bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract SY12-04: Lowering the TCR signaling threshold with a DGKa/z dual inhibitor potentiates anti-tumor immunity
Authors: Dougan Stephanie K.
Published: April 2023

Checkpoint blockade immunotherapies expand neoantigen- or virus-specific T cells, and poor responsiveness to immunotherapy is associated with lower mutational burden in tumors of non-viral origin. Although mouse models demonstrate that lower affinity T cells recognizing self-antigens can contribute to tumor control if sufficiently activated, therapeutic options for enhancing T cell priming are limited. Diacylglycerol kinases (DGKs) suppress DAG signaling by converting DAG to phosphatidic acid, thereby attenuating pathways downstream of TCR signaling. Using a novel dual DGKa/z inhibitor (DGKi), tumor-specific CD8 T cells with different affinities (TRP1high and TRP1low), and a series of altered peptide ligands, we demonstrate that inhibition of DGKa/z can lower the signaling threshold for T cell priming. TRP1high and TRP1low CD8 T cells produced more IL-2 and IFNγ in the presence of cognate antigen and DGKi. Effector TRP1high- and TRP1low-mediated cytolysis of tumor cells with low antigen load was MHC-restricted, mediated by IFNg and augmented by DGKi. Adoptive T cell transfer into mice bearing pancreatic or melanoma tumors synergized with single-agent DGKi or DGKi and αPD1, with increased expansion of low affinity T cells and increased cytokine production observed in tumor infiltrates of treated mice. Collectively, our findings highlight DGKa/z as therapeutic targets for augmenting tumor-specific CD8 T cell function.

Citation Format: Stephanie K. Dougan. Lowering the TCR signaling threshold with a DGKa/z dual inhibitor potentiates anti-tumor immunity. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr SY12-04.
Kinome Scan Binding Assay from Honokiol Decreases Lung Cancer Metastasis through Inhibition of the STAT3 Signaling Pathway
Authors: Pan Jing , Lee Yongik , Zhang Qi , Xiong Donghai , Wan Tina C. , Wang Yian , You Ming
Published: April 2023

Kinome Scan Binding Assay
Supplementary Figures and Tables from Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection
Authors: Pavel Ana B. , Campbell Joshua D. , Liu Gang , Elashoff David , Dubinett Steven , Smith Kate , Whitney Duncan , Lenburg Marc E. , Spira Avrum
Published: April 2023

Supplementary Figure 1. Principal Components Analysis (PCA) of global microRNA expression. Supplementary Figure 2. Significantly differentially expressed microRNAs between current and former smokers (q<0.01). Supplementary Table 1. Patient demographics stratified by cancer status. Supplementary Table 2. Smoking associated microRNAs (p<0.05) Supplementary Table 3. Gender associated microRNAs (p<0.05) Supplementary Table 4. Age associated microRNAs (p<0.05) Supplementary Table 5. Pack-years (PY) associated microRNAs (p<0.05) Supplementary Table 6. Cancer associated microRNAs (p<0.05) Supplementary Table 7. Biomarker performance in the test set (* significant increase in AUC compared to mRNA biomarker p<0.05; â€ ROC-curve Operating Point set to 90% sensitivity in the training set).
Supplementary Figures 1-4 from Inhibitory Effects of γ- and δ-Tocopherols on Estrogen-Stimulated Breast Cancer In Vitro and In Vivo
Authors: Bak Min Ji , Das Gupta Soumyasri , Wahler Joseph , Lee Hong Jin , Li Xiaowei , Lee Mao-Jung , Yang Chung S. , Suh Nanjoo
Published: April 2023

Supplementary Figure S1. Effects of tocopherols on protein levels of cyclinD1 and c-Myc in MDA-MB-231 cells. Western blot analysis of effects of tocopherols (10 μM) in MDA-MB-231 in the presence of estrogen (1 nM) at 1 and 4 days. Supplementary Figure S2. Effects of tocopherols on expression of estrogen-related genes encoding TFF1, cathepsin D and PGR in MDA-MB-231 cells. Supplementary Figure S3. Effects of tocopherols on estrogen-induced oxidative and nitrosative stress in MDA-MB-231 cells. Supplementary Figure S4. Effects of tocopherols on estrogen- and etoposide-induced γ-H2AX formation in MDA-MB-231 cells.
Supplementary Tables 1, 2, 3, 4 from Sleep Duration across the Adult Lifecourse and Risk of Lung Cancer Mortality: A Cohort Study in Xuanwei, China
Authors: Wong Jason Y. , Bassig Bryan A. , Vermeulen Roel , Hu Wei , Ning Bofu , Seow Wei Jie , Ji Bu-Tian , Downward George S. , Katki Hormuzd A. , Barone-Adesi Francesco , Rothman Nathaniel , Chapman Robert S. , Lan Qing
Published: April 2023

Supplementary Table 1: Average Sleep Duration in Various Age-Periods and Risk of Lung Cancer Mortality Among Ever Smoky Coal Users of Xuanwei, China (1994-2011), Stratified by Average Tons of Fuel/Coal Used Per Year Supplementary Table 2: Average Sleep Duration in Various Age-Periods Across the Adult Lifecourse and Risk of Lung Cancer Mortality (1994-2011) Among those Alive in 1992 and Self-Responded (Excluding Surrogate Reported Data) Supplementary Table 3: Average Sleep Duration in Various Age-Periods Across the Adult Lifecourse and Risk of Lung Cancer Mortality in Xuanwei, China (1976-2011) Supplementary Table 4: Average Sleep Duration in Various Age-Periods Across the Adult Lifecourse and Risk of Lung Cancer Mortality in Farmers of Xuanwei, China (1994-2011) using 8-9 Sleep Hours/day as the Reference Group
Supplementary Table 1. from Targeting mTOR and p53 Signaling Inhibits Muscle Invasive Bladder Cancer In Vivo
Authors: Madka Venkateshwar , Mohammed Altaf , Li Qian , Zhang Yuting , Biddick Laura , Patlolla Jagan M.R. , Lightfoot Stan , Towner Rheal A. , Wu Xue-Ru , Steele Vernon E. , Kopelovich Levy , Rao Chinthalapally V.
Published: April 2023

List of primers used for real-time PCR analysis.
Supplementary Table from Prevention of Carcinogen-Induced Oral Cancer by Sulforaphane
Authors: Bauman Julie E. , Zang Yan , Sen Malabika , Li Changyou , Wang Lin , Egner Patricia A. , Fahey Jed W. , Normolle Daniel P. , Grandis Jennifer R. , Kensler Thomas W. , Johnson Daniel E.
Published: April 2023

Supplementary Table 1 This Table presence of SF metabolites in patient urine specimens.
Supplementary Materials and Methods from Prevention of Carcinogen-Induced Oral Cancer by Sulforaphane
Authors: Bauman Julie E. , Zang Yan , Sen Malabika , Li Changyou , Wang Lin , Egner Patricia A. , Fahey Jed W. , Normolle Daniel P. , Grandis Jennifer R. , Kensler Thomas W. , Johnson Daniel E.
Published: April 2023

Supplementary Materials and Methods.
Supplementary Figures from Prevention of Carcinogen-Induced Oral Cancer by Sulforaphane
Authors: Bauman Julie E. , Zang Yan , Sen Malabika , Li Changyou , Wang Lin , Egner Patricia A. , Fahey Jed W. , Normolle Daniel P. , Grandis Jennifer R. , Kensler Thomas W. , Johnson Daniel E.
Published: April 2023

Supplementary Figures 1, 2, 3, 4, 5 Supplementary Fig 1 shows SF induction of NRF2 in HPV-negative and HPV-positive cell lines. Supplementary Fig 2 shows induction of NRF2 by proteasome inhibitors. Supplementary Fig 3 shows SF induction of the NRF2 target gene NQO1 in HPV-negative and HPV-positive cell lines. Supplementary Fig 4 shows SF induction of the NRF2 target gene GCLC in HPV-negative and HPV-positive cell lines. Supplementary Fig 5 shows dose-response (cell death) curves for SF in HPV-negative and HPV-positive cell lines.
Table S2 from Evaluation of Biodistribution of Sulforaphane after Administration of Oral Broccoli Sprout Extract in Melanoma Patients with Multiple Atypical Nevi
Authors: Tahata Shawn , Singh Shivendra V. , Lin Yan , Hahm Eun-Ryeong , Beumer Jan H. , Christner Susan M. , Rao Uma N. , Sander Cindy , Tarhini Ahmad A. , Tawbi Hussein , Ferris Laura K. , Wilson Melissa , Rose Amy , Dietz Catherine M. , Hughes Ellen , Fahey Jed W. , Leachman Sancy A. , Cassidy Pamela B. , Butterfield Lisa H. , Zarour Hassane M. , Kirkwood John M.
Published: April 2023

Skin sulforaphane concentration post-BSE-SFN administration by dose group and day
Table S1, Table S2, Table S3, Table S4, Details for immunohistochemical staining from Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population
Authors: Wu Si , Zhang Yang , Zhang Lian , Ma Jun-Ling , Zhou Tong , Li Zhe-Xuan , Liu Wei-Dong , Li Wen-Qing , You Wei-Cheng , Pan Kai-Feng
Published: April 2023

Table S1. Differentially methylated CpGs of non-clustered PCDHs by H. pylori eradication in the whole-genome methylation profiling. Table S2. The association between major characteristics and methylation of four PCDH genes. Table S3. Associations between DNA methylation levels and expression. Table S4. PCR primers and experiment condition of candidate genes. Details for immunohistochemical staining
Supplementary Figure from Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids
Authors: Devall Matthew A.M. , Drew David A. , Dampier Christopher H. , Plummer Sarah J. , Eaton Stephen , Bryant Jennifer , Díez-Obrero Virginia , Mo Jiancheng , Kedrin Dmitriy , Zerjav Dylan C. , Takacsi-Nagy Oliver , Jennelle Lucas T. , Ali Mourad W. , Yilmaz Ömer H. , Moreno Victor , Powell Steven M. , Chan Andrew T. , Peters Ulrike , Casey Graham
Published: April 2023

Supplementary Figure from Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids
Supplementary Data from Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids
Authors: Devall Matthew A.M. , Drew David A. , Dampier Christopher H. , Plummer Sarah J. , Eaton Stephen , Bryant Jennifer , Díez-Obrero Virginia , Mo Jiancheng , Kedrin Dmitriy , Zerjav Dylan C. , Takacsi-Nagy Oliver , Jennelle Lucas T. , Ali Mourad W. , Yilmaz Ömer H. , Moreno Victor , Powell Steven M. , Chan Andrew T. , Peters Ulrike , Casey Graham
Published: April 2023

Supplementary Data from Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids
All Supplementary Figures and Tables from DNA Methylation of Telomere-Related Genes and Cancer Risk
Authors: Joyce Brian T. , Zheng Yinan , Nannini Drew , Zhang Zhou , Liu Lei , Gao Tao , Kocherginsky Masha , Murphy Robert , Yang Hushan , Achenbach Chad J. , Roberts Lewis R. , Hoxha Mirjam , Shen Jincheng , Vokonas Pantel , Schwartz Joel , Baccarelli Andrea , Hou Lifang
Published: April 2023

Table S1: Detailed information on all CpGs of interest Table S2: Cancer-associated CpGs in TRGs by pathway at FDR < 0.05, with unspecified skin malignancies excluded Table S3: Methylation trajectory over time by cancer status Table S4: Logistic regression results for DNA methylation measured over 8 years before diagnosis/censoring Table S5: Regulatory elements enrichment analysis results Figure S1: Plots of Beta-coefficients by genomic location for all CpGs on six genes of interest Figure S2: DNA methylation by years to cancer diagnosis/censoring and cancers status with 95% confidence intervals Figure S3: DNA methylation by years to cancer diagnosis/censoring and cancer status for CpG additional sites Figure S4: Regulatory enrichment analysis results
Supplementary Figure 1 from Gene Methylation and Cytological Atypia in Random Fine-Needle Aspirates for Assessment of Breast Cancer Risk
Authors: Stearns Vered , Fackler Mary Jo , Hafeez Sidra , Bujanda Zoila Lopez , Chatterton Robert T. , Jacobs Lisa K. , Khouri Nagi F. , Ivancic David , Kenney Kara , Shehata Christina , Jeter Stacie C. , Wolfman Judith A. , Zalles Carola M. , Huang Peng , Khan Seema A. , Sukumar Saraswati
Published: April 2023

Figure S1: Performance of a minimal 5-gene marker panel.
Supplementary Table from Associations between Preserved Foods and Breast Cancer Risk in Hong Kong Chinese Women
Authors: Lee Priscilla Ming Yi , Kwok Chi-Hei , Tsoi Yee-Kei , Wu Cherry , Law Sze-Hong , Tsang Koon-Ho , Yeung Yiu-Cheong , Chan W.C. , Tse Gary M. , Yuen Karen Ka-Wan , Hung Ray Ka Wai , Wang Feng , Tse Lap Ah
Published: April 2023

Supplementary Table from Associations between Preserved Foods and Breast Cancer Risk in Hong Kong Chinese Women
Supplementary Table 4 from Comparison of Performance Between a Short Categorized Lifestyle Exposure-based Colon Cancer Risk Prediction Tool and a Model Using Continuous Measures
Authors: Liu Ying , Colditz Graham A. , Rosner Bernard A. , Dart Hank , Wei Esther , Waters Erika A.
Published: April 2023

Reclassification of predicted risk by two colon cancer risk prediction models among men in the Health Professionals Followup Study: the model with categorized predictor variables versus the model with continuous predictor variables (reference).
Supplementary Table 1 from Comparison of Performance Between a Short Categorized Lifestyle Exposure-based Colon Cancer Risk Prediction Tool and a Model Using Continuous Measures
Authors: Liu Ying , Colditz Graham A. , Rosner Bernard A. , Dart Hank , Wei Esther , Waters Erika A.
Published: April 2023

Baseline age and age-standardized characteristics of cohort participants who developed colon cancer (cases) and those who remained free from cancer (noncases) among women in the Nurses' Health Study and men in the Health Professionals Follow-up Study in 1986
Supplementary Figure from Comparison of Performance Between a Short Categorized Lifestyle Exposure-based Colon Cancer Risk Prediction Tool and a Model Using Continuous Measures
Authors: Liu Ying , Colditz Graham A. , Rosner Bernard A. , Dart Hank , Wei Esther , Waters Erika A.
Published: April 2023

Flow chart of participant inclusion and exclusion criteria and the number of women in the Nurses' Health Study (NHS) and men in the Health Professional Follow-up Study (HPFS).
Supplementary Table from Bisphosphonates Zometa and Fosamax Synergize with Metformin to Prevent AOM-Induced Colon Cancer in F344 Rat Model
Authors: Madka Venkateshwar , Kumar Gaurav , Pathuri Gopal , Zhang Yuting , Lightfoot Stanley , Asch Adam S. , Mohammed Altaf , Steele Vernon E. , Rao Chinthalapally V.
Published: April 2023

Supplementary Table 1
Supplementary Figures from Bisphosphonates Zometa and Fosamax Synergize with Metformin to Prevent AOM-Induced Colon Cancer in F344 Rat Model
Authors: Madka Venkateshwar , Kumar Gaurav , Pathuri Gopal , Zhang Yuting , Lightfoot Stanley , Asch Adam S. , Mohammed Altaf , Steele Vernon E. , Rao Chinthalapally V.
Published: April 2023

Suppl. Figs 1 & 2
Supplementary Data legends from Bisphosphonates Zometa and Fosamax Synergize with Metformin to Prevent AOM-Induced Colon Cancer in F344 Rat Model
Authors: Madka Venkateshwar , Kumar Gaurav , Pathuri Gopal , Zhang Yuting , Lightfoot Stanley , Asch Adam S. , Mohammed Altaf , Steele Vernon E. , Rao Chinthalapally V.
Published: April 2023

Supplementary Data legends
Supplementary Data from Reducing Fatty Acid Oxidation Improves Cancer-free Survival in a Mouse Model of Li-Fraumeni Syndrome
Authors: Wang Ping-Yuan , Ma Jin , Li Jie , Starost Matthew F. , Wolfgang Michael J. , Singh Komudi , Pirooznia Mehdi , Kang Ju-Gyeong , Hwang Paul M.
Published: April 2023

Supplementary Table and Figures
Tables S1-5, Figures S1-S6, 3 Methods from Identification of a Human Airway Epithelial Cell Subpopulation with Altered Biophysical, Molecular, and Metastatic Properties
Authors: Pagano Paul C. , Tran Linh M. , Bendris Nawal , O'Byrne Sean , Tse Henry T. , Sharma Shivani , Hoech Jonathan W. , Park Stacy J. , Liclican Elvira L. , Jing Zhe , Li Rui , Krysan Kostyantyn , Paul Manash K. , Fontebasso Yari , Larsen Jill E. , Hakimi Shaina , Seki Atsuko , Fishbein Michael C. , Gimzewski James K. , Carlo Dino Di , Minna John D. , Walser Tonya C. , Dubinett Steven M.
Published: April 2023

Supplemental Tables, Figures, and Methods
Supplementary Data from Adiposity, Adulthood Weight Change, and Risk of Incident Hepatocellular Carcinoma
Authors: Simon Tracey G. , Kim Mi Na , Luo Xiao , Liu Xing , Yang Wanshui , Ma Yanan , Chong Dawn Q. , Fuchs Charles S. , Stampfer Meir , Giovannucci Edward L. , Chan Andrew T. , Zhang Xuehong
Published: April 2023

Supplementary Methods Supplementary Tables Table S1. Age-standardized Characteristics of Participants from NHS (n=56,224) and HPFS (n=35,975) With Available Waist Circumference Data in 1986 (NHS) and 1987 (HPFS), According to Adulthood Weight Change Table S2. Waist Circumference and Risk of Incident HCC in the NHS and HPFS Cohorts Table S3. Jointly Classified Analyses of Waist Circumference and BMI and Incident HCC Risk in the Combined NHS and HPFS Cohorts Table S4. Multivariate Risk of Incident HCC According to Weight Change Between Early Adulthood and Mid-life Table S5. Multivariate Risk of Incident HCC According to Weight Change Between Mid-Life and Present Table S6. Multivariate Risk of Incident HCC using an Alternate Definition of Weight Change During Adulthood Table S7. Lagged Analyses of Incident HCC Risk According to Weight Change During Overall Adulthood Table S8. Multivariate Risk of Incident HCC According to Adulthood Weight Change After Excluding Persons with Established Cirrhosis at Baseline Table S9. Multivariate Risk of Incident HCC According to Overall Adulthood Weight Change After Further Accounting for Incident Viral Hepatitis or Cirrhosis Supplementary References
supp data figure legend from Effects of Black Raspberry Extract and Protocatechuic Acid on Carcinogen-DNA Adducts and Mutagenesis, and Oxidative Stress in Rat and Human Oral Cells
Authors: Guttenplan Joseph B. , Chen Kun-Ming , Sun Yuan-Wan , Kosinska Wieslawa , Zhou Ying , Kim Seungjin (Agatha) , Sung Youngjae , Gowda Krishne , Amin Shantu , Stoner Gary D. , El-Bayoumy Karam
Published: April 2023

Legend for Supplementary Figure 1.
Table S3 from A Distinct Epidemiologic Pattern of Precancerous Lesions of Esophageal Squamous Cell Carcinoma in a High-risk Area of Huai'an, Jiangsu Province, China
Authors: Pan Da , Su Ming , Zhang Ting , Miao Caiyun , Fu Lingmeng , Yang Ligang , Song Guang , Raine Philip J. , Wang Shaokang , Sun Guiju
Published: April 2023

Table S3 shows the insignificant dietary results of univariate logistic regression analysis without adjustment for confounders. These insignificant data are not further analysed in the adjusted logistic regression model.
Table S2 from A Distinct Epidemiologic Pattern of Precancerous Lesions of Esophageal Squamous Cell Carcinoma in a High-risk Area of Huai'an, Jiangsu Province, China
Authors: Pan Da , Su Ming , Zhang Ting , Miao Caiyun , Fu Lingmeng , Yang Ligang , Song Guang , Raine Philip J. , Wang Shaokang , Sun Guiju
Published: April 2023

Table S2 shows the significant dietary results of univariate logistic regression analysis without adjustment for confounders. As mentioned in the article, each food or food type listed in Fig. 2 was analyzed to be statistically significant when conducting univariate logistic regression analysis, and some of them remained significant associations after performing adjusted logistic regression model (Fig. 2).
Table S1 from A Distinct Epidemiologic Pattern of Precancerous Lesions of Esophageal Squamous Cell Carcinoma in a High-risk Area of Huai'an, Jiangsu Province, China
Authors: Pan Da , Su Ming , Zhang Ting , Miao Caiyun , Fu Lingmeng , Yang Ligang , Song Guang , Raine Philip J. , Wang Shaokang , Sun Guiju
Published: April 2023

Table S1 shows the raw result with adjustment for gender, age, education, income and BMI. provided by SPSS software. The joint effects by cumulative amount of smoking and alcohol drinking are assessed here, but no significant interaction is observed (p=0.088).
Supplementary Data from Upper Gastrointestinal Cancer in China: Spatial Epidemiologic Evidence from Screening Areas
Authors: Li Peng , Jing Jing , Li Rui , Ge Miao , Jia Peng , Hu Wenbiao , Qi Xin , Wei Wen-Qiang , Zhuang Guihua
Published: April 2023

Original data and the calculation of relative risks
Supplementary material 2 from Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women
Authors: Ritu Wu , Enqi Wu , Zheng Siriguleng , Wang Jiandong , Ling Yaqin , Wang Yan
Published: April 2023

Adonis and db-RDA analysis on the association of microbiota and different variables of risk factor based on five distance matrixes
Supplementary material 1 from Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women
Authors: Ritu Wu , Enqi Wu , Zheng Siriguleng , Wang Jiandong , Ling Yaqin , Wang Yan
Published: April 2023

HPV genotyping before and after follow-up
Supplementary Table S2 from Myeloid Differentiation Factor 88 Signaling in Bone Marrow–Derived Cells Promotes Gastric Tumorigenesis by Generation of Inflammatory Microenvironment
Authors: Maeda Yusuke , Echizen Kanae , Oshima Hiroko , Yu Liang , Sakulsak Natthiya , Hirose Osamu , Yamada Yoichi , Taniguchi Tadatsugu , Jenkins Brendan J. , Saya Hideyuki , Oshima Masanobu
Published: April 2023

IPA analysis of human gastric cancer subtypes.
Supplementary Table S1 from Myeloid Differentiation Factor 88 Signaling in Bone Marrow–Derived Cells Promotes Gastric Tumorigenesis by Generation of Inflammatory Microenvironment
Authors: Maeda Yusuke , Echizen Kanae , Oshima Hiroko , Yu Liang , Sakulsak Natthiya , Hirose Osamu , Yamada Yoichi , Taniguchi Tadatsugu , Jenkins Brendan J. , Saya Hideyuki , Oshima Masanobu
Published: April 2023

Real-time RT-PCR primer information.
Supplementary Table S1-S5 from Physical Activity and Risk of Hepatocellular Carcinoma Among U.S. Men and Women
Authors: Luo Xiao , Yang Wanshui , Ma Yanan , Simon Tracey G. , Meyerhardt Jeffrey A. , Chan Andrew T. , Giovannucci Edward L. , Zhang Xuehong
Published: April 2023

Additional analyses for revised manuscript.
Supplementary Tables from A Novel Biomarker Panel for the Early Detection and Risk Assessment of Hepatocellular Carcinoma in Patients with Cirrhosis
Authors: Khan Ilvira M. , Gjuka Donjeta , Jiao Jingjing , Song Xiaoling , Wang Ying , Wang Jing , Wei Peng , El-Serag Hashem B. , Marrero Jorge A. , Beretta Laura
Published: April 2023

Supplementary Tables
Table S4 from Simultaneous Measurement of 92 Serum Protein Biomarkers for the Development of a Multiprotein Classifier for Ovarian Cancer Detection
Authors: Skubitz Amy P.N. , Boylan Kristin L.M. , Geschwind Kate , Cao Qing , Starr Timothy K. , Geller Melissa A. , Celestino Joseph , Bast Robert C. , Lu Karen H. , Koopmeiners Joseph S.
Published: April 2023

Supplemental Table S4
Table S2 from Simultaneous Measurement of 92 Serum Protein Biomarkers for the Development of a Multiprotein Classifier for Ovarian Cancer Detection
Authors: Skubitz Amy P.N. , Boylan Kristin L.M. , Geschwind Kate , Cao Qing , Starr Timothy K. , Geller Melissa A. , Celestino Joseph , Bast Robert C. , Lu Karen H. , Koopmeiners Joseph S.
Published: April 2023

Supplemental Table S2
Table S1 from Simultaneous Measurement of 92 Serum Protein Biomarkers for the Development of a Multiprotein Classifier for Ovarian Cancer Detection
Authors: Skubitz Amy P.N. , Boylan Kristin L.M. , Geschwind Kate , Cao Qing , Starr Timothy K. , Geller Melissa A. , Celestino Joseph , Bast Robert C. , Lu Karen H. , Koopmeiners Joseph S.
Published: April 2023

Supplemental Table S1
Supplemental Movie S1 from Simultaneous Measurement of 92 Serum Protein Biomarkers for the Development of a Multiprotein Classifier for Ovarian Cancer Detection
Authors: Skubitz Amy P.N. , Boylan Kristin L.M. , Geschwind Kate , Cao Qing , Starr Timothy K. , Geller Melissa A. , Celestino Joseph , Bast Robert C. , Lu Karen H. , Koopmeiners Joseph S.
Published: April 2023

Animation of PCA for Figure 1
Supplementary Data from Interaction Between Susceptibility Loci in MAVS and TRAF3 Genes, and High-risk HPV Infection on the Risk of Cervical Precancerous Lesions in Chinese Population
Authors: Xiao Di , Liu Dandan , Wen Zihao , Huang Xiuxia , Zeng Chengli , Zhou Zixing , Han Yajing , Ye Xiaohong , Wu Jing , Wang Yao , Guo Congcong , Ou Meiling , Huang Shiqi , Huang Chuican , Wei Xiangcai , Yang Guang , Jing Chunxia
Published: April 2023

Table S1. The distribution of demographic characteristics. Table S2. Primer sequences and amplified length of 8 SNPs in MAVS and TRAF3 gene. Table S3. Distribution of SNPs in MAVS and TRAF3 genes. Table S4. The haplotype frequencies of MAVS and TRAF3 polymorphisms and cervical precancerous lesions. Figure S1. AIC values of five genetic models in relating each SNP loci to the SIL cases and control groups.
Supplementary Data from A Multistage Murine Breast Cancer Model Reveals Long-Lived Premalignant Clones Refractory to Parity-Induced Protection
Authors: Li Shuo , Gestl Shelley A. , Gunther Edward J.
Published: April 2023

SFig. 1
Suppl Fig S4 from Analysis of Immune Cells from Human Mammary Ductal Epithelial Organoids Reveals Vδ2+ T Cells That Efficiently Target Breast Carcinoma Cells in the Presence of Bisphosphonate
Authors: Zumwalde Nicholas A. , Haag Jill D. , Sharma Deepak , Mirrielees Jennifer A. , Wilke Lee G. , Gould Michael N. , Gumperz Jenny E.
Published: April 2023

IFN-gamma and IL-17 production by T cells in organoid preps.
Suppl Fig S3 from Analysis of Immune Cells from Human Mammary Ductal Epithelial Organoids Reveals Vδ2+ T Cells That Efficiently Target Breast Carcinoma Cells in the Presence of Bisphosphonate
Authors: Zumwalde Nicholas A. , Haag Jill D. , Sharma Deepak , Mirrielees Jennifer A. , Wilke Lee G. , Gould Michael N. , Gumperz Jenny E.
Published: April 2023

Comparison of human Vd2+ T cell proliferation in response to two FDA-approved bisphosphonate drugs.
Suppl Fig S2 from Analysis of Immune Cells from Human Mammary Ductal Epithelial Organoids Reveals Vδ2+ T Cells That Efficiently Target Breast Carcinoma Cells in the Presence of Bisphosphonate
Authors: Zumwalde Nicholas A. , Haag Jill D. , Sharma Deepak , Mirrielees Jennifer A. , Wilke Lee G. , Gould Michael N. , Gumperz Jenny E.
Published: April 2023

Further characterization of the phenotypes of T cells in organoid preps.
Figure S1, Table S1 from Risk Factors for Recurrence in Patients with Atypical Endometrial Hyperplasia and Endometrioid Adenocarcinoma after Fertility-Sparing Treatments
Authors: Yin Jie , Ma Shuai , Shan Ying , Wang Yongxue , Li Yan , Jin Ying , Pan Lingya
Published: April 2023

Figure S1,study profile. Table S1, variable compare among different patients with different progestogen.
Table S2 from Association of IgG Glycosylation and Esophageal Precancerosis Beyond Inflammation
Authors: Wu Zhiyuan , Pan Huiying , Liu Di , Zhou Di , Tao Lixin , Zhang Jie , Wang Xiaonan , Wang Youxin , Wang Wei , Guo Xiuhua
Published: April 2023

The detailed description of the IgG glycans and traits.
Figure S2 from Association of IgG Glycosylation and Esophageal Precancerosis Beyond Inflammation
Authors: Wu Zhiyuan , Pan Huiying , Liu Di , Zhou Di , Tao Lixin , Zhang Jie , Wang Xiaonan , Wang Youxin , Wang Wei , Guo Xiuhua
Published: April 2023

The nonlinear relationship of IgG glycosylation and esophageal precancerosis in the multivariate model.
Supplementary Figure S5 from Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma
Authors: Chung Andrew S. , Mettlen Marcel , Ganguly Debolina , Lu Tianshi , Wang Tao , Brekken Rolf A. , Hsiehchen David , Zhu Hao
Published: April 2023

Two animals randomly selected from each group were sacrificed and showed no difference in tumor burden or T cells.
Supplementary Figure S4 from Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma
Authors: Chung Andrew S. , Mettlen Marcel , Ganguly Debolina , Lu Tianshi , Wang Tao , Brekken Rolf A. , Hsiehchen David , Zhu Hao
Published: April 2023

Image analysis pipeline for quantifying CD3, CD4, and CD8 cells in whole liver sections.
Supplementary Figure S2 from Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma
Authors: Chung Andrew S. , Mettlen Marcel , Ganguly Debolina , Lu Tianshi , Wang Tao , Brekken Rolf A. , Hsiehchen David , Zhu Hao
Published: April 2023

There were no microscopic tumors at initiation of antibody therapy.
Supplementary Figure S1 from Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma
Authors: Chung Andrew S. , Mettlen Marcel , Ganguly Debolina , Lu Tianshi , Wang Tao , Brekken Rolf A. , Hsiehchen David , Zhu Hao
Published: April 2023

Neoantigens tend to increase with worsening fibrosis stage.
Supplementary Figure Legends from Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma
Authors: Chung Andrew S. , Mettlen Marcel , Ganguly Debolina , Lu Tianshi , Wang Tao , Brekken Rolf A. , Hsiehchen David , Zhu Hao
Published: April 2023

Figure Legends for Supplementary Figures S1-S5.
Supplementary Figure from The COX-2–PGE2 Pathway Promotes Tumor Evasion in Colorectal Adenomas
Authors: Wei Jie , Zhang Jinyu , Wang Dingzhi , Cen Bo , Lang Jessica D. , DuBois Raymond N.
Published: April 2023

Supplementary Figure from The COX-2–PGE2 Pathway Promotes Tumor Evasion in Colorectal Adenomas
Supplementary information from A Phase II Randomized Placebo-Controlled Trial of Oral N-acetylcysteine for Protection of Melanocytic Nevi against UV-Induced Oxidative Stress In Vivo
Authors: Cassidy Pamela B. , Liu Tong , Florell Scott R. , Honeggar Matthew , Leachman Sancy A. , Boucher Kenneth M. , Grossman Douglas
Published: April 2023

Contains detailed methods for solar-simulated radiation and RT-PCR reactions, table of subjects' characteristics for phase II trial, results of open-label post-trial study, photographs of UV-irradiated nevi, and GSH data from pilot study.
Supplementary Tables from Baseline Oral Microbiome and All-cancer Incidence in a Cohort of Nonsmoking Mexican American Women
Authors: Zhang Xiaotao , Hoffman Kristi L. , Wei Peng , Elhor Gbito Kplola Y. , Joseph Reji , Li Fangyu , Scheet Paul , Chang Shine , Petrosino Joseph F. , Daniel Carrie R.
Published: April 2023

Supplemental tables 1 through 3
Supplementary Figures from Baseline Oral Microbiome and All-cancer Incidence in a Cohort of Nonsmoking Mexican American Women
Authors: Zhang Xiaotao , Hoffman Kristi L. , Wei Peng , Elhor Gbito Kplola Y. , Joseph Reji , Li Fangyu , Scheet Paul , Chang Shine , Petrosino Joseph F. , Daniel Carrie R.
Published: April 2023

Supplemental Figures 1 through 4
Supplementary Table 1 from Colonoscopy and Sigmoidoscopy Use among the Average-Risk Population for Colorectal Cancer: A Systematic Review and Trend Analysis
Authors: Cardoso Rafael , Niedermaier Tobias , Chen Chen , Hoffmeister Michael , Brenner Hermann
Published: April 2023

In Supplementary Table 1 prevalence estimates of colonoscopy use by age and sex in 2008-2011 and 2014-2015 in Germany are presented.
Supplementary Data from Evidence that EZH2 Deregulation is an Actionable Therapeutic Target for Prevention of Prostate Cancer
Authors: Burkhart Deborah L. , Morel Katherine L. , Wadosky Kristine M. , Labbé David P. , Galbo Phillip M. , Dalimov Zafardjan , Xu Bo , Loda Massimo , Ellis Leigh
Published: April 2023

Supplementary Data
Supplementary Figure from Cancer Prevention with Resistant Starch in Lynch Syndrome Patients in the CAPP2-Randomized Placebo Controlled Trial: Planned 10-Year Follow-up
Authors: Mathers John C. , Elliott Faye , Macrae Finlay , Mecklin Jukka-Pekka , Möslein Gabriela , McRonald Fiona E. , Bertario Lucio , Evans D. Gareth , Gerdes Anne-Marie , Ho Judy W.C. , Lindblom Annika , Morrison Patrick J. , Rashbass Jem , Ramesar Raj S. , Seppälä Toni T. , Thomas Huw J.W. , Sheth Harsh J. , Pylvänäinen Kirsi , Reed Lynn , Borthwick Gillian M. , Bishop D. Timothy , Burn John
Published: April 2023

Supplementary Figure from Cancer Prevention with Resistant Starch in Lynch Syndrome Patients in the CAPP2-Randomized Placebo Controlled Trial: Planned 10-Year Follow-up
Figure S1, S2, S3, Table S1, S2, S3, S4, S5, S6, S7 from Metabolomics Profiles of Hepatocellular Carcinoma in a Korean Prospective Cohort: The Korean Cancer Prevention Study-II
Authors: Jee Sun Ha , Kim Minjoo , Kim Minkyung , Yoo Hye Jin , Kim Hyungyoon , Jung Keum Ji , Hong Seri , Lee Jong Ho
Published: April 2023

S1: Permutation plots for the OPLS-DA model showing R2 (black triangle) and Q2 (blue square) values. S2. Correlation matrix among the clinical parameters and major metabolites in the control and HCC groups. S3. ROC curves for L-tyrosine, AST, 5-hydroxyhexanoic acid, and tauroursodeoxycholic acid for the incidence of hepatocellular cancer. Supplementary Table S1. Detailed method for pathway analysis. Supplementary Table S2. Levels of liver enzymes according to the mean diagnostic time after inclusion. Supplementary Table S3. CV-ANOVA assessing the reliability of the generated models. Supplementary Table S4. Peak intensities of the seven major metabolites according to the mean diagnostic time after inclusion. Supplementary Table S5. Metabolic pathway analysis of all subjects. Supplementary Table S6. Area under the ROC curve (AUC) for the risk factors of HCC incidence. Supplementary Table S7. List of unidentified peaks with VIP values >1.5.
Supplementary Tables from Vitamin D Signaling Suppresses Early Prostate Carcinogenesis in TgAPT121 Mice
Authors: Fleet James C. , Kovalenko Pavlo L. , Li Yan , Smolinski Justin , Spees Colleen , Yu Jun-Ge , Thomas-Ahner Jennifer M. , Cui Min , Neme Antonio , Carlberg Carsten , Clinton Steven K.
Published: April 2023

Five Supplemental tables
Supplementary Figure Legends, Table Legends, Table 1 from Targeting Translation Initiation Bypasses Signaling Crosstalk Mechanisms That Maintain High MYC Levels in Colorectal Cancer
Authors: Wiegering Armin , Uthe Friedrich W. , Jamieson Thomas , Ruoss Yvonne , Hüttenrauch Melanie , Küspert Maritta , Pfann Christina , Nixon Colin , Herold Steffi , Walz Susanne , Taranets Lyudmyla , Germer Christoph-Thomas , Rosenwald Andreas , Sansom Owen J. , Eilers Martin
Published: April 2023

Supplementary Figure Legends, Table Legends. Table 1. Reagents used in this study.
Supplementary Figure 4 from Targeting Translation Initiation Bypasses Signaling Crosstalk Mechanisms That Maintain High MYC Levels in Colorectal Cancer
Authors: Wiegering Armin , Uthe Friedrich W. , Jamieson Thomas , Ruoss Yvonne , Hüttenrauch Melanie , Küspert Maritta , Pfann Christina , Nixon Colin , Herold Steffi , Walz Susanne , Taranets Lyudmyla , Germer Christoph-Thomas , Rosenwald Andreas , Sansom Owen J. , Eilers Martin
Published: April 2023

Supplementary Figure 4. Characterization of the 4E-BP1(4A) allele and eIF4A inhibitors.
Supplementary Figure 3 from Targeting Translation Initiation Bypasses Signaling Crosstalk Mechanisms That Maintain High MYC Levels in Colorectal Cancer
Authors: Wiegering Armin , Uthe Friedrich W. , Jamieson Thomas , Ruoss Yvonne , Hüttenrauch Melanie , Küspert Maritta , Pfann Christina , Nixon Colin , Herold Steffi , Walz Susanne , Taranets Lyudmyla , Germer Christoph-Thomas , Rosenwald Andreas , Sansom Owen J. , Eilers Martin
Published: April 2023

Supplementary Figure 3. Effect of BEZ235 on MAP-kinase signaling.
Supplementary Figure, Table Legends from Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer
Authors: Carter Hannah , Marty Rachel , Hofree Matan , Gross Andrew M. , Jensen James , Fisch Kathleen M. , Wu Xingyu , DeBoever Christopher , Van Nostrand Eric L. , Song Yan , Wheeler Emily , Kreisberg Jason F. , Lippman Scott M. , Yeo Gene W. , Gutkind J. Silvio , Ideker Trey
Published: April 2023

Supplementary Figure, Table Legends
Supplementary Tables 8 - 9 from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Table 8. Sequence of primers for real-time PCR. Supplementary Table 9. Sequence of primers for CHIP real-time PCR.
Supplementary Tables 6 - 7 from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Table 6. A, ChIP-Seq Library Statistics. B, ChIP-Seq Library Peak Calls. C, WDR5 and KAT2A peaks within 2kb of RefSeq gene promoters where read coverage were significant decreased in BGC823 GC cells after transduction of GClnc1 shRNA virus,compared with transduction of control shRNA virus. D, the differentiated expression genes in BGC823 cells after downregulation of GClnc1. E, Intersection of ChIP-Seq and RNA seq data. Supplementary Table 7. The association between GClnc1 with target genes in the coexpression network analysis.
Supplementary Tables 1 - 3 from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Table 1. Identification of eight lncRNAs candidates upregulation from 10 pairs GC and adjacent tissues. Supplementary Table 2. Clinical information of 165 cases GC patients (fresh tissues). Supplementary Table 3. Clinical information of 105 cases GC patients (paraffin tissues).
Supplementary Methods from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Methods
Supplementary Figures 1 - 7 from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Figure 1, related to Figure 1. Clinical relevance of lncRNA candidate BC041951 in gastric cancer. Supplementary Figure 2, related to Figure 2. Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) in gastric cancer cells and gastric cancer patients with high and low GClnc1 expression. Supplementary Figure 3, related to Figure 3. GClnc1 is an oncogenic lncRNA in gastric cancer. Supplementary Figure 4, related to Figure 4. GClnc1 interacts with WDR5 and KAT2A epigenetic modification complex. Supplementary Figure 5, related to Figure 5. GClnc1 coordinates the localization of WDR5 and KAT2A genome-wide. Supplementary Figure 6, related to Figure 6. GClnc1 promotes gastric cancer progression via SOD2. Supplementary Figure 7, related to Figure 7. GClnc1 is a molecular link among WDR5/KAT2A and SOD2.
Supplementary Figure Legends from LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern
Authors: Sun Tian-Tian , He Jie , Liang Qian , Ren Lin-Lin , Yan Ting-Ting , Yu Ta-Chung , Tang Jia-Yin , Bao Yu-Jie , Hu Ye , Lin Yanwei , Sun Danfeng , Chen Ying-Xuan , Hong Jie , Chen Haoyan , Zou Weiping , Fang Jing-Yuan
Published: April 2023

Supplementary Figure Legends
Supplementary Methods, Figures S1 - S4 from Autocrine Complement Inhibits IL10-Dependent T-cell–Mediated Antitumor Immunity to Promote Tumor Progression
Authors: Wang Yu , Sun Sheng-Nan , Liu Qing , Yu Yang-Yang , Guo Jian , Wang Kun , Xing Bao-Cai , Zheng Qing-Feng , Campa Michael J. , Patz Edward F. , Li Shi-You , He You-Wen
Published: April 2023

Supplementary Figure S1. Complement regulates IL-10 production in CD8+ TILs. Supplementary Figure S2. Non-CD8+ T cell responses in tumor bearing mice. Supplementary Figure S3. T cell exhaustion markers expressed on CD8+ TILs after IL-10 culture. Supplementary Figure S4. Anaphylatoxins regulate IL-10 production through C3aR and C5aR.
Supplementary Methods from Activating ESR1 Mutations Differentially Affect the Efficacy of ER Antagonists
Authors: Toy Weiyi , Weir Hazel , Razavi Pedram , Lawson Mandy , Goeppert Anne U. , Mazzola Anne Marie , Smith Aaron , Wilson Joanne , Morrow Christopher , Wong Wai Lin , De Stanchina Elisa , Carlson Kathryn E. , Martin Teresa S. , Uddin Sharmeen , Li Zhiqiang , Fanning Sean , Katzenellenbogen John A. , Greene Geoffrey , Baselga José , Chandarlapaty Sarat
Published: April 2023

Supplementary Methods
Supplementary Figures 1 - 8, Tables 1 - 3 from Activating ESR1 Mutations Differentially Affect the Efficacy of ER Antagonists
Authors: Toy Weiyi , Weir Hazel , Razavi Pedram , Lawson Mandy , Goeppert Anne U. , Mazzola Anne Marie , Smith Aaron , Wilson Joanne , Morrow Christopher , Wong Wai Lin , De Stanchina Elisa , Carlson Kathryn E. , Martin Teresa S. , Uddin Sharmeen , Li Zhiqiang , Fanning Sean , Katzenellenbogen John A. , Greene Geoffrey , Baselga José , Chandarlapaty Sarat
Published: April 2023

Supplementary Figures 1 - 8, Tables 1 - 3
Supplementary Tables 1 through 8 from Immune Escape in Breast Cancer During In Situ to Invasive Carcinoma Transition
Authors: Gil Del Alcazar Carlos R. , Huh Sung Jin , Ekram Muhammad B. , Trinh Anne , Liu Lin L. , Beca Francisco , Zi Xiaoyuan , Kwak Minsuk , Bergholtz Helga , Su Ying , Ding Lina , Russnes Hege G. , Richardson Andrea L. , Babski Kirsten , Min Hui Kim Elizabeth , McDonnell Charles H. , Wagner Jon , Rowberry Ron , Freeman Gordon J. , Dillon Deborah , Sorlie Therese , Coussens Lisa M. , Garber Judy E. , Fan Rong , Bobolis Kristie , Allred D. Craig , Jeong Joon , Park So Yeon , Michor Franziska , Polyak Kornelia
Published: April 2023

Supplementary Table S1. List of tissue samples used. Supplementary Table S2. Raw FACS data in each sample. Supplementary Table S3. List of differentially expressed genes. Supplementary Table S4. Results of GSEA analyses. Supplementary Table S5. Gene lists used for functional analyses. Supplementary Table S6. Statistical modeling of ERBB2 and CC co-amplification; and PDL1 amplification. Supplementary Table S7. ERBB2 and 17q12 FISH data. Supplementary Table S8. List of antibodies used.
Supplementary Figures 1 through 7, Supplementary Methods from Immune Escape in Breast Cancer During In Situ to Invasive Carcinoma Transition
Authors: Gil Del Alcazar Carlos R. , Huh Sung Jin , Ekram Muhammad B. , Trinh Anne , Liu Lin L. , Beca Francisco , Zi Xiaoyuan , Kwak Minsuk , Bergholtz Helga , Su Ying , Ding Lina , Russnes Hege G. , Richardson Andrea L. , Babski Kirsten , Min Hui Kim Elizabeth , McDonnell Charles H. , Wagner Jon , Rowberry Ron , Freeman Gordon J. , Dillon Deborah , Sorlie Therese , Coussens Lisa M. , Garber Judy E. , Fan Rong , Bobolis Kristie , Allred D. Craig , Jeong Joon , Park So Yeon , Michor Franziska , Polyak Kornelia
Published: April 2023

Supplementary Figure S1. Leukocyte frequencies in breast tissues. Supplementary Figure S2. Genes expressed in T cells. Supplementary Figure S3. Activity status of T cells. Supplementary Figure S4. TCR clonotypes in breast tissues. Supplementary Figure S5. Functional state of T cells. Supplementary Figure S6. Tumor topology. Supplementary Figure S7. Immune-related amplicons in breast cancer.
Supplementary methods from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

Supplementary methods
Supplementary Tables 3, 6, 7, 9, 11, 12 from Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma
Authors: Kalaora Shelly , Wolf Yochai , Feferman Tali , Barnea Eilon , Greenstein Erez , Reshef Dan , Tirosh Itay , Reuben Alexandre , Patkar Sushant , Levy Ronen , Quinkhardt Juliane , Omokoko Tana , Qutob Nouar , Golani Ofra , Zhang Jianhua , Mao Xizeng , Song Xingzhi , Bernatchez Chantale , Haymaker Cara , Forget Marie-Andrée , Creasy Caitlin , Greenberg Polina , Carter Brett W. , Cooper Zachary A. , Rosenberg Steven A. , Lotem Michal , Sahin Ugur , Shakhar Guy , Ruppin Eytan , Wargo Jennifer A. , Friedman Nir , Admon Arie , Samuels Yardena
Published: April 2023

Supplementary Tables 3, 6, 7, 9, 11, 12
Table S4 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

TCGA Source Data
Table S3 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

Patient Characteristics and Treatment History, Select RNA-seq data, and Response Data