bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Fig. S3 from Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab
Authors: Filho Otto Metzger , Viale Giuseppe , Stein Shayna , Trippa Lorenzo , Yardley Denise A. , Mayer Ingrid A. , Abramson Vandana G. , Arteaga Carlos L. , Spring Laura M. , Waks Adrienne G. , Wrabel Eileen , DeMeo Michelle K. , Bardia Aditya , Dell'Orto Patrizia , Russo Leila , King Tari A. , Polyak Kornelia , Michor Franziska , Winer Eric P. , Krop Ian E.
Published: April 2023

Assessment of spatial HER2 heterogeneity. A, The maximum area fraction of HER2 non-amplified cells in each patient. P-value is from a Wilcoxon test. The lower and upper hinges correspond to the 1st and 3rd quartiles, respectively. The lower and upper whiskers extend to the smallest and largest values, respectively, no further than 1.5*IQR from the hinge, where the IQR is the distance between the 1st and 3rd quartiles. All data points are plotted. B, Association between the minimum and maximum area fractions of HER2 non-amplified cells in each patient. R and p-value are from a Pearson correlation test of association. C, Asso-ciation between the overall and minimum area fractions of HER2 non-amplified cells in each patient. R and p-value are from a Pearson correlation test of association. D, Association between the overall and maximum area frequencies of HER2 non-amplified cells in each patient. R and p-value are from a Pearson correlation test of association. A-D, Red represents patients without pCR and blue represents patients with pCR.
Supplementary Table 1 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

SWISNF mutations in thyroid cancers
Figure S7 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Impact of acute MAPK blockade on chromatin accessibility in TBraf and TBraf/Swi-Snf deficient tumors.
Figure S3 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Validation of tumor derived TBraf, TBraf/A1a, TBraf/A2 and TBraf/Sb1 cell lines.
Figure S2 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Loss of Arid1a or Smarcb1 in the context of endogenous BrafV600E expression promotes tumor growth in mice.
Figure S12 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Restoration of Nis (SLC5A5) expression upon MEK inhibition is attenuated in Braf-tumors with Swi/Snf loss.
Supplementary Data from Six-Month Efficacy and Toxicity Profile of BNT162b2 Vaccine in Cancer Patients with Solid Tumors
Authors: Waldhorn Ithai , Holland Roy , Goshen-Lago Tal , Shirman Yelena , Szwarcwort-Cohen Moran , Reiner-Benaim Anat , Shachor-Meyouhas Yael , Hussein Khetam , Fahoum Liana , Peer Avivit , Almog Ronit , Shaked Yuval , Halberthal Michael , Ben-Aharon Irit
Published: April 2023

Seropositivity persistence six months after vaccination
Supplementary Table S1 from Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity
Authors: Mahadevan Navin R. , Knelson Erik H. , Wolff Jacquelyn O. , Vajdi Amir , Saigí Maria , Campisi Marco , Hong Deli , Thai Tran C. , Piel Brandon , Han Saemi , Reinhold Bruce B. , Duke-Cohan Jonathan S. , Poitras Michael J. , Taus Luke J. , Lizotte Patrick H. , Portell Andrew , Quadros Victor , Santucci Alison D. , Murayama Takahiko , Cañadas Israel , Kitajima Shunsuke , Akitsu Aoi , Fridrikh Maya , Watanabe Hideo , Reardon Brendan , Gokhale Prafulla C. , Paweletz Cloud P. , Awad Mark M. , Van Allen Eliezer M. , Lako Ana , Wang Xi-Tao , Chen Benjamin , Hong Fangxin , Sholl Lynette M. , Tolstorukov Michael Y. , Pfaff Kathleen , Jänne Pasi A. , Gjini Evisa , Edwards Robin , Rodig Scott , Reinherz Ellis L. , Oser Matthew G. , Barbie David A.
Published: April 2023

Supplementary Table S1
Table S1 from Obesity-Dependent Adipokine Chemerin Suppresses Fatty Acid Oxidation to Confer Ferroptosis Resistance
Authors: Tan Sze Kiat , Mahmud Iqbal , Fontanesi Flavia , Puchowicz Michelle , Neumann Chase K.A. , Griswold Anthony J. , Patel Rutulkumar , Dispagna Marco , Ahmed Hamzah H. , Gonzalgo Mark L. , Brown J. Mark , Garrett Timothy J. , Welford Scott M.
Published: April 2023

Differential expression matrix
Supplementary table from Paradigms on Immunotherapy Combinations with Chemotherapy
Authors: Salas-Benito Diego , Pérez-Gracia José L. , Ponz-Sarvisé Mariano , Rodriguez-Ruiz María E. , Martínez-Forero Iván , Castañón Eduardo , López-Picazo José M. , Sanmamed Miguel F. , Melero Ignacio
Published: April 2023

Supplementary information regarding chemoimmunotehrapy clinical trials other than phase III or ongoing.
Figure S6 from RTK-Dependent Inducible Degradation of Mutant PI3Kα Drives GDC-0077 (Inavolisib) Efficacy
Authors: Song Kyung W. , Edgar Kyle A. , Hanan Emily J. , Hafner Marc , Oeh Jason , Merchant Mark , Sampath Deepak , Nannini Michelle A. , Hong Rebecca , Phu Lilian , Forrest William F. , Stawiski Eric , Schmidt Stephen , Endres Nicholas , Guan Jane , Wallin Jeffrey J. , Cheong Jonathan , Plise Emile G. , Lewis Phillips Gail D. , Salphati Laurent , Heffron Timothy P. , Olivero Alan G. , Malek Shiva , Staben Steven T. , Kirkpatrick Donald S. , Dey Anwesha , Friedman Lori S.
Published: April 2023

RTK activity plays a key role in regulating p110a degradation
Supplemental-Figures-and-Legends from Mutations in the RAS/MAPK Pathway Drive Replication Repair–Deficient Hypermutated Tumors and Confer Sensitivity to MEK Inhibition
Authors: Campbell Brittany B. , Galati Melissa A. , Stone Simone C. , Riemenschneider Alexandra N. , Edwards Melissa , Sudhaman Sumedha , Siddaway Robert , Komosa Martin , Nunes Nuno M. , Nobre Liana , Morrissy A. Sorana , Zatzman Matthew , Zapotocky Michal , Joksimovic Lazar , Kalimuthu Sangeetha N. , Samuel David , Mason Gary , Bouffet Eric , Morgenstern Daniel A. , Aronson Melyssa , Durno Carol , Malkin David , Maris John M. , Taylor Michael D. , Shlien Adam , Pugh Trevor J. , Ohashi Pamela S. , Hawkins Cynthia E. , Tabori Uri
Published: April 2023

All Supplementary Figures: Fig S1: Major subtypes in 1215 pediatric cancers. Fig S2: Frequency of protein coding point mutations in 1215 pediatric tumors. Fig S3: Confirmatory tissue specific preferences for MAPK pathway mutations in cBioPortal CRCs and gliomas. Fig S4: Unsupervised clustering of CMMRD tumors, normal fetal brain, and normal adult brain based on RNA-sequencing. Fig S5: Phospho-ERK immunohistochemical staining of hypermutant RRD brain and CRCs. Fig S6: Genomic characterization and treatment of 3 CRC MMRD cell lines with Trametinib. Fig S7: Combination anti-PD1 and MEKi promotes an anti-tumor immune response.
Table S1 from Blocking Short-Form Ron Eliminates Breast Cancer Metastases through Accumulation of Stem-Like CD4+ T Cells That Subvert Immunosuppression
Authors: Lai Shu-Chin Alicia , Gundlapalli Harika , Ekiz H. Atakan , Jiang Amanda , Fernandez Elvelyn , Welm Alana L.
Published: April 2023

Table S1 - List of antibodies and reagents
Table S2 from Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Authors: Penter Livius , Gohil Satyen H. , Lareau Caleb , Ludwig Leif S. , Parry Erin M. , Huang Teddy , Li Shuqiang , Zhang Wandi , Livitz Dimitri , Leshchiner Ignaty , Parida Laxmi , Getz Gad , Rassenti Laura Z. , Kipps Thomas J. , Brown Jennifer R. , Davids Matthew S. , Neuberg Donna S. , Livak Kenneth J. , Sankaran Vijay G. , Wu Catherine J.
Published: April 2023

Supplementary Table 2 - %CLL cells marked by mtDNA mutations
Supplementary Data from Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Authors: Penter Livius , Gohil Satyen H. , Lareau Caleb , Ludwig Leif S. , Parry Erin M. , Huang Teddy , Li Shuqiang , Zhang Wandi , Livitz Dimitri , Leshchiner Ignaty , Parida Laxmi , Getz Gad , Rassenti Laura Z. , Kipps Thomas J. , Brown Jennifer R. , Davids Matthew S. , Neuberg Donna S. , Livak Kenneth J. , Sankaran Vijay G. , Wu Catherine J.
Published: April 2023

Supplementary methods, Table S1, supplementary figures 1-9
Supplementary Table 2 from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia
Authors: Wei Yiliang , Huang Yu-Han , Skopelitis Damianos S. , Iyer Shruti V. , Costa Ana S.H. , Yang Zhaolin , Kramer Melissa , Adelman Emmalee R. , Klingbeil Olaf , Demerdash Osama E. , Polyanskaya Sofya A. , Chang Kenneth , Goodwin Sara , Hodges Emily , McCombie W. Richard , Figueroa Maria E. , Vakoc Christopher R.
Published: April 2023

Supplementary Table 2
Supplementary Table 1 from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia
Authors: Wei Yiliang , Huang Yu-Han , Skopelitis Damianos S. , Iyer Shruti V. , Costa Ana S.H. , Yang Zhaolin , Kramer Melissa , Adelman Emmalee R. , Klingbeil Olaf , Demerdash Osama E. , Polyanskaya Sofya A. , Chang Kenneth , Goodwin Sara , Hodges Emily , McCombie W. Richard , Figueroa Maria E. , Vakoc Christopher R.
Published: April 2023

Supplementary Table 1
Supplementary Figures S1-S17 from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia
Authors: Wei Yiliang , Huang Yu-Han , Skopelitis Damianos S. , Iyer Shruti V. , Costa Ana S.H. , Yang Zhaolin , Kramer Melissa , Adelman Emmalee R. , Klingbeil Olaf , Demerdash Osama E. , Polyanskaya Sofya A. , Chang Kenneth , Goodwin Sara , Hodges Emily , McCombie W. Richard , Figueroa Maria E. , Vakoc Christopher R.
Published: April 2023

Figures S1 to S17
Supplementary Figures from Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia
Authors: Malani Disha , Kumar Ashwini , Brück Oscar , Kontro Mika , Yadav Bhagwan , Hellesøy Monica , Kuusanmäki Heikki , Dufva Olli , Kankainen Matti , Eldfors Samuli , Potdar Swapnil , Saarela Jani , Turunen Laura , Parsons Alun , Västrik Imre , Kivinen Katja , Saarela Janna , Räty Riikka , Lehto Minna , Wolf Maija , Gjertsen Bjorn Tore , Mustjoki Satu , Aittokallio Tero , Wennerberg Krister , Heckman Caroline A. , Kallioniemi Olli , Porkka Kimmo
Published: April 2023

15 Supplement figures and legends
Table S3 from Cholesterol Auxotrophy as a Targetable Vulnerability in Clear Cell Renal Cell Carcinoma
Authors: Riscal Romain , Bull Caroline J. , Mesaros Clementina , Finan Jennifer M. , Carens Madeleine , Ho Elaine S. , Xu Jimmy P. , Godfrey Jason , Brennan Paul , Johansson Mattias , Purdue Mark P. , Chanock Stephen J. , Mariosa Daniela , Timpson Nicholas J. , Vincent Emma E. , Keith Brian , Blair Ian A. , Skuli Nicolas , Simon M. Celeste
Published: April 2023

LogOR RCC per SD circulating metabolite, excluding rs67053123
Figure S6 from Cholesterol Auxotrophy as a Targetable Vulnerability in Clear Cell Renal Cell Carcinoma
Authors: Riscal Romain , Bull Caroline J. , Mesaros Clementina , Finan Jennifer M. , Carens Madeleine , Ho Elaine S. , Xu Jimmy P. , Godfrey Jason , Brennan Paul , Johansson Mattias , Purdue Mark P. , Chanock Stephen J. , Mariosa Daniela , Timpson Nicholas J. , Vincent Emma E. , Keith Brian , Blair Ian A. , Skuli Nicolas , Simon M. Celeste
Published: April 2023

Figure S6 shows that BLT-1 treated ccRCC cells exhibit proliferation defects in vitro and in vivo, related to Figure 5.
Figure S2 from Cholesterol Auxotrophy as a Targetable Vulnerability in Clear Cell Renal Cell Carcinoma
Authors: Riscal Romain , Bull Caroline J. , Mesaros Clementina , Finan Jennifer M. , Carens Madeleine , Ho Elaine S. , Xu Jimmy P. , Godfrey Jason , Brennan Paul , Johansson Mattias , Purdue Mark P. , Chanock Stephen J. , Mariosa Daniela , Timpson Nicholas J. , Vincent Emma E. , Keith Brian , Blair Ian A. , Skuli Nicolas , Simon M. Celeste
Published: April 2023

Figure S2 shows that ccRCC cells depend on exogenous cholesterol levels for growth, related to Figure 2.
Supplementary Data from Low-Dose Radiotherapy Reverses Tumor Immune Desertification and Resistance to Immunotherapy
Authors: Herrera Fernanda G. , Ronet Catherine , Ochoa de Olza Maria , Barras David , Crespo Isaac , Andreatta Massimo , Corria-Osorio Jesus , Spill Aodrenn , Benedetti Fabrizio , Genolet Raphael , Orcurto Angela , Imbimbo Martina , Ghisoni Eleonora , Navarro Rodrigo Blanca , Berthold Dominik R. , Sarivalasis Apostolos , Zaman Khalil , Duran Rafael , Dromain Clarisse , Prior John , Schaefer Niklaus , Bourhis Jean , Dimopoulou Georgia , Tsourti Zoi , Messemaker Marius , Smith Thomas , Warren Sarah E. , Foukas Periklis , Rusakiewicz Sylvie , Pittet Mikaël J. , Zimmermann Stefan , Sempoux Christine , Dafni Urania , Harari Alexandre , Kandalaft Lana E. , Carmona Santiago J. , Dangaj Laniti Denarda , Irving Melita , Coukos George
Published: April 2023

Supplementary Data from Low-Dose Radiotherapy Reverses Tumor Immune Desertification and Resistance to Immunotherapy
Supplementary Data from Rates and Patterns of Clonal Oncogenic Mutations in the Normal Human Brain
Authors: Ganz Javier , Maury Eduardo A. , Becerra Basheer , Bizzotto Sara , Doan Ryan N. , Kenny Connor J. , Shin Taehwan , Kim Junho , Zhou Zinan , Ligon Keith L. , Lee Eunjung Alice , Walsh Christopher A.
Published: April 2023

Supplementary methods and figures.
Supplementary Table S6 from PRC2 Inhibitors Overcome Glucocorticoid Resistance Driven by NSD2 Mutation in Pediatric Acute Lymphoblastic Leukemia
Authors: Li Jianping , Hlavka-Zhang Julia , Shrimp Jonathan H. , Piper Crissandra , Dupéré-Richér Daphne , Roth Jacob S. , Jing Duohui , Casellas Román Heidi L. , Troche Catalina , Swaroop Alok , Kulis Marta , Oyer Jon A. , Will Christine M. , Shen Min , Riva Alberto , Bennett Richard L. , Ferrando Adolfo A. , Hall Matthew D. , Lock Richard B. , Licht Jonathan D.
Published: April 2023

Differentially expressed genes in NSD2 p.E1099K RCH-ACV cells with the change of H3K27me3 peaks
Supplementary Table S1 from PRC2 Inhibitors Overcome Glucocorticoid Resistance Driven by NSD2 Mutation in Pediatric Acute Lymphoblastic Leukemia
Authors: Li Jianping , Hlavka-Zhang Julia , Shrimp Jonathan H. , Piper Crissandra , Dupéré-Richér Daphne , Roth Jacob S. , Jing Duohui , Casellas Román Heidi L. , Troche Catalina , Swaroop Alok , Kulis Marta , Oyer Jon A. , Will Christine M. , Shen Min , Riva Alberto , Bennett Richard L. , Ferrando Adolfo A. , Hall Matthew D. , Lock Richard B. , Licht Jonathan D.
Published: April 2023

The full drug screen results
Supplementary Data from Efficacy, Safety, and Biomarker Analysis of Combined PD-L1 (Atezolizumab) and VEGF (Bevacizumab) Blockade in Advanced Malignant Peritoneal Mesothelioma
Authors: Raghav Kanwal , Liu Suyu , Overman Michael J. , Willett Anneleis F. , Knafl Mark , Fu Szu-Chin , Malpica Anais , Prasad Seema , Royal Richard E. , Scally Christopher P. , Mansfield Paul F. , Wistuba Ignacio I. , Futreal Andrew P. , Maru Dipen M. , Solis Soto Luisa M. , Parra Cuentas Edwin R. , Chen Honglei , Villalobos Pamela , Verma Anuj , Mahvash Armeen , Hwu Patrick , Cortazar Patricia , McKenna Edward , Yun Cindy , Dervin Shannon , Schulze Katja , Darbonne Walter C. , Morani Ajaykumar C. , Kopetz Scott , Fournier Keith F. , Woodman Scott E. , Yao James C. , Varadhachary Gauri R. , Halperin Daniel M.
Published: April 2023

Supplementary Methods, Figures and Tables
Supplementary Tables from NKX3.1 Localization to Mitochondria Suppresses Prostate Cancer Initiation
Authors: Papachristodoulou Alexandros , Rodriguez-Calero Antonio , Panja Sukanya , Margolskee Elizabeth , Virk Renu K. , Milner Teresa A. , Martina Luis Pina , Kim Jaime Y. , Di Bernardo Matteo , Williams Alanna B. , Maliza Elvis A. , Caputo Joseph M. , Haas Christopher , Wang Vinson , De Castro Guarionex Joel , Wenske Sven , Hibshoosh Hanina , McKiernan James M. , Shen Michael M. , Rubin Mark A. , Mitrofanova Antonina , Dutta Aditya , Abate-Shen Cory
Published: April 2023

This files contains all of the supplementary tables included in the manuscript.
Supplementary Materials and Methods from NKX3.1 Localization to Mitochondria Suppresses Prostate Cancer Initiation
Authors: Papachristodoulou Alexandros , Rodriguez-Calero Antonio , Panja Sukanya , Margolskee Elizabeth , Virk Renu K. , Milner Teresa A. , Martina Luis Pina , Kim Jaime Y. , Di Bernardo Matteo , Williams Alanna B. , Maliza Elvis A. , Caputo Joseph M. , Haas Christopher , Wang Vinson , De Castro Guarionex Joel , Wenske Sven , Hibshoosh Hanina , McKiernan James M. , Shen Michael M. , Rubin Mark A. , Mitrofanova Antonina , Dutta Aditya , Abate-Shen Cory
Published: April 2023

Detailed materials and methods including references.
Supplementary Figures from NKX3.1 Localization to Mitochondria Suppresses Prostate Cancer Initiation
Authors: Papachristodoulou Alexandros , Rodriguez-Calero Antonio , Panja Sukanya , Margolskee Elizabeth , Virk Renu K. , Milner Teresa A. , Martina Luis Pina , Kim Jaime Y. , Di Bernardo Matteo , Williams Alanna B. , Maliza Elvis A. , Caputo Joseph M. , Haas Christopher , Wang Vinson , De Castro Guarionex Joel , Wenske Sven , Hibshoosh Hanina , McKiernan James M. , Shen Michael M. , Rubin Mark A. , Mitrofanova Antonina , Dutta Aditya , Abate-Shen Cory
Published: April 2023

Supplementary Figures and Figure legends
Supplementary Table 2 from Nongenetic Evolution Drives Lung Adenocarcinoma Spatial Heterogeneity and Progression
Authors: Tavernari Daniele , Battistello Elena , Dheilly Elie , Petruzzella Aaron S. , Mina Marco , Sordet-Dessimoz Jessica , Peters Solange , Krueger Thorsten , Gfeller David , Riggi Nicolo , Oricchio Elisa , Letovanec Igor , Ciriello Giovanni
Published: April 2023

Supplementary Table 2
Supplementary Table 1 from Nongenetic Evolution Drives Lung Adenocarcinoma Spatial Heterogeneity and Progression
Authors: Tavernari Daniele , Battistello Elena , Dheilly Elie , Petruzzella Aaron S. , Mina Marco , Sordet-Dessimoz Jessica , Peters Solange , Krueger Thorsten , Gfeller David , Riggi Nicolo , Oricchio Elisa , Letovanec Igor , Ciriello Giovanni
Published: April 2023

Supplementary Table 1
Video from Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Authors: Yi Eunhee , Gujar Amit D. , Guthrie Molly , Kim Hoon , Zhao Dacheng , Johnson Kevin C. , Amin Samirkumar B. , Costa Megan L. , Yu Qianru , Das Sunit , Jillette Nathaniel , Clow Patricia A. , Cheng Albert W. , Verhaak Roel G.W.
Published: April 2023

Video from Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer
Supplementary Figures from TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin
Authors: Torres-Ayuso Pedro , An Elvira , Nyswaner Katherine M. , Bensen Ryan C. , Ritt Daniel A. , Specht Suzanne I. , Das Sudipto , Andresson Thorkell , Cachau Raul E. , Liang Roger J. , Ries Amy L. , Robinson Christina M. , Difilippantonio Simone , Gouker Brad , Bassel Laura , Karim Baktiar O. , Miller Chad J. , Turk Benjamin E. , Morrison Deborah K. , Brognard John
Published: April 2023

Supplementary Figures S1-S7
Supplementary Figure from A Cancer Cell–Intrinsic GOT2–PPARδ Axis Suppresses Antitumor Immunity
Authors: Abrego Jaime , Sanford-Crane Hannah , Oon Chet , Xiao Xu , Betts Courtney B. , Sun Duanchen , Nagarajan Shanthi , Diaz Luis , Sandborg Holly , Bhattacharyya Sohinee , Xia Zheng , Coussens Lisa M. , Tontonoz Peter , Sherman Mara H.
Published: April 2023

Supplementary Figure from A Cancer Cell–Intrinsic GOT2–PPARδ Axis Suppresses Antitumor Immunity
Supplementary Table from Subversion of Serotonin Receptor Signaling in Osteoblasts by Kynurenine Drives Acute Myeloid Leukemia
Authors: Galán-Díez Marta , Borot Florence , Ali Abdullah Mahmood , Zhao Junfei , Gil-Iturbe Eva , Shan Xiaochuan , Luo Na , Liu Yongfeng , Huang Xi-Ping , Bisikirska Brygida , Labella Rossella , Kurland Irwin , Roth Bryan L. , Quick Matthias , Mukherjee Siddhartha , Rabadán Raul , Carroll Martin , Raza Azra , Kousteni Stavroula
Published: April 2023

Supplementary Table from Subversion of Serotonin Receptor Signaling in Osteoblasts by Kynurenine Drives Acute Myeloid Leukemia
Supplementary Data from Common Trajectories of Highly Effective CD19-Specific CAR T Cells Identified by Endogenous T-cell Receptor Lineages
Authors: Wilson Taylor L. , Kim Hyunjin , Chou Ching-Heng , Langfitt Deanna , Mettelman Robert C. , Minervina Anastasia A. , Allen E. Kaitlynn , Métais Jean-Yves , Pogorelyy Mikhail V. , Riberdy Janice M. , Velasquez M. Paulina , Kottapalli Pratibha , Trivedi Sanchit , Olsen Scott R. , Lockey Timothy , Willis Catherine , Meagher Michael M. , Triplett Brandon M. , Talleur Aimee C. , Gottschalk Stephen , Crawford Jeremy Chase , Thomas Paul G.
Published: April 2023

Supplementary Data from Common Trajectories of Highly Effective CD19-Specific CAR T Cells Identified by Endogenous T-cell Receptor Lineages
RNA-seq (cell line) 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 isogenic SMARCA4-WT and -KO cell lines
Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Authors: Myer Parvathi A. , Lee Jessica K. , Madison Russell W. , Pradhan Kith , Newberg Justin Y. , Isasi Carmen R. , Klempner Samuel J. , Frampton Garrett M. , Ross Jeffery S. , Venstrom Jeffrey M. , Schrock Alexa B. , Das Sudipto , Augenlicht Leonard , Verma Amit , Greally John M. , Raj Srilakshmi M. , Goel Sanjay , Ali Siraj M.
Published: April 2023

Supplementary Figure from The Genomics of Colorectal Cancer in Populations with African and European Ancestry
Supplementary Data from Precision Combination Therapies Based on Recurrent Oncogenic Coalterations
Authors: Li Xubin , Dowling Elisabeth K. , Yan Gonghong , Dereli Zeynep , Bozorgui Behnaz , Imanirad Parisa , Elnaggar Jacob H. , Luna Augustin , Menter David G. , Pilié Patrick G. , Yap Timothy A. , Kopetz Scott , Sander Chris , Korkut Anil
Published: April 2023

Supplementary Data from Precision Combination Therapies Based on Recurrent Oncogenic Coalterations
Supplementary Figure from Zenocutuzumab, a HER2xHER3 Bispecific Antibody, Is Effective Therapy for Tumors Driven by NRG1 Gene Rearrangements
Authors: Schram Alison M. , Odintsov Igor , Espinosa-Cotton Madelyn , Khodos Inna , Sisso Whitney J. , Mattar Marissa S. , Lui Allan J.W. , Vojnic Morana , Shameem Sara H. , Chauhan Thrusha , Torrisi Jean , Ford Jim , O'Connor Marie N. , Geuijen Cecile A.W. , Schackmann Ron C.J. , Lammerts van Bueren Jeroen J. , Wasserman Ernesto , de Stanchina Elisa , O'Reilly Eileen M. , Ladanyi Marc , Drilon Alexander , Somwar Romel
Published: April 2023

Supplementary Figure from Zenocutuzumab, a HER2xHER3 Bispecific Antibody, Is Effective Therapy for Tumors Driven by NRG1 Gene Rearrangements
Supplementary Figure from Preclinical Characterization and Phase I Trial Results of a Bispecific Antibody Targeting PD-L1 and 4-1BB (GEN1046) in Patients with Advanced Refractory Solid Tumors
Authors: Muik Alexander , Garralda Elena , Altintas Isil , Gieseke Friederike , Geva Ravit , Ben-Ami Eytan , Maurice-Dror Corinne , Calvo Emiliano , LoRusso Patricia M. , Alonso Guzman , Rodriguez-Ruiz Maria E. , Schoedel Kristina B. , Blum Jordan M. , Sänger Bianca , Salcedo Theodora W. , Burm Saskia M. , Stanganello Eliana , Verzijl Dennis , Vascotto Fulvia , Sette Angelica , Quinkhardt Juliane , Plantinga Theo S. , Toker Aras , van den Brink Edward N. , Fereshteh Mark , Diken Mustafa , Satijn David , Kreiter Sebastian , Breij Esther C.W. , Bajaj Gaurav , Lagkadinou Eleni , Sasser Kate , Türeci Özlem , Forssmann Ulf , Ahmadi Tahamtan , Şahin Uğur , Jure-Kunkel Maria , Melero Ignacio
Published: April 2023

Supplementary Figure from Preclinical Characterization and Phase I Trial Results of a Bispecific Antibody Targeting PD-L1 and 4-1BB (GEN1046) in Patients with Advanced Refractory Solid Tumors
Table S2 from Mesenchymal Lineage Heterogeneity Underlies Nonredundant Functions of Pancreatic Cancer–Associated Fibroblasts
Authors: Helms Erin J. , Berry Mark W. , Chaw R. Crystal , DuFort Christopher C. , Sun Duanchen , Onate M. Kathrina , Oon Chet , Bhattacharyya Sohinee , Sanford-Crane Hannah , Horton Wesley , Finan Jennifer M. , Sattler Ariana , Makar Rosemary , Dawson David W. , Xia Zheng , Hingorani Sunil R. , Sherman Mara H.
Published: April 2023

Table S2
Supplementary Methods from Mesenchymal Lineage Heterogeneity Underlies Nonredundant Functions of Pancreatic Cancer–Associated Fibroblasts
Authors: Helms Erin J. , Berry Mark W. , Chaw R. Crystal , DuFort Christopher C. , Sun Duanchen , Onate M. Kathrina , Oon Chet , Bhattacharyya Sohinee , Sanford-Crane Hannah , Horton Wesley , Finan Jennifer M. , Sattler Ariana , Makar Rosemary , Dawson David W. , Xia Zheng , Hingorani Sunil R. , Sherman Mara H.
Published: April 2023

Supplementary Methods
Supplementary Table from Early Tumor–Immune Microenvironmental Remodeling and Response to First-Line Fluoropyrimidine and Platinum Chemotherapy in Advanced Gastric Cancer
Authors: Kim Ryul , An Minae , Lee Hyuk , Mehta Arnav , Heo You Jeong , Kim Kyoung-Mee , Lee Song-Yi , Moon Jeonghyeon , Kim Seung Tae , Min Byung-Hoon , Kim Tae Jun , Rha Sun Young , Kang Won Ki , Park Woong-Yang , Klempner Samuel J. , Lee Jeeyun
Published: April 2023

Supplementary Table from Early Tumor–Immune Microenvironmental Remodeling and Response to First-Line Fluoropyrimidine and Platinum Chemotherapy in Advanced Gastric Cancer
Supplementary Data from Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants
Authors: Hofmann Marco H. , Gerlach Daniel , Misale Sandra , Petronczki Mark , Kraut Norbert
Published: April 2023

Supplementary Data from Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants
Supplementary Data from Sequential Single-Cell Transcriptional and Protein Marker Profiling Reveals TIGIT as a Marker of CD19 CAR-T Cell Dysfunction in Patients with Non-Hodgkin Lymphoma
Authors: Jackson Zachary , Hong Changjin , Schauner Robert , Dropulic Boro , Caimi Paolo F. , de Lima Marcos , Giraudo Maria Florencia , Gupta Kalpana , Reese Jane S. , Hwang Tae Hyun , Wald David N.
Published: April 2023

Supplementary Data from Sequential Single-Cell Transcriptional and Protein Marker Profiling Reveals TIGIT as a Marker of CD19 CAR-T Cell Dysfunction in Patients with Non-Hodgkin Lymphoma
Supplementary Figure from Temozolomide Treatment Alters Mismatch Repair and Boosts Mutational Burden in Tumor and Blood of Colorectal Cancer Patients
Authors: Crisafulli Giovanni , Sartore-Bianchi Andrea , Lazzari Luca , Pietrantonio Filippo , Amatu Alessio , Macagno Marco , Barault Ludovic , Cassingena Andrea , Bartolini Alice , Luraghi Paolo , Mauri Gianluca , Battuello Paolo , Personeni Nicola , Zampino Maria Giulia , Pessei Valeria , Vitiello Pietro Paolo , Tosi Federica , Idotta Laura , Morano Federica , Valtorta Emanuele , Bonoldi Emanuela , Germano Giovanni , Di Nicolantonio Federica , Marsoni Silvia , Siena Salvatore , Bardelli Alberto
Published: April 2023

Supplementary Figure from Temozolomide Treatment Alters Mismatch Repair and Boosts Mutational Burden in Tumor and Blood of Colorectal Cancer Patients
Supplementary Data from Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer
Authors: Kumar Vikrant , Ramnarayanan Kalpana , Sundar Raghav , Padmanabhan Nisha , Srivastava Supriya , Koiwa Mayu , Yasuda Tadahito , Koh Vivien , Huang Kie Kyon , Tay Su Ting , Ho Shamaine Wei Ting , Tan Angie Lay Keng , Ishimoto Takatsugu , Kim Guowei , Shabbir Asim , Chen Qingfeng , Zhang Biyan , Xu Shengli , Lam Kong-Peng , Lum Huey Yew Jeffrey , Teh Ming , Yong Wei Peng , So Jimmy Bok Yan , Tan Patrick
Published: April 2023

Supplementary Data from Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer
Supplementary Data from Melanoma-Secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis
Authors: Kleffman Kevin , Levinson Grace , Rose Indigo V.L. , Blumenberg Lili M. , Shadaloey Sorin A.A. , Dhabaria Avantika , Wong Eitan , Galán-Echevarría Francisco , Karz Alcida , Argibay Diana , Von Itter Richard , Floristán Alfredo , Baptiste Gillian , Eskow Nicole M. , Tranos James A. , Chen Jenny , Vega y Saenz de Miera Eleazar C. , Call Melissa , Rogers Robert , Jour George , Wadghiri Youssef Zaim , Osman Iman , Li Yue-Ming , Mathews Paul , DeMattos Ronald B. , Ueberheide Beatrix , Ruggles Kelly V. , Liddelow Shane A. , Schneider Robert J. , Hernando Eva
Published: April 2023

Supplementary Data from Melanoma-Secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis
Supplementary Figure from Stress Granules Determine the Development of Obesity-Associated Pancreatic Cancer
Authors: Fonteneau Guillaume , Redding Alexandra , Hoag-Lee Hannah , Sim Edward S. , Heinrich Stefan , Gaida Matthias M. , Grabocka Elda
Published: April 2023

Supplementary Figure from Stress Granules Determine the Development of Obesity-Associated Pancreatic Cancer
Supplementary Table from Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts
Authors: Ellegast Jana M. , Alexe Gabriela , Hamze Amanda , Lin Shan , Uckelmann Hannah J. , Rauch Philipp J. , Pimkin Maxim , Ross Linda S. , Dharia Neekesh V. , Robichaud Amanda L. , Conway Amy Saur , Khalid Delan , Perry Jennifer A. , Wunderlich Mark , Benajiba Lina , Pikman Yana , Nabet Behnam , Gray Nathanael S. , Orkin Stuart H. , Stegmaier Kimberly
Published: April 2023

Supplementary Table from Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts
Supplementary Data from DIPG Harbors Alterations Targetable by MEK Inhibitors, with Acquired Resistance Mechanisms Overcome by Combinatorial Inhibition
Authors: Izquierdo Elisa , Carvalho Diana M. , Mackay Alan , Temelso Sara , Boult Jessica K.R. , Pericoli Giulia , Fernandez Elisabet , Das Molina , Molinari Valeria , Grabovska Yura , Rogers Rebecca F. , Ajmone-Cat Maria Antonietta , Proszek Paula Z. , Stubbs Mark , Depani Sarita , O'Hare Patricia , Yu Lu , Roumelioti Georgia , Choudhary Jyoti S. , Clarke Matthew , Fairchild Amy R. , Jacques Thomas S. , Grundy Richard G. , Howell Lisa , Picton Susan , Adamski Jenny , Wilson Shaun , Gray Juliet C. , Zebian Bassel , Marshall Lynley V. , Carceller Fernando , Grill Jacques , Vinci Maria , Robinson Simon P. , Hubank Michael , Hargrave Darren , Jones Chris
Published: April 2023

Supplementary Data from DIPG Harbors Alterations Targetable by MEK Inhibitors, with Acquired Resistance Mechanisms Overcome by Combinatorial Inhibition
Supp Table 6 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 6 qRT PCR Probes
Supplementary Table 1 from Dysregulated Lipid Synthesis by Oncogenic IDH1 Mutation Is a Targetable Synthetic Lethal Vulnerability
Authors: Thomas Daniel , Wu Manhong , Nakauchi Yusuke , Zheng Ming , Thompson-Peach Chloe A.L. , Lim Kelly , Landberg Niklas , Köhnke Thomas , Robinson Nirmal , Kaur Satinder , Kutyna Monika , Stafford Melissa , Hiwase Devendra , Reinisch Andreas , Peltz Gary , Majeti Ravindra
Published: April 2023

Table S1 showing AML primary cell details for metabolomics
Supplementary Methods, Tables, Figures from Osimertinib + Savolitinib to Overcome Acquired MET-Mediated Resistance in Epidermal Growth Factor Receptor–Mutated, MET-Amplified Non–Small Cell Lung Cancer: TATTON
Authors: Hartmaier Ryan J. , Markovets Aleksandra A. , Ahn Myung Ju , Sequist Lecia V. , Han Ji-Youn , Cho Byoung Chul , Yu Helena A. , Kim Sang-We , Yang James Chih-Hsin , Lee Jong-Seok , Su Wu-Chou , Kowalski Dariusz M. , Orlov Sergey , Ren Song , Frewer Paul , Ou Xiaoling , Cross Darren A.E. , Kurian Nisha , Cantarini Mireille , Jänne Pasi A.
Published: April 2023

Supplementary methods, 8 tables, 7 figures
Supplementary Table S4 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

HPV42 integration sites in DPA.
Supplementary Figure 5 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

Oncoprint of baseline alterations in CRC patients who developed resistance to KRAS G12C and EGFR inhibitors
Supplementary Figure 2 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

C106 cell lines single cell sequencing analysis
Table S6 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 6. OncoLoop summary table
Table S1 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 1: Phenotypic analysis of the GEMMs
Supplementary Figures S1-S9 from A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia
Authors: Zhou Fengbiao , Aroua Nesrine , Liu Yi , Rohde Christian , Cheng Jingdong , Wirth Anna-Katharina , Fijalkowska Daria , Göllner Stefanie , Lotze Michelle , Yun Haiyang , Yu Xiaobing , Pabst Caroline , Sauer Tim , Oellerich Thomas , Serve Hubert , Röllig Christoph , Bornhäuser Martin , Thiede Christian , Baldus Claudia , Frye Michaela , Raffel Simon , Krijgsveld Jeroen , Jeremias Irmela , Beckmann Roland , Trumpp Andreas , Müller-Tidow Carsten
Published: April 2023

Supplementary Figure S1 shows enrichment of FBL in LSC, correlation of FBL with LSC signature and rRNA 2'-O-Me in healthy hematopoietic cells.
Supplementary Figure S2 shows the association of rRNA 2’-O-Me with LSC and hematopoietic differentiation signatures.
Supplementary Figure S3 shows strategy for LSC sorting and distribution of LSC methylation sites on ribosomes.
Supplementary Figure S4 shows the effect of FBL knockdown on rRNA 2’-O-methylation and in vitro proliferation of leukemia cells.
Supplementary Figure S5 show the effect of FBL overexpression on in vivo engraftment of primary AML cells.
Supplementary Figure S6 shows the effect of FBL knockdown on nascent proteome and metabolism of AML cells.
Supplementary Figure S7 shows the ribosome footprinting analysis after FBL knockdown.
Supplementary Figure S8 shows the association of Gm1447 with LSC signature and the effect of Gm1447 supression on cellular amino acid levels.
Supplementary Figure S9 shows regulatory effect of Gm1447 on in vivo leukemic self-renewal.
Supplementary Figure from Impaired Proteolysis of Noncanonical RAS Proteins Drives Clonal Hematopoietic Transformation
Authors: Chen Sisi , Vedula Rahul S. , Cuevas-Navarro Antonio , Lu Bin , Hogg Simon J. , Wang Eric , Benbarche Salima , Knorr Katherine , Kim Won Jun , Stanley Robert F. , Cho Hana , Erickson Caroline , Singer Michael , Cui Dan , Tittley Steven , Durham Benjamin H. , Pavletich Tatiana S. , Fiala Elise , Walsh Michael F. , Inoue Daichi , Monette Sebastien , Taylor Justin , Rosen Neal , McCormick Frank , Lindsley R. Coleman , Castel Pau , Abdel-Wahab Omar
Published: April 2023

Supplementary Figure from Impaired Proteolysis of Noncanonical RAS Proteins Drives Clonal Hematopoietic Transformation
Supplementary Figure from Pharmacologic Inhibition of NT5C2 Reverses Genetic and Nongenetic Drivers of 6-MP Resistance in Acute Lymphoblastic Leukemia
Authors: Reglero Clara , Dieck Chelsea L. , Zask Arie , Forouhar Farhad , Laurent Anouchka P. , Lin Wen-Hsuan W. , Albero Robert , Miller Hannah I. , Ma Cindy , Gastier-Foster Julie M. , Loh Mignon L. , Tong Liang , Stockwell Brent R. , Palomero Teresa , Ferrando Adolfo A.
Published: April 2023

Supplementary Figure from Pharmacologic Inhibition of NT5C2 Reverses Genetic and Nongenetic Drivers of 6-MP Resistance in Acute Lymphoblastic Leukemia
Supplementary Figures from A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin–MLL Inhibition
Authors: Soto-Feliciano Yadira M. , Sánchez-Rivera Francisco J. , Perner Florian , Barrows Douglas W. , Kastenhuber Edward R. , Ho Yu-Jui , Carroll Thomas , Xiong Yijun , Anand Disha , Soshnev Alexey A. , Gates Leah , Beytagh Mary Clare , Cheon David , Gu Shengqing , Liu X. Shirley , Krivtsov Andrei V. , Meneses Maximiliano , de Stanchina Elisa , Stone Richard M. , Armstrong Scott A. , Lowe Scott W. , Allis C. David
Published: April 2023

Supplementary Figures S1-S25
Supplementary Figures 1-15 from Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA
Authors: Cortes-Ciriano Isidro , Steele Christopher D. , Piculell Katherine , Al-Ibraheemi Alyaa , Eulo Vanessa , Bui Marilyn M. , Chatzipli Aikaterini , Dickson Brendan C. , Borcherding Dana C. , Feber Andrew , Galor Alon , Hart Jesse , Jones Kevin B. , Jordan Justin T. , Kim Raymond H. , Lindsay Daniel , Miller Colin , Nishida Yoshihiro , Proszek Paula Z. , Serrano Jonathan , Sundby R. Taylor , Szymanski Jeffrey J. , Ullrich Nicole J. , Viskochil David , Wang Xia , Snuderl Matija , Park Peter J. , Flanagan Adrienne M. , Hirbe Angela C. , Pillay Nischalan , Miller David T.
Published: April 2023

Supplementary figures provide additional details on the genomic landscape of MPNST and interesting cases within the cohort.
Supplementary Table S2 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 S2 shows the differential expressed genes in dTAG-13 vs DMSO treatment at 24hr in OCI-AML3-NPM1c-degron2 cells.
Supplementary Figures S1-S14 from Detecting Liver Cancer Using Cell-Free DNA Fragmentomes
Authors: Foda Zachariah H. , Annapragada Akshaya V. , Boyapati Kavya , Bruhm Daniel C. , Vulpescu Nicholas A. , Medina Jamie E. , Mathios Dimitrios , Cristiano Stephen , Niknafs Noushin , Luu Harry T. , Goggins Michael G. , Anders Robert A. , Sun Jing , Meta Shruti H. , Thomas David L. , Kirk Gregory D. , Adleff Vilmos , Phallen Jillian , Scharpf Robert B. , Kim Amy K. , Velculescu Victor E.
Published: April 2023

Supplementary Figure S1 shows contributions of individual genomic regions to the final trained DELFI surveillance model.
Supplementary Figure S2 shows DELFI scores in individuals without cancer by age and sex.
Supplementary Figure S3 shows DELFI scores in high-risk individuals without cancer across racial or ethnic groups.
Supplementary Figure S4 shows DELFI scores in cirrhotic patients in relation to severity.
Supplementary Figure S5 shows DELFI scores in individuals in relation to BMI.
Supplementary Figure S6 Shows Performance of alternative DELFI models.
Supplementary Figure S7 shows Correlation between rank ordered DELFI.
Supplementary Figure S8 shows DELFI scores in patients with HCC were related to tumor characteristics.
Supplementary Figure S9 shows DELFI scores in by etiology of underlying liver disease.
Supplementary Figure S10 shows the DELFI score in patients with HCC is correlated to AFP levels.
Supplementary Figure S11 shows the correlation of fragmentation profiles.
Supplementary Figure S12 shows Genome wide fragmentation profiles in the Hong Kong validation cohort
Supplementary Figure S13 shows chromosomal copy number in Hong Kong cohort.
Supplementary Figure S14 shows the implementation of DELFI in liver cancer screening.
Supplementary Figures and Tables from A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas
Authors: Cervia Lisa D. , Shibue Tsukasa , Borah Ashir A. , Gaeta Benjamin , He Linh , Leung Lisa , Li Naomi , Moyer Sydney M. , Shim Brian H. , Dumont Nancy , Gonzalez Alfredo , Bick Nolan R. , Kazachkova Mariya , Dempster Joshua M. , Krill-Burger John Michael , Piccioni Federica , Udeshi Namrata D. , Olive Meagan E. , Carr Steven A. , Root David E. , McFarland James M. , Vazquez Francisca , Hahn William C.
Published: April 2023

Supplementary Figure S1 shows the strategy and result of co-essentiality module identificationfrom the DepMap CRISPR screen dataset and further characterization of the BIRC6 module.
Supplementary Figure S2 shows the viability effect of BIRC6 depletion in BIRC6-dependent and -nondependent cancer cells lines as well asin nontransformed cells.
Supplementary Figure S3 shows in vitro confirmations of the inducible BIRC6 depletion (by RNAi and CRISPR) systems as well as the effect of BIRC6 depletion on metastasis in xenograft models.
Supplementary Figure S4 shows detailed results for the allele competition assay to evaluate the role of the BIR and UBC domains of BIRC6 and further evidence for the physical assembly of BIRC6 ubiquitin ligase complex.
Supplementary Figure S5 shows evidence for the selective activation of the p-eIF2alpha/ATF4 arm of UPR (or ISR) upon BIRC6 depletion.
Supplementary Figure S6 shows evidence supporting the importance of HRI-mediated ISR activation as a mechanism underlying the loss of viability caused by BIRC6 complex suppression.
Supplementary Figure S7 shows evidence for the direct regulation of HRI ubiquitination and degradation by the BIRC6 complex
Supplementary Figure S8 shows elevated expression of HRI mRNA in the tumor samples compared to the normal samples in large-scale datasets (TCGA, TARGET and GTEx).
Supplementary Figure S9 shows the inefficiency of the gene expression and copy number of the functionally related genes in predicting BIRC6 dependency.
Supplementary Table S1 lists the top 50 co-essentiality modules identified in the analysis explained in Supplementary Figure S1A.
Supplementary Table S2 lists the key DNA and RNA sequences used in this study.
Supplementary Tables S1-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

Table S1. List of ubiquitylated peptides from DiGly proteomics assay.
Table S2. List of proteins differentially abundant in LZTR1-/- compared toLZTR1+/+ cells quantified by TMT.Table S3. List of top scoring LZTR1 interacting proteins from immunoprecipitation/mass spectrometry.