SHANK2 is a frequently amplified oncogene with evolutionarily conserved roles in regulating Hippo signaling

Leveraging FAM features to predict the prognosis of LGG patients and immunotherapy outcome

Heterogeneity at biological and transcriptomic levels poses a challenge in defining and typing low-grade glioma (LGG), leading to a critical need for specific molecular signatures to enhance diagnosis, therapy, and prognostic evaluation of LGG. This study focused on fatty acid metabolism (FAM) related genes and prognostic features to investigate the mechanisms and treatment strategies for LGG cell metastasis and invasion. By screening 158 FAM-related genes and clustering 512 LGG samples into two subtypes (C1 and C2), differential gene expression analysis and functional enrichment were performed. The immune cell scores and prognosis were compared between the two subtypes, with C1 showing poorer outcomes and higher immune scores. A four-gene signature (PHEX, SHANK2, HOPX, and LGALS1) was identified and validated across different datasets, demonstrating a stable predictive effect. Cellular experiments confirmed the roles of LGALS1 and HOPX in promoting tumor cell proliferation, migration, and invasion, while SHANK2 exhibited a suppressive effect. This four-gene signature based on FAM-related genes offers valuable insights for understanding the pathogenesis and clinical management of LGG.

Impact of HBV Integration on Hepatocellular Carcinoma After Long-Term Antiviral Therapy

Purpose

Few studies have reported the integrated characteristics of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) after long-term antiviral therapy. This study aimed to investigate the HBV integration features in HBV-HCC patients who had undergone long-term antiviral therapy, evaluate their impact on clinical indicators, and analyze the potential mechanisms involved.

Patients and Methods

We utilized genome-wide association study (GWAS) to analyze liver cancer tissues and detect the presence of HBV integration. Seventeen patients with HBV integration were included in the integration (Int) group, while the remaining five patients were included in the non-integration (N-int) group. Clinical indicators were regularly monitored and compared between the two groups. The characteristics of HBV integration patterns were analyzed, and differences between the groups were explored at the chromosome and genomic levels.

Results

After long-term antiviral therapy, although the frequency of HBV integration in HBV-HCC was reduced, residual HBV integration still accelerated the development of HCC. It affected the diagnosis, treatment, and prognosis of patients. HBV integration events led to changes in chromosome structure, which were closely related to HCC. Novel fusion genes were detected at a high frequency and had the potential to be specific detection sites for HBV-HCC.

Conclusion

HBV integration events are synergistically involved in the human genome and HBV, which can lead to chromosome structural instability, gene rearrangement events closely related to HCC production, and the formation of new specific fusion genes.

A cuproptosis-related lncRNA signature predicts the prognosis and immune cell status in head and neck squamous cell carcinoma

Introduction

The incidence of head and neck squamous cell carcinoma (HNSCC), one of the most prevalent tumors, is increasing rapidly worldwide. Cuproptosis, as a new copper-dependent cell death form, was proposed recently. However, the prognosis value and immune effects of cuproptosis-related lncRNAs (CRLs) have not yet been elucidated in HNSCC.

Methods

In the current study, the expression pattern, differential profile, clinical correlation, DNA methylation, functional enrichment, univariate prognosis factor, and the immune effects of CRLs were analyzed. A four-CRL signature was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm.

Results

Results showed that 20 CRLs had significant effects on the stage progression of HNSCC. Sixteen CRLs were tightly correlated with the overall survival (OS) of HNSCC patients. Particularly, lnc-FGF3-4 as a single risk factor was upregulated in HNSCC tissues and negatively impacted the prognosis of HNSCC. DNA methylation probes of cg02278768 (MIR9-3HG), cg07312099 (ASAH1-AS1), and cg16867777 (TIAM1-AS1) were also correlated with the prognosis of HNSCC. The four-CRL signature that included MAP4K3-DT, lnc-TCEA3-1, MIR9-3HG, and CDKN2A-DT had a significantly negative effect on the activation of T cells follicular helper and OS probability of HNSCC. Functional analysis revealed that cell cycle, DNA replication, and p53 signal pathways were enriched.

Discussion

A novel CRL-related signature has the potential of prognosis prediction in HNSCC. Targeting CRLs may be a promising therapeutic strategy for HNSCC.

Bioinformatics analysis of ceRNA regulatory network of baicalin in alleviating pathological joint alterations in CIA rats

Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inffammation of synovium, leading to cartilage damage, bone erosion,even joint destruction and deformity. The conventional treatment modalities in RA are associated with side effects, emphasizing the need for alternative therapeutic remedies. Baicalin possesses multiple pharmacological effects and the advantage of low toxicity. This study aimed to reveal the potential gene regulatory mechanisms underlying the alleviating effects of baicalin in joint pathological alterations in Collagen-Induced Arthritis (CIA) rat models. At 28 days after the primary immunization, 60mg/kg/d of baicalin was administered via intraperitoneal injection once daily for 40 days, and the pathological alterations of hind paw joints were examined with X-ray imaging. Subsequently, the synovial tissue of knee joints was isolated, from which total RNA was extracted, and mRNA and miRNA sequencing libraries were established. Finally, High-throughput transcriptome sequencing(RNA-seq) technology was performed, and the lncRNAs/miRNAs/mRNAs competing endogenous RNA(ceRNA) regulatory network was analyzed. The CIA model was successfully established, and baicalin treatment significantly alleviated the destruction of distal joints of CIA rat models (p < 0.01). We found that 3 potential ceRNA regulatory networks of baicalin were established, including lncRNA ENSRNOT00000076420/miR-144-3p/Fosb, lncRNA MSTRG.1448.13/miR-144-3p/Atp2b2 and lncRNA MSTRG.1448.13/miR-144-3p/Shanks. The validation results from synovial tissue of CIA rats were consistent with the RNA-Seq results. Overall, this study revealed potentially important genes and ceRNA regulatory network that mediate the alleviating effects of baicalin on joint pathological alterations in CIA rats.

Genome-wide methylation profiling identifies a novel gene signature for patients with synchronous colorectal cancer

BACKGROUND

There are no robust tools for the diagnosis of synchronous colorectal cancer (SyCRC). Herein, we developed the first methylation signature to identify and characterise patients with SyCRC.

METHODS

For biomarker discovery, we analysed the genome-wide methylation profiles of 16 SyCRC and 18 solitary colorectal cancer (SoCRC) specimens. We thereafter established a methylation signature risk-scoring model to identify SyCRC in an independent cohort of 38 SyCRC and 42 SoCRC patients. In addition, we evaluated the prognostic value of the identified methylation profile.

RESULTS

We identified six differentially methylated CpG probes/sites that distinguished SyCRC from SoCRC. In the validation cohort, we developed a methylation panel that identified patients with SyCRC from not only larger tumour (AUC = 0.91) but also the paired remaining tumour (AUC = 0.93). Moreover, high risk scores of our panel were associated with the development of metachronous CRC among patients with SyCRC (AUC = 0.87) and emerged as an independent predictor for relapse-free survival (hazard ratio = 2.72; 95% CI = 1.12-6.61). Furthermore, the risk stratification model which combined with clinical risk factors was a diagnostic predictor of recurrence (AUC = 0.90).

CONCLUSIONS

Our novel six-gene methylation panel robustly identifies patients with SyCRC, which has the clinical potential to improve the diagnosis and management of patients with CRC.

SHANK family on stem cell fate and development

SH3 and multiple ankyrin repeat domains protein (SHANK) 1, SHANK2, and SHANK3 encode a family of postsynaptic scaffolding proteins present at glutamatergic synapses and play a crucial role in synaptogenesis. In the past years, studies have provided a preliminary appreciation and understanding of the influence of the SHANK family in controlling stem cell fate. Here, we review the modulation of SHANK gene expression and their related signaling pathways, allowing for an in-depth understanding of the role of SHANK in stem cells. Besides, their role in governing stem cell self-renewal, proliferation, differentiation, apoptosis, and metabolism are explored in neural stem cells (NSCs), stem cells from apical papilla (SCAPs), and induced pluripotent stem cells (iPSCs). Moreover, iPSCs and embryonic stem cells (ESCs) have been utilized as model systems for analyzing their functions in terms of neuronal development. SHANK-mediated stem cell fate determination is an intricate and multifactorial process. This study aims to achieve a better understanding of the role of SHANK in these processes and their clinical applications, thereby advancing the field of stem cell therapy. This review unravels the regulatory role of the SHANK family in the fate of stem cells.

Genetic Analysis Implicates Dysregulation of SHANK2 in Renal Cell Carcinoma Progression

SH3 and multiple ankyrin repeat domains (SHANK) is a family of scaffold proteins that were first identified to be involved in balancing synaptic transmission via regulation of intracellular signalling crosstalk and have been linked to various cancers. However, the role of the SHANK genes in renal cell carcinoma (RCC) remains to be elucidated. In this study, we aimed to evaluate whether genetic variants in SHANK family genes affect the risk of RCC and survival of patients. A genetic association study was conducted using logistic regression and Cox regression analyses, followed by the correction for a false discovery rate (FDR), in 630 patients with RCC and controls. A pooled analysis was further performed to summarise the clinical relevance of SHANK gene expression in RCC. After adjustment for known risk factors and the FDR, the SHANK2 rs10792565 T allele was found to be associated with an increased risk of RCC (adjusted odds ratio = 1.79, 95% confidence interval = 1.32-2.44, p = 1.96 × 10^-4, q = 0.030), whereas no significant association was found with RCC survival. A pooled analysis of 19 independent studies, comprising 1509 RCC and 414 adjacent normal tissues, showed that the expression of SHANK2 was significantly lower in RCC than in normal tissues (p < 0.001). Furthermore, low expression of SHANK2 was correlated with an advanced stage and poor prognosis for patients with clear cell and papillary RCC. This study suggests that SHANK2 rs10792565 is associated with an increased risk of RCC and that SHANK2 may play a role in RCC progression.

Recognition of a Novel Gene Signature for Human Glioblastoma

Glioblastoma (GBM) is one of the most common malignant and incurable brain tumors. The identification of a gene signature for GBM may be helpful for its diagnosis, treatment, prediction of prognosis and even the development of treatments. In this study, we used the GSE108474 database to perform GSEA and machine learning analysis, and identified a 33-gene signature of GBM by examining astrocytoma or non-GBM glioma differential gene expression. The 33 identified signature genes included the overexpressed genes COL6A2, ABCC3, COL8A1, FAM20A, ADM, CTHRC1, PDPN, IBSP, MIR210HG, GPX8, MYL9 and PDLIM4, as well as the underexpressed genes CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C, SHANK2 and VIPR2. Protein functional analysis by CELLO2GO implied that these signature genes might be involved in regulating various aspects of biological function, including anatomical structure development, cell proliferation and adhesion, signaling transduction and many of the genes were annotated in response to stress. Of these 33 signature genes, 23 have previously been reported to be functionally correlated with GBM; the roles of the remaining 10 genes in glioma development remain unknown. Our results were the first to reveal that GBM exhibited the overexpressed GPX8 gene and underexpressed signature genes including CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C and SHANK2, which might play crucial roles in the tumorigenesis of different gliomas.

SHANK1 facilitates non-small cell lung cancer processes through modulating the ubiquitination of Klotho by interacting with MDM2

SH3 and multiple ankyrin repeat domains 1 (SHANK1) is a scaffold protein, plays an important role in the normal function of neuron system. It has recently been shown to be a potential oncogene. In the present study, we report that the expression of SHANK1 is upregulated in non-small cell lung cancer (NSCLC), and is correlated with clinic pathological characteristics of NSCLC. Moreover, SHANK1 overexpression enhances the proliferation, migration and invasion of NSCLC cells. Mouse cell-derived xenograft model also confirmed the effects of SHANK1 on tumor growth in vivo. Furthermore, we found that SHANK1 increases the protein degradation of Klotho (KL), an important tumor suppressor, through ubiquitination-dependent pathway. In particular, we report discovery of KL as a SHANK1-interacting protein that acts as a new substate of the E3 ubiquitin ligase MDM2. SHANK1 can form a complex with KL and MDM2 and enhance the interaction between KL and MDM2. Our findings reveal an important oncogenic role and mechanism of SHANK1, suggesting SHANK1 can be a potential therapeutic target in NSCLC.

Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis (IPF)

Idiopathic pulmonary fibrosis (IPF), a devastating, fibro-proliferative chronic lung disorder, is associated with expansion of fibroblasts/myofibroblasts, which leads to excessive production and deposition of extracellular matrix (ECM). IPF is typically clinically identified as end-stage lung disease, after fibrotic processes are well-established and advanced. Fibroblasts have been shown to be critically important in the development and progression of IPF. We hypothesize that differential chromatin access can drive genetic differences in IPF fibroblasts relative to healthy fibroblasts. To this end, we performed Assay of Transposase-Accessible Chromatin (ATAC)-sequencing to identify differentially accessible regions within the genomes of fibroblasts from healthy and IPF lungs. Multiple motifs were identified to be enriched in IPF fibroblasts compared to healthy fibroblasts, including binding motifs for TWIST1 and FOXA1. RNA-sequencing identified 93 genes that could be annotated to differentially accessible regions. Pathway analysis of the annotated genes identified cellular adhesion, cytoskeletal anchoring, and cell differentiation as important biological processes. In addition, single nucleotide polymorphisms (SNPs) analysis showed that linkage disequilibrium (LD) blocks of IPF risk SNPs with IPF accessible regions that have been identified to be located in genes which are important in IPF, including MUC5B, TERT and TOLLIP. Validation studies in isolated lung tissue confirmed increased expression for TWIST1 and FOXA1 in addition to revealing SHANK2 and CSPR2 as novel targets. Thus, modulation of differential chromatin access may be an important mechanism in the pathogenesis of lung fibrosis.

Mutations and Copy Number Abnormalities of Hippo Pathway Components in Human Cancers

The Hippo pathway is highly conserved from Drosophila to mammals. As a key regulator of cell proliferation, the Hippo pathway controls tissue homeostasis and has a major impact on tumorigenesis. The originally defined core components of the Hippo pathway in mammals include STK3/4, LATS1/2, YAP1/TAZ, TEAD, VGLL4, and NF2. However, for most of these genes, mutations and copy number variations are relatively uncommon in human cancer. Several other recently identified upstream and downstream regulators of Hippo signaling, including FAT1, SHANK2, Gq/11, and SWI/SNF complex, are more commonly dysregulated in human cancer at the genomic level. This review will discuss major genomic events in human cancer that enable cancer cells to escape the tumor-suppressive effects of Hippo signaling.