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Wu J, Zhang X, Lin S, Wei Q, Lin Z, Jin O, Gu J. Alterations in peripheral T- and B-cell subsets in patients with systemic sclerosis. Int J Rheum Dis 2024; 27:e15145. [PMID: 38661314 DOI: 10.1111/1756-185x.15145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
OBJECTIVES To determine the alteration of peripheral T and B cell subsets in patients with systemic sclerosis (SSc) and to evaluate their correlation with the progression of SSc. METHODS We recruited 47 SSc patients and 45 healthy controls (HCs) in this study. Demographic and clinical data were then collected. Flow cytometry was used to detect the proportions of 44 different T and B cell subsets in circulating blood. RESULTS The proportion of total B cells (p = .043) decreased in SSc patients, together with similar frequencies of total T cells, CD4+ T cells, and CD8+ T cells in both groups. Several subsets of T and B cells differed significantly between these two groups. Follicular helper T cells-1 (Tfh1) (p < .001), helper T cells-1 (Th1) (p = .001), regulatory T cells (Treg) (p = .004), effector memory CD8+ T cells (p = .041), and cytotoxic T cells-17 (Tc17) (p = .01) were decreased in SSc patients. Follicular helper T cells-2 (Tfh2) (p = .001) and, helper T cells-2 (Th2) (p = .001) levels increased in the SSc group. Regulatory B cells (Breg) (p = .015) were lower in the SSc group, together with marginal zone (MZ) B cells (p < .001), memory B cells (p = .001), and non-switched B cells (p = .005). The modified Rodnan skin score (mRSS) correlated with helper T cells-17 (Th17) (r = -.410, p = .004), Tfh1 (r = -.321, p = .028), peripheral helper T cells (Tph) (r = -.364, p = .012) and plasma cells (r = -.312, p = .033). CONCLUSIONS The alterations in T and B cells implied immune dysfunction, which may play an essential role in systemic sclerosis.
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Affiliation(s)
- Jialing Wu
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xi Zhang
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shen Lin
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Qiujing Wei
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhiming Lin
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Ou Jin
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jieruo Gu
- Department of Rheumatology and Immunology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
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Merkouris E, Mavroudi T, Miliotas D, Tsiptsios D, Serdari A, Christidi F, Doskas TK, Mueller C, Tsamakis K. Probiotics' Effects in the Treatment of Anxiety and Depression: A Comprehensive Review of 2014-2023 Clinical Trials. Microorganisms 2024; 12:411. [PMID: 38399815 PMCID: PMC10893170 DOI: 10.3390/microorganisms12020411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Changes in the gut microbiome can affect cognitive and psychological functions via the microbiota-gut-brain (MGB) axis. Probiotic supplements are thought to have largely positive effects on mental health when taken in sufficient amounts; however, despite extensive research having been conducted, there is a lack of consistent findings on the effects of probiotics on anxiety and depression and the associated microbiome alterations. The aim of our study is to systematically review the most recent literature of the last 10 years in order to clarify whether probiotics could actually improve depression and anxiety symptoms. Our results indicate that the majority of the most recent literature suggests a beneficial role of probiotics in the treatment of depression and anxiety, despite the existence of a substantial number of less positive findings. Given probiotics' potential to offer novel, personalized treatment options for mood disorders, further, better targeted research in psychiatric populations is needed to address concerns about the exact mechanisms of probiotics, dosing, timing of treatment, and possible differences in outcomes depending on the severity of anxiety and depression.
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Affiliation(s)
- Ermis Merkouris
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | - Theodora Mavroudi
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | - Daniil Miliotas
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | - Dimitrios Tsiptsios
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
- 3rd Neurology Department, Aristotle University, 54124 Thessaloniki, Greece
| | - Aspasia Serdari
- Department of Child and Adolescent Psychiatry, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Foteini Christidi
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | | | - Christoph Mueller
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London SE5 8AB, UK;
- Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London SE5 8AF, UK
| | - Konstantinos Tsamakis
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London SE5 8AB, UK;
- Institute of Medical and Biomedical Education, St George’s, University of London, London SW17 0RE, UK
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3
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Valdivia-Zúñiga CA, Bobadilla-Lescano G, Martínez-Escalante FA, Balam-May AJ, Cámara-Arrigunaga F. [Frequency of spinopelvic alterations in postoperative total hip arthroplasty patients and their association with functional outcomes]. Acta Ortop Mex 2024; 38:3-9. [PMID: 38657145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
INTRODUCTION the analysis of spinopelvic imbalance in patients undergoing total hip arthroplasty has gained significance in recent years, being recognized as a risk factor for instability. Few reports exist regarding the prevalence of spinopelvic alterations in Latin American literature. The aim of this study is to determine the frequency of spinopelvic imbalance in our patients and to associate them with functional outcomes. MATERIAL AND METHODS 29 patients who underwent total hip arthroplasty using a lateral approach (32 arthroplasties) were included. All patients completed clinical outcome questionnaires preoperatively. Twelve months after surgery, they underwent anteroposterior pelvic and lateral pelvic X-rays, both standing and sitting, and clinical outcome questionnaires were completed. The radiographic parameters examined were: pelvic incidence, lumbar lordosis, sacral slope, anterior pelvic plane and pelvic femoral angle. Functional outcome was assessed with the Harris Hip Score and WOMAC scales. Patients were classified according to their spinopelvic alteration and statistical analysis was performed to identify significant differences between the groups and the correlation with functional outcomes. RESULTS there was a high frequency of spinopelvic balance alterations (46.8%); 6.2% (n = 2/32) presented isolated spinal stiffness (group 1B), 37.5% (n = 12/29) spinal deformity without spinal stiffness (group 2A) and 3.1% (n = 1/29) spinal deformity associated with stiffness (group 2B). We found no improvement in HHS and WOMAC scores in the groups with spinal stiffness (1B and 2B) (p = 0.98 y 0.15). There is association between spinal stiffness (SS < 10°) and poor functional outcomes (p = 0.02). CONCLUSIONS the frequency of spinopelvic balance alterations was high. While there was no observed rise in prosthetic dislocations, the existence of spinal stiffness, defined by a SS of less than 10°, was associated to poor outcomes on functional scales.
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Affiliation(s)
- C A Valdivia-Zúñiga
- Departamento de Cirugía Articular, Hospital de Ortopedia Cruz Roja Mexicana. Mérida, Yucatán. México
| | - G Bobadilla-Lescano
- Departamento de Cirugía Articular, Hospital de Ortopedia Cruz Roja Mexicana. Mérida, Yucatán. México
| | - F A Martínez-Escalante
- Departamento de Cirugía Articular, Hospital de Ortopedia Cruz Roja Mexicana. Mérida, Yucatán. México
| | - A J Balam-May
- Universidad Autónoma de Yucatán. Mérida, Yucatán. México
| | - F Cámara-Arrigunaga
- Departamento de Cirugía Articular, Hospital de Ortopedia Cruz Roja Mexicana. Mérida, Yucatán. México
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4
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Abdullah M, Rehman MSU, Rehman MSNU, AlKahtane AA, Al-Hazani TM, Hassan FU, Rehman SU. Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family. Animals (Basel) 2023; 13:2246. [PMID: 37508024 PMCID: PMC10376873 DOI: 10.3390/ani13142246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo.
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Affiliation(s)
- Muhammad Abdullah
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muhammad Saif-Ur Rehman
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Abdullah A AlKahtane
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Tahani Mohamed Al-Hazani
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj 11940, Saudi Arabia
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
- Department of Breeding and Genetics, Cholistan University of Veterinary and Animal Sciences, Bahawalpur 63100, Pakistan
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
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5
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Lukashchuk N, Barnicle A, Adelman CA, Armenia J, Kang J, Barrett JC, Harrington EA. Impact of DNA damage repair alterations on prostate cancer progression and metastasis. Front Oncol 2023; 13:1162644. [PMID: 37434977 PMCID: PMC10331135 DOI: 10.3389/fonc.2023.1162644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/01/2023] [Indexed: 07/13/2023] Open
Abstract
Prostate cancer is among the most common diseases worldwide. Despite recent progress with treatments, patients with advanced prostate cancer have poor outcomes and there is a high unmet need in this population. Understanding molecular determinants underlying prostate cancer and the aggressive phenotype of disease can help with design of better clinical trials and improve treatments for these patients. One of the pathways often altered in advanced prostate cancer is DNA damage response (DDR), including alterations in BRCA1/2 and other homologous recombination repair (HRR) genes. Alterations in the DDR pathway are particularly prevalent in metastatic prostate cancer. In this review, we summarise the prevalence of DDR alterations in primary and advanced prostate cancer and discuss the impact of alterations in the DDR pathway on aggressive disease phenotype, prognosis and the association of germline pathogenic alterations in DDR genes with risk of developing prostate cancer.
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Affiliation(s)
- Natalia Lukashchuk
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Alan Barnicle
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Carrie A. Adelman
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Joshua Armenia
- Oncology Data Science, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
| | - Jinyu Kang
- Global Medicines Development, Oncology Research and Development (R&D), AstraZeneca, Gaithersburg, MD, United States
| | - J. Carl Barrett
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Waltham, MA, United States
| | - Elizabeth A. Harrington
- Translational Medicine, Oncology Research and Development (R&D), AstraZeneca, Cambridge, United Kingdom
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6
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Masud N. Symphony in the crowd: Key genetic alterations in prostate cancer. Cancer Innov 2023; 2:203-209. [PMID: 38089408 PMCID: PMC10686121 DOI: 10.1002/cai2.52] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 02/02/2024]
Abstract
Androgen receptor (AR) signaling have been frequently targeted for treating prostate cancer (PCa). Even though primarily patients receive a good therapeutic outcome by targeting AR signaling axis, eventually it emerges resistance by altering the genetic makeup of prostate cells. However, to develop an effective therapeutic regime, it is essential to recognize key genetic alterations in PCa. The most common genetic alterations that give rise to distinct androgen different differentiation states are gene fusion of TMPRSS2 with ETS family genes, deletion, or mutation of tumor suppressor PTEN and TP53 gene, amplification or splicing of AR, altered DNA repair genes. In this review, we describe key genes and genetic changes that have been recognized to contribute to altered prostate environment.
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Affiliation(s)
- Neshat Masud
- Department of PharmacologyUniversity of Louisiana at MonroeMonroeLAUSA
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7
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Chen C, Liu X, Chang CY, Wang HY, Wang RF. The Interplay between T Cells and Cancer: The Basis of Immunotherapy. Genes (Basel) 2023; 14:genes14051008. [PMID: 37239368 DOI: 10.3390/genes14051008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Over the past decade, immunotherapy has emerged as one of the most promising approaches to cancer treatment. The use of immune checkpoint inhibitors has resulted in impressive and durable clinical responses in the treatment of various cancers. Additionally, immunotherapy utilizing chimeric antigen receptor (CAR)-engineered T cells has produced robust responses in blood cancers, and T cell receptor (TCR)-engineered T cells are showing promising results in the treatment of solid cancers. Despite these noteworthy advancements in cancer immunotherapy, numerous challenges remain. Some patient populations are unresponsive to immune checkpoint inhibitor therapy, and CAR T cell therapy has yet to show efficacy against solid cancers. In this review, we first discuss the significant role that T cells play in the body's defense against cancer. We then delve into the mechanisms behind the current challenges facing immunotherapy, starting with T cell exhaustion due to immune checkpoint upregulation and changes in the transcriptional and epigenetic landscapes of dysfunctional T cells. We then discuss cancer-cell-intrinsic characteristics, including molecular alterations in cancer cells and the immunosuppressive nature of the tumor microenvironment (TME), which collectively facilitate tumor cell proliferation, survival, metastasis, and immune evasion. Finally, we examine recent advancements in cancer immunotherapy, with a specific emphasis on T-cell-based treatments.
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Affiliation(s)
- Christina Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xin Liu
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Che-Yu Chang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Helen Y Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rong-Fu Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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8
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Brcic I, Scheipl S, Bergovec M, Leithner A, Szkandera J, Sotlar K, Suda A, Smolle MA, Kraus T, Rosenberg AE, Liegl-Atzwanger B, Igrec J. Implementation of Copy Number Variations-Based Diagnostics in Morphologically Challenging EWSR1/FUS::NFATC2 Neoplasms of the Bone and Soft Tissue. Int J Mol Sci 2022; 23:ijms232416196. [PMID: 36555836 PMCID: PMC9784784 DOI: 10.3390/ijms232416196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
In the last decade, new tumor entities have been described, including EWSR1/FUS::NFATC2-rearranged neoplasms of different biologic behavior. To gain further insights into the behavior of these tumors, we analyzed a spectrum of EWSR1/FUS::NFATC2-rearranged neoplasms and discuss their key diagnostic and molecular features in relation to their prognosis. We report five patients with EWSR1/FUS::NFATC2-rearranged neoplasms, including one simple bone cyst (SBC), two complex cystic bone lesions lacking morphological characteristics of SBC, and two sarcomas. In three cases, fluorescence in situ hybridization (FISH) and in all cases copy number variation (CNV) profiling and fusion analyses were performed. All patients were male, three cystic lesions occurred in children (aged 10, 14, and 17 years), and two sarcomas in adults (69 and 39 years). Fusion analysis revealed two FUS::NFATC2 rearrangements in two cystic lesions and three EWSR1::NFATC2 rearrangements in one complex cystic lesion and two sarcomas. EWSR1 FISH revealed tumor cells with break-apart signal without amplification in one complex cystic lesion and EWSR1 amplification in both sarcomas was documented. CNV analysis showed simple karyotypes in all cystic lesions, while more complex karyotypes were found in NFATC2-rearranged sarcomas. Our study supports and expands previously reported molecular findings of EWSR1/FUS::NFATC2-rearranged neoplasms. The study highlights the importance of combining radiology and morphologic features with molecular aberrations. The use of additional molecular methods, such as CNV and FISH in the routine diagnostic workup, can be crucial in providing a correct diagnosis and avoiding overtreatment.
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Affiliation(s)
- Iva Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Susanne Scheipl
- Department of Orthopedics and Trauma, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Marko Bergovec
- Department of Orthopedics and Trauma, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Andreas Leithner
- Department of Orthopedics and Trauma, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Joanna Szkandera
- Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Karl Sotlar
- Institute of Pathology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Arnold Suda
- Department of Orthopedics and Trauma Surgery, AUVA Trauma Center Salzburg, 5010 Salzburg, Austria
| | - Maria Anna Smolle
- Department of Orthopedics and Trauma, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Tanja Kraus
- Department of Orthopedics and Trauma, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
| | - Andrew Eric Rosenberg
- Department of Pathology and Laboratory Medicine, University of Miami, Miami, FL 33136, USA
| | - Bernadette Liegl-Atzwanger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-385-71717
| | - Jasminka Igrec
- Division of General Radiology, Department of Radiology, Medical University of Graz, Comprehensive Cancer Centre, 8010 Graz, Austria
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9
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Katayama A, Starczynski J, Toss MS, Shaaban AM, Provenzano E, Quinn CM, Callagy G, Purdie CA, Millican-Slater R, Purnell D, Chagla L, Oyama T, Pinder SE, Chan S, Ellis I, Lee AHS, Rakha EA. The frequency and clinical significance of centromere enumeration probe 17 alterations in HER2 immunohistochemistry-equivocal invasive breast cancer. Histopathology 2022; 81:511-519. [PMID: 35879836 PMCID: PMC9545957 DOI: 10.1111/his.14728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Background and aims Chromosome 17 alterations affect the assessment of HER2 gene amplification in breast cancer (BC), but its clinical significance remains unclear. This study aimed to identify the prevalence of centromere enumeration probe 17 (CEP17) alterations, and its correlation with response to neoadjuvant therapy (NAT) in BC patients with human epidermal growth factor receptor 2 (HER2) immunohistochemistry‐equivocal score. Methods and results A large BC cohort (n = 6049) with HER2 immunohistochemistry score 2+ and florescent in‐situ hybridisation (FISH) results was included to assess the prevalence of CEP17 alterations. Another cohort (n = 885) with available clinicopathological data was used to evaluate the effect of CEP17 in the setting of NAT. HER2‐amplified tumours with monosomy 17 (CEP17 copy number < 1.5 per nucleus), normal 17 (CEP17 1.5–< 3.0) and polysomy 17 (CEP17 ≥ 3.0) were observed in 16, 59 and 25%, respectively, compared with 3, 74 and 23%, respectively, in HER2‐non‐amplified tumours. There was no significant relationship between CEP17 alterations and pathological complete response (pCR) rate in both HER2‐amplified and HER2‐non‐amplified tumours. The independent predictors of pCR were oestrogen (ER) negativity in HER2‐amplified tumours [ER negative versus positive; odds ratio (OR) = 11.80; 95% confidence interval (CI) = 1.37–102.00; P = 0.02], and histological grade 3 in HER2 non‐amplified tumours (3 versus 1, 2; OR = 5.54; 95% CI = 1.61–19.00; P = 0.007). Conclusion The impacts of CEP17 alterations are not as strong as those of HER2/CEP17 ratio and HER2 copy number. The hormonal receptors status and tumour histological grade are more useful to identify BC patients with a HER2 immunohistochemistry‐equivocal score who would benefit from NAT.
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Affiliation(s)
- Ayaka Katayama
- Translational Medical Sciences Unit, School of Medicine, University of Nottingham, Nottingham, UK.,Diagnostic Pathology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Jane Starczynski
- Department of Cellular Pathology, University Hospitals Birmingham NHS Foundation Trust, Edgebaston, Birmingham, UK
| | - Michael S Toss
- Translational Medical Sciences Unit, School of Medicine, University of Nottingham, Nottingham, UK
| | - Abeer M Shaaban
- Department of Cellular Pathology, University Hospitals Birmingham NHS Foundation Trust, Edgebaston, Birmingham, UK.,Institute of Cancer and Genomic Sciences, The University of Birmingham, Edgebaston, Birmingham, UK
| | - Elena Provenzano
- Department of Histopathology, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Cecily M Quinn
- Department of Histopathology, St. Vincent's University Hospital, Dublin, and School of Medicine, University College Dublin, Ireland
| | - Grace Callagy
- Discipline of Pathology, School of Medicine, Lambe Institute for Translational Research, NUI, Galway, Ireland
| | - Colin A Purdie
- Department of Breast Pathology, Ninewells Hospital and Medical School, Dundee, UK
| | | | - David Purnell
- Histopathology department, University Hospitals of Leicester, Leicester, UK
| | - Leena Chagla
- Burney Breast Unit , St Helens and Knowsley Teaching Hospital NHS Trust, UK
| | - Tetsunari Oyama
- Diagnostic Pathology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Sarah E Pinder
- Division of Cancer Studies, King's College London, Guy's Hospital, London, UK
| | - Steve Chan
- Department of Oncology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Ian Ellis
- Translational Medical Sciences Unit, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, Nottingham, City Hospital Nottingham, UK
| | - Andrew H S Lee
- Department of Histopathology, Nottingham University Hospitals NHS Trust, Nottingham, City Hospital Nottingham, UK
| | - Emad A Rakha
- Translational Medical Sciences Unit, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, Nottingham, City Hospital Nottingham, UK
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10
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Venkataramany AS, Schieffer KM, Lee K, Cottrell CE, Wang PY, Mardis ER, Cripe TP, Chandler DS. Alternative RNA Splicing Defects in Pediatric Cancers: New Insights in Tumorigenesis and Potential Therapeutic Vulnerabilities. Ann Oncol 2022; 33:578-592. [PMID: 35339647 DOI: 10.1016/j.annonc.2022.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Compared to adult cancers, pediatric cancers are uniquely characterized by a genomically stable landscape and lower tumor mutational burden. However, alternative splicing, a global cellular process that produces different mRNA/protein isoforms from a single mRNA transcript, has been increasingly implicated in the development of pediatric cancers. DESIGN We review the current literature on the role of alternative splicing in adult cancer, cancer predisposition syndromes, and pediatric cancers. We also describe multiple splice variants identified in adult cancers and confirmed through comprehensive genomic profiling in our institutional cohort of rare, refractory and relapsed pediatric and adolescent young adult cancer patients. Finally, we summarize the contributions of alternative splicing events to neoantigens and chemoresistance and prospects for splicing-based therapies. RESULTS Published dysregulated splicing events can be categorized as exon inclusion, exon exclusion, splicing factor upregulation, or splice site alterations. We observe these phenomena in cancer predisposition syndromes (Lynch syndrome, Li-Fraumeni syndrome, CHEK2) and pediatric leukemia (B-ALL), sarcomas (Ewing sarcoma, rhabdomyosarcoma, osteosarcoma), retinoblastoma, Wilms tumor, and neuroblastoma. Within our institutional cohort, we demonstrate splice variants in key regulatory genes (CHEK2, TP53, PIK3R1, MDM2, KDM6A, NF1) that resulted in exon exclusion or splice site alterations, which were predicted to impact functional protein expression and promote tumorigenesis. Differentially spliced isoforms and splicing proteins also impact neoantigen creation and treatment resistance, such as imatinib or glucocorticoid regimens. Additionally, splice-altering strategies with the potential to change the therapeutic landscape of pediatric cancers include antisense oligonucleotides, adeno-associated virus gene transfers, and small molecule inhibitors. CONCLUSIONS Alternative splicing plays a critical role in the formation and growth of pediatric cancers, and our institutional cohort confirms and highlights the broad spectrum of affected genes in a variety of cancers. Further studies that elucidate the mechanisms of disease-inducing splicing events will contribute toward the development of novel therapeutics.
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Affiliation(s)
- A S Venkataramany
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States; Medical Scientist Training Program, The Ohio State University, Columbus, Ohio, United States
| | - K M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States
| | - K Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - C E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - P Y Wang
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States
| | - E R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - T P Cripe
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States; Division of Hematology, Oncology and Blood and Marrow Transplant, Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States
| | - D S Chandler
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States; Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States.
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11
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Li X, Hu Y, Lv Y, Gao Y, Yuwen L, Yang W, Weng L, Teng Z, Wang L. Gut microbiota and lipid metabolism alterations in mice induced by oral cadmium telluride quantum dots. J Appl Toxicol 2020; 40:1131-1140. [PMID: 32167196 DOI: 10.1002/jat.3972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023]
Abstract
The potential toxicity of cadmium-containing quantum dots (QDs) has received much attention because of increasing biomedical applications. However, little has been known about how cadmium telluride (CdTe) QDs influence the gut microbiota and lipid metabolism. In this study, mice were exposed orally to CdTe QDs (200 μL of 0.2, 2, 20 or 200 μm; twice per week) for 4 weeks. The oral experiments showed CdTe QD exposure led to a decrease of the Firmicutes/Bacteroidetes (F/B) ratio of gut microbiota, which highly negatively correlated with the low-density lipoprotein (LDL), triglyceride (TG) and total cholesterol (TC) levels in serum. In addition, the low-dose (0.2 and 2 μm) CdTe QDs significantly increased the diversity of gut microbiota, and did not elevate the LDL, TG and TC levels in serum. The medium dose (20 μm) of CdTe QDs caused the biggest decrease of the F/B ratio, so it significantly increased the LDL, TG and TC levels compared with the control. Furthermore, high-dose (200 μm) CdTe QDs caused various toxicities in the histopathology of liver and intestine, liver function and intestinal immunity, but did not significantly lead to changes of the LDL, TG and TC levels in serum. This study demonstrates that high-dose oral CdTe QDs mainly lead to tissue damage of the liver and intestine, while the medium and low doses of oral CdTe QDs induce shifts of gut microbiota structure, which are associated with blood lipid levels.
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Affiliation(s)
- Xiaohui Li
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China.,Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yun Hu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yangfan Lv
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yu Gao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Lihui Yuwen
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Wenjing Yang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Lixing Weng
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zhaogang Teng
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China.,Department of Medical Imaging, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
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12
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Abstract
Metabolism is defined as the collection of complex biochemical processes that living cells use to generate energy and maintain their growth and survival. Metabolism encompasses the synthesis and breakdown of glucose, fatty acids, and amino acids; the generation of energy (ATP); and oxidative phosphorylation. In cancer cells, metabolism can be commandeered to promote tumor growth and cellular proliferation. These alterations in metabolism have emerged as an additional hallmark of various cancers. In this review we focus on metabolic alterations in multiple myeloma (MM) - a malignancy of plasma cells - including derangements in glycolysis, gluconeogenesis, the tricarboxylic acid cycle, oxidative phosphorylation, and fatty acid/amino acid synthesis and degradation. Particular focus is given to metabolic alterations that contribute to myeloma cell growth, proliferation and drug resistance. Finally, novel approaches that target metabolic pathways for the treatment of MM are discussed.
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Affiliation(s)
- Dustin Rizzieri
- Division of Hematological Malignancies and Cellular Therapy, Duke University Medical Center, Durham, NC 27710, USA
| | - Barry Paul
- Division of Hematological Malignancies and Cellular Therapy, Duke University Medical Center, Durham, NC 27710, USA
| | - Yubin Kang
- Division of Hematological Malignancies and Cellular Therapy, Duke University Medical Center, Durham, NC 27710, USA
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13
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Hodzic E, Shrestha R, Zhu K, Cheng K, Collins CC, Cenk Sahinalp S. Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. Gigascience 2019; 8:giz024. [PMID: 30978274 PMCID: PMC6458499 DOI: 10.1093/gigascience/giz024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/12/2018] [Accepted: 02/21/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Advances in large-scale tumor sequencing have led to an understanding that there are combinations of genomic and transcriptomic alterations specific to tumor types, shared across many patients. Unfortunately, computational identification of functionally meaningful and recurrent alteration patterns within gene/protein interaction networks has proven to be challenging. FINDINGS We introduce a novel combinatorial method, cd-CAP (combinatorial detection of conserved alteration patterns), for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not) and simultaneously detects multiple alteration profile conserved subnetworks. CONCLUSIONS In a number of The Cancer Genome Atlas datasets, cd-CAP identified large biologically significant subnetworks with conserved alteration patterns, shared across many tumor samples.
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Affiliation(s)
- Ermin Hodzic
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- School of Computing Science, Simon Fraser University, 8888 University Dr, Burnaby, BC, V5A 1S6, Canada
| | - Raunak Shrestha
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- Department of Urologic Sciences, University of British Columbia, 2775 Laurel St, Vancouver, BC, V5Z 1M9, Canada
| | - Kaiyuan Zhu
- Department of Computer Science, Indiana University Bloomington, 700 N. Woodlawn Ave, Bloomington, IN, 47408, USA
| | - Kuoyuan Cheng
- Center for Bioinformatics and Computational Biology, University of Maryland, 8125 Paint Branch Dr, College Park, MD, 20742, USA
| | - Colin C Collins
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- Department of Urologic Sciences, University of British Columbia, 2775 Laurel St, Vancouver, BC, V5Z 1M9, Canada
| | - S Cenk Sahinalp
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- Department of Computer Science, Indiana University Bloomington, 700 N. Woodlawn Ave, Bloomington, IN, 47408, USA
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14
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Zaami S, Tagliabracci A, Berretta P, Busardò FP, Marinelli E. Use of Methylphenidate Analogues as Cognitive Enhancers: The Prelude to Cosmetic Neurology and an Ethical Issue. Front Psychiatry 2019; 10:1006. [PMID: 32038333 PMCID: PMC6989549 DOI: 10.3389/fpsyt.2019.01006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/20/2019] [Indexed: 01/01/2023] Open
Affiliation(s)
- Simona Zaami
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University, Rome, Italy
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence-Biomedical Sciences and Public Health, Ancona, Italy
| | - Paolo Berretta
- National Centre on Addiction and Doping, Istituto Superiore di Sanità, Rome, Italy
| | - Francesco Paolo Busardò
- Section of Legal Medicine, Department of Excellence-Biomedical Sciences and Public Health, Ancona, Italy
| | - Enrico Marinelli
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University, Rome, Italy
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15
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Paracka L, Wegner F, Blahak C, Abdallat M, Saryyeva A, Dressler D, Karst M, Krauss JK. Sensory Alterations in Patients with Isolated Idiopathic Dystonia: An Exploratory Quantitative Sensory Testing Analysis. Front Neurol 2017; 8:553. [PMID: 29089923 PMCID: PMC5650962 DOI: 10.3389/fneur.2017.00553] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/28/2017] [Indexed: 02/04/2023] Open
Abstract
Abnormalities in the somatosensory system are increasingly being recognized in patients with dystonia. The aim of this study was to investigate whether sensory abnormalities are confined to the dystonic body segments or whether there is a wider involvement in patients with idiopathic dystonia. For this purpose, we recruited 20 patients, 8 had generalized, 5 had segmental dystonia with upper extremity involvement, and 7 had cervical dystonia. In total, there were 13 patients with upper extremity involvement. We used Quantitative Sensory Testing (QST) at the back of the hand in all patients and at the shoulder in patients with cervical dystonia. The main finding on the hand QST was impaired cold detection threshold (CDT), dynamic mechanical allodynia (DMA), and thermal sensory limen (TSL). The alterations were present on both hands, but more pronounced on the side more affected with dystonia. Patients with cervical dystonia showed a reduced CDT and hot detection threshold (HDT), enhanced TSL and DMA at the back of the hand, whereas the shoulder QST only revealed increased cold pain threshold and DMA. In summary, QST clearly shows distinct sensory abnormalities in patients with idiopathic dystonia, which may also manifest in body regions without evident dystonia. Further studies with larger groups of dystonia patients are needed to prove the consistency of these findings.
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Affiliation(s)
- Lejla Paracka
- Department of Neurology, Hannover Medical School, Hannover, Germany.,Center for Systems Neuroscience, Hannover, Germany
| | - Florian Wegner
- Department of Neurology, Hannover Medical School, Hannover, Germany.,Center for Systems Neuroscience, Hannover, Germany
| | - Christian Blahak
- Faculty of Medicine Mannheim, Department of Neurology, University of Heidelberg, Mannheim, Germany
| | - Mahmoud Abdallat
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Assel Saryyeva
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Dirk Dressler
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Matthias Karst
- Department of Anesthesiology, Hannover Medical School, Hannover, Germany
| | - Joachim K Krauss
- Center for Systems Neuroscience, Hannover, Germany.,Department of Neurosurgery, Hannover Medical School, Hannover, Germany
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16
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Abstract
MicroRNAs (miRNAs) directly and indirectly affect tumorigenesis. To be able to perform their myriad roles, miRNA machinery genes, such as Drosha, DGCR8, Dicer1, XPO5, TRBP, and AGO2, must generate precise miRNAs. These genes have specific expression patterns, protein-binding partners, and biochemical capabilities in different cancers. Our preliminary analysis of data from The Cancer Genome Atlas consortium on multiple types of cancer revealed significant alterations in these miRNA machinery genes. Here, we review their biological structures and functions with an eye toward understanding how they could serve as cancer biomarkers.
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Affiliation(s)
- Jing-Tao Huang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University , Wuhan , China
| | - Jin Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | - Vibhuti Srivastava
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center , Houston, TX , USA
| | - Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University , Wuhan , China
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17
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Wujcicka W, Wilczyński J, Nowakowska D. Alterations in TLRs as new molecular markers of congenital infections with Human cytomegalovirus? Pathog Dis 2013; 70:3-16. [PMID: 23929630 DOI: 10.1111/2049-632x.12083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/28/2013] [Accepted: 07/31/2013] [Indexed: 12/14/2022] Open
Abstract
Toll-like receptors (TLRs) play a crucial role in non-specific immunity against various infections. The most common intrauterine infection, caused by Human cytomegalovirus (HCMV), results in perinatal morbidity and mortality of primary infected fetuses. The induction of immune response by TLRs was observed in HCMV infections in murine models and cell lines cultured in vitro. Studies reported an immunological response in pregnant women with primary HCMV infection and TLR2 activity in collecting of HCMV particles in placental syncytiotrophoblasts (STs) in vivo and cultured ST, and in stimulation of tumor necrosis factor (TNF)-α expression and damage of villous trophoblast. Expression levels of TLRs are associated with cell type, stage of pregnancy and response to microorganisms. We show the effect of HCMV infection on the development of pregnancy as well as the effect of TLR single-nucleotide polymorphisms on the occurrence and course of infectious diseases, immune response and diseases of pregnancy. We report the impact of TLRs on the function of miRNAs and the altered expression levels of these molecules, as observed in HCMV infections. We suggest that the methylation status of TLR gene promoter regions as epigenetic modifications may be significant in the immune response to HCMV infections. We conclude that it is important to study in detail the molecular mechanisms of TLR function in the immune response to HCMV infections in pregnancy.
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Affiliation(s)
- Wioletta Wujcicka
- Department of Fetal-Maternal Medicine and Gynecology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
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18
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Naumov VA, Generozov EV, Zaharjevskaya NB, Matushkina DS, Larin AK, Chernyshov SV, Alekseev MV, Shelygin YA, Govorun VM. Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips. Epigenetics 2013; 8:921-34. [PMID: 23867710 DOI: 10.4161/epi.25577] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Illumina's Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data. In general, at the CpG-site level, we found that common CRC-specific methylation patterns consist of at least 15,667 CpG sites that were significantly different from either adjacent healthy tissue or tissue from cancer-free subjects. Of these sites, 10,342 were hypermethylated in CRC, and 5,325 were hypomethylated. Hypermethylated sites were common in the maximum number of sample pairs and were mostly located in CpG islands, where they were significantly enriched for differentially methylated regions known to be cancer-specific. In contrast, hypomethylated sites were mostly located in CpG shores and were generally sample-specific. Despite the considerable variability in methylation data, we selected a panel of 14 highly robust candidates showing methylation marks in genes SND1, ADHFE1, OPLAH, TLX2, C1orf70, ZFP64, NR5A2, and COL4A. This set was successfully cross-validated using methylation data from 209 CRC samples and 38 healthy tissue samples from The Cancer Genome Atlas consortium (AUC = 0.981 [95% CI: 0.9677-0.9939], sensitivity = 100% and specificity = 82%). In summary, this study reports a large number of loci with novel differential methylation statuses, some of which may serve as candidate markers for diagnostic purposes.
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Affiliation(s)
- Vladimir A Naumov
- Research Institute of Physical Chemical Medicine of Federal Medical Biology Agency of Russian Federation; Moscow, Russia
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19
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Shen J, Wang S, Zhang YJ, Wu HC, Kibriya MG, Jasmine F, Ahsan H, Wu DPH, Siegel AB, Remotti H, Santella RM. Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigenetics 2012. [PMID: 23208076 DOI: 10.4161/epi.23062] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) incidence has increased in the US and also has one of the fastest growing death rates of any cancer. The purpose of the current study was to discover novel genome-wide aberrant DNA methylation patterns in HCC tumors that are predominantly HCV-related. Infinium HumanMethylation 450K BeadChip arrays were used to examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared with non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Absolute tumor/non-tumor methylation differences ≥ 20% were found in 24.9% of the hypermethylated and 43.1% of the hypomethylated CpG sites; almost 10,000 CpG sites have ≥ 30% DNA methylation differences. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands, with 21.6% in CpG shores and 3.6% in shelves. In contrast, only a small proportion (8.2%) of significantly hypomethylated CpG sites are situated in islands, while most are found in open sea (60.2%), shore (17.3%) or shelf (14.3%) regions. A total of 2,568 significant CpG sites (2,441 hypermethylated and 127 hypomethylated) covering 589 genes are located within 684 differentially methylated regions defined as regions with at least two significant CpG sites displaying > 20% methylation differences in the same direction within 250-bp. The top 500 significant CpG sites can significantly distinguish HCC tumor from adjacent tissues with one misclassification. Within adjacent non-tumor tissues, we also identified 75 CpG sites significantly associated with gender, 228 with HCV infection, 17,207 with cirrhosis, and 56 with both HCV infection and cirrhosis after multiple comparisons adjustment. Aberrant DNA methylation profiles across the genome were identified in tumor tissues from US HCC cases that are predominantly related to HCV infection. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis.
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Affiliation(s)
- Jing Shen
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY, USA
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