Publications

A comprehensive list of lab publications are available here:

Please view PubMed for a comprehensive list of Sweet-Cordero lab publications.

Complete Response to PD-1 Inhibition in an Adolescent With Relapsed Clear Cell Adenocarcinoma of the Cervix Predicted by Neoepitope Burden and APOBEC Signature.
Levinson A, Lee AG, Martell HJ, Breese MR, Zaloudek C, Van Ziffle J, Laguna B, Leung SG, Chen MD, Chen LM, Pfeil J, Ladwig NR, Shah AT, Behroozfard I, Rao AA, Salama SR, Sweet-Cordero EA, Stieglitz E
JCO precision oncology, 2020

An Expanded Tool Kit for Modeling the Oncogenic Functions of KRAS.
Kostyrko K, Sweet-Cordero EA
Cancer discovery, 2020

Advances and Challenges in Pediatric and Childhood Cancers.
Hawkins C, Pfister S, Jones DTW, Shah NN, Gilbertson RJ, Sweet-Cordero EA, Dyer MA, Mossé YP, Haber M, DuBois SG
Cancer cell, 2020

Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.
Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A
Nature biotechnology, 2020

NUP98-NSD1 Driven MDS/MPN in Childhood Masquerading as JMML.
Behnert A, Lee AG, Young EP, Breese MR, Leung SG, Behroozfard I, Maruffi M, Sweet-Cordero EA, Dvorak CC, Chu J, Stieglitz E
Journal of pediatric hematology/oncology, 2020

Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities.
Kelly MR, Kostyrko K, Han K, Mooney NA, Jeng EE, Spees K, Dinh PT, Abbott KL, Gwinn DM, Sweet-Cordero EA, Bassik MC, Jackson PK
Cancer discovery, 2020

Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand.
Kim JW, Marquez CP, Sperberg RAP, Wu J, Bae WG, Huang PS, Sweet-Cordero EA, Cochran JR
Proceedings of the National Academy of Sciences of the United States of America, 2020

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures.
Pfeil J, Sanders LM, Anastopoulos I, Lyle AG, Weinstein AS, Xue Y, Blair A, Beale HC, Lee A, Leung SG, Dinh PT, Shah AT, Breese MR, Devine WP, Bjork I, Salama SR, Sweet-Cordero EA, Haussler D, Vaske OM
PLoS computational biology, 2020

CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities.
Han K, Pierce SE, Li A, Spees K, Anderson GR, Seoane JA, Lo YH, Dubreuil M, Olivas M, Kamber RA, Wainberg M, Kostyrko K, Kelly MR, Yousefi M, Simpkins SW, Yao D, Lee K, Kuo CJ, Jackson PK, Sweet-Cordero A, Kundaje A, Gentles AJ, Curtis C, Winslow MM, Bassik MC
Nature, 2020

Genomic Complexity of Osteosarcoma and Its Implication for Preclinical and Clinical Targeted Therapies.
Schott C, Shah AT, Sweet-Cordero EA
Advances in experimental medicine and biology, 2020

The mir181ab1 cluster promotes kras-driven oncogenesis and progression in lung and pancreas.
Valencia K, Erice O, Kostyrko K, Hausmann S, Guruceaga E, Thathireddy A, Flores NM, Sayles LC, Lee AG, Fragoso R, Sun TQ, Vallejo A, Roman M, Entrialgo-Cadierno R, Migueliz I, Razquin N, Fortes P, Lecanda F, Lu J, Ponz-Sarvise M, Chen CZ, Mazur PK, Sweet-Cordero EA, Vicent S
The Journal of clinical investigation, 2019

Antitumor activity of an engineered decoy receptor targeting CLCF1-CNTFR signaling in lung adenocarcinoma.
Kim JW, Marquez CP, Kostyrko K, Koehne AL, Marini K, Simpson DR, Lee AG, Leung SG, Sayles LC, Shrager J, Ferrer I, Paz-Ares L, Gephart MH, Vicent S, Cochran JR, Sweet-Cordero EA
Nature medicine, 2019

Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor.
Sanders LM, Rangaswami A, Bjork I, Lam DL, Beale HC, Kephart ET, Durbin A, Learned K, Currie R, Lyle AG, Pfeil J, Shah AT, Lee AG, Leung SG, Behroozfard IH, Breese MR, Peralez J, Hazard FK, Lacayo N, Spunt SL, Haussler D, Salama SR, Sweet-Cordero EA, Vaske OM
Cold Spring Harbor molecular case studies, 2019

Ewing sarcoma in a child with neurofibromatosis type 1.
Fernandez KS, Turski ML, Shah AT, Bastian BC, Horvai A, Hardee S, Sweet-Cordero EA
Cold Spring Harbor molecular case studies, 2019

Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer.
Vaske OM, Bjork I, Salama SR, Beale H, Tayi Shah A, Sanders L, Pfeil J, Lam DL, Learned K, Durbin A, Kephart ET, Currie R, Newton Y, Swatloski T, McColl D, Vivian J, Zhu J, Lee AG, Leung SG, Spillinger A, Liu HY, Liang WS, Byron SA, Berens ME, Resnick AC, Lacayo N, Spunt SL, Rangaswami A, Huynh V, Torno L, Plant A, Kirov I, Zabokrtsky KB, Rassekh SR, Deyell RJ, Laskin J, Marra MA, Sender LS, Mueller S, Sweet-Cordero EA, Goldstein TC, Haussler D
JAMA network open, 2019

Fusion driven JMML: a novel CCDC88C-FLT3 fusion responsive to sorafenib identified by RNA sequencing.
Chao AK, Meyer JA, Lee AG, Hecht A, Tarver T, Van Ziffle J, Koegel AK, Golden C, Braun BS, Sweet-Cordero EA, Smith CC, Dvorak CC, Loh ML, Stieglitz E
Leukemia, 2019

Provocative questions in osteosarcoma basic and translational biology: A report from the Children's Oncology Group.
Roberts RD, Lizardo MM, Reed DR, Hingorani P, Glover J, Allen-Rhoades W, Fan T, Khanna C, Sweet-Cordero EA, Cash T, Bishop MW, Hegde M, Sertil AR, Koelsche C, Mirabello L, Malkin D, Sorensen PH, Meltzer PS, Janeway KA, Gorlick R, Crompton BD
Cancer, 2019

Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules.
Ren Y, Huang S, Dai C, Xie D, Zheng L, Xie H, Zheng H, She Y, Zhou F, Wang Y, Li P, Fei K, Jiang G, Zhang Y, Su B, Sweet-Cordero EA, Tran NL, Yang Y, Patel JN, Rolfo C, Rocco G, Cardona AF, Tuzi A, Suter MB, Yang P, Xu W, Chen C
Frontiers in oncology, 2019

The genomic landscape of pediatric cancers: Implications for diagnosis and treatment.
Sweet-Cordero EA, Biegel JA
Science (New York, N.Y.), 2019

Genome-Informed Targeted Therapy for Osteosarcoma.
Sayles LC, Breese MR, Koehne AL, Leung SG, Lee AG, Liu HY, Spillinger A, Shah AT, Tanasa B, Straessler K, Hazard FK, Spunt SL, Marina N, Kim GE, Cho SJ, Avedian RS, Mohler DG, Kim MO, Dubois SG, Hawkins DS, Sweet-Cordero EA
Cancer discovery, 2018

Inhibition of activin signaling in lung adenocarcinoma increases the therapeutic index of platinum chemotherapy.
Marini KD, Croucher DR, McCloy RA, Vaghjiani V, Gonzalez-Rajal A, Hastings JF, Chin V, Szczepny A, Kostyrko K, Marquez C, Jayasekara WSN, Alamgeer M, Boolell V, Han JZR, Waugh T, Lee HC, Oakes SR, Kumar B, Harrison CA, Hedger MP, Lorensuhewa N, Kita B, Barrow R, Robinson BW, de Kretser DM, Wu J, Ganju V, Sweet-Cordero EA, Burgess A, Martelotto LG, Rossello FJ, Cain JE, Watkins DN
Science translational medicine, 2018

Oncogenic KRAS Regulates Amino Acid Homeostasis and Asparagine Biosynthesis via ATF4 and Alters Sensitivity to L-Asparaginase.
Gwinn DM, Lee AG, Briones-Martin-Del-Campo M, Conn CS, Simpson DR, Scott AI, Le A, Cowan TM, Ruggero D, Sweet-Cordero EA
Cancer cell, 2018

Statistical algorithms improve accuracy of gene fusion detection.
Hsieh G, Bierman R, Szabo L, Lee AG, Freeman DE, Watson N, Sweet-Cordero EA, Salzman J
Nucleic acids research, 2017

Improvement in treatment abandonment in pediatric patients with cancer in Guatemala.
Alvarez E, Seppa M, Rivas S, Fuentes L, Valverde P, Antillón-Klussmann F, Castellanos M, Sweet-Cordero EA, Messacar K, Kurap J, Bustamante M, Howard SC, Efron B, Luna-Fineman S
Pediatric blood & cancer, 2017

An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer.
Vallejo A, Perurena N, Guruceaga E, Mazur PK, Martinez-Canarias S, Zandueta C, Valencia K, Arricibita A, Gwinn D, Sayles LC, Chuang CH, Guembe L, Bailey P, Chang DK, Biankin A, Ponz-Sarvise M, Andersen JB, Khatri P, Bozec A, Sweet-Cordero EA, Sage J, Lecanda F, Vicent S
Nature communications, 2017

Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis.
Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Ma RK, Caswell DR, Chiou SH, Winters AF, Grüner BM, Ramaswami G, Spencley AL, Kopecky KE, Sayles LC, Sweet-Cordero EA, Li JB, Kundaje A, Winslow MM
Nature medicine, 2017

An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency.
Brady JJ, Chuang CH, Greenside PG, Rogers ZN, Murray CW, Caswell DR, Hartmann U, Connolly AJ, Sweet-Cordero EA, Kundaje A, Winslow MM
Cancer cell, 2016

Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma.
Mazur PK, Herner A, Mello SS, Wirth M, Hausmann S, Sánchez-Rivera FJ, Lofgren SM, Kuschma T, Hahn SA, Vangala D, Trajkovic-Arsic M, Gupta A, Heid I, Noël PB, Braren R, Erkan M, Kleeff J, Sipos B, Sayles LC, Heikenwalder M, Heßmann E, Ellenrieder V, Esposito I, Jacks T, Bradner JE, Khatri P, Sweet-Cordero EA, Attardi LD, Schmid RM, Schneider G, Sage J, Siveke JT
Nature medicine, 2015

Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis.
Marques Howarth M, Simpson D, Ngok SP, Nieves B, Chen R, Siprashvili Z, Vaka D, Breese MR, Crompton BD, Alexe G, Hawkins DS, Jacobson D, Brunner AL, West R, Mora J, Stegmaier K, Khavari P, Sweet-Cordero EA
The Journal of clinical investigation, 2014

A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma.
Chen R, Khatri P, Mazur PK, Polin M, Zheng Y, Vaka D, Hoang CD, Shrager J, Xu Y, Vicent S, Butte AJ, Sweet-Cordero EA
Cancer research, 2014

Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma.
Valdmanis PN, Roy-Chaudhuri B, Kim HK, Sayles LC, Zheng Y, Chuang CH, Caswell DR, Chu K, Zhang Y, Winslow MM, Sweet-Cordero EA, Kay MA
Oncogene, 2013

A rare population of CD24(+)ITGB4(+)Notch(hi) cells drives tumor propagation in NSCLC and requires Notch3 for self-renewal.
Zheng Y, de la Cruz CC, Sayles LC, Alleyne-Chin C, Vaka D, Knaak TD, Bigos M, Xu Y, Hoang CD, Shrager JB, Fehling HJ, French D, Forrest W, Jiang Z, Carano RA, Barck KH, Jackson EL, Sweet-Cordero EA
Cancer cell, 2013

The phosphatase PP2A links glutamine to the tumor suppressor p53.
Gwinn D, Sweet-Cordero EA
Molecular cell, 2013

Mathematical modeling of tumor cell proliferation kinetics and label retention in a mouse model of lung cancer.
Zheng Y, Moore H, Piryatinska A, Solis T, Sweet-Cordero EA
Cancer research, 2013

Blocking NRG1 and other ligand-mediated Her4 signaling enhances the magnitude and duration of the chemotherapeutic response of non-small cell lung cancer.
Hegde GV, de la Cruz CC, Chiu C, Alag N, Schaefer G, Crocker L, Ross S, Goldenberg D, Merchant M, Tien J, Shao L, Roth L, Tsai SP, Stawicki S, Jin Z, Wyatt SK, Carano RA, Zheng Y, Sweet-Cordero EA, Wu Y, Jackson EL
Science translational medicine, 2013

Residual tumor cells that drive disease relapse after chemotherapy do not have enhanced tumor initiating capacity.
Hegde GV, de la Cruz C, Eastham-Anderson J, Zheng Y, Sweet-Cordero EA, Jackson EL
PloS one, 2012

Cross-species functional analysis of cancer-associated fibroblasts identifies a critical role for CLCF1 and IL-6 in non-small cell lung cancer in vivo.
Vicent S, Sayles LC, Vaka D, Khatri P, Gevaert O, Chen R, Zheng Y, Gillespie AK, Clarke N, Xu Y, Shrager J, Hoang CD, Plevritis S, Butte AJ, Sweet-Cordero EA
Cancer research, 2012

Wilms tumor 1 (WT1) regulates KRAS-driven oncogenesis and senescence in mouse and human models.
Vicent S, Chen R, Sayles LC, Lin C, Walker RG, Gillespie AK, Subramanian A, Hinkle G, Yang X, Saif S, Root DE, Huff V, Hahn WC, Sweet-Cordero EA
The Journal of clinical investigation, 2010

Loss of p130 accelerates tumor development in a mouse model for human small-cell lung carcinoma.
Schaffer BE, Park KS, Yiu G, Conklin JF, Lin C, Burkhart DL, Karnezis AN, Sweet-Cordero EA, Sage J
Cancer research, 2010

Chronic cisplatin treatment promotes enhanced damage repair and tumor progression in a mouse model of lung cancer.
Oliver TG, Mercer KL, Sayles LC, Burke JR, Mendus D, Lovejoy KS, Cheng MH, Subramanian A, Mu D, Powers S, Crowley D, Bronson RT, Whittaker CA, Bhutkar A, Lippard SJ, Golub T, Thomale J, Jacks T, Sweet-Cordero EA
Genes & development, 2010

Comparison of gene expression and DNA copy number changes in a murine model of lung cancer.
Sweet-Cordero A, Tseng GC, You H, Douglass M, Huey B, Albertson D, Jacks T
Genes, chromosomes & cancer, 2006

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis.
Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T
Nature genetics, 2004