Neuroprotective protein ADNP-dependent histone remodeling complex promotes T helper 2 immune cell differentiation

Proteomics reveals the key transcription-related factors mediating obstructive nephropathy in pediatric patients and mice

BACKGROUND

Obstructive nephropathy is one of the leading causes of kidney injury in infants and children. Increasing evidence has shown that transcription-related factors (TRFs), including transcription factors and cofactors, are associated with kidney diseases. However, a global landscape of dysregulated TRFs in pediatric patients with obstructive nephropathy is lacking.

METHODS

We mined the data from our previous proteomic study for the TRF profile in pediatric patients with obstructive nephropathy and unilateral ureteral obstruction (UUO) mice. Gene ontology (GO) analysis was performed to determine pathways that were enriched in the dysregulated TRFs. We then took advantage of kidney samples from patients and UUO mice to verify the selected TRFs by immunoblots.

RESULTS

The proteomes identified a total of 140 human TRFs with 28 upregulated and 1 downregulated, and 160 murine TRFs with 88 upregulated and 1 downregulated (fold change >2 or <0.5). These dysregulated TRFs were enriched in the inflammatory signalings, such as janus kinase/signal transducer and activator of transcription (JAK-STAT) and tumor necrosis factor (TNF) pathways. Of note, the transforming growth factor (TGF)-β signaling pathway, which is the master regulator of organ fibrosis, was enriched in both patients and mice. Cross-species analysis showed 16 key TRFs that might mediate obstructive nephropathy in patients and UUO mice. Moreover, we verified a significant dysregulation of three previously unexplored TRFs; prohibitin (PHB), regulatory factor X 1 (RFX1), and activity-dependent neuroprotector homeobox protein (ADNP), in patients and mice.

CONCLUSIONS

Our study uncovered key TRFs in the obstructed kidneys and provided additional molecular insights into obstructive nephropathy.

Single-cell RNA sequencing indicates AP-1 as a potential therapeutic target for autoimmune uveitis

Autoimmune uveitis (AU) is a sight-threatening eye disease, marked by a complex pathogenesis and limited treatment options. Herein, we conducted single-cell RNA sequencing (scRNA-seq) on the spleen and cervical draining lymph nodes (CDLNs) of both normal and experimental autoimmune uveitis (EAU) mice and found common alterations in celluar composition and transcriptional regulation occurred throughout the EAU process. Moreover, we identified activator protein-1 (AP-1) as a pivotal disease-related molecule in the pathogenesis of EAU. Inhibiting AP-1 alleviated symptoms of EAU and reduced the retina infiltration of T helper 17 cells (Th17) and Th1 cells. Additionally, following treatment with the AP-1 inhibitor, both the spleen and CDLNs showed decreased Th17 and Th1 cell proportions. Meanwhile, in vitro studies revealed that treatment with AP-1 inhibitor reduced the level of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-23 (IL-23), two pivotal molecules implicated in the Th17 cell pathogenicity, during EAU. The adoptive transfer experiment also showed that inhibiting AP-1 in CD4+ T cells suppressed their ability to elicit EAU. Altogether, our study demonstrates that AP-1 might involved in EAU pathogenesis by supporting Th17 cell pathogenicity via the GM-CSF/IL-23 feedback loop. Thus, AP-1 inhibition might be a novel treatment strategy for uveitis.

Overexpression of GNPDA1 in head and neck squamous cell carcinoma: Prognostic significance, immune infiltration, and correlation with cancer cell immune evasion

To evaluate the correlation between glucosamine-6-phosphate isomerase 1 (GNPDA1) expression and prognosis, immune infiltration, and immune evasion in head and neck squamous cell carcinoma (HNSCC). We analyzed the expression of GNPDA1 in HNSCC tissues and obtained RNA sequence data from the Cancer Genome Atlas (TCGA) database. Kaplan-Meier survival analysis evaluated the relationship between GNPDA1 expression and advanced tumor stage, TNM stage, grading, and gender. Co-expressed genes with GNPDA1 were identified using TCGA data and annotated through gene ontology and Kyoto encyclopedia of genes and genomes analyses. A protein-protein interaction network was constructed using the STRING database. Single-sample gene set enrichment analysis was conducted based on TCGA and TIMER 2.0 databases to assess the correlation between GNPDA1 and immune infiltration. In addition, the location of GNPDA1 in tumor cell and immune cell structures was identified by the tumor immune stromal cells helper database, and potential protein-interacting molecules of GNPDA1 were elucidated in the STRING database. Potential GNPDA1 gene functions were assessed using gene set enrichment analysis. Our results indicate that the expression of GNPDA1 is elevated in HNSCC tissues (P < .05). GNPDA1 expression was positively correlated with tumor malignancy (P < .05) and negatively correlated with patient prognosis (P < .05). There was a significant correlation between high expression of GNPDA1 and advanced tumor stage, N-stage, or G-grade, and it was associated with gender. High GNPDA1 expression was associated with increased infiltration of resting CD4+T cells, macrophages M1 and M2, resting natural killer cells, monocytes, eosinophils, and naïve B cells (P < .05). In contrast, low GNPDA1 expression was associated with increased infiltration of activated natural killer cells, neutrophils, activated mast cells, macrophages M0, plasma cells, activated dendritic cells, CD8+T cells, memory B cells, regulatory T cells (Tregs), and naïve CD4+T cells (P < .05). In addition, GNPDA1 was observed to be closely associated with various immune evasion-related genes in HNSCC. The results of this study suggest that GNPDA1 can serve as a potential prognostic marker and therapeutic target for HNSCC and may be a key gene mediating immune evasion in HNSCC.

Deficiency of Toll-like receptor 4 attenuates airway inflammation and remodeling in an ovalbumine-induced mouse asthma model

Background

Previous research has demonstrated elevated levels of Toll-like receptor 4 (TLR4) in the lung tissues of asthmatic mice compared to healthy counterparts, with a notable association between asthmatic inflammation and the sustained activation of the nuclear factor kappa-B (NF-κB) pathway. The specific role of TLR4 in modulating airway inflammation and remodeling, however, remains unclear. This study aimed to explore the impact of TLR4 deficiency on airway inflammation and remodeling in an ovalbumin (OVA)-induced mouse asthma model and to elucidate the underlying mechanisms involved.

Methods

To induce murine airway remodeling, an acute OVA sensitization and challenge protocol was employed. Pathological alterations in the lung tissues were assessed using hematoxylin and eosin, periodic acid-Schiff, and Masson trichrome staining.

Results

Our findings indicated that there were significant reductions in inflammatory cell infiltration in TLR4 knockout (KO) mice, including eosinophils, lymphocytes, neutrophils and the levels of Th2 cytokines interleukin-4, 5, 13 (IL-4, IL-5, IL-13), while showing increased expression of Th1 cytokines [interferon-gamma (IFN-γ)] and a higher T-bet/GATA-3 ratio. Furthermore, TLR4 deficiency markedly decreased airway mucous production, collagen deposition and airway smooth muscle thickness, all of which are strongly associated with airway remodeling. Additionally, TLR4 KO enhanced inhibitor of NF-κB (IκB) protein expression in lung tissues, suggesting an inhibition of the TLR4/NF-κB pathway.

Conclusions

These results demonstrate that TLR4 deficiency attenuates airway inflammation and remodeling, potentially through the inhibition of the TLR4/NF-κB signaling pathway in an OVA-induced mouse asthma model.

Tissue-Resident Th2 Cells in Type 2 Immunity and Allergic Diseases

Type 2 immunity represents a unique immune module that provides host protection against macro-parasites and noxious agents such as venoms and toxins. In contrast, maladaptive type 2 immune responses cause allergic diseases. While multiple cell types play important roles in type 2 immunity, recent studies in humans and murine models of chronic allergic diseases have shown that a distinct population of tissue-resident, CD4+ T helper type 2 (Th2) cells play a critical role in chronic allergic inflammation. The rules regulating Th2 cell differentiation have remained less well defined than other T cell subsets, but recent studies have shed new light into the specific mechanisms controlling Th2 cell biology in vivo. Here, we review our current understanding of the checkpoints regulating the development and function of tissue-resident Th2 cells with a focus on chronic allergic diseases. We discuss evidence for a barrier tissue checkpoint in initial Th2 cell priming, including the role of neuropeptides, damage-associated molecular patterns, and dendritic cell macro-clusters. Furthermore, we review the evidence for a second barrier tissue checkpoint that instructs the development of multi-cytokine producing, tissue-resident Th2 cells that orchestrate allergic inflammation. Lastly, we discuss potential approaches to therapeutically target tissue-resident Th2 cells in chronic allergic diseases.

Update on type 2 immunity

This review article summarizes and comments on the mechanistic work on type 2 immunity published between January 2022 and September 2024. Type 2 immunity is characterized by the production of IL-4, IL-5, IL-9, and IL-13 and is primarily known for its detrimental roles in allergic diseases and its protective roles in helminth infections. Other functions of type 2 immunity include protection against venoms and toxins, wound healing, tissue remodeling, regeneration, and metabolic homeostasis. This review article discusses novel findings on regulation of these processes and disease states by select cells and humoral factors of type 2 immunity, including group 2 innate lymphoid cells, CD4 T cells, mast cells, peripheral neurons, and IgE. The article also describes novel discoveries on regulation of these factors and cells by environmental exposures and the host. Further, the article discusses select genetic mouse models that were developed recently and have the potential to accelerate the field. Finally, the article comments on the significance of novel discoveries to clinical medicine, including drug development.

Epigenetic regulation of macrophage function in kidney disease: New perspective on the interaction between epigenetics and immune modulation

The interaction between renal intrinsic cells and macrophages plays a crucial role in the onset and progression of kidney diseases. In recent years, epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA regulation have become essential windows for understanding these processes. This review focuses on how renal intrinsic cells (including tubular epithelial cells, podocytes, and endothelial cells), renal cancer cells, and mesenchymal stem cells influence the function and polarization status of macrophages through their own epigenetic alterations, and how the epigenetic regulation of macrophages themselves responds to kidney damage, thus participating in renal inflammation, fibrosis, and repair. Moreover, therapeutic studies targeting these epigenetic interaction mechanisms have found that the application of histone deacetylase inhibitors, histone methyltransferase inhibitors, various nanomaterials, and locked nucleic acids against non-coding RNA have positive effects on the treatment of multiple kidney diseases. This review summarizes the latest research advancements in these epigenetic regulatory mechanisms and therapies, providing a theoretical foundation for further elucidating the pathogenesis of kidney diseases and the development of novel therapeutic strategies.

Mitochondrial Control of Proteasomal Psmb5 Drives the Differentiation of Tissue-Resident Memory T Cells in Patients with Rheumatoid Arthritis

OBJECTIVE

To explore T cell-intrinsic mechanisms underpinning the mal-differentiation of tissue-resident memory T (Trm) cells in patients with rheumatoid arthritis (RA).

METHODS

Circulating T cells from patient with RA and healthy individuals were used for Trm cell differentiation. The role of Hobit in Trm differentiation was investigated through targeted silencing experiments. Psmb5 expression regulation was explored by identifying BRD2 as a key transcription factor, with the interaction validated through chromatin immunoprecipitation-quantitative polymerase chain reaction. The impact of BRD2 succinylation on Trm differentiation was examined by manipulating succinyl-CoA levels in T cells. Humanized NSG chimeras representing synovitis provided insights into Trm infiltration in RA synovitis and were used for translational experiments.

RESULTS

In patients with RA, a notable predisposition of CD4+ T cells toward differentiation into Trm cells was observed, demonstrating a positive correlation with the disease activity score 28. Remarkably, Hobit was a pivotal facilitator in the formation of RA CD4+ Trm cells. Mechanistic studies unveiled the dysregulation of proteasomal Psmb5 in T cells of patients with RA as the key factor contributing to elevated Hobit protein levels. The deficiency of proteasomal Psmb5 was intricately linked to BRD2, with succinylation exerting a significant impact on Psmb5 transcription and Trm cell differentiation. This heightened BRD2 succinylation was attributed to elevated levels of mitochondrial succinyl-CoA in RA T cells. Consequently, targeting succinyl-CoA within CD4+ T cells controlled the inflammation of synovial tissues in humanized chimeras.

CONCLUSION

Mitochondrial succinyl-CoA fosters the succinylation of BRD2, resulting in compromised transcription of proteasomal Psmb5 and the differentiation of Trm cells in RA.

Molecular mechanisms regulating T helper 2 cell differentiation and function

T helper 2 (TH2) cells orchestrate type 2 immunity during protective antihelminth immunity and help restore tissue homoeostasis. Their misdirected activities against innocuous substances also underlie atopic diseases, such as asthma and allergy. Recent technological advances are uncovering novel insights into the molecular mechanisms governing TH2 cell differentiation and function.

Recent Advances in Therapeutics for the Treatment of Alzheimer's Disease

The most prevalent chronic neurodegenerative illness in the world is Alzheimer's disease (AD). It results in mental symptoms including behavioral abnormalities and cognitive impairment, which have a substantial financial and psychological impact on the relatives of the patients. The review discusses various pathophysiological mechanisms contributing to AD, including amyloid beta, tau protein, inflammation, and other factors, while emphasizing the need for effective disease-modifying therapeutics that alter disease progression rather than merely alleviating symptoms. This review mainly covers medications that are now being studied in clinical trials or recently approved by the FDA that fall under the disease-modifying treatment (DMT) category, which alters the progression of the disease by targeting underlying biological mechanisms rather than merely alleviating symptoms. DMTs focus on improving patient outcomes by slowing cognitive decline, enhancing neuroprotection, and supporting neurogenesis. Additionally, the review covers amyloid-targeting therapies, tau-targeting therapies, neuroprotective therapies, and others. This evaluation specifically looked at studies on FDA-approved novel DMTs in Phase II or III development that were carried out between 2021 and 2024. A thorough review of the US government database identified clinical trials of biologics and small molecule drugs for 14 agents in Phase I, 34 in Phase II, and 11 in Phase III that might be completed by 2028.

Mef2d potentiates type-2 immune responses and allergic lung inflammation

Innate lymphoid cells (ILCs) and adaptive T lymphocytes promote tissue homeostasis and protective immune responses. Their production depends on the transcription factor GATA3, which is further elevated specifically in ILC2s and T helper 2 cells to drive type-2 immunity during tissue repair, allergic disorders, and anti-helminth immunity. The control of this crucial up-regulation is poorly understood. Using CRISPR screens in ILCs we identified previously unappreciated myocyte-specific enhancer factor 2d (Mef2d)-mediated regulation of GATA3-dependent type-2 lymphocyte differentiation. Mef2d-deletion from ILC2s and/or T cells specifically protected against an allergen lung challenge. Mef2d repressed Regnase-1 endonuclease expression to enhance IL-33 receptor production and IL-33 signaling and acted downstream of calcium-mediated signaling to translocate NFAT1 to the nucleus to promote type-2 cytokine-mediated immunity.

ADNP dysregulates methylation and mitochondrial gene expression in the cerebellum of a Helsmoortel-Van der Aa syndrome autopsy case

BACKGROUND

Helsmoortel-Van der Aa syndrome is a neurodevelopmental disorder in which patients present with autism, intellectual disability, and frequent extra-neurological features such as feeding and gastrointestinal problems, visual impairments, and cardiac abnormalities. All patients exhibit heterozygous de novo nonsense or frameshift stop mutations in the Activity-Dependent Neuroprotective Protein (ADNP) gene, accounting for a prevalence of 0.2% of all autism cases worldwide. ADNP fulfills an essential chromatin remodeling function during brain development. In this study, we investigated the cerebellum of a died 6-year-old male patient with the c.1676dupA/p.His559Glnfs*3 ADNP mutation.

RESULTS

The clinical presentation of the patient was representative of the Helsmoortel-Van der Aa syndrome. During his lifespan, he underwent two liver transplantations after which the child died because of multiple organ failure. An autopsy was performed, and various tissue samples were taken for further analysis. We performed a molecular characterization of the cerebellum, a brain region involved in motor coordination, known for its highest ADNP expression and compared it to an age-matched control subject. Importantly, epigenome-wide analysis of the ADNP cerebellum identified CpG methylation differences and expression of multiple pathways causing neurodevelopmental delay. Interestingly, transcription factor motif enrichment analysis of differentially methylated genes showed that the ADNP binding motif was the most significantly enriched. RNA sequencing of the autopsy brain further identified downregulation of the WNT signaling pathway and autophagy defects as possible causes of neurodevelopmental delay. Ultimately, label-free quantification mass spectrometry identified differentially expressed proteins involved in mitochondrial stress and sirtuin signaling pathways amongst others. Protein-protein interaction analysis further revealed a network including chromatin remodelers (ADNP, SMARCC2, HDAC2 and YY1), autophagy-related proteins (LAMP1, BECN1 and LC3) as well as a key histone deacetylating enzyme SIRT1, involved in mitochondrial energy metabolism. The protein interaction of ADNP with SIRT1 was further biochemically validated through the microtubule-end binding proteins EB1/EB3 by direct co-immunoprecipitation in mouse cerebellum, suggesting important mito-epigenetic crosstalk between chromatin remodeling and mitochondrial energy metabolism linked to autophagy stress responses. This is further supported by mitochondrial activity assays and stainings in patient-derived fibroblasts which suggest mitochondrial dysfunctions in the ADNP deficient human brain.

CONCLUSION

This study forms the baseline clinical and molecular characterization of an ADNP autopsy cerebellum, providing novel insights in the disease mechanisms of the Helsmoortel-Van der Aa syndrome. By combining multi-omic and biochemical approaches, we identified a novel SIRT1-EB1/EB3-ADNP protein complex which may contribute to autophagic flux alterations and impaired mitochondrial metabolism in the Helsmoortel-Van der Aa syndrome and holds promise as a new therapeutic target.

CRISPR-Cas9 applications in T cells and adoptive T cell therapies

T cell immunity is central to contemporary cancer and autoimmune therapies, encompassing immune checkpoint blockade and adoptive T cell therapies. Their diverse characteristics can be reprogrammed by different immune challenges dependent on antigen stimulation levels, metabolic conditions, and the degree of inflammation. T cell-based therapeutic strategies are gaining widespread adoption in oncology and treating inflammatory conditions. Emerging researches reveal that clustered regularly interspaced palindromic repeats-associated protein 9 (CRISPR-Cas9) genome editing has enabled T cells to be more adaptable to specific microenvironments, opening the door to advanced T cell therapies in preclinical and clinical trials. CRISPR-Cas9 can edit both primary T cells and engineered T cells, including CAR-T and TCR-T, in vivo and in vitro to regulate T cell differentiation and activation states. This review first provides a comprehensive summary of the role of CRISPR-Cas9 in T cells and its applications in preclinical and clinical studies for T cell-based therapies. We also explore the application of CRISPR screen high-throughput technology in editing T cells and anticipate the current limitations of CRISPR-Cas9, including off-target effects and delivery challenges, and envisioned improvements in related technologies for disease screening, diagnosis, and treatment.

Recent Developments in the Role of Histone Acetylation in Asthma

BACKGROUND

Epigenetic modifications are known to mediate both beneficial and unfavorable effects of environmental exposures on the development and clinical course of asthma. On the molecular level, epigenetic mechanisms participate in multiple aspects of the emerging and ongoing asthma pathology.

SUMMARY

Studies performed in the last several years expand our knowledge on the role of histone acetylation, a classical epigenetic mark, in the regulation of (patho)physiological processes of diverse cells playing a central role in asthma, including those belonging to the immune system (e.g., CD4+ T cells, macrophages) and lung structure (e.g., airway epithelial cells, pulmonary fibroblasts). Those studies demonstrate a number of specific histone acetylation-associated mechanisms and pathways underlying pathological processes characteristic for asthma, as well as report their modification modalities.

KEY MESSAGES

Dietary modulation of histone acetylation levels in the immune system might protect against the development of asthma and other allergies. Interfering with the enzymes controlling the histone acetylation status of structural lung and (local) immune cells might provide future therapeutic options for asthmatics. Despite some methodological obstacles, analysis of the histone acetylation levels might improve asthma diagnostics.

High-throughput CRISPR technology: a novel horizon for solid organ transplantation

Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.

Tau, ADNP, and sex

With 50 years to the original discovery of Tau, I gave here my perspective, looking through the prism of activity-dependent neuroprotective protein (ADNP), and the influence of sex. My starting point was vasoactive intestinal peptide (VIP), a regulator of ADNP. I then moved to the original discovery of ADNP and its active neuroprotective site, NAP, drug candidate, davunetide. Tau-ADNP-NAP interactions were then explained with emphasis on sex and future translational medicine.

NAP (Davunetide): The Neuroprotective ADNP Drug Candidate Penetrates Cell Nuclei Explaining Pleiotropic Mechanisms

(1) Background: Recently, we showed aberrant nuclear/cytoplasmic boundaries/activity-dependent neuroprotective protein (ADNP) distribution in ADNP-mutated cells. This malformation was corrected upon neuronal differentiation by the ADNP-derived fragment drug candidate NAP (davunetide). Here, we investigated the mechanism of NAP nuclear protection. (2) Methods: CRISPR/Cas9 DNA-editing established N1E-115 neuroblastoma cell lines that express two different green fluorescent proteins (GFPs)-labeled mutated ADNP variants (p.Tyr718* and p.Ser403*). Cells were exposed to NAP conjugated to Cy5, followed by live imaging. Cells were further characterized using quantitative morphology/immunocytochemistry/RNA and protein quantifications. (3) Results: NAP rapidly distributed in the cytoplasm and was also seen in the nucleus. Furthermore, reduced microtubule content was observed in the ADNP-mutated cell lines. In parallel, disrupting microtubules by zinc or nocodazole intoxication mimicked ADNP mutation phenotypes and resulted in aberrant nuclear-cytoplasmic boundaries, which were rapidly corrected by NAP treatment. No NAP effects were noted on ADNP levels. Ketamine, used as a control, was ineffective, but both NAP and ketamine exhibited direct interactions with ADNP, as observed via in silico docking. (4) Conclusions: Through a microtubule-linked mechanism, NAP rapidly localized to the cytoplasmic and nuclear compartments, ameliorating mutated ADNP-related deficiencies. These novel findings explain previously published gene expression results and broaden NAP (davunetide) utilization in research and clinical development.