bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 1 from A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes
Authors: Krishnan Neeraja M. , Dhas Kunal , Nair Jayalakshmi , Palve Vinayak , Bagwan Jamir , Siddappa Gangotri , Suresh Amritha , Kekatpure Vikram D. , Kuriakose Moni Abraham , Panda Binay
Published: April 2023

Clinical information for all patients used in the study
Supplementary Figures from A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes
Authors: Krishnan Neeraja M. , Dhas Kunal , Nair Jayalakshmi , Palve Vinayak , Bagwan Jamir , Siddappa Gangotri , Suresh Amritha , Kekatpure Vikram D. , Kuriakose Moni Abraham , Panda Binay
Published: April 2023

All the supplementary figures
Supplementary Table 3 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis
Authors: Shen He , Yang Nuo , Truskinovsky Alexander , Chen Yanmin , Mussell Ashley L. , Nowak Norma J. , Kobzik Lester , Frangou Costa , Zhang Jianmin
Published: April 2023

GO biological analysis using DAVID.
Supplementary Table 2 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis
Authors: Shen He , Yang Nuo , Truskinovsky Alexander , Chen Yanmin , Mussell Ashley L. , Nowak Norma J. , Kobzik Lester , Frangou Costa , Zhang Jianmin
Published: April 2023

Functional enrichment analysis for pathway.
Supplementary Data for Article from p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes
Authors: Pappas Kyrie , Xu Jia , Zairis Sakellarios , Resnick-Silverman Lois , Abate Francesco , Steinbach Nicole , Ozturk Sait , Saal Lao H. , Su Tao , Cheung Pamela , Schmidt Hank , Aaronson Stuart , Hibshoosh Hanina , Manfredi James , Rabadan Raul , Parsons Ramon
Published: April 2023

Supplementary Fig. S1. Basally expressed p53 may have important tumor suppressor targets. Supplementary Fig. S2. Binding targets of basal p53 in MCF10A cells. Supplementary Fig. S3. Exploring the binding targets of basal p53. Supplementary Fig. S4. Wild-type p53 maintains expression of tumor suppressor target genes. Supplementary Fig. S5. Long range chromatin interactions of enhancers with transcriptional start sites of basal p53 targets. Supplementary Fig. S6. Enhancer for PTEN is present in multiple cell types. Supplementary Fig. S7. The binding and regulation of the PTEN locus by basal p53. Supplementary Fig. S8. PTEN-eP53RE is a highly conserved p53 response element in a p53-dependent enhancer. Supplementary Fig. S9. Deletion of endogenous PTEN-eP53RE by CRISPR/Cas9. Supplementary Fig. S10. Depletion of p53 causes a PTEN-eP53RE-dependent decrease in PTEN expression, deletion of PTEN-eP53RE alters some tumor cell phenotypes. Supplementary Table S1. Information on tumor suppressor genes identified as basal p53 targets. Supplementary Table S2. Predicted p53 response elements within basal p53 binding sites using JASPAR. Supplementary Table S3. Chromatin properties of basal p53 binding sites near tumor suppressor genes. Legends for Supplementary Spreadsheets S1-S5. Additional Materials and Methods. References for Supplementary Material.
Figure S2 from Targeting TAZ-Driven Human Breast Cancer by Inhibiting a SKP2-p27 Signaling Axis
Authors: Shen He , Yang Nuo , Truskinovsky Alexander , Chen Yanmin , Mussell Ashley L. , Nowak Norma J. , Kobzik Lester , Frangou Costa , Zhang Jianmin
Published: April 2023

TAZ induced tumor growth and regression in response to Dox treatment and removal.
Supplementary Results from A Transcriptional Program for Detecting TGFβ-Induced EMT in Cancer
Authors: Foroutan Momeneh , Cursons Joseph , Hediyeh-Zadeh Soroor , Thompson Erik W. , Davis Melissa J.
Published: April 2023

Expanded and additional figures supporting this manuscript.
Supplementary Methods from A Transcriptional Program for Detecting TGFβ-Induced EMT in Cancer
Authors: Foroutan Momeneh , Cursons Joseph , Hediyeh-Zadeh Soroor , Thompson Erik W. , Davis Melissa J.
Published: April 2023

Detailed description of computational methods used in this manuscript.
Table S1 from Inhibition of Aurora-A Promotes CD8+ T-Cell Infiltration by Mediating IL10 Production in Cancer Cells
Authors: Han Jing , Jiang Zhen , Wang Chennan , Chen Xin , Li Rongqing , Sun Na , Liu Xiangye , Wang Hui , Hong Li , Zheng Kuiyang , Yang Jing , Ikezoe Takayuki
Published: April 2023

Table S1 shows Real time RT-PCR primers.
Figure S2 from IKKβ-Mediated Resistance to Skin Cancer Development Is Ink4a/Arf-Dependent
Authors: Page Angustias , Bravo Ana , Suarez-Cabrera Cristian , Alameda Josefa P. , Casanova M. Llanos , Lorz Corina , Segrelles Carmen , Segovia José C. , Paramio Jesús M. , Navarro Manuel , Ramirez Angel
Published: April 2023

CD34+ cell chaacterization in K5-IKKbeta skin.
Figure S1 from IKKβ-Mediated Resistance to Skin Cancer Development Is Ink4a/Arf-Dependent
Authors: Page Angustias , Bravo Ana , Suarez-Cabrera Cristian , Alameda Josefa P. , Casanova M. Llanos , Lorz Corina , Segrelles Carmen , Segovia José C. , Paramio Jesús M. , Navarro Manuel , Ramirez Angel
Published: April 2023

Immune cell populations in wt and K5-IKKbeta skin.
Supplementary Data from E-Cadherin Represses Anchorage-Independent Growth in Sarcomas through Both Signaling and Mechanical Mechanisms
Authors: Jolly Mohit Kumar , Ware Kathryn E. , Xu Shengnan , Gilja Shivee , Shetler Samantha , Yang Yanjun , Wang Xueyang , Austin R. Garland , Runyambo Daniella , Hish Alexander J. , Bartholf DeWitt Suzanne , George Jason T. , Kreulen R. Timothy , Boss Mary-Keara , Lazarides Alexander L. , Kerr David L. , Gerber Drew G. , Sivaraj Dharshan , Armstrong Andrew J. , Dewhirst Mark W. , Eward William C. , Levine Herbert , Somarelli Jason A.
Published: April 2023

Supplementary Data
Figure S6 from E-Cadherin Represses Anchorage-Independent Growth in Sarcomas through Both Signaling and Mechanical Mechanisms
Authors: Jolly Mohit Kumar , Ware Kathryn E. , Xu Shengnan , Gilja Shivee , Shetler Samantha , Yang Yanjun , Wang Xueyang , Austin R. Garland , Runyambo Daniella , Hish Alexander J. , Bartholf DeWitt Suzanne , George Jason T. , Kreulen R. Timothy , Boss Mary-Keara , Lazarides Alexander L. , Kerr David L. , Gerber Drew G. , Sivaraj Dharshan , Armstrong Andrew J. , Dewhirst Mark W. , Eward William C. , Levine Herbert , Somarelli Jason A.
Published: April 2023

S6. A mechanical model relates cell-cell adhesion to spheroid size.
Supplementary Methods from Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation
Authors: Kumar Pankaj , Dillon Laura W. , Shibata Yoshiyuki , Jazaeri Amir A. , Jones David R. , Dutta Anindya
Published: April 2023

Supplementary Methods
Supplementary Figure S8 from Potent EMT and CSC Phenotypes Are Induced By Oncostatin-M in Pancreatic Cancer
Authors: Smigiel Jacob M. , Parameswaran Neetha , Jackson Mark W.
Published: April 2023

Normal tissue expression of OSM, OSMR, JAK and STAT3
Supplementary Figure S4 from Potent EMT and CSC Phenotypes Are Induced By Oncostatin-M in Pancreatic Cancer
Authors: Smigiel Jacob M. , Parameswaran Neetha , Jackson Mark W.
Published: April 2023

OSM induces expression of the CSC marker CD133
Supplementary Data 7 from Abemaciclib Is Effective Against Pancreatic Cancer Cells and Synergizes with HuR and YAP1 Inhibition
Authors: Dhir Teena , Schultz Christopher W. , Jain Aditi , Brown Samantha Z. , Haber Alex , Goetz Austin , Xi Chunhua , Su Gloria H. , Xu Liang , Posey James , Jiang Wei , Yeo Charles J. , Golan Talia , Pishvaian Michael J. , Brody Jonathan R.
Published: April 2023

Supplemental figure 7: (A) GR50 comparison of Mia PaCa2 (top) or Panc-1 (bottom) parental cells, and their respective "chronic" abemaciclib therapy cells once treated with abemaciclib. These "chronic" abemaciclib therapy cells were then liberated from abemaciclib exposure and cultured for 14 and 21 days and GR50 was re-tested after abemaciclib exposure. Mia PaCa 2 parental, Mia PaCa2 "chronic" abemaciclib therapy (denoted as MP CA, without abemaciclib 14 days or 21 days), Panc-1 parental and Panc-1 "chronic" abemaciclib therapy (denoted as P CA, without abemaciclib 14 days or 21 days) cells GR curves are plotted together on the same graph and shown in Supplemental figure 7A. MP CA= Mia PaCa2 "chronic" abemaciclib therapy cells, P CA= Panc-1 "chronic" abemaciclib therapy cells, w/o= without. (B) β-galactosidase staining quantification of Mia PaCa2 parental/ Mia PaCa2 "chronic" abemaciclib therapy cells (top), or Panc-1 parental/ Panc-1 "chronic" abemaciclib therapy cells (bottom), as collected 3, 5, or 7 days after plating with no additional drug treatment. (C) qPCR results of Mia PaCa2 (top) or Panc-1 (bottom) parental or "chronic" abemaciclib therapy cells evaluating for SASP markers. Samples were collected 3, 5, or 7 days after plating and normalized to the same day no treatment. MP CA= Mia PaCa2 "chronic" abemaciclib therapy cells, P CA= Panc-1 "chronic" abemaciclib therapy cells.
Table S8 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate
Authors: Elfandy Habiba , Armenia Joshua , Pederzoli Filippo , Pullman Eli , Pertega-Gomes Nelma , Schultz Nikolaus , Viswanathan Kartik , Vosoughi Aram , Blattner Mirjam , Stopsack Konrad H. , Zadra Giorgia , Penney Kathryn L. , Mosquera Juan Miguel , Tyekucheva Svitlana , Mucci Lorelei A. , Barbieri Christopher , Loda Massimo
Published: April 2023

Function and effect of aberrations of differentially expressed genes between Cribriform and Noncribriform
Supplementary Table 1 from Distinct Afatinib Resistance Mechanisms Identified in Lung Adenocarcinoma Harboring an EGFR Mutation
Authors: Yamaoka Toshimitsu , Ohmori Tohru , Ohba Motoi , Arata Satoru , Murata Yasunori , Kusumoto Sojiro , Ando Koichi , Ishida Hiroo , Ohnishi Tsukasa , Sasaki Yasutsuna
Published: April 2023

Primer sequences for candidate normalization genes and those used for direct-sequencing of the EGFR gene.
Supplementary Figure Legends from Distinct Afatinib Resistance Mechanisms Identified in Lung Adenocarcinoma Harboring an EGFR Mutation
Authors: Yamaoka Toshimitsu , Ohmori Tohru , Ohba Motoi , Arata Satoru , Murata Yasunori , Kusumoto Sojiro , Ando Koichi , Ishida Hiroo , Ohnishi Tsukasa , Sasaki Yasutsuna
Published: April 2023

Figure Legends for Supplementary data
Figure S3 from Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate
Authors: Elfandy Habiba , Armenia Joshua , Pederzoli Filippo , Pullman Eli , Pertega-Gomes Nelma , Schultz Nikolaus , Viswanathan Kartik , Vosoughi Aram , Blattner Mirjam , Stopsack Konrad H. , Zadra Giorgia , Penney Kathryn L. , Mosquera Juan Miguel , Tyekucheva Svitlana , Mucci Lorelei A. , Barbieri Christopher , Loda Massimo
Published: April 2023

Examples of PTEN Immunostaining of Tissue Microarray (TMA) Cores, HPFS/ PHS Prostate Cancer Cohorts.
Supplementary Figure 3 from Distinct Afatinib Resistance Mechanisms Identified in Lung Adenocarcinoma Harboring an EGFR Mutation
Authors: Yamaoka Toshimitsu , Ohmori Tohru , Ohba Motoi , Arata Satoru , Murata Yasunori , Kusumoto Sojiro , Ando Koichi , Ishida Hiroo , Ohnishi Tsukasa , Sasaki Yasutsuna
Published: April 2023

Increased IGFBP3 expression results in MET overexpression in AFR2 cells.
Table S3 from Aberrant Induction of a Mesenchymal/Stem Cell Program Engages Senescence in Normal Mammary Epithelial Cells
Authors: Bryson Benjamin L. , Tamagno Ilaria , Taylor Sarah E. , Parameswaran Neetha , Chernosky Noah M. , Balasubramaniam Nikhila , Jackson Mark W.
Published: April 2023

Source Data
Supplementary Figure 1 from Vasohibin-2 Expressed in Human Serous Ovarian Adenocarcinoma Accelerates Tumor Growth by Promoting Angiogenesis
Authors: Takahashi Yoshifumi , Koyanagi Takahiro , Suzuki Yasuhiro , Saga Yasushi , Kanomata Naoki , Moriya Takuya , Suzuki Mitsuaki , Sato Yasufumi
Published: April 2023

PDF file - 39K, Possible splicing variants of human VASH2
Supplementary Figures 1-2 from The mRNA Stability Factor HuR Inhibits MicroRNA-16 Targeting of COX-2
Authors: Young Lisa E. , Moore Ashleigh E. , Sokol Lena , Meisner-Kober Nicole , Dixon Dan A.
Published: April 2023

PDF file - 4.7MB
Supplemental Figure 1 from DNA-Directed Polymerase Subunits Play a Vital Role in Human Telomeric Overhang Processing
Authors: Diotti Raffaella , Kalan Sampada , Matveyenko Anastasiya , Loayza Diego
Published: April 2023

Supplemental Figure 1. A. FACS data showing DNA content of HeLaII transfected with the indicated siRNAs. B. Percentages of the cells found in subG1, G1, S, and G2/M for figure A (mean of four experiments). C. The p53BP1 foci do not show obvious co-localization with telomeres: cells processed as in figure 2A (see legends), with telomeres detected by FISH (green: PNA-FISH C-rich probe).
Supplementary Figure 1 from The ATM Substrate KAP1 Controls DNA Repair in Heterochromatin: Regulation by HP1 Proteins and Serine 473/824 Phosphorylation
Authors: White David , Rafalska-Metcalf Ilona U. , Ivanov Alexey V. , Corsinotti Andrea , Peng Hongzhuang , Lee Sheng-Chung , Trono Didier , Janicki Susan M. , Rauscher Frank J.
Published: April 2023

PDF file - 168K
Supplementary Figure Legends 1-4, Table Legend from Yes-Associated Protein 1 Is Activated and Functions as an Oncogene in Meningiomas
Authors: Baia Gilson S. , Caballero Otavia L. , Orr Brent A. , Lal Anita , Ho Janelle S. Y. , Cowdrey Cynthia , Tihan Tarik , Mawrin Christian , Riggins Gregory J.
Published: April 2023

PDF file - 17K
Supplementary Table 2 from Fibroblast Growth Factor-2 Is an Important Factor that Maintains Cellular Immaturity and Contributes to Aggressiveness of Osteosarcoma
Authors: Shimizu Takatsune , Ishikawa Tomoki , Iwai Sayaka , Ueki Arisa , Sugihara Eiji , Onishi Nobuyuki , Kuninaka Shinji , Miyamoto Takeshi , Toyama Yoshiaki , Ijiri Hiroshi , Mori Hajime , Matsuzaki Yumi , Yaguchi Tomonori , Nishio Hiroshi , Kawakami Yutaka , Ikeda Yasuo , Saya Hideyuki
Published: April 2023

PDF file - 19K
Supplementary Table 1 from Fibroblast Growth Factor-2 Is an Important Factor that Maintains Cellular Immaturity and Contributes to Aggressiveness of Osteosarcoma
Authors: Shimizu Takatsune , Ishikawa Tomoki , Iwai Sayaka , Ueki Arisa , Sugihara Eiji , Onishi Nobuyuki , Kuninaka Shinji , Miyamoto Takeshi , Toyama Yoshiaki , Ijiri Hiroshi , Mori Hajime , Matsuzaki Yumi , Yaguchi Tomonori , Nishio Hiroshi , Kawakami Yutaka , Ikeda Yasuo , Saya Hideyuki
Published: April 2023

PDF file - 10K
Supplementary Figure 5 from Fibroblast Growth Factor-2 Is an Important Factor that Maintains Cellular Immaturity and Contributes to Aggressiveness of Osteosarcoma
Authors: Shimizu Takatsune , Ishikawa Tomoki , Iwai Sayaka , Ueki Arisa , Sugihara Eiji , Onishi Nobuyuki , Kuninaka Shinji , Miyamoto Takeshi , Toyama Yoshiaki , Ijiri Hiroshi , Mori Hajime , Matsuzaki Yumi , Yaguchi Tomonori , Nishio Hiroshi , Kawakami Yutaka , Ikeda Yasuo , Saya Hideyuki
Published: April 2023

PDF file - 227K
Supplementary Figures 1 - 3 from The Role of Versican in Modulating Breast Cancer Cell Self-renewal
Authors: Du William Weidong , Fang Ling , Yang Xiangling , Sheng Wang , Yang Bing L. , Seth Arun , Zhang Yaou , Yang Burton B. , Yee Albert J.
Published: April 2023

PDF file - 269K, Figure S1. The mammosphere cells expressed high levels of versican V1, Sca-1, Sox2, and ALDH1. Figure S2. Versican G3 enhanced breast cancer colony formation. Figure S3. Expression of versican G3 domain promoted breast cancer cells expression of cell self-renewal markers.
Supplementary Figure 2 from New Insight into the SDF-1/CXCR4 Axis in a Breast Carcinoma Model: Hypoxia-Induced Endothelial SDF-1 and Tumor Cell CXCR4 Are Required for Tumor Cell Intravasation
Authors: Jin Fengyan , Brockmeier Ulf , Otterbach Friedrich , Metzen Eric
Published: April 2023

PDF file - 126K, SDF-1 effects on HUVEC are mediated by CXCR4
Supplementary Figure 7 from Group I p21-Activated Kinases (PAKs) Promote Tumor Cell Proliferation and Survival through the AKT1 and Raf–MAPK Pathways
Authors: Menges Craig W. , Sementino Eleonora , Talarchek Jacqueline , Xu Jinfei , Chernoff Jonathan , Peterson Jeffrey R. , Testa Joseph R.
Published: April 2023

PDF file - 75K, Reverse-phase antibody array of phospho-kinases in Meso 22 cells treated with DMSO or IPA-3 (left panels) or nucleofected with pcDNA or pcDNA-PID (right panels) for 24 hours
Supplementary Figures S1-S5 from Active Ras Triggers Death in Glioblastoma Cells through Hyperstimulation of Macropinocytosis
Authors: Overmeyer Jean H. , Kaul Aparna , Johnson Erin E. , Maltese William A.
Published: April 2023

Supplementary Figures S1-S5 from Active Ras Triggers Death in Glioblastoma Cells through Hyperstimulation of Macropinocytosis
Supplementary Table 1 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas
Authors: Cheng Yingduan , Liang Pei , Geng Hua , Wang Zhaohui , Li Lili , Cheng Suk Hang , Ying Jianming , Su Xianwei , Ng Ka Man , Ng Margaret H.L. , Mok Tony S.K. , Chan Anthony T.C. , Tao Qian
Published: April 2023

PDF file - 25K, Summary of ZNF545 methylation in cell lines and primary carcinomas
Supplementary Table S1 from Interference of Macrophage Migration Inhibitory Factor Expression in a Mouse Melanoma Inhibits Tumor Establishment by Up-Regulating Thrombospondin-1
Authors: Culp W. David , Tsagozis Panagiotis , Burgio Michael , Russell Paul , Pisa Pavel , Garland Donita
Published: April 2023

Supplementary Table S1 from Interference of Macrophage Migration Inhibitory Factor Expression in a Mouse Melanoma Inhibits Tumor Establishment by Up-Regulating Thrombospondin-1
Supplementary Figures S1-S3 from Transforming Growth Factor-β1 Induces Tissue Inhibitor of Metalloproteinase-1 Expression via Activation of Extracellular Signal-Regulated Kinase and Sp1 in Human Fibrosarcoma Cells
Authors: Kwak Hee-Jin , Park Myung-Jin , Cho Hyeyoung , Park Chang-Min , Moon Sang-Ik , Lee Hyung-Chan , Park In-Chul , Kim Mi-Suk , Rhee Chang Hun , Hong Seok-Il
Published: April 2023

Supplementary Figures S1-S3 from Transforming Growth Factor-β1 Induces Tissue Inhibitor of Metalloproteinase-1 Expression via Activation of Extracellular Signal-Regulated Kinase and Sp1 in Human Fibrosarcoma Cells
Supplementary Figure S1 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment
Authors: Schwartz Donald R. , Moin Kamiar , Yao Bin , Matrisian Lynn M. , Coussens Lisa M. , Bugge Thomas H. , Fingleton Barbara , Acuff Heath B. , Sinnamon Mark , Nassar Hind , Platts Adrian E. , Krawetz Stephen A. , Linebaugh Bruce E. , Sloane Bonnie F.
Published: April 2023

Supplementary Figure S1 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment
Supplementary Data from HMGA2 Participates in Transformation in Human Lung Cancer
Authors: Di Cello Francescopaolo , Hillion Joelle , Hristov Alexandra , Wood Lisa J. , Mukherjee Mita , Schuldenfrei Andrew , Kowalski Jeanne , Bhattacharya Raka , Ashfaq Raheela , Resar Linda M.S.
Published: April 2023

Supplementary Data from HMGA2 Participates in Transformation in Human Lung Cancer
Supplementary Methods from Meta-Analysis and Systematic Review of the Genomics of Mucosal Melanoma
Authors: Broit Natasa , Johansson Peter A. , Rodgers Chloe B. , Walpole Sebastian T. , Newell Felicity , Hayward Nicholas K. , Pritchard Antonia L.
Published: April 2023

Supplementary Methods
Supplementary Table 1 from SPANX Control of Lamin A/C Modulates Nuclear Architecture and Promotes Melanoma Growth
Authors: Lazar Ikrame , Fabre Bertrand , Feng Yongmei , Khateb Ali , Turko Patrick , Martinez Gomez Julia M. , Frederick Dennie T. , Levesque Mitchell P. , Feld Lea , Zhang Gao , Zhang Tongwu , James Brian , Shklover Jeny , Avitan-Hersh Emily , Livneh Ido , Scortegagna Marzia , Brown Kevin , Larsson Ola , Topisirovic Ivan , Wolfenson Haguy , Herlyn Meenhard , Flaherty Keith , Dummer Reinhard , Ronai Ze'ev A.
Published: April 2023

Supplementary Table S1: Clinical information related to the PDX used in Fig1A
Figure S4: Expression of key erythroid marker genes. from 5-Azacytidine Transiently Restores Dysregulated Erythroid Differentiation Gene Expression in TET2-Deficient Erythroleukemia Cells
Authors: Reilly Brian M. , Luger Timothy , Park Soo , Lio Chan-Wang Jerry , González-Avalos Edahí , Wheeler Emily C. , Lee Minjung , Williamson Laura , Tanaka Tiffany , Diep Dinh , Zhang Kun , Huang Yun , Rao Anjana , Bejar Rafael
Published: April 2023

A) Expression of hemoglobin genes which increase in terminally differentiated erythroid cells. B) Expression of key erythrocyte marker genes. TPM=Transcripts per kilobase million; a gene expression measure for RNAseq that normalizes for gene-length and the sample sequencing depth.
Figure S3 from NF-κB Blockade with Oral Administration of Dimethylaminoparthenolide (DMAPT), Delays Prostate Cancer Resistance to Androgen Receptor (AR) Inhibition and Inhibits AR Variants
Authors: Morel Katherine L. , Hamid Anis A. , Clohessy John G. , Pandell Nicole , Ellis Leigh , Sweeney Christopher J.
Published: April 2023

Comparison of AR-v7 and AR-FL mRNA expression in parental vs empty vector control cell lines.
Supplementary Figures 1-4 from Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment
Authors: Shiota Hitoshi , Alekseyenko Artyom A. , Wang Zhipeng A. , Filic Ivona , Knox Tatiana M. , Luong Nhi M. , Huang Yeying , Scott David A. , Jones Kristen L. , Gokhale Prafulla C. , Lemieux Madeleine E. , Cole Philip A. , Kuroda Mitzi I. , French Christopher A.
Published: April 2023

Figure S1. Rationale and readout for the dCAS9-NUT chemical screen. Figure S2. IRBM6 is highly active in vitro and in vivo. Figure S3. IRBM6 induces transcriptional programs leading to growth arrest and differentiation in NC. Figure S4. IRBM6 treatment induces redistribution of BRD4-NUT and H3K27ac.
Supplementary Figures 1-5 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Authors: Schaafsma Evelien , Zhao Yanding , Zhang Lanjing , Li Yong , Cheng Chao
Published: April 2023

S1. Characteristics of MYC signatures. S2. MYC activity scores capture MYC pathway activity. S3. Diverse mechanisms of MYC alterations captured by MYC activity scores. S4. Prognostic relevance of MYC score. S5. High MYC activity is associated with high proliferative rate of tumor cells.
Supplemental Figure 6 from In Situ Analysis of N-Linked Glycans as Potential Biomarkers of Clinical Course in Human Prostate Cancer
Authors: Conroy Lindsey R. , Stanback Alexandra E. , Young Lyndsay E.A. , Clarke Harrison A. , Austin Grant L. , Liu Jinze , Allison Derek B. , Sun Ramon C.
Published: April 2023

Supplemental Figure 6. Differential N-glycan profiles for Appalachian versus non-Appalachian prostate tumor patients, separated by grade.
Supplementary Video: HPV+ (UMSCC47) from Palbociclib Renders Human Papilloma Virus–Negative Head and Neck Squamous Cell Carcinoma Vulnerable to the Senolytic Agent Navitoclax
Authors: Gadsden Nicholas J. , Fulcher Cory D. , Li Daniel , Shrivastava Nitisha , Thomas Carlos , Segall Jeffrey E. , Prystowsky Michael B. , Schlecht Nicolas F. , Gavathiotis Evripidis , Ow Thomas J.
Published: April 2023

Supplementary Video: HPV+ (UMSCC47) is a time-lapse video illustrating a HPV+ cell line's response to palbociclib treatment.
Supplementary Figure 2 from EMT-Derived Alterations in Glutamine Metabolism Sensitize Mesenchymal Breast Cells to mTOR Inhibition
Authors: Karvelsson Sigurdur Trausti , Sigurdsson Arnar , Seip Kotryna , Grinde Maria Tunset , Wang Qiong , Johannsson Freyr , Mælandsmo Gunhild Mari , Moestue Siver Andreas , Rolfsson Ottar , Halldorsson Skarphedinn
Published: April 2023

UPLC-MS label enrichment in various metabolites after culturing of D492 and D492M with 1,2-13C-glucose for 6 hours. Results are shown as mean + standard deviation (n = 3).
Video S1 from Hypoxic Induction of Exosome Uptake through Proteoglycan-Dependent Endocytosis Fuels the Lipid Droplet Phenotype in Glioma
Authors: Cerezo-Magaña Myriam , Christianson Helena C. , van Kuppevelt Toin H. , Forsberg-Nilsson Karin , Belting Mattias
Published: April 2023

High-resolution Airyscan live-cell confocal microscopy visualization of internalized EVs in hypoxic U87 MG cells. The sequence was captured at 4 s interval for 8 min. Scale bar, 20 µm.
Supplementary Data from Heparan Sulfate Synthesized by Ext1 Regulates Receptor Tyrosine Kinase Signaling and Promotes Resistance to EGFR Inhibitors in GBM
Authors: Ohkawa Yuki , Wade Anna , Lindberg Olle R. , Chen Katharine Y. , Tran Vy M. , Brown Spencer J. , Kumar Anupam , Kalita Mausam , James C. David , Phillips Joanna J.
Published: April 2023

Supplementary Materials and Methods.
Supplementary Fig. S2 from AXL Inhibition Induces DNA Damage and Replication Stress in Non–Small Cell Lung Cancer Cells and Promotes Sensitivity to ATR Inhibitors
Authors: Ramkumar Kavya , Stewart C. Allison , Cargill Kasey R. , Della Corte Carminia M. , Wang Qi , Shen Li , Diao Lixia , Cardnell Robert J. , Peng David H. , Rodriguez B. Leticia , Fan You-Hong , Heymach John V. , Wang Jing , Gay Carl M. , Gibbons Don L. , Byers Lauren A.
Published: April 2023

Supplementary Fig. S2: Spectra of EMT score and AXL expression across different tumor types.
Table S3 from IQ Motif-Containing GTPase-Activating Protein 2 Inhibits Breast Cancer Angiogenesis by Suppressing VEGFR2–AKT Signaling
Authors: Kumar Dinesh , Patel Saket Awadhesbhai , Khan Rehan , Chawla Saurabh , Mohapatra Nachiketa , Dixit Manjusha
Published: April 2023

Association between the expression of IQGAP2 and MVD in breast cancer patients*
Supplementary Tables 1-15 from Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions
Authors: Kim Jong Hyuk , Megquier Kate , Thomas Rachael , Sarver Aaron L. , Song Jung Min , Kim Yoon Tae , Cheng Nuojin , Schulte Ashley J. , Linden Michael A. , Murugan Paari , Oseth LeAnn , Forster Colleen L. , Elvers Ingegerd , Swofford Ross , Turner-Maier Jason , Karlsson Elinor K. , Breen Matthew , Lindblad-Toh Kerstin , Modiano Jaime F.
Published: April 2023

Table S1. Demographic and pathological features of human patients with angiosarcoma Table S2. Demographic and pathological features of dogs with HSA Table S3. Primary antibodies for immunohistochemical evaluation Table S4. Gene ontology and biological functions of fusion partner genes in human angiosarcomas Table S5. Gene ontology and biological functions of fusion partner genes in canine HSAs Table S6. Detection of fusion genes in canine HSAs by RT-PCR Table S7. Biological functions associated with 490 upregulated genes in human angiosarcomas Table S8. Association of frequency between fusion genes, TP53 and PIK3CA mutations Table S9. Association of fusion genes with dog signalment and tumor histology Table S10. Association of frequency between fusion genes, TP53 and PIK3CA mutations Table S11. 41 differentially expressed genes in PF (n = 4) compared to P (n = 9) group Table S12. 212 differentially expressed genes in PF (n = 4) compared to PK (n = 6) group Table S13. 377 differentially expressed genes in PF (n = 4) compared to PFK (n = 4) group Table S14. Immunohistochemical features of human angiosarcomas Table S15. Immunohistochemical features of canine HSAs
Table S1 from IQ Motif-Containing GTPase-Activating Protein 2 Inhibits Breast Cancer Angiogenesis by Suppressing VEGFR2–AKT Signaling
Authors: Kumar Dinesh , Patel Saket Awadhesbhai , Khan Rehan , Chawla Saurabh , Mohapatra Nachiketa , Dixit Manjusha
Published: April 2023

List of qRT-PCR primers
Supplementary Figures 1-5 and Table S1 from Platelet-Coated Circulating Tumor Cells Are a Predictive Biomarker in Patients with Metastatic Castrate-Resistant Prostate Cancer
Authors: Chai Shoujie , Matsumoto Nicholas , Storgard Ryan , Peng Chen-Ching , Aparicio Ana , Ormseth Benjamin , Rappard Kate , Cunningham Katherine , Kolatkar Anand , Nevarez Rafael , Tu Kai-Han , Hsu Ching-Ju , Malihi Paymaneh , Corn Paul , Zurita Amado , Hicks James , Kuhn Peter , Ruiz-Velasco Carmen
Published: April 2023

S1. Platelet confirmation with CD61 staining in the SKBR3-spiked NBD sample S2. Enumeration of CTC subtypes S3. Survival analysis using AVPC-MS-CTC status S4. Survival analysis in patients without pc.CTC S5. Treatment decision tree Table S1. Correlation between CTC and clinical characteristics
Supplementary Figures 1-8 from p53 Frameshift Mutations Couple Loss-of-Function with Unique Neomorphic Activities
Authors: Tong David R. , Zhou Wen , Katz Chen , Regunath Kausik , Venkatesh Divya , Ihuegbu Chinyere , Manfredi James J. , Laptenko Oleg , Prives Carol
Published: April 2023

This file contain Supplementary Information that is relevant to the main body of the text. Supplementary Figure S1. Supplementary Figure S2. Half-lives of WT and mutant I332fs*14 p53 in U2OS and HCT116 cells. Supplementary Figure S3. Subcellular localization of p53 FS mutants expressed in U2OS and HCT116 cells. Supplementary Figure S4. Cross-linked species detected in cells grown in the absence or presence of Photo-Met. Supplementary Figure S5. Transcriptional activity of p53 FS mutants in U2OS and HCT116 cells. Supplementary Figure S6. Transactivation potential of N345K* and N345fs*26 mutants in U2OS cells. Supplementary Figure S7. Cell cycle profiles of I332fs*14-expressing HCT116 and U2OS cells. Supplementary Figure S8. Pro-apoptotic activity of I332fs*14 p53.
Supplementary Figure S3 from Cross-talk between YAP and RAR-RXR Drives Expression of Stemness Genes to Promote 5-FU Resistance and Self-Renewal in Colorectal Cancer Cells
Authors: Bauzone Marjolaine , Souidi Mouloud , Dessein Anne-Frédérique , Wisztorski Maxence , Vincent Audrey , Gimeno Jean-Pascal , Monté Didier , Van Seuningen Isabelle , Gespach Christian , Huet Guillemette
Published: April 2023

Supplementary Figure S3 shows the validation of the YAP/RAR-RXR crosstalk in control and YAPdc-RKO colorectal cancer cells.
Supplementary Tables 1-5 and Figures 1-6 from LncIHAT Is Induced by Hypoxia-Inducible Factor 1 and Promotes Breast Cancer Progression
Authors: Chen Lin , Bao Lei , Niu Yanling , Wang Jennifer E. , Kumar Ashwani , Xing Chao , Wang Yingfei , Luo Weibo
Published: April 2023

Supplementary Table 1. The shRNA and sgRNA Oligonucleotide Sequences Supplementary Table 2. 5'-and 3' RACE Primers Supplementary Table 3. qPCR Primers Supplementary Table 4. Hypoxia-induced lncRNAs in TNBC cells. Supplementary Table 5. Abundance of hypoxia-induced lncRNAs in both MDA-MB-231 and SUM159 cells. Supplementary Figure 1. The nucleotide sequence alignment of lncIHAT. Supplementary Figure 2. LncIHAT promotes TNBC growth and metastasis in mice. Supplementary Figure 3. LncIHATis required for expression of PDK1 and ITGA6 in TNBC cells. Supplementary Figure 4 .LncIHAT overexpression has no effect on PDK1 and ITGA6 expression. Supplementary Figure 5. Time-dependent induction of lncIHAT and PDK1 by hypoxia in TNBC cells. Supplementary Figure 6. PDK1 and ITGA6 mediate the effect of lncIHAT on TNBC cell growth in vitro.
Supplementary Figure 3 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum
Authors: Penney Kathryn L. , Tyekucheva Svitlana , Rosenthal Jacob , El Fandy Habiba , Carelli Ryan , Borgstein Stephanie , Zadra Giorgia , Fanelli Giuseppe Nicolò , Stefanizzi Lavinia , Giunchi Francesca , Pomerantz Mark , Peisch Samuel , Coulson Hannah , Lis Rosina , Kibel Adam S. , Fiorentino Michelangelo , Umeton Renato , Loda Massimo
Published: April 2023

Supplementary Figure 3. Scatterplots for metabolites with high correlations between their abundances in tissue and serum.
Supplementary Figure 1 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum
Authors: Penney Kathryn L. , Tyekucheva Svitlana , Rosenthal Jacob , El Fandy Habiba , Carelli Ryan , Borgstein Stephanie , Zadra Giorgia , Fanelli Giuseppe Nicolò , Stefanizzi Lavinia , Giunchi Francesca , Pomerantz Mark , Peisch Samuel , Coulson Hannah , Lis Rosina , Kibel Adam S. , Fiorentino Michelangelo , Umeton Renato , Loda Massimo
Published: April 2023

Supplemental Figure 1. Fresh radical prostatectomy specimens were inked and transverse sliced from apex to base.
Table S2 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes
Authors: DelaCourt Andrew , Black Alyson , Angel Peggi , Drake Richard , Hoshida Yujin , Singal Amit , Lewin David , Taouli Bachir , Lewis Sara , Schwarz Myron , Fiel M. Isabel , Mehta Anand S.
Published: April 2023

Full list of glycans analyzed on the FT-ICR mass spectrometer.
Supplementary Table 1 from ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression
Authors: Sheldon Helen , Bridges Esther , Silva Ildefonso , Masiero Massimo , Favara David M. , Wang Dian , Leek Russell , Snell Cameron , Roxanis Ioannis , Kreuzer Mira , Gileadi Uzi , Buffa Francesca M. , Banham Alison , Harris Adrian L.
Published: April 2023

Supplementary Table 1. QPCR primer sequences
Supplementary Figure 8 from ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression
Authors: Sheldon Helen , Bridges Esther , Silva Ildefonso , Masiero Massimo , Favara David M. , Wang Dian , Leek Russell , Snell Cameron , Roxanis Ioannis , Kreuzer Mira , Gileadi Uzi , Buffa Francesca M. , Banham Alison , Harris Adrian L.
Published: April 2023

S8. Tumour vascular ADGRL4/ELTD1 is differentially expressed between primary breast cancer and regional node metastases and expression correlates with improved relapse free survival (RFS).
Supplementary Figure 7 from ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression
Authors: Sheldon Helen , Bridges Esther , Silva Ildefonso , Masiero Massimo , Favara David M. , Wang Dian , Leek Russell , Snell Cameron , Roxanis Ioannis , Kreuzer Mira , Gileadi Uzi , Buffa Francesca M. , Banham Alison , Harris Adrian L.
Published: April 2023

S7. Mice with Eltd1 expressing tumours have less specific T CD8+ cells raised against the tumour NY-ESO-1 antigen.
Supplementary Figure 2 from Identification and Characterization of Cancer Cells That Initiate Metastases to the Brain and Other Organs
Authors: Berghoff Anna. S. , Liao Yunxiang , Karreman Matthia A. , Ilhan-Mutlu Ayseguel , Gunkel Katharina , Sprick Martin R. , Eisen Christian , Kessler Tobias , Osswald Matthias , Wünsche Susanne , Feinauer Manuel , Gril Brunhilde , Marmé Frederic , Michel Laura L. , Bago-Horvath Zuszanna , Sahm Felix , Becker Natalia , Breckwoldt Michael O. , Solecki Gergely , Gömmel Miriam , Huang Lulu , Rübmann Petra , Thome Carina M. , Ratliff Miriam , Trumpp Andreas , Steeg Patricia S. , Preusser Matthias , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Figure 2 cell index of PKH26 stained cells, the overlap of PKH26 loss and 2 other methods of cell division analysis as well as the reversion of a slow cycling cell population to a mixed cycling population.
Figure S2 from Deubiquitinase UCHL1 Maintains Protein Homeostasis through the PSMA7–APEH–Proteasome Axis in High-grade Serous Ovarian Carcinoma
Authors: Tangri Apoorva , Lighty Kinzie , Loganathan Jagadish , Mesmar Fahmi , Podicheti Ram , Zhang Chi , Iwanicki Marcin , Drapkin Ronny , Nakshatri Harikrishna , Mitra Sumegha
Published: April 2023

Figure S2 shows effect of UCHL1 epigenetic upregulation in HGSOC.
Supplemental Figure 4 from Autophagy-Dependent Sensitization of Triple-Negative Breast Cancer Models to Topoisomerase II Poisons by Inhibition of the Nucleosome Remodeling Factor
Authors: Tyutyunyk-Massey Liliya , Sun Yilun , Dao Nga , Ngo Hannah , Dammalapati Mallika , Vaidyanathan Ashish , Singh Manjulata , Haqqani Syed , Haueis Joshua , Finnegan Ryan , Deng Xiaoyan , Kirberger Steve E. , Bos Paula D. , Bandyopadhyay Dipankar , Pomerantz William C.K. , Pommier Yves , Gewirtz David A. , Landry Joseph W.
Published: April 2023

Supplemental Figure 4. Selective BPTF Bromdomain Inhibitor AU1 Recapitulates Effects from BPTF KD in 4T1 Cells and Tumors.
Supplementary Figures 1-6 from Neoadjuvant Chemotherapy Induces IL34 Signaling and Promotes Chemoresistance via Tumor-Associated Macrophage Polarization in Esophageal Squamous Cell Carcinoma
Authors: Nakajima Shotaro , Mimura Kosaku , Saito Katsuharu , Thar Min Aung Kyi , Endo Eisei , Yamada Leo , Kase Koji , Yamauchi Naoto , Matsumoto Takuro , Nakano Hiroshi , Kanke Yasuyuki , Okayama Hirokazu , Saito Motonobu , Neupane Prajwal , Saze Zenichiro , Watanabe Yohei , Hanayama Hiroyuki , Hayase Suguru , Kaneta Akinao , Momma Tomoyuki , Ohki Shinji , Ohira Hiromasa , Kono Koji
Published: April 2023

S1. Measurement of the number of CD163+ cells and their expression intensities in ESCC specimens. S2. IHC staining of CSF-1, IL-34, E-cadherin, and vimentin in ESCC specimens. S3. Correlation between mRNA expression of CD163 and CSF-1 in patients with ESCC who underwent curative esophagectomy without any preoperative therapy. S4. The effect of CSF-1 expression of NAC responsivity and tumor progression after NAC in ESCC. S5. Involvement of higher fold-change of IL-34 expression after CDDP treatment to poorer chemo-sensitivity in ESCC cells. S6. Enhanced mRNA expression of IL-34 in CDDP-resistant human ESCC cells.
Supplementary Methods, Supplementary Figures 1-10 from EGR1 Addiction in Diffuse Large B-cell Lymphoma
Authors: Kimpara Shuichi , Lu Li , Hoang Nguyet M. , Zhu Fen , Bates Paul D. , Daenthanasanmak Anusara , Zhang Shanxiang , Yang David T. , Kelm Amanda , Liu Yunxia , Li Yangguang , Rosiejka Alexander , Kondapelli Apoorv , Bebel Samantha , Chen Madelyn , Waldmann Thomas A. , Capitini Christian M. , Rui Lixin
Published: April 2023

Supplementary Methods, Supplementary Figures and Figure Legends. Figure S1. EGR1 is a downstream target of BCR and JAK1 signaling (related to Figure 1). Figure S2. Sensitivity of MCL cell lines to EGR1 shRNAs and statistical analysis (related to Figure 2). Figure S3. EGR1 motif analysis and gene set enrichment analysis of RNA-seq data (related to Figure 3). Figure S4. Enrichment of E2F pathway genes in ABC DLBCL after EGR1 knockdown (related to Figure 4). Figure S5. EGR1 regulates expression of MYC and MYC targets and OCI-Ly10 xenografts (related to Figure 4). Figure S6. Enrichment of EGR1 on EGR1 own promoter and EP300 regulatory (5'UTR and enhancer) regions (related to Figure 4). Figure S7. Inhibition of EGR1 transcription and tumor growth by mithramycin (related to Figure 4). Figure S8. Synergism of mithramycin and lenalidomide in ABC DLBCL (related to Figure 6). Figure S9. Expression of MYC and MYC target genes is higher in ABC DLBCL than GCB DLBCL patient samples (related to the Discussion). Figure S10. No correlation between EGR1 and MYC expression in DLBCL cell lines and patient samples (related to the Discussion).
Supplementary Data from REX-1 Represses RASSF1a and Activates the MEK/ERK Pathway to Promote Tumorigenesis in Prostate Cancer
Authors: Liu Weijing , Xie An , Tu Chunhua , Liu Weipeng
Published: April 2023

Supplementary Figures 1 and 2
Supplementary Table from MUC16 Promotes Liver Metastasis of Pancreatic Ductal Adenocarcinoma by Upregulating NRP2-Associated Cell Adhesion
Authors: Marimuthu Saravanakumar , Lakshmanan Imayavaramban , Muniyan Sakthivel , Gautam Shailendra K. , Nimmakayala Rama Krishna , Rauth Sanchita , Atri Pranita , Shah Ashu , Bhyravbhatla Namita , Mallya Kavita , Grandgenett Paul M. , Hollingsworth Michael A. , Datta Kaustubh , Jain Maneesh , Ponnusamy Moorthy P. , Batra Surinder K.
Published: April 2023

Supplementary Table from MUC16 Promotes Liver Metastasis of Pancreatic Ductal Adenocarcinoma by Upregulating NRP2-Associated Cell Adhesion
Supplementary Tables 1-5 from Activation of the JAK/STAT Pathway Leads to BRAF Inhibitor Resistance in BRAFV600E Positive Thyroid Carcinoma
Authors: Limberg Jessica , Egan Caitlin E. , Gray Katherine D. , Singh Mandeep , Loewenstein Zachary , Yang Yanping , Riascos Maria Cristina , Al Asadi Hala , Safe Parima , El Eshaky Steve , Liang Heng , Ullmann Timothy M. , Wang Weibin , Li Wei , Zhang Tuo , Xiang Jenny , Stefanova Dessislava , Jin Moonsoo M. , Zarnegar Rasa , Fahey Thomas J. , Min Irene M.
Published: April 2023

Supplementary Table 1. Gene expression changes in 8505C after vemurafenib treatment.Supplementary Table 2. Gene expression changes in WRO after vemurafenib treatment.Supplementary Table 3. Gene expression changes in 8505C -Vem-Res 1 relative to parental 8505C.Supplementary Table 4. Gene expression changes in WRO -Vem-Res 6 relative to parental WRO.Supplementary Table 5. Clinical features of thyroid tumors used in Fig. 5.
Supplementary Figure from Origins and Timing of Emerging Lesions in Advanced Renal Cell Carcinoma
Authors: Wallace Andrew , Porten Sima P. , Lo Amy A. , Oreper Daniel , Lounsbury Nicolas , Havnar Charles , Pechuan-Jorge Ximo , Zill Oliver A. , Meng Maxwell V.
Published: April 2023

Supplementary Figure from Origins and Timing of Emerging Lesions in Advanced Renal Cell Carcinoma
Supplementary Data from Molecular Profile Changes in Patients with Castrate-Resistant Prostate Cancer Pre- and Post-Abiraterone/Prednisone Treatment
Authors: Sicotte Hugues , Kalari Krishna R. , Qin Sisi , Dehm Scott M. , Bhargava Vipul , Gormley Michael , Tan Winston , Sinnwell Jason P. , Hillman David W. , Li Ying , Vedell Peter T. , Carlson Rachel E. , Bryce Alan H. , Jimenez Raphael E. , Weinshilboum Richard M. , Kohli Manish , Wang Liewei
Published: April 2023

Supplementary Data from Molecular Profile Changes in Patients with Castrate-Resistant Prostate Cancer Pre- and Post-Abiraterone/Prednisone Treatment
Supplementary Figure from Identifying Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole-Genome Sequencing
Authors: Pham Minh-Tam , Gupta Anuj , Gupta Harshath , Vaghasia Ajay , Skaist Alyza , Garrison McKinzie A. , Coulter Jonathan B. , Haffner Michael C. , Zheng S. Lilly , Xu Jianfeng , DeStefano Shields Christina , Isaacs William B. , Wheelan Sarah J. , Nelson William G. , Yegnasubramanian Srinivasan
Published: April 2023

Supplementary Figure from Identifying Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole-Genome Sequencing
Supplementary Data from Epigenetic Regulation of Fanconi Anemia Genes Implicates PRMT5 Blockage as a Strategy for Tumor Chemosensitization
Authors: Du Changzheng , Li Steven W. , Singh Simranjit X. , Roso Kristen , Sun Michael A. , Pirozzi Christopher J. , Yang Rui , Li Jian-Liang , He Yiping
Published: April 2023

Supplementary Data from Epigenetic Regulation of Fanconi Anemia Genes Implicates PRMT5 Blockage as a Strategy for Tumor Chemosensitization
Supplementary Table from Loss of VOPP1 Contributes to BET Inhibitor Acquired Resistance in Non–Small Cell Lung Cancer Cells
Authors: Sun Lin , Wu Qian , Huan Xia-Juan , Tian Chang-Qing , Wang Ying-Qing , Miao Ze-Hong
Published: April 2023

Supplementary Table from Loss of VOPP1 Contributes to BET Inhibitor Acquired Resistance in Non–Small Cell Lung Cancer Cells
Supplementary Figure from TFAP4 Activates IGF2BP1 and Promotes Progression of Non–Small Cell Lung Cancer by Stabilizing TK1 Expression through m6A Modification
Authors: Shen Qiming , Xu Zhe , Sun Guanghao , Wang Haoyou , Zhang Lin
Published: April 2023

Supplementary Figure from TFAP4 Activates IGF2BP1 and Promotes Progression of Non–Small Cell Lung Cancer by Stabilizing TK1 Expression through m6A Modification
Supplementary Figure 1 from DCLK1-Short Splice Variant Promotes Esophageal Squamous Cell Carcinoma Progression via the MAPK/ERK/MMP2 Pathway
Authors: Ge Yang , Fan Xiaona , Huang Xuying , Weygant Nathaniel , Xiao Zeru , Yan Rui , Liu Heshu , Liu Jian , An Guangyu , Yao Jiannan
Published: April 2023

Figure S1 shows DCLK1 isoforms.
Supplementary Figure 2 from The Spatial Context of Tumor-Infiltrating Immune Cells Associates with Improved Ovarian Cancer Survival
Authors: Steinhart Benjamin , Jordan Kimberly R. , Bapat Jaidev , Post Miriam D. , Brubaker Lindsay W. , Bitler Benjamin G. , Wrobel Julia
Published: April 2023

S2. Kaplan-Meier curves for CD8 T cell infiltration into tumor regions.
Supplementary Figure 1 from The Spatial Context of Tumor-Infiltrating Immune Cells Associates with Improved Ovarian Cancer Survival
Authors: Steinhart Benjamin , Jordan Kimberly R. , Bapat Jaidev , Post Miriam D. , Brubaker Lindsay W. , Bitler Benjamin G. , Wrobel Julia
Published: April 2023

S1: Kaplan-Meier curves of disease-free survival for B cell presence and B cell-macrophage interaction.
Supplementary Data from The Spatial Context of Tumor-Infiltrating Immune Cells Associates with Improved Ovarian Cancer Survival
Authors: Steinhart Benjamin , Jordan Kimberly R. , Bapat Jaidev , Post Miriam D. , Brubaker Lindsay W. , Bitler Benjamin G. , Wrobel Julia
Published: April 2023

The supplementary document includes a sensitivity analysis on the distance threshold chosen. Additionally, it contains disease free survival analysis. Lastly, it contains cell infiltration analysis for CD8+ T cells.
Figure S5 from The Elongin BC Complex Negatively Regulates AXL and Marks a Differentiated Phenotype in Melanoma
Authors: Schieven Sebastiaan M. , Traets Joleen J.H. , Vliet Alex v. , Baalen Martijn v. , Song Ji-Ying , Guimaraes Marcos Da Silva , Kuilman Thomas , Peeper Daniel S.
Published: April 2023

Extended data on Figure 5: Low expression of ELOB/C is associated with phenotype switching and EMT.
Data from Adaptation to HIF1α Deletion in Hypoxic Cancer Cells by Upregulation of GLUT14 and Creatine Metabolism
Authors: Valli Alessandro , Morotti Matteo , Zois Christos E. , Albers Patrick K. , Soga Tomoyoshi , Feldinger Katharina , Fischer Roman , Frejno Martin , McIntyre Alan , Bridges Esther , Haider Syed , Buffa Francesca M. , Baban Dilair , Rodriguez Miguel , Yanes Oscar , Whittington Hannah J. , Lake Hannah A. , Zervou Sevasti , Lygate Craig A. , Kessler Benedikt M. , Harris Adrian L.
Published: April 2023

Abstract
Hypoxia-inducible factor 1α is a key regulator of the hypoxia response in normal and cancer tissues. It is well recognized to regulate glycolysis and is a target for therapy. However, how tumor cells adapt to grow in the absence of HIF1α is poorly understood and an important concept to understand for developing targeted therapies is the flexibility of the metabolic response to hypoxia via alternative pathways. We analyzed pathways that allow cells to survive hypoxic stress in the absence of HIF1α, using the HCT116 colon cancer cell line with deleted HIF1α versus control. Spheroids were used to provide a 3D model of metabolic gradients. We conducted a metabolomic, transcriptomic, and proteomic analysis and integrated the results. These showed surprisingly that in three-dimensional growth, a key regulatory step of glycolysis is Aldolase A rather than phosphofructokinase. Furthermore, glucose uptake could be maintained in hypoxia through upregulation of GLUT14, not previously recognized in this role. Finally, there was a marked adaptation and change of phosphocreatine energy pathways, which made the cells susceptible to inhibition of creatine metabolism in hypoxic conditions. Overall, our studies show a complex adaptation to hypoxia that can bypass HIF1α, but it is targetable and it provides new insight into the key metabolic pathways involved in cancer growth.
Implications:
Under hypoxia and HIF1 blockade, cancer cells adapt their energy metabolism via upregulation of the GLUT14 glucose transporter and creatine metabolism providing new avenues for drug targeting.