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Omics: a Journal of Integrative Biology

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https://www.readbyqxmd.com/read/28486096/key-pharmacogenomic-considerations-for-sickle-cell-disease-patients
#1
Alexandra Kolliopoulou, Apostolos Stratopoulos, Stavroula Siamoglou, Argyro Sgourou, Adamantia Papachatzopoulou, Theodora Katsila, George P Patrinos
Sickle cell disease (SCD), although a monogenic disease, exhibits a complex clinical phenotype that hampers optimum patient stratification and disease management, especially on hydroxyurea treatment. Moreover, theranostics, the combination of diagnostics to individualize and optimize therapeutic interventions, has not been firmly on the forefront of SCD research and clinical management to date. We suggest that if tailor-made theranostics in SCD is envisaged, pharmacogenomics is anticipated to be the way forward...
May 9, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28486083/progress-in-mass-spectrometry-based-proteomics-in-hypoxia-related-diseases-and-high-altitude-medicine
#2
Zhiqi Gao, Gang Luo, Bing Ni
Human migration, influenced by social conflict and natural disasters as well as global climate change, has become recognized as a major "planetary force." It has also brought to the forefront, new specialties of integrative biology-such as high-altitude medicine-and the impact of hitherto understudied environmental factors on human pathophysiology in these new geographical settings. For people migrating to or living in high-altitude regions, environmental hypoxia is a primary challenge. Decreased partial pressure of oxygen in environmental air, caused by lower barometric pressure, puts living organisms in a hypoxic state...
May 9, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28402209/culturomics-a-new-kid-on-the-block-of-omics-to-enable-personalized-medicine
#3
Manousos E Kambouris, Cristiana Pavlidis, Efthymios Skoufas, Michael Arabatzis, Maria Kantzanou, Aristea Velegraki, George P Patrinos
This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine...
April 12, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28282257/human-microbiome-and-learning-healthcare-systems-integrating-research-and-precision-medicine-for-inflammatory-bowel-disease
#4
Kim H Chuong, David R Mack, Alain Stintzi, Kieran C O'Doherty
Healthcare institutions face widespread challenges of delivering high-quality and cost-effective care, while keeping up with rapid advances in biomedical knowledge and technologies. Moreover, there is increased emphasis on developing personalized or precision medicine targeted to individuals or groups of patients who share a certain biomarker signature. Learning healthcare systems (LHS) have been proposed for integration of research and clinical practice to fill major knowledge gaps, improve care, reduce healthcare costs, and provide precision care...
March 10, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481734/hlj1-dnajb4-gene-is-a-novel-biomarker-candidate-in-breast-cancer
#5
Tolga Acun, Natalie Doberstein, Jens K Habermann, Timo Gemoll, Christoph Thorns, Emin Oztas, Thomas Ried
Breast cancer is the most common cancer type and cause of cancer-related mortality among women worldwide. New biomarker discovery is crucial for diagnostic innovation and personalized medicine in breast cancer. Heat shock proteins (HSPs) have been increasingly reported as biomarkers and potential drug targets for cancers. HLJ1 (DNAJB4) belongs to the DNAJ (HSP40) family of HSPs and is regarded as a tumor suppressor gene in lung, colon, and gastric cancers. However, the role of the HLJ1 gene in breast cancer is currently unknown...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481733/tissue-proteome-analysis-of-different-grades-of-human-gliomas-provides-major-cues-for-glioma-pathogenesis
#6
Kishore Gollapalli, Saicharan Ghantasala, Apurva Atak, Srikanth Rapole, Aliasgar Moiyadi, Sridhar Epari, Sanjeeva Srivastava
Gliomas are heterogeneous and most commonly occurring brain tumors. Blood-brain barrier restricts the entry of brain tumor proteins into blood stream thus limiting the usage of serum or plasma for proteomic analysis. Our study aimed at understanding the molecular basis of aggressiveness of various grades of brain tumors using isobaric tagging for relative and absolute quantification (iTRAQ) based mass spectrometry. Tissue proteomic analysis of various grades of gliomas was performed using four-plex iTRAQ. We labeled five sets (each set consists of control, grade-II, III, and IV tumor samples) of individual glioma patients using iTRAQ reagents...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481732/human-cap10-like-protein-46%C3%A2-kda-gene-promotes-malignancy-in-colorectal-cancer
#7
Honghong Fang, Qiaoyun Chu, Jie Zhang, Hao Wang, Xinwei Yu, Siqi Ge, Manshu Song, Lijuan Wu, Minglin Lang, Naibai Chang, Youxin Wang, Wei Wang
Colon cancer patients have major unmet needs in terms of robust diagnostics and molecular biomarkers for personalized therapeutics. We have previously reported that human CAP10-like protein 46 kDa (hCLP46) is overexpressed in human acute myelogenous leukemia, T acute lymphoblastic leukemia, and leukemia cell lines. We extend this line of biomarker and diagnostic discovery research by investigating hCLP46 expression in colorectal cancer (CRC) tissues and examine the possibility of hCLP46 as a candidate biomarker for diagnosis and prognosis of CRC...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481731/posttranslational-modifications-in-spermatozoa-and-effects-on-male-fertility-and-sperm-viability
#8
Rahim Dad Brohi, Li-Jun Huo
Spermatogenesis is a complex and highly regulated process. The ability of spermatozoa to perform its function depends on multiple physiological and genetic factors that are not fully understood. Notably, due to lack of transcriptional and translational activity in spermatozoa, posttranslational modifications (PTMs) play key roles in determining their viability. PTMs not only confer structural changes in the proteome of the spermatozoa cells, but also increase the diversity of the proteome and introduce specific modifications that could be translated into functional changes in the affected spermatozoa...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28481730/next-generation-sequencing-reveals-novel-mutations-in-x-linked-intellectual-disability
#9
Babylakshmi Muthusamy, Lakshmi Dhevi N Selvan, Thong T Nguyen, Jesna Manoj, Eric W Stawiski, Bijay S Jaiswal, Weiru Wang, Remya Raja, Vedam Laxmi Ramprasad, Ravi Gupta, Sakthivel Murugan, Jayarama S Kadandale, T S Keshava Prasad, Kavita Reddy, Andrew Peterson, Akhilesh Pandey, Somasekar Seshagiri, Satish Chandra Girimaji, Harsha Gowda
Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next-generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28375712/ovarian-cancer-differential-interactome-and-network-entropy-analysis-reveal-new-candidate-biomarkers
#10
Dilara Ayyildiz, Esra Gov, Raghu Sinha, Kazim Yalcin Arga
Ovarian cancer is one of the most common cancers and has a high mortality rate due to insidious symptoms and lack of robust diagnostics. A hitherto understudied concept in cancer pathogenesis may offer new avenues for innovation in ovarian cancer biomarker development. Cancer cells are characterized by an increase in network entropy, and several studies have exploited this concept to identify disease-associated gene and protein modules. We report in this study the changes in protein-protein interactions (PPIs) in ovarian cancer within a differential network (interactome) analysis framework utilizing the entropy concept and gene expression data...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388302/genome-wide-association-and-replication-study-of-hepatotoxicity-induced-by-antiretrovirals-alone-or-with-concomitant-anti-tuberculosis-drugs
#11
Zelalem Petros, Ming Ta Michael Lee, Atsushi Takahashi, Yanfei Zhang, Getnet Yimer, Abiy Habtewold, Ina Schuppe-Koistinen, Taisei Mushiroda, Eyasu Makonnen, Michiaki Kubo, Eleni Aklillu
Drug-induced hepatotoxicity (DIH) is a common adverse event that is associated with both antiretroviral (ARV) and anti-tuberculosis drugs (ATD). Moreover, the genetic variations predisposing ARV- and ARV-ATD-induced liver toxicity in African populations are not well investigated, despite the two diseases being the major global health problems in sub-Saharan Africa. We performed a genome-wide association study (GWAS) and replication study to identify the genetic variants linked to the risk of developing DIH due to ARV drugs alone, and ARV-ATD co-treatment in Ethiopian HIV-positive patients...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388301/procalcitonin-biomarker-algorithm-reduces-antibiotic-prescriptions-duration-of-therapy-and-costs-in-chronic-obstructive-pulmonary-disease-a-comparison-in-the-netherlands-germany-and-the-united-kingdom
#12
Marloes E van der Maas, Gertjan Mantjes, Lotte M G Steuten
Antibiotics are often recommended as treatment for patients with chronic obstructive pulmonary disease (COPD) exacerbations. However, not all COPD exacerbations are caused by bacterial infections and there is consequently considerable misuse and overuse of antibiotics among patients with COPD. This poses a severe burden on healthcare resources such as increased risk of developing antibiotic resistance. The biomarker procalcitonin (PCT) displays specificity to distinguish bacterial inflammations from nonbacterial inflammations and may therefore help to rationalize antibiotic prescriptions...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388300/minimal-standards-for-reporting-microrna-target-interactions
#13
Klara Piletič, Tanja Kunej
Epigenomics is one of the leading frontiers of postgenomics medicine. The challenges and prospects ahead in epigenomics are related not merely to technology innovation and clinical implementation but also to science communication. In this context, microRNAs (miRNAs) are an important part of the epigenomic regulatory machinery. As the number of publications reporting miRNA-target interactions (MTIs) is growing rapidly, there is an urgent need to standardize reporting. This study reports (1) an analysis of the published literature and databases reporting validated MTIs, and for the first time to the best of our knowledge (2) suggests a solution as a way forward, the minimum information required for MTI standard reporting...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388299/innovation-analysis-on-postgenomic-biomarkers-glycomics-for-chronic-diseases
#14
Eric Adua, Alyce Russell, Peter Roberts, Youxin Wang, Manshu Song, Wei Wang
Despite decades of investment in biomarker research, we still do not have robust and field-tested biomarkers for many chronic diseases so as to anticipate clinical outcomes and thus move toward personalized medicine. Biomarker innovations have tended to focus on genomics, but next-generation biomarkers from the nascent field of glycomics now offer fresh vistas for innovation in chronic disease biomarkers and systems diagnostics. Glycosylation, regarded as a complex enzymatic process where sugars (glycans) bind to proteins and lipids, affects many human biological functions, including cell signaling, adhesion, and motility...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388298/nf-%C3%AE%C2%BAb-is-a-potential-molecular-drug-target-in-triple-negative-breast-cancers
#15
Paola Poma, Manuela Labbozzetta, Natale D'Alessandro, Monica Notarbartolo
Breast cancer continues to cause significant burden in global health morbidity and mortality. Triple-negative breast cancers (TNBCs) are highly aggressive with poor prognosis and are characterized by lack of expression of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor (Her-2). TNBCs are often resistant to cytotoxic chemotherapy and pose major difficulty in achieving personalized medicine due to their molecular heterogeneity. There is increasing evidence that the aberrant activation of nuclear factor (NF)-κB signaling is a frequent characteristic of TNBCs...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28388297/cancer-transcriptome-dataset-analysis-comparing-methods-of-pathway-and-gene-regulatory-network-based-cluster-identification
#16
Seungyoon Nam
Cancer transcriptome analysis is one of the leading areas of Big Data science, biomarker, and pharmaceutical discovery, not to forget personalized medicine. Yet, cancer transcriptomics and postgenomic medicine require innovation in bioinformatics as well as comparison of the performance of available algorithms. In this data analytics context, the value of network generation and algorithms has been widely underscored for addressing the salient questions in cancer pathogenesis. Analysis of cancer trancriptome often results in complicated networks where identification of network modularity remains critical, for example, in delineating the "druggable" molecular targets...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253088/association-between-telomere-length-chronic-kidney-disease-and-renal-traits-a-systematic-review
#17
Oluwatoyin I Ameh, Ikechi G Okpechi, Collet Dandara, André-Pascal Kengne
Telomere length (TL) is an important biological variable that can influence a variety of disease-related complex traits as well as host-environment interactions such as drug and nutritional responses. Chronic kidney disease (CKD) is a common global health challenge especially with the currently aging world population. We conducted a PubMed database search according to the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines for systematic reviews. Studies in adults (18 years and above) in which TL was determined and correlated with CKD, renal traits, and function were included, while animal model studies were excluded...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253087/genome-wide-association-studies-for-idiosyncratic-drug-induced-hepatotoxicity-looking-back-looking-forward-to-next-generation-innovation
#18
Zelalem Petros, Eyasu Makonnen, Eleni Aklillu
Idiosyncratic drug-induced hepatotoxicity is a formidable challenge for rational drug discovery and development, as well as the science of personalized medicine. There is evidence that hereditary factors, in part, contribute to drug toxicity. This expert analysis and review offer the insights gained, and the challenges ahead, for genome-wide association studies (GWASs) of idiosyncratic drug-induced hepatotoxicity. Published articles on genome-wide and subsequent replication studies were systematically searched in the PubMed electronic database...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253086/oocyte-developmental-competence-insights-from-cross-species-differential-gene-expression-and-human-oocyte-specific-functional-gene-networks
#19
Fernando H Biase
Understanding oocyte developmental competence remains a key challenge for reproductive biology and systems sciences. The transcriptome of oocytes in eutherians is highly complex and is associated with the success of embryo development. Due to sample limitations from humans, animal models are used for investigation of the oocyte transcriptome. Nonetheless, little is known about the diversity of the oocyte transcriptome across eutherians. In this report, comprehensive investigation of 7 public data sets in 4 species, human, macaque, mice, and cattle, shows that 16,572 genes are expressed in oocytes...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28253085/water-pipe-shisha-hookah-arghile-smoking-and-secondhand-tobacco-smoke-effects-on-cyp1a2-and-cyp2a6-phenotypes-as-measured-by-caffeine-urine-test
#20
Şenay Görücü Yılmaz, Adrián Llerena, Fernando De Andrés, Ümit Karakaş, Hasan Gündoğar, Kamile Erciyas, Sabit Kimyon, Alper Mete, Kıvanç Güngör, Vural Özdemir
Public policies to stop or reduce cigarette smoking and exposure to secondhand smoke and associated diseases have yielded successful results over the past decade. Yet, the growing worldwide popularity of another form of tobacco consumption, water pipe smoking, has received relatively less attention. To the best of our knowledge, no study to date has evaluated the effects of water pipe smoking on cytochrome P450 (CYP450) activities and drug interaction potential in humans, whereas only limited information is available on the impact of secondhand smoke on drug metabolism...
March 2017: Omics: a Journal of Integrative Biology
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