1
|
Fogarty EA, Buchert EM, Ma Y, Nicely AB, Buttitta LA. Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592773. [PMID: 38766255 PMCID: PMC11100713 DOI: 10.1101/2024.05.06.592773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in the Drosophila wing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of the Drosophila eye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and show that they encode dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset, and find that the principles of cell cycle gene regulation identified in terminally differentiating Drosophila tissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle gens, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.
Collapse
Affiliation(s)
- Elizabeth A. Fogarty
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Elli M. Buchert
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Yiqin Ma
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Ava B. Nicely
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Laura A. Buttitta
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| |
Collapse
|
2
|
Yin W, Jiang Z, Guo Y, Cao Y, Wu Z, Zhou Y, Chen Q, Liu W, Jiang X, Ren C. Identification of Anoikis-Related Genes in Spinal Cord Injury: Bioinformatics and Experimental Validation. Mol Neurobiol 2024:10.1007/s12035-024-04121-8. [PMID: 38519735 DOI: 10.1007/s12035-024-04121-8] [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: 01/26/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
Spinal cord injury (SCI) is a serious disease without effective therapeutic strategies. To identify the potential treatments for SCI, it is extremely important to explore the underlying mechanism. Current studies demonstrate that anoikis might play an important role in SCI. In this study, we aimed to identify the key anoikis-related genes (ARGs) providing therapeutic targets for SCI. The mRNA expression matrix of GSE45006 was downloaded from the Gene Expression Omnibus (GEO) database, and the ARGs were downloaded from the Molecular Signatures Database (MSigDB database). Then, the potential differentially expressed ARGs were identified. Next, correlation analysis, gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) analysis were employed for the differentially expressed ARGs. Moreover, miRNA-gene networks were constructed by the hub ARGs. Finally, RNA expression of the top ten hub ARGs was validated in the SCI cell model and rat SCI model. A total of 27 common differentially expressed ARGs were identified at different time points (1, 3, 7, and 14 days) following SCI. The GO and KEGG enrichment analysis of these ARGs indicated several enriched terms related to proliferation, cell cycle, and apoptotic process. The PPI results revealed that most of the ARGs interacted with each other. Ten hub ARGs were further screened, and all the 10 genes were validated in the SCI cell model. In the rat model, only seven genes were validated eventually. We identified 27 differentially expressed ARGs of the SCI through bioinformatic analysis. Seven real hub ARGs (CCND1, FN1, IGF1, MYC, STAT3, TGFB1, and TP53) were identified eventually. These results may expand our understanding of SCI and contribute to the exploration of potential SCI targets.
Collapse
Affiliation(s)
- Wen Yin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Zhipeng Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Youwei Guo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Yudong Cao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Zhaoping Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Yi Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Quan Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
| | - Weidong Liu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
| | - Caiping Ren
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
3
|
Lee K, Kim SI, Kim EE, Shim YM, Won JK, Park CK, Choi SH, Yun H, Lee H, Park SH. Genomic profiles of IDH-mutant gliomas: MYCN-amplified IDH-mutant astrocytoma had the worst prognosis. Sci Rep 2023; 13:6761. [PMID: 37185778 PMCID: PMC10130138 DOI: 10.1038/s41598-023-32153-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
This study aimed to find any ambiguous genetic outlier for "oligodendroglioma, IDH-mutant and 1p/19q-codeleted (O_IDH_mut)" and "astrocytoma, IDH-mutant (A_IDH_mut)" and to redefine the genetic landscape and prognostic factors of IDH-mutant gliomas. Next-generation sequencing (NGS) using a brain tumor-targeted gene panel, methylation profiles, and clinicopathological features were analyzed for O_IDH_mut (n = 74) in 70 patients and for A_IDH_mut (n = 95) in 90 patients. 97.3% of O_IDH_mut and 98.9% of A_IDH_mut displayed a classic genomic landscape. Combined CIC (75.7%) and/or FUBP1 (45.9%) mutations were detected in 93.2% and MGMTp methylation in 95.9% of O_IDH_mut patients. In A_IDH_mut, TP53 mutations were found in 86.3% and combined ATRX (82.1%) and TERTp (6.3%) mutations in 88.4%. Although there were 3 confusing cases, NOS (not otherwise specified) category, based on genetic profiles, but they were clearly classified by combining histopathology and DKFZ methylation classifier algorithms. The patients with MYCN amplification and/or CDKN2A/2B homozygous deletion in the A_IDH_mut category had a worse prognosis than those without these gene alterations and MYCN-amplified A_IDH_mut showed the worst prognosis. However, there was no prognostic genetic marker in O_IDH_mut. In histopathologically or genetically ambiguous cases, methylation profiles can be used as an objective tool to avoid a diagnosis of NOS or NEC (not elsewhere classified), as well as for tumor classification. The authors have not encountered a case of true mixed oligoastrocytoma using an integrated diagnosis of histopathological, genetic and methylation profiles. MYCN amplification, in addition to CDKN2A/2B homozygous deletion, should be included in the genetic criteria for CNS WHO grade 4 A_IDH_mut.
Collapse
Affiliation(s)
- Kwanghoon Lee
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seong-Ik Kim
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eric Eunshik Kim
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yu-Mi Shim
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae-Kyung Won
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung Hong Choi
- Department of Radiology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyunju Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
- Artificial Intelligence Graduate School, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
4
|
The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency. J Virol 2021; 95:JVI.01247-20. [PMID: 33239456 PMCID: PMC7851559 DOI: 10.1128/jvi.01247-20] [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] [Indexed: 12/12/2022] Open
Abstract
HIV transcription requires assembly of cellular transcription factors at the HIV-1promoter. The TFIIH general transcription factor facilitates transcription initiation by opening the DNA strands around the transcription start site and phosphorylating the C-terminal domain for RNA polymerase II (RNAPII) for activation. Spironolactone (SP), an FDA approved aldosterone antagonist, triggers the proteasomal degradation of the XPB subunit of TFIIH, and concurrently suppresses acute HIV infection in vitro Here we investigated SP as a possible block-and-lock agent for a functional cure aimed at the transcriptional silencing of the viral reservoir. The long-term activity of SP was investigated in primary and cell line models of HIV-1 latency and reactivation. We show that SP rapidly inhibits HIV-1 transcription by reducing RNAPII recruitment to the HIV-1 genome. shRNA knockdown of XPB confirmed XPB degradation as the mechanism of action. Unfortunately, long-term pre-treatment with SP does not result in epigenetic suppression of HIV upon SP treatment interruption, since virus rapidly rebounds when XPB reemerges; however, SP alone without ART maintains the transcriptional suppression. Importantly, SP inhibits HIV reactivation from latency in both cell line models and resting CD4+T cells isolated from aviremic infected individuals upon cell stimulation with latency reversing agents. Furthermore, long-term treatment with concentrations of SP that potently degrade XPB does not lead to global dysregulation of cellular mRNA expression. Overall, these results suggest that XPB plays a key role in HIV transcriptional regulation and XPB degradation by SP strengthens the potential of HIV transcriptional inhibitors in block-and-lock HIV cure approaches.IMPORTANCE Antiretroviral therapy (ART) effectively reduces an individual's HIV loads to below the detection limit, nevertheless rapid viral rebound immediately ensues upon treatment interruption. Furthermore, virally suppressed individuals experience chronic immune activation from ongoing low-level virus expression. Thus, the importance of identifying novel therapeutics to explore in block-and-lock HIV functional cure approaches, aimed at the transcriptional and epigenetic silencing of the viral reservoir to block reactivation from latency. We investigated the potential of repurposing the FDA-approved spironolactone (SP), as one such drug. SP treatment rapidly degrades a host transcription factor subunit, XPB, inhibiting HIV transcription and blocking reactivation from latency. Long-term SP treatment does not affect cellular viability, cell cycle progression or global cellular transcription. SP alone blocks HIV transcription in the absence of ART but does not delay rebound upon drug removal as XPB rapidly reemerges. This study highlights XPB as a novel drug target in block-and-lock therapeutic approaches.
Collapse
|
5
|
Abstract
Neuroblastoma (NB) is a pediatric cancer of the sympathetic nervous system and one of the most common solid tumors in infancy. Amplification of MYCN, copy number alterations, numerical and segmental chromosomal aberrations, mutations, and rearrangements on a handful of genes, such as ALK, ATRX, TP53, RAS/MAPK pathway genes, and TERT, are attributed as underlying causes that give rise to NB. However, the heterogeneous nature of the disease-along with the relative paucity of recurrent somatic mutations-reinforces the need to understand the interplay of genetic factors and epigenetic alterations in the context of NB. Epigenetic mechanisms tightly control gene expression, embryogenesis, imprinting, chromosomal stability, and tumorigenesis, thereby playing a pivotal role in physio- and pathological settings. The main epigenetic alterations include aberrant DNA methylation, disrupted patterns of posttranslational histone modifications, alterations in chromatin composition and/or architecture, and aberrant expression of non-coding RNAs. DNA methylation and demethylation are mediated by DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) proteins, respectively, while histone modifications are coordinated by histone acetyltransferases and deacetylases (HATs, HDACs), and histone methyltransferases and demethylases (HMTs, HDMs). This article focuses predominately on the crosstalk between the epigenome and NB, and the implications it has on disease diagnosis and treatment.
Collapse
|
6
|
MYC in Brain Development and Cancer. Int J Mol Sci 2020; 21:ijms21207742. [PMID: 33092025 PMCID: PMC7588885 DOI: 10.3390/ijms21207742] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 12/27/2022] Open
Abstract
The MYC family of transcriptional regulators play significant roles in animal development, including the renewal and maintenance of stem cells. Not surprisingly, given MYC's capacity to promote programs of proliferative cell growth, MYC is frequently upregulated in cancer. Although members of the MYC family are upregulated in nervous system tumours, the mechanisms of how elevated MYC promotes stem cell-driven brain cancers is unknown. If we are to determine how increased MYC might contribute to brain cancer progression, we will require a more complete understanding of MYC's roles during normal brain development. Here, we evaluate evidence for MYC family functions in neural stem cell fate and brain development, with a view to better understand mechanisms of MYC-driven neural malignancies.
Collapse
|
7
|
Zheng Y, Dubois W, Benham C, Batchelor E, Levens D. FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells. Commun Biol 2020; 3:545. [PMID: 33005010 PMCID: PMC7530719 DOI: 10.1038/s42003-020-01264-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/01/2020] [Indexed: 11/24/2022] Open
Abstract
Physiologically, MYC levels must be precisely set to faithfully amplify the transcriptome, but in cancer MYC is quantitatively misregulated. Here, we study the variation of MYC amongst single primary cells (B-cells and murine embryonic fibroblasts, MEFs) for the repercussions of variable cellular MYC-levels and setpoints. Because FUBPs have been proposed to be molecular “cruise controls” that constrain MYC expression, their role in determining basal or activated MYC-levels was also examined. Growing cells remember low and high-MYC setpoints through multiple cell divisions and are limited by the same expression ceiling even after modest MYC-activation. High MYC MEFs are enriched for mRNAs regulating inflammation and immunity. After strong stimulation, many cells break through the ceiling and intensify MYC expression. Lacking FUBPs, unstimulated MEFs express levels otherwise attained only with stimulation and sponsor MYC chromatin changes, revealed by chromatin marks. Thus, the FUBPs enforce epigenetic setpoints that restrict MYC expression. Ying Zheng et al. characterize MYC gene and protein expression in single mammalian cells in response to various external signals. They find that individual cells show either high or low basal MYC expression setpoints, and that adherence to these setpoints as well as the magnitude of the response of MYC to stimulation, is controlled by FUBP1 and FUBP2.
Collapse
Affiliation(s)
- Ying Zheng
- Lab of Pathology, National Cancer Institutes, Bethesda, MD, USA
| | - Wendy Dubois
- Lab of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institutes, Bethesda, MD, USA
| | - Craig Benham
- Biomedical Engineering, University of California, Davis, CA, USA
| | - Eric Batchelor
- Masonic Cancer Center and Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - David Levens
- Lab of Pathology, National Cancer Institutes, Bethesda, MD, USA.
| |
Collapse
|
8
|
Zaytseva O, Mitchell NC, Guo L, Marshall OJ, Parsons LM, Hannan RD, Levens DL, Quinn LM. Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in Drosophila. Development 2020; 147:147/11/dev190231. [PMID: 32527935 PMCID: PMC7295588 DOI: 10.1242/dev.190231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/27/2020] [Indexed: 12/29/2022]
Abstract
Here, we report novel tumour suppressor activity for the Drosophila Argonaute family RNA-binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth inhibition does not, however, involve canonical roles as part of the RISC; rather, AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion and cell growth in a manner dependent on Myc abundance. Moreover, increased Myc promoter activity and elevated Myc mRNA in AGO1-depleted animals requires RNA polymerase II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA polymerase II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on the Myc promoter and AGO1 interacts with the Myc transcriptional activator Psi. Together, our data show that Drosophila AGO1 functions outside of the RISC to repress Myc transcription and inhibit developmental cell and tissue growth. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: In the Drosophila wing, the Argonaute family protein AGO1 acts independently of the miRNA-silencing pathway to restrict tissue growth by directly repressing transcription of the master growth regulator Myc.
Collapse
Affiliation(s)
- Olga Zaytseva
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Linna Guo
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | | | - Ross D Hannan
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - David L Levens
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Leonie M Quinn
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| |
Collapse
|
9
|
Zurita M, Murillo-Maldonado JM. Drosophila as a Model Organism to Understand the Effects during Development of TFIIH-Related Human Diseases. Int J Mol Sci 2020; 21:ijms21020630. [PMID: 31963603 PMCID: PMC7013941 DOI: 10.3390/ijms21020630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/20/2022] Open
Abstract
Human mutations in the transcription and nucleotide excision repair (NER) factor TFIIH are linked with three human syndromes: xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS). In particular, different mutations in the XPB, XPD and p8 subunits of TFIIH may cause one or a combination of these syndromes, and some of these mutations are also related to cancer. The participation of TFIIH in NER and transcription makes it difficult to interpret the different manifestations observed in patients, particularly since some of these phenotypes may be related to problems during development. TFIIH is present in all eukaryotic cells, and its functions in transcription and DNA repair are conserved. Therefore, Drosophila has been a useful model organism for the interpretation of different phenotypes during development as well as the understanding of the dynamics of this complex. Interestingly, phenotypes similar to those observed in humans caused by mutations in the TFIIH subunits are present in mutant flies, allowing the study of TFIIH in different developmental processes. Furthermore, studies performed in Drosophila of mutations in different subunits of TFIIH that have not been linked to any human diseases, probably because they are more deleterious, have revealed its roles in differentiation and cell death. In this review, different achievements made through studies in the fly to understand the functions of TFIIH during development and its relationship with human diseases are analysed and discussed.
Collapse
|
10
|
Paglia S, Sollazzo M, Di Giacomo S, Strocchi S, Grifoni D. Exploring MYC relevance to cancer biology from the perspective of cell competition. Semin Cancer Biol 2019; 63:49-59. [PMID: 31102666 DOI: 10.1016/j.semcancer.2019.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022]
Abstract
Cancer has long been regarded and treated as a foreign body appearing by mistake inside a living organism. However, now we know that cancer cells communicate with neighbours, thereby creating modified environments able to support their unusual need for nutrients and space. Understanding the molecular basis of these bi-directional interactions is thus mandatory to approach the complex nature of cancer. Since their discovery, MYC proteins have been showing to regulate a steadily increasing number of processes impacting cell fitness, and are consistently found upregulated in almost all human tumours. Of interest, MYC takes part in cell competition, an evolutionarily conserved fitness comparison strategy aimed at detecting weakened cells, which are then committed to death, removed from the tissue and replaced by fitter neighbours. During physiological development, MYC-mediated cell competition is engaged to eliminate cells with suboptimal MYC levels, so as to guarantee selective growth of the fittest and proper homeostasis, while transformed cells expressing high levels of MYC coopt cell competition to subvert tissue constraints, ultimately disrupting homeostasis. Therefore, the interplay between cells with different MYC levels may result in opposite functional outcomes, depending on the nature of the players. In the present review, we describe the most recent findings on the role of MYC-mediated cell competition in different contexts, with a special emphasis on its impact on cancer initiation and progression. We also discuss the relevance of competition-associated cell death to cancer disease.
Collapse
Affiliation(s)
- Simona Paglia
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Manuela Sollazzo
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Simone Di Giacomo
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Silvia Strocchi
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| | - Daniela Grifoni
- CanceЯEvolutionLab, University of Bologna, Department of Pharmacy and Biotechnology, Via Selmi 3, 40126, Bologna, Italy.
| |
Collapse
|
11
|
Li X, Zhang Y, Wang L, Lin Y, Gao Z, Zhan X, Huang Y, Sun C, Wang D, Liang S, Wu L. Integrated Analysis of Brain Transcriptome Reveals Convergent Molecular Pathways in Autism Spectrum Disorder. Front Psychiatry 2019; 10:706. [PMID: 31649562 PMCID: PMC6795181 DOI: 10.3389/fpsyt.2019.00706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/02/2019] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a set of complex neurodevelopmental disorders with etiology that remains elusive. Although there is a mounting body of investigation in different brain regions related to ASD, our knowledge about the common and distinct perturb condition between them is at the threshold of accumulation. In this study, based on protein-protein interactions, post-mortem transcriptome analysis was performed with corpus callosum (CC) and prefrontal cortex (PFC) samples from ASD individuals and controls. Co-expression network analysis revealed that a total of seven (four for CC set, three for PFC set) core dysfunctional modules strongly enriched for known ASD-risk genes. Three quarters of them in CC set (M4, M6, M29) significantly enriched for genes annotated by genetically associated variants in our previous whole genome sequencing data. We further determined transcriptional and post-transcriptional regulation subnetwork for each ASD-correlated module, including 47 pivot transcription factors, 130 pivot miRNAs, and 7 pivot lncRNAs. Moreover, there were significantly more interactions between CC-M4, -M6, and PFC-M2, mainly involved in synaptic functions and neuronal development. Our integrated multifactor analysis of ASD brain transcriptome profile illustrated underlying common and distinct molecular mechanisms and the module crosstalk between CC and PFC, helping to shed light on the molecular neuropathological underlying ASD.
Collapse
Affiliation(s)
- Xiaodan Li
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Yuncong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Luxi Wang
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Yunqing Lin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhaomin Gao
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Xiaolei Zhan
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Yan Huang
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Caihong Sun
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Department of Bioinformatics, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Shuang Liang
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| | - Lijie Wu
- Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.,Province Key Laboratory of Children Development and Genetic Research, Heilongjiang, China
| |
Collapse
|
12
|
Enane FO, Saunthararajah Y, Korc M. Differentiation therapy and the mechanisms that terminate cancer cell proliferation without harming normal cells. Cell Death Dis 2018; 9:912. [PMID: 30190481 PMCID: PMC6127320 DOI: 10.1038/s41419-018-0919-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/24/2022]
Abstract
Chemotherapeutic drugs have a common intent to activate apoptosis in tumor cells. However, master regulators of apoptosis (e.g., p53, p16/CDKN2A) are frequently genetically inactivated in cancers, resulting in multidrug resistance. An alternative, p53-independent method for terminating malignant proliferation is to engage terminal-differentiation. Normally, the exponential proliferation of lineage-committed progenitors, coordinated by the master transcription factor (TF) MYC, is self-limited by forward-differentiation to terminal lineage-fates. In cancers, however, this exponential proliferation is disengaged from terminal-differentiation. The mechanisms underlying this decoupling are mostly unknown. We performed a systematic review of published literature (January 2007-June 2018) to identify gene pathways linked to differentiation-failure in three treatment-recalcitrant cancers: hepatocellular carcinoma (HCC), ovarian cancer (OVC), and pancreatic ductal adenocarcinoma (PDAC). We analyzed key gene alterations in various apoptosis, proliferation and differentiation pathways to determine whether it is possible to predict treatment outcomes and suggest novel therapies. Poorly differentiated tumors were linked to poorer survival across histologies. Our analyses suggested loss-of-function events to master TF drivers of lineage-fates and their cofactors as being linked to differentiation-failure: genomic data in TCGA and ICGC databases demonstrated frequent haploinsufficiency of lineage master TFs (e.g., GATA4/6) in poorly differentiated tumors; the coactivators that these TFs use to activate genes (e.g. ARID1A, PBRM1) were also frequently inactivated by genetic mutation and/or deletion. By contrast, corepressor components (e.g., DNMT1, EED, UHRF1, and BAZ1A/B), that oppose coactivators to repress or turn off genes, were frequently amplified instead, and the level of amplification was highest in poorly differentiated lesions. This selection by neoplastic evolution towards unbalanced activity of transcriptional corepressors suggests these enzymes as candidate targets for inhibition aiming to re-engage forward-differentiation. This notion is supported by both pre-clinical and clinical trial literature.
Collapse
Affiliation(s)
- Francis O Enane
- Department of Medicine, Indiana University School of Medicine Indianapolis, Indianapolis, IN, 46202, USA.
| | - Yogen Saunthararajah
- Department of Hematology and Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Translational Hematology and Oncology Research, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Murray Korc
- Department of Medicine, Indiana University School of Medicine Indianapolis, Indianapolis, IN, 46202, USA.
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- The Pancreatic Cancer Signature Center at Indiana University Purdue University Indianapolis and Indiana University Simon Cancer, Indianapolis, IN, 46202, USA.
| |
Collapse
|
13
|
Wang H, Dolezal JM, Kulkarni S, Lu J, Mandel J, Jackson LE, Alencastro F, Duncan AW, Prochownik EV. Myc and ChREBP transcription factors cooperatively regulate normal and neoplastic hepatocyte proliferation in mice. J Biol Chem 2018; 293:14740-14757. [PMID: 30087120 DOI: 10.1074/jbc.ra118.004099] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/02/2018] [Indexed: 12/31/2022] Open
Abstract
Analogous to the c-Myc (Myc)/Max family of bHLH-ZIP transcription factors, there exists a parallel regulatory network of structurally and functionally related proteins with Myc-like functions. Two related Myc-like paralogs, termed MondoA and MondoB/carbohydrate response element-binding protein (ChREBP), up-regulate gene expression in heterodimeric association with the bHLH-ZIP Max-like factor Mlx. Myc is necessary to support liver cancer growth, but not for normal hepatocyte proliferation. Here, we investigated ChREBP's role in these processes and its relationship to Myc. Unlike Myc loss, ChREBP loss conferred a proliferative disadvantage to normal murine hepatocytes, as did the combined loss of ChREBP and Myc. Moreover, hepatoblastomas (HBs) originating in myc-/-, chrebp-/-, or myc-/-/chrebp-/- backgrounds grew significantly more slowly. Metabolic studies on livers and HBs in all three genetic backgrounds revealed marked differences in oxidative phosphorylation, fatty acid β-oxidation (FAO), and pyruvate dehydrogenase activity. RNA-Seq of livers and HBs suggested seven distinct mechanisms of Myc-ChREBP target gene regulation. Gene ontology analysis indicated that many transcripts deregulated in the chrebp-/- background encode enzymes functioning in glycolysis, the TCA cycle, and β- and ω-FAO, whereas those dysregulated in the myc-/- background encode enzymes functioning in glycolysis, glutaminolysis, and sterol biosynthesis. In the myc-/-/chrebp-/- background, additional deregulated transcripts included those involved in peroxisomal β- and α-FAO. Finally, we observed that Myc and ChREBP cooperatively up-regulated virtually all ribosomal protein genes. Our findings define the individual and cooperative proliferative, metabolic, and transcriptional roles for the "Extended Myc Network" under both normal and neoplastic conditions.
Collapse
Affiliation(s)
- Huabo Wang
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC
| | - James M Dolezal
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC
| | - Sucheta Kulkarni
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC
| | - Jie Lu
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC
| | - Jordan Mandel
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC
| | - Laura E Jackson
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC
| | | | | | - Edward V Prochownik
- From the Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, .,the Pittsburgh Liver Center.,the Hillman Cancer Center of UPMC, and.,the Department of Microbiology and Molecular Genetics, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15224
| |
Collapse
|
14
|
Goetzman ES, Prochownik EV. The Role for Myc in Coordinating Glycolysis, Oxidative Phosphorylation, Glutaminolysis, and Fatty Acid Metabolism in Normal and Neoplastic Tissues. Front Endocrinol (Lausanne) 2018; 9:129. [PMID: 29706933 PMCID: PMC5907532 DOI: 10.3389/fendo.2018.00129] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 12/24/2022] Open
Abstract
That cancer cells show patterns of metabolism different from normal cells has been known for over 50 years. Yet, it is only in the past decade or so that an appreciation of the benefits of these changes has begun to emerge. Altered cancer cell metabolism was initially attributed to defective mitochondria. However, we now realize that most cancers do not have mitochondrial mutations and that normal cells can transiently adopt cancer-like metabolism during periods of rapid proliferation. Indeed, an encompassing, albeit somewhat simplified, conceptual framework to explain both normal and cancer cell metabolism rests on several simple premises. First, the metabolic pathways used by cancer cells and their normal counterparts are the same. Second, normal quiescent cells use their metabolic pathways and the energy they generate largely to maintain cellular health and organelle turnover and, in some cases, to provide secreted products necessary for the survival of the intact organism. By contrast, undifferentiated cancer cells minimize the latter functions and devote their energy to producing the anabolic substrates necessary to maintain high rates of unremitting cellular proliferation. Third, as a result of the uncontrolled proliferation of cancer cells, a larger fraction of the metabolic intermediates normally used by quiescent cells purely as a source of energy are instead channeled into competing proliferation-focused and energy-consuming anabolic pathways. Fourth, cancer cell clones with the most plastic and rapidly adaptable metabolism will eventually outcompete their less well-adapted brethren during tumor progression and evolution. This attribute becomes increasingly important as tumors grow and as their individual cells compete in a constantly changing and inimical environment marked by nutrient, oxygen, and growth factor deficits. Here, we review some of the metabolic pathways whose importance has gained center stage for tumor growth, particularly those under the control of the c-Myc (Myc) oncoprotein. We discuss how these pathways differ functionally between quiescent and proliferating normal cells, how they are kidnapped and corrupted during the course of transformation, and consider potential therapeutic strategies that take advantage of common features of neoplastic and metabolic disorders.
Collapse
Affiliation(s)
- Eric S. Goetzman
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, United States
| | - Edward V. Prochownik
- Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, United States
- Department of Microbiology and Molecular Genetics, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, United States
- *Correspondence: Edward V. Prochownik,
| |
Collapse
|
15
|
Di Giacomo S, Sollazzo M, Paglia S, Grifoni D. MYC, Cell Competition, and Cell Death in Cancer: The Inseparable Triad. Genes (Basel) 2017; 8:genes8040120. [PMID: 28420161 PMCID: PMC5406867 DOI: 10.3390/genes8040120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 01/07/2023] Open
Abstract
Deregulation of MYC family proteins in cancer is associated with a global reprogramming of gene expression, ultimately promoting glycolytic pathways, cell growth, and proliferation. It is well known that MYC upregulation triggers cell-autonomous apoptosis in normal tissues, while frankly malignant cells develop resistance to apoptotic stimuli, partly resulting from MYC addiction. As well as inducing cell-autonomous apoptosis, MYC upregulation is able to trigger non cell-autonomous apoptotic death through an evolutionarily conserved mechanism known as “cell competition”. With regard to this intimate and dual relationship between MYC and cell death, recent evidence obtained in Drosophila models of cancer has revealed that, in early tumourigenesis, MYC upregulation guides the clonal expansion of mutant cells, while the surrounding tissue undergoes non-cell autonomous death. Apoptosis inhibition in this context was shown to restrain tumour growth and to restore a wild-type phenotype. This suggests that cell-autonomous and non cell-autonomous apoptosis dependent on MYC upregulation may shape tumour growth in different ways, soliciting the need to reconsider the role of cell death in cancer in the light of this new level of complexity. Here we review recent literature about MYC and cell competition obtained in Drosophila, with a particular emphasis on the relevance of cell death to cell competition and, more generally, to cancer. Possible implications of these findings for the understanding of mammalian cancers are also discussed.
Collapse
Affiliation(s)
- Simone Di Giacomo
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Manuela Sollazzo
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Simona Paglia
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Daniela Grifoni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| |
Collapse
|