Single-cell transcriptomics reveals apolipoprotein A4-mediated metabolic-immune reprogramming in lymphocytes during early obesity-related chronic kidney disease

Abstract

Obesity-induced metabolic inflammation is a key driver of chronic kidney disease (CKD), with immune dysregulation, particularly among lymphocytes, contributing to early disease pathology. To explore the role of apolipoprotein A4 (Apoa4) in regulating immune cell metabolism and function, we establish high-fat diet-induced obese (DIO) models using wild-type and Apoa4-knockout (KO) mice. KO mice exhibit exacerbated insulin resistance and renal lipid accumulation. Single-cell RNA sequencing reveals that Apoa4 deletion remodeled the renal immune-metabolic landscape. This remodeling broadly compromises the immune functions of T, NK, and B cells, even as it expands the proportions of cytotoxic Gzma+ NK cells and Derl3+ plasma cells. Mechanistically, Apoa4 deletion aggravates metabolic dysregulation and oxidative stress and downregulates the expression levels of key effector genes, including Ifng and Il1b. Furthermore, the regulatory network activities of key transcription factors, such as Lef1 and Runx3 in Cd8+ T cells; Irf8, T-bet, and Eomes in NK cells; and Tcf4, Lmo2, and Xbp1 in B cells, are perturbed. CellChat analysis predicts disruptions in pro-inflammatory (IFN-II and IL-1), immunoregulatory (FASLG), and metabolic regulatory (ENHO and ANGPTL) signaling, alongside enhanced IL-2-mediated suppression. These findings are corroborated by flow cytometry, immunofluorescence staining, and qPCR. Our results establish Apoa4 as a crucial regulator of lymphocyte metabolic and immune homeostasis in the early stages of obesity-associated CKD.

1. Introduction

Obesity-induced metabolic inflammation, insulin resistance and lipid deposition in the kidney are major contributors to the onset and progression of obesity-related chronic kidney disease (CKD) [1,2]. The increasing prevalence of obesity-related CKD has become a major global public health challenge [3]. The immune system plays a crucial role in maintaining immunological homeostasis in healthy kidneys, and its dysregulation, whether overactive or underactive, accelerates disease progression [4]. Recent advances in single-cell RNA sequencing (scRNA-seq) have revealed the intricate diversity of immune cell populations in both healthy and diseased kidneys [5–7], providing unprecedented insights into the heterogeneity of immune cells and their diverse roles in inflammation and tissue remodeling.

Immune cell activation and function are tightly regulated by environmental cues and intercellular interactions. For example, tissue-resident memory T cells and B cells rapidly activate and exhibit effector functions upon re-encountering antigens [8,9], whereas natural killer (NK) cells respond to stimulatory signals, becoming activated and directly exerting cytotoxic effects on target cells. These cells release pro-inflammatory mediators such as interferon-γ (IFN-γ) and tumor necrosis factor (TNF), which modulate innate immune cells, underscoring the critical role of lymphocytes in early inflammatory kidney disease [10]. The macrophage phenotype is dynamically regulated by the microenvironment, with M1 and M2 macrophages playing opposing roles in renal inflammation [11]. In CKD, immune cell activation is closely linked to the activation of signaling pathways, such as the MAPK signaling, NLRP3 inflammasome signaling, PI3K/Akt signaling, NF-κB signaling, JAK-STAT signaling, and Toll-like receptor signaling pathways [12].

Metabolic pathways are fundamental to immune cell function and influence immune cell proliferation, differentiation, and activation. Under healthy conditions, glucose, fatty acid, and amino acid metabolism maintain immune metabolism homeostasis. However, in diseases, including obese kidneys, disruption of cellular metabolism leads to aberrant immune responses [13–15]. Aerobic glycolysis appears to drive the activation of most lymphoid and myeloid cells, whereas oxidative phosphorylation predominates in regulatory, resting, and memory immune cells [16]. Importantly, lipids play dual roles as both metabolic fuels and signaling molecules in immune regulation. The dynamic processes of extracellular lipid uptake, membrane lipid remodeling and intracellular lipid synthesis/catabolism collectively orchestrate immune cell function and disease development.