bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods and References from Integrative Genome-Scale Analysis Identifies Epigenetic Mechanisms of Transcriptional Deregulation in Unfavorable Neuroblastomas
Authors: Henrich Kai-Oliver , Bender Sebastian , Saadati Maral , Dreidax Daniel , Gartlgruber Moritz , Shao Chunxuan , Herrmann Carl , Wiesenfarth Manuel , Parzonka Martha , Wehrmann Lea , Fischer Matthias , Duffy David J. , Bell Emma , Torkov Alica , Schmezer Peter , Plass Christoph , Höfer Thomas , Benner Axel , Pfister Stefan M. , Westermann Frank
Published: April 2023

Description of additional methods and procedures used in the study. Also includes Supplementary References.
Supplemental Table 1 from Herbacetin Is a Novel Allosteric Inhibitor of Ornithine Decarboxylase with Antitumor Activity
Authors: Kim Dong Joon , Roh Eunmiri , Lee Mee-Hyun , Oi Naomi , Lim Do Young , Kim Myoung Ok , Cho Yong-Yeon , Pugliese Angelo , Shim Jung-Hyun , Chen Hanyong , Cho Eun Jin , Kim Jong-Eun , Kang Sun Chul , Paul Souren , Kang Hee Eun , Jung Ji Won , Lee Sung-Young , Kim Sung-Hyun , Reddy Kanamata , Yeom Young Il , Bode Ann M. , Dong Zigang
Published: April 2023

List of potential ODC inhibitors generated by using computer screening.
Supplemental Materials and Methods from Herbacetin Is a Novel Allosteric Inhibitor of Ornithine Decarboxylase with Antitumor Activity
Authors: Kim Dong Joon , Roh Eunmiri , Lee Mee-Hyun , Oi Naomi , Lim Do Young , Kim Myoung Ok , Cho Yong-Yeon , Pugliese Angelo , Shim Jung-Hyun , Chen Hanyong , Cho Eun Jin , Kim Jong-Eun , Kang Sun Chul , Paul Souren , Kang Hee Eun , Jung Ji Won , Lee Sung-Young , Kim Sung-Hyun , Reddy Kanamata , Yeom Young Il , Bode Ann M. , Dong Zigang
Published: April 2023

Supplemental Materials and Methods
Supplemental Figure Legend from Herbacetin Is a Novel Allosteric Inhibitor of Ornithine Decarboxylase with Antitumor Activity
Authors: Kim Dong Joon , Roh Eunmiri , Lee Mee-Hyun , Oi Naomi , Lim Do Young , Kim Myoung Ok , Cho Yong-Yeon , Pugliese Angelo , Shim Jung-Hyun , Chen Hanyong , Cho Eun Jin , Kim Jong-Eun , Kang Sun Chul , Paul Souren , Kang Hee Eun , Jung Ji Won , Lee Sung-Young , Kim Sung-Hyun , Reddy Kanamata , Yeom Young Il , Bode Ann M. , Dong Zigang
Published: April 2023

Supplemental Figure Legend
Supplementary Figure 1 from Systemic Chromosome Instability Resulted in Colonic Transcriptomic Changes in Metabolic, Proliferation, and Stem Cell Regulators in Sgo1−/+ Mice
Authors: Rao Chinthalapally V. , Sanghera Saira , Zhang Yuting , Biddick Laura , Reddy Arun , Lightfoot Stan , Janakiram Naveena B. , Mohammed Altaf , Dai Wei , Yamada Hiroshi Y.
Published: April 2023

List of 349 differentially expressed genes in normal-looking colonic mucosal tissues in Sgo1, compared with control wild type. (P<0.05, 2-fold cutoff)
Supplementary Figure S1 from Inhibition of PAI-1 Limits Tumor Angiogenesis Regardless of Angiogenic Stimuli in Malignant Pleural Mesothelioma
Authors: Takayama Yusuke , Hattori Noboru , Hamada Hironobu , Masuda Takeshi , Omori Keitaro , Akita Shin , Iwamoto Hiroshi , Fujitaka Kazunori , Kohno Nobuoki
Published: April 2023

Structure of SK-216
Supplementary Table S3 from Long Noncoding RNA MALAT1 Promotes Aggressive Renal Cell Carcinoma through Ezh2 and Interacts with miR-205
Authors: Hirata Hiroshi , Hinoda Yuji , Shahryari Varahram , Deng Guoren , Nakajima Koichi , Tabatabai Z. Laura , Ishii Nobuhisa , Dahiya Rajvir
Published: April 2023

22 transcription factors (related to cancer pathway) potentially binding to MALAT1 promoter.
Supplementary Figures 1-8 from Hyperthermia Synergizes with Chemotherapy by Inhibiting PARP1-Dependent DNA Replication Arrest
Authors: Schaaf Lea , Schwab Matthias , Ulmer Christoph , Heine Simon , Mürdter Thomas E. , Schmid Jens O. , Sauer Georg , Aulitzky Walter E. , van der Kuip Heiko
Published: April 2023

Supplemental Figures (Supplementary Fig. 1-8): Cell lines are HR proficient (Supplementary Fig. 1); Influence of hyperthermia on the quantity of intra-nuclear Pt-DNA adducts and intracellular doxorubicin concentration (Supplementary Fig. 2); Hyperthermia sensitizes tumor cells to drugs which induce PARylation without altering PARP of PARG protein levels (Supplementary Fig. 3); Hyperthermia leads to a delayed DNA strand break repair capacity in different cell lines from ovarian and colon cancer (Supplementary Fig. 4); HR competence in 14 of 15 samples from PC patients (Supplementary Fig. 5); Gamma-irradiation leads to induction of γH2AX foci in all cells independent of proliferation status (Supplementary Fig. 6); Hyperthermia has no acute effect on cisplatin or doxorubicin induced apoptosis (Supplementary Fig. 7); Combined treatment of cells with hyperthermia and PARPi slightly enhanced the potentiating effect of either treatment alone (Supplementary Fig. 8).
Supplemental Table 2 from G0S2 Suppresses Oncogenic Transformation by Repressing a MYC-Regulated Transcriptional Program
Authors: Yim Christina Y. , Sekula David J. , Hever-Jardine Mary P. , Liu Xi , Warzecha Joshua M. , Tam Janice , Freemantle Sarah J. , Dmitrovsky Ethan , Spinella Michael J.
Published: April 2023

Expression of G0S2 in breast cancer versus normal breast tissue
SUPPLEMENTARY DATA from Genome-Wide Association Study of Bladder Cancer in a Chinese Cohort Reveals a New Susceptibility Locus at 5q12.3
Authors: Wang Meilin , Li Zhiqiang , Chu Haiyan , Lv Qiang , Ye Dingwei , Ding Qiang , Xu Chuanliang , Guo Jianming , Du Mulong , Chen Jianhua , Song Zhijian , Yin Changjun , Qin Chao , Gu Chengyuan , Zhu Yao , Xia Guowei , Liu Fang , Zhang Zhengsheng , Yuan Lin , Fu Guangbo , Hu Zhibin , Tong Na , Shen Jiawei , Liu Ke , Sun Jielin , Sun Yinghao , Li Jue , Li Xingwang , Shen Hongbing , Xu Jianfeng , Shi Yongyong , Zhang Zhengdong
Published: April 2023

Supplemental Methods and References, Supplemental Tables S1-S10, Supplemental Figures S1-S11
Supplementary figures from Preclinical Anticancer Efficacy of BET Bromodomain Inhibitors Is Determined by the Apoptotic Response
Authors: Conery Andrew R. , Centore Richard C. , Spillane Kerry L. , Follmer Nicole E. , Bommi-Reddy Archana , Hatton Charlie , Bryant Barbara M. , Greninger Patricia , Amzallag Arnaud , Benes Cyril H. , Mertz Jennifer A. , Sims Robert J.
Published: April 2023

This file contains six supplementary figures: Figure S1 (related to Figure 1) provides additional characterization of the BETi tolerant cell lines; Figure S2 (related to Figure 1) provides additional information regarding gene expression changes in the BETi tolerant cell lines; Figure S3 (related to Figure 2) provides further support for the importance of BCL2 and BCL2L1 expression in the BETi tolerant cell lines; Figure S4 (related to Figures 3 and 4) quantifies Figure 3C, and provides supporting data and additional analysis for BCL2/BCL2L1/BAD as predictive biomarkers; Figure S5 (related to Figure 4) provides supporting data for BCL2 family expression as predictive biomarkers; Figure S6 (related to Figure 4) shows that BCL2/BCL2L1 protein expression can serve as predictive biomarkers for BETi response.
Figure S2 from Heme Oxygenase-1 Controls an HDAC4-miR-206 Pathway of Oxidative Stress in Rhabdomyosarcoma
Authors: Ciesla Maciej , Marona Paulina , Kozakowska Magdalena , Jez Mateusz , Seczynska Marta , Loboda Agnieszka , Bukowska-Strakova Karolina , Szade Agata , Walawender Magdalena , Kusior Magdalena , Stepniewski Jacek , Szade Krzysztof , Krist Bart , Yagensky Oleksandr , Urbanik Aleksandra , Kazanowska Bernarda , Dulak Jozef , Jozkowicz Alicja
Published: April 2023

Expression of miR-328, miR-338-3p and miR-485-5p in SMS-CTR eRMS (SMS) and CW9019 aRMS (CW).
Figure S10 from Heme Oxygenase-1 Controls an HDAC4-miR-206 Pathway of Oxidative Stress in Rhabdomyosarcoma
Authors: Ciesla Maciej , Marona Paulina , Kozakowska Magdalena , Jez Mateusz , Seczynska Marta , Loboda Agnieszka , Bukowska-Strakova Karolina , Szade Agata , Walawender Magdalena , Kusior Magdalena , Stepniewski Jacek , Szade Krzysztof , Krist Bart , Yagensky Oleksandr , Urbanik Aleksandra , Kazanowska Bernarda , Dulak Jozef , Jozkowicz Alicja
Published: April 2023

Scheme showing the proposed relation between Pax3-FoxO1 induced expression of HO-1 and miR-206 dependent pathway.
Figure S1 from Heme Oxygenase-1 Controls an HDAC4-miR-206 Pathway of Oxidative Stress in Rhabdomyosarcoma
Authors: Ciesla Maciej , Marona Paulina , Kozakowska Magdalena , Jez Mateusz , Seczynska Marta , Loboda Agnieszka , Bukowska-Strakova Karolina , Szade Agata , Walawender Magdalena , Kusior Magdalena , Stepniewski Jacek , Szade Krzysztof , Krist Bart , Yagensky Oleksandr , Urbanik Aleksandra , Kazanowska Bernarda , Dulak Jozef , Jozkowicz Alicja
Published: April 2023

Comparison of SMS-CTR eRMS (SMS) and CW9019 aRMS (CW) cell lines cultured under standard conditions. Expression of VEGF, VEGFR-1, VEGFR-2, HIF-1, HIF-2 and miR-146a genes.
Supplemental Tables S1-S2 from Forced Activation of Notch in Macrophages Represses Tumor Growth by Upregulating miR-125a and Disabling Tumor-Associated Macrophages
Authors: Zhao Jun-Long , Huang Fei , He Fei , Gao Chun-Chen , Liang Shi-Qian , Ma Peng-Fei , Dong Guang-Ying , Han Hua , Qin Hong-Yan
Published: April 2023

Table S1: Primers and oligonucleotides used for PCR. Table S2: Antibodies and related reagents used in this study.
Supplemental Figures S1-4 from Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits BET Bromodomain Proteins
Authors: Nilsson Lisa M. , Green Lydia C. , Muralidharan Somsundar Veppil , Demir Dağsu , Welin Martin , Bhadury Joydeep , Logan Derek T. , Walse Björn , Nilsson Jonas A.
Published: April 2023

Figure S1: Molecular modelling and structure determination by X ray crystallography. Expanded data related to Figure 1B. Figure S2-S3: Ingenuity Pathway analyses of microarray data. Expanded analyses related to Figure 4 and Supplemental dataset 1. Figure S4: Gene-set enrichment analyses of microarray data. Expanded analyses related to Figure 4 and Supplemental dataset 1.
Supplementary Materials and Methods, Supplementary Tables 1 and 2 and Supplementary Figures 1 through 5 from PTP1B Deficiency Enables the Ability of a High-Fat Diet to Drive the Invasive Character of PTEN-Deficient Prostate Cancers
Authors: Labbé David P. , Uetani Noriko , Vinette Valérie , Lessard Laurent , Aubry Isabelle , Migon Eva , Sirois Jacinthe , Haigh Jody J. , Bégin Louis R. , Trotman Lloyd C. , Paquet Marilène , Tremblay Michel L.
Published: April 2023

Supplementary Materials and Methods. Table S1: List of the different oligonucleotides used for mouse genotyping. Table S2: Phenotypic evaluation of prostate-specific PTP1B-overexpressing mice. Figure S1: Ptpn1 status does not alter the transition to mPIN in PtenPE-/- mice. Figure S2: Examples of mild and moderate desmoplasia. Figure S3: HFD drives invasive prostate cancer in the AP only in absence of Ptpn1. Figure S4: Ptpn1 status does not modulate mPIN formation in PtenPE+/- mice. Figure S5: Ptpn1 status influences PtenPE-/- phenotype in a dose-dependent manner.
Supplementary from miR-214 and miR-148b Targeting Inhibits Dissemination of Melanoma and Breast Cancer
Authors: Orso Francesca , Quirico Lorena , Virga Federico , Penna Elisa , Dettori Daniela , Cimino Daniela , Coppo Roberto , Grassi Elena , Elia Angela Rita , Brusa Davide , Deaglio Silvia , Brizzi Maria Felice , Stadler Michael B. , Provero Paolo , Caselle Michele , Taverna Daniela
Published: April 2023

Supplementary tables and figure legends
Supplementary Table 6 from Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma
Authors: De Rienzo Assunta , Archer Michael A. , Yeap Beow Y. , Dao Nhien , Sciaranghella Daniele , Sideris Antonios C. , Zheng Yifan , Holman Alexander G. , Wang Yaoyu E. , Dal Cin Paola S. , Fletcher Jonathan A. , Rubio Renee , Croft Larry , Quackenbush John , Sugarbaker Peter E. , Munir Kiara J. , Battilana Jesse R. , Gustafson Corinne E. , Chirieac Lucian R. , Ching Soo Meng , Wong James , Tay Liang Chung , Rudd Stephen , Hercus Robert , Sugarbaker David J. , Richards William G. , Bueno Raphael
Published: April 2023

List of the Tumor types having mutations in both MYH9 and RHOA genes in the cBioPortal for Cancer Genomics database
Figure S10 from miR-214 and miR-148b Targeting Inhibits Dissemination of Melanoma and Breast Cancer
Authors: Orso Francesca , Quirico Lorena , Virga Federico , Penna Elisa , Dettori Daniela , Cimino Daniela , Coppo Roberto , Grassi Elena , Elia Angela Rita , Brusa Davide , Deaglio Silvia , Brizzi Maria Felice , Stadler Michael B. , Provero Paolo , Caselle Michele , Taverna Daniela
Published: April 2023

miR-214 inhibition and miR-148b overexpression impair melanoma cell extravasation
Supplementary Table 4 from Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma
Authors: De Rienzo Assunta , Archer Michael A. , Yeap Beow Y. , Dao Nhien , Sciaranghella Daniele , Sideris Antonios C. , Zheng Yifan , Holman Alexander G. , Wang Yaoyu E. , Dal Cin Paola S. , Fletcher Jonathan A. , Rubio Renee , Croft Larry , Quackenbush John , Sugarbaker Peter E. , Munir Kiara J. , Battilana Jesse R. , Gustafson Corinne E. , Chirieac Lucian R. , Ching Soo Meng , Wong James , Tay Liang Chung , Rudd Stephen , Hercus Robert , Sugarbaker David J. , Richards William G. , Bueno Raphael
Published: April 2023

List of the 51 canonical pathways significantly enriched (p<0.05) for the mutated genes identify by Ingenuity Pathway Analysis
Supplementary Figure S3 from Oxygen-Enhanced MRI Accurately Identifies, Quantifies, and Maps Tumor Hypoxia in Preclinical Cancer Models
Authors: O'Connor James P.B. , Boult Jessica K.R. , Jamin Yann , Babur Muhammad , Finegan Katherine G. , Williams Kaye J. , Little Ross A. , Jackson Alan , Parker Geoff J.M. , Reynolds Andrew R. , Waterton John C. , Robinson Simon P.
Published: April 2023

R1 changes in Oxy-E and Oxy-R sub-regions
Supplemental Table 3 from Integrated Genomic Analysis of Pancreatic Ductal Adenocarcinomas Reveals Genomic Rearrangement Events as Significant Drivers of Disease
Authors: Murphy Stephen J. , Hart Steven N. , Halling Geoffrey C. , Johnson Sarah H. , Smadbeck James B. , Drucker Travis , Lima Joema Felipe , Rohakhtar Fariborz Rakhshan , Harris Faye R. , Kosari Farhad , Subramanian Subbaya , Petersen Gloria M. , Wiltshire Timothy D. , Kipp Benjamin R. , Truty Mark J. , McWilliams Robert R. , Couch Fergus J. , Vasmatzis George
Published: April 2023

Comparison of current data with published data sets of PDAC.
Supplementary Figure Legends from Inhibition of MUC1-C Suppresses MYC Expression and Attenuates Malignant Growth in KRAS Mutant Lung Adenocarcinomas
Authors: Bouillez Audrey , Rajabi Hasan , Pitroda Sean , Jin Caining , Alam Maroof , Kharbanda Akriti , Tagde Ashujit , Wong Kwok-Kin , Kufe Donald
Published: April 2023

Supplementary Figure Legends
Fig.S5 from Dual Roles for CXCL4 Chemokines and CXCR3 in Angiogenesis and Invasion of Pancreatic Cancer
Authors: Quemener Cathy , Baud Jessica , Boyé Kevin , Dubrac Alexandre , Billottet Clotilde , Soulet Fabienne , Darlot Florence , Dumartin Laurent , Sire Marie , Grepin Renaud , Daubon Thomas , Rayne Fabienne , Wodrich Harald , Couvelard Anne , Pineau Raphael , Schilling Martin , Castronovo Vincent , Sue Shih-Che , Clarke Kim , Lomri Abderrahim , Khatib Abdel-Majid , Hagedorn Martin , Prats Hervé , Bikfalvi Andreas
Published: April 2023

Effect of CXCL4L1 and CXCL4 on apoptosis in pancreatic adenocarcinoma cells and endothelial cells
Supplementary Movie 3 from Metabolic Stress-Induced Phosphorylation of KAP1 Ser473 Blocks Mitochondrial Fusion in Breast Cancer Cells
Authors: Cheng Chun-Ting , Kuo Ching-Ying , Ouyang Ching , Li Chien-Feng , Chung Yiyin , Chan David C. , Kung Hsing-Jien , Ann David K.
Published: April 2023

Movie 3. Time-lapse imaging of MDA-MB-231/shKAP1/S473A-KAP1 cells in glucose-depleted medium.
Supplementary Figure S2 from Mutational Landscape and Antiproliferative Functions of ELF Transcription Factors in Human Cancer
Authors: Ando Mizuo , Kawazu Masahito , Ueno Toshihide , Koinuma Daizo , Ando Koji , Koya Junji , Kataoka Keisuke , Yasuda Takahiko , Yamaguchi Hiroyuki , Fukumura Kazutaka , Yamato Azusa , Soda Manabu , Sai Eirin , Yamashita Yoshihiro , Asakage Takahiro , Miyazaki Yasushi , Kurokawa Mineo , Miyazono Kohei , Nimer Stephen D. , Yamasoba Tatsuya , Mano Hiroyuki
Published: April 2023

Expression level of ELF4 in stably transduced T3M-1 Cl-10 cells
Supplemental Figures from STK11/LKB1 Deficiency Promotes Neutrophil Recruitment and Proinflammatory Cytokine Production to Suppress T-cell Activity in the Lung Tumor Microenvironment
Authors: Koyama Shohei , Akbay Esra A. , Li Yvonne Y. , Aref Amir R. , Skoulidis Ferdinandos , Herter-Sprie Grit S. , Buczkowski Kevin A. , Liu Yan , Awad Mark M. , Denning Warren L. , Diao Lixia , Wang Jing , Parra-Cuentas Edwin R. , Wistuba Ignacio I. , Soucheray Margaret , Thai Tran , Asahina Hajime , Kitajima Shunsuke , Altabef Abigail , Cavanaugh Jillian D. , Rhee Kevin , Gao Peng , Zhang Haikuo , Fecci Peter E. , Shimamura Takeshi , Hellmann Matthew D. , Heymach John V. , Hodi F. Stephen , Freeman Gordon J. , Barbie David A. , Dranoff Glenn , Hammerman Peter S. , Wong Kwok-Kin
Published: April 2023

This file contains figures which include: additional immune proofing data of mouse tumors, RNA sequencing data of neutrophils, cytokine and chemokine profile of Kras, p53, LKB1/STK11 mutant cell lines, data for neutrophil depletion, chemokine and cytokine profile of human cell lines transducer with hairpins for LKB1/STK11 or non-target, immune and survival analysis of mice treated with combination of IL6 antibody and PD-1 antibody.
Supplementary Figure S7 from Eva1 Maintains the Stem-like Character of Glioblastoma-Initiating Cells by Activating the Noncanonical NF-κB Signaling Pathway
Authors: Ohtsu Naoki , Nakatani Yuka , Yamashita Daisuke , Ohue Shiro , Ohnishi Takanori , Kondo Toru
Published: April 2023

RelB is essential for the NSCL61 proliferation and tumorigenesis.
Supplementary Figure S2 from Eva1 Maintains the Stem-like Character of Glioblastoma-Initiating Cells by Activating the Noncanonical NF-κB Signaling Pathway
Authors: Ohtsu Naoki , Nakatani Yuka , Yamashita Daisuke , Ohue Shiro , Ohnishi Takanori , Kondo Toru
Published: April 2023

Generation of rabbit polyclonal anti-Eva1 antibodies.
Supplementary Figure S1 from Eva1 Maintains the Stem-like Character of Glioblastoma-Initiating Cells by Activating the Noncanonical NF-κB Signaling Pathway
Authors: Ohtsu Naoki , Nakatani Yuka , Yamashita Daisuke , Ohue Shiro , Ohnishi Takanori , Kondo Toru
Published: April 2023

Eva1 expression level in mouse GICs, human GIC and glioma tissues.
Supplementary Fig 6 from Neuropilin-2 Regulates Endosome Maturation and EGFR Trafficking to Support Cancer Cell Pathobiology
Authors: Dutta Samikshan , Roy Sohini , Polavaram Navatha S. , Stanton Marissa J. , Zhang Heyu , Bhola Tanvi , Hönscheid Pia , Donohue Terrence M. , Band Hamid , Batra Surinder K. , Muders Michael H. , Datta Kaustubh
Published: April 2023

Maturation of Cathepsin following depletion of NRP2 axis in Du145 and PC3 cells
Supplementary Figure S7 from Upregulation of Cytosolic Phosphoenolpyruvate Carboxykinase Is a Critical Metabolic Event in Melanoma Cells That Repopulate Tumors
Authors: Li Yong , Luo Shunqun , Ma Ruihua , Liu Jing , Xu Pingwei , Zhang Huafeng , Tang Ke , Ma Jingwei , Zhang Yi , Liang Xiaoyu , Sun Yanling , Ji Tiantian , Wang Ning , Huang Bo
Published: April 2023

Supplementary Figure S7. High methylation in promoter region of PCK1 gene. B16 TRCs and control cells were used for DNA isolation.
Supplementary Figure S3 from Rapalogs Efficacy Relies on the Modulation of Antitumor T-cell Immunity
Authors: Beziaud Laurent , Mansi Laura , Ravel Patrice , Marie-Joseph Elodie Lauret , Laheurte Caroline , Rangan Laurie , Bonnefoy Francis , Pallandre Jean-René , Boullerot Laura , Gamonet Clémentine , Vrecko Sindy , Queiroz Lise , Maurina Tristan , Mouillet Guillaume , Hon Thierry Nguyen Tan , Curtit Elsa , Royer Bernard , Gaugler Béatrice , Bayry Jagadeesh , Tartour Eric , Thiery-Vuillemin Antoine , Pivot Xavier , Borg Christophe , Godet Yann , Adotévi Olivier
Published: April 2023

This file contains the antiviral response in patients: Supplementary figure 3
Supplementary Figure S5 from Upregulation of Cytosolic Phosphoenolpyruvate Carboxykinase Is a Critical Metabolic Event in Melanoma Cells That Repopulate Tumors
Authors: Li Yong , Luo Shunqun , Ma Ruihua , Liu Jing , Xu Pingwei , Zhang Huafeng , Tang Ke , Ma Jingwei , Zhang Yi , Liang Xiaoyu , Sun Yanling , Ji Tiantian , Wang Ning , Huang Bo
Published: April 2023

Supplementary Figure S5. Inhibition of PCK1 enzymatic activity repressed TRC growth and PCK1 knockdown didn't affect B16 TRC apoptosis.
supplementary figure legends from The E3-ligase E6AP Represses Breast Cancer Metastasis via Regulation of ECT2-Rho Signaling
Authors: Mansour Mariam , Haupt Sue , Chan Ai-Leen , Godde Nathan , Rizzitelli Alexandra , Loi Sherene , Caramia Franco , Deb Siddhartha , Takano Elena A. , Bishton Mark , Johnstone Cameron , Monahan Brendon , Levav-Cohen Yarra , Jiang Yong-Hui , Yap Alpha S. , Fox Stephen , Bernard Ora , Anderson Robin , Haupt Ygal
Published: April 2023

legends for supplemantry figures
Supplemental Figures and Tables from FAP Promotes Immunosuppression by Cancer-Associated Fibroblasts in the Tumor Microenvironment via STAT3–CCL2 Signaling
Authors: Yang Xuguang , Lin Yuli , Shi Yinghong , Li Bingji , Liu Weiren , Yin Wei , Dang Yongjun , Chu Yiwei , Fan Jia , He Rui
Published: April 2023

Supplemental Figures and Tables Figure S1. The purity of the isolated fibroblasts. Figure S2. Knockdown of FAP or STAT3 impairs the inflammatory phenotype of CAFs. Figure S3. Forced FAP expression in the normal fibroblasts. Figure S4. Knockdown of STAT3 or uPAR has no effect on the expression of inflammatory genes in control fibroblasts. Figure S5. FAP knockdown abolishes the tumor-promoting effects of CAFs in Hepa1-6 tumor. Figure S6. FAP expression is dispensable for the direct effect of CAFs on the cancer stemness or the immune function of MDSCs or CD8+T cells. Figure S7. Stromal expression of p-STAT3 or CCL2 is negatively associated with the survival of ICC patients.
Supplementary Methods from CSN1 Somatic Mutations in Penile Squamous Cell Carcinoma
Authors: Feber Andrew , Worth Daniel C. , Chakravarthy Ankur , de Winter Patricia , Shah Kunal , Arya Manit , Saqib Muhammad , Nigam Raj , Malone Peter R. , Tan Wei Shen , Rodney Simon , Freeman Alex , Jameson Charles , Wilson Gareth A. , Powles Tom , Beck Stephan , Fenton Tim , Sharp Tyson V. , Muneer Asif , Kelly John D.
Published: April 2023

Supplementary methods
Supplemental Figure S3 from Fibroblast-Mediated Collagen Remodeling Within the Tumor Microenvironment Facilitates Progression of Thyroid Cancers Driven by BrafV600E and Pten Loss
Authors: Jolly Lee Ann , Novitskiy Sergey , Owens Phillip , Massoll Nicole , Cheng Nikki , Fang Wei , Moses Harold L. , Franco Aime T.
Published: April 2023

Supplemental Figure S3 LOX expression in murine BrafV600E/Pten-/-/TPO-Cre cell lines.
Supplemental Figure S2 from Fibroblast-Mediated Collagen Remodeling Within the Tumor Microenvironment Facilitates Progression of Thyroid Cancers Driven by BrafV600E and Pten Loss
Authors: Jolly Lee Ann , Novitskiy Sergey , Owens Phillip , Massoll Nicole , Cheng Nikki , Fang Wei , Moses Harold L. , Franco Aime T.
Published: April 2023

Supplemental Figure S2 Braf conditioned media does not induce TGFβ activation in CAFs.
Supplementary Table S3 from An Epigenetic Reprogramming Strategy to Resensitize Radioresistant Prostate Cancer Cells
Authors: Peitzsch Claudia , Cojoc Monica , Hein Linda , Kurth Ina , Mäbert Katrin , Trautmann Franziska , Klink Barbara , Schröck Evelin , Wirth Manfred P. , Krause Mechthild , Stakhovsky Eduard A. , Telegeev Gennady D. , Novotny Vladimir , Toma Marieta , Muders Michael , Baretton Gustavo B. , Frame Fiona M. , Maitland Norman J. , Baumann Michael , Dubrovska Anna
Published: April 2023

Regulation of the genes involved in WNT signaling pathway in the entire population of DU145 parental (P) cells versus DU145 radioresistant (RR) cells.
Supplementary Figures 1-5 from Feasibility of Telomerase-Specific Adoptive T-cell Therapy for B-cell Chronic Lymphocytic Leukemia and Solid Malignancies
Authors: Sandri Sara , Bobisse Sara , Moxley Kelly , Lamolinara Alessia , De Sanctis Francesco , Boschi Federico , Sbarbati Andrea , Fracasso Giulio , Ferrarini Giovanna , Hendriks Rudi W. , Cavallini Chiara , Scupoli Maria Teresa , Sartoris Silvia , Iezzi Manuela , Nishimura Michael I. , Bronte Vincenzo , Ugel Stefano
Published: April 2023

In supplementary figure S1 we show that malignant B-CLL cells isolated from IgH.TEμ+ splenocytes express high levels of telomerase and are recognized by mTERT198-205-specific CTLs; supplementary figure S2 shows a schematic representation of flow cytometry cytotoxicity assay; supplementary figure S3 demonstrates that Leukemic cells isolated from IgH.TEμ+ mice preserves the original phenotype during several in vivo transplantations; supplementary figure S4 shows the phenotypical and functional evaluation of engineered T-cells and finally supplementary figure S5 demonstrates that B-CLL cells are a preferential target of anti-TERT T cells and reports the schematic representation of the experiments on human chimeras.
Supplementary Figure 5 from NOTCH Signaling Regulates Asymmetric Cell Fate of Fast- and Slow-Cycling Colon Cancer–Initiating Cells
Authors: Srinivasan Tara , Walters Jewell , Bu Pengcheng , Than Elaine Bich , Tung Kuei-Ling , Chen Kai-Yuan , Panarelli Nicole , Milsom Jeff , Augenlicht Leonard , Lipkin Steven M. , Shen Xiling
Published: April 2023

NOTCH modulation in CCIC-1 line.
Supplementary Figure S2 from The Ubiquitin-like Protein FAT10 Stabilizes eEF1A1 Expression to Promote Tumor Proliferation in a Complex Manner
Authors: Liu Xiuxia , Chen Leifeng , Ge Jin , Yan Chen , Huang Zixi , Hu Junwen , Wen Chongyu , Li Ming , Huang Da , Qiu Yumin , Hao Haibin , Yuan Rongfa , Lei Jun , Yu Xin , Shao Jianghua
Published: April 2023

Supplementary Fig. S2 shRNA-resistant FAT10 plasmid rescues the expression of eEF1A1 and recovers cell proliferation in shFAT10 cancer cells.
SUPPLEMENTARY figure 3 from IGFBP2 Activates the NF-κB Pathway to Drive Epithelial–Mesenchymal Transition and Invasive Character in Pancreatic Ductal Adenocarcinoma
Authors: Gao Song , Sun Yan , Zhang Xuebin , Hu Limei , Liu Yuexin , Chua Corrine Yingxuan , Phillips Lynette M. , Ren He , Fleming Jason B. , Wang Huamin , Chiao Paul J. , Hao Jihui , Zhang Wei
Published: April 2023

Quantification of western blotting results from main Figures 2, 3, and 4.
Supplementary Figure 2 from PAK4 Phosphorylates p53 at Serine 215 to Promote Liver Cancer Metastasis
Authors: Xu Hai-Tao , Lai Wai-Lung , Liu Heong-Fai , Wong Leo Lap-Yan , Ng Irene Oi-Lin , Ching Yick Pang
Published: April 2023

Similar to Fig. 3D, cytoplasmic (Cyto) and nuclear (Nu) lysates were extracted from HeLa cells by fractionation.
Supplementary Figure 1 from PAK4 Phosphorylates p53 at Serine 215 to Promote Liver Cancer Metastasis
Authors: Xu Hai-Tao , Lai Wai-Lung , Liu Heong-Fai , Wong Leo Lap-Yan , Ng Irene Oi-Lin , Ching Yick Pang
Published: April 2023

mRNA expression of PAK4alpha and PAK4beta in HCC and LO2 cells was detected by RT-PCR.
Supplementary Materials and Methods, Supplementary Figures 1 through 9, and Supplementary Tables 1 through 5 and 7 and 8 from PROTOCADHERIN 7 Acts through SET and PP2A to Potentiate MAPK Signaling by EGFR and KRAS during Lung Tumorigenesis
Authors: Zhou Xiaorong , Updegraff Barrett L. , Guo Yabin , Peyton Michael , Girard Luc , Larsen Jill E. , Xie Xian-Jin , Zhou Yunyun , Hwang Tae Hyun , Xie Yang , Rodriguez-Canales Jaime , Villalobos Pamela , Behrens Carmen , Wistuba Ignacio I. , Minna John D. , O'Donnell Kathryn A.
Published: April 2023

Supplementary Methods, References, and Figure Legends, Supplementary Fig. S1-High magnification images of PCDH7 IHC staining in normal human lung and lung adenocarcinomas. Supplementary Fig. S2-NSCLC tissue microarray analysis of PCDH7 immunoexpression. Supplementary Fig. S3-PCDH7 induces cellular transformation of HBEC cells and induces a gene expression program that promotes cell proliferation. Supplementary Fig. S4-All PCDH7 isoforms induce MAPK signaling in HBEC-shp53-KRASG12V cells. Supplementary Fig. S5-PCDH7 synergizes with mutant EGFR to promote tumor formation. Supplementary Fig. S6-CRISPR/Cas9-mediated inhibition of PCDH7 sensitizes NSCLC cells to MEK and ERK inhibitors. Supplementary Fig. S7-PCDH7 isoforms A, C, and D bind SET in EGFR-mutant cells. Supplementary Fig. S8-SET localization studies in HBECs and NSCLC cells and requirement of SET for PCDH7-induced MAPK pathway activation. Supplementary Fig. S9-Treatment of NSCLC cells with a SET inhibitor FTY720 induces cell death. Supplementary Table S1. Expression and survival analysis of PCDH family members in lung adenocarcinoma. Supplementary Table S2. Affymetrix probe IDs analyzed for each PCDH family member. Supplementary Table S3. Summary of clinical and pathologic information of the cohort of NSCLC patient tissue blocks used for TMA generation. Supplementary Table S4. Analysis of tissue microarray correlations. Supplementary Table S5. Correlation between PCDH7 upregulation and alterations in KRAS or EGFR. Supplementary Table S7. List of antibodies utilized in this study. Supplementary Table S8. List of primer sequences utilized in this study.
Supplementary Figures from TRPA1 Mediates Aromatase Inhibitor–Evoked Pain by the Aromatase Substrate Androstenedione
Authors: De Logu Francesco , Tonello Raquel , Materazzi Serena , Nassini Romina , Fusi Camilla , Coppi Elisabetta , Li Puma Simone , Marone Ilaria M. , Sadofsky Laura R. , Morice Alyn H. , Susini Tommaso , Terreni Alessandro , Moneti Gloriano , Di Tommaso Mariarosaria , Geppetti Pierangelo , Benemei Silvia
Published: April 2023

Supplementary Figure 1 shows the chemical structure of exemestane, androstenedione and testosterone, and responses (calcium mobilization or currents) evoked by androstenedione and other steroid hormones in cells that express the native or recombinant (including a mutated form) TRPA1 channel. Supplementary Figure 2 shows the inhibitory effect of the ROS scavenger, alpha lipoic acid, on the mechanical allodynia induced by intragastric administration of letrozole. Supplementary Figure 3 shows that the combination of per se ineffective doses of androstenedione, letrozole or H202 is able to evoke mechanical allodynia. Supplementary Figure 4 shows the ability of the TRPA1 antagonist, HC-030031, and TRPV1 antagonist, capsazepine, to modulate the responses (mechanical allodynia, grip strength reduction) evoked by buthionine sulfoximine and androstenedione.
Supplementary figure legend from Hypoxia-Induced Downregulation of DUSP-2 Phosphatase Drives Colon Cancer Stemness
Authors: Hou Pei-Chi , Li Yo-Hua , Lin Shih-Chieh , Lin Shau-Chieh , Lee Jenq-Chang , Lin Bo-Wen , Liou Jing-Ping , Chang Jang-Yang , Kuo Ching-Chuan , Liu Yi-Min , Sun H. Sunny , Tsai Shaw-Jenq
Published: April 2023

Legends for supplementary figures S1-S7
Supplementary Figure S4 from Predicting Barrett's Esophagus in Families: An Esophagus Translational Research Network (BETRNet) Model Fitting Clinical Data to a Familial Paradigm
Authors: Sun Xiangqing , Elston Robert C. , Barnholtz-Sloan Jill S. , Falk Gary W. , Grady William M. , Faulx Ashley , Mittal Sumeet K. , Canto Marcia , Shaheen Nicholas J. , Wang Jean S. , Iyer Prasad G. , Abrams Julian A. , Tian Ye D. , Willis Joseph E. , Guda Kishore , Markowitz Sanford D. , Chandar Apoorva , Warfe James M. , Brock Wendy , Chak Amitabh
Published: April 2023

The linear relationship between the continuous covariates and susceptibility on the logit scale
Supplementary Tables 1-2 from Phase II, Open-Label, Randomized Trial of the MEK1/2 Inhibitor Selumetinib as Monotherapy versus Temozolomide in Patients with Advanced Melanoma
Authors: Kirkwood John M. , Bastholt Lars , Robert Caroline , Sosman Jeff , Larkin James , Hersey Peter , Middleton Mark , Cantarini Mireille , Zazulina Victoria , Kemsley Karin , Dummer Reinhard
Published: April 2023

PDF file - 46K
Supplementary Figure 5 from BRAF Fusions Define a Distinct Molecular Subset of Melanomas with Potential Sensitivity to MEK Inhibition
Authors: Hutchinson Katherine E. , Lipson Doron , Stephens Philip J. , Otto Geoff , Lehmann Brian D. , Lyle Pamela L. , Vnencak-Jones Cindy L. , Ross Jeffrey S. , Pietenpol Jennifer A. , Sosman Jeffrey A. , Puzanov Igor , Miller Vincent A. , Pao William
Published: April 2023

PDF file - 89K, Supplementary Figure S5. Comparison of reverse phase protein array (RPPA) data in TCGA skin cutaneous melanoma dataset.
Supplementary Figure 4 from BRAF Fusions Define a Distinct Molecular Subset of Melanomas with Potential Sensitivity to MEK Inhibition
Authors: Hutchinson Katherine E. , Lipson Doron , Stephens Philip J. , Otto Geoff , Lehmann Brian D. , Lyle Pamela L. , Vnencak-Jones Cindy L. , Ross Jeffrey S. , Pietenpol Jennifer A. , Sosman Jeffrey A. , Puzanov Igor , Miller Vincent A. , Pao William
Published: April 2023

PDF file - 237K, Supplementary Figure S4. Potential TAX1BP1-BRAF and CDC27-BRAF fusions identified in data from The Cancer Genome Atlas.
Supplementary Figure 2 from Expression of Interleukin-4 Receptor Alpha in Human Pleural Mesothelioma Is Associated with Poor Survival and Promotion of Tumor Inflammation
Authors: Burt Bryan M. , Bader Andrew , Winter Daniel , Rodig Scott J. , Bueno Raphael , Sugarbaker David J.
Published: April 2023

PDF file - 362K
Supplementary Table 2 from The Zinc Finger Gene ZIC2 Has Features of an Oncogene and Its Overexpression Correlates Strongly with the Clinical Course of Epithelial Ovarian Cancer
Authors: Marchini Sergio , Poynor Elizabeth , Barakat Richard R. , Clivio Luca , Cinquini Michela , Fruscio Robert , Porcu Luca , Bussani Cecilia , D’Incalci Maurizio , Erba Eugenio , Romano Michela , Cattoretti Giorgio , Katsaros Dionyssios , Koff Andrew , Luzzatto Lucio
Published: April 2023

PDF file, 64K, ZIC2 expression and clinical course of patients tested.
Supplementary Figure 2 from MSH3 Protein Expression and Nodal Status in MLH1-Deficient Colorectal Cancers
Authors: Laghi Luigi , Bianchi Paolo , Delconte Gabriele , Celesti Giuseppe , Di Caro Giuseppe , Pedroni Monica , Chiaravalli Anna Maria , Jung Barbara , Capella Carlo , de Leon Maurizio Ponz , Malesci Alberto
Published: April 2023

PDF file, 1877KB, Supplemental Material 3. Disease-free survival after resection of stage 11/111 CRC.
Supplementary Figure 1 from MSH3 Protein Expression and Nodal Status in MLH1-Deficient Colorectal Cancers
Authors: Laghi Luigi , Bianchi Paolo , Delconte Gabriele , Celesti Giuseppe , Di Caro Giuseppe , Pedroni Monica , Chiaravalli Anna Maria , Jung Barbara , Capella Carlo , de Leon Maurizio Ponz , Malesci Alberto
Published: April 2023

PDF file, 6805KB, Supplemental Material 1. Frameshifts at MSH3/MSH6 codin~crep_eats in microdissected areas of MLHI-deficient CRC with or without secondary MMR-protein loss.
Supplementary Table 7 from FoxM1 Inhibition Sensitizes Resistant Glioblastoma Cells to Temozolomide by Downregulating the Expression of DNA-Repair Gene Rad51
Authors: Zhang Nu , Wu Xinjian , Yang Lixuan , Xiao Feizhe , Zhang Heng , Zhou Aidong , Huang Zhengsong , Huang Suyun
Published: April 2023

XLSX file - 10370K, Microarray analysis of gene expression after knockdown of FoxM1 by siRNA in U87 cells
Supplementary Figure 4 from Transcriptional Characterization of a Prospective Series of Primary Plasma Cell Leukemia Revealed Signatures Associated with Tumor Progression and Poorer Outcome
Authors: Todoerti Katia , Agnelli Luca , Fabris Sonia , Lionetti Marta , Tuana Giacomo , Mosca Laura , Lombardi Luigia , Grieco Vitina , Bianchino Gabriella , D'Auria Fiorella , Statuto Teodora , Mazzoccoli Carmela , De Luca Luciana , Petrucci Maria Teresa , Morabito Fortunato , Offidani Massimo , Di Raimondo Francesco , Falcone Antonietta , Omede' Paola , Tassone Pierfrancesco , Boccadoro Mario , Palumbo Antonio , Neri Antonino , Musto Pellegrino
Published: April 2023

PDF file - 862K, Boxplot distributions of the expression levels of the 26 progression-associated genes.
Supplementary Figure 1 from Transcriptional Characterization of a Prospective Series of Primary Plasma Cell Leukemia Revealed Signatures Associated with Tumor Progression and Poorer Outcome
Authors: Todoerti Katia , Agnelli Luca , Fabris Sonia , Lionetti Marta , Tuana Giacomo , Mosca Laura , Lombardi Luigia , Grieco Vitina , Bianchino Gabriella , D'Auria Fiorella , Statuto Teodora , Mazzoccoli Carmela , De Luca Luciana , Petrucci Maria Teresa , Morabito Fortunato , Offidani Massimo , Di Raimondo Francesco , Falcone Antonietta , Omede' Paola , Tassone Pierfrancesco , Boccadoro Mario , Palumbo Antonio , Neri Antonino , Musto Pellegrino
Published: April 2023

PDF file - 749K, Histogram of the expression values of MAFA gene in the 21 PPCL and the 55 MM patients.
Supplementary Table S1 from Clinical, Pathologic, and Biologic Features Associated with BRAF Mutations in Non–Small Cell Lung Cancer
Authors: Cardarella Stephanie , Ogino Atsuko , Nishino Mizuki , Butaney Mohit , Shen Jeanne , Lydon Christine , Yeap Beow Y. , Sholl Lynette M. , Johnson Bruce E. , Jänne Pasi A.
Published: April 2023

Supplementary Table S1 - XLS file 32K, Baseline characteristics of the patients with driver alterations in EGFR, KRAS or ALK
Supplementary Figure 6 from Mutual Regulation between Raf/MEK/ERK Signaling and Y-Box–Binding Protein-1 Promotes Prostate Cancer Progression
Authors: Imada Kenjiro , Shiota Masaki , Kohashi Kenichi , Kuroiwa Kentaro , Song YooHyun , Sugimoto Masaaki , Naito Seiji , Oda Yoshinao
Published: April 2023

Supplementary Figure 6 - Supplementary Figure 6. Densitometric analyses of Figure 4D - PDF file 76K, Protein expression level of p-Raf-1, p-MEK, p-ERK1, p-ERK2, p-RSK and p-YB-1 in LNCaP cells transfected with control siRNA and not treated with EGF was defined as 1. Boxes, mean; bars, plus-minus s.d.; *P < 0.05 versus cells with transfected with control siRNA -
Supplementary Table 3 from Targeted Therapy for BRAFV600E Malignant Astrocytoma
Authors: Nicolaides Theodore P. , Li Huifang , Solomon David A. , Hariono Sujatmi , Hashizume Rintaro , Barkovich Krister , Baker Suzanne J. , Paugh Barbara S. , Jones Chris , Forshew Tim , Hindley Guy F. , Hodgson J. Graeme , Kim Jung-Sik , Rowitch David H. , Weiss William A. , Waldman Todd A. , James C. David
Published: April 2023

PDF file - 52K
Supplementary Figure 4 from Mutual Regulation between Raf/MEK/ERK Signaling and Y-Box–Binding Protein-1 Promotes Prostate Cancer Progression
Authors: Imada Kenjiro , Shiota Masaki , Kohashi Kenichi , Kuroiwa Kentaro , Song YooHyun , Sugimoto Masaaki , Naito Seiji , Oda Yoshinao
Published: April 2023

Supplementary Figure 4 - Supplementary Figure 4. YB-1 down-regulates HER2 expression but HER2 down-regulation does not affect the MEK/ERK pathway - PDF file 196K, (A) LNCaP and PC-3 cells were transfected with 40 nmol/L of the indicated siRNA, and incubated for 72 h. Whole-cell extracts were subjected to SDS-PAGE and western blotting analysis. (B) LNCaP and PC-3 cells were transfected with 40 nmol/L of the indicated siRNA and incubated for 72 h, and then quantitative RT-PCR was performed for HER2 and GAPDH. The target transcript expression was adjusted to GAPDH expression. Each target transcript expression level in cells transfected with control siRNA was defined as 1. Boxes, mean; bars, plus-minus s.d.; *P < 0.05. (C) LNCaP and PC-3 cells were transfected with 40 nmol/L of the indicated siRNA, incubated for 72 h, incubated with serum-free media for 24 h, and treated with 50 ng/mL of EGF for 30 min. Whole-cell extracts were subjected to SDS-PAGE and western blotting analysis
RT-PCR Results for FFPE ROS positive tumors from Analysis of Receptor Tyrosine Kinase ROS1-Positive Tumors in Non–Small Cell Lung Cancer: Identification of a FIG-ROS1 Fusion
Authors: Rimkunas Victoria M. , Crosby Katherine E. , Li Daiqiang , Hu Yerong , Kelly Meghan E. , Gu Ting-Lei , Mack Jennifer S. , Silver Matthew R. , Zhou Xinmin , Haack Herbert
Published: April 2023

Supplemental Table I RT-PCR Results for FFPE ROS1 positive tumors
Supplementary Figure 1 from FOXM1 Promotes the Warburg Effect and Pancreatic Cancer Progression via Transactivation of LDHA Expression
Authors: Cui Jiujie , Shi Min , Xie Dacheng , Wei Daoyan , Jia Zhiliang , Zheng Shaojiang , Gao Yong , Huang Suyun , Xie Keping
Published: April 2023

PDF file - 1072KB, Supplementary Fig. S1. Regulation of LDHA, LDHB and PGK-1 by FOXM1.
Supplementary Tables from Tumor-Reactive CD8+ T Cells in Metastatic Gastrointestinal Cancer Refractory to Chemotherapy
Authors: Turcotte Simon , Gros Alena , Tran Eric , Lee Chyi-Chia R. , Wunderlich John R. , Robbins Paul F. , Rosenberg Steven A.
Published: April 2023

PDF file 44K, Table S1 shows Class I HLA genotyping of TIL and cancer cell lines; Table S2 shows the recognition of autologous and allogeneic cell lines by TIL and TCR-transduced lymphocytes; Table S3 contains the TCR variable alpha and beta chains of CD8+ TIL clones reactive to autologous gastrointestinal tumors
Supplementary Figure 2 from Activity of the Hypoxia-Activated Prodrug, TH-302, in Preclinical Human Acute Myeloid Leukemia Models
Authors: Portwood Scott , Lal Deepika , Hsu Yung-Chun , Vargas Rodrigo , Johnson Megan K. , Wetzler Meir , Hart Charles P. , Wang Eunice S.
Published: April 2023

PDF file - 179K, Supplemental Figure 2. The number of hypoxic marrow cells correlate with AML burden.
Supplementary Figure 1 from Activity of the Hypoxia-Activated Prodrug, TH-302, in Preclinical Human Acute Myeloid Leukemia Models
Authors: Portwood Scott , Lal Deepika , Hsu Yung-Chun , Vargas Rodrigo , Johnson Megan K. , Wetzler Meir , Hart Charles P. , Wang Eunice S.
Published: April 2023

PDF file - 372K, Supplemental Figure 1. AML marrow progression is associated with increased hypoxia.
Supplementary Figures S1-S8 from A Poor Prognosis Subtype of HNSCC Is Consistently Observed across Methylome, Transcriptome, and miRNome Analysis
Authors: Jung Alain C. , Job Sylvie , Ledrappier Sonia , Macabre Christine , Abecassis Joseph , de Reyniès Aurélien , Wasylyk Bohdan
Published: April 2023

Supplementary Figures S1-S8 - PDF file 275K, This files contains the Supplementary Figures S1-S8. The contents are: Figure S1: Venn diagram showing the overlap between patients analyzed at the level of the genome, transcriptome, methylome and miRNome. Figure S2: Metastasis free survival curves of the predicted R1 subgroup (A) and the predicted Me.1 and Me.2+3 (C) clusters for the methylation data for 101 independent patient samples and on the R1 subgroup (B) and the T.1-3 clusters (D) for gene expression data for 44 independent patient samples from Cohen et al. Figure S3: Metastasis free survival curves of the three unsupervised clusters vMe.1-3 generated by RPMM using the methylation validation data. Figure S4: Box-and-whisker plots of the expression of the AIM2, KRT16, DSG3, SFRP1 and Col9A3 mRNAs, as well as miR-345 and miR-1, measured by qRT-PCR on RNA extracts from R1 and non-R1 tumor samples. Figure S5: Evaluation of the methylation levels of candidate CpG islands. Figure S6: Combined Bisulfite Restriction Analysis (COBRA) of the DNA amplicons obtained with the GRP55 primers on bisulfite-converted DNA from the six R1 and four non-R1 samples. Figure S7: Pangenomic profiles of the R1 subgroup and of the other samples. Figure S8: Chi2 p values of the comparison of gains (red) and losses (green) between R1 and the other samples
Supplementary Figure S2 from Molecular Imaging of Death Receptor 5 Occupancy and Saturation Kinetics In Vivo by Humanized Monoclonal Antibody CS-1008
Authors: Burvenich Ingrid J.G. , Lee Fook T. , Cartwright Glenn A. , O'Keefe Graeme J. , Makris Dahna , Cao Diana , Gong Sylvia , Chueh Anderly C. , Mariadason John M. , Brechbiel Martin W. , Beckman Robert A. , Fujiwara Kosaku , von Roemeling Reinhard , Scott Andrew M.
Published: April 2023

Supplementary Figure S2 - PDF file 357K, TUNEL assay for apoptosis. A, TACS-Nuclease treated positive control of a COLO 205 tumor section; B, unlabeled experimental negative control; C, a characteristic area for COLO 205 tumors treated with 0.2 mg/kg CS-1008; D, a characteristic area for COLO 205 tumors treated with 10 mg/kg CS-1008. Magnification: x 200
Supplementary Table from PIK3CA and AKT1 Mutations Have Distinct Effects on Sensitivity to Targeted Pathway Inhibitors in an Isogenic Luminal Breast Cancer Model System
Authors: Beaver Julia A. , Gustin John P. , Yi Kyung H. , Rajpurohit Anandita , Thomas Matthew , Gilbert Samuel F. , Rosen D. Marc , Ho Park Ben , Lauring Josh
Published: April 2023

PDF file, 55K, Supplementary table of antibodies used for western blotting.
Supplementary Methods from Tumor Imaging and Interferon-γ–Inducible Protein-10 Gene Transfer Using a Highly Efficient Transferrin-Conjugated Liposome System in Mice
Authors: Zhuo Huiqin , Peng Yi , Yao Qin , Zhou Nuo , Zhou Sufang , He Jian , Fang Yuan , Li Xi , Jin Hongwei , Lu Xiaoling , Zhao Yongxiang
Published: April 2023

Supplementary Methods - PDF file 121K, Supplementary Methods
Supplementary Figure 1 from Rb Loss Is Characteristic of Prostatic Small Cell Neuroendocrine Carcinoma
Authors: Tan Hsueh-Li , Sood Akshay , Rahimi Hameed A. , Wang Wenle , Gupta Nilesh , Hicks Jessica , Mosier Stacy , Gocke Christopher D. , Epstein Jonathan I. , Netto George J. , Liu Wennuan , Isaacs William B. , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

PDF file - 284K, Supplementary Figure S1: (A) High grade prostatic adenocarcinoma with neuroendocrine differentiation by diffuse expression of immunohistochemical markers. This case shows lack of small cell differentiation by hematoxylin and eosin staining (left panel, 200x and inset) based on presence of prominent nucleoli and abundant cytoplasms, without nuclear molding. However, neuroendocrine immunohistochemical markers are diffusely positive (middle panel). Rb protein is present in this case (right panel). (B) Large cell neuroendocrine prostate carcinoma (LCNEC) shows cords and trabeculae of cells, but with abundant pink cytoplasm, which is inconsistent with a diagnosis of small cell carcinoma (left panel and inset). Neuroendocrine markers are diffusely positive (middle panel), however Rb protein is preserved (right panel). (C) Castrate resistant prostate cancer metastasis from autopsy study that has been previously reported (reference 30). This liver metastasis from case 30 (Supplementary Table 1) is heterogeneously positive for Rb protein, with one nodule staining positive (lower left) and nearby nodules staining negative, despite Rb protein in endothelial cells (arrowhead) as an internal positive control. Additional liver and bone tumors from this patient were found to have homozygous deletion of RB1, suggesting inter-metastatic heterogeneity in RB1 status.
Supplementary Tables 1-2 from Breast Cancer Index Identifies Early-Stage Estrogen Receptor–Positive Breast Cancer Patients at Risk for Early- and Late-Distant Recurrence
Authors: Zhang Yi , Schnabel Catherine A. , Schroeder Brock E. , Jerevall Piiha-Lotta , Jankowitz Rachel C. , Fornander Tommy , Stål Olle , Brufsky Adam M. , Sgroi Dennis , Erlander Mark G.
Published: April 2023

Supplementary Tables 1-2 - PDF file 101K, Supplementary Table 1. Kaplan-Meier estimates of overall distant recurrence free survival (DRFS) for 3 BCI risk groups in Stockholm TAM-treated and Multi-institutional cohorts. Supplementary Table 2. Overall distant recurrence: Univariate and multivariate Cox model analysis after stepwise variable selection by AIC of likelihood of overall distant recurrence in Stockholm TAM and Multi-institutional cohorts for all ER+ and ER+, HER2- patients
Supplementary Table 1 from LINE-1 Hypomethylation, DNA Copy Number Alterations, and CDK6 Amplification in Esophageal Squamous Cell Carcinoma
Authors: Baba Yoshifumi , Watanabe Masayuki , Murata Asuka , Shigaki Hironobu , Miyake Keisuke , Ishimoto Takatsugu , Iwatsuki Masaaki , Iwagami Shiro , Yoshida Naoya , Oki Eiji , Sakamaki Kentaro , Nakao Mitsuyoshi , Baba Hideo
Published: April 2023

PDF file - 40K, Clinical and pathological characteristics of 6 cases selected for CGH array.