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Yan Han

Publications and source records attributed to Yan Han.

4 recordsLinked to original sources
PubMed2026

Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Journal Article↗
PubMed2026

Genomic and transcriptomic features of HBV integration in treatment-naïve, HBeAg-positive children with chronic HBV infection.

BACKGROUND: Hepatitis B virus (HBV) integration represents a major obstacle to curing HBV; however, the landscape of HBV integration and local immune response to transcriptionally active viral integration in children with chronic HBV infection remain unclear. Herein, we aimed to elucidate this landscape in this population. METHODS: Genomic analyses using a probe-based capture strategy were performed on 18 children and 28 adults with chronic HBV infection. Spatial transcriptomics (ST) was performed on 12 children from our cohort and 3 adults from a public database. FINDINGS: All patients were hepatitis B e antigen (HBeAg)-positive and treatment-naïve. Genomically, children exhibited significantly lower clonal expansion level of HBV-integrated hepatocytes than adults, despite comparable unique breakpoint counts. After adjusting for confounding variables, age was identified as an independent risk factor for total frequency of unique integration breakpoints (b = 3.22, P = 0.005). Spatially, ST revealed that spots with transcriptionally active viral integration exhibited a sparse distribution and accounted for a low proportion of all spots in children. Notably, at these spots, children showed reduced adaptive immune cells (e.g., CD8+ T cells) but increased innate components (myeloid cells, Kupffer cells, activated dendritic cells) and APC co-stimulation, whereas adults exhibited a uniform reduction of immune cell populations. INTERPRETATION: Compared with adults, children exhibit lower clonal expansion of HBV-integrated hepatocytes and distinct immune profiles in response to transcriptionally active viral integration, offering new insights into their differing clinical course. FUNDING: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education).

Humans↗
PubMed2026

Exploring the potential mechanism of Huang'e capsule against spontaneous benign prostatic hyperplasia in beagle dogs using high-performance liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry, gas chromatography-mass spectrometry, and network pharmacology.

OBJECTIVE: To investigate the therapeutic efficacy and potential mechanisms of Huang'e capsule (, HEC) against benign prostatic hyperplasia (BPH). METHODS: The chemical profile of HEC was characterized using high-performance liquid chromatographyquadrupole-time-of-flight tandem mass spectrometry (HPLC-Q-TOF-MS/MS) and gas chromatography-mass spectrometry (GC-MS) techniques. Network pharmacology was employed to analyze potential active compounds, core targets, and key signaling pathways. A spontaneous canine BPH model was used to evaluate the efficacy of HEC and to validate the predictions from network pharmacology. RESULTS: A total of 51 chemical components of HEC were identified, comprising 19 from HPLC-Q-TOF-MS/MS and 32 from GC-MS analyses. The "components-targets-pathways-disease" network analysis predicted active compounds including (s)-coriolic acid, ethyl linoleate, peroxysimulenoline, physcion, and kaempferol. Core targets identified included cytochrome P450 family 19 subfamily A member 1, estrogen receptor 2 (ESR2), ESR1, and androgen receptor (AR). Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that HEC's effects on BPH involve pathways related to cancer, phosphatidylinositol 3-kinase (PI3K) -protein kinase B (Akt)-signaling, proteoglycans in cancer, and prostate cancer signaling. Animal experiments showed that HEC significantly improved maximum urinary flow rates, reduced prostate weight, volume, and prostate index, and ameliorated histopathological changes. HEC regulated the balance between apoptosis and proliferation by downregulating AR and estrogen receptor alpha expression, while upregulating estrogen receptor beta expression. CONCLUSION: These findings indicate that HEC effectively ameliorates spontaneous BPH in beagle dogs, likely by regulating the balance between cell apoptosis and proliferation through multiple signaling pathways.

Animals↗
PubMed2025

Enrichment of G-to-U Substitution in SARS-CoV-2 Functional Regions and Its Compensation via Concurrent Mutations.

We surveyed single nucleotide variant (SNV) patterns from 5 903 647 complete SARS-CoV-2 genomes. Among 10 012 SNVs, APOBEC-mediated C-to-U (C > U) deamination was the most prevalent, followed by G > U and other RNA editing-related substitutions including (A > G, U > C, G > A). However, C > U mutations were less frequent in functional regions, for example, S protein, intrinsic disordered regions, and nonsynonymous mutations, where G > U were over-represented. Notably, G-loss substitutions rarely appeared together. Instead, G-gain mutations tended to more frequently co-occur with others, with a marked preference in the S protein, suggesting a compensatory mechanism for G loss in G > U mutations. The temporal patterns revealed C > U frequency declined until late 2021 then resurged in early 2022. Conversely, G > U steadily decreased, with a pronounced drop in January 2022, coinciding with reduced COVID-19 severity. Vaccinated individuals exhibited a slightly but significantly higher C > U frequency and a notably lower G > U frequency compared to the unvaccinated group. Additionally, cancer patients had higher G > U frequency than general patients during the same period. Interestingly, none of the C > U SNVs were uniquely identified in 2724 environmental samples. These findings suggest novel functional roles of G > U in COVID-19 symptoms, potentially linked to oxidative stress and reactive oxygen species, while C > U remains the dominant substitution, likely driven by host immune-mediated RNA editing.

SARS-CoV-2↗