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Journal of Parkinson's Disease 2019Gut microbiota have been studied in relation to the pathophysiology of Parkinson's disease (PD) due to the early gastrointestinal symptomatology and presence of...
Gut microbiota have been studied in relation to the pathophysiology of Parkinson's disease (PD) due to the early gastrointestinal symptomatology and presence of alpha-synuclein pathology in the enteric nervous system, hypothesized to ascend via the vagal nerve to the central nervous system. Accordingly, sixteen human case-control studies have published gut microbiome composition changes in PD and reported over 100 differentially abundant taxa covering all taxonomic levels from phylum to genus or species, depending on methodology. While certain findings were replicated across several studies, various contradictory findings were reported. Here, differences in methodologies and the presence of possible confounders in the study populations are assessed for their potential to confound the results of gut microbiome studies in PD. Gut microbiome studies in PD exhibited considerable variability with respect to the study population, sample transport conditions, laboratory protocols and sequencing, bioinformatics pipelines, and biostatistical methods. To move from the current heterogeneous dataset towards clinically relevant biomarkers and the identification of putative therapeutic targets, recommendations are derived from the limitations of the available studies to increase the future comparability of microbiome studies in PD. In addition, integration of currently available data on the gut microbiome in PD is proposed to identify robust gut microbiome profiles in PD. Furthermore, expansion of the current dataset with atypical parkinsonism cohorts, prodromal and treatment-naïve de novo PD subjects, measurements of fecal microbial concentrations and multi-omics assessments are required to provide clinically relevant biomarkers and reveal therapeutic targets within the gut microbiome of PD.
Topics: Gastrointestinal Microbiome; Humans; Parkinson Disease
PubMed: 31498131
DOI: 10.3233/JPD-191711 -
Clinical Breast Cancer Dec 2019Optimal treatment of breast cancer brain metastases (BCBM) is often hampered by limitations in diagnostic abilities. Developing innovative tools for BCBM diagnosis is...
Optimal treatment of breast cancer brain metastases (BCBM) is often hampered by limitations in diagnostic abilities. Developing innovative tools for BCBM diagnosis is vital for early detection and effective treatment. In this study we explored the advances in trial for the diagnosis of BCBM, with review of the literature. On May 8, 2019, we searched ClinicalTrials.gov for interventional and diagnostic clinical trials involving BCBM, without limiting for date or location. Information on trial characteristics, experimental interventions, results, and publications were collected and analyzed. In addition, a systematic review of the literature was conducted to explore published studies related to BCBM diagnosis. Only 9 diagnostic trials explored BCBM. Of these, 1 trial was withdrawn because of low accrual numbers. Three trials were completed; however, none had published results. Modalities in trial for BCBM diagnosis entailed magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), PET-CT, nanobodies, and circulating tumor cells (CTCs), along with a collection of novel tracers and imaging biomarkers. MRI continues to be the diagnostic modality of choice, whereas CT is best suited for acute settings. Advances in PET and PET-CT allow the collection of metabolic and functional information related to BCBM. CTC characterization can help reflect on the molecular foundations of BCBM, whereas cell-free DNA offers new genetic material for further exploration in trials. The integration of machine learning in BCBM diagnosis seems inevitable as we continue to aim for rapid and accurate detection and better patient outcomes.
Topics: Brain Neoplasms; Breast Neoplasms; Clinical Trials as Topic; Female; Humans; Magnetic Resonance Imaging; Neoplastic Cells, Circulating; Positron Emission Tomography Computed Tomography; Prognosis
PubMed: 31262686
DOI: 10.1016/j.clbc.2019.05.018 -
Cold Spring Harbor Molecular Case... Jun 2019In the current era of personalized medicine, the field of oncology is witnessing a paradigm shift in patient care that is driving a tighter integration of genomic...
In the current era of personalized medicine, the field of oncology is witnessing a paradigm shift in patient care that is driving a tighter integration of genomic analysis modalities in patient care decision. This is driven by the expanding category of targeted therapies that require a broader understanding of the mutational profile of patient samples to more precisely guided personalized treatment decisions. Next-generation sequencing (NGS) has proved to be of tremendous power in detecting and characterizing a broad spectrum of activating or loss-of-function mutations across many gene targets. This power of NGS also results in significant challenges related to technical expertise, bioinformatics, computing infrastructure, laboratory practices, and integration into clinical decision-making. These challenges are particularly relevant to smaller and mid-tier hospital networks that are faced with the need to modernize their clinical practices and offer their patients access to advanced genomic technologies to improve outcomes. Adoption of such personalized medicine relies on information about a patient's cancer genome and the identification of its variants. This is best achieved using NGS. However, there are challenges to the adoption of such a complex technology and workflow, especially in smaller hospital systems. This commentary summarizes key considerations and challenges related to implementation of NGS in a community hospital setting.
Topics: Computational Biology; Genomics; High-Throughput Nucleotide Sequencing; Hospitals, Community; Humans; Medical Oncology; Mutation; Neoplasms; Precision Medicine; Sequence Analysis, DNA
PubMed: 31160354
DOI: 10.1101/mcs.a003707 -
Annals of Global Health Jul 2018Children are susceptible to environmental contaminants and are at risk of developing diseases, more so if the exposure begins at an early age. Epidemiological studies...
BACKGROUND
Children are susceptible to environmental contaminants and are at risk of developing diseases, more so if the exposure begins at an early age. Epidemiological studies have postulated the hypothesis of the fetal origin of disease, which is mediated by epigenetic changes. Epigenetic marks are inheritable; they modulate the gene expression and can affect human health due to the presence of environmental factors.
OBJECTIVE
This review focuses on DNA-methylation and its association with environmental-related diseases in children.
METHODS
A search for studies related to DNA-methylation in children by pre- or post-natal environmental exposures was conducted, and those studies with appropriate designs and statistical analyses and evaluations of the exposure were selected.
FINDINGS
Prenatal and early life environmental factors, from diet to exposure to pollutants, have been associated with epigenetic changes, specifically DNA-methylation. Thus, maternal nutrition and smoking and exposure to air particulate matter, polycyclic aromatic hydrocarbons, arsenic, heavy metals, persistent organic pollutants, and some endocrine disrupters during pregnancy have been associated with genomic and gene-specific newborns' DNA-methylation changes that have shown in some cases sex-specific patterns. In addition, these maternal factors may deregulate the placental DNA-methylation balance and could induce a fetal reprogramming and later-in-life diseases.
CONCLUSIONS
Exposure to environmental pollutants during prenatal and early life can trigger epigenetic imbalances and eventually the development of diseases in children. The integration of epigenetic data should be considered in future risk assessments.
Topics: Child; Child Health; DNA Methylation; Environmental Exposure; Environmental Health; Epigenesis, Genetic; Female; Humans; Maternal Exposure; Risk Factors
PubMed: 30873799
DOI: 10.29024/aogh.909 -
Ontario Health Technology Assessment... 2019Pregnant people have a risk of carrying a fetus affected by a chromosomal anomaly. Prenatal screening is offered to pregnant people to assess their risk. In recent... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Pregnant people have a risk of carrying a fetus affected by a chromosomal anomaly. Prenatal screening is offered to pregnant people to assess their risk. In recent years, noninvasive prenatal testing (NIPT) has been introduced clinically, which uses the presence of circulating cell-free fetal DNA in the maternal blood to quantify the risk of a chromosomal anomaly. At present, NIPT is publicly funded for pregnancies at high risk of a chromosomal anomaly, and available to pregnant people at average risk if they choose to pay out of pocket.
METHODS
We performed a systematic review of primary, empirical qualitative research that describes the experiences and perspectives of pregnant people, their families, clinicians, and others with lived experience relevant to NIPT. We were interested in the beliefs, experiences, preferences, and perspectives of these groups. We analyzed the evidence available in 36 qualitative and mixed-methods studies using the integrative technique of qualitative meta-synthesis.
RESULTS
Most people (pregnant people, clinicians, and others with relevant lived experience) said that NIPT offered important information to pregnant people and their partners. Most people were very enthusiastic about widening access to NIPT because it can provide information about chromosomal anomalies quite early in pregnancy, with relatively high accuracy, and without risk of procedure-related pregnancy loss. However, many groups cautioned that widening access to NIPT may result in routinization of this test, causing potential harm to pregnant people, their families, the health care system, people living with disabilities, and society as a whole. Widened logistical, financial, emotional, and informational access may be perceived as a benefit, but it can also confer harm on various groups. Many of these challenges echo historical critiques of other forms of prenatal testing, with some issues mitigated or exacerbated by the particular features of NIPT.
CONCLUSIONS
Noninvasive prenatal testing offers significant benefit for pregnant people but may also be associated with potential harms related to informed decision-making, inequitable use, social pressure to test, and reduced support for people with disabilities.
Topics: Female; Humans; Pregnancy; Attitude of Health Personnel; Patient Acceptance of Health Care; Patient Preference; Patient Satisfaction; Prenatal Diagnosis; Qualitative Research
PubMed: 30838086
DOI: No ID Found -
BMC Pregnancy and Childbirth Jan 2019Non-invasive prenatal testing (NIPT) can be used to accurately detect fetal chromosomal anomalies early in pregnancy by assessing cell-free fetal DNA present in maternal...
BACKGROUND
Non-invasive prenatal testing (NIPT) can be used to accurately detect fetal chromosomal anomalies early in pregnancy by assessing cell-free fetal DNA present in maternal blood. The rapid diffusion of NIPT, as well as the ease and simplicity of the test raises concerns around informed decision-making and the potential for routinization. Introducing NIPT in a way that facilitates informed and autonomous decisions is imperative to the ethical application of this technology. We approach this imperative by systematically reviewing and synthesizing primary qualitative research on women's experiences with and preferences for informed decision-making around NIPT.
METHODS
We searched multiple bibliographic databases including Ovid MEDLINE, EBSCO Cumulative Index to Nursing & Allied Health Literature (CINAHL), and ISI Web of Science Social Sciences Citation Index (SSCI). Our review was guided by integrative qualitative meta-synthesis, and we used a staged coding process similar to that of grounded theory to conduct our analysis.
RESULTS
Thirty empirical primary qualitative research studies were eligible for inclusion. Women preferred to learn about NIPT from their clinicians, but they expressed dissatisfaction with the quality and quantity of information provided during counselling and often sought information from a variety of other sources. Women generally had a good understanding of test characteristics, and the factors of accuracy, physical risk, and test timing were the critical information elements that they used to make informed decisions around NIPT. Women often described NIPT as easy or just another blood test, highlighting threats to informed decision-making such as routinization or a pressure to test.
CONCLUSIONS
Women's unique circumstances modulate the information that they value and require most in the context of making an informed decision. Widened availability of trustworthy information about NIPT as well as careful attention to the facilitation of counselling may help facilitate informed decision-making.
TRIAL REGISTRATION
PROSPERO 2018 CRD42018086261 .
Topics: Cell-Free Nucleic Acids; Choice Behavior; Decision Making; Down Syndrome; Female; Humans; Informed Consent; Patient Preference; Pregnancy; Pregnant Women; Prenatal Diagnosis; Qualitative Research; Trisomy 13 Syndrome; Trisomy 18 Syndrome
PubMed: 30642270
DOI: 10.1186/s12884-018-2168-4 -
Systematic Reviews Nov 2018There is scanty or inconclusive evidence on which cervical cancer screening tool is effective and suitable for human immunodeficiency virus (HIV)-seropositive women. The...
BACKGROUND
There is scanty or inconclusive evidence on which cervical cancer screening tool is effective and suitable for human immunodeficiency virus (HIV)-seropositive women. The aim of this review was to assess, synthesise and document published evidence relating to the available cervical cancer screening modalities for HIV-seropositive women in developing countries. This paper did not review the issue of human papillomavirus (HPV) prophylactic vaccine on HIV-seropositive women.
METHODS
Five electronic databases were systematically searched from inception to January 2018 for relevant published original research examining cervical cancer prevention modalities for HPV infection, abnormal cytology and direct visualisation of the cervix amongst HIV-seropositive women in developing countries. Extra studies were identified through reference list and citation tracking.
RESULTS
Due to methodological and clinical heterogeneity, a narrative synthesis was presented. Of the 2559 articles, 149 underwent full-text screening and 25 were included in the review. Included studies were of moderate quality, and no exclusions were made based on quality or bias. There is no standard cervical cancer screening test or programme for HIV-seropositive women and countries screening according to available resources and expertise. The screening methods used for HIV-seropositive women are the same for HIV-negative women, with varying clinical performance and accuracy. The main cervical cancer screening methods described for HIV-seropositive women are HPV deoxyribonucleic acid/messenger RNA (DNA/mRNA) testing (n = 16, 64.0%), visual inspection with acetic acid (VIA) (n = 13, 52.0%) and Pap smear (n = 11, 44.0%). HPV testing has a better accuracy/efficiency than other methods with a sensitivity of 80.0-97.0% and specificity of 51.0-78.0%. Sequential screening using VIA or visual inspection with Lugol's iodine (VILI) and HPV testing has shown better clinical performance in screening HIV-seropositive women.
CONCLUSION
Although cervical cancer screening exists in almost all developing countries, what is missing is both opportunistic and systematic organised population-based screenings. Cervical cancer screening programmes need to be integrated into already existing HIV services to enable early detection and treatment. There is a need to offer opportunistic and coordinated screening programmes that are provider-initiated to promote early identification of cervical precancerous lesions.
SYSTEMATIC REVIEW REGISTRATION
PROSPERO CRD42018095702.
Topics: Adult; Developing Countries; Early Detection of Cancer; Female; HIV Seropositivity; Human Papillomavirus DNA Tests; Humans; Papillomaviridae; Papillomavirus Infections; Uterine Cervical Neoplasms; Vaginal Smears
PubMed: 30447695
DOI: 10.1186/s13643-018-0874-7 -
Inflammation and Regeneration 2018In the era of precision medicine, transcriptome analysis of whole gene expression is an essential technology. While DNA microarray has a limited dynamic range and a... (Review)
Review
In the era of precision medicine, transcriptome analysis of whole gene expression is an essential technology. While DNA microarray has a limited dynamic range and a problem of background hybridization, RNA sequencing (RNA-seq) has a broader dynamic range and a lower background signal that increase the sensitivity and reproducibility. While transcriptome analyses in rheumatoid arthritis (RA) have generally focused on whole peripheral blood mononuclear cells (PBMC), analyses of detailed cell subsets have an increased need for understanding the pathophysiology of disease because the involvement of CD4 T cells in the pathogenesis of RA has been established. Transcriptome analysis of detailed CD4 T cell subsets or neutrophils shed new light on the pathophysiology of RA. There are several analyses about the effect of biological treatment. Many studies report the association between type I interferon signature gene expression and response to therapy.
PubMed: 30410636
DOI: 10.1186/s41232-018-0078-5 -
Journal of Animal Science Dec 2018Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency....
Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of genes shared between different traits was observed, indicating a high impact of the population genetic structure and environmental effects. Several chromosomal regions were enriched for functional candidate genes associated with fertility traits. Moreover, multiple functional candidate genes were enriched for markers in a species-specific basis, taurine (Bos taurus) or indicine (Bos indicus). For the different candidate regions identified in the GWAS in the literature, functional candidate genes were detected as follows: B. Taurus chromosome X (BTX) (TEX11, IRAK, CDK16, ATP7A, ATRX, HDAC6, FMR1, L1CAM, MECP2, etc.), BTA17 (TRPV4 and DYNLL1), and BTA14 (MOS, FABP5, ZFPM2). These genes are responsible for regulating important metabolic pathways or biological processes associated with fertility, such as progression of spermatogenesis, control of ciliary activity, development of Sertoli cells, DNA integrity in spermatozoa, and homeostasis of testicular cells. This study represents the first systematic review on male fertility traits in cattle using a system biology approach to identify key candidate genes for these traits.
Topics: Animals; Cattle; Genome-Wide Association Study; Male; Polymorphism, Single Nucleotide; Spermatozoa; Testis
PubMed: 30304443
DOI: 10.1093/jas/sky382 -
Biology of Sex Differences May 2018Differences in cardiovascular diseases are evident in men and women throughout life and are mainly attributed to the presence of sex hormones and chromosomes. Epigenetic...
BACKGROUND
Differences in cardiovascular diseases are evident in men and women throughout life and are mainly attributed to the presence of sex hormones and chromosomes. Epigenetic mechanisms drive the regulation of the biological processes that may lead to CVD and are possibly influenced by sex. In order to gain an overview of the status quo on sex differences in cardiovascular epigenetics, we performed a systematic review.
MATERIALS AND METHODS
A systematic search was performed on PubMed and Embase for studies mentioning cardiovascular disease, epigenetics, and anything related to sex differences. The search returned 3071 publications to be screened. Primary included publications focused on cardiovascular and epigenetics research. Subsequently, papers were assessed for including both sexes in their studies and checked for appropriate sex stratification of results.
RESULTS
Two independent screeners identified 75 papers in the proper domains that had included both sexes. Only 17% (13 papers out of 75) of these publications stratified some of their data according to sex. All remaining papers focused on DNA methylation solely as an epigenetic mechanism. Of the excluded papers that included only one sex, 86% (24 out 28) studied males, while 14% (4 out of 28) studied females.
CONCLUSION
Our overview indicates that the majority of studies into cardiovascular epigenetics do not show their data stratified by sex, despite the well-known sex differences in CVD. All included and sex-stratified papers focus on DNA methylation, indicating that a lot of ground is still to gain regarding other epigenetic mechanisms, like chromatin architecture, and histone modifications. More attention to sex in epigenetic studies is warranted as such integration will advance our understanding of cardiovascular disease mechanisms in men and women.
Topics: Cardiovascular Diseases; Epigenesis, Genetic; Female; Humans; Male; Sex Characteristics
PubMed: 29792221
DOI: 10.1186/s13293-018-0180-z