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https://www.readbyqxmd.com/read/29345573/precision-medicine-update-on-diagnosis-and-therapeutic-strategies-of-hepatocellular-carcinoma
#1
Qing Liang, Xiaoying Shen, Guangchun Sun
Recent advances in multiple omics technologies and the advent of massively parallel sequencing provide technical supports for the implementation of precision medicine. The precision medicine emphasizes that heterogeneous diseases can be well classified into more precise subtypes by the powerful detection methods and integration of clinical features, so that the clinicians should develop more accurate diagnosis and therapeutic strategies for the disease subtype population, in an effort to maximize the efficacy and minimize the unnecessary side effects...
January 16, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29344888/perseus-a-bioinformatics-platform-for-integrative-analysis-of-proteomics-data-in-cancer-research
#2
Stefka Tyanova, Juergen Cox
Mass spectrometry-based proteomics is a continuously growing field marked by technological and methodological improvements. Cancer proteomics is aimed at pursuing goals such as accurate diagnosis, patient stratification, and biomarker discovery, relying on the richness of information of quantitative proteome profiles. Translating these high-dimensional data into biological findings of clinical importance necessitates the use of robust and powerful computational tools and methods. In this chapter, we provide a detailed description of standard analysis steps for a clinical proteomics dataset performed in Perseus, a software for functional analysis of large-scale quantitative omics data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344009/evaluation-of-nipple-aspirate-fluid-as-a-diagnostic-tool-for-early-detection-of-breast-cancer
#3
REVIEW
Sadr-Ul Shaheed, Catherine Tait, Kyriacos Kyriacou, Richard Linforth, Mohamed Salhab, Chris Sutton
There has been tremendous progress in detection of breast cancer in postmenopausal women, resulting in two-thirds of women surviving more than 20 years after treatment. However, breast cancer remains the leading cause of cancer-related deaths in premenopausal women. Breast cancer is increasing in younger women due to changes in life-style as well as those at high risk as carriers of mutations in high-penetrance genes. Premenopausal women with breast cancer are more likely to be diagnosed with aggressive tumours and therefore have a lower survival rate...
2018: Clinical Proteomics
https://www.readbyqxmd.com/read/29335008/multi-omics-differentially-classify-disease-state-and-treatment-outcome-in-pediatric-crohn-s-disease
#4
Gavin M Douglas, Richard Hansen, Casey M A Jones, Katherine A Dunn, André M Comeau, Joseph P Bielawski, Rachel Tayler, Emad M El-Omar, Richard K Russell, Georgina L Hold, Morgan G I Langille, Johan Van Limbergen
BACKGROUND: Crohn's disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been confounded with patients' ongoing treatments. Additionally, most analyses of CD patients' microbiomes have focused on microbes in stool samples, which yield different insights than profiling biopsy samples. RESULTS: We sequenced the 16S rRNA gene (16S) and carried out shotgun metagenomics (MGS) from the intestinal biopsies of 20 treatment-naïve CD and 20 control pediatric patients...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29325019/deep-molecular-phenotypes-link-complex-disorders-and-physiological-insult-to-cpg-methylation
#5
Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Maija Pezer, Gordan Lauc, Johannes Graumann, Joel A Malek, Karsten Suhre
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle, and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29322918/a-linear-programming-computational-framework-integrates-phosphor-proteomics-and-prior-knowledge-to-predict-drug-efficacy
#6
Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi
BACKGROUND: In recent years, the integration of 'omics' technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the way of approaching drug discovery. The LINCS public data warehouse provides detailed information about cell responses with various genetic and environmental stressors. It can be greatly helpful in developing new drugs and therapeutics, as well as improving the situations of lacking effective drugs, drug resistance and relapse in cancer therapies, etc...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29319603/population-neuroscience-dementia-epidemiology-serving-precision-medicine-and-population-health
#7
Mary Ganguli, Emiliano Albanese, Sudha Seshadri, David A Bennett, Constantine Lyketsos, Walter A Kukull, Ingmar Skoog, Hugh C Hendrie
Over recent decades, epidemiology has made significant contributions to our understanding of dementia, translating scientific discoveries into population health. Here, we propose reframing dementia epidemiology as "population neuroscience," blending techniques and models from contemporary neuroscience with those of epidemiology and biostatistics. On the basis of emerging evidence and newer paradigms and methods, population neuroscience will minimize the bias typical of traditional clinical research, identify the relatively homogenous subgroups that comprise the general population, and investigate broader and denser phenotypes of dementia and cognitive impairment...
January 9, 2018: Alzheimer Disease and Associated Disorders
https://www.readbyqxmd.com/read/29316700/sea-anemones-quiet-achievers-in-the-field-of-peptide-toxins
#8
REVIEW
Peter J Prentis, Ana Pavasovic, Raymond S Norton
Sea anemones have been understudied as a source of peptide and protein toxins, with relatively few examined as a source of new pharmacological tools or therapeutic leads. This is surprising given the success of some anemone peptides that have been tested, such as the potassium channel blocker from Stichodactyla helianthus known as ShK. An analogue of this peptide, ShK-186, which is now known as dalazatide, has successfully completed Phase 1 clinical trials and is about to enter Phase 2 trials for the treatment of autoimmune diseases...
January 8, 2018: Toxins
https://www.readbyqxmd.com/read/29315503/the-clinical-implications-of-immunogenomics-in-colorectal-cancer-a-path-for-precision-medicine
#9
REVIEW
Jenny M Riley, Ashley W Cross, Chrystal M Paulos, Mark P Rubinstein, John Wrangle, E Ramsay Camp
Colorectal cancer (CRC) remains the third most common malignancy and the second-leading cause of cancer-related deaths in the United States. Large multi-omic databases, such as The Cancer Genome Atlas and the International Colorectal Cancer Subtyping Consortium, have identified distinct molecular subtypes related to anatomy. The identification of genomic alterations in CRC is now critical because of the recent success and US Food and Drug Administration approval of pembrolizumab and nivolumab for microsatellite-instable tumors...
January 9, 2018: Cancer
https://www.readbyqxmd.com/read/29309763/manipulating-cell-fate-while-confronting-reproducibility-concerns
#10
REVIEW
Jeannette M Osterloh, Kevin Mullane
Biomedical research is being transformed by the discovery and use of human pluripotent stem cells (hPSCs). Remarkable progress has been made, and assorted clinical trials are underway related to the application of stem cell therapy, including transplantation of hPSC-derived cells, in situ reprogramming or transdifferentiation, and utilization of targets and compounds identified from patient-derived stem cells. However, the pace of discovery is overwhelming efforts to replicate the work of others, prompting a concern over validity and reproducibility...
January 5, 2018: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29302075/foxo1-a2m-and-tgf-%C3%AE-1-three-novel-genes-predicting-depression-in-gene-x-environment-interactions-are-identified-using-cross-species-and-cross-tissues-transcriptomic-and-mirnomic-analyses
#11
Annamaria Cattaneo, Nadia Cattane, Chiara Malpighi, Darina Czamara, Anna Suarez, Nicole Mariani, Eero Kajantie, Alessia Luoni, Johan G Eriksson, Jari Lahti, Valeria Mondelli, Paola Dazzan, Katri Räikkönen, Elisabeth B Binder, Marco A Riva, Carmine M Pariante
To date, gene-environment (GxE) interaction studies in depression have been limited to hypothesis-based candidate genes, since genome-wide (GWAS)-based GxE interaction studies would require enormous datasets with genetics, environmental, and clinical variables. We used a novel, cross-species and cross-tissues "omics" approach to identify genes predicting depression in response to stress in GxE interactions. We integrated the transcriptome and miRNome profiles from the hippocampus of adult rats exposed to prenatal stress (PNS) with transcriptome data obtained from blood mRNA of adult humans exposed to early life trauma, using a stringent statistical analyses pathway...
January 4, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29296236/combined-microrna-and-mrna-microfluidic-taqman-array-cards-for-the-diagnosis-of-malignancy-of-multiple-types-of-pancreatico-biliary-tumors-in-fine-needle-aspiration-material
#12
Thomas M Gress, Ludwig Lausser, Lyn-Rouven Schirra, Lisa Ortmüller, Ramona Diels, Bo Kong, Christoph W Michalski, Thilo Hackert, Oliver Strobel, Nathalia A Giese, Miriam Schenk, Rita T Lawlor, Aldo Scarpa, Hans A Kestler, Malte Buchholz
Pancreatic ductal adenocarcinoma (PDAC) continues to carry the lowest survival rates among all solid tumors. A marked resistance against available therapies, late clinical presentation and insufficient means for early diagnosis contribute to the dismal prognosis. Novel biomarkers are thus required to aid treatment decisions and improve patient outcomes. We describe here a multi-omics molecular platform that allows for the first time to simultaneously analyze miRNA and mRNA expression patterns from minimal amounts of biopsy material on a single microfluidic TaqMan Array card...
December 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/29288656/functional-bowel-disorders-a-roadmap-to-guide-the-next-generation-of-research
#13
Lin Chang, Carlo Di Lorenzo, Gianrico Farrugia, Frank A Hamilton, Gary M Mawe, Pankaj J Pasricha, John W Wiley
In June 2016, the National Institutes of Health hosted a workshop on functional bowel disorders (FBDs), particularly irritable bowel syndrome, with the objective of elucidating gaps in current knowledge and recommending strategies to address these gaps. The workshop aimed to provide a roadmap to help strategically guide research efforts during the next decade. Attendees were a diverse group of internationally recognized leaders in basic and clinical FBD research. This document summarizes the results of their deliberations, including the following general conclusions and recommendations...
December 27, 2017: Gastroenterology
https://www.readbyqxmd.com/read/29288185/cohort-profile-the-emory-cardiovascular-biobank-emcab
#14
Yi-An Ko, Salim Hayek, Pratik Sandesara, Ayman Samman Tahhan, Arshed Quyyumi
PURPOSE: The Emory Cardiovascular Biobank (EmCAB) is an ongoing prospective registry of patients undergoing cardiac catheterisation, which was established to identify novel factors associated with the pathobiological process and treatment of cardiovascular disease. PARTICIPANTS: Individuals aged 18 years and older undergoing cardiac catheterisation at three Emory Healthcare sites in Atlanta are asked to participate in this prospective registry. Around 95% agree to participate...
December 29, 2017: BMJ Open
https://www.readbyqxmd.com/read/29288091/the-importance-of-accounting-for-sex-in-the-search-of-proteomic-signatures-of-mycotoxin-exposure
#15
L Soler, I P Oswald
Mycotoxins are natural food and feed contaminants that are toxic to human and animals. Proteomics is an adequate toolbox to investigate the mode of action and the effects of mycotoxins, as these toxicants often alter protein synthesis and degradation, as well as induce changes of important post-translational modifications. For instance, the contaminant deoxynivalenol induces a severe ribosomal stress that affects protein production, whereas the toxin Fumonisin B1 can alter the phosphorylation of a large number of proteins, and patulin is a potent proteotoxic molecule...
December 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29286146/immune-response-associated-gene-profiling-in-japanese-melanoma-patients-using-multi-omics-analysis
#16
Yasuto Akiyama, Yoshio Kiyohara, Shusuke Yoshikawa, Masaki Otsuka, Ryota Kondou, Chizu Nonomura, Haruo Miyata, Akira Iizuka, Tadashi Ashizawa, Keiichi Ohshima, Kenichi Urakami, Takeshi Nagashima, Masatoshi Kusuhara, Takashi Sugino, Ken Yamaguchi
Project High-tech Omics-based Patient Evaluation (HOPE), including comprehensive whole-exome sequencing (WES) and gene expression profiling (GEP) using freshly resected tumor specimens, has been in progress since its implementation in 2014. Among a total of 1,685 cancer patients, 13 melanoma patients were registered in the HOPE Project and were characterized using multi-omics analyses. Among the 13 melanoma patients, 4 were deceased, and 9 were alive. The mean overall survival (OS) and relapse‑free survival (RFS) times of the melanoma patients were 16...
December 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29278737/network-science-in-clinical-trials-a-patient-centered-approach
#17
REVIEW
Venkata Manem, Roberto Salgado, Philippe Aftimos, Christos Sotiriou, Benjamin Haibe-Kains
There has been a paradigm shift in translational oncology with the advent of novel molecular diagnostic tools in the clinic. However, several challenges are associated with the integration of these sophisticated tools into clinical oncology and daily practice. High-throughput profiling at the DNA, RNA and protein levels (omics) generate a massive amount of data. The analysis and interpretation of these is non-trivial but will allow a more thorough understanding of cancer. Linear modelling of the data as it is often used today is likely to limit our understanding of cancer as a complex disease, and at times under-performs to capture a phenotype of interest...
December 23, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29275822/screening-for-fetal-growth-restriction-using-fetal-biometry-combined-with-maternal-biomarkers
#18
REVIEW
Francesca Gaccioli, Irving L M H Aye, Ulla Sovio, D Stephen Charnock-Jones, Gordon C S Smith
Fetal growth restriction is a major determinant of perinatal morbidity and mortality. Screening for fetal growth restriction is a key element of prenatal care but it is recognized to be problematic. Screening using clinical risk assessment and targeting ultrasound to high-risk women is the standard of care in the United States and United Kingdom, but the approach is known to have low sensitivity. Systematic reviews of randomized controlled trials do not demonstrate any benefit from universal ultrasound screening for fetal growth restriction in the third trimester, but the evidence base is not strong...
December 22, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29261660/genetic-analysis-of-japanese-primary-open-angle-glaucoma-patients-and-clinical-characterization-of-risk-alleles-near-cdkn2b-as1-six6-and-gas7
#19
Yukihiro Shiga, Koji M Nishiguchi, Yosuke Kawai, Kaname Kojima, Kota Sato, Kosuke Fujita, Mai Takahashi, Kazuko Omodaka, Makoto Araie, Kenji Kashiwagi, Makoto Aihara, Takeshi Iwata, Fumihiko Mabuchi, Mitsuko Takamoto, Mineo Ozaki, Kazuhide Kawase, Nobuo Fuse, Masayuki Yamamoto, Jun Yasuda, Masao Nagasaki, Toru Nakazawa
PURPOSE: To test the genetic association between Japanese patients with primary open-angle glaucoma (POAG) and the previously reported POAG susceptibility loci and to perform genotype-phenotype analysis. METHODS: Genetic associations for 27 SNPs from 16 loci previously linked to POAG were assessed using genome-wide SNP data of the primary cohort (565 Japanese POAG patients and 1,104 controls). Reproducibility of the assessment was tested in 607 POAG cases and 455 controls (second cohort) with a targeted genotyping approach...
2017: PloS One
https://www.readbyqxmd.com/read/29259349/are-fusion-transcripts-in-relapsed-metastatic-head-and-neck-cancer-patients-predictive-of-response-to-anti-egfr-therapies
#20
Paolo Bossi, Marco Siano, Cristiana Bergamini, Maria Cossu Rocca, Andrea P Sponghini, Marco Giannoccaro, Luca Tonella, Alessandro Paoli, Edoardo Marchesi, Federica Perrone, Silvana Pilotti, Laura D Locati, Silvana Canevari, Lisa Licitra, Loris De Cecco
Prediction of benefit from combined chemotherapy and the antiepidermal growth factor receptor cetuximab is a not yet solved question in head and neck squamous cell carcinoma (HNSCC). In a selected series of 14 long progression-free survival (PFS) and 26 short PFS patients by whole gene and microRNA expression analysis, we developed a model potentially predictive of cetuximab sensitivity. To better decipher the "omics" profile of our patients, we detected transcript fusions by RNA-seq through a Pan-Cancer panel targeting 1385 cancer genes...
2017: Disease Markers
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