Identifying novel genes involved in both deer physiological and human pathological osteoporosis

Use of the Phylobone database for the annotation of bone extracellular matrix proteins in reindeer (Rangifer tarandus)

Bone extracellular matrix (ECM) proteins play a key role in bone formation and regeneration, including structural and regulatory functions. The Phylobone database consists of 255 ECM protein groups from 39 species and can be used to support bone research. Here, we gathered bone ECM proteins from reindeer (Rangifer tarandus), a member of the Cervidae family. The importance of reindeer lies in their ability to regenerate their antlers, in both male and female individuals. Protein sequences were extracted from the National Center for Biotechnology Information's repository and selected by homology searches. We identified 215 proteins and their corresponding functional domains, which are putatively present in the bone ECM of reindeer. Protein sequence alignments have shown a high degree of conservation between R. tarandus and other members of the Cervidae family. This update expands the Phylobone database and shows that it is a useful resource for the preliminary annotation of bone ECM proteins in novel proteomes.

Phylobone: a comprehensive database of bone extracellular matrix proteins in human and model organisms

The bone extracellular matrix (ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of non-collagenous proteins. Some of these proteins are key to the regulation of bone formation and regeneration via signaling pathways, and play important regulatory and structural roles. However, the complete list of bone extracellular matrix proteins, their roles, and the extent of individual and cross-species variations have not been fully captured in both humans and model organisms. Here, we introduce the most comprehensive resource of bone extracellular matrix (ECM) proteins that can be used in research fields such as bone regeneration, osteoporosis, and mechanobiology. The Phylobone database (available at https://phylobone.com ) includes 255 proteins potentially expressed in the bone extracellular matrix (ECM) of humans and 30 species of vertebrates. A bioinformatics pipeline was used to identify the evolutionary relationships of bone ECM proteins. The analysis facilitated the identification of potential model organisms to study the molecular mechanisms of bone regeneration. A network analysis showed high connectivity of bone ECM proteins. A total of 214 functional protein domains were identified, including collagen and the domains involved in bone formation and resorption. Information from public drug repositories was used to identify potential repurposing of existing drugs. The Phylobone database provides a platform to study bone regeneration and osteoporosis in light of (biological) evolution, and will substantially contribute to the identification of molecular mechanisms and drug targets.

Concentration of Macroelements and Trace Elements in Farmed Fallow Deer Antlers Depending on Age

The mineral content of the antlers reflects the nutritional status and specific stage of bone growth in cervid males. Therefore, this research aimed to analyze the concentration of Ca, P, Mg, K, Na, Li, V, Cr, Mn, Co, Cu, Zn, Se and Mo in three characteristic antler positions selected based on the observation of fights between males. These were compared between farmed fallow deer (Dama dama) of different ages. The mineral compositions of tissues were analyzed using inductively coupled plasma mass spectrometry. The highest mean concentrations of macroelements (except K) were recorded in the youngest animals aged 2 or 3 years in the proximal position of the antlers. With age and distance from the skull, Ca, P, Mg and Na contents decreased, while K increased. Higher mean concentrations of most trace elements (Cr, Mn, Co, Cu, Zn) were recorded in 3-year-old animals in antler distal positions. With an increase in the age, body mass and antler mass of fallow deer, the concentration of Ca, P, Mg, K, Mn, Cu and Zn decreased (−0.414 ≤ R ≤ −0.737, p < 0.05) in the studied tissue, whereas Li increased (0.470 ≤ R ≤ 0.681, p < 0.05). The obtained results confirm that the antlers’ chemical composition changes with age, also changing the Ca:P ratio.

The Mineral Composition of Bone Marrow, Plasma, Bones and the First Antlers of Farmed Fallow Deer

An adequate supply of essential nutrients is particularly important during the skeletal growth and development of young deer, especially in males, who build new antlers each year. The aim of the research was to analyze the levels of 21 mineral elements (including the bulk elements: Ca, P, Mg, K, Na; trace elements: Li, Cr, Mn, Co, Cu, Zn, Se, Mo; and toxic elements: Be, Al, As, Cd, Sb, Ba, Pb, Ni) in the bone marrow, plasma, bones, and first antlers of farmed fallow deer (Dama dama). The mineral compositions of tissues were analyzed using inductively coupled plasma mass spectrometry. Higher concentrations of Ca, P, Mg, Cr, Zn, Se, Al, Ba and Ni were found in bone marrow than in plasma. The highest concentrations of Ca, P and Ba were recorded in fallow deer bone, while the highest concentrations of Mg, K, Na, Li, Cr, Mn, Co, Cu, Zn, Se, Mo, Be, Al, As, Sb, Pb and Ni were found in the antlers. Moreover, the research showed a significant negative relationship between Ca and Cd, and between Ca and Pb, and P and Pb (rS = −0.70, rS = −0.80, and rS = −0.66, respectively; p < 0.05) in the tissues.

Osteoporotic bone recovery by a bamboo-structured bioceramic with controlled release of hydroxyapatite nanoparticles

While most bone defects can be repaired spontaneously, the healing process can be complicated due to insufficient bone regeneration when osteoporosis occurs. Synthetic materials that intrinsically stimulate bone formation without inclusion of exogenous cells or growth factors represent a highly desirable alternative to current grafting strategies for the management of osteoporotic defects. Herein, we developed a series of hydroxyapatite bioceramics composed of a microwhiskered scaffold (wHA) reinforced with multiple layers of releasable hydroxyapatite nanoparticles (nHA). These novel bioceramics (nwHA) are tunable to optimize the loading amount of nHA for osteoporotic bone formation. The utility of nwHA bioceramics for the proliferation or differentiation of osteoporotic osteoblasts in vitro is demonstrated. A much more compelling response is seen when bioceramics are implanted in critical-sized femur defects in osteoporotic rats, as nwHA bioceramics promote significantly higher bone regeneration and delay adjacent bone loss. Moreover, the nwHA bioceramics loaded with a moderate amount of nHA can induce new bone formation with a higher degree of ossification and homogenization. Two types of osteogenesis inside the nwHA bioceramic pores were discovered for the first time, depending on the direction of growth of the new bone. The current study recommends that these tailored hybrid micro/nanostructured bioceramics represent promising candidates for osteoporotic bone repair.

Factors affecting antler growth period and casting date in red deer

Antlers are unique structures because they grow rapidly and are cast annually, representing an important energetic and mineral cost for deer. Variables related to the timing of antler growth, such as date of antler casting and length of growth period, therefore, should be affected by somatic resources and availability of food. We examined the effects of body and antler weight, age, and climatic variables, on antler casting date and the period of time antlers were grown as well as possible random effects of individual, year, cohort, and pedigree, based on 244 antlers in a population of 109 males of Iberian red deer (Cervus elaphus) over a 17-year study from 1999 to 2016. Body weight affected casting date, with heavier males casting antlers earlier than lighter males. Antlers also grew faster and were cast earlier among older males than young males. Antler weight influenced casting date and the duration of the growth period: males with heavier antlers cast them earlier and grow them faster than males with light antlers. Nevertheless, age and antler weight interacted; as such, older males grew their antlers slower and delay casting date because they produce heavier antlers, in contrast to younger males, where those with the heaviest antlers grow them faster and cast first. The date of the end of antler growth also influenced casting date, so that antlers that took the longest to develop were cast later than those that finished growing early. We conclude that older and heavier males cast their antlers earlier and grow them faster than younger and lighter males, likely to correlate the subsequent antler growth with the spring peak in plant nutrients, but that this early development is limited physiologically by the size of the antlers.

Comparison of the accumulation of macro- and microelements in the bone marrow and bone of wild and farmed red deer (Cervus elaphus)

Background

The cells of the entire body, including the skeletal system, especially of young animals, may derive from the bone marrow in which they multiply. Therefore, it is important to assess whether the diet and quality of life of deer have a significant impact on the elemental composition of bone and bone marrow, which can directly affect their health and growth. The aim of this study was to determine the concentrations of macro- (Ca, calcium, P, phosphorus, Mg, magnesium, K, potassium, Na, sodium) and microelements (Li, lithium, Cr, chromium, Mn, manganese, Co, cobalt, Cu, copper, Zn, zinc, Se, selenium, Mo, molybdenum, and Sn, tin) accumulated in the bone marrow and bones of deer (Cervus elaphus). The study was carried out on 15 young stags divided into two groups: farmed and wild animals. The concentrations of macro- and microelements were analysed using the inductively coupled plasma mass spectrometry technique. This research expands our knowledge on this topic, which so far has not been extensively studied.

Results

The mean content of K, Na, Zn and Se in the bone marrow of farmed animals was significantly higher than in wild deer, whereas the mean content of Ca, P, Mg, K, Na and Li in the bones was higher in wild animals than in farmed individuals (p < 0.05). In addition, the mean concentration of Cr, Mn, Cu, Se and Mo in the bones of the analysed animals differed significantly (p < 0.05) and was higher in the farmed deer. The mean concentration of Se in the bone marrow of wild deer decreased with the increase of the body weight (p < 0.05). In turn, the mean content of Mn in the bone marrow and of Mo in the bones of the animals was significantly positively correlated with the animals’ body weight (p < 0.05).

Conclusions

The obtained results indicated different levels of micro- and macro-components in the body of farmed and wild deer, though without clear and strong variations. Generally, the higher level of macronutrients in the bones of wild deer may be related to the higher physiological importance of these minerals for life activities in the natural environment and to the limited supply of balanced food. On the other hand, the higher levels of microelements in the tissues of farmed animals may result from their significantly better nutritional status in the first year of life, achieved through appropriate nutrition as well as diet supplementation of adult females.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-03041-2.

The mechanism of Epimedin B in treating osteoporosis as revealed by RNA sequencing-based analysis

With the ageing of populations, the management of osteoporosis is a priority of society in general. Epimedin B, a major ingredient of Herba Epimedii, which has the advantages of high content and hypotoxicity has been proved to be effective in preventing osteoporosis in vitro. However, the efficacy and mechanism of Epimedin B on osteoporosis in vivo have not been well elucidated yet. This study aimed to investigate the effects and the potential mechanisms of 8-week repeated oral administration of Epimedin B (10 and 20 mg/kg/day) on a mouse osteoporosis model. Effects of Epimedin B were evaluated by examinations of serum bone turnover markers, bone mineral density, bone microstructure parameters and histopathological section. Epimedin B significantly rose N-terminal propeptide of type I procollagen (P1NP) and dropped C-telopeptide of type I collagen (CTX1). Connectivity density (Conn.D) increased significantly while structure model index (DA) decreased significantly after treated by Epimedin B. Meanwhile, Epimedin B administration significantly increased the number of trabecular bones while significantly decreased the gap between them. Overall, Epimedin B showed beneficial effects on osteoporosis. Furthermore, RNA sequencing-based analysis revealed 5 significantly down-regulated transcripts and 107 significantly up-regulated transcripts between the Epimedin B administration group and the model group. These transcripts were mapped to 15 pathways by KEGG enrichment analysis, of which PI3K-Akt signalling pathway, MAPK signalling pathway and PPAR signalling pathway were most connected to osteoporosis. To conclude, Epimedin B is effective in treating osteoporosis in mice via regulating PI3K-Akt, MAPK and PPAR signalling pathway.

SWATH-MS Quantitative Proteomic Analysis of Deer Antler from Two Regenerating and Mineralizing Sections

Simple Summary

Deer antler is a unique and astonishing case of annual regeneration in mammalians. Several studies have pointed out the potential for use of velvet antler extract as a nutraceutical supplement, among others, because of its anti-cancer activity. The study of antler regeneration and growth allow us to identify the main proteins and regulatory pathways involved in cell differentiation and regeneration. For this purpose, two sections of antlers (tips and middle sections) using ribs as controls were analyzed from a proteomic point of view. A total of 259 proteins mainly associated with antioxidant mechanisms and Wnt signalling pathways could be responsible for deer antler regeneration and these proteins may be linked to human health benefits. Further studies should be focused on discovering which proteins from velvet antler extracts are associated with these beneficial effects.

Abstract

Antlers are the only organ in the mammalian body that regenerates each year. They can reach growth rates of 1–3 cm/day in length and create more than 20 cm²/day of skin in the antler tips (their growth centers). Previous proteomic studies regarding antlers have focused on antler growth centers (tips) compared to the standard bone to detect the proteins involved in tissue growth. However, proteins of cell differentiation and regeneration will be more accurately detected considering more growing tissues. Thus, we set out to compare proteins expressed in antler tips (the highest metabolism rate and cell differentiation) vs. middle sections (moderate cell growth involving bone calcification), using ribs as controls. Samples were obtained in mid-June with antlers’ phenology corresponding to the middle of their growth period. Quantitative proteomic analysis identified 259 differentially abundant proteins mainly associated with antioxidant metabolic mechanisms, protein formation and Wnt signalling pathway, meanwhile, the mid antler section was linked to blood proteins. The high metabolic rate and subsequent risk of oxidative stress also seem to have resulted in strong antioxidant mechanisms. These results suggest that redox regulation of proteins is a key factor in the model of deer antler regeneration.

Accumulation of Toxic Elements in Bone and Bone Marrow of Deer Living in Various Ecosystems. A Case Study of Farmed and Wild-Living Deer

The aim of the study was to determine the concentrations of toxic elements accumulated in the bone marrow and bones (Cervus elaphus). The studies were carried out on two groups of young stags: farmed (n = 6) and wild (n = 9). Their body weights were measured and bone and bone marrow samples were collected. The concentrations of toxic elements were analyzed using the inductively coupled plasma mass spectrometry technique. The mean aluminum content in the bone marrow and bones of the farmed animals was significantly higher than in the wild group (p < 0.05). The mean concentration of arsenic, barium and lead in the bones of the wild red deer was significantly higher than in the bones of the farmed animals (p < 0.05), while the cadmium concentration in the bones of the farmed red deer exceeded the value determined in the wild animals. A significant difference was found between the mean concentrations of aluminum, arsenic, barium, lead, vanadium and nickel in the bone marrow and bones of both red deer groups (p < 0.05). Although the study involved animals living in an uncontaminated area, the concentrations of some heavy metals were higher than values reported from industrial regions.

Comparative Metabolomics Study Revealed Difference in Central Carbon Metabolism between Sika Deer and Red Deer Antler

The antler regeneration has been well studied for the past two decades and adopted in the regenerative medicine model for studying on developmental biology. Despite our growing knowledge of functional molecules regulating antler regeneration, we still do not know whether antler from different deer species possess the exact same mechanism or not. Our previous comparative study between sika deer and red deer suggests that the metabolic pathways between them are profoundly different based on protein level. Therefore, the metabolomic technology is used to identify and quantify the metabolites in antler samples, providing interesting insights into differential metabolite profile of antlers between sika deer and red deer. The distinct metabolic characteristics of sika deer compared to red deer provide an opportunity to explain why the red deer antler with a larger size. The enrichment analysis of differential metabolites showed that three pathways including glycine and serine metabolism, methionine metabolism, and pterine biosynthesis had a significant difference between two antler groups.

Quality of main types of hunted red deer meat obtained in Spain compared to farmed venison from New Zealand

Deer venison is increasingly valued as a natural meat. This study examines the three main sources of venison: farmed venison from New Zealand (NZ), the world's leading producer, and wild deer from Spain (SP), the second largest producer, which mainly supplies venison from traditional autumn-winter driven hunts (monteria), involving packs of dogs, and a smaller proportion culled through summer selective stalking. Meat from NZ contained more protein, lower shear force and lower n-6/n-3 ratio (P < 0.01). Spanish meat had a greater content of total, essential and non-essential amino acids (P < 0.01). Meat from deer culled in winter had lower intramuscular fat and saturated fatty acids (FA) but higher polyunsaturated FA (P < 0.01) and pH (P < 0.001) than meat from summer stalked deer. Therefore, venison presents differences by country of origin for composition, FA and texture that are likely to affect its health characteristics. Anomalies observed in meat between the winter driven hunt and non-stressful summer stalking may be attributed to the level of death stress in the case of variables such as pH. However, the effect on fat and mineral composition seems to be seasonal, depending respectively on wild diet or cyclic osteoporosis in males.

Effects of supplementation with different levels of calcium and phosphorus on mineral content of first antler, bone, muscle, and liver of farmed fallow deer (Dama dama)

Nutrition is one of the main factors influencing physiological processes, e.g., growth and antler development, in Cervidae. The aim of this study was to demonstrate a possible effect of supplementation with different levels of calcium (Ca) and phosphorus (P) on the mineral composition of antlers and bones, and its effect on the content of macroelements — Ca, potassium (K), magnesium (Mg), sodium (Na), and P — in the muscle tissue, liver, and blood of farmed fallow deer fawns. The results show a positive effect of increased doses of Ca and P on body weight at the age of 14 mo. Additionally, there was a significant increase in the content of Ca, Mg, Na, and P in antlers and Ca, Na, and P in bones. The muscle tissue was characterised by a significant increase only in the content of Na, whereas Ca, K, and P levels increased significantly in the liver. In turn, the serum P content decreased significantly. Adequate Ca and P supplementation exerts a positive effect on the mineral composition of bones and whole antlers of farmed fallow deer fawns, and it enhances the concentrations of macroelements in tissues, which may constitute a reservoir used for future development of antlers. It also has a positive effect on body weight.

Antlers - Evolution, development, structure, composition, and biomechanics of an outstanding type of bone

Antlers are bony appendages of deer that undergo periodic regeneration from the top of permanent outgrowths (the pedicles) of the frontal bones. Of the "less familiar" bone types whose study was advocated by John Currey to gain a better understanding of structure-function relationships of mineralized tissues and organs, antlers were of special interest to him. The present review summarizes our current knowledge about the evolution, development, structure, mineralization, and biomechanics of antlers and how their formation is affected by environmental factors like nutrition. Furthermore, the potential role of antlers as a model in bone biology and several fields of biomedicine as well as their use as a monitoring tool in environmental studies are discussed.

Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer

Deer antler, as the only mammalian regenerative appendage, provides an optimal model to study regenerative medicine. Antler harvested from red deer or sika deer were mainly study objects used to disclose the mechanism underlying antler regeneration over past decades. A previous study used proteomic technology to reveal the signaling pathways of antler stem cell derived from red deer. Moreover, transcriptome of antler tip from sika deer provide us with the essential genes, which regulated antler development and regeneration. However, antler comparison between red deer and sika deer has not been well studied. In our current study, proteomics were employed to analyze the biological difference of antler regeneration between sika deer and red deer. The proteomics profile was completed by searching the UniProt database, and differentially expressed proteins were identified by bioinformatic software. Thirty-six proteins were highly expressed in red deer antler, while 144 proteins were abundant in sika deer. GO and KEGG analysis revealed that differentially expressed proteins participated in the regulation of several pathways including oxidative phosphorylation, ribosome, extracellular matrix interaction, and PI3K-Akt pathway.

Altered morpho-functional features of bones in autoimmune disease-prone BXSB/MpJ- Yaa mice

IMPACT STATEMENT

Bone disease, such as osteoporosis and rheumatoid arthritis, increases because of the progression of an aging society. Autoimmune disease are important and predisposing factors for the pathogenesis of the bone disease; however, the pathological mechanism is unclear. We have demonstrated that systemic autoimmune disease in BXSB/MpJ- Yaa is closely associated with the morpho-functional abnormalities of bones including bone marrow and has complicated pathology. The abnormalities are characterized by altered regulations of serum calcium, anemia tendency, and hematopoiesis with increased WBCs and decreased PLs, short length and low mass of long bones, imbalance in the populations of osteoclasts and osteoblasts, and increased expression of candidate genes for causing and/or exacerbating their phenotypes. Therefore, BXSB/MpJ- Yaa serves as a model to elucidate bone phenotypes in systemic autoimmune disease that would be affected by the factors in the bone as well as the other immune and/or mineral metabolism organs both in human and experimental medicine.

Dietary calcium supplementation affects nutrient digestibility and antler-production performance during the antler-velvet growth period of male sika deer

Effects of calcium (Ca) supplementation on nutrient digestibility, physiochemical characteristics and antler growth in farmed male sika deer were investigated. Eighteen sika deer (6 years old, 105.50 ± 5.05 kg) were assigned into the following three treatments where they had ad libitum access to water for 90 days: (1) control (C), basal diet containing 0.5% Ca; (2) Ca1.10, basal diet supplemented with 0.6% Ca; and (3) Ca1.70, basal diet supplemented with 1.2% Ca. The basal diet contained 0.50% Ca and 0.34% phosphorus (P). Each group consisted of the same ratio of Ca to P (provided as CaCO3 and CaHPO4). The results showed that the digestibility of dry matter (DM) and crude protein in the Ca1.70 group was lower than in the other two groups. The digestibilities of Ca, P and neutral detergent fibre in the Ca1.10 group were higher than those in the C group and Ca1.70 group (P &lt; 0.05). Concentrations of Ca and P in faeces increased with an increasing supplementation level of Ca and the highest concentrations were observed in the Ca1.70 group (P &lt; 0.05). There were no differences in the concentrations of parathyroid hormone, alkaline phosphatase and osteocalcin among the treatments. Testosterone and oestradiol concentrations of the Ca1.7 group were higher than those of the C and Ca1.10 groups (P &lt; 0.05). Average daily gains of fresh antler weight and dry antler weight of the groups Ca1.10 and Ca1.70 were greater than those of the C (P &lt; 0.05). Fresh and dry antler yields of the Ca1.10 group were higher than those of the other groups (P &lt; 0.05). In conclusion, optimal level of Ca supplement was found to be total Ca concentration of 1.10–1.70%, on the basis of DM, which significantly increased feed digestibility and antler daily gain for the 6-year-old sika deer.

The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes

We present here the de novo genome assembly CerEla1.0 for the red deer, Cervus elaphus, an emblematic member of the natural megafauna of the Northern Hemisphere. Humans spread the species in the South. Today, the red deer is also a farm-bred animal and is becoming a model animal in biomedical and population studies. Stag DNA was sequenced at 74× coverage by Illumina technology. The ALLPATHS-LG assembly of the reads resulted in 34.7 × 10³ scaffolds, 26.1 × 10³ of which were utilized in Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red deer pseudochromosomes, a pre-established genetic map was used for main anchor points. A nearly complete co-linearity was found between the mapmarker sequences of the deer genetic map and the order and orientation of the orthologous sequences in the syntenic bovine regions. Syntenies were also conserved at the in-scaffold level. The cM distances corresponded to 1.34 Mbp uniformly along the deer genome. Chromosomal rearrangements between deer and cattle were demonstrated. 2.8 × 10⁶ SNPs, 365 × 10³ indels and 19368 protein-coding genes were identified in CerEla1.0, along with positions for centromerons. CerEla1.0 demonstrates the utilization of dual references, i.e., when a target genome (here C. elaphus) already has a pre-established genetic map, and is combined with the well-established whole genome sequence of a closely related species (here Bos taurus). Genome-wide association studies (GWAS) that CerEla1.0 (NCBI, MKHE00000000) could serve for are discussed.

Selective effect of hydroxyapatite nanoparticles on osteoporotic and healthy bone formation correlates with intracellular calcium homeostasis regulation

Adequate bone substitutes osseointegration has been difficult to achieve in osteoporosis. Hydroxyapatite of the osteoporotic bone, secreted by pathologic osteoblasts, had a smaller crystal size and lower crystallinity than that of the normal. To date, little is known regarding the interaction of synthetic hydroxyapatite nanoparticles (HANPs) with osteoblasts born in bone rarefaction. The present study investigated the biological effects of HANPs on osteoblastic cells derived from osteoporotic rat bone (OVX-OB), in comparison with the healthy ones (SHM-OB). A selective effect of different concentrations of HANPs on the two cell lines was observed that the osteoporotic osteoblasts had a higher tolerance. Reductions in cell proliferation, ALP activity, collagen secretion and osteoblastic gene expressions were found in the SHM-OB when administered with HANPs concentration higher than 25µg/ml. In contrast, those of the OVX-OB suffered no depression but benefited from 25 to 250µg/ml HANPs in a dose-dependent manner. We demonstrated that the different effects of HANPs on osteoblasts were associated with the intracellular calcium influx into the endoplasmic reticulum. The in vivo bone defect model further confirmed that, with a critical HANPs concentration administration, the osteoporotic rats had more and mechanically matured new bone formation than the non-treated ones, whilst the sham rats healed no better than the natural healing control. Collectively, the observed epigenetic regulation of osteoblastic cell function by HANPs has significant implication on defining design parameters for a potential therapeutic use of nanomaterials.

STATEMENT OF SIGNIFICANCE

In this study, we investigated the biological effects of hydroxyapatite nanoparticles (HANPs) on osteoporotic rat bone and the derived osteoblast. Our findings revealed a previously unrecognized phenomenon that the osteoporotic individuals could benefit from higher concentrations of HANPs, as compared with the healthy individuals. The in vivo bone defect model confirmed that, with a critical HANPs concentration administration, the osteoporotic rats had more mechanically matured new bone formation than the non-treated ones, whilst the sham rats healed no better than the natural healing control. The selective effect of HANPs might be associated with the intracellular calcium influx into the endoplasmic reticulum. Collectively, the observed epigenetic regulation by HANPs has significant implication on defining design parameters for a potential therapeutic use of nanomaterials in a pathological condition.

Identification of calgranulin B interacting proteins and network analysis in gastrointestinal cancer cells

Calgranulin B is known to be involved in tumor development, but the underlying molecular mechanism is not clear. To gain insight into possible roles of calgranulin B, we screened for calgranulin B-interacting molecules in the SNU-484 gastric cancer and the SNU-81 colon cancer cells. Calgranulin B-interacting partners were identified by yeast two-hybrid and functional information was obtained by computational analysis. Most of the calgranulin B-interacting partners were involved in metabolic and cellular processes, and found to have molecular function of binding and catalytic activities. Interestingly, 46 molecules in the network of the calgranulin B-interacting proteins are known to be associated with cancer and FKBP2 was found to interact with calgranulin B in both SNU-484 and SNU-81 cells. Polyubiquitin-C encoded by UBC, which exhibited an interaction with calgranulin B, has been associated with various molecules of the extracellular space and plasma membrane identified in our screening, including Na-K-Cl cotransporter 1 and dystonin in SNU-484 cells, and ATPase subunit beta-1 in SNU-81 cells. Our data provide novel insight into the roles of calgranulin B of gastrointestinal cancer cells, and offer new clues suggesting calgranulin B acts as an effector molecule through which the cell can communicate with the tumor microenvironment via polyubiquitin-C.

Transcriptome analysis of sika deer in China

Sika deer is of great commercial value because their antlers are used in tonics and alternative medicine and their meat is healthy and delicious. The goal of this study was to generate transcript sequences from sika deer for functional genomic analyses and to identify the transcripts that demonstrate tissue-specific, age-dependent differential expression patterns. These sequences could enhance our understanding of the molecular mechanisms underlying sika deer growth and development. In the present study, we performed de novo transcriptome assembly and profiling analysis across ten tissue types and four developmental stages (juvenile, adolescent, adult, and aged) of sika deer, using Illumina paired-end tag (PET) sequencing technology. A total of 1,752,253 contigs with an average length of 799 bp were generated, from which 1,348,618 unigenes with an average length of 590 bp were defined. Approximately 33.2 % of these (447,931 unigenes) were then annotated in public protein databases. Many sika deer tissue-specific, age-dependent unigenes were identified. The testes have the largest number of tissue-enriched unigenes, and some of them were prone to develop new functions for other tissues. Additionally, our transcriptome revealed that the juvenile-adolescent transition was the most complex and important stage of the sika deer life cycle. The present work represents the first multiple tissue transcriptome analysis of sika deer across four developmental stages. The generated data not only provide a functional genomics resource for future biological research on sika deer but also guide the selection and manipulation of genes controlling growth and development.

Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases

Gene expression profiling in clinical genomics has yet to deliver robust and reliable approaches for developing diagnostics and contributing to personalized medicine. Owing to technological developments and the recent accumulation of expression profiles, it is a timely and relevant question whether peripheral blood gene expression profiling can be used routinely in clinical decision making. Here, we review the available gene expression profiling data of peripheral blood in autoimmune and chronic inflammatory diseases and suggest that peripheral blood mononuclear cells are suitable for descriptive and comparative gene expression analyses. A gene-disease interaction network in chronic inflammatory diseases, a general protocol for future studies and a decision tree for researchers are presented to facilitate standardization and adoption of this approach.

Molecular genetic studies of gene identification for osteoporosis: the 2009 update

Osteoporosis is a complex human disease that results in increased susceptibility to fragility fractures. It can be phenotypically characterized using several traits, including bone mineral density, bone size, bone strength, and bone turnover markers. The identification of gene variants that contribute to osteoporosis phenotypes, or responses to therapy, can eventually help individualize the prognosis, treatment, and prevention of fractures and their adverse outcomes. Our previously published reviews have comprehensively summarized the progress of molecular genetic studies of gene identification for osteoporosis and have covered the data available to the end of September 2007. This review represents our continuing efforts to summarize the important and representative findings published between October 2007 and November 2009. The topics covered include genetic association and linkage studies in humans, transgenic and knockout mouse models, as well as gene-expression microarray and proteomics studies. Major results are tabulated for comparison and ease of reference. Comments are made on the notable findings and representative studies for their potential influence and implications on our present understanding of the genetics of osteoporosis.

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes

Background

With the completion of the whole genome sequence for many organisms, investigations into genomic structure have revealed that gene distribution is variable, and that genes with similar function or expression are located within clusters. This clustering suggests that there are evolutionary constraints that determine genome architecture. However, as most of the evidence for constraints on genome evolution comes from studies on yeast, it is unclear how much of this prior work can be extrapolated to mammalian genomes. Therefore, in this work we wished to examine the constraints on regions of the mammalian genome containing conserved gene clusters.

Results

We first identified regions of the mouse genome with microsynteny conservation by comparing gene arrangement in the mouse genome to the human, rat, and dog genomes. We then asked if any particular gene types were found preferentially in conserved regions. We found a significant correlation between conserved microsynteny and the density of mouse orthologs of human disease genes, suggesting that disease genes are clustered in genomic regions of increased microsynteny conservation.

Conclusion

The correlation between microsynteny conservation and disease gene locations indicates that regions of the mouse genome with microsynteny conservation may contain undiscovered human disease genes. This study not only demonstrates that gene function constrains mammalian genome organization, but also identifies regions of the mouse genome that can be experimentally examined to produce mouse models of human disease.