Overexpression of genes in health and sickness. A bird's eye view

In Silico Pleiotropy Analysis in KEGG Signaling Networks Using a Boolean Network Model

Pleiotropy, which refers to the ability of different mutations on the same gene to cause different pathological effects in human genetic diseases, is important in understanding system-level biological diseases. Although some biological experiments have been proposed, still little is known about pleiotropy on gene–gene dynamics, since most previous studies have been based on correlation analysis. Therefore, a new perspective is needed to investigate pleiotropy in terms of gene–gene dynamical characteristics. To quantify pleiotropy in terms of network dynamics, we propose a measure called in silico Pleiotropic Scores (sPS), which represents how much a gene is affected against a pair of different types of mutations on a Boolean network model. We found that our model can identify more candidate pleiotropic genes that are not known to be pleiotropic than the experimental database. In addition, we found that many types of functionally important genes tend to have higher sPS values than other genes; in other words, they are more pleiotropic. We investigated the relations of sPS with the structural properties in the signaling network and found that there are highly positive relations to degree, feedback loops, and centrality measures. This implies that the structural characteristics are principles to identify new pleiotropic genes. Finally, we found some biological evidence showing that sPS analysis is relevant to the real pleiotropic data and can be considered a novel candidate for pleiotropic gene research. Taken together, our results can be used to understand the dynamics pleiotropic characteristics in complex biological systems in terms of gene–phenotype relations.

Differential Gene Expression in Post-Finasteride Syndrome Patients

BACKGROUND

An organic etiology underpinning post-finasteride syndrome, a constellation of persistent sexual, neuropsychiatric, and somatic symptoms reported by men exposed to 5-alpha-reductase inhibitors (5ARIs), is debated. Persistent changes in neurosteroid levels or androgen receptor expression have been implicated.

AIM

To determine whether differences in gene expression, especially in relevant biologic pathways, exist between patients reporting post-finasteride syndrome symptoms and healthy controls.

METHODS

This was a single center, prospective case-control study taking place between March 2013 and September 2018. Men 18 years and older being evaluated for sexual dysfunction (study) or circumcision (control) were eligible for inclusion. Twenty-six men with a history of 5ARI use reporting symptoms consistent with post-finasteride syndrome were included in the patient group. Twenty-six men consented to inclusion in the control group.

OUTCOMES

The primary outcome measure is gene expression data for genes affecting neurosteroid levels and androgen receptor activity from penile skin cells.

RESULTS

Gene expression of cells from penile skin samples from twenty-six men of median age 38 years (IQR, 33-42) in the study group was compared with that from twenty-six men of median age 41 years (IQR, 35-62) in the control group (P = .13), with 1,446 genes significantly over-expressed and 2,318 genes significantly under-expressed in study patients. Androgen receptor expression was significantly higher in study patients compared to controls (9.961 vs 9.494, adjusted P value = .01). Serum levels of androgen receptor activity markers 5α-androstanediol (0.950 ng/mL [0.749-1.587] vs 0.949 [0.817-1.337], P = .34) or 3α-androstanedione (3.1 ng/mL [1.925-5.475] vs 6.7 [3.375-11.4], P = .31) revealed no significant differences. No significant differences were found between the number of trinucleotide repeats (21.5 [20-23.75], 22 [19-25], P = .94).

CLINICAL IMPLICATIONS

In this study we present evidence of gene expression correlating with observed biologic differences in patients with post-finasteride syndrome; providers who prescribe 5ARIs should be aware and advise their patients accordingly.

STRENGTHS & LIMITATIONS

Strengths of this study include the evaluation of multiple proposed etiologies for post-finasteride syndrome. The study is also strengthened by the fact that not all data matched the initial hypotheses, qualifying the argument for the existence of PFS. Limitations include potential selection bias arising from more severe phenotypes seeking care; lack of gene expression data prior to 5ARI exposure; lack of non-penile tissue samples supposedly involved; and a lack of mechanistic data to imply causality.

CONCLUSION

This study is the first to consider and demonstrate gene expression differences in patients with PFS as a potential etiology of sexual dysfunction. Howell S, Song W, Pastuszak A, et al. Differential Gene Expression in Post-Finasteride Syndrome Patients. J Sex Med 2021;18:1479-1490.

RMut: R package for a Boolean sensitivity analysis against various types of mutations

There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. In addition, RMut can specify the mutation area and the duration time for more precise analysis. RMut can be used to analyze large-scale networks because it is implemented in a parallel algorithm using the OpenCL library. In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. In the second case study, we showed that edgetic mutations can predict drug-targets better than node-based mutations. Finally, we examined the network sensitivity to double edge-removal mutations and found an interesting synergistic effect. Taken together, these findings indicate that RMut is a flexible R package to efficiently analyze network sensitivity to various types of mutations. RMut is available at https://github.com/csclab/RMut.

Independent validation of induced overexpression efficiency across 242 experiments shows a success rate of 39

Although numerous studies containing induced gene expression have already been published, independent authentication of their results has not yet been performed. Here, we utilized available transcriptomic data to validate the achieved efficiency in overexpression studies. Microarray data of experiments containing cell lines with induced overexpression in one or more genes were analyzed. All together 342 studies were processed, these include 242 different genes overexpressed in 184 cell lines. The final database includes 4,755 treatment-control sample pairs. Successful gene induction (fold change induction over 1.44) was validated in 39.3% of all genes at p < 0.05. Number of repetitions within a study (p < 0.0001) and type of used vector (p = 0.023) had significant impact on successful overexpression efficacy. In summary, over 60% of studies failed to deliver a reproducible overexpression. To achieve higher efficiency, robust and strict study design with multi-level quality control will be necessary.

The application of 'kisser' probes for resolving the distribution and microenvironment of membrane proteins in situ

Membrane proteins play a lead role in the formation and function of synapses, but, despite revolutions in immunology and molecular genetics, limitations persist in our ability to investigate membrane proteins in the context of an intact synapse. Here, we introduce a simple but novel approach to resolving the distribution of endogenous membrane proteins in either live or fixed tissues. The technique involves transgenic expression of a protein with an extracellular tag, a generic transmembrane domain, and an intracellular terminus that mimics the intracellular anchoring motifs of the endogenous protein of interest. We provide three examples where these kisser probes can be used to answer questions regarding the synaptic distribution of endogenous proteins and their microenvironment that would be difficult to resolve by other contemporary means: (i) the live distribution of untagged proteins at the neuromuscular junction (Cacophony and Shaker), (ii) the relative distribution of an untagged protein (PMCA) in pre- versus post-synaptic membranes separated by only 20 nm across the cleft of a fixed synapse, and (iii) the live targeting of functional probes (chemical and protein fluorescent pH reporters) to membrane protein-defined subcellular domains.

Polymer Microneedle Mediated Local Aptamer Delivery for Blocking the Function of Vascular Endothelial Growth Factor

Overexpression of proteins in the body can cause severe diseases and other physiological disturbances. The development of protein blockers and local delivery systems would offer opportunities for addressing the health problems caused by protein overexpression. Nucleic acid aptamers are an emerging class of ligands with the potential to block proteins effectively; however, little effort has been made in developing polymer systems for local aptamer delivery. In this work, polymer microneedles capable of delivering DNA aptamers locally to inhibit the function of vascular endothelial growth factor (VEGF) were developed and studied. The presence of anti-VEGF aptamer in the polymer matrix did not change the apparent mechanical strength of the microneedles. Once in contact with a physiological solution, the polymer microneedles quickly dissolved, generating a high concentration of anti-VEGF aptamer in the surrounding local microenvironment. Aptamer delivery by way of dissolving polymer microneedles in a tissue phantom reduced VEGF-mediated endothelial cell tube formation. Thus, aptamer-loaded polymer microneedles hold great potential as a therapeutic tool for the treatment of human diseases resulting from protein overexpression.

Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN

The Zebrafish Model Organism Database (ZFIN; https://zfin.org) is the central resource for genetic, genomic, and phenotypic data for zebrafish (Danio rerio) research. ZFIN continuously assesses trends in zebrafish research, adding new data types and providing data repositories and tools that members of the research community can use to navigate data. The many research advantages and flexibility of manipulation of zebrafish have made them an increasingly attractive animal to model and study human disease.To facilitate disease-related research, ZFIN developed support to provide human disease information as well as annotation of zebrafish models of human disease. Human disease term pages at ZFIN provide information about disease names, synonyms, and references to other databases as well as a list of publications reporting studies of human diseases in which zebrafish were used. Zebrafish orthologs of human genes that are implicated in human disease etiology are routinely studied to provide an understanding of the molecular basis of disease. Therefore, a list of human genes involved in the disease with their corresponding zebrafish ortholog is displayed on the disease page, with links to additional information regarding the genes and existing mutations. Studying human disease often requires the use of models that recapitulate some or all of the pathologies observed in human diseases. Access to information regarding existing and published models can be critical, because they provide a tractable way to gain insight into the phenotypic outcomes of the disease. ZFIN annotates zebrafish models of human disease and supports retrieval of these published models by listing zebrafish models on the disease term page as well as by providing search interfaces and data download files to access the data. The improvements ZFIN has made to annotate, display, and search data related to human disease, especially zebrafish models for disease and disease-associated gene information, should be helpful to researchers and clinicians considering the use of zebrafish to study human disease.

A novel dual lock method for down-regulation of genes, in which a target mRNA is captured at 2 independent positions by linked locked nucleic acid antisense oligonucleotides

Nuclear factor κB (NFκB), which is composed of the RelA and p50 subunits, binds to NFκB response elements (NREs) and stimulates the transcription of inflammation-related genes. Here, locked nucleic acid (LNA) antisense oligonucleotides (ASOs) complementary to the termini of the 3'- and 5'-untranslated regions (UTRs) of the RelA mRNA were generated; these molecules were named 3'-LNA and 5'-LNA, respectively. To evaluate their effects on NFκB activity, HeLa cells were co-transfected with the LNA ASOs and a luciferase reporter gene carrying an NRE. Transfection of the cells with 3'-LNA reduced NFκB activity by 30-40%, without affecting RelA mRNA accumulation. Concomitant transfection of HeLa cells with 5'-LNA and 3'-LNA resulted in a 70% reduction in NFκB activity. Furthermore, partial poly(A) tail shortening occurred in LNA ASO-transfected cells. We also employed triethylene glycol as a spacer to link 5'-LNA and 3'-LNA. Reporter gene assays showed that the spacer-linked LNA ASO reduced NFκB activity similarly to a combination of 5'-LNA and 3'-LNA. In addition, an in vitro translation assay revealed that spacer-linked LNA ASOs inhibited the translation of a target mRNA in a specific manner. In summary, this study describes a novel antisense method capturing the target mRNA at independent positions.

Winter temperatures decrease swimming performance and limit distributions of tropical damselfishes

Coral reefs within 10° of the equator generally experience ≤3°C seasonal variation in water temperature. Ectotherms that have evolved in these conditions are therefore expected to exhibit narrow thermal optima and be very sensitive to the greater thermal variability (>6°C) experienced at higher latitudes (≥10°N/S). The impact of increased thermal variability on the fitness and distribution of thermally sensitive reef ectotherms is currently unknown. Here, we examine site-attached planktivorous coral reef damselfishes that rely on their physiological capacity to swim and forage in the water column year round. We focus on 10 species spanning four evolutionarily distinct genera from a region of the Great Barrier Reef that experiences ≥6°C difference between seasons. Four ecologically important indicators showed reduced performance during the winter low (23°C) compared with the summer peak (29°C), with effect sizes varying among species and genera, as follows: (i) the energy available for activity (aerobic scope) was reduced by 35-45% in five species and three genera; (ii) the energetically most efficient swimming speed was reduced by 17% across all species; and (iii) the maximal critical swimming speed and (iv) the gait transition speed (the swimming mode predominantly used for foraging) were reduced by 16-42% in six species spanning all four genera. Comparisons with field surveys within and across latitudes showed that species-specific distributions were strongly correlated with these performance indicators. Species occupy habitats where they can swim faster than prevailing habitat currents year round, and >95% of individuals were observed only in habitats where the gait transition speed can be maintained at or above habitat currents. Thermal fluctuation at higher latitudes appears to reduce performance as well as the possible distribution of species and genera within and among coral reef habitats. Ultimately, thermal variability across latitudes may progressively cause sublethal changes to species performance and lead to a contraction of biogeographical range.

Assessing constraints on the path of regulatory sequence evolution

Structural and functional constraints are known to play a major role in restricting the path of evolution of protein activities. However, constraints acting on evolving transcriptional regulatory sequences, e.g. enhancers, are largely unknown. Recently, we elucidated how a novel expression pattern of the Neprilysin-1 (Nep1) gene in the optic lobe of Drosophila santomea evolved via co-option of existing enhancer activities. Drosophila santomea, which has diverged from Drosophila yakuba by approximately 400 000 years has accumulated four fixed mutations that each contribute to the full activity of this enhancer. Recreating and testing the optic lobe enhancer of the ancestor of D. santomea and D. yakuba revealed that the strong D. santomea enhancer activity evolved from a weak ancestral activity. Because each mutation on the path from the D. yakuba/santomea ancestor to modern-day D. santomea contributes to the newly derived optic lobe enhancer activity, we sought here to use this system to study the path of evolution of enhancer sequences. We inferred likely paths of evolution of this enhancer by observing the transcriptional output of all possible intermediate steps between the ancestral D. yakuba/santomea enhancer and the modern D. santomea enhancer. Many possible paths had epistatic and cooperative effects. Furthermore, we found that several paths significantly increased ectopic transcriptional activity or affected existing enhancer activities from which the novel activity was co-opted. We suggest that these attributes highlight constraints that guide the path of evolution of enhancers.

Gene overexpression: uses, mechanisms, and interpretation

The classical genetic approach for exploring biological pathways typically begins by identifying mutations that cause a phenotype of interest. Overexpression or misexpression of a wild-type gene product, however, can also cause mutant phenotypes, providing geneticists with an alternative yet powerful tool to identify pathway components that might remain undetected using traditional loss-of-function analysis. This review describes the history of overexpression, the mechanisms that are responsible for overexpression phenotypes, tests that begin to distinguish between those mechanisms, the varied ways in which overexpression is used, the methods and reagents available in several organisms, and the relevance of overexpression to human disease.

Key amino acids in the aryl hydrocarbon receptor predict dioxin sensitivity in avian species

Dioxin-like compounds are toxic to most vertebrates, but significant differences in sensitivity exist among species. A recent study suggests that the amino acid residues corresponding to Ile324 and Ser380 in the chicken aryl hydrocarbon receptor 1 (AHR1) are important determinants of differential biochemical responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in chickens and common terns. Here, we investigate whether the identity of these amino acid residues can predict embryonic sensitivity to dioxin-like compounds in a wide range of birds. AHR1 sequences were determined in species for which sensitivity data were available. Of all the species surveyed, chickens were unique in having the Ile/Ser genotype and were also the most sensitive to dioxin-like compounds. Turkeys, ring-necked pheasants, and Eastern bluebirds (intermediate Ile/Ala genotype) were less sensitive than chickens but more sensitive than American kestrels, common terns, double-crested cormorants, Japanese quail, herring gulls, or ducks (Val/ Ala genotype). Our work suggests that key amino acids in the AHR1 ligand binding domain are predictive of broad categories of dioxin sensitivity in avian species. Given the large degree of variation in species sensitivity and the paucity of species-specific toxicity data, a genetic screen based on these findings could substantially improve risk assessment for dioxin-like compounds in wild birds.

Altered DNA methylation: a secondary mechanism involved in carcinogenesis

This review focuses on the role that DNA methylation plays in the regulation of normal and aberrant gene expression and on how, in a hypothesis-driven fashion, altered DNA methylation may be viewed as a secondary mechanism involved in carcinogenesis. Research aimed at discerning the mechanisms by which chemicals can transform normal cells into frank carcinomas has both theoretical and practical implications. Through an increased understanding of the mechanisms by which chemicals affect the carcinogenic process, we learn more about basic biology while, at the same time, providing the type of information required to make more rational safety assessment decisions concerning their actual potential to cause cancer under particular conditions of exposure. One key question is: does the mechanism of action of the chemical in question involve a secondary mechanism and, if so, what dose may be below its threshold?

Molecular genetics of Rett syndrome

Rett syndrome is a neurodevelopmental disorder affecting almost exclusively females. It affects approximately one in 15000 females and is characterized by a loss of purposeful hand use, autism, ataxia and seizure. The disorder is usually sporadic, but rare familial cases have also been reported. Recently it has been shown that familial cases are an X-linked dominant disorder and the disease locus maps to Xq28. A candidate gene called methyl-CpG-binding protein 2 was identified from the Xq28 region and was shown to contain mutations in about 77% of Rett syndrome patients. Since the encoded protein was previously shown to be a global transcriptional repressor, undesired expression of yet unidentified genes that are normally repressed is considered to be pathogenic in Rett syndrome.

Response to "Epigenetic mechanisms of carcinogenesis" by Klaunig JE, Kamendulis LM and Xu Y

It is now quite clear that carcinogenesis involves more than mutagenesis and an increased focus on epigenetic events underlying the transformation of a normal cell into a frank malignancy is appropriate.