richard , Giannakis Marios , Song Mingyang , Phipps Amanda I. , Figueiredo Jane C. , Zaidi Syed H. , Toland Amanda E. , Amitay Efrat L. , Berndt Sonja I. , Borozan Ivan , Chan Andrew T. , Gallinger Steven , Gunter Marc J. , Guinter Mark A. , Harlid Sophia , Hampel Heather , Jenkins Mark A. , Lin Yi , Moreno Victor , Newcomb Polly A. , Nishihara Reiko , Ogino Shuji , Obón-Santacana Mireia , Parfrey Patrick S. , Potter John D. , Slattery Martha L. , Steinfelder Robert S. , Um Caroline Y. , Wang Xiaoliang , Woods Michael O. , Van Guelpen Bethany , Thibodeau Stephen N. , Hoffmeister Michael , Sun Wei , Hsu Li , Buchanan Daniel D. , Campbell Peter T. , Peters Ulrike
Published: April 2023

Supplementary Table S5
Supplemental Figure S3 from Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma
Authors: Gartrell-Corrado Robyn D. , Chen Andrew X. , Rizk Emanuelle M. , Marks Douglas K. , Bogardus Margaret H. , Hart Thomas D. , Silverman Andrew M. , Bayan Claire-Audrey Y. , Finkel Grace G. , Barker Luke W. , Komatsubara Kimberly M. , Carvajal Richard D. , Horst Basil A. , Chang Rui , Monod Anthea , Rabadan Raul , Saenger Yvonne M.
Published: April 2023

DSP identifies differences in immune marker expression between patients with high and low HLA-DR- macrophage density. DSP analysis of immune markers per total CD45 including CD3, CD4, CD8A, CD68, CD163 as well as immunosuppressive or checkpoint markers B7-H3, B7-H4, STING, VISTA, ICOS, and OX40L comparing patients with high and low density of HLA-DR- macrophages. Statistical analysis performed using Mann-Whitney U test. ***, p<0.001; **, p< 0.01; *, p<0.05; n.s., p{greater than or equal to}0.05.
Figure S1 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion
Authors: Voli Florida , Valli Emanuele , Lerra Luigi , Kimpton Kathleen , Saletta Federica , Giorgi Federico M. , Mercatelli Daniele , Rouaen Jourdin R.C. , Shen Sylvie , Murray Jayne E. , Ahmed-Cox Aria , Cirillo Giuseppe , Mayoh Chelsea , Beavis Paul A. , Haber Michelle , Trapani Joseph A. , Kavallaris Maria , Vittorio Orazio
Published: April 2023

Co-expression plots of VST-normalized gene expression profiles derived from TCGA datasets for PD-L1 and four copper-responsive genes
Supplementary Materials and Methods from Slow-Cycling Cancer Stem Cells Regulate Progression and Chemoresistance in Colon Cancer
Authors: Shiokawa Daisuke , Sakai Hiroaki , Ohata Hirokazu , Miyazaki Toshiaki , Kanda Yusuke , Sekine Shigeki , Narushima Daichi , Hosokawa Masahito , Kato Mamoru , Suzuki Yutaka , Takeyama Haruko , Kambara Hideki , Nakagama Hitoshi , Okamoto Koji
Published: April 2023

Supplementary Materials and Methods
Supplementary Table 1 from Cellular and Genetic Determinants of the Sensitivity of Cancer to α-Particle Irradiation
Authors: Yard Brian D. , Gopal Priyanka , Bannik Kristina , Siemeister Gerhard , Hagemann Urs B. , Abazeed Mohamed E.
Published: April 2023

CCLE cell lines profiled and radiation sensitivity data.
Supplementary Data from Hes1 Is Essential in Proliferating Ductal Cell–Mediated Development of Intrahepatic Cholangiocarcinoma
Authors: Matsumori Tomoaki , Kodama Yuzo , Takai Atsushi , Shiokawa Masahiro , Nishikawa Yoshihiro , Matsumoto Tomonori , Takeda Haruhiko , Marui Saiko , Okada Hirokazu , Hirano Tomonori , Kuwada Takeshi , Sogabe Yuko , Kakiuchi Nobuyuki , Tomono Teruko , Mima Atsushi , Morita Toshihiro , Ueda Tatsuki , Tsuda Motoyuki , Yamauchi Yuki , Kuriyama Katsutoshi , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Marusawa Hiroyuki , Kageyama Ryoichiro , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Supplemental Data
Supplementary Figure 1 from Cellular and Genetic Determinants of the Sensitivity of Cancer to α-Particle Irradiation
Authors: Yard Brian D. , Gopal Priyanka , Bannik Kristina , Siemeister Gerhard , Hagemann Urs B. , Abazeed Mohamed E.
Published: April 2023

High-throughput profiling of cellular survival after gamma irradiation.
Fig. S3 from Hes1 Is Essential in Proliferating Ductal Cell–Mediated Development of Intrahepatic Cholangiocarcinoma
Authors: Matsumori Tomoaki , Kodama Yuzo , Takai Atsushi , Shiokawa Masahiro , Nishikawa Yoshihiro , Matsumoto Tomonori , Takeda Haruhiko , Marui Saiko , Okada Hirokazu , Hirano Tomonori , Kuwada Takeshi , Sogabe Yuko , Kakiuchi Nobuyuki , Tomono Teruko , Mima Atsushi , Morita Toshihiro , Ueda Tatsuki , Tsuda Motoyuki , Yamauchi Yuki , Kuriyama Katsutoshi , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Marusawa Hiroyuki , Kageyama Ryoichiro , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Relative mRNA expression levels of downstream effectors of Notch signaling in the liver tissues of 8-week-old Albcre and Albcre; RosaNotchOE/+ mice.
Supplemental Tables from Palmitoylated Proteins on AML-Derived Extracellular Vesicles Promote Myeloid-Derived Suppressor Cell Differentiation via TLR2/Akt/mTOR Signaling
Authors: Tohumeken Sehmus , Baur Rebecca , Böttcher Martin , Stoll Andrej , Loschinski Romy , Panagiotidis Konstantinos , Braun Martina , Saul Domenica , Völkl Simon , Baur Andreas S. , Bruns Heiko , Mackensen Andreas , Jitschin Regina , Mougiakakos Dimitrios
Published: April 2023

Information regarding patient characteristics, antibodies, and primers.
Supplemental Figure 2 from Palmitoylated Proteins on AML-Derived Extracellular Vesicles Promote Myeloid-Derived Suppressor Cell Differentiation via TLR2/Akt/mTOR Signaling
Authors: Tohumeken Sehmus , Baur Rebecca , Böttcher Martin , Stoll Andrej , Loschinski Romy , Panagiotidis Konstantinos , Braun Martina , Saul Domenica , Völkl Simon , Baur Andreas S. , Bruns Heiko , Mackensen Andreas , Jitschin Regina , Mougiakakos Dimitrios
Published: April 2023

(A) CD33 expression on AML-EVs, (B) Cytokine-content of AML-EVs, (C) Localization analysis of AML-EVs in monocytes, (D) Control experiment regarding EV-independent uptake of PKH26.
Supplemental Figure 1 from Palmitoylated Proteins on AML-Derived Extracellular Vesicles Promote Myeloid-Derived Suppressor Cell Differentiation via TLR2/Akt/mTOR Signaling
Authors: Tohumeken Sehmus , Baur Rebecca , Böttcher Martin , Stoll Andrej , Loschinski Romy , Panagiotidis Konstantinos , Braun Martina , Saul Domenica , Völkl Simon , Baur Andreas S. , Bruns Heiko , Mackensen Andreas , Jitschin Regina , Mougiakakos Dimitrios
Published: April 2023

(A) Induction of an MDSC phenotype by AML-derived soluble factors, (B) Induction of IDO-activity by AML-EVs, (C) ZetaView-based analysis of AML-EVs, and (D) Impact of chemotherapy on EV release by AML cells.
Figure S3 from Oncogenic BRAFV600E Governs Regulatory T-cell Recruitment during Melanoma Tumorigenesis
Authors: Shabaneh Tamer B. , Molodtsov Aleksey K. , Steinberg Shannon M. , Zhang Peisheng , Torres Gretel M. , Mohamed Gadisti A. , Boni Andrea , Curiel Tyler J. , Angeles Christina V. , Turk Mary Jo
Published: April 2023

Treg accumulation kinetics in induced Braf/Pten skin grafts
Supplementary Figure 2 from Loss of ARID1A Promotes Epithelial–Mesenchymal Transition and Sensitizes Pancreatic Tumors to Proteotoxic Stress
Authors: Tomihara Hideo , Carbone Federica , Perelli Luigi , Huang Justin K. , Soeung Melinda , Rose Johnathon L. , Robinson Frederick S. , Lissanu Deribe Yonathan , Feng Ningping , Takeda Mitsunobu , Inoue Akira , Poggetto Edoardo Del , Deem Angela K. , Maitra Anirban , Msaouel Pavlos , Tannir Nizar M. , Draetta Giulio F. , Viale Andrea , Heffernan Timothy P. , Bristow Christopher A. , Carugo Alessandro , Genovese Giannicola
Published: April 2023

Supplementary Figure 2. Knocking out ARID1A does not impair viability in PDAC cell lines.
Supplementary Table 4 from Bladder Tumor Subtype Commitment Occurs in Carcinoma In Situ Driven by Key Signaling Pathways Including ECM Remodeling
Authors: Wullweber Adrian , Strick Reiner , Lange Fabienne , Sikic Danijel , Taubert Helge , Wach Sven , Wullich Bernd , Bertz Simone , Weyerer Veronika , Stoehr Robert , Breyer Johannes , Burger Maximilian , Hartmann Arndt , Strissel Pamela L. , Eckstein Markus
Published: April 2023

Pairwise group P-values of analyses with multiple group comparisons tested by non-parametric Kruskal-Wallis tests.
Supplementary Table 3 from Bladder Tumor Subtype Commitment Occurs in Carcinoma In Situ Driven by Key Signaling Pathways Including ECM Remodeling
Authors: Wullweber Adrian , Strick Reiner , Lange Fabienne , Sikic Danijel , Taubert Helge , Wach Sven , Wullich Bernd , Bertz Simone , Weyerer Veronika , Stoehr Robert , Breyer Johannes , Burger Maximilian , Hartmann Arndt , Strissel Pamela L. , Eckstein Markus
Published: April 2023

Genes and proteins used for calculation of gene- and protein-expression scores (luminal-ness/basal-ness/ECM/EMT/signature scores).
Supplementary Table 1 from Bladder Tumor Subtype Commitment Occurs in Carcinoma In Situ Driven by Key Signaling Pathways Including ECM Remodeling
Authors: Wullweber Adrian , Strick Reiner , Lange Fabienne , Sikic Danijel , Taubert Helge , Wach Sven , Wullich Bernd , Bertz Simone , Weyerer Veronika , Stoehr Robert , Breyer Johannes , Burger Maximilian , Hartmann Arndt , Strissel Pamela L. , Eckstein Markus
Published: April 2023

(A) Clinico-pathological cohort data and molecular genetic features of the mapping bladder (Case ID4). (B) Clinico-pathological cohort data of the tissue microarray cohort of papillary high grade carcinomas and CIS.
Supplementary Figure 3 from Bladder Tumor Subtype Commitment Occurs in Carcinoma In Situ Driven by Key Signaling Pathways Including ECM Remodeling
Authors: Wullweber Adrian , Strick Reiner , Lange Fabienne , Sikic Danijel , Taubert Helge , Wach Sven , Wullich Bernd , Bertz Simone , Weyerer Veronika , Stoehr Robert , Breyer Johannes , Burger Maximilian , Hartmann Arndt , Strissel Pamela L. , Eckstein Markus
Published: April 2023

(A) Unsupervised hierarchical clustering reveals three lesion clusters (lesion cluster A-C) designated below the heat map. Histological classifications are shown above the heatmap and gene cluster families A*-D* are depicted on the left-sided cluster. Distribution of the lesion types in each cluster A-C are illustrated as pie diagrams below the heatmap. (B) Gene families from gene clusters C* and D* are mainly expressed in lesion clusters A/B in tumor associated urothelium, non-invasive urothelial lesions and CIS, while gene family A* is upregulated in CIS and pT1/MIBC samples. P-values were derived by nonparametric Kruskal-Wallis tests and are depicted above the graphs. P-values of single group comparisons derived by nonparametric Mann-Whitney tests are depicted in Suppl. Table 5. (C) Distribution of lesion cluster assignments (A-C) in the WBHM scheme. (D) Boxplots depicting differential expression of ERBB2, ERBB3, EGFR, STAT3 and CADM1 (STAT3-regulator) in luminal and basal tumors from the TCGA bladder cancer cohort. CIS = Carcinoma in situ; DYS = Dysplasia; UPUMP/HYP = urothelial proliferation of unknown malignant potential/ hyperplasia (abbreviated as "HYP" in graphs); MIBC = Muscle-invasive bladder cancer; pT1 = Stroma invasive bladder cancer; U = Tumor associated urothelium.
Supplementary Data 7 from SLFN5 Regulates LAT1-Mediated mTOR Activation in Castration-Resistant Prostate Cancer
Authors: Martinez Rafael S. , Salji Mark J. , Rushworth Linda , Ntala Chara , Rodriguez Blanco Giovanny , Hedley Ann , Clark William , Peixoto Paul , Hervouet Eric , Renaude Elodie , Kung Sonia H.Y. , Galbraith Laura C.A. , Nixon Colin , Lilla Sergio , MacKay Gillian M. , Fazli Ladan , Gaughan Luke , Sumpton David , Gleave Martin E. , Zanivan Sara , Blomme Arnaud , Leung Hing Y.
Published: April 2023

List of primers
Table S2 from Alterations in the Global Proteome and Phosphoproteome in Third Generation EGFR TKI Resistance Reveal Drug Targets to Circumvent Resistance
Authors: Zhang Xu , Maity Tapan K. , Ross Karen E. , Qi Yue , Cultraro Constance M. , Bahta Meriam , Pitts Stephanie , Keswani Meghana , Gao Shaojian , Nguyen Khoa Dang P. , Cowart Julie , Kirkali Fatos , Wu Cathy , Guha Udayan
Published: April 2023

Table S2
Supplementary Table from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a TP53-Dependent Manner
Authors: McDonald James I. , Diab Noor , Arthofer Elisa , Hadley Melissa , Kanholm Tomas , Rentia Uzma , Gomez Stephanie , Yu Angela , Grundy Erin E. , Cox Olivia , Topper Michael J. , Xing Xiaoyun , Strissel Pamela L. , Strick Reiner , Wang Ting , Baylin Stephen B. , Chiappinelli Katherine B.
Published: April 2023

Supplementary Table from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a TP53-Dependent Manner
Supplementary Table S1 from The Evolving Genomic Landscape of Esophageal Squamous Cell Carcinoma Under Chemoradiotherapy
Authors: Hirata Hidenari , Niida Atsushi , Kakiuchi Nobuyuki , Uchi Ryutaro , Sugimachi Keishi , Masuda Takaaki , Saito Tomoko , Kageyama Shun-Ichiro , Motomura Yushi , Ito Shuhei , Yoshitake Tadamasa , Tsurumaru Daisuke , Nishimuta Yusuke , Yokoyama Akira , Hasegawa Takanori , Chiba Kenichi , Shiraishi Yuichi , Du Junyan , Miura Fumihito , Morita Masaru , Toh Yasushi , Hirakawa Masakazu , Shioyama Yoshiyuki , Ito Takashi , Akimoto Tetsuo , Miyano Satoru , Shibata Tatsuhiro , Mori Masaki , Suzuki Yutaka , Ogawa Seishi , Ishigami Kousei , Mimori Koshi
Published: April 2023

Supplementary Table S1
Supplementary Figure S1 from The Evolving Genomic Landscape of Esophageal Squamous Cell Carcinoma Under Chemoradiotherapy
Authors: Hirata Hidenari , Niida Atsushi , Kakiuchi Nobuyuki , Uchi Ryutaro , Sugimachi Keishi , Masuda Takaaki , Saito Tomoko , Kageyama Shun-Ichiro , Motomura Yushi , Ito Shuhei , Yoshitake Tadamasa , Tsurumaru Daisuke , Nishimuta Yusuke , Yokoyama Akira , Hasegawa Takanori , Chiba Kenichi , Shiraishi Yuichi , Du Junyan , Miura Fumihito , Morita Masaru , Toh Yasushi , Hirakawa Masakazu , Shioyama Yoshiyuki , Ito Takashi , Akimoto Tetsuo , Miyano Satoru , Shibata Tatsuhiro , Mori Masaki , Suzuki Yutaka , Ogawa Seishi , Ishigami Kousei , Mimori Koshi
Published: April 2023

Supplementary Figure S1 and legend
Table S2 from ALDH1A1 Activity in Tumor-Initiating Cells Remodels Myeloid-Derived Suppressor Cells to Promote Breast Cancer Progression
Authors: Liu Cuicui , Qiang Jiankun , Deng Qiaodan , Xia Jie , Deng Lu , Zhou Lei , Wang Dong , He Xueyan , Liu Ying , Zhao Botao , Lv Jinhui , Yu Zuoren , Lei Qun-Ying , Shao Zhi-Ming , Zhang Xiao-Yong , Zhang Lixing , Liu Suling
Published: April 2023

Primer sequences for plasmid construction
Figure S2 from MYC- and MIZ1-Dependent Vesicular Transport of Double-Strand RNA Controls Immune Evasion in Pancreatic Ductal Adenocarcinoma
Authors: Krenz Bastian , Gebhardt-Wolf Anneli , Ade Carsten P. , Gaballa Abdallah , Roehrig Florian , Vendelova Emilia , Baluapuri Apoorva , Eilers Ursula , Gallant Peter , D'Artista Luana , Wiegering Armin , Gasteiger Georg , Rosenfeldt Mathias T. , Bauer Stefan , Zender Lars , Wolf Elmar , Eilers Martin
Published: April 2023

Histological analyses of transplanted tumors.
uncut gels from Hepatitis B–Induced IL8 Promotes Hepatocellular Carcinoma Venous Metastasis and Intrahepatic Treg Accumulation
Authors: Zhang Changlu , Gao Yanan , Du Chengzhi , Markowitz Geoffrey J. , Fu Jing , Zhang Zhenxing , Liu Chunliang , Qin Wenhao , Wang Hongyang , Wang Fan , Yang Pengyuan
Published: April 2023

uncut gels shows figure 1, figure 2, figure 3 and figure 6 uncut gels
Figure S6 from Human Endogenous Retrovirus Type K Promotes Proliferation and Confers Sensitivity to Antiretroviral Drugs in Merlin-Negative Schwannoma and Meningioma
Authors: Maze Emmanuel A. , Agit Bora , Reeves Shona , Hilton David A. , Parkinson David B. , Laraba Liyam , Ercolano Emanuela , Kurian Kathreena M. , Hanemann C. Oliver , Belshaw Robert D. , Ammoun Sylwia
Published: April 2023

Figure S6
Figure S6 and figure legend
Supplementary Data from Host-Derived Matrix Metalloproteinase-13 Activity Promotes Multiple Myeloma–Induced Osteolysis and Reduces Overall Survival
Authors: Lo Chen Hao , Shay Gemma , McGuire Jeremy J. , Li Tao , Shain Kenneth H. , Choi Jun Yong , Fuerst Rita , Roush William R. , Knapinska Anna M. , Fields Gregg B. , Lynch Conor C.
Published: April 2023

All Supplementary Figures and Legends
Supplementary Data from Combined Inhibition of G9a and EZH2 Suppresses Tumor Growth via Synergistic Induction of IL24-Mediated Apoptosis
Authors: Casciello Francesco , Kelly Gregory M. , Ramarao-Milne Priya , Kamal Nabilah , Stewart Teneale A. , Mukhopadhyay Pamela , Kazakoff Stephen H. , Miranda Mariska , Kim Dorim , Davis Felicity M. , Hayward Nicholas K. , Vertino Paula M. , Waddell Nicola , Gannon Frank , Lee Jason S.
Published: April 2023

Supplementary Data from Combined Inhibition of G9a and EZH2 Suppresses Tumor Growth via Synergistic Induction of IL24-Mediated Apoptosis
Figure SF5 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
Authors: Lopes-Ramos Camila M. , Belova Tatiana , Brunner Tess H. , Ben Guebila Marouen , Osorio Daniel , Quackenbush John , Kuijjer Marieke L.
Published: April 2023

A) Comparison of distributions of immune scores from xCell between the two survival groups in the discovery and validation datasets. In the boxplots, boxes represent the median and first and third quantiles, whiskers represent 1.5Ã-IQR. B) Association of the immune scores with PD1 targeting scores in the discovery and validation datasets. Regression lines with confidence intervals of 0.95 are shown for the long-term (blue) and short-term (red) groups.
Figure SF4 from Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme
Authors: Lopes-Ramos Camila M. , Belova Tatiana , Brunner Tess H. , Ben Guebila Marouen , Osorio Daniel , Quackenbush John , Kuijjer Marieke L.
Published: April 2023

xCell values for cell types with significant abundance levels (xCell scores >0.2 in at least one sample) as well as total immune and microenvironment scores. Boxplots represent the median and first and third quantiles, whisker represent 1.5Ã-IQR and are visualized for the long-term and short-term survival groups separately, in the two discovery datasets (A-B) and the validation dataset (C). Cell types with significantly different abundance between long- and short-term survival groups are indicated with asterisks (t-test, **FDR<0.05, *FDR<0.1).
Supplementary Tables from N6-methyladenosine–Mediated Upregulation of WTAPP1 Promotes WTAP Translation and Wnt Signaling to Facilitate Pancreatic Cancer Progression
Authors: Deng Junge , Zhang Jialiang , Ye Ying , Liu Kaijing , Zeng Lingxing , Huang Jingyi , Pan Ling , Li Mei , Bai Ruihong , Zhuang Lisha , Huang Xudong , Wu Guandi , Wei Lusheng , Zheng Yanfen , Su Jiachun , Zhang Shaoping , Chen Rufu , Lin Dongxin , Zheng Jian
Published: April 2023

Supplementary Table S1-S6
Figure S2 from Targeting HER2 Exon 20 Insertion–Mutant Lung Adenocarcinoma with a Novel Tyrosine Kinase Inhibitor Mobocertinib
Authors: Han Han , Li Shuai , Chen Ting , Fitzgerald Michael , Liu Shengwu , Peng Chengwei , Tang Kwan Ho , Cao Shougen , Chouitar Johara , Wu Jiansheng , Peng David , Deng Jiehui , Gao Zhendong , Baker Theresa E. , Li Fei , Zhang Hua , Pan Yuanwang , Ding Hailin , Hu Hai , Pyon Val , Thakurdin Cassandra , Papadopoulos Eleni , Tang Sittinon , Gonzalvez Francois , Chen Haiquan , Rivera Victor M. , Brake Rachael , Vincent Sylvie , Wong Kwok-Kin
Published: April 2023

Figure S2
Supplementary Data from Mapping Mechanical Properties of the Tumor Microenvironment by Laser Speckle Rheological Microscopy
Authors: Hajjarian Zeinab , Brachtel Elena F. , Tshikudi Diane M. , Nadkarni Seemantini K.
Published: April 2023

Supplementary Methods 1-5
Table S3 from Neural Crest-Like Stem Cell Transcriptome Analysis Identifies LPAR1 in Melanoma Progression and Therapy Resistance
Authors: Liu Jianglan , Rebecca Vito W. , Kossenkov Andrew V. , Connelly Thomas , Liu Qin , Gutierrez Alexis , Xiao Min , Li Ling , Zhang Gao , Samarkina Anastasia , Zayasbazan Delaine , Zhang Jie , Cheng Chaoran , Wei Zhi , Alicea Gretchen M. , Fukunaga-Kalabis Mizuho , Krepler Clemens , Aza-Blanc Pedro , Yang Chih-Cheng , Delvadia Bela , Tong Cynthia , Huang Ye , Delvadia Maya , Morias Alice S. , Sproesser Katrin , Brafford Patricia , Wang Joshua X. , Beqiri Marilda , Somasundaram Rajasekharan , Vultur Adina , Hristova Denitsa M. , Wu Lawrence W. , Lu Yiling , Mills Gordon B. , Xu Wei , Karakousis Giorgos C. , Xu Xiaowei , Schuchter Lynn M. , Mitchell Tara C. , Amaravadi Ravi K. , Kwong Lawrence N. , Frederick Dennie T. , Boland Genevieve M. , Salvino Joseph M. , Speicher David W. , Flaherty Keith T. , Ronai Ze'ev A. , Herlyn Meenhard
Published: April 2023

Supplementary Table
Data from Maximizing the Efficacy of MAPK-Targeted Treatment in PTENLOF/BRAFMUT Melanoma through PI3K and IGF1R Inhibition
Authors: Herkert Barbara , Kauffmann Audrey , Mollé Sandra , Schnell Christian , Ferrat Thomas , Voshol Hans , Juengert Janina , Erasimus Hélène , Marszalek Grégory , Kazic-Legueux Malika , Billy Eric , Ruddy David , Stump Mark , Guthy Daniel , Ristov Mitko , Calkins Keith , Maira Sauveur-Michel , Sellers William R. , Hofmann Francesco , Hall Michael N. , Brachmann Saskia M.
Published: April 2023

Abstract
The introduction of MAPK pathway inhibitors paved the road for significant advancements in the treatment of BRAF-mutant (BRAFMUT) melanoma. However, even BRAF/MEK inhibitor combination therapy has failed to offer a curative treatment option, most likely because these pathways constitute a codependent signaling network. Concomitant PTEN loss of function (PTENLOF) occurs in approximately 40% of BRAFMUT melanomas. In this study, we sought to identify the nodes of the PTEN/PI3K pathway that would be amenable to combined therapy with MAPK pathway inhibitors for the treatment of PTENLOF/BRAFMUT melanoma. Large-scale compound sensitivity profiling revealed that PTENLOF melanoma cell lines were sensitive to PI3Kβ inhibitors, albeit only partially. An unbiased shRNA screen (7,500 genes and 20 shRNAs/genes) across 11 cell lines in the presence of a PI3Kβ inhibitor identified an adaptive response involving the IGF1R–PI3Kα axis. Combined inhibition of the MAPK pathway, PI3Kβ, and PI3Kα or insulin-like growth factor receptor 1 (IGF1R) synergistically sustained pathway blockade, induced apoptosis, and inhibited tumor growth in PTENLOF/BRAFMUT melanoma models. Notably, combined treatment with the IGF1R inhibitor, but not the PI3Kα inhibitor, failed to elevate glucose or insulin signaling. Taken together, our findings provide a strong rationale for testing combinations of panPI3K, PI3Kβ + IGF1R, and MAPK pathway inhibitors in PTENLOF/BRAFMUT melanoma patients to achieve maximal response. Cancer Res; 76(2); 390–402. ©2015 AACR.
Data from Modulation of EZH2 Expression by MEK-ERK or PI3K-AKT Signaling in Lung Cancer Is Dictated by Different KRAS Oncogene Mutations
Authors: Riquelme Erick , Behrens Carmen , Lin Heather Y. , Simon George , Papadimitrakopoulou Vassiliki , Izzo Julie , Moran Cesar , Kalhor Neda , Lee J. Jack , Minna John D. , Wistuba Ignacio I.
Published: April 2023

Abstract
EZH2 overexpression promotes cancer by increasing histone methylation to silence tumor suppressor genes, but how EZH2 levels become elevated in cancer is not understood. In this study, we investigated the mechanisms by which EZH2 expression is regulated in non–small cell lung carcinoma cells by oncogenic KRAS. In cells harboring KRASG12C and KRASG12D mutations, EZH2 expression was modulated by MEK–ERK and PI3K/AKT signaling, respectively. Accordingly, MEK–ERK depletion decreased EZH2 expression in cells harboring the KRASG12C mutation, whereas PI3K/AKT depletion decreased EZH2 expression, EZH2 phosphorylation, and STAT3 activity in KRASG12D-mutant cell lines. Combined inhibition of EZH2 and MEK–ERK or PI3K/AKT increased the sensitivity of cells with specific KRAS mutations to MEK–ERK and PI3K/AKT–targeted therapies. Our work defines EZH2 as a downstream effector of KRAS signaling and offers a rationale for combining EZH2 inhibitory strategies with MEK–ERK- or PI3K/AKT–targeted therapies to treat lung cancer patients, as stratified into distinct treatment groups based on specific KRAS mutations. Cancer Res; 76(3); 675–85. ©2015 AACR.
Data from Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications
Authors: Popova Tatiana , Manié Elodie , Boeva Valentina , Battistella Aude , Goundiam Oumou , Smith Nicholas K. , Mueller Christopher R. , Raynal Virginie , Mariani Odette , Sastre-Garau Xavier , Stern Marc-Henri
Published: April 2023

Abstract
CDK12 is a recurrently mutated gene in serous ovarian carcinoma, whose downregulation is associated with impaired expression of DNA damage repair genes and subsequent hypersensitivity to DNA-damaging agents and PARP1/2 inhibitors. In this study, we investigated the genomic landscape associated with CDK12 inactivation in patients with serous ovarian carcinoma. We show that CDK12 loss was consistently associated with a particular genomic instability pattern characterized by hundreds of tandem duplications of up to 10 megabases (Mb) in size. Tandem duplications were characterized by a bimodal (∼0.3 and ∼3 Mb) size distribution and overlapping microhomology at the breakpoints. This genomic instability, denoted as the CDK12 TD-plus phenotype, is remarkably distinct from other alteration patterns described in breast and ovarian cancers. The CDK12 TD-plus phenotype was associated with a greater than 10% gain in genomic content and occurred at a 3% to 4% rate in The Cancer Genome Atlas–derived and in-house cohorts of patients with serous ovarian carcinoma. Moreover, CDK12-inactivating mutations together with the TD-plus phenotype were also observed in prostate cancers. Our finding provides new insight toward deciphering the function of CDK12 in genome maintenance and oncogenesis. Cancer Res; 76(7); 1882–91. ©2016 AACR.
Data from Mutational Landscape and Antiproliferative Functions of ELF Transcription Factors in Human Cancer
Authors: Ando Mizuo , Kawazu Masahito , Ueno Toshihide , Koinuma Daizo , Ando Koji , Koya Junji , Kataoka Keisuke , Yasuda Takahiko , Yamaguchi Hiroyuki , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Sai Eirin , Yamashita Yoshihiro , Asakage Takahiro , Miyazaki Yasushi , Kurokawa Mineo , Miyazono Kohei , Nimer Stephen D. , Yamasoba Tatsuya , Mano Hiroyuki
Published: April 2023

Abstract
ELF4 (also known as MEF) is a member of the ETS family of transcription factors. An oncogenic role for ELF4 has been demonstrated in hematopoietic malignancies, but its function in epithelial tumors remains unclear. Here, we show that ELF4 can function as a tumor suppressor and is somatically inactivated in a wide range of human tumors. We identified a missense mutation affecting the transactivation potential of ELF4 in oral squamous cell carcinoma cells. Restoration of the transactivation activity through introduction of wild-type ELF4 significantly inhibited cell proliferation in vitro and tumor xenograft growth. Furthermore, we found that ELF1 and ELF2, closely related transcription factors to ELF4, also exerted antiproliferative effects in multiple cancer cell lines. Mutations in ELF1 and ELF2, as in ELF4, were widespread across human cancers, but were almost all mutually exclusive. Moreover, chromatin immunoprecipitation coupled with high-throughput sequencing revealed ELF4-binding sites in genomic regions adjacent to genes related to cell-cycle regulation and apoptosis. Finally, we provide mechanistic evidence that the antiproliferative effects of ELF4 were mediated through the induction of HRK, an activator of apoptosis, and DLX3, an inhibitor of cell growth. Collectively, our findings reveal a novel subtype of human cancer characterized by inactivating mutations in the ELF subfamily of proteins, and warrant further investigation of the specific settings where ELF restoration may be therapeutically beneficial. Cancer Res; 76(7); 1814–24. ©2016 AACR.
Data from The CDK9 Inhibitor Dinaciclib Exerts Potent Apoptotic and Antitumor Effects in Preclinical Models of MLL-Rearranged Acute Myeloid Leukemia
Authors: Baker Adele , Gregory Gareth P. , Verbrugge Inge , Kats Lev , Hilton Joshua J. , Vidacs Eva , Lee Erwin M. , Lock Richard B. , Zuber Johannes , Shortt Jake , Johnstone Ricky W.
Published: April 2023

Abstract
Translocations of the mixed lineage leukemia (MLL) gene occur in 60% to 80% of all infant acute leukemias and are markers of poor prognosis. MLL-AF9 and other MLL fusion proteins aberrantly recruit epigenetic regulatory proteins, including histone deacetylases (HDAC), histone methyltransferases, bromodomain-containing proteins, and transcription elongation factors to mediate chromatin remodeling and regulate tumorigenic gene expression programs. We conducted a small-molecule inhibitor screen to test the ability of candidate pharmacologic agents targeting epigenetic and transcriptional regulatory proteins to induce apoptosis in leukemic cells derived from genetically engineered mouse models of MLL-AF9–driven acute myeloid leukemia (AML). We found that the CDK inhibitor dinaciclib and HDAC inhibitor panobinostat were the most potent inducers of apoptosis in short-term in vitro assays. Treatment of MLL-rearranged leukemic cells with dinaciclib resulted in rapidly decreased expression of the prosurvival protein Mcl-1, and accordingly, overexpression of Mcl-1 protected AML cells from dinaciclib-induced apoptosis. Administration of dinaciclib to mice bearing MLL-AF9–driven human and mouse leukemias elicited potent antitumor responses and significantly prolonged survival. Collectively, these studies highlight a new therapeutic approach to potentially overcome the resistance of MLL-rearranged AML to conventional chemotherapies and prompt further clinical evaluation of CDK inhibitors in AML patients harboring MLL fusion proteins. Cancer Res; 76(5); 1158–69. ©2015 AACR.