FERM domain-containing protein FRMD6 activates the mTOR signaling pathway and promotes lung cancer progression

Exploring Prognostic Gene Factors in Breast Cancer via Machine Learning

Breast cancer remains the most prevalent cancer in women. To date, its underlying molecular mechanisms have not been fully uncovered. The determination of gene factors is important to improve our understanding on breast cancer, which can correlate the specific gene expression and tumor staging. However, the knowledge in this regard is still far from complete. Thus, this study aimed to explore these knowledge gaps by analyzing existing gene expression profile data from 3149 breast cancer samples, where each sample was represented by the expression of 19,644 genes and classified into Nottingham histological grade (NHG) classes (Grade 1, 2, and 3). To this end, a machine learning-based framework was designed. First, the profile data were analyzed by using seven feature ranking algorithms to evaluate the importance of features (genes). Seven feature lists were generated, each of which sorted features in accordance with feature importance evaluated from a special aspect. Then, the incremental feature selection method was applied to each list to determine essential features for classification and building efficient classifiers. Consequently, overlapping genes, such as AURKA, CBX2, and MYBL2, were deemed as potentially related to breast cancer malignancy and prognosis, indicating that such genes were identified to be important by multiple feature ranking algorithms. In addition, the study formulated classification rules to reflect special gene expression patterns for three NHG classes. Some genes and rules were analyzed and supported by recent literature, providing new references for studying breast cancer.

FRMD6 determines the cell fate towards senescence: involvement of the Hippo-YAP-CCN3 axis

Cellular senescence, a hallmark of aging, is pathogenically linked to the development of aging-related diseases. This study demonstrates that FRMD6, an upstream component of the Hippo/YAP signaling cascade, is a key regulator of senescence. Proteomic analysis revealed that FRMD6 is upregulated in senescent IMR90 fibroblasts under various senescence-inducing conditions. Silencing FRMD6 mitigated the senescence of IMR90 cells, suggesting its requirement in senescence. Conversely, the overexpression of FRMD6 alone induced senescence in cells and in lung tissue, establishing a causal link. The elevated FRMD6 levels correlated well with increased levels of the inhibitory phosphorylated YAP/TAZ. We identified cellular communication network factor 3 (CCN3), a key component of the senescence-associated secretory phenotype regulated by YAP, whose administration attenuated FRMD6-induced senescence in a dose-dependent manner. Mechanistically, FRMD6 interacted with and activated MST kinase, which led to YAP/TAZ inactivation. The expression of FRMD6 was regulated by the p53 and SMAD transcription factors in senescent cells. Accordingly, the expression of FRMD6 was upregulated by TGF-β treatment that activates those transcription factors. In TGF-β-treated IMR90 cells, FRMD6 mainly segregated with p21, a senescence marker, but rarely segregated with α-SMA, a myofibroblast marker, which suggests that FRMD6 has a role in directing cells towards senescence. Similarly, in TGF-β-enriched environments, such as fibroblastic foci (FF) from patients with idiopathic pulmonary fibrosis, FRMD6 co-localized with p16 in FF lining cells, while it was rarely detected in α-SMA-positive myofibroblasts that are abundant in FF. In sum, this study identifies FRMD6 as a novel regulator of senescence and elucidates the contribution of the FRMD6-Hippo/YAP-CCN3 axis to senescence.

Identification of Tumor Budding-Associated Genes in Breast Cancer through Transcriptomic Profiling and Network Diffusion Analysis

Breast cancer has the highest diagnosis rate among all cancers. Tumor budding (TB) is recognized as a recent prognostic marker. Identifying genes specific to high-TB samples is crucial for hindering tumor progression and metastasis. In this study, we utilized an RNA sequencing technique, called TempO-Seq, to profile transcriptomic data from breast cancer samples, aiming to identify biomarkers for high-TB cases. Through differential expression analysis and mutual information, we identified seven genes (NOL4, STAR, C8G, NEIL1, SLC46A3, FRMD6, and SCARF2) that are potential biomarkers in breast cancer. To gain more relevant proteins, further investigation based on a protein-protein interaction network and the network diffusion technique revealed enrichment in the Hippo signaling and Wnt signaling pathways, promoting tumor initiation, invasion, and metastasis in several cancer types. In conclusion, these novel genes, recognized as overexpressed in high-TB samples, along with their associated pathways, offer promising therapeutic targets, thus advancing treatment and diagnosis for breast cancer.

Spatiotemporally Controlled T-Cell Combination Therapy for Solid Tumor

Due to multidimensional complexity of solid tumor, development of rational T-cell combinations and corresponding formulations is still challenging. Herein, a triple combination of T cells are developed with Indoleamine 2,3-dioxygenase inhibitors (IDOi) and Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i). To maximize synergism, a spatiotemporally controlled T-cell engineering technology to formulate triple drugs into one cell therapeutic, is established. Specifically, a sequentially responsive core-shell nanoparticle (SRN) encapsulating IDOi and CDK4/6i is anchored onto T cells. The yielded SRN-T cells migrated into solid tumor, and achieved a 1st release of IDOi in acidic tumor microenvironment (TME). Released IDOi restored tryptophan supply in TME, which activated effector T cells and inhibited Tregs. Meanwhile, 1st released core is internalized by tumor cells and degraded by glutathione (GSH), to realize a 2nd release of CDK4/6i, which induced up-regulated expression of C-X-C motif chemokine ligand 10 (CXCL10) and C-C motif chemokine ligand 5 (CCL5), and thus significantly increased tumor infiltration of T cells. Together, with an enhanced recruitment and activation, T cells significantly suppressed tumor growth, and prolonged survival of tumor-bearing mice. This study demonstrated rationality and superiority of a tri-drug combination mediated by spatiotemporally controlled cell-engineering technology, which provides a new treatment regimen for solid tumor.

ZEB1 hypermethylation is associated with better prognosis in patients with colon cancer

BACKGROUND

Colon cancer (CC) is a heterogeneous disease that is categorized into four Consensus Molecular Subtypes (CMS) according to gene expression. Patients with loco-regional CC (stages II/III) lack prognostic factors, making it essential to analyze new molecular markers that can delineate more aggressive tumors. Aberrant methylation of genes that are essential in crucial mechanisms such as epithelial mesenchymal transition (EMT) contributes to tumor progression in CC. We evaluate the presence of hyper- and hypomethylation in subrogate IHC markers used for CMS classification (CDX2, FRMD6, HTR2B, ZEB1) of 144 stage II/III patients and CC cell lines by pyrosequencing. ZEB1 expression was also studied in control and shRNA-silenced CC cell lines and in paired normal tissue/tumors by quantitative PCR. The pattern of ZEB1 staining was also analyzed in methylated/unmethylated tumors by immunohistochemistry.

RESULTS

We describe for the first time the hypermethylation of ZEB1 gene and the hypomethylation of the FRMD6 gene in 32.6% and 50.9% of tumors, respectively. Additionally, we confirm the ZEB1 re-expression by epigenetic drugs in methylated cell lines. ZEB1 hypermethylation was more frequent in CMS1 patients and, more importantly, was a good prognostic factor related to disease-free survival (p = 0.015) and overall survival (p = 0.006) in our patient series, independently of other significant clinical parameters such as patient age, stage, lymph node involvement, and blood vessel and perineural invasion.

CONCLUSIONS

Aberrant methylation is present in the subrogate genes used for CMS classification. Our results are the first evidence that ZEB1 is hypermethylated in CC and that this alteration is an independent factor of good prognosis.

Development of cancer-associated fibroblast-related gene signature for predicting the survival and immunotherapy response in lung adenocarcinoma

The present study aims to construct a predictive model for prognosis and immunotherapy response in lung adenocarcinoma (LUAD). Transcriptome data were extracted from the Cancer Genome Atlas (TCGA), GSE41271, and IMvigor210. The weighted gene correlation network analysis was utilized to identify the hub modules related to immune/stromal cells. Then, univariate, LASSO, and multivariate Cox regression analyses were employed to develop a predictive signature based on genes of the hub module. Moreover, the association between the predictive signature and immunotherapy response was also investigated. As a result, seven genes (FGF10, SERINE2, LSAMP, STXBP5, PDE5A, GLI2, FRMD6) were screened to develop the cancer associated fibroblasts (CAFs)-related risk signature (CAFRS). LUAD patients with high-risk score underwent shortened Overall survival (OS). A strong correlation was found between CAFRS and immune infiltrations/functions. The gene set variation analysis showed that G2/M checkpoint, epithelial-mesenchymal transition, hypoxia, glycolysis, and PI3K-Akt-mTOR pathways were greatly enriched in the high-risk subgroup. Moreover, patients with higher risk score were less likely to respond to immunotherapy. A nomogram based on CAFRS and Stage presented a stronger predictive performance for OS than the single indicator. In conclusion, the CAFRS exhibited a potent predictive value for OS and immunotherapy response in LUAD.