Yunliang Wang’s research while affiliated with Zhengzhou University and other places

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Publications (68)


Spike protein genome and phases of vaccination in COVID-19. Spike genome organization includes two S1 and S2 subunits. The top mutation occurrences in spike were analyzed in two phases of vaccination progress.
Methodology overview. This is a schematic representation of the data mining process, categorized into two distinct phases: data refining and analysis, followed by data reporting. Countries were categorized into two phases based on number of received doses of COVID-19 vaccines. Overlapping areas between groups were hatched. 1) Data from GISAID were extracted and analyzed, and the NGS data criteria for each country and group were applied. 2) Geographical data categorized based on doses of vaccination with a chance of 50% occurrence in each phase of vaccination were reported. 3) The Wuhan genome was considered the reference genome. Next, the obtained mutations were processed. The common mutations with more than 50% at the different vaccination phases were concluded. 4) The top mutations of each period of vaccination were compared, and common or unique mutations were presented to help the vaccine design industry.
Variant calling rate in investigated samples in each group in the first phase of immunization and booster dose. Phase 1 (A) Group with 20-50% receiving two doses of vaccine; a significant number of sequences demonstrated no mutation in their spike. (B) Group with 50-70% receiving two vaccine doses; a significant number of sequences demonstrated no mutation in their spike. However, four mutations in the investigated samples were nearly equal to no mutation. (C) In the group with 70-100% two-dose-vaccinated population in phase 1, with the progress of the vaccination, a significant number of sequences demonstrated no mutation in their spike. Phase 2 (Booster) (D, E) Booster group, 50% of the population receiving booster dose; a significant number of sequences demonstrated more than one mutation in their spike.
Heatmap represents the occurrence of spike mutations at various phases of vaccination. Phase 1, (A) In the 20-50% group of phase 1, 254-381, 762-889, and 1,016-1,270 were shown as conserved regions. (B) In the 50%-70% group of phase 1, the hot spots of mutation incidence are 127-254 regions in spike. Furthermore, 254-1,270 were detected as the conserved site. (C) In the 70%-100% group of phase 1, sequences 254-381, 762-889, and 1,143-1,270 are conserved to the mutation incidence, whereas 1-127, 381-508, 635-762, and 889-1,143 were more susceptible to mutations. Phase 2 (Booster), (D) In phase 2 of vaccination, the hot spots of mutation incidence are next to each other in this group as 381-762 regions. Besides them, 254-381 and 762-1,016 are shown as conserved regions.
Heatmap of p-values for Kruskal–Wallis and Mann–Whitney U tests. A p-value heatmap was created to illustrate the significance of differences in mutation counts, employing a sequential color scheme to signify p-value gradations, with darker hues indicating lower p-values.

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Intersecting SARS-CoV-2 spike mutations and global vaccine efficacy against COVID-19
  • Article
  • Full-text available

March 2025

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11 Reads

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Samira Salami Ghaleh

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Youping Deng

In line with encountering the world with the emergence of vaccine-resistance variants of SARS-CoV-2, 15,669,529 samples that received COVID-19 vaccines until April 2023 were investigated as two doses in the first phase and booster vaccinations in the second phase. The analysis shows that D614G and P681 mutations occurred in both phases. The E484 and Y655 mutations significantly emerged during the second phase. The 762-889 and 254-381 regions are revealed as conserved parts and could be considered in vaccine design. The Kruskal–Wallis test revealed a significant reduction in single mutations between populations with 20%–50% and those with 70%–100% vaccination coverage (p=0.017). The Mann–Whitney U test proposes a link between vaccination and suppression of viral mutation rates. Dynamic modeling suggests that key mutations have facilitated the virus’ evolution and immune escape. The study’s findings are crucial for understanding virus genome mutations, especially E614 and P681 in Delta and E484 and H655 in Omicron. This highlights the need to adjust strategies and strengthen global efforts in combating the pandemic.

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Curcumin prevents Alzheimer's disease progression by upregulating JMJD3

August 2022

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12 Reads

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2 Citations

American Journal of Translational Research

The main purpose of this research was to explore the molecular mechanisms of Jumonji Domain-Containing Protein 3 (JMJD3) in Alzheimer's disease (AD) and to analyze its role in the anti-AD mechanism of curcumin (CUR). In the in vitro study of AD, JMJD3 overexpression promoted the trimethylation of histone H3 lysine 27 (H3K27me3), downregulated brain-derived neurotrophic factor (BDNF ), improved the abnormality of mitochondrial stress response (MSR) markers, Aβ accumulation, increased cell proliferation and inhibited apoptosis. Upregulating BDNF also achieved above similar results. Knockout of JMJD3 could downregulate BDNF, upregulate the level of H3K27me3 methylation and inhibit MSR markers, while transfection of JMJD3 RNAi could counteract the upregulated effect of BDNF. Then, MSR activator could also improve AD. In addition, JMJD3 in AD in vitro models was obviously upregulated under CUR stimulation, and it triggered a series of reactions as mentioned above. In the in vivo study, the levels of JMJD3, the mRNA and protein levels of BDNF in the right brain tissues of AD mice were downregulated, the methylation of H3K27me3 increased, and the MSR markers (ClpP, HSP6, HSP-60, ATFS-1, etc.) were downregulated; the above indexes were improved in varying degrees with the intervention of CUR. Thus, we conclude that CUR can induce the upregulation of JMJD3 and improve BDNF expression by promoting the demethylation of H3K27me3, thereby maintaining the balance of MSR and thus, preventing AD development.


Citations (52)


... All included studies provided cross-sectional data for participants with LBD, although two studies reported longitudinal data relating to participants with prodromal LBD [31,32] and one interventional study for PDD reported inflammatory outcomes at two timepoints [33]. Study sizes were small, with a median of n = 14 (interquartile range (IQR) 9-27.5) ...

Reference:

Investigation of Inflammation in Lewy Body Dementia: A Systematic Scoping Review
Effect of Butylphthalide soft capsules on cognitive function and dementia-related factors in elderly patients with Parkinson's disease dementia during the COVID-19 pandemic
  • Citing Article
  • February 2024

American Journal of Translational Research

... Osteoporosis is a disease characterized by low bone mass, deterioration of bone tissue and destruction of bone microarchitecture, which can lead to impaired bone strength and increased risk of fracture (1). As a chronic disease of bone metabolism, it is the result of an imbalance between osteoblasts and osteoclasts (2,3) and is ranked as one of the most serious diseases affecting health, being the second most common disease after heart disease. With the change of diet and lifestyle, the incidence of osteoporosis is increasing year by year, showing the characteristics of more and more young people. ...

Hypermethylation of the ALOX12 and CBS promoters in osteoporosis: Potential biomarkers for early diagnosis
  • Citing Article
  • April 2023

Genes & Diseases

... (4)(5)(6) However, apart from the achievements, it still lacks effective medication for TBI treatment currently (7) and results from previous clinical trials were mostly unsatisfying. (8,9) During the recent exploration, bile acids and their potential effects on the central nervous system have been noticed. It has been noted that bile acids might be beneficial in both neurodegenerative diseases and acute brain injuries such as intracranial hemorrhage or ischemic stroke. ...

Guideline of clinical neurorestorative treatment for brain trauma (2022 China version)

Journal of Neurorestoratology

... High expression of JMJD3 has been documented to enhance H3K27me3 demethylation of disstal-less homeobox2, mixed lineage leukemia 1, mammalian achaete-scute homologue-1, and other genes related to neuronal development [52]; however, whether it has this effect on AD is unknown. Evidence showed that medium and high doses of curcumin inhibited Aβ aggregation and attenuated mitochondrial stress response by modulating the JMJD3-H3K27me3-BDNF pathway in APP/PS1 mice and SH-SY5Y cells [53]. In addition, a study in caenorhabditis elegans discovered that elevated UTX activated the insulin/IGF-1 signaling pathway (IIS) and prevented the transcription factor DAF-16 from entering the nucleus to activate anti-aging genes. ...

Curcumin slows the progression of Alzheimer's disease by modulating mitochondrial stress responses via JMJD3-H3K27me3-BDNF axis
  • Citing Article
  • December 2021

American Journal of Translational Research

... Human adult olfactory neurons are special cells which can automatically regenerate. After being transplanted, they seem to migrate where they are needed, and become local functional neurons as they need to be compensated or replaced [114]; so the indications of human olfactory neuron therapy should be neurological diseases in which many neurons are lost or die and neurological functions are impaired, such as dementia, PD, etc. Pilot clinical studies demonstrated that patients with PD and VD got benefits from the human olfactory neuron therapy [9,10]. The prospect of the human olfactory neuron therapy is promising, but needs to be proved by multicenter, randomized, double blind, placebo-controlled clinical trials. ...

A pilot study of clinical cell therapies in Alzheimer’s disease

Journal of Neurorestoratology

... We first compared CpG sites that had been detected in all of the ONT-generated HG002 data sets (R9, R10, and whole-genome bisulfite sequencing [WGBS]). Because previous studies have revealed the questionable quality of some WGBS techniques and data sets (Ji et al. 2014;Olova et al. 2018), we compared the ONT WGBS data set to an extensively validated HG002 WGBS data set generated as part of an epigenomics quality control (EpiQC) study (Foox et al. 2021). Details about the generation of this data set, and links to the files used, are included in the Methods section. ...

The SEQC2 epigenomics quality control (EpiQC) study

Genome Biology

... Recently, olfactory neuron (ON) transplantation showed promising neurorestorative effects in patients with AD and vascular dementia (VD) in clinical pilot studies. 13,14 ONs are promising candidates for the neuronal replacement in neurotrauma and/or neurodegenerative diseases. ...

A pilot study of clinical cell therapy for patients with vascular dementia

Journal of Neurorestoratology

... Decreased expression of RMST could improve the function of dopaminergic neurons and reduce neuroinflammation in PD rats. 91 For this reason, this study aimed to investigate the role of RMST in modulating PD progression by quantitating changes in neurobehavioral tasks, oxidative stress, and TLR/NF-κB pathway. Research indicated that reducing RMST-enhanced movement reduced oxidative stress, reduced the extent of neuronal damage, and inhibited astrogliosis. ...

Down-regulated long non-coding RNA RMST ameliorates dopaminergic neuron damage in Parkinson’s disease rats via regulation of TLR/NF-κB signaling pathway
  • Citing Article
  • April 2021

Brain Research Bulletin

... The study also evaluated the use of nanopore sequencing methods that can directly detect modified bases, as well as the use of ATAC-seq protocols to profile chromatin accessibility. These NGS-based methods were further compared to established DNA methylation microarray assays within and between laboratories [16]. ...

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

... MiR-218-5p is an important regulator of neuronal function, whose reduction has been linked to amyotrophic lateral sclerosis [14], cognitive impairment [15] and depression [16]. In PD, miR-218-5p is downregulated in the brain of 6-hydroxydopamine (6-OHDA)treated rats [17] and patients with PD [18], and its overexpression attenuates survival of dopaminergic neurons by regulating apoptosis and oxidative stress [17]. However, it remains unclear whether miR-218-5p inhibits microglia-mediated neuroinflammation. ...

Up-regulated microRNA-218-5p ameliorates the damage of dopaminergic neurons in rats with Parkinson’s disease via suppression of LASP1
  • Citing Article
  • November 2020

Brain Research Bulletin