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González-Arzola K. The nucleolus: Coordinating stress response and genomic stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195029. [PMID: 38642633 DOI: 10.1016/j.bbagrm.2024.195029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
The perception that the nucleoli are merely the organelles where ribosome biogenesis occurs is challenged. Only around 30 % of nucleolar proteins are solely involved in producing ribosomes. Instead, the nucleolus plays a critical role in controlling protein trafficking during stress and, according to its dynamic nature, undergoes continuous protein exchange with nucleoplasm under various cellular stressors. Hence, the concept of nucleolar stress has evolved as cellular insults that disrupt the structure and function of the nucleolus. Considering the emerging role of this organelle in DNA repair and the fact that rDNAs are the most fragile genomic loci, therapies targeting the nucleoli are increasingly being developed. Besides, drugs that target ribosome synthesis and induce nucleolar stress can be used in cancer therapy. In contrast, agents that regulate nucleolar activity may be a potential treatment for neurodegeneration caused by abnormal protein accumulation in the nucleolus. Here, I explore the roles of nucleoli beyond their ribosomal functions, highlighting the factors triggering nucleolar stress and their impact on genomic stability.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain.
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2
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Jain V, Foo SH, Chooi S, Moss C, Goodwin R, Berland S, Clarke AJ, Davies SJ, Corrin S, Murch O, Doyle S, Graham GE, Greenhalgh L, Holder SE, Johnson D, Kumar A, Ladda RL, Sell S, Begtrup A, Lynch SA, McCann E, Østern R, Pottinger C, Splitt M, Fry AE. Börjeson-Forssman-Lehmann syndrome: delineating the clinical and allelic spectrum in 14 new families. Eur J Hum Genet 2023; 31:1421-1429. [PMID: 37704779 PMCID: PMC10689765 DOI: 10.1038/s41431-023-01447-0] [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: 02/06/2023] [Revised: 05/15/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Börjeson-Forssman-Lehmann syndrome (BFLS) is an X-linked intellectual disability syndrome caused by variants in the PHF6 gene. We ascertained 19 individuals from 15 families with likely pathogenic or pathogenic PHF6 variants (11 males and 8 females). One family had previously been reported. Six variants were novel. We analysed the clinical and genetic findings in our series and compared them with reported BFLS patients. Affected males had classic features of BFLS including intellectual disability, distinctive facies, large ears, gynaecomastia, hypogonadism and truncal obesity. Carrier female relatives of affected males were unaffected or had only mild symptoms. The phenotype of affected females with de novo variants overlapped with the males but included linear skin hyperpigmentation and a higher frequency of dental, retinal and cortical brain anomalies. Complications observed in our series included keloid scarring, digital fibromas, absent vaginal orifice, neuropathy, umbilical hernias, and talipes. Our analysis highlighted sex-specific differences in PHF6 variant types and locations. Affected males often have missense variants or small in-frame deletions while affected females tend to have truncating variants or large deletions/duplications. Missense variants were found in a minority of affected females and clustered in the highly constrained PHD2 domain of PHF6. We propose recommendations for the evaluation and management of BFLS patients. These results further delineate and extend the genetic and phenotypic spectrum of BFLS.
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Affiliation(s)
- Vani Jain
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
| | - Seow Hoong Foo
- Department of Dermatology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, UK
- Department of Dermatology, Gleneagles Hospital Medini, Nusajaya, 79250, Johor, Malaysia
| | - Stephen Chooi
- School of Medicine, Cardiff University, Heath Park Campus, Cardiff, CF14 4YS, UK
| | - Celia Moss
- Department of Dermatology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B4 6NH, UK
- University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Richard Goodwin
- Department of Dermatology, Royal Gwent Hospital, Newport, NP20 2UB, UK
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Angus J Clarke
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
- Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sally J Davies
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Sian Corrin
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Oliver Murch
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Samantha Doyle
- Department of Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, D12 N512, Ireland
- Department of Clinical Genetics, The National Maternity Hospital, Holles Street, Dublin, D02 YH21, Ireland
| | - Gail E Graham
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, K1H 8L1, Canada
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, L8 7SS, UK
| | - Susan E Holder
- North West Thames Regional Genetic Service, Kennedy Galton Centre, Northwick Park Hospital, Harrow, HA1 3UJ, UK
| | - Diana Johnson
- Department of Clinical Genetics, Northern General Hospital, Sheffield, S5 7AU, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, WC1N 3JH, UK
| | - Roger L Ladda
- Department of Pediatrics, Division of Human Genetics, Penn State Health Children's Hospital, Hershey, Pennsylvania, 17033, USA
| | - Susan Sell
- Department of Pediatrics, Division of Human Genetics, Penn State Health Children's Hospital, Hershey, Pennsylvania, 17033, USA
| | | | - Sally A Lynch
- Department of Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, D12 N512, Ireland
| | - Emma McCann
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, L8 7SS, UK
| | - Rune Østern
- Department of Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, 7030, Trondheim, Norway
| | - Caroline Pottinger
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 3BZ, UK
| | - Andrew E Fry
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
- Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
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3
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Bataller A, Chien KS, Sasaki K, Montalban-Bravo G, Kanagal-Shamanna R, Urrutia S, Almanza-Huante E, Gener-Ricos G, Ravandi F, Jabbour E, Kadia T, Borthakur G, Garcia-Manero G. PHF6 mutations in myelodysplastic syndromes, chronic myelomonocytic leukemia and acute myeloid leukemia. Leuk Res 2023; 127:107044. [PMID: 36801700 DOI: 10.1016/j.leukres.2023.107044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Affiliation(s)
- Alex Bataller
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly S Chien
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Koji Sasaki
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samuel Urrutia
- Department of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Georgina Gener-Ricos
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Farhad Ravandi
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elias Jabbour
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tapan Kadia
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gautam Borthakur
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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4
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Eisa YA, Guo Y, Yang FC. The Role of PHF6 in Hematopoiesis and Hematologic Malignancies. Stem Cell Rev Rep 2023; 19:67-75. [PMID: 36008597 DOI: 10.1007/s12015-022-10447-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2022] [Indexed: 01/29/2023]
Abstract
Epigenetic regulation of gene expression represents an important mechanism in the maintenance of stem cell function. Alterations in epigenetic regulation contribute to the pathogenesis of hematological malignancies. Plant homeodomain finger protein 6 (PHF6) is a member of the plant homeodomain (PHD)-like zinc finger family of proteins that is involved in transcriptional regulation through the modification of the chromatin state. Germline mutation of PHF6 is the causative genetic alteration of the X-linked mental retardation Borjeson-Forssman-Lehmann syndrome (BFLS). Somatic mutations in PHF6 are identified in human leukemia, such as adult T-cell acute lymphoblastic leukemia (T-ALL, ~ 38%), pediatric T-ALL (~ 16%), acute myeloid leukemia (AML, ~ 3%), chronic myeloid leukemia (CML, ~ 2.5%), mixed phenotype acute leukemia (MPAL, ~ 20%), and high-grade B-cell lymphoma (HGBCL, ~ 3%). More recent studies imply an oncogenic effect of PHF6 in B-cell acute lymphoblastic leukemia (B-ALL) and solid tumors. These data demonstrate that PHF6 could act as a double-edged sword, either a tumor suppressor or an oncogene, in a lineage-dependent manner. However, the underlying mechanisms of PHF6 in normal hematopoiesis and leukemogenesis remain largely unknown. In this review, we summarize current knowledge of PHF6, emphasizing the role of PHF6 in hematological malignancies. Epigenetic regulation of PHF6 in B-ALL. PHF6 maintains a chromatin structure that is permissive to B-cell identity genes, but not T-cell-specific genes (left). Loss of PHF6 leads to aberrant expression of B-cell- and T-cell-specific genes resulting from lineage promiscuity and binding of T-cell transcription factors (right).
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Affiliation(s)
- Yusra A Eisa
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Ying Guo
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Feng-Chun Yang
- Department of Cell Systems & Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA. .,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, USA.
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5
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Tsai HI, Wu Y, Huang R, Su D, Wu Y, Liu X, Wang L, Xu Z, Pang Y, Sun C, He C, Shu F, Zhu H, Wang D, Cheng F, Huang L, Chen H. PHF6 functions as a tumor suppressor by recruiting methyltransferase SUV39H1 to nucleolar region and offers a novel therapeutic target for PHF6-muntant leukemia. Acta Pharm Sin B 2022; 12:1913-1927. [PMID: 35847518 PMCID: PMC9279718 DOI: 10.1016/j.apsb.2021.10.025] [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: 07/11/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in the plant homeodomain-like finger protein 6 (PHF6) gene are strongly associated with acute myeloid (AML) and T-cell acute lymphoblastic leukemia (T-ALL). In this study, we demonstrated that PHF6 can bind to H3K9me3 and H3K27me1 on the nucleolar chromatin and recruit histone methyltransferase SUV39H1 to the rDNA locus. The deletion of PHF6 caused a decrease in the recruitment of SUV39H1 to rDNA gene loci, resulting in a reduction in the level of H3K9me3 and the promotion of rDNA transcription. The knockdown of either SUV39H1 or PHF6 significantly attenuated the effects of increase in H3K9me3 and suppressed the transcription of rDNA induced by the overexpression of the other interacting partner, thereby establishing an interdependent relationship between PHF6 and SUV39H1 in their control of rRNA transcription. The PHF6 clinical mutants significantly impaired the ability to bind and recruit SUV39H1 to the rDNA loci, resulting in an increase in rDNA transcription activity, the proliferation of in vitro leukemia cells, and the growth of in vivo mouse xenografts. Importantly, significantly elevated levels of pre-rRNA were observed in clinical AML patients who possessed a mutated version of PHF6. The specific rDNA transcription inhibitor CX5461 significantly reduced the resistance of U937 AML cells deficient in PHF6 to cytarabine, the drug that is most commonly used to treat AML. Collectively, we revealed a novel molecular mechanism by which PHF6 recruits methyltransferase SUV39H1 to the nucleolar region in leukemia and provided a potential therapeutic target for PHF6-mutant leukemia.
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Affiliation(s)
- Hsiang-i Tsai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
- Department of Medical Imaging, the Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Yanping Wu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Rui Huang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510000, China
| | - Dandan Su
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Yingyi Wu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Xiaoyan Liu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Linglu Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Zhanxue Xu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Yuxin Pang
- School of Traditional Medicine Materials Resource, Guangdong Pharmaceutical University, Yunfu 527322, China
| | - Chong Sun
- Immune Regulation in Cancer, German Cancer Research Center, Heidelberg 69120, Germany
| | - Chao He
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Fan Shu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Haitao Zhu
- Department of Medical Imaging, the Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Dongqing Wang
- Department of Medical Imaging, the Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Fang Cheng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
- Corresponding authors.
| | - Laiqiang Huang
- The Shenzhen Key Lab of Gene and Antibody Therapy, Center for Biotechnology & Biomedicine, Division of Life and Health Sciences, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
- Corresponding authors.
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
- Corresponding authors.
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Afkhami M, Ally F, Pullarkat V, Pillai RK. Genetics and Diagnostic Approach to Lymphoblastic Leukemia/Lymphoma. Cancer Treat Res 2021; 181:17-43. [PMID: 34626353 DOI: 10.1007/978-3-030-78311-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Our understanding of the genetics and biology of lymphoblastic leukemia/lymphoma (acute lymphoblastic leukemia, ALL) has advanced rapidly in the past decade with advances in sequencing and other molecular techniques. Besides recurrent chromosomal abnormalities detected by karyotyping or fluorescence in situ hybridization, these leukemias/lymphomas are characterized by a variety of mutations, gene rearrangements as well as copy number alterations. This is particularly true in the case of Philadelphia-like (Ph-like) ALL, a major subset which has the same gene expression signature as Philadelphia chromosome-positive ALL but lacks BCR-ABL1 translocation. Ph-like ALL is associated with a worse prognosis and hence its detection is critical. However, techniques to detect this entity are complex and are not widely available. This chapter discusses various subsets of ALL and describes our approach to the accurate classification and prognostication of these cases.
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Affiliation(s)
- Michelle Afkhami
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA.
| | - Feras Ally
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Vinod Pullarkat
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Raju K Pillai
- City of Hope Medical Center, 1500 E Duarte Rd., Duarte, CA, 91010, USA
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7
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Kurzer JH, Weinberg OK. PHF6 Mutations in Hematologic Malignancies. Front Oncol 2021; 11:704471. [PMID: 34381727 PMCID: PMC8350393 DOI: 10.3389/fonc.2021.704471] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/28/2021] [Indexed: 11/23/2022] Open
Abstract
Next generation sequencing has uncovered several genes with associated mutations in hematologic malignancies that can serve as potential biomarkers of disease. Keeping abreast of these genes is therefore of paramount importance in the field of hematology. This review focuses on PHF6, a highly conserved epigenetic transcriptional regulator that is important for neurodevelopment and hematopoiesis. PHF6 serves as a tumor suppressor protein, with PHF6 mutations and deletions often implicated in the development of T-lymphoblastic leukemia and less frequently in acute myeloid leukemia and other myeloid neoplasms. PHF6 inactivation appears to be an early event in T-lymphoblastic leukemogenesis, requiring cooperating events, including NOTCH1 mutations or overexpression of TLX1 and TLX3 for full disease development. In contrast, PHF6 mutations tend to occur later in myeloid malignancies, are frequently accompanied by RUNX1 mutations, and are often associated with disease progression. Moreover, PHF6 appears to play a role in lineage plasticity within hematopoietic malignancies, with PHF6 mutations commonly present in mixed phenotype acute leukemias with a predilection for T-lineage marker expression. Due to conflicting data, the prognostic significance of PHF6 mutations remains unclear, with a subset of studies showing no significant difference in outcomes compared to malignancies with wild-type PHF6, and other studies showing inferior outcomes in certain patients with mutated PHF6. Future studies are necessary to elucidate the role PHF6 plays in development of T-lymphoblastic leukemia, progression of myeloid malignancies, and its overall prognostic significance in hematopoietic neoplasms.
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Affiliation(s)
- Jason H. Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Olga K. Weinberg
- Department of Pathology, UT Southwestern, Dallas, TX, United States
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8
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Mousa NO, Gado M, Assem MM, Dawood KM, Osman A. Expression profiling of some Acute Myeloid Leukemia - associated markers to assess their diagnostic / prognostic potential. Genet Mol Biol 2021; 44:e20190268. [PMID: 33432966 PMCID: PMC7802071 DOI: 10.1590/1678-4685-gmb-2019-0268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/21/2020] [Indexed: 12/19/2022] Open
Abstract
Investigating the etiological causes of acute myeloid leukemia (AML) at the
molecular level should help in identifying targets and strategies that would
increase the efficacy of the current management regimens. Some genes may act as
molecular diagnostics, of these ASXL1 and PHF6
are involved in regulation of gene expression, and BAX , and ARC, are pro- and anti-apoptotic molecules,
respectively. In this study, peripheral blood samples were collected from 54
recently diagnosed AML patients in addition to 20 healthy individuals (the
control group). Cellular RNA was extracted from all the samples and were
subjected to quantitative analysis of the transcript levels of the four selected
markers. Our data showed a significant elevation in the expression levels of
PHF6 and ARC in AML patients, when
compared to the controls (77.8% and 83.3%, respectively). On the other hand,
ASXL1 and BAX exhibited increase, to a
lesser extent, in the expression levels of the AML patients (52% and 55.6%,
respectively). Our study also showed that the expression levels of
ARC and PHF6 exhibited a concomitant
increase and this could be correlated with poor prognosis of the cases. Thus, we
can suggest these markers as reliable prognostic markers for prediction of AML
outcomes.
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Affiliation(s)
- Nahla O Mousa
- Egypt-Japan University of Science and Technology (E-JUST), Basic and Applied Sciences Institute, Alexandria, Egypt.,Cairo University, Faculty of Science, Department of Chemistry, Giza, Egypt
| | - Marwa Gado
- Cairo University, Faculty of Science, Department of Chemistry, Giza, Egypt
| | - Magda M Assem
- Cairo University, National Cancer Institute, Department of Clinical pathology, Giza, Egypt
| | - Kamal M Dawood
- Cairo University, Faculty of Science, Department of Chemistry, Giza, Egypt
| | - Ahmed Osman
- Egypt-Japan University of Science and Technology (E-JUST), Basic and Applied Sciences Institute, Alexandria, Egypt.,Ain shams University, Faculty of Science, Department of Biochemistry, Cairo, Egypt
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Zia S, Shahid R. Mutagenic players in ALL progression and their associated signaling pathways. Cancer Genet 2019; 233-234:7-20. [DOI: 10.1016/j.cancergen.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/10/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
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Yu Q, Yin L, Jian Y, Li P, Zeng W, Zhou J. Downregulation of PHF6 Inhibits Cell Proliferation and Migration in Hepatocellular Carcinoma. Cancer Biother Radiopharm 2019; 34:245-251. [PMID: 30888215 DOI: 10.1089/cbr.2018.2671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: The plant homeodomain finger 6 (PHF6) was originally identified as single gene mutated in Börjeson-Forssman-Lehmann syndrome, which was reported to be a tumor suppressor in T-cell acute lymphoblastic leukemia. However, the biological function of PHF6 in hepatocellular carcinoma (HCC) has been poorly characterized. Materials and Methods: In this study, we first determined the mRNA levels of PHF6 in HCC tissues and adjacent normal tissues using quantitative real-time PCR. Then the expression of PHF6 was knocked down in HCC cell lines (HepG2, SMMC-7721, and Bel-7402) by siRNA transfection. A series of functional experiments, including EdU proliferation assay, colony formation assay, and Transwell assay, were performed in HCC cells. Western blot analysis was used to detect the expression of PHF6, E-cadherin, and Vimentin. Results: We found that PHF6 was significantly elevated in HCC tissues and positively correlated with TNM stage, differentiation, and lymph node metastasis. Silencing PHF6 significantly inhibited cell proliferation, colony formation, and migration in HCC cells. Furthermore, silencing PHF6 obviously increased E-cadherin and decreased Vimentin expression. Conclusions: These findings suggest that PHF6 plays a positive role in the growth of HCC cells, and targeting PHF6 could serve as a promising therapeutic strategy for human HCC.
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Affiliation(s)
- Qiangfeng Yu
- 1 Department of Hepatobiliary Surgery, the Second Hospital of Longyan, Longyan, China.,2 Department of Hepatobiliary Surgery, Nanfang Hospital Affiliated to Southern Medical University, Guangzhou, China
| | - Libo Yin
- 3 Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral & Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Yizeng Jian
- 1 Department of Hepatobiliary Surgery, the Second Hospital of Longyan, Longyan, China
| | - Pengtao Li
- 4 Department of Hepatobiliary and Pancreatic Surgery, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Wenlong Zeng
- 1 Department of Hepatobiliary Surgery, the Second Hospital of Longyan, Longyan, China
| | - Jianyin Zhou
- 4 Department of Hepatobiliary and Pancreatic Surgery, Zhongshan Hospital, Xiamen University, Xiamen, China
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11
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Lindström MS, Jurada D, Bursac S, Orsolic I, Bartek J, Volarevic S. Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis. Oncogene 2018; 37:2351-2366. [PMID: 29429989 PMCID: PMC5931986 DOI: 10.1038/s41388-017-0121-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
The nucleolus is the major site for synthesis of ribosomes, complex molecular machines that are responsible for protein synthesis. A wealth of research over the past 20 years has clearly indicated that both quantitative and qualitative alterations in ribosome biogenesis can drive the malignant phenotype via dysregulation of protein synthesis. However, numerous recent proteomic, genomic, and functional studies have implicated the nucleolus in the regulation of processes that are unrelated to ribosome biogenesis, including DNA-damage response, maintenance of genome stability and its spatial organization, epigenetic regulation, cell-cycle control, stress responses, senescence, global gene expression, as well as assembly or maturation of various ribonucleoprotein particles. In this review, the focus will be on features of rDNA genes, which make them highly vulnerable to DNA damage and intra- and interchromosomal recombination as well as built-in mechanisms that prevent and repair rDNA damage, and how dysregulation of this interplay affects genome-wide DNA stability, gene expression and the balance between euchromatin and heterochromatin. We will also present the most recent insights into how malfunction of these cellular processes may be a central driving force of human malignancies, and propose a promising new therapeutic approach for the treatment of cancer.
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Affiliation(s)
- Mikael S Lindström
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Deana Jurada
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Sladana Bursac
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Ines Orsolic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- The Danish Cancer Society Research Centre, Copenhagen, Denmark.
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia.
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia.
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Choi J, Polcher A, Joas A. Systematic literature review on Parkinson's disease and Childhood Leukaemia and mode of actions for pesticides. ACTA ACUST UNITED AC 2016. [DOI: 10.2903/sp.efsa.2016.en-955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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The relationship between the nucleolus and cancer: Current evidence and emerging paradigms. Semin Cancer Biol 2015; 37-38:36-50. [PMID: 26721423 DOI: 10.1016/j.semcancer.2015.12.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/15/2015] [Accepted: 12/19/2015] [Indexed: 12/13/2022]
Abstract
The nucleolus is the most prominent nuclear substructure assigned to produce ribosomes; molecular machines that are responsible for carrying out protein synthesis. To meet the increased demand for proteins during cell growth and proliferation the cell must increase protein synthetic capacity by upregulating ribosome biogenesis. While larger nucleolar size and number have been recognized as hallmark features of many tumor types, recent evidence has suggested that, in addition to overproduction of ribosomes, decreased ribosome biogenesis as well as qualitative changes in this process could also contribute to tumor initiation and cancer progression. Furthermore, the nucleolus has become the focus of intense attention for its involvement in processes that are clearly unrelated to ribosome biogenesis such as sensing and responding to endogenous and exogenous stressors, maintenance of genome stability, regulation of cell-cycle progression, cellular senescence, telomere function, chromatin structure, establishment of nuclear architecture, global regulation of gene expression and biogenesis of multiple ribonucleoprotein particles. The fact that dysregulation of many of these fundamental cellular processes may contribute to the malignant phenotype suggests that normal functioning of the nucleolus safeguards against the development of cancer and indicates its potential as a therapeutic approach. Here we review the recent advances made toward understanding these newly-recognized nucleolar functions and their roles in normal and cancer cells, and discuss possible future research directions.
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Luan C, Yang Z, Chen B. The functional role of microRNA in acute lymphoblastic leukemia: relevance for diagnosis, differential diagnosis, prognosis, and therapy. Onco Targets Ther 2015; 8:2903-14. [PMID: 26508875 PMCID: PMC4610789 DOI: 10.2147/ott.s92470] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs), a new class of noncoding RNAs, which can hybridize to target messenger RNAs and regulate their expression posttranscriptionally, express differentially in distinct stages of lymphopoiesis and influence the direction of lymphoid precursor maturation. Hence, there is aberrant expression of miRNAs involved in malignant lymphopoiesis, and these aberrations can be used as signatures of acute lymphoblastic leukemia (ALL) with different subtypes. In addition, changes in the expression of several miRNAs may have functional relevance with leukemogenesis or drug resistance. As a result, the reversal of the expression of these miRNAs may alleviate the disease to some extent and improve clinical outcomes. However, among the studies of miRNAs, there are still some problems that need to be solved to understand the function of miRNAs in ALL more thoroughly.
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Affiliation(s)
- Chengxin Luan
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, People's Republic of China
| | - Zixue Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Baoan Chen
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, People's Republic of China
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15
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Peirs S, Van der Meulen J, Van de Walle I, Taghon T, Speleman F, Poppe B, Van Vlierberghe P. Epigenetics in T-cell acute lymphoblastic leukemia. Immunol Rev 2015; 263:50-67. [PMID: 25510271 DOI: 10.1111/imr.12237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Normal T-cell development is a strictly regulated process in which hematopoietic progenitor cells migrate from the bone marrow to the thymus and differentiate from early T-cell progenitors toward mature and functional T cells. During this maturation process, cooperation between a variety of oncogenes and tumor suppressors can drive immature thymocytes into uncontrolled clonal expansion and cause T-cell acute lymphoblastic leukemia (T-ALL). Despite improved insights in T-ALL disease biology and comprehensive characterization of its genetic landscape, clinical care remained largely similar over the past decades and still consists of high-dose multi-agent chemotherapy potentially followed by hematopoietic stem cell transplantation. Even with such aggressive treatment regimens, which are often associated with considerable side effects, clinical outcome is still extremely poor in a significant subset of T-ALL patients as a result of therapy resistance or hematological relapses. Recent genetic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in T-ALL, suggesting that epigenetic homeostasis is critically required in restraining tumor development in the T-cell lineage. In this review, we provide an overview of the epigenetic regulators that could be implicated in T-ALL disease biology and speculate how the epigenetic landscape of T-ALL could trigger the development of epigenetic-based therapies to further improve the treatment of human T-ALL.
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Affiliation(s)
- Sofie Peirs
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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16
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PHF6 Degrees of Separation: The Multifaceted Roles of a Chromatin Adaptor Protein. Genes (Basel) 2015; 6:325-52. [PMID: 26103525 PMCID: PMC4488667 DOI: 10.3390/genes6020325] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 12/13/2022] Open
Abstract
The importance of chromatin regulation to human disease is highlighted by the growing number of mutations identified in genes encoding chromatin remodeling proteins. While such mutations were first identified in severe developmental disorders, or in specific cancers, several genes have been implicated in both, including the plant homeodomain finger protein 6 (PHF6) gene. Indeed, germline mutations in PHF6 are the cause of the Börjeson–Forssman–Lehmann X-linked intellectual disability syndrome (BFLS), while somatic PHF6 mutations have been identified in T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). Studies from different groups over the last few years have made a significant impact towards a functional understanding of PHF6 protein function. In this review, we summarize the current knowledge of PHF6 with particular emphasis on how it interfaces with a distinct set of interacting partners and its functional roles in the nucleoplasm and nucleolus. Overall, PHF6 is emerging as a key chromatin adaptor protein critical to the regulation of neurogenesis and hematopoiesis.
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17
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Meacham CE, Lawton LN, Soto-Feliciano YM, Pritchard JR, Joughin BA, Ehrenberger T, Fenouille N, Zuber J, Williams RT, Young RA, Hemann MT. A genome-scale in vivo loss-of-function screen identifies Phf6 as a lineage-specific regulator of leukemia cell growth. Genes Dev 2015; 29:483-8. [PMID: 25737277 PMCID: PMC4358400 DOI: 10.1101/gad.254151.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Meacham et al. performed a genome-scale shRNA screen for modulators of B-cell leukemia progression in vivo and revealed dramatic distinctions between the relative effects of shRNAs on the growth of tumor cells in culture versus in their native microenvironment. They identified “context-specific” regulators of leukemia development, including the gene encoding the zinc finger protein Phf6. While inactivating mutations in Phf6 are commonly observed in human myeloid and T-cell malignancies, they found that Phf6 suppression in B-cell malignancies impairs tumor progression. We performed a genome-scale shRNA screen for modulators of B-cell leukemia progression in vivo. Results from this work revealed dramatic distinctions between the relative effects of shRNAs on the growth of tumor cells in culture versus in their native microenvironment. Specifically, we identified many “context-specific” regulators of leukemia development. These included the gene encoding the zinc finger protein Phf6. While inactivating mutations in PHF6 are commonly observed in human myeloid and T-cell malignancies, we found that Phf6 suppression in B-cell malignancies impairs tumor progression. Thus, Phf6 is a “lineage-specific” cancer gene that plays opposing roles in developmentally distinct hematopoietic malignancies.
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Affiliation(s)
- Corbin E Meacham
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lee N Lawton
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Yadira M Soto-Feliciano
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Justin R Pritchard
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tobias Ehrenberger
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nina Fenouille
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Johannes Zuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Richard T Williams
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Michael T Hemann
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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18
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Yohe S. Molecular Genetic Markers in Acute Myeloid Leukemia. J Clin Med 2015; 4:460-78. [PMID: 26239249 PMCID: PMC4470139 DOI: 10.3390/jcm4030460] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/15/2015] [Accepted: 02/03/2015] [Indexed: 12/19/2022] Open
Abstract
Genetics play an increasingly important role in the risk stratification and management of acute myeloid leukemia (AML) patients. Traditionally, AML classification and risk stratification relied on cytogenetic studies; however, molecular detection of gene mutations is playing an increasingly important role in classification, risk stratification, and management of AML. Molecular testing does not take the place of cytogenetic testing results, but plays a complementary role to help refine prognosis, especially within specific AML subgroups. With the exception of acute promyelocytic leukemia, AML therapy is not targeted but the intensity of therapy is driven by the prognostic subgroup. Many prognostic scoring systems classify patients into favorable, poor, or intermediate prognostic subgroups based on clinical and genetic features. Current standard of care combines cytogenetic results with targeted testing for mutations in FLT3, NPM1, CEBPA, and KIT to determine the prognostic subgroup. Other gene mutations have also been demonstrated to predict prognosis and may play a role in future risk stratification, although some of these have not been confirmed in multiple studies or established as standard of care. This paper will review the contribution of cytogenetic results to prognosis in AML and then will focus on molecular mutations that have a prognostic or possible therapeutic impact.
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Affiliation(s)
- Sophia Yohe
- Department of Laboratory Medicine and Pathology, Divisions of Hematopathology and Molecular Genetic Pathology, University of Minnesota, MMC Box 609 Mayo, 420 Delaware St. SE. Minneapolis, MN 55455, USA.
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19
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Mets E, Van Peer G, Van der Meulen J, Boice M, Taghon T, Goossens S, Mestdagh P, Benoit Y, De Moerloose B, Van Roy N, Poppe B, Vandesompele J, Wendel HG, Van Vlierberghe P, Speleman F, Rondou P. MicroRNA-128-3p is a novel oncomiR targeting PHF6 in T-cell acute lymphoblastic leukemia. Haematologica 2014; 99:1326-33. [PMID: 24895337 DOI: 10.3324/haematol.2013.099515] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
T-cell acute lymphoblastic leukemia arises from the leukemic transformation of developing thymocytes and results from cooperative genetic lesions. Inactivation of the PHF6 gene is frequently observed in T-cell acute lymphoblastic leukemia, suggesting an important tumor suppressive role for PHF6 in the pathobiology of this leukemia. Although the precise function of PHF6 is still unknown, this gene is most likely involved in chromatin regulation, a strongly emerging theme in T-cell acute lymphoblastic leukemia. In this context, our previous description of a cooperative microRNA regulatory network controlling several well-known T-cell acute lymphoblastic leukemia tumor suppressor genes, including PHF6, is of great importance. Given the high frequency of PHF6 lesions in T-cell acute lymphoblastic leukemia and the integration of PHF6 in this microRNA regulatory network, we aimed to identify novel oncogenic microRNAs in T-cell acute lymphoblastic leukemia which suppress PHF6. To this end, we performed an unbiased PHF6 3'UTR-microRNA library screen and combined the results with microRNA profiling data of samples from patients with T-cell acute lymphoblastic leukemia and normal thymocyte subsets. We selected miR-128-3p as a candidate PHF6-targeting, oncogenic microRNA and demonstrated regulation of PHF6 expression upon modulation of this microRNA in T-cell acute lymphoblastic leukemia cell lines. In vivo evidence of an oncogenic role of this microRNA in T-cell acute lymphoblastic leukemia was obtained through accelerated leukemia onset in a NOTCH1-induced T-cell acute lymphoblastic leukemia mouse model upon miR-128-3p over-expression. We conclude that miR-128-3p is a strong novel candidate oncogenic microRNA in T-cell acute lymphoblastic leukemia which targets the PHF6 tumor suppressor gene.
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Affiliation(s)
- Evelien Mets
- Center for Medical Genetics, Ghent University, Belgium
| | - Gert Van Peer
- Center for Medical Genetics, Ghent University, Belgium
| | | | - Michael Boice
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Tom Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Belgium
| | - Steven Goossens
- Unit for Molecular Oncology, Inflammation Research Center, VIB, Ghent, Belgium Department for Molecular Biomedical Research, Ghent University, Belgium
| | | | - Yves Benoit
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Belgium
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Belgium
| | | | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Belgium
| | | | - Hans-Guido Wendel
- Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | | | - Pieter Rondou
- Center for Medical Genetics, Ghent University, Belgium
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20
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Van der Meulen J, Van Roy N, Van Vlierberghe P, Speleman F. The epigenetic landscape of T-cell acute lymphoblastic leukemia. Int J Biochem Cell Biol 2014; 53:547-57. [PMID: 24786297 DOI: 10.1016/j.biocel.2014.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 12/29/2022]
Abstract
The genetic landscape of T-ALL has been very actively explored during the past decades. This leads to an overwhelming body of exciting novel findings providing insight into (1) the genetic heterogeneity of the disease with marked genetic subsets, (2) the mechanisms by which aberrant T-cell development drive leukemogenesis and (3) emerging opportunities for novel therapeutic interventions. Of further interest, recent genome wide sequencing studies identified proteins that actively participate in the regulation of the T-cell epigenome as novel oncogenes and tumor suppressor genes in T-ALL. The identification of these perturbed molecular epigenetic events in the pathogenesis of T-ALL will contribute to the further exploration of novel therapies in this cancer type. As some epigenetic therapies have recently been approved for a number of hematological neoplasms, one could speculate that targeted therapies against epigenetic regulators might offer good prospects for T-ALL treatment in the near future. In this review, we summarize the epigenetic discoveries made in T-ALL hitherto and discuss possible new venues for epigenetic therapeutic intervention in this aggressive subtype of human leukemia. This article is part of a Directed Issue entitled: Rare Cancers.
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Affiliation(s)
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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21
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Pastor-Barriuso R, López-Abente G. Changes in period and cohort effects on haematological cancer mortality in Spain, 1952-2006. BMC Cancer 2014; 14:250. [PMID: 24716829 PMCID: PMC4021557 DOI: 10.1186/1471-2407-14-250] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/31/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In contrast to other haematological cancers, mortality from non-Hodgkin's lymphoma and multiple myeloma increased dramatically during the second half of the 20th century in most developed countries. This widespread upward trend remains controversial, as it may be attributable either to progressive improvements in diagnosis and certification or to increasing exposures to little-known but relevant risk factors. METHODS To assess the relative contribution of these factors, we analysed the independent effects of age, death period, and birth cohort on haematological cancer mortality rates in Spain across the period 1952-2006. Weighted joinpoint regression analyses were performed to detect and estimate changes in period and cohort curvatures. RESULTS Although mortality rates were consistently higher among men, trends across periods and cohorts were virtually identical in both sexes. There was an early period trend reversal in the 1960s for Hodgkin's disease and leukaemia, which was delayed to the 1980s for multiple myeloma and the 1990s for non-Hodgkin's lymphoma. Birth cohort patterns showed a first downturn for generations born in the 1900s and 1910s for all haematological cancers, and a second trend reversal for more recent cohorts born in the 1950s and 1960s for non-Hodgkin's lymphoma and leukaemia. CONCLUSIONS The sustained decline in Hodgkin's disease mortality and the levelling off in leukaemia seem to be driven by an early period effect linked to improvements in disease treatment, whereas the steep upward trends in non-Hodgkin's lymphoma and multiple myeloma mortality in Spain are more likely explained by a cohort effect linked to better diagnosis and death certification in the elderly. The consistent male excess mortality across all calendar periods and age groups points to the importance of possible sex-related genetic markers of susceptibility in haematological cancers.
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Affiliation(s)
- Roberto Pastor-Barriuso
- National Center for Epidemiology, Carlos III Institute of Health, Monforte de Lemos 5, 28029, Madrid, Spain.
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22
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Kechavarzi B, Janga SC. Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol 2014; 15:R14. [PMID: 24410894 PMCID: PMC4053825 DOI: 10.1186/gb-2014-15-1-r14] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/10/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA-binding proteins (RBPs) play important roles in cellular homeostasis by controlling gene expression at the post-transcriptional level. RESULTS We explore the expression of more than 800 RBPs in sixteen healthy human tissues and their patterns of dysregulation in cancer genomes from The Cancer Genome Atlas project. We show that genes encoding RBPs are consistently and significantly highly expressed compared with other classes of genes, including those encoding regulatory components such as transcription factors, miRNAs and long non-coding RNAs. We also demonstrate that a set of RBPs, numbering approximately 30, are strongly upregulated (SUR) across at least two-thirds of the nine cancers profiled in this study. Analysis of the protein-protein interaction network properties for the SUR and non-SUR groups of RBPs suggests that path length distributions between SUR RBPs is significantly lower than those observed for non-SUR RBPs. We further find that the mean path lengths between SUR RBPs increases in proportion to their contribution to prognostic impact. We also note that RBPs exhibiting higher variability in the extent of dysregulation across breast cancer patients have a higher number of protein-protein interactions. We propose that fluctuating RBP levels might result in an increase in non-specific protein interactions, potentially leading to changes in the functional consequences of RBP binding. Finally, we show that the expression variation of a gene within a patient group is inversely correlated with prognostic impact. CONCLUSIONS Overall, our results provide a roadmap for understanding the impact of RBPs on cancer pathogenesis.
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Affiliation(s)
- Bobak Kechavarzi
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University – Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University – Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, USA
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23
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Current world literature. Curr Opin Oncol 2012; 24:756-68. [PMID: 23079785 DOI: 10.1097/cco.0b013e32835a4c91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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24
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Kim MS, Chung NG, Kim MS, Yoo NJ, Lee SH. Somatic mutation of IL7R exon 6 in acute leukemias and solid cancers. Hum Pathol 2012; 44:551-5. [PMID: 23069254 DOI: 10.1016/j.humpath.2012.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 06/27/2012] [Accepted: 06/29/2012] [Indexed: 12/14/2022]
Abstract
Inframe insertion and deletion/insertion (delins) mutations of the IL7R gene in exon 6 have recently been reported in childhood T-cell acute lymphoblastic leukemia (T-ALL). The recurrent nature of the IL7R mutations in the same region strongly suggests that the IL7R mutations may play an important role in the pathogenesis of childhood T-ALL. The aim of this study was to address whether IL7R exon 6 mutation occurs in other human tumors besides childhood T-ALL. For this, we analyzed 1792 tumor tissues from various origins, including 432 hematologic and 1360 nonhematopoietic tumors by single-strand conformation polymorphism analysis to detect the exon 6 mutations. Overall, we found 10 IL7R exon 6 mutations in seven hematologic malignancies (three childhood T-ALL [12%], one adult T-ALL [7%], two childhood precursor B-cell acute lymphoblastic leukemia (B-ALL) [2%] and one adult acute myelogenous leukemia (AML) [1%]) and three nonhematopoietic malignancies (one lung cancer [0.6%] and two colorectal cancer [0.5%]), but none in other tumors. IL7R mutations detected in hematologic tumors were exclusively inframe insertion and delins mutations, whereas those detected in non-hematologic tumors were missense and frameshift mutations. Our data indicate that IL7R exon 6 inframe mutations occur not only in childhood T-ALL but also other acute leukemias at slightly lower frequencies. Our data suggest that the IL7R mutations may contribute to the development of diverse types of acute leukemias, and that possible therapies targeting the IL7R exon 6 mutation should include not only childhood T-ALL but also T-ALL, childhood precursor B-ALL, and adult AML.
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Affiliation(s)
- Min Sung Kim
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul 137-701, South Korea
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25
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Todd MAM, Picketts DJ. PHF6 interacts with the nucleosome remodeling and deacetylation (NuRD) complex. J Proteome Res 2012; 11:4326-37. [PMID: 22720776 DOI: 10.1021/pr3004369] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mutations in PHF6 are the cause of Börjeson-Forssman-Lehman syndrome (BFLS), an X-linked intellectual disability (XLID) disorder, and both T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). The PHF6 gene encodes a protein with two plant homeodomain (PHD)-like zinc finger domains. As many PHD-like domains function to target chromatin remodelers to post-translationally modified histones, this suggests a role for PHF6 in chromatin regulation. However, PHD domains are usually found in association with a catalytic domain, a feature that is lacking in PHF6. This distinct domain structure and the minimal information on its cellular function prompted us to perform a proteomic screen to identify PHF6 binding partners. We expressed recombinant Flag-tagged PHF6 in HEK 293T cells for coimmunoprecipitation, and analyzed the purified products by mass spectrometry. We identified proteins involved in ribosome biogenesis, RNA splicing, and chromatin regulation, consistent with PHF6 localization to both the nucleoplasm and nucleolus. Notably, PHF6 copurified with multiple constituents of the nucleosome remodeling and deacetylation (NuRD) complex, including CHD4, HDAC1, and RBBP4. We demonstrate that this PHF6-NuRD complex is not present in the nucleolus but is restricted to the nucleoplasm. The association with NuRD represents the first known interaction for PHF6 and implicates it in chromatin regulation.
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Affiliation(s)
- Matthew A M Todd
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8L6
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Abstract
Cancer cells silence autosomal tumor suppressor genes by Knudson's two-hit mechanism in which loss-of-function mutations and then loss of heterozygosity occur at the tumor suppressor gene loci. However, the identification of X-linked tumor suppressor genes has challenged the traditional theory of 'two-hit inactivation' in tumor suppressor genes, introducing the novel concept that a single genetic hit can cause loss of tumor suppressor function. The mechanism through which these genes are silenced in human cancer is unclear, but elucidating the details will greatly enhance our understanding of the pathogenesis of human cancer. Here, we review the identification of X-linked tumor suppressor genes and discuss the potential mechanisms of their inactivation. In addition, we also discuss how the identification of X-linked tumor suppressor genes can potentially lead to new approaches in cancer therapy.
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Affiliation(s)
- Runhua Liu
- Division of Immunotherapy, Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham and Comprehensive Cancer Center, Birmingham, AL, USA
| | - Mandy Kain
- Division of Immunotherapy, Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Lizhong Wang
- Division of Immunotherapy, Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA
- Department of Genetics, School of Medicine, University of Alabama at Birmingham and Comprehensive Cancer Center, Birmingham, AL, USA
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