bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S3 from Molecular Targeted Therapies Elicit Concurrent Apoptotic and GSDME-Dependent Pyroptotic Tumor Cell Death
Authors: Lu Haijiao , Zhang Shengzhe , Wu Jie , Chen Minjiang , Cai Mei-Chun , Fu Yujie , Li Wenfeng , Wang Jing , Zhao Xiaojing , Yu Zhuang , Ma Pengfei , Zhuang Guanglei
Published: April 2023

A. TCGA pan-cancer genomic analysis of all the gasdermin family members. B. DFNA5 gene expression in TCGA lung adenocarcinomas classified by indicated genetic alterations. C. Western blot analysis of indicated proteins in nucleus, cytosol, mitochondria-enriched membrane, and cytoskeleton fractions prepared from A549, PC9 and NCI-H3122 cells. D. Immunofluorescent staining of GSDME (green), F-actin (red) and nuclear 4',6-diamidino-2-phenylindole (DAPI; blue) in A549, PC9 and NCI-H3122 cells.
Table S1 from A Novel TGFβ Trap Blocks Chemotherapeutics-Induced TGFβ1 Signaling and Enhances Their Anticancer Activity in Gynecologic Cancers
Authors: Zhu Haiyan , Gu Xiang , Xia Lu , Zhou You , Bouamar Hakim , Yang Junhua , Ding Xiaofei , Zwieb Christian , Zhang Jianan , Hinck Andrew P. , Sun Lu-Zhe , Zhu Xueqiong
Published: April 2023

Supplementary Table 1. Differentially Expressed Probesets comparing samples from ovarian cancer patients with chemotherapy treatment to samples without chemotherapy treatment
Figure S1-5 from A Novel TGFβ Trap Blocks Chemotherapeutics-Induced TGFβ1 Signaling and Enhances Their Anticancer Activity in Gynecologic Cancers
Authors: Zhu Haiyan , Gu Xiang , Xia Lu , Zhou You , Bouamar Hakim , Yang Junhua , Ding Xiaofei , Zwieb Christian , Zhang Jianan , Hinck Andrew P. , Sun Lu-Zhe , Zhu Xueqiong
Published: April 2023

Supplementary Figure 1. Chemotherapy-associated differentially expressed genes that are regulated by TGF-β. Supplementary Figure 2. Density analysis of P-Smad2 and P-Smad3 bands in Figure 3. The density of corresponding total Smad2 (T-Smad2) and total Smad3 (T-Smad3) bands were used for normalization. Supplementary Figure 3. HeLa and C-41cellswere treated with TGF-β1 (80pM), RER (40nM) or HTS (100nM) alone or in combination for 6 h. The cell extracts were used for Western immunoblotting analysis to measure the levels of P-Smad2, P-Smad3, T-Smad2, and T-Smad3 with their respective antibodies. Supplementary Figure 4. Forward and side scatter (FSC and SSC) density plots for excluding dead cells and debris. Supplementary Figure 5. OVCAR-3 cells were treated with TGF-β1 (80pM), cisplatin (1μM), HTS (100nM), or RER (40nM) alone or in combination for 4 days.
Supplementary Table 2 from Pericytes Elicit Resistance to Vemurafenib and Sorafenib Therapy in Thyroid Carcinoma via the TSP-1/TGFβ1 Axis
Authors: Prete Alessandro , Lo Agnes S. , Sadow Peter M. , Bhasin Swati S. , Antonello Zeus A. , Vodopivec Danica M. , Ullas Soumya , Sims Jennifer N. , Clohessy John , Dvorak Ann M. , Sciuto Tracey , Bhasin Manoj , Murphy-Ullrich Joanne E. , Lawler Jack , Karumanchi S. Ananth , Nucera Carmelo
Published: April 2023

Suppl. Table 2. Log2 Fold Changes (FC) of some genes differentially expressed in BRAFV600E-PTC vs BRAFWT-PTC
Supplementary Table 1 from Pericytes Elicit Resistance to Vemurafenib and Sorafenib Therapy in Thyroid Carcinoma via the TSP-1/TGFβ1 Axis
Authors: Prete Alessandro , Lo Agnes S. , Sadow Peter M. , Bhasin Swati S. , Antonello Zeus A. , Vodopivec Danica M. , Ullas Soumya , Sims Jennifer N. , Clohessy John , Dvorak Ann M. , Sciuto Tracey , Bhasin Manoj , Murphy-Ullrich Joanne E. , Lawler Jack , Karumanchi S. Ananth , Nucera Carmelo
Published: April 2023

Supplementary Table 1 Antibodies list and experimental conditions for immunohistochemistry (IHC)
Supplementary from Identification of Novel Pathways of Osimertinib Disposition and Potential Implications for the Outcome of Lung Cancer Therapy
Authors: MacLeod A. Kenneth , Lin De , Huang Jeffrey T.–J. , McLaughlin Lesley A. , Henderson Colin J. , Wolf C. Roland
Published: April 2023

Supplementary Table 1: MRM parameters for osimertinib, metabolites and internal standard. Supplementary Table 2. Correlation coefficients for formation of osimertinib metabolites. Supplementary Table 3. Metabolic phenotyping of osimertinib in pooled HLM. Supplementary Table 4. Apparent kinetic parameters of osimertinib metabolite formation by CYP1A1 and CYP3A4. Supplementary Table 5. PK parameters of osimertinib in WT and hCYP2D6*2 mice. Supplementary Table 6. PK parameters of osimertinib in hPXR/hCAR/h3A4 and hPXR/hCAR/3aKO mice. Supplementary Table 7. PK parameters of osimertinib in h1A1/1A2 and 1aKO mice. Supplementary Figure 1. Metabolite identification. Supplementary Figure 2. Stress reporter activation by osimertinib.
Supplementary Data from Long Noncoding RNA MPRL Promotes Mitochondrial Fission and Cisplatin Chemosensitivity via Disruption of Pre-miRNA Processing
Authors: Tian Tian , Lv Xiaobin , Pan Guokai , Lu Yingjuan , Chen Weixiong , He Wang , Lei Xinyuan , Zhang Hanqing , Liu Mo , Sun Sheng , Ou Zhanpeng , Lin Xinyu , Cai Lei , He Lile , Tu Zhiming , Wang Xinhui , Tannous Bakhos A. , Ferrone Soldano , Li Jinsong , Fan Song
Published: April 2023

Supplementary Materials and Methods,Supplementary Figures and Supplementary Tables.
Table S1 from An Effective Epigenetic-PARP Inhibitor Combination Therapy for Breast and Ovarian Cancers Independent of BRCA Mutations
Authors: Pulliam Nicholas , Fang Fang , Ozes Ali R. , Tang Jessica , Adewuyi Adeoluwa , Keer Harold , Lyons John , Baylin Stephen B. , Matei Daniela , Nakshatri Harikrishna , Rassool Feyruz V. , Miller Kathy D. , Nephew Kenneth P.
Published: April 2023

Description of cell lines used in the study
Supplementary tables from Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition
Authors: Chen Xian , Low Kwang-Huei , Alexander Angela , Jiang Yufeng , Karakas Cansu , Hess Kenneth R. , Carey Jason P.W. , Bui Tuyen N. , Vijayaraghavan Smruthi , Evans Kurt W. , Yi Min , Ellis D. Christian , Cheung Kwok-Leung , Ellis Ian O. , Fu Siqing , Meric-Bernstam Funda , Hunt Kelly K. , Keyomarsi Khandan
Published: April 2023

The file contains a total of 12 supplementary figures that were referred to in the main text.
Supplementary Methods from Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition
Authors: Chen Xian , Low Kwang-Huei , Alexander Angela , Jiang Yufeng , Karakas Cansu , Hess Kenneth R. , Carey Jason P.W. , Bui Tuyen N. , Vijayaraghavan Smruthi , Evans Kurt W. , Yi Min , Ellis D. Christian , Cheung Kwok-Leung , Ellis Ian O. , Fu Siqing , Meric-Bernstam Funda , Hunt Kelly K. , Keyomarsi Khandan
Published: April 2023

The file contains all the methods pertaining to the data presented in the supplemental figures.
Materials and Methods from An Effective Epigenetic-PARP Inhibitor Combination Therapy for Breast and Ovarian Cancers Independent of BRCA Mutations
Authors: Pulliam Nicholas , Fang Fang , Ozes Ali R. , Tang Jessica , Adewuyi Adeoluwa , Keer Harold , Lyons John , Baylin Stephen B. , Matei Daniela , Nakshatri Harikrishna , Rassool Feyruz V. , Miller Kathy D. , Nephew Kenneth P.
Published: April 2023

Materials and Methods
redacted protocol from Safety and Antitumor Activity of Pembrolizumab in Patients with Estrogen Receptor–Positive/Human Epidermal Growth Factor Receptor 2–Negative Advanced Breast Cancer
Authors: Rugo Hope S. , Delord Jean-Pierre , Im Seock-Ah , Ott Patrick A. , Piha-Paul Sarina A. , Bedard Philippe L. , Sachdev Jasgit , Tourneau Christophe Le , van Brummelen Emilie M.J. , Varga Andrea , Salgado Roberto , Loi Sherene , Saraf Sanatan , Pietrangelo Dina , Karantza Vassiliki , Tan Antoinette R.
Published: April 2023

redacted protocol
Figure S13-S16 from Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition
Authors: Chen Xian , Low Kwang-Huei , Alexander Angela , Jiang Yufeng , Karakas Cansu , Hess Kenneth R. , Carey Jason P.W. , Bui Tuyen N. , Vijayaraghavan Smruthi , Evans Kurt W. , Yi Min , Ellis D. Christian , Cheung Kwok-Leung , Ellis Ian O. , Fu Siqing , Meric-Bernstam Funda , Hunt Kelly K. , Keyomarsi Khandan
Published: April 2023

supplementary figure 13-16
supplementary data from Clinical Relevance and Suppressive Capacity of Human Myeloid-Derived Suppressor Cell Subsets
Authors: Lang Stephan , Bruderek Kirsten , Kaspar Cordelia , Höing Benedikt , Kanaan Oliver , Dominas Nina , Hussain Timon , Droege Freya , Eyth Christian , Hadaschik Boris , Brandau Sven
Published: April 2023

includes two suppl figures, suppl legends and suppl methods
Figure S1-S6 from Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition
Authors: Chen Xian , Low Kwang-Huei , Alexander Angela , Jiang Yufeng , Karakas Cansu , Hess Kenneth R. , Carey Jason P.W. , Bui Tuyen N. , Vijayaraghavan Smruthi , Evans Kurt W. , Yi Min , Ellis D. Christian , Cheung Kwok-Leung , Ellis Ian O. , Fu Siqing , Meric-Bernstam Funda , Hunt Kelly K. , Keyomarsi Khandan
Published: April 2023

supplementary figure 1-6
Supplementary Figure and Supplementary Tables from Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome
Authors: Forget Marie-Andrée , Haymaker Cara , Hess Kenneth R. , Meng Yuzhong Jeff , Creasy Caitlin , Karpinets Tatiana , Fulbright Orenthial J. , Roszik Jason , Woodman Scott E. , Kim Young Uk , Sakellariou-Thompson Donastas , Bhatta Ankit , Wahl Arely , Flores Esteban , Thorsen Shawne T. , Tavera René J. , Ramachandran Renjith , Gonzalez Audrey M. , Toth Christopher L. , Wardell Seth , Mansaray Rahmatu , Patel Vruti , Carpio Destiny Joy , Vaughn Carol , Farinas Chantell M. , Velasquez Portia G. , Hwu Wen-Jen , Patel Sapna P. , Davies Michael A. , Diab Adi , Glitza Isabella C. , Tawbi Hussein , Wong Michael K. , Cain Suzanne , Ross Merrick I. , Lee Jeffrey E. , Gershenwald Jeffrey E. , Lucci Anthony , Royal Richard , Cormier Janice N. , Wargo Jennifer A. , Radvanyi Laszlo G. , Torres-Cabala Carlos A. , Beroukhim Rameen , Hwu Patrick , Amaria Rodabe N. , Bernatchez Chantale
Published: April 2023

Supplementary figures and tables
Supplementary figure 4 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients
Authors: Khanna Swati , Graef Suzanne , Mussai Francis , Thomas Anish , Wali Neha , Yenidunya Bahar Guliz , Yuan Constance , Morrow Betsy , Zhang Jingli , Korangy Firouzeh , Greten Tim F. , Steinberg Seth M. , Stetler-Stevenson Maryalice , Middleton Gary , De Santo Carmela , Hassan Raffit
Published: April 2023

GM-CSF drives ROS release in granulocytes
Supplementary Table S1 from Comparison of Biomarker Assays for EGFR: Implications for Precision Medicine in Patients with Glioblastoma
Authors: Lassman Andrew B. , Roberts-Rapp Lisa , Sokolova Irina , Song Minghao , Pestova Ekaterina , Kular Rupinder , Mullen Carolyn , Zha Zheng , Lu Xin , Gomez Erica , Bhathena Anahita , Maag David , Kumthekar Priya , Gan Hui K. , Scott Andrew M. , Guseva Maria , Holen Kyle D. , Ansell Peter J. , van den Bent Martin J.
Published: April 2023

Supplementary Table S1. Data for tumor samples and all assays performed.
Supplementary figure 2 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients
Authors: Khanna Swati , Graef Suzanne , Mussai Francis , Thomas Anish , Wali Neha , Yenidunya Bahar Guliz , Yuan Constance , Morrow Betsy , Zhang Jingli , Korangy Firouzeh , Greten Tim F. , Steinberg Seth M. , Stetler-Stevenson Maryalice , Middleton Gary , De Santo Carmela , Hassan Raffit
Published: April 2023

Mesothelioma granulocytes suppress T cell activation
Supplementary figure 1 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients
Authors: Khanna Swati , Graef Suzanne , Mussai Francis , Thomas Anish , Wali Neha , Yenidunya Bahar Guliz , Yuan Constance , Morrow Betsy , Zhang Jingli , Korangy Firouzeh , Greten Tim F. , Steinberg Seth M. , Stetler-Stevenson Maryalice , Middleton Gary , De Santo Carmela , Hassan Raffit
Published: April 2023

Arginase activity does not drive immunosuppressive granulocyte function
Supporting information from A Gallium-67/68–Labeled Antibody Fragment for Immuno-SPECT/PET Shows Low Renal Radioactivity Without Loss of Tumor Uptake
Authors: Uehara Tomoya , Yokoyama Miki , Suzuki Hiroyuki , Hanaoka Hirofumi , Arano Yasushi
Published: April 2023

Table S1. Biodistribution of radioactivity in mice after injection of 67Ga-NOTA-Fab, 67Ga-NOTA-MI-Fab and 67Ga-NOTA-MVK-Fab. Table S2. Biodistribution of radioactivity in nude mice bearing SY cells after 3 h injection of 67Ga-NOTA-Fab, 67Ga-NOTA-MI-Fab and 67Ga-NOTA-MVK-Fab. Table S3. Stability of 67Ga-labeled Fab fragments in murine serum. Scheme S1. Synthetic procedure for NOTA-MVK-Mal. Scheme S2. Synthetic procedure for NOTA-MVK-Bzo.
Table S1 from Rapid Clearance Profile of Plasma Circulating Tumor HPV Type 16 DNA during Chemoradiotherapy Correlates with Disease Control in HPV-Associated Oropharyngeal Cancer
Authors: Chera Bhishamjit S. , Kumar Sunil , Beaty Brian T. , Marron David , Jefferys Stuart , Green Rebecca , Goldman Emily C. , Amdur Robert , Sheets Nathan , Dagan Roi , Hayes D. Neil , Weiss Jared , Grilley-Olson Juneko E. , Zanation Adam , Hackman Trevor , Blumberg Jeffrey M. , Patel Samip , Weissler Mark , Tan Xianming M. , Parker Joel S. , Mendenhall William , Gupta Gaorav P.
Published: April 2023

Primers, probes, plasmids and gBlocks used in the HPV assay
Supplementary Table S4 from Impact of Emergent Circulating Tumor DNA RAS Mutation in Panitumumab-Treated Chemoresistant Metastatic Colorectal Cancer
Authors: Kim Tae Won , Peeters Marc , Thomas Anne , Gibbs Peter , Hool Kristina , Zhang Jianqi , Ang Agnes Lee , Bach Bruce Allen , Price Timothy
Published: April 2023

Five patients who were RAS mutant at baseline reverted to wild-type at SFU
Figure S3 from Rapid Clearance Profile of Plasma Circulating Tumor HPV Type 16 DNA during Chemoradiotherapy Correlates with Disease Control in HPV-Associated Oropharyngeal Cancer
Authors: Chera Bhishamjit S. , Kumar Sunil , Beaty Brian T. , Marron David , Jefferys Stuart , Green Rebecca , Goldman Emily C. , Amdur Robert , Sheets Nathan , Dagan Roi , Hayes D. Neil , Weiss Jared , Grilley-Olson Juneko E. , Zanation Adam , Hackman Trevor , Blumberg Jeffrey M. , Patel Samip , Weissler Mark , Tan Xianming M. , Parker Joel S. , Mendenhall William , Gupta Gaorav P.
Published: April 2023

Baseline ctHPV16DNA levels stratified by AJCC 8th edition N staging
Figure S2 from Rapid Clearance Profile of Plasma Circulating Tumor HPV Type 16 DNA during Chemoradiotherapy Correlates with Disease Control in HPV-Associated Oropharyngeal Cancer
Authors: Chera Bhishamjit S. , Kumar Sunil , Beaty Brian T. , Marron David , Jefferys Stuart , Green Rebecca , Goldman Emily C. , Amdur Robert , Sheets Nathan , Dagan Roi , Hayes D. Neil , Weiss Jared , Grilley-Olson Juneko E. , Zanation Adam , Hackman Trevor , Blumberg Jeffrey M. , Patel Samip , Weissler Mark , Tan Xianming M. , Parker Joel S. , Mendenhall William , Gupta Gaorav P.
Published: April 2023

Multiplexed dPCR assay for non-16 HPV strains
eFigure 2 supplemental from A Phase I Clinical Trial of AZD1775 in Combination with Neoadjuvant Weekly Docetaxel and Cisplatin before Definitive Therapy in Head and Neck Squamous Cell Carcinoma
Authors: Méndez Eduardo , Rodriguez Cristina P. , Kao Michael C. , Raju Sharat , Diab Ahmed , Harbison R. Alex , Konnick Eric Q. , Mugundu Ganesh M. , Santana-Davila Rafael , Martins Renato , Futran Neal D. , Chow Laura Q.M.
Published: April 2023

Correlative translational pharmacodynamics data revised
Supplementary Data from Nivolumab in Patients with Recurrent or Metastatic Squamous Cell Carcinoma of the Head and Neck: Efficacy and Safety in CheckMate 141 by Prior Cetuximab Use
Authors: Ferris Robert L. , Licitra Lisa , Fayette Jerome , Even Caroline , Blumenschein George , Harrington Kevin J. , Guigay Joel , Vokes Everett E. , Saba Nabil F. , Haddad Robert , Ramkumar Shanmugasundaram , Russell Jeffery , Brossart Peter , Tahara Makoto , Colevas A. Dimitrios , Concha-Benavente Fernando , Lynch Mark , Li Li , Gillison Maura L.
Published: April 2023

Tables S1-S5, Figures S1, S2 Supplementary Table S1. Summary of prior systemic cancer therapies in {greater than or equal to}2% of patients with prior cetuximab exposure Supplementary Table S2. Summary of prior systemic cancer therapies in {greater than or equal to}2% of patients without prior cetuximab exposure Supplementary Table S3. Summary of prior cetuximab-containing regimens in all treated patients Supplementary Table S4. Treatment-related adverse events by prior cetuximab exposure reported in {greater than or equal to}10% of patients in any subgroup Supplementary Table S5. Select treatment-related adverse events by prior cetuximab exposure Supplementary Figure S1. CONSORT diagram. Supplementary Figure S2. Best reduction from baseline in target lesions among patients treated with nivolumab.
eFigure 1 supplemental from A Phase I Clinical Trial of AZD1775 in Combination with Neoadjuvant Weekly Docetaxel and Cisplatin before Definitive Therapy in Head and Neck Squamous Cell Carcinoma
Authors: Méndez Eduardo , Rodriguez Cristina P. , Kao Michael C. , Raju Sharat , Diab Ahmed , Harbison R. Alex , Konnick Eric Q. , Mugundu Ganesh M. , Santana-Davila Rafael , Martins Renato , Futran Neal D. , Chow Laura Q.M.
Published: April 2023

Study Schema Supplemental figure 1 (no revisions, reuploaded)
Supplementary Figure 1 from Comprehensive Molecular Profiling of Intrahepatic and Extrahepatic Cholangiocarcinomas: Potential Targets for Intervention
Authors: Lowery Maeve A. , Ptashkin Ryan , Jordan Emmet , Berger Michael F. , Zehir Ahmet , Capanu Marinela , Kemeny Nancy E. , O'Reilly Eileen M. , El-Dika Imane , Jarnagin William R. , Harding James J. , D'Angelica Michael I. , Cercek Andrea , Hechtman Jaclyn F. , Solit David B. , Schultz Nikolaus , Hyman David M. , Klimstra David S. , Saltz Leonard B. , Abou-Alfa Ghassan K.
Published: April 2023

Overall survival from diagnosis with advanced disease by KRAS, ERBB2 and CDKN2A/B status
Supplementary tables from Targeting Galectin-1 Impairs Castration-Resistant Prostate Cancer Progression and Invasion
Authors: Shih Tsung-Chieh , Liu Ruiwu , Wu Chun-Te , Li Xiaocen , Xiao Wenwu , Deng Xiaojun , Kiss Sophie , Wang Ting , Chen Xiao-Jia , Carney Randy , Kung Hsing-Jien , Duan Yong , Ghosh Paramita M. , Lam Kit S.
Published: April 2023

Supplementary tables
Supplementary materials and methods from Targeting Galectin-1 Impairs Castration-Resistant Prostate Cancer Progression and Invasion
Authors: Shih Tsung-Chieh , Liu Ruiwu , Wu Chun-Te , Li Xiaocen , Xiao Wenwu , Deng Xiaojun , Kiss Sophie , Wang Ting , Chen Xiao-Jia , Carney Randy , Kung Hsing-Jien , Duan Yong , Ghosh Paramita M. , Lam Kit S.
Published: April 2023

Supplementary materials and methods
Supplementary Figures from Targeting Galectin-1 Impairs Castration-Resistant Prostate Cancer Progression and Invasion
Authors: Shih Tsung-Chieh , Liu Ruiwu , Wu Chun-Te , Li Xiaocen , Xiao Wenwu , Deng Xiaojun , Kiss Sophie , Wang Ting , Chen Xiao-Jia , Carney Randy , Kung Hsing-Jien , Duan Yong , Ghosh Paramita M. , Lam Kit S.
Published: April 2023

Supplementary Figures
Supplementary materials and methods from HERC3-Mediated SMAD7 Ubiquitination Degradation Promotes Autophagy-Induced EMT and Chemoresistance in Glioblastoma
Authors: Li Hong , Li Junjie , Chen Lei , Qi Songtao , Yu Shishi , Weng Zhijian , Hu Ziyou , Zhou Qiang , Xin Zong , Shi Linyong , Ma Liyi , Huang Annie , Lu Yuntao
Published: April 2023

Supplementary materials and methods
Figure S5 from HERC3-Mediated SMAD7 Ubiquitination Degradation Promotes Autophagy-Induced EMT and Chemoresistance in Glioblastoma
Authors: Li Hong , Li Junjie , Chen Lei , Qi Songtao , Yu Shishi , Weng Zhijian , Hu Ziyou , Zhou Qiang , Xin Zong , Shi Linyong , Ma Liyi , Huang Annie , Lu Yuntao
Published: April 2023

The biological function of HERC3 depends on the Smad7 protein level
Figure S4 from HERC3-Mediated SMAD7 Ubiquitination Degradation Promotes Autophagy-Induced EMT and Chemoresistance in Glioblastoma
Authors: Li Hong , Li Junjie , Chen Lei , Qi Songtao , Yu Shishi , Weng Zhijian , Hu Ziyou , Zhou Qiang , Xin Zong , Shi Linyong , Ma Liyi , Huang Annie , Lu Yuntao
Published: April 2023

The correlation of HERC3 expression to the clinical outcome of different molecular subtypes of GBM, and the Molecular features and TMZ sensitivity of malignant glioma cells
Supplementary Figure S1 from Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck
Authors: Lee Jong Woo , Parameswaran Janaki , Sandoval-Schaefer Teresa , Eoh Kyung Jin , Yang Dong-hua , Zhu Fang , Mehra Ranee , Sharma Roshan , Gaffney Stephen G. , Perry Elizabeth B. , Townsend Jeffrey P. , Serebriiskii Ilya G. , Golemis Erica A. , Issaeva Natalia , Yarbrough Wendell G. , Koo Ja Seok , Burtness Barbara
Published: April 2023

Supplementary Figure S1. Overview of the identified mutations in UNC7 HNSCC cell line by whole exome sequencing.
Supplementary Data from Deep Learning Predicts Lung Cancer Treatment Response from Serial Medical Imaging
Authors: Xu Yiwen , Hosny Ahmed , Zeleznik Roman , Parmar Chintan , Coroller Thibaud , Franco Idalid , Mak Raymond H. , Aerts Hugo J.W.L.
Published: April 2023

Supplementary Figures, Data, and Results Figure S1: Patient Missed Scans. Figure S2: Overall Survival Prediction Performance. Figure S3: Performance Deep Learning Biomarkers with Increase in Number of Time-points. Table S1: Event percentages for overall survival and prognostic factors for the definitive radiation therapy training/validation and independent test set. Table S2: Patient and treatment characteristics of Dataset A. Median (range) is reported for continuous and counts (percentage) for categorical variables for the training and testing cohorts with not significant differences found with the Wilcoxon's Rank Sums test. Table S3: AUC values for the clinical model and pre-treatment only images, with regards to predictions of overall survival and prognostic factors.
Figure S3 from Deep Learning Predicts Lung Cancer Treatment Response from Serial Medical Imaging
Authors: Xu Yiwen , Hosny Ahmed , Zeleznik Roman , Parmar Chintan , Coroller Thibaud , Franco Idalid , Mak Raymond H. , Aerts Hugo J.W.L.
Published: April 2023

Performance Deep Learning Biomarkers with Increase in Number of Time-points. AUC values were evaluated on an independent test set from the deep learning models for one-year survival, distant metastasis, progression and locoregional recurrence (LRR)-free status. Values were significantly separated with the Wilcoxon rank-sums test (p < 0.05) in Dataset A, the definitive radiation therapy cohort with the input of the pre-treatment scan along with the addition of one, two or three follow-up scans at one, three and six months follow-up.
Supplementary Data 2 from A Survey on Data Reproducibility and the Effect of Publication Process on the Ethical Reporting of Laboratory Research
Authors: Boulbes Delphine R. , Costello Tracy , Baggerly Keith , Fan Fan , Wang Rui , Bhattacharya Rajat , Ye Xiangcang , Ellis Lee M.
Published: April 2023

Answers to Question 28. All comments provided in the â€œfree commentsâ€� section at the end of the survey.
Supplementary Data 1 from A Survey on Data Reproducibility and the Effect of Publication Process on the Ethical Reporting of Laboratory Research
Authors: Boulbes Delphine R. , Costello Tracy , Baggerly Keith , Fan Fan , Wang Rui , Bhattacharya Rajat , Ye Xiangcang , Ellis Lee M.
Published: April 2023

Raw data from our survey. Tab 1. All survey responses, including date of response. Tab 2. Survey responses from eligible respondents only (graduate students or postdoctoral fellows performing bench research). Tab 3. Extrapolated results from those who answered â€œotherâ€� to certain questions. Tab 4. Responses compiled in bar graphs.
Supplementary Data from Combination of Trastuzumab Emtansine and Stereotactic Radiosurgery Results in High Rates of Clinically Significant Radionecrosis and Dysregulation of Aquaporin-4
Authors: Stumpf Priscilla K. , Cittelly Diana M. , Robin Tyler P. , Carlson Julie A. , Stuhr Kelly A. , Contreras-Zarate Maria Jose , Lai Steven , Ormond D. Ryan , Rusthoven Chad G. , Gaspar Laurie E. , Rabinovitch Rachel , Kavanagh Brian D. , Liu Arthur , Diamond Jennifer R. , Kabos Peter , Fisher Christine M.
Published: April 2023

Chemotherapy effects on astrocytes
Supplementary Figure 3 from The Dual PI3K/mTOR Pathway Inhibitor GDC-0084 Achieves Antitumor Activity in PIK3CA-Mutant Breast Cancer Brain Metastases
Authors: Ippen Franziska M. , Alvarez-Breckenridge Christopher A. , Kuter Benjamin M. , Fink Alexandria L. , Bihun Ivanna V. , Lastrapes Matthew , Penson Tristan , Schmidt Stephen P. , Wojtkiewicz Gregory R. , Ning Jianfang , Subramanian Megha , Giobbie-Hurder Anita , Martinez-Lage Maria , Carter Scott L. , Cahill Daniel P. , Wakimoto Hiroaki , Brastianos Priscilla K.
Published: April 2023

Photomicrographs illustrating p-MEK1/2 (Ser221) and p-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) expression in mouse brains harboring either JIMT-1 BR-3 or MDA-MB-231 BrM2 intracranial tumors, stratified by treatment with sham or GDC-0084.
Supplementary Figure 2 from The Dual PI3K/mTOR Pathway Inhibitor GDC-0084 Achieves Antitumor Activity in PIK3CA-Mutant Breast Cancer Brain Metastases
Authors: Ippen Franziska M. , Alvarez-Breckenridge Christopher A. , Kuter Benjamin M. , Fink Alexandria L. , Bihun Ivanna V. , Lastrapes Matthew , Penson Tristan , Schmidt Stephen P. , Wojtkiewicz Gregory R. , Ning Jianfang , Subramanian Megha , Giobbie-Hurder Anita , Martinez-Lage Maria , Carter Scott L. , Cahill Daniel P. , Wakimoto Hiroaki , Brastianos Priscilla K.
Published: April 2023

GDC-0084-induced changes in cell cycle in the PIK3CA-mutant cell line MDA-MB-361 and in the PIK3CA-wildtype cell line BS-004
Supplementary Methods from Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples
Authors: Verlaat Wina , Snoek Barbara C. , Heideman Daniëlle A.M. , Wilting Saskia M. , Snijders Peter J.F. , Novianti Putri W. , van Splunter Annina P. , Peeters Carel F.W. , van Trommel Nienke E. , Massuger Leon F.A.G. , Bekkers Ruud L.M. , Melchers Willem J.G. , van Kemenade Folkert J. , Berkhof Johannes , van de Wiel Mark A. , Meijer Chris J.L.M. , Steenbergen Renske D.M.
Published: April 2023

Further detailed description of methods
Supplementary Figures and Tables from Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples
Authors: Verlaat Wina , Snoek Barbara C. , Heideman Daniëlle A.M. , Wilting Saskia M. , Snijders Peter J.F. , Novianti Putri W. , van Splunter Annina P. , Peeters Carel F.W. , van Trommel Nienke E. , Massuger Leon F.A.G. , Bekkers Ruud L.M. , Melchers Willem J.G. , van Kemenade Folkert J. , Berkhof Johannes , van de Wiel Mark A. , Meijer Chris J.L.M. , Steenbergen Renske D.M.
Published: April 2023

Supplementary Figure S1: Overview of study populations. Supplementary Figure S2: Correlation heatmap of all 72 hrHPV-positive self-samples analyzed by Infinium Methylation 450K Array. Supplementary Figure S3: The effect of informative co-data. Supplementary Figure S4: Approach to build a 3-gene methylation classifier applicable to both lavage and brush self-samples. Supplementary Figure S5: DNA methylation levels of all 28 methylation targets in hrHPV-positive lavage self-samples. Supplementary Figure S6: DNA methylation-positivity determined by the 3-gene methylation classifier. Supplementary Figure S7: Classification tree model for lavage self-samples. Supplementary Figure S8: Classification tree model for brush self-samples. Supplementary Figure S9: DNA methylation-positivity in hrHPV-positive self-samples from women with glandular lesions and cancer. Supplementary Figure S10: Predicted probabilities in self-samples from women with and without CIN3. Supplementary Figure S11: DNA methylation levels of ASCL1, LHX8 and ST6GALNAC5 in self-samples from women with HPV16 or with other hrHPV types (non-HPV16). Supplementary Table S1: Primers and probes used in multiplex qMSP. Supplementary Table S2: Logistic regression analysis results of the 3-gene methylation classifier for CIN3 detection in hrHPV-positive self-samples. Supplementary Table S3: The comparison of the performance of logistic regression and CART models.
Supplemental Figure 2 from A Phase I Trial of a Guadecitabine (SGI-110) and Irinotecan in Metastatic Colorectal Cancer Patients Previously Exposed to Irinotecan
Authors: Lee Valerie , Wang Judy , Zahurak Marianna , Gootjes Elske , Verheul Henk M. , Parkinson Rose , Kerner Zachary , Sharma Anup , Rosner Gary , De Jesus-Acosta Ana , Laheru Daniel , Le Dung T. , Oganesian Aram , Lilly Ellen , Brown Thomas , Jones Peter , Baylin Stephen , Ahuja Nita , Azad Nilofer
Published: April 2023

LINE1 changes in tumor CpG 1-3 on cycle 1 day 8 from baseline. LINE1 changes in tumor DNA in individual patient biopsy samples.
Supplemental Figure 1 from A Phase I Trial of a Guadecitabine (SGI-110) and Irinotecan in Metastatic Colorectal Cancer Patients Previously Exposed to Irinotecan
Authors: Lee Valerie , Wang Judy , Zahurak Marianna , Gootjes Elske , Verheul Henk M. , Parkinson Rose , Kerner Zachary , Sharma Anup , Rosner Gary , De Jesus-Acosta Ana , Laheru Daniel , Le Dung T. , Oganesian Aram , Lilly Ellen , Brown Thomas , Jones Peter , Baylin Stephen , Ahuja Nita , Azad Nilofer
Published: April 2023

LINE1 changes in circulating DNA CpG 1-3 as compared to baseline.
Supplemental Figure legends from Regulatory T Cells in Ovarian Cancer Are Characterized by a Highly Activated Phenotype Distinct from that in Melanoma
Authors: Toker Aras , Nguyen Linh T. , Stone Simone C. , Yang S.Y. Cindy , Katz Sarah Rachel , Shaw Patricia A. , Clarke Blaise A. , Ghazarian Danny , Al-Habeeb Ayman , Easson Alexandra , Leong Wey L. , McCready David R. , Reedijk Michael , Guidos Cynthia J. , Pugh Trevor J. , Bernardini Marcus Q. , Ohashi Pamela S.
Published: April 2023

Legends to supplemental figures 1-6
Figure S6 from Regulatory T Cells in Ovarian Cancer Are Characterized by a Highly Activated Phenotype Distinct from that in Melanoma
Authors: Toker Aras , Nguyen Linh T. , Stone Simone C. , Yang S.Y. Cindy , Katz Sarah Rachel , Shaw Patricia A. , Clarke Blaise A. , Ghazarian Danny , Al-Habeeb Ayman , Easson Alexandra , Leong Wey L. , McCready David R. , Reedijk Michael , Guidos Cynthia J. , Pugh Trevor J. , Bernardini Marcus Q. , Ohashi Pamela S.
Published: April 2023

Analysis of PD-1 expression by CD8 T cells
Figure S1 from Tracking Cell Transplants in Femoral Osteonecrosis with Magnetic Resonance Imaging: A Proof-of-Concept Study in Patients
Authors: Theruvath Ashok J. , Nejadnik Hossein , Muehe Anne M. , Gassert Felix , Lacayo Norman J. , Goodman Stuart B. , Daldrup-Link Heike E.
Published: April 2023

Figure S1 shows that quantity of transplanted cells may predict outcome of osteonecrosis.
Figure S5 from Regulatory T Cells in Ovarian Cancer Are Characterized by a Highly Activated Phenotype Distinct from that in Melanoma
Authors: Toker Aras , Nguyen Linh T. , Stone Simone C. , Yang S.Y. Cindy , Katz Sarah Rachel , Shaw Patricia A. , Clarke Blaise A. , Ghazarian Danny , Al-Habeeb Ayman , Easson Alexandra , Leong Wey L. , McCready David R. , Reedijk Michael , Guidos Cynthia J. , Pugh Trevor J. , Bernardini Marcus Q. , Ohashi Pamela S.
Published: April 2023

Analysis of Treg-hi and Treg-lo subpopulations by mass and flow cytometry
Supplementary Materials, Figures and Tables from A Multi-center Phase I Trial of Ipilimumab in Patients with Myelodysplastic Syndromes following Hypomethylating Agent Failure
Authors: Zeidan Amer M. , Knaus Hanna A. , Robinson Tara M. , Towlerton Andrea M.H. , Warren Edus H. , Zeidner Joshua F. , Blackford Amanda L. , Duffield Amy S. , Rizzieri David , Frattini Mark G. , Levy Yair M. , Schroeder Mark A. , Ferguson Anna , Sheldon Katherine E. , DeZern Amy E. , Gojo Ivana , Gore Steven D. , Streicher Howard , Luznik Leo , Smith B. Douglas
Published: April 2023

Supplementary Methods (Flow cytometry, cell sorting and TCR sequencing); Figure S1 shows Kaplan-Meir curve; Figure S2 shows absolute lymphocyte counts (ALC); Figure S3 shows differentiation of BM T cells; Figure S4 shows absolute numbers of ICOS+ T cells; Figure S5 shows ICOS expression in bone marrow T cells; Figure S6 shows CTLA-s and PD-1 expression; Figure S7 shows T-regulatory cells (Tregs); Figure S8 shows T cell receptor diversity; Figure S9 shows the top 20 most frequent T cell clones; Table S1 shows antibodies used for correlative studies; Table S2 shows immune related adverse events for each patient
Figure S3 from Regulatory T Cells in Ovarian Cancer Are Characterized by a Highly Activated Phenotype Distinct from that in Melanoma
Authors: Toker Aras , Nguyen Linh T. , Stone Simone C. , Yang S.Y. Cindy , Katz Sarah Rachel , Shaw Patricia A. , Clarke Blaise A. , Ghazarian Danny , Al-Habeeb Ayman , Easson Alexandra , Leong Wey L. , McCready David R. , Reedijk Michael , Guidos Cynthia J. , Pugh Trevor J. , Bernardini Marcus Q. , Ohashi Pamela S.
Published: April 2023

Analysis of CD27, CD28 and DNAM-1 expression by Treg cells
Table S2 from Phase I Study of Oncolytic Vaccinia Virus GL-ONC1 in Patients with Peritoneal Carcinomatosis
Authors: Lauer Ulrich M. , Schell Martina , Beil Julia , Berchtold Susanne , Koppenhöfer Ursula , Glatzle Jörg , Königsrainer Alfred , Möhle Robert , Nann Dominik , Fend Falko , Pfannenberg Christina , Bitzer Michael , Malek Nisar P.
Published: April 2023

Characterization of ascites sample contents based on cytological analyses (patient 01).
Figure S3 from Phase I Study of Oncolytic Vaccinia Virus GL-ONC1 in Patients with Peritoneal Carcinomatosis
Authors: Lauer Ulrich M. , Schell Martina , Beil Julia , Berchtold Susanne , Koppenhöfer Ursula , Glatzle Jörg , Königsrainer Alfred , Möhle Robert , Nann Dominik , Fend Falko , Pfannenberg Christina , Bitzer Michael , Malek Nisar P.
Published: April 2023

Cytological analyses of further study patients.
Figure S2 from Phase I Study of Oncolytic Vaccinia Virus GL-ONC1 in Patients with Peritoneal Carcinomatosis
Authors: Lauer Ulrich M. , Schell Martina , Beil Julia , Berchtold Susanne , Koppenhöfer Ursula , Glatzle Jörg , Königsrainer Alfred , Möhle Robert , Nann Dominik , Fend Falko , Pfannenberg Christina , Bitzer Michael , Malek Nisar P.
Published: April 2023

Inflammatory response following GL-ONC1 therapy.
Supplementary Figures from LIMS1 Promotes Pancreatic Cancer Cell Survival under Oxygen–Glucose Deprivation Conditions by Enhancing HIF1A Protein Translation
Authors: Huang Chongbiao , Li Yang , Li Zengxun , Xu Yang , Li Na , Ge Yi , Dong Jie , Chang Antao , Zhao Tiansuo , Wang Xiuchao , Wang Hongwei , Yang Shengyu , Xie Keping , Hao Jihui , Ren He
Published: April 2023

15 Supplementary Figures: Supplementary Figure S1. The expression and subcellular localization of LIMS1 in PDAC cell lines. Supplementary Figure S2. LIMS1 is overexpressed in esophageal carcinoma and negatively correlated with survival. Supplementary Figure S3. LIMS1 is overexpressed in lung adenocarcinoma and negatively correlated with survival. Supplementary Figure S4. LIMS1 had no effect on cell viability under normal culture condition. Supplementary Figure S5. LIMS1 facilitates glucose uptaking and surviving of esophageal carcinoma. Supplementary Figure S6. LIMS1 facilitates glucose uptaking and surviving of lung adenocarcinoma. Supplementary Figure S7. LIMS1 expression does not alter the half-life of HIF1A. Supplementary Figure S8. LIMS1 plays important roles in maintain the activation of AKT signaling. Supplementary Figure S9. Impact of altered expression of LIMS1 on tumorigenicity and therapeutic efficacy. Supplementary Figure S10. The effect of altered LIMS1 expression on extracellular acidification. Supplementary Figure S11. LIMS1 expression level positively correlates with glucose uptaking in PETCT scanning of patients with PDAC, esophageal carcinoma and lung adenocarcinoma. Supplementary Figure S12. The LIMS1-HIF1 positive feedback loop is pivotal to oxygen-glucose deprivation stress resistance. Supplementary Figure S13. Impact of altered expression on LIMS1 on cell survival under hypoxia. Supplementary Figure S14. Impact of altered expression of LIMS1 and HIF1 on tumorigenicity. Supplementary Figure S15. The effect of LIMS1 on IRES-dependent translation of HIF1A.
Supplemental Tables and Figures from Hybrid Capture–Based Genomic Profiling of Circulating Tumor DNA from Patients with Advanced Cancers of the Gastrointestinal Tract or Anus
Authors: Schrock Alexa B. , Pavlick Dean , Klempner Samuel J. , Chung Jon H. , Forcier Brady , Welsh Allison , Young Lauren , Leyland-Jones Bryan , Bordoni Rodolfo , Carvajal Richard D. , Chao Joseph , Kurzrock Razelle , Sicklick Jason K. , Ross Jeffrey S. , Stephens Philip J. , Devoe Craig , Braiteh Fadi , Ali Siraj M. , Miller Vincent A.
Published: April 2023

Supplemental Figure 1. Distribution of EGFR extracellular domain (ECD) mutations in ctDNA samples from patients with CRC. Supplemental Figure 2. Response to crizotinib in a patient with small bowel adenocarcinoma and GOPC-ROS1 fusion. Supplemental Figure 3. Detection of copy number amplification is associated with increased ctDNA fraction. Supplemental Table 1. List of 62 genes sequenced in this study using the FoundationACT ctDNA assay. Supplemental Table 2. Genomic alterations detected in temporally matched ctDNA and tissue samples.
Supplementary Table S1 from Loss of Nuclear Localized Parathyroid Hormone-Related Protein in Primary Breast Cancer Predicts Poor Clinical Outcome and Correlates with Suppressed Stat5 Signaling
Authors: Tran Thai H. , Utama Fransiscus E. , Sato Takahiro , Peck Amy R. , Langenheim John F. , Udhane Sameer S. , Sun Yunguang , Liu Chengbao , Girondo Melanie A. , Kovatich Albert J. , Hooke Jeffrey A. , Shriver Craig D. , Hu Hai , Palazzo Juan P. , Bibbo Marluce , Auer Paul W. , Flister Michael J. , Hyslop Terry , Mitchell Edith P. , Chervoneva Inna , Rui Hallgeir
Published: April 2023

Clinical Characteristics of Outcome Cohorts 1 and 2.
Figure S6 from Loss of Nuclear Localized Parathyroid Hormone-Related Protein in Primary Breast Cancer Predicts Poor Clinical Outcome and Correlates with Suppressed Stat5 Signaling
Authors: Tran Thai H. , Utama Fransiscus E. , Sato Takahiro , Peck Amy R. , Langenheim John F. , Udhane Sameer S. , Sun Yunguang , Liu Chengbao , Girondo Melanie A. , Kovatich Albert J. , Hooke Jeffrey A. , Shriver Craig D. , Hu Hai , Palazzo Juan P. , Bibbo Marluce , Auer Paul W. , Flister Michael J. , Hyslop Terry , Mitchell Edith P. , Chervoneva Inna , Rui Hallgeir
Published: April 2023

Supplementary Figure 6: Nuclear PTHrP and nuclear pY-Stat5 protein levels are strongly positively correlated independent of breast cancer subtype. Scatterplot of nuclear PTHrP protein levels against nuclear pY-Stat5 levels according to immunohistochemistry-based subtyping. Regression lines were fitted using robust MM-estimation illustrating strong positive correlations between nuclear PTHrP and nuclear pY-Stat5 in Luminal A (R=0.460), Luminal B (R=0.460), HER2-positive (R=0.690) and triple negative (R=0.630) human breast cancer tissues.
Figure S5 from Loss of Nuclear Localized Parathyroid Hormone-Related Protein in Primary Breast Cancer Predicts Poor Clinical Outcome and Correlates with Suppressed Stat5 Signaling
Authors: Tran Thai H. , Utama Fransiscus E. , Sato Takahiro , Peck Amy R. , Langenheim John F. , Udhane Sameer S. , Sun Yunguang , Liu Chengbao , Girondo Melanie A. , Kovatich Albert J. , Hooke Jeffrey A. , Shriver Craig D. , Hu Hai , Palazzo Juan P. , Bibbo Marluce , Auer Paul W. , Flister Michael J. , Hyslop Terry , Mitchell Edith P. , Chervoneva Inna , Rui Hallgeir
Published: April 2023

Supplementary Figure 5: Higher nuclear PTHrP protein levels are associated with lower grade and estrogen receptor-positive (ER+) breast cancer. Nuclear PTHrP protein levels are significantly higher in well-differentiated, grade 1 tumors compared to grade 3 tumors (A) and significantly higher in ER-positive (ER pos) than in ER-negative (ER neg) breast cancer (B). **p<0.02; ***p<001.
Table S3 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Toca 511 signal in tumor and nonneoplastic brain samples taken at time of autopsy from a Study 8 patient.
Table S2 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Tg 511-13-01 (Study 13) dosing table.
Table S1 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Tg 511-11-01 (Study 11) dosing table.
Figure S5 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Figure S5
Table S2 from Increased Synthesis of MCL-1 Protein Underlies Initial Survival of EGFR-Mutant Lung Cancer to EGFR Inhibitors and Provides a Novel Drug Target
Authors: Song Kyung-A , Hosono Yasuyuki , Turner Crystal , Jacob Sheeba , Lochmann Timothy L. , Murakami Yoshiko , Patel Neha U. , Ham Jungoh , Hu Bin , Powell Krista M. , Coon Colin M. , Windle Brad E. , Oya Yuko , Koblinski Jennifer E. , Harada Hisashi , Leverson Joel D. , Souers Andrew J. , Hata Aaron N. , Boikos Sosipatros , Yatabe Yasushi , Ebi Hiromichi , Faber Anthony C.
Published: April 2023

Sup. Table 2. Top 3 functional pathways from ingenuity pathways analysis (IPA) in DTC.
Supplementary Figure Legends from Increased Synthesis of MCL-1 Protein Underlies Initial Survival of EGFR-Mutant Lung Cancer to EGFR Inhibitors and Provides a Novel Drug Target
Authors: Song Kyung-A , Hosono Yasuyuki , Turner Crystal , Jacob Sheeba , Lochmann Timothy L. , Murakami Yoshiko , Patel Neha U. , Ham Jungoh , Hu Bin , Powell Krista M. , Coon Colin M. , Windle Brad E. , Oya Yuko , Koblinski Jennifer E. , Harada Hisashi , Leverson Joel D. , Souers Andrew J. , Hata Aaron N. , Boikos Sosipatros , Yatabe Yasushi , Ebi Hiromichi , Faber Anthony C.
Published: April 2023

Supplementary figure legends
Figure S2 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Figure S2
Figure S12 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Figure S12
Supplemental Figures and Table from Preclinical Antitumor Activity of a Novel Anti–c-KIT Antibody–Drug Conjugate against Mutant and Wild-type c-KIT–Positive Solid Tumors
Authors: Abrams Tinya , Connor Anu , Fanton Christie , Cohen Steven B. , Huber Thomas , Miller Kathy , Hong E. Erica , Niu Xiaohong , Kline Janine , Ison-Dugenny Marjorie , Harris Sarah , Walker Dana , Krauser Klaus , Galimi Francesco , Wang Zhen , Ghoddusi Majid , Mansfield Keith , Lee-Hoeflich Si Tuen , Holash Jocelyn , Pryer Nancy , Kluwe William , Ettenberg Seth A. , Sellers William R. , Lees Emma , Kwon Paul , Abraham Judith A. , Schleyer Siew C.
Published: April 2023

Figure S1. RNASeq data across multiple tumor types indicate c-KIT overexpression in a subset of cancer types such as AML, melanoma, testicular germ cell cancer and lung cancer. This was obtained from the TCGA data set. Figure S2. Western blot analysis of phosphorylated c-KIT and total c-KIT protein levels. Cells were starved overnight in 0.1% serum and then left untreated or treated with 10 ng/ml of SCF +/- 5 ug/ml of ADC together for 15 minutes before preparing cell lysates for immunoblotting. Figure S3. Correlation between c-KIT expression level and sensitivity to LOP628. GIST, SCLC and AML cell lines were analyzed for surface c-KIT expression by flow cytometry and assessed for sensitivity to LOP cell proliferation assays. Sensitivity to LOP628 was enriched if the cell line expressed >20,000 surface c-KIT receptors. Figure S4. Representative images of c-KIT immunostained GIST-T1, GIST430, NCI-H1048 and NCI-H2170 tumor xenografts in SCID-beige mice Figure S5. Lack of LOP628 efficacy in the c-KIT low/negative NCI-H2170 tumor xenograft model in SCID-beige mice after a single 10 mg/kg i.v. dose. Table S1. Activity of antagonist vs non-ligand blocking c-Kit ADCs in panel of GIST, AML and SCLC cell lines. Cell line sensitivity to the S-DM1-ME payload was also evaluated. There were no significant differences in activity between the two classes of ADCs. (A) refers to antagonist or ligand-blocking Abs. Table S2. Surface c-KIT expression on human and cynomolgus monkey mast cells and bone marrow cells as quantified by IHC or flow cytometry.
Supplementary Online Content from Polygenic Determinants for Subsequent Breast Cancer Risk in Survivors of Childhood Cancer: The St Jude Lifetime Cohort Study (SJLIFE)
Authors: Wang Zhaoming , Liu Qi , Wilson Carmen L. , Easton John , Mulder Heather , Chang Ti-Cheng , Rusch Michael C. , Edmonson Michael N. , Rice Stephen V. , Ehrhardt Matthew J. , Howell Rebecca M. , Kesserwan Chimene A. , Wu Gang , Nichols Kim E. , Downing James R. , Hudson Melissa M. , Zhang Jinghui , Yasui Yutaka , Robison Leslie L.
Published: April 2023

Figure S1. Population Admixture Revealed by STRUCTURE Analysis Figure S2. Distribution of Polygenic Risk Score among Female Survivors of European Ancestry Figure S3. Cumulative Incidence of Subsequent Breast Cancer Differs by Polygenic Risk Score after Excluding Breast Cancer Predisposing Mutation Carriers Table S1. Previously Reported Loci Associated with Overall Breast Cancer Table S2. Polygenic Risk Score for 1133 Female Childhood Cancer Survivors of European Ancestry Table S3. Quintile Cutoffs for Polygenic Risk Score Based on 1133 Female Survivors or Estimated with Minor Allele Frequencies within OncoArray Control Population Table S4. Pathogenic or Likely Pathogenic Mutations in 11 Breast Cancer Predisposition Genes for 1133 Female Survivors of European Ancestry Table S5. Baseline Risk Model for Subsequent Breast Cancer Table S6. Association of Polygenic Risk Score with Rate of Subsequent Breast Cancer in Survivors of Childhood Cancer after Excluding Predisposing Mutation Carriers Table S7. Association of Polygenic Risk Score with Rate of Subsequent Breast Cancer in Survivors of Childhood Cancer after Excluding Predisposing Mutation Carriers (top 10% of PRS)
Dataset S2 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Locations of Toca 511 Integration Sites
Dataset S1 from Molecular Analyses Support the Safety and Activity of Retroviral Replicating Vector Toca 511 in Patients
Authors: Hogan Daniel J. , Zhu Jay-Jiguang , Diago Oscar R. , Gammon Dawn , Haghighi Ali , Lu Guangrong , Das Asha , Gruber Harry E. , Jolly Douglas J. , Ostertag Derek
Published: April 2023

Toca 511 qPCR detection results