Preeclampsia is a life-threating pregnancy disorder, especially preterm preeclampsia and early-onset preeclampsia, the heterogeneity and complexity of preeclampsia make it difficult to predict risk and develop treatments. Plasma cell-free RNA carries unique information from human tissue and may be useful for noninvasive monitoring of maternal, placental, and fetal dynamics during pregnancy. This study aimed to investigate various RNA biotypes associated with preeclampsia in plasma and develop classifiers to predict preterm preeclampsia and early-onset preeclampsia before diagnosis. We performed a novel cell-free RNA sequencing method named PALM-Seq to investigate the cell-free RNA characteristics of 715 healthy and 202 preeclampsia pregnancies before symptom onset. We explored changes in the abundance of different RNA biotypes in plasma between healthy and preeclampsia samples and built preterm preeclampsia and early-onset preeclampsia prediction classifiers using machine learning methods. Furthermore, we validated the performance of the classifiers using the external and internal validation cohorts and assessed the area under the curve and positive predictive value. We detected 77 differentially expressed genes including mRNA (44%) and miRNA (26%) between healthy and preterm preeclampsia mothers before symptom onset, which could separate preterm preeclampsia from healthy samples and play critical functional roles in preeclampsia physiology. We developed two classifiers for predicting preterm preeclampsia and early-onset preeclampsia before diagnosis based on 13 cell-free RNA signatures and two clinical features (IVF and MAP), respectively. Notably, both classifiers showed enhanced performance compared to the existing methods: the preterm preeclampsia prediction model achieved 81% area under the curve and 68% positive predictive value in an independent validation cohort (preterm PE, n=46; control, n=151); the early-onset preeclampsia prediction model had an area under the curve of 88% and a positive predictive value of 73% in an external validation cohort (early-onset PE, n=28; control, n=234). Furthermore, we demonstrated downregulation of miRNAs may play vital roles in preeclampsia through the upregulation of preeclampsia-relevant target genes. Our cohort study presented the first comprehensive transcriptomic landscape of different RNA biotypes in preeclampsia and developed two advanced classifiers with significant clinical importance for preterm preeclampsia and early-onset preeclampsia prediction before symptom onset. We demonstrated for the first time that messenger RNA, microRNA, and long noncoding RNA can simultaneously serve as potential biomarkers of preeclampsia, holding the promise of prevention of preeclampsia in advance. Abnormal cell-free messenger RNA, microRNA and long noncoding RNA molecular changes help to elucidate the pathogenic determinants of preeclampsia, and open new therapeutic windows to effectively reduce pregnancy complications and fetal morbidity.

Cell‐specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single‐cell mono‐omics techniques are unable to directly capture the relationships and dynamics between different layers of molecular information within the same cells. While advanced algorithm facilitates merging scRNA‐seq and scATAC‐seq datasets, accurate data integration remains a challenge, particularly when investigating cell‐type‐specific TRNs. By examining gene expression and chromatin accessibility simultaneously in 16,670 Arabidopsis root tip nuclei, the TRNs are reconstructed that govern root tip development under osmotic stress. In contrast to commonly used computational integration at cell‐type level, 12,968 peak‐to‐gene linkage is captured at the bona fide single‐cell level and construct TRNs at an unprecedented resolution. Furthermore, the unprecedented datasets allow to more accurately reconstruct the coordinated changes of gene expression and chromatin states during cellular state transition. During root tip development, chromatin accessibility of initial cells precedes gene expression, suggesting that changes in chromatin accessibility may prime cells for subsequent differentiation steps. Pseudo‐time trajectory analysis reveal that osmotic stress can shift the functional differentiation of trichoblast. Candidate stress‐related gene‐linked cis‐regulatory elements (gl‐cCREs) as well as potential target genes are also identified, and uncovered large cellular heterogeneity under osmotic stress.

: Numerous studies have investigated the risk factors of Alzheimer’s disease (AD); however, AD-risk factors related miRNAs were rarely reported. In this study, AD-risk factor related miRNAs of 105 Chinese individuals (45 AD patients and 60 cognitively normal controls) were investigated. The results showed that Hsa-miR-185-5p, Hsa-miR-20a-5p, and Hsa-miR-497-5p were related to AD and education, Hsa-miR-185-5p, Hsa-miR-181c-5p, Hsa-miR-664a-3p, Hsa-miR-27a-3p, Hsa-miR-451a, and Hsa-miR-320a were related to AD and depression. Target prediction of above miRNAs showed that these miRNAs were involved in the generation and clearance of amyloid-beta (Aβ), important molecules related to cognition, and disease-activated microglia response to AD. It is worth noting that Hsa-miR-185-5p was related to both education and depression, whose decreased expression pattern in AD patients was alleviated by education and enhanced by depression, and participates in Aβ generation and accumulation. Our results indicated that certain education and depression factors can contribute to AD progression by modulating miRNA expression, implying that preventive interventions might alter AD progression in Chinese patients.

Deer antlers constitute a unique mammalian model for the study of both organ formation in postnatal life and annual full regeneration. Previous studies revealed that these events are achieved through the proliferation and differentiation of antlerogenic periosteum (AP) cells and pedicle periosteum (PP) cells, respectively. As the cells resident in the AP and the PP possess stem cell attributes, both antler generation and regeneration are stem cell-based processes. However, the cell composition of each tissue type and molecular events underlying antler development remain poorly characterized. Here, we took the approach of single-cell RNA sequencing (scRNA-Seq) and identified eight cell types (mainly THY1⁺ cells, progenitor cells, and osteochondroblasts) and three core subclusters of the THY1⁺ cells (SC2, SC3, and SC4). Endothelial and mural cells each are heterogeneous at transcriptional level. It was the proliferation of progenitor, mural, and endothelial cells in the activated antler-lineage-specific tissues that drove the rapid formation of the antler. We detected the differences in the initial differentiation process between antler generation and regeneration using pseudotime trajectory analysis. These may be due to the difference in the degree of stemness of the AP-THY1⁺ and PP-THY1⁺ cells. We further found that androgen-RXFP2 axis may be involved in triggering initial antler full regeneration. Fully deciphering the cell composition for these antler tissue types will open up new avenues for elucidating the mechanism underlying antler full renewal in specific and regenerative medicine in general.

Soil salinization threatens the yield and quality of wheat. Roots are critical for the salt stress response, yet their cell‐type‐specific mechanisms remain unclear. We conducted the first single‐nucleus RNA sequencing analysis of wheat root tips from salt‐sensitive (CS) and ‐tolerant (DK) varieties under salt stress, profiling 188 270 high‐quality root cells. Seventeen cell types were identified and validated using reported marker genes and reference atlases. Cell‐type‐specific analyses found that root hair cells exhibited the strongest association with salt stress, with variety‐specific transcriptional changes potentially contributing to DK's superior salt tolerance. Comparative gene profiling of root hair cells highlighted that CS prioritized rapid stress signaling and osmolyte accumulation, whereas DK emphasized metabolic reprogramming and cellular repair mechanisms. Pseudotime analysis pinpointed TaGSTU1‐5B as a key candidate for wheat salt tolerance, and it was validated as improving salt tolerance by mediating ROS scavenging by overexpression. Additionally, subgenomic analysis revealed that salt stress enhanced asymmetric expression of the homeologs in polyploid wheat roots, and A‐ and D‐dominant homologs were more related to salt response. This study reports the first single‐cell atlas of salt‐stressed wheat roots, uncovering cell‐type‐specific and variety‐specific salt responses, providing novel insights into the molecular basis of salt adaptation and tolerance in wheat.