bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from The sTRA Plasma Biomarker: Blinded Validation of Improved Accuracy Over CA19-9 in Pancreatic Cancer Diagnosis
Authors: Staal Ben , Liu Ying , Barnett Daniel , Hsueh Peter , He Zonglin , Gao ChongFeng , Partyka Katie , Hurd Mark W. , Singhi Aatur D. , Drake Richard R. , Huang Ying , Maitra Anirban , Brand Randall E. , Haab Brian B.
Published: April 2023

Supplementary Methods: 1. Sandwich immunoassays on microarrays. 2. Processing the samples and the biomarker data. 3. Immunofluorescence on tissue microarrays. 4. Cell culture and measuring cell-surface sTRA and CA19-9. 5. Patient-derived xenografts. Supplementary Tables (provided as separate Excel files): Table S1. Training and validation set data. Table S2. Covariates. Table S3. Application of the specificity-optimized panel to the test set. Table S4. Application of the specificity-optimized panel to the test set. Supplementary Figures: Figure S1. Correlations between secreted levels and cellular expression. Figure S2. Individual marker performance in stage I-II and stage III-IV cancers.
Supplementary Methods from NKT Cells Coexpressing a GD2-Specific Chimeric Antigen Receptor and IL15 Show Enhanced In Vivo Persistence and Antitumor Activity against Neuroblastoma
Authors: Xu Xin , Huang Wei , Heczey Andras , Liu Daofeng , Guo Linjie , Wood Michael , Jin Jingling , Courtney Amy N. , Liu Bin , Di Pierro Erica J. , Hicks John , Barragan Gabriel A. , Ngai Ho , Chen Yuhui , Savoldo Barbara , Dotti Gianpietro , Metelitsa Leonid S.
Published: April 2023

Supplementary methods
Figure S7 from A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)
Authors: Mazzu Ying Z. , Armenia Joshua , Chakraborty Goutam , Yoshikawa Yuki , Coggins Si'Ana A. , Nandakumar Subhiksha , Gerke Travis A. , Pomerantz Mark M. , Qiu Xintao , Zhao Huiyong , Atiq Mohammad , Khan Nabeela , Komura Kazumasa , Lee Gwo-Shu Mary , Fine Samson W. , Bell Connor , O'Connor Edward , Long Henry W. , Freedman Matthew L. , Kim Baek , Kantoff Philip W.
Published: April 2023

Figure S7
Supplementary figure legends from Combination of TMB and CNA Stratifies Prognostic and Predictive Responses to Immunotherapy Across Metastatic Cancer
Authors: Liu Li , Bai Xue , Wang Jian , Tang Xin-Ran , Wu De-Hua , Du Sha-Sha , Du Xiu-Ju , Zhang Yao-Wei , Zhu Hong-Bo , Fang Yuan , Guo Ze-Qin , Zeng Qin , Guo Xue-Jun , Liu Zhu , Dong Zhong-Yi
Published: April 2023

Supplementary figure legends
Figure S4 from A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)
Authors: Mazzu Ying Z. , Armenia Joshua , Chakraborty Goutam , Yoshikawa Yuki , Coggins Si'Ana A. , Nandakumar Subhiksha , Gerke Travis A. , Pomerantz Mark M. , Qiu Xintao , Zhao Huiyong , Atiq Mohammad , Khan Nabeela , Komura Kazumasa , Lee Gwo-Shu Mary , Fine Samson W. , Bell Connor , O'Connor Edward , Long Henry W. , Freedman Matthew L. , Kim Baek , Kantoff Philip W.
Published: April 2023

Figure S4
Figure S2 from A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)
Authors: Mazzu Ying Z. , Armenia Joshua , Chakraborty Goutam , Yoshikawa Yuki , Coggins Si'Ana A. , Nandakumar Subhiksha , Gerke Travis A. , Pomerantz Mark M. , Qiu Xintao , Zhao Huiyong , Atiq Mohammad , Khan Nabeela , Komura Kazumasa , Lee Gwo-Shu Mary , Fine Samson W. , Bell Connor , O'Connor Edward , Long Henry W. , Freedman Matthew L. , Kim Baek , Kantoff Philip W.
Published: April 2023

Figure S2
Figure S3 from Combination of TMB and CNA Stratifies Prognostic and Predictive Responses to Immunotherapy Across Metastatic Cancer
Authors: Liu Li , Bai Xue , Wang Jian , Tang Xin-Ran , Wu De-Hua , Du Sha-Sha , Du Xiu-Ju , Zhang Yao-Wei , Zhu Hong-Bo , Fang Yuan , Guo Ze-Qin , Zeng Qin , Guo Xue-Jun , Liu Zhu , Dong Zhong-Yi
Published: April 2023

Kaplan-Meier curves of overall survival (OS) and progression-free survival (PFS) according to TMB and CNA in patients receiving immune checkpoint inhibitor treatment. (A) Kaplan-Meier curves of OS based on TMB or CNA classification in SKCM ICI cohort treated with anti-CTLA-4. (B) Kaplan-Meier curves of PFS based on TMB or CNA classification in MSK NSCLC ICI cohort treated with anti-PD1/L1. Kaplan-Meier curves of (C) OS and (D) PFS based on TMB or CNA classification in Dana-Farber ICI cohort treated with anti-PD1/L1. We calculated p values using the log-rank test.
Figure S1 from A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2)
Authors: Mazzu Ying Z. , Armenia Joshua , Chakraborty Goutam , Yoshikawa Yuki , Coggins Si'Ana A. , Nandakumar Subhiksha , Gerke Travis A. , Pomerantz Mark M. , Qiu Xintao , Zhao Huiyong , Atiq Mohammad , Khan Nabeela , Komura Kazumasa , Lee Gwo-Shu Mary , Fine Samson W. , Bell Connor , O'Connor Edward , Long Henry W. , Freedman Matthew L. , Kim Baek , Kantoff Philip W.
Published: April 2023

Figure S1
Figure S2 from Combination of TMB and CNA Stratifies Prognostic and Predictive Responses to Immunotherapy Across Metastatic Cancer
Authors: Liu Li , Bai Xue , Wang Jian , Tang Xin-Ran , Wu De-Hua , Du Sha-Sha , Du Xiu-Ju , Zhang Yao-Wei , Zhu Hong-Bo , Fang Yuan , Guo Ze-Qin , Zeng Qin , Guo Xue-Jun , Liu Zhu , Dong Zhong-Yi
Published: April 2023

Relationship between CNA level and TMB in (A) MSK pan-cancer non-ICI treated cohort and (B) other three ICI-treated cohorts (MSK NSCLC, SKCM, and Dana-Farber ICI cohort). For each cancer type and each cohort, a plot is shown containing the CNA level versus tumor mutation burden. The spearman correlation coefficient and P value are shown.
Figure S1 from Combination of TMB and CNA Stratifies Prognostic and Predictive Responses to Immunotherapy Across Metastatic Cancer
Authors: Liu Li , Bai Xue , Wang Jian , Tang Xin-Ran , Wu De-Hua , Du Sha-Sha , Du Xiu-Ju , Zhang Yao-Wei , Zhu Hong-Bo , Fang Yuan , Guo Ze-Qin , Zeng Qin , Guo Xue-Jun , Liu Zhu , Dong Zhong-Yi
Published: April 2023

Study flow: The flowchart of our study design and specific cohort selected.
Supplementary Legend from EZH2 Is Overexpressed in BRCA1-like Breast Tumors and Predictive for Sensitivity to High-Dose Platinum-Based Chemotherapy
Authors: Puppe Julian , Opdam Mark , Schouten Philip C. , Jóźwiak Katarzyna , Lips Esther , Severson Tesa , van de Ven Marieke , Brambillasca Chiara , Bouwman Peter , van Tellingen Olaf , Bernards René , Wesseling Jelle , Eichler Christian , Thangarajah Fabinshy , Malter Wolfram , Pandey Gaurav Kumar , Ozretić Luka , Caldas Carlos , van Lohuizen Maarten , Hauptmann Michael , Rhiem Kerstin , Hahnen Eric , Reinhardt H. Christian , Büttner Reinhard , Mallmann Peter , Schömig-Markiefka Birgid , Schmutzler Rita , Linn Sabine , Jonkers Jos
Published: April 2023

Supplementary Legend
Supplemental Table 1 from Prospective Genotyping of Hepatocellular Carcinoma: Clinical Implications of Next-Generation Sequencing for Matching Patients to Targeted and Immune Therapies
Authors: Harding James J. , Nandakumar Subhiksha , Armenia Joshua , Khalil Danny N. , Albano Melanie , Ly Michele , Shia Jinru , Hechtman Jaclyn F. , Kundra Ritika , El Dika Imane , Do Richard K. , Sun Yichao , Kingham T. Peter , D'Angelica Michael I. , Berger Michael F. , Hyman David M. , Jarnagin William , Klimstra David S. , Janjigian Yelena Y. , Solit David B. , Schultz Nikolaus , Abou-Alfa Ghassan K.
Published: April 2023

MSK IMPACT Gene Panels
Supplemental Figure 1 from Prospective Genotyping of Hepatocellular Carcinoma: Clinical Implications of Next-Generation Sequencing for Matching Patients to Targeted and Immune Therapies
Authors: Harding James J. , Nandakumar Subhiksha , Armenia Joshua , Khalil Danny N. , Albano Melanie , Ly Michele , Shia Jinru , Hechtman Jaclyn F. , Kundra Ritika , El Dika Imane , Do Richard K. , Sun Yichao , Kingham T. Peter , D'Angelica Michael I. , Berger Michael F. , Hyman David M. , Jarnagin William , Klimstra David S. , Janjigian Yelena Y. , Solit David B. , Schultz Nikolaus , Abou-Alfa Ghassan K.
Published: April 2023

Supplemental Figure 1: Distribution of tumor mutation burden (TMB) across different tumor types, comparing TMB in this HCC cohort (N=127) to the most common other tumor types in the MSK-IMPACT clinical sequencing cohort. The mutation rate was plotted as in (Zehir et al. Nat Med 2017).47
Figure S6 from Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations
Authors: Rodrigues Manuel , Mobuchon Lenha , Houy Alexandre , Alsafadi Samar , Baulande Sylvain , Mariani Odette , Marande Benjamin , Ait Rais Khadija , Van der Kooij Monique K. , Kapiteijn Ellen , Gassama Sieta , Gardrat Sophie , Barnhill Raymond L. , Servois Vincent , Dendale Rémi , Putterman Marc , Tick Sarah , Piperno-Neumann Sophie , Cassoux Nathalie , Pierron Gaëlle , Waterfall Joshua J. , Roman-Roman Sergio , Mariani Pascale , Stern Marc-Henri
Published: April 2023

Supplementary figure 6 - Comparisons of CCFs between samples including inter- and intra-metastatic comparisons in MBD4pro samples.
Figure S5 from Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations
Authors: Rodrigues Manuel , Mobuchon Lenha , Houy Alexandre , Alsafadi Samar , Baulande Sylvain , Mariani Odette , Marande Benjamin , Ait Rais Khadija , Van der Kooij Monique K. , Kapiteijn Ellen , Gassama Sieta , Gardrat Sophie , Barnhill Raymond L. , Servois Vincent , Dendale Rémi , Putterman Marc , Tick Sarah , Piperno-Neumann Sophie , Cassoux Nathalie , Pierron Gaëlle , Waterfall Joshua J. , Roman-Roman Sergio , Mariani Pascale , Stern Marc-Henri
Published: April 2023

Supplementary figure 5 - Pyclone profiles of all 25 cases
Table S5 from Germline DNA Sequencing Reveals Novel Mutations Predictive of Overall Survival in a Cohort of Patients with Pancreatic Cancer
Authors: Goldstein Jennifer B. , Zhao Li , Wang Xuemei , Ghelman Yael , Overman Michael J. , Javle Milind M. , Shroff Rachna T. , Varadhachary Gauri R. , Wolff Robert A. , McAllister Florencia , Futreal Andrew , Fogelman David R.
Published: April 2023

Chemotherapy Response Rate by Mutation Status of Sequenced Cohort (n = 133)
Table S4 from Germline DNA Sequencing Reveals Novel Mutations Predictive of Overall Survival in a Cohort of Patients with Pancreatic Cancer
Authors: Goldstein Jennifer B. , Zhao Li , Wang Xuemei , Ghelman Yael , Overman Michael J. , Javle Milind M. , Shroff Rachna T. , Varadhachary Gauri R. , Wolff Robert A. , McAllister Florencia , Futreal Andrew , Fogelman David R.
Published: April 2023

Univariate Cox proportional hazards model for overall survival among all 233 patients (n deaths=211).
Supplementary Tables S1-S4 from AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses MCL-1 and Induces Apoptosis in Hematologic Cancer Cells
Authors: Cidado Justin , Boiko Scott , Proia Theresa , Ferguson Douglas , Criscione Steven W. , San Martin Maryann , Pop-Damkov Petar , Su Nancy , Roamio Franklin Valar Nila , Sekhar Reddy Chilamakuri Chandra , D'Santos Clive S. , Shao Wenlin , Saeh Jamal C. , Koch Raphael , Weinstock David M. , Zinda Michael , Fawell Stephen E. , Drew Lisa
Published: April 2023

List of antibodies (S1), PK/PD/efficacy model parameters (S2), putative cancer-associated genes (S3), and transcripts modulated by AZD4573 (S4).
Table S3 from Germline DNA Sequencing Reveals Novel Mutations Predictive of Overall Survival in a Cohort of Patients with Pancreatic Cancer
Authors: Goldstein Jennifer B. , Zhao Li , Wang Xuemei , Ghelman Yael , Overman Michael J. , Javle Milind M. , Shroff Rachna T. , Varadhachary Gauri R. , Wolff Robert A. , McAllister Florencia , Futreal Andrew , Fogelman David R.
Published: April 2023

Univariate Cox proportional hazards model for overall survival among 133 patients (n deaths = 130).
Supplementary Figure S5 from AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses MCL-1 and Induces Apoptosis in Hematologic Cancer Cells
Authors: Cidado Justin , Boiko Scott , Proia Theresa , Ferguson Douglas , Criscione Steven W. , San Martin Maryann , Pop-Damkov Petar , Su Nancy , Roamio Franklin Valar Nila , Sekhar Reddy Chilamakuri Chandra , D'Santos Clive S. , Shao Wenlin , Saeh Jamal C. , Koch Raphael , Weinstock David M. , Zinda Michael , Fawell Stephen E. , Drew Lisa
Published: April 2023

In vitro sensitivity to AZD4573 accurately predicts in vivo efficacy in hematological tumor xenograft models, and combinations with venetoclax are efficacious and tolerated.
Supplementary Figure S4 from AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses MCL-1 and Induces Apoptosis in Hematologic Cancer Cells
Authors: Cidado Justin , Boiko Scott , Proia Theresa , Ferguson Douglas , Criscione Steven W. , San Martin Maryann , Pop-Damkov Petar , Su Nancy , Roamio Franklin Valar Nila , Sekhar Reddy Chilamakuri Chandra , D'Santos Clive S. , Shao Wenlin , Saeh Jamal C. , Koch Raphael , Weinstock David M. , Zinda Michael , Fawell Stephen E. , Drew Lisa
Published: April 2023

Intermittent dosing of AZD4573 drives regression of hematological tumor xenografts as predicted by a PK/PD/efficacy model.
Supplementary Data from Development of 2 Bromodomain and Extraterminal Inhibitors With Distinct Pharmacokinetic and Pharmacodynamic Profiles for the Treatment of Advanced Malignancies
Authors: Falchook Gerald , Rosen Seth , LoRusso Patricia , Watts Justin , Gupta Shilpa , Coombs Catherine C. , Talpaz Moshe , Kurzrock Razelle , Mita Monica , Cassaday Ryan , Harb Wael , Peguero Julio , Smith David C. , Piha-Paul Sarina A. , Szmulewitz Russ , Noel Marcus S. , Yeleswaram Swamy , Liu Phillip , Switzky Julie , Zhou Gongfu , Zheng Fred , Mehta Amitkumar
Published: April 2023

Supplementary Figure 1
Supplementary Data from Development of 2 Bromodomain and Extraterminal Inhibitors With Distinct Pharmacokinetic and Pharmacodynamic Profiles for the Treatment of Advanced Malignancies
Authors: Falchook Gerald , Rosen Seth , LoRusso Patricia , Watts Justin , Gupta Shilpa , Coombs Catherine C. , Talpaz Moshe , Kurzrock Razelle , Mita Monica , Cassaday Ryan , Harb Wael , Peguero Julio , Smith David C. , Piha-Paul Sarina A. , Szmulewitz Russ , Noel Marcus S. , Yeleswaram Swamy , Liu Phillip , Switzky Julie , Zhou Gongfu , Zheng Fred , Mehta Amitkumar
Published: April 2023

Supplementary Figure 2
Supplementary Data from Targeting EZH2 Enhances Antigen Presentation, Antitumor Immunity, and Circumvents Anti–PD-1 Resistance in Head and Neck Cancer
Authors: Zhou Liye , Mudianto Tenny , Ma Xiaojing , Riley Rachel , Uppaluri Ravindra
Published: April 2023

8 supplementary figures
Table S1 from Photodynamic Therapy for the Treatment of Vertebral Metastases: A Phase I Clinical Trial
Authors: Fisher Carl , Ali Zakariya , Detsky Jay , Sahgal Arjun , David Elizabeth , Kunz Monica , Akens Margarete , Chow Edward , Whyne Cari , Burch Shane , Wilson Brian C. , Yee Albert
Published: April 2023

Table S1 highlights the inclusion/exclusion criteria for the PDT clinical trial in table format.
Figure S1 from Photodynamic Therapy for the Treatment of Vertebral Metastases: A Phase I Clinical Trial
Authors: Fisher Carl , Ali Zakariya , Detsky Jay , Sahgal Arjun , David Elizabeth , Kunz Monica , Akens Margarete , Chow Edward , Whyne Cari , Burch Shane , Wilson Brian C. , Yee Albert
Published: April 2023

Figure S1 shows an overview of the PDT fiber set-up and placement for a kyphoplasty case.
Figures S1, S2, S3, S4, S5 from A Pilot Trial of the Combination of Transgenic NY-ESO-1–reactive Adoptive Cellular Therapy with Dendritic Cell Vaccination with or without Ipilimumab
Authors: Nowicki Theodore S. , Berent-Maoz Beata , Cheung-Lau Gardenia , Huang Rong Rong , Wang Xiaoyan , Tsoi Jennifer , Kaplan-Lefko Paula , Cabrera Paula , Tran Justin , Pang Jia , Macabali Mignonette , Garcilazo Ivan Perez , Carretero Ignacio Baselga , Kalbasi Anusha , Cochran Alistair J. , Grasso Catherine S. , Hu-Lieskovan Siwen , Chmielowski Bartosz , Comin-Anduix Begoña , Singh Arun , Ribas Antoni
Published: April 2023

Supplemental Figures
Table S1 from Functional Genomics Identifies Hepatitis-Induced STAT3–TYRO3–STAT3 Signaling as a Potential Therapeutic Target of Hepatoma
Authors: Tsai Chia-Liang , Chang Jeng-Shou , Yu Ming-Chin , Lee Chern-Horng , Chen Tse-Ching , Chuang Wen-Yu , Kuo Wei-Liang , Lin Chen-Chun , Lin Shi-Ming , Hsieh Sen-Yung
Published: April 2023

RTK expression profiles in normal, early HCC, and advanced HCC tissues.
Figure S1 from Preclinical Comparison of the Blood–brain barrier Permeability of Osimertinib with Other EGFR TKIs
Authors: Colclough Nicola , Chen Kan , Johnström Peter , Strittmatter Nicole , Yan Yumei , Wrigley Gail L. , Schou Magnus , Goodwin Richard , Varnäs Katarina , Adua Sally J. , Zhao Minghui , Nguyen Don X. , Maglennon Gareth , Barton Peter , Atkinson James , Zhang Lin , Janefeldt Annika , Wilson Joanne , Smith Aaron , Takano Akihiro , Arakawa Ryosuke , Kondrashov Mikhail , Malmquist Jonas , Revunov Evgeny , Vazquez-Romero Ana , Moein Mohammad Mahdi , Windhorst Albert D. , Karp Natasha A. , Finlay M. Raymond V. , Ward Richard A. , Yates James W.T. , Smith Paul D. , Farde Lars , Cheng Zack , Cross Darren A.E.
Published: April 2023

Supplementary Figure S1 - Structure and position of label for compounds assessed for BBB penetrance in non human primates (NHP). Majority of compounds were labelled with carbon-11 except afatinib which was labelled with fluorine-18. (*) Indicates position for carbon-11 label
Supplementary Data (for Review only) from Functional Genomics Identifies Hepatitis-Induced STAT3–TYRO3–STAT3 Signaling as a Potential Therapeutic Target of Hepatoma
Authors: Tsai Chia-Liang , Chang Jeng-Shou , Yu Ming-Chin , Lee Chern-Horng , Chen Tse-Ching , Chuang Wen-Yu , Kuo Wei-Liang , Lin Chen-Chun , Lin Shi-Ming , Hsieh Sen-Yung
Published: April 2023

Supplemental information of Materials and Methods
Suppl Fig 6 from Targeting Resistance against the MDM2 Inhibitor RG7388 in Glioblastoma Cells by the MEK Inhibitor Trametinib
Authors: Berberich Anne , Kessler Tobias , Thomé Carina M. , Pusch Stefan , Hielscher Thomas , Sahm Felix , Oezen Iris , Schmitt Lara-Marie , Ciprut Sara , Hucke Nanina , Ruebmann Petra , Fischer Manuel , Lemke Dieter , Breckwoldt Michael O. , von Deimling Andreas , Bendszus Martin , Platten Michael , Wick Wolfgang
Published: April 2023

IGFBP1 expression in glioblastoma cell lines and after occurrence of RG7388 resistance.
Supplementary Tables 1-6 from Inactivating NF1 Mutations Are Enriched in Advanced Breast Cancer and Contribute to Endocrine Therapy Resistance
Authors: Pearson Alex , Proszek Paula , Pascual Javier , Fribbens Charlotte , Shamsher Monee K. , Kingston Belinda , O'Leary Ben , Herrera-Abreu Maria T. , Cutts Rosalind J. , Garcia-Murillas Isaac , Bye Hannah , Walker Brian A. , Gonzalez De Castro David , Yuan Lina , Jamal Sabri , Hubank Mike , Lopez-Knowles Elena , Schuster Eugene F. , Dowsett Mitch , Osin Peter , Nerurkar Ashutosh , Parton Marina , Okines Alicia F.C. , Johnston Stephen R.D. , Ring Alistair , Turner Nicholas C.
Published: April 2023

Supplementary Table 1. Targets of The Breast NGS v1.0 capture panel. Supplementary Table 2. Gene list of NanoString nCounter{trade mark, serif} custom codeset. Supplementary Table 3. Gene list of Human Estrogen Receptor RT2 Profiler PCR Array (330231, PAHS-005ZA-24, Qiagen) Supplementary Table 4. Lines of treatment of patients with ESR1 and NF1 mutations. Supplementary Table 5. Disease free survival for mutated genes with incidence {greater than or equal to}5% presented by HR+/HER2-, HER2+ and TNBC subtype. Supplementary Table 6. Advanced overall survival for mutated genes with incidence {greater than or equal to}5% presented by HR+/HER2-, HER2+ and TNBC subtype
Supplementary Figure Legend from Inactivating NF1 Mutations Are Enriched in Advanced Breast Cancer and Contribute to Endocrine Therapy Resistance
Authors: Pearson Alex , Proszek Paula , Pascual Javier , Fribbens Charlotte , Shamsher Monee K. , Kingston Belinda , O'Leary Ben , Herrera-Abreu Maria T. , Cutts Rosalind J. , Garcia-Murillas Isaac , Bye Hannah , Walker Brian A. , Gonzalez De Castro David , Yuan Lina , Jamal Sabri , Hubank Mike , Lopez-Knowles Elena , Schuster Eugene F. , Dowsett Mitch , Osin Peter , Nerurkar Ashutosh , Parton Marina , Okines Alicia F.C. , Johnston Stephen R.D. , Ring Alistair , Turner Nicholas C.
Published: April 2023

Supplementary Figure Legend
Suppl Fig 2 from Targeting Resistance against the MDM2 Inhibitor RG7388 in Glioblastoma Cells by the MEK Inhibitor Trametinib
Authors: Berberich Anne , Kessler Tobias , Thomé Carina M. , Pusch Stefan , Hielscher Thomas , Sahm Felix , Oezen Iris , Schmitt Lara-Marie , Ciprut Sara , Hucke Nanina , Ruebmann Petra , Fischer Manuel , Lemke Dieter , Breckwoldt Michael O. , von Deimling Andreas , Bendszus Martin , Platten Michael , Wick Wolfgang
Published: April 2023

Synergistic effects of RG7388 treatment and radiotherapy on inhibition of proliferation.
Supplementary Figure 5 from Inactivating NF1 Mutations Are Enriched in Advanced Breast Cancer and Contribute to Endocrine Therapy Resistance
Authors: Pearson Alex , Proszek Paula , Pascual Javier , Fribbens Charlotte , Shamsher Monee K. , Kingston Belinda , O'Leary Ben , Herrera-Abreu Maria T. , Cutts Rosalind J. , Garcia-Murillas Isaac , Bye Hannah , Walker Brian A. , Gonzalez De Castro David , Yuan Lina , Jamal Sabri , Hubank Mike , Lopez-Knowles Elena , Schuster Eugene F. , Dowsett Mitch , Osin Peter , Nerurkar Ashutosh , Parton Marina , Okines Alicia F.C. , Johnston Stephen R.D. , Ring Alistair , Turner Nicholas C.
Published: April 2023

CDK4/6 inhibition partly overcomes NF1 loss in T47D cells
Figure S4 from Elastography Can Map the Local Inverse Relationship between Shear Modulus and Drug Delivery within the Pancreatic Ductal Adenocarcinoma Microenvironment
Authors: Wang Hexuan , Mislati Reem , Ahmed Rifat , Vincent Phuong , Nwabunwanne Solumtochukwu F. , Gunn Jason R. , Pogue Brian W. , Doyley Marvin M.
Published: April 2023

The analysis for collagen density for the AsPC-1 (left) and BxPC-3 (right) tumor in relation to tumor shear modulus. (a) and (b) sonograms of representative AsPC-1 tumor and a BxPC-3 tumors. The corresponding shear modulus elastograms (c) and (d). The Masson's Trichrome stained histological images are shown in (e) to (f). (g) scatter plot of mean collagen density as a function of mean shear modulus.
Figure S3 from Elastography Can Map the Local Inverse Relationship between Shear Modulus and Drug Delivery within the Pancreatic Ductal Adenocarcinoma Microenvironment
Authors: Wang Hexuan , Mislati Reem , Ahmed Rifat , Vincent Phuong , Nwabunwanne Solumtochukwu F. , Gunn Jason R. , Pogue Brian W. , Doyley Marvin M.
Published: April 2023

Illustrates the color segmentation technique that was applied to Masson's Trichrome (MT) stained images. The MT stained image was converted from RGB color space (a) to La*b* color space. The red arrows marked the proteoglycans from degenerated tissue and remnants from the gelatin phantom. The black arrows marked the collagen fibers in the PDAC tumor stroma. The a* and b* channels of the MT stained image in La*b* color space were shown in (c) and (d). Four sample regions of different colors matching distinct tumor features were selected, and their average a* and b* channel values were calculated in (e). Each pixel in the MT stained image was classified into the four sample regions by calculating the Euclidean distance between the pixel and each sample region. Shortest Euclidean distance to a sample region determined the tumor feature classification of the pixel. The blue collagen fibers were segmented in (f); (g) shows the proteoglycans and gelatin remnants; (h) shows the cytoplasms and (i) shows the white, vacant background of the MT image.
Supplementary Data from Multicenter Phase I Study of Erdafitinib (JNJ-42756493), Oral Pan-Fibroblast Growth Factor Receptor Inhibitor, in Patients with Advanced or Refractory Solid Tumors
Authors: Bahleda Rastislav , Italiano Antoine , Hierro Cinta , Mita Alain , Cervantes Andres , Chan Nancy , Awad Mark , Calvo Emiliano , Moreno Victor , Govindan Ramaswamy , Spira Alexander , Gonzalez Martha , Zhong Bob , Santiago-Walker Ademi , Poggesi Italo , Parekh Trilok , Xie Hong , Infante Jeffrey , Tabernero Josep
Published: April 2023

Supplementary Table S1. Arithmetic Mean {plus minus} SD Plasma Erdafitinib Pharmacokinetic Parameters after the First Erdafitinib Administration (Cycle 1 Day 1) or at Steady-State (Cycle 2 Day 1) in Patients Assigned to the Continuous Daily Dosing or the Intermittent (7 Days on/7 Days off) Dosing Regimen (Part 1 and Part 2 of the Study)
Figure S1B from Multicenter Phase I Study of Erdafitinib (JNJ-42756493), Oral Pan-Fibroblast Growth Factor Receptor Inhibitor, in Patients with Advanced or Refractory Solid Tumors
Authors: Bahleda Rastislav , Italiano Antoine , Hierro Cinta , Mita Alain , Cervantes Andres , Chan Nancy , Awad Mark , Calvo Emiliano , Moreno Victor , Govindan Ramaswamy , Spira Alexander , Gonzalez Martha , Zhong Bob , Santiago-Walker Ademi , Poggesi Italo , Parekh Trilok , Xie Hong , Infante Jeffrey , Tabernero Josep
Published: April 2023

Supplementary Figure S1. Mean concentration-time erdafitinib profiles after a single dose (cycle 1 day 1 [C1D1]) and at steady-state (cycle 2 day 1 [C2D1]) after daily dosing (Panel A) or intermittent dosing (Panel B). 9 mg QD Part 1 at Cycle 2 Day 1 (C2D1) was not reported as n=1.
Supplementary Data from Role of KEAP1/NFE2L2 Mutations in the Chemotherapeutic Response of Patients with Non–Small Cell Lung Cancer
Authors: Jeong Youngtae , Hellyer Jessica A. , Stehr Henning , Hoang Ngoc T. , Niu Xiaomin , Das Millie , Padda Sukhmani K. , Ramchandran Kavitha , Neal Joel W. , Wakelee Heather , Diehn Maximilian
Published: April 2023

Legend for supplementary figure
Supplementary Figure S4 from Targeting the KIF4A/AR Axis to Reverse Endocrine Therapy Resistance in Castration-resistant Prostate Cancer
Authors: Cao Qi , Song Zhengshuai , Ruan Hailong , Wang Cheng , Yang Xiong , Bao Lin , Wang Keshan , Cheng Gong , Xu TianBo , Xiao Wen , Xiong Zhiyong , Liu Di , Yang Ming , Zhou Diwei , Yang Hongmei , Chen Ke , Zhang Xiaoping
Published: April 2023

A, The half-life of AR-V7 was calculated for C4-2-ENZ-R cells upon KIF4A knockdown. B, The half-life of AR was calculated for 22Rv1 cells upon overexpression of KIF4A. *p < 0.05; **p < 0.01, ***p < 0.001.
Supplementary Figure S3 from Targeting the KIF4A/AR Axis to Reverse Endocrine Therapy Resistance in Castration-resistant Prostate Cancer
Authors: Cao Qi , Song Zhengshuai , Ruan Hailong , Wang Cheng , Yang Xiong , Bao Lin , Wang Keshan , Cheng Gong , Xu TianBo , Xiao Wen , Xiong Zhiyong , Liu Di , Yang Ming , Zhou Diwei , Yang Hongmei , Chen Ke , Zhang Xiaoping
Published: April 2023

Characterization of the enzalutamide-resistant prostate cancer cell line. A, schematic representation of the process of establishment of C4-2-ENZ-R cells. B, Cell lines were treated with enzalutamide for 48 hrs, and growth inhibition was determined by a cell viability assay. The results are shown as the mean {plus minus} SD. ***p < 0.001. C, Immunoblot detection of AR and AR-V7 protein levels in C4-2 and C4-2-ENZ-R cells. D, Cell morphology changes in C4-2 and C4-2-ENZ-R cells.
Supplementary Figure S2 from Targeting the KIF4A/AR Axis to Reverse Endocrine Therapy Resistance in Castration-resistant Prostate Cancer
Authors: Cao Qi , Song Zhengshuai , Ruan Hailong , Wang Cheng , Yang Xiong , Bao Lin , Wang Keshan , Cheng Gong , Xu TianBo , Xiao Wen , Xiong Zhiyong , Liu Di , Yang Ming , Zhou Diwei , Yang Hongmei , Chen Ke , Zhang Xiaoping
Published: April 2023

A, LNCaP cells were treated with or without DHT for 48 h. ChIP analysis of AR binding at the P1, P2, P3, P4, P5, and P6 loci in LNCaP cells. B, Whole-cell lysates of 22Rv1 cells were immunoprecipitated with anti-AR-V7 antibodies and blotted with the indicated antibodies. *p < 0.05; **p < 0.01, ***p < 0.001.
Supplementary Data from FLASH Irradiation Spares Lung Progenitor Cells and Limits the Incidence of Radio-induced Senescence
Authors: Fouillade Charles , Curras-Alonso Sandra , Giuranno Lorena , Quelennec Eddy , Heinrich Sophie , Bonnet-Boissinot Sarah , Beddok Arnaud , Leboucher Sophie , Karakurt Hamza Umut , Bohec Mylène , Baulande Sylvain , Vooijs Marc , Verrelle Pierre , Dutreix Marie , Londoño-Vallejo Arturo , Favaudon Vincent
Published: April 2023

Supplementary data: text with embedded figures.
Supplementary Methods from Comprehensive Transcriptome Profiling of Cryptic CBFA2T3–GLIS2 Fusion–Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study
Authors: Smith Jenny L. , Ries Rhonda E. , Hylkema Tiffany , Alonzo Todd A. , Gerbing Robert B. , Santaguida Marianne T. , Eidenschink Brodersen Lisa , Pardo Laura , Cummings Carrie L. , Loeb Keith R. , Le Quy , Imren Suzan , Leonti Amanda R. , Gamis Alan S. , Aplenc Richard , Kolb E. Anders , Farrar Jason E. , Triche Timothy J. , Nguyen Cu , Meerzaman Daoud , Loken Michael R. , Oehler Vivian G. , Bolouri Hamid , Meshinchi Soheil
Published: April 2023

Supplemental methods that provides additional detail on statistical methods and laboratory protocols and reagents.
Supplementary Data from Evaluation of Eribulin Combined with Irinotecan for Treatment of Pediatric Cancer Xenografts
Authors: Robles Andrew J. , Kurmasheva Raushan T. , Bandyopadhyay Abhik , Phelps Doris A. , Erickson Stephen W. , Lai Zhao , Kurmashev Dias , Chen Yidong , Smith Malcom A. , Houghton Peter J.
Published: April 2023

Supplementary Tables and Figures
Supplementary material from A Th1/IFNγ Gene Signature Is Prognostic in the Adjuvant Setting of Resectable High-Risk Melanoma but Not in Non–Small Cell Lung Cancer
Authors: Dizier Benjamin , Callegaro Andrea , Debois Muriel , Dreno Brigitte , Hersey Peter , Gogas Helen J. , Kirkwood John M. , Vansteenkiste Johan F. , Sequist Lecia V. , Atanackovic Djordje , Goeman Jelle , van Houwelingen Hans , Salceda Susana , Wang Fawn , Therasse Patrick , Debruyne Channa , Spiessens Bart , Brichard Vincent G. , Louahed Jamila , Ulloa-Montoya Fernando
Published: April 2023

Supplementary material
Supplementary Data from Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites
Authors: Nassar Amin H. , Umeton Renato , Kim Jaegil , Lundgren Kevin , Harshman Lauren , Van Allen Eliezer M. , Preston Mark , Dong Fei , Bellmunt Joaquim , Mouw Kent W. , Choueiri Toni K. , Sonpavde Guru , Kwiatkowski David J.
Published: April 2023

Mutation signature projections for 462 UC cases. Each tumor SNV was projected onto A) 30 COSMIC signatures, and B) 6 COSMIC signatures. Counts are calculated as the aggregate probabilities of each mutation signature activity for each tumor sample, and shown graphically color-coded to indicate the count.
Supplementary Data from Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites
Authors: Nassar Amin H. , Umeton Renato , Kim Jaegil , Lundgren Kevin , Harshman Lauren , Van Allen Eliezer M. , Preston Mark , Dong Fei , Bellmunt Joaquim , Mouw Kent W. , Choueiri Toni K. , Sonpavde Guru , Kwiatkowski David J.
Published: April 2023

Comparison of tumor mutation burden for each UC subtype according to presence or absence of DNA damage repair (DDR) gene alteration. P values were calculated by two-sided Wilcoxon rank sum test (p<0.05).
Supplementary Data from Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites
Authors: Nassar Amin H. , Umeton Renato , Kim Jaegil , Lundgren Kevin , Harshman Lauren , Van Allen Eliezer M. , Preston Mark , Dong Fei , Bellmunt Joaquim , Mouw Kent W. , Choueiri Toni K. , Sonpavde Guru , Kwiatkowski David J.
Published: April 2023

Kaplan-Meier curves for overall survival in patients with FGFR3, EP300, or PIK3CA-altered compared to wild-type HG-UTUC tumors. WT= wild type.
Supplementary Data from A Phase II, Prospective, Randomized, Multicenter, Open-Label Study of GX-188E, an HPV DNA Vaccine, in Patients with Cervical Intraepithelial Neoplasia 3
Authors: Choi Youn Jin , Hur Soo Young , Kim Tae-Jin , Hong Sung Ran , Lee Jae Kwan , Cho Chi-Heum , Park Ki Seok , Woo Jung Won , Sung Young Chul , Suh You Suk , Park Jong Sup
Published: April 2023

Supplementary Data Table S1. Characteristics of the patients who participated the clinical trial Table S2. IFN-γ ELISPOT responses. Table S3. List of HPV16 nucleotide variations among 52 patients included at V8 visit Table S4. Association between "average sum of IFN-γ ELISPOT responses/ baseline IFN-γ ELISPOT responses (fold-change)" and HPV variations (Cutoff p-value <0.05)
Figure S2 from A Phase II, Prospective, Randomized, Multicenter, Open-Label Study of GX-188E, an HPV DNA Vaccine, in Patients with Cervical Intraepithelial Neoplasia 3
Authors: Choi Youn Jin , Hur Soo Young , Kim Tae-Jin , Hong Sung Ran , Lee Jae Kwan , Cho Chi-Heum , Park Ki Seok , Woo Jung Won , Sung Young Chul , Suh You Suk , Park Jong Sup
Published: April 2023

Figure S2. Clinical efficacy according to does difference (1 mg and 4 mg).
Supplementary Information from NOTCH1 Represses MCL-1 Levels in GSI-resistant T-ALL, Making them Susceptible to ABT-263
Authors: Dastur Anahita , Choi AHyun , Costa Carlotta , Yin Xunqin , Williams August , McClanaghan Joseph , Greenberg Max , Roderick Justine , Patel Neha U. , Boisvert Jessica , McDermott Ultan , Garnett Mathew J. , Almenara Jorge , Grant Steven , Rizzo Kathryn , Engelman Jeffrey A. , Kelliher Michelle , Faber Anthony C. , Benes Cyril H.
Published: April 2023

Materials & Methods
Supplementary Figs S1-S15 from NOTCH1 Represses MCL-1 Levels in GSI-resistant T-ALL, Making them Susceptible to ABT-263
Authors: Dastur Anahita , Choi AHyun , Costa Carlotta , Yin Xunqin , Williams August , McClanaghan Joseph , Greenberg Max , Roderick Justine , Patel Neha U. , Boisvert Jessica , McDermott Ultan , Garnett Mathew J. , Almenara Jorge , Grant Steven , Rizzo Kathryn , Engelman Jeffrey A. , Kelliher Michelle , Faber Anthony C. , Benes Cyril H.
Published: April 2023

Figures S1-S15 support the data in the main paper.
Supplementary Material and methods from Tumor-Associated Fibroblasts Promote HER2-Targeted Therapy Resistance through FGFR2 Activation
Authors: Fernández-Nogueira Patricia , Mancino Mario , Fuster Gemma , López-Plana Anna , Jauregui Patricia , Almendro Vanesa , Enreig Estel , Menéndez Silvia , Rojo Federico , Noguera-Castells Aleix , Bill Anke , Gaither L. Alex , Serrano Laia , Recalde-Percaz Leire , Moragas Núria , Alonso Raul , Ametller Elisabet , Rovira Ana , Lluch Ana , Albanell Joan , Gascon Pere , Bragado Paloma
Published: April 2023

File describing the supplementary material and methods and the table for the antibodies and drugs used for treatment
eTable6 from Comprehensive Transcriptomic Profiling Identifies Breast Cancer Patients Who May Be Spared Adjuvant Systemic Therapy
Authors: Sjöström Martin , Chang S. Laura , Fishbane Nick , Davicioni Elai , Hartman Linda , Holmberg Erik , Feng Felix Y. , Speers Corey W. , Pierce Lori J. , Malmström Per , Fernö Mårten , Karlsson Per
Published: April 2023

Reactome pathway enrichment
eTable5 from Comprehensive Transcriptomic Profiling Identifies Breast Cancer Patients Who May Be Spared Adjuvant Systemic Therapy
Authors: Sjöström Martin , Chang S. Laura , Fishbane Nick , Davicioni Elai , Hartman Linda , Holmberg Erik , Feng Felix Y. , Speers Corey W. , Pierce Lori J. , Malmström Per , Fernö Mårten , Karlsson Per
Published: April 2023

Signature pathway enrichment
eTable4 from Comprehensive Transcriptomic Profiling Identifies Breast Cancer Patients Who May Be Spared Adjuvant Systemic Therapy
Authors: Sjöström Martin , Chang S. Laura , Fishbane Nick , Davicioni Elai , Hartman Linda , Holmberg Erik , Feng Felix Y. , Speers Corey W. , Pierce Lori J. , Malmström Per , Fernö Mårten , Karlsson Per
Published: April 2023

Genes in common for signatures
Supplementary Figure S3 from Tumor-Associated Fibroblasts Promote HER2-Targeted Therapy Resistance through FGFR2 Activation
Authors: Fernández-Nogueira Patricia , Mancino Mario , Fuster Gemma , López-Plana Anna , Jauregui Patricia , Almendro Vanesa , Enreig Estel , Menéndez Silvia , Rojo Federico , Noguera-Castells Aleix , Bill Anke , Gaither L. Alex , Serrano Laia , Recalde-Percaz Leire , Moragas Núria , Alonso Raul , Ametller Elisabet , Rovira Ana , Lluch Ana , Albanell Joan , Gascon Pere , Bragado Paloma
Published: April 2023

Characterization of the anti-HER2 targeted therapies resistant breast cancer cell lines panel
Supplementary Data from Epigenetic Silencing Affects l-Asparaginase Sensitivity and Predicts Outcome in T-ALL
Authors: Touzart Aurore , Lengliné Etienne , Latiri Mehdi , Belhocine Mohamed , Smith Charlotte , Thomas Xavier , Spicuglia Salvatore , Puthier Denis , Pflumio Françoise , Leguay Thibaut , Graux Carlos , Chalandon Yves , Huguet Françoise , Leprêtre Stéphane , Ifrah Norbert , Dombret Hervé , Macintyre Elizabeth , Hunault Mathilde , Boissel Nicolas , Asnafi Vahid
Published: April 2023

supplementary data Figure S1. Gene expression signatures define distinct molecular groups of T-ALL. Figure S2. Global flow chart of the patients Figure S3. Comparison of outcomes between LALA94 patients with central lab onco-genetic study performed (dotted line) and patients without (full line). Figure S4. Epigenetic histone marks. Figure S5. Kaplan-Meier graph for OS is shown for TAL1+ patients treated on LALA-94 vs. GRAALL-2003/2005 trials. Figure S6. TAL1 expression normalised to GAPDH by RTQ-PCR in 8 PDX treated with L-asparaginase (Rf. Figure 4H). Figure S7. (A) Correlation analysis between ASNS expression and ASNS promoter methylation ratio. (B) ASNS transcriptional expression normalized to GAPDH in T-ALL, in normal Bone Marrow (BM) (100%, 50%, 10% and 1%) and in normal Peripheral Blood Cells (PBL) (100%, 50%, 10% and 1. (C) comparison of ASNS transcriptional expression in non-sorted diagnostic sample, blast and non-blast sorted cells in two patients with a hypermethylated ASNS promoter (UPNT-573 and UPNT-498) and high ASNS expression (T3 tertile) (left) and, in primary samples and PDX (Primary Derived Xenograft) using a human specific Taqman system for two hypermethylated cases (UPNT-485 and UPNT-419) and two hypomethylated cases (UPNT-615 and UPNT-241) (right). (D) Correlation analysis between ASNS expression and ASNS promoter methylation ratio in purified blasts cells (PDX n=8 )and sorted primary samples (n=3). (E) Correlation analysis between ASNS expression (RNA-seq) and ASNS promoter methylation ratio in a series of 13 T-ALL cell lines (LOUCY, DND41, RPMI8402, HPB-ALL, ALL-SIL, TALL1, MOLT3, PEER, SUPT1, PF382, MOLT3, MOLT16, JURKAT). Table S1. Clinico-biological characteristics of patients included in the LALA94 trial according to their inclusion in the present study. Table S2. GRAALL03, 05 and LALA94 trials overview and drug administration schedule. Table S3. SiRNA sequences Table S4. Probes sequences for ASNS MS-MLPA analysis Table S5. DNA Global Methylation study Table S6. Characteristics of TLX1+, TLX3+ and TLX neg patients Table S7. Clinico-biological characteristics of T1 (lower ASNS methylation tertile) and T2+T3 (higher methylation tertiles) adult T-ALL. Table S8. Univariate and multivariate analysis for EFS and OS
Supplementary Table 1 from Liver- and Microbiome-derived Bile Acids Accumulate in Human Breast Tumors and Inhibit Growth and Improve Patient Survival
Authors: Tang Wei , Putluri Vasanta , Ambati Chandrashekar R. , Dorsey Tiffany H. , Putluri Nagireddy , Ambs Stefan
Published: April 2023

Characteristics of the 67 breast tumors in the NCI-Maryland Breast Cancer Study
Supplemental Table 1 from Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer
Authors: Rotow Julia K. , Gui Philippe , Wu Wei , Raymond Victoria M. , Lanman Richard B. , Kaye Frederic J. , Peled Nir , Fece de la Cruz Ferran , Nadres Brandon , Corcoran Ryan B. , Yeh Iwei , Bastian Boris C. , Starostik Petr , Newsom Kimberly , Olivas Victor R. , Wolff Alexander M. , Fraser James S. , Collisson Eric A. , McCoach Caroline E. , Camidge D. Ross , Pacheco Jose , Bazhenova Lyudmila , Li Tianhong , Bivona Trever G. , Blakely Collin M.
Published: April 2023

Demographics of the METex14-mutated and EGFR-mutated cohorts.
Supplemental Figure S5 from Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer
Authors: Rotow Julia K. , Gui Philippe , Wu Wei , Raymond Victoria M. , Lanman Richard B. , Kaye Frederic J. , Peled Nir , Fece de la Cruz Ferran , Nadres Brandon , Corcoran Ryan B. , Yeh Iwei , Bastian Boris C. , Starostik Petr , Newsom Kimberly , Olivas Victor R. , Wolff Alexander M. , Fraser James S. , Collisson Eric A. , McCoach Caroline E. , Camidge D. Ross , Pacheco Jose , Bazhenova Lyudmila , Li Tianhong , Bivona Trever G. , Blakely Collin M.
Published: April 2023

Relative cell viability of Ba/F3 METex14-mutant expressing cells treated with trametinib monotherapy
Supplementary Methods, Figures and Tables from Cooperative Immune-Mediated Mechanisms of the HDAC Inhibitor Entinostat, an IL15 Superagonist, and a Cancer Vaccine Effectively Synergize as a Novel Cancer Therapy
Authors: Hicks Kristin C. , Knudson Karin M. , Lee Karin L. , Hamilton Duane H. , Hodge James W. , Figg William D. , Ordentlich Peter , Jones Frank R. , Rabizadeh Shahrooz , Soon-Shiong Patrick , Schlom Jeffrey , Gameiro Sofia R.
Published: April 2023

Methods: depletion studies, immunofluorescence, assays, serum cytokines and plasma TGFbeta, RNA extraction and NanoString analysis, Human HD PBMCs. Figures: effects of entinostat and combination therapy. Tables: antibodies used for flow cytometry staining, gating strategies for flow cytometry
Supplemental Figure S1 from Co-occurring Alterations in the RAS–MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer
Authors: Rotow Julia K. , Gui Philippe , Wu Wei , Raymond Victoria M. , Lanman Richard B. , Kaye Frederic J. , Peled Nir , Fece de la Cruz Ferran , Nadres Brandon , Corcoran Ryan B. , Yeh Iwei , Bastian Boris C. , Starostik Petr , Newsom Kimberly , Olivas Victor R. , Wolff Alexander M. , Fraser James S. , Collisson Eric A. , McCoach Caroline E. , Camidge D. Ross , Pacheco Jose , Bazhenova Lyudmila , Li Tianhong , Bivona Trever G. , Blakely Collin M.
Published: April 2023

Flowchart describing sample filtering for predicted functional impact.
Supplementary Figure 3 from SMAD4 Loss in Colorectal Cancer Patients Correlates with Recurrence, Loss of Immune Infiltrate, and Chemoresistance
Authors: Wasserman Isaac , Lee Lik Hang , Ogino Shuji , Marco Michael R. , Wu Chao , Chen Xi , Datta Jashodeep , Sadot Eran , Szeglin Bryan , Guillem Jose G. , Paty Philip B. , Weiser Martin R. , Nash Garrett M. , Saltz Leonard , Barlas Afsar , Manova-Todorova Katia , Uppada Srijaya Prakash Babu , Elghouayel Arthur E. , Ntiamoah Peter , Glickman Jonathan N. , Hamada Tsuyoshi , Kosumi Keisuke , Inamura Kentaro , Chan Andrew T. , Nishihara Reiko , Cercek Andrea , Ganesh Karuna , Kemeny Nancy E. , Dhawan Punita , Yaeger Rona , Sawyers Charles L. , Garcia-Aguilar Julio , Giannakis Marios , Shia Jinru , Smith J. Joshua
Published: April 2023

Kaplan-Meier graphs in the validation cohort with number of subjects at risk showing colorectal cancer-specific survival according to SMAD4 status.
Supplementary Figure 1 from SMAD4 Loss in Colorectal Cancer Patients Correlates with Recurrence, Loss of Immune Infiltrate, and Chemoresistance
Authors: Wasserman Isaac , Lee Lik Hang , Ogino Shuji , Marco Michael R. , Wu Chao , Chen Xi , Datta Jashodeep , Sadot Eran , Szeglin Bryan , Guillem Jose G. , Paty Philip B. , Weiser Martin R. , Nash Garrett M. , Saltz Leonard , Barlas Afsar , Manova-Todorova Katia , Uppada Srijaya Prakash Babu , Elghouayel Arthur E. , Ntiamoah Peter , Glickman Jonathan N. , Hamada Tsuyoshi , Kosumi Keisuke , Inamura Kentaro , Chan Andrew T. , Nishihara Reiko , Cercek Andrea , Ganesh Karuna , Kemeny Nancy E. , Dhawan Punita , Yaeger Rona , Sawyers Charles L. , Garcia-Aguilar Julio , Giannakis Marios , Shia Jinru , Smith J. Joshua
Published: April 2023

Kaplan-Meier graphs with number of subjects at risk comparing recurrence-free survival (RFS) by (a) TIL status, or (b) PLA status, with arrows indicating patients whose tumors were also SMAD4 loss.
Supplementary Table S4 from Loss of SMAD4 Promotes Colorectal Cancer Progression by Recruiting Tumor-Associated Neutrophils via the CXCL1/8–CXCR2 Axis
Authors: Ogawa Ryotaro , Yamamoto Takamasa , Hirai Hideyo , Hanada Keita , Kiyasu Yoshiyuki , Nishikawa Gen , Mizuno Rei , Inamoto Susumu , Itatani Yoshiro , Sakai Yoshiharu , Kawada Kenji
Published: April 2023

List of antibodies used for Flow cytometry
Supplementary Table S3 from Loss of SMAD4 Promotes Colorectal Cancer Progression by Recruiting Tumor-Associated Neutrophils via the CXCL1/8–CXCR2 Axis
Authors: Ogawa Ryotaro , Yamamoto Takamasa , Hirai Hideyo , Hanada Keita , Kiyasu Yoshiyuki , Nishikawa Gen , Mizuno Rei , Inamoto Susumu , Itatani Yoshiro , Sakai Yoshiharu , Kawada Kenji
Published: April 2023

List of primers for ChIP assay
Supplementary Table S2 from Loss of SMAD4 Promotes Colorectal Cancer Progression by Recruiting Tumor-Associated Neutrophils via the CXCL1/8–CXCR2 Axis
Authors: Ogawa Ryotaro , Yamamoto Takamasa , Hirai Hideyo , Hanada Keita , Kiyasu Yoshiyuki , Nishikawa Gen , Mizuno Rei , Inamoto Susumu , Itatani Yoshiro , Sakai Yoshiharu , Kawada Kenji
Published: April 2023

Kinase Inhibitors
Supplementary Figure S1 from Loss of SMAD4 Promotes Colorectal Cancer Progression by Recruiting Tumor-Associated Neutrophils via the CXCL1/8–CXCR2 Axis
Authors: Ogawa Ryotaro , Yamamoto Takamasa , Hirai Hideyo , Hanada Keita , Kiyasu Yoshiyuki , Nishikawa Gen , Mizuno Rei , Inamoto Susumu , Itatani Yoshiro , Sakai Yoshiharu , Kawada Kenji
Published: April 2023

Supplementary Figure 1. A, Chemokine array using the SW837 cells engineered with stable SMAD4-knockdown (SW837-shSMAD4 #2) and scramble control
Supplementary Data from Sustained Therapeutic Efficacy of Humanized Anti-CD19 Chimeric Antigen Receptor T Cells in Relapsed/Refractory Acute Lymphoblastic Leukemia
Authors: Heng Gang , Jia Jiankun , Li Shiqi , Fu Gang , Wang Meiling , Qin Dabing , Li Yunyan , Pei Li , Tian Xiaobo , Zhang Jiasi , Wu Yi , Xiang Shali , Wan Jia , Zhu Wei , Zhang Pei , Zhang Qianzhen , Peng Xi , Wang Linling , Wang Ping , Wei Zhihao , Zhang Yingzi , Wang Guiqin , Chen Xue , Zhang Chengcheng , Sun Yanni , Zhao Wenxu , Fan Yahan , Yang Zhi , Chen Jieping , Qian Cheng
Published: April 2023

This Supplementary information consists of (1) materials and methods of FCM; (2) 1 table and 8 supplementary figures.
Supplementary Methods from Potent Cell-Cycle Inhibition and Upregulation of Immune Response with Abemaciclib and Anastrozole in neoMONARCH, Phase II Neoadjuvant Study in HR+/HER2− Breast Cancer
Authors: Hurvitz Sara A. , Martin Miguel , Press Michael F. , Chan David , Fernandez-Abad María , Petru Edgar , Rostorfer Regan , Guarneri Valentina , Huang Chiun-Sheng , Barriga Susana , Wijayawardana Sameera , Brahmachary Manisha , Ebert Philip J. , Hossain Anwar , Liu Jiangang , Abel Adam , Aggarwal Amit , Jansen Valerie M. , Slamon Dennis J.
Published: April 2023

Materials and methods.
Supplementary Figure S4 from Potent Cell-Cycle Inhibition and Upregulation of Immune Response with Abemaciclib and Anastrozole in neoMONARCH, Phase II Neoadjuvant Study in HR+/HER2− Breast Cancer
Authors: Hurvitz Sara A. , Martin Miguel , Press Michael F. , Chan David , Fernandez-Abad María , Petru Edgar , Rostorfer Regan , Guarneri Valentina , Huang Chiun-Sheng , Barriga Susana , Wijayawardana Sameera , Brahmachary Manisha , Ebert Philip J. , Hossain Anwar , Liu Jiangang , Abel Adam , Aggarwal Amit , Jansen Valerie M. , Slamon Dennis J.
Published: April 2023

Relative changes in tumor-infiltrating lymphocyte category in stroma after 2 and 16 weeks of treatment.
Table S6 from Colony-Stimulating Factor 1 Receptor (CSF1R) Activates AKT/mTOR Signaling and Promotes T-Cell Lymphoma Viability
Authors: Murga-Zamalloa Carlos , Rolland Delphine C.M. , Polk Avery , Wolfe Ashley , Dewar Hiran , Chowdhury Pinki , Onder Ozlem , Dewar Rajan , Brown Noah A. , Bailey Nathanael G. , Inamdar Kedar , Lim Megan S. , Elenitoba-Johnson Kojo S.J. , Wilcox Ryan A.
Published: April 2023

List of primers.