bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1 from LncRNA AGPG Confers Endocrine Resistance in Breast Cancer by Promoting E2F1 Activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: October 2023

Figure S1
Supplementary Figure 6 from Galectin-1 Mediates Chronic STING Activation in Tumors to Promote Metastasis through MDSC Recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda Jeanette , von Eyben Rie , Plevritis Sylvia , Li Lingyin , Giaccia Amato , Engleman Edgar , Le Quynh Thu
Published: October 2023

Immunoblot showing knockdown of STING in MOC2 WT/KO cells.
Supplementary Figure 4 from Galectin-1 Mediates Chronic STING Activation in Tumors to Promote Metastasis through MDSC Recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda Jeanette , von Eyben Rie , Plevritis Sylvia , Li Lingyin , Giaccia Amato , Engleman Edgar , Le Quynh Thu
Published: October 2023

A. Gating strategy for CD8+ T cells in the spleen of mice treated with either MOC2 WT/KO-Gal1 CM. B. Quantitation of PMN-MDSCs and T cells in the spleen of mice bearing KO-Gal1 tumors injected with either WT- or KO-Gal1 CM for 3 weeks. C. Graph showing the 48-plex mouse cytokine Luminex assay results performed on the 10x concentrated condition media from MOC2 WT/KO-Gal1 tumor cells. The media was collected in 3 independent experiments and run as a single batch. D. Gating strategy for CXCR2 staining on PMN-MDSCs isolated from the tumor and pre-metastatic lungs.
Supplementary Table S3 from Socioeconomic Status at Birth and Breast Tissue Composition in Adolescence and Adulthood
Authors: Kehm Rebecca D. , Lilge Lothar , Walter E. Jane , White Melissa , Herbstman Julie B. , Perera Frederica P. , Miller Rachel L. , Terry Mary Beth , Tehranifar Parisa
Published: October 2023

Supplementary Table S3 shows the characteristics of adult women by maternal education at birth in the Columbia Breast Cancer and the Environment Research Program (Columbia-BCERP) Study, n = 160.
Supplementary Table S1 from Socioeconomic Status at Birth and Breast Tissue Composition in Adolescence and Adulthood
Authors: Kehm Rebecca D. , Lilge Lothar , Walter E. Jane , White Melissa , Herbstman Julie B. , Perera Frederica P. , Miller Rachel L. , Terry Mary Beth , Tehranifar Parisa
Published: October 2023

Supplementary Table S1 shows the characteristics of adolescent girls by household income at birth in the Columbia Breast Cancer and the Environment Research Program (Columbia-BCERP) Study, n=165.
Supplementary Table S6 from Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes
Authors: Chen Ji-Qing , Salas Lucas A. , Wiencke John K. , Koestler Devin C. , Molinaro Annette M. , Andrew Angeline S. , Seigne John D. , Karagas Margaret R. , Kelsey Karl T. , Christensen Brock C.
Published: October 2023

Supplementary Table S6: Characteristics of subjects of each group based on the grouping results from both partDSA and SS-RPMM in all NMIBC patients
Supplementary Table S1 from Sex-Specific Associations between Adiponectin and Leptin Signaling and Pancreatic Cancer Survival
Authors: Babic Ana , Wang Qiao-Li , Lee Alice A. , Yuan Chen , Rifai Nader , Luo Juhua , Tabung Fred K. , Shadyab Aladdin H. , Wactawski-Wende Jean , Saquib Nazmus , Kim Jihye , Kraft Peter , Sesso Howard D. , Buring Julie E. , Giovannucci Edward L. , Manson JoAnn E. , Stampfer Meir J. , Ng Kimmie , Fuchs Charles S. , Wolpin Brian M.
Published: October 2023

Number of pancreatic cancer cases with available plasma adipokine levels and SNPs in adiponectin and leptin receptor genes
Supplementary Figure 1 from Germline Genetic Variants Associated with Somatic TMPRSS2:ERG Fusion Status in Prostate Cancer: A Genome-Wide Association Study
Authors: Ma Chaoran , Wang Xiaoyu , Dai James Y. , Turman Constance , Kraft Peter , Stopsack Konrad H. , Loda Massimo , Pettersson Andreas , Mucci Lorelei A. , Stanford Janet L. , Penney Kathryn L.
Published: October 2023

Quantile-quantile plots of GWAS in the pooled analysis of ERG (+) vs. ERG (-) tumor (A) ERG (+) tumors vs. controls (B) and ERG (-) tumors vs. controls (C).
Supplementary Figure S1 from Heritable Traits and Lung Cancer Risk: A Two-Sample Mendelian Randomization Study
Authors: Pettit Rowland W. , Byun Jinyoung , Han Younghun , Ostrom Quinn T. , Coarfa Cristian , Bondy Melissa L. , Amos Christopher I.
Published: October 2023

Supplementary Figure S1. IVW multivariate MR estimation of direct impact of traits on lung adenocarcinoma development, conditioned on smoking (pack years per lifespan), income, and years of schooling.
Supplementary Table 2 from Patterns of Evidence-Based Care for the Diagnosis, Staging, and First-line Treatment of Breast Cancer by Race–Ethnicity: A SEER-Medicare Study
Authors: Herbach Emma L. , Nash Sarah H. , Lizarraga Ingrid M. , Carnahan Ryan M. , Wang Kai , Ogilvie Amy C. , Curran Michaela , Charlton Mary E.
Published: October 2023

Supplementary Table 2 shows crude and adjusted rate ratios for all applicable outcomes stratified by stage at diagnosis.
Supplemental Table 2 from Germline Mutations in 12 Genes and Risk of Ovarian Cancer in Three Population-Based Cohorts
Authors: Kotsopoulos Joanne , Hathaway Cassandra A. , Narod Steven A. , Teras Lauren R. , Patel Alpa V. , Hu Chunling , Yadav Siddhartha , Couch Fergus J. , Tworoger Shelley S.
Published: October 2023

Supplemental Table 2: Mutation frequencies in ovarian cancer cases and controls and risk of ovarian cancer in the NHS, NHSII, and CPSII cohorts combined
Supplementary Table 2 from Changes in Geographic Variation and Socioeconomic Inequalities in Esophageal Cancer Mortality in China, 1973–2017
Authors: Ran Xianhui , Zheng Rongshou , Zeng Hongmei , Zhang Siwei , Sun Kexin , Han Bingfeng , Wang Shaoming , Chen Ru , Li Li , Wei Wenqiang , He Jie
Published: October 2023

Supplementary Table 2 shows the change in esophageal cancer mortality rates in counties with and without screening programs.
Supplementary Table 1 from Changes in Geographic Variation and Socioeconomic Inequalities in Esophageal Cancer Mortality in China, 1973–2017
Authors: Ran Xianhui , Zheng Rongshou , Zeng Hongmei , Zhang Siwei , Sun Kexin , Han Bingfeng , Wang Shaoming , Chen Ru , Li Li , Wei Wenqiang , He Jie
Published: October 2023

Supplementary Table 1 shows three major measures of data quality of cancer registries included in this study.
Supplementary Figure 2 from Changes in Geographic Variation and Socioeconomic Inequalities in Esophageal Cancer Mortality in China, 1973–2017
Authors: Ran Xianhui , Zheng Rongshou , Zeng Hongmei , Zhang Siwei , Sun Kexin , Han Bingfeng , Wang Shaoming , Chen Ru , Li Li , Wei Wenqiang , He Jie
Published: October 2023

Supplementary Figure 2 was a scatter diagram of the age-standardized esophageal cancer mortality rate in 1973-1975 and the absolute change in mortality rates from 1973–1975 to 2015–2017.
Supplementary Table 5 from The Association of Kidney Function and Inflammatory Biomarkers with Epithelial Ovarian Cancer Risk
Authors: Hathaway Cassandra A. , Townsend Mary K. , Sklar Elliot M. , Thomas-Purcell Kamilah B. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: October 2023

Hazard ratios (HR) and 95% confidence intervals (95%CI) of kidney related markers measured in urine and ovarian cancer risk by C Reactive Protein (CRP) in the UK Biobank.
Supplementary Table 3 from The Association of Kidney Function and Inflammatory Biomarkers with Epithelial Ovarian Cancer Risk
Authors: Hathaway Cassandra A. , Townsend Mary K. , Sklar Elliot M. , Thomas-Purcell Kamilah B. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: October 2023

Hazard ratios (HR) and 95% confidence intervals (95%CI) of kidney related markers measured in urine and ovarian cancer risk by histological subtype in the UK Biobank.
Supplemental Methods and Results from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative
Authors: Karra Prasoona , Hardikar Sheetal , Winn Maci , Anderson Garnet L. , Haaland Benjamin , Krick Benjamin , Thomson Cynthia A. , Shadyab Aladdin , Luo Juhua , Saquib Nazmus , Strickler Howard D. , Chlebowski Rowan , Arthur Rhonda S. , Summers Scott A. , Holland William L. , Jalili Thunder , Playdon Mary C.
Published: October 2023

Describes the methods and results for cancer-free cohort analysis.
Supplementary Table S5 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Table S5: Antibiotics use in relation to overall and cancer specific survival among stage IV colorectal cancer patients by sex
Supplementary Table S4 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Table S4: Characteristics of stage IV colorectal cancer patients
Supplementary Figure S6 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Figure S6: Sensitivity analyses for antibiotics use in relation to overall and cancer-specific survival in stage I-III and stage IV
colorectal cancer.
(A) Multilevel mix-effect analyses, assuming Weibull distribution and including operating hospitals as a second-level
variable (n =36 061). (B) Analyses limited to colon cancer patients who underwent elective surgery (n= 21 096). (C) Analyses
limited to colon cancer patients who underwent emergency surgery (n= 2 897). (D) Analyses excluding cases who died
within 90 days after surgery, i.e., fatal perioperative complications (n=35 200). (E) Multilevel mix-effect analyses, assuming
Weibull distribution and including treating hospitals as a second-level variable (n =11 242). (F) Analyses limited to cases
with complete covariate information (n= 4 729).
Supplementary Figure S5 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Figure S5: Antibiotics use in relation to overall and cancer-specific survival in stage I-III colorectal cancer patients by
antibiotics classes, typical indications and specific antibiotics drugs.
The hazards ratios (HR) are derived from the Cox proportional hazards models, stratified by tumour sites (proximal
colon/distal colon/rectum/unspecified colorectum categories) and tumour stage (stage I-III), age at diagnosis (</≥
50 years), prediagnostic Charlson comorbidity index (no/any CCI), family history of colorectal cancer (0/1/≥2 first
degree relatives ), and adjusted for: age and calendar year of diagnosis and prediagnostic Charlson comorbidity
index as continuous variables, and sex, place of birth, county of residence, marital status, level of education and
income status as categorical variables, defined as presented in Table 1. Antibiotics use during one year before
colorectal cancer diagnosis was excluded to account for potential use due to undiagnosed but clinically manifest
colorectal cancer. Any use of specific antibiotics class was compared with no use of the specific antibiotics class
(reference category). Antibiotics that primarily or only affect aerobic bacteria were categorized as aerobic
antibiotics. Antibiotics with effect on both anaerobic and aerobic bacteria, and metrodinazoles and/or tinidazoles
(which only affect anaerobic bacteria) were categorized as anti-anaerobic antibiotics. Phenoxymethylpenicillin is
presented as a specific antibiotic drug but was also the sole typical drug for the indication uncomplicated
respiratory infections and some skin and soft tissue infections. Clindamycin is presented as a specific antibiotic
drug but was also the sole typical drug for the indication complicated skin and soft tissue and deep-seated
infections. Amoxicillin includes amoxicillin with beta-lactamase inhibitor. UTI = urinary tract infection, CI =
confidence interval. Detailed antibiotics classification and typical indications are presented in Supplementary
Table S1.
Supplementary Figure S3 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Figure S3: Kaplan-Meier estimates for antibiotics use in relation to overall and cancer-specific survival in stage
I-III and stage IV colorectal cancer.
Prediagnostic antibiotics use was categorized as no use, any use, low use (1-10 days), moderate use (11-60
days), high use (61-180 days) and very high use (>180 days), based on defined daily doses. Antibiotics use during
one year before colorectal cancer diagnosis was excluded to account to account for potential use due to
undiagnosed but clinically manifest colorectal cancer. P represents P-value for the log-rank test.
Figure S1 from A Phase II Study of Durvalumab for Bacillus Calmette-Guerin (BCG) Unresponsive Urothelial Carcinoma In Situ of the Bladder
Authors: Li Roger , Sexton Wade J. , Dhillon Jasreman , Berglund Anders , Naidu Shreyas , Borjas Gustavo , Rose Kyle , Kim Youngchul , Wang Xuefeng , Conejo-Garcia Jose R. , Jain Rohit K. , Poch Michael A. , Spiess Philippe E. , Pow-Sang Julio , Gilbert Scott M. , Zhang Jingsong
Published: October 2023

12-CK Score from RNA Sequencing
Supplementary Table S3 from Safety and Efficacy of Anlotinib Hydrochloride Plus Temozolomide in Patients with Recurrent Glioblastoma
Authors: Xu Qingsheng , Huang Kaiyuan , Meng Xiangqi , Weng Yuxiang , Zhang Luyuan , Bu Linghao , Zheng Xiujue , Cai Jinquan , Zhan Renya , Chen Qun
Published: October 2023

Supplementary Table S3. Summary of other trial results for recurrent glioblastoma.
Supplementary Table S1 from Safety and Efficacy of Anlotinib Hydrochloride Plus Temozolomide in Patients with Recurrent Glioblastoma
Authors: Xu Qingsheng , Huang Kaiyuan , Meng Xiangqi , Weng Yuxiang , Zhang Luyuan , Bu Linghao , Zheng Xiujue , Cai Jinquan , Zhan Renya , Chen Qun
Published: October 2023

Supplementary Table S1. Patient Characteristics.
Supplementary Table S3 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Recurrent regions of chromothripsis and chromoplexy together with the candidate genes located within the regions. A. CHromothripsis B. Templated Instertion
Supplementary Table S2 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Recurrent regions of copy number gain and loss together with the candidate genes located within the regions.
Supplementary Spreadsheet S5 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Differential expression between normal chr1 and gain(1q) MM patients with t(4;14) translocation
Supplementary Spreadsheet S11 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Differentially methylated Illumina HM27 probes in MM vs PC
Supplementary Methods S1 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Methods
Supplementary Figure S9 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Impact of additional chromosome 1 structural events on outcome A.Effect of amp(1q) with or without a total (TT) gain on PFS B. Effect of amp(1q) on OS
Supplementary Figure S8 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Co-occurrence of regions of gain(1q) and loss(1p). A. The percentage of patients top and per patient (bottom) with specific region of gain B. A histogram summarising the number of gained regions per patient. C. The percentage of patients top and per patient (bottom) with specific regions of copy number loss D. Histogram summarizing the number of gained regions per patient.
Supplementary Figure S7 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Hi-C interaction and TAD map of TI2 and G8 regions. A comparison of the chromatin conformation of the region which encompasses TI2 and G8 across the 3 HMCLs (U266, RPMI8226, and KMS11) and PC. We note that there are noticeable loss of TAD boundary within the G8 region between PC and U266 and RPMI8226 that may allow accessibility to distal super-enhancers and result in overexpression. A similar change is seen in KMS11 at the ELF3 locus.
Supplementary Figure S6 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Chromatin state of different SV regions. The CT1 region at 1p36.11-1p34.3 is comprised of greater than 74% A-compartment (range 74-100%); CT2 at 1p33-1p32.3 comprises both inactive (range 35-59%) and active chromatin (range 41-65%) and, CT3 at 1p13.3-1p12, overlaps with TI1, had greater variability with 86% A-compartment in U266 while only 1% in KMS11. TI1 region predominantly laid in B-compartment (range 63-73%) and TI2 lay in an almost entirely active compartment (range 91-100%). NBC=Naïve B-cell, MBC=Memory B-cell, GCBC=Germinal Center B-cell, PC=plasma cell.
Supplementary Figure S2 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Chromatin state of different gain region. The regions of gain tend to fall within active chromatin regions with G3, G4, G5, G6, and G8 lying exclusively within A-compartments (100%) across B-cell differentiation states and MM cell lines (U266, RPMI8226, and KMS11). The G1 region also followed this pattern with the exception of KMS11 (where A-compartment represented only 78% of the region). The G2 region showed variability between the normal and malignant phenotype, with moderate switching from to B-compartments of 24%, 21%, and 37% in U266, RPMI8226, and KMS11 respectively. The compartment profile of the G7 region is interesting as each sample contained considerable B-compartment percentage (range 16-82%) but within the conserved A-compartment across all samples lies the well characterised oncogene ABL2. The G9 region showed the greatest variability across all samples and was shifted more towards inactive chromatin (range 45-97%). NBC=Naïve B-cell, MBC=Memory B-cell, GCBC=Germinal Center B-cell, PC=plasma cell.
Supplementary Figure S18 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Concurrent Hypomethylation and Overexpression Probes. The dot plot (top) displays the distribution of statistically significant CpG probes with difference in group mean methylation beta value, where the greater the value is a proxy for loss of methylation at the CpG probe. The probes are oriented by genomic locus across chromosome 1 with annotations for the midpoint of the recurrent gained regions on the 1q arm. The area graph (bottom) displays the ratio of probes that are significantly differentially methylated in any given 2MB window across chromosome 1. The highlighted region corresponds to the 1q arm.
Supplementary Figure S14 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Genes with increased dependency in cell lines with gain(1q).
Supplementary Figure S1 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzsky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: October 2023

Recurrent chromosome 1 mutations. Ninety-five genes on chromosome 1 that are mutated in more than 1% of cases in the Myeloma Genome Project dataset.
Figure S1A and S1B from Liquid Biopsies with Circulating Plasma HPV–DNA Measurements—A Clinically Applicable Surveillance Tool for Patients with HPV-Positive Oropharyngeal Cancer
Authors: Jakobsen Kathrine K. , Bendtsen Simone K. , Pallisgaard Niels , Friborg Jeppe , Lelkaitis Giedrius , Grønhøj Christian , von Buchwald Christian
Published: October 2023

HPV VisionArray scans of tumor samples in patients with HPV-negative pre-treatment plasma samples.
Supplementary Material 1 from Neoadjuvant Cabazitaxel plus Abiraterone/Leuprolide Acetate in Patients with High-Risk Prostate Cancer: ACDC-RP Phase II Trial
Authors: Fleshner Neil E. , Sayyid Rashid K. , Hansen Aaron R. , Chin Joseph L.K. , Fernandes Ricardo , Winquist Eric , van der Kwast Theodorus , Sweet Joan , Lajkosz Katherine , Kenk Miran , Hersey Karen , Veloso Rosette , Berlin Doron , Herrera-Caceres Jaime O. , Sridhar Srikala , Moussa Madeleine , Finelli Antonio , Hamilton Robert J. , Kulkarni Girish S. , Zlotta Alexandre R. , Joshua Anthony M.
Published: October 2023

Supplementary Material. Study protocol
Supplementary Table S2 from Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial
Authors: Kessler Tobias , Schrimpf Daniel , Doerner Laura , Hai Ling , Kaulen Leon D. , Ito Jakob , van den Bent Martin , Taphoorn Martin , Brandes Alba A. , Idbaih Ahmed , Dômont Julien , Clement Paul M. , Campone Mario , Bendszus Martin , von Deimling Andreas , Sahm Felix , Platten Michael , Wick Wolfgang , Wick Antje
Published: October 2023

Supplementary Table 2: Characteristics of patients with RTK1 tumors compared to RTK2 and MES according to classifier version v12.5. P-value was calculated for comparison between RTK1 and both other groups (RTK2 and MES) combined. NA, not available.
Supplementary Table S1 from Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial
Authors: Kessler Tobias , Schrimpf Daniel , Doerner Laura , Hai Ling , Kaulen Leon D. , Ito Jakob , van den Bent Martin , Taphoorn Martin , Brandes Alba A. , Idbaih Ahmed , Dômont Julien , Clement Paul M. , Campone Mario , Bendszus Martin , von Deimling Andreas , Sahm Felix , Platten Michael , Wick Wolfgang , Wick Antje
Published: October 2023

Supplementary Table 1: Representativeness of study participants.
Supplementary Figure S5 from Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial
Authors: Kessler Tobias , Schrimpf Daniel , Doerner Laura , Hai Ling , Kaulen Leon D. , Ito Jakob , van den Bent Martin , Taphoorn Martin , Brandes Alba A. , Idbaih Ahmed , Dômont Julien , Clement Paul M. , Campone Mario , Bendszus Martin , von Deimling Andreas , Sahm Felix , Platten Michael , Wick Wolfgang , Wick Antje
Published: October 2023

Supplementary Figure 5: Copy number variants in the three main glioblastoma groups according to classifier v12.5. A Copy number variants in all patients combined (n = 295), B in RTK1 tumors (n = 89), C in RTK2 tumors (n = 140) and D in MES tumors (n = 66). PDGFRA amplifications are enriched in RTK1 tumors and gains of chromosomes 19 and 20 are enriched in RTK2 tumors.
Supplementary Figure S3 from Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial
Authors: Kessler Tobias , Schrimpf Daniel , Doerner Laura , Hai Ling , Kaulen Leon D. , Ito Jakob , van den Bent Martin , Taphoorn Martin , Brandes Alba A. , Idbaih Ahmed , Dômont Julien , Clement Paul M. , Campone Mario , Bendszus Martin , von Deimling Andreas , Sahm Felix , Platten Michael , Wick Wolfgang , Wick Antje
Published: October 2023

Supplementary Figure 3: Characteristics of RTK1 tumors in comparison to RTK2 and MES. A Distribution of MGMT promotor methylation in main glioblastoma methylation subgroups. Classifier assignment is based on the v12.5 version (n = 295). Mutational profiles in B RTK1 tumors (n = 89), C RTK2 tumors (n = 140) and D MES tumors (n = 66).
Supplementary Figure S1 from Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial
Authors: Kessler Tobias , Schrimpf Daniel , Doerner Laura , Hai Ling , Kaulen Leon D. , Ito Jakob , van den Bent Martin , Taphoorn Martin , Brandes Alba A. , Idbaih Ahmed , Dômont Julien , Clement Paul M. , Campone Mario , Bendszus Martin , von Deimling Andreas , Sahm Felix , Platten Michael , Wick Wolfgang , Wick Antje
Published: October 2023

Supplementary Figure 1: Overview of the clinical trial and biomarker analysis. Out of 596 patients in the EORTC-26101 trial, patient tumor tissue to perform DNA methylation (Meth) and NGS sequencing analysis was available from 380 patients (63.8%). Of these, 99 patients treated with lomustine and 189 patients treated with lomustine and bevacizumab were eligible to detect biomarkers for bevacizumab response.
Supplementary Table S4 from Autocrine 17-β-Estradiol/Estrogen Receptor-α Loop Determines the Response to Immune Checkpoint Inhibitors in Non–Small Cell Lung Cancer
Authors: Anobile Dario P. , Salaroglio Iris C. , Tabbò Fabrizio , La Vecchia Sofia , Akman Muhlis , Napoli Francesca , Bungaro Maristella , Benso Federica , Aldieri Elisabetta , Bironzo Paolo , Kopecka Joanna , Passiglia Francesco , Righi Luisella , Novello Silvia , Scagliotti Giorgio V. , Riganti Chiara
Published: October 2023

Primers list for RT-PCR
Supplementary Figure S5 from Autocrine 17-β-Estradiol/Estrogen Receptor-α Loop Determines the Response to Immune Checkpoint Inhibitors in Non–Small Cell Lung Cancer
Authors: Anobile Dario P. , Salaroglio Iris C. , Tabbò Fabrizio , La Vecchia Sofia , Akman Muhlis , Napoli Francesca , Bungaro Maristella , Benso Federica , Aldieri Elisabetta , Bironzo Paolo , Kopecka Joanna , Passiglia Francesco , Righi Luisella , Novello Silvia , Scagliotti Giorgio V. , Riganti Chiara
Published: October 2023

Disaggregated data of ERα, 17-β-estradiol and PD-L1 levels in non-small cell lung cancer cells.
a-c. Expression of ERα mRNA, measured by RT-PCR (technical triplicates) (panel a), levels of 17-β-estradiol, measured by ELISA (technical triplicates) (panel b), expression of surface PD-L1 (panel c), measured by flow cytometry (technical triplicates) in 29 human NSCLC cell lines, divided in female (F)- or male (M)-derived cell lines, primary tumor (P) or metastatic (MTS) localization-derived cell lines, non-smoker (NSm) or smoker (Sm) patients. *p<0.05, **p<0.01: F versus M, P versus MTS, NSm versus Sm (ANOVA).
Supplementary Figure S16 from Autocrine 17-β-Estradiol/Estrogen Receptor-α Loop Determines the Response to Immune Checkpoint Inhibitors in Non–Small Cell Lung Cancer
Authors: Anobile Dario P. , Salaroglio Iris C. , Tabbò Fabrizio , La Vecchia Sofia , Akman Muhlis , Napoli Francesca , Bungaro Maristella , Benso Federica , Aldieri Elisabetta , Bironzo Paolo , Kopecka Joanna , Passiglia Francesco , Righi Luisella , Novello Silvia , Scagliotti Giorgio V. , Riganti Chiara
Published: October 2023

Molecular circuitries linking ERα and PD-L1.
ERα, activated by the binding of 17-β-estradiol and by the phosphorylation on Ser118 via the EGFR/Akt and EGFR/ERK1/2 axes, upregulates PD-L1 and predicts a better response to pembrolizumab. However, lowering the synthesis of 17-β-estradiol with letrozole or the activity of ERα with fulvestrant sensitizes non-small cell lung cancer to pembrolizumab, relieving the PD-L1-dependent immune-suppression, allowing the expansion and activity of anti-tumor infiltrating lymphocytes, such as CD8+T-cells, NK cells and Vγ9Vδ2+T cells. We suggest the existence of four possible scenarios, depending on sex, EGFR activity, 17-β-estradiol/ERα and PD-L1 status, with a differential sensitivity to pembrolizumab and aromatase inhibitors:1) male patients with low 17-β-estradiol synthesis, low EGFR signaling, low ERα amount/activity and low PD-L1 amount; 2) male patients with high EGFR signaling, high ERα amount/activity but low 17-β-estradiol synthesis, with intermediate PD-L1 amount; 3) female patients with low EGFR signaling, low ERα amount/activity but high 17-β-estradiol synthesis, with intermediate PD-L1 amount; 4) female patients with high EGFR signaling, high ERα amount/activity, high 17-β-estradiol synthesis and high PD-L1 amount. The efficacy of pembrolizumab and the additional benefit of aromatase inhibitors increased progressively from scenario 1 to 4.
Supplementary Figure S12 from Autocrine 17-β-Estradiol/Estrogen Receptor-α Loop Determines the Response to Immune Checkpoint Inhibitors in Non–Small Cell Lung Cancer
Authors: Anobile Dario P. , Salaroglio Iris C. , Tabbò Fabrizio , La Vecchia Sofia , Akman Muhlis , Napoli Francesca , Bungaro Maristella , Benso Federica , Aldieri Elisabetta , Bironzo Paolo , Kopecka Joanna , Passiglia Francesco , Righi Luisella , Novello Silvia , Scagliotti Giorgio V. , Riganti Chiara
Published: October 2023

Dose-dependent inhibition of Akt, ERK1/2 and EGFR.
ERα highNCI-H1975 cells were grown 24 h in fresh medium (Ctrl) or in medium containing 10 nM, 100 nM, 1 μM of the Akt inhibitor MK-2206 (Akti, panel a), 0.1 μM, 1 μM, 10 μM of the ERK1/2 inhibitor U-0126 (ERKi, panel b), 10 nM, 100 nM, 1 μM of the EGFR inhibitor AZD9291/Osimertinib (EGFRi, panel c). As read-out assays, Akt and ERK1/2 activity were measured by ELISA (technical duplicates), EGFR kinase activity was measured by a chemiluminescence-based assay (technical duplicates). Data are means + SD (n=3, biological replicates). *p<0.05, ***p<0.001: treated cells versus Ctrl cells (ANOVA).
Supplementary Figure S11 from Autocrine 17-β-Estradiol/Estrogen Receptor-α Loop Determines the Response to Immune Checkpoint Inhibitors in Non–Small Cell Lung Cancer
Authors: Anobile Dario P. , Salaroglio Iris C. , Tabbò Fabrizio , La Vecchia Sofia , Akman Muhlis , Napoli Francesca , Bungaro Maristella , Benso Federica , Aldieri Elisabetta , Bironzo Paolo , Kopecka Joanna , Passiglia Francesco , Righi Luisella , Novello Silvia , Scagliotti Giorgio V. , Riganti Chiara
Published: October 2023

Activity of ERβ on CD274/PD-L1 promoter.
Chromatin immunoprecipitation of ERE1 and ERE2 regions from CD274/PD-L1 promoter, using an anti-ERα or an anti-ERβ antibody, followed by RT-PCR (technical triplicates) of the precipitated products, in ERα highNCI-H1975 cells, grown 24 h in fresh medium (Ctrl) or in medium containing 10 nM fluvestrant (Fulv), an ERα inhibitor, or 10 nM letrozole (Letr), an aromatase inhibitor. Data are means+SD (n=3). **p<0.01, ***p<0.001: treated cells versus Ctrl cells; °°°p<0.001: anti-ERβ versus anti-ERα.
Supplementary Tables S1-S5 from Novel Genomic Risk Stratification Model for Primary Gastrointestinal Stromal Tumors (GIST) in the Adjuvant Therapy Era
Authors: Dermawan Josephine K. , Kelly Ciara , Gao Zhidong , Smith Shaleigh , Jadeja Bhumika , Singer Samuel , Tap William D. , Chi Ping , Antonescu Cristina R.
Published: October 2023

Supplementary Table S1. Metastasis Frequencies by Traditional vs. Genomic Risk Stratification
Supplementary Table S2. List of gene level and chromosomal arm level genomic variables used in OncoCast.
Supplementary Table S3-S4. Frequencies of genomic alterations by OncoCast risk groups in primary gastric and small bowel GISTs.
Supplementary Table S5. Number and frequencies of specific KIT/PDGFRA mutations in primary localized gastric and small bowel GISTs.
Supplementary Figure S5 from Novel Genomic Risk Stratification Model for Primary Gastrointestinal Stromal Tumors (GIST) in the Adjuvant Therapy Era
Authors: Dermawan Josephine K. , Kelly Ciara , Gao Zhidong , Smith Shaleigh , Jadeja Bhumika , Singer Samuel , Tap William D. , Chi Ping , Antonescu Cristina R.
Published: October 2023

Supplementary Figure S5. RFS in primary localized gastric GIST excluding SDH-deficient cases.
Supplementary Figure S4 from Novel Genomic Risk Stratification Model for Primary Gastrointestinal Stromal Tumors (GIST) in the Adjuvant Therapy Era
Authors: Dermawan Josephine K. , Kelly Ciara , Gao Zhidong , Smith Shaleigh , Jadeja Bhumika , Singer Samuel , Tap William D. , Chi Ping , Antonescu Cristina R.
Published: October 2023

Supplementary Figure S4. RFS in primary localized gastric (A) and small bowel (B) GISTs by types of primary KIT and PDGFRA mutations [del: deletion; ex: exon; INS: insertion; PM: point mutation].
Supplementary Figure 1 from Unique Spectrum of Activating BRAF Alterations in Prostate Cancer
Authors: Chehrazi-Raffle Alex , Tukachinsky Hanna , Toye Eamon , Sivakumar Smruthy , Schrock Alexa B. , Bergom Hannah E. , Ebrahimi Hedyeh , Pal Sumanta , Dorff Tanya , Agarwal Neeraj , Mahal Brandon A. , Oxnard Geoffrey R. , Hwang Justin , Antonarakis Emmanuel S.
Published: October 2023

Supplementary Figure 1
Supplementary Table S7 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Table S7. KEGG analysis for DE genes between C1(Low) and High(C2).
Supplementary Table S6 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Table S6. GO analysis for DE genes between C1(Low) and High(C2).
Supplementary Table S3 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Table S3. DE genes in C2 (High) compared with C1 (Low) subtype.
Supplementary Table S15 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Table S15. Pearson Correlation Coefficient between target lncRNA and target mRNA of key miRNAs.
Supplementary Table S12 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Table S12. MREs between mRNAs and miRNAs in the survival-related ceRNA network.
Supplementary Table S11 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Table S11. MREs between lncRNAs and miRNAs in the survival-related ceRNA network.
Supplementary Figure S7 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Figure S7. Investigation of therapeutic effects of TSA on SARC.
Supplementary Figure S3 from Comprehensive Analysis of Tumor Microenvironment Reveals Prognostic ceRNA Network Related to Immune Infiltration in Sarcoma
Authors: Leng Dongliang , Yang Ziyi , Sun Heng , Song Chengcheng , Huang Chen , Ip Ka U. , Chen Guokai , Deng Chu-Xia , Zhang Xiaohua Douglas , Zhao Qi
Published: October 2023

Supplementary Figure S3. Characterization of subtypes of SARC.
Circulating Tumor DNA Analysis in Advanced Urothelial Carcinoma: Insights from Biological Analysis and Extended Clinical Follow-up
Authors: Lindskrog Sia V. , Birkenkamp-Demtröder Karin , Nordentoft Iver , Laliotis George , Lamy Philippe , Christensen Emil , Renner Derrick , Andreasen Tine G. , Lange Naja , Sharma Shruti , ElNaggar Adam C. , Liu Minetta C. , Sethi Himanshu , Aleshin Alexey , Agerbæk Mads , Jensen Jørgen B. , Dyrskjøt Lars
Published: October 2023

Purpose:

To investigate whether circulating tumor DNA (ctDNA) assessment in patients with muscle-invasive bladder cancer predicts treatment response and provides early detection of metastatic disease.

Experimental Design:

We present full follow-up results (median follow-up: 68 months) from a previously described cohort of 68 neoadjuvant chemotherapy (NAC)-treated patients who underwent longitudinal ctDNA testing (712 plasma samples). In addition, we performed ctDNA evaluation of 153 plasma samples collected before and after radical cystectomy (RC) in a separate cohort of 102 NAC-naïve patients (median follow-up: 72 months). Total RNA sequencing of tumors was performed to investigate biological characteristics of ctDNA shedding tumors.

Results:

Assessment of ctDNA after RC identified metastatic relapse with a sensitivity of 94% and specificity of 98% using the expanded follow-up data for the NAC-treated patients. ctDNA dynamics during NAC was independently associated with patient outcomes when adjusted for pathologic downstaging (HR = 4.7; P = 0.029). For the NAC-naïve patients, ctDNA was a prognostic predictor before (HR = 3.4; P = 0.0005) and after RC (HR = 17.8; P = 0.0002). No statistically significant difference in recurrence-free survival for patients without detectable ctDNA at diagnosis was observed between the cohorts. Baseline ctDNA positivity was associated with the Basal/Squamous (Ba/Sq) subtype and enrichment of epithelial-to-mesenchymal transition and cell cycle–associated gene sets.

Conclusions:

ctDNA is prognostic in NAC-treated and NAC-naïve patients with more than 5 years follow-up and outperforms pathologic downstaging in predicting treatment efficacy. Patients without detectable ctDNA at diagnosis may benefit significantly less from NAC, but additional studies are needed.
Figure S6 from Intratumoral IL15 Improves Efficacy of Near-Infrared Photoimmunotherapy
Authors: Fukushima Hiroshi , Furusawa Aki , Kato Takuya , Wakiyama Hiroaki , Takao Seiichiro , Okuyama Shuhei , Choyke Peter L. , Kobayashi Hisataka
Published: October 2023

Supplementary Fig. S6. Expression of immunogenic signals after in vitro CD44-targeted NIR-PIT in hIL-15-MC38 or parental MC38 cells.
Figure S5 from Intratumoral IL15 Improves Efficacy of Near-Infrared Photoimmunotherapy
Authors: Fukushima Hiroshi , Furusawa Aki , Kato Takuya , Wakiyama Hiroaki , Takao Seiichiro , Okuyama Shuhei , Choyke Peter L. , Kobayashi Hisataka
Published: October 2023

Supplementary Fig. S5. In vitro CD44-targeted NIR-PIT in hIL-15-MC38 or parental MC38 cells.
Figure S2 from Intratumoral IL15 Improves Efficacy of Near-Infrared Photoimmunotherapy
Authors: Fukushima Hiroshi , Furusawa Aki , Kato Takuya , Wakiyama Hiroaki , Takao Seiichiro , Okuyama Shuhei , Choyke Peter L. , Kobayashi Hisataka
Published: October 2023

Supplementary Fig. S2. Estimation of IL-15 secreted in a hIL-15-MC38 tumor in vivo.
Supplementary Fig. S7 from Dual Targeting of the PDZ1 and PDZ2 Domains of MDA-9/Syntenin Inhibits Melanoma Metastasis
Authors: Pradhan Anjan K. , Modi Jinkal , Maji Santanu , Kumar Amit , Bhoopathi Praveen , Mannangatti Padmanabhan , Guo Chunqing , Afosah Daniel K. , Mochel Mark C. , Mukhopadhyay Nitai D. , Kirkwood John M. , Wang Xiang-Yang , Desai Umesh R. , Sarkar Devanand , Emdad Luni , Das Swadesh K. , Fisher Paul B.
Published: October 2023

IVMT-Rx-3 suppressed tumor cell derived pro-inflammatory cytokines expression.
Supplementary Figure Legends from A Multivalent Peptoid Conjugate Modulates Androgen Receptor Transcriptional Activity to Inhibit Therapy-resistant Prostate Cancer
Authors: Habault Justine , Schneider Jeffrey A. , Ha Susan , Ruoff Rachel , Pereira Luiza D. , Puccini Joseph , Ranieri Michela , Ayasun Ruveyda , Deng Jiehui , Kasper Amanda C. , Bar-Sagi Dafna , Wong Kwok-Kin , Zoubeidi Amina , Claessens Frank , Wise David R. , Logan Susan K. , Kirshenbaum Kent , Garabedian Michael J.
Published: October 2023

Figure legends for the supplemental data
Supplementary Figure S5 from A Carbonic Anhydrase IX/SLC1A5 Axis Regulates Glutamine Metabolism Dependent Ferroptosis in Hypoxic Tumor Cells
Authors: Venkateswaran Geetha , McDonald Paul C. , Chafe Shawn C. , Brown Wells S. , Gerbec Zachary J. , Awrey Shannon J. , Parker Seth J. , Dedhar Shoukat
Published: October 2023

Supplementary Figure S5 shows heatmaps demonstrating that combined inhibition of CAIX activity and GCLC or RSL3 synergize to increase cytotoxicity of hypoxic cancer cells.