bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure_S2 from Phase Ib Dose Expansion and Translational Analyses of Olaparib in Combination with Capivasertib in Recurrent Endometrial, Triple-Negative Breast, and Ovarian Cancer
Authors: Westin Shannon N. , Labrie Marilyne , Litton Jennifer K. , Blucher Aurora , Fang Yong , Vellano Christopher P. , Marszalek Joseph R. , Feng Ningping , Ma XiaoYan , Creason Allison , Fellman Bryan , Yuan Ying , Lee Sanghoon , Kim Tae-Beom , Liu Jinsong , Chelariu-Raicu Anca , Chen Tsun Hsuan , Kabil Nashwa , Soliman Pamela T. , Frumovitz Michael , Schmeler Katheleen M. , Jazaeri Amir , Lu Karen H. , Murthy Rashmi , Meyer Larissa A. , Sun Charlotte C. , Sood Anil K. , Coleman Robert L. , Mills Gordon B.
Published: April 2023

Supplementary Figure S2
Figure_S1 from Phase Ib Dose Expansion and Translational Analyses of Olaparib in Combination with Capivasertib in Recurrent Endometrial, Triple-Negative Breast, and Ovarian Cancer
Authors: Westin Shannon N. , Labrie Marilyne , Litton Jennifer K. , Blucher Aurora , Fang Yong , Vellano Christopher P. , Marszalek Joseph R. , Feng Ningping , Ma XiaoYan , Creason Allison , Fellman Bryan , Yuan Ying , Lee Sanghoon , Kim Tae-Beom , Liu Jinsong , Chelariu-Raicu Anca , Chen Tsun Hsuan , Kabil Nashwa , Soliman Pamela T. , Frumovitz Michael , Schmeler Katheleen M. , Jazaeri Amir , Lu Karen H. , Murthy Rashmi , Meyer Larissa A. , Sun Charlotte C. , Sood Anil K. , Coleman Robert L. , Mills Gordon B.
Published: April 2023

Supplementary Figure S1
Supplementary Table from CUB Domain-Containing Protein 1 (CDCP1) Is a Target for Radioligand Therapy in Castration-Resistant Prostate Cancer, including PSMA Null Disease
Authors: Zhao Ning , Chopra Shalini , Trepka Kai , Wang Yung-Hua , Sakhamuri Sasank , Hooshdaran Nima , Kim Hyunjung , Zhou Jie , Lim Shion A. , Leung Kevin K. , Egusa Emily A. , Zhu Jun , Zhang Li , Foye Adam , Sriram Renuka , Chan Emily , Seo Youngho , Feng Felix Y. , Small Eric J. , Chou Jonathan , Wells James A. , Aggarwal Rahul , Evans Michael J.
Published: April 2023

Supplementary Table from CUB Domain-Containing Protein 1 (CDCP1) Is a Target for Radioligand Therapy in Castration-Resistant Prostate Cancer, including PSMA Null Disease
Supplementary Table from Highly Sensitive EGFRvIII Detection in Circulating Extracellular Vesicle RNA of Glioma Patients
Authors: Batool Syeda Maheen , Muralidharan Koushik , Hsia Tiffany , Falotico Sarah , Gamblin Austin S. , Rosenfeld Yulia B. , Khanna Sirena K. , Balaj Leonora , Carter Bob S.
Published: April 2023

Supplementary Table from Highly Sensitive EGFRvIII Detection in Circulating Extracellular Vesicle RNA of Glioma Patients
Supplementary Data from Spatial and Transcriptomic Analysis of Perineural Invasion in Oral Cancer
Authors: Schmitd Ligia B. , Perez-Pacheco Cindy , Bellile Emily L. , Wu Weisheng , Casper Keith , Mierzwa Michelle , Rozek Laura S. , Wolf Gregory T. , Taylor Jeremy M.G. , D'Silva Nisha J.
Published: April 2023

Supplementary Data from Spatial and Transcriptomic Analysis of Perineural Invasion in Oral Cancer
Supplementary Data from Biomarkers of Angiogenesis and Clinical Outcomes to Cabozantinib and Everolimus in Patients with Metastatic Renal Cell Carcinoma from the Phase III METEOR Trial
Authors: Denize Thomas , Farah Subrina , Cimadamore Alessia , Flaifel Abdallah , Walton Emily , Sticco-Ivins Maura A. , Labaki Chris , Braun David A. , Sun Maxine , Wang Evelyn , Xie Wanling , Choueiri Toni K. , Signoretti Sabina
Published: April 2023

Supplementary Data from Biomarkers of Angiogenesis and Clinical Outcomes to Cabozantinib and Everolimus in Patients with Metastatic Renal Cell Carcinoma from the Phase III METEOR Trial
Supplementary Figure from Phase Ib/II Trial of Ribociclib in Combination with Binimetinib in Patients with NRAS-mutant Melanoma
Authors: Schuler Martin , Zimmer Lisa , Kim Kevin B. , Sosman Jeffrey A. , Ascierto Paolo A. , Postow Michael A. , De Vos Filip Y.F.L. , van Herpen Carla M.L. , Carlino Matteo S. , Johnson Douglas B. , Berking Carola , Reddy Micaela B. , Harney Allison S. , Berlin Jordan D. , Amaria Rodabe N.
Published: April 2023

Supplementary Figure from Phase Ib/II Trial of Ribociclib in Combination with Binimetinib in Patients with NRAS-mutant Melanoma
Supplementary Figure from Clinical Outcomes and Immune Markers by Race in a Phase I/II Clinical Trial of Durvalumab Concomitant with Neoadjuvant Chemotherapy in Early-Stage TNBC
Authors: Foldi Julia , Kahn Adriana , Silber Andrea , Qing Tao , Reisenbichler Emily , Fischbach Neal , Persico Justin , Adelson Kerin , Katoch Anamika , Chagpar Anees , Park Tristen , Blanchard Adam , Blenman Kim , Rimm David L. , Pusztai Lajos
Published: April 2023

Supplementary Figure from Clinical Outcomes and Immune Markers by Race in a Phase I/II Clinical Trial of Durvalumab Concomitant with Neoadjuvant Chemotherapy in Early-Stage TNBC
Supplementary Table from Association of Tumor Mutational Burden with Efficacy of Pembrolizumab±Chemotherapy as First-Line Therapy for Gastric Cancer in the Phase III KEYNOTE-062 Study
Authors: Lee Keun-Wook , Van Cutsem Eric , Bang Yung-Jue , Fuchs Charles S. , Kudaba Iveta , Garrido Marcelo , Chung Hyun Cheol , Lee Jeeyun , Castro Hugo R. , Chao Joseph , Wainberg Zev A. , Cao Z. Alexander , Aurora-Garg Deepti , Kobie Julie , Cristescu Razvan , Bhagia Pooja , Shah Sukrut , Tabernero Josep , Shitara Kohei , Wyrwicz Lucjan
Published: April 2023

Supplementary Table from Association of Tumor Mutational Burden with Efficacy of Pembrolizumab±Chemotherapy as First-Line Therapy for Gastric Cancer in the Phase III KEYNOTE-062 Study
Supplementary Figure from Association of Tumor Mutational Burden with Efficacy of Pembrolizumab±Chemotherapy as First-Line Therapy for Gastric Cancer in the Phase III KEYNOTE-062 Study
Authors: Lee Keun-Wook , Van Cutsem Eric , Bang Yung-Jue , Fuchs Charles S. , Kudaba Iveta , Garrido Marcelo , Chung Hyun Cheol , Lee Jeeyun , Castro Hugo R. , Chao Joseph , Wainberg Zev A. , Cao Z. Alexander , Aurora-Garg Deepti , Kobie Julie , Cristescu Razvan , Bhagia Pooja , Shah Sukrut , Tabernero Josep , Shitara Kohei , Wyrwicz Lucjan
Published: April 2023

Supplementary Figure from Association of Tumor Mutational Burden with Efficacy of Pembrolizumab±Chemotherapy as First-Line Therapy for Gastric Cancer in the Phase III KEYNOTE-062 Study
Supplementary Figure from Safety and Efficacy of Irradiation Boost Based on 18F-FET-PET in Patients with Newly Diagnosed Glioblastoma
Authors: Harat Maciej , Blok Maciej , Miechowicz Izabela , Wiatrowska Izabela , Makarewicz Karolina , Małkowski Bogdan
Published: April 2023

Supplementary Figure from Safety and Efficacy of Irradiation Boost Based on 18F-FET-PET in Patients with Newly Diagnosed Glioblastoma
Supplementary Data from Novel DNA Methylation Biomarker Panel for Detection of Esophageal Adenocarcinoma and High-Grade Dysplasia
Authors: Yu Ming , Moinova Helen R. , Willbanks Amber , Cannon Victoria K. , Wang Ting , Carter Kelly , Kaz Andrew , Reddi Deepti , Inadomi John , Luebeck Georg , Iyer Prasad G. , Canto Marcia I. , Wang Jean S. , Shaheen Nicholas J. , Thota Prashanti N. , Willis Joseph E. , LaFramboise Thomas , Chak Amitabh , Markowitz Sanford D. , Grady William M.
Published: April 2023

Supplementary Data from Novel DNA Methylation Biomarker Panel for Detection of Esophageal Adenocarcinoma and High-Grade Dysplasia
Supplementary Figure from Distinct Immune Gene Programs Associated with Host Tumor Immunity, Neoadjuvant Chemotherapy, and Chemoimmunotherapy in Resectable NSCLC
Authors: Rocha Pedro , Zhang Jiexin , Laza-Briviesca Raquel , Cruz-Bermúdez Alberto , Bota-Rabassedas Neus , Sanchez-Espiridon Beatriz , Yoshimura Katsuhiro , Behrens Carmen , Lu Wei , Tang Ximing , Pataer Apar , Parra Edwin R. , Haymaker Cara , Fujimoto Junya , Swisher Stephen G. , Heymach John V. , Gibbons Don L. , Lee J. Jack , Sepesi Boris , Cascone Tina , Solis Luisa M. , Provencio Mariano , Wistuba Ignacio I. , Kadara Humam
Published: April 2023

Supplementary Figure from Distinct Immune Gene Programs Associated with Host Tumor Immunity, Neoadjuvant Chemotherapy, and Chemoimmunotherapy in Resectable NSCLC
Supplementary Data from Distinct Immune Gene Programs Associated with Host Tumor Immunity, Neoadjuvant Chemotherapy, and Chemoimmunotherapy in Resectable NSCLC
Authors: Rocha Pedro , Zhang Jiexin , Laza-Briviesca Raquel , Cruz-Bermúdez Alberto , Bota-Rabassedas Neus , Sanchez-Espiridon Beatriz , Yoshimura Katsuhiro , Behrens Carmen , Lu Wei , Tang Ximing , Pataer Apar , Parra Edwin R. , Haymaker Cara , Fujimoto Junya , Swisher Stephen G. , Heymach John V. , Gibbons Don L. , Lee J. Jack , Sepesi Boris , Cascone Tina , Solis Luisa M. , Provencio Mariano , Wistuba Ignacio I. , Kadara Humam
Published: April 2023

Supplementary Data from Distinct Immune Gene Programs Associated with Host Tumor Immunity, Neoadjuvant Chemotherapy, and Chemoimmunotherapy in Resectable NSCLC
Supplementary Data from Anti-CD79B Antibody–Drug Conjugate DCDS0780A in Patients with B-Cell Non-Hodgkin Lymphoma: Phase 1 Dose-Escalation Study
Authors: Herrera Alex F. , Patel Manish R. , Burke John M. , Advani Ranjana , Cheson Bruce D. , Sharman Jeff P. , Penuel Elicia , Polson Andrew G. , Liao Chen Di , Li Chunze , Schuth Eva , Vaze Anjali , Samineni Divya , Elstrom Rebecca , Cooper James , Diefenbach Catherine
Published: April 2023

Supplementary Data from Anti-CD79B Antibody–Drug Conjugate DCDS0780A in Patients with B-Cell Non-Hodgkin Lymphoma: Phase 1 Dose-Escalation Study
Supplementary Data from Phase Ib/II Dose Expansion Study of Lenvatinib Combined with Letrozole in Postmenopausal Women with Hormone Receptor–Positive Breast Cancer
Authors: Lim Joline S.J. , Wong Andrea L.A. , Ow Samuel G.W. , Ngoi Natalie Y.L. , Chan Gloria H.J. , Ang Yvonne L.E. , Chong Wan Qin , Lim Siew Eng , Lim Yi Wan , Lee Matilda , Choo Joan R.E. , Tan Hon Lyn , Yong Wei Peng , Soo Ross A. , Tan David S.P. , Chee Cheng Ean , Sundar Raghav , Yadav Kritika , Jain Supriya , Wang Lingzhi , Tai Bee Choo , Goh Boon Cher , Lee Soo-Chin
Published: April 2023

Supplementary Data from Phase Ib/II Dose Expansion Study of Lenvatinib Combined with Letrozole in Postmenopausal Women with Hormone Receptor–Positive Breast Cancer
Supplementary Table from A Randomized Phase II Study of MEDI0680 in Combination with Durvalumab versus Nivolumab Monotherapy in Patients with Advanced or Metastatic Clear-cell Renal Cell Carcinoma
Authors: Voss Martin H. , Azad Arun A. , Hansen Aaron R. , Gray Jhanelle E. , Welsh Sarah J. , Song Xuyang , Kuziora Michael , Meinecke Lina , Blando Jorge , Achour Ikbel , Wang Yi , Walcott Farzana L. , Oosting Sjoukje F.
Published: April 2023

Supplementary Table from A Randomized Phase II Study of MEDI0680 in Combination with Durvalumab versus Nivolumab Monotherapy in Patients with Advanced or Metastatic Clear-cell Renal Cell Carcinoma
Supplementary Data from HSP90 Inhibition Overcomes Resistance to Molecular Targeted Therapy in BRAFV600E-mutant High-grade Glioma
Authors: Sasame Jo , Ikegaya Naoki , Kawazu Masahito , Natsumeda Manabu , Hayashi Takahiro , Isoda Masataka , Satomi Kaishi , Tomiyama Arata , Oshima Akito , Honma Hirokuni , Miyake Yohei , Takabayashi Katsuhiro , Nakamura Taishi , Ueno Toshihide , Matsushita Yuko , Iwashita Hiromichi , Kanemaru Yu , Murata Hidetoshi , Ryo Akihide , Terashima Keita , Yamanaka Shoji , Fujii Yukihiko , Mano Hiroyuki , Komori Takashi , Ichimura Koichi , Cahill Daniel P. , Wakimoto Hiroaki , Yamamoto Tetsuya , Tateishi Kensuke
Published: April 2023

Supplementary Data from HSP90 Inhibition Overcomes Resistance to Molecular Targeted Therapy in BRAFV600E-mutant High-grade Glioma
Supplementary Table from Transcriptomic Profiling of MSI-H/dMMR Gastrointestinal Tumors to Identify Determinants of Responsiveness to Anti–PD-1 Therapy
Authors: Chida Keigo , Kawazoe Akihito , Suzuki Toshihiro , Kawazu Masahito , Ueno Toshihide , Takenouchi Kazumasa , Nakamura Yoshiaki , Kuboki Yasutoshi , Kotani Daisuke , Kojima Takashi , Bando Hideaki , Mishima Saori , Kuwata Takeshi , Sakamoto Naoya , Watanabe Jun , Mano Hiroyuki , Ikeda Masafumi , Shitara Kohei , Endo Itaru , Nakatsura Tetsuya , Yoshino Takayuki
Published: April 2023

Supplementary Table from Transcriptomic Profiling of MSI-H/dMMR Gastrointestinal Tumors to Identify Determinants of Responsiveness to Anti–PD-1 Therapy
Supplementary Data from The Role of the TP53 Pathway in Predicting Response to Neoadjuvant Therapy in Esophageal Adenocarcinoma
Authors: Sihag Smita , Nussenzweig Samuel C. , Walch Henry S. , Hsu Meier , Tan Kay See , De La Torre Sergio , Janjigian Yelena Y. , Maron Steven B. , Ku Geoffrey Y. , Tang Laura H. , Shah Pari M. , Wu Abraham , Jones David R. , Solit David B. , Schultz Nikolaus , Ganesh Karuna , Berger Michael F. , Molena Daniela
Published: April 2023

Supplementary Data from The Role of the TP53 Pathway in Predicting Response to Neoadjuvant Therapy in Esophageal Adenocarcinoma
Supplementary Data from Genetic Subtyping and Phenotypic Characterization of the Immune Microenvironment and MYC/BCL2 Double Expression Reveal Heterogeneity in Diffuse Large B-cell Lymphoma
Authors: Xu-Monette Zijun Y. , Wei Li , Fang Xiaosheng , Au Qingyan , Nunns Harry , Nagy Máté , Tzankov Alexandar , Zhu Feng , Visco Carlo , Bhagat Govind , Dybkaer Karen , Chiu April , Tam Wayne , Zu Youli , Hsi Eric D. , Hagemeister Fredrick B. , Sun Xiaoping , Han Xin , Go Heounjeong , Ponzoni Maurilio , Ferreri Andrés J.M. , Møller Michael B. , Parsons Benjamin M. , van Krieken J. Han , Piris Miguel A. , Winter Jane N. , Li Yong , Xu Bing , Albitar Maher , You Hua , Young Ken H.
Published: April 2023

Supplementary Data from Genetic Subtyping and Phenotypic Characterization of the Immune Microenvironment and MYC/BCL2 Double Expression Reveal Heterogeneity in Diffuse Large B-cell Lymphoma
Supplementary Data from PD-1T TILs as a Predictive Biomarker for Clinical Benefit to PD-1 Blockade in Patients with Advanced NSCLC
Authors: Hummelink Karlijn , van der Noort Vincent , Muller Mirte , Schouten Robert D. , Lalezari Ferry , Peters Dennis , Theelen Willemijn S.M.E. , Koelzer Viktor H. , Mertz Kirsten D. , Zippelius Alfred , van den Heuvel Michel M. , Broeks Annegien , Haanen John B.A.G. , Schumacher Ton N. , Meijer Gerrit A. , Smit Egbert F. , Monkhorst Kim , Thommen Daniela S.
Published: April 2023

Supplementary Data from PD-1T TILs as a Predictive Biomarker for Clinical Benefit to PD-1 Blockade in Patients with Advanced NSCLC
Supplementary Table from Mutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers
Authors: Batalini Felipe , Gulhan Doga C. , Mao Victor , Tran Antuan , Polak Madeline , Xiong Niya , Tayob Nabihah , Tung Nadine M. , Winer Eric P. , Mayer Erica L. , Knappskog Stian , Lønning Per E. , Matulonis Ursula A. , Konstantinopoulos Panagiotis A. , Solit David B. , Won Helen , Eikesdal Hans P. , Park Peter J. , Wulf Gerburg M.
Published: April 2023

Supplementary Table from Mutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers
Supplementary Figure from Mutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers
Authors: Batalini Felipe , Gulhan Doga C. , Mao Victor , Tran Antuan , Polak Madeline , Xiong Niya , Tayob Nabihah , Tung Nadine M. , Winer Eric P. , Mayer Erica L. , Knappskog Stian , Lønning Per E. , Matulonis Ursula A. , Konstantinopoulos Panagiotis A. , Solit David B. , Won Helen , Eikesdal Hans P. , Park Peter J. , Wulf Gerburg M.
Published: April 2023

Supplementary Figure from Mutational Signature 3 Detected from Clinical Panel Sequencing is Associated with Responses to Olaparib in Breast and Ovarian Cancers
Supplementary Figures S1-S4 from A Novel B7-H6–Targeted IgG-Like T Cell–Engaging Antibody for the Treatment of Gastrointestinal Tumors
Authors: Zhang Wei , Auguste Aurélie , Liao Xiaoyun , Walterskirchen Christian , Bauer Kathrin , Lin Yu-Hsi , Yang Ling , Sayedian Farzaneh , Fabits Markus , Bergmann Michael , Binder Carina , Corrales Leticia , Vogt Anne B. , Hudson Lindsey J. , Barnes Martin P. , Bisht Arnima , Giragossian Craig , Voynov Vladimir , Adam Paul J. , Hipp Susanne
Published: April 2023

Supplementary Figure 1
(A) OGAP® Screen of tumor and non-tumorous (normal, non-diseased tissues).
(B) B7-H6 mRNA expression in gastrointestinal cancer tissues (TCGA).
Supplementary Figure 2
B7-H6 expression on cell lines
Supplementary Figure 3
Influence of B7-H6/CD3 ITE on the B7-H6-induced activation of NK-92® MI cells.
Supplementary Figure 4
Pharmacokinetic profile in NOG mice.
Supplementary Figure S7 from Obesity Is Associated with Altered Tumor Metabolism in Metastatic Melanoma
Authors: Hahn Andrew W. , Menk Ashley V. , Rivadeneira Dayana B. , Augustin Ryan C. , Xu Mingchu , Li Jun , Wu Xiaogang , Mishra Aditya K. , Gide Tuba N. , Quek Camelia , Zang Yan , Spencer Christine N. , Menzies Alexander M. , Daniel Carrie R. , Hudgens Courtney W. , Nowicki Theodore , Haydu Lauren E. , Khan M.A. Wadud , Gopalakrishnan Vancheswaran , Burton Elizabeth M. , Malke Jared , Simon Julie M. , Bernatchez Chantale , Putluri Nagireddy , Woodman Scott E. , Vashisht Gopal Y.N. , Guerrieri Renato , Fischer Grant M. , Wang Jian , Wani Khalida M. , Thompson John F. , Lee Jeffrey E. , Hwu Patrick , Ajami Nadim , Gershenwald Jeffrey E. , Long Georgina V. , Scolyer Richard A. , Tetzlaff Michael T. , Lazar Alexander J. , Schadendorf Dirk , Wargo Jennifer A. , Kirkwood John M. , DeBerardinis Ralph J. , Liang Han , Futreal Andrew , Zhang Jianhua , Wilmott James S. , Peng Weiyi , Davies Michael A. , Delgoffe Greg M. , Najjar Yana G. , McQuade Jennifer L.
Published: April 2023

Beta-diversity analysis stratified by sex based on Bray-Curtis dissimilarity represents microbiome samples with metastatic melanoma in terms of the two top principal components (explaining around 17% of variance) obtained from the principal coordinate analysis. Red dots are from overweight/obese (OW/OB) BMI patients, and blue dots are from normal (NL) BMI patients. Shading inside the dots indicates the female gender. This is a subgroup analysis of Figure 5B.
Supplementary Figure S2 from Obesity Is Associated with Altered Tumor Metabolism in Metastatic Melanoma
Authors: Hahn Andrew W. , Menk Ashley V. , Rivadeneira Dayana B. , Augustin Ryan C. , Xu Mingchu , Li Jun , Wu Xiaogang , Mishra Aditya K. , Gide Tuba N. , Quek Camelia , Zang Yan , Spencer Christine N. , Menzies Alexander M. , Daniel Carrie R. , Hudgens Courtney W. , Nowicki Theodore , Haydu Lauren E. , Khan M.A. Wadud , Gopalakrishnan Vancheswaran , Burton Elizabeth M. , Malke Jared , Simon Julie M. , Bernatchez Chantale , Putluri Nagireddy , Woodman Scott E. , Vashisht Gopal Y.N. , Guerrieri Renato , Fischer Grant M. , Wang Jian , Wani Khalida M. , Thompson John F. , Lee Jeffrey E. , Hwu Patrick , Ajami Nadim , Gershenwald Jeffrey E. , Long Georgina V. , Scolyer Richard A. , Tetzlaff Michael T. , Lazar Alexander J. , Schadendorf Dirk , Wargo Jennifer A. , Kirkwood John M. , DeBerardinis Ralph J. , Liang Han , Futreal Andrew , Zhang Jianhua , Wilmott James S. , Peng Weiyi , Davies Michael A. , Delgoffe Greg M. , Najjar Yana G. , McQuade Jennifer L.
Published: April 2023

Reverse phase protein array of the PI3K pathway expression by BMI. Box plot represents the median bar with the box bounding IQR and whiskers the minimum and maximum values.
Supplementary Table 2 from Therapy-related Myeloid Neoplasms Following PARP Inhibitors: Real-life Experience
Authors: Marmouset Vincent , Decroocq Justine , Garciaz Sylvain , Etienne Gabriel , Belhabri Amine , Bertoli Sarah , Gastaud Lauris , Simand Célestine , Chantepie Sylvain , Uzunov Madalina , Genthon Alexis , Berthon Céline , Chiche Edmond , Dumas Pierre-Yves , Vargaftig Jacques , Salmeron Géraldine , Lemasle Emilie , Tavernier Emmanuelle , Delage Jérémy , Loirat Marion , Morineau Nadine , Blanc-Durand Félix , Pautier Patricia , Vergé Véronique , Auger Nathalie , Thomas Myrtille , Stefani Laetitia , Lepelley Marion , Boyer Thomas , Thepot Sylvain , Gourin Marie-Pierre , Bourquard Pascal , Duchmann Matthieu , Morice Pierre-Marie , Michallet Mauricette , Adès Lionel , Fenaux Pierre , Récher Christian , Dombret Hervé , Pagès Arnaud , Marzac Christophe , Leary Alexandra , Micol Jean-Baptiste
Published: April 2023

TP53 mutations characteristics among t-MN PARPi national cohort.
Supplementary Tables S1-S5 from Associations between Pretreatment Body Composition Features and Clinical Outcomes among Patients with Metastatic Clear Cell Renal Cell Carcinoma Treated with Immune Checkpoint Blockade
Authors: Ged Yasser , Sanchez Alejandro , Patil Sujata , Knezevic Andrea , Stein Emily , Petruzella Stacey , Weiss Kate , Duzgol Cihan , Chaim Joshua , Akin Oguz , Mourtzakis Marina , Paris Michael T. , Scott Jessica , Kuo Fengshen , Kotecha Ritesh , Hakimi A. Ari , Lee Chung-Han , Motzer Robert J. , Voss Martin H. , Furberg Helena
Published: April 2023

Associations of Body Composition and Clinical Characteristics
Supplementary Figure from Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors
Authors: van IJzendoorn David G.P. , Matusiak Magdalena , Charville Gregory W. , Spierenburg Geert , Varma Sushama , Colburg Deana R.C. , van de Sande Michiel A.J. , van Langevelde Kirsten , Mohler David G. , Ganjoo Kristen N. , Bui Nam Q. , Avedian Raffi S. , Bovée Judith V.M.G. , Steffner Robert , West Robert B. , van de Rijn Matt
Published: April 2023

Supplementary Figure from Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors
Supplementary Figure 4 from A Single-Arm Phase Ib/II Study of Lenvatinib plus Eribulin in Advanced Liposarcoma and Leiomyosarcoma
Authors: Chen Tom Wei-Wu , Hsu Chia-Lang , Hong Ruey-Long , Lee Jen-Chieh , Chang Koping , Yu Chih-Wei , Chen San-Chi , Guo Jhe-Cyuan , Chen Mei-Lu , Hsu Meng-Chi , Kung Ting-Fang , Cheng Ann-Lii , Yen Chueh-Chuan
Published: April 2023

Volcano plots of differentially expressed genes of different clinical scenarios (a) partial responders vs non-partial responders (b) progression-free survival longer vs shorter than 6 months (c) post- and pre-treatment samples.
Supplementary Figure S1 from Safety, Outcomes, and T-Cell Characteristics in Patients with Relapsed or Refractory MDS or CMML Treated with Atezolizumab in Combination with Guadecitabine
Authors: O'Connell Casey L. , Baer Maria R. , Ørskov Andreas Due , Saini Sunil Kumar , Duong Vu H. , Kropf Patricia , Hansen Jakob Werner , Tsao-Wei Denice , Jang Hyo Sik , Emadi Ashkan , Holmberg-Thyden Staffan , Cowland Jack , Brinker Brett T. , Horwood Kristin , Burgos Ryan , Hostetter Galen , Youngblood Benjamin A. , Hadrup Sine Reker , Issa Jean-Pierre , Jones Peter , Baylin Stephen B. , Siddiqi Imran , Grønbaek Kirsten
Published: April 2023

Median overall survival was longer among patients whose T cells harbored ASXL1 mutations (green) than for those without the mutation (red) or with only myeloid mutations (blue), but ASXL1 mutation status was not associated with survival in a univariate analysis by the logrank test (p=0.11). In a multivariate analysis using a Cox proportional model and adjusted by age at study entry, gender, diagnosis, and the number of prior treatment regimens, ASXL1 was significantly associated with survival (p=0.001 based on likelihood ratio test).
Supplementary Figure S5 from NPY Methylated ctDNA is a Promising Biomarker for Treatment Response Monitoring in Metastatic Colorectal Cancer
Authors: Janssens Katleen , Vanhoutte Greetje , Lybaert Willem , Demey Wim , Decaestecker Jochen , Hendrickx Koen , Rezaei Kalantari Hassan , Zwaenepoel Karen , Pauwels Patrick , Fransen Erik , Op de Beeck Ken , Van Camp Guy , Rolfo Christian , Peeters Marc
Published: April 2023

Normalized methylation ratio.
Supplementary Figure 7 from Biology and Targetability of the Extended Spectrum of PIK3CA Mutations Detected in Breast Carcinoma
Authors: Rugo Hope S. , Raskina Kira , Schrock Alexa B. , Madison Russell W. , Graf Ryon P. , Sokol Ethan S. , Sivakumar Smruthy , Lee Jessica K. , Fisher Virginia , Oxnard Geoffrey R. , Tukachinsky Hanna
Published: April 2023

Supplementary Figure 7. Individual covariate balance before and after inverse probabilityof treatment weighting.
Supplementary Figure 5 from Biology and Targetability of the Extended Spectrum of PIK3CA Mutations Detected in Breast Carcinoma
Authors: Rugo Hope S. , Raskina Kira , Schrock Alexa B. , Madison Russell W. , Graf Ryon P. , Sokol Ethan S. , Sivakumar Smruthy , Lee Jessica K. , Fisher Virginia , Oxnard Geoffrey R. , Tukachinsky Hanna
Published: April 2023

Supplementary Figure 5. Comparison of performance of comprehensive genomicprofiling by next-generation sequencing (NGS) and PCR hotspot testing.
Supplemental Table 3 from Response to Neoadjuvant Targeted Therapy in Operable Head and Neck Cancer Confers Survival Benefit
Authors: Mascarella Marco A. , Olonisakin Tolani F. , Rumde Purva , Vendra Varun , Nance Melonie A. , Kim Seungwon , Kubik Mark W. , Sridharan Shaum S. , Ferris Robert L. , Fenton Moon J. , Clayburgh Daniel R. , Ohr James P. , Joyce Sonali C. , Sen Malabika , Herman James G. , Grandis Jennifer R. , Zandberg Dan P. , Duvvuri Umamaheswar
Published: April 2023

Comparison of clinical to pathologic stage migration between patients enrolled in 1 of 4 window trials compared to a second control group
Supplementary Table S8 from A Phase II Window of Opportunity Study of Neoadjuvant PD-L1 versus PD-L1 plus CTLA-4 Blockade for Patients with Malignant Pleural Mesothelioma
Authors: Lee Hyun-Sung , Jang Hee-Jin , Ramineni Maheshwari , Wang Daniel Y. , Ramos Daniela , Choi Jong Min , Splawn Taylor , Espinoza Monica , Almarez Michelle , Hosey Leandria , Jo Eunji , Hilsenbeck Susan , Amos Christopher I. , Ripley R. Taylor , Burt Bryan M.
Published: April 2023

Supplementary Table 8. IMC antibody panel relevant to Figure 5.
Supplementary Figure S3. from Multi-Maintenance Olaparib Therapy in Relapsed, Germline BRCA1/2-Mutant High-Grade Serous Ovarian Cancer (MOLTO): A Phase II Trial
Authors: Morgan Robert D. , Clamp Andrew R. , White Daniel J. , Price Marcus , Burghel George J. , Ryder W. David J. , Mahmood Reem D. , Murphy Alexander D. , Hasan Jurjees , Mitchell Claire L. , Salih Zena , Wheeler Chelsey , Buckley Emma , Truelove Joanna , King Georgia , Ainaoui Yasmina , Bhaskar Sanjeev S. , Shaw Joseph , Evans D. Gareth R. , Kilerci Bedirhan , Pearce Simon P. , Brady Gerard , Dive Caroline , O'Connor James P.B. , Wallace Andrew J. , Rothwell Dominic G. , Edmondson Richard J. , Jayson Gordon C.
Published: April 2023

Cell-free circulating DNA yields at each time point.
Supplementary Figure S2 from Elucidating the Genetic Landscape of Oral Leukoplakia to Predict Malignant Transformation
Authors: Wils Leon J. , Poell Jos B. , Brink Arjen , Evren Ilkay , Brouns Elisabeth R. , de Visscher Jan G.A.M. , Bloemena Elisabeth , Brakenhoff Ruud H.
Published: April 2023

Overview of laboratory methods for the processing of oral leukoplakia biopsies for next generation sequencing.
Supplementary Figure S3 from Impact of RNA Signatures on pCR and Survival after 12-Week Neoadjuvant Pertuzumab plus Trastuzumab with or without Paclitaxel in the WSG-ADAPT HER2+/HR− Trial
Authors: Graeser Monika , Gluz Oleg , Biehl Claudia , Ulbrich-Gebauer Daniel , Christgen Matthias , Palatty Jenci , Kuemmel Sherko , Grischke Eva-Maria , Augustin Doris , Braun Michael , Potenberg Jochem , Wuerstlein Rachel , Krauss Katja , Schumacher Claudia , Forstbauer Helmut , Reimer Toralf , Stefek Andrea , Fischer Hans Holger , Pelz Enrico , zu Eulenburg Christine , Kates Ronald , Ni Hua , Kolberg-Liedtke Cornelia , Feuerhake Friedrich , Kreipe Hans Heinrich , Nitz Ulrike , Harbeck Nadia
Published: April 2023

Supplementary Figure 3 shows association between RNA signatures and overall survival
Supplementary Table S1 from Loss of CDKN2A Cooperates with WWTR1(TAZ)–CAMTA1 Gene Fusion to Promote Tumor Progression in Epithelioid Hemangioendothelioma
Authors: Seavey Caleb N. , Hallett Andrea , Li Shuo , Che Kepeng , Pobbati Ajaybabu V. , Ma Shuang , Burtscher Ashley , Kanai Ryan , Lamar John M. , Rubin Brian P.
Published: April 2023

Supplemental Table 1. Mouse Short Tandem Repeat (STR) loci for all three cell lines
Short tandem repeat analysis of each EHE cell line and using both mouse and human loci. Human defining loci were undetected in all three cell lines.
Data from Analysis of the MammaPrint Breast Cancer Assay in a Predominantly Postmenopausal Cohort
Authors: Wittner Ben S. , Sgroi Dennis C. , Ryan Paula D. , Bruinsma Tako J. , Glas Annuska M. , Male Anitha , Dahiya Sonika , Habin Karleen , Bernards Rene , Haber Daniel A. , Van't Veer Laura J. , Ramaswamy Sridhar
Published: April 2023

Abstract
Purpose: Most node-negative breast cancer patients are older and postmenopausal and are increasingly being offered adjuvant chemotherapy despite their low overall risk of distant relapse. A molecular diagnostic test with high negative predictive value (NPV) for distant metastasis in this subgroup would spare many older breast cancer patients adjuvant treatment.

Experimental Design: We determined the NPV and positive predictive value of the MammaPrint assay in breast cancer patients who were consecutively diagnosed and treated at the Massachusetts General Hospital between 1985 and 1997. Primary tumors from 100 patients with node-negative, invasive breast cancer (median age, 62.5 years; median follow-up, 11.3 years) were subjected to MammaPrint analysis and classified as being at either low or high risk for distant metastasis.

Results: The MammaPrint 70-gene signature displayed excellent NPV as in previous studies, correctly identifying 100% of women at low risk for distant metastases at 5 years. However, this assay had a lower positive predictive value (12% at 5 years) than previously observed.

Conclusions: The MammaPrint assay was originally designed to identify younger breast cancer patients at low risk for distant metastasis, who might consequently be spared systemic treatment. We show here that the same signature has a very high NPV for distant recurrence after adjuvant treatment in older breast cancer patients.
Data from In vivo Knockdown of the Androgen Receptor Results in Growth Inhibition and Regression of Well-Established, Castration-Resistant Prostate Tumors
Authors: Snoek Robert , Cheng Helen , Margiotti Katia , Wafa Latif A. , Wong Charmaine A. , Wong Erica Chan , Fazli Ladan , Nelson Colleen C. , Gleave Martin E. , Rennie Paul S.
Published: April 2023

Abstract
Purpose: Progression to the castration-resistant state is the incurable and lethal end stage of prostate cancer, and there is strong evidence that androgen receptor (AR) still plays a central role in this process. We hypothesize that knocking down AR will have a major effect on inhibiting growth of castration-resistant tumors.

Experimental Design: Castration-resistant C4-2 human prostate cancer cells stably expressing a tetracycline-inducible AR-targeted short hairpin RNA (shRNA) were generated to directly test the effects of AR knockdown in C4-2 human prostate cancer cells and tumors.

Results:In vitro expression of AR shRNA resulted in decreased levels of AR mRNA and protein, decreased expression of prostate-specific antigen (PSA), reduced activation of the PSA-luciferase reporter, and growth inhibition of C4-2 cells. Gene microarray analyses revealed that AR knockdown under hormone-deprived conditions resulted in activation of genes involved in apoptosis, cell cycle regulation, protein synthesis, and tumorigenesis. To ensure that tumors were truly castration-resistant in vivo, inducible AR shRNA expressing C4-2 tumors were grown in castrated mice to an average volume of 450 mm3. In all of the animals, serum PSA decreased, and in 50% of them, there was complete tumor regression and disappearance of serum PSA.

Conclusions: Whereas castration is ineffective in castration-resistant prostate tumors, knockdown of AR can decrease serum PSA, inhibit tumor growth, and frequently cause tumor regression. This study is the first direct evidence that knockdown of AR is a viable therapeutic strategy for treatment of prostate tumors that have already progressed to the castration-resistant state.
Data from Prognostic Value of LISCH7 mRNA in Plasma and Tumor of Colon Cancer Patients
Authors: García José M. , Peña Cristina , García Vanesa , Domínguez Gemma , Muñoz Concepción , Silva Javier , Millán Isabel , Diaz Raquel , Lorenzo Yolanda , Rodriguez Rufo , Bonilla Félix
Published: April 2023

Abstract
Purpose:LISCH7 is a gene potentially regulated by p53 that is up-regulated in metastasis development. Our hypothesis was that the expression of LISCH7 in primary colorectal tumors determined certain characteristics of the tumors, as well as their behavior, and that its identification in plasma could serve as a prognostic marker.

Experimental Design: We tested this hypothesis in a series of 115 tumors and normal tissues and in 83 plasmas from patients with sporadic colorectal carcinomas, as well as in 20 healthy control plasmas in which the expression levels of the gene were measured by real-time PCR. The expression data were contrasted with clinicopathologic variables.

Results: Although LISCH7 expression was not detected in any control plasma samples, it was positive in 25 (30.1%) plasmas from patients (P = 0.002). LISCH7 mRNA in plasma was significantly associated with the pathologic stage (P = 0.019), with lymph node metastasis (P = 0.008) and with vascular invasion (P = 0.005). Expression was not detected in any normal tissues but was detected in 80 tumor tissues, with a clear association found with vascular invasion (P = 0.027). Moreover, we show that LISCH7 was specifically expressed by the epithelial tumor cells. The adjusted overall survival study showed independent prognostic values for LISCH7 expression levels in tumor tissues (hazard ratio, 3.45; 95% confidence interval, 1.19-9.98).

Conclusions: Our results suggest that LISCH7 is a good tumor marker whose expression levels could be considered as a poor prognosis factor in human colon cancer. Furthermore, plasma is suggested as a feasible source of nucleic acids for subsequent noninvasive prognostic studies.
Data from Intracellular MUC1 Peptides Inhibit Cancer Progression
Authors: Bitler Benjamin G. , Menzl Ina , Huerta Carmen L. , Sands Barbara , Knowlton Wendy , Chang Andrew , Schroeder Joyce A.
Published: April 2023

Abstract
Purpose: During cancer progression, the oncoprotein MUC1 binds β-catenin while simultaneously inhibiting the degradation of the epidermal growth factor receptor (EGFR), resulting in enhanced transformation and metastasis. The purpose of this study was to design a peptide-based therapy that would block these intracellular protein-protein interactions as a treatment for metastatic breast cancer.

Experimental Design: The amino acid residues responsible for these interactions lie in tandem in the cytoplasmic domain of MUC1, and we have targeted this sequence to produce a MUC1 peptide that blocks the protumorigenic functions of MUC1. We designed the MUC1 inhibitory peptide (MIP) to block the intracellular interactions between MUC1/β-catenin and MUC1/EGFR. To allow for cellular uptake we synthesized MIP adjacent to the protein transduction domain, PTD4 (PMIP).

Results: We have found that PMIP acts in a dominant-negative fashion, blocking both MUC1/β-catenin and MUC1/EGFR interactions. In addition, PMIP induces ligand-dependent reduction of EGFR levels. These effects correspond to a significant reduction in proliferation, migration, and invasion of metastatic breast cancer cells in vitro, and inhibition of tumor growth and recurrence in an established MDA-MB-231 immunocompromised (SCID) mouse model. Importantly, PMIP also inhibits genetically driven breast cancer progression, as injection of tumor-bearing MMTV-pyV mT transgenic mice with PMIP results in tumor regression and a significant inhibition of tumor growth rate.

Conclusions: These data show that intracellular MUC1 peptides possess significant antitumor activity and have important clinical applications in the treatment of cancer.
Data from Enhanced Antitumor Efficacy of Clinical-Grade Vasculature-Targeted Liposomal Doxorubicin
Authors: Pastorino Fabio , Di Paolo Daniela , Piccardi Federica , Nico Beatrice , Ribatti Domenico , Daga Antonio , Baio Gabriella , Neumaier Carlo E. , Brignole Chiara , Loi Monica , Marimpietri Danilo , Pagnan Gabriella , Cilli Michele , Lepekhin Eugene A. , Garde Seema V. , Longhi Renato , Corti Angelo , Allen Theresa M. , Wu Jinzi J. , Ponzoni Mirco
Published: April 2023

Abstract
Purpose:In vivo evaluation of good manufacturing practice-grade targeted liposomal doxorubicin (TVT-DOX), bound to a CD13 isoform expressed on the vasculature of solid tumors, in human tumor xenografts of neuroblastoma, ovarian cancer, and lung cancer.

Experimental Design: Mice were implanted with lung, ovarian, or neuroblastoma tumor cells via the pulmonary, peritoneal, or orthotopic (adrenal gland) routes, respectively, and treated, at different days post inoculation, with multiple doses of doxorubicin, administered either free or encapsulated in untargeted liposomes (Caelyx) or in TVT-DOX. The effect of TVT-DOX treatment on tumor cell proliferation, viability, apoptosis, and angiogenesis was studied by immunohistochemical analyses of neoplastic tissues and using the chick embryo chorioallantoic membrane assay.

Results: Compared with the three control groups (no doxorubicin, free doxorubicin, or Caelyx), statistically significant improvements in survival was seen in all three animal models following treatment with 5 mg/kg (maximum tolerated dose) of TVT-DOX, with long-term survivors occurring in the neuroblastoma group; increased survival was also seen at a dose of 1.7 mg/kg in mice bearing neuroblastoma or ovarian cancer. Minimal residual disease after surgical removal of neuroblastoma primary mass, and the enhanced response to TVT-DOX, was visualized and quantified by bioluminescence imaging and with magnetic resonance imaging. When treated with TVT-DOX, compared with Caelyx, all three tumor models, as assayed by immunohistochemistry and chorioallantoic membrane, showed statistically significant reductions in cell proliferation, blood vessel density, and microvessel area, showing increased cell apoptosis.

Conclusion: TVT-DOX should be evaluated as a novel angiostatic strategy for adjuvant therapy of solid tumors.
Data from Clinical Usefulness of EGFR Gene Copy Number as a Predictive Marker in Colorectal Cancer Patients Treated with Cetuximab: A Fluorescent In situ Hybridization Study
Authors: Personeni Nicola , Fieuws Steffen , Piessevaux Hubert , De Hertogh Gert , De Schutter Jef , Biesmans Bart , De Roock Wendy , Capoen An , Debiec-Rychter Maria , Van Laethem Jean-Luc , Peeters Marc , Humblet Yves , Van Cutsem Eric , Tejpar Sabine
Published: April 2023

Abstract
Purpose: To evaluate the usefulness and the pitfalls inherent to the assessment of the epidermal growth factor receptor (EGFR) gene copy number (GCN) by fluorescence in situ hybridization (FISH) for outcome prediction to cetuximab in metastatic colorectal cancer. The value of testing KRAS mutation status, in addition to EGFR GCN, was also explored.

Experimental Design: FISH analysis of 87 metastatic colorectal cancer patients treated with cetuximab was done, recording individual GCN per cell and using different samples per tumor. Performances of published cutoff points and different summaries of EGFR GCN distribution were assessed for response prediction.

Results: In our data set, two published cutoff points performed less well than in their training set, yielding positive predictive values and negative predictive values between 40.0% and 48.3% and between 81.0% and 86.5%, respectively. Among summaries of GCN distribution explored, mean and right-tailed distribution of GCN yielded the highest performances. A mean EGFR GCN ≥2.83 provided an area under the curve of 0.71. Important heterogeneity of repeated measures of mean EGFR GCN was observed within tumors (intraclass correlation, 0.61; within-class SD, 0.40), leading to potential misclassifications of FISH status in 7 of 18 (38.8%) patients if a cutoff point were used. In multivariable analysis, EGFR GCN testing provided significant information independent of the KRAS status to predict response (P = 0.016) and overall survival (P = 0.005).

Conclusions: We confirm the association between increased EGFR GCN and outcome after cetuximab. However, because of reproducibility concerns, any decision making based on published cutoff points is not warranted.
Data from Trastuzumab Activates Allogeneic or Autologous Antibody-Dependent Cellular Cytotoxicity against Malignant Rhabdoid Tumor Cells and Interleukin-2 Augments the Cytotoxicity
Authors: Katsumi Yoshiki , Kuwahara Yasumichi , Tamura Shinichi , Kikuchi Ken , Otabe Osamu , Tsuchiya Kunihiko , Iehara Tomoko , Kuroda Hiroshi , Hosoi Hajime , Sugimoto Tohru
Published: April 2023

Abstract
Purpose: Malignant rhabdoid tumor (MRT) is an early childhood cancer with poor prognosis. Trastuzumab, a humanized monoclonal antibody against human epidermal growth factor receptor-2 (HER-2), has been shown to be effective against breast cancer and other cancers. We investigated the effect of trastuzumab on MRT cell lines.

Experimental Design: We examined expression of HER-2 on four MRT cell lines and two tumor tissues by indirect immunofluorescence, flow cytometry, and immunohistochemistry. The effect of trastuzumab against MRT cells was examined by cell growth assay. To observe the antibody-dependent cellular cytotoxicity of effector cells, we examined the cytotoxicity of trastuzumab in combination with allogeneic or autologous human peripheral blood mononuclear cells with and without IL-2 using the chromium release assay.

Results: All four MRT cell lines and both MRT tissues expressed HER-2 protein. Trastuzumab alone did not reduce the viability of the MRT cell lines. On the other hand, the cytotoxicity of trastuzumab against each of the MRT cell lines was significantly increased by the presence of allogeneic and autologous peripheral blood mononuclear cells (P < 0.01). There was a strong correlation coefficient (r = 0.825) between HER-2 expression and the cytotoxicity enhanced by trastuzumab. Moreover, trastuzumab in combination with peripheral blood mononuclear cells augmented by interleukin-2 (IL-2) was significantly more cytotoxic than trastuzumab alone or IL-2 alone (P < 0.01).

Conclusions: Our results indicate that (1) trastuzumab can exert antitumor effects on MRT cells by using the antibody-dependent cellular cytotoxicity of effector cells and (2) IL-2 can enhance the cytotoxicity of trastuzumab against MRT cells.
Data from Gene Expression Profiles of Luteal Phase Fallopian Tube Epithelium from BRCA Mutation Carriers Resemble High-Grade Serous Carcinoma
Authors: Tone Alicia A. , Begley Heather , Sharma Monika , Murphy Joan , Rosen Barry , Brown Theodore J. , Shaw Patricia A.
Published: April 2023

Abstract
Purpose: To identify molecular alterations potentially involved in predisposition to adnexal serous carcinoma (SerCa) in the nonmalignant fallopian tube epithelium (FTE) of BRCA1/2 mutation carriers, given recent evidence implicating the distal FTE as a common source for SerCa.

Experimental Design: We obtained and compared gene expression profiles of laser capture microdissected nonmalignant distal FTE from 12 known BRCA1/2 mutation carriers (FTEb) and 12 control women (FTEn) during the luteal and follicular phase, as well as 13 high-grade tubal and ovarian SerCa.

Results: Gene expression profiles of tubal and ovarian SerCa specimens were indistinguishable by unsupervised cluster analysis and significance analysis of microarrays. FTEb samples as a group, and four individual FTEb samples from the luteal phase in particular, clustered closely with SerCa rather than normal control FTE. Differentially expressed genes from these four samples relative to other FTEb samples, as well as differentially expressed genes in all FTEb luteal samples relative to follicular samples, were mapped to the I2D protein-protein interaction database, revealing a complex network affecting signaling pathways previously implicated in tumorigenesis. Two candidates, disabled homolog 2 mitogen-responsive phosphoprotein (DAB2) and Ski-like (SKIL), were further validated by real-time reverse transcription–PCR and tissue arrays. FTEb luteal and SerCa samples expressed higher levels of oncogenic SKIL and decreased levels of tumor suppressor DAB2, relative to FTEb follicular samples.

Conclusions: These findings support a common molecular pathway for adnexal SerCa and implicate factors associated with the luteal phase in predisposition to ovarian cancer in BRCA mutation carriers.
Data from Serial Analysis of Gene Expression Identifies Connective Tissue Growth Factor Expression as a Prognostic Biomarker in Gallbladder Cancer
Authors: Alvarez Hector , Corvalan Alejandro , Roa Juan C. , Argani Pedram , Murillo Francisco , Edwards Jennifer , Beaty Robert , Feldmann Georg , Hong Seung-Mo , Mullendore Michael , Roa Ivan , Ibañez Luis , Pimentel Fernando , Diaz Alfonso , Riggins Gregory J. , Maitra Anirban
Published: April 2023

Abstract
Background: Gallbladder cancer (GBC) is an uncommon neoplasm in the United States, but one with high mortality rates. This malignancy remains largely understudied at the molecular level such that few targeted therapies or predictive biomarkers exist.

Experimental Design: We built the first series of serial analysis of gene expression (SAGE) libraries from GBC and nonneoplastic gallbladder mucosa, composed of 21-bp long-SAGE tags. SAGE libraries were generated from three stage-matched GBC patients (representing Hispanic/Latino, Native American, and Caucasian ethnicities, respectively) and one histologically alithiasic gallbladder. Real-time quantitative PCR was done on microdissected epithelium from five matched GBC and corresponding nonneoplastic gallbladder mucosa. Immunohistochemical analysis was done on a panel of 182 archival GBC in high-throughput tissue microarray format.

Results: SAGE tags corresponding to connective tissue growth factor (CTGF) transcripts were identified as differentially overexpressed in all pairwise comparisons of GBC (P < 0.001). Real-time quantitative PCR confirmed significant overexpression of CTGF transcripts in microdissected primary GBC (P < 0.05), but not in metastatic GBC, compared with nonneoplastic gallbladder epithelium. By immunohistochemistry, 66 of 182 (36%) GBC had high CTGF antigen labeling, which was significantly associated with better survival on univariate analysis (P = 0.0069, log-rank test).

Conclusions: An unbiased analysis of the GBC transcriptome by SAGE has identified CTGF expression as a predictive biomarker of favorable prognosis in this malignancy. The SAGE libraries from GBC and nonneoplastic gallbladder mucosa are publicly available at the Cancer Genome Anatomy Project web site and should facilitate much needed research into this lethal neoplasm.