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Sui X, Liu T, Zou Z, Zhang B, Zhang G. Effects and mechanisms of puerarin against neuroblastoma: insights from bioinformatics and in vitro experiments. BMC Complement Med Ther 2024; 24:257. [PMID: 38982456 PMCID: PMC11234716 DOI: 10.1186/s12906-024-04569-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Neuroblastoma, a prevalent solid tumor in children, often manifests with hidden onset sites, rapid growth, and high metastatic potential. The prognosis for children with high-risk neuroblastoma remains poor, highlighting the urgent need for novel prognostic models and therapeutic avenues. In recent years, puerarin, as a kind of small molecule drug extracted from Chinese medicine Pueraria lobata, has demonstrated significant anticancer effects on various cancer cell types. In this study, through bioinformatics analysis and in vitro experiments, the potential and mechanism of puerarin in the treatment of neuroblastoma were investigated, and a prognostic model was established. METHODS A total of 9 drug-disease related targets were observed by constructing a database of drug targets and disease genes. Besides, GO and KEGG enrichment analysis was performed to explore the potential mechanism of its therapeutic effect. To construct the prognostic model, risk regression analysis and LASSO analysis were carried out for validation. Finally, the prognostic genes were identified. Parachute test and immunofluorescence staining were performed to verify the potential mechanism of puerarin in neuroblastoma treatment. RESULTS Three prognostic genes, i.e., BIRC5, TIMP2 and CASP9, were identified. In vitro studies verified puerarin's impact on BIRC5, TIMP2, and CASP9 expression, inhibiting proliferation in neuroblastoma SH-SY5Y cells. Puerarin disrupts the cytoskeleton, boosts gap junctional communication, curtailing invasion and migration, and induces mitochondrial damage in SH-SY5Y cells. CONCLUSIONS Based on network pharmacology and bioinformatics analysis, combined with in vitro experimental verification, puerarin was hereby observed to enhance GJIC in neuroblastoma, destroy cytoskeleton and thus inhibit cell invasion and migration, cause mitochondrial damage of tumor cells, and inhibit cell proliferation. Overall, puerarin, as a natural medicinal compound, does hold potential as a novel therapy for neuroblastoma.
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Affiliation(s)
- Xiaohui Sui
- Shandong University of Traditional Chinese Medicine, Jinan Shandong, 250014, China
| | - Tingting Liu
- Shandong University of Traditional Chinese Medicine, Jinan Shandong, 250014, China
| | - Zhiyun Zou
- Shandong University of Traditional Chinese Medicine, Jinan Shandong, 250014, China
| | - Baoqing Zhang
- Affiliated Hospital of Shandong, University of Traditional Chinese Medicine, Jinan Shandong, 250011, China
| | - Guiju Zhang
- Affiliated Hospital of Shandong, University of Traditional Chinese Medicine, Jinan Shandong, 250011, China.
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2
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Matsui Y, Djekidel MN, Lindsay K, Samir P, Connolly N, Wu G, Yang X, Fan Y, Xu B, Peng JC. SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development. Nat Commun 2023; 14:4754. [PMID: 37553330 PMCID: PMC10409800 DOI: 10.1038/s41467-023-40487-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Stem cell survival versus death is a developmentally programmed process essential for morphogenesis, sizing, and quality control of genome integrity and cell fates. Cell death is pervasive during development, but its programming is little known. Here, we report that Smad nuclear interacting protein 1 (SNIP1) promotes neural progenitor cell survival and neurogenesis and is, therefore, integral to brain development. The SNIP1-depleted brain exhibits dysplasia with robust induction of caspase 9-dependent apoptosis. Mechanistically, SNIP1 regulates target genes that promote cell survival and neurogenesis, and its activities are influenced by TGFβ and NFκB signaling pathways. Further, SNIP1 facilitates the genomic occupancy of Polycomb complex PRC2 and instructs H3K27me3 turnover at target genes. Depletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and to partially restore genetic programs in the SNIP1-depleted brain in vivo. These findings suggest a loci-specific regulation of PRC2 and H3K27 marks to toggle cell survival and death in the developing brain.
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Affiliation(s)
- Yurika Matsui
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Katherine Lindsay
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Parimal Samir
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Medical Research Building, Room 7, 138E, Galveston, TX, 77550, USA
| | - Nina Connolly
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xiaoyang Yang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jamy C Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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3
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Khan MQ, Mubeen H, Khan ZQ, Masood A, Zafar A, Wattoo JI, Nisa AU. Computational insights into missense mutations in HTT gene causing Huntington's disease and its interactome networks. Ir J Med Sci 2022:10.1007/s11845-022-03043-5. [PMID: 35829908 DOI: 10.1007/s11845-022-03043-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Huntington's disease is a rare neurodegenerative illness of the central nervous system that is inherited in an autosomal dominant pattern. Mutant huntingtin protein is produced as a result of enlargement of CAG repeat in the N-terminal of the polyglutamine tract. AIM OF THE STUDY Herein, we aim to investigate the mutations and their effects on the HTT gene and its genetic variants. Additionally, the protein-protein interaction of HTT with other proteins and receptor-ligand interaction with the three-dimensional structure of huntingtin protein were identified. METHODS A comprehensive analysis of the HTT interactome and protein-ligand interaction has been carried out to provide a global picture of structure-function analysis of huntingtin protein. Mutations were analyzed and mutation verification tools were used to check the effect of mutation on protein function. RESULTS The results showed, mutations in a single gene are not only responsible for causing a particular disease but may also cause other hereditary disorders as well. Moreover, the modification at the nucleotide level also cause the change in the specific amino acid which may disrupt the function of HTT and its interacting proteins contributing in disease pathogenesis. Furthermore, the interaction between MECP2 and BDNF lowers the rate of transcriptional activity. Molecular docking further confirmed the strong interaction between MECP2 and BDNF with highest affinity. Amino acid residues of the HTT protein, involved in the interaction with tetrabenazine were N912, Y890, G2385, and V2320. These findings proved, tetrabenazine as one of the potential therapeutic agent for treatment of Huntington's disease. CONCLUSION These results give further insights into the genetics of Huntington's disease for a better understanding of disease models which will be beneficial for the future therapeutic studies.
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Affiliation(s)
| | - Hira Mubeen
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan.
| | | | - Ammara Masood
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Asma Zafar
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Javed Iqbal Wattoo
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Alim Un Nisa
- Pakistan Council of Scientific and Industrial Research, Lahore, Pakistan
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A Novel Classification Model for Lower-Grade Glioma Patients Based on Pyroptosis-Related Genes. Brain Sci 2022; 12:brainsci12060700. [PMID: 35741587 PMCID: PMC9221219 DOI: 10.3390/brainsci12060700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023] Open
Abstract
Recent studies demonstrated that pyroptosis plays a crucial role in shaping the tumor-immune microenvironment. However, the influence of pyroptosis on lower-grade glioma regarding immunotherapy and targeted therapy is still unknown. This study analyzed the variations of 33 pyroptosis-related genes in lower-grade glioma and normal tissues. Our study found considerable genetic and expression alterations in heterogeneity among lower-grade gliomas and normal brain tissues. There are two pyroptosis phenotypes in lower-grade glioma, and they exhibited differences in cell infiltration characteristics and clinical characters. Then, a PyroScore model using the lasso-cox method was constructed to measure the level of pyroptosis in each patient. PyroScore can refine the lower-grade glioma patients with a stratified prognosis and a distinct tumor immune microenvironment. Pyscore may also be an effective factor in predicting potential therapeutic benefits. In silico analysis showed that patients with a lower PyroScore are expected to be more sensitive to targeted therapy and immunotherapy. These findings may enhance our understanding of pyroptosis in lower-grade glioma and might help optimize risk stratification for the survival and personalized management of lower-grade glioma patients.
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Avrutsky MI, Troy CM. Caspase-9: A Multimodal Therapeutic Target With Diverse Cellular Expression in Human Disease. Front Pharmacol 2021; 12:701301. [PMID: 34305609 PMCID: PMC8299054 DOI: 10.3389/fphar.2021.701301] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
Caspase-9, a cysteine-aspartic protease known for its role as an initiator of intrinsic apoptosis, regulates physiological cell death and pathological tissue degeneration. Its nonapoptotic functions, including regulation of cellular differentiation/maturation, innate immunity, mitochondrial homeostasis, and autophagy, reveal a multimodal landscape of caspase-9 functions in health and disease. Recent work has demonstrated that caspase-9 can drive neurovascular injury through nonapoptotic endothelial cell dysfunction. CASP9 polymorphisms have been linked with various cancers, neurological disorders, autoimmune pathologies and lumbar disc disease. Clinical reports suggest alterations in caspase-9 expression, activity or function may be associated with acute and chronic neurodegeneration, retinal neuropathy, slow-channel myasthenic syndrome, lumbar disc disease, cardiomyopathies, atherosclerosis and autoimmune disease. Healthy tissues maintain caspase-9 activity at low basal levels, rendering supraphysiological caspase-9 activation a tractable target for therapeutic interventions. Strategies for selective inhibition of caspase-9 include dominant negative caspase-9 mutants and pharmacological inhibitors derived from the XIAP protein, whose Bir3 domain is an endogenous highly selective caspase-9 inhibitor. However, the mechanistic implications of caspase-9 expression and activation remain indeterminate in many pathologies. By assembling clinical reports of caspase-9 genetics, signaling and cellular localization in human tissues, this review identifies gaps between experimental and clinical studies on caspase-9, and presents opportunities for further investigations to examine the consequences of caspase activity in human disease.
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Affiliation(s)
- Maria I Avrutsky
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Carol M Troy
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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6
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Bu L, Hameed NUF, Luo C, Hong P, Zhou X, Wang S, Wu S. Germline ALK variations are associated with a poor prognosis in glioma and IDH-wildtype glioblastoma. J Neurooncol 2021; 152:27-36. [PMID: 33486679 DOI: 10.1007/s11060-020-03676-5] [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: 10/07/2020] [Accepted: 12/12/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Glioma is the most common primary brain tumor. Clear classification is crucial for accurate diagnosis and individualized treatment. Histopathological characteristics and genetic alterations have shown to be related to prognosis and treatment response. Germline variants are important components of genetic alterations. However, the distribution of germline variations in glioma patients and their association with survival remain unknown. METHODS We carried out whole-exome sequencing on 99 cases to explore germline variants in glioma. We also analyzed the association of germline variants with clinicopathological features and other prognostic indicators. RESULTS All the glioma cases harbored rare germline variants. Germline ALK variants (gALK-Mut) were identified in 12/99 (12.12%) patients. The gALK-Mut patients had significantly shorter overall survival than germline ALK wildtype (gALK-WT) patients in the all glioma group (99 cases) and the subset of patients with IDH-wildtype glioblastoma (IDH-WT-GBM, 39 cases) (P = 0.013 and 0.027, respectively). The gALK-Mut patients also had higher frequency of BIRC5, PIK3CA and RPN1 somatic mutations than the gALK-WT patients in IDH-WT-GBM. Other confounding factors appeared to contribute to patient survival. The subgroup of patients in IDH-WT-GBM with gALK-Mut/TP53-Mut had worse prognosis than the gALK-WT/TP53-Mut subgroup (P = 0.031); The gALK-Mut/TERT-WT and gALK-Mut/TERT-Mut subgroups both had a worse prognosis than the gALK-WT/TERT-Mut subgroup (P = 0.031 and 0.018, respectively). CONCLUSIONS Our study revealed ALK variation was an independent indicator of poor prognosis in glioma and IDH-WT-GBM. It could be a promising biomarker and tractable therapeutic target for this deadly disease.
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Affiliation(s)
- Linghao Bu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Neurosurgical Institute of Fudan University, Shanghai, China.,Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.,Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
| | - N U Farrukh Hameed
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Neurosurgical Institute of Fudan University, Shanghai, China.,Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.,Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
| | - Chen Luo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Neurosurgical Institute of Fudan University, Shanghai, China.,Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.,Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
| | - Pengjie Hong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Neurosurgical Institute of Fudan University, Shanghai, China.,Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China.,Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China
| | - Xiaoyu Zhou
- GenomiCare Biotechnology (Shanghai) Co. Ltd.,, Shanghai, China
| | - Shengzhou Wang
- GenomiCare Biotechnology (Shanghai) Co. Ltd.,, Shanghai, China
| | - Shuai Wu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China. .,Neurosurgical Institute of Fudan University, Shanghai, China. .,Shanghai Clinical Medical Center of Neurosurgery, Shanghai, China. .,Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, China.
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7
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Sepulveda-Villegas M, Rojo R, Garza-Hernandez D, de la Rosa-Garza M, Treviño V. A systematic review of genes affecting mitochondrial processes in cancer. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165846. [PMID: 32473387 DOI: 10.1016/j.bbadis.2020.165846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/01/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Malignant conversion of cancer cells requires efficient mitochondria reprogramming orchestrated by hundreds of genes. The transformation includes increased energy demand, biosynthesis of precursors, and reactive oxygen species needed to accelerate cell growth, proliferation, and survival. Reprogramming involves complex gene alterations that have not been methodically curated. Therefore, we systematically analyzed the literature of cancer-related genes in mitochondria. Through the analysis of >2500 PubMed abstracts and >1600 human genes, we identified 228 genes showing clear roles in cancer. Each gene was classified according to their homeostatic function, together with the pathological transitions that contribute to specific cancer hallmarks. The potential clinical relevance of these hallmarks and genes is discussed by representative examples and validated by detecting differences in gene expression levels across 16 different types of cancer. A compendium, including the gene functions and alterations underpinning cancer progression, can be explored at http://bioinformatica.mty.itesm.mx/MitoCancer.
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Affiliation(s)
- Maricruz Sepulveda-Villegas
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Rocio Rojo
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Debora Garza-Hernandez
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Mauricio de la Rosa-Garza
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Victor Treviño
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico.
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8
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Muskens IS, de Smith AJ, Zhang C, Hansen HM, Morimoto L, Metayer C, Ma X, Walsh KM, Wiemels JL. Germline cancer predisposition variants and pediatric glioma: a population-based study in California. Neuro Oncol 2020; 22:864-874. [PMID: 31970404 PMCID: PMC7283023 DOI: 10.1093/neuonc/noaa014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Pediatric astrocytoma constitutes a majority of malignant pediatric brain tumors. Previous studies that investigated pediatric cancer predisposition have primarily been conducted in tertiary referral centers and focused on cancer predisposition genes. In this study, we investigated the contribution of rare germline variants to risk of malignant pediatric astrocytoma on a population level. METHODS DNA samples were extracted from neonatal dried bloodspots from 280 pediatric astrocytoma patients (predominantly high grade) born and diagnosed in California and were subjected to whole-exome sequencing. Sequencing data were analyzed using agnostic exome-wide gene-burden testing and variant identification for putatively pathogenic variants in 175 a priori candidate cancer-predisposition genes. RESULTS We identified 33 putatively pathogenic germline variants among 31 patients (11.1%) which were located in 24 genes largely involved in DNA repair and cell cycle control. Patients with pediatric glioblastoma were most likely to harbor putatively pathogenic germline variants (14.3%, N = 9/63). Five variants were located in tumor protein 53 (TP53), of which 4 were identified among patients with glioblastoma (6.3%, N = 4/63). The next most frequently mutated gene was neurofibromatosis 1 (NF1), in which putatively pathogenic variants were identified in 4 patients with astrocytoma not otherwise specified. Gene-burden testing also revealed that putatively pathogenic variants in TP53 were significantly associated with pediatric glioblastoma on an exome-wide level (odds ratio, 32.8, P = 8.04 × 10-7). CONCLUSION A considerable fraction of pediatric glioma patients, especially those of higher grade, harbor a putatively pathogenic variant in a cancer predisposition gene. Some of these variants may be clinically actionable or may warrant genetic counseling.
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Affiliation(s)
- Ivo S Muskens
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, California
| | | | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale University, New Haven, Connecticut
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Children’s Health and Discovery Institute, Duke University, Durham, North Carolina
- Department of Neurosurgery, Duke University, Durham, North Carolina
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
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9
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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10
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Muskens IS, Zhou M, Mccoy L, Bracci PM, Hansen HM, Gauderman WJ, Wiencke JK, Wrensch MR, Wiemels JL. Immune factors preceding diagnosis of glioma: a Prostate Lung Colorectal Ovarian Cancer Screening Trial nested case-control study. Neurooncol Adv 2019; 1:vdz031. [PMID: 31807733 PMCID: PMC6881819 DOI: 10.1093/noajnl/vdz031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Epidemiological studies of adult glioma have identified genetic and environmental risk factors, but much remains unclear. The aim of the current study was to evaluate anthropometric, disease-related, and prediagnostic immune-related factors for relationship with glioma risk. Methods We conducted a nested case–control study among the intervention arm of the Prostate, Lung, Colorectal, and Ovarian Cancer (PLCO) Screening Trial. One hundred and twenty-four glioma cases were identified and each matched to four controls. Baseline characteristics were collected at enrollment and were evaluated for association with glioma status. Serum specimens were collected at yearly intervals and were analyzed for immune-related factors including TGF-β1, TNF-α, total IgE, and allergen-specific IgE. Immune factors were evaluated at baseline in a multivariate conditional logistic regression model, along with one additional model that incorporated the latest available measurement. Results A family history of glioma among first-degree relatives was associated with increased glioma risk (OR = 4.41, P = .002). In multivariate modeling of immune factors at baseline, increased respiratory allergen-specific IgE was inversely associated with glioma risk (OR for allergen-specific IgE > 0.35 PAU/L: 0.59, P = .03). A logistic regression model that incorporated the latest available measurements found a similar association for allergen-specific IgE (P = .005) and showed that elevated TGF-β1 was associated with increased glioma risk (P-value for trend <.0001). Conclusion The results from this prospective prediagnostic study suggest that several immune-related factors are associated with glioma risk. The association observed for TGF-β1 when sampling closer to the time of diagnosis may reflect the nascent brain tumor’s feedback on immune function.
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Affiliation(s)
- Ivo S Muskens
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Mi Zhou
- Department of Epidemiology and Biostatistics
| | - Lucie Mccoy
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA
| | | | - Helen M Hansen
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA
| | - W James Gauderman
- Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - John K Wiencke
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA
| | - Margaret R Wrensch
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA.,Department of Epidemiology and Biostatistics
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11
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Penkert J, Schmidt G, Hofmann W, Schubert S, Schieck M, Auber B, Ripperger T, Hackmann K, Sturm M, Prokisch H, Hille-Betz U, Mark D, Illig T, Schlegelberger B, Steinemann D. Breast cancer patients suggestive of Li-Fraumeni syndrome: mutational spectrum, candidate genes, and unexplained heredity. Breast Cancer Res 2018; 20:87. [PMID: 30086788 PMCID: PMC6081832 DOI: 10.1186/s13058-018-1011-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/27/2018] [Indexed: 01/07/2023] Open
Abstract
Background Breast cancer is the most prevalent tumor entity in Li-Fraumeni syndrome. Up to 80% of individuals with a Li-Fraumeni-like phenotype do not harbor detectable causative germline TP53 variants. Yet, no systematic panel analyses for a wide range of cancer predisposition genes have been conducted on cohorts of women with breast cancer fulfilling Li-Fraumeni(-like) clinical diagnostic criteria. Methods To specifically help explain the diagnostic gap of TP53 wild-type Li-Fraumeni(-like) breast cancer cases, we performed array-based CGH (comparative genomic hybridization) and panel-based sequencing of 94 cancer predisposition genes on 83 breast cancer patients suggestive of Li-Fraumeni syndrome who had previously had negative test results for causative BRCA1, BRCA2, and TP53 germline variants. Results We identified 13 pathogenic or likely pathogenic germline variants in ten patients and in nine genes, including four copy number aberrations and nine single-nucleotide variants or small indels. Three patients presented as double-mutation carriers involving two different genes each. In five patients (5 of 83; 6% of cohort), we detected causative pathogenic variants in established hereditary breast cancer susceptibility genes (i.e., PALB2, CHEK2, ATM). Five further patients (5 of 83; 6% of cohort) were found to harbor pathogenic variants in genes lacking a firm association with breast cancer susceptibility to date (i.e., Fanconi pathway genes, RECQ family genes, CDKN2A/p14ARF, and RUNX1). Conclusions Our study details the mutational spectrum in breast cancer patients suggestive of Li-Fraumeni syndrome and indicates the need for intensified research on monoallelic variants in Fanconi pathway and RECQ family genes. Notably, this study further reveals a large portion of still unexplained Li-Fraumeni(-like) cases, warranting comprehensive investigation of recently described candidate genes as well as noncoding regions of the TP53 gene in patients with Li-Fraumeni(-like) syndrome lacking TP53 variants in coding regions. Electronic supplementary material The online version of this article (10.1186/s13058-018-1011-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Penkert
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Stephanie Schubert
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Partner Site Dresden, Dresden, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ursula Hille-Betz
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Dorothea Mark
- Department of Internal Medicine, Hematology/Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Thomas Illig
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Brigitte Schlegelberger
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
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