Self-incompatibility (SI) is an intraspecific reproductive barrier widely present in angiosperms. The SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box (SLF) genes found in the Solanaceae, Plantaginaceae, Rosaceae, and Rutaceae. Recent studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box (SCF)SLF -mediated ubiquitin-proteasome system in a collaborative manner in Petunia, but how self-RNase functions largely remains mysterious. Here, we show that S-RNases form S-RNase condensates (SRCs) in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia hybrida. We further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs, which then sequester several actin-binding proteins, including the actin polymerization factor PhABRACL, the actin polymerization activity of which is reduced by S-RNase in vitro. Meanwhile, we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth inhibition. Taken together, our results demonstrate that phase separation of S-RNase promotes SI response in P. hybrida, revealing a new mode of S-RNase action.

Colorectal cancer (CRC) is the most prevalent malignancy of the digestive system. Glucose metabolism plays a crucial role in CRC development. However, the heterogeneity of glucose metabolic patterns in CRC is not well characterized. Here, we classified CRC into specific glucose metabolic subtypes and identified the key regulators. 2228 carbohydrate metabolism-related genes were screened out from the GeneCards database, 202 of them were identified as prognosis genes in the TCGA database. Based on the expression patterns of the 202 genes, three metabolic subtypes were obtained by the non-negative matrix factorization clustering method. The C1 subtype had the worst survival outcome and was characterized with higher immune cell infiltration and more activation in extracellular matrix pathways than the other two subtypes. The C2 subtype was the most prevalent in CRC and was characterized by low immune cell infiltration. The C3 subtype had the smallest number of individuals and had a better prognosis, with higher levels of NRF2 and TP53 pathway expression. Secreted frizzled-related protein 2 (SFRP2) and thrombospondin-2 (THBS2) were confirmed as biomarkers for the C1 subtype. Their expression levels were elevated in high glucose condition, while their knockdown inhibited migration and invasion of HCT 116 cells. The analysis of therapeutic potential found that the C1 subtype was more sensitive to immune and PI3K-Akt pathway inhibitors than the other subtypes. To sum up, this study revealed a novel glucose-related CRC subtype, characterized by SFRP2 and THBS2, with poor prognosis but possible therapeutic benefits from immune and targeted therapies.

Abstract The synovium, a thin layer of tissue that is adjacent to the joints and secretes synovial fluid, undergoes changes in aging that contribute to intense shoulder pain and other joint diseases. However, the mechanism underlying human synovial aging remains poorly characterized. Here, we generated a comprehensive transcriptomic profile of synovial cells present in the subacromial synovium from young and aged individuals. By delineating aging-related transcriptomic changes across different cell types and their associated regulatory networks, we identified two subsets of mesenchymal stromal cells (MSCs) in human synovium, which are lining and sublining MSCs, and found that angiogenesis and fibrosis-associated genes were upregulated whereas genes associated with cell adhesion and cartilage development were downregulated in aged MSCs. Moreover, the specific cell-cell communications in aged synovium mirrors that of aging-related inflammation and tissue remodeling, including vascular hyperplasia and tissue fibrosis. In particular, we identified forkhead box O1 (FOXO1) as one of the major regulons for aging differentially expressed genes (DEGs) in synovial MSCs, and validated its downregulation in both lining and sublining MSC populations of the aged synovium. In human FOXO1-depleted MSCs derived from human embryonic stem cells, we recapitulated the senescent phenotype observed in the subacromial synovium of aged donors. These data indicate an important role of FOXO1 in the regulation of human synovial aging. Overall, our study improves our understanding of synovial aging during joint degeneration, thereby informing the development of novel intervention strategies aimed at rejuvenating the aged joint.

Bifidobacteria are key gut commensals that confer various health benefits and are commonly used as probiotics. However, little is known about the population-level variation in gut bifidobacterial composition and its affecting factors. Therefore, we analyzed Bifidobacterium species with amplicon sequencing of the groEL gene on fecal samples of 1674 healthy individuals, who belonged to eight ethnic groups and resided in 60 counties/cities of 28 provinces across China. We found that the composition of the bifidobacterial community was associated with geographical factors, demographic characteristics, staple food type, and urbanization. First, geography, which reflects a mixed effect of other variables, explained the largest variation in the bifidobacterial profile. Second, middle adolescence (age 14–17) and age 30 were two key change points in the bifidobacterial community development, and a bifidobacterial community resembling that of adults occurred in middle adolescence, which is much later than the maturation of the whole gut microbial community at approximately age 3. Third, each ethnicity showed a distinct bifidobacterial profile, and the remarkable amount of unknown Bifidobacterium species in the Tibetan gut suggested undiscovered biodiversity. Fourth, wheat as the main staple food promoted the flourish of B. adolescentis and B. longum. Fifth, alpha diversity of the bifidobacterial community decreased with urbanization. Collectively, our findings provide insight into the environmental and host factors that shape the human gut bifidobacterial community, which is fundamental for precision probiotics.

Since its outbreak in December 2019, SARS-CoV-2 has spread rapidly across the world, posing significant threats and challenges to global public health. SARS-CoV-2, together with SARS-CoV and MERS-CoV, is a highly pathogenic coronavirus that contributes to fatal pneumonia. Understanding the similarities and differences at the transcriptome level between SARS-CoV-2, SARS-CoV, as well as MERS-CoV is critical for developing effective strategies against these viruses. In this article, we comparatively analyzed publicly available transcriptome data of human cell lines infected with highly pathogenic SARS-CoV-2, SARS-CoV, MERS-CoV, and lowly pathogenic HCoV-229E. The host gene expression profiles during human coronavirus (HCoV) infections were generated, and the pathways and biological functions involved in immune responses, antiviral efficacy, and organ damage were intensively elucidated. Our results indicated that SARS-CoV-2 induced a stronger immune response versus the other two highly pathogenic HCoVs. Specifically, SARS-CoV-2 induced robust type I and type III IFN responses, marked by higher upregulation of type I and type III IFNs, as well as numerous interferon-stimulated genes (ISGs). Further Ingenuity Pathway Analysis (IPA) revealed the important role of ISGs for impeding SARS-CoV-2 infection, and the interferon/ISGs could be potential targets for therapeutic interventions. Moreover, our results uncovered that SARS-CoV-2 infection was linked to an enhanced risk of multi-organ toxicity in contrast to the other two highly pathogenic HCoVs. These findings provided valuable insights into the pathogenic mechanism of SARS-CoV-2, which showed a similar pathological feature but a lower fatality rate compared to SARS-CoV and MERS-CoV.

Abstract Aging is a complex and heterogeneous process, raising important questions about how aging is differently impacted by underlying genetics and external factors. Recently, migrasomes, newly discovered organelles, have been identified to play important roles in various physiological and pathological processes by facilitating cell-to-cell communication. Thus far, their involvement in cellular senescence and aging remains largely unexplored. In this study, we aimed to investigate how migrasomes impact on cellular aging by leveraging multiple cellular senescence models, including replicatively senescent (RS), pathologically senescent and stress-induced senescent human mesenchymal stem cells (hMSCs), as well as RS human primary fibroblasts. In all cellular aging models, we detected an enhanced formation of migrasomes. Notably, migrasomes in senescent cells exhibited an accumulation of numerous aging hallmarks, such as dysfunctional mitochondria, endogenous retroviruses, and senescence-associated pro-inflammatory cytokines. Furthermore, we discovered that migrasomes derived from senescent cells can be taken up by young cells, thereby transferring aging signals and subsequently causing premature senescence phenotypes in recipient cells. Mechanistically, we found that treatment with migrasomes derived from senescent cells activated the innate immune response. Thus, our study sheds light on a pivotal role of migrasomes in mediating the contagiousness of aging.

The epigenetic modification 5-hydroxymethylcytosine (5hmC) plays a crucial role in the regulation of gene expression. Although some methods have been developed to detect 5hmC, direct genome-wide mapping of 5hmC at base resolution is still highly desirable. Herein, we proposed a single-step deamination sequencing (SSD-seq) method, designed to precisely map 5hmC across the genome at single-base resolution. SSD-seq takes advantage of a screened engineered human apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (A3A) protein, known as eA3A-v10, to selectively deaminate cytosine (C) and 5-methylcytosine (5mC) but not 5hmC. During sequencing, the deaminated C and 5mC are converted to uracil (U) and thymine (T), read as T in the sequencing data. However, 5hmC remains unaffected by eA3A-v10 and is read as C during sequencing. Consequently, the presence of C in the sequence reads indicates the original 5hmC. We applied SSD-seq to generate a base-resolution map of 5hmC in human lung tissue. Our findings revealed that 5hmC was predominantly localized to CpG dinucleotides. Furthermore, the base-resolution map of 5hmC generated by SSD-seq demonstrated a strong correlation with prior ACE-seq results. The advantages of SSD-seq are its single-step process, absence of bisulfite treatment or DNA glycosylation, cost effectiveness, and ability to detect and quantify 5hmC directly at single-base resolution.

BackgroundMetabolic homeostasis is closely related to early impairment of cell fate determination and embryo development. The protein kinase mechanistic target of rapamycin (mTOR) is a key regulator of cellular metabolism in the body. Inhibition of mTOR signaling in early embryo causes postimplantation development failure, yet the mechanisms are still poorly understood.MethodsPregnancy mice and preimplantation mouse embryo were treated with mTOR inhibitor in vivo and in vitro respectively, and subsequently examined the blastocyst formation, implantation, and post-implantation development. We used immunofluorescence staining, RNA-Seq smart2, and genome-wide bisulfite sequencing technologies to investigate the impact of mTOR inhibitors on the quality, cell fate determination, and molecular alterations in developing embryos.ResultsWe showed mTOR suppression during preimplantation decreases the rate of blastocyst formation and the competency of implantation, impairs the post implantation embryonic development. We discovered that blocking mTOR signaling negatively affected the transformation of 8-cell embryos into blastocysts and caused various deficiencies in blastocyst quality. These included problems with compromised trophectoderm cell differentiation, as well as disruptions in cell fate specification. mTOR suppression significantly affected the transcription and DNA methylation of embryos. Treatment with mTOR inhibitors increase lysosomal activation and disrupts the organization and dynamics of the actin cytoskeleton in blastocysts.ConclusionsThese results demonstrate that mTOR plays a crucial role in 8-cell to blastocyst transition and safeguards embryo quality during early embryo development.

Bcakground: Pediatric acute megakaryoblastic leukemia (AMKL) without Down syndrome (DS) is a genetically heterogenous myeloid malignancy and with dismal prognosis. Refractory and relapse remains a major challenge. Given to the young age distribution of AMKL and high frequency of abandonment in middle-income countries, we conducted a multicenter clinical trial (ChiCTR1800015875) in aims to lower the intensity of induction while without compromise the remission rate and survival. Methods: From June 2018 to December 2022, there were consecutively 43 cases with de novo non-DS AMKL, which accounted for 7.6% cases of acute myeloid leukemia (AML) during the same period, enrolled in this trial. All the patients received at least one cycle of low-dose induction with HAG regimen (homoharringtonine 1 mg/m 2, intravenous daily, days 1-7; cytarabine 10 mg/m 2, subcutaneously every 12 hours, 20 doses, and G-CSF 5µ/kg subcutaneous, daily, 10 doses) followed by 3 to 4 courses of intensive chemotherapy or HSCT as post-remission consolidation. Besides conventional molecule testing, RNA-sequencing and whole exon sequencing (WES) were performed as well to reveal underlying genetic landscape of this type of disease. Results: The median age of the 43 patients at diagnosis was 18.5 (range 4-114) months. The median while blood cell (WBC) counts and platelet at diagnosis were 17.2×10 9/L (range 1.8-105.7 ×10 9/L) and 36.5×10 9/L (range 4-472 ×10 9/L), respectively. Among them, 39.5% of cases exhibited hepatosplenomegaly. A diversity of genetic fusions and mutations were uncovered. The recurrent fusions in this cohort include CBFA2T3-GLIS2 (16.3%), MLLr (11.6%), NUP98-(9.3%), RBM15-MKL1 (7.0%), HOX fusions (7.0%) and PICALM-MLLT10 (4.7%). Other non-recurrent fusions accounted for 18.6% (Figure 1A). The common mutations detected in our pediatric AMKL were JAK2, NRAS, MPL, BCOR, CTCF, KRAS and PTPN11. Regarding treatment response, 20 of 43 cases (46.5%) attained complete remission (CR) or complete remission with incomplete blood cell recovery (CRi) after one cycle of induction. Among the 20 cases, 9 of them got minimal residual disease (MRD) negative by flow cytometry. Ten patients (23.2%) achieved partial remission (PR) while 13 patients (30.2%) showed no response (NR) to treatment. Thirty-one patients continued with another cycle of the same regimen and 21 of the 28 cases who were available for evaluation (75.0%) attained CR/CRi. Disease relapse was observed in 16/43 (37.2%) cases, with 7/43 (16.2%) patients relapsed after transplantation. The 3-year overall survival (OS) and event-free survival (EFS) were 49.6±8.2% and 29.5±7.1%, respectively (Figure 1B). In total, more than half of patients (22/43, 51.5%) underwent HSCT. The 3-year OS of transplant group and chemotherapy group were 57.9±11.7% versus 39.5±11.2%, P=0.036. As genetic characteristics often predict treatment response and prognosis, we wonder which subgroup could benefit from the reduced intensive induction. We further compared the features of patients who got CR/CRi after induction I with those achieved PR/NR. Interestingly, we found more patients with adverse fusions in PR/NR group, such as CBFA2T3-GLIS2 (26.0% vs. 5.0%), NUP98- (17.4% vs. 0%), MLLs (13.0% vs. 10.0%), and RBM15-MKL1 (8.7% vs. 5.0%); while other non-recurrent fusions were more common in CR/CRi group (4.3% vs. 35.0%). Two thirds of patients (67.4%) experienced refractory or relapse and almost half of them harbored adverse fusions or mutations such as CBFA2T3-GLIS2, MLLr, NUP98- fusions, NRAS and PTPN11. On the other hand, 14 patients without refractory or relapse had genetic features with more JAK2 and MPL mutations. No treatment-related mortality (TRM) occurred during induction. Only one patient with KRAS mutation died of infection after consolidation III. Conclusion: Insight into the genetic and molecular landscape improved our understanding of pediatric AMKL. Distinct molecular features can serve as a tool to tailor the therapy. Though treatment still lags behind and novel therapy is urgent for the adverse subgroups, our low-dose induction with HAG regimen could benefit for a subgroup with non-recurrent fusions, which showed efficiency while is tolerable for the young age group. Based on our results, we provide an induction option for these AMKL patients, especially for those in the middle-income countries.

Backgroun d: Intensive chemotherapy is recommended for remission induction of pediatric acute myeloid leukemia (AML). However, life-threatening complications are common especially in vulnerable populations. We investigated whether a low-dose chemotherapy (LDC) regimen would be noninferior to a standard-dose chemotherapy (SDC) regimen for induction remission.This study also aimed to assess whether LDC is not inferior to SDC in terms of survival outcomes. Methods: We conducted a randomized, noninferiority study in children with AML who were admitted to 14 medical centers in China. Patients were randomly assigned to receive two remission-induction courses of either low-dose chemotherapy (LDC) (cytarabine 10 mg/m 2, subcutaneous, q12 hours, 20 doses; mitoxantrone or idarubicin 5 mg/m 2, intravenous, days 1, 3 and 5; and G-CSF 5 mcg/kg, subcutaneous, daily, 10 doses) (n = 246) or standard-dose chemotherapy (SDC) (cytarabine 100 mg/m 2, intravenous, q12 hours, 20 doses; daunomycin 50 mg/m 2, intravenous, days 1, 3, 5; and etoposide 100 mg 2, intravenous, days 1 to 5) (n = 251). Depending on the risk of relapse, patients in complete remission (CR) in both arms received two to three cycles of intensive consolidation chemotherapy and/or underwent hematopoietic stem cell transplantation (HSCT). The primary endpoint was to compare CR rates in patients randomized to the LDC or SDC regimens. The secondary endpoints were to determine the safety of the LDC regimen and to compare the time to platelet and neutrophil count recovery in the two groups. Finally, in a multivariate analysis, we determined the impact of the type of remission induction on the outcome. This trial is registered at chictr.org as # ChiCTR-18000015883 and has been completed. Results: From June 2018 to June 2022,497 participants aged <18 years with de novo AML were randomized. Patients with Down syndrome, promyelocytic leukemia, or megakaryoblastic leukemia were excluded. There were no significant differences in age, sex, or genotype between the two arms. Complete morphologic remission with or without platelet recovery (CR/CRi) was attained in 72.8% and 70.3% of patients assigned to the LDC and SDC arms, respectively, after Induction I and in 95.5% and 95.7%, respectively, after Induction II ( P = .545 for Induction I and .898 for Induction II). Residual disease < 0.1%, as measured by flow cytometry, was observed in 54.8% and 58.9% of patients in the LDC and SDC arms, respectively, after Induction I and in 85.9% and 84.4%, respectively, after Induction II ( P = .229 for Induction I and .827 for induction II). Median time to neutrophil count recovery was 15 days for patients in the LDC arm vs. 22 days for those in the SCD arm after Induction I ( P< .001) and 12 days vs. 18 days for patients in the respective arms after Induction II ( P < .001). Median time to platelet count recovery was 13 days for patients in the LDC arm vs. 19 days for those in the SCD arm after Induction I ( P < .001) and 3 days vs. 8 days for patients in the respective arms after Induction II ( P< .001). Grade 3 and 4 toxicities were significantly lower in patients in the LDC arm than those in the SDC arm. In Induction I, febrile neutropenia occurred in 75.2% and 93.2% ( P < .001), colitis in 3.7% and 10.7% ( P = .003), and gastrointestinal hemorrhage in 0.4% and 4.4% ( P = .006) in the LDC and SDC arms, respectively. In Induction II, febrile neutropenia occurred in 34.4% and 66.9% ( P < .001), lung or sinus infection in 2.8% and 9.3% ( P = .008), and sepsis in 3.3% and 10.7% ( P = .004), in the LDC and SDC arms, respectively. There was no significant difference in treatment-related mortality between the two treatment arms ( P = 204).Compared to patients in the SDC arm, patients in the LDC arm had noninferior 3-year EFS of 61.9% (95% CI: 55.7 to 68.8) vs. 62.2% (95% CI: 56.1 to 68.8)( P = .994) (Figure 1A), and 3-year OS of 81.0% (95% CI: 75.7 to 86.6) vs. 83.2% (95% CI: 78.2 to 88.5) ( P = .485) (Figure 1B). In a multivariate analysis considering known prognostic indicators in pediatric AML, treatment arm was not associated with outcome. Conclusion: In children with AML, remission induction with a low-dose chemotherapy regimen with concurrent G-CSF administration was well tolerated and was associated with CR, EFS, and OS rates that were not inferior to those of patients treated with a standard chemotherapy regimen.