Begell House Inc.
Critical Reviews™ in Eukaryotic Gene Expression
CRE
1045-4403
26
2
2016
Clinical Genomics: Challenges and Opportunities
97-113
10.1615/CritRevEukaryotGeneExpr.2016015724
Priyanka
Vijay
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Tri-Institutional Training
Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
Alexa B. R.
McIntyre
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Tri-Institutional Training
Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
Christopher E.
Mason
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York. Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York. Feil Family Brain and Mind Research Institute, New York, New York
Jeffrey P.
Greenfield
Department of Neurological Surgery, New York-Presbyterian Hospital, Weill
Cornell Medical College, New York, New York
Sheng
Li
Department of Neurological Surgery, New York-Presbyterian Hospital, Weill
Cornell Medical College, New York, New York
Sequencing
genomics
clinical utility
Next-generation sequencing (NGS) approaches are highly applicable to clinical studies. We review
recent advances in sequencing technologies, as well as their benefits and tradeoffs, to provide an overview of clinical genomics from study design to computational analysis. Sequencing technologies enable genomic, transcriptomic, and epigenomic evaluations. Studies that use a combination of whole genome, exome, mRNA, and bisulfite sequencing are now feasible due to decreasing sequencing costs. Single-molecule sequencing increases read length, with the MinIONTM nanopore sequencer, which offers a uniquely portable option at a lower cost. Many of the published comparisons we review here address the challenges associated with different sequencing methods. Overall, NGS
techniques, coupled with continually improving analysis algorithms, are useful for clinical studies in many realms,
including cancer, chronic illness, and neurobiology. We, and others in the field, anticipate the clinical use of NGS
approaches will continue to grow, especially as we shift into an era of precision medicine.
Macrophage Polarization: Implications on Metabolic Diseases and the Role of Exercise
115-132
10.1615/CritRevEukaryotGeneExpr.2016015920
Loreana Sanches
Silveira
Immunometabolism Research Group, Institute of Biomedical Sciences, Department of Cell Biology and Development, University of Sao Paulo, Av. Prof Lineu Prestes, 1524, 05508-000 Sao Paulo, SP, Brazil; Exercise and Immunometabolism Research Group, Department of Physical Education, University of the State of Sao Paulo, Rua Roberto Simonsen, 305, 19060-900 Presidente Prudente, SP, Brazil
Barbara de Moura Mello
Antunes
Exercise and Immunometabolism Research Group, Department of Physical Education, University of the State of Sao Paulo, Rua Roberto Simonsen, 305, 19060-900 Presidente Prudente, SP, Brazil
Andre Luis Araujo
Minari
Psychobiology Department, Federal University of Sao Paulo, UNIFESP, Sao Paulo, Brazil
Ronaldo Vagner Thomatieli
dos Santos
Psychobiology Department, Federal University of Sao Paulo, UNIFESP, Sao Paulo, Brazil; Bioscience Department, Campus Baixada Santista, Federal University of Sao Paulo, UNIFESP, Santos, Brazil
José Cesar Rosa
Neto
Immunometabolism Research Group, Department of Cell Biology and Development − Institute of Biomedical Sciences I − University of Sao Paulo (USP), Sao Paulo, Brazil
Fábio Santos
Lira
Immunometabolism Research Group, Department of Cell Biology and Development − Institute of Biomedical Sciences I − University of Sao Paulo (USP), Sao Paulo, Brazil
macrophages
immune system
inflammation
exercise
transcriptional factor
Macrophages are cells of the innate immune response that trigger inflammation resolution. The phenotype of "classically activated macrophages" (M1) has anti-tumoricidal and anti-bactericidal activities. On the
other hand, "alternatively activated macrophages" (M2) are involved in tissue remodeling and immunomodulatory
functions. The change in the polarization of macrophages varies according to the diversity of cytokines present
in the microenvironment or by the stimuli of an antigen. It involves such factors as interferon-regulatory factors,
peroxisome proliferator-activated receptors (PPARs), hypoxia-inducible factors (HIFs), and signal transducers and
activators of transcription (STATs). Switching the phenotype of macrophages can help attenuate the development
of an inflammatory disease. Exercise can promote alterations in the number of innate immune cells and stimulates phagocytic function. Chronic exercise seems to inhibit macrophage infiltration into adipose tissue by attenuating the expression of F4/80 mRNA. Furthermore, exercise may also increase the expression of M2 markers and reduce TNF-α and TLR4 mRNA expression, which activates the inflammatory pathway of NF-κB. Chronic exercise reduces β2-adrenergic receptors in monocytes and macrophages by modulating TLR4 signaling as well as suppressing IL-12 production, a stimulator of interferon Y. In this review, we discuss macrophage polarization in metabolic diseases and how exercise can modulate macrophage plasticity.
Ethical Dilemmas for Oocyte Donations: Slippery Slope for Conflicts of Interest
133-136
10.1615/CritRevEukaryotGeneExpr.2016015927
Pinar
Tulay
Near East University
oocyte donation
donor
genetic screening
reproductive risk
Oocyte donations have increased with improvements in oocyte cryopreservation procedures in recent years. Women with medical conditions that require chemotherapy or radiotherapy have begun to opt for oocyte cryo¬preservation prior to their treatment or to enroll in an oocyte donation program. Alternatively, some women apply for "third-party" oocyte donation programs for nonmedical reasons such as delayed childbearing. Although society seems to accept oocyte donations for medical reasons, it appears that there are still some moral issues surrounding nonmedical oocyte donations. In this review, the ethical aspects of oocyte donations and donors' perspectives are discussed. With developing technologies, the genetic screening of donors has expanded to include diseases. This review explores the ethical issues involved in genetic screening of gamete donors.
The Impacts of miRNAs in Glioblastoma Progression
137-142
10.1615/CritRevEukaryotGeneExpr.2016015964
Rasime
Kalkan
European University of Lefke
Emine İkbal
Atli
Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
miRNA
GBM
Glioblastoma
therapy
survival
miRNAs are short noncoding RNA sequences that cause translational repression or mRNA degradation.
A growing number of studies have sought new biomarkers in GBM that will be important in disease progression and prognosis and as potential therapeutic targets. miRNA-profiling studies in glioblastoma patients have found that aberrant miRNA expression can be used as a target to develop new biomarkers for disease detection and for determining prognosis or therapeutic response. In evaluating the tumor or its therapeutic response, genetic abnormalities such as mutations, epigenetic abnormalities, and aberrant miRNA expressions can be useful markers. This review summarizes the known miRNAs according their therapeutic importance and their use as disease progression biomarkers.
Recent Investigations for Discovery of Natural Antioxidants: A Comprehensive Review
143-160
10.1615/CritRevEukaryotGeneExpr.2016015974
Amna
Parveen
Pharmaceutical Resources Botany Laboratory, Department of Pharmacognosy, College of Pharmacy, Chung-ang University, Seoul, Republic of Korea; Department of Pharmaceutical Chemistry, Government College University
Faisalabad, Pakistan
Muhammad Sajid Hamid
Akash
Department of Pharmaceutical Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
Kanwal
Rehman
Department of Pharmacy, University of Agriculture, Faisalabad, Pakistan
Whang Wan
Kyunn
Pharmaceutical Resources Botany Laboratory, Department of Pharmacognosy, College of Pharmacy, Chung-ang
University, Seoul, Republic of Korea
Antioxidants
medicinal plants
reactive oxygen species
In the biological system, reactive oxygen species (ROS) play a crucial role in the defense mechanisms of the body. ROS is responsible for the initiation of several cellular responses that can impart the harmful effects on the body, initiating biomolecular damage. Therefore, it is essential to counteract the dangerous effects produced by ROS, which is only possible through the use of antioxidants. Researchers are evaluating medicinal plants to discover and investigate the new antioxidant sources. Using natural antioxidants, beneficial effects on human health can be achieved. In this article, we summarize the recent investigations of the sources of naturally occurring antioxidants.
Challenges Facing the Use of Endothelial Progenitor Cells in Stem Cell Therapies
161-162
10.1615/CritRevEukaryotGeneExpr.2016016325
Carolina N.
Franca
University of Santo Amaro, Health Sciences Post Graduation, Sao Paulo, Brazil; Federal University of Sao Paulo,
Department of Medicine, Sao Paulo, Brazil
Jonatas B.
Amaral
Federal University of Sao Paulo, Department of Otorhinolaryngology
-Head and Neck Surgery, São Paulo, Brazil
Izabela D.
Tuleta
University of Bonn, Department of Internal Medicine II - Cardiology, Pneumology, Angiology, Bonn, Germany
Fábio
Siviero
University of Sao Paulo, Department of Cell and Tissue Biology, Institute
of Biomedical Sciences, Sao Paulo, Brazil
Carlos E. S.
Ferreira
Federal University of Sao Paulo,
Department of Medicine, Sao Paulo, Brazil;
Albert Einstein Israeli Hospital, Clinical Laboratory, Sao Paulo, Brazil
Maria C. O.
Izar
Federal University of Sao Paulo,
Department of Medicine, Sao Paulo, Brazil
Francisco A. H.
Fonseca
Federal University of Sao Paulo,
Department of Medicine, Sao Paulo, Brazil
bone marrow
clinical trials as topic
cryopreservation
endothelial progenitor cells
cluster of differentiation markers
The paper summarizes the difficulties to study the rare population of endothelial progenitor cells in clinical trials, based on the experience of our group in many publications in this area.
Events of Molecular Changes in Epithelial-Mesenchymal Transition
163-171
10.1615/CritRevEukaryotGeneExpr.2016016307
Srishti
Kotiyal
Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh, India
Susinjan
Bhattacharya
Department of Biotechnology, Jaypee Institute of Information Technology
Cell junctions
Cytoskeletal changes
EMT
GTPase
miRNA
EMT is the process by which epithelial cells, characterized by well-developed intercellular contacts, transdifferentiate into motile and invasive mesenchymal cells. This process is associated with the loss of transmembrane intercellular adhesion molecule E-cadherin and disruption of cell-cell junctions along with acquisition of migratory properties. EMT is integral in embryonic development, wound healing, and stem cell behavior; however, its aberrant activation by micro-environmental alterations and abnormal stimuli can lead to cancer progression. Here, we review the different molecular changes associated with EMT that are responsible for downregulation of epithelial genes. Increased knowledge of the EMT process is essential for therapeutic targeting of cancer cells.
The Changes of Energy Interactions between Nucleus Function and Mitochondria Functions Causing Transmutation of Chronic Inflammation into Cancer Metabolism
173-186
10.1615/CritRevEukaryotGeneExpr.2016016308
Michail R.
Ponizovskiy
A.A.Bogomoletz Kiev National Medical Universary; Laboratory Biochemistry and Toxicology, Kiev Regional p/n Hospital, Kiev, Ukraine
balance of catabolic and anabolic processes
cellular internal energy
ROS/H2O2/O2*/free radicals
cellular capacitors
mitochondrial fusion and fission
Interactions between nucleus and mitochondria functions induce the mechanism of maintenance stability of cellular internal energy according to the first law of thermodynamics in able-bodied cells and changes the mechanisms of maintenance stability of cellular internal energy creating a transition stationary state of ablebodied cells into quasi-stationary pathologic states of acute inflammation transiting then into chronic inflammation and then transmuting into cancer metabolism. The mechanisms’ influences of intruding etiologic pathologic agents (microbe, virus, etc.) lead to these changes of energy interactions between nucleus and mitochondria functions causing general acute inflammation, then passing into local chronic inflammation, and reversing into cancer metabolism transmutation. Interactions between biochemical processes and biophysical processes of cellular capacitors’ operations create a supplementary mechanism of maintenance stability of cellular internal energy in the norm and in pathology. Discussion of some scientific works eliminates doubts of the authors of these works.