Integrin activation is an indispensable step for various integrin-mediated biological functions. Kindlin-2 is known to coactivate integrins with Talin; however, molecules that restrict integrin activation are elusive. Here, we demonstrate that the E3 ubiquitin ligase Smurf1 controls the amount of Kindlin-2 protein in cells and hinders integrin activation. Smurf1 interacts with and promotes Kindlin-2 ubiquitination and degradation. Smurf1 selectively mediates degradation of Kindlin-2 but not Talin, leading to inhibition of αIIbβ3 integrin activation in Chinese hamster ovary cells and β1 integrin activation in fibroblasts. Enhanced activation of β1 integrin was found in Smurf1-knockout mouse embryonic fibroblasts, which correlates with an increase in Kindlin-2 protein levels. Similarly, a reciprocal relationship between Smurf1 and Kindlin-2 protein levels is found in tissues from colon cancer patients, suggesting that Smurf1 mediates Kindlin-2 degradation in vivo. Collectively, we demonstrate that Smurf1 acts as a brake for integrin activation by controlling Kindlin-2 protein levels, a new mechanism that permits precise modulation of integrin-mediated cellular functions.

FRMD5, FERM-domain protein 5, has been reported to be associated with tumors progession and neurodevelopment, however its molecular mechanisms in normal cells and its functions during urinary epithelium development remain unknown. In this study, we identified that Frmd5 interacts with Jak2 and Stat3, leading to the enhanced Jak2/Stat3 complex formation and subsquently promoting phosphorylation of Stat3. In a urinary epithelium specific knockout of Frmd5 mouse, Jak2-Stat3 signaling pathway was significantly inactivated and apoptosis of epithelium was significantly downregulated compared with Cdh16-Cre-; Frmd5flox/floxcontrol mouse. In Cdh16-Cre+; Frmd5flox/flox vaginal epithelium pro-apoptotic genes (Casp3, Casp8) was decreased and anti-apoptotic genes (Bcl2, Bcl-XL) was increased compared with Cdh16-Cre-; Frmd5flox/flox vaginal epithelium. A total of 56.7% Cdh16-Cre+; Frmd5flox/flox mice failed to form vaginal lumen and developed longitudinal vaginal septum coupled with infertility in these mice. In summary, we demonstrated that Frmd5 is essential for activation of Jak2-Stat3 signaling pathway and is required for vaginal lumen development in mice.

Hepatocellular carcinoma (HCC) remains a major global health challenge due to its molecular heterogeneity, late diagnosis, and limited therapeutic options. Recent studies have identified isonicotinylation (Kinic), a novel lysine acylation, as a regulatory modification influencing carcinogenic protein activity and liver cancer progression. In this study, we established the Kinic Index (KinicI), an artificial intelligence (AI)-driven predictive model that integrates multi-omics data and consensus clustering to classify HCC patients into two distinct Kinic subgroups. Patients in the high-Kinic subgroup exhibited significantly worse overall survival, demonstrating the value of KinicI for risk stratification and outcome prediction. Machine learning approaches (LASSO, RSF) coupled with Shapley additive explanation (SHAP) analysis identified CYP2C9 and G6PD as the most influential prognostic variables associated with HCC progression. Single-cell and spatial transcriptomic analyses confirmed that CYP2C9 and G6PD are primarily localized in malignant hepatocytes with high metastatic potential, underscoring their clinical relevance. Importantly, using the GraphBAN deep learning framework and ADMET-AI screening, we prioritized candidate compounds targeting CYP2C9 and G6PD, followed by molecular docking that validated strong binding affinities, suggesting their potential as novel therapeutics. Together, our study demonstrates that KinicI is a powerful AI-enabled platform for prognostic modeling, molecular stratification, and multitarget drug discovery, providing a foundation for precision oncology and resistance-aware treatment strategies in HCC patients.

Paclitaxel and nab-paclitaxel differ in therapeutic efficacy and modulation of the tumor immune microenvironment, yet the molecular basis remains poorly defined. Here, based on a meta-analysis, we first show that treatment with nab-paclitaxel results in a higher overall response rate and pathological complete response compared to paclitaxel in female patients with breast cancer. Notably, TREM2 expression in macrophages is elevated in primary tumors of paclitaxel- but not nab-paclitaxel-treated female patients. In metastatic breast cancer, TREM2+ macrophage infiltration is increased in primary tumors. In breast cancer models in female mice, paclitaxel, but not nab-paclitaxel, promotes lung metastasis by recruiting TREM2+ macrophages to primary tumors. Mechanistically, paclitaxel enhances the ATF3-FGF2 axis in breast cancer cells; secreted FGF2 activates the EGR1-TREM2-EMT cytokine axis in macrophages. Genetic ablation of Trem2 or pharmacologic targeting with antisense oligonucleotides suppress paclitaxel-induced breast cancer lung metastasis in vivo. Collectively, our findings demonstrate that paclitaxel, but not nab-paclitaxel, stimulates TREM2 expression and expands TREM2+ macrophages, suggesting that TREM2 targeting could enhance paclitaxel efficacy while limiting metastasis.

BRCA1 is a critical tumor suppressor, mutations in which greatly increase risks for many tumors in carriers, most notably breast cancer. Luminal progenitor cells (LPs) are the currently recognized cells origin of BRCA1-deficient breast cancers. However, the reason why LPs are prone to transform with BRCA1 deficiency has not been elucidated. Here, using single-cell sequencing of human BRCA1 mutant breast cancers and RNA sequencing (RNA-seq) of BRCA1-deficient normal mammary cells, we reveal that replication stress is a feature of LPs and a driving factor during BRCA1-associated tumorigenesis. Mechanistically, replication stress and BRCA1 deficiency lead to significant upregulation of ELF3 expression. ELF3 can help suppress excessive genomic instability and promote LP transformation with BRCA1 deficiency. Moreover, ELF3 emerged as a core transcription factor regulating LP genes, leading to LP expansion. Our findings suggest that replication stress is a driving factor during BRCA1-associated tumorigenesis in luminal progenitor cells and elucidates the key role of ELF3 during this process.

Metabolic syndrome increases the risk of endometrial cancer development and progression, but the mechanism remains unclear. We find that polyamine metabolites are notably elevated in the sera and tumor tissues of endometrial cancer patients with metabolic syndrome. Oleic acid, one of the many components in hyperlipidemia, is the key factor for upregulating Ornithine Decarboxylase 1 (ODC1) (the rate-limiting enzyme in polyamine metabolism) and downstream polyamines. Mechanistically, Oleic acid binds to and stabilizes Homeobox B9 (HOXB9) by inhibiting the binding of HOXB9 to E3 ligase Praja2. Stable HOXB9 then competes with OAZ1 and combines with ODC1 to block ODC1 degradation. Targeting HOXB9 or ODC1 reduces polyamine levels and suppresses tumor growth/spread. Oleic acid-HOXB9-ODC1 stable cascading axis then is confirmed in patient tissues, and ODC1 inhibitors boost patient-derived tumor cells' chemosensitivity. This study links fatty acids to polyamine buildup, reveals a mechanism for metabolic syndrome-driven endometrial cancer, and points to HOXB9 and ODC1 as potential therapeutic targets.

N6-methyladenosine (m6A) is the most common epigenetic modification of RNA, but whether m6A RNA methylation modulates cardiovascular development or congenital heart diseases (CHDs) has not been determined. The published high-throughput sequencing data suggested that transcripts of genes related to CHDs were prone to m6A modification, while the expression of methyltransferase-like 3 (METTL3)-involved methyltransferase complex was downregulated in mouse embryonic hearts following prenatal alcohol exposure as a critical CHD risk factor, indicating the association of insufficient m6A RNA methylation with CHDs. Using cardiovascular-specific Mettl3 knockout mice (Tagln-Cre; Mettl3flox/flox ), we observed that cardiovascular Mettl3 deficiency resulted in postnatal lethality and profound congenital cardiac defects, including left pulmonary stenosis, ventricular septal defects, and right ventricular hypoplasia. The m6A-specific methylated RNA-immunoprecipitation sequencing identified Sox4, Sox11, and Mef2a, the critical transcription factors involved in the right ventricle and outflow tract development, were the regulatory targets of METTL3-catalyzed m6A RNA methylation. Mettl3 deficiency-caused insufficient m6A RNA methylation downregulated the expression of SOX4, SOX11, and MEF2A in mouse embryonic hearts. In conclusion, cardiovascular Mettl3 deficiency directly led to congenital cardiac defects by downregulating the m6A-dependent expression of Mef2a, Sox4, and Sox11. METTL3-catalyzed m6A RNA methylation may become a potential target for preventing and treating CHDs.

Approximately 40% ERα-positive breast cancer patients suffer from therapeutic resistance to tamoxifen. Although reduced ERα level is the major cause of tamoxifen resistance, the underlying mechanisms remain elusive. Here, we report that FRMD8 raises the level of ERα at both transcriptional and post-translational layers. FRMD8 deficiency in MMTV-Cre + ; Frmd8 fl/fl ; PyMT mice accelerates mammary tumor growth and loss of luminal phenotype, and confers tamoxifen resistance. Single-cell RNA profiling reveals that Frmd8 loss decreases the proportion of hormone-sensing differentiated epithelial cells and downregulates the levels of ERα. Mechanically, on one hand, loss of FRMD8 inhibits ESR1 transcription via suppressing the expression of FOXO3A, a transcription factor of ESR1 . On the other hand, FRMD8 interacts both with ERα and UBE3A, and disrupts the interaction of UBE3A with ERα, thereby blocking UBE3A-mediated ERα degradation. In breast cancer patients, FRMD8 gene promoter is found hypermethylated and low level of FRMD8 predicts poor prognosis. Therefore, FRMD8 is an important regulator of ERα and may control therapeutic sensitivity to tamoxifen in ERα-positive breast cancer patients.

The luminal-to-basal transition in mammary epithelial cells (MECs) is accompanied by changes in epithelial cell lineage plasticity; however, the underlying mechanism remains elusive. Here, we report that deficiency of Frmd3 inhibits mammary gland lineage development and induces stemness of MECs, subsequently leading to the occurrence of triple-negative breast cancer. Loss of Frmd3 in PyMT mice results in a luminal-to-basal transition phenotype. Single-cell RNA sequencing of MECs indicated that knockout of Frmd3 inhibits the Notch signaling pathway. Mechanistically, FERM domain-containing protein 3 (FRMD3) promotes the degradation of Disheveled-2 by disrupting its interaction with deubiquitinase USP9x. FRMD3 also interrupts the interaction of Disheveled-2 with CK1, FOXK1/2, and NICD and decreases Disheveled-2 phosphorylation and nuclear localization, thereby impairing Notch-dependent luminal epithelial lineage plasticity in MECs. A low level of FRMD3 predicts poor outcomes for breast cancer patients. Together, we demonstrated that FRMD3 is a tumor suppressor that functions as an endogenous activator of the Notch signaling pathway, facilitating the basal-to-luminal transformation in MECs.

Abstract Vitamin B3 is the major precursor of NAD+ and NADP+, however it was unknown whether this vitamin supplementation could modify histone epigenetically. Here, we report nicotinic acid (NA), a component of vitamin B3, suppresses liver cancer metastasis specifically, via stimulating histone lysine nicotinylation (Knic). Importantly, nicotinyl-CoA, that metabolically generated by NA via ACSS2, stimulates histone Knic in vivo and in vitro. Histone Knic regulates chromatin accessibility and inhibits binding of transcription factor HOXB9 to the promoter of oncogene PPFIA1, resulting in inhibition of hepatocyte carcinoma progression. Notably, we found that NA specific induces histone Knic and suppresses hepatocyte carcinoma progression, whereas nicotinamide, an amide form of nicotinic acid, does not stimulate nicotinylation, instead promotes tumour growth and metastasis. These findings suggest that vitamin B3 supplementation may contribute to cancer progression depending on its composition. Collectively, we demonstrated that histone lysine nicotinylation is a histone mark controlling gene expression and NA supresses liver cancer progression by inducing histone lysine nicotinylation.

Protein post-translational modifications (PTMs) are crucial for cancer growth and metastasis. Vitamin B3, a key precursor of NAD + and NADP+, however its epigenetic functions in physiology and disease remain unclear. Herein we report a nicotinic acid (NA), a component of vitamin B3, induces a histone PTM, lysine nicotinylation (Knic), and demonstrate 17 Knic site across core histones in cells. Tandem mass spectrometry and stable isotope tracing revealed that NA-derived nicotinyl-CoA, catalysed by ACSS2, enhances histone Knic in vivo and in vitro. Analysis of chromatin accessibility revealed that histone Knic downregulates chromatin accessibility and therefore inhibits gene expression, for instance, restrain the binding of transcription factor HOXB9 to the promoter of oncogene PPFIA1. PPFIA1 level is correlated with malignancy and poor prognosis of hepatocellular carcinoma. These findings suggest that vitamin B3 supplementation may affects the chromatin accessibility depending on its composition. Collectively, we propose that NA induces histone Knic, a histone mark controlling gene expression.

Liver metastasis is the primary factor contributing to unfavorable prognosis in colorectal cancer (CRC). Although N-glycosylation is implicated in metastasis, there is a notable paucity of comprehensive studies addressing the N-glycosylation proteomics associated with liver metastasis in CRC. In this study, N-glycosylated proteins and N-glycosylation sites of differential expression between primary lesions and paired liver metastatic lesions are identified. Cathepsin D (CTSD) is further screened as a potentially pivotal N-glycosylated protein in CRC liver metastasis. Glycosyltransferases complex DDOST and STT3B can regulate N-glycosylation modification at residue 263 of CTSD (a protease), thereby affecting CTSD protease to lyse ACADM. ACADM can regulate ferroptosis-related proteins (ACSL4, SLC7A11, and GPX4) to further influence the invasion and metastasis of CRC cells. This newly discovered mechanism provides potential therapeutic targets for CRC treatment and insights for controlling CRC progression and metastasis.

FRMD6, a member of the 4.1 ezrin-radixin-moesin domain-containing protein family, has been reported to inhibit tumor progression in multiple cancers. Here, we demonstrate the involvement of FRMD6 in lung cancer progression. We find that FRMD6 is overexpressed in lung cancer tissues relative to in normal lung tissues. In addition, the enhanced expression of FRMD6 is associated with poor outcomes in patients with lung squamous cell carcinoma (n = 75, P = 0.0054) and lung adenocarcinoma (n = 94, P = 0.0330). Cell migration and proliferation in vitro and tumor formation in vivo are promoted by FRMD6 but are suppressed by the depletion of FRMD6. Mechanistically, FRMD6 interacts and colocalizes with mTOR and S6K, which are the key molecules of the mTOR signaling pathway. FRMD6 markedly enhances the interaction between mTOR and S6K, subsequently increasing the levels of endogenous pS6K and downstream pS6 in lung cancer cells. Furthermore, knocking out FRMD6 inhibits the activation of the mTOR signaling pathway in Frmd6(-/-) gene KO MEFs and mice. Altogether, our results show that FRMD6 contributes to lung cancer progression by activating the mTOR signaling pathway.

Figure S3 shows that PHACTR2-AS1 promotes H3K9 methylation on rDNA

Figure S1 shows that PHACTR2-AS1 is a target gene of EZH2.

Figure S6 shows PHACTR2-AS1-30nt-RNA inhibits cancer cell growth and metastasis in vivo.

Figure S5 shows that PHACTR2-AS1 inhibits cancer cell growth and migration.

BRCA1 expression is highly regulated to prevent genomic instability and tumorigenesis. Dysregulation of BRCA1 expression correlates closely with sporadic basal-like breast cancer and ovarian cancer. The most significant characteristic of BRCA1 regulation is periodic expression fluctuation throughout the cell cycle, which is important for the orderly progression of different DNA repair pathways throughout the various cell cycle phases and for further genomic stability. However, the underlying mechanism driving this phenomenon is poorly understood. Here, we demonstrate that RBM10-mediated RNA alternative splicing coupled to nonsense-mediated mRNA decay (AS-NMD), rather than transcription, determines the periodic fluctuations in G1/S-phase BRCA1 expression. Furthermore, AS-NMD broadly regulates the expression of period genes, such as DNA replication-related genes, in an uneconomical but more rapid manner. In summary, we identified an unexpected posttranscriptional mechanism distinct from canonical processes that mediates the rapid regulation of BRCA1 as well as other period gene expression during the G1/S-phase transition and provided insights into potential targets for cancer therapy.