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The ability of pulmonary surfactant to reduce alveolar surface tension requires adequate levels of surfactant protein B (SP-B). Dexamethasone (DEX) increases human SP-B expression, in part, through increased SP-B mRNA stability. A 30-nt-long hairpin element (RBE) in the 3′-untranslated region of human SP-B mRNA mediates both DEX-induced and intrinsic mRNA stabilities, but the mechanism is unknown. Proteomic analysis of RBE-interacting proteins identified a primate-specific protein, RNA-binding motif X-linked-like-3 (RBMXL3). siRNA directed against RBMXL3 reduces DEX-induced SP-B mRNA expression in human bronchoalveolar cells. Human SP-B mRNA stability, measured by our dual cistronic plasmid assay, is unaffected by DEX in mouse lung epithelial cells lacking RBMXL3, but DEX increases human SP-B mRNA stability when RBMXL3 is expressed and requires the RBE. In the absence of DEX, RBE interacts with cellular proteins, reducing intrinsic SP-B mRNA stability in human and mouse lung epithelial cells. RBMXL3 specifically binds the RBE in vitro, whereas RNA immunoprecipitation and affinity chromatography analyses indicate that binding is enhanced in the presence of DEX. These results describe a model where intrinsic stability of human SP-B mRNA is reduced through binding of cellular mRNA decay factors to RBE, which is then relieved through DEX-enhanced binding of primate-specific RBMXL3.

The biological functions of primate-specific astroglia, interlaminar astrocytes (IAs), remain enigmatic due to the lack of access to experimental materials, especially in humans. Here, we develop a protocol for the derivation of IAs from healthy normal and schizophrenia patient (SCZ)-specific human pluripotent stem cells. We find that IAs possess a functional profile which is distinct from that of protoplasmic astrocytes, particularly in synapse-associated functions such as neuroactive ligand-receptor interactions, calcium signaling, and long-term potentiation. These synaptic functions are further corroborated by our findings that IAs respond to glutamate, which mediates Ca2+ signaling and in turn leads to the release of gliotransmitters to interact with neurons and astrocytes. We further show that SCZ IAs shift their functional characteristic from synaptic signaling to Matrix-associated functions, with a notable impairment in the levels of gliotransmitters. We anticipate that these findings will prompt more penetrating investigations into the role of IAs in glia biology and brain disorders.

Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics. Here, we have summarized the studies regarding regulatory roles of some key primate-specific lncRNAs and miRNAs.

// Xingrong Qing 1 , Jian Shi 1 , Tingting Dong 1, 2 , Chunlin Wu 1, 3 , Lian Hu 1, 4 and Honggang Li 1, 4 1 Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China 2 Center of Reproductive Medicine, Tengzhou Central People’s Hospital, Tengzhou, China 3 Center of Reproductive Medicine, The No.1 Hospital of Wuhan, Wuhan, China 4 Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China Correspondence to: Honggang Li, email: lhgyx@hotmail.com Keywords: unexplained asthenozoospermia, primate specific, epididymal miRNA, sperm maturation, epigenetic basis Received: March 29, 2017 Accepted: April 25, 2017 Published: May 23, 2017 ABSTRACT Asthenoszoopermia, characterized by reduced sperm motility, is one of the primary forms of male infertility. Whereas most cases were diagnosed into unexplained asthenozoospermia (UA) because the etiology cannot be identified. In animal models, epigenetic dysregulation in epididymis can impair sperm maturation and result in asthenozoospermia. However, researches of epididymal epigenetic regulation on humans are impeded by the difficulty in obtaining epididymal tissues. We previously identified cell-free seminal microRNAs predominately derived from epididymis in human ejaculate. In the present study, these microRNAs were used to screen and validate the microRNA dysregulation in men with UA, which were divided into screening set and validation set. The expression of five miRNAs (miR-891b, miR-892b, miR-892a, miR-888 and miR-890) was found and confirmed to be dysregulated in men with UA. Interestingly, these five miRNAs belong to a primate-specific miRNA cluster located on the X chromosome with epididymis specific expression. Moreover, obvious coherent dysregulation of these miRNAs were observed in 13% men with UA. Regression analysis demonstrated that levels of these miRNAs were significantly correlated with progressive sperm motility. Functions and pathways of predicted target genes of this cluster suggested its role in sperm maturation. Dysregulation of this miRNA cluster might be an epigenetic basis for some patients with UA. We also showed a noninvasive and feasible approach to get epigenetic information of human epididymis.

The largest proportion of microRNAs in humans (ca. 40-50%) originated in the phylogenetic grouping defined as primates. The dynamic evolution of this family of non-coding RNA is further demonstrated by the presence of microRNA unique to the human species. Investigations into the role of microRNA in cancer have until recently mainly focused on the more ancient members of this RNA family that are widely conserved in the animal kingdom. As I describe in this review the evolutionary young lineage and species-specific microRNA could be important contributors to cancers, especially in particular organs in primates compared to more distantly-related research models. Elucidating the biological significance of primate and human-specific microRNA in cancer could have important implications for cancer research and the use of non-primate animal models.

Although the requirement of pituitary-derived LH for ovulation is well documented, the intrafollicular paracrine and autocrine processes elicited by LH necessary for follicle rupture are not fully understood. Evaluating a published rhesus macaque periovulatory transcriptome database revealed that mRNA encoding leukemia inhibitory factor (LIF) and its downstream signaling effectors are up-regulated in the follicle after animals receive an ovulatory stimulus (human chorionic gonadotropin [hCG]). Follicular LIF mRNA and protein levels are below the limit of detection before the administration of hCG but increase significantly 12 hours thereafter. Downstream LIF receptor (LIFR) signaling components including IL-6 signal transducer, the receptor associated Janus kinase 1, and the transcription factor signal transducer and activator of transcription 3 also exhibit increased expression in the rhesus macaque follicle 12 hours after administration of an ovulatory hCG bolus. A laparoscopic ovarian evaluation 72 hours after the injection of a LIF antagonist (soluble LIFR) into the rhesus macaque preovulatory follicle and hCG administration revealed blocking LIF action prevented ovulation (typically occurs 36–44 h after hCG). Moreover, ovaries removed 52 hours after both hCG and intrafollicular soluble LIFR administration confirmed ovulation was blocked as evidenced by the presence of an intact follicle and a trapped cumulus-oocyte complex. These findings give new insight into the role of LIF in the primate ovary and could lead to the development of new approaches for the control of fertility.

Evidence of primate-specific genes and gene regulatory mechanisms linked to bipolar disorder (BD) lend support to evolutionary/adaptive processes in the pathogenesis of this disorder. Following a genome-scale analysis of the entire protein coding genes annotated in the GeneCards database, we have recently reported that cytohesin-4 (CYTH4) contains the longest tetra-nucleotide short tandem repeat (STR) identified in a human protein-coding gene core promoter, which may be of adaptive advantage to this species. In the current study, we analyzed the evolutionary trend of this STR across evolution. We also analyzed the functional implication and distribution of this STR in a group of patients with type 1 BD (n=233) and controls (n=262). We found that this STR is exceptionally expanded in primates (Fisher exact p0.00003). Association was observed between type I BD and the 6-repeat allele of this STR, (GTTT)₆ (Yates corrected Χ(2)=12.68, p0.0001, OR: 1.68). This allele is the shortest length of the GTTT-repeat identified in the human subjects studied. Consistent with that finding, excess homozygosity was observed for the shorter alleles, (GTTT)₆ and (GTTT)₇, vs. the longer alleles, (GTTT)₈ and (GTTT)₉ in the BD group (Yates corrected Χ(2)=5.18, p0.01, 1 df, OR: 1.96). Using Dual Glo luciferase system in HEK-293 cells, a trend for gene expression repression was observed from the 6- to the 9-repeat allele (p0.003), and the GTTT-repeat significantly down-regulated gene expression, per se (p0.0006). This is the first evidence of a link between a primate-specific STR and a major psychiatric disorder in human. It may be speculated that the CYTH4 GTTT-repeat in primates may have conferred selective advantage to this order, reflected in neural function and neurophenotypes. The role of the CYTH4 gene in the pathogenesis of type I BD remains to be clarified in the future studies.

As cancers with a high incidence rate, colorectal cancers are a main cause of cancer-related death. MicroRNAs are often deregulated in cancers. The primate-specific miR-944, located in a p63 intron, is known to be highly expressed in patients exhibiting low colorectal cancer recurrence rates. However, the biological functions of miR-944 in colorectal cancers remain unclear. In this study, we found that miR-944 was downregulated in colorectal cancer tissues, and inhibited cancer cell growth in a xenograft mouse model. The overexpression of miR-944 caused G1 phase arrest and increased p53 expression in cancer cells. p53 stability was enhanced by miR-944s targeting E3 ligases COP1 and MDM2. Overexpression of COP1 and MDM2 restored cell growth inhibition caused by miR-944. Taken together, our results suggest that miR-944 acts as a potential tumor suppressor in colorectal cancers through the ubiquitin-proteasome system.

To understand the relationship between the structure and function of primate neocortical areas at a molecular level, we have been screening for genes differentially expressed across macaque neocortical areas by restriction landmark cDNA scanning (RLCS). Here, we report enriched expression of the paraneoplastic antigen-like 5 gene (PNMA5) in association areas but not in primary sensory areas, with the lowest expression level in primary visual cortex. In situ hybridization in the primary sensory areas revealed PNMA5 mRNA expression restricted to layer II. Along the ventral visual pathway, the expression gradually increased in the excitatory neurons from the primary to higher visual areas. This differential expression pattern was very similar to that of retinol-binding protein (RBP) mRNA, another association-area-enriched gene that we reported previously. Additional expression analysis for comparison of other genes in the PNMA gene family, PNMA1, PNMA2, PNMA3, and MOAP1 (PNMA4), showed that they were widely expressed across areas and layers but without the differentiated pattern of PNMA5. In mouse brains, PNMA1 was only faintly expressed and PNMA5 was not detected. Sequence analysis showed divergence of PNMA5 sequences among mammals. These findings suggest that PNMA5 acquired a certain specialized role in the association areas of the neocortex during primate evolution.

Lineage-specific microRNA (miRNA) families may contribute to developmental novelties during evolution. However, little is known about the origin and evolution of new miRNA families. We report evidence of an Alu-mediated rapid expansion of miRNA genes in a previously identified primate-specific miRNA family, drawn from sequencing and comparative analysis of 9 diverse primate species. Evolutionary analysis reveals similar divergence among miRNA copies whether they are within or between species, lineage-specific gain and loss of miRNAs, and gene pseudolization in multiple species. These observations support a birth-and-death process of miRNA genes in this family, implicating functional diversification during primate evolution. In addition, both secondary structure conservation and reduced single nucleotide polymorphisms density attest to functional constraint of this family in primates. Finally, we observed preferential expression of miRNAs in human placenta and fetal brain, suggesting a functional importance of this family for primate development.

We thank Backes and Keller (1) for their comments on our recent publication (2). With regard to the first example in their cluster analysis point, it is great to see that Backes and Keller (1) uncovered more clusters among our reported data, as this provides further support for the nonaccidental nature of these molecules. With regard to the second example, where they did not find a direct overlap, it is indeed because of variations in individual samples, as Backes and Keller already speculated; there are a handful of … [↵][1]1To whom correspondence should be addressed. Email: Isidore.Rigoutsos{at}jefferson.edu. [1]: #xref-corresp-1-1

Evolutionary expansion and complexification of the primate cerebral cortex are largely linked to the emergence of the outer subventricular zone (OSVZ), a uniquely structured germinal zone that generates the expanded primate supragranular layers. The primate OSVZ departs from rodent germinal zones in that it includes a higher diversity of precursor types, inter-related in bidirectional non-hierarchical lineages. In addition, primate-specific regulatory mechanisms are operating in primate cortical precursors via the occurrence of novel miRNAs. Here, we propose that the origin and evolutionary importance of the OSVZ is related to genetic changes in multiple regulatory loops and that cell-cycle regulation is a favored target for evolutionary adaptation of the cortex.

Recently, pathophysiology of human psychiatry originates from abnormal numbers of synapses/spines. There are generally two-types of development of spines from birth depending on species. One is, after birth, synaptogenesis occurs, and there is a clear peak of spines, and then rapidly pruning occurring, which are called “overshoot-type” of development of synapses/spines. Primates including human belong to this type. In other type including rodents, even after a peak, general number of spines does not decrease so much. Although these differences, most of human psychiatric models have been genetic modified rodents. Now, transgenic primate (the common marmoset) became available. In near future, we can, examine pathophysiology of psychiatric disorders using this animal model, which is closer to human being. To begin with this endeavor, we should know how synapses/spines of normal marmosets developed, and molecular mechanisms of “overshoot-type” of spine development, which human being also shows. Here, we will present our recent effort to explore these questions, and future experiments will be discussed.

Accurate human-specific DNA quantification is essential for forensic casework analysis. In this work, we describe a microplate-based quantification assay that utilizes the PCR amplification of human-specific TH01 primers. This method enables the reliable quantification of human DNA samples from 0.2 to 40 ng, even in mixtures with nonhuman DNA. Analysis of samples can be semi-automated using 96-well microplates and a spreadsheet-based concentration calculator for high-throughput demands. We have used this quantification method with more than 15 000 forensic samples.

Purpose: Estrogen is a proliferative hormone that regulates the growth of estrogen receptor positive cells, including breast cancer cells. Although estrogen is a global regulator of protein-coding genes as well as non-coding RNA (ncRNA) genes, its effects on long ncRNA (lncRNA) genes, the most abundant class of human ncRNAs, remain poorly understood. We previously used custom microarrays and Taqman qRTPCR to identify 127 estrogen-responsive lncRNAs, and demonstrated a direct role for 25 of these in breast cancer cell viability and proliferation: estrogen-induced lncRNAs cause cell proliferation (reversed upon siRNA knockdown of these lncRNAs) and estrogen-repressed lncRNAs cause cell death (induced upon overexpression of those lncRNAs). Furthermore, since over 60% of human lncRNAs, including CR593775, are primate-specific, eight additional primate-specific lncRNAs were used in functional assays to determine whether primate-specific lncRNAs are functional in breast cancer. Methods/Results: We ablated two new estrogen-induced primate-specific lncRNAs with two independent siRNAs each and validated the knockdowns by qRTPCR. Post-transfection MTT and crystal violet cell proliferation assays revealed that for one lncRNA, both knockdowns reduced cell viability and proliferation. We also used Stellaris RNA fluorescent in situ hybridization (FISH) to determine that the primate-specific estrogen-repressed cell death inducer lncRNA BC041455 is cytoplasmic in MCF7 cells. In addition, CR593775, our top estrogen-induced lncRNA, does not regulate the viability and proliferation of nonmalignant MCF10A breast cells as compared to breast cancer cells that are estrogen receptor positive (T47D, MCF7) and negative (MDA-MB-231). Conclusion: The primate-specific estrogen-induced lncRNAs are cytoplasmic targets for breast cancer treatment that leads to reduced proliferation and cell viability. Citation Format: Donghong Ju, Daniel Xie, Juan Cai, Anton Scott Goustin, Mary A. Kosir, Leonard Lipovich. Primate-specific estrogen-induced long noncoding RNAs as targets for breast cancer treatment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1262.

Schizophrenia is a human mental disorder that affects an individual's thoughts, perception, affect and behavior, which is caused by a complex interaction of genetic and environmental factors. Genetic studies have implicated the evolutionary novel, anthropoid primate-specific gene locus G72/G30 in the etiology of schizophrenia and other psychiatric disorders. This gene encodes the protein LG72, which has been discussed as a modulator of the peroxisomal enzyme d-amino-acid-oxidase (DAO), or, alternatively as a mitochondrial protein. Recently, G72 transgenic (G72Tg) mice were generated that express the protein throughout the brain. These mice show several behavioral deficits that are related to schizophrenia. Further, G72Tg mice have a reduced activity of mitochondrial complex I, with a concomitantly increased production of reactive oxygen species, as well as deficits in short-term plasticity. Results from these studies demonstrate that expression of the human G72/G30 gene locus in mice produces behavioral phenotypes that are relevant to schizophrenia. They implicate LG72-induced mitochondrial and synaptic defects as a possible pathomechanism of this disease.

Computer analyses of the 3′-flanking DNA sequence of the human elastase I gene revealed a significant degree of similarity with seven human gene sequences in the CenBank and EMBL databases. Cenomic Southern analysis indicates that the shared nucleotide sequences are a primate-specific family of short interspersed elements. These elements are members of MERI sequences (medium reiteration frequency sequences). The consensus sequence of MERI repeats spans 543 nucleot-ides and contains several inverted repeats. Since the copy number of MERI elements seems to be much smaller than that of Alu and L1 repeats, MERI elements may provide useful landmarks for human genome mapping.

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link. Four presumptive blood tests, Hexagon OBTI, Hemastix , Leucomalachite green (LMG), and Kastle-Meyer (KM) were compared for their sensitivity in the identification of dried bloodstains. Stains of varying blood dilutions were subjected to each presumptive test and the results compared. The Hexagon OBTI buffer volume was also reduced to ascertain whether this increased the sensitivity of the kit. The study found that Hemastix was the most sensitive test for trace blood detection. Only with the reduced buffer volume was the Hexagon OBTI kit as sensitive as the LMG and KM tests. However, the Hexagon OBTI kit has the advantage of being a primate specific blood detection kit. This study also investigated whether the OBTI buffer within the kit could be utilized for DNA profiling after presumptive testing. The results show that DNA profiles can be obtained from the Hexagon OBTI kit buffer directly.

Purpose: miRNAs (microRNAs) have recently been recognized as important regulators of cancer biological behavior. However, the expression patterns and prognostic significance of miRNAs in GBM remain elusive due to the lack of large pools of clinical specimens for screening. This study was performed to identify miR-663 as a potential regulator of glioblastoma (GBM) malignant behaviors from miRNA profiles. The prognostic significance of miR-663 in GBM, its effect in tumor progression and the underlying mechanism were determined. Methods: Specimens from 256 cases of glioma patients, including 239 patients with follow-up information, were used to analyze the association between miR-663 and patients’ prognosis by Kaplan-Meier and multivariate Cox regression analyses. The effects of miR-663 on GBM cell proliferation and invasion were examined both in vitro and in vivo. Bioinformatics prediction and signal network analysis were applied to identify the putative targets of miR-663, which were further verified by luciferase reporter assay, rescue experiments as well as the immunohistochemistry (IHC) and Western blotting examination of downstream effectors. Quantitative reverse transcriptase-PCR (qRT-PCR) and IHC were applied to investigate the clinical association between miR-663 and its target in human GBM specimens. Results: miR-663 was identified from miRNA profiles and inversely correlated with glioma grades but positively correlated with patients’ survival. Furthermore, two distinct subgroups of GBM patients with different prognoses were identified based on miR-663 expression in our specimens and that from TCGA database. Overexpression of miR-663 significantly suppressed the proliferation and invasion of GBM cells in vitro and in vivo. Mechanistically, we discovered PIK3CD as a direct target of miR-663 and found that phosphorylated AKT and three key downstream effectors of PIK3CD, were down-regulated by miR-663 overexpression. Moreover, PIK3CD was inversely correlated with miR-663 in GBM specimens and predicted poor prognosis of GBM patients. Conclusion: miR-663 is a novel prognostic biomarker and a potential therapeutic candidate for GBM. Citation Format: Yu Shi, Yi-fang Ping, Xiu-wu Bian. Primate-specific miR-663 suppresses glioblastoma progression and predicts patient prognosis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3113. doi:10.1158/1538-7445.AM2015-3113

The biased distribution of dispersed repeat insertions in various types of primate specific alpha satellites (AS) is being discussed in the literature in relation to the modes of AS evolution and their possible roles in maintenance and disruption of functional centromeres. However, such a bias has not been properly documented on a genome-wide scale so far. In this work, using a representative sample of about 100 insertions we show that the "old" AS contains at least 10 times more dispersed repeats than the "new" one. In the new arrays insertions accumulate mostly in poorly homogenized areas, presumably in the edges, and in the old AS, throughout the whole array length. Dating of L1 insertions in the old AS revealed that their massive accumulation started at or after the time when the new AS emerged and expanded in the genome and the centromere function had shifted to the new AS arrays.

Current procedures for human DNA quantitation reach their limit at 150 pg DNA, which is above the limit of the PCR profiling range using Profiler-Plus (Applied Biosystems, CA). This study tested the potential for the use of primate specific Alu sequences in forensic science for the sensitive detection and quantitaion of DNA. A fluorescently labelled primer pair was designed enabling high efficiency amplification of the core Alu sequence within primate DNA. Quantitation was performed by measurement of fluorescence intensity and comparison to a series of standard template DNA amounts via the construction of a standard curve. The new Alu-based quantitation protocol developed has shown its feasibility in more sensitively quantitating (100-2.5 pg) unknown amounts of human DNA for forensic use. The method is compatible with the use and throughput of current forensic procedures.

Constituting one of the three subfamilies of the retroviruses the lentivirinae comprise genetically and structurally highly related agents (Frank, 1987; Gelderblom et al., 1985a; Gonda et al., 1985; Levy, 1988; Matthews, 1982; Weiss et. al., 1984). Lentiviruses are transmitted as exogenous agents, show a strong leucotropism and induce persistent, progressive infections in vivo (for review see Georgsson et al., 1989; Haase, 1989; Levy, 1989; Narayan and Clements, 1989). Lentiviruses are cytopathogenic in vitro and partially serologically related. Primate specific lentiviruses share approximately 60% of homology in conserved proteins (Desrosiers et al., 1989). Serological cross-reactivities localized mainly to the viral core, but also to the envelope, have been described for HIV and EIAV (Montagnier et al., 1984; Montelaro et al., 1988; Schneider et al., 1986, 1987).

Our laboratory has developed an automated real-time quantitative PCR assay for detecting human DNA. The assay utilizes an in-house, custom-designed TaqMan-MGB sequence-specific probe (CFS-HumRT) and the ABD 7900HT SDS platform. Developmental validation has followed TWGDAM (1) guidelines and demonstrates that the assay is primate specific, is highly sensitive, yields consistent results, and works with human DNA extracted from a variety of body fluid stains. When operating within the dynamic range of the system using high-quality DNA samples. the technique yields similar quantification results to our current QuantiBlot assay with the added benefit of time saving through automation. Furthermore, the QPCR assay identifies how much amplifiable DNA is in a sample and thus has the potential to predict PCR success in downstream applications such as STR analysis.

In the last few years with the recent emergence of high-throughput technologies, thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome. However, assigning functional annotation and determining cellular contexts for these RNAs are still in its infancy. As information gained about lncRNA structure, interacting partners, and roles in human diseases may be helpful in the characterization of novel lncRNAs, we review our knowledge on a selected group of lncRNAs that were identified serendipitously years ago by large-scale gene expression methods used to study human diseases. In particular, we focus on the Psoriasis-susceptibility-Related RNA Gene Induced by Stress (PRINS) lncRNA, first identified by our research group as a transcript highest expressed in psoriatic non-lesional epidermis. Results gathered for PRINS in the last 10 years indicate that it is conserved in primates and plays a role in keratinocyte stress response. Elevated levels of PRINS expression in psoriatic non-lesional keratinocytes alter the stress response of non-lesional epidermis and contribute to disease pathogenesis. Finally, we propose a categorization for the PRINS lncRNA based on a recently elaborated system for lncRNA classification.

SummaryA relative quantitative estimation of cathodal esterase in normal and malignant tissues has been performed. The highest concentration of esterase was found in the kidney. A comparison shows that human hepatomas have a distinctly increased level of the esterase over normal liver.