Single nucleotide variations in the development of diabetic foot ulcer: A narrative review

Diabetes mellitus has become a global health problem,and the number of patients with diabetic foot ulcers(DFU)is rapidly increasing.Currently,DFU still poses great challenges to physicians,as the treatment is complex,with high risks of infection,recurrence,limb amputation,and even death.Therefore,a comprehensive understanding of DFU pathogenesis is of great importance.In this review,we summarized recent findings regarding the DFU development from the perspective of single-nucleotide variations(SNVs).Studies have shown that SNVs located in the genes encoding C-reactive protein,interleukin-6,tumor necrosis factor-alpha,stromal cell-derived factor-1,vascular endothelial growth factor,nuclear factor erythroid-2-related factor 2,sirtuin 1,intercellular adhesion molecule 1,monocyte chemoattractant protein-1,endothelial nitric oxide synthase,heat shock protein 70,hypoxia inducible factor 1 alpha,lysyl oxidase,intelectin 1,mitogen-activated protein kinase 14,toll-like receptors,osteoprotegerin,vitamin D receptor,and fibrinogen may be associated with the development of DFU.However,considering the limitations of the present investigations,future multi-center studies with larger sample sizes,as well as in-depth mechanistic research are warranted.

Nucleotide Variation in the NCED3 Region of Arabidopsis thaliana and its Association Study with Abscisic Acid Content under Drought Stress

Drought tolerance is a comprehensive quantitative trait that is being understood further at the molecular genetic level. Abscisic acid （ABA） is the main drought-induced hormone that regulates the expression of many genes related to drought responses. 9-cis-epoxycarotenoid dioxygenase （NCED3） is thought to be a key enzyme in ABA biosynthesis. In this paper, we measured the ABA content increase under drought stress, and sequenced and compared the sequence of AtNCED3 among 22 Arabidopsis thaliana accessions. The results showed that the fold of ABA content increase under drought stress was highly variable among these accessions. High density single nucleotide polymorphism （SNP） and insertion/deletion （indel） were found in the AtNCED3 region, on average one SNP per 87.4 bp and one indel per 502 bp. Nucleotide diversity was significantly lower in the coding region than that in non-coding regions. The results of an association study with ANOVA analysis suggested that the 274th site （P←→S） and the 327th site （P←→R） amino acid variations might be the cause of ABA content increase of 163av accession under drought stress.

Circulating tumor DNA and its role in detection, prognosis and therapeutics of hepatocellular carcinoma

Hepatocellular carcinoma(HCC) is considered the fifth most prevalent cancer among all types of cancers and has the third most morbidity value. It has the most frequent duplication time and a high recurrence rate. Recently, the most unique technique used is liquid biopsies, which carry many markers;the most prominent is circulating tumor DNA(ctDNA). Varied methods are used to investigate ctDNA, including various forms of polymerase chain reaction(PCR) [emulsion PCR(ePCR), digital PCR(dPCR), and bead, emulsion, amplification, magnetic(BEAMing) PCR]. Hence ctDNA is being recognized as a potential biomarker that permits early cancer detection,treatment monitoring, and predictive data on tumor burden are subjective to therapy or surgery. Numerous ctDNA biomarkers have been investigated based on their alterations such as 1) single nucleotide variations(either insertion or deletion of a nucleotide) markers including TP53, KRAS, and CCND1;2) copy number variations which include markers such as CDK6, EFGR, MYC and BRAF;3) DNA methylation(RASSF1A, SEPT9, KMT2C and CCNA2);4) homozygous mutation includes ctDNA markers as CDKN2A, AXIN1;and 5) gain or loss of function of the genes, particularly for HCC. Various researchers have conducted many studies and gotten fruitful results.Still, there are some drawbacks to ctDNA namely low quantity, fragment heterogeneity, less stability, limited mutant copies and standards, and differential sensitivity. However, plenty of investigations demonstrate ctDNA's significance as a polyvalent biomarker for cancer and can be viewed as a future diagnostic, prognostic and therapeutic agent. This article overviews many conditions in genetic changes linked to the onset and development of HCC, such as dysregulated signaling pathways, somatic mutations, single-nucleotide polymorphisms, and genomic instability. Additionally, efforts are also made to develop treatments for HCC that are molecularly targeted and to unravel some of the genetic pathways that facilitate its early identification.

Gene testing for osteonecrosis of the femoral head in systemic lupus erythematosus using targeted next-generation sequencing:A pilot study

BACKGROUND Previous publications indicated that genetic predisposition might play important roles in the onset of osteonecrosis of the femoral head(ONFH)in systemic lupus erythematosus(SLE).Some gene loci such as complement C3d receptor 2(CR2),nitric oxide synthase 3(NOS3),collagen type II alpha 1 chain(COL2A1),protein tyrosine phosphatase non-receptor type 22(PTPN22),and transient receptor potential cation channel subfamily V member 4(TRPV4)were reported to be involved in this process.AIM To investigate whether the risk of ONFH in SLE is associated with single nucleotide variations(SNVs)in these five genes.METHODS SNVs in the CR2,NOS3,COL2A1,PTPN22,and TRPV4 genes were examined by using FastTarget and Illumina Miseq sequencing technologies in 49 cases of SLE with ONFH.Burrows–wheeler aligner was used to align the sequencing reads to hg19,and GATK and Varscan programs were used to perform SNV calling.PolyPhen-2,SIFT,and MutationTaster were used to assess the functional effects of non-synonymous SNVs.RESULTS Six of the 49 patients were confirmed to have low frequency SNVs,including one patient with SNVs in NOS3(exon 6:c.814G>A:p.E272K and exon 7:c.814G>A:p.E272K.),four in COL2A1(rs41263847:exon 29:c.1913C>T:p.T638I,exon 28:c.1706C>T:p.T569I,and rs371445823:exon 8:c.580G>A:p.A194T,exon 7:c.373G>A:p.A125T),and one in CR2(rs45573035:exon 2:c.200C>G:p.T67S).CONCLUSION The onset of ONFH in SLE might be associated with the identified SNVs in NOS3,COL2A1,and CR2.

Prevalence,variation,and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei,China during 2020–2021

Human respiratory syncytial virus(RSV)is a severe threat to children and a main cause of acute lower respiratory tract infections.Nevertheless,the intra-host evolution and inter-regional diffusion of RSV are little known.In this study,we performed a systematic surveillance in hospitalized children in Hubei during 2020–2021,in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing(mNGS).RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant.About 46 high-quality genomes were used for further analyses.A total of 163 intra-host nucleotide variation(iSNV)sites distributed in 34 samples were detected,and glycoprotein(G)gene was the most enriched gene for iSNVs,with non-synonymous substitutions more than synonymous substitutions.Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher,and the population size of RSV groups changed over time.We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B,respectively.This study highlighted the intra-host and inter-host evolution of RSV,and provided some evi-dences for understanding the evolution of RSV.

Intra-host Ebola viral adaption during human infection

The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this virus.Herein,we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015,during the late phase of the outbreak.The surviving EBOV patients had a recovery process characterized by decreasing viremia,fever,and biochemical parameters.EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection,including the previously described short stretches of 13 serial TNC mutations.Remarkably,within individual patients,samples collected during the early phase of infection possessed Ts at these nucleotide sites,whereas they were replaced by Cs in samples collected in the later phase,suggesting that these short stretches of TNC mutations could emerge independently.In addition,up to a total of 35 nucleotide sites spanning the EBOV genome were mutated coincidently.Our study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions.

Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft

We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations(iSNVs)in a confined space.Thirty-three patients with COVID-19 were sampled,and 14 were resampled 3-31 days later.All 47 nasopharyngeal swabs were deep-sequenced.iSNVs and similarities in the consensus genome sequence were analyzed.Three SARS-CoV-2 variants of concern,Delta(n=31),Beta(n=1),and C.1.2(n=1),were detected among the 33 patients.The viral genome sequences from 30 Delta-positive patients had similar SNVs;14 of these patients provided two successive samples.Overall,the 47 sequenced genomes contained 164 iSNVs.Of the 14 paired(successive)samples,the second samples(T2)contained more iSNVs(median:3;95%confidence interval[95%CI]:2.77-10.22)than did the first samples(T1;median:2;95%CI:1.63-3.74;Wilcoxon test,P=0.021).38 iSNVs were detected in T1 samples,and only seven were also detectable in T2 samples.Notably,T2 samples from two of the 14 paired samples had additional mutations than the T1 samples.The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event.Intra-host diversity increased gradually with time,and new site mutations occurred in vivo without a population transmission bottleneck.Therefore,we could not determine the generational relationship from the mutation site changes alone.