Biomedical subjects

Lu Li

Publications and source records attributed to Lu Li.

7 recordsLinked to original sources

PubMed2026

3D chromatin remodeling during domestication defines novel targets for crop improvement.

Three-dimensional (3D) genome folding shapes gene regulation, yet the genetic underpinnings linking 3D genome evolution to phenotypic innovation during domestication remain elusive. Using population-scale Hi-C profiling of 34 semi-wild and 267 cultivated allotetraploid cottons, we generated a pan-3D genome atlas capturing extensive diversity in topologically associating domains (TADs) and chromatin loops. Chromatin interactome-wide association studies identified 105 TAD reconfigurations and 58 loop rewirings that were established as the 3D chromatin basis of fiber quality, boosting heritability estimates for fiber strength by 16% and fiber length by 20%. We reveal that domestication selection within sequence-defined sweeps fixed 57% of 3D conformation signatures, thereby decoupling sequence-level from chromatin-level selection and shifting the subgenome expression balance of 39 homoeologs in cultivated cotton. Sequence-based modeling and mutational analyses identified the C2H2 zinc-finger protein YY1 as a conserved mediator of 3D genome organization. This study provides a resource for redefining precision-breeding paradigms by harnessing cryptic 3D chromatin targets.

3D genome↗

PubMed2026

Transcriptional and phytohormonal regulation of positional ear development reveals yield strategies in maize.

Maize (Zea mays L.) is a vital global crop, contributing ∼37% of annual grain production. Enhancing yield per unit area is crucial for food security, yet research has primarily focused on single-ear traits, overlooking the regulation of double ears-a key determinant of prolificacy. While secondary ears drive yield variability under prolificacy-favoring conditions, the mechanisms governing ear formation across shoot positions remain poorly understood. Here, we performed high-resolution transcriptomic analysis of 66 samples from three ear types (primary, secondary and third) in maize inbred B73. We uncovered distinct hormonal developmental dynamics: strigolactone (SL) signaling genes, particularly SBP transcription factors, dominated in primary (I) ears, whereas ethylene-related genes (e.g., ZmEREB131, ZmACCO35) were enriched in third (III) ears. Functional validation confirmed that knockout of ZmEREB131 and ZmACCO35 accelerated development and elongated ears compared to wild-type, implicating ethylene (ETH) signaling in ear maturation arrest. Notably, SL inhibitor application synchronized primary and secondary ear development, boosting total yield by >20% without compromising primary ear performance. Our study elucidates the transcriptional networks underlying differential ear development and provides actionable strategies for yield improvement through targeted hormonal modulation. These findings advance the understanding of maize inflorescence biology and offer molecular tools for breeding high-yielding varieties.

RNA-seq↗

PubMed2026

Enhanced Performance in All-Inorganic AgBiS2 Photodetectors via Oxygen-Inhibited Spray Pyrolysis Deposition.

AgBiS2 has emerged as a promising optoelectronic material due to its broad spectral response and strong light absorption. However, the current use of high-boiling solvents and organic buffers restricts fundamental studies and further performance optimization of AgBiS2's intrinsic properties. In this study, we develop an organic buffer-free AgBiS2 photodetector prepared using a low-temperature ultrasonic spray pyrolysis technique. Our theoretical analysis revealed that oxygen doping alters the optoelectronic characteristics by enhancing the density of states near the Fermi level, leading to consequent severe nonradiative charge carrier recombination. By incorporating excess thiourea while maintaining optimal substrate temperature for enhanced crystallinity, we successfully suppress oxygen defects and consequently improve photodetection performance. The optimized device exhibits a high responsivity of 0.046 A W-1 at 1050 nm, a low noise level (<8.5 × 10-19 A2 Hz-1), and a fast response time (0.07 μs rise, 0.60 μs decay). Benefiting from the rapid response, the photodetector delivers high-resolution imaging with sharp edge definition. This work eliminates the interference of organic buffer layers to directly reveal how oxygen defect modulation affects the intrinsic optoelectronic properties of AgBiS2, offering a scalable pathway for high-performance, solution-processed photodetectors.

near-infrared detector↗

PubMed2026

Genome-guided stage- and tissue-resolved transcriptome analysis of Serrodes campana identifies sex-biased antennal expression and candidate chemosensory-related genes.

Serrodes campana is an erebid moth of ecological and forestry relevance; its larvae are mainly associated with the soapberry tree, Sapindus mukorossi, whereas adults exhibit fruit-piercing behavior. However, stage- and tissue-resolved transcriptomic resources for this species remain limited. Here, using a chromosome-level reference genome, we performed a genome-guided transcriptome analysis of S. campana based on 12 RNA-seq libraries representing major developmental stages and key adult tissues. Global transcriptomic analyses revealed pronounced transcriptional differentiation across developmental stages and tissue types. Tissue-enriched gene sets and functional enrichment analyses identified distinct molecular signatures associated with developmental, sensory, and pheromone-associated tissues. Comparative analysis of female and male antennae further revealed sex-biased expression of several candidate chemosensory-related genes. Among 153 curated chemosensory-related candidate genes, most odorant receptor genes showed strong antennal enrichment, whereas other major chemosensory gene families displayed broader but still tissue-preferential expression patterns. In addition, an exploratory comparison of female terminal abdominal gland tissue and male terminal abdominal coremata revealed divergent expression profiles and highlighted candidate genes potentially associated with pheromone-related physiology, reproduction, and tissue-specific signaling. Together, this study provides the first genome-guided stage- and tissue-resolved transcriptomic resource for S. campana and offers a useful foundation for future studies of chemosensory detection, sex-biased gene expression, and pheromone-associated biology in this species.

Animals↗

PubMed2026

Genome-Wide In Vivo RNAi Screening Identifies HOXD4 as a Tumor Metastasis Suppressor in Colorectal Cancer.

Metastasis remains a major therapeutic challenge in colorectal cancer, highlighting an urgent need to elucidate its underlying molecular mechanisms. In this study, an in vivo screening system integrating genome-wide short hairpin RNA library and next-generation sequencing identifies six candidate metastasis suppressors, among which Homeobox D4 (HOXD4) shows the most pronounced effects. Clinicopathological analyses reveal significant HOXD4 downregulation in tumor tissues relative to adjacent normal tissues, with reduced expression strongly correlating with aggressive tumor features. Functional assays demonstrate that HOXD4 depletion enhances migration, invasion, and tumorsphere formation in HCT116 cells, while ectopic HOXD4 overexpression reverses these malignant phenotypes in SW620 cells. Mechanistically, HOXD4 suppresses epithelial-mesenchymal transition (EMT) by directly binding to the promoter of Forkhead box Q1 (FOXQ1), a key driver of EMT and stemness, and thereby transcriptionally repressing its expression. Immunohistochemistry confirms an inverse correlation between HOXD4 and FOXQ1 expression in clinical specimens. Rescue experiments substantiate that HOXD4 exerts its metastasis-suppressing functions via FOXQ1 regulation. Collectively, these findings not only establish an efficient platform for screening tumor metastasis suppressors, but also identify HOXD4 as a master transcriptional regulator of the FOXQ1-EMT axis, providing a promising target for metastasis interception.

Humans↗

PubMed2025

Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.

Humans↗

PubMed2024

Association between Branched-Chain amino acids and Epilepsy: A Mendelian randomized study.

BACKGROUND: Branched-chain amino acids (BCAAs) have been affected epilepsy, yet conclusions remain inconclusive, lacking causal evidence regarding whether BCAAs affect epilepsy. Systematic exploration of the causal relationship between BCAAs and epilepsy could hand out new ideas for the treatment of epilepsy. METHODS: Utilizing bidirectional Mendelian randomization (MR) study, we investigated the causal relationship between BCAA levels and epilepsy. BCAA levels from genome-wide association studies (GWAS), including total BCAAs, leucine levels, isoleucine levels, and valine levels, were employed. Causal relationships were explored applying the method of inverse variance-weighted (IVW) and MR-Egger, followed by sensitivity analyses of the results to evaluate heterogeneity and pleiotropy. RESULTS: Through strict genetic variant selection, we find some related SNPs, total BCAA levels (9), leucine levels (11), isoleucine levels (7), and valine levels (6) as instrumental variables for our MR analysis. Following IVW and sensitivity analysis, total BCAAs levels (OR = 1.14, 95 % CI = 1.019 ∼ 1.285, P = 0.022) and leucine levels (OR = 1.15, 95 % CI = 1.018 ∼ 1.304, P = 0.025) had significant correlation with epilepsy. CONCLUSIONS: There exists a causal relationship between the levels of total BCAAs and leucine with epilepsy, offering the new ideas into epilepsy potential mechanisms, holding significant implications for its prevention and treatment.

Humans↗