Breast Cancer Outcomes of Neoadjuvant Versus Adjuvant Chemotherapy by Receptor Subtype: A Scoping Review.

BACKGROUND: Trials demonstrate equivalent survival for breast cancers treated with neoadjuvant chemotherapy (NAC) or adjuvant chemotherapy (AC). However, these were conducted before the recognition of the importance of receptor subtype for survival and chemotherapy response. Therefore, chemotherapy timing may impact survival for certain receptor subtypes. A scoping review of studies assessing outcomes by chemotherapy timing based on receptor subtype was conducted to evaluate gaps in the existing literature. METHODS: Three databases were searched in February 2019 with terms related to breast cancer, NAC/AC, and survival. Inclusion criteria were original peer-reviewed studies published in English after 1989 comparing breast cancer outcomes for females based on chemotherapy timing. Studies/sections of studies lacking outcomes by receptor subtype or including patients missing appropriate targeted therapy were excluded. RESULTS: Of 7354 articles, 262 abstracts and 60 full texts were reviewed. Three studies met criteria. All were single-institution retrospective studies analyzing outcomes for triple negative (TN) patients with one study also examining luminal A patients. Significant differences in clinical characteristics existed between patients selected for NAC versus AC. Two studies demonstrated no survival difference by chemotherapy timing for TN patients, with the third showing improved likelihood of survival after AC for TN patients. No difference was seen for patients with luminal A cancer. CONCLUSIONS: Our scoping review reveals a significant gap in the existing literature regarding optimal timing of chemotherapy for modern-era patients receiving targeted therapy based on receptor subtype. Review of the identified studies identified methodological challenges to answering this question through observational study designs.

iNR-2L: A two-level sequence-based predictor developed via Chou's 5-steps rule and general PseAAC for identifying nuclear receptors and their families.

Nuclear receptor proteins (NRPs) perform a vital role in regulating gene expression. With the rapidity growth of NRPs in post-genomic era, it is highly recommendable to identify NRPs and their sub-families accurately from their primary sequences. Several conventional methods have been used for discrimination of NRPs and their sub-families, but did not achieve considerable results. In a sequel, a two-level new computational model "iNR-2 L" is developed. Two discrete methods namely: Dipeptide Composition and Tripeptide Composition were used to formulate NRPs sequences. Further, both the descriptor spaces were merged to construct hybrid space. Furthermore, feature selection technique minimum redundancy and maximum relevance was employed in order to select salient features as well as reduce the noise and redundancy. The experiential outcomes exhibited that the proposed model iNR-2 L achieved outstanding results. It is anticipated that the proposed computational model might be a practical and effective tool for academia and research community.

RF-NR: Random Forest Based Approach for Improved Classification of Nuclear Receptors.

The Nuclear Receptor (NR) superfamily plays an important role in key biological, developmental, and physiological processes. Developing a method for the classification of NR proteins is an important step towards understanding the structure and functions of the newly discovered NR protein. The recent studies on NR classification are either unable to achieve optimum accuracy or are not designed for all the known NR subfamilies. In this study, we developed RF-NR, which is a Random Forest based approach for improved classification of nuclear receptors. The RF-NR can predict whether a query protein sequence belongs to one of the eight NR subfamilies or it is a non-NR sequence. The RF-NR uses spectrum-like features namely: Amino Acid Composition, Di-peptide Composition, and Tripeptide Composition. Benchmarking on two independent datasets with varying sequence redundancy reduction criteria, the RF-NR achieves better (or comparable) accuracy than other existing methods. The added advantage of our approach is that we can also obtain biological insights about the important features that are required to classify NR subfamilies. RF-NR is freely available at http://bcb.ncat.edu/RF_NR.

An emerging link between LIM domain proteins and nuclear receptors.

Nuclear receptors are ligand-activated transcription factors that partake in several biological processes including development, reproduction and metabolism. Over the last decade, evidence has accumulated that group 2, 3 and 4 LIM domain proteins, primarily known for their roles in actin cytoskeleton organization, also partake in gene transcription regulation. They shuttle between the cytoplasm and the nucleus, amongst other as a consequence of triggering cells with ligands of nuclear receptors. LIM domain proteins act as important coregulators of nuclear receptor-mediated gene transcription, in which they can either function as coactivators or corepressors. In establishing interactions with nuclear receptors, the LIM domains are important, yet pleiotropy of LIM domain proteins and nuclear receptors frequently occurs. LIM domain protein-nuclear receptor complexes function in diverse physiological processes. Their association is, however, often linked to diseases including cancer.

Phospholipid regulation of the nuclear receptor superfamily.

Nuclear receptors are ligand-activated transcription factors whose diverse biological functions are classically regulated by cholesterol-based small molecules. Over the past few decades, a growing body of evidence has demonstrated that phospholipids and other similar amphipathic molecules can also specifically bind and functionally regulate the activity of certain nuclear receptors, suggesting a critical role for these non-cholesterol-based molecules in transcriptional regulation. Phosphatidylcholines, phosphoinositides and sphingolipids are a few of the many phospholipid like molecules shown to quite specifically regulate nuclear receptors in mouse models, cell lines and in vitro. More recent evidence has also shown that certain nuclear receptors can "present" a bound phospholipid headgroup to key lipid signaling enzymes, which can then modify the phospholipid headgroup with very unique kinetic properties. Here, we review the broad array of phospholipid/nuclear receptor interactions, from the perspective of the chemical nature of the phospholipid, and the cellular abundance of the phospholipid. We also view the data in the light of well established paradigms for phospholipid mediated transcriptional regulation, as well as newer models of how phospholipids might effect transcription in the acute regulation of complex nuclear signaling pathways. Thus, this review provides novel insight into the new, non-membrane associated roles nuclear phospholipids play in regulating complex nuclear events, centered on the nuclear receptor superfamily of transcription factors.

Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome.

BACKGROUND: Anguilla japonica (Japanese eel) is currently one of the most important research subjects in eastern Asia aquaculture. Enigmatic life cycle of the organism makes study of artificial reproduction extremely limited. Henceforth genomic and transcriptomic resources of eels are urgently needed to help solving the problems surrounding this organism across multiple fields. We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided expressed sequence tags were used to annotate the currently available draft genome sequence. Homologous information derived from the annotation result was applied to improve the group of scaffolds into available linkage groups. RESULTS: With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were structurally and functionally annotated on the draft genome. Among them, 3,921 genes were located in the 19 linkage groups. 137 scaffolds covering 13 million bases were grouped into the linkage groups in additional to the original partial linkage groups, increasing the linkage group coverage from 13 to 14%. CONCLUSIONS: This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived homologous evidences pave the way for phylogenetic analysis of important genetic traits and the improvement of the genome assembly.

Accurate prediction of nuclear receptors with conjoint triad feature.

BACKGROUND: Nuclear receptors (NRs) form a large family of ligand-inducible transcription factors that regulate gene expressions involved in numerous physiological phenomena, such as embryogenesis, homeostasis, cell growth and death. These nuclear receptors-related pathways are important targets of marketed drugs. Therefore, the design of a reliable computational model for predicting NRs from amino acid sequence has now been a significant biomedical problem. RESULTS: Conjoint triad feature (CTF) mainly considers neighbor relationships in protein sequences by encoding each protein sequence using the triad (continuous three amino acids) frequency distribution extracted from a 7-letter reduced alphabet. In addition, chaos game representation (CGR) can investigate the patterns hidden in protein sequences and visually reveal previously unknown structure. In this paper, three methods, CTF, CGR, amino acid composition (AAC), are applied to formulate the protein samples. By considering different combinations of three methods, we study seven groups of features, and each group is evaluated by the 10-fold cross-validation test. Meanwhile, a new non-redundant dataset containing 474 NR sequences and 500 non-NR sequences is built based on the latest NucleaRDB database. Comparing the results of numerical experiments, the group of combined features with CTF and AAC gets the best result with the accuracy of 96.30% for identifying NRs from non-NRs. Moreover, if it is classified as a NR, it will be further put into the second level, which will classify a NR into one of the eight main subfamilies. At the second level, the group of combined features with CTF and AAC also gets the best accuracy of 94.73%. Subsequently, the proposed predictor is compared with two existing methods, and the comparisons show that the accuracies of two levels significantly increase to 98.79% (NR-2L: 92.56 %; iNR-PhysChem: 98.18%; the first level) and 93.71% (NR-2L: 88.68%; iNR-PhysChem: 92.45%; the second level) with the introduction of our CTF-based method. Finally, each component of CTF features is analyzed via the statistical significant test, and a simplified model only with the resulting top-50 significant features achieves accuracy of 95.28%. CONCLUSIONS: The experimental results demonstrate that our CTF-based method is an effective way for predicting nuclear receptor proteins. Furthermore, the top-50 significant features obtained from the statistical significant test are considered as the "intrinsic features" in predicting NRs based on the analysis of relative importance.

Families of nuclear receptors in vertebrate models: characteristic and comparative toxicological perspective.

Various synthetic chemicals are ligands for nuclear receptors (NRs) and can cause adverse effects in vertebrates mediated by NRs. While several model vertebrates, such as mouse, chicken, western clawed frog and zebrafish, are widely used in toxicity testing, few NRs have been well described for most of these classes. In this report, NRs in genomes of 12 vertebrates are characterized via bioinformatics approaches. Although numbers of NRs varied among species, with 40-42 genes in birds to 66-74 genes in teleost fishes, all NRs had clear homologs in human and could be categorized into seven subfamilies defined as NR0B-NR6A. Phylogenetic analysis revealed conservative evolutionary relationships for most NRs, which were consistent with traditional morphology-based systematics, except for some exceptions in Dolphin (Tursiops truncatus). Evolution of PXR and CAR exhibited unexpected multiple patterns and the existence of CAR possibly being traced back to ancient lobe-finned fishes and tetrapods (Sarcopterygii). Compared to the more conservative DBD of NRs, sequences of LBD were less conserved: Sequences of THRs, RARs and RXRs were ≥90% similar to those of the human, ERs, AR, GR, ERRs and PPARs were more variable with similarities of 60%-100% and PXR, CAR, DAX1 and SHP were least conserved among species.

Nuclear receptors in nematode development: Natural experiments made by a phylum.

The development of complex multicellular organisms is dependent on regulatory decisions that are necessary for the establishment of specific differentiation and metabolic cellular states. Nuclear receptors (NRs) form a large family of transcription factors that play critical roles in the regulation of development and metabolism of Metazoa. Based on their DNA binding and ligand binding domains, NRs are divided into eight NR subfamilies from which representatives of six subfamilies are present in both deuterostomes and protostomes indicating their early evolutionary origin. In some nematode species, especially in Caenorhabditis, the family of NRs expanded to a large number of genes strikingly exceeding the number of NR genes in vertebrates or insects. Nematode NRs, including the multiplied Caenorhabditis genes, show clear relation to vertebrate and insect homologues belonging to six of the eight main NR subfamilies. This review summarizes advances in research of nematode NRs and their developmental functions. Nematode NRs can reveal evolutionarily conserved mechanisms that regulate specific developmental and metabolic processes as well as new regulatory adaptations. They represent the results of a large number of natural experiments with structural and functional potential of NRs for the evolution of the phylum. The conserved and divergent character of nematode NRs adds a new dimension to our understanding of the general biology of regulation by NRs. This article is part of a Special Issue entitled: Nuclear receptors in animal development.

Computational characterization of modes of transcriptional regulation of nuclear receptor genes.

BACKGROUND: Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, development and reproduction. They are activated through the binding of small ligands, which can be replaced by drug molecules, making nuclear receptors promising drug targets. Transcriptional regulation of the genes that encode them is central to gaining a deeper understanding of the diversity of their biochemical and biophysical roles and their role in disease and therapy. Even though they share evolutionary history, nuclear receptor genes have fundamentally different expression patterns, ranging from ubiquitously expressed to tissue-specific and spatiotemporally complex. However, current understanding of regulation in nuclear receptor gene family is still nascent. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we investigate the relationship between long-range regulation of nuclear receptor family and their known functionality. Towards this goal, we identify the nuclear receptor genes that are potential targets based on counts of highly conserved non-coding elements. We validate our results using publicly available expression (RNA-seq) and histone modification (ChIP-seq) data from the ENCODE project. We find that nuclear receptor genes involved in developmental roles show strong evidence of long-range mechanism of transcription regulation with distinct cis-regulatory content they feature clusters of highly conserved non-coding elements distributed in regions spanning several Megabases, long and multiple CpG islands, bivalent promoter marks and statistically significant higher enrichment of enhancer mark around their gene loci. On the other hand nuclear receptor genes that are involved in tissue-specific roles lack these features, having simple transcriptional controls and a greater variety of mechanisms for producing paralogs. We further examine the combinatorial patterns of histone maps associated with dynamic functional elements in order to explore the regulatory landscape of the gene family. The results show that our proposed classification capturing long-range regulation is strongly indicative of the functional roles of the nuclear receptors compared to existing classifications. CONCLUSIONS/SIGNIFICANCE: We present a new classification for nuclear receptor gene family capturing whether a nuclear receptor is a possible target of long-range regulation or not. We compare our classification to existing structural (mechanism of action) and homology-based classifications. Our results show that understanding long-range regulation of nuclear receptors can provide key insight into their functional roles as well as evolutionary history; and this strongly merits further study.

Nuclear hormone receptor expression in mouse kidney and renal cell lines.

Nuclear hormone receptors (NHRs) are transcription factors that regulate carbohydrate and lipid metabolism, immune responses, and inflammation. Although several NHRs, including peroxisome proliferator-activated receptor-γ (PPARγ) and PPARα, demonstrate a renoprotective effect in the context of diabetic nephropathy (DN), the expression and role of other NHRs in the kidney are still unrecognized. To investigate potential roles of NHRs in the biology of the kidney, we used quantitative real-time polymerase chain reaction to profile the expression of all 49 members of the mouse NHR superfamily in mouse kidney tissue (C57BL/6 and db/m), and cell lines of mesangial (MES13), podocyte (MPC), proximal tubular epithelial (mProx24) and collecting duct (mIMCD3) origins in both normal and high-glucose conditions. In C57BL/6 mouse kidney cells, hepatocyte nuclear factor 4α, chicken ovalbumin upstream promoter transcription factor II (COUP-TFII) and COUP-TFIII were highly expressed. During hyperglycemia, the expression of the NHR 4A subgroup including neuron-derived clone 77 (Nur77), nuclear receptor-related factor 1, and neuron-derived orphan receptor 1 significantly increased in diabetic C57BL/6 and db/db mice. In renal cell lines, PPARδ was highly expressed in mesangial and proximal tubular epithelial cells, while COUP-TFs were highly expressed in podocytes, proximal tubular epithelial cells, and collecting duct cells. High-glucose conditions increased the expression of Nur77 in mesangial and collecting duct cells, and liver x receptor α in podocytes. These data demonstrate NHR expression in mouse kidney cells and cultured renal cell lines and suggest potential therapeutic targets in the kidney for the treatment of DN.

Recent progresses in identifying nuclear receptors and their families.

Nuclear receptors (NRs) are members of a large superfamily of evolutionarily related DNA-binding transcription factors. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. As nuclear receptors bind small molecules that can easily be modified by drug design, and control functions associated with major diseases (e.g. cancer, osteoporosis and diabetes), they are promising pharmacological targets. According to their different action mechanisms or functions, NR superfamily has been classified into seven families: NR1 (thyroid hormone like), NR2 (HNF4-like), NR3 (estrogen like), NR4 (nerve growth factor IB-like), NR5 (fushi tarazu-F1 like), NR6 (germ cell nuclear factor like), and NR0 (knirps or DAX like). With the avalanche of protein sequences generated in the postgenomic age, Scientists are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what family even subfamily it belongs to? To address these problems, many cheminformatics tools have been developed for nuclear receptor prediction. The current review is mainly focused on this field, including the functions, computational methods and limitations of these tools.

The role of nuclear receptors in embryonic stem cells.

Embryonic stem (ES) cells, isolated from pre-implantation embryos, can grow indefinitely invitro (self-renewal) and have potential to differentiate into all cell types in the body (pluripotency). The nuclear receptor gene family is very important for controlling development, differentiation and homeostasis. Here, we review the new progress in understanding the role of nuclear receptors in ES cells focusing on the structure, expression and function of several nuclear receptors. LRH1, DAX1, Esrrß and TR2 play critical roles in maintaining pluripotency, while, GCNF, COUP-TFs and sumoylated TR2 are critical in regulating the exit from pluripotency. Nuclear receptors hold great potential as targets of manipulation of ES and iPS cells for applications in regenerative medicine, because they are ligand-activated transcription factors that can be regulated by small molecule agonists and antagonists.

Retinoid X receptor (RXR), estrogen receptor (ER) and other nuclear receptors in tissues of the mussel Mytilus galloprovincialis: cloning and transcription pattern.

Bivalve molluscs accumulate chemical compounds from the environment that could cause alterations in lipid homeostasis and endocrine system. In vertebrates such cell processes are modulated by transcription factors belonging to the superfamily of nuclear receptors (NRs). The goal of this study was to clone fragments of mussel Mytilus galloprovincialis NR genes that could mediate cell responses such as peroxisome proliferation and endocrine disruption. PCR-based screening of mussel digestive gland cDNA using degenerate primers provided cDNA fragments or whole ORFs of retinoid X receptor (RXR), estrogen receptor (ER) and 5 proteins belonging to the NR1 subfamily highly similar to the arthropod ecdysone inducible protein E75. NR1G, whose whole ORF was cloned, is related to the nematode and trematode G group of NR1 receptors; NR1DEF is related to the D, E and F groups, and NR1Dv1, NR1Dv2 and NR1DΔ belong to the D group. mRNA transcripts for all these receptors were detected in gill, mantle and digestive gland. In all cases, except ER, transcript levels were lower in June than in January. NR1Dv1 and NR1DΔ did not show identical transcription levels, although both were at their lowest in digestive gland in June. On the contrary, NR1Dv2 and NR1DΔ transcription profiles were similar. Further studies are needed to determine the function(s) of mussel RXR, ER and novel NR1 subfamily receptors and their possible role in the regulation of physiological cell responses and/or adaptive response to xenobiotic exposures.

RACK1 regulates mesenchymal cell recruitment during sexual and asexual reproduction of budding tunicates.

A homolog of receptor for activated protein kinase C1 (RACK1) was cloned from the budding tunicate Polyandrocarpa misakiensis. By RT-PCR and in situ hybridization analyses, PmRACK1 showed biphasic gene expression during asexual and sexual reproduction. In developing buds, the signal was exclusively observed in the multipotent atrial epithelium and undifferentiated mesenchymal cells that contributed to morphogenesis by the mesenchymal-epithelial transition (MET). In juvenile zooids, the signal was first observable in germline precursor cells that arose as mesenchymal cell aggregated in the ventral hemocoel. In mature zooids, the germinal epithelium in the ovary and the pharynx were the most heavily stained parts. GFP reporter assay indicated that the ovarian expression of PmRACK1 was constitutive from germline precursor cells to oocytes. To elucidate the in vivo function of PmRACK1, RNA interference was challenged. When growing buds were incubated with 5 nmol/mL siRNA, most mesenchymal cells remained round and appeared to have no interactions with the extracellular matrix (ECM), causing lower activity of MET without any apparent effects on cell proliferation. The resultant zooids became growth-deficient. The dwarf zooids did not form buds or mature gonads. Prior to RNAi, buds were treated with human BMP4 that could induce PmRACK1 expression, which resulted in MET activity. We conclude that in P. misakiensis, PmRACK1 plays roles in mesenchymal cell recruitment during formation of somatic and gonad tissues, which contributes to zooidal growth and sexual and asexual reproduction.

Evolution of JAK-STAT pathway components: mechanisms and role in immune system development.

BACKGROUND: Lying downstream of a myriad of cytokine receptors, the Janus kinase (JAK)-Signal transducer and activator of transcription (STAT) pathway is pivotal for the development and function of the immune system, with additional important roles in other biological systems. To gain further insight into immune system evolution, we have performed a comprehensive bioinformatic analysis of the JAK-STAT pathway components, including the key negative regulators of this pathway, the SH2-domain containing tyrosine phosphatase (SHP), Protein inhibitors against Stats (PIAS), and Suppressor of cytokine signaling (SOCS) proteins across a diverse range of organisms. RESULTS: Our analysis has demonstrated significant expansion of JAK-STAT pathway components co-incident with the emergence of adaptive immunity, with whole genome duplication being the principal mechanism for generating this additional diversity. In contrast, expansion of upstream cytokine receptors appears to be a pivotal driver for the differential diversification of specific pathway components. CONCLUSION: Diversification of JAK-STAT pathway components during early vertebrate development occurred concurrently with a major expansion of upstream cytokine receptors and two rounds of whole genome duplications. This produced an intricate cell-cell communication system that has made a significant contribution to the evolution of the immune system, particularly the emergence of adaptive immunity.

NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.

Nuclear receptors (NRs) are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1) thyroid hormone like (NR1), (2) HNF4-like (NR2), (3) estrogen like, (4) nerve growth factor IB-like (NR4), (5) fushi tarazu-F1 like (NR5), (6) germ cell nuclear factor like (NR6), and (7) knirps like (NR0). The identification was made by the Fuzzy K nearest neighbor (FK-NN) classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will usually be. All the program codes for NR-2L are available for non-commercial purpose upon request.

Analysis of nuclear receptor acetylation.

Acetylation is an essential post-translational modification in which an acetyl group is covalently conjugated to a protein substrate. Histone acetylation was first proposed nearly half a century ago by Dr. Vincent Allfrey. Subsequent studies have shown that acetylated core histones are often associated with transcriptionally active chromatin. Acetylation at lysine residues of histone tails neutralizes the positive charge, which decreases the binding ability to DNA and increases the accessibility of transcription factors and co-activators to the chromatin template. In addition to histones, a number of non-histone substrates are acetylated. Acetylation of non-histone proteins governs biological processes, including cellular proliferation and survival, transcriptional activity, and intracellular trafficking. We demonstrated that acetylation of transcription factors can regulate cellular growth. Further, we have shown that nuclear receptors are acetylated at a phylogenetically conserved motif. Since our initial observations with the estrogen and androgen receptors, more than a dozen nuclear receptors have been shown to function as substrates for acetyltransferases with a variety of new methods (Fig. 11.1). This chapter focuses on the protocol used in the studies of NR acetylation and de-acetylation. We will discuss the potential pitfalls of each method.