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Tan KT, Slevin MK, Leibowitz ML, Garrity-Janger M, Shan J, Li H, Meyerson M. Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. CELL GENOMICS 2024; 4:100588. [PMID: 38917803 PMCID: PMC11293586 DOI: 10.1016/j.xgen.2024.100588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 11/09/2023] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Alterations in the structure and location of telomeres are pivotal in cancer genome evolution. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeats, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. These results provide a framework for the systematic study of telomeric repeats in cancer genomes, which could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
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Affiliation(s)
- Kar-Tong Tan
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - Mitchell L Leibowitz
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Max Garrity-Janger
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jidong Shan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Heng Li
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA.
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Tan KT, Slevin MK, Leibowitz ML, Garrity-Janger M, Li H, Meyerson M. Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569101. [PMID: 38077026 PMCID: PMC10705422 DOI: 10.1101/2023.11.30.569101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Alterations in the structure and location of telomeres are key events in cancer genome evolution. However, previous genomic approaches, unable to span long telomeric repeat arrays, could not characterize the nature of these alterations. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeat arrays, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. Analysis of lung adenocarcinoma genome sequences identified somatic neotelomere and telomere-spanning fusion alterations. These results provide a framework for systematic study of telomeric repeat arrays in cancer genomes, that could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
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Affiliation(s)
- Kar-Tong Tan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Michael K. Slevin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mitchell L. Leibowitz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Max Garrity-Janger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Lead contact
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Geller JI, Hong AL, Vallance KL, Evageliou N, Aldrink JH, Cost NG, Treece AL, Renfro LA, Mullen EA. Children's Oncology Group's 2023 blueprint for research: Renal tumors. Pediatr Blood Cancer 2023; 70 Suppl 6:e30586. [PMID: 37477907 PMCID: PMC10529605 DOI: 10.1002/pbc.30586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
Every year, approximately 600 infants, children, and adolescents are diagnosed with renal cancer in the United States. In addition to Wilms tumor (WT), which accounts for about 80% of all pediatric renal cancers, clear cell sarcoma of the kidney, renal cell carcinoma, malignant rhabdoid tumor, as well as more rare cancers (other sarcomas, rare carcinomas, lymphoma) and benign tumors can originate within the kidney. WT itself can be divided into favorable histology (FHWT), with a 5-year overall survival (OS) exceeding 90%, and anaplastic histology, with 4-year OS of 73.7%. Outcomes of the other pediatric renal cancers include clear cell sarcoma (5-year OS: 90%), malignant rhabdoid tumor (5-year OS: 10% for stages 3 and 4), and renal cell carcinoma (4-year OS: 84.8%). Recent clinical trials have identified novel biological prognostic markers for FHWT, and a series of Children's Oncology Group (COG) trials have demonstrated improving outcomes with therapy modification, and opportunities for further care refinement.
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Affiliation(s)
- James I Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Andrew L Hong
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kelly L Vallance
- Hematology and Oncology, Cook Children's Medical Center, Fort Worth, Texas, USA
| | - Nick Evageliou
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer H Aldrink
- Division of Pediatric Surgery, Department of Surgery, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Nicholas G Cost
- Department of Surgery, Division of Urology and the Surgical Oncology Program at Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Amy L Treece
- Department of Pathology and Laboratory Medicine, Children's of Alabama, Birmingham, Alabama, USA
| | | | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Blood Disorders and Cancer Center, Boston, Massachusetts, USA
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Severseike BO, Schafernak KT, Willard SD, Goncalves LF, Kothari AK, Eshun FK, Mangum R. Diagnostic challenges of renal medullary carcinoma and the role for cytologic assessment: Case report and literature review. J Clin Lab Anal 2023; 37:e24854. [PMID: 36843202 PMCID: PMC10020844 DOI: 10.1002/jcla.24854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/18/2023] [Accepted: 02/11/2023] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND Renal medullary carcinoma (RMC) is a diagnostically challenging, aggressive primary renal malignancy associated with abysmal survival. Delays in diagnosis contribute to most patients having diffusely metastatic disease at the time of initial presentation. METHODS We present the case of a 13-year-old African American male with sickle cell trait who presented with a renal mass and hematuria. Evaluation included imaging, fluid cultures, and cytologic assessment. RESULTS Patient was diagnosed with RMC based on cytologic assessment of sub-centimeter fluid collections aspirated from the left kidney at the time of cortical biopsy for suspected renal mass. The additional fluid aspiration in conjunction with renal biopsy was an atypical but crucial step in early diagnosis. CONCLUSION Cytomorphologic evaluation of fluid biospecimens is not currently part of the standard work-up for patients with renal masses but, when available, can provide crucial information that reduces time to diagnosis. Prompt symptom recognition and treatment initiation may improve patient outcomes.
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Affiliation(s)
- Benjamin O. Severseike
- Phoenix Children's Hospital Residency Program Alliance (PCHRP)Phoenix Children's HospitalPhoenixArizonaUSA
| | - Kristian T. Schafernak
- Pathology and Laboratory MedicinePhoenix Children's HospitalPhoenixArizonaUSA
- Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
- Creighton University School of MedicinePhoenixArizonaUSA
- Mayo Clinic Alix School of MedicinePhoenixArizonaUSA
| | - Scott D. Willard
- Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
- Creighton University School of MedicinePhoenixArizonaUSA
- Mayo Clinic Alix School of MedicinePhoenixArizonaUSA
- Interventional RadiologyPhoenix Children's HospitalPhoenixArizonaUSA
| | - Luis F. Goncalves
- Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
- Creighton University School of MedicinePhoenixArizonaUSA
- Mayo Clinic Alix School of MedicinePhoenixArizonaUSA
- Radiology DepartmentPhoenix Children's HospitalPhoenixArizonaUSA
| | - Alok K. Kothari
- Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
- Creighton University School of MedicinePhoenixArizonaUSA
- Mayo Clinic Alix School of MedicinePhoenixArizonaUSA
- Center for Cancer and Blood DisordersPhoenix Children's HospitalPhoenixArizonaUSA
| | - Francis K. Eshun
- Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
- Creighton University School of MedicinePhoenixArizonaUSA
- Mayo Clinic Alix School of MedicinePhoenixArizonaUSA
- Center for Cancer and Blood DisordersPhoenix Children's HospitalPhoenixArizonaUSA
| | - Ross Mangum
- Department of Child HealthUniversity of Arizona College of MedicinePhoenixArizonaUSA
- Creighton University School of MedicinePhoenixArizonaUSA
- Mayo Clinic Alix School of MedicinePhoenixArizonaUSA
- Center for Cancer and Blood DisordersPhoenix Children's HospitalPhoenixArizonaUSA
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Su Y, Hong AL. Recent Advances in Renal Medullary Carcinoma. Int J Mol Sci 2022; 23:ijms23137097. [PMID: 35806102 PMCID: PMC9266801 DOI: 10.3390/ijms23137097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 02/05/2023] Open
Abstract
Renal medullary carcinoma (RMC) is a rare renal malignancy that has been associated with sickle hemoglobinopathies. RMC is aggressive, difficult to treat, and occurs primarily in adolescents and young adults of African ancestry. This cancer is driven by the loss of SMARCB1, a tumor suppressor seen in a number of primarily rare childhood cancers (e.g., rhabdoid tumor of the kidney and atypical teratoid rhabdoid tumor). Treatment options remain limited due in part to the limited knowledge of RMC biology. However, significant advances have been made in unraveling the biology of RMC, from genomics to therapeutic targets, over the past 5 years. In this review, we will present these advances and discuss what new questions exist in the field.
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Affiliation(s)
- Yongdong Su
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Andrew L. Hong
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
- Correspondence:
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Shapiro DD, Soeung M, Perelli L, Dondossola E, Surasi DS, Tripathi DN, Bertocchio JP, Carbone F, Starbuck MW, Van Alstine ML, Rao P, Katz MHG, Parker NH, Shah AY, Carugo A, Heffernan TP, Schadler KL, Logothetis C, Walker CL, Wood CG, Karam JA, Draetta GF, Tannir NM, Genovese G, Msaouel P. Association of High-Intensity Exercise with Renal Medullary Carcinoma in Individuals with Sickle Cell Trait: Clinical Observations and Experimental Animal Studies. Cancers (Basel) 2021; 13:cancers13236022. [PMID: 34885132 PMCID: PMC8656882 DOI: 10.3390/cancers13236022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/25/2021] [Accepted: 11/28/2021] [Indexed: 01/25/2023] Open
Abstract
Renal medullary carcinoma (RMC) is a lethal malignancy affecting individuals with sickle hemoglobinopathies. Currently, no modifiable risk factors are known. We aimed to determine whether high-intensity exercise is a risk factor for RMC in individuals with sickle cell trait (SCT). We used multiple approaches to triangulate our conclusion. First, a case-control study was conducted at a single tertiary-care facility. Consecutive patients with RMC were compared to matched controls with similarly advanced genitourinary malignancies in a 1:2 ratio and compared on rates of physical activity and anthropometric measures, including skeletal muscle surface area. Next, we compared the rate of military service among our RMC patients to a similarly aged population of black individuals with SCT in the U.S. Further, we used genetically engineered mouse models of SCT to study the impact of exercise on renal medullary hypoxia. Compared with matched controls, patients with RMC reported higher physical activity and had higher skeletal muscle surface area. A higher proportion of patients with RMC reported military service than expected compared to the similarly-aged population of black individuals with SCT. When exposed to high-intensity exercise, mice with SCT demonstrated significantly higher renal medulla hypoxia compared to wild-type controls. These data suggest high-intensity exercise is the first modifiable risk factor for RMC in individuals with SCT.
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Affiliation(s)
- Daniel D. Shapiro
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.D.S.); (C.G.W.); (J.A.K.)
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.S.); (G.F.D.)
| | - Luigi Perelli
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
| | - Eleonora Dondossola
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Devaki Shilpa Surasi
- Department of Nuclear Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Durga N. Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA; (D.N.T.); (C.L.W.)
| | - Jean-Philippe Bertocchio
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA; (D.N.T.); (C.L.W.)
| | - Federica Carbone
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
| | - Michael W. Starbuck
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
| | | | - Priya Rao
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Matthew H. G. Katz
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Nathan H. Parker
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Amishi Y. Shah
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
| | - Alessandro Carugo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.C.); (T.P.H.)
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy P. Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.C.); (T.P.H.)
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Keri L. Schadler
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cheryl L. Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA; (D.N.T.); (C.L.W.)
| | - Christopher G. Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.D.S.); (C.G.W.); (J.A.K.)
| | - Jose A. Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.D.S.); (C.G.W.); (J.A.K.)
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giulio F. Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.S.); (G.F.D.)
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nizar M. Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (M.S.); (G.F.D.)
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (G.G.); (P.M.)
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.P.); (E.D.); (J.-P.B.); (F.C.); (M.W.S.); (A.Y.S.); (C.L.); (N.M.T.)
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA; (D.N.T.); (C.L.W.)
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (G.G.); (P.M.)
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