Contemporary Approaches for Identifying Rare Bone Disease Causing Genes

Recent improvements in the speed and accuracy of DNA sequencing, together with increasingly sophisti- cated mathematical approaches for annotating gene networks, have revolutionized the field of human genetics and made these once time consuming approaches assessable to most investigators. In the field of bone research, a particularly active area of gene discovery has occurred in patients with rare bone disorders such as osteogenesis imperfecta （OI） that are caused by mutations in single genes. In this perspective, we highlight some of these technological advances and describe how they have been used to identify the genetic determinants underlying two previously unexplained cases of OI. The widespread availability of advanced methods for DNA sequencing and bioinformatics analysis can be expected to greatly facilitate identification of novel gene networks that normally function to control bone formation and maintenance.

Current evidence on potential of adipose derived stem cells to enhance bone regeneration and future projection

Injuries to the postnatal skeleton are naturally repaired through successive stepsinvolving specific cell types in a process collectively termed “bone regeneration”.Although complex, bone regeneration occurs through a series of well-orchestratedstages wherein endogenous bone stem cells play a central role. In most situations,bone regeneration is successful;however, there are instances when it fails andcreates non-healing injuries or fracture nonunion requiring surgical or therapeuticinterventions. Transplantation of adult or mesenchymal stem cells (MSCs) definedby the International Society for Cell and Gene Therapy (ISCT) as CD105+-CD90+CD73+CD45-CD34-CD14orCD11b-CD79αorCD19-HLA-DR- is beinginvestigated as an attractive therapy for bone regeneration throughout the world.MSCs isolated from adipose tissue, adipose-derived stem cells (ADSCs), aregaining increasing attention since this is the most abundant source of adult stemcells and the isolation process for ADSCs is straightforward. Currently, there isnot a single Food and Drug Administration (FDA) approved ADSCs product forbone regeneration. Although the safety of ADSCs is established from their usagein numerous clinical trials, the bone-forming potential of ADSCs and MSCs, ingeneral, is highly controversial. Growing evidence suggests that the ISCT definedphenotype may not represent bona fide osteoprogenitors. Transplantation of bothADSCs and the CD105- sub-population of ADSCs has been reported to induce bone regeneration. Most notably, cells expressing other markers such as CD146,AlphaV, CD200, PDPN, CD164, CXCR4, and PDGFRα have been shown torepresent osteogenic sub-population within ADSCs. Amongst other strategies toimprove the bone-forming ability of ADSCs, modulation of VEGF, TGF-β1 andBMP signaling pathways of ADSCs has shown promising results. The U.S. FDAreveals that 73% of Investigational New Drug applications for stem cell-basedproducts rely on CD105 expression as the “positive” marker for adult stem cells.A concerted effort involving the scientific community, clinicians, industries, andregulatory bodies to redefine ADSCs using powerful selection markers andstrategies to modulate signaling pathways of ADSCs will speed up thetherapeutic use of ADSCs for bone regeneration.

RECOGNICER:A coarse-graining approach for identifying broad domains from ChIP-seq data

Background:Histone modifications are major factors that define chromatin states and have functions in regulating gene expression in eukaryotic cells.Chromatin immunoprecipitation coupled with high-throughput sequencing(ChIP-seq)technique has been widely used for profiling the genome-wide distribution of chromatin-associating protein factors.Some histone modifications,such as H3K27me3 and H3K9me3,usually mark broad domains in the genome ranging from kilobases(kb)to megabases(Mb)long,resulting in diffuse patterns in the ChIP-seq data that are challenging for signal separation.While most existing ChIP-seq peak-calling algorithms are based on local statistical models without account of multi-scale features,a principled method to identify scale-free board domains has been lacking.Methods:Here we present RECOGNICER(Recursive coarse-graining identification for ChIP-seq enriched regions),a computational method for identifying ChIP-seq enriched domains on a large range of scales.The algorithm is based on a coarse-graining approach,which uses recursive block transformations to determine spatial clustering of local enriched elements across multiple length scales.Results:We apply RECOGNICER to call H3K27me3 domains from ChIP-seq data,and validate the results based on H3K27me3's association with repressive gene expression.We show that RECOGNICER outperforms existing ChIP-seq broad domain calling tools in identifying more whole domains than separated pieces.Conclusion:RECOGNICER can be a useful bioinformatics tool for next-generation sequencing data analysis in epigenomics research.

Ectopic Tcf1 expression instills a stem-like program in exhausted CD8^(+) T cells to enhance viral and tumor immunity

Exhausted CD8^(+)T(Tex)cells are dysfunctional due to persistent antigen exposure in chronic viral infection and tumor contexts.A stem cell-like Tex(Tex-stem)subset can self-renew and differentiate into terminally exhausted(Tex-term)cells.Here,we show that ectopic Tcf1 expression potently promoted the generation of Tex-stem cells in both a chronic viral infection and preclinical tumor models.Tcf1 overexpression diminished coinhibitory receptor expression and enhanced polycytokine-producing capacity while retaining a heightened responses to checkpoint blockade,leading to enhanced viral and tumor control.Mechanistically,ectopically expressed Tcf1 exploited existing and novel chromatin accessible sites as transcriptional enhancers or repressors and modulated the transcriptome by enforcing pre-existing expression patterns in Tex-stem cells,such as enhanced suppression of Blimp1 and Bim and acquisition of new downstream genes,including Mx1,Tox2,and Runx3.These findings reveal a pronounced impact of ectopic Tcf1 expression on Tex functional restoration and highlight the therapeutic potential of harnessing Tcf1-enforced transcriptional programs.