Single-Cell Genomics for Investigating Pathogenesis of Inflammatory Diseases

Roles of PEG10 in cancer and neurodegenerative disorder (Review)

Paternally expressed gene 10 (PEG10) is an imprinting gene. In addition to its known roles in placental development, as well as mouse embryonic stem cell and trophoblast stem cell differentiation, PEG10 has recently been shown to have significance in cancers. High expression of PEG10 is observed in various cancer types and is associated with poor prognosis. Of note, disruption of PEG10 expression leads to increased apoptosis, as well as decreased proliferation, invasion and migration of cancer cells. PEG10 is expected to become a target for cancer and neurodegenerative disorder therapy. This article reviewed the latest progress in the role of PEG10 in cancers.

Inflammatory Cell Interactions in the Rotator Cuff Microenvironment: Insights From Single-Cell Sequencing

Rotator cuff injuries are a common cause of shoulder pain and dysfunction, with chronic inflammation complicating recovery. Recent advances in single-cell RNA sequencing (scRNA-seq) have provided new insights into the immune cell interactions within the rotator cuff microenvironment during injury and healing. This review focuses on the application of scRNA-seq to explore the roles of immune and nonimmune cells, including macrophages, T-cells, fibroblasts, and myofibroblasts, in driving inflammation, tissue repair, and fibrosis. We discuss how immune cell crosstalk and interactions with the extracellular matrix influence the progression of healing or pathology. Single-cell analyses have identified distinct molecular signatures associated with chronic inflammation, which may contribute to persistent tissue damage. Additionally, we highlight the therapeutic potential of targeting inflammation in rotator cuff repair, emphasizing personalized medicine approaches. Overall, the integration of scRNA-seq in studying rotator cuff injuries enhances our understanding of the cellular mechanisms involved and offers new perspectives for developing targeted treatments in regenerative medicine.

Differential pathological changes in colon microenvironments in acute and chronic mouse models of inflammatory bowel disease

Inflammatory bowel disease is a chronic condition characterized by inflammation of the gastrointestinal tract, resulting from an abnormal immune response to normal stimuli, such as food and intestinal flora. Since the etiology of this disease remains largely unknown, murine models induced by the consumption of dextran-sodium sulfate serve as a pivotal tool for studying colon inflammation. In this study, we employed both acute and chronic colitis mouse models induced by varying durations of dextran-sodium sulfate consumption to investigate the pathological and immunologic characteristics throughout the disease course. During the acute phase, activated innate inflammation marked by M1 macrophage infiltration was prominent. In contrast, the chronic phase was characterized by tissue remodeling, with a significant increase in M2 macrophages and lymphocytes. RNA-sequencing revealed genetic changes in acute and chronic colitis, marked by the maintenance of genomic integrity in the acute phase and extracellular matrix dynamics in the chronic phase. These phase-specific alterations reflect the multifaceted physiological processes involved in the initiation and progression of inflammation in the large intestine, underscoring the necessity for distinct experimental approaches for each phase. The findings demonstrate that the factors shaping the large intestinal immune microenvironment change specifically during the acute and chronic phases of experimental inflammatory bowel disease, highlighting the importance of developing therapeutic strategies that align with the disease course.

Therapeutic single-cell landscape: methotrexate exacerbates interstitial lung disease by compromising the stemness of alveolar epithelial cells under systemic inflammation

BACKGROUND

Interstitial lung disease (ILD) poses a serious threat in patients with rheumatoid arthritis (RA). However, the impact of cornerstone drugs, including methotrexate (MTX) and TNF inhibitor, on RA-associated ILD (RA-ILD) remains controversial.

METHODS

Using an SKG mouse model and single-cell transcriptomics, we investigated the effects of MTX and TNF blockade on ILD.

FINDINGS

Our study revealed that MTX exacerbates pulmonary inflammation by promoting immune cell infiltration, Th17 activation, and fibrosis. In contrast, TNF inhibitor ameliorates these features and inhibits ILD progression. Analysis of data from a human RA-ILD cohort revealed that patients with ILD progression had persistently higher systemic inflammation than those without progression, particularly among the subgroup undergoing MTX treatment.

INTERPRETATION

These findings highlight the need for personalized therapeutic approaches in RA-ILD, given the divergent outcomes of MTX and TNF inhibitor.

FUNDING

This work was funded by GENINUS Inc., and the National Research Foundation of Korea, and Seoul National University Hospital.

Molecular profiling and therapeutic tailoring to address disease heterogeneity in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a chronic, heterogeneous, systemic autoimmune disease characterized by autoantibody production, complement activation, and immune complex deposition. SLE predominantly affects young, middle-aged, and child-bearing women with episodes of flare-up and remission, although it affects males at a much lower frequency (female: male; 7:1 to 15:1). Technological and molecular advancements have helped in patient stratification and improved patient prognosis, morbidity, and treatment regimens overall, impacting quality of life. Despite several attempts to comprehend the pathogenesis of SLE, knowledge about the precise molecular mechanisms underlying this disease is still lacking. The current treatment options for SLE are pragmatic and aim to develop composite biomarkers for daily practice, which necessitates the robust development of novel treatment strategies and drugs targeting specific responsive pathways. In this communication, we review and aim to explore emerging therapeutic modalities, including multiomics-based approaches, rational drug design, and CAR-T-cell-based immunotherapy, for the management of SLE.

Comparative Assessment of Risk and Turn-Around Time between Sequence-Based Typing and Next-Generation Sequencing for HLA Typing

This study compared laboratory risk and turn-around time (TAT) between sequence-based typing (SBT) and next-generation sequencing (NGS) for human leukocyte antigen (HLA) typing. For risk assessment, we utilized the risk priority number (RPN) score based on failure mode and effect analysis (FMEA) and a risk acceptability matrix (RAM) according to the Clinical Laboratory Standards Institute (CLSI) guidelines (EP23-A). Total TAT was documented for the analytical phase, and hands-on time was defined as manual processes conducted by medical technicians. NGS showed a significantly higher total RPN score than SBT (1169 vs. 465). NGS indicated a higher mean RPN score, indicating elevated severity and detectability scores in comparison to SBT (RPN 23 vs. 12, p = 0.001; severity 5 vs. 3, p = 0.005; detectability 5 vs. 4, p < 0.001, respectively). NGS required a greater number of steps than SBT (44 vs. 25 steps), all of which were acceptable for the RAM. NGS showed a longer total TAT, total hands-on time, and hands-on time per step than SBT (26:47:20 vs. 12:32:06, 03:59:35 vs. 00:47:39, 00:05:13 vs. 00:01:54 hh:mm:ss, respectively). Transitioning from SBT to NGS for HLA typing involves increased risk and an extended TAT. This study underscored the importance of evaluating these factors to optimize laboratory efficiency in HLA typing.

Unlocking biological mechanisms with integrative functional genomics approaches

Reverse genetics offers precise functional insights into genes through the targeted manipulation of gene expression followed by phenotypic assessment. While these approaches have proven effective in model organisms such as Saccharomyces cerevisiae, large-scale genetic manipulations in human cells were historically unfeasible due to methodological limitations. However, recent advancements in functional genomics, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-based screening technologies and next-generation sequencing platforms, have enabled pooled screening technologies that allow massively parallel, unbiased assessments of biological phenomena in human cells. This review provides a comprehensive overview of cutting-edge functional genomic screening technologies applicable to human cells, ranging from short hairpin RNA screens to modern CRISPR screens. Additionally, we explore the integration of CRISPR platforms with single-cell approaches to monitor gene expression, chromatin accessibility, epigenetic regulation, and chromatin architecture following genetic perturbations at the omics level. By offering an in-depth understanding of these genomic screening methods, this review aims to provide insights into more targeted and effective strategies for genomic research and personalized medicine.

Psoriasis and Psoriatic Arthritis-Associated Genes, Cytokines, and Human Leukocyte Antigens

In recent years, research has intensified in exploring the genetic basis of psoriasis (PsO) and psoriatic arthritis (PsA). Genome-wide association studies (GWASs), including tools like ImmunoChip, have significantly deepened our understanding of disease mechanisms by pinpointing risk-associated genetic loci. These efforts have elucidated biological pathways involved in PsO pathogenesis, particularly those related to the innate immune system, antigen presentation, and adaptive immune responses. Specific genetic loci, such as TRAF3IP2, REL, and FBXL19, have been identified as having a significant impact on disease development. Interestingly, different genetic variants at the same locus can predispose individuals to either PsO or PsA (e.g., IL23R and deletion of LCE3B and LCE3C), with some variants being uniquely linked to PsA (like HLA B27 on chromosome 6). This article aims to summarize known and new data on the genetics of PsO and PsA, their associated genes, and the involvement of the HLA system and cytokines.

Single-cell transcriptome analysis reveals periodontal ligament fibroblast heterogeneity with distinct IL-1β and RANKL expression in periodontitis

Periodontitis (PD) is an inflammatory disease with alveolar bone destruction by osteoclasts (OCs). In PD, both inflammation and OC activation are significantly influenced by periodontal ligament fibroblasts (PDL-Fib). Yet, whether PDL-Fib has heterogeneity and whether distinct PDL-Fib subsets have specific functions have not been investigated. In this study, we discovered the complexity of PDL-Fib in PD, utilizing single-cell RNA sequencing data from human PD patients. We identified distinct subpopulations of PDL-Fib: one expressing interleukin-1 beta (IL-1β) and another expressing the receptor activator of nuclear factor-kappa B ligand (RANKL), both crucial in OC differentiation and bone resorption. In periodontal tissues of mice with PD, active IL-1β, cleaved caspase 1, and nucleotide-binding oligomerization domain-like receptor 3 (NLPR3) were significantly elevated, implicating the NLRP3 inflammasome in IL-1β production. Upon stimulation of PDL-Fib with LPS from Porphyromonas gingivalis (pg), the most well-characterized periodontal bacteria, a more rapid increase in IL-1β, followed by RANKL induction, was observed. IL-1β and tumor necrosis factor alpha (TNF-α), another LPS-responsive cytokine, effectively increased RANKL in PDL-Fib, suggesting an indirect effect of pgLPS through IL-1β and TNF-α on RANKL induction. Immunohistological analyses of mouse periodontal tissues also showed markedly elevated levels of IL-1β and RANKL upon PD induction and displayed separate locations of IL-1β-expressing PDL-Fib and RANKL-expressing PDL-Fib in PD. The heterogenic feature of fibroblasts expressing IL-1β and RANKL was also mirrored in our combined cross-tissue single-cell RNA sequencing datasets analysis. In summary, our study elucidates the heterogeneity of PDL-Fib, highlighting distinct functional groups for producing RANKL and IL-1β, which collectively promote OC generation and bone destruction in PD.

Adipose tissue macrophage heterogeneity in the single-cell genomics era

It is now well-accepted that obesity-induced inflammation plays an important role in the development of insulin resistance and type 2 diabetes. A key source of the inflammation is the murine epididymal and human visceral adipose tissue. The current paradigm is that obesity activates multiple proinflammatory immune cell types in adipose tissue, including adipose-tissue macrophages (ATMs), T Helper 1 (Th1) T cells, and natural killer (NK) cells, while concomitantly suppressing anti-inflammatory immune cells such as T Helper 2 (Th2) T cells and regulatory T cells (Tregs). A key feature of the current paradigm is that obesity induces the anti-inflammatory M2 ATMs in lean adipose tissue to polarize into proinflammatory M1 ATMs. However, recent single-cell transcriptomics studies suggest that the story is much more complex. Here we describe the single-cell genomics technologies that have been developed recently and the emerging results from studies using these technologies. While further studies are needed, it is clear that ATMs are highly heterogeneous. Moreover, while a variety of ATM clusters with quite distinct features have been found to be expanded by obesity, none truly resemble classical M1 ATMs. It is likely that single-cell transcriptomics technology will further revolutionize the field, thereby promoting our understanding of ATMs, adipose-tissue inflammation, and insulin resistance and accelerating the development of therapies for type 2 diabetes.