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Lee RH, Roy R, Li H, Hechmer A, Zhu TR, Izgutdina A, Olshen AB, Johnson DE, Grandis JR. Therapeutic implications of transcriptomics in head and neck cancer patient-derived xenografts. PLoS One 2023; 18:e0282177. [PMID: 36857322 PMCID: PMC9977000 DOI: 10.1371/journal.pone.0282177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
There are currently no clinical strategies utilizing tumor gene expression to inform therapeutic selection for patients with head and neck squamous cell carcinoma (HNSCC). One of the challenges in developing predictive biomarkers is the limited characterization of preclinical HNSCC models. Patient-derived xenografts (PDXs) are increasingly recognized as translationally relevant preclinical avatars for human tumors; however, the overall transcriptomic concordance of HNSCC PDXs with primary human HNSCC is understudied, especially in human papillomavirus-associated (HPV+) disease. Here, we characterized 64 HNSCC PDXs (16 HPV+ and 48 HPV-) at the transcriptomic level using RNA-sequencing. The range of human-specific reads per PDX varied from 64.6%-96.5%, with a comparison of the most differentially expressed genes before and after removal of mouse transcripts revealing no significant benefit to filtering out mouse mRNA reads in this cohort. We demonstrate that four previously established HNSCC molecular subtypes found in The Cancer Genome Atlas (TCGA) are also clearly recapitulated in HNSCC PDXs. Unsupervised hierarchical clustering yielded a striking natural division of HNSCC PDXs by HPV status, with C19orf57 (BRME1), a gene previously correlated with positive response to cisplatin in cervical cancer, among the most significantly differentially expressed genes between HPV+ and HPV- PDXs. In vivo experiments demonstrated a possible relationship between increased C19orf57 expression and superior anti-tumor responses of PDXs to cisplatin, which should be investigated further. These findings highlight the value of PDXs as models for HPV+ and HPV- HNSCC, providing a resource for future discovery of predictive biomarkers to guide treatment selection in HNSCC.
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Affiliation(s)
- Rex H. Lee
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Hua Li
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Tian Ran Zhu
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Adila Izgutdina
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Adam B. Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Daniel E. Johnson
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Jennifer R. Grandis
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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Zavala VA, Casavilca-Zambrano S, Navarro-Vásquez J, Castañeda CA, Valencia G, Morante Z, Calderón M, Abugattas JE, Gómez H, Fuentes HA, Liendo-Picoaga R, Cotrina JM, Monge C, Neciosup SP, Huntsman S, Hu D, Sánchez SE, Williams MA, Núñez-Marrero A, Godoy L, Hechmer A, Olshen AB, Dutil J, Ziv E, Zabaleta J, Gelaye B, Vásquez J, Gálvez-Nino M, Enriquez-Vera D, Vidaurre T, Fejerman L. Association between Ancestry-Specific 6q25 Variants and Breast Cancer Subtypes in Peruvian Women. Cancer Epidemiol Biomarkers Prev 2022; 31:1602-1609. [PMID: 35654312 PMCID: PMC9662925 DOI: 10.1158/1055-9965.epi-22-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/07/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Breast cancer incidence in the United States is lower in Hispanic/Latina (H/L) compared with African American/Black or Non-Hispanic White women. An Indigenous American breast cancer-protective germline variant (rs140068132) has been reported near the estrogen receptor 1 gene. This study tests the association of rs140068132 and other polymorphisms in the 6q25 region with subtype-specific breast cancer risk in H/Ls of high Indigenous American ancestry. METHODS Genotypes were obtained for 5,094 Peruvian women with (1,755) and without (3,337) breast cancer. Associations between genotype and overall and subtype-specific risk for the protective variant were tested using logistic regression models and conditional analyses, including other risk-associated polymorphisms in the region. RESULTS We replicated the reported association between rs140068132 and breast cancer risk overall [odds ratio (OR), 0.53; 95% confidence interval (CI), 0.47-0.59], as well as the lower odds of developing hormone receptor negative (HR-) versus HR+ disease (OR, 0.77; 95% CI, 0.61-0.97). Models, including HER2, showed further heterogeneity with reduced odds for HR+HER2+ (OR, 0.68; 95% CI, 0.51-0.92), HR-HER2+ (OR, 0.63; 95% CI, 0.44-0.90) and HR-HER2- (OR, 0.77; 95% CI, 0.56-1.05) compared with HR+HER2-. Inclusion of other risk-associated variants did not change these observations. CONCLUSIONS The rs140068132 polymorphism is associated with decreased risk of breast cancer in Peruvians and is more protective against HR- and HER2+ diseases independently of other breast cancer-associated variants in the 6q25 region. IMPACT These results could inform functional analyses to understand the mechanism by which rs140068132-G reduces risk of breast cancer development in a subtype-specific manner. They also illustrate the importance of including diverse individuals in genetic studies.
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Affiliation(s)
- Valentina A. Zavala
- Department of Public Health Sciences, University of California Davis, Davis, California
| | | | | | | | | | - Zaida Morante
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | | | - Henry Gómez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | | | | | - Claudia Monge
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | - Scott Huntsman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Sixto E. Sánchez
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru and Asociación Civil Proyectos en Salud (PROESA), Lima, Peru
| | - Michelle A. Williams
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Angel Núñez-Marrero
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Lenin Godoy
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Aaron Hechmer
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Adam B. Olshen
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Julie Dutil
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Jovanny Zabaleta
- Department of Pediatrics and Stanley S. Scott Cancer Center LSUHSC, New Orleans, Louisiana
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jule Vásquez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | | | | | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, California
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California
- Corresponding Author: Laura Fejerman, UC Davis Comprehensive Cancer Center, 451 Health Sciences Drive, Davis, CA 95616. Phone: 530-754-1690; E-mail:
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3
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Behnert A, Meyer J, Parsa JY, Hechmer A, Loh ML, Olshen A, de Smith AJ, Stieglitz E. Exploring the genetic and epigenetic origins of juvenile myelomonocytic leukemia using newborn screening samples. Leukemia 2022; 36:279-282. [PMID: 34183765 PMCID: PMC8720242 DOI: 10.1038/s41375-021-01331-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 01/09/2023]
Affiliation(s)
- Astrid Behnert
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA
| | | | - Aaron Hechmer
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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4
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Bouhaddou M, Lee RH, Li H, Bhola NE, O'Keefe RA, Naser M, Zhu TR, Nwachuku K, Duvvuri U, Olshen AB, Roy R, Hechmer A, Bolen J, Keysar SB, Jimeno A, Mills GB, Vandenberg S, Swaney DL, Johnson DE, Krogan NJ, Grandis JR. Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. JCI Insight 2021; 6:151982. [PMID: 34546978 PMCID: PMC8564908 DOI: 10.1172/jci.insight.151982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) inhibitor cetuximab is the only FDA-approved oncogene-targeting therapy for head and neck squamous cell carcinoma (HNSCC). Despite variable treatment response, no biomarkers exist to stratify patients for cetuximab therapy in HNSCC. Here, we applied unbiased hierarchical clustering to reverse-phase protein array molecular profiles from patient-derived xenograft (PDX) tumors and revealed 2 PDX clusters defined by protein networks associated with EGFR inhibitor resistance. In vivo validation revealed unbiased clustering to classify PDX tumors according to cetuximab response with 88% accuracy. Next, a support vector machine classifier algorithm identified a minimalist biomarker signature consisting of 8 proteins — caveolin-1, Sox-2, AXL, STING, Brd4, claudin-7, connexin-43, and fibronectin — with expression that strongly predicted cetuximab response in PDXs using either protein or mRNA. A combination of caveolin-1 and Sox-2 protein levels was sufficient to maintain high predictive accuracy, which we validated in tumor samples from patients with HNSCC with known clinical response to cetuximab. These results support further investigation into the combined use of caveolin-1 and Sox-2 as predictive biomarkers for cetuximab response in the clinic.
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Affiliation(s)
- Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology and.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.,J. David Gladstone Institutes, San Francisco, California, USA
| | - Rex H Lee
- Department of Otolaryngology - Head and Neck Surgery and
| | - Hua Li
- Department of Otolaryngology - Head and Neck Surgery and
| | - Neil E Bhola
- Department of Otolaryngology - Head and Neck Surgery and
| | | | - Mohammad Naser
- Histology and Biomarkers Core, Helen Diller Family Comprehensive Cancer Center Biorepository and Tissue Biomarker Technology, University of California, San Francisco, San Francisco, California, USA
| | - Tian Ran Zhu
- Department of Otolaryngology - Head and Neck Surgery and
| | | | - Umamaheswar Duvvuri
- Department of Otolaryngology and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam B Olshen
- Computational Biology and Informatics Core and.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Ritu Roy
- Computational Biology and Informatics Core and
| | | | - Jennifer Bolen
- Histology and Biomarkers Core, Helen Diller Family Comprehensive Cancer Center Biorepository and Tissue Biomarker Technology, University of California, San Francisco, San Francisco, California, USA
| | - Stephen B Keysar
- Department of Medicine, University of Colorado Hospital, Aurora, Colorado, USA
| | - Antonio Jimeno
- Department of Medicine, University of Colorado Hospital, Aurora, Colorado, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Scott Vandenberg
- Histology and Biomarkers Core, Helen Diller Family Comprehensive Cancer Center Biorepository and Tissue Biomarker Technology, University of California, San Francisco, San Francisco, California, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology and.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.,J. David Gladstone Institutes, San Francisco, California, USA
| | | | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology and.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.,J. David Gladstone Institutes, San Francisco, California, USA
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5
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Snijders A, Zhou M, Whitehead T, Fitch B, Pandey P, Hechmer A, Huang A, Schick S, de Smith A, Olshen A, Metayer C, Mao JH, Wiemels J, Kogan S. In utero and early-life exposure to thirdhand smoke causes profound changes to the immune system. Clin Sci (Lond) 2021; 135:1053-1063. [PMID: 33851706 PMCID: PMC8086195 DOI: 10.1042/cs20201498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/01/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Thirdhand smoke (THS) is the residual tobacco contamination that remains after the smoke clears. We investigated the effects of THS exposure in utero and during early life in a transgenic Cdkn2a knockout mouse model that is vulnerable to the development of leukemia/lymphoma. Female mice, and their offspring, were exposed from the first day of pregnancy to weaning. Plasma cytokines, body weight and hematologic parameters were measured in the offspring. To investigate THS exposure effects on the development of leukemia/lymphoma, bone marrow (BM) was collected from control and THS-exposed mice and transplanted into BM-ablated recipient mice, which were followed for tumor development for 1 year. We found that in utero and early-life THS exposure caused significant changes in plasma cytokine concentrations and in immune cell populations; changes appeared more pronounced in male mice. Spleen (SP) and BM B-cell populations were significantly lower in THS-exposed mice. We furthermore observed that THS exposure increased the leukemia/lymphoma-free survival in BM transplantation recipient mice, potentially caused by THS-induced B-cell toxicity. A trend towards increased solid tumors in irradiated mice reconstituted with THS-exposed BM stimulates the hypothesis that the immunosuppressive effects of in utero and early-life THS exposure might contribute to carcinogenesis by lowering the host defense to other toxic exposures. Our study adds to expanding evidence that THS exposure alters the immune system and that in utero and early-life developmental periods represent vulnerable windows of susceptibility for these effects.
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Affiliation(s)
- Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Mi Zhou
- Department of Laboratory Medicine, University of California, San Francisco, CA, U.S.A
| | - Todd P. Whitehead
- School of Public Health, University of California, Berkeley, CA, U.S.A
| | - Briana Fitch
- Department of Laboratory Medicine, University of California, San Francisco, CA, U.S.A
| | - Priyatama Pandey
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, U.S.A
| | - Aaron Hechmer
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
| | - Abel Huang
- Division of Occupational and Environmental Medicine, Department of Medicine, University of California, San Francisco, CA, U.S.A
| | - Suzaynn F. Schick
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
- Division of Occupational and Environmental Medicine, Department of Medicine, University of California, San Francisco, CA, U.S.A
| | - Adam J. de Smith
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, U.S.A
| | - Adam B. Olshen
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, U.S.A
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, CA, U.S.A
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, U.S.A
| | - Scott C. Kogan
- Department of Laboratory Medicine, University of California, San Francisco, CA, U.S.A
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, U.S.A
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6
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Hecht A, Meyer JA, Behnert A, Wong E, Chehab F, Olshen A, Hechmer A, Aftandilian C, Bhat R, Choi SW, Chonat S, Farrar JE, Fluchel M, Frangoul H, Han JH, Kolb EA, Kuo DJ, MacMillan ML, Maese L, Maloney KW, Narendran A, Oshrine B, Schultz KR, Sulis ML, Van Mater D, Tasian SK, Hofmann WK, Loh ML, Stieglitz E. Molecular and phenotypic diversity of CBL-mutated juvenile myelomonocytic leukemia. Haematologica 2020; 107:178-186. [PMID: 33375775 PMCID: PMC8719097 DOI: 10.3324/haematol.2020.270595] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 11/22/2022] Open
Abstract
Mutations in the CBL gene were first identified in adults with various myeloid malignancies. Some patients with juvenile myelomonocytic leukemia (JMML) were also noted to harbor mutations in CBL, but were found to have generally less aggressive disease courses compared to patients with other forms of Ras pathway-mutant JMML. Importantly, and in contrast to most reports in adults, the majority of CBL mutations in JMML patients are germline with acquired uniparental disomy occurring in affected marrow cells. Here, we systematically studied a large cohort of 33 JMML patients with CBL mutations and found that this disease is highly diverse in presentation and overall outcome. Moreover, we discovered somatically acquired CBL mutations in 15% of pediatric patients who presented with more aggressive disease. Neither clinical features nor methylation profiling were able to distinguish patients with somatic CBL mutations from those with germline CBL mutations, highlighting the need for germline testing. Overall, we demonstrate that disease courses are quite heterogeneous even among patients with germline CBL mutations. Prospective clinical trials are warranted to find ideal treatment strategies for this diverse cohort of patients.
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Affiliation(s)
- Anna Hecht
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA; Department of Hematology/Oncology, University Hospital Mannheim, Heidelberg University
| | - Julia A Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco
| | - Astrid Behnert
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco
| | - Eric Wong
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco
| | - Farid Chehab
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco
| | - Adam Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA; Department of Epidemiology and Biostatistics, University of California
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco
| | | | - Rukhmi Bhat
- Northwestern University Feinberg School of Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Sung Won Choi
- Blood and Marrow Transplantation Program, University of Michigan, Ann Arbor, MI
| | - Satheesh Chonat
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA; Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Jason E Farrar
- Arkansas Children's Research Institute, Little Rock, AR; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Mark Fluchel
- University of Utah, Department of Pediatrics, Division of Pediatric Hematology-Oncology, Salt Lake City, UT
| | - Haydar Frangoul
- The Children's Hospital at TriStar Centennial and Sarah Cannon Research Institute, Nashville, TN
| | - Jennifer H Han
- Division of Pediatric Hematology-Oncology, University of California, San Diego/ Rady Children's Hospital San Diego
| | - Edward A Kolb
- Nemours Center for Cancer and Blood Disorders/Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Dennis J Kuo
- Division of Pediatric Hematology-Oncology, University of California, San Diego/ Rady Children's Hospital San Diego
| | - Margaret L MacMillan
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Luke Maese
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | | | - Aru Narendran
- Pediatric Hematology and Oncology, Alberta Children's Hospital, Calgary, Alberta
| | | | - Kirk R Schultz
- British Columbia Children's Hospital and Research Institute, Vancouver, British Columbia
| | - Maria L Sulis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center. 1275 York Avenue. 10065 New York, NY
| | - David Van Mater
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia; Department of Pediatrics and Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Wolf-Karsten Hofmann
- Department of Hematology/Oncology, University Hospital Mannheim, Heidelberg University
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco.
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7
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Meyer LK, Huang BJ, Delgado-Martin C, Roy RP, Hechmer A, Wandler AM, Vincent TL, Fortina P, Olshen AB, Wood BL, Horton TM, Shannon KM, Teachey DT, Hermiston ML. Glucocorticoids paradoxically facilitate steroid resistance in T cell acute lymphoblastic leukemias and thymocytes. J Clin Invest 2020; 130:863-876. [PMID: 31687977 PMCID: PMC6994137 DOI: 10.1172/jci130189] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Glucocorticoids (GCs) are a central component of therapy for patients with T cell acute lymphoblastic leukemia (T-ALL), and although resistance to GCs is a strong negative prognostic indicator in T-ALL, the mechanisms of GC resistance remain poorly understood. Using diagnostic samples from patients enrolled in the frontline Children's Oncology Group (COG) T-ALL clinical trial AALL1231, we demonstrated that one-third of primary T-ALLs were resistant to GCs when cells were cultured in the presence of IL-7, a cytokine that is critical for normal T cell function and that plays a well-established role in leukemogenesis. We demonstrated that in these T-ALLs and in distinct populations of normal developing thymocytes, GCs paradoxically induced their own resistance by promoting upregulation of IL-7 receptor (IL-7R) expression. In the presence of IL-7, this augmented downstream signal transduction, resulting in increased STAT5 transcriptional output and upregulation of the prosurvival protein BCL-2. Taken together, we showed that IL-7 mediates an intrinsic and physiologic mechanism of GC resistance in normal thymocyte development that is retained during leukemogenesis in a subset of T-ALLs and is reversible with targeted inhibition of the IL-7R/JAK/STAT5/BCL-2 axis.
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Affiliation(s)
- Lauren K. Meyer
- Department of Pediatrics, UCSF, San Francisco, California, USA
| | | | | | - Ritu P. Roy
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | | | - Tiffaney L. Vincent
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Adam B. Olshen
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Brent L. Wood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Terzah M. Horton
- Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Kevin M. Shannon
- Department of Pediatrics, UCSF, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - David T. Teachey
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michelle L. Hermiston
- Department of Pediatrics, UCSF, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
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8
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MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SVE, Knowles DW, Stapleton M, Bickel P, Biggin MD, Eisen MB. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 2009; 10:R80. [PMID: 19627575 PMCID: PMC2728534 DOI: 10.1186/gb-2009-10-7-r80] [Citation(s) in RCA: 267] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 05/15/2009] [Accepted: 07/23/2009] [Indexed: 01/05/2023] Open
Abstract
Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions. Background We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. Results Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. Conclusions It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.
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Affiliation(s)
- Stewart MacArthur
- Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84-181, Berkeley, CA 94720, USA
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Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Hendriks CLL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 2008; 6:e27. [PMID: 18271625 PMCID: PMC2235902 DOI: 10.1371/journal.pbio.0060027] [Citation(s) in RCA: 353] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 12/19/2007] [Indexed: 01/22/2023] Open
Abstract
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. We used whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over 40 well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.
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Affiliation(s)
- Xiao-yong Li
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Stewart MacArthur
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Richard Bourgon
- Statistics Department, University of California Berkeley, Berkeley, California, United States of America
| | - David Nix
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Daniel A Pollard
- Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America
| | - Venky N Iyer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Aaron Hechmer
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Lisa Simirenko
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mark Stapleton
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Cris L. Luengo Hendriks
- Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America
| | - Hou Cheng Chu
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nobuo Ogawa
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - William Inwood
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Victor Sementchenko
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Amy Beaton
- Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America
| | - Richard Weiszmann
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Susan E Celniker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - David W Knowles
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Tom Gingeras
- Affymetrix, Inc., Santa Clara, California, United States of America
| | - Terence P Speed
- Statistics Department, University of California Berkeley, Berkeley, California, United States of America
| | - Michael B Eisen
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail: (MBE); (MDB)
| | - Mark D Biggin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail: (MBE); (MDB)
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