bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplemental Materials and Methods from SMO Gene Amplification and Activation of the Hedgehog Pathway as Novel Mechanisms of Resistance to Anti-Epidermal Growth Factor Receptor Drugs in Human Lung Cancer
Authors: Della Corte Carminia Maria , Bellevicine Claudio , Vicidomini Giovanni , Vitagliano Donata , Malapelle Umberto , Accardo Marina , Fabozzi Alessio , Fiorelli Alfonso , Fasano Morena , Papaccio Federica , Martinelli Erika , Troiani Teresa , Troncone Giancarlo , Santini Mario , Bianco Roberto , Ciardiello Fortunato , Morgillo Floriana
Published: April 2023

Supplemental matherial and methods
Figure S2 from PKCα Attenuates Jagged-1–Mediated Notch Signaling in ErbB-2–Positive Breast Cancer to Reverse Trastuzumab Resistance
Authors: Pandya Kinnari , Wyatt Debra , Gallagher Brian , Shah Deep , Baker Andrew , Bloodworth Jeffrey , Zlobin Andrei , Pannuti Antonio , Green Andrew , Ellis Ian O. , Filipovic Aleksandra , Sagert Jason , Rana Ajay , Albain Kathy S. , Miele Lucio , Denning Mitchell F. , Osipo Clodia
Published: April 2023

A. Mib-1 is required for trastuzumab or lapatinib-induced increase of HES-1 protein expression in MDA-MB-453 cells. B. Notch-1, JAG-1, and HES-1 proteins are increases in trastuzumab resistant BT474 cells compared to sensitive cells.
Supplementary Figure 2 from A Phase I/II Study of the mTOR Inhibitor Everolimus in Combination with HyperCVAD Chemotherapy in Patients with Relapsed/Refractory Acute Lymphoblastic Leukemia
Authors: Daver Naval , Boumber Yanis , Kantarjian Hagop , Ravandi Farhad , Cortes Jorge , Rytting Michael E. , Kawedia Jitesh D. , Basnett Jordan , Culotta Kirk S. , Zeng Zhihong , Lu Hongbo , Richie Mary Ann , Garris Rebecca , Xiao Lianchun , Liu Wenbin , Baggerly Keith A. , Jabbour Elias , O'Brien Susan , Burger Jan , Bendall Linda J. , Thomas Deborah , Konopleva Marina
Published: April 2023

Supplementary Figure 2. OS and EFS by salvage status.
Supplemental Figure S6 from Chemotherapy Resistance in Diffuse-Type Gastric Adenocarcinoma Is Mediated by RhoA Activation in Cancer Stem-Like Cells
Authors: Yoon Changhwan , Cho Soo-Jeong , Aksoy Bülent Arman , Park Do Joong , Schultz Nikolaus , Ryeom Sandra W. , Yoon Sam S.
Published: April 2023

Kaplan-Meier overall survival curves for all patients and patients with intestinal tumors.
Supplemental Figures- Legends from Toxicity Attribution in Phase I Trials: Evaluating the Effect of Dose on the Frequency of Related and Unrelated Toxicities
Authors: Eaton Anne , Iasonos Alexia , Gounder Mrinal M. , Pamer Erika G. , Drilon Alexander , Vulih Diana , Smith Gary L. , Ivy S. Percy , Spriggs David R. , Hyman David M.
Published: April 2023

Legends to Supplemental Figures
Supplemental Figure 3 from Toxicity Attribution in Phase I Trials: Evaluating the Effect of Dose on the Frequency of Related and Unrelated Toxicities
Authors: Eaton Anne , Iasonos Alexia , Gounder Mrinal M. , Pamer Erika G. , Drilon Alexander , Vulih Diana , Smith Gary L. , Ivy S. Percy , Spriggs David R. , Hyman David M.
Published: April 2023

Demonstrates hypothetically the effect that systematic misattribution of disease-related toxicities as drug-related could have on the observed rate of drug-related toxicity as well as its relationship with dose. In this example, the observed rate of drug-related toxicity increases by 10% across all dose levels but the relationship with dose (as demonstrated by the slope of the curve) remains unchanged.
Supplemental Figure 1. from Toxicity Attribution in Phase I Trials: Evaluating the Effect of Dose on the Frequency of Related and Unrelated Toxicities
Authors: Eaton Anne , Iasonos Alexia , Gounder Mrinal M. , Pamer Erika G. , Drilon Alexander , Vulih Diana , Smith Gary L. , Ivy S. Percy , Spriggs David R. , Hyman David M.
Published: April 2023

Dose-toxicity curves by agent class (cytotoxic or molecular) and attribution (2-tier system). Black points represent the proportion of patients in a dose group experiencing grade {greater than or equal to}1 toxicity with the specified category and attribution. Red points represent the proportion of patients experiencing grade {greater than or equal to}3 toxicity within the specified category and attribution. Lines represent a fitted logistic regression curve with % of maximum administered dose (MAD) as a continuous covariate and p-values are from the same model.
Supplemental Table 2 from A Phase I Study of Oral ARRY-614, a p38 MAPK/Tie2 Dual Inhibitor, in Patients with Low or Intermediate-1 Risk Myelodysplastic Syndromes
Authors: Garcia-Manero Guillermo , Khoury Hanna J. , Jabbour Elias , Lancet Jeffrey , Winski Shannon L. , Cable LouAnn , Rush Selena , Maloney Lara , Hogeland Grant , Ptaszynski Mieke , Calvo Monica Cabrero , Bohannan Zach , List Alan , Kantarjian Hagop , Komrokji Rami
Published: April 2023

Supplemental Table 2. Dose escalation PK parameters for ARRY-614
Supplemental Figure 1 from Toxicity Attribution in Phase I Trials: Evaluating the Effect of Dose on the Frequency of Related and Unrelated Toxicities
Authors: Eaton Anne , Iasonos Alexia , Gounder Mrinal M. , Pamer Erika G. , Drilon Alexander , Vulih Diana , Smith Gary L. , Ivy S. Percy , Spriggs David R. , Hyman David M.
Published: April 2023

Dose-toxicity curves by agent class (cytotoxic or molecular) and attribution (2-tier system). Black points represent the proportion of patients in a dose group experiencing grade {greater than or equal to}1 toxicity with the specified category and attribution. Red points represent the proportion of patients experiencing grade {greater than or equal to}3 toxicity within the specified category and attribution. Lines represent a fitted logistic regression curve with % of maximum administered dose (MAD) as a continuous covariate and p-values are from the same model.
Supplemental Table 1 from A Phase I Study of Oral ARRY-614, a p38 MAPK/Tie2 Dual Inhibitor, in Patients with Low or Intermediate-1 Risk Myelodysplastic Syndromes
Authors: Garcia-Manero Guillermo , Khoury Hanna J. , Jabbour Elias , Lancet Jeffrey , Winski Shannon L. , Cable LouAnn , Rush Selena , Maloney Lara , Hogeland Grant , Ptaszynski Mieke , Calvo Monica Cabrero , Bohannan Zach , List Alan , Kantarjian Hagop , Komrokji Rami
Published: April 2023

Supplemental Table 1. Treatment-emergent AEs (safety population)
Supplementary Tables 1-4 from Soluble Vascular Endothelial Growth Factor (sVEGF) and the Risk of Venous Thromboembolism in Patients with Cancer: Results from the Vienna Cancer and Thrombosis Study (CATS)
Authors: Posch Florian , Thaler Johannes , Zlabinger Gerhard-Johann , Königsbrügge Oliver , Koder Silvia , Zielinski Christoph , Pabinger Ingrid , Ay Cihan
Published: April 2023

Table S1: Mean change in sVEGF according to selected variables - Simple linear regression models Table S2: Mean change in sVEGF* according to selected variables - "Multiple Model 1" Table S3: Mean change in sVEGF according to selected variables - "Multiple Model 2" Table S4: sVEGF and the risk of death-from-any-cause - Multivariable Cox regression model
Figure S4 from Statins Synergize with Hedgehog Pathway Inhibitors for Treatment of Medulloblastoma
Authors: Gordon Renata E. , Zhang Li , Peri Suraj , Kuo Yin-Ming , Du Fang , Egleston Brian L. , Ng Jessica M. Y. , Andrews Andrew J. , Astsaturov Igor , Curran Tom , Yang Zeng-Jie
Published: April 2023

SmoM2 MB cells are resistant to simvastatin treatment
Supplementary Table 3 from Image Analysis–based Assessment of PD-L1 and Tumor-Associated Immune Cells Density Supports Distinct Intratumoral Microenvironment Groups in Non–small Cell Lung Carcinoma Patients
Authors: Parra Edwin R. , Behrens Carmen , Rodriguez-Canales Jaime , Lin Heather , Mino Barbara , Blando Jorge , Zhang Jianjun , Gibbons Don L. , Heymach John V. , Sepesi Boris , Swisher Stephen G. , Weissferdt Annikka , Kalhor Neda , Izzo Julie , Kadara Humam , Moran Cesar , Lee Jack J. , Wistuba Ignacio I.
Published: April 2023

Correlation between immunohistochemical PD-L1 H-score expression in MCs and TAIC density by mm2 in the intratumoral and peritumoral compartments in lung ADC and SqCC specimens.
Figure S1 from Statins Synergize with Hedgehog Pathway Inhibitors for Treatment of Medulloblastoma
Authors: Gordon Renata E. , Zhang Li , Peri Suraj , Kuo Yin-Ming , Du Fang , Egleston Brian L. , Ng Jessica M. Y. , Andrews Andrew J. , Astsaturov Igor , Curran Tom , Yang Zeng-Jie
Published: April 2023

Cholesterol availability influences proliferation of Ptch1+/- MB proliferation cells
Supplementary Figure S2 from Global Hypomethylation (LINE-1) and Gene-Specific Hypermethylation (GSTP1) on Initial Negative Prostate Biopsy as Markers of Prostate Cancer on a Rebiopsy
Authors: Zelic Renata , Fiano Valentina , Zugna Daniela , Grasso Chiara , Delsedime Luisa , Daniele Lorenzo , Galliano Diego , Pettersson Andreas , Gillio-Tos Anna , Merletti Franco , Richiardi Lorenzo
Published: April 2023

Association between LINE-1 methylation on a negative biopsy and risk of prostate cancer diagnosis on a rebiopsy in the two Wards separately. Estimates are, adjusted for matching variables and time between the two samples, number of cores sampled at the biopsy, number of biopsies prior to the index biopsy and GSTP1 methylation (the upper 95% limit is restricted to <200 and the lower 95% limit is restricted to >0.03).
Supplemental Figure 2 from KDR Amplification Is Associated with VEGF-Induced Activation of the mTOR and Invasion Pathways but does not Predict Clinical Benefit to the VEGFR TKI Vandetanib
Authors: Nilsson Monique B. , Giri Uma , Gudikote Jayanthi , Tang Ximing , Lu Wei , Tran Hai , Fan Youhong , Koo Andrew , Diao Lixia , Tong Pan , Wang Jing , Herbst Roy , Johnson Bruce E. , Ryan Andy , Webster Alan , Rowe Philip , Wistuba Ignacio I. , Heymach John V.
Published: April 2023

Supplemental Figure 2. VEGFR TKIs inhibit the migration of NSCLC cells with KDR CNGs.
Supplemental Figure Legends from Overexpression of Smad7 Blocks Primary Tumor Growth and Lung Metastasis Development in Osteosarcoma
Authors: Lamora Audrey , Talbot Julie , Bougras Gwenola , Amiaud Jérôme , Leduc Marion , Chesneau Julie , Taurelle Julien , Stresing Verena , Le Deley Marie Cécile , Heymann Marie Françoise , Heymann Dominique , Redini Françoise , Verrecchia Franck
Published: April 2023

Supplemental Figure Legends from Overexpression of Smad7 Blocks Primary Tumor Growth and Lung Metastasis Development in Osteosarcoma
Supplementary Figures 1 - 4, Tables 1 - 3 from Essential Role of Aldehyde Dehydrogenase 1A3 for the Maintenance of Non–Small Cell Lung Cancer Stem Cells Is Associated with the STAT3 Pathway
Authors: Shao Chunli , Sullivan James P. , Girard Luc , Augustyn Alexander , Yenerall Paul , Rodriguez-Canales Jaime , Liu Hui , Behrens Carmen , Shay Jerry W. , Wistuba Ignacio I. , Minna John D.
Published: April 2023

PDF file - 465K, Supplementary Table S1. The correlation between ALDH1A3 protein expression and percentage of ALDH+ cells in NSCLC lines (Data for Figure 2D). Supplementary Table S2. Incidence of xenograft tumors derived from control or ALDH1A3 knockdown lung cancer cells. Supplementary Table S3. The association between ALDH1A3 protein expression and clinicopathological variables for 455 NSCLC patient samples. Figure S1. ALDH profiling of 8 NSCLC lines using the flow cytometry based Aldefluor assay. Figure S2. Anchorage dependent colony formation efficiency was determined by growing serial dilutions of sorted ALDH+ and ALDH- cells for 2 weeks in liquid culture. Figure S3. A, ALDH1A3 protein expression in a set of NSCLC lines was detected by western blots. The corresponding percentage of ALDH+ cells was analyzed by Aldefluor assay. B, western blot showed ALDH1A1 protein expression in certain HBEC and NSCLC lines. C, ALDH1A3 was knocked down using three siRNAs in a panel of NSCLC lines with different driver mutations followed by liquid colony formation assays. RT-PCR was performed to examine ALDH1A3 mRNA expression. Figure S4. Ectopic expression of ALDH1A3 does not affect tumorigenicity of lung cancer cells.
Supplementary table and figure legends from KEAP1 Genetic Polymorphisms Associate with Breast Cancer Risk and Survival Outcomes
Authors: Hartikainen Jaana M. , Tengström Maria , Winqvist Robert , Jukkola-Vuorinen Arja , Pylkäs Katri , Kosma Veli-Matti , Soini Ylermi , Mannermaa Arto
Published: April 2023

Supplementary table and figure legends
Supplementary Figure S1 from KEAP1 Genetic Polymorphisms Associate with Breast Cancer Risk and Survival Outcomes
Authors: Hartikainen Jaana M. , Tengström Maria , Winqvist Robert , Jukkola-Vuorinen Arja , Pylkäs Katri , Kosma Veli-Matti , Soini Ylermi , Mannermaa Arto
Published: April 2023

Supplementary Figure S1. Immunohistochemical staining of KEAP1 in breast tumor tissue.
Supplementary Figures S1-6 from Aspirin Suppresses the Growth and Metastasis of Osteosarcoma through the NF-κB Pathway
Authors: Liao Dan , Zhong Li , Duan Tingmei , Zhang Ru-Hua , Wang Xin , Wang Gang , Hu Kaishun , Lv Xiaobin , Kang Tiebang
Published: April 2023

Supplementary Figures S1-6. Figure S1. Aspirin enhances chemosensitivity to DDP in both U2OS and ZOS cells using the clone formation assay; Figure S2. Aspirin promotes the DDP-induced apoptosis in osteosarcoma cell lines; Figure S3. Aspirin inhibits the migration and invasion of OS cells; Figure S4. The orthotopic model of osteosarcoma in vivo; Figure S5. Aspirin has no effect on the migration and invasion in both U2OS and ZOS cells knockdown of p65; Figure S6. The impairment of Aspirin on migration and invasion are rescued in both U2OS and ZOS cells stably overexpressing p65.
Related Article from Myeloid Suppressors Decrease Melanoma Survival by Abating Tumor-Fighting T Cells
Authors: Kiessling Rolf , Mao Yumeng , de Coaña Yago Pico
Published: April 2023

Related Article from Myeloid Suppressors Decrease Melanoma Survival by Abating Tumor-Fighting T Cells
Supplementary Table 4 from FGFR1/3 Tyrosine Kinase Fusions Define a Unique Molecular Subtype of Non–Small Cell Lung Cancer
Authors: Wang Rui , Wang Lei , Li Yuan , Hu Haichuan , Shen Lei , Shen Xuxia , Pan Yunjian , Ye Ting , Zhang Yang , Luo Xiaoyang , Zhang Yiliang , Pan Bin , Li Bin , Li Hang , Zhang Jie , Pao William , Ji Hongbin , Sun Yihua , Chen Haiquan
Published: April 2023

PDF file - 91KB, Independent predictors of FGFR1/3 fusions in 1328 patients with NSCLCs in multivariate analysis.
Supplementary Figures S1-7 from CD73 Expression Is an Independent Prognostic Factor in Prostate Cancer
Authors: Leclerc Bruno G. , Charlebois Roxanne , Chouinard Guillaume , Allard Bertrand , Pommey Sandra , Saad Fred , Stagg John
Published: April 2023

Supplementary Figures S1-7. Fig. S1: CD73 and CD8 protein expression Fig. S2: Distribution of CD73 and CD8 expression Fig. S3: Prognostic impact of CD73 using ROC-based cut-off Fig. S4: Prognostic impact of CD73 using ROC-based cut-off Fig. S5: Prognostic impact of CD73/CD8 combined score using ROC-based cut-off Fig. S6: Correlation between CD73 and TGF-β genes Fig. S7: Graphical summary
Supplementary Figure S2 from Analysis of mTOR Gene Aberrations in Melanoma Patients and Evaluation of Their Sensitivity to PI3K–AKT–mTOR Pathway Inhibitors
Authors: Kong Yan , Si Lu , Li Yiqian , Wu Xiaowen , Xu Xiaowei , Dai Jie , Tang Huan , Ma Meng , Chi Zhihong , Sheng Xinan , Cui Chuanliang , Guo Jun
Published: April 2023

Supplementary Figure S2. Overall survival of melanoma patients in relation to mTOR nonsynonymous mutations.
Supplementary Figure S1 from Analysis of mTOR Gene Aberrations in Melanoma Patients and Evaluation of Their Sensitivity to PI3K–AKT–mTOR Pathway Inhibitors
Authors: Kong Yan , Si Lu , Li Yiqian , Wu Xiaowen , Xu Xiaowei , Dai Jie , Tang Huan , Ma Meng , Chi Zhihong , Sheng Xinan , Cui Chuanliang , Guo Jun
Published: April 2023

Supplementary Figure S1. Typical staining results of immunohistochemistry.
Supplementary Figure 1 from FGFR1/3 Tyrosine Kinase Fusions Define a Unique Molecular Subtype of Non–Small Cell Lung Cancer
Authors: Wang Rui , Wang Lei , Li Yuan , Hu Haichuan , Shen Lei , Shen Xuxia , Pan Yunjian , Ye Ting , Zhang Yang , Luo Xiaoyang , Zhang Yiliang , Pan Bin , Li Bin , Li Hang , Zhang Jie , Pao William , Ji Hongbin , Sun Yihua , Chen Haiquan
Published: April 2023

PDF file - 69KB, FGFR3-TACC3 fusion variants and BAG4-FGFR1 fusion in NSCLCs.
Supplemental Figure 1 from SRRM4 Expression and the Loss of REST Activity May Promote the Emergence of the Neuroendocrine Phenotype in Castration-Resistant Prostate Cancer
Authors: Zhang Xiaotun , Coleman Ilsa M. , Brown Lisha G. , True Lawrence D. , Kollath Lori , Lucas Jared M. , Lam Hung-Ming , Dumpit Ruth , Corey Eva , Chéry Lisly , Lakely Bryce , Higano Celestia S. , Montgomery Bruce , Roudier Martine , Lange Paul H. , Nelson Peter S. , Vessella Robert L. , Morrissey Colm
Published: April 2023

(A) Representative examples of marker response by IHC for CHGA, SYP, and AR in CRPC bone metastases. 05-114: CHGA+/SYP+/AR-, 05-221: CHGA+/SYP+/AR- (white arrow), CHGA-/SYP-AR+ (black arrow). 07-042: CHGA+/SYP+AR+. Percent of (B) CHGA and (C) SYP positive cells in 22 CRPC CHGA+/SYP+ metastases. Virtually all cells in CHGA+/SYP+ metastases had a neuroendocrine phenotype.
Supplementary data from Whole-Exome Sequencing Reveals Defective CYP3A4 Variants Predictive of Paclitaxel Dose-Limiting Neuropathy
Authors: Apellániz-Ruiz María , Lee Mi-Young , Sánchez-Barroso Lara , Gutiérrez-Gutiérrez Gerardo , Calvo Isabel , García-Estévez Laura , Sereno María , García-Donás Jesús , Castelo Beatriz , Guerra Eva , Leandro-García Luis J. , Cascón Alberto , Johansson Inger , Robledo Mercedes , Ingelman-Sundberg Magnus , Rodríguez-Antona Cristina
Published: April 2023

Supplementary data. Supplementary figure legends and supplementary tables
Supplementary Figure 2 from Whole-Exome Sequencing Reveals Defective CYP3A4 Variants Predictive of Paclitaxel Dose-Limiting Neuropathy
Authors: Apellániz-Ruiz María , Lee Mi-Young , Sánchez-Barroso Lara , Gutiérrez-Gutiérrez Gerardo , Calvo Isabel , García-Estévez Laura , Sereno María , García-Donás Jesús , Castelo Beatriz , Guerra Eva , Leandro-García Luis J. , Cascón Alberto , Johansson Inger , Robledo Mercedes , Ingelman-Sundberg Magnus , Rodríguez-Antona Cristina
Published: April 2023

Supplementary Figure 2. Neuropathy risk conditions confer an increased risk of paclitaxel-induced neuropathy and a trend towards treatment modifications.
Table S2 from Sequence Variation in Mature MicroRNA-499 Confers Unfavorable Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy
Authors: Qiu Fuman , Yang Lei , Ling Xiaoxuan , Yang Rongrong , Yang Xiaorong , Zhang Lisha , Fang Wenxiang , Xie Chenli , Huang Dongsheng , Zhou Yifeng , Lu Jiachun
Published: April 2023

Table S2. Information on the TaqMan assay of SNPs in the microRNAs.
File S1 from Sequence Variation in Mature MicroRNA-499 Confers Unfavorable Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy
Authors: Qiu Fuman , Yang Lei , Ling Xiaoxuan , Yang Rongrong , Yang Xiaorong , Zhang Lisha , Fang Wenxiang , Xie Chenli , Huang Dongsheng , Zhou Yifeng , Lu Jiachun
Published: April 2023

File S1. Differentially expressed genes between A549-miRNA-499-T cells and A549-miRNA-499-C cells using microarray analysis. Column A. TargetID: Gene symbol in the genechip; Column B. DiffScore: Difference in the expression score of target gene between the A549-miRNA-499-T cells and A549-miRNA-499-C cells; Column C. DiffPval: P value of the difference calculated by the student's t test. Column D. DEFINITION: Full name of target genes based on the NCBI RefSeq (Build 36.2, Rel 22)database. Column E. ONTOLOGY_FUNCTION: Possible function of the target genes.
Figure S3 from Sequence Variation in Mature MicroRNA-499 Confers Unfavorable Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy
Authors: Qiu Fuman , Yang Lei , Ling Xiaoxuan , Yang Rongrong , Yang Xiaorong , Zhang Lisha , Fang Wenxiang , Xie Chenli , Huang Dongsheng , Zhou Yifeng , Lu Jiachun
Published: April 2023

Figure S3. MicroRNA-499 expression levels in A549 cells transfected with the miR-499-T vector, the miR-499-C vector and an "empty" vector.
Supplementary Figure S5: Cosmic 30 consensus from Mutational Signatures in Breast Cancer: The Problem at the DNA Level
Authors: Nik-Zainal Serena , Morganella Sandro
Published: April 2023

Supplementary Figure S5: Cosmic 30 consensus
Supplementary Table 3 from Deletion of 11q in Neuroblastomas Drives Sensitivity to PARP Inhibition
Authors: Sanmartín Elena , Muñoz Lisandra , Piqueras Marta , Sirerol J. Antoni , Berlanga Pablo , Cañete Adela , Castel Victoria , Font de Mora Jaime
Published: April 2023

Potential pathogenic variants detected by next generation sequencing in 17 11q-deleted neuroblastoma patients (see tab "Patients") as well as in neuroblastoma cell lines used in this study (tab "cell lines"), and functional effect predictions.
Supplementary Legend from Deletion of 11q in Neuroblastomas Drives Sensitivity to PARP Inhibition
Authors: Sanmartín Elena , Muñoz Lisandra , Piqueras Marta , Sirerol J. Antoni , Berlanga Pablo , Cañete Adela , Castel Victoria , Font de Mora Jaime
Published: April 2023

Supplementary Legend
Supplementary Figure 3 from Deletion of 11q in Neuroblastomas Drives Sensitivity to PARP Inhibition
Authors: Sanmartín Elena , Muñoz Lisandra , Piqueras Marta , Sirerol J. Antoni , Berlanga Pablo , Cañete Adela , Castel Victoria , Font de Mora Jaime
Published: April 2023

Molecular karyotype in circos plots of the indicated cell lines. Name of cell line is indicated in the middle of each plot. Allele peacks (inner plots) and weigthed Log2ratio (middle plots) information were obtained from Affymetrix software ChAS and further used to generate circus plots.
Supplemental R File 1-Lab222 from Cytoplasmic Cyclin E Predicts Recurrence in Patients with Breast Cancer
Authors: Hunt Kelly K. , Karakas Cansu , Ha Min Jin , Biernacka Anna , Yi Min , Sahin Aysegul A. , Adjapong Opoku , Hortobagyi Gabriel N. , Bondy Melissa L. , Thompson Patricia A. , Cheung Kwok Leung , Ellis Ian O. , Bacus Sarah , Symmans W. Fraser , Do Kim-Anh , Keyomarsi Khandan
Published: April 2023

R File codes pertaining to the Lab222 cohort
Supplementary Figure S5. Cell proliferation inhibition of cetuximab, FASN inhibitor (EGCG or C75) and the combination. from Preclinical Evaluation of Fatty Acid Synthase and EGFR Inhibition in Triple-Negative Breast Cancer
Authors: Giró-Perafita Ariadna , Palomeras Sònia , Lum David H. , Blancafort Adriana , Viñas Gemma , Oliveras Glòria , Pérez-Bueno Ferran , Sarrats Ariadna , Welm Alana L. , Puig Teresa
Published: April 2023

(A) 231 and 231DXR and (B) HCC and HCCDXR cells were treated with doxorubicin (50-100-150nM) and C75 (20µM for HCC, HCCDXR; 40µM for 231, 231DXR) or the combination for 48h. (C) 231 and 231DXR and (D) HCC and HCCDXR cells were treated with doxorubicin (50-100-150nM), EGCG (100µM for 231, 231DXR; 120µM for HCC, HCCDXR) or the combination of both for 48h. Results shown are mean {plus minus} SEM. *(p < 0.05), **(p < 0.01) and ***(p < 0.001) indicate levels of statistically significance.
Supplemental Table 2 from Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen
Authors: Brechbuhl Heather M. , Finlay-Schultz Jessica , Yamamoto Tomomi M. , Gillen Austin E. , Cittelly Diana M. , Tan Aik-Choon , Sams Sharon B. , Pillai Manoj M. , Elias Anthony D. , Robinson William A. , Sartorius Carol A. , Kabos Peter
Published: April 2023

Tamoxifen responsive genes up-regulated in ER+ breast cancer cells influenced by CD146pos fibroblasts.
supplemental figures from Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients
Authors: Van Roy Nadine , Van Der Linden Malaïka , Menten Björn , Dheedene Annelies , Vandeputte Charlotte , Van Dorpe Jo , Laureys Geneviève , Renard Marleen , Sante Tom , Lammens Tim , De Wilde Bram , Speleman Frank , De Preter Katleen
Published: April 2023

Supplemental figure 1: Comparison of the copy number profiles of 4 cases generated with sWGS on cfDNA (at 100 kb binsize), sWGS on tumor DNA (at 100 kb binsize), sWGS on tumor DNA (at 15 kb binsize) and arrayCGH on tumor DNA (at 180k resolution). Supplemental figure 2 : Heatmap describing the concordance between arrayCGH data on tumor DNA vs sWGS of cfDNA. Numbers on the right reflect the case numbers, followed by a 1 for aCGH data on the tumor, and 2 for sWGS data on the cfDNA; the numbers on the top and bottom indicate the chromosome numbers. Red=copy number gain, blue=copy number loss. Supplemental figure 3: Validation of LIN28B amplification by Q-PCR.Y-axis represents the haploid copy number, X-axis represents the samples. NGP is a NB cell line that was used as a positive control, since this cell line showed gain of LIN28B in arrayCGH, gDNA:genomic DNA, NTC: no template control
Table S3 from Single Dose of the CXCR4 Antagonist BL-8040 Induces Rapid Mobilization for the Collection of Human CD34+ Cells in Healthy Volunteers
Authors: Abraham Michal , Pereg Yaron , Bulvik Baruch , Klein Shiri , Mishalian Inbal , Wald Hana , Eizenberg Orly , Beider Katia , Nagler Arnon , Golan Rottem , Vainstein Abi , Aharon Arnon , Galun Eithan , Caraco Yoseph , Or Reuven , Peled Amnon
Published: April 2023

Drug-related adverse events by preferred term and treatment group
Supplementary Figure 5 from Inhibition of Age-Related Therapy Resistance in Melanoma by Rosiglitazone-Mediated Induction of Klotho
Authors: Behera Reeti , Kaur Amanpreet , Webster Marie R. , Kim Suyeon , Ndoye Abibatou , Kugel Curtis H. , Alicea Gretchen M. , Wang Joshua , Ghosh Kanad , Cheng Phil , Lisanti Sofia , Marchbank Katie , Dang Vanessa , Levesque Mitchell , Dummer Reinhard , Xu Xiaowei , Herlyn Meenhard , Aplin Andrew E. , Roesch Alexander , Caino Cecilia , Altieri Dario C. , Weeraratna Ashani T.
Published: April 2023

Supplementary Figure 5
Supplementary Figure 2 from Inhibition of Age-Related Therapy Resistance in Melanoma by Rosiglitazone-Mediated Induction of Klotho
Authors: Behera Reeti , Kaur Amanpreet , Webster Marie R. , Kim Suyeon , Ndoye Abibatou , Kugel Curtis H. , Alicea Gretchen M. , Wang Joshua , Ghosh Kanad , Cheng Phil , Lisanti Sofia , Marchbank Katie , Dang Vanessa , Levesque Mitchell , Dummer Reinhard , Xu Xiaowei , Herlyn Meenhard , Aplin Andrew E. , Roesch Alexander , Caino Cecilia , Altieri Dario C. , Weeraratna Ashani T.
Published: April 2023

Supplementary Figure 2
Supplementary Table S5 from Improved Risk Assessment by Integrating Molecular and Clinicopathological Factors in Early-stage Endometrial Cancer—Combined Analysis of the PORTEC Cohorts
Authors: Stelloo Ellen , Nout Remi A. , Osse Elisabeth M. , Jürgenliemk-Schulz Ina J. , Jobsen Jan J. , Lutgens Ludy C. , van der Steen-Banasik Elzbieta M. , Nijman Hans W. , Putter Hein , Bosse Tjalling , Creutzberg Carien L. , Smit Vincent T.H.B.M.
Published: April 2023

Univariable analysis of clinicopathological characteristics, molecular subgroups, and potential other classifiers in low-risk early-stage endometrial cancer (n=242).
Supplementary figure 2 from Time-Degenerative Factors and the Risk of Hepatocellular Carcinoma after Antiviral Therapy among Hepatitis C Virus Patients: A Model for Prioritization of Treatment
Authors: Yu Ming-Lung , Huang Chung-Feng , Yeh Ming-Lun , Tsai Pei-Chien , Huang Ching-I. , Hsieh Meng-Hsuan , Hsieh Ming-Yen , Lin Zu-Yau , Chen Shinn-Cherng , Huang Jee-Fu , Dai Chia-Yen , Chuang Wan-Long
Published: April 2023

Risk of HCC in patients with or without SVR stratified by different fibrotic stages
Supplementary Data S1-S16 from Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component
Authors: Avigdor Bracha Erlanger , Beierl Katie , Gocke Christopher D. , Zabransky Daniel J. , Cravero Karen , Kyker-Snowman Kelly , Button Berry , Chu David , Croessmann Sarah , Cochran Rory L. , Connolly Roisin M. , Park Ben H. , Wheelan Sarah J. , Cimino-Mathews Ashley
Published: April 2023

vcf files for 16 WES samples analyzed in this study
Figure S1 from Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component
Authors: Avigdor Bracha Erlanger , Beierl Katie , Gocke Christopher D. , Zabransky Daniel J. , Cravero Karen , Kyker-Snowman Kelly , Button Berry , Chu David , Croessmann Sarah , Cochran Rory L. , Connolly Roisin M. , Park Ben H. , Wheelan Sarah J. , Cimino-Mathews Ashley
Published: April 2023

Supplemental figure S1
Supplementary Table 2 from A Multi-Institution Phase I Trial of Ruxolitinib in Patients with Chronic Myelomonocytic Leukemia (CMML)
Authors: Padron Eric , Dezern Amy , Andrade-Campos Marcio , Vaddi Kris , Scherle Peggy , Zhang Qing , Ma Yan , Balasis Maria E. , Tinsley Sara , Ramadan Hanadi , Zimmerman Cassandra , Steensma David P. , Roboz Gail J. , Lancet Jeffrey E. , List Alan F. , Sekeres Mikkael A. , Komrokji Rami S.
Published: April 2023

Table summarizing all toxicities reported on study.
'Supplemental Table 1' from Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component
Authors: Avigdor Bracha Erlanger , Beierl Katie , Gocke Christopher D. , Zabransky Daniel J. , Cravero Karen , Kyker-Snowman Kelly , Button Berry , Chu David , Croessmann Sarah , Cochran Rory L. , Connolly Roisin M. , Park Ben H. , Wheelan Sarah J. , Cimino-Mathews Ashley
Published: April 2023

Supplemental table S1
Supplementary Methods, Supplementary Table 1, Supplementary Figure Legends from Liquid Biopsies Using Plasma Exosomal Nucleic Acids and Plasma Cell-Free DNA Compared with Clinical Outcomes of Patients with Advanced Cancers
Authors: Möhrmann Lino , Huang Helen J. , Hong David S. , Tsimberidou Apostolia M. , Fu Siqing , Piha-Paul Sarina A. , Subbiah Vivek , Karp Daniel D. , Naing Aung , Krug Anne , Enderle Daniel , Priewasser Tina , Noerholm Mikkel , Eitan Erez , Coticchia Christine , Stoll Georg , Jordan Lisa-Marie , Eng Cathy , Kopetz E. Scott , Skog Johan , Meric-Bernstam Funda , Janku Filip
Published: April 2023

Supplementary Table 1. Sensitivity and specificity for BRAF, KRAS, and EGFR mutations testing of plasma exosomal nucleic acids and cell-free DNA (exoNA) using the next-generation sequencing and plasma cell-free DNA using droplet digital PCR or BEAMing digital PCR.
SFigure 4 from Macropinocytosis of Bevacizumab by Glioblastoma Cells in the Perivascular Niche Affects their Survival
Authors: Müller-Greven Gaëlle , Carlin Cathleen R. , Burgett Monica E. , Ahluwalia Manmeet S. , Lauko Adam , Nowacki Amy S. , Herting Cameron J. , Qadan Maha A. , Bredel Markus , Toms Steven A. , Lathia Justin D. , Hambardzumyan Dolores , Sarkaria Jann N. , Hamerlik Petra , Gladson Candece L.
Published: April 2023

Figure S4 shows FcRn staining largely colocalizes with the endothelial cell marker vWf in xenograft GBM tumors.
Supplementary Tables S7-S10 from The Genomic Landscape of Male Breast Cancers
Authors: Piscuoglio Salvatore , Ng Charlotte K.Y. , Murray Melissa P. , Guerini-Rocco Elena , Martelotto Luciano G. , Geyer Felipe C. , Bidard Francois-Clement , Berman Samuel , Fusco Nicola , Sakr Rita A. , Eberle Carey A. , De Mattos-Arruda Leticia , Macedo Gabriel S. , Akram Muzaffar , Baslan Timour , Hicks James B. , King Tari A. , Brogi Edi , Norton Larry , Weigelt Britta , Hudis Clifford A. , Reis-Filho Jorge S.
Published: April 2023

Supplementary Table S7: Comparative analysis of the frequencies of mutations in luminal A-like and luminal B-like male breast cancer. Supplementary Table S8: Comparative analysis of genes affecting selected functional pathways. Supplementary Table S9: Mutational frequency of male breast cancer vs subsets of female breast cancer from the TCGA study. Supplementary Table S10: Potentially targetable genes mutated exclusively in ER-positive/HER2-negative male breast cancer.
Supplementary Tables S1-S3 from The Genomic Landscape of Male Breast Cancers
Authors: Piscuoglio Salvatore , Ng Charlotte K.Y. , Murray Melissa P. , Guerini-Rocco Elena , Martelotto Luciano G. , Geyer Felipe C. , Bidard Francois-Clement , Berman Samuel , Fusco Nicola , Sakr Rita A. , Eberle Carey A. , De Mattos-Arruda Leticia , Macedo Gabriel S. , Akram Muzaffar , Baslan Timour , Hicks James B. , King Tari A. , Brogi Edi , Norton Larry , Weigelt Britta , Hudis Clifford A. , Reis-Filho Jorge S.
Published: April 2023

Supplementary Table S1: Histologic and immunohistochemical profiling and molecular classification of 59 male breast cancers. Supplementary Table S2: Antibody clones and amplification primers used. Supplementary Table S3: List of 241 genes included in the targeted capture massively parallel sequencing platform.
Supplementary Table S1: Complex Signature Oncology In Vitro Diagnostic Devices from An FDA Perspective on the Regulatory Implications of Complex Signatures to Predict Response to Targeted Therapies
Authors: Beaver Julia A. , Tzou Abraham , Blumenthal Gideon M. , McKee Amy E. , Kim Geoffrey , Pazdur Richard , Philip Reena
Published: April 2023

Supplementary Table S1: Complex Signature Oncology In Vitro Diagnostic Devices
Figure S1 from Clinical Features and Outcomes of Patients with Colorectal Cancers Harboring NRAS Mutations
Authors: Cercek Andrea , Braghiroli Maria Ignez , Chou Joanne F. , Hechtman Jaclyn F. , Kemeny Nancy , Saltz Leonard , Capanu Marinela , Yaeger Rona
Published: April 2023

Supplementary Figure 1
Supplementary Tables S1-S8 from Selective Targeting of Cyclin E1-Amplified High-Grade Serous Ovarian Cancer by Cyclin-Dependent Kinase 2 and AKT Inhibition
Authors: Au-Yeung George , Lang Franziska , Azar Walid J. , Mitchell Chris , Jarman Kate E. , Lackovic Kurt , Aziz Diar , Cullinane Carleen , Pearson Richard B. , Mileshkin Linda , Rischin Danny , Karst Alison M. , Drapkin Ronny , Etemadmoghadam Dariush , Bowtell David D.L.
Published: April 2023

Supplementary Table S1 - RT-PCR Primer sequences used in the study Supplementary Table S2 - CDK2 shRNA sequences used in the study Supplementary Table S3 - Cell lines and genes used in the analysis from Project Achilles Supplementary Table S4 - EC50 values for compounds from primary screen for OVCAR3 and SKOV3 cell lines Supplementary Table S5 - EC50 values for compounds from primary screen for OVCAR3 and OVCAR3-R1 cell lines Supplementary Table S7 - List of compounds and their primary targets tested in the secondary screen for OVCAR3 and OVCAR3-R1 cell lines Supplementary Table S8 - List of combination indexes and type of interaction between compounds tested in the matrix screen
Figure S7 from Hypoxia-Inducible PIM Kinase Expression Promotes Resistance to Antiangiogenic Agents
Authors: Casillas Andrea L. , Toth Rachel K. , Sainz Alva G. , Singh Neha , Desai Ankit A. , Kraft Andrew S. , Warfel Noel A.
Published: April 2023

Simultaneous inhibition of PIM and VEGF reduces colon cancer metastasis
Table S1 from EGFR Mutations and ALK Rearrangements Are Associated with Low Response Rates to PD-1 Pathway Blockade in Non–Small Cell Lung Cancer: A Retrospective Analysis
Authors: Gainor Justin F. , Shaw Alice T. , Sequist Lecia V. , Fu Xiujun , Azzoli Christopher G. , Piotrowska Zofia , Huynh Tiffany G. , Zhao Ling , Fulton Linnea , Schultz Katherine R. , Howe Emily , Farago Anna F. , Sullivan Ryan J. , Stone James R. , Digumarthy Subba , Moran Teresa , Hata Aaron N. , Yagi Yukako , Yeap Beow Y. , Engelman Jeffrey A. , Mino-Kenudson Mari
Published: April 2023

Clinicopathologic Features of EGFR-Mutant and ALK-Positive Patients Included in PD-L1 Expression Analysis
Figure S1 from Hypoxia-Inducible PIM Kinase Expression Promotes Resistance to Antiangiogenic Agents
Authors: Casillas Andrea L. , Toth Rachel K. , Sainz Alva G. , Singh Neha , Desai Ankit A. , Kraft Andrew S. , Warfel Noel A.
Published: April 2023

Treatment with anti-angiogenic agents increases CAIX expression
Supplemental Table 1 from Combined KIT and CTLA-4 Blockade in Patients with Refractory GIST and Other Advanced Sarcomas: A Phase Ib Study of Dasatinib plus Ipilimumab
Authors: D'Angelo Sandra P. , Shoushtari Alexander N. , Keohan Mary Louise , Dickson Mark A. , Gounder Mrinal M. , Chi Ping , Loo Jennifer K. , Gaffney Leigh , Schneider Lee , Patel Zarine , Erinjeri Joseph Patrick , Bluth Mark J. , Sjoberg Ana , Streicher Howard , Takebe Naoko , Qin Li-Xuan , Antonescu Cristina , DeMatteo Ronald P. , Carvajal Richard D. , Tap William D.
Published: April 2023

Table of adverse events grade 1-4, at least possibly related to treatment. All G1-G4 at least possible related toxicity.
Supplemental Materials and Methods from Tumor Resection Recruits Effector T Cells and Boosts Therapeutic Efficacy of Encapsulated Stem Cells Expressing IFNβ in Glioblastomas
Authors: Choi Sung Hugh , Stuckey Daniel W. , Pignatta Sara , Reinshagen Clemens , Khalsa Jasneet Kaur , Roozendaal Nicolaas , Martinez-Quintanilla Jordi , Tamura Kaoru , Keles Erhan , Shah Khalid
Published: April 2023

Supplemental Materials and Methods from Tumor Resection Recruits Effector T Cells and Boosts Therapeutic Efficacy of Encapsulated Stem Cells Expressing IFNβ in Glioblastomas
Supplemental Figure 8 from Tumor Resection Recruits Effector T Cells and Boosts Therapeutic Efficacy of Encapsulated Stem Cells Expressing IFNβ in Glioblastomas
Authors: Choi Sung Hugh , Stuckey Daniel W. , Pignatta Sara , Reinshagen Clemens , Khalsa Jasneet Kaur , Roozendaal Nicolaas , Martinez-Quintanilla Jordi , Tamura Kaoru , Keles Erhan , Shah Khalid
Published: April 2023

MSCs co-expressing HSV-TK and mIFNÃŽÂ² can be selectively eliminated in vitro
Supplementary Figure S2 from Targeted Exome Sequencing of Krebs Cycle Genes Reveals Candidate Cancer–Predisposing Mutations in Pheochromocytomas and Paragangliomas
Authors: Remacha Laura , Comino-Méndez Iñaki , Richter Susan , Contreras Laura , Currás-Freixes María , Pita Guillermo , Letón Rocío , Galarreta Antonio , Torres-Pérez Rafael , Honrado Emiliano , Jiménez Scherezade , Maestre Lorena , Moran Sebastian , Esteller Manel , Satrústegui Jorgina , Eisenhofer Graeme , Robledo Mercedes , Cascón Alberto
Published: April 2023

(A) GOT2 western blot of HeLa cells stably silenced for GOT2 expression by shRNA transfection compared to non-silenced scrambled (Scr) control cells. β-actin was used as a loading control. (B) Number of GOT2 KD HeLa cells after transfection with empty vector (EV), GOT2- WT cDNA, and GOT2- c.357A>T. Cells were seeded into 12-well plates and incubated for various times, as indicated. The counts are reported as means (n=3). A t-test was applied to test for differences. n.s.: not significant.
Suppl. data and methods from Combined Inhibition of Both p110α and p110β Isoforms of Phosphatidylinositol 3-Kinase Is Required for Sustained Therapeutic Effect in PTEN-Deficient, ER+ Breast Cancer
Authors: Hosford Sarah R. , Dillon Lloye M. , Bouley Stephanie J. , Rosati Rachele , Yang Wei , Chen Vivian S. , Demidenko Eugene , Morra Rocco P. , Miller Todd W.
Published: April 2023

Contains suppl. methods, and suppl. figures S1-S13. Fig. S1- Genetic lesions in PTEN predict sensitization to p110β-selective inhibitors. Fig. S2- ER+, PTEN-mutant breast cancer cell lines show reduced PTEN protein expression and increased PIP3 levels. Fig. S3- Treatment with BYL719 or GSK2636771 suppresses PI3K signaling in p110α-driven, PIK3CAmutant T47D or p110β-driven, PTEN-mutant MDA-MB-415 cells, respectively. Fig. S4- p110β inhibition suppresses response to growth factor stimulation. Fig. S5- Growth factor receptor signaling engages both p110α and p110β. Fig. S6- PTEN depletion in ER+, PIK3CA-mutant breast cancer cells increases AKT activation via p110α. Fig. S7- Growth of PTEN-deficient, ER+ breast cancer cells is dependent on ER and p110β. Fig. S8- PTEN-deficient breast cancer cells maintain dependence on p110β for PI3K/AKT signaling upon acquisition of anti-estrogen resistance. Fig. S9- mTORC1 hyperactivation by TSC2 depletion provides minimal protection against a PI3K inhibitor in ER+, PTEN-deficient breast cancer cells. Fig. S10- PI3K inhibition-induced inactivation of Rb predicts subsequent apoptosis in PTEN-deficient, ER+ CAMA-1 breast cancer cells. Fig. S11- ER+, PTEN-deficient breast cancer cells adapted to growth in the presence of a p110β inhibitor exhibit continued dependence on p110β for PIP3/AKT signaling. Fig. S12- Growth of ER+, PTEN-deficient, parental ZR75-1 tumors is inhibited by anti-estrogen treatment. Fig. S13- Combined inhibition of ER and PI3K suppresses tumor cell proliferation in fulv-resistant, ER+, PTEN-deficient breast tumors. Fig. S14- Combined inhibition of ER and PI3K induces early apoptosis in fulv-resistant, ER+, PTENdeficient breast tumors.
Supplemental Figure 10 from Tumor Resection Recruits Effector T Cells and Boosts Therapeutic Efficacy of Encapsulated Stem Cells Expressing IFNβ in Glioblastomas
Authors: Choi Sung Hugh , Stuckey Daniel W. , Pignatta Sara , Reinshagen Clemens , Khalsa Jasneet Kaur , Roozendaal Nicolaas , Martinez-Quintanilla Jordi , Tamura Kaoru , Keles Erhan , Shah Khalid
Published: April 2023

mIFNÃŽÂ² does not activate Chk1 in CT2A mouse GBM cells
Supplementary Figure 1 and 2 from Dual ALK and CDK4/6 Inhibition Demonstrates Synergy against Neuroblastoma
Authors: Wood Andrew C. , Krytska Kateryna , Ryles Hannah T. , Infarinato Nicole R. , Sano Renata , Hansel Theodore D. , Hart Lori S. , King Frederick J. , Smith Timothy R. , Ainscow Edward , Grandinetti Kathryn B. , Tuntland Tove , Kim Sunkyu , Caponigro Giordano , He You Qun , Krupa Shiva , Li Nanxin , Harris Jennifer L. , Mossé Yaël P.
Published: April 2023

1.Western blot analysis of the cleaved caspase-3 and p53 pathways in Ceritinib and Ribociclib treated cells. 2.Combination ALK and CDK 4/6 inhibition leads to enhanced G0/G1 arrest.
Supplementary Figures from Bortezomib Treatment Sensitizes Oncolytic HSV-1–Treated Tumors to NK Cell Immunotherapy
Authors: Yoo Ji Young , Jaime-Ramirez Alena Cristina , Bolyard Chelsea , Dai Hongsheng , Nallanagulagari Tejaswini , Wojton Jeffrey , Hurwitz Brian S. , Relation Theresa , Lee Tae Jin , Lotze Michael T. , Yu Jun-Ge , Zhang Jianying , Croce Carlo M. , Yu Jianhua , Caligiuri Michael A. , Old Matthew , Kaur Balveen
Published: April 2023

Supplementary Figure S1. Effects of combination treatment of both bortezomib and oHSV on cancer cell killing. Supplementary Figure S2. Necrostatin-1 (Nec-1) treatment and RIPK1 knock down did not reduce the bortezomib-induced increase in virus replication. Supplementary Figure S3. Single treatment with bortezomib or oHSV enhances NK cell mediated glioma killing. Supplementary Figure S4. Combination treatment with bortezomib and oHSV enhance mice survival in vivo.
Supplementary Figures S1, S2A, S2B, S3, S4A, S4B from Transcriptional Mechanisms of Resistance to Anti–PD-1 Therapy
Authors: Ascierto Maria L. , Makohon-Moore Alvin , Lipson Evan J. , Taube Janis M. , McMiller Tracee L. , Berger Alan E. , Fan Jinshui , Kaunitz Genevieve J. , Cottrell Tricia R. , Kohutek Zachary A. , Favorov Alexander , Makarov Vladimir , Riaz Nadeem , Chan Timothy A. , Cope Leslie , Hruban Ralph H. , Pardoll Drew M. , Taylor Barry S. , Solit David B. , Iacobuzio-Donahue Christine A. , Topalian Suzanne L.
Published: April 2023

Supplementary figures
Supplementary Figure Legend from Bortezomib Treatment Sensitizes Oncolytic HSV-1–Treated Tumors to NK Cell Immunotherapy
Authors: Yoo Ji Young , Jaime-Ramirez Alena Cristina , Bolyard Chelsea , Dai Hongsheng , Nallanagulagari Tejaswini , Wojton Jeffrey , Hurwitz Brian S. , Relation Theresa , Lee Tae Jin , Lotze Michael T. , Yu Jun-Ge , Zhang Jianying , Croce Carlo M. , Yu Jianhua , Caligiuri Michael A. , Old Matthew , Kaur Balveen
Published: April 2023

Supplementary Figure Legend
Differentially expressed chemokine genes (fold change >2) in esophageal cancer tissues from Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis
Authors: Yamamura Kensuke , Baba Yoshifumi , Nakagawa Shigeki , Mima Kosuke , Miyake Keisuke , Nakamura Kenichi , Sawayama Hiroshi , Kinoshita Koichi , Ishimoto Takatsugu , Iwatsuki Masaaki , Sakamoto Yasuo , Yamashita Yoichi , Yoshida Naoya , Watanabe Masayuki , Baba Hideo
Published: April 2023

Differentially expressed chemokine genes (fold change >2) in esophageal cancer tissues
Supplementary Tables from TOP2A and EZH2 Provide Early Detection of an Aggressive Prostate Cancer Subgroup
Authors: Labbé David P. , Sweeney Christopher J. , Brown Myles , Galbo Phillip , Rosario Spencer , Wadosky Kristine M. , Ku Sheng-Yu , Sjöström Martin , Alshalalfa Mohammed , Erho Nicholas , Davicioni Elai , Karnes R. Jeffrey , Schaeffer Edward M. , Jenkins Robert B. , Den Robert B. , Ross Ashley E. , Bowden Michaela , Huang Ying , Gray Kathryn P. , Feng Felix Y. , Spratt Daniel E. , Goodrich David W. , Eng Kevin H. , Ellis Leigh
Published: April 2023

Supplement Table 1: Prostate cancer cohorts used for genome wide expression profiling Supplement Table 2: GSEA Hallmark - Significant enrichments Supplement Table 3: GSEA Oncogenic Signatures - Significant enrichments Supplement Table 4: Dana Farber Cancer Institute tissue microarray (TMA) sample information Supplement Table 5: Differentially expressed genes (DEG) Supplement Table 6: Overlapping differentially expressed genes (DEG) Supplement Table 7: Univariate survival analysis including TOP2A/EZH2 expression together with other variables and their association on clinical outcomes (Meta Cohort, N = 631) Supplement Table 8: Multivariate survival analysis including TOP2A/EZH2 expression together with standard clinical variables and their association on clinical outcomes (meta cohort, N = 631) Supplement Table 9: Multivariate survival analysis including TOP2A/EZH2 expression together with Decipher and standard clinical variables and their association on clinical outcomes (Meta Cohort, N = 631)
Table S2 from T2–FLAIR Mismatch, an Imaging Biomarker for IDH and 1p/19q Status in Lower-grade Gliomas: A TCGA/TCIA Project
Authors: Patel Sohil H. , Poisson Laila M. , Brat Daniel J. , Zhou Yueren , Cooper Lee , Snuderl Matija , Thomas Cheddhi , Franceschi Ana M. , Griffith Brent , Flanders Adam E. , Golfinos John G. , Chi Andrew S. , Jain Rajan
Published: April 2023

GSEA results comparing gene pathway expression differences between the 125 TCGA/TCIA gliomas differentiated by the T2-FLAIR mismatch sign. ES = Enrichment Score. NES = Normalized Enrichment Score. NOM = Nominal. FDR = False Discovery Rate. FWER = Family-wise error rate.
Supplemental Figure S9 from Targeting the Leukemia Antigen PR1 with Immunotherapy for the Treatment of Multiple Myeloma
Authors: Alatrash Gheath , Perakis Alexander A. , Kerros Celine , Peters Haley L. , Sukhumalchandra Pariya , Zhang Mao , Jakher Haroon , Zope Madhushree , Patenia Rebecca , Sergeeva Anna , Yi Shuhua , Young Ken H. , Philips Anne V. , Cernosek Amanda M. , Garber Haven R. , Qiao Na , Weng Jinsheng , St John Lisa S. , Lu Sijie , Clise-Dwyer Karen , Mittendorf Elizabeth A. , Ma Qing , Molldrem Jeffrey J.
Published: April 2023

Gating strategy used to determine PR1 expression and co-stimulatory molecule expression on patient bone marrow multiple myeloma cells
Supplemental Figure 3 from Ensartinib (X-396) in ALK-Positive Non–Small Cell Lung Cancer: Results from a First-in-Human Phase I/II, Multicenter Study
Authors: Horn Leora , Infante Jeffrey R. , Reckamp Karen L. , Blumenschein George R. , Leal Ticiana A. , Waqar Saiama N. , Gitlitz Barbara J. , Sanborn Rachel E. , Whisenant Jennifer G. , Du Liping , Neal Joel W. , Gockerman Jon P. , Dukart Gary , Harrow Kimberly , Liang Chris , Gibbons James J. , Holzhausen Allison , Lovly Christine M. , Wakelee Heather A.
Published: April 2023

Supplemental Figure 3. Best percentage change from baseline in sum of target lesions is presented for the ALK-positive evaluable patients at 200 mg who had received prior crizotinib and as second-generation ALK TKI. Dashed lines indicate RECIST v1.1 cut-offs for partial response and progressive disease. Of the 16 patients, four had partial responses and four had stable disease. The color scheme represents which second-generation ALK TKI that patient received after crizotinib. Of note, the primary lesion of one of the 16 patients was too small, and thus indeterminate, at the post-baseline assessment, therefore a change in tumor size is not available. This patient had received, in order, prior crizotinib, alectinib, and ceritinib, and developed progression on ensartinib in a non-target brain lesion prior to cycle 3. *Denotes those patients with progressive disease as the best response. >Denotes patients still on study at the time of data cutoff.