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Mofunanya A, Cameron ER, Braun CJ, Celeste F, Zhao X, Hemann MT, Scott KL, Li J, Powers S. Simultaneous screening of overexpressed genes in breast cancer for oncogenic drivers and tumor dependencies. Sci Rep 2024; 14:13227. [PMID: 38851782 PMCID: PMC11162420 DOI: 10.1038/s41598-024-64297-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024] Open
Abstract
There are hundreds of genes typically overexpressed in breast cancer cells and it's often assumed that their overexpression contributes to cancer progression. However, the precise proportion of these overexpressed genes contributing to tumorigenicity remains unclear. To address this gap, we undertook a comprehensive screening of a diverse set of seventy-two genes overexpressed in breast cancer. This systematic screening evaluated their potential for inducing malignant transformation and, concurrently, assessed their impact on breast cancer cell proliferation and viability. Select genes including ALDH3B1, CEACAM5, IL8, PYGO2, and WWTR1, exhibited pronounced activity in promoting tumor formation and establishing gene dependencies critical for tumorigenicity. Subsequent investigations revealed that CEACAM5 overexpression triggered the activation of signaling pathways involving β-catenin, Cdk4, and mTOR. Additionally, it conferred a growth advantage independent of exogenous insulin in defined medium and facilitated spheroid expansion by inducing multiple layers of epithelial cells while preserving a hollow lumen. Furthermore, the silencing of CEACAM5 expression synergized with tamoxifen-induced growth inhibition in breast cancer cells. These findings underscore the potential of screening overexpressed genes for both oncogenic drivers and tumor dependencies to expand the repertoire of therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Adaobi Mofunanya
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
| | - Eleanor R Cameron
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christian J Braun
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Frank Celeste
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Xiaoyu Zhao
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jinyu Li
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA
| | - Scott Powers
- Department of Pathology, Stony Brook Cancer Center, Stony Brook, NY, 11794, USA.
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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2
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Jangam SV, Briere LC, Jay KL, Andrews JC, Walker MA, Rodan LH, High FA, Yamamoto S, Sweetser DA, Wangler MF. A de novo missense variant in EZH1 associated with developmental delay exhibits functional deficits in Drosophila melanogaster. Genetics 2023; 224:iyad110. [PMID: 37314226 PMCID: PMC10411565 DOI: 10.1093/genetics/iyad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/13/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
EZH1, a polycomb repressive complex-2 component, is involved in a myriad of cellular processes. EZH1 represses transcription of downstream target genes through histone 3 lysine27 (H3K27) trimethylation (H3K27me3). Genetic variants in histone modifiers have been associated with developmental disorders, while EZH1 has not yet been linked to any human disease. However, the paralog EZH2 is associated with Weaver syndrome. Here we report a previously undiagnosed individual with a novel neurodevelopmental phenotype identified to have a de novo missense variant in EZH1 through exome sequencing. The individual presented in infancy with neurodevelopmental delay and hypotonia and was later noted to have proximal muscle weakness. The variant, p.A678G, is in the SET domain, known for its methyltransferase activity, and an analogous somatic or germline mutation in EZH2 has been reported in patients with B-cell lymphoma or Weaver syndrome, respectively. Human EZH1/2 are homologous to fly Enhancer of zeste (E(z)), an essential gene in Drosophila, and the affected residue (p.A678 in humans, p.A691 in flies) is conserved. To further study this variant, we obtained null alleles and generated transgenic flies expressing wildtype [E(z)WT] and the variant [E(z)A691G]. When expressed ubiquitously the variant rescues null-lethality similar to the wildtype. Overexpression of E(z)WT induces homeotic patterning defects but notably the E(z)A691G variant leads to dramatically stronger morphological phenotypes. We also note a dramatic loss of H3K27me2 and a corresponding increase in H3K27me3 in flies expressing E(z)A691G, suggesting this acts as a gain-of-function allele. In conclusion, here we present a novel EZH1 de novo variant associated with a neurodevelopmental disorder. Furthermore, we found that this variant has a functional impact in Drosophila.
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Affiliation(s)
- Sharayu V Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kristy L Jay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Jonathan C Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lance H Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Frances A High
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | | | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
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3
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Zeng Z, Gao J, Chen T, Zhang Z, Li M, Fan Q, Liu G, Li X, Li Z, Zhong C, Yao F, Sun L, Deng Y, Li M. Nicotinamide adenine dinucleotide kinase promotes lymph node metastasis of NSCLC via activating ID1 expression through BMP pathway. Int J Biol Sci 2023; 19:3184-3199. [PMID: 37416767 PMCID: PMC10321276 DOI: 10.7150/ijbs.84322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/11/2023] [Indexed: 07/08/2023] Open
Abstract
Metastasis is a significant cause of high mortality in lung cancer. Lymph node (LN) metastasis is the most common metastatic pathway in non-small cell lung cancer and the most crucial factor affecting the prognosis of NSCLC. Nevertheless, the molecular mechanism underlying metastasis is unknown. We demonstrated that higher NADK expression suggests worsened survival prognosis, and NADK expression positively correlates with the lymph node metastasis rate and TNM and AJCC stages in NSCLC patients. Moreover, patients with LN metastasis show higher NADK expression than those without LN metastasis. NADK can promote NSCLC progression by enhancing the migration, invasion, lymph node metastasis and growth of NSCLC cells. Mechanistically, NADK inhibits the ubiquitination and degradation of BMPR1A by interacting with Smurf1, further activating the BMPs signalling pathway and promoting ID1 transcription. In conclusion, NADK may be a potential diagnostic indicator and a novel therapeutic target for metastatic NSCLC.
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Affiliation(s)
- Zimei Zeng
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
| | - Jie Gao
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
| | - Tao Chen
- State Key Laboratory of Respiratory Diseases at People's Hospital of Yangjiang, Yangjiang, Guangdong 529500, China
- Yangjiang Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong 529500, China
| | - Ziyu Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Mengwei Li
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
| | - Qi Fan
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, Shanghai, China
| | - Guoqian Liu
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
| | - Xuebing Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhi Li
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
| | - Chenxi Zhong
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, Shanghai, China
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, Shanghai, China
| | - Lunquan Sun
- Department of Oncology, Xiangya Cancer Center, Xiangya Hospital, Central South University, Hunan Province, Changsha 410008, China
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Hunan Province, Changsha 410008, China
- Hunan International Science and Technology Collaboration Base of Precision Medicine for Cancer, Hunan Province, Changsha 410008, China
| | - Yuezhen Deng
- State Key Laboratory of Respiratory Diseases at People's Hospital of Yangjiang, Yangjiang, Guangdong 529500, China
- Yangjiang Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong 529500, China
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, 200030, Shanghai, China
| | - Min Li
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
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4
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Choi DJ, Armstrong G, Lozzi B, Vijayaraghavan P, Plon SE, Wong TC, Boerwinkle E, Muzny DM, Chen HC, Gibbs RA, Ostrom QT, Melin B, Deneen B, Bondy ML, Bainbridge MN. The genomic landscape of familial glioma. SCIENCE ADVANCES 2023; 9:eade2675. [PMID: 37115922 PMCID: PMC10146888 DOI: 10.1126/sciadv.ade2675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Glioma is a rare brain tumor with a poor prognosis. Familial glioma is a subset of glioma with a strong genetic predisposition that accounts for approximately 5% of glioma cases. We performed whole-genome sequencing on an exploratory cohort of 203 individuals from 189 families with a history of familial glioma and an additional validation cohort of 122 individuals from 115 families. We found significant enrichment of rare deleterious variants of seven genes in both cohorts, and the most significantly enriched gene was HERC2 (P = 0.0006). Furthermore, we identified rare noncoding variants in both cohorts that were predicted to affect transcription factor binding sites or cause cryptic splicing. Last, we selected a subset of discovered genes for validation by CRISPR knockdown screening and found that DMBT1, HP1BP3, and ZCH7B3 have profound impacts on proliferation. This study performs comprehensive surveillance of the genomic landscape of familial glioma.
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Affiliation(s)
- Dong-Joo Choi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Georgina Armstrong
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | | | - Sharon E. Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Terence C. Wong
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric Boerwinkle
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Chi Chen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Quinn T. Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Melissa L. Bondy
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - The Gliogene Consortium
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Genomics England Research Consortium
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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5
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Yu K, Kong K, Lozzi B, Luna-Figueroa E, Cervantes A, Curry R, Mohila CA, Rao G, Jalali A, Mills GB, Scott KL, Deneen B. In vivo functional characterization of EGFR variants identifies novel drivers of glioblastoma. Neuro Oncol 2023; 25:471-481. [PMID: 36044040 PMCID: PMC10013639 DOI: 10.1093/neuonc/noac215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common and aggressive primary brain tumor. Large-scale sequencing initiatives have cataloged its mutational landscape in hopes of elucidating mechanisms driving this deadly disease. However, a major bottleneck in harnessing this data for new therapies is deciphering "driver" and "passenger" events amongst the vast volume of information. METHODS We utilized an autochthonous, in vivo screening approach to identify driver, EGFR variants. RNA-Seq identified unique molecular signatures of mouse gliomas across these variants, which only differ by a single amino acid change. In particular, we identified alterations to lipid metabolism, which we further validated through an unbiased lipidomics screen. RESULTS Our screen identified A289I as the most potent EGFR variant, which has previously not been characterized. One of the mechanisms through which A289I promotes gliomagenesis is to alter cellular triacylglycerides through MTTP. Knockout of Mttp in mouse gliomas, reduces gliomagenesis in multiple models. CONCLUSIONS EGFR variants that differ by a single amino acid residue differentially promote gliomagenesis. Among the identified mechanism that drives glioma growth include lipid metabolism through MTTP. Understanding triacylglyceride accumulation may present a prospective therapeutic pathway for this deadly disease.
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Affiliation(s)
- Kwanha Yu
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kathleen Kong
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brittney Lozzi
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Estefania Luna-Figueroa
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alexis Cervantes
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rachel Curry
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- The Integrative Molecular and Biomedical Sciences Graduate Program (IMBS), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carrie A Mohila
- Department of Pathology, Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Ganesh Rao
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health Science University, Portland, OR 97239, USA
| | - Kenneth L Scott
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benjamin Deneen
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
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6
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Curry RN, Aiba I, Meyer J, Lozzi B, Ko Y, McDonald MF, Rosenbaum A, Cervantes A, Huang-Hobbs E, Cocito C, Greenfield JP, Jalali A, Gavvala J, Mohila C, Serin Harmanci A, Noebels J, Rao G, Deneen B. Glioma epileptiform activity and progression are driven by IGSF3-mediated potassium dysregulation. Neuron 2023; 111:682-695.e9. [PMID: 36787748 PMCID: PMC9991983 DOI: 10.1016/j.neuron.2023.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/11/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023]
Abstract
Seizures are a frequent pathophysiological feature of malignant glioma. Recent studies implicate peritumoral synaptic dysregulation as a driver of brain hyperactivity and tumor progression; however, the molecular mechanisms that govern these phenomena remain elusive. Using scRNA-seq and intraoperative patient ECoG recordings, we show that tumors from seizure patients are enriched for gene signatures regulating synapse formation. Employing a human-to-mouse in vivo functionalization pipeline to screen these genes, we identify IGSF3 as a mediator of glioma progression and dysregulated neural circuitry that manifests as spreading depolarization (SD). Mechanistically, we discover that IGSF3 interacts with Kir4.1 to suppress potassium buffering and found that seizure patients exhibit reduced expression of potassium handlers in proliferating tumor cells. In vivo imaging reveals that dysregulated synaptic activity emanates from the tumor-neuron interface, which we confirm in patients. Our studies reveal that tumor progression and seizures are enabled by ion dyshomeostasis and identify SD as a driver of disease.
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Affiliation(s)
- Rachel Naomi Curry
- The Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isamu Aiba
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jochen Meyer
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yeunjung Ko
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Malcolm Ford McDonald
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Development, Disease, Models, and Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Rosenbaum
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexis Cervantes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emmet Huang-Hobbs
- The Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carolina Cocito
- Department of Pediatric Neurological Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Ali Jalali
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jay Gavvala
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carrie Mohila
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Akdes Serin Harmanci
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey Noebels
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ganesh Rao
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Benjamin Deneen
- The Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Development, Disease, Models, and Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
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7
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Jangam S, Briere LC, Jay K, Andrews JC, Walker MA, Rodan LH, High FA, Yamamoto S, Sweetser DA, Wangler M. A de novo missense variant in EZH1 associated with developmental delay exhibits functional deficits in Drosophila melanogaster. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.31.23285113. [PMID: 36778246 PMCID: PMC9915809 DOI: 10.1101/2023.01.31.23285113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
EZH1 ( Enhancer of Zeste, homolog 1) , a Polycomb Repressive Complex-2 (PRC2) component, is involved in a myriad of cellular processes through modifying histone 3 lysine27 (H3K27) residues. EZH1 represses transcription of downstream target genes through H3K27 trimethylation (H3K27me3). Genetic mutations in histone modifiers have been associated with developmental disorders, while EZH1 has not yet been linked to any human disease. However, the paralog EZH2 is associated with Weaver syndrome. Here we report a previously undiagnosed individual with a novel neurodevelopmental phenotype identified to have a de novo variant in EZH1 , p.Ala678Gly, through exome sequencing. The individual presented in infancy with neurodevelopmental delay and hypotonia and was later noted to have proximal muscle weakness. The variant, p.A678G, is in the SET domain, known for its methyltransferase activity, and was the best candidate variant found in the exome. Human EZH1 / 2 are homologous to fly Enhancer of zeste E(z) , an essential gene in flies, and the residue (A678 in humans, A691 in Drosophila ) is conserved. To further study this variant, we obtained Drosophila null alleles and generated transgenic flies expressing wild-type (E(z) WT ) and the variant (E(z) A691G ) . The E(z) A691G variant led to hyper H3K27me3 while the E(z) WT did not, suggesting this is as a gain-of-function allele. When expressed under the tubulin promotor in vivo the variant rescued null-lethality similar to wild-type but the E(z) A691G flies exhibit bang sensitivity and shortened lifespan. In conclusion, here we present a novel EZH1 de novo variant associated with a neurodevelopmental disorder. Furthermore, we found that this variant has a functional impact in Drosophila . Biochemically this allele leads to increased H3K27me3 suggesting gain-of-function, but when expressed in adult flies the E(z) A691G has some characteristics of partial loss-of-function which may suggest it is a more complex allele in vivo .
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Affiliation(s)
- Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, 77030 USA
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kristy Jay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, 77030 USA
- Genetics and Genomics program, Baylor College of Medicine, Houston, Texas, 77030 USA
| | - Jonathan C Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, 77030 USA
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lance H Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Frances A High
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, 77030 USA
- Genetics and Genomics program, Baylor College of Medicine, Houston, Texas, 77030 USA
| | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, 77030 USA
- Genetics and Genomics program, Baylor College of Medicine, Houston, Texas, 77030 USA
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8
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Oka SI, Titus AS, Zablocki D, Sadoshima J. Molecular properties and regulation of NAD + kinase (NADK). Redox Biol 2022; 59:102561. [PMID: 36512915 PMCID: PMC9763689 DOI: 10.1016/j.redox.2022.102561] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 11/27/2022] [Indexed: 12/11/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) kinase (NADK) phosphorylates NAD+, thereby producing nicotinamide adenine dinucleotide phosphate (NADP). Both NADK genes and the NADP(H)-producing mechanism are evolutionarily conserved among archaea, bacteria, plants and mammals. In mammals, NADK is activated by phosphorylation and protein-protein interaction. Recent studies conducted using genetically altered models validate the essential role of NADK in cellular redox homeostasis and metabolism in multicellular organisms. Here, we describe the evolutionary conservation, molecular properties, and signaling mechanisms and discuss the pathophysiological significance of NADK.
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Affiliation(s)
| | | | | | - Junichi Sadoshima
- Rutgers New Jersey Medical School Department of Cell Biology and Molecular Medicine, Rutgers Biomedical and Health Sciences, Newark, NJ, 07101, USA.
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9
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Liu T, Shi W, Ding Y, Wu Q, Zhang B, Zhang N, Wang M, Du D, Zhang H, Han B, Guo D, Zheng J, Li Q, Luo C. (-)-Epigallocatechin Gallate is a Noncompetitive Inhibitor of NAD Kinase. ACS Med Chem Lett 2022; 13:1699-1706. [PMID: 36385933 PMCID: PMC9661698 DOI: 10.1021/acsmedchemlett.2c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/26/2022] [Indexed: 11/29/2022] Open
Abstract
Nicotinamide adenine dinucleotide kinase (NADK) controls the intracellular NADPH content and provides reducing power for the synthesis of macromolecules and anti-ROS. Moreover, NADK is considered to be a synthetic lethal gene for KRAS mutations. To discover NADK-targeted probes, a high-throughput screening assay was established and optimized with a Z factor of 0.71. The natural product (-)-epigallocatechin gallate (EGCG) was found to be a noncompetitive inhibitor of NADK with K i = 3.28 ± 0.32 μΜ. The direct binding of EGCG to NADK was determined by several biophysical methods, including NMR spectroscopy, surface plasmon resonance (SPR) assay, and hydrogen-deuterium exchange mass spectrometry (HDX-MS). The SPR assay showed a K d of 1.78 ± 1.15 μΜ. The HDX-MS experiment showed that EGCG was bound at the non-substrate-binding sites of NADK. Besides, binding mode prediction and derivative activity analysis revealed a potential structure-activity relationship between EGCG and NADK. Furthermore, EGCG can specifically inhibit the proliferation of KRAS-mutated lung cancer cell lines without affecting KRAS wild-type lung cancer cell lines.
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Affiliation(s)
- Tonghai Liu
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjia Shi
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
| | - Yiluan Ding
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qiqi Wu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
| | - Bei Zhang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Naixia Zhang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingliang Wang
- Zhongshan
Institute for Drug Discovery, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
| | - Daohai Du
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hao Zhang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bo Han
- School
of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and
Utilization, Ministry of Education, Shihezi
University, Shihezi 832003, China
| | - Dean Guo
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Zheng
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Li
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
- Zhongshan
Institute for Drug Discovery, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
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10
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Zhang Y, Xu Y, Lu W, Li J, Yu S, Brown EJ, Stanger BZ, Rabinowitz JD, Yang X. G6PD-mediated increase in de novo NADP + biosynthesis promotes antioxidant defense and tumor metastasis. SCIENCE ADVANCES 2022; 8:eabo0404. [PMID: 35857842 PMCID: PMC9299539 DOI: 10.1126/sciadv.abo0404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/03/2022] [Indexed: 05/11/2023]
Abstract
Metastasizing cancer cells are able to withstand high levels of oxidative stress through mechanisms that are poorly understood. Here, we show that under various oxidative stress conditions, pancreatic cancer cells markedly expand NADPH and NADP+ pools. This expansion is due to up-regulation of glucose-6-phosphate dehydrogenase (G6PD), which stimulates the cytoplasmic nicotinamide adenine dinucleotide kinase (NADK1) to produce NADP+ while converting NADP+ to NADPH. G6PD is activated by the transcription factor TAp73, which is, in turn, regulated by two pathways. Nuclear factor-erythroid 2 p45-related factor-2 suppresses expression of the ubiquitin ligase PIRH2, stabilizing the TAp73 protein. Checkpoint kinases 1/2 and E2F1 induce expression of the TAp73 gene. Levels of G6PD and its upstream activators are elevated in metastatic pancreatic cancer. Knocking down G6PD impedes pancreatic cancer metastasis, whereas forced G6PD expression promotes it. These findings reveal an intracellular network that maintains redox homeostasis through G6PD-mediated increase in de novo NADP+ biosynthesis, which may be co-opted by tumor cells to enable metastasis.
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Affiliation(s)
- Yang Zhang
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Jinyang Li
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sixiang Yu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric J. Brown
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben Z. Stanger
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua D. Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Xiaolu Yang
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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11
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Abstract
Eukaryotic cells have developed complex systems to regulate the production and response to reactive oxygen species (ROS). Different ROS control diverse aspects of cell behaviour from signalling to death, and deregulation of ROS production and ROS limitation pathways are common features of cancer cells. ROS also function to modulate the tumour environment, affecting the various stromal cells that provide metabolic support, a blood supply and immune responses to the tumour. Although it is clear that ROS play important roles during tumorigenesis, it has been difficult to reliably predict the effect of ROS modulating therapies. We now understand that the responses to ROS are highly complex and dependent on multiple factors, including the types, levels, localization and persistence of ROS, as well as the origin, environment and stage of the tumours themselves. This increasing understanding of the complexity of ROS in malignancies will be key to unlocking the potential of ROS-targeting therapies for cancer treatment.
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12
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Marcogliese PC, Deal SL, Andrews J, Harnish JM, Bhavana VH, Graves HK, Jangam S, Luo X, Liu N, Bei D, Chao YH, Hull B, Lee PT, Pan H, Bhadane P, Huang MC, Longley CM, Chao HT, Chung HL, Haelterman NA, Kanca O, Manivannan SN, Rossetti LZ, German RJ, Gerard A, Schwaibold EMC, Fehr S, Guerrini R, Vetro A, England E, Murali CN, Barakat TS, van Dooren MF, Wilke M, van Slegtenhorst M, Lesca G, Sabatier I, Chatron N, Brownstein CA, Madden JA, Agrawal PB, Keren B, Courtin T, Perrin L, Brugger M, Roser T, Leiz S, Mau-Them FT, Delanne J, Sukarova-Angelovska E, Trajkova S, Rosenhahn E, Strehlow V, Platzer K, Keller R, Pavinato L, Brusco A, Rosenfeld JA, Marom R, Wangler MF, Yamamoto S. Drosophila functional screening of de novo variants in autism uncovers damaging variants and facilitates discovery of rare neurodevelopmental diseases. Cell Rep 2022; 38:110517. [PMID: 35294868 PMCID: PMC8983390 DOI: 10.1016/j.celrep.2022.110517] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/23/2021] [Accepted: 02/18/2022] [Indexed: 12/30/2022] Open
Abstract
Individuals with autism spectrum disorder (ASD) exhibit an increased burden of de novo mutations (DNMs) in a broadening range of genes. While these studies have implicated hundreds of genes in ASD pathogenesis, which DNMs cause functional consequences in vivo remains unclear. We functionally test the effects of ASD missense DNMs using Drosophila through "humanization" rescue and overexpression-based strategies. We examine 79 ASD variants in 74 genes identified in the Simons Simplex Collection and find 38% of them to cause functional alterations. Moreover, we identify GLRA2 as the cause of a spectrum of neurodevelopmental phenotypes beyond ASD in 13 previously undiagnosed subjects. Functional characterization of variants in ASD candidate genes points to conserved neurobiological mechanisms and facilitates gene discovery for rare neurodevelopmental diseases.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Samantha L Deal
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Jonathan Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - V Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Hematology/Oncology, BCM, Houston, TX 77030, USA
| | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Yu-Hsin Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Brooke Hull
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pradnya Bhadane
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Colleen M Longley
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Nele A Haelterman
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sathiya N Manivannan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Linda Z Rossetti
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | | | - Sarah Fehr
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Annalisa Vetro
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Eleina England
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Isabelle Sabatier
- Department of Pediatric Neurology, Lyon University Hospitals, Lyon, France
| | - Nicolas Chatron
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Thomas Courtin
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Laurence Perrin
- Genetic Department, Robert Debré Hospital, APHP.Nord-Université de Paris, Paris 75019, France
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Timo Roser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Lindwurmstraße 4, 80337 Munich, Germany
| | - Steffen Leiz
- Department of Pediatrics and Adolescent Medicine, Hospital Dritter Orden, Munich, Germany
| | - Frederic Tran Mau-Them
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France; Laboratoire de Génétique, Innovation en Diagnostic Génomique des Maladies Rares UF6254, Plateau Technique de Biologie, CHU Dijon, 14 Rue Paul Gaffarel, BP 77908, 21079 Dijon, France
| | - Julian Delanne
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, Republic of Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Erik Rosenhahn
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Roberto Keller
- Adult Autism Center, Mental Health Department, Health Unit ASL Città di Torino, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy; Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, Turin, Italy
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
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13
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Saliakoura M, Sebastiano MR, Nikdima I, Pozzato C, Konstantinidou G. Restriction of extracellular lipids renders pancreatic cancer dependent on autophagy. J Exp Clin Cancer Res 2022; 41:16. [PMID: 34998392 PMCID: PMC8742413 DOI: 10.1186/s13046-021-02231-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/21/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND KRAS is the predominant oncogene mutated in pancreatic ductal adenocarcinoma (PDAC), the fourth cause of cancer-related deaths worldwide. Mutant KRAS-driven tumors are metabolically programmed to support their growth and survival, which can be used to identify metabolic vulnerabilities. In the present study, we aimed to understand the role of extracellularly derived fatty acids in KRAS-driven pancreatic cancer. METHODS To assess the dependence of PDAC cells on extracellular fatty acids we employed delipidated serum or RNAi-mediated suppression of ACSL3 (to inhibit the activation and cellular retention of extracellular fatty acids) followed by cell proliferation assays, qPCR, apoptosis assays, immunoblots and fluorescence microscopy experiments. To assess autophagy in vivo, we employed the KrasG12D/+;p53flox/flox;Pdx1-CreERT2 (KPC) mice crossed with Acsl3 knockout mice, and to assess the efficacy of the combination therapy of ACSL3 and autophagy inhibition we used xenografted human cancer cell-derived tumors in immunocompromised mice. RESULTS Here we show that depletion of extracellularly derived lipids either by serum lipid restriction or suppression of ACSL3, triggers autophagy, a process that protects PDAC cells from the reduction of bioenergetic intermediates. Combined extracellular lipid deprivation and autophagy inhibition exhibits anti-proliferative and pro-apoptotic effects against PDAC cell lines in vitro and promotes suppression of xenografted human pancreatic cancer cell-derived tumors in mice. Therefore, we propose lipid deprivation and autophagy blockade as a potential co-targeting strategy for PDAC treatment. CONCLUSIONS Our work unravels a central role of extracellular lipid supply in ensuring fatty acid provision in cancer cells, unmasking a previously unappreciated metabolic vulnerability of PDAC cells.
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Affiliation(s)
- Maria Saliakoura
- Institute of Pharmacology, University of Bern, 3010, Bern, Switzerland
| | | | - Ioanna Nikdima
- Institute of Pharmacology, University of Bern, 3010, Bern, Switzerland
| | - Chiara Pozzato
- Institute of Pharmacology, University of Bern, 3010, Bern, Switzerland
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14
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Wang G, Han JJ. Connections between metabolism and epigenetic modifications in cancer. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:199-221. [PMID: 37724300 PMCID: PMC10388788 DOI: 10.1515/mr-2021-0015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/19/2021] [Indexed: 09/20/2023]
Abstract
How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.
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Affiliation(s)
- Guangchao Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jingdong J. Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
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15
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Schild T, McReynolds MR, Shea C, Low V, Schaffer BE, Asara JM, Piskounova E, Dephoure N, Rabinowitz JD, Gomes AP, Blenis J. NADK is activated by oncogenic signaling to sustain pancreatic ductal adenocarcinoma. Cell Rep 2021; 35:109238. [PMID: 34133937 DOI: 10.1016/j.celrep.2021.109238] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/02/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
Metabolic adaptations and the signaling events that control them promote the survival of pancreatic ductal adenocarcinoma (PDAC) at the fibrotic tumor site, overcoming stresses associated with nutrient and oxygen deprivation. Recently, rewiring of NADPH production has been shown to play a key role in this process. NADPH is recycled through reduction of NADP+ by several enzymatic systems in cells. However, de novo NADP+ is synthesized only through one known enzymatic reaction, catalyzed by NAD+ kinase (NADK). In this study, we show that oncogenic KRAS promotes protein kinase C (PKC)-mediated NADK phosphorylation, leading to its hyperactivation, thus sustaining both NADP+ and NADPH levels in PDAC cells. Together, our data show that increased NADK activity is an important adaptation driven by oncogenic signaling. Our findings indicate that NADK could serve as a much-needed therapeutic target for PDAC.
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Affiliation(s)
- Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Christie Shea
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY 10021, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bethany E Schaffer
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Elena Piskounova
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA; Department of Dermatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Ana P Gomes
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA.
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16
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Niu L, Dang C, Li L, Guo N, Xu Y, Li X, Xu Q, Cheng L, Zhang L, Liu L. Next-generation sequencing-based identification of EGFR and NOTCH2 complementary mutations in non-small cell lung cancer. Oncol Lett 2021; 22:594. [PMID: 34149905 PMCID: PMC8200943 DOI: 10.3892/ol.2021.12855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022] Open
Abstract
Although targeted therapy has emerged as an effective treatment strategy for non-small cell lung cancer (NSCLC), some patients cannot benefit from such therapy due to the limited number of therapeutic targets. The present study aimed to identify mutated genes associated with clinicopathological characteristics and prognosis and to screen for mutations that are not concurrent with applicable drug target sites in patients with NSCLC. Tumor tissue and blood samples were obtained from 97 patients with NSCLC. A lung cancer-specific panel of 55 genes was established and analyzed using next-generation sequencing (NGS). The results obtained from the clinical cohort were compared with the NSCLC dataset from The Cancer Genome Atlas (TCGA). Subsequently, 25 driver genes were identified by taking the intersection of the 55 lung-cancer-specific genes with three databases, namely, the Catalog of Somatic Mutations in Cancer database, the Network of Cancer Genes database and Vogelstein's list. Functional annotation and protein-protein interaction analysis were conducted on these 25 driver genes. The χ2 test and logistic regression were used to evaluate the association between mutations in the 25 driver genes and the clinicopathological characteristics of 97 patients, and phosphatase and tensin homolog (PTEN) and kirsten rat sarcoma viral oncogene homolog (KRAS) were associated with stage at diagnosis and sex, respectively, while epidermal growth factor receptor (EGFR) was associated with sex, stage at diagnosis, metastasis, CEA and CYFRA21-1. Moreover, the association between the 25 driver gene mutations and overall survival were examined using Cox regression analysis. Age and Notch homolog 2 (NOTCH2) mutations were independent prognostic factors in TCGA dataset. The correlations between statistically significant mutations in EGFR, KRAS, PTEN and NOTCH2 were further examined, both in the clinical data and TCGA dataset. There was a negative correlation between EGFR and NOTCH2 mutations (correlation coefficient, −0.078; P=0.027). Thus, the present study highlights the importance of NOTCH2 mutations and might provide novel therapeutic options for patients with NSCLC who do not harbor EGFR mutations.
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Affiliation(s)
- Lin Niu
- Department of Human Anatomy, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Chunyan Dang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Lin Li
- Department of Human Anatomy, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Na Guo
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Ying Xu
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Xiangling Li
- Department of Pathology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Qian Xu
- Basic Medical Institute, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Luyang Cheng
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Li Zhang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Lei Liu
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
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17
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Precision oncology for breast cancer through clinical trials. Clin Exp Metastasis 2021; 39:71-78. [PMID: 33950412 DOI: 10.1007/s10585-021-10092-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Precision treatment for breast cancers has made several notable advances in recent decades, but challenges of tumor heterogeneity, drug resistance, and aggressive recurrence and metastases remain. To meet and overcome these challenges, we must refine our understanding of breast subtypes and treatment biomarkers according to the knowledge afforded across the spectrum of 'omics assays. A critical aspect of harnessing this knowledge into actionable biomarkers for treatment decision relies on our ability to integrate knowledge across data types and leverage our insight in evidence-based clinical trials. We review recent advances in cutting-edge clinical trials for precision treatment of breast cancer, including chemotherapies, targeted therapies, immunotherapies, and combination therapies. We comment on promising future areas of development for this exciting point in precision breast cancer research.
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18
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Rather GM, Pramono AA, Szekely Z, Bertino JR, Tedeschi PM. In cancer, all roads lead to NADPH. Pharmacol Ther 2021; 226:107864. [PMID: 33894275 DOI: 10.1016/j.pharmthera.2021.107864] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
Cancer cells require increased levels of NADPH for increased nucleotide synthesis and for protection from ROS. Recent studies show that increased NADPH is generated in several ways. Activated AKT phosphorylates NAD kinase (NADK), increasing its activity. NADP formed, is rapidly converted to NADPH by glucose 6-phosphate dehydrogenase and malic enzymes, overexpressed in tumor cells with mutant p53. Calmodulin, overexpressed in some cancers, also increases NADK activity. Also, in IDH1/2 mutant cancer, NADPH serves as the cofactor to generate D-2 hydroxyglutarate, an oncometabolite. The requirement of cancer cells for elevated levels of NADPH provides an opportunity to target its synthesis for cancer treatment.
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Affiliation(s)
- Gulam Mohmad Rather
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Alvinsyah Adhityo Pramono
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Research Center of Medical Genetics, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Zoltan Szekely
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Joseph R Bertino
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA; Department of Medicine and Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
| | - Philip Michael Tedeschi
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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19
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Yachida N, Yoshihara K, Suda K, Nakaoka H, Ueda H, Sugino K, Yamaguchi M, Mori Y, Yamawaki K, Tamura R, Ishiguro T, Kase H, Motoyama T, Enomoto T. Biological significance of KRAS mutant allele expression in ovarian endometriosis. Cancer Sci 2021; 112:2020-2032. [PMID: 33675098 PMCID: PMC8088964 DOI: 10.1111/cas.14871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/17/2022] Open
Abstract
KRAS is the most frequently mutated in ovarian endometriosis. However, it is unclear whether the KRAS mutant allele's mRNA is expressed and plays a biological role in ovarian endometriosis. Here, we performed mutation-specific RNA in situ hybridization to evaluate mutant allele expression of KRAS p.G12V, the most frequently detected mutation in ovarian endometriosis in our previous study, in formalin-fixed paraffin-embedded tissue (FFPE) samples of ovarian endometriosis, cancer cell lines, and ovarian cancers. First, we verified that mutant or wild-type allele of KRAS were expressed in all 5 cancer cell lines and 9 ovarian cancer cases corresponding to the mutation status. Next, we applied this assay to 26 ovarian endometriosis cases, and observed mutant allele expression of KRAS p.G12V in 10 cases. Mutant or wild-type allele of KRAS were expressed in line with mutation status in 12 available endometriosis cases for which KRAS gene sequence was determined. Comparison of clinical features between ovarian endometriosis with KRAS p.G12V mutant allele expression and with KRAS wild-type showed that KRAS p.G12V mutant allele expression was significantly associated with inflammation in ovarian endometriosis. Finally, we assessed the spatial distribution of KRAS mutant allele expression in 5 endometriosis cases by performing multiregional sampling. Intratumor heterogeneity of KRAS mutant allele expression was observed in two endometriosis cases, whereas the spatial distribution of KRAS p.G12V mutation signals were diffuse and homogenous in ovarian cancer. In conclusion, evaluation of oncogene mutant expression will be useful for clarifying the biological significance of oncogene mutations in benign tumors.
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Affiliation(s)
- Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kentaro Sugino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroaki Kase
- Department of Obstetrics and Gynecology, Nagaoka Chuo General Hospital, Nagaoka, Japan
| | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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20
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Rabani R, Cossette C, Graham F, Powell WS. Protein kinase C activates NAD kinase in human neutrophils. Free Radic Biol Med 2020; 161:50-59. [PMID: 33011272 DOI: 10.1016/j.freeradbiomed.2020.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/14/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022]
Abstract
NAD kinase (NADK) is required for the de novo synthesis of NADP+ from NAD+. In neutrophils, NADK plays an essential role by providing sufficient levels of NADPH to support a robust oxidative burst. Activation of NADPH oxidase-2 (NOX-2) in neutrophils by stimulators of protein kinase C (PKC), such as phorbol myristate acetate (PMA), results in the rapid generation of superoxide at the expense of oxidation of NADPH to NADP+. In this study, we measured the levels of pyridine nucleotides following the addition of PMA to neutrophils. PMA elicited a rapid increase in NADP+ in neutrophils, which was not due to oxidation of NADPH, the levels of which also rose. This was mirrored by a rapid reduction in NAD+ levels, suggesting that NADK had been activated. PMA-induced depletion of NAD+ in neutrophils was blocked by PKC inhibitors, but was not dependent on NOX-2, as it was not blocked by the NOX inhibitor, diphenyleneiodonium. PMA also increased NADK activity in neutrophil lysates as well as NADK phosphorylation, as revealed by a monoclonal antibody selective for phospho-NADK. Human recombinant NADK was phosphorylated by PKCδ, resulting in increased immunoreactivity, but unchanged enzyme activity, suggesting that PKC-induced phosphorylation alone is insufficient to increase NADK activity in neutrophils. This leads us to speculate that phosphorylation of NADK promotes the dissociation of an inhibitory molecule from a complex, thereby increasing enzyme activity. Activation of NADK by PKC in phagocytic cells could be critical for the rapid provision of sufficient levels of superoxide for host defence against invading microorganisms.
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Affiliation(s)
- Razieh Rabani
- Meakins-Christie Laboratories, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
| | - Chantal Cossette
- Meakins-Christie Laboratories, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
| | - François Graham
- Meakins-Christie Laboratories, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada
| | - William S Powell
- Meakins-Christie Laboratories, Centre for Translational Biology, Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC H4A 3J1, Canada.
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21
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NADPH homeostasis in cancer: functions, mechanisms and therapeutic implications. Signal Transduct Target Ther 2020; 5:231. [PMID: 33028807 PMCID: PMC7542157 DOI: 10.1038/s41392-020-00326-0] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/09/2020] [Accepted: 09/14/2020] [Indexed: 02/08/2023] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms, and provides the reducing power for anabolic reactions and redox balance. NADPH homeostasis is regulated by varied signaling pathways and several metabolic enzymes that undergo adaptive alteration in cancer cells. The metabolic reprogramming of NADPH renders cancer cells both highly dependent on this metabolic network for antioxidant capacity and more susceptible to oxidative stress. Modulating the unique NADPH homeostasis of cancer cells might be an effective strategy to eliminate these cells. In this review, we summarize the current existing literatures on NADPH homeostasis, including its biological functions, regulatory mechanisms and the corresponding therapeutic interventions in human cancers, providing insights into therapeutic implications of targeting NADPH metabolism and the associated mechanism for cancer therapy.
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22
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Weber J, Braun CJ, Saur D, Rad R. In vivo functional screening for systems-level integrative cancer genomics. Nat Rev Cancer 2020; 20:573-593. [PMID: 32636489 DOI: 10.1038/s41568-020-0275-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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23
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Rossi Sebastiano M, Pozzato C, Saliakoura M, Yang Z, Peng RW, Galiè M, Oberson K, Simon HU, Karamitopoulou E, Konstantinidou G. ACSL3-PAI-1 signaling axis mediates tumor-stroma cross-talk promoting pancreatic cancer progression. SCIENCE ADVANCES 2020; 6:6/44/eabb9200. [PMID: 33127675 PMCID: PMC7608806 DOI: 10.1126/sciadv.abb9200] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/15/2020] [Indexed: 05/16/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by marked fibrosis and low immunogenicity, features that are linked to treatment resistance and poor clinical outcomes. Therefore, understanding how PDAC regulates the desmoplastic and immune stromal components is of great clinical importance. We found that acyl-CoA synthetase long-chain 3 (ACSL3) is up-regulated in PDAC and correlates with increased fibrosis. Our in vivo results show that Acsl3 knockout hinders PDAC progression, markedly reduces tumor fibrosis and tumor-infiltrating immunosuppressive cells, and increases cytotoxic T cell infiltration. This effect is, at least in part, due to decreased plasminogen activator inhibitor-1 (PAI-1) secretion from tumor cells. Accordingly, PAI-1 expression in PDAC positively correlates with markers of fibrosis and immunosuppression and predicts poor patient survival. We found that PAI-1 pharmacological inhibition strongly enhances chemo- and immunotherapeutic response against PDAC, increasing survival of mice. Thus, our results unveil ACSL3-PAI-1 signaling as a requirement for PDAC progression with druggable attributes.
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Affiliation(s)
| | - Chiara Pozzato
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland
| | - Maria Saliakoura
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland
| | - Zhang Yang
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, 3008 Bern, Switzerland
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, 3008 Bern, Switzerland
| | - Mirco Galiè
- Department of Neuroscience, Biomedicine and Movement, University of Verona, 37134 Verona, Italy
| | - Kevin Oberson
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland
- Department of Clinical Immunology and Allergology, Sechenov University, Moscow, Russia
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24
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Bioinformatics Data Mining Repurposes the JAK2 (Janus Kinase 2) Inhibitor Fedratinib for Treating Pancreatic Ductal Adenocarcinoma by Reversing the KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog)-Driven Gene Signature. J Pers Med 2020; 10:jpm10030130. [PMID: 32947833 PMCID: PMC7563462 DOI: 10.3390/jpm10030130] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is still one of the most aggressive and lethal cancer types due to the late diagnosis, high metastatic potential, and drug resistance. The development of novel therapeutic strategies is urgently needed. KRAS (Kirsten rat sarcoma 2 viral oncogene homolog) is the major driver mutation gene for PDAC tumorigenesis. In this study, we mined cancer genomics data and identified a common KRAS-driven gene signature in PDAC, which is related to cell–cell and cell–extracellular matrix (ECM) interactions. Higher expression of this gene signature was associated with poorer overall survival of PDAC patients. Connectivity Map (CMap) analysis and drug sensitivity profiling predicted that a clinically approved JAK2 (Janus kinase 2)-selective inhibitor, fedratinib (also known as TG-101348), could reverse the KRAS-driven gene signature and exhibit KRAS-dependent anticancer activity in PDAC cells. As an approved treatment for myelofibrosis, the pharmacological and toxicological profiles of fedratinib have been well characterized. It may be repurposed for treating KRAS-driven PDAC in the future.
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Beyond the Genomic Mutation: Rethinking the Molecular Biomarkers of K-RAS Dependency in Pancreatic Cancers. Int J Mol Sci 2020; 21:ijms21145023. [PMID: 32708716 PMCID: PMC7404119 DOI: 10.3390/ijms21145023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
Oncogenic v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-RAS) plays a key role in the development and maintenance of pancreatic ductal adenocarcinoma (PDAC). The targeting of K-RAS would be beneficial to treat tumors whose growth depends on active K-RAS. The analysis of K-RAS genomic mutations is a clinical routine; however, an emerging question is whether the mutational status is able to identify tumors effectively dependent on K-RAS for tailoring targeted therapies. With the emergence of novel K-RAS inhibitors in clinical settings, this question is relevant. Several studies support the notion that the K-RAS mutation is not a sufficient biomarker deciphering the effective dependency of the tumor. Transcriptomic and metabolomic profiles of tumors, while revealing K-RAS signaling complexity and K-RAS-driven molecular pathways crucial for PDAC growth, are opening the opportunity to specifically identify K-RAS-dependent- or K-RAS-independent tumor subtypes by using novel molecular biomarkers. This would help tumor selection aimed at tailoring therapies against K-RAS. In this review, we will present studies about how the K-RAS mutation can also be interpreted in a state of K-RAS dependency, for which it is possible to identify specific K-RAS-driven molecular biomarkers in certain PDAC subtypes, beyond the genomic K-RAS mutational status.
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26
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Negrao MV, Raymond VM, Lanman RB, Robichaux JP, He J, Nilsson MB, Ng PKS, Amador BE, Roarty EB, Nagy RJ, Banks KC, Zhu VW, Ng C, Chae YK, Clarke JM, Crawford JA, Meric-Bernstam F, Ignatius Ou SH, Gandara DR, Heymach JV, Bivona TG, McCoach CE. Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations. J Thorac Oncol 2020; 15:1611-1623. [PMID: 32540409 DOI: 10.1016/j.jtho.2020.05.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/22/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Approximately 4% of NSCLC harbor BRAF mutations, and approximately 50% of these are non-V600 mutations. Treatment of tumors harboring non-V600 mutations is challenging because of functional heterogeneity and lack of knowledge regarding their clinical significance and response to targeted agents. METHODS We conducted an integrative analysis of BRAF non-V600 mutations using genomic profiles of BRAF-mutant NSCLC from the Guardant360 database. BRAF mutations were categorized by clonality and class (1 and 2: RAS-independent; 3: RAS-dependent). Cell viability assays were performed in Ba/F3 models. Drug screens were performed in NSCLC cell lines. RESULTS A total of 305 unique BRAF mutations were identified. Missense mutations were most common (276, 90%), and 45% were variants of unknown significance. F468S and N581Y were identified as novel activating mutations. Class 1 to 3 mutations had higher clonality than mutations of unknown class (p < 0.01). Three patients were treated with MEK with or without BRAF inhibitors. Patients harboring G469V and D594G mutations did not respond, whereas a patient with the L597R mutation had a durable response. Trametinib with or without dabrafenib, LXH254, and lifirafenib had more potent inhibition of BRAF non-V600-mutant NSCLC cell lines than other MEK, BRAF, and ERK inhibitors, comparable with the inhibition of BRAF V600E cell line. CONCLUSIONS In BRAF-mutant NSCLC, clonality is higher in known functional mutations and may allow identification of variants of unknown significance that are more likely to be oncogenic drivers. Our data indicate that certain non-V600 mutations are responsive to MEK and BRAF inhibitors. This integration of genomic profiling and drug sensitivity may guide the treatment for BRAF-mutant NSCLC.
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Affiliation(s)
- Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junqin He
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick K S Ng
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bianca E Amador
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily B Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Viola W Zhu
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine, Orange, California
| | - Chun Ng
- Kaiser Permanente, Stockton, California
| | - Young Kwang Chae
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology-Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine, Orange, California
| | - David R Gandara
- Division of Hematology-Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trever G Bivona
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, California
| | - Caroline E McCoach
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, California.
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27
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Mitra A, Andrews MC, Roh W, De Macedo MP, Hudgens CW, Carapeto F, Singh S, Reuben A, Wang F, Mao X, Song X, Wani K, Tippen S, Ng KS, Schalck A, Sakellariou-Thompson DA, Chen E, Reddy SM, Spencer CN, Wiesnoski D, Little LD, Gumbs C, Cooper ZA, Burton EM, Hwu P, Davies MA, Zhang J, Bernatchez C, Navin N, Sharma P, Allison JP, Wargo JA, Yee C, Tetzlaff MT, Hwu WJ, Lazar AJ, Futreal PA. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma. Nat Commun 2020; 11:1839. [PMID: 32296058 PMCID: PMC7160105 DOI: 10.1038/s41467-020-15538-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Complex tumor microenvironmental (TME) features influence the outcome of cancer immunotherapy (IO). Here we perform immunogenomic analyses on 67 intratumor sub-regions of a PD-1 inhibitor-resistant melanoma tumor and 2 additional metastases arising over 8 years, to characterize TME interactions. We identify spatially distinct evolution of copy number alterations influencing local immune composition. Sub-regions with chromosome 7 gain display a relative lack of leukocyte infiltrate but evidence of neutrophil activation, recapitulated in The Cancer Genome Atlas (TCGA) samples, and associated with lack of response to IO across three clinical cohorts. Whether neutrophil activation represents cause or consequence of local tumor necrosis requires further study. Analyses of T-cell clonotypes reveal the presence of recurrent priming events manifesting in a dominant T-cell clonotype over many years. Our findings highlight the links between marked levels of genomic and immune heterogeneity within the physical space of a tumor, with implications for biomarker evaluation and immunotherapy response.
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Affiliation(s)
- Akash Mitra
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Quantitative Sciences Graduate Training Program, Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Miles C Andrews
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Heidelberg, VIC, Australia
| | - Whijae Roh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Courtney W Hudgens
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fernando Carapeto
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shailbala Singh
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xizeng Mao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xingzhi Song
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Khalida Wani
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samantha Tippen
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Aislyn Schalck
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Eveline Chen
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sangeetha M Reddy
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Diana Wiesnoski
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Latasha D Little
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Elizabeth M Burton
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicholas Navin
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - James P Allison
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Michael T Tetzlaff
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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Tsang YH, Wang Y, Kong K, Grzeskowiak C, Zagorodna O, Dogruluk T, Lu H, Villafane N, Bhavana VH, Moreno D, Elsea SH, Liang H, Mills GB, Scott KL. Differential expression of MAGEA6 toggles autophagy to promote pancreatic cancer progression. eLife 2020; 9:48963. [PMID: 32270762 PMCID: PMC7164953 DOI: 10.7554/elife.48963] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/06/2020] [Indexed: 12/19/2022] Open
Abstract
The melanoma-associated antigen family A (MAGEA) antigens are expressed in a wide variety of malignant tumors but not in adult somatic cells, rendering them attractive targets for cancer immunotherapy. Here we show that a number of cancer-associated MAGEA mutants that undergo proteasome-dependent degradation in vitro could negatively impact their utility as immunotherapeutic targets. Importantly, in pancreatic ductal adenocarcinoma cell models, MAGEA6 suppresses macroautophagy (autophagy). The inhibition of autophagy is released upon MAGEA6 degradation, which can be induced by nutrient deficiency or by acquisition of cancer-associated mutations. Using xenograft mouse models, we demonstrated that inhibition of autophagy is critical for tumor initiation whereas reinstitution of autophagy as a consequence of MAGEA6 degradation contributes to tumor progression. These findings could inform cancer immunotherapeutic strategies for targeting MAGEA antigens and provide mechanistic insight into the divergent roles of MAGEA6 during pancreatic cancer initiation and progression.
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Affiliation(s)
- Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Cell, Develop & Cancer Biology, Oregon Health & Science University, Portland, United States
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Caitlin Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Nicole Villafane
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Michael E DeBakey Department of Surgery, Baylor College of Medicine, Houston, United States
| | | | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, United States.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Gordon B Mills
- Cell, Develop & Cancer Biology, Oregon Health & Science University, Portland, United States.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
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29
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Chen QY, Shen S, Sun H, Wu F, Kluz T, Kibriya MG, Chen Y, Ahsan H, Costa M. PBMC gene expression profiles of female Bangladeshi adults chronically exposed to arsenic-contaminated drinking water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113672. [PMID: 31918125 PMCID: PMC11062206 DOI: 10.1016/j.envpol.2019.113672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/06/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Arsenic, a class I human carcinogen, is ubiquitously found throughout the environment and around the globe, posing a great public health concern. Notably, Bangladesh and regions of West Bengal have been found to have high levels (0.5-4600 μg/L) of arsenic drinking water contamination, and approximately 50 million of the world's 200 million people chronically exposed to arsenic in Bangladesh alone. This study was carried out to examine genome-wide gene expression changes in individuals chronically exposed to arsenic-contaminated drinking water. Our study population includes twenty-nine Bangladeshi female participants with urinary arsenic levels ranging from 22.32 to 1828.12 μg/g creatinine. RNA extracted from peripheral blood mononuclear cells (PBMCs) were evaluated using RNA-Sequencing analysis. Our results indicate that a total of 1,054 genes were significantly associated with increasing urinary arsenic levels (FDR p < 0.05), which include 418 down-regulated and 636 up-regulated genes. Further Ingenuity Pathway Analysis revealed potential target genes (DAPK1, EGR2, APP), microRNAs (miR-155, -338, -210) and pathways (NOTCH signaling pathway) related to arsenic carcinogenesis. The selection of female-only participants provides a homogenous study population since arsenic has significant sex dependent effects, and the wide exposure range provides new insight for key gene expression changes that correlate with increasing urinary arsenic levels.
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Affiliation(s)
- Qiao Yi Chen
- Department of Environmental Medicine, New York University School of Medicine, 10010, New York, NY, USA.
| | - Steven Shen
- Institute of Health Informatics, University of Minnesota, 55455, Minneapolis, MN, USA
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, 10010, New York, NY, USA
| | - Fen Wu
- Department of Population Health and Environmental Medicine, 10016, New York University School of Medicine, New York, NY, USA
| | - Thomas Kluz
- Department of Environmental Medicine, New York University School of Medicine, 10010, New York, NY, USA
| | - Muhammad G Kibriya
- Institute for Population and Precision Health, Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Yu Chen
- Department of Population Health and Environmental Medicine, 10016, New York University School of Medicine, New York, NY, USA
| | - Habibul Ahsan
- Institute for Population and Precision Health, Department of Public Health Sciences, The University of Chicago, Chicago, IL, 60637, USA
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, 10010, New York, NY, USA.
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30
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Chen H, Li J, Wang Y, Ng PKS, Tsang YH, Shaw KR, Mills GB, Liang H. Comprehensive assessment of computational algorithms in predicting cancer driver mutations. Genome Biol 2020; 21:43. [PMID: 32079540 PMCID: PMC7033911 DOI: 10.1186/s13059-020-01954-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/07/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the decade, many computational algorithms have been developed to predict the effects of missense single-nucleotide variants, and they are frequently employed to prioritize mutation candidates. These algorithms employ diverse molecular features to build predictive models, and while some algorithms are cancer-specific, others are not. However, the relative performance of these algorithms has not been rigorously assessed. RESULTS We construct five complementary benchmark datasets: mutation clustering patterns in the protein 3D structures, literature annotation based on OncoKB, TP53 mutations based on their effects on target-gene transactivation, effects of cancer mutations on tumor formation in xenograft experiments, and functional annotation based on in vitro cell viability assays we developed including a new dataset of ~ 200 mutations. We evaluate the performance of 33 algorithms and found that CHASM, CTAT-cancer, DEOGEN2, and PrimateAI show consistently better performance than the other algorithms. Moreover, cancer-specific algorithms show much better performance than those designed for a general purpose. CONCLUSIONS Our study is a comprehensive assessment of the performance of different algorithms in predicting cancer driver mutations and provides deep insights into the best practice of computationally prioritizing cancer mutation candidates for end-users and for the future development of new algorithms.
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Affiliation(s)
- Hu Chen
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yiu Huen Tsang
- Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - Kenna R Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gordon B Mills
- Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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31
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Yu K, Lin CCJ, Hatcher A, Lozzi B, Kong K, Huang-Hobbs E, Cheng YT, Beechar VB, Zhu W, Zhang Y, Chen F, Mills GB, Mohila CA, Creighton CJ, Noebels JL, Scott KL, Deneen B. PIK3CA variants selectively initiate brain hyperactivity during gliomagenesis. Nature 2020; 578:166-171. [PMID: 31996845 PMCID: PMC7577741 DOI: 10.1038/s41586-020-1952-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/12/2019] [Indexed: 12/21/2022]
Abstract
Glioblastoma is a universally lethal form of brain cancer that exhibits an array of pathophysiological phenotypes, many of which are mediated by interactions with the neuronal microenvironment1,2. Recent studies have shown that increases in neuronal activity have an important role in the proliferation and progression of glioblastoma3,4. Whether there is reciprocal crosstalk between glioblastoma and neurons remains poorly defined, as the mechanisms that underlie how these tumours remodel the neuronal milieu towards increased activity are unknown. Here, using a native mouse model of glioblastoma, we develop a high-throughput in vivo screening platform and discover several driver variants of PIK3CA. We show that tumours driven by these variants have divergent molecular properties that manifest in selective initiation of brain hyperexcitability and remodelling of the synaptic constituency. Furthermore, secreted members of the glypican (GPC) family are selectively expressed in these tumours, and GPC3 drives gliomagenesis and hyperexcitability. Together, our studies illustrate the importance of functionally interrogating diverse tumour phenotypes driven by individual, yet related, variants and reveal how glioblastoma alters the neuronal microenvironment.
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Affiliation(s)
- Kwanha Yu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Chia-Ching John Lin
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Asante Hatcher
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Kathleen Kong
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Emmet Huang-Hobbs
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Yi-Ting Cheng
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Vivek B Beechar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Wenyi Zhu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Cancer Center, Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Fengju Chen
- Dan L. Duncan Cancer Center, Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health Science University, Portland, OR, USA
| | - Carrie A Mohila
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey L Noebels
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Kenneth L Scott
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA.
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32
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Hoxhaj G, Manning BD. The PI3K-AKT network at the interface of oncogenic signalling and cancer metabolism. Nat Rev Cancer 2020; 20:74-88. [PMID: 31686003 PMCID: PMC7314312 DOI: 10.1038/s41568-019-0216-7] [Citation(s) in RCA: 1004] [Impact Index Per Article: 251.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 02/06/2023]
Abstract
The altered metabolic programme of cancer cells facilitates their cell-autonomous proliferation and survival. In normal cells, signal transduction pathways control core cellular functions, including metabolism, to couple the signals from exogenous growth factors, cytokines or hormones to adaptive changes in cell physiology. The ubiquitous, growth factor-regulated phosphoinositide 3-kinase (PI3K)-AKT signalling network has diverse downstream effects on cellular metabolism, through either direct regulation of nutrient transporters and metabolic enzymes or the control of transcription factors that regulate the expression of key components of metabolic pathways. Aberrant activation of this signalling network is one of the most frequent events in human cancer and serves to disconnect the control of cell growth, survival and metabolism from exogenous growth stimuli. Here we discuss our current understanding of the molecular events controlling cellular metabolism downstream of PI3K and AKT and of how these events couple two major hallmarks of cancer: growth factor independence through oncogenic signalling and metabolic reprogramming to support cell survival and proliferation.
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Affiliation(s)
- Gerta Hoxhaj
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Brendan D Manning
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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33
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Computer-aided drug repurposing for cancer therapy: Approaches and opportunities to challenge anticancer targets. Semin Cancer Biol 2019; 68:59-74. [PMID: 31562957 DOI: 10.1016/j.semcancer.2019.09.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022]
Abstract
Despite huge efforts made in academic and pharmaceutical worldwide research, current anticancer therapies achieve effective treatment in a limited number of neoplasia cases only. Oncology terms such as big killers - to identify tumours with yet a high mortality rate - or undruggable cancer targets, and chemoresistance, represent the current therapeutic debacle of cancer treatments. In addition, metastases, tumour microenvironments, tumour heterogeneity, metabolic adaptations, and immunotherapy resistance are essential features controlling tumour response to therapies, but still, lack effective therapeutics or modulators. In this scenario, where the pharmaceutical productivity and drug efficacy in oncology seem to have reached a plateau, the so-called drug repurposing - i.e. the use of old drugs, already in clinical use, for a different therapeutic indication - is an appealing strategy to improve cancer therapy. Opportunities for drug repurposing are often based on occasional observations or on time-consuming pre-clinical drug screenings that are often not hypothesis-driven. In contrast, in-silico drug repurposing is an emerging, hypothesis-driven approach that takes advantage of the use of big-data. Indeed, the extensive use of -omics technologies, improved data storage, data meaning, machine learning algorithms, and computational modeling all offer unprecedented knowledge of the biological mechanisms of cancers and drugs' modes of action, providing extensive availability for both disease-related data and drugs-related data. This offers the opportunity to generate, with time and cost-effective approaches, computational drug networks to predict, in-silico, the efficacy of approved drugs against relevant cancer targets, as well as to select better responder patients or disease' biomarkers. Here, we will review selected disease-related data together with computational tools to be exploited for the in-silico repurposing of drugs against validated targets in cancer therapies, focusing on the oncogenic signaling pathways activation in cancer. We will discuss how in-silico drug repurposing has the promise to shortly improve our arsenal of anticancer drugs and, likely, overcome certain limitations of modern cancer therapies against old and new therapeutic targets in oncology.
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Mottini C, Tomihara H, Carrella D, Lamolinara A, Iezzi M, Huang JK, Amoreo CA, Buglioni S, Manni I, Robinson FS, Minelli R, Kang Y, Fleming JB, Kim MP, Bristow CA, Trisciuoglio D, Iuliano A, Del Bufalo D, Di Bernardo D, Melisi D, Draetta GF, Ciliberto G, Carugo A, Cardone L. Predictive Signatures Inform the Effective Repurposing of Decitabine to Treat KRAS-Dependent Pancreatic Ductal Adenocarcinoma. Cancer Res 2019; 79:5612-5625. [PMID: 31492820 DOI: 10.1158/0008-5472.can-19-0187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/24/2019] [Accepted: 08/29/2019] [Indexed: 11/16/2022]
Abstract
Mutated KRAS protein is a pivotal tumor driver in pancreatic cancer. However, despite comprehensive efforts, effective therapeutics that can target oncogenic KRAS are still under investigation or awaiting clinical approval. Using a specific KRAS-dependent gene signature, we implemented a computer-assisted inspection of a drug-gene network to in silico repurpose drugs that work like inhibitors of oncogenic KRAS. We identified and validated decitabine, an FDA-approved drug, as a potent inhibitor of growth in pancreatic cancer cells and patient-derived xenograft models that showed KRAS dependency. Mechanistically, decitabine efficacy was linked to KRAS-driven dependency on nucleotide metabolism and its ability to specifically impair pyrimidine biosynthesis in KRAS-dependent tumors cells. These findings also showed that gene signatures related to KRAS dependency might be prospectively used to inform on decitabine sensitivity in a selected subset of patients with KRAS-mutated pancreatic cancer. Overall, the repurposing of decitabine emerged as an intriguing option for treating pancreatic tumors that are addicted to mutant KRAS, thus offering opportunities for improving the arsenal of therapeutics for this extremely deadly disease. SIGNIFICANCE: Decitabine is a promising drug for cancer cells dependent on RAS signaling.
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Affiliation(s)
- Carla Mottini
- Department of Tumor Immunology and Immunotherapy, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Hideo Tomihara
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Alessia Lamolinara
- Department of Medicine and Aging Science, Center for Advanced Studies and Technology (CAST), G. D'Annunzio University, Chieti-Pescara, Italy
| | - Manuela Iezzi
- Department of Medicine and Aging Science, Center for Advanced Studies and Technology (CAST), G. D'Annunzio University, Chieti-Pescara, Italy
| | - Justin K Huang
- Department of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carla A Amoreo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Simonetta Buglioni
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Isabella Manni
- Animal Facility (SAFU), IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Frederick S Robinson
- Department of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rosalba Minelli
- Department of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ya'an Kang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Michael P Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher A Bristow
- Department of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniela Trisciuoglio
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | | | - Donatella Del Bufalo
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Davide Melisi
- Department of Medicine, University of Verona, Verona, Italy
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Alessandro Carugo
- Department of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Luca Cardone
- Department of Tumor Immunology and Immunotherapy, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
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Zhu Y, Liu J, Park J, Rai P, Zhai RG. Subcellular compartmentalization of NAD + and its role in cancer: A sereNADe of metabolic melodies. Pharmacol Ther 2019; 200:27-41. [PMID: 30974124 PMCID: PMC7010080 DOI: 10.1016/j.pharmthera.2019.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/02/2019] [Indexed: 02/07/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential biomolecule involved in many critical processes. Its role as both a driver of energy production and a signaling molecule underscores its importance in health and disease. NAD+ signaling impacts multiple processes that are dysregulated in cancer, including DNA repair, cell proliferation, differentiation, redox regulation, and oxidative stress. Distribution of NAD+ is highly compartmentalized, with each subcellular NAD+ pool differentially regulated and preferentially involved in distinct NAD+-dependent signaling or metabolic events. Emerging evidence suggests that targeting NAD+ metabolism is likely to repress many specific mechanisms underlying tumor development and progression, including proliferation, survival, metabolic adaptations, invasive capabilities, heterotypic interactions with the tumor microenvironment, and stress response including notably DNA maintenance and repair. Here we provide a comprehensive overview of how compartmentalized NAD+ metabolism in mitochondria, nucleus, cytosol, and extracellular space impacts cancer formation and progression, along with a discussion of the therapeutic potential of NAD+-targeting drugs in cancer.
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Affiliation(s)
- Yi Zhu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong 264005, China; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jiaqi Liu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong 264005, China
| | - Joun Park
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Priyamvada Rai
- Department of Medicine/Medical Oncology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Rong G Zhai
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong 264005, China.
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Purohit V, Simeone DM, Lyssiotis CA. Metabolic Regulation of Redox Balance in Cancer. Cancers (Basel) 2019; 11:cancers11070955. [PMID: 31288436 PMCID: PMC6678865 DOI: 10.3390/cancers11070955] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) are chemically active free radicals produced by partial reduction of oxygen that can activate discrete signaling pathways or disrupt redox homeostasis depending on their concentration. ROS interacts with biomolecules, including DNA, and can cause mutations that can transform normal cells into cancer cells. Furthermore, certain cancer-causing mutations trigger alterations in cellular metabolism that can increase ROS production, resulting in genomic instability, additional DNA mutations, and tumor evolution. To prevent excess ROS-mediated toxicity, cancer-causing mutations concurrently activate pathways that manage this oxidative burden. Hence, an understanding of the metabolic pathways that regulate ROS levels is imperative for devising therapies that target tumor cells. In this review, we summarize the dual role of metabolism as a generator and inhibitor of ROS in cancer and discuss current strategies to target the ROS axis.
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Affiliation(s)
- Vinee Purohit
- Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Diane M Simeone
- Perlmutter Cancer Center, New York University, New York, NY 10016, USA
- Department of Surgery, New York University, New York, NY 10016, USA
- Department of Pathology, New York University, New York, NY 10016, USA
| | - Costas A Lyssiotis
- Departments of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
- Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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Das B, Senapati S. Functional and mechanistic studies reveal MAGEA3 as a pro-survival factor in pancreatic cancer cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:294. [PMID: 31287009 PMCID: PMC6615156 DOI: 10.1186/s13046-019-1272-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/10/2019] [Indexed: 12/17/2022]
Abstract
Background In the era of personalized therapy, functional annotation of less frequent genetic aberrations will be instrumental in adapting effective therapeutic in clinic. Overexpression of Melanoma associated antigen A3 (MAGEA3) is reported in certain pancreatic cancer (PCA) patients. The major objective of the current study was to investigate the functional role of MAGEA3 in pancreatic cancer cells (PCCs) growth and survival. Methods Using overexpression (tet-on regulated system and constitutive expression system) and knockdown (by siRNA and shRNA) approach, we dissected the mechanistic role of MAGEA3 in pancreatic cancer pathogenesis. We generated MAGEA3 expressing stable PCA cell lines and mouse primary pancreatic epithelial cells. MAGEA3 was also depleted in certain MAGEA3 positive PCCs by siRNA or shRNA. The stable cells were subjected to in vitro assays like proliferation and survival assays under growth factor deprivation or in the presence of cytotoxic drugs. The MAGEA3 overexpressing or depleted stable PCCs were evaluated in vivo using xenograft model to check the role of MAGEA3 in tumor progression. We also dissected the mechanism behind the MAGEA3 role in tumor progression using western blot analysis and CCL2 neutralization. Results MAGEA3 overexpression in PCA cells did not alter the cell proliferation but protected the cells during growth factor deprivation and also in the presence of cytotoxic drugs. However, depletion of MAGEA3 in MAGEA3 positive cells resulted in reduced cell proliferation and increased apoptosis upon growth factor deprivation and also in response to cytotoxic drugs. The in vivo xenograft study revealed that overexpression of MAGEA3 promoted tumor growth however depleting the same hindered the tumor progression. Mechanistically, our in vitro and in vivo study revealed that MAGEA3 has tumor-promoting role by reducing macro-autophagy and overexpressing pro-survival molecules like CCL2 and survivin. Conclusion Our data proves tumor-promoting role of MAGEA3 and provides the rationale to target MAGEA3 and/or its functional mediators like CCL2 for PCA, which may have a better impact in PCA therapy. Electronic supplementary material The online version of this article (10.1186/s13046-019-1272-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biswajit Das
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, 751023, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shantibhusan Senapati
- Tumor Microenvironment and Animal Models Lab, Institute of Life Sciences, Bhubaneswar, Odisha, 751023, India.
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38
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Scholl C, Fröhling S. Exploiting rare driver mutations for precision cancer medicine. Curr Opin Genet Dev 2019; 54:1-6. [PMID: 30844512 DOI: 10.1016/j.gde.2019.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/03/2019] [Indexed: 12/23/2022]
Abstract
Catalyzed by the ability to develop precision therapies targeting the unique genetic changes that drive individual tumors, sequencing patients' tumor genomes is an increasingly common practice in oncology. In most cancer types, however, a limited number of common mutations are accompanied by a plethora of low-frequency variants whose functional consequences and clinical actionability are often unknown. We here illustrate that this 'long tail' of infrequent molecular alterations includes oncogenic drivers of biological significance that can be the genetic basis of extraordinary responses to systemic cancer therapies. Furthermore, we review current strategies to identify, prioritize, and experimentally validate novel long-tail driver mutations, efforts that will likely provide new insights into the clinically actionable genome and improve outcomes for patients.
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Affiliation(s)
- Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and DKFZ, 69120 Heidelberg, Germany; DKFZ-Heidelberg Center for Personalized Oncology (HIPO), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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39
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NADP + is an endogenous PARP inhibitor in DNA damage response and tumor suppression. Nat Commun 2019; 10:693. [PMID: 30741937 PMCID: PMC6370829 DOI: 10.1038/s41467-019-08530-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 12/05/2018] [Accepted: 12/30/2018] [Indexed: 11/15/2022] Open
Abstract
ADP-ribosylation is a unique posttranslational modification catalyzed by poly(ADP-ribose) polymerases (PARPs) using NAD+ as ADP-ribose donor. PARPs play an indispensable role in DNA damage repair and small molecule PARP inhibitors have emerged as potent anticancer drugs. However, to date, PARP inhibitor treatment has been restricted to patients with BRCA1/2 mutation-associated breast and ovarian cancer. One of the major challenges to extend the therapeutic potential of PARP inhibitors to other cancer types is the absence of predictive biomarkers. Here, we show that ovarian cancer cells with higher level of NADP+, an NAD+ derivative, are more sensitive to PARP inhibitors. We demonstrate that NADP+ acts as a negative regulator and suppresses ADP-ribosylation both in vitro and in vivo. NADP+ impairs ADP-ribosylation-dependent DNA damage repair and sensitizes tumor cell to chemically synthesized PARP inhibitors. Taken together, our study identifies NADP+ as an endogenous PARP inhibitor that may have implications in cancer treatment. Cancer cells respond differently to inhibitors of Poly (ADP-ribose) polymerase. Here the authors reveal that ovarian cancer cells with higher cellular NADP+ levels are more sensitive to clinically relevant PARP1 inhibitors and show that NADP+ act as an endogenous inhibitor of PARP enzymes.
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40
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Vaziri-Gohar A, Zarei M, Brody JR, Winter JM. Metabolic Dependencies in Pancreatic Cancer. Front Oncol 2018; 8:617. [PMID: 30631752 PMCID: PMC6315177 DOI: 10.3389/fonc.2018.00617] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a highly lethal cancer with a long-term survival rate under 10%. Available cytotoxic chemotherapies have significant side effects, and only marginal therapeutic efficacy. FDA approved drugs currently used against PDA target DNA metabolism and DNA integrity. However, alternative metabolic targets beyond DNA may prove to be much more effective. PDA cells are forced to live within a particularly severe microenvironment characterized by relative hypovascularity, hypoxia, and nutrient deprivation. Thus, PDA cells must possess biochemical flexibility in order to adapt to austere conditions. A better understanding of the metabolic dependencies required by PDA to survive and thrive within a harsh metabolic milieu could reveal specific metabolic vulnerabilities. These molecular requirements can then be targeted therapeutically, and would likely be associated with a clinically significant therapeutic window since the normal tissue is so well-perfused with an abundant nutrient supply. Recent work has uncovered a number of promising therapeutic targets in the metabolic domain, and clinicians are already translating some of these discoveries to the clinic. In this review, we highlight mitochondria metabolism, non-canonical nutrient acquisition pathways (macropinocytosis and use of pancreatic stellate cell-derived alanine), and redox homeostasis as compelling therapeutic opportunities in the metabolic domain.
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Affiliation(s)
- Ali Vaziri-Gohar
- School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Mahsa Zarei
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Jonathan R Brody
- Division of Surgical Research, Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Jordan M Winter
- School of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Department of Surgery and Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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41
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Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng PKS, Jeong KJ, Tsang YH, Moreno D, Bhavana VH, Peng X, Ge Z, Chen H, Li J, Chen Z, Zhang H, Han L, Du D, Creighton CJ, Mills GB, Camargo F, Liang H. Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer. Cell Rep 2018; 25:1304-1317.e5. [PMID: 30380420 PMCID: PMC6326181 DOI: 10.1016/j.celrep.2018.10.001] [Citation(s) in RCA: 277] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 01/15/2023] Open
Abstract
Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform a comprehensive molecular characterization of 19 Hippo core genes in 9,125 tumor samples across 33 cancer types using multidimensional "omic" data from The Cancer Genome Atlas. We identify somatic drivers among Hippo genes and the related microRNA (miRNA) regulators, and using functional genomic approaches, we experimentally characterize YAP and TAZ mutation effects and miR-590 and miR-200a regulation for TAZ. Hippo pathway activity is best characterized by a YAP/TAZ transcriptional target signature of 22 genes, which shows robust prognostic power across cancer types. Our elastic-net integrated modeling further reveals cancer-type-specific pathway regulators and associated cancer drivers. Our results highlight the importance of Hippo signaling in squamous cell cancers, characterized by frequent amplification of YAP/TAZ, high expression heterogeneity, and significant prognostic patterns. This study represents a systems-biology approach to characterizing key cancer signaling pathways in the post-genomic era.
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Affiliation(s)
- Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoyan Xu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathophysiology, College of Basic Medicine Science, China Medical University, Shenyang, Liaoning Province 110122, China
| | - Dejan Maglic
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Michael T Dill
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiu Huen Tsang
- Department of Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniela Moreno
- Department of Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xinxin Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongqi Ge
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hu Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongyuan Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Huiwen Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Di Du
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chad J Creighton
- Duncan Cancer Center-Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fernando Camargo
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Kundu ST, Grzeskowiak CL, Fradette JJ, Gibson LA, Rodriguez LB, Creighton CJ, Scott KL, Gibbons DL. TMEM106B drives lung cancer metastasis by inducing TFEB-dependent lysosome synthesis and secretion of cathepsins. Nat Commun 2018; 9:2731. [PMID: 30013069 PMCID: PMC6048095 DOI: 10.1038/s41467-018-05013-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 05/10/2018] [Indexed: 12/19/2022] Open
Abstract
Metastatic lung cancer is the leading cause of cancer-associated mortality worldwide, therefore necessitating novel approaches to identify specific genetic drivers for lung cancer progression and metastasis. We recently performed an in vivo gain-of-function genetic screen to identify driver genes of lung cancer metastasis. In the study reported here, we identify TMEM106B as a primary robust driver of lung cancer metastasis. Ectopic expression of TMEM106B could significantly promote the synthesis of enlarged vesicular lysosomes that are laden with elevated levels of active cathepsins. In a TFEB-dependent manner, TMEM106B could modulate the expression of lysosomal genes of the coordinated lysosomal expression and regulation (CLEAR) pathway in lung cancer cells and patient samples. We also demonstrate that TMEM106B-induced lysosomes undergo calcium-dependent exocytosis, thereby releasing active lysosomal cathepsins necessary for TMEM106B-mediated cancer cell invasion and metastasis in vivo, which could be therapeutically prevented by pharmacological inhibition of cathepsins. Further, in TCGA LUAD data sets, 19% of patients show elevated expression of TMEM106B, which predicts for poor disease-free and overall-survival.
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Affiliation(s)
- Samrat T Kundu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jared J Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Laura A Gibson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Leticia B Rodriguez
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chad J Creighton
- Department of Medicine and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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43
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Grzeskowiak CL, Kundu ST, Mo X, Ivanov AA, Zagorodna O, Lu H, Chapple RH, Tsang YH, Moreno D, Mosqueda M, Eterovic K, Fradette JJ, Ahmad S, Chen F, Chong Z, Chen K, Creighton CJ, Fu H, Mills GB, Gibbons DL, Scott KL. In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer. Nat Commun 2018; 9:2732. [PMID: 30013058 PMCID: PMC6048166 DOI: 10.1038/s41467-018-04572-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 05/02/2018] [Indexed: 12/26/2022] Open
Abstract
Genetic aberrations driving pro-oncogenic and pro-metastatic activity remain an elusive target in the quest of precision oncology. To identify such drivers, we use an animal model of KRAS-mutant lung adenocarcinoma to perform an in vivo functional screen of 217 genetic aberrations selected from lung cancer genomics datasets. We identify 28 genes whose expression promoted tumor metastasis to the lung in mice. We employ two tools for examining the KRAS-dependence of genes identified from our screen: 1) a human lung cell model containing a regulatable mutant KRAS allele and 2) a lentiviral system permitting co-expression of DNA-barcoded cDNAs with Cre recombinase to activate a mutant KRAS allele in the lungs of mice. Mechanistic evaluation of one gene, GATAD2B, illuminates its role as a dual activity gene, promoting both pro-tumorigenic and pro-metastatic activities in KRAS-mutant lung cancer through interaction with c-MYC and hyperactivation of the c-MYC pathway.
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Affiliation(s)
- Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Samrat T Kundu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiulei Mo
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Andrei A Ivanov
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard H Chapple
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maribel Mosqueda
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Karina Eterovic
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jared J Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sumreen Ahmad
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fengju Chen
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zechen Chong
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haian Fu
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, 77030, USA.
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
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Ng PKS, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB. Systematic Functional Annotation of Somatic Mutations in Cancer. Cancer Cell 2018; 33:450-462.e10. [PMID: 29533785 PMCID: PMC5926201 DOI: 10.1016/j.ccell.2018.01.021] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.
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Affiliation(s)
- Patrick Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shan Shao
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hu Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sohini Sengupta
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Zixing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Richard Tran
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie Soewito
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Collin Tokheim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Daniel Cui Zhou
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Amber M Johnson
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Zeng
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carman Ka Man Ip
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Wester
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shuangxing Yu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher P Vellano
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins Medicine, Baltimore, MD 21287, USA
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63108, USA
| | - Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lydia Wai Ting Cheung
- HKU Shenzhen Institute of Research and Innovation, Shenzhen, China; School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenna R Shaw
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Song Yi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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45
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Yau EH, Kummetha IR, Lichinchi G, Tang R, Zhang Y, Rana TM. Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers. Cancer Res 2017; 77:6330-6339. [PMID: 28954733 DOI: 10.1158/0008-5472.can-17-2043] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022]
Abstract
Targeting mutant KRAS signaling pathways continues to attract attention as a therapeutic strategy for KRAS-driven tumors. In this study, we exploited the power of the CRISPR-Cas9 system to identify genes affecting the tumor xenograft growth of human mutant KRAS (KRASMUT) colorectal cancers. Using pooled lentiviral single-guide RNA libraries, we conducted a genome-wide loss-of-function genetic screen in an isogenic pair of human colorectal cancer cell lines harboring mutant or wild-type KRAS. The screen identified novel and established synthetic enhancers or synthetic lethals for KRASMUT colorectal cancer, including targetable metabolic genes. Notably, genetic disruption or pharmacologic inhibition of the metabolic enzymes NAD kinase or ketohexokinase was growth inhibitory in vivo In addition, the chromatin remodeling protein INO80C was identified as a novel tumor suppressor in KRASMUT colorectal and pancreatic tumor xenografts. Our findings define a novel targetable set of therapeutic targets for KRASMUT tumors. Cancer Res; 77(22); 6330-9. ©2017 AACR.
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Affiliation(s)
- Edwin H Yau
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California.,Division of Hematology-Oncology, Department of Internal Medicine, University of California San Diego School of Medicine, La Jolla, California.,Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Indrasena Reddy Kummetha
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Gianluigi Lichinchi
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Rachel Tang
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Yunlin Zhang
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Tariq M Rana
- Department of Pediatrics and Institute for Genomic Medicine, University of California San Diego School of Medicine, La Jolla, California. .,Solid Tumor Therapeutics Program, Moores Cancer Center, University of California, San Diego, La Jolla, California
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46
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Sun C, Fang Y, Yin J, Chen J, Ju Z, Zhang D, Chen X, Vellano CP, Jeong KJ, Ng PKS, Eterovic AKB, Bhola NH, Lu Y, Westin SN, Grandis JR, Lin SY, Scott KL, Peng G, Brugge J, Mills GB. Rational combination therapy with PARP and MEK inhibitors capitalizes on therapeutic liabilities in RAS mutant cancers. Sci Transl Med 2017; 9:eaal5148. [PMID: 28566428 PMCID: PMC5919217 DOI: 10.1126/scitranslmed.aal5148] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/29/2017] [Indexed: 12/11/2022]
Abstract
Mutant RAS has remained recalcitrant to targeted therapy efforts. We demonstrate that combined treatment with poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors and mitogen-activated protein kinase (MAPK) kinase (MEK) inhibitors evokes unanticipated, synergistic cytotoxic effects in vitro and in vivo in multiple RAS mutant tumor models across tumor lineages where RAS mutations are prevalent. The effects of PARP and MEK inhibitor combinations are independent of BRCA1/2 and p53 mutation status, suggesting that the synergistic activity is likely to be generalizable. Synergistic activity of PARP and MEK inhibitor combinations in RAS mutant tumors is associated with (i) induction of BIM-mediated apoptosis, (ii) decrease in expression of components of the homologous recombination DNA repair pathway, (iii) decrease in homologous recombination DNA damage repair capacity, (iv) decrease in DNA damage checkpoint activity, (v) increase in PARP inhibitor-induced DNA damage, (vi) decrease in vascularity that could increase PARP inhibitor efficacy by inducing hypoxia, and (vii) elevated PARP1 protein, which increases trapping activity of PARP inhibitors. Mechanistically, enforced expression of FOXO3a, which is a target of the RAS/MAPK pathway, was sufficient to recapitulate the functional consequences of MEK inhibitors including synergy with PARP inhibitors. Thus, the ability of mutant RAS to suppress FOXO3a and its reversal by MEK inhibitors accounts, at least in part, for the synergy of PARP and MEK inhibitors in RAS mutant tumors. The rational combination of PARP and MEK inhibitors warrants clinical investigation in patients with RAS mutant tumors where there are few effective therapeutic options.
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Affiliation(s)
- Chaoyang Sun
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yong Fang
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Yin
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Chen
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of General Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang Province, Hangzhou 310000, China
| | - Zhenlin Ju
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dong Zhang
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaohua Chen
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher P Vellano
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kang Jin Jeong
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Kwok-Shing Ng
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Agda Karina B Eterovic
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neil H Bhola
- Provost Office, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yiling Lu
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer R Grandis
- Provost Office, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joan Brugge
- Department of Cell Biology, Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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47
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Lu H, Villafane N, Dogruluk T, Grzeskowiak CL, Kong K, Tsang YH, Zagorodna O, Pantazi A, Yang L, Neill NJ, Kim YW, Creighton CJ, Verhaak RG, Mills GB, Park PJ, Kucherlapati R, Scott KL. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. Cancer Res 2017; 77:3502-3512. [PMID: 28512244 DOI: 10.1158/0008-5472.can-16-2745] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Oncogenic gene fusions drive many human cancers, but tools to more quickly unravel their functional contributions are needed. Here we describe methodology permitting fusion gene construction for functional evaluation. Using this strategy, we engineered the known fusion oncogenes, BCR-ABL1, EML4-ALK, and ETV6-NTRK3, as well as 20 previously uncharacterized fusion genes identified in The Cancer Genome Atlas datasets. In addition to confirming oncogenic activity of the known fusion oncogenes engineered by our construction strategy, we validated five novel fusion genes involving MET, NTRK2, and BRAF kinases that exhibited potent transforming activity and conferred sensitivity to FDA-approved kinase inhibitors. Our fusion construction strategy also enabled domain-function studies of BRAF fusion genes. Our results confirmed other reports that the transforming activity of BRAF fusions results from truncation-mediated loss of inhibitory domains within the N-terminus of the BRAF protein. BRAF mutations residing within this inhibitory region may provide a means for BRAF activation in cancer, therefore we leveraged the modular design of our fusion gene construction methodology to screen N-terminal domain mutations discovered in tumors that are wild-type at the BRAF mutation hotspot, V600. We identified an oncogenic mutation, F247L, whose expression robustly activated the MAPK pathway and sensitized cells to BRAF and MEK inhibitors. When applied broadly, these tools will facilitate rapid fusion gene construction for subsequent functional characterization and translation into personalized treatment strategies. Cancer Res; 77(13); 3502-12. ©2017 AACR.
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Affiliation(s)
- Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Nicole Villafane
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angeliki Pantazi
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lixing Yang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Young Won Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Roel G Verhaak
- The Jackson Laboratory, Genomic Medicine, Farmington, Connecticut
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Raju Kucherlapati
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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48
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Kumar S, Peng X, Daley J, Yang L, Shen J, Nguyen N, Bae G, Niu H, Peng Y, Hsieh HJ, Wang L, Rao C, Stephan CC, Sung P, Ira G, Peng G. Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells. Oncogenesis 2017; 6:e319. [PMID: 28414320 PMCID: PMC5520492 DOI: 10.1038/oncsis.2017.15] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/10/2017] [Indexed: 02/06/2023] Open
Abstract
Replication stress is a characteristic feature of cancer cells, which is resulted from sustained proliferative signaling induced by activation of oncogenes or loss of tumor suppressors. In cancer cells, oncogene-induced replication stress manifests as replication-associated lesions, predominantly double-strand DNA breaks (DSBs). An essential mechanism utilized by cells to repair replication-associated DSBs is homologous recombination (HR). In order to overcome replication stress and survive, cancer cells often require enhanced HR repair capacity. Therefore, the key link between HR repair and cellular tolerance to replication-associated DSBs provides us with a mechanistic rationale for exploiting synthetic lethality between HR repair inhibition and replication stress. DNA2 nuclease is an evolutionarily conserved essential enzyme in replication and HR repair. Here we demonstrate that DNA2 is overexpressed in pancreatic cancers, one of the deadliest and more aggressive forms of human cancers, where mutations in the KRAS are present in 90–95% of cases. In addition, depletion of DNA2 significantly reduces pancreatic cancer cell survival and xenograft tumor growth, suggesting the therapeutic potential of DNA2 inhibition. Finally, we develop a robust high-throughput biochemistry assay to screen for inhibitors of the DNA2 nuclease activity. The top inhibitors were shown to be efficacious against both yeast Dna2 and human DNA2. Treatment of cancer cells with DNA2 inhibitors recapitulates phenotypes observed upon DNA2 depletion, including decreased DNA double strand break end resection and attenuation of HR repair. Similar to genetic ablation of DNA2, chemical inhibition of DNA2 selectively attenuates the growth of various cancer cells with oncogene-induced replication stress. Taken together, our findings open a new avenue to develop a new class of anticancer drugs by targeting druggable nuclease DNA2. We propose DNA2 inhibition as new strategy in cancer therapy by targeting replication stress, a molecular property of cancer cells that is acquired as a result of oncogene activation instead of targeting currently undruggable oncoprotein itself such as KRAS.
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Affiliation(s)
- S Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - X Peng
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, China
| | - J Daley
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - L Yang
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Shen
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - N Nguyen
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - G Bae
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - H Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA.,Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Y Peng
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H-J Hsieh
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Wang
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Rao
- Department of Internal Medicine, University of Oklahoma, Oklahoma City, OK, USA
| | - C C Stephan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - P Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - G Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - G Peng
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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49
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50
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Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K, Chen WW, Lander ES, Sabatini DM. Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras. Cell 2017. [PMID: 28162770 DOI: 10.1016/j.cell.2017.01.013.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
The genetic dependencies of human cancers widely vary. Here, we catalog this heterogeneity and use it to identify functional gene interactions and genotype-dependent liabilities in cancer. By using genome-wide CRISPR-based screens, we generate a gene essentiality dataset across 14 human acute myeloid leukemia (AML) cell lines. Sets of genes with correlated patterns of essentiality across the lines reveal new gene relationships, the essential substrates of enzymes, and the molecular functions of uncharacterized proteins. Comparisons of differentially essential genes between Ras-dependent and -independent lines uncover synthetic lethal partners of oncogenic Ras. Screens in both human AML and engineered mouse pro-B cells converge on a surprisingly small number of genes in the Ras processing and MAPK pathways and pinpoint PREX1 as an AML-specific activator of MAPK signaling. Our findings suggest general strategies for defining mammalian gene networks and synthetic lethal interactions by exploiting the natural genetic and epigenetic diversity of human cancer cells.
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Affiliation(s)
- Tim Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Haiyan Yu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas W Hughes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bingxu Liu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arek Kendirli
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Klara Klein
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Walter W Chen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric S Lander
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - David M Sabatini
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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