bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from Spatial Organization and Prognostic Significance of NK and NKT-like Cells via Multimarker Analysis of the Colorectal Cancer Microenvironment
Authors: Väyrynen Juha P. , Haruki Koichiro , Lau Mai Chan , Väyrynen Sara A. , Ugai Tomotaka , Akimoto Naohiko , Zhong Rong , Zhao Melissa , Dias Costa Andressa , Borowsky Jennifer , Bell Phoenix , Takashima Yasutoshi , Fujiyoshi Kenji , Arima Kota , Kishikawa Junko , Shi Shan-shan , Twombly Tyler S. , Song Mingyang , Wu Kana , Chan Andrew T. , Zhang Xuehong , Fuchs Charles S. , Meyerhardt Jeffrey A. , Giannakis Marios , Ogino Shuji , Nowak Jonathan A.
Published: April 2023

Supplementary Data
Supplementary Tables and Figures
Supplementary Table S1 from APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell–Mediated Antitumor Immune Responses
Authors: DiMarco Ashley V. , Qin Xiaodi , McKinney Brock J. , Garcia Nina Marie G. , Van Alsten Sarah C. , Mendes Elizabeth A. , Force Jeremy , Hanks Brent A. , Troester Melissa A. , Owzar Kouros , Xie Jichun , Alvarez James V.
Published: April 2023

Supplementary Table S1
Supplementary Video 3 from Imaging α-GalCer–Activated iNKT Cells in a Hepatic Metastatic Environment
Authors: Babes Liane , Shim Raymond , Kubes Paul
Published: April 2023

Supplementary Video 3
Supplementary Video 1 from Imaging α-GalCer–Activated iNKT Cells in a Hepatic Metastatic Environment
Authors: Babes Liane , Shim Raymond , Kubes Paul
Published: April 2023

Supplementary Video 1
Supplementary Data from Spatial UMAP and Image Cytometry for Topographic Immuno-oncology Biomarker Discovery
Authors: Giraldo Nicolas A. , Berry Sneha , Becht Etienne , Ates Deniz , Schenk Kara M. , Engle Elizabeth L. , Green Benjamin , Nguyen Peter , Soni Abha , Stein Julie E. , Succaria Farah , Ogurtsova Aleksandra , Xu Haiying , Gottardo Raphael , Anders Robert A. , Lipson Evan J. , Danilova Ludmila , Baras Alexander S. , Taube Janis M.
Published: April 2023

Supplementary Table S1. Clinicopathologic characteristics of the cohort separated by death at the 5-year time point. Supplementary Table S2. Primary and secondary antibody information and TSA dye pairings for multiplex IF panel. Supplementary Table S3. Twenty highest ranking variables associating with overall survival by univariate Cox regression analysis. Supplementary Table S4. Density and proximity variables selected by least absolute shrinkage and selection operator (LASSO) methods using a 5-fold cross-validation. Supplementary Figure S1. Image cytometry to quantify immune cell biomarkers in metastatic melanoma. Supplementary Figure S2. The expression of PD-L1 on tumor cells and 'Other' cells is determined by their proximity to CD8+ cells. Supplementary Figure S3. Characterization of immune neighborhoods associated with overall survival. Supplementary Computational Methods. Survival and clinical statistical analysis - R markdown document.
Supplementary Figures from Intracellular Factor H Drives Tumor Progression Independently of the Complement Cascade
Authors: Daugan Marie V. , Revel Margot , Thouenon Romane , Dragon-Durey Marie-Agnès , Robe-Rybkine Tania , Torset Carine , Merle Nicolas S. , Noé Rémi , Verkarre Virginie , Oudard Stephane Marie , Mejean Arnaud , Validire Pierre , Cathelineau Xavier , Sanchez-Salas Rafael , Pickering Mathew C. , Cremer Isabelle , Mansuet-Lupo Audrey , Alifano Marco , Sautès-Fridman Catherine , Damotte Diane , Fridman Wolf H. , Roumenina Lubka T.
Published: April 2023

Supplementary figures
Supplementary Figure from Sensory Nerves Impede the Formation of Tertiary Lymphoid Structures and Development of Protective Antimelanoma Immune Responses
Authors: Vats Kavita , Kruglov Oleg , Sahoo Bikram , Soman Vishal , Zhang Jiying , Shurin Galina V. , Chandran Uma R. , Skums Pavel , Shurin Michael R. , Zelikovsky Alex , Storkus Walter J. , Bunimovich Yuri L.
Published: April 2023

Supplementary Figure from Sensory Nerves Impede the Formation of Tertiary Lymphoid Structures and Development of Protective Antimelanoma Immune Responses
Supplementary Data from Immuno-PET Monitoring of Lymphocytes Using the CD8-Specific Antibody REGN5054
Authors: Tavaré Richard , Danton Makenzie , Giurleo Jason T. , Makonnen Sosina , Hickey Carlos , Arnold Tomas C. , Kelly Marcus P. , Fredriksson Fanny , Bruestle Karina , Hermann Aynur , Ullman Erica , Edelmann Kurt H. , Potocky Terra , Dudgeon Drew , Bhatt Nikunj B. , Doubrovin Mikhail , Barry Thomas , Kyratsous Christos A. , Gurer Cagan , Tu Naxin , Gartner Hans , Murphy Andrew , Macdonald Lynn E. , Popke Jon , Mintz Akiva , Griesemer Adam , Olson William C. , Thurston Gavin , Ma Dangshe , Kirshner Jessica R.
Published: April 2023

Supplementary Data from Immuno-PET Monitoring of Lymphocytes Using the CD8-Specific Antibody REGN5054
Supplementary Figures legends from Extracellular Vesicle–Packaged circATP2B4 Mediates M2 Macrophage Polarization via miR-532-3p/SREBF1 Axis to Promote Epithelial Ovarian Cancer Metastasis
Authors: Wang Fang , Niu Yuequn , Chen Kelie , Yuan Xiaoyu , Qin Yuheng , Zheng Fang , Cui Zhenyan , Lu Weiguo , Wu Yihua , Xia Dajing
Published: April 2023

Supplementary Figures legends
Supplementary Tables and Figures from CD73 Inhibits cGAS–STING and Cooperates with CD39 to Promote Pancreatic Cancer
Authors: Jacoberger-Foissac Célia , Cousineau Isabelle , Bareche Yacine , Allard David , Chrobak Pavel , Allard Bertrand , Pommey Sandra , Messaoudi Nouredin , McNicoll Yannic , Soucy Geneviève , Koseoglu Secil , Masia Ricard , Lake Andrew C. , Seo Heewon , Eeles Christopher B. , Rohatgi Neha , Robson Simon C. , Turcotte Simon , Haibe-Kains Benjamin , Stagg John
Published: April 2023

supplementary Table S1 to S3; Supplementary Figure S1 to S9
Supplementary Tables from HRS Regulates Small Extracellular Vesicle PD-L1 Secretion and Is Associated with Anti–PD-1 Treatment Efficacy
Authors: Xiao Bo-Lin , Wang Xiao-Le , Xia Hou-Fu , Zhang Lin-Zhou , Wang Kui-Ming , Chen Zhuo-Kun , Zhong Ya-Hua , Jiang Huan-Gang , Zhou Fu-Xiang , Wang Wei , Chen Gai-Li , Chen Gang
Published: April 2023

Supplementary Tables S1-S4
Data from Combination IFNβ and Membrane-Stable CD40L Maximize Tumor Dendritic Cell Activation and Lymph Node Trafficking to Elicit Systemic T-cell Immunity
Authors: Zheng Hong , Yu Xiaoqing , Ibrahim Mohammed L. , Foresman Dana , Xie Mengyu , Johnson Joseph O. , Boyle Theresa A. , Ruffell Brian , Perez Bradford A. , Antonia Scott J. , Ready Neal , Saltos Andreas N. , Cantwell Mark J. , Beg Amer A.
Published: April 2023

Abstract
Oncolytic virus therapies induce the direct killing of tumor cells and activation of conventional dendritic cells (cDC); however, cDC activation has not been optimized with current therapies. We evaluated the adenoviral delivery of engineered membrane-stable CD40L (MEM40) and IFNβ to locally activate cDCs in mouse tumor models. Combined tumor MEM40 and IFNβ expression induced the highest cDC activation coupled with increased lymph node migration, increased systemic antitumor CD8+ T-cell responses, and regression of established tumors in a cDC1-dependent manner. MEM40 + IFNβ combined with checkpoint inhibitors led to effective control of distant tumors and lung metastases. An oncolytic adenovirus (MEM-288) expressing MEM40 + IFNβ  in phase I clinical testing induced cancer cell loss concomitant with enhanced T-cell infiltration and increased systemic presence of tumor T-cell clonotypes in non–small cell lung cancer (NSCLC) patients. This approach to simultaneously target two major DC-activating pathways has the potential to significantly affect the solid tumor immunotherapy landscape.
Table S1 from An Autochthonous Mouse Model of Myd88- and BCL2-Driven Diffuse Large B-cell Lymphoma Reveals Actionable Molecular Vulnerabilities
Authors: Flümann Ruth , Rehkämper Tim , Nieper Pascal , Pfeiffer Pauline , Holzem Alessandra , Klein Sebastian , Bhatia Sanil , Kochanek Moritz , Kisis Ilmars , Pelzer Benedikt W. , Ahlert Heinz , Hauer Julia , da Palma Guerreiro Alexandra , Ryan Jeremy A. , Reimann Maurice , Riabinska Arina , Wiederstein Janica , Krüger Marcus , Deckert Martina , Altmüller Janine , Klatt Andreas R. , Frenzel Lukas P. , Pasqualucci Laura , Béguelin Wendy , Melnick Ari M. , Sander Sandrine , Montesinos-Rongen Manuel , Brunn Anna , Lohneis Philipp , Büttner Reinhard , Kashkar Hamid , Borkhardt Arndt , Letai Anthony , Persigehl Thorsten , Peifer Martin , Schmitt Clemens A. , Reinhardt Hans Christian , Knittel Gero
Published: April 2023

WES Mutations Table
Supplementary Tables from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia
Authors: Roels Juliette , Thénoz Morgan , Szarzyńska Bronisława , Landfors Mattias , De Coninck Stien , Demoen Lisa , Provez Lien , Kuchmiy Anna , Strubbe Steven , Reunes Lindy , Pieters Tim , Matthijssens Filip , Van Loocke Wouter , Erarslan-Uysal Büşra , Richter-Pechańska Paulina , Declerck Ken , Lammens Tim , De Moerloose Barbara , Deforce Dieter , Van Nieuwerburgh Filip , Cheung Laurence C. , Kotecha Rishi S. , Mansour Marc R. , Ghesquière Bart , Van Camp Guy , Berghe Wim Vanden , Kowalczyk Jerzy R. , Szczepański Tomasz , Davé Utpal P. , Kulozik Andreas E. , Goossens Steven , Curtis David J. , Taghon Tom , Dawidowska Małgorzata , Degerman Sofie , Van Vlierberghe Pieter
Published: April 2023

Supplementary Tables 1-15
Supplementary Figure 16 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia
Authors: Roels Juliette , Thénoz Morgan , Szarzyńska Bronisława , Landfors Mattias , De Coninck Stien , Demoen Lisa , Provez Lien , Kuchmiy Anna , Strubbe Steven , Reunes Lindy , Pieters Tim , Matthijssens Filip , Van Loocke Wouter , Erarslan-Uysal Büşra , Richter-Pechańska Paulina , Declerck Ken , Lammens Tim , De Moerloose Barbara , Deforce Dieter , Van Nieuwerburgh Filip , Cheung Laurence C. , Kotecha Rishi S. , Mansour Marc R. , Ghesquière Bart , Van Camp Guy , Berghe Wim Vanden , Kowalczyk Jerzy R. , Szczepański Tomasz , Davé Utpal P. , Kulozik Andreas E. , Goossens Steven , Curtis David J. , Taghon Tom , Dawidowska Małgorzata , Degerman Sofie , Van Vlierberghe Pieter
Published: April 2023

Supplementary Figure 16
Supplementary Figure 15 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia
Authors: Roels Juliette , Thénoz Morgan , Szarzyńska Bronisława , Landfors Mattias , De Coninck Stien , Demoen Lisa , Provez Lien , Kuchmiy Anna , Strubbe Steven , Reunes Lindy , Pieters Tim , Matthijssens Filip , Van Loocke Wouter , Erarslan-Uysal Büşra , Richter-Pechańska Paulina , Declerck Ken , Lammens Tim , De Moerloose Barbara , Deforce Dieter , Van Nieuwerburgh Filip , Cheung Laurence C. , Kotecha Rishi S. , Mansour Marc R. , Ghesquière Bart , Van Camp Guy , Berghe Wim Vanden , Kowalczyk Jerzy R. , Szczepański Tomasz , Davé Utpal P. , Kulozik Andreas E. , Goossens Steven , Curtis David J. , Taghon Tom , Dawidowska Małgorzata , Degerman Sofie , Van Vlierberghe Pieter
Published: April 2023

Supplementary Figure 15
Supplementary Data overview from Mutation Signatures of Pediatric Acute Myeloid Leukemia and Normal Blood Progenitors Associated with Differential Patient Outcomes
Authors: Brandsma Arianne M. , Bertrums Eline J.M. , van Roosmalen Markus J. , Hofman Damon A. , Oka Rurika , Verheul Mark , Manders Freek , Ubels Joske , Belderbos Mirjam E. , van Boxtel Ruben
Published: April 2023

Overview of supplementary data of this manuscript
Supplementary Table S5 from Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers
Authors: Feusier Julie E. , Arunachalam Sasi , Tashi Tsewang , Baker Monika J. , VanSant-Webb Chad , Ferdig Amber , Welm Bryan E. , Rodriguez-Flores Juan L. , Ours Christopher , Jorde Lynn B. , Prchal Josef T. , Mason Clinton C.
Published: April 2023

Unique mutations allowed at hotspots
Supplementary Table S2 from Large-scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers
Authors: Feusier Julie E. , Arunachalam Sasi , Tashi Tsewang , Baker Monika J. , VanSant-Webb Chad , Ferdig Amber , Welm Bryan E. , Rodriguez-Flores Juan L. , Ours Christopher , Jorde Lynn B. , Prchal Josef T. , Mason Clinton C.
Published: April 2023

Comparison of identified hotspots
Supplementary Tables S1-S19 from ZBTB33 Is Mutated in Clonal Hematopoiesis and Myelodysplastic Syndromes and Impacts RNA Splicing
Authors: Beauchamp Ellen M. , Leventhal Matthew , Bernard Elsa , Hoppe Emma R. , Todisco Gabriele , Creignou Maria , Gallì Anna , Castellano Cecilia A. , McConkey Marie , Tarun Akansha , Wong Waihay , Schenone Monica , Stanclift Caroline , Tanenbaum Benjamin , Malolepsza Edyta , Nilsson Björn , Bick Alexander G. , Weinstock Joshua S. , Miller Mendy , Niroula Abhishek , Dunford Andrew , Taylor-Weiner Amaro , Wood Timothy , Barbera Alex , Anand Shankara , Psaty Bruce M. , Desai Pinkal , Cho Michael H. , Johnson Andrew D. , Loos Ruth , MacArthur Daniel G. , Lek Monkol , Neuberg Donna S. , Lage Kasper , Carr Steven A. , Hellstrom-Lindberg Eva , Malcovati Luca , Papaemmanuil Elli , Stewart Chip , Getz Gad , Bradley Robert K. , Jaiswal Siddhartha , Ebert Benjamin L.
Published: April 2023

Supplementary Tables S1-S19
Table S5 from Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Koya Junji , Saito Yuki , Kameda Takuro , Kogure Yasunori , Yuasa Mitsuhiro , Nagasaki Joji , McClure Marni B. , Shingaki Sumito , Tabata Mariko , Tahira Yuki , Akizuki Keiichi , Kamiunten Ayako , Sekine Masaaki , Shide Kotaro , Kubuki Yoko , Hidaka Tomonori , Kitanaka Akira , Nakano Nobuaki , Utsunomiya Atae , Togashi Yosuke , Ogawa Seishi , Shimoda Kazuya , Kataoka Keisuke
Published: April 2023

TCR repertoire analysis
Table S3 from Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Koya Junji , Saito Yuki , Kameda Takuro , Kogure Yasunori , Yuasa Mitsuhiro , Nagasaki Joji , McClure Marni B. , Shingaki Sumito , Tabata Mariko , Tahira Yuki , Akizuki Keiichi , Kamiunten Ayako , Sekine Masaaki , Shide Kotaro , Kubuki Yoko , Hidaka Tomonori , Kitanaka Akira , Nakano Nobuaki , Utsunomiya Atae , Togashi Yosuke , Ogawa Seishi , Shimoda Kazuya , Kataoka Keisuke
Published: April 2023

Clusters identified in this study
Table S1 from Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Koya Junji , Saito Yuki , Kameda Takuro , Kogure Yasunori , Yuasa Mitsuhiro , Nagasaki Joji , McClure Marni B. , Shingaki Sumito , Tabata Mariko , Tahira Yuki , Akizuki Keiichi , Kamiunten Ayako , Sekine Masaaki , Shide Kotaro , Kubuki Yoko , Hidaka Tomonori , Kitanaka Akira , Nakano Nobuaki , Utsunomiya Atae , Togashi Yosuke , Ogawa Seishi , Shimoda Kazuya , Kataoka Keisuke
Published: April 2023

Sample information and sequencing metrics in this study
Supplementary Data from Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Koya Junji , Saito Yuki , Kameda Takuro , Kogure Yasunori , Yuasa Mitsuhiro , Nagasaki Joji , McClure Marni B. , Shingaki Sumito , Tabata Mariko , Tahira Yuki , Akizuki Keiichi , Kamiunten Ayako , Sekine Masaaki , Shide Kotaro , Kubuki Yoko , Hidaka Tomonori , Kitanaka Akira , Nakano Nobuaki , Utsunomiya Atae , Togashi Yosuke , Ogawa Seishi , Shimoda Kazuya , Kataoka Keisuke
Published: April 2023

Supplementary methods, Supplementary Figures, Supplementary Figure Legends, Supplementary Table Legends, Supplementary references, and Key resource table.
Supplementary Data from Scalable Manufacturing of CAR T Cells for Cancer Immunotherapy
Authors: Abou-el-Enein Mohamed , Elsallab Magdi , Feldman Steven A. , Fesnak Andrew D. , Heslop Helen E. , Marks Peter , Till Brian G. , Bauer Gerhard , Savoldo Barbara
Published: April 2023

Supplementary Data from Scalable Manufacturing of CAR T Cells for Cancer Immunotherapy
Supplementary Method from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Methods, compound synthesis, Supplementary Materials and Supplementary References
Supplementary Figure S6 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Figure S6 shows that genome-wide H3K4me3 and RNAPII changes after treatment with JQKD82 or knockdown of KDM5A in MM.1S cells
Supplementary Figure S5 from Lysine Demethylase 5A Is Required for MYC-Driven Transcription in Multiple Myeloma
Authors: Ohguchi Hiroto , Park Paul M.C. , Wang Tingjian , Gryder Berkley E. , Ogiya Daisuke , Kurata Keiji , Zhang Xiaofeng , Li Deyao , Pei Chengkui , Masuda Takeshi , Johansson Catrine , Wimalasena Virangika K. , Kim Yong , Hino Shinjiro , Usuki Shingo , Kawano Yawara , Samur Mehmet K. , Tai Yu-Tzu , Munshi Nikhil C. , Matsuoka Masao , Ohtsuki Sumio , Nakao Mitsuyoshi , Minami Takashi , Lauberth Shannon , Khan Javed , Oppermann Udo , Durbin Adam D. , Anderson Kenneth C. , Hideshima Teru , Qi Jun
Published: April 2023

Supplementary Figure S5 shows the genome-wide localization of KDM5A in MM.1S cells.
Supplementary Figure from CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Preestablished Immunity
Authors: Shree Tanaya , Shankar Vishnu , Lohmeyer Julian J.K. , Czerwinski Debra K. , Schroers-Martin Joseph G. , Rodriguez Gladys M. , Beygi Sara , Kanegai Alyssa M. , Corbelli Karen S. , Gabriel Etelka , Kurtz David M. , Khodadoust Michael S. , Gupta Neel K. , Maeda Lauren S. , Advani Ranjana H. , Alizadeh Ash A. , Levy Ronald
Published: April 2023

Supplementary Figure from CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Preestablished Immunity
Supplementary Figure from The Cell Type–Specific 5hmC Landscape and Dynamics of Healthy Human Hematopoiesis and TET2-Mutant Preleukemia
Authors: Nakauchi Yusuke , Azizi Armon , Thomas Daniel , Corces M. Ryan , Reinisch Andreas , Sharma Rajiv , Cruz Hernandez David , Köhnke Thomas , Karigane Daiki , Fan Amy , Martinez-Krams Daniel , Stafford Melissa , Kaur Satinder , Dutta Ritika , Phan Paul , Ediriwickrema Asiri , McCarthy Erin , Ning Yuhong , Phillips Tierney , Ellison Christopher K. , Guler Gulfem D. , Bergamaschi Anna , Ku Chin-Jen , Levy Samuel , Majeti Ravindra
Published: April 2023

Supplementary Figure from The Cell Type–Specific 5hmC Landscape and Dynamics of Healthy Human Hematopoiesis and TET2-Mutant Preleukemia
Supplementary Table S4 from Extracellular Vesicle Secretion by Leukemia Cells In Vivo Promotes CLL Progression by Hampering Antitumor T-cell Responses
Authors: Gargiulo Ernesto , Viry Elodie , Morande Pablo Elías , Largeot Anne , Gonder Susanne , Xian Feng , Ioannou Nikolaos , Benzarti Mohaned , Kleine Borgmann Felix Bruno , Mittelbronn Michel , Dittmar Gunnar , Nazarov Petr V. , Meiser Johannes , Stamatopoulos Basile , Ramsay Alan G. , Moussay Etienne , Paggetti Jérôme
Published: April 2023

Supplemental Table S4 - Flow cytometry antibody list
Supplementary Figures S1 to S12 from Distinct Genetically Determined Origins of Myd88/BCL2-Driven Aggressive Lymphoma Rationalize Targeted Therapeutic Intervention Strategies
Authors: Flümann Ruth , Hansen Julia , Pelzer Benedikt W. , Nieper Pascal , Lohmann Tim , Kisis Ilmars , Riet Tobias , Kohlhas Viktoria , Nguyen Phuong-Hien , Peifer Martin , Abedpour Nima , Bosco Graziella , Thomas Roman K. , Kochanek Moritz , Knüfer Jacqueline , Jonigkeit Lorenz , Beleggia Filippo , Holzem Alessandra , Büttner Reinhard , Lohneis Philipp , Meinel Jörn , Ortmann Monika , Persigehl Thorsten , Hallek Michael , Calado Dinis Pedro , Chmielewski Markus , Klein Sebastian , Göthert Joachim R. , Chapuy Bjoern , Zevnik Branko , Wunderlich F. Thomas , von Tresckow Bastian , Jachimowicz Ron D. , Melnick Ari M. , Reinhardt Hans Christian , Knittel Gero
Published: April 2023

This file contains the Supplementary Figures S1 to S12.
Supplementary Tables S1-S11 from Adult Low-Hypodiploid Acute Lymphoblastic Leukemia Emerges from Preleukemic TP53-Mutant Clonal Hematopoiesis
Authors: Kim Rathana , Bergugnat Hugo , Larcher Lise , Duchmann Matthieu , Passet Marie , Gachet Stéphanie , Cuccuini Wendy , Lafage-Pochitaloff Marina , Pastoret Cédric , Grardel Nathalie , Asnafi Vahid , Schäfer Beat W. , Delabesse Eric , Itzykson Raphaël , Adès Lionel , Hicheri Yosr , Chalandon Yves , Graux Carlos , Chevallier Patrice , Hunault Mathilde , Leguay Thibaut , Huguet Françoise , Lhéritier Véronique , Dombret Hervé , Soulier Jean , Rousselot Philippe , Boissel Nicolas , Clappier Emmanuelle
Published: April 2023

Supplementary Table 1. Karyotypes of LH-ALL patients at diagnosis.
Supplementary Table 2. Somatic variants detected in LH-ALL patients at diagnosis.
Supplementary Table 3. ARCH related variants detected in LH-ALL patients at remission.
Supplementary Table 4. Minimal residual disease values of remission samples used for mutation analysis.
Supplementary Table 5. Somatic alterations in cell populations from diagnostic samples (BMMC) based on single-cell analyses.
Supplementary Table 6. Somatic alterations in FACS-sorted cell populations from diagnostic samples.
Supplementary Table 7. Panel of genes for targeted sequencing.
Supplementary Table 8. Single cell DNA amplicons for genotyping and LOH analyses.
Supplementary Table 9. Single cell DNA amplicons for B-ALL clono-specific IG/TR detection.
Supplementary Table 10. ADT-seq panel and spike-in antibodies.
Supplementary Table 11. Single cell sequencing metrics.
Supplementary Figure Legends from Peripheral Blood Monocyte Abundance Predicts Outcomes in Patients with Breast Cancer
Authors: Axelrod Margaret L. , Wang Yu , Xu Yaomin , Sun Xiaopeng , Bejan Cosmin A. , Gonzalez-Ericsson Paula I. , Nunnery Sara , Bergman Riley E. , Donaldson Joshua , Guerrero-Zotano Angel L. , Massa Chiara , Seliger Barbara , Sanders Melinda , Mayer Ingrid A. , Balko Justin M.
Published: April 2023

Legends for Supplementary Figures 1-3
Supplementary Materials and Methods from Repurposing Itraconazole and Hydroxychloroquine to Target Lysosomal Homeostasis in Epithelial Ovarian Cancer
Authors: Marastoni Stefano , Madariaga Ainhoa , Pesic Aleksandra , Nair Sree Narayanan , Li Zhu Juan , Shalev Zvi , Ketela Troy , Colombo Ilaria , Mandilaras Victoria , Cabanero Michael , Bruce Jeff P. , Li Xuan , Garg Swati , Wang Lisa , Chen Eric X. , Gill Sarbjot , Dhani Neesha C. , Zhang Wenjiang , Pintilie Melania , Bowering Valerie , Koritzinsky Marianne , Rottapel Robert , Wouters Bradly G. , Oza Amit M. , Joshua Anthony M. , Lheureux Stephanie
Published: April 2023

- List of cell lines

- Lentiviral constructs, lentivirus generation and infection

- Apoptosis Assay

- FILIPIN staining

- Lysosomal assay and immunofluorescence
Supplementary Table 7 from Cancer Stem Cells, not Bulk Tumor Cells, Determine Mechanisms of Resistance to SMO Inhibitors
Authors: George Joshy , Chen Yaohui , Abdelfattah Nourhan , Yamamoto Keiko , Gallup Thomas D. , Adamson Scott I. , Rybinski Brad , Srivastava Anuj , Kumar Parveen , Lee Min Gyu , Baskin David S. , Jiang Wen , Choi Jong Min , Flavahan William , Chuang Jeffrey H. , Kim Betty Y.S. , Xu Jiaqiong , Jung Sung Yun , Yun Kyuson
Published: April 2023

Supplementary Table 7: DEG in LDE vs. control treated SI-CSC Ptch;p53 tumors
Table S1 from Type-I Interferon Signaling Is Essential for Robust Metronomic Chemo-Immunogenic Tumor Regression in Murine Breast Cancer
Authors: Vergato Cameron , Doshi Kshama A. , Roblyer Darren , Waxman David J.
Published: April 2023

Table S1. RNAseq analysis of cultured 4T1 and E0771 tumor cell RNA.
Figure S3 from Increased Microtubule Growth Triggered by Microvesicle-mediated Paracrine Signaling is Required for Melanoma Cancer Cell Invasion
Authors: Pudelko Karoline , Wieland Angela , Hennecke Magdalena , Räschle Markus , Bastians Holger
Published: April 2023

Figure S3 shows that conditioned media from invasive melanoma cells or from non.-invasive cells overexpressing PLK4 or STIL do not induce supernumerary centrosomes.
Supplementary Materials and Methods from A Preclinical and Phase Ib Study of Palbociclib plus Nab-Paclitaxel in Patients with Metastatic Adenocarcinoma of the Pancreas
Authors: Hidalgo Manuel , Garcia-Carbonero Rocio , Lim Kian-Huat , Messersmith Wells A. , Garrido-Laguna Ignacio , Borazanci Erkut , Lowy Andrew M. , Medina Rodriguez Laura , Laheru Daniel , Salvador-Barbero Beatriz , Malumbres Marcos , Shields David J. , Grossman Joseph E. , Huang Xin , Tammaro Meggan , Martini Jean-François , Yu Yanke , Kern Kenneth , Macarulla Teresa
Published: April 2023

Supplementary Materials and Methods
Supplementary Figure S2 from A Preclinical and Phase Ib Study of Palbociclib plus Nab-Paclitaxel in Patients with Metastatic Adenocarcinoma of the Pancreas
Authors: Hidalgo Manuel , Garcia-Carbonero Rocio , Lim Kian-Huat , Messersmith Wells A. , Garrido-Laguna Ignacio , Borazanci Erkut , Lowy Andrew M. , Medina Rodriguez Laura , Laheru Daniel , Salvador-Barbero Beatriz , Malumbres Marcos , Shields David J. , Grossman Joseph E. , Huang Xin , Tammaro Meggan , Martini Jean-François , Yu Yanke , Kern Kenneth , Macarulla Teresa
Published: April 2023

Swimmer's Plot of Best Response.
Supplementary Figure S1 from A Preclinical and Phase Ib Study of Palbociclib plus Nab-Paclitaxel in Patients with Metastatic Adenocarcinoma of the Pancreas
Authors: Hidalgo Manuel , Garcia-Carbonero Rocio , Lim Kian-Huat , Messersmith Wells A. , Garrido-Laguna Ignacio , Borazanci Erkut , Lowy Andrew M. , Medina Rodriguez Laura , Laheru Daniel , Salvador-Barbero Beatriz , Malumbres Marcos , Shields David J. , Grossman Joseph E. , Huang Xin , Tammaro Meggan , Martini Jean-François , Yu Yanke , Kern Kenneth , Macarulla Teresa
Published: April 2023

A) Palbociclib and nab-paclitaxel combination dose escalation and de-escalation sequence. B) Number of patients with dose-limiting toxicities for dose escalation decisions at a dose level.
Supplementary Data S1-S3 from Under-Representation of Racial Groups in Genomics Studies of Gastroenteropancreatic Neuroendocrine Neoplasms
Authors: Herring Brendon R. , Bonner Andrew , Guenter Rachael E. , Vickers Selwyn , Yates Clayton , Lee Goo , Dhall Deepti , Chen Herbert , Rose J. Bart
Published: April 2023

AACR Genie Comparisons (SD.1), STRING Interactions (SD.2), GO Enrichment of STRING data (SD.3)
Supplementary Table TS4 from Circulating Tumor DNA Monitoring Reveals Molecular Progression before Radiologic Progression in a Real-life Cohort of Patients with Advanced Non–small Cell Lung Cancer
Authors: Frank Malene S. , Andersen Christina S.A. , Ahlborn Lise B. , Pallisgaard Niels , Bodtger Uffe , Gehl Julie
Published: April 2023

Analyses of variables for ctDNA detection
Supplementary Figure S14 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer
Authors: Chen Hao , Cresswell Gregory M. , Libring Sarah , Ayers Mitchell G. , Miao Jinmin , Zhang Zhong-Yin , Solorio Luis , Ratliff Timothy L. , Wendt Michael K.
Published: April 2023

PD-L1 expression is induced by growth factor stimulation in the D2.A1 cells.
Supplementary Figure S12 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer
Authors: Chen Hao , Cresswell Gregory M. , Libring Sarah , Ayers Mitchell G. , Miao Jinmin , Zhang Zhong-Yin , Solorio Luis , Ratliff Timothy L. , Wendt Michael K.
Published: April 2023

Analyses of Tregs and macrophage scores in clinical datasets with respect to SHP2 phosphorylation.
Supplementary Figure FS7 from Circulating Tumor DNA Monitoring Reveals Molecular Progression before Radiologic Progression in a Real-life Cohort of Patients with Advanced Non–small Cell Lung Cancer
Authors: Frank Malene S. , Andersen Christina S.A. , Ahlborn Lise B. , Pallisgaard Niels , Bodtger Uffe , Gehl Julie
Published: April 2023

All patient cases
Supplementary Figure S10 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer
Authors: Chen Hao , Cresswell Gregory M. , Libring Sarah , Ayers Mitchell G. , Miao Jinmin , Zhang Zhong-Yin , Solorio Luis , Ratliff Timothy L. , Wendt Michael K.
Published: April 2023

Representative dot plots for data shown in figure 4D-F and additional exhaustion marker analysis of CD8+ T cells in mice bearing SHP2 manipulated 4T1 metastases.
Supplementary Figure FS3 from Circulating Tumor DNA Monitoring Reveals Molecular Progression before Radiologic Progression in a Real-life Cohort of Patients with Advanced Non–small Cell Lung Cancer
Authors: Frank Malene S. , Andersen Christina S.A. , Ahlborn Lise B. , Pallisgaard Niels , Bodtger Uffe , Gehl Julie
Published: April 2023

OS and PFS – above/below median
Figure S8 from CD47-blocking Antibody ZL-1201 Promotes Tumor-associated Macrophage Phagocytic Activity and Enhances the Efficacy of the Therapeutic Antibodies and Chemotherapy
Authors: Cao Anthony , Yi Jiaqing , Tang Xinyan , Szeto Christopher W. , Wu Renyi , Wan Bing , Fang Xu , Li Shou , Wang Lei , Wang Lina , Li Jing , Ye Qiuping , Huang Tom , Hsu Karl , Kabbarah Omar , Zhou Haiying
Published: April 2023

Body weights of mice in HCC1954(A), SKOV3(B), ST-02-0077(C), FaDu (D), and Raji(E) xenograft efficacy studies shown in Figure 5 at days post-treatment as shown
Figure S3 from Cell-free DNA Predicts Prolonged Response to Multi-agent Chemotherapy in Pancreatic Ductal Adenocarcinoma
Authors: Christenson Eric S. , Lim Su Jin , Durham Jennifer , De Jesus-Acosta Ana , Bever Katherine , Laheru Daniel , Ryan Amy , Agarwal Parul , Scharpf Robert B. , Le Dung T. , Wang Hao
Published: April 2023

Supplemental Figure 3. Post-treatment KRAS and change in KRAS VAF following treatment. To determine whether KRAS VAF following 2 cycles of treatment or the change in KRAS VAF from pre-treatment to after 2 cycles of treatment is correlated with CT response at 2 months, each patient’s CT response to treatment was plotted against KRAS VAF and calculated Spearman’s rank correlation coefficient. There was a significant correlation between post-treatment KRAS VAF and CT response (panel A) (R=0.58) and change in KRAS and CT response (panel B) (R=0.59)
Supplementary Tables S1-S2, Figures S1-S8 from Targeting OCT2 with Duloxetine to Prevent Oxaliplatin-induced Peripheral Neurotoxicity
Authors: Nepal Mahesh R. , Taheri Hanieh , Li Yang , Talebi Zahra , Uddin Muhammad Erfan , Jin Yan , DiGiacomo Duncan F. , Gibson Alice A. , Lustberg Maryam B. , Hu Shuiying , Sparreboom Alex
Published: April 2023

Supplementary Table S1. Percentage of OCT2 inhibition by compounds reported to reduce platinum-induced toxicities. Supplementary Table S2. Validation of human, rat, and murine overexpressed cells by evaluating their ability to accumulate known prototypical transport substrates. Supplementary Figure S1. Chemical structure of duloxetine. Supplementary Figure S2. IVIS imaging of tumor bearing mice. Supplementary Figure S3. Metabolites of duloxetine do not inhibit OCT2 function. Supplementary Figure S4. Duloxetine is an OCT2 inhibitor that extensively binds to extracellular membrane. Supplementary Figure S5. Duloxetine does not prevent peripheral neurotoxicity associated with vincristine and paclitaxel. Supplementary Figure S6. Paw withdrawal force measured by VFH instrument before the start of the treatment in wild-type (WT) and OCT1/2(-/-) mice (n=5-10 per group). Supplementary Figure S7. Activity of oxaliplatin in various colorectal cancer cell lines. Supplementary Figure S8. Effect of duloxetine on sciatic and caudal nerve velocity and amplitude.
Figure FS6 from Loss of the Volume-regulated Anion Channel Components LRRC8A and LRRC8D Limits Platinum Drug Efficacy
Authors: Widmer Carmen A. , Klebic Ismar , Domanitskaya Natalya , Decollogny Morgane , Howald Denise , Siffert Myriam , Essers Paul , Nowicka Zuzanna , Stokar-Regenscheit Nadine , van de Ven Marieke , de Korte-Grimmerink Renske , Galván José A. , Pritchard Colin E.J. , Huijbers Ivo J. , Fendler Wojciech , Vens Conchita , Rottenberg Sven
Published: April 2023

Analysis of publicly available ovarian cancer dataset to identify the association of LRRC8A or LRRC8D expression with outcome of chemotherapy with cisplatin
Figure FS3 from Loss of the Volume-regulated Anion Channel Components LRRC8A and LRRC8D Limits Platinum Drug Efficacy
Authors: Widmer Carmen A. , Klebic Ismar , Domanitskaya Natalya , Decollogny Morgane , Howald Denise , Siffert Myriam , Essers Paul , Nowicka Zuzanna , Stokar-Regenscheit Nadine , van de Ven Marieke , de Korte-Grimmerink Renske , Galván José A. , Pritchard Colin E.J. , Huijbers Ivo J. , Fendler Wojciech , Vens Conchita , Rottenberg Sven
Published: April 2023

Pt-drug treatment of polyclonal cell lines with wild type as well as Lrrc8a or Lrrc8d knockout alleles shows positive selection for knockout alleles
Supplementary Table S5 from Mixed Response to Cancer Immunotherapy is Driven by Intratumor Heterogeneity and Differential Interlesion Immune Infiltration
Authors: Morinaga Takao , Inozume Takashi , Kawazu Masahito , Ueda Youki , Sax Nicolas , Yamashita Kazuo , Kawashima Shusuke , Nagasaki Joji , Ueno Toshihide , Lin Jason , Ohara Yuuki , Kuwata Takeshi , Yukami Hiroki , Kawazoe Akihito , Shitara Kohei , Honobe-Tabuchi Akiko , Ohnuma Takehiro , Kawamura Tatsuyoshi , Umeda Yoshiyasu , Kawahara Yu , Nakamura Yasuhiro , Kiniwa Yukiko , Morita Ayako , Ichihara Eiki , Kiura Katsuyuki , Enokida Tomohiro , Tahara Makoto , Hasegawa Yoshinori , Mano Hiroyuki , Suzuki Yutaka , Nishikawa Hiroyoshi , Togashi Yosuke
Published: April 2023

Comparison of RNA-seq.
Figure S7 from Phase I Trial of Intravenous Mistletoe Extract in Advanced Cancer
Authors: Paller Channing J. , Wang Lin , Fu Wei , Kumar Rajendra , Durham Jennifer N. , Azad Nilofer S. , Laheru Daniel A. , Browner Ilene , Kachhap Sushant K. , Boyapati Kavya , Odeny Thomas , Armstrong Deborah K. , Meyer Christian F. , Gaillard Stephanie , Brahmer Julie R. , Page Ivelisse , Wang Hao , Diaz Luis A.
Published: April 2023

Figure S7 shows social/family well-being over time
Figure S1 from Phase I Trial of Intravenous Mistletoe Extract in Advanced Cancer
Authors: Paller Channing J. , Wang Lin , Fu Wei , Kumar Rajendra , Durham Jennifer N. , Azad Nilofer S. , Laheru Daniel A. , Browner Ilene , Kachhap Sushant K. , Boyapati Kavya , Odeny Thomas , Armstrong Deborah K. , Meyer Christian F. , Gaillard Stephanie , Brahmer Julie R. , Page Ivelisse , Wang Hao , Diaz Luis A.
Published: April 2023

Figure S1 shows tumor marker over time
Supplementary Figure SF4 from Antibody Binding and Neutralization of Live SARS-CoV-2 Variants Including BA.4/5 Following Booster Vaccination of Patients with B-cell Malignancies
Authors: Chang Andres , Akhtar Akil , Lai Lilin , Orellana-Noia Victor M. , Linderman Susanne L. , McCook-Veal Ashley A. , Switchenko Jeffrey M. , Saini Manpreet , Valanparambil Rajesh M. , Blum Kristie A. , Allen Pamela B. , Lechowicz Mary Jo , Romancik Jason T. , Ayers Amy , Leal Alyssa , O'Leary Colin B. , Churnetski Michael C. , Baird Katelin , Kives Melissa , Wrammert Jens , Nooka Ajay K. , Koff Jean L. , Dhodapkar Madhav V. , Suthar Mehul S. , Cohen Jonathon B. , Ahmed Rafi
Published: April 2023

Supplemental Figure 4. Anti-spike binding IgG titers after booster correlate with conventional B cell numbers in the blood prior booster.
Figure S6 from MEK5-ERK5 Axis Promotes Self-renewal and Tumorigenicity of Glioma Stem Cells
Authors: Fukasawa Kazuya , Lyu Jiajun , Kubo Takuya , Tanaka Yuki , Suzuki Akane , Horie Tetsuhiro , Tomizawa Akane , Osumi Ryoma , Iwahashi Sayuki , Tokumura Kazuya , Murata Misato , Kobayashi Masaki , Todo Tomoki , Hirao Atsushi , Hinoi Eiichi
Published: April 2023

Figure S6
Supplementary Figure SF2 from Antibody Binding and Neutralization of Live SARS-CoV-2 Variants Including BA.4/5 Following Booster Vaccination of Patients with B-cell Malignancies
Authors: Chang Andres , Akhtar Akil , Lai Lilin , Orellana-Noia Victor M. , Linderman Susanne L. , McCook-Veal Ashley A. , Switchenko Jeffrey M. , Saini Manpreet , Valanparambil Rajesh M. , Blum Kristie A. , Allen Pamela B. , Lechowicz Mary Jo , Romancik Jason T. , Ayers Amy , Leal Alyssa , O'Leary Colin B. , Churnetski Michael C. , Baird Katelin , Kives Melissa , Wrammert Jens , Nooka Ajay K. , Koff Jean L. , Dhodapkar Madhav V. , Suthar Mehul S. , Cohen Jonathon B. , Ahmed Rafi
Published: April 2023

Supplemental Figure 2. Positive correlations in antibody binding titers between anti-Spike IgG and anti-RBD, anti-NTD IgG, and anti-spike IgA and IgM
Supplementary Tables S1-S10 from Complex Patterns of Genomic Heterogeneity Identified in 42 Tumor Samples and ctDNA of a Pulmonary Atypical Carcinoid Patient
Authors: Robb Tamsin J. , Tsai Peter , Fitzgerald Sandra , Shields Paula , Houseman Pascalene S. , Patel Rachna , Fan Vicky , Curran Ben , Tse Rexson , Ting Jacklyn , Kramer Nicole , Woodhouse Braden J. , Coats Esther , Le Quesne Stabej Polona , Reeve Jane , Parker Kate , Lawrence Ben , Blenkiron Cherie , Print Cristin G.
Published: April 2023

Supplementary Table S1 includes a description of the tumour samples analysed.

Supplementary Table S2 includes DNA WES summary statistics.

Supplementary Table S3 includes RNA-Seq summary statistics.

Supplementary Table S4 includes WGS linked-read summary statistics.

Supplementary Table S5 includes regions covered in the custom ThermoFisher Scientific Ampliseq HD panel. Supplementary Table S6 includes targeted DNA sequencing custom panel summary statistics. Supplementary Table S7 includes low-coverage DNA WES summary statistics.

Supplementary Table S8 includes gene set enrichment of genes lost from Chr 11.

Supplementary Table S9 includes variants identified in two or more tumour sites.

Supplementary Table S10 includes the consequence of somatic variants in Biopsy 1.
Table TS3 from Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma
Authors: Wong Derek , Luo Ping , Znassi Nadia , Arteaga Diana P. , Gray Diana , Danesh Arnavaz , Han Ming , Zhao Eric Y. , Pedersen Stephanie , Prokopec Stephenie , Sundaravadanam Yogi , Torti Dax , Marsh Kayla , Keshavarzi Sareh , Xu Wei , Krema Hatem , Joshua Anthony M. , Butler Marcus O. , Pugh Trevor J.
Published: April 2023

sample schedule
Table S2 from Loss of Dok-3 in Non-tumor Cells Induces Malignant Transformation of Benign Epithelial Tumor Cells of the Intestine
Authors: Arimura Sumimasa , Inoue-Yamauchi Akane , Katayama Kotoe , Kanno Tatsuo , Jozawa Hiroki , Imoto Seiya , Yamanashi Yuji
Published: April 2023

Dok-3 KO mice bearing Csf1 homozygous mutations are not observed at the expected Mendelian ratios at weaning.
Figure S1 from Targeting MLL Methyltransferases Enhances the Antitumor Effects of PI3K Inhibition in Hormone Receptor–positive Breast Cancer
Authors: Jones Robert B. , Farhi Jonathan , Adams Miranda , Parwani Kiran K. , Cooper Garrett W. , Zecevic Milica , Lee Richard S. , Hong Andrew L. , Spangle Jennifer M.
Published: April 2023

Figure S1 shows combined effects of PI3K and MLL1 inhibition in clonogenic assays
Supplementary Figure S5 from Targeting NEDDylation is a Novel Strategy to Attenuate Cisplatin-induced Nephrotoxicity
Authors: Jones Trace M. , Espitia Claudia M. , Chipollini Juan , Lee Benjamin R. , Wertheim Jason A. , Carew Jennifer S. , Nawrocki Steffan T.
Published: April 2023

Quantification of IHC staining.
Supplementary Figure S2 from Targeting NEDDylation is a Novel Strategy to Attenuate Cisplatin-induced Nephrotoxicity
Authors: Jones Trace M. , Espitia Claudia M. , Chipollini Juan , Lee Benjamin R. , Wertheim Jason A. , Carew Jennifer S. , Nawrocki Steffan T.
Published: April 2023

Pevonedistat stabilizes NRF2 expression in RPTECs.
Data from Detection of MET Polysomy by Next-generation Sequencing and Its Clinical Relevance for MET Inhibitors
Authors: Sun Boyang , Qiu Tian , Zeng Xiaoling , Duan Jianchun , Bai Hua , Xu Jiachen , Li Jin , Li Junling , Hao Xuezhi , Liu Yutao , Lin Lin , Wang Hongyu , Zhang Xin , Zhong Jia , Wang Jie , Ying Jianming , Wang Zhijie
Published: April 2023

Next-generation sequencing (NGS) has failed to detect mesenchymal epithelial transition factor gene (MET) polysomy in previous studies. We included three non–small cell lung cancer (NSCLC) cohorts in this retrospective study to establish new criteria for detecting MET polysomy and to explore the clinical relevance of MET polysomy. Cohort 1 included 53 patients whose tissues were available for both FISH and NGS assays. Paired plasma and tissue samples were obtained from 261 patients with NSCLC as cohort 2. Cohort 3 included 46 patients with metastatic NSCLC, who presented with MET copy-number gain assessed by NGS. ROC analysis demonstrated that a cut-off point of 2.3 copies achieved the maximum Youden index in discriminating polysomy from normal copy number. Compared with the FISH test for MET polysomy, the sensitivity, specificity, and agreement of NGS were 90%, 90%, and 96.2%, respectively. Following optimization using maximum somatic allele frequency, the sensitivity and specificity of NGS for defining polysomy using plasma samples according to different circulating tumor DNA mutation frequencies were 42% and 63%. The concordance rate between tissue and plasma samples for detecting polysomy was 85%. Regarding the response to MET inhibitor, the median progression-free survival (PFS) of the MET amplification group was significantly higher than that of the polysomy group. The median PFS was similar between the polysomy and normal groups. Our results indicated that NGS may serve as an alternative method for detecting MET polysomy in NSCLC tissues. Moreover, patients with MET polysomy may not benefit from MET inhibitors.
Significance:
In this study, we established a methodology to differentiate polysomy from normal copy numbers and amplification using NGS. Moreover, this study suggests that it is critical to discriminate MET polysomy from amplification, for the former may dilute the clinical benefit of MET inhibitors.
Data from The GPER Agonist LNS8801 Induces Mitotic Arrest and Apoptosis in Uveal Melanoma Cells
Authors: Ambrosini Grazia , Natale Christopher A. , Musi Elgilda , Garyantes Tina , Schwartz Gary K.
Published: April 2023

Uveal melanoma is the most common primary intraocular malignancy in adults and has a high incidence of metastatic disease. Current treatments have shown limited clinical activity in patients with uveal melanoma with metastasis and there is an urgent need for new effective therapies. Recent findings have shown that women with uveal melanoma have better survival rates than men. The G protein–coupled estrogen receptor-1 (GPER) has distinct functions from those of the classic estrogen receptors ERα/β and its activation by specific agonists has tumor-suppressive roles in several cancers. However, the role of GPER had not previously been investigated in uveal melanoma. We demonstrated that downregulation of GPER in uveal melanoma cells decreased expression of p53 and stimulated cell growth. In contrast, the clinical GPER agonist, LNS8801, upregulated p53 and p21, induced melanocytic differentiation markers, inhibited cell proliferation and cell migration, and induced apoptosis. Furthermore, LNS8801 treatment arrested the cells in G2–M-phase of the cell cycle with concomitant activation of mitotic markers and disruption of the mitotic spindle apparatus. LNS8801 significantly inhibited tumor growth of uveal melanoma xenografts in vivo, suggesting that GPER agonists may be a novel treatment for uveal melanoma.
Significance:
Current treatments against metastatic uveal melanoma have shown limited clinical activity and there is an urgent need for effective therapies. Here, we demonstrate that the GPER agonist LNS8801 induced both GPER-dependent and GPER-independent effects and elicited potent anticancer activities in vitro and in vivo. Our results complement and support the ongoing clinical trial of LNS8801 in advanced uveal melanoma.
The effects of chemotherapy, primary tumor location and histological subtype on the survival of stage III colon cancer patients
Authors: Zhou Chenghui , Lu Liqing , Huang Qiulin , Tang Zhen , Tang Rong , Xiao Zhongsheng , Xiao Shuai
Published: April 2023

Objective

Colon cancer (CC) is one of the most common cancers worldwide and has a poor prognosis. Surgery followed by adjuvant chemotherapy is the standard treatment strategy for stage III CC patients. Primary tumor location (PTL) is an important factor for the long-term survival of CC. However, the difference in the prognosis between the histological subtypes of mucinous adenocarcinoma (MAC) and nonspecific adenocarcinoma (AC) in stage III CC patients is unclear. The correlation of chemotherapy, PTL and histological subtype with the overall survival (OS) of stage III CC patients has not yet been explored.

Methods

Patients diagnosed with stage III CC from 2010 to 2016 in the Surveillance, Epidemiology, and End Results (SEER) database were retrieved. The clinicopathological features and OS were analyzed according to the chemotherapy, PTL and histological subtype.

Results

A total of 28,765 eligible stage III CC patients were enrolled in this study. The results showed that chemotherapy, left-sided CC (LCC) and AC were favorable prognostic factors for OS. Right-sided CC (RCC) had worse OS than LCC regardless of chemotherapy. MAC had worse OS than AC in the patients with chemotherapy, but the survival benefits disappeared in the patients without chemotherapy. Additionally, in LCC, MAC had worse OS than AC regardless of chemotherapy. However, in RCC, MAC had worse OS than AC in patients with chemotherapy but had similar OS to AC in patients without chemotherapy. In the AC group, RCC had worse OS than LCC regardless of chemotherapy. In the MAC group, RCC had comparable OS to LCC regardless of chemotherapy. Four subgroups, i.e., RCC/MAC, RCC/AC, LCC/MAC and LCC/AC, all showed benefits from chemotherapy. Among them, LCC/AC had the best OS, and RCC/MAC had the worst OS compared with the other three subgroups.

Conclusion

The prognosis of MAC is worse than that of AC in stage III CC. LCC/AC has the best OS, while RCC/MAC has the worst OS but still benefits from chemotherapy. The impact of chemotherapy on survival is greater than that of histological subtype, but the impact of histological subtype on survival is similar to that of PTL.