A novel phosphoprotein is induced during bone marrow commitment to dendritic cells

Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes

Both age-dependent and age-independent alteration of DNA methylation in human tissues are functionally associated with the development of many malignant and non-malignant human diseases. TCGA-KIRC data were biometrically analyzed to identify new loci with age-dependent DNA methylation that may contribute to tumor risk in normal kidney tissue. ANKRD34B and ZIC1 were evaluated as candidate genes by pyrosequencing of 539 tissues, including 239 normal autopsy, 157 histopathologically tumor-adjacent normal, and 143 paired tumor kidney samples. All candidate CpG loci demonstrated a strong correlation between relative methylation levels and age (R = 0.70−0.88, p < 2 × 10−16) and seven out of 10 loci were capable of predicting chronological age in normal kidney tissues, explaining 84% of the variance (R = 0.92). Moreover, significantly increased age-independent methylation was found for 9 out of 10 CpG loci in tumor-adjacent tissues, compared to normal autopsy tissues (p = 0.001−0.028). Comparing tumor and paired tumor-adjacent tissues revealed two patient clusters showing hypermethylation, one cluster without significant changes in methylation, and a smaller cluster demonstrating hypomethylation in the tumors (p < 1 × 10−10). Taken together, our results show the presence of additional methylation risk factors besides age for renal cancer in normal kidney tissue. Concurrent tumor-specific hypermethylation suggests a subset of these loci are candidates for epigenetic renal cancer susceptibility.

Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.

Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds

We performed genome-wide CNV detection based on SNP genotyping data of 96 Chinese-native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions (CNVRs) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVRs selected randomly were validated by quantitative real-time PCR. Comparison with previous studies revealed 25 (23.81%) novel CNVRs, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVRs confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVRs were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes (i.e., ANKRD34B, FAM110B and ABCG1). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVRs harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVRs in the pig genome and provide valuable resources for follow-up-associated studies of CNVs in pig complex traits as well as important implications of human diseases.

Characteristics of highly polymorphic segmental copy-number variations observed in Japanese by BAC-array-CGH

Segmental copy-number variations (CNVs) may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH). We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals.

A novel cell-surface protein CSP82 on bone marrow stem cells and a cytosolic phosphoprotein DP58 (ankyrinRD 34B) are involved in promyeloid progenitor induction

The molecular events associated with the development of common myeloid progenitor (CMP) remain largely unknown. This study reports that a novel glycosylphosphatidylinositol (GPI)-anchored lactoferrin CSP82 on uninitiated mouse bone marrow cells (BMC) may be involved in inducing pro-DC from CMP. By peptide mass fingerprinting, CSP82 has been identified as the mouse lactoferrin precursor, but unlike the latter, it occurs as a GPI-linked cell-surface protein. The GPI-linkage was demonstrated on BMC-derived immunoprecipitates and by other techniques. Furthermore, BMC and hematopoietic stem BM cells following incubation with either CSP82 peptide antibody or purified Reagent A yielded CMP-like progenitors (BM4 cells). These progenitors expressed a previously reported cytosolic phosphoprotein DP58 (AnkRD 34B protein). Continued cultivation of BMC in media containing only anti-CSP82 antibody led to DC-like cells, that bore phenotypic and endocytic resemblance with those obtained using GM-CSF. The results suggest that a receptor lactoferrin on BMC may be an important non-cytokine mechanism for early promyeloid progenitor differentiation.

Mycobacterial HSP70 as an adjuvant in the design of an idiotype vaccine against a murine lymphoma

Mycobacterial HSP70 protein coupled with ovalbumin is known to elicit antigen-specific CD8(+) T-cell response. We investigated whether anti-idiotype immunity can likewise be enhanced using a conjugate of recombinant mycHSP70 and the Ig Id in a murine lymphoma model, A20. Plasmids were constructed of A20 tumor to generate A20Id-HSP70 (scFv-H), unconjugated A20Id (scFv), and mycHSP70 (H) recombinant proteins. We evaluated their relative efficacy in activating anti-tumor immunity that can reduce the mortality of tumor-challenged BALB/c mice; significantly, a longer term protection (>50% of the population) was observed in mice vaccinated with scFv-H compared to those receiving the scFv or H proteins. Concomitantly a much higher-level activation in anti-A20 cytotoxic T-cell activity, IFN-gamma secretion and predominantly anti-A20 IgG2a response was also observed with the scFv-H group. Thus, conjugating HSP70 with the A20Id renders the latter significantly immunogenic and affords longer protection against A20 tumor progression.