LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis.

Single-cell RNA-sequencing (scRNA-seq) has become a powerful tool for biomedical research by providing a variety of valuable information with the advancement of computational tools. Lineage analysis based on scRNA-seq provides key insights into the fate of individual cells in various systems. However, such analysis is limited by several technical challenges. On top of the considerable computational expertise and resources, these analyses also require specific types of matching data such as exogenous barcode information or bulk assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) data. To overcome these technical challenges, we developed a user-friendly computational algorithm called "LINEAGE" (label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis). Aiming to screen out endogenous markers of lineage located on mitochondrial reads from label-free scRNA-seq data to conduct lineage inference, LINEAGE integrates a marker selection strategy by feature subspace separation and de novo "low cross-entropy subspaces" identification. In this process, the mutation type and subspace-subspace "cross-entropy" of features were both taken into consideration. LINEAGE outperformed three other methods, which were designed for similar tasks as testified with two standard datasets in terms of biological accuracy and computational efficiency. Applied on a label-free scRNA-seq dataset of BRAF-mutated cancer cells, LINEAGE also revealed genes that contribute to BRAF inhibitor resistance. LINEAGE removes most of the technical hurdles of lineage analysis, which will remarkably accelerate the discovery of the important genes or cell-lineage clusters from scRNA-seq data.

The physiological functions of lymphangiocrine signals.

It has been demonstrated that the lymphatic system plays important roles in tissue development and the progress of diseases. Recent studies identified that lymphatic endothelial cells can secret many proteins with diverse functions. This article highlights the physiological significances of these lymphangiocrine signals in different tissues.

BCAA insufficiency leads to premature ovarian insufficiency via ceramide-induced elevation of ROS.

Premature ovarian insufficiency (POI) is a disease featured by early menopause before 40 years of age, accompanied by an elevation of follicle-stimulating hormone. Though POI affects many aspects of women's health, its major causes remain unknown. Many clinical studies have shown that POI patients are generally underweight, indicating a potential correlation between POI and metabolic disorders. To understand the pathogenesis of POI, we performed metabolomics analysis on serum and identified branch-chain amino acid (BCAA) insufficiency-related metabolic disorders in two independent cohorts from two clinics. A low BCAA diet phenotypically reproduced the metabolic, endocrine, ovarian, and reproductive changes of POI in young C57BL/6J mice. A mechanism study revealed that the BCAA insufficiency-induced POI is associated with abnormal activation of the ceramide-reactive oxygen species (ROS) axis and consequent impairment of ovarian granulosa cell function. Significantly, the dietary supplement of BCAA prevented the development of ROS-induced POI in female mice. The results of this pathogenic study will lead to the development of specific therapies for POI.

The Storage Conditions of High-Fat Diet Are the Key Factors for Diet-Induced Obesity and Liver Damage.

The diet-induced obesity (DIO) mouse model has been widely used for obesity studies. The effects of storage conditions on the composition of nutrients in high-fat diets (HFDs) and their impact on metabolic homeostasis have not been systemically investigated. In the current study, we tested the effects of HFDs stored under different conditions and found that mice fed a HFD stored in the fridge (HFDfri) gained less weight than those fed HFDs stored in the freezer (HFDfre). Further analysis revealed that changes in the relative abundance of medium-chain triglyceride (MCT) in the HFDfri, which have much lower intestinal absorption rates, contributed to the body weight differences. In contrast, exacerbated liver damage and elevated levels of unfolded protein response (UPR) was observed in the mice fed by HFDfri. Depletion of the UPR-regulated gene Nnmt alleviated liver damage via the inhibition of the integrated stress response (ISR). Our study, for the first time, provides evidence that HFD storage conditions can have a significant impact on both body weight changes and liver damage in the DIO model.

Identification of clinical and molecular features of recurrent serous borderline ovarian tumour.

Background: Serous borderline ovarian tumour (SBOT) is the most common type of BOT. Fertility sparing surgery (FSS) is an option for patients with SBOT, though it may increase the risk of recurrence. The clinical and molecular features of its recurrence are important and need to be investigated in detail. Methods: An internal cohort of 319 patients with SBOT was collected from Aug 1, 2009 to July 31, 2019 from the Obstetrics and Gynecology Hospital of Fudan University in China. An external cohort of 100 patients with SBOT was collected from Aug 1, 2009 to Nov 30, 2019 from the Shandong Provincial Hospital in China. The risk factors for the recurrence were identified by multivariate cox analysis. Several computational methods were tested to establish a prediction tool for recurrence. Whole genome sequencing, RNA-seq, metabolomics and lipidomics were used to understand the molecular characteristics of the recurrence of SBOT. Findings: Five factors were significantly correlated with SBOT recurrence in a Han population: micropapillary pattern, advanced stage, FSS, microinvasion, and lymph node invasion. A random forest-based online recurrence prediction tool was established and validated using an internal cohort and an independent external cohort for patients with SBOT. The multi-omics analysis on the original SBOT samples revealed that recurrence is related to metabolic regulation of immunological suppression. Interpretation: Our study identified several important clinical and molecular features of recurrent SBOT. The prediction tool we established could help physicians to estimate the prognosis of patients with SBOT. These findings will contribute to the development of personalised and targeted therapies to improve prognosis. Funding: JL was funded by MOST 2020YFA0803600, 2018YFA0801300, NSFC 32071138, and SKLGE-2118 to Jin Li; JY was funded by the Initial Project for Young and Middle-aged Medical Talents of Wuhan City, Hubei Province ([2014] 41); HH was funded by MOST 2019YFA0801900 and 2020YF1402600 to He Huang; JS was funded by NSFC 22,104,080; CG was funded by Natural Science Foundation of Shanghai 20ZR1408800 and NSFC82171633; BL was funded by Natural Science Foundation of Shanghai 19ZR1406800.

HCV poly U/UC sequence-induced inflammation leads to metabolic disorders in vulvar lichen sclerosis.

Vulvar lichen sclerosis (VLS) is a dermatologic disorder that affects women worldwide. Women with VLS have white, atrophic papules on the vulva. They suffer from life-long intense pruritus. Corticosteroids are the first-line of treatments and the most effective medicines for VLS. Although VLS has been speculated as an autoimmune disease for a long time, its pathogenesis and the molecular mechanism is largely unknown. We performed a comprehensive multi-omics analysis of paired samples from VLS patients as well as healthy donors. From the RNA-seq analysis, we found that VLS is correlated to abnormal antivirus response because of the presence of Hepatitis C Virus poly U/UC sequences. Lipidomic and metabolomic analysis revealed that inflammation-induced metabolic disorders of fatty acids and glutathione were likely the reasons for pruritus, atrophy, and pigment loss in the vulva. Thus, the present study provides an initial interpretation of the pathogenesis and molecular mechanism of VLS and suggests that metabolic disorders that affect the vulva may serve as therapeutic targets for VLS.

Stimuli-Responsive Hydrogels with Antibacterial Activity Assembled from Guanosine, Aminoglycoside, and a Bifunctional Anchor.

Multistimuli-responsive hydrogels with specific functions have attracted great interest for biomedical applications; however, these smart hydrogels usually require the presynthesis of macromolecular building blocks with multiple ligands and the integration of bioactive cargoes into the gels. Here, a multistimuli-responsive hydrogel with potent antibacterial activity by a combination of supramolecular assembly and iminoboronate chemistry is reported. The hydrogel consists of all-small-molecule building blocks including aminoglycoside, guanosine, potassium ion, and a bifunctional anchor bearing both boronic acid and aldehyde groups. Guanosines form quadruplexes in the presence of potassium ions via supramolecular assembly, and the bifunctional anchor connects aminoglycosides, a class of potent antibiotics to cis-diol groups on quadruplexes via dynamic iminoboronate chemistry, yielding a smart hydrogel containing abundant antibiotics. The hydrogel is sensitive to multistimuli such as heat, acids, oxidants, glucose and crown ether, which promote the release of antibiotics from the gels. Moreover, the prepared hydrogels show potent antibacterial activities both in vitro and in vivo. The results provide a new option to prepare antibacterial hydrogels with multistimuli responsiveness via facile chemistry using all-small-molecule building blocks.

A pH-responsive hydrogel with potent antibacterial activity against both aerobic and anaerobic pathogens.

Aminoglycosides are a family of antibiotics with a wide-spread antibacterial spectrum and high antibacterial activity. However, they are less effective against anaerobic pathogens due to the requirement of aerobic respiration to exert their antibacterial functions. Here, we prepared a pH-responsive hydrogel with potent antibacterial activities against both aerobic and anaerobic pathogens. The hydrogel was prepared by reacting oxidized dextran with aminoglycoside and an ornidazole analogue via an acid-labile Schiff base linkage. The prepared hydrogel was injectable, self-healing, biocompatible, and showed a pH-responsive drug release behavior. More importantly, the gel was efficient in killing both aerobic and anaerobic pathogens. This study provides a facile strategy to expand the antibacterial spectrum of aminoglycoside hydrogels.