Urinary microbiota and serum metabolite analysis in patients with diabetic kidney disease.

Background: Diabetic kidney disease (DKD) is a common and potentially fatal consequence of diabetes. Chronic renal failure or end-stage renal disease may result over time. Numerous studies have demonstrated the function of the microbiota in health and disease.

Microbiome and metabolome analysis to clarify the interaction between the urine microbiota and serum metabolites in Chinese patients with immunoglobulin A nephropathy.

Background: The bacterial and metabolic networks in immunoglobin A nephropathy (IgAN), the most common type of primary chronic glomerulonephritis worldwide, have not been extensively studied. To help develop better methods for the diagnosis, treatment, and prognosis of IgAN, we characterized the alterations of the urinary microbiome and serum metabolome in patients with IgAN.

Methods: We analyzed serum and urine samples from Chinese patients with IgAN and healthy controls (HCs) using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S ribosomal RNA gene sequencing.

Combined proteomics and single cell RNA-sequencing analysis to identify biomarkers of disease diagnosis and disease exacerbation for systemic lupus erythematosus.

Introduction: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease for which there is no cure. Effective diagnosis and precise assessment of disease exacerbation remains a major challenge.

Methods: We performed peripheral blood mononuclear cell (PBMC) proteomics of a discovery cohort, including patients with active SLE and inactive SLE, patients with rheumatoid arthritis (RA), and healthy controls (HC).

Absolute quantification and characterization of oxylipins in lupus nephritis and systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with multi-organ inflammation and defect, which is linked to many molecule mediators. Oxylipins as a class of lipid mediator have not been broadly investigated in SLE. Here, we applied targeted mass spectrometry analysis to screen the alteration of oxylipins in serum of 98 SLE patients and 106 healthy controls.

Integrated single-cell analyses decode the developmental landscape of the human fetal spine.

The spine has essential roles in supporting body weight, and passaging the neural elements between the body and the brain. In this study, we used integrated single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing analyses to reveal the cellular heterogeneity, lineage, and transcriptional regulatory network of the developing human spine. We found that  + + fibroblasts with stem cell characteristics could differentiate into chondrocytes by highly expressing the chondrogenic markers and .

Gene regulatory network study of rheumatoid arthritis in single-cell chromatin landscapes of peripheral blood mononuclear cells.

Objectives: Assays for transposase-accessible chromatin with single-cell sequencing (scATAC-seq) contribute to the progress in epigenetic studies. The purpose of our project was to discover the transcription factors (TFs) that were involved in the pathogenesis of rheumatoid arthritis (RA) at a single-cell resolution using epigenetic technology.

Methods: Peripheral blood mononuclear cells of seven RA patients and seven natural controls were extracted nuclei suspensions for library construction.

Single-Cell RNA and ATAC Sequencing Reveal Hemodialysis-Related Immune Dysregulation of Circulating Immune Cell Subpopulations.

Background: An increased risk of infection, malignancy, and cardiovascular diseases in maintenance hemodialysis patients is associated with hemodialysis-related immunity disturbances. Although defects in T-lymphocyte-dependent immune responses and preactivation of antigen-presenting cells have been documented in hemodialysis patients, the effects of long-term hemodialysis on the transcriptional program and chromosomal accessibility of circulating immune cell subpopulations remain poorly defined.

Methods: We integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to characterize the transcriptome profiles of peripheral mononuclear cells (PBMCs) from healthy controls and maintenance hemodialysis patients.

Multiomics landscape of the autosomal dominant osteopetrosis type II disease-specific induced pluripotent stem cells.

Background: Autosomal dominant osteopetrosis type II (ADO2) is a genetically and phenotypically metabolic bone disease, caused by osteoclast abnormalities. The pathways dysregulated in ADO2 could lead to the defects in osteoclast formation and function. However, the mechanism remains elusive.

Intestinal microbiome and metabolome analyses reveal metabolic disorders in the early stage of renal transplantation.

Renal transplantation is the most effective treatment for end-stage renal disease, but the long-term prognosis of organs after transplantation is not ideal. In recent years, the importance of gut microbes and metabolites in the study of disease mechanisms has gradually received attention. However, the coordination between gut microbes and the metabolism of renal transplant patients needs further study.

Analysis of gut microbiota and metabolites in patients with rheumatoid arthritis and identification of potential biomarkers.

Rheumatoid arthritis (RA) is an autoimmune disease described by joint destruction, synovitis and pannus formation. The gut microbiota acts as an environmental factor that plays an important role in RA, but little research regarding the etiopathogenic mechanisms of the microbiome in RA has been carried out. We used an integrated approach of 16S rRNA gene sequencing and ultrahigh-performance liquid chromatography-mass spectrometry-based metabolomics to analyze the structure and diversity of the intestinal flora and metabolites of the gut microbiota in RA patients compared with healthy subjects.

Label-free quantitative proteomic and phosphoproteomic analyses of renal biopsy tissues in membranous nephropathy.

Purpose: Membranous nephropathy (MN) is a common cause of nephrotic syndrome in adults. However, the underlying mechanisms of its occurrence and development are not completely clear. Thus, it is essential to explore the mechanisms.

The Landscape and Potential Regulatory Mechanism of Lysine 2-Hydroxyisobutyrylation of Protein in End-Stage Renal Disease.

Background: Acetylation has a vital role in the pathogenesis of end-stage renal disease (ESRD). Lysine 2-hydroxyisobutyrylation (Khib) is a novel type of acetylation. In this study, we aimed to reveal the key features of Khib in peripheral blood monocytes (PBMCs) of patients with ESRD.

Integrated analysis of competing endogenous RNA networks in peripheral blood mononuclear cells of systemic lupus erythematosus.

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease with a complicated pathogenesis, and its aetiology has not been clearly unveiled. The lack of effective diagnosis and treatment methods makes it necessary to explore the molecular mechanism of SLE. We aimed to identify some critical signalling pathways and key competing endogenous RNAs (ceRNAs) underlying the molecular mechanism of SLE and to map out the systematic signalling networks by integrating the data on different kinds of RNAs.

Integrative multiplatform-based molecular profiling of human colorectal cancer reveals proteogenomic alterations underlying mitochondrial inactivation.

Mitochondria play leading roles in initiation and progression of colorectal cancer (CRC). Proteogenomic analyses of mitochondria of CRC tumor cells would likely enhance our understanding of CRC pathogenesis and reveal new independent prognostic factors and treatment targets. However, comprehensive investigations focused on mitochondria of CRC patients are lacking.

Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndrome.

Background: Trisomy 18 syndrome (Edwards syndrome, ES) is a type of aneuploidy caused by the presence of an extra chromosome 18. Aneuploidy is the leading cause of early pregnancy loss, intellectual disability, and multiple congenital anomalies. The research of trisomy 18 is progressing slowly, and the molecular characteristics of the disease mechanism and phenotype are still largely unclear.

Multi-omics analyses of human colorectal cancer revealed three mitochondrial genes potentially associated with poor outcomes of patients.

Background: The identification of novel functional biomarkers is essential for recognizing high-risk patients, predicting recurrence, and searching for appropriate treatment. However, no prognostic biomarker has been applied for colorectal cancer (CRC) in the clinic.

Methods: Integrated with transcriptomic data from public databases, multi-omics examinations were conducted to search prognostic biomarkers for CRC.

The Chromatin Accessibility Landscape of Peripheral Blood Mononuclear Cells in Patients With Systemic Lupus Erythematosus at Single-Cell Resolution.

Objective: Systemic lupus erythematosus (SLE) is a complex autoimmune disease, and various immune cells are involved in the initiation, progression, and regulation of SLE. Our goal was to reveal the chromatin accessibility landscape of peripheral blood mononuclear cells (PBMCs) in SLE patients at single-cell resolution and identify the transcription factors (TFs) that may drive abnormal immune responses.

Methods: The assay for transposase accessible chromatin in single-cell sequencing (scATAC-seq) method was applied to map the landscape of active regulatory DNA in immune cells from SLE patients at single-cell resolution, followed by clustering, peak annotation and motif analysis of PBMCs in SLE.

Single-cell sequencing reveals the potential oncogenic expression atlas of human iPSC-derived cardiomyocytes.

Human induced pluripotent stem cells (iPSCs) are important source for regenerative medicine. However, the links between pluripotency and oncogenic transformation raise safety issues. To understand the characteristics of iPSC-derived cells at single-cell resolution, we directly reprogrammed two human iPSC lines into cardiomyocytes and collected cells from four time points during cardiac differentiation for single-cell sequencing.

Quantitative proteomics analysis of lysine 2-hydroxyisobutyrylation in IgA nephropathy.

Background: Protein posttranslational modification is an indispensable regulatory element that can fine-tune protein functions and regulate diverse cellular processes. Lysine 2-hydroxyisobutyrylation (Khib) is a protein posttranslational modification that was recently identified and is thought to play a role in a wide variety of active cellular functions.

Methods: In this report, for the first time, we comparatively studied the 2-hydroxyisobutyrylation proteome in peripheral blood mononuclear cells from a biopsy-proven immunoglobulin A nephropathy (IgAN) group and a normal control group based on liquid chromatography-tandem mass spectrometry.

Integrated proteome and phosphoproteome analyses of peripheral blood mononuclear cells in primary Sjögren syndrome patients.

Primary Sjögren syndrome (pSS) is a common autoimmune disease. Here, we performed the first proteome and phosphoproteome analyses of peripheral blood mononuclear cells in pSS patients to obtain a comprehensive profile and identify the potential crucial proteins and pathways for the screening and evaluation of pSS patients. Peripheral blood mononuclear cells from 8 pSS-confirmed patients (American-European Consensus Group Criteria, 2002) and 10 normal controls were selected.

Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay.

A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) is a suitable method for revealing such networks. Thus, scATAC-seq was applied to define the landscape of active regulatory DNA in AS.

Microbiome and Metabolome Analyses Reveal the Disruption of Lipid Metabolism in Systemic Lupus Erythematosus.

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that affects thousands of people worldwide. Recently, alterations in metabolism and gut microbiome have emerged as key regulators of SLE pathogenesis. However, it is not clear about the coordination of gut commensal bacteria and SLE metabolism.

The potential role of tRNAs and small RNAs derived from tRNAs in the occurrence and development of systemic lupus erythematosus.

Background: Emerging evidence has shown the involvement of dysregulated transfer RNAs (tRNAs) and small RNAs derived from transfer RNAs (tsRNAs) in the pathophysiology of human diseases. The role of tRNAs and tsRNAs in systemic lupus erythematosus (SLE) remains unclear. Therefore, this study aims to investigate the possible regulatory roles of tRNAs and tsRNAs in the pathological mechanism of SLE.

Advances in applying of multi-omics approaches in the research of systemic lupus erythematosus.

Systemic lupus erythematosus (SLE), an autoimmune disease that causes multiorgan injury, has an unclear etiology and complex pathogenesis. Numerous studies have found abnormal alterations in mRNAs, proteins and/or metabolites in SLE patients. These findings have extended our understanding of the pathogenesis of SLE.

Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy.

Posttranslational modifications (PTMs) to histones such as lysine crotonylation are classified as epigenetic changes. Lysine crotonylation participates in various cellular processes and occurs in active promoters, directly accelerating transcription. The present study performed a proteomics analysis of crotonylation between healthy controls and patients with immunoglobulin A (IgA) nephropathy using tandem mass spectrometry and high‑resolution liquid chromatography.