bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S4 from Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression
Authors: Barnabas Georgina D. , Lee Joo Sang , Shami Tamar , Harel Michal , Beck Lir , Selitrennik Michael , Jerby-Arnon Livnat , Erez Neta , Ruppin Eytan , Geiger Tamar
Published: April 2023

Supplementary Table S4: Degree and eigenvector centrality measure for TN module proteins
Supplementary Data from A Genome-Wide Pooled shRNA Screen Identifies PPP2R2A as a Predictive Biomarker for the Response to ATR and CHK1 Inhibitors
Authors: Qiu Zhaojun , Fa Pengyan , Liu Tao , Prasad Chandra B. , Ma Shanhuai , Hong Zhipeng , Chan Ernest R. , Wang Hongbing , Li Zaibo , He Kai , Wang Qi-En , Williams Terence M. , Yan Chunhong , Sizemore Steven T. , Narla Goutham , Zhang Junran
Published: April 2023

Supplementary Materials and Methods.
Supplementary Table S3 from Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression
Authors: Barnabas Georgina D. , Lee Joo Sang , Shami Tamar , Harel Michal , Beck Lir , Selitrennik Michael , Jerby-Arnon Livnat , Erez Neta , Ruppin Eytan , Geiger Tamar
Published: April 2023

Supplementary Table S3: Eigenprotein modules and the metabolic pathway enrichments
Supplementary Figure S7 from Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression
Authors: Barnabas Georgina D. , Lee Joo Sang , Shami Tamar , Harel Michal , Beck Lir , Selitrennik Michael , Jerby-Arnon Livnat , Erez Neta , Ruppin Eytan , Geiger Tamar
Published: April 2023

Supplementary Figure S7. Metabolic effects of PHGDH and PSAT1 knockouts with mCherry (control) overexpression A-F - Isotopologue abundances of glutamate (A), alpha-ketoglutarate (B), citrate (C), fumarate (D) malate (E) and aspartate (F) from 13C5-glutamine upon PHGDH & PSAT1 knockout with transiently overexpressed mCherry (mCh). G - Contribution of 13C5-glutamine to 13C5-alpha-ketoglutarate (% of total pool) in cells with high IDH2 and active PHGDH and PSAT1 compared to cells with high IDH2 and PHGDH or PSAT1 CRISPR-Cas9 knockouts. (*p-value <0.05; **p-value <0.01).
Supplementary Figure S6 from Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression
Authors: Barnabas Georgina D. , Lee Joo Sang , Shami Tamar , Harel Michal , Beck Lir , Selitrennik Michael , Jerby-Arnon Livnat , Erez Neta , Ruppin Eytan , Geiger Tamar
Published: April 2023

Supplementary Figure S6. Decreased serine synthesis with CRISPR knockout of PHGDH and PSAT1 with IDH2 overexpression A - Western blot shows the CRISPR-Cas9 based knockout of PSAT1 and the partial and complete knockout of two PHGDH clones (different guides). HSC-70 was used as a loading control. B - Proteomic analysis shows the protein expression levels of PHGDH and PSAT1 in the control and knockout HCC38 cells. C - Bar plots show the transient IDH2 overexpression (vs. mCherry control) in Control-ko (no gRNA), PHGDH-ko1, PHGDH-ko2 and PSAT1-ko cells from proteomic analysis in HCC38 cells. D-E - Decreased serine synthesis pathway traced using 13C6-glucose labeling in PHGDH & PSAT1 knockout cells show decreased abundance of serine (m3) and glycine (m2) in the knockouts. F - Isotope tracing scheme: Labeling using 15N2-glutamine towards serine synthesis; grey-unlabeled carbon atoms, blue-labeled nitrogen atoms and green-unlabeled hydrogen atoms. G-I - Fraction of glutamate (m1), serine (m1) and glycine (m1) from 15N2- glutamine upon PHGDH and PSAT1 knockout in HCC38 cells.
Supplementary Figure S1 from Serine Biosynthesis Is a Metabolic Vulnerability in IDH2-Driven Breast Cancer Progression
Authors: Barnabas Georgina D. , Lee Joo Sang , Shami Tamar , Harel Michal , Beck Lir , Selitrennik Michael , Jerby-Arnon Livnat , Erez Neta , Ruppin Eytan , Geiger Tamar
Published: April 2023

Supplementary Figure S1. Analysis of the integrated cohort of breast tumors A - Correlation of proteomic data of all the tumor samples in the integrated cohort of 145 samples. Pearson correlation coefficients between the tumor samples ranged from 0.35 to 0.85. The color code in the vertical dendrogram represent the datasets and the one in the horizontal dendrogram represent the tumor subtypes. B-D - mRNA expression of IDH1, ACLY and IDH2 in the tumors of the Pan Cancer Atlas study (TCGA). Expression levels in breast invasive carcinoma is highlighted. E - mRNA expression (TCGA) of the subunits of IDH3 enzyme (IDH3A, IDH3B and IDH3G) in four breast cancer subtypes. IDH3 subunits showed inconsistent expression patterns between the subtypes.
Table S2 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

Canine quality of life evaluation
Supplementary Table S7 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 S7
Supplementary Figure S5 from Blocking Angiopoietin-2 Promotes Vascular Damage and Growth Inhibition in Mouse Tumors Treated with Small Doses of Radiation
Authors: Kallio Pauliina , Jokinen Elina , Högström Jenny , Das Suvendu , Heino Sarika , Lähde Marianne , Brodkin Jefim , Korhonen Emilia A. , Alitalo Kari
Published: April 2023

Supplementary Figure S5
Figure S7 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

TEPA did not affect tumor growth in an immunocompromised neuroblastoma xenograft model
Supplementary Methods from FTO-Dependent N6-Methyladenosine Modifications Inhibit Ovarian Cancer Stem Cell Self-Renewal by Blocking cAMP Signaling
Authors: Huang Hao , Wang Yinu , Kandpal Manoj , Zhao Guangyuan , Cardenas Horacio , Ji Yanrong , Chaparala Anusha , Tanner Edward J. , Chen Jianjun , Davuluri Ramana V. , Matei Daniela
Published: April 2023

Detailed information regarding materials and methods are included in this file.
Figure S6 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

Copper lowering drugs increased NK-mediated cell death in vitro
Figure S4 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

TEPA increases tumor-infiltrating immune cells in Th-MYCN mice
Figure S2 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

Effect of copper levels on PD-L1 expression and interferon stimulation in cancer cells
legends from Oligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors
Authors: Lopez Sambrooks Cecilia , Baro Marta , Quijano Amanda , Narayan Azeet , Cui Wei , Greninger Patricia , Egan Regina , Patel Abhijit , Benes Cyril H. , Saltzman W. Mark , Contessa Joseph N.
Published: April 2023

Legends for supplementary figures 1 and 2
Suppl. Table 2 from Oligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors
Authors: Lopez Sambrooks Cecilia , Baro Marta , Quijano Amanda , Narayan Azeet , Cui Wei , Greninger Patricia , Egan Regina , Patel Abhijit , Benes Cyril H. , Saltzman W. Mark , Contessa Joseph N.
Published: April 2023

Deep sequencing of lung cancer cell lines to determine the proportion of EGFR mutations.
Supplementary Table 4 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

Gene mutations and survival after irradiation.
Supplementary Table 2 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

ssGSEA and survival after irradiation.
Table. 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

Leading edge genes in gene set enrichment analysys using HALLMARK gene set of KRAS_SIGNALING_UP.
Table. S2 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

Differentially expressed genes between 48-week-old AlbcreK; Hes1WT/WT and AlbcreK; Hes1flox/flox mice.
Supplemental Figure 5 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

Nrf2 activation and alpha-particle irradiation.
Supplementary Movie 1 from The Amino-Terminal Oligomerization Domain of Angiopoietin-2 Affects Vascular Remodeling, Mammary Gland Tumor Growth, and Lung Metastasis in Mice
Authors: Kapiainen Emmi , Kihlström Minna K. , Pietilä Riikka , Kaakinen Mika , Ronkainen Veli-Pekka , Tu Hongmin , Heikkinen Anne , Devarajan Raman , Miinalainen Ilkka , Laitakari Anna , Ansarizadeh Mohammadhassan , Zhang Qin , Wei Gong-Hong , Ruddock Lloyd , Pihlajaniemi Taina , Elamaa Harri , Eklund Lauri
Published: April 2023

Visualization of basal cell surface of GFP-HUVECs
Supplementary Materials and Methods from The Amino-Terminal Oligomerization Domain of Angiopoietin-2 Affects Vascular Remodeling, Mammary Gland Tumor Growth, and Lung Metastasis in Mice
Authors: Kapiainen Emmi , Kihlström Minna K. , Pietilä Riikka , Kaakinen Mika , Ronkainen Veli-Pekka , Tu Hongmin , Heikkinen Anne , Devarajan Raman , Miinalainen Ilkka , Laitakari Anna , Ansarizadeh Mohammadhassan , Zhang Qin , Wei Gong-Hong , Ruddock Lloyd , Pihlajaniemi Taina , Elamaa Harri , Eklund Lauri
Published: April 2023

Supplementary Materials and Methods
Supplementary Data from 5-Fluorouracil Enhances the Antitumor Activity of the Glutaminase Inhibitor CB-839 against PIK3CA-Mutant Colorectal Cancers
Authors: Zhao Yiqing , Feng Xiujing , Chen Yicheng , Selfridge J. Eva , Gorityala Shashank , Du Zhanwen , Wang Janet M. , Hao Yujun , Cioffi Gino , Conlon Ronald A. , Barnholtz-Sloan Jill S. , Saltzman Joel , Krishnamurthi Smitha S. , Vinayak Shaveta , Veigl Martina , Xu Yan , Bajor David L. , Markowitz Sanford D. , Meropol Neal J. , Eads Jennifer R. , Wang Zhenghe
Published: April 2023

Supplementary Figures 1-6 and Tables 1-3. Figure S1. PIK3CA mutant cells are more sensitive to a glutaminase inhibitor CB-839 than their WT counterparts. Figure S2. CB-839 enhances 5-FU tumor inhibitory effect in PIK3CA mutant CRC. Figure S3. Genes and pathways that are up-regulated in PIK3CA mutant cells after glutamine deprivation. Figure S4. Characterization of Nrf2 and its targets in CRC cells. Figure S5. CB-839 and 5-FU combinational treatment induces more DNA damage. Figure S6. Phase I clinical trial. Table S1: Patient Baseline Characteristics. Table S2. Patient information. Table S3. Treatment Related Adverse Events (all grade 3/4 AEs and grade 1/2 AEs seen in {greater than or equal to} 10% of patients).
Supplementary Figures from The Amino-Terminal Oligomerization Domain of Angiopoietin-2 Affects Vascular Remodeling, Mammary Gland Tumor Growth, and Lung Metastasis in Mice
Authors: Kapiainen Emmi , Kihlström Minna K. , Pietilä Riikka , Kaakinen Mika , Ronkainen Veli-Pekka , Tu Hongmin , Heikkinen Anne , Devarajan Raman , Miinalainen Ilkka , Laitakari Anna , Ansarizadeh Mohammadhassan , Zhang Qin , Wei Gong-Hong , Ruddock Lloyd , Pihlajaniemi Taina , Elamaa Harri , Eklund Lauri
Published: April 2023

Supplementary Figure S1: Amino acid sequence of ANGPT2, ANGPT2443 and ANGTPT2DAP. Supplementary Figure S2: Competitive inhibition of ANGPT4-induced TIE2 phosphorylation by ANGPT2 isoforms. Supplementary Figure S3. TIE2 phosphorylation by ANGPT2 isoforms at the retracting cell edges. Supplementary Figure S4. Generation of Angpt2443 allele and the effects of Angpt2443 expression on the retina. Supplementary Figure S5. MMTV-PyMT mammary gland tumor model. Supplementary Figure S6. ANGPT2 at the Weibel-Palade bodies and the subendothelial space. Supplementary Figure S7. B16F10 melanoma lung colonization model. Supplementary Figure S8. E0771 breast cancer cell transplantation model.
Figure S2 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

Tumor Ag-specific Tregs expand in draining lymph nodes
Supplementary Table 1 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

Comparison of IC50 values based on the gene mutation status
Dataset S2 from Inhibition of Histone H3K27 Demethylases Inactivates Brachyury (TBXT) and Promotes Chordoma Cell Death
Authors: Cottone Lucia , Cribbs Adam P. , Khandelwal Garima , Wells Graham , Ligammari Lorena , Philpott Martin , Tumber Anthony , Lombard Patrick , Hookway Edward S. , Szommer Tamas , Johansson Catrine , Brennan Paul E. , Pillay Nischalan , Jenner Richard G. , Oppermann Udo , Flanagan Adrienne M.
Published: April 2023

Chordoma RNAseq_all cell lines_gene lists
Supplementary Data from HDAC11 Regulates Glycolysis through the LKB1/AMPK Signaling Pathway to Maintain Hepatocellular Carcinoma Stemness
Authors: Bi Lei , Ren Yidan , Feng Maoxiao , Meng Peng , Wang Qin , Chen Weiping , Jiao Qinlian , Wang Yuli , Du Lutao , Zhou Fuqiong , Jiang Yucui , Chen Feiyan , Wang Chuanxin , Tang Bo , Wang Yunshan
Published: April 2023

Supplementary Data
Figure S2 from Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer Therapy
Authors: Amjadi-Moheb Fatemeh , Paniri Alireza , Akhavan-Niaki Haleh
Published: April 2023

Schematic representation of quadruplex structure and role of the NHEIII1 region in transcriptional regulation of MYC. NHEIII1 is located upstream of MYC promoter 1 and consists of the G-rich and C-rich strands which form G-quadruplex and i-motif, respectively. The formation of G-quadruplex in the MYC NHEIII1 region is considered to be a transcriptional silencer. Signals for initiation of cancer, recruit SP1 to bind to NHEIII1 region through denaturation of G-quadruplex and i-motif which results in FUSE element melting and recruitment of FBP and FIR by FUSE region to mediate a loop structure with MYC promoter. Besides, the denatured NHEIII1 region gets filled with hnRNP and CNBP. Then, other transcriptional machinery factors including TFIIH and RNA pol II are recruited to the region to transcribe MYC. NHEIII1: nuclease hypersensitivity element III1; FUSE: far upstream element; FBP: FUSE binding protein; FIR: FUSE-binding protein-interacting repressor; CNBP: cellular nucleic acid-binding protein.
Supplementary Data 3 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

Pathway Enrichment_RNASeq
Supplementary Data 2 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

RNASeq_SLFN5 KO
Supplementary Data 1 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

Proteomics_CRPC
Figure S3 from Pharmacological Disruption of the Notch1 Transcriptional Complex Inhibits Tumor Growth by Selectively Targeting Cancer Stem Cells
Authors: Alvarez-Trotta Annamil , Guerrant William , Astudillo Luisana , Lahiry Mohini , Diluvio Giulia , Shersher Elena , Kaneku Hugo , Robbins David J. , Orton Darren , Capobianco Anthony J.
Published: April 2023

Inputs of DNA pull downs
Table S5 from Targeting Pyruvate Kinase M2 Phosphorylation Reverses Aggressive Cancer Phenotypes
Authors: Apostolidi Maria , Vathiotis Ioannis A. , Muthusamy Viswanathan , Gaule Patricia , Gassaway Brandon M. , Rimm David L. , Rinehart Jesse
Published: April 2023

CDK/cyclin gene expression analysis in TCGA BRCA database.
Figure S1 from Pharmacological Disruption of the Notch1 Transcriptional Complex Inhibits Tumor Growth by Selectively Targeting Cancer Stem Cells
Authors: Alvarez-Trotta Annamil , Guerrant William , Astudillo Luisana , Lahiry Mohini , Diluvio Giulia , Shersher Elena , Kaneku Hugo , Robbins David J. , Orton Darren , Capobianco Anthony J.
Published: April 2023

Structures and additional docking detail for NADI-351
Supplementary Table from Targeting Glucose Metabolism Sensitizes Pancreatic Cancer to MEK Inhibition
Authors: Yan Liang , Tu Bo , Yao Jun , Gong Jing , Carugo Alessandro , Bristow Christopher A. , Wang Qiuyun , Zhu Cihui , Dai Bingbing , Kang Ya'an , Han Leng , Feng Ningping , Jin Yanqing , Fleming Jason , Heffernan Timothy P. , Yao Wantong , Ying Haoqiang
Published: April 2023

Supplementary Tables 1-7.
Table S3 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 S3
Figure S2 from Mesothelin-Specific CAR T Cells Target Ovarian Cancer
Authors: Schoutrop Esther , El-Serafi Ibrahim , Poiret Thomas , Zhao Ying , Gultekin Okan , He Rui , Moyano-Galceran Lidia , Carlson Joseph W. , Lehti Kaisa , Hassan Moustapha , Magalhaes Isabelle , Mattsson Jonas
Published: April 2023

Figure S2
Figure S7 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

Supplementary Fig.S7
Supplementary Methods 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 Methods
Supplementary Figure S4 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 S4 and legend
Supplementary Figure S2 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 S2 and legend
Figure S5 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

Characterization of dsRNA and ssDNA in KPC cells.
Supplementary Data from A Spatial and Functional Interaction of a Heterotetramer Survivin–DNA-PKcs Complex in DNA Damage Response
Authors: Güllülü Ömer , Hehlgans Stephanie , Mayer Benjamin E. , Gößner Ines , Petraki Chrysi , Hoffmann Melanie , Dombrowsky Maximilian J. , Kunzmann Patrick , Hamacher Kay , Strebhardt Klaus , Fokas Emmanouil , Rödel Claus , Münch Christian , Rödel Franz
Published: April 2023

supplementary figures 1-6, table 1 and materials and methods.
Figure S4 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

Characterization of MYC depletion.
Supplementary Table S5 from Mutant Idh2 Cooperates with a NUP98-HOXD13 Fusion to Induce Early Immature Thymocyte Precursor ALL
Authors: Goldberg Liat , Negi Vijay , Chung Yang Jo , Onozawa Masahiro , Zhu Yuelin J. , Walker Robert L. , Pierce Rachel , Patel Daxesh P. , Krausz Kristopher W. , Gonzalez Frank J. , Goodell Margaret A. , Rodriguez Benjamin A.T. , Meltzer Paul S. , Aplan Peter D.
Published: April 2023

Whole exome sequencing data with indels.
Supplementary Data from Gut Microbiota Condition the Therapeutic Efficacy of Trastuzumab in HER2-Positive Breast Cancer
Authors: Di Modica Martina , Gargari Giorgio , Regondi Viola , Bonizzi Arianna , Arioli Stefania , Belmonte Beatrice , De Cecco Loris , Fasano Elena , Bianchi Francesca , Bertolotti Alessia , Tripodo Claudio , Villani Laura , Corsi Fabio , Guglielmetti Simone , Balsari Andrea , Triulzi Tiziana , Tagliabue Elda
Published: April 2023

1. Supplementary Materials and Methods Table S1. List of the antibodies used for flow cytometry 2. Supplementary Figures Supplementary Fig. S1. Impact of antibiotic treatment on trastuzumab efficacy and the tumor microenvironment. Supplementary Fig. S2. Depletion of commensal microbiota by antibiotic cocktail (ABX) treatment and fecal microbiota transplantation. Supplementary Fig. S3. Impact of vancomycin on trastuzumab efficacy in Î"16HER2 transgenic FVB mice. Supplementary Fig. S4. Differentially abundant bacteria in the gut microbiota of antibiotic-treated mice. Supplementary Fig. S5. Short-chain fatty acids (SCFAs) quantification in fecal samples from antibiotic-treated mice. Supplementary Fig. S6. Analysis of intratumor and stromal cell staining in tumors of antibiotic-treated mice. Supplementary Fig. S7. Impact of antibiotic treatment on tumor immune infiltrate. Supplementary Fig. S8. Analysis of intratumor and stromal cell staining in tumors from FMT mice. Supplementary Fig. S9. Impact of vancomycin treatment on intestinal and systemic immune features. Supplementary Fig. S10. Impact of IL12p70 and CD4+ cell depletion on trastuzumab antitumor efficacy and on tumor immune infiltrate. Supplementary Fig. S11. Causal role of human commensal bacteria in immune-mediated trastuzumab antitumor efficacy. 3. Supplementary References
Supplementary Data from BRD4 Regulates Transcription Factor ΔNp63α to Drive a Cancer Stem Cell Phenotype in Squamous Cell Carcinomas
Authors: Fisher Matthew L. , Balinth Seamus , Hwangbo Yon , Wu Caizhi , Ballon Carlos , Wilkinson John E. , Goldberg Gary L. , Mills Alea A.
Published: April 2023

Supplemental Figures 1-6
Supplementary Movie B from Platelet TLR4-ERK5 Axis Facilitates NET-Mediated Capturing of Circulating Tumor Cells and Distant Metastasis after Surgical Stress
Authors: Ren Jinghua , He Jiayi , Zhang Hongji , Xia Yujia , Hu Zhiwei , Loughran Patricia , Billiar Timothy , Huang Hai , Tsung Allan
Published: April 2023

Supplementary Movie B
Table S3 from ZIP9 Is a Druggable Determinant of Sex Differences in Melanoma
Authors: Aguirre-Portolés Cristina , Payne Riley , Trautz Aspen , Foskett J. Kevin , Natale Christopher A. , Seykora John T. , Ridky Todd W.
Published: April 2023

RPPA analysis in WM46 cells treated with testosterone
Supplementary Figure S2 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

Supplementary Figure S2 shows HBV induces IL-8 expression mainly through HBx
Supplementary Table 2 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

Supplementary Table 2
Table 2 and legend
Figure S7 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 S7
Figure S7 and figure legend
Supplementary Tables from STIM1 Mediates Calcium-Dependent Epigenetic Reprogramming in Pancreatic Cancer
Authors: Kutschat Ana P. , Hamdan Feda H. , Wang Xin , Wixom Alexander Q. , Najafova Zeynab , Gibhardt Christine S. , Kopp Waltraut , Gaedcke Jochen , Ströbel Philipp , Ellenrieder Volker , Bogeski Ivan , Hessmann Elisabeth , Johnsen Steven A.
Published: April 2023

Supplementary Tables S4 to S8
Figure S3 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 S3
Figure S3 and figure legend
Supplementary Table 1 from Diverse Oncogenic Fusions and Distinct Gene Expression Patterns Define the Genomic Landscape of Pediatric Papillary Thyroid Carcinoma
Authors: Stosic Ana , Fuligni Fabio , Anderson Nathaniel D. , Davidson Scott , de Borja Richard , Acker Meryl , Forte Vito , Campisi Paolo , Propst Evan J. , Wolter Nikolaus E. , Chami Rose , Mete Ozgur , Malkin David , Shlien Adam , Wasserman Jonathan D.
Published: April 2023

Chromosomes, Genes, Breakpoints, and Fusion Validator Scores for Oncogenic Fusions. In the event of multiple splicing confirmations, the fusion with highest validator score is displayed.
Table S1 from Polypharmacologic Reprogramming of Tumor-Associated Macrophages toward an Inflammatory Phenotype
Authors: Nishida-Aoki Nao , Gujral Taranjit S.
Published: April 2023

Table S1
Table S1
Supplementary Data from Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk
Authors: Boonen Rick A.C.M. , Wiegant Wouter W. , Celosse Nandi , Vroling Bas , Heijl Stephan , Kote-Jarai Zsofia , Mijuskovic Martina , Cristea Simona , Solleveld-Westerink Nienke , van Wezel Tom , Beerenwinkel Niko , Eeles Rosalind , Devilee Peter , Vreeswijk Maaike P.G. , Marra Giancarlo , van Attikum Haico
Published: April 2023

Supplementary Data from Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk
Table S6 from The Protein Kinase Activity of NME7 Activates Wnt/β-Catenin Signaling to Promote One-Carbon Metabolism in Hepatocellular Carcinoma
Authors: Ren Xinxin , Rong Zhuoxian , Liu Xiaoyu , Gao Jie , Xu Xu , Zi Yuyuan , Mu Yun , Guan Yidi , Cao Zhen , Zhang Yuefang , Zeng Zimei , Fan Qi , Wang Xitao , Pei Qian , Wang Xiang , Xin Haiguang , Li Zhi , Nie Yingjie , Qiu Zilong , Li Nan , Sun Lunquan , Deng Yuezhen
Published: April 2023

Supplemental Table 6 Differentially expressed genes in PVTT cells with knockdown of NME7.
Table S5 from The Protein Kinase Activity of NME7 Activates Wnt/β-Catenin Signaling to Promote One-Carbon Metabolism in Hepatocellular Carcinoma
Authors: Ren Xinxin , Rong Zhuoxian , Liu Xiaoyu , Gao Jie , Xu Xu , Zi Yuyuan , Mu Yun , Guan Yidi , Cao Zhen , Zhang Yuefang , Zeng Zimei , Fan Qi , Wang Xitao , Pei Qian , Wang Xiang , Xin Haiguang , Li Zhi , Nie Yingjie , Qiu Zilong , Li Nan , Sun Lunquan , Deng Yuezhen
Published: April 2023

Supplemental Table 5 Correlation between the protein level of NME7 and the clinical features of patients with HCC in the tissue array.
Supplementary Figure from Disruption of Prostaglandin E2 Signaling in Cancer-Associated Fibroblasts Limits Mammary Carcinoma Growth but Promotes Metastasis
Authors: Elwakeel Eiman , Brüggemann Mirko , Wagih Jessica , Lityagina Olga , Elewa Mohammed A.F. , Han Yingying , Frömel Timo , Popp Rüdiger , Nicolas Adele M. , Schreiber Yannick , Gradhand Elise , Thomas Dominique , Nüsing Rolf , Steinmetz-Späh Julia , Savai Rajkumar , Fokas Emmanouil , Fleming Ingrid , Greten Florian R. , Zarnack Kathi , Brüne Bernhard , Weigert Andreas
Published: April 2023

Supplementary Figure from Disruption of Prostaglandin E2 Signaling in Cancer-Associated Fibroblasts Limits Mammary Carcinoma Growth but Promotes Metastasis
Table 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

GSEA analysis of mobocertinib and T-DM1 treated tumors versus mobocertinib-only treated tumors
Genes involved in "INTERFERON ALPHA RESPONSE", "INFLAMMATORY RESPONSE", "INTERFERON GAMMA RESPONSE", "IL2 STAT5 SIGNALING", "TNFA SIGNALING VIA NFKB" and "IL6 JAK STAT3 SIGNALING" pathways of HALLMARK gene sets.
Figure S4 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 S4
Data from Immune-Dependent and Independent Antitumor Activity of GM-CSF Aberrantly Expressed by Mouse and Human Colorectal Tumors
Authors: Urdinguio Rocio G. , Fernandez Agustin F. , Moncada-Pazos Angela , Huidobro Covadonga , Rodriguez Ramon M. , Ferrero Cecilia , Martinez-Camblor Pablo , Obaya Alvaro J. , Bernal Teresa , Parra-Blanco Adolfo , Rodrigo Luis , Santacana Maria , Matias-Guiu Xavier , Soldevilla Beatriz , Dominguez Gemma , Bonilla Felix , Cal Santiago , Lopez-Otin Carlos , Fraga Mario F.
Published: April 2023

Abstract
Granulocyte-macrophage colony-stimulating factor (GM-CSF/CSF2) is a cytokine produced in the hematologic compartment that may enhance antitumor immune responses, mainly by activation of dendritic cells. Here, we show that more than one-third of human colorectal tumors exhibit aberrant DNA demethylation of the GM-CSF promoter and overexpress the cytokine. Mouse engraftment experiments with autologous and homologous colon tumors engineered to repress the ectopic secretion of GM-CSF revealed the tumor-secreted GM-CSF to have an immune-associated antitumor effect. Unexpectedly, an immune-independent antitumor effect was observed that depended on the ectopic expression of GM-CSF receptor subunits by tumors. Cancer cells expressing GM-CSF and its receptor did not develop into tumors when autografted into immunocompetent mice. Similarly, 100% of the patients with human colon tumors that overexpressed GM-CSF and its receptor subunits survived at least 5 years after diagnosis. These data suggest that expression of GM-CSF and its receptor subunits by colon tumors may be a useful marker for prognosis as well as for patient stratification in cancer immunotherapy. Cancer Res; 73(1); 395–405. ©2012 AACR.
Data from Impact of Intertumoral Heterogeneity on Predicting Chemotherapy Response of BRCA1-Deficient Mammary Tumors
Authors: Rottenberg Sven , Vollebergh Marieke A. , de Hoon Bas , de Ronde Jorma , Schouten Philip C. , Kersbergen Ariena , Zander Serge A.L. , Pajic Marina , Jaspers Janneke E. , Jonkers Martijn , Lodén Martin , Sol Wendy , van der Burg Eline , Wesseling Jelle , Gillet Jean-Pierre , Gottesman Michael M. , Gribnau Joost , Wessels Lodewyk , Linn Sabine C. , Jonkers Jos , Borst Piet
Published: April 2023

Abstract
The lack of markers to predict chemotherapy responses in patients poses a major handicap in cancer treatment. We searched for gene expression patterns that correlate with docetaxel or cisplatin response in a mouse model for breast cancer associated with BRCA1 deficiency. Array-based expression profiling did not identify a single marker gene predicting docetaxel response, despite an increase in Abcb1 (P-glycoprotein) expression that was sufficient to explain resistance in several poor responders. Intertumoral heterogeneity explained the inability to identify a predictive gene expression signature for docetaxel. To address this problem, we used a novel algorithm designed to detect differential gene expression in a subgroup of the poor responders that could identify tumors with increased Abcb1 transcript levels. In contrast, standard analytical tools, such as significance analysis of microarrays, detected a marker only if it correlated with response in a substantial fraction of tumors. For example, low expression of the Xist gene correlated with cisplatin hypersensitivity in most tumors, and it also predicted long recurrence-free survival of HER2-negative, stage III breast cancer patients treated with intensive platinum-based chemotherapy. Our findings may prove useful for selecting patients with high-risk breast cancer who could benefit from platinum-based therapy. Cancer Res; 72(9); 2350–61. ©2012 AACR.
Data from Bevacizumab-Induced Normalization of Blood Vessels in Tumors Hampers Antibody Uptake
Authors: Arjaans Marlous , Oude Munnink Thijs H. , Oosting Sjoukje F. , Terwisscha van Scheltinga Anton G.T. , Gietema Jourik A. , Garbacik Erik T. , Timmer-Bosscha Hetty , Lub-de Hooge Marjolijn N. , Schröder Carolina P. , de Vries Elisabeth G.E.
Published: April 2023

Abstract
In solid tumors, angiogenesis occurs in the setting of a defective vasculature and impaired lymphatic drainage that is associated with increased vascular permeability and enhanced tumor permeability. These universal aspects of the tumor microenvironment can have a marked influence on intratumoral drug delivery that may often be underappreciated. In this study, we investigated the effect of blood vessel normalization in tumors by the antiangiogenic drug bevacizumab on antibody uptake by tumors. In mouse xenograft models of human ovarian and esophageal cancer (SKOV-3 and OE19), we evaluated antibody uptake in tumors by positron emission tomographic imaging 24 and 144 hours after injection of 89Zr-trastuzumab (SKOV-3 and OE19), 89Zr-bevacizumab (SKOV-3), or 89Zr-IgG (SKOV-3) before or after treatment with bevacizumab. Intratumor distribution was assessed by fluorescence microscopy along with mean vessel density (MVD) and vessel normalization. Notably, bevacizumab treatment decreased tumor uptake and intratumoral accumulation compared with baseline in the tumor models relative to controls. Bevacizumab treatment also reduced MVD in tumors and increased vessel pericyte coverage. These findings are clinically important, suggesting caution in designing combinatorial trials with therapeutic antibodies due to a possible reduction in tumoral accumulation that may be caused by bevacizumab cotreatment. Cancer Res; 73(11); 3347–55. ©2013 AACR.
Data from Serial Magnetic Resonance Spectroscopy Reveals a Direct Metabolic Effect of Cediranib in Glioblastoma
Authors: Kim Heisoog , Catana Ciprian , Ratai Eva-Maria , Andronesi Ovidiu C. , Jennings Dominique L. , Batchelor Tracy T. , Jain Rakesh K. , Sorensen A. Gregory
Published: April 2023

Abstract
Proton magnetic resonance spectroscopy is increasingly used in clinical studies of brain tumor to provide information about tissue metabolic profiles. In this study, we evaluated changes in the levels of metabolites predominant in recurrent glioblastoma multiforme (rGBM) to characterize the response of rGBM to antiangiogenic therapy. We examined 31 rGBM patients treated with daily doses of cediranib, acquiring serial chemical shift imaging data at specific time points during the treatment regimen. We defined spectra from three regions of interest (ROI)—enhancing tumor (ET), peritumoral tissue, and normal tissue on the contralateral side (cNT)—in post-contrast T1-weighted images, and normalized the concentrations of N-acetylaspartate (NAA) and choline (Cho) in each ROI to the concentration of creatine in cNT (norCre). We analyzed the ratios of these normalized metabolites (i.e., NAA/Cho, NAA/norCre, and Cho/norCre) by averaging all patients and categorizing two different survival groups. Relative to pretreatment values, NAA/Cho in ET was unchanged through day 28. However, after day 28, NAA/Cho significantly increased in relation to a significant increase in NAA/norCre and a decrease in Cho/norCre; interestingly, the observed trend was reversed after day 56, consistent with the clinical course of GBM recurrence. Notably, receiver operating characteristic analysis indicated that NAA/Cho in tumor shows a high prediction to 6-month overall survival. These metabolic changes in these rGBM patients strongly suggest a direct metabolic effect of cediranib and might also reflect an antitumor response to antiangiogenic treatment during the first 2 months of treatment. Further study is needed to confirm these findings. Cancer Res; 71(11); 3745–52. ©2011 AACR.
Data from B-Raf Activation Cooperates with PTEN Loss to Drive c-Myc Expression in Advanced Prostate Cancer
Authors: Wang Jingqiang , Kobayashi Takashi , Floc'h Nicolas , Kinkade Carolyn Waugh , Aytes Alvaro , Dankort David , Lefebvre Celine , Mitrofanova Antonina , Cardiff Robert D. , McMahon Martin , Califano Andrea , Shen Michael M. , Abate-Shen Cory
Published: April 2023

Abstract
Both the PI3K → Akt → mTOR and mitogen-activated protein kinase (MAPK) signaling pathways are often deregulated in prostate tumors with poor prognosis. Here we describe a new genetically engineered mouse model of prostate cancer in which PI3K-Akt-mTOR signaling is activated by inducible disruption of PTEN, and extracellular signal-regulated kinase 1/2 (ERK1/2) MAPK signaling is activated by inducible expression of a BRAFV600E oncogene. These tissue-specific compound mutant mice develop lethal prostate tumors that are inherently resistant to castration. These tumors bypass cellular senescence and disseminate to lymph nodes, bone marrow, and lungs where they form overt metastases in approximately 30% of the cases. Activation of PI3K → Akt → mTOR and MAPK signaling pathways in these prostate tumors cooperate to upregulate c-Myc. Accordingly, therapeutic treatments with rapamycin and PD0325901 to target these pathways, respectively, attenuate c-Myc levels and reduce tumor and metastatic burden. Together, our findings suggest a generalized therapeutic approach to target c-Myc activation in prostate cancer by combinatorial targeting of the PI3K → Akt → mTOR and ERK1/2 MAPK signaling pathways. Cancer Res; 72(18); 4765–76. ©2012 AACR.
Data from Twist1 Induces CCL2 and Recruits Macrophages to Promote Angiogenesis
Authors: Low-Marchelli Janine M. , Ardi Veronica C. , Vizcarra Edward A. , van Rooijen Nico , Quigley James P. , Yang Jing
Published: April 2023

Abstract
The transcription factor Twist1 induces epithelial–mesenchymal transition and extracellular matrix degradation to promote tumor metastasis. Although Twist1 also plays a role in embryonic vascular development and tumor angiogenesis, the molecular mechanisms that underlie these processes are not as well understood. Here, we report a novel function for Twist1 in modifying the tumor microenvironment to promote progression. We found that expression of Twist1 in human mammary epithelial cells potently promoted angiogenesis. Surprisingly, Twist1 expression did not increase the secretion of the common proangiogenic factors VEGF and basic fibroblast growth factor but rather induced expression of the macrophage chemoattractant CCL2. Attenuation of endogenous Twist1 in vivo blocked macrophage recruitment and angiogenesis, whereas exogenous CCL2 rescued the ability of tumor cells lacking Twist1 to attract macrophages and promote angiogenesis. Macrophage recruitment also was essential for the ability of Twist1-expressing cells to elicit a strong angiogenic response. Together, our findings show that how Twist1 recruits stromal macrophages through CCL2 induction to promote angiogenesis and tumor progression. As Twist1 expression has been associated with poor survival in many human cancers, this finding suggests that anti-CCL2 therapy may offer a rational strategy to treat Twist1-positive metastatic cancers. Cancer Res; 73(2); 662–71. ©2012 AACR.