bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table from Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms
Authors: Bertrums Eline J.M. , Rosendahl Huber Axel K.M. , de Kanter Jurrian K. , Brandsma Arianne M. , van Leeuwen Anaïs J.C.N. , Verheul Mark , van den Heuvel-Eibrink Marry M. , Oka Rurika , van Roosmalen Markus J. , de Groot-Kruseman Hester A. , Zwaan C. Michel , Goemans Bianca F. , van Boxtel Ruben
Published: April 2023

Supplementary Table from Elevated Mutational Age in Blood of Children Treated for Cancer Contributes to Therapy-Related Myeloid Neoplasms
Supplementary Figures S1-S7 from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung
Authors: Concepcion Carla P. , Ma Sai , LaFave Lindsay M. , Bhutkar Arjun , Liu Manyuan , DeAngelo Lydia P. , Kim Jonathan Y. , Del Priore Isabella , Schoenfeld Adam J. , Miller Manon , Kartha Vinay K. , Westcott Peter M.K. , Sánchez-Rivera Francisco J. , Meli Kevin , Gupta Manav , Bronson Roderick T. , Riely Gregory J. , Rekhtman Natasha , Rudin Charles M. , Kim Carla F. , Regev Aviv , Buenrostro Jason D. , Jacks Tyler
Published: April 2023

Supplementary Figures related to Figures 1-6
RNA-seq (primary tumors) Supplementary Data from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung
Authors: Concepcion Carla P. , Ma Sai , LaFave Lindsay M. , Bhutkar Arjun , Liu Manyuan , DeAngelo Lydia P. , Kim Jonathan Y. , Del Priore Isabella , Schoenfeld Adam J. , Miller Manon , Kartha Vinay K. , Westcott Peter M.K. , Sánchez-Rivera Francisco J. , Meli Kevin , Gupta Manav , Bronson Roderick T. , Riely Gregory J. , Rekhtman Natasha , Rudin Charles M. , Kim Carla F. , Regev Aviv , Buenrostro Jason D. , Jacks Tyler
Published: April 2023

Processed data for bulk RNA-seq of primary tumors isolated from KP, KPS-HET and KPS animals
Supplementary Figure from NCOA4-Mediated Ferritinophagy Is a Pancreatic Cancer Dependency via Maintenance of Iron Bioavailability for Iron–Sulfur Cluster Proteins
Authors: Santana-Codina Naiara , del Rey Maria Quiles , Kapner Kevin S. , Zhang Huan , Gikandi Ajami , Malcolm Callum , Poupault Clara , Kuljanin Miljan , John Kristen M. , Biancur Douglas E. , Chen Brandon , Das Nupur K. , Lowder Kristen E. , Hennessey Connor J. , Huang Wesley , Yang Annan , Shah Yatrik M. , Nowak Jonathan A. , Aguirre Andrew J. , Mancias Joseph D.
Published: April 2023

Supplementary Figure from NCOA4-Mediated Ferritinophagy Is a Pancreatic Cancer Dependency via Maintenance of Iron Bioavailability for Iron–Sulfur Cluster Proteins
Supplementary Figure from The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution
Authors: Nirmal Ajit J. , Maliga Zoltan , Vallius Tuulia , Quattrochi Brian , Chen Alyce A. , Jacobson Connor A. , Pelletier Roxanne J. , Yapp Clarence , Arias-Camison Raquel , Chen Yu-An , Lian Christine G. , Murphy George F. , Santagata Sandro , Sorger Peter K.
Published: April 2023

Supplementary Figure from The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution
Table S4 from Transcription Elongation Machinery Is a Druggable Dependency and Potentiates Immunotherapy in Glioblastoma Stem Cells
Authors: Qiu Zhixin , Zhao Linjie , Shen Jia Z. , Liang Zhengyu , Wu Qiulian , Yang Kailin , Min Lihua , Gimple Ryan C. , Yang Qiyuan , Bhargava Shruti , Jin Chunyu , Kim Cheryl , Hinz Denise , Dixit Deobrat , Bernatchez Jean A. , Prager Briana C. , Zhang Guoxin , Dong Zhen , Lv Deguan , Wang Xujun , Kim Leo J.Y. , Zhu Zhe , Jones Katherine A. , Zheng Ye , Wang Xiuxing , Siqueira-Neto Jair L. , Chavez Lukas , Fu Xiang-Dong , Spruck Charles , Rich Jeremy N.
Published: April 2023

Table S4. YY1 expression correlated drug responses in brain cancer cells lines.
Supplementary Figure from Modulation of BCL-2 in Both T Cells and Tumor Cells to Enhance Chimeric Antigen Receptor T-cell Immunotherapy against Cancer
Authors: Lee Yong Gu , Guruprasad Puneeth , Ghilardi Guido , Pajarillo Raymone , Sauter Christopher Tor , Patel Ruchi , Ballard Hatcher J. , Hong Seok Jae , Chun Inkook , Yang Nicholas , Amelsberg Kimberly V. , Cummins Katherine D. , Svoboda Jakub , Gill Saar , Chong Elise A. , North Khrystyna , Church Sarah E. , Fraietta Joseph A. , Chang Wan-Jung , Lacey Simon F. , Lu Xueqing Maggie , Zhang Yunlin , Whig Kanupriya , Schultz David C. , Cherry Sara , Gerson James , Schuster Stephen J. , Porazzi Patrizia , Ruella Marco
Published: April 2023

Supplementary Figure from Modulation of BCL-2 in Both T Cells and Tumor Cells to Enhance Chimeric Antigen Receptor T-cell Immunotherapy against Cancer
Supplementary Figure from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer
Authors: Ruiz-Fernández de Córdoba Borja , Moreno Haritz , Valencia Karmele , Perurena Naiara , Ruedas Pablo , Walle Thomas , Pezonaga-Torres Alberto , Hinojosa Juan , Guruceaga Elisabet , Pineda-Lucena Antonio , Abengózar-Muela Marta , Cochonneau Denis , Zandueta Carolina , Martínez-Canarias Susana , Teijeira Álvaro , Ajona Daniel , Ortiz-Espinosa Sergio , Morales Xabier , Ortiz de Solórzano Carlos , Santisteban Marta , Ramos-García Luis I. , Guembe Laura , Strnad Vratislav , Heymann Dominique , Hervás-Stubbs Sandra , Pío Rubén , Rodríguez-Ruiz María E. , de Andrea Carlos E. , Vicent Silvestre , Melero Ignacio , Lecanda Fernando , Martínez-Monge Rafael
Published: April 2023

Supplementary Figure from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer
Supplementary Data from Improving the Affordability of Anticancer Medicines Demands Evidence-Based Policy Solutions
Authors: Franzen Nora , Romagnoli Giorgia , Ziegler Andreas , Retèl Valesca P. , Offerman Theo J.S. , van Harten Wim H.
Published: April 2023

Supplementary Data
Brief description of important policy proposals to reduce treatment prices in oncology.
Supplementary Figure from Targeting S100A9–ALDH1A1–Retinoic Acid Signaling to Suppress Brain Relapse in EGFR-Mutant Lung Cancer
Authors: Biswas Anup Kumar , Han Seoyoung , Tai Yifan , Ma Wanchao , Coker Courtney , Quinn S. Aidan , Shakri Ahmad Rushdi , Zhong Timothy James , Scholze Hanna , Lagos Galina G. , Mela Angeliki , Manova-Todorova Katia , de Stanchina Elisa , Ferrando Adolfo A. , Mendelsohn Cathy , Canoll Peter , Yu Helena A. , Paik Paul K. , Saqi Anjali , Shu Catherine A. , Kris Mark G. , Massague Joan , Acharyya Swarnali
Published: April 2023

Supplementary Figure from Targeting S100A9–ALDH1A1–Retinoic Acid Signaling to Suppress Brain Relapse in EGFR-Mutant Lung Cancer
Supplementary Data from Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse
Authors: Gambacorta Valentina , Beretta Stefano , Ciccimarra Martina , Zito Laura , Giannetti Kety , Andrisani Angela , Gnani Daniela , Zanotti Lucia , Oliveira Giacomo , Carrabba Matteo Giovanni , Cittaro Davide , Merelli Ivan , Ciceri Fabio , Di Micco Raffaella , Vago Luca
Published: April 2023

Supplementary Data from Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse
Supplementary Figure from SETD2 Haploinsufficiency Enhances Germinal Center–Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis
Authors: Leung Wilfred , Teater Matt , Durmaz Ceyda , Meydan Cem , Chivu Alexandra G. , Chadburn Amy , Rice Edward J. , Muley Ashlesha , Camarillo Jeannie M. , Arivalagan Jaison , Li Ziyi , Flowers Christopher R. , Kelleher Neil L. , Danko Charles G. , Imielinski Marcin , Dave Sandeep S. , Armstrong Scott A. , Mason Christopher E. , Melnick Ari M.
Published: April 2023

Supplementary Figure from SETD2 Haploinsufficiency Enhances Germinal Center–Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis
Supplementary Figure from AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer
Authors: Noronha Ashish , Belugali Nataraj Nishanth , Lee Joo Sang , Zhitomirsky Benny , Oren Yaara , Oster Sara , Lindzen Moshit , Mukherjee Saptaparna , Will Rainer , Ghosh Soma , Simoni-Nieves Arturo , Verma Aakanksha , Chatterjee Rishita , Borgoni Simone , Robinson Welles , Sinha Sanju , Brandis Alexander , Kerr D. Lucas , Wu Wei , Sekar Arunachalam , Giri Suvendu , Chung Youngmin , Drago-Garcia Diana , Danysh Brian P. , Lauriola Mattia , Fiorentino Michelangelo , Ardizzoni Andrea , Oren Moshe , Blakely Collin M. , Ezike Jideofor , Wiemann Stefan , Parida Laxmi , Bivona Trever G. , Aqeilan Rami I. , Brugge Joan S. , Regev Aviv , Getz Gad , Ruppin Eytan , Yarden Yosef
Published: April 2023

Supplementary Figure from AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer
Supp Table 5 from Human Bone Marrow Organoids for Disease Modeling, Discovery, and Validation of Therapeutic Targets in Hematologic Malignancies
Authors: Khan Abdullah O. , Rodriguez-Romera Antonio , Reyat Jasmeet S. , Olijnik Aude-Anais , Colombo Michela , Wang Guanlin , Wen Wei Xiong , Sousos Nikolaos , Murphy Lauren C. , Grygielska Beata , Perrella Gina , Mahony Christopher B. , Ling Rebecca E. , Elliott Natalina E. , Karali Christina Simoglou , Stone Andrew P. , Kemble Samuel , Cutler Emily A. , Fielding Adele K. , Croft Adam P. , Bassett David , Poologasundarampillai Gowsihan , Roy Anindita , Gooding Sarah , Rayes Julie , Machlus Kellie R. , Psaila Bethan
Published: April 2023

Supplementary Table 5 Antibodies
Supplementary Figure 2 from A Small Molecule Reacts with the p53 Somatic Mutant Y220C to Rescue Wild-type Thermal Stability
Authors: Guiley Keelan Z. , Shokat Kevan M.
Published: April 2023

Supplementary Figure S2: Differential scanning fluorimetry (A) Carbazole series plot of average values from differential scanning fluorimetry. (B) Indole series plot of average values from differential scanning fluorimetry. (C) Azaindole series plot of average values from differential scanning fluorimetry. (D) p53 Y220C-CL D228A DMSO or KG11 adduct plot of average values from differential scanning fluorimetry.
Supplementary Video 4 from Bone Metastasis Initiation Is Coupled with Bone Remodeling through Osteogenic Differentiation of NG2+ Cells
Authors: Zhang Weijie , Xu Zhan , Hao Xiaoxin , He Tiancheng , Li Jiasong , Shen Yichao , Liu Kai , Gao Yang , Liu Jun , Edwards David G. , Muscarella Aaron M. , Wu Ling , Yu Liqun , Xu Longyong , Chen Xi , Wu Yi-Hsuan , Bado Igor L. , Ding Yunfeng , Aguirre Sergio , Wang Hai , Gugala Zbigniew , Satcher Robert L. , Wong Stephen T.C. , Zhang Xiang H.-F.
Published: April 2023

Supplemantary Video 4, LLC1 cells cocultured with NG2+ Ncadherin KO BMSCs
Supplementary Figure S1-S7 from Bone Metastasis Initiation Is Coupled with Bone Remodeling through Osteogenic Differentiation of NG2+ Cells
Authors: Zhang Weijie , Xu Zhan , Hao Xiaoxin , He Tiancheng , Li Jiasong , Shen Yichao , Liu Kai , Gao Yang , Liu Jun , Edwards David G. , Muscarella Aaron M. , Wu Ling , Yu Liqun , Xu Longyong , Chen Xi , Wu Yi-Hsuan , Bado Igor L. , Ding Yunfeng , Aguirre Sergio , Wang Hai , Gugala Zbigniew , Satcher Robert L. , Wong Stephen T.C. , Zhang Xiang H.-F.
Published: April 2023

Supplementary figures and corresponding figure legends
Supplementary Figures and Tables from Cell Competition Shapes Metastatic Latency and Relapse
Authors: Kim Kangsan , Huang Huocong , Parida Pravat Kumar , He Lan , Marquez-Palencia Mauricio , Reese Tanner C. , Kapur Payal , Brugarolas James , Brekken Rolf A. , Malladi Srinivas
Published: April 2023

This document includes the followings:
Supplementary Fig. S1-6 and legends
Supplementary Table. S1-2 and legends
Supplementary Video. S1 legend
Supplementary Figure S4 from Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma
Authors: Suresh Shruthy , Rabbie Roy , Garg Manik , Lumaquin Dianne , Huang Ting-Hsiang , Montal Emily , Ma Yilun , Cruz Nelly M , Tang Xinran , Nsengimana Jérémie , Newton-Bishop Julia , Hunter Miranda V. , Zhu Yuxin , Chen Kevin , de Stanchina Elisa , Adams David J. , White Richard M.
Published: April 2023

An in vivo screen identifies metastasis suppressors in melanoma.
Supp Table S4 from Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma
Authors: Suresh Shruthy , Rabbie Roy , Garg Manik , Lumaquin Dianne , Huang Ting-Hsiang , Montal Emily , Ma Yilun , Cruz Nelly M , Tang Xinran , Nsengimana Jérémie , Newton-Bishop Julia , Hunter Miranda V. , Zhu Yuxin , Chen Kevin , de Stanchina Elisa , Adams David J. , White Richard M.
Published: April 2023

Supp Table S4 has a list of antibodies and other resources
Supp Table S3 from Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma
Authors: Suresh Shruthy , Rabbie Roy , Garg Manik , Lumaquin Dianne , Huang Ting-Hsiang , Montal Emily , Ma Yilun , Cruz Nelly M , Tang Xinran , Nsengimana Jérémie , Newton-Bishop Julia , Hunter Miranda V. , Zhu Yuxin , Chen Kevin , de Stanchina Elisa , Adams David J. , White Richard M.
Published: April 2023

Supp Table S3 has a List of Oligonucleotides Sequences
Supplementary Figure from BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma
Authors: Panditharatna Eshini , Marques Joana G. , Wang Tingjian , Trissal Maria C. , Liu Ilon , Jiang Li , Beck Alexander , Groves Andrew , Dharia Neekesh V. , Li Deyao , Hoffman Samantha E. , Kugener Guillaume , Shaw McKenzie L. , Mire Hafsa M. , Hack Olivia A. , Dempster Joshua M. , Lareau Caleb , Dai Lingling , Sigua Logan H. , Quezada Michael A. , Stanton Ann-Catherine J. , Wyatt Meghan , Kalani Zohra , Goodale Amy , Vazquez Francisca , Piccioni Federica , Doench John G. , Root David E. , Anastas Jamie N. , Jones Kristen L. , Conway Amy Saur , Stopka Sylwia , Regan Michael S. , Liang Yu , Seo Hyuk-Soo , Song Kijun , Bashyal Puspalata , Jerome William P. , Mathewson Nathan D. , Dhe-Paganon Sirano , Suvà Mario L. , Carcaboso Angel M. , Lavarino Cinzia , Mora Jaume , Nguyen Quang-De , Ligon Keith L. , Shi Yang , Agnihotri Sameer , Agar Nathalie Y.R. , Stegmaier Kimberly , Stiles Charles D. , Monje Michelle , Golub Todd R. , Qi Jun , Filbin Mariella G.
Published: April 2023

Supplementary Figure from BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma
Supplementary Figure 1 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
Authors: Yaeger Rona , Mezzadra Riccardo , Sinopoli Jenna , Bian Yu , Marasco Michelangelo , Kaplun Esther , Gao Yijun , Zhao HuiYong , Paula Arnaud Da Cruz , Zhu Yingjie , Perez Almudena Chaves , Chadalavada Kalyani , Tse Edison , Chowdhry Sudhir , Bowker Sydney , Chang Qing , Qeriqi Besnik , Weigelt Britta , Nanjangud Gouri J. , Berger Michael F. , Der-Torossian Hirak , Anderes Kenna , Socci Nicholas D. , Shia Jinru , Riely Gregory J. , Murciano-Goroff Yonina R. , Li Bob T. , Christensen James G. , Reis-Filho Jorge S. , Solit David B. , de Stanchina Elisa , Lowe Scott W. , Rosen Neal , Misale Sandra
Published: April 2023

Characterization of acquired resistance in vitro models
Supplementary Figures S1-S9 from Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell–like Program Conserved in HPV-Positive Cancers
Authors: Leiendecker Lukas , Neumann Tobias , Jung Pauline S. , Cronin Shona M. , Steinacker Thomas L. , Schleiffer Alexander , Schutzbier Michael , Mechtler Karl , Kervarrec Thibault , Laurent Estelle , Bachiri Kamel , Coyaud Etienne , Murali Rajmohan , Busam Klaus J. , Itzinger-Monshi Babak , Kirnbauer Reinhard , Cerroni Lorenzo , Calonje Eduardo , Rütten Arno , Stubenrauch Frank , Griewank Klaus G. , Wiesner Thomas , Obenauf Anna C.
Published: April 2023

Supplementary data depicted in Supplementary Figures S1-S9
Table S5 from OncoLoop: A Network-Based Precision Cancer Medicine Framework
Authors: Vasciaveo Alessandro , Arriaga Juan Martín , de Almeida Francisca Nunes , Zou Min , Douglass Eugene F. , Picech Florencia , Shibata Maho , Rodriguez-Calero Antonio , de Brot Simone , Mitrofanova Antonina , Chua Chee Wai , Karan Charles , Realubit Ronald , Pampou Sergey , Kim Jaime Y. , Afari Stephanie N. , Mukhammadov Timur , Zanella Luca , Corey Eva , Alvarez Mariano J. , Rubin Mark A. , Shen Michael M. , Califano Andrea , Abate-Shen Cory
Published: April 2023

Supplementary Table 5. Drug perturbation and OncoTreat analysis
A. Summary of drugs and concentrations used
B. Drug perturbation data for DU145
C. OncoTreat for drugs to SU2C patients using DU145
D. OncoTreat for drugs to GEMMs using DU145
Table S4 from OncoLoop: A Network-Based Precision Cancer Medicine Framework
Authors: Vasciaveo Alessandro , Arriaga Juan Martín , de Almeida Francisca Nunes , Zou Min , Douglass Eugene F. , Picech Florencia , Shibata Maho , Rodriguez-Calero Antonio , de Brot Simone , Mitrofanova Antonina , Chua Chee Wai , Karan Charles , Realubit Ronald , Pampou Sergey , Kim Jaime Y. , Afari Stephanie N. , Mukhammadov Timur , Zanella Luca , Corey Eva , Alvarez Mariano J. , Rubin Mark A. , Shen Michael M. , Califano Andrea , Abate-Shen Cory
Published: April 2023

Supplementary Table 4: OncoMatch
A. OncoMatch TCGA
B. OncoMatch SU2C
Supplementary Materials from Efficacy of a Small-Molecule Inhibitor of KrasG12D in Immunocompetent Models of Pancreatic Cancer
Authors: Kemp Samantha B. , Cheng Noah , Markosyan Nune , Sor Rina , Kim Il-Kyu , Hallin Jill , Shoush Jason , Quinones Liz , Brown Natalie V. , Bassett Jared B. , Joshi Nikhil , Yuan Salina , Smith Molly , Vostrejs William P. , Perez-Vale Kia Z. , Kahn Benjamin , Mo Feiyan , Donahue Timothy R. , Radu Caius G. , Clendenin Cynthia , Christensen James G. , Vonderheide Robert H. , Stanger Ben Z.
Published: April 2023

Supplementary Figures and Table with legend arranged in a single presentable package
Supplementary Figure S7 from Efficacy of a Small-Molecule Inhibitor of KrasG12D in Immunocompetent Models of Pancreatic Cancer
Authors: Kemp Samantha B. , Cheng Noah , Markosyan Nune , Sor Rina , Kim Il-Kyu , Hallin Jill , Shoush Jason , Quinones Liz , Brown Natalie V. , Bassett Jared B. , Joshi Nikhil , Yuan Salina , Smith Molly , Vostrejs William P. , Perez-Vale Kia Z. , Kahn Benjamin , Mo Feiyan , Donahue Timothy R. , Radu Caius G. , Clendenin Cynthia , Christensen James G. , Vonderheide Robert H. , Stanger Ben Z.
Published: April 2023

Effects of MRTX1133 in KPC/Y and subcutaneous models
Supplementary Figure S3 from Efficacy of a Small-Molecule Inhibitor of KrasG12D in Immunocompetent Models of Pancreatic Cancer
Authors: Kemp Samantha B. , Cheng Noah , Markosyan Nune , Sor Rina , Kim Il-Kyu , Hallin Jill , Shoush Jason , Quinones Liz , Brown Natalie V. , Bassett Jared B. , Joshi Nikhil , Yuan Salina , Smith Molly , Vostrejs William P. , Perez-Vale Kia Z. , Kahn Benjamin , Mo Feiyan , Donahue Timothy R. , Radu Caius G. , Clendenin Cynthia , Christensen James G. , Vonderheide Robert H. , Stanger Ben Z.
Published: April 2023

MRTX1133 reduces metastatic burden in a tail vein model
Supplementary Figure from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion
Authors: Deborde Sylvie , Gusain Laxmi , Powers Ann , Marcadis Andrea , Yu Yasong , Chen Chun-Hao , Frants Anna , Kao Elizabeth , Tang Laura H. , Vakiani Efsevia , Amisaki Masataka , Balachandran Vinod P. , Calo Annalisa , Omelchenko Tatiana , Jessen Kristjan R. , Reva Boris , Wong Richard J.
Published: April 2023

Supplementary Figure from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion
Supplementary Figure from Geospatial Immune Heterogeneity Reflects the Diverse Tumor–Immune Interactions in Intrahepatic Cholangiocarcinoma
Authors: Lin Youpei , Peng Lihua , Dong Liangqing , Liu Dongbing , Ma Jiaqiang , Lin Jian , Chen Xiaofang , Lin Penghui , Song Guohe , Zhang Mao , Liu Yuming , Rao Junhua , Wei Chen , Lu Ye , Zhang Shu , Ding Guangyu , Peng Zhenyu , Lu Haorong , Wang Xiaoying , Zhou Jian , Fan Jia , Wu Kui , Gao Qiang
Published: April 2023

Supplementary Figure from Geospatial Immune Heterogeneity Reflects the Diverse Tumor–Immune Interactions in Intrahepatic Cholangiocarcinoma
Supplementary Table S1 from Mutant NPM1 Hijacks Transcriptional Hubs to Maintain Pathogenic Gene Programs in Acute Myeloid Leukemia
Authors: Wang Xue Qing David , Fan Dandan , Han Qinyu , Liu Yiman , Miao Hongzhi , Wang Xinyu , Li Qinglan , Chen Dong , Gore Haley , Himadewi Pamela , Pfeifer Gerd P. , Cierpicki Tomasz , Grembecka Jolanta , Su Jianzhong , Chong Shasha , Wan Liling , Zhang Xiaotian
Published: April 2023

Supplementary Table S1 shows the high-confident NPM1c binding peaks in OCI-AML3 cells.
Supplementary Figure S8 from LZTR1 Mutation Mediates Oncogenesis through Stabilization of EGFR and AXL
Authors: Ko Aram , Hasanain Mohammad , Oh Young Taek , D'Angelo Fulvio , Sommer Danika , Frangaj Brulinda , Tran Suzanne , Bielle Franck , Pollo Bianca , Paterra Rosina , Mokhtari Karima , Soni Rajesh Kumar , Peyre Matthieu , Eoli Marica , Papi Laura , Kalamarides Michel , Sanson Marc , Iavarone Antonio , Lasorella Anna
Published: April 2023

Vulnerability of LZTR1 inactive cells to combination treatment of EGFR and AXL inhibitors
Supplementary Figure S7 from LZTR1 Mutation Mediates Oncogenesis through Stabilization of EGFR and AXL
Authors: Ko Aram , Hasanain Mohammad , Oh Young Taek , D'Angelo Fulvio , Sommer Danika , Frangaj Brulinda , Tran Suzanne , Bielle Franck , Pollo Bianca , Paterra Rosina , Mokhtari Karima , Soni Rajesh Kumar , Peyre Matthieu , Eoli Marica , Papi Laura , Kalamarides Michel , Sanson Marc , Iavarone Antonio , Lasorella Anna
Published: April 2023

Protein expression of LZTR1 substrates and pathway analysis in human schwannoma A
Supplementary Figure S5 from LZTR1 Mutation Mediates Oncogenesis through Stabilization of EGFR and AXL
Authors: Ko Aram , Hasanain Mohammad , Oh Young Taek , D'Angelo Fulvio , Sommer Danika , Frangaj Brulinda , Tran Suzanne , Bielle Franck , Pollo Bianca , Paterra Rosina , Mokhtari Karima , Soni Rajesh Kumar , Peyre Matthieu , Eoli Marica , Papi Laura , Kalamarides Michel , Sanson Marc , Iavarone Antonio , Lasorella Anna
Published: April 2023

Phenotype alterations in the liver and brain of Lztr1-deleted mice
Supplementary Figure S3 from LZTR1 Mutation Mediates Oncogenesis through Stabilization of EGFR and AXL
Authors: Ko Aram , Hasanain Mohammad , Oh Young Taek , D'Angelo Fulvio , Sommer Danika , Frangaj Brulinda , Tran Suzanne , Bielle Franck , Pollo Bianca , Paterra Rosina , Mokhtari Karima , Soni Rajesh Kumar , Peyre Matthieu , Eoli Marica , Papi Laura , Kalamarides Michel , Sanson Marc , Iavarone Antonio , Lasorella Anna
Published: April 2023

Mechanism of LZTR1-mediated degradation of RIT1 and the effect of LZTR1 mutations
Figure S3 from CD19/CD20 Bispecific Chimeric Antigen Receptor (CAR) in Naive/Memory T Cells for the Treatment of Relapsed or Refractory Non-Hodgkin Lymphoma
Authors: Larson Sarah M. , Walthers Christopher M. , Ji Brenda , Ghafouri Sanaz N. , Naparstek Jacob , Trent Jacqueline , Chen Jia Ming , Roshandell Mobina , Harris Caitlin , Khericha Mobina , Schweppe Thomas , Berent-Maoz Beata , Gosliner Stanley B. , Almaktari Amr , Ceja Melanie Ayala , Allen-Auerbach Martin S. , Said Jonathan , Nawaly Karla , Mead Monica , de Vos Sven , Young Patricia A. , Oliai Caspian , Schiller Gary J. , Timmerman John M. , Ribas Antoni , Chen Yvonne Y.
Published: April 2023

Patient 009 exhibited elevated cytokine, C-reactive protein, and ferritin levels prior to and after CART19/20 cell infusion. (A) Serum levels of various cytokines measured by Luminex multiplex assay. (B) C-reactive protein (CRP) levels for Patient 009 (left-most) and all patients (second from left). Peak and median CRP levels are shown in box-and-whisker plots. (C) Ferritin levels for Patient 009 (left-most) and all patients (second from left). Peak and median ferritin levels are shown in box-and-whisker plots.
Supplementary Figures S1-S6 and Tables S1-S5 from Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration
Authors: Akagi Keiko , Symer David E. , Mahmoud Medhat , Jiang Bo , Goodwin Sara , Wangsa Darawalee , Li Zhengke , Xiao Weihong , Dan Dunn Joe , Ried Thomas , Coombes Kevin R. , Sedlazeck Fritz J. , Gillison Maura L.
Published: April 2023

Figure S1.1. Circos plots of human genomes.
Figure S1.2. Circos plots of HPV genomes.
Figure S1.3. PacBio HiFi read length distributions.
Figure S1.4. Oxford Nanopore (ONT) read length distributions.
Figure S2.1. Detection of circularized mitochondrial DNA by LR-seq reads.
Figure S2.2. Detection of HPV concatemers by LR-seq reads.
Figure S2.3. ONT reads show structural rearrangements in HPV concatemers.
Figure S3.1. Absence of sequence variants at breakpoints.
Figure S3.2. AmpliconArchitect predicts inaccurate HPV ecDNA structures.
Figure S4.1. Evolution of structural variants at Chr. 22 of Tumor 2.
Figure S4.2. Evidence of heterocateny in Tumor 5 and Tumor 3.
Figure S5.1. HPV integration into icDNA in GUMC-395, HeLa, and HTEC.
Figure S5.2. HPV integrants at Chr. 17 and Chr. X of VU147.
Figure S5.3. Metaphase FISH identifies HPV-containing ecDNAs in cell lines.
Figure S5.4. Circle-seq analysis of HeLa, GUMC-395, VU147, and HTEC cells.
Figure S6. Transcription levels of HPV genes.
Table S1.1. Depths of autosomal and mitochondrial genome sequencing coverage from WGS and LR-seq.
Table S1.2. Depths of autosomal and HPV genome sequencing coverage from WGS and LR-seq.
Table S2.1. Breakpoints and normal segment junctions in Tumor 4.
Table S2.2. Definition of genomic segments flanking HPV integrants in Tumor 4.
Table S3.1. Breakpoints and normal segment junctions in Tumor 2.
Table S3.2. Definition of genomic segments flanking HPV integrants in Tumor 2.
Table S3.3. Breakpoints and normal segment junctions in Tumor 5.
Table S3.4. Definition of genomic segments flanking HPV integrants in Tumor 5.
Table S3.5. Breakpoints and normal segment junctions in Tumor 3.
Table S3.6. Definition of genomic segments flanking HPV integrants in Tumor 3.
Table S4.1. Breakpoints and normal segment junctions in GUMC-395 cells.
Table S4.2. Definition of genomic segments flanking HPV integrants in GUMC-395 cells.
Table S5.1. Breakpoints and normal segment junctions in HeLa cells.
Table S5.2. Definition of genomic segments flanking HPV integrants in HeLa cells.
Table S5.3. Breakpoints and normal segment junctions in VU147 cells.
Table S5.4. Definition of genomic segments flanking HPV integrants in VU147 cells.
Table S5.5. Breakpoints and normal segment junctions in HTEC cells.
Table S5.6. Definition of genomic segments flanking HPV integrants in HTEC cells.
Tables S2, S7, S8, S9 from Dynamics of Age- versus Therapy-Related Clonal Hematopoiesis in Long-term Survivors of Pediatric Cancer
Authors: Hagiwara Kohei , Natarajan Sivaraman , Wang Zhaoming , Zubair Haseeb , Mulder Heather L. , Dong Li , Plyler Emily M. , Thimmaiah Padma , Ma Xiaotu , Ness Kristen K. , Li Zhenghong , Mulrooney Daniel A. , Wilson Carmen L. , Yasui Yutaka , Hudson Melissa M. , Easton John , Robison Leslie L. , Zhang Jinghui
Published: April 2023

Table S2:
List of CH mutations identified.
Table S7:
Mutations analyzed in serial analysis.
Table S8:
Clinical features of the survivors.
Table S9:
List of primers used in ddPCR validation.
Table S8 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Authors: Pongor Lőrinc Sándor , Schultz Christopher W. , Rinaldi Lorenzo , Wangsa Darawalee , Redon Christophe E. , Takahashi Nobuyuki , Fialkoff Gavriel , Desai Parth , Zhang Yang , Burkett Sandra , Hermoni Nadav , Vilk Noa , Gutin Jenia , Gergely Rona , Zhao Yongmei , Nichols Samantha , Vilimas Rasa , Sciuto Linda , Graham Chante , Caravaca Juan Manuel , Turan Sevilay , Tsai-wei Shen , Rajapakse Vinodh N. , Kumar Rajesh , Upadhyay Deep , Kumar Suresh , Kim Yoo Sun , Roper Nitin , Tran Bao , Hewitt Stephen M. , Kleiner David E. , Aladjem Mirit I. , Friedman Nir , Hager Gordon L. , Pommier Yves , Ried Thomas , Thomas Anish
Published: April 2023

Experimental validation of copy-number of the MYC locus in NCI-H889, DMS-114, NCI-H446 and RA022 patient derived cell lines and number of ecDNA and HSR positive cells in the RA022 patient derived cell lines
Table S7 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Authors: Pongor Lőrinc Sándor , Schultz Christopher W. , Rinaldi Lorenzo , Wangsa Darawalee , Redon Christophe E. , Takahashi Nobuyuki , Fialkoff Gavriel , Desai Parth , Zhang Yang , Burkett Sandra , Hermoni Nadav , Vilk Noa , Gutin Jenia , Gergely Rona , Zhao Yongmei , Nichols Samantha , Vilimas Rasa , Sciuto Linda , Graham Chante , Caravaca Juan Manuel , Turan Sevilay , Tsai-wei Shen , Rajapakse Vinodh N. , Kumar Rajesh , Upadhyay Deep , Kumar Suresh , Kim Yoo Sun , Roper Nitin , Tran Bao , Hewitt Stephen M. , Kleiner David E. , Aladjem Mirit I. , Friedman Nir , Hager Gordon L. , Pommier Yves , Ried Thomas , Thomas Anish
Published: April 2023

Amplified genes identified from cell-free ChIP-seq of patient plasma samples.
Figure S2 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Authors: Pongor Lőrinc Sándor , Schultz Christopher W. , Rinaldi Lorenzo , Wangsa Darawalee , Redon Christophe E. , Takahashi Nobuyuki , Fialkoff Gavriel , Desai Parth , Zhang Yang , Burkett Sandra , Hermoni Nadav , Vilk Noa , Gutin Jenia , Gergely Rona , Zhao Yongmei , Nichols Samantha , Vilimas Rasa , Sciuto Linda , Graham Chante , Caravaca Juan Manuel , Turan Sevilay , Tsai-wei Shen , Rajapakse Vinodh N. , Kumar Rajesh , Upadhyay Deep , Kumar Suresh , Kim Yoo Sun , Roper Nitin , Tran Bao , Hewitt Stephen M. , Kleiner David E. , Aladjem Mirit I. , Friedman Nir , Hager Gordon L. , Pommier Yves , Ried Thomas , Thomas Anish
Published: April 2023

Validation of ecDNA in SCLC, related to Figure 2
Figure 1 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Authors: Pongor Lőrinc Sándor , Schultz Christopher W. , Rinaldi Lorenzo , Wangsa Darawalee , Redon Christophe E. , Takahashi Nobuyuki , Fialkoff Gavriel , Desai Parth , Zhang Yang , Burkett Sandra , Hermoni Nadav , Vilk Noa , Gutin Jenia , Gergely Rona , Zhao Yongmei , Nichols Samantha , Vilimas Rasa , Sciuto Linda , Graham Chante , Caravaca Juan Manuel , Turan Sevilay , Tsai-wei Shen , Rajapakse Vinodh N. , Kumar Rajesh , Upadhyay Deep , Kumar Suresh , Kim Yoo Sun , Roper Nitin , Tran Bao , Hewitt Stephen M. , Kleiner David E. , Aladjem Mirit I. , Friedman Nir , Hager Gordon L. , Pommier Yves , Ried Thomas , Thomas Anish
Published: April 2023

Patient sample AmpliconArchitect assemblies, related to Figure 1
Table S3 from Targeting Microglial Metabolic Rewiring Synergizes with Immune-Checkpoint Blockade Therapy for Glioblastoma
Authors: Ye Zengpanpan , Ai Xiaolin , Yang Kailin , Yang Zhengnan , Fei Fan , Liao Xiaoling , Qiu Zhixin , Gimple Ryan C. , Yuan Huairui , Huang Hao , Gong Yanqiu , Xiao Chaoxin , Yue Jing , Huang Liang , Saulnier Olivier , Wang Wei , Zhang Peidong , Dai Lunzhi , Wang Xin , Wang Xiuxing , Ahn Young Ha , You Chao , Xu Jianguo , Wan Xiaoxiao , Taylor Michael D. , Zhao Linjie , Rich Jeremy N. , Zhou Shengtao
Published: April 2023

Table S3 describes primer information for qPCR analysis.
Data from Targeting Microglial Metabolic Rewiring Synergizes with Immune-Checkpoint Blockade Therapy for Glioblastoma
Authors: Ye Zengpanpan , Ai Xiaolin , Yang Kailin , Yang Zhengnan , Fei Fan , Liao Xiaoling , Qiu Zhixin , Gimple Ryan C. , Yuan Huairui , Huang Hao , Gong Yanqiu , Xiao Chaoxin , Yue Jing , Huang Liang , Saulnier Olivier , Wang Wei , Zhang Peidong , Dai Lunzhi , Wang Xin , Wang Xiuxing , Ahn Young Ha , You Chao , Xu Jianguo , Wan Xiaoxiao , Taylor Michael D. , Zhao Linjie , Rich Jeremy N. , Zhou Shengtao
Published: April 2023

Abstract
Glioblastoma (GBM) constitutes the most lethal primary brain tumor for which immunotherapy has provided limited benefit. The unique brain immune landscape is reflected in a complex tumor immune microenvironment (TIME) in GBM. Here, single-cell sequencing of the GBM TIME revealed that microglia were under severe oxidative stress, which induced nuclear receptor subfamily 4 group A member 2 (NR4A2)–dependent transcriptional activity in microglia. Heterozygous Nr4a2 (Nr4a2+/−) or CX3CR1+ myeloid cell–specific Nr4a2 (Nr4a2fl/flCx3cr1Cre) genetic targeting reshaped microglia plasticity in vivo by reducing alternatively activated microglia and enhancing antigen presentation capacity for CD8+ T cells in GBM. In microglia, NR4A2 activated squalene monooxygenase (SQLE) to dysregulate cholesterol homeostasis. Pharmacologic NR4A2 inhibition attenuated the protumorigenic TIME, and targeting the NR4A2 or SQLE enhanced the therapeutic efficacy of immune-checkpoint blockade in vivo. Collectively, oxidative stress promotes tumor growth through NR4A2–SQLE activity in microglia, informing novel immune therapy paradigms in brain cancer.
Significance:
Metabolic reprogramming of microglia in GBM informs synergistic vulnerabilities for immune-checkpoint blockade therapy in this immunologically cold brain tumor.

This article is highlighted in the In This Issue feature, p. 799
Data from IDO Is a Nodal Pathogenic Driver of Lung Cancer and Metastasis Development
Authors: Smith Courtney , Chang Mee Young , Parker Katherine H. , Beury Daniel W. , DuHadaway James B. , Flick Hollie E. , Boulden Janette , Sutanto-Ward Erika , Soler Alejandro Peralta , Laury-Kleintop Lisa D. , Mandik-Nayak Laura , Metz Richard , Ostrand-Rosenberg Suzanne , Prendergast George C. , Muller Alexander J.
Published: April 2023

Abstract
Indoleamine 2,3-dioxygenase (IDO) enzyme inhibitors have entered clinical trials for cancer treatment based on preclinical studies, indicating that they can defeat immune escape and broadly enhance other therapeutic modalities. However, clear genetic evidence of the impact of IDO on tumorigenesis in physiologic models of primary or metastatic disease is lacking. Investigating the impact of Ido1 gene disruption in mouse models of oncogenic KRAS-induced lung carcinoma and breast carcinoma–derived pulmonary metastasis, we have found that IDO deficiency resulted in reduced lung tumor burden and improved survival in both models. Micro-computed tomographic (CT) imaging further revealed that the density of the underlying pulmonary blood vessels was significantly reduced in Ido1-nullizygous mice. During lung tumor and metastasis outgrowth, interleukin (IL)-6 induction was greatly attenuated in conjunction with the loss of IDO. Biologically, this resulted in a consequential impairment of protumorigenic myeloid-derived suppressor cells (MDSC), as restoration of IL-6 recovered both MDSC suppressor function and metastasis susceptibility in Ido1-nullizygous mice. Together, our findings define IDO as a prototypical integrative modifier that bridges inflammation, vascularization, and immune escape to license primary and metastatic tumor outgrowth.

Significance: This study provides preclinical, genetic proof-of-concept that the immunoregulatory enzyme IDO contributes to autochthonous carcinoma progression and to the creation of a metastatic niche. IDO deficiency in vivo negatively impacted both vascularization and IL-6–dependent, MDSC-driven immune escape, establishing IDO as an overarching factor directing the establishment of a protumorigenic environment. Cancer Discov; 2(8); 722–35. ©2012 AACR.

Read the Commentary on this article by Novitskiy et al., p. 673.

This article is highlighted in the In This Issue feature, p. 653.
Data from Functional Metabolic Screen Identifies 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 as an Important Regulator of Prostate Cancer Cell Survival
Authors: Ros Susana , Santos Claudio R. , Moco Sofia , Baenke Franziska , Kelly Gavin , Howell Michael , Zamboni Nicola , Schulze Almut
Published: April 2023

Abstract
Alterations in metabolic activity contribute to the proliferation and survival of cancer cells. We investigated the effect of siRNA-mediated gene silencing of 222 metabolic enzymes, transporters, and regulators on the survival of 3 metastatic prostate cancer cell lines and a nonmalignant prostate epithelial cell line. This approach revealed significant complexity in the metabolic requirements of prostate cancer cells and identified several genes selectively required for their survival. Among these genes was 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (PFKFB4), an isoform of phosphofructokinase 2 (PFK2). We show that PFKFB4 is required to balance glycolytic activity and antioxidant production to maintain cellular redox balance in prostate cancer cells. Depletion of PFKFB4 inhibited tumor growth in a xenograft model, indicating that it is required under physiologic nutrient levels. PFKFB4 mRNA expression was also found to be greater in metastatic prostate cancer compared with primary tumors. Taken together, these results indicate that PFKFB4 is a potential target for the development of antineoplastic agents.

Significance: Cancer cells undergo several changes in their metabolism that promote growth and survival. Using an unbiased functional screen, we found that the glycolytic enzyme PFKFB4 is essential for prostate cancer cell survival by maintaining the balance between the use of glucose for energy generation and the synthesis of antioxidants. Targeting PFKFB4 may therefore present new therapeutic opportunities. Cancer Discov; 2(4); 328–43. ©2012 AACR.

Read the Commentary on this article by Dang, p. 304

This article is highlighted in the In This Issue feature, 288
Data from Obligate Progression Precedes Lung Adenocarcinoma Dissemination
Authors: Caswell Deborah R. , Chuang Chen-Hua , Yang Dian , Chiou Shin-Heng , Cheemalavagu Shashank , Kim-Kiselak Caroline , Connolly Andrew , Winslow Monte M.
Published: April 2023

Abstract
Despite its clinical importance, very little is known about the natural history and molecular underpinnings of lung cancer dissemination and metastasis. Here, we used a genetically engineered mouse model of metastatic lung adenocarcinoma in which cancer cells are fluorescently marked to determine whether dissemination is an inherent ability or a major acquired phenotype during lung adenocarcinoma metastasis. We find very little evidence for dissemination from oncogenic KRAS-driven hyperplasias or most adenocarcinomas. p53 loss is insufficient to drive dissemination but rather enables rare cancer cells in a small fraction of primary adenocarcinomas to gain alterations that drive dissemination. Molecular characterization of disseminated tumor cells indicates that downregulation of the transcription factor Nkx2-1 precedes dissemination. Finally, we show that metastatic primary tumors possess a highly proliferative subpopulation of cells with characteristics matching those of disseminating cells. We propose that dissemination is a major hurdle during the natural course of lung adenocarcinoma metastasis.

Significance: Because of its aggressively metastatic nature, lung cancer is the top cancer killer of both men and women in the United States. We show that, unlike in other cancer types, lung cancer dissemination is a major initial barrier to metastasis. Our findings provide insight into the effect of p53 deficiency and downregulation of Nkx2-1 during lung adenocarcinoma progression. Cancer Discov; 4(7); 781–9. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 745
Data from Targeting MYCN in Neuroblastoma by BET Bromodomain Inhibition
Authors: Puissant Alexandre , Frumm Stacey M. , Alexe Gabriela , Bassil Christopher F. , Qi Jun , Chanthery Yvan H. , Nekritz Erin A. , Zeid Rhamy , Gustafson William Clay , Greninger Patricia , Garnett Matthew J. , McDermott Ultan , Benes Cyril H. , Kung Andrew L. , Weiss William A. , Bradner James E. , Stegmaier Kimberly
Published: April 2023

Abstract
Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between MYCN amplification and sensitivity to bromodomain inhibition. We characterized the mechanistic and translational significance of this finding in neuroblastoma, a childhood cancer with frequent amplification of MYCN. Genome-wide expression analysis showed downregulation of the MYCN transcriptional program accompanied by suppression of MYCN transcription. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knockdown phenocopied these effects, establishing BET bromodomains as transcriptional regulators of MYCN. BET inhibition conferred a significant survival advantage in 3 in vivo neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma.

Significance: Biomarkers of response to small-molecule inhibitors of BET bromodomains, a new compound class with promising anticancer activity, have been lacking. Here, we reveal MYCN amplification as a strong genetic predictor of sensitivity to BET bromodomain inhibitors, show a mechanistic rationale for this finding, and provide a translational framework for clinical trial development of BET bromodomain inhibitors for pediatric patients with MYCN-amplified neuroblastoma. Cancer Discov; 3(3); 308–23. ©2012 AACR.

See related commentary by Schnepp and Maris, p. 255

This article is highlighted in the In This Issue feature, p. 239
Data from Mutation-Specific RAS Oncogenicity Explains NRAS Codon 61 Selection in Melanoma
Authors: Burd Christin E. , Liu Wenjin , Huynh Minh V. , Waqas Meriam A. , Gillahan James E. , Clark Kelly S. , Fu Kailing , Martin Brit L. , Jeck William R. , Souroullas George P. , Darr David B. , Zedek Daniel C. , Miley Michael J. , Baguley Bruce C. , Campbell Sharon L. , Sharpless Norman E.
Published: April 2023

Abstract
NRAS mutation at codons 12, 13, or 61 is associated with transformation; yet, in melanoma, such alterations are nearly exclusive to codon 61. Here, we compared the melanoma susceptibility of an NrasQ61R knock-in allele to similarly designed KrasG12D and NrasG12D alleles. With concomitant p16INK4a inactivation, KrasG12D or NrasQ61R expression efficiently promoted melanoma in vivo, whereas NrasG12D did not. In addition, NrasQ61R mutation potently cooperated with Lkb1/Stk11 loss to induce highly metastatic disease. Functional comparisons of NrasQ61R and NrasG12D revealed little difference in the ability of these proteins to engage PI3K or RAF. Instead, NrasQ61R showed enhanced nucleotide binding, decreased intrinsic GTPase activity, and increased stability when compared with NrasG12D. This work identifies a faithful model of human NRAS-mutant melanoma, and suggests that the increased melanomagenecity of NrasQ61R over NrasG12D is due to heightened abundance of the active, GTP-bound form rather than differences in the engagement of downstream effector pathways.

Significance: This work explains the curious predominance in human melanoma of mutations of codon 61 of NRAS over other oncogenic NRAS mutations. Using conditional “knock-in” mouse models, we show that physiologic expression of NRASQ61R, but not NRASG12D, drives melanoma formation. Cancer Discov; 4(12); 1418–29. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 1355
Data from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Authors: Grasso Catherine S. , Giannakis Marios , Wells Daniel K. , Hamada Tsuyoshi , Mu Xinmeng Jasmine , Quist Michael , Nowak Jonathan A. , Nishihara Reiko , Qian Zhi Rong , Inamura Kentaro , Morikawa Teppei , Nosho Katsuhiko , Abril-Rodriguez Gabriel , Connolly Charles , Escuin-Ordinas Helena , Geybels Milan S. , Grady William M. , Hsu Li , Hu-Lieskovan Siwen , Huyghe Jeroen R. , Kim Yeon Joo , Krystofinski Paige , Leiserson Mark D.M. , Montoya Dennis J. , Nadel Brian B. , Pellegrini Matteo , Pritchard Colin C. , Puig-Saus Cristina , Quist Elleanor H. , Raphael Ben J. , Salipante Stephen J. , Shin Daniel Sanghoon , Shinbrot Eve , Shirts Brian , Shukla Sachet , Stanford Janet L. , Sun Wei , Tsoi Jennifer , Upfill-Brown Alexander , Wheeler David A. , Wu Catherine J. , Yu Ming , Zaidi Syed H. , Zaretsky Jesse M. , Gabriel Stacey B. , Lander Eric S. , Garraway Levi A. , Hudson Thomas J. , Fuchs Charles S. , Ribas Antoni , Ogino Shuji , Peters Ulrike
Published: April 2023

Abstract
To understand the genetic drivers of immune recognition and evasion in colorectal cancer, we analyzed 1,211 colorectal cancer primary tumor samples, including 179 classified as microsatellite instability–high (MSI-high). This set includes The Cancer Genome Atlas colorectal cancer cohort of 592 samples, completed and analyzed here. MSI-high, a hypermutated, immunogenic subtype of colorectal cancer, had a high rate of significantly mutated genes in important immune-modulating pathways and in the antigen presentation machinery, including biallelic losses of B2M and HLA genes due to copy-number alterations and copy-neutral loss of heterozygosity. WNT/β-catenin signaling genes were significantly mutated in all colorectal cancer subtypes, and activated WNT/β-catenin signaling was correlated with the absence of T-cell infiltration. This large-scale genomic analysis of colorectal cancer demonstrates that MSI-high cases frequently undergo an immunoediting process that provides them with genetic events allowing immune escape despite high mutational load and frequent lymphocytic infiltration and, furthermore, that colorectal cancer tumors have genetic and methylation events associated with activated WNT signaling and T-cell exclusion.

Significance: This multi-omic analysis of 1,211 colorectal cancer primary tumors reveals that it should be possible to better monitor resistance in the 15% of cases that respond to immune blockade therapy and also to use WNT signaling inhibitors to reverse immune exclusion in the 85% of cases that currently do not. Cancer Discov; 8(6); 730–49. ©2018 AACR.

This article is highlighted in the In This Issue feature, p. 663