bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data Tables S1-S2 from Targeting UGCG Overcomes Resistance to Lysosomal Autophagy Inhibition
Authors: Jain Vaibhav , Harper Sandra L. , Versace Amanda M. , Fingerman Dylan , Brown Gregory Schuyler , Bhardwaj Monika , Crissey Mary Ann S. , Goldman Aaron R. , Ruthel Gordon , Liu Qin , Zivkovic Aleksandra , Stark Holgar , Herlyn Meenhard , Gimotty Phyllis A. , Speicher David W. , Amaravadi Ravi K.
Published: April 2023

Supplemental Table S1: Patient Characteristics by UGCG expression defined Risk Groups in the Learning Dataset; Supplemental Table S2: Patient Characteristics by UGCG expression defined Risk Groups in the Validation Dataset (Cirenajwis et al., 2015)
Supplementary Data Figures S1-S5 from Targeting UGCG Overcomes Resistance to Lysosomal Autophagy Inhibition
Authors: Jain Vaibhav , Harper Sandra L. , Versace Amanda M. , Fingerman Dylan , Brown Gregory Schuyler , Bhardwaj Monika , Crissey Mary Ann S. , Goldman Aaron R. , Ruthel Gordon , Liu Qin , Zivkovic Aleksandra , Stark Holgar , Herlyn Meenhard , Gimotty Phyllis A. , Speicher David W. , Amaravadi Ravi K.
Published: April 2023

Supplemental Figure S1: LAI remodels the lipidome of melanoma cells. Supplemental Figure S2: LAI induces UGCG, and UGCG inhibition augments DC661 cytotoxicity, and this effect is not seen by blocking cholesterol synthesis and key earlier steps of autophagy. Supplemental Figure S3: LAI increases the formation of GMM in cancer cells. Supplemental Figure S4: UGCG inhibition synergistically augments LAI induced cytotoxicity and abrogates GMM formation without elevating ceramide levels. Supplemental Figure S5: LAI induces UGCG-associated GMM formation in PDX cells, a combination of DC661 and eliglustat impairs tumor growth in a therapy-resistant PDX tumor model.
Supplementary Data from Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia
Authors: Liu Yiman , Li Qinglan , Alikarami Fatemeh , Barrett Declan R. , Mahdavi Leila , Li Hangpeng , Tang Sylvia , Khan Tanweer A. , Michino Mayako , Hill Connor , Song Lele , Yang Lu , Li Yuanyuan , Pokharel Sheela Pangeni , Stamford Andrew W. , Liverton Nigel , Renzetti Louis M. , Taylor Simon , Watt Gillian F. , Ladduwahetty Tammy , Kargman Stacia , Meinke Peter T. , Foley Michael A. , Shi Junwei , Li Haitao , Carroll Martin , Chen Chun-Wei , Gardini Alessandro , Maillard Ivan , Huggins David J. , Bernt Kathrin M. , Wan Liling
Published: April 2023

Supplementary Data from Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia
Table S1 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

X-ray crystallography data collection and refinement statistics
Supplementary Figure 7 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 S7: Extended p53 Y220C KG13 cellular activity (A) Western blot for isogenic cell panel treated with 10 μM Nutlin-3a constant or 10 μM KG13 for 1 hr at 28°C, washed out, then moved to 37°C for 8hr. (B) ChIP p53 enrichment for U2OS cells expressing p53 Y220C. (C) p53 ChIP enrichment at CDKN1A and MDM2 promoters relative to IgG following KG13 treatment in H1299 cells expressing p53 Y220C. (D) RT-qPCR results for 25 μM KG13 treated NUGC-4, NUGC-3, and BxPC-3ß cells. (E) Viability assay for KG13 treatment. (F) Viability assay for Nutlin-3a treatment.
Supplementary Figure 4 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 S4: Ligand electron density maps (A) 1σ 2Fo-Fc electron density map and 1.5σ Fo-Fc simulated annealing omit density map for KG3. (B) 1σ 2Fo-Fc electron density map and 1.5σ Fo-Fc simulated annealing omit density map for KG6. (C) 1σ 2Fo-Fc electron density map and 1.5σ Fo-Fc simulated annealing omit density map for KG10. (D) 1σ 2Fo-Fc electron density map and 1.5σ Fo-Fc simulated annealing omit density map for KG13. (E) Allosteric stabilization by KG6. D228 makes intramolecular contacts with V147 amine rather through a small molecule directly.
Supplementary Figure 3 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 S3: Example LC/MS spectra from carbazole and indole series (A) LC/MS spectra from p53 WT-CL or p53 Y220C-CL labeling with KG1. (B) LC/MS spectra from p53 WT or p53 Y220C labeling with KG5. (C) LC/MS spectra from p53 WT or p53 Y220C labeling with PK11000. (D) LC/MS spectra from p53 WT or p53 Y220C labeling with KG6. (E) LC/MS spectra from p53 WT or p53 Y220C labeling with KG13.
Supplementary Figure 1 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 S1: p53 hotspot mutations (A) Crystal structure of p53 bound to DNA PDB 1TUP with structural and DNA-contact mutations highlighted. (B) Frequency of hotspot mutations out of total p53 alterations based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga. (C) The urea-denaturation free energy values from hotspot mutations and stabilizing mutations plotted from previous studies (7). (D) SDS-PAGE of recombinant protein used in study stained with Coomassie blue.
Table S4 from Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti–PD-1 Immunotherapy in Endometrial Carcinoma
Authors: Chow Ryan D. , Michaels Tai , Bellone Stefania , Hartwich Tobias M.P. , Bonazzoli Elena , Iwasaki Akiko , Song Eric , Santin Alessandro D.
Published: April 2023

Supplementary Table S4: Metadata annotations for the scRNA-seq dataset.
Table S1 from Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti–PD-1 Immunotherapy in Endometrial Carcinoma
Authors: Chow Ryan D. , Michaels Tai , Bellone Stefania , Hartwich Tobias M.P. , Bonazzoli Elena , Iwasaki Akiko , Song Eric , Santin Alessandro D.
Published: April 2023

Supplementary Table S1: Genomic and clinical characteristics of the study cohort.
Supplementary Table from A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma
Authors: Rappold Phillip M. , Vuong Lynda , Leibold Josef , Chakiryan Nicholas H. , Curry Michael , Kuo Fengshen , Sabio Erich , Jiang Hui , Nixon Briana G. , Liu Ming , Berglund Anders E. , Silagy Andrew W. , Mascareno Eduardo A. , Golkaram Mahdi , Marker Mahtab , Reising Albert , Savchenko Alexander , Millholland John , Chen Ying-Bei , Russo Paul , Coleman Jonathan , Reznik Ed , Manley Brandon J. , Ostrovnaya Irina , Makarov Vladimir , DiNatale Renzo G. , Blum Kyle A. , Ma Xiaoxiao , Chowell Diego , Li Ming O. , Solit David B. , Lowe Scott W. , Chan Timothy A. , Motzer Robert J. , Voss Martin H. , Hakimi A. Ari
Published: April 2023

Supplementary Table from A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma
Supplementary Table from Spatial Positioning and Matrix Programs of Cancer-Associated Fibroblasts Promote T-cell Exclusion in Human Lung Tumors
Authors: Grout John A. , Sirven Philemon , Leader Andrew M. , Maskey Shrisha , Hector Eglantine , Puisieux Isabelle , Steffan Fiona , Cheng Evan , Tung Navpreet , Maurin Mathieu , Vaineau Romain , Karpf Lea , Plaud Martin , Begue Anne-Laure , Ganesh Koushik , Mesple Jérémy , Casanova-Acebes Maria , Tabachnikova Alexandra , Keerthivasan Shilpa , Lansky Alona , Berichel Jessica Le , Walker Laura , Rahman Adeeb H. , Gnjatic Sacha , Girard Nicolas , Lefevre Marine , Damotte Diane , Adam Julien , Martin Jerome C. , Wolf Andrea , Flores Raja M. , Beasley Mary Beth , Pradhan Rachana , Muller Soren , Marron Thomas U. , Turley Shannon J. , Merad Miriam , Kenigsberg Ephraim , Salmon Hélène
Published: April 2023

Supplementary Table from Spatial Positioning and Matrix Programs of Cancer-Associated Fibroblasts Promote T-cell Exclusion in Human Lung Tumors
Supplementary Figure from A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma
Authors: Rappold Phillip M. , Vuong Lynda , Leibold Josef , Chakiryan Nicholas H. , Curry Michael , Kuo Fengshen , Sabio Erich , Jiang Hui , Nixon Briana G. , Liu Ming , Berglund Anders E. , Silagy Andrew W. , Mascareno Eduardo A. , Golkaram Mahdi , Marker Mahtab , Reising Albert , Savchenko Alexander , Millholland John , Chen Ying-Bei , Russo Paul , Coleman Jonathan , Reznik Ed , Manley Brandon J. , Ostrovnaya Irina , Makarov Vladimir , DiNatale Renzo G. , Blum Kyle A. , Ma Xiaoxiao , Chowell Diego , Li Ming O. , Solit David B. , Lowe Scott W. , Chan Timothy A. , Motzer Robert J. , Voss Martin H. , Hakimi A. Ari
Published: April 2023

Supplementary Figure from A Targetable Myeloid Inflammatory State Governs Disease Recurrence in Clear-Cell Renal Cell Carcinoma
Supplementary Video 1B 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

Video shows displacement of Lat-M cells in cell competition. Lat-M cells (Green) surrounded by PA (Red) cells being displaced under
cell competition assay conditions.
Supplementary Table from Developmental Deconvolution for Classification of Cancer Origin
Authors: Moiso Enrico , Farahani Alexander , Marble Hetal D. , Hendricks Austin , Mildrum Samuel , Levine Stuart , Lennerz Jochen K. , Garg Salil
Published: April 2023

Supplementary Table from Developmental Deconvolution for Classification of Cancer Origin
Supplementary Figure from Spatial Positioning and Matrix Programs of Cancer-Associated Fibroblasts Promote T-cell Exclusion in Human Lung Tumors
Authors: Grout John A. , Sirven Philemon , Leader Andrew M. , Maskey Shrisha , Hector Eglantine , Puisieux Isabelle , Steffan Fiona , Cheng Evan , Tung Navpreet , Maurin Mathieu , Vaineau Romain , Karpf Lea , Plaud Martin , Begue Anne-Laure , Ganesh Koushik , Mesple Jérémy , Casanova-Acebes Maria , Tabachnikova Alexandra , Keerthivasan Shilpa , Lansky Alona , Berichel Jessica Le , Walker Laura , Rahman Adeeb H. , Gnjatic Sacha , Girard Nicolas , Lefevre Marine , Damotte Diane , Adam Julien , Martin Jerome C. , Wolf Andrea , Flores Raja M. , Beasley Mary Beth , Pradhan Rachana , Muller Soren , Marron Thomas U. , Turley Shannon J. , Merad Miriam , Kenigsberg Ephraim , Salmon Hélène
Published: April 2023

Supplementary Figure from Spatial Positioning and Matrix Programs of Cancer-Associated Fibroblasts Promote T-cell Exclusion in Human Lung Tumors
Supplementary Figure from Developmental Deconvolution for Classification of Cancer Origin
Authors: Moiso Enrico , Farahani Alexander , Marble Hetal D. , Hendricks Austin , Mildrum Samuel , Levine Stuart , Lennerz Jochen K. , Garg Salil
Published: April 2023

Supplementary Figure from Developmental Deconvolution for Classification of Cancer Origin
Supplementary Data from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma
Authors: Hao Dapeng , Han Guangchun , Sinjab Ansam , Gomez-Bolanos Lorena Isabel , Lazcano Rossana , Serrano Alejandra , Hernandez Sharia D. , Dai Enyu , Cao Xuanye , Hu Jian , Dang Minghao , Wang Ruiping , Chu Yanshuo , Song Xingzhi , Zhang Jianhua , Parra Edwin R. , Wargo Jennifer A. , Swisher Stephen G. , Cascone Tina , Sepesi Boris , Futreal Andrew P. , Li Mingyao , Dubinett Steven M. , Fujimoto Junya , Solis Soto Luisa M. , Wistuba Ignacio I. , Stevenson Christopher S. , Spira Avrum , Shalapour Shabnam , Kadara Humam , Wang Linghua
Published: April 2023

Supplementary Data from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma
Supplementary Data from The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation
Authors: Yeaton Anna , Cayanan Geraldine , Loghavi Sanam , Dolgalev Igor , Leddin Emmett M. , Loo Christian E. , Torabifard Hedieh , Nicolet Deedra , Wang Jingjing , Corrigan Kate , Paraskevopoulou Varvara , Starczynowski Daniel T , Wang Eric , Abdel-Wahab Omar , Viny Aaron D , Stone Richard M. , Byrd John C. , Guryanova Olga A. , Kohli Rahul M. , Cisneros G. Andrés , Tsirigos Aristotelis , Eisfeld Ann-Kathrin , Aifantis Iannis , Guillamot Maria
Published: April 2023

Supplementary Data from The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation
Supplementary Figures and Tables from MinimuMM-seq: Genome Sequencing of Circulating Tumor Cells for Minimally Invasive Molecular Characterization of Multiple Myeloma Pathology
Authors: Dutta Ankit K. , Alberge Jean-Baptiste , Lightbody Elizabeth D. , Boehner Cody J. , Dunford Andrew , Sklavenitis-Pistofidis Romanos , Mouhieddine Tarek H. , Cowan Annie N. , Su Nang Kham , Horowitz Erica M. , Barr Hadley , Hevenor Laura , Beckwith Jenna B. , Perry Jacqueline , Cao Amanda , Lin Ziao , Kuhr Frank K. , Mastro Richard G. Del , Nadeem Omar , Greipp Patricia T. , Stewart Chip , Auclair Daniel , Getz Gad , Ghobrial Irene M.
Published: April 2023

Supplementary data contains additional Materials and Methods used to generate results presented only in the supplementary figures and tables, as well as more detailed bioinformatics methods.
Figure S1 shows correlation between clinical measures of disease pathology, survival, and circulating tumor cells enumeration.
Figure S2 shows characteristics of isolated circulating tumor cells from peripheral blood of precursor disease patients.
Figure S3 shows cohort-level genomic characterization of tumor in MM precursor stages with CTCs.
Figure S4 shows longitudinal and tissue-matched genomic characterization of driver mutations.
Figure S5 shows comparison of mutational processes between BMPCs and CTCs assigned to most likely PCAWG composite reference signature.
Table S1 shows clinical characteristics and sampling of participants in this study.
Table S2 shows whole-genome sequencing coverage and library metrics.
Table S3 shows clinical BM FISH results and cells recovered for cohort with matched samples.
Table S4 shows comparison of BCR sequence between BMPCs and CTCs.
Table S5 shows clinical BM FISH results of peripheral blood only cohort and CTCs recovered.
Table S6 shows enumeration of single nucleotide variants and short insertions and deletions discovered from WGS of CTCs.
Table S7 shows enumeration of structural variants reconstructed from WGS of CTCs.
Supplementary Table from Stromal Reprogramming by FAK Inhibition Overcomes Radiation Resistance to Allow for Immune Priming and Response to Checkpoint Blockade
Authors: Lander Varintra E. , Belle Jad I. , Kingston Natalie L. , Herndon John M. , Hogg Graham D. , Liu Xiuting , Kang Liang-I , Knolhoff Brett L. , Bogner Savannah J. , Baer John M. , Zuo Chong , Borcherding Nicholas C. , Lander Daniel P. , Mpoy Cedric , Scott Jalen , Zahner Michael , Rogers Buck E. , Schwarz Julie K. , Kim Hyun , DeNardo David G.
Published: April 2023

Supplementary Table from Stromal Reprogramming by FAK Inhibition Overcomes Radiation Resistance to Allow for Immune Priming and Response to Checkpoint Blockade
Supplementary Figure from Stromal Reprogramming by FAK Inhibition Overcomes Radiation Resistance to Allow for Immune Priming and Response to Checkpoint Blockade
Authors: Lander Varintra E. , Belle Jad I. , Kingston Natalie L. , Herndon John M. , Hogg Graham D. , Liu Xiuting , Kang Liang-I , Knolhoff Brett L. , Bogner Savannah J. , Baer John M. , Zuo Chong , Borcherding Nicholas C. , Lander Daniel P. , Mpoy Cedric , Scott Jalen , Zahner Michael , Rogers Buck E. , Schwarz Julie K. , Kim Hyun , DeNardo David G.
Published: April 2023

Supplementary Figure from Stromal Reprogramming by FAK Inhibition Overcomes Radiation Resistance to Allow for Immune Priming and Response to Checkpoint Blockade
Supplementary Data from Trastuzumab Deruxtecan in HER2-Positive Metastatic Breast Cancer Patients with Brain Metastases: A DESTINY-Breast01 Subgroup Analysis
Authors: Jerusalem Guy , Park Yeon Hee , Yamashita Toshinari , Hurvitz Sara A. , Modi Shanu , Andre Fabrice , Krop Ian E. , Gonzàlez Farré Xavier , You Benoit , Saura Cristina , Kim Sung-Bae , Osborne Cynthia R. , Murthy Rashmi K. , Gianni Lorenzo , Takano Toshimi , Liu Yali , Cathcart Jillian , Lee Caleb , Perrin Christophe
Published: April 2023

Supplementary Data from Trastuzumab Deruxtecan in HER2-Positive Metastatic Breast Cancer Patients with Brain Metastases: A DESTINY-Breast01 Subgroup Analysis
Supplementary Figure S7 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

Loss of GRAMD1B suppresses de novo cholesterol synthesis in melanoma cells.
Supplementary Figure from Escherichia coli–Specific CXCL13-Producing TFH Are Associated with Clinical Efficacy of Neoadjuvant PD-1 Blockade against Muscle-Invasive Bladder Cancer
Authors: Goubet Anne-Gaëlle , Lordello Leonardo , Alves Costa Silva Carolina , Peguillet Isabelle , Gazzano Marianne , Mbogning-Fonkou Maxime Descartes , Thelemaque Cassandra , Lebacle Cédric , Thibault Constance , Audenet François , Pignot Géraldine , Gravis Gwenaelle , Helissey Carole , Campedel Luca , Roupret Morgan , Xylinas Evanguelos , Ouzaid Idir , Dubuisson Agathe , Mazzenga Marine , Flament Caroline , Ly Pierre , Marty Virginie , Signolle Nicolas , Sauvat Allan , Sbarrato Thomas , Filahi Mounia , Davin Caroline , Haddad Gabriel , Bou Khalil Jacques , Bleriot Camille , Danlos François-Xavier , Dunsmore Garett , Mulder Kevin , Silvin Aymeric , Raoult Thibault , Archambaud Baptiste , Belhechmi Shaima , Gomperts Boneca Ivo , Cayet Nadège , Moya-Nilges Maryse , Mallet Adeline , Daillere Romain , Rouleau Etienne , Radulescu Camelia , Allory Yves , Fieschi Jacques , Rouanne Mathieu , Ginhoux Florent , Le Teuff Gwénaël , Derosa Lisa , Marabelle Aurélien , Van Dorp Jeroen , Van Dijk Nick , Van Der Heijden Michiel S. , Besse Benjamin , Andre Fabrice , Merad Miriam , Kroemer Guido , Scoazec Jean-Yves , Zitvogel Laurence , Loriot Yohann
Published: April 2023

Supplementary Figure from Escherichia coli–Specific CXCL13-Producing TFH Are Associated with Clinical Efficacy of Neoadjuvant PD-1 Blockade against Muscle-Invasive Bladder Cancer
Supplementary Figure S1 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

The AVAST-M trial identifies a signature predictive of metastatic relapse
Supplementary Table 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 Table from BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma
Supp Table S2 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

Supplementary Table S2. David GO analysis of AVAST-M signature
Supplementary Table from Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer
Authors: Anurag Meenakshi , Jaehnig Eric J. , Krug Karsten , Lei Jonathan T. , Bergstrom Erik J. , Kim Beom-Jun , Vashist Tanmayi D. , Huynh Anh Minh Tran , Dou Yongchao , Gou Xuxu , Huang Chen , Shi Zhiao , Wen Bo , Korchina Viktoriya , Gibbs Richard A. , Muzny Donna M. , Doddapaneni Harshavardhan , Dobrolecki Lacey E. , Rodriguez Henry , Robles Ana I. , Hiltke Tara , Lewis Michael T. , Nangia Julie R. , Nemati Shafaee Maryam , Li Shunqiang , Hagemann Ian S. , Hoog Jeremy , Lim Bora , Osborne C. Kent , Mani D.R. , Gillette Michael A. , Zhang Bing , Echeverria Gloria V. , Miles George , Rimawi Mothaffar F. , Carr Steven A. , Ademuyiwa Foluso O. , Satpathy Shankha , Ellis Matthew J.
Published: April 2023

Supplementary Table from Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer
Supplementary Table from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent
Authors: Martini Rachel , Delpe Princesca , Chu Timothy R. , Arora Kanika , Lord Brittany , Verma Akanksha , Bedi Deepa , Karanam Balasubramanyam , Elhussin Isra , Chen Yalei , Gebregzabher Endale , Oppong Joseph K. , Adjei Ernest K. , Jibril Suleiman Aisha , Awuah Baffour , Muleta Mahteme Bekele , Abebe Engida , Kyei Ishmael , Aitpillah Frances S. , Adinku Michael O. , Ankomah Kwasi , Osei-Bonsu Ernest Baawuah , Chitale Dhananjay A. , Bensenhaver Jessica M. , Nathanson David S. , Jackson LaToya , Petersen Lindsay F. , Proctor Erica , Stonaker Brian , Gyan Kofi K. , Gibbs Lee D. , Monojlovic Zarko , Kittles Rick A. , White Jason , Yates Clayton C. , Manne Upender , Gardner Kevin , Mongan Nigel , Cheng Esther , Ginter Paula , Hoda Syed , Elemento Olivier , Robine Nicolas , Sboner Andrea , Carpten John D. , Newman Lisa , Davis Melissa B.
Published: April 2023

Supplementary Table from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent
Supplementary Data from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent
Authors: Martini Rachel , Delpe Princesca , Chu Timothy R. , Arora Kanika , Lord Brittany , Verma Akanksha , Bedi Deepa , Karanam Balasubramanyam , Elhussin Isra , Chen Yalei , Gebregzabher Endale , Oppong Joseph K. , Adjei Ernest K. , Jibril Suleiman Aisha , Awuah Baffour , Muleta Mahteme Bekele , Abebe Engida , Kyei Ishmael , Aitpillah Frances S. , Adinku Michael O. , Ankomah Kwasi , Osei-Bonsu Ernest Baawuah , Chitale Dhananjay A. , Bensenhaver Jessica M. , Nathanson David S. , Jackson LaToya , Petersen Lindsay F. , Proctor Erica , Stonaker Brian , Gyan Kofi K. , Gibbs Lee D. , Monojlovic Zarko , Kittles Rick A. , White Jason , Yates Clayton C. , Manne Upender , Gardner Kevin , Mongan Nigel , Cheng Esther , Ginter Paula , Hoda Syed , Elemento Olivier , Robine Nicolas , Sboner Andrea , Carpten John D. , Newman Lisa , Davis Melissa B.
Published: April 2023

Supplementary Data from African Ancestry–Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent
Supplementary Table 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

HPV42- and HPV16-E7 BioID.
Supplementary Table 3 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

Patients Longitudinal Cell Free DNA data
Supplementary Table S6 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 protein-coding mutations.
Supplementary Table 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

Patients Progression Cell Free DNA data
Supplementary Table 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

Patients Characteristics
Supplementary Table from Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis
Authors: SanMiguel Jennifer M. , Eudy Elizabeth , Loberg Matthew A. , Young Kira A. , Mistry Jayna J. , Mujica Kristina D. , Schwartz Logan S. , Stearns Timothy M. , Challen Grant A. , Trowbridge Jennifer J.
Published: April 2023

Supplementary Table from Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis
Table S7 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 7. Transcriptomic analyses of the PDX models
A. PDX interactome
B. OncoTreat for drugs to PDX using DU145 cell perturbation data
Supplementary Table from Epigenome Programming by H3.3K27M Mutation Creates a Dependence of Pediatric Glioma on SMARCA4
Authors: Mo Yan , Duan Shoufu , Zhang Xu , Hua Xu , Zhou Hui , Wei Hong-Jian , Watanabe Jun , McQuillan Nicholas , Su Zhenyi , Gu Wei , Wu Cheng-Chia , Vakoc Christopher R. , Hashizume Rintaro , Chang Kenneth , Zhang Zhiguo
Published: April 2023

Supplementary Table from Epigenome Programming by H3.3K27M Mutation Creates a Dependence of Pediatric Glioma on SMARCA4
Supplementary Table 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

Antibody lists
Supplementary Figure S6 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

KRASG12D inhibition alters the tumor immune microenvironment
Index of Supplementary Data 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

Index of Supplementary Data
Supplementary Figure S4 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 elicits changes in the tumor stroma and vasculature
Supplementary Tables S1-S4 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 table S1 shows all rRNA 2’-O-methylation sites identified in human AMLs.
Supplementary table S2 shows dynamic rRNA 2’-O-methylation sites in each DyMeC cluster.
Supplementary table S3 shows the location of rRNA 2’-O-methylation static sites in ribosome regions.
Supplementary table S4 shows proteins with altered translation after FBL knockdown.
Supplementary Figure S1 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 selectively inhibits KRASG12D and downstream MAPK signaling in vitro
Supplementary Table from Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma
Authors: Wu Lingxiang , Wu Wei , Zhang Junxia , Zhao Zheng , Li Liangyu , Zhu Mengyan , Wu Min , Wu Fan , Zhou Fengqi , Du Yuxin , Chai Rui-Chao , Zhang Wei , Qiu Xiaoguang , Liu Quanzhong , Wang Ziyu , Li Jie , Li Kening , Chen Apeng , Jiang Yinan , Xiao Xiangwei , Zou Han , Srivastava Rashmi , Zhang Tingting , Cai Yun , Liang Yuan , Huang Bin , Zhang Ruohan , Lin Fan , Hu Lang , Wang Xiuxing , Qian Xu , Lv Sali , Hu Baoli , Zheng Siyuan , Hu Zhibin , Shen Hongbing , You Yongping , Verhaak Roel G.W. , Jiang Tao , Wang Qianghu
Published: April 2023

Supplementary Table from Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma
Supplementary Video 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 Video from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion
Supplementary Data from Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma
Authors: Wu Lingxiang , Wu Wei , Zhang Junxia , Zhao Zheng , Li Liangyu , Zhu Mengyan , Wu Min , Wu Fan , Zhou Fengqi , Du Yuxin , Chai Rui-Chao , Zhang Wei , Qiu Xiaoguang , Liu Quanzhong , Wang Ziyu , Li Jie , Li Kening , Chen Apeng , Jiang Yinan , Xiao Xiangwei , Zou Han , Srivastava Rashmi , Zhang Tingting , Cai Yun , Liang Yuan , Huang Bin , Zhang Ruohan , Lin Fan , Hu Lang , Wang Xiuxing , Qian Xu , Lv Sali , Hu Baoli , Zheng Siyuan , Hu Zhibin , Shen Hongbing , You Yongping , Verhaak Roel G.W. , Jiang Tao , Wang Qianghu
Published: April 2023

Supplementary Data from Natural Coevolution of Tumor and Immunoenvironment in Glioblastoma
Supplementary Data 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 Data from Reprogrammed Schwann Cells Organize into Dynamic Tracks that Promote Pancreatic Cancer Invasion
Supplementary Table 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 Table from Pharmacologic Inhibition of NT5C2 Reverses Genetic and Nongenetic Drivers of 6-MP Resistance in Acute Lymphoblastic Leukemia
Supplementary Table 3 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

ChIP-Seq results
Supplementary Table 2 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

CRISPR screen results
Supplementary Table 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 Table from Geospatial Immune Heterogeneity Reflects the Diverse Tumor–Immune Interactions in Intrahepatic Cholangiocarcinoma
Supplementary Table S5 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 S5 shows all the oligos used in this study
Supplementary Table S3 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 S3 shows the differential expressed genes in NPM1c-koncked in HOXB8 cell lines vs parental cells
Supplementary Figure S1-S8 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 Figure S1 is associated with Figure1 and it shows the NPM1-WT binds to the rDNA arrays and NPM1c binds to non-repetitive genomic regions.
Supplementary Figure S2 is associated with Figure1 and it shows NPM1c’s chromatin binding and association with gene expression.
Supplementary Figure S3 is associated with Figure2 and shows NPM1c regulates the transcription of its target genes with BRU-seq.
Supplementary Figure S4 is associated with Figure2 and it shows the characterization of NPM1c condensate with biochemical assay and imaging assay.
Supplementary Figure S5 is associated with figure 3. The figure shows NPM1c and chromatin landacpe dymanics during dTag-13 treatment and wash-off.
Supplementary Figure S6 is associated with figure 4. It shows the supplemental data of HOXB8-NPM1c-knock-in model.
Supplementary figure S7 is associated with figure 5. It shows the supplemental data of XPO1's binding to chromatin in various leukemia cell lines and normal HSPCs.
Supplementary Figure S8 is associated with figure 6. It shows the supplemental information of synergy between Menin and XPO1 inhibitor in the NPM1c AML cell line model.
Supplementary Figures S1-S16 from NVL-520 Is a Selective, TRK-Sparing, and Brain-Penetrant Inhibitor of ROS1 Fusions and Secondary Resistance Mutations
Authors: Drilon Alexander , Horan Joshua C. , Tangpeerachaikul Anupong , Besse Benjamin , Ou Sai-Hong Ignatius , Gadgeel Shirish M. , Camidge D. Ross , van der Wekken Anthonie J. , Nguyen-Phuong Linh , Acker Adam , Keddy Clare , Nicholson Katelyn S. , Yoda Satoshi , Mente Scot , Sun Yuting , Soglia John R. , Kohl Nancy E. , Porter James R. , Shair Matthew D. , Zhu Viola , Davare Monika A. , Hata Aaron N. , Pelish Henry E. , Lin Jessica J.
Published: April 2023

NVL-520 Modeling, Properties, Biochemical Activity, Cellular Activity, and In Vivo Activity
Supplementary Tables S1-S5 and Figures S1-S4 from Racial/Ethnic and Sex Differences in Somatic Cancer Gene Mutations among Patients with Early-Onset Colorectal Cancer
Authors: Holowatyj Andreana N. , Wen Wanqing , Gibbs Timothy , Seagle Hannah M. , Keller Samantha R. , Edwards Digna R. Velez , Washington Mary K. , Eng Cathy , Perea Jose , Zheng Wei , Guo Xingyi
Published: April 2023

Table S1. Clinical and demographic characteristics of the colorectal cancer (CRC) patient study population by race/ethnicity and age at sequencing: AACR Project GENIE.Table S2. Baseline mutation probability, comparison and heterogeneity of non-silent somatic gene mutations among patients with early-onset and late-onset nonhypermutated colorectal cancer. Genes ranked by false discovery rate (FDR).Table S3. Racial/ethnic patterns in baseline mutation probability, comparison and heterogeneity of all non-silent somatic gene mutations among patients with early-onset and late-onset non-hypermutated colorectal cancer.Table S4. Baseline mutation probability, comparison and heterogeneity of non-silent somatic gene mutations among patients with earlyonset and late-onset non-hypermutated colorectal cancer by sex.Table S5. Read depth for clinical-grade targeting sequencing data from tumor tissues and case counts by early-onset and late-onset groups and sequencing center. Figure S1. Mutation rates among 6,903 tumor samples from colorectal cancer patients across racial/ethnic groups.Figure S2. Adjusted mutation rates in 653 hypermutated colorectal tumors: AACR GENIE.Figure S3. Tumor mutational burden (TMB) across sequencing assay/platform for early-onset and late-onset non-hypermutated colorectal cancer cases: AACR Project GENIE.Figure S4. Frequency of non-silent somatic mutations in commonly assayed and mutated genes between early-onset and late-onset non-hypermutated CRC cases (mutation frequency >10%).
Supplementary Figure S6 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

EGFR and AXL protein expression in the brain and immunohistochemical characterization of tumors of Lztr1fl/fl;Cdkn2afl/fl;GFAP-Cre+ mice
Supplementary Figure S4 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

LZTR1 co-localized with EGFR and AXL at the cellular membrane upon ligand stimulation
Supplementary Figure S1. 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

LZTR1 regulates EGFR and AXL protein stability
Figures S1-S10 and Tables S1, S3-S6 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

Figure S1: Age distribution of the cohort. Figure S2: The distribution of bleomycin 3rd tertile. Figure S3: Distribution of cancer types treated without alkylating agents, platinum, anthracyclines, bleomycin, dactinomycin, epipodophyllotoxins, methotrexate, vinca alkaloids. Figure S4: Conceptual illustration for age- and therapy-related clonal hematopoiesis. Figure S5: Distribution of cell phenotypes harboring STAT3 Y640F mutation. Figure S6: Regression analysis on public dataset to reproduce the clone expansion pattern in main Figure 4A. Figure S7: Longitudinal view of the serial samples. Figure S8: Simulation analysis to reproduce the pattern in main Figure 4B. Figure S9: Comparison of clone growth rates and clone sizes between age- and therapy-related CH. Figure S10: Additional sequencing for PPM1D. Table S1: Gene panel. Table S3: Comparison between CH and sex, race and age. Table S4: Comparison between CH status and pathogenic germline mutations. Separately analyzed for cancer predisposition genes and DNA damage repair genes. Table S5: Enrichment of STAT3 mutations in Hodgkin lymphoma survivors. Table S6: Association between procarbazine exposure and mutation pattern in Hodgkin lymphoma survivors.
Supplementary Data from Targeted MDM2 Degradation Reveals a New Vulnerability for p53-Inactivated Triple-Negative Breast Cancer
Authors: Adams Clare M. , Mitra Ramkrishna , Xiao Youcai , Michener Peter , Palazzo Juan , Chao Allen , Gour Jitendra , Cassel Joel , Salvino Joseph M. , Eischen Christine M.
Published: April 2023

Supplementary Materials and Methods, Tables S1-S3, Figures S1-S7
Figure S7 from LKB1-Dependent Regulation of TPI1 Creates a Divergent Metabolic Liability between Human and Mouse Lung Adenocarcinoma
Authors: Stein Benjamin D. , Ferrarone John R. , Gardner Eric E. , Chang Jae Won , Wu David , Hollstein Pablo E. , Liang Roger J. , Yuan Min , Chen Qiuying , Coukos John S. , Sindelar Miriam , Ngo Bryan , Gross Steven S. , Shaw Reuben J. , Zhang Chen , Asara John M. , Moellering Raymond E. , Varmus Harold , Cantley Lewis C.
Published: April 2023

Figure S7. Tpi1 is required for tumor growth in KP and KPL LUAD models.