Understanding the early stages of carcinogenesis requires detailed insight into the abnormalities present in normal cells before cancer onset. In the past, it was difficult to analyze genomic abnormalities in small clones in normal tissues. However, recent technological advances in genomic analysis have shed light on the process of accumulation of somatic mutations in normal cells, which is driven by factors such as aging and environmental influences. Even in normal tissues, clones that have acquired driver mutations-either directly contributing to carcinogenesis or adapting to specific pathological or genetic backgrounds-are frequently selected, leading to clonal expansion. Normal cells undergo clonal evolution into cancer cells over several decades, with the initial acquisition of a driver mutation occurring in early life. Here this review presents recent findings concerning the accumulation of somatic mutations in normal cells, acquisition of driver mutations and clonal evolution toward cancer.

Despite therapeutic advances, ovarian cancer remains a major clinical challenge owing to its frequent metastasis and chemoresistance, which are often driven by cancer stem cells (CSCs) and proangiogenic signaling. Here we demonstrated that dihydroartemisinin (DHA), a derivative of the antimalarial drug artemisinin, inhibits CSC characteristics, tumor neovascularization and resistance to carboplatin via a microRNA-dependent mechanism in ovarian cancer. DHA substantially inhibited CSC properties, tumorigenicity and vascular endothelial growth factor A (VEGF-A)-mediated tumor neovascularization in ovarian cancer. Moreover, the combined treatment with DHA and carboplatin produced a synergistic effect that reduced tumor burden, chemoresistance and peritoneal dissemination in vivo. Mechanistically, DHA downregulated BMI-1 and VEGF-A/vascular endothelial growth factor receptor 2 (VEGFR2), which are critical factors in CSC maintenance and metastasis, via the upregulation of miR-200b. An analysis of ovarian tumor tissues collected from patients enrolled in our clinical cohort revealed that dual positivity for BMI-1 and VEGF-A was associated with poor progression-free survival. Overall, DHA targets the miR-200b-BMI-1/VEGF-A axis to suppress cancer stemness and metastatic potential, highlighting its therapeutic promise in overcoming the limitations of standard chemotherapy for ovarian cancer. The clinical trial number for this study is not applicable.

Artificial intelligence (AI) is reshaping biomedical research by providing scalable computational frameworks suited to the complexity of biological systems. Central to this revolution are bio/chemical language models, including large language models, which are reconceptualizing molecular structures as a form of 'language' amenable to advanced computational techniques. Here we critically examine the role of these models in biology and chemistry, tracing their evolution from molecular representation to molecular generation and optimization. This review covers key molecular representation strategies for both biological macromolecules and small organic compounds-ranging from protein and nucleotide sequences to single-cell data, string-based chemical formats, graph-based encodings and three-dimensional point clouds-highlighting their respective advantages and inherent limitations in AI applications. The discussion further explores core model architectures, such as bidirectional encoder representations from transformers-like encoders, generative pretrained transformer-like decoders and encoder-decoder transformers, alongside their sophisticated pretraining strategies such as self-supervised learning, multitask learning and retrieval-augmented generation. Key biomedical applications, spanning protein structure and function prediction, de novo protein design, genomic analysis, molecular property prediction, de novo molecular design, reaction prediction and retrosynthesis, are explored through representative studies and emerging trends. Finally, the review considers the emerging landscape of agentic and interactive AI systems, showcasing briefly their potential to automate and accelerate scientific discovery while addressing critical technical, ethical and regulatory considerations that will shape the future trajectory of AI in biomedicine.

A recent ground-breaking study suggested that small RNA from mammalian cells can undergo N-glycan modifications (termed glycoRNA). The discovery relied upon a metabolic glycan labeling strategy in combination with commonly used phase-separation-based RNA isolation. Following the reported procedure, here we likewise identify an N-glycosylated species in the RNA fraction. However, our results suggest that the reported RNase sensitivity of the glycosylated species depends on the specific RNA purification method. This suggests the possibility of copurifying unexpected RNase-insensitive N-glycoconjugates during glycoRNA isolation. The co-existence of two independent, yet highly similar molecular entities, complicates biochemical assays on glycoRNA and calls for more specific approaches for glycoRNA analysis. To address this, we propose a control experiment that can help distinguish genuine glycoRNA species from copurified glycoconjugates.

Alternative splicing significantly contributes to gene expression heterogeneity and disease progression, yet analyzing its dynamics in short genetic regions such as microexons remains challenging. Here we identified notable variations in ribosomal protein S24 (RPS24) splicing patterns across breast cancer subtypes and investigated this novel regulatory mechanism. To overcome the complexity of analyzing three consecutive microexons (3 bp, 18 bp and 22 bp), we developed a specialized approach combining splice junction read analysis with fragment analysis for accurate isoform quantification. We observed distinct isoform compositions across breast cancer cell lines. The 3-bp exon-containing isoform (ex4:3 bp) of RPS24 showed significantly higher expression in estrogen receptor-positive (ER) cells, demonstrating the strongest association with estrogen receptor signaling among all analyzed genes. This isoform functions as a molecular sensor for therapeutic interventions, being consistently upregulated following mTOR or CDK4/6 inhibition but consistently reduced across diverse drug-resistant cell lines, regardless of resistance mechanism. Through systematic RNA-binding protein screening and crosslinking immunoprecipitation followed by high-throughput sequencing analysis, we identified PTBP1 as a critical upstream regulator mediating microexon skipping. Analysis of multiple patient cohorts demonstrated that decreased ex4:3 bp expression strongly correlated with poor epithelial differentiation and metastatic progression specifically in ER breast cancer. Our findings suggest that RPS24 alternative splicing is associated with a multilayered regulatory network integrating ER signaling, cell cycle and PTBP1-mediated splicing. The ex4:3 bp isoform serves as a potential biomarker for drug resistance and treatment response in ER breast cancer.

RNA molecules are now recognized as active regulators of DNA double-strand break repair. In end-joining pathways, nascent transcripts promote repair through RNA:DNA hybrids, end bridging and RNA-templated synthesis. In homologous recombination, RNA:DNA hybrids modulate DNA end resection, recruit repair factors and enable RNA-templated repair, with DNA polymerase ζ emerging as a key reverse transcriptase in this process. Transcription at double-strand break sites generates regulatory RNAs that further influence pathway choice and repair fidelity. Long noncoding RNAs, RNA-binding proteins and RNA modifications add additional control layers. Advances in genomic mapping, reporter assays and in vitro methods are now dissecting these complex RNA-mediated processes, although important challenges remain in capturing their full kinetics and contributions. Finally, RNA-templated genome editing platforms, such as prime editing, harness these principles for precise, programmable DNA repair. Together, these findings position RNA as a multifunctional player in genome maintenance and engineering.

Although angiogenesis following tendon injury was expected to provide nutrients for regeneration and repair, excessive angiogenesis may be associated with poor long-term outcomes in tendinopathy. Here we aim to explore the pathological role of angiogenesis in the progression of tendinopathy. Patients with tendinopathy were categorized into a hypervascularization group (HyperV) and a hypovascularization group (HypoV), and postarthroscopic outcome and histopathology were compared. In addiiton, tendon injury models and tenocyte stress models were employed to investigate the temporal-spatial vascular pattern characteristics and mechanisms involved in the progression of tendinopathy. This study finds that the HyperV group exhibited worse postoperative pain and functional outcomes and higher Bonar's pathological scores and vascular density. Bulk RNA sequencing and pathological staining revealed that decreased FHL2 and increased YAP1/sFRP2 expression in tenocytes were strongly associated with disorganized tissue pathology, aggravated inflammation and increased vascular abundance in the HyperV group and tendon injury models (Td-Inj and Td-Sut groups). Three-dimensional vascular imaging demonstrated the formation of morphologically complex and abnormally distributed blood vessels in the Td-Inj and Td-Sut groups, which was significantly alleviated by YAP1 knockdown. In activated tenocytes, FHL2 deficiency-mediated YAP1 overexpression led to the overexpression and extracellular secretion of sFRP2, thereby enhancing endothelial angiogenesis. FHL2 overexpression partly mitigated vascular remodeling and improved tendon blood perfusion in rats. In summary, FHL2/YAP1/sFRP2-mediated pathological vascular remodeling disrupts the homeostasis of tendon repair and regeneration. This study underscores the importance of a systematic vascular assessment, incorporating abundance, morphology, and spatial distribution, in tendinopathy.

B cell malfunction is implicated in the pathogenesis of systemic lupus erythematosus (SLE) through the release of proinflammatory cytokines and the production of autoreactive antibodies. RNA N-methyladenosine (mA) is the predominant post-transcriptional RNA modification that has been reported to control various biological processes. Whether RNA mA alteration and mA reader protein YTHDF1 contribute to B cell activation and terminal B cell differentiation in SLE has not been fully demonstrated. Here we observed that SLE peripheral B cell subsets, activated B cells and differentiated plasma cells (PCs) had abnormally elevated levels of YTHDF1, the deficit of which attenuated PC differentiation both in vitro and in mouse models that have been immunized with keyhole limpet hemocyanin (KLH) or N-propionyl polysialic acid (NP-KLH). Utilizing RNA sequencing, RNA immunoprecipitation, mA immunoprecipitation and other functional experiments, we have identified and described a PC-promoting role of YTHDF1. YTHDF1 binds to the mA-marked 3' untranslated region of transcription factor IRF4 messenger RNA to enhance its stability, thereby facilitating PC differentiation. Depletion of YTHDF1 hindered the differentiation of PCs, reduced the generation of autoantibodies and ameliorated the lupus-like phenotypes in an imiquimod-treated mouse model. Overall, this study highlights a distinct role of YTHDF1 in promoting PC differentiation through the direct regulation of IRF4 in an mA-dependent manner and identifies YTHDF1 as a potential target for the treatment of SLE.

The neurokinin-1 receptor (NK1R) has been investigated as a potential target for major depressive disorder owing to its role in stress regulation and neuroinflammation. However, clinical trials of NK1R antagonists have yielded inconsistent results, leaving it unclear whether these outcomes reflect limitations of NK1R as a therapeutic target or shortcomings inherent to the clinical candidates tested. The majority of previously developed NK1R antagonists contain a 3,5-bis-trifluoromethylphenyl moiety, which enhances receptor binding but may also influence drug metabolism, pharmacokinetics or receptor interactions, potentially affecting therapeutic efficacy. Whether structurally distinct NK1R antagonists exhibit different antidepressant potential remains an open question. Here we used computational approaches to identify NK1R antagonists lacking the 3,5-bis-trifluoromethylphenyl group and evaluated their effects in preclinical models of depression. Several compounds exhibited NK1R antagonistic activity and reduced depressive-like behaviors, with compound #15 demonstrating the most pronounced effects. Molecular docking and molecular dynamics simulations revealed a distinct binding mode for compound #15, characterized by a hydrogen bond interaction with Asn109 and π-π stacking with His197, suggesting structural differences that may influence NK1R modulation. These findings support the potential of structurally diverse NK1R antagonists to modulate behavior and neuroinflammatory responses in preclinical models. While the relevance of these structural differences to clinical outcomes remains to be determined, our results provide a preliminary framework for further investigation of chemically novel NK1R antagonists in the context of major depressive disorder.

Tumor cells rearrange cytoskeletal networks, harmonize signaling pathways and modulate cell fate to initiate tumor growth and metastasis. Activating mutations in the canonical Wnt-β-catenin pathway are associated with aggressiveness and poor prognosis in adrenocortical carcinoma (ACC). However, the contribution of noncanonical Wnt pathways, which are known to regulate cell polarity and migration, is still widely unknown. Here we comprehensively investigated canonical and noncanonical Wnt signaling along with cytoskeleton networks, stemness programs and HOX gene expression in recently developed 2D and 3D cultures of primary, local and distant metastatic ACC models. We report that tumor spheroids derived from nonmetastatic primary tumors correlated strongly with the overexpression of canonical Wnt signaling components, while metastatic ACC models demonstrated shifts toward noncanonical Wnt pathways together with perturbed expression of matrix-cytoskeleton-nucleoskeleton markers and related changes in the cytoarchitecture of respective tumor spheroids. Consistent with a potential noncanonical Wnt activation in the metastatic models, an abundance and relocalization of proteins associated with tumor aggressiveness such as β-catenin, β-actin, vimentin and nucleolin as well as specific HOX-cluster activation was detected, suggesting strong potential for specific reconfigurations of metastatic tumor niches. Furthermore, all models demonstrated key properties of cancer stem cells, although with varying degrees of expression of progenitor and stem cell markers, which could be dynamically modulated by treatments and therapies. Overall, our results draw parallels between canonical and noncanonical Wnt signaling, differential cytoskeletal remodeling, stemness properties and various cellular plasticities in primary tumor and metastasis-derived models of ACC.

Tumor necrosis factor receptor 2-positive regulatory T (TNFR2 T) cells, the most suppressive subset of T cells, are enriched in malignant pleural effusion (MPE), contributing to disease progression. However, the underlying mechanisms responsible for their accumulation remain unclear. Here we demonstrate that the C-X-C motif chemokine ligand 16 (CXCL16)/C-X-C chemokine receptor type 6 (CXCR6) axis plays a critical role in recruiting TNFR2 T cells to MPE, with cancer-associated fibroblasts serving as the primary source of CXCL16. Mechanistically, under the hypoxic conditions prevailing in the pleural cavity, cancer-associated fibroblasts in MPE undergo glycolysis, which in turn leads to an increase in the production of endogenous lactate. This elevated lactate induces histone H3 lysine 18 lactylation (H3K18la) at the promoter regions of both the CXCL16 gene and its transcription factor forkhead box O3 (FOXO3), which may contribute to CXCL16 transcription. TNFR2 T cells that express high levels of CXCR6, the only receptor for CXCL16, are subsequently recruited into MPE. The infiltration of TNFR2 T cells may reinforce the immunosuppressive milieu of MPE, facilitating disease progression. Collectively, these findings uncover a novel mechanism governing immunosuppression in MPE, providing new insights into potential therapeutic strategies to disrupt this process.

Ferroptosis is a distinct form of programmed cell death that differs from other pathways. It is characterized by iron-dependent lipid peroxidation and results in morphologically lethal cellular damage. With advancing insight, triggering ferroptosis is a promising strategy for cancer therapy. RNA-binding proteins (RBPs) comprise a diverse group of molecules that regulate various RNA processes through interactions with transcripts. Research has highlighted the pivotal role of RBPs in controlling biological functions. Evidence indicates that RBPs play important roles in regulating ferroptosis. Heterogeneous nuclear ribonucleoprotein U (HnRNPU) is a well-known RBP involved in RNA splicing, messenger RNA stability and chromatin organization. Elevated HnRNPU expression has been implicated in cancer progression and is associated with poor prognosis. However, the function and underlying mechanisms of HnRNPU in colon adenocarcinoma (COAD) remain poorly understood. Here we identify increased HnRNPU expression in patients with COAD, with higher levels correlating with poor patient survival. HnRNPU knockdown inhibited cell proliferation and induced cell cycle arrest by suppressing cyclin E1 and CDK2. RNA-sequencing analysis revealed HnRNPU's involvement in ferroptosis regulation. In line with this, HnRNPU deletion induced ferroptosis and increased sensitivity to RSL3 treatment and cysteine deprivation. xCT overexpression (SLC3A2/SLC7A11) counteracted the antiproliferative and proferroptotic effects of HnRNPU knockdown. Mechanistically, HnRNPU stabilized the mRNAs of SLC7A11 and SLC3A2 by binding to their 3' untranslated regions, thereby promoting cysteine uptake and glutathione synthesis. Findings demonstrate that HnRNPU promotes proliferation and inhibits ferroptosis by regulating the mRNA stability of SLC7A11 and SLC3A2. Targeting HnRNPU is a potential therapeutic approach for COAD treatment.

Tumor fibrosis is recognized as a malignant hallmark in various solid tumors; however, the clinical importance and associated molecular characteristics of tumor fibrosis in liver metastases (LM) from colorectal cancer (CRLM) remain poorly understood. Here we show that patients with CRLM whose liver metastases (LM) exhibited tumor fibrosis (Fibrosis+ LM) had significantly worse progression-free survival (P = 0.025) and overall survival (P = 0.008). Single-cell RNA sequencing revealed that the tumor microenvironment of the Fibrosis+ LM was characterized by T cells with an exhausted phenotype, macrophages displaying a profibrotic and suppressive phenotype and fibrosis-promoting fibroblasts. Further investigation highlighted the pivotal role of VCAN_eCAF in remodeling the tumor fibrosis in the tumor microenvironment of Fibrosis+ LM, emphasizing potential targetable interactions such as FGF23 or FGF3-FGFR1. Validation through multiplex immunohistochemistry/immunofluorescence and spatial transcriptomics supported these findings. Here we present a comprehensive single-cell atlas of tumor fibrosis in LM, revealing the intricate multicellular environment and molecular features associated with it. These insights deepen our understanding of tumor fibrosis mechanisms and inform improved clinical diagnosis and treatment strategies.

Melanosomes are highly specialized organelles responsible for melanin synthesis, storage and transport in melanocytes, playing a central role in pigmentation and skin homeostasis. Although melanosome biogenesis and trafficking have been well characterized, emerging evidence emphasizes the importance of melanosome degradation in regulating pigment levels. Among the degradation pathways, melanophagy-a selective form of autophagy targeting melanosomes-has recently emerged as an important mechanism for the turnover of damaged, immature, or excess melanosomes. Here we highlight current insights into melanophagy mechanisms, including molecular regulators and signaling pathways. We also discuss the potential of modulating melanophagy as a novel cosmetic or therapeutic approach for managing hyperpigmentation, offering an alternative to traditional strategies focused solely on inhibiting melanin synthesis. By emphasizing the role of organelle clearance, melanophagy provides a new paradigm in the regulation of skin pigmentation.

Extensive research has underscored the pivotal role of DNA methylation in the development of various diseases, including osteoarthritis (OA). DNA methylation is regulated by methylation writers, readers, and erasers. As a crucial methylation reader, methyl-CpG-binding domain2 (MBD2) has been implicated in modulating the occurrence and progression of multiple inflammatory diseases. This study aims to investigate whether MBD2 contributes to the pathogenesis of OA through its regulation of DNA methylation. Our study confirmed that MBD2 was increased in OA cartilage tissues from humans as well as mice with destabilization of the medial meniscus, despite a reduction in its nuclear import. Specific knockout of Mbd2 in cartilage exacerbated cartilage degradation and accelerated OA progression. Mechanistically, RNA sequencing studies demonstrated that the deletion of MBD2 induced ferroptosis in chondrocytes. Subsequent CUT&Tag and reduced representation bisulfite sequencing analyses revealed that MBD2 binds to the Steap3 promoter region and modulates its methylation state in chondrocytes. STEAP3 catalyzes the reduction of ferric iron (Fe) to ferrous iron (Fe), contributing to the induction of ferroptosis. The administration of a ferroptosis inhibitor and adeno-associated virus-mediated Steap3 knockdown alleviated OA induced by MBD2 deletion. Adeno-associated virus-mediated overexpression of Mbd2 partially mitigated destabilization of the medial meniscus-induced OA. Our findings provide evidence linking DNA methylation readers to OA development, and targeting MBD2 may offer a promising therapeutic strategy for OA treatment.

Recent epidemiological studies have shown that dietary fructose intake is associated with an increased risk of colorectal cancer, yet its specific molecular mechanisms in colon carcinogenesis remain underexplored. Here we investigate the molecular mechanisms by which dietary fructose contributes to colon carcinogenesis, focusing on the role of mitochondrial NADP-dependent isocitrate dehydrogenase 2 (IDH2). Using an unbiased multiomics approach (transcriptomics and proteomics), liver and colon tissues from fructose-fed wild-type mice were analyzed to identify key genes involved in cancer-related pathways. In addition, human liver transcriptomic data (GSE256398) were analyzed to confirm alterations in aryl hydrocarbon receptor (AhR) signaling and the sirtuin (SIRT)3-IDH2 axis. IDH2-knockout mice were exposed to a dietary carcinogen, 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP), to validate IDH2's role in colon cancer development. In vitro, fructose's effects on SIRT3 expression and IDH2 activity were assessed. Fructose-fed wild-type mice exhibited suppressed AhR signaling, increased oxidative stress and mitochondrial dysfunction via the SIRT3-IDH2 axis. In human liver datasets, AhR-associated genes and SIRT3-IDH2 expression were reduced in metabolic dysfunction-associated steatotic liver disease and cirrhosis. The IDH2-knockout mice showed heightened DNA damage, colonic tumorigenesis and mitochondrial and glutathione-mediated detoxification disruptions following PhIP exposure. In vitro, fructose reduced SIRT3 expression and IDH2 activity, further supporting its role in promoting colon carcinogenesis. Fructose promotes colon carcinogenesis by disrupting mitochondrial function and impairing DNA damage response mechanisms, particularly through SIRT3-IDH2 axis suppression. These findings highlight the critical role of mitochondrial dysfunction in fructose-induced carcinogenesis and suggest the SIRT3-IDH2 axis as a potential therapeutic target.

The abnormal deposition of α-synuclein (α-syn) and neuroinflammation are key features of synucleinopathies. We recently demonstrated that leucine-rich repeat kinase 2 (LRRK2) and nuclear factor of activated T cells 1 (NFAT1) modulate the neurotoxic inflammation in synucleinopathies mediated by microglia. Therefore, we hypothesized that targeting NFAT1 might ameliorate the microglial neurotoxicity in synucleinopathies. Here we utilized 11R-VIVIT, an NFAT1 inhibitory peptide, in in vivo, ex vivo and in vitro synucleinopathy models to evaluate the effects of NFAT1 inhibition to test this hypothesis. The microglia in synucleinopathy mouse models become excessively activated due to chronic disease conditions, thereby increasing the expressions of proinflammatory cytokines in these cells and decreasing the expressions of genes associated with microglial mobility and phagocytosis, strongly associated with neurodegeneration and pathogenic α-syn deposition. However, we observed that the inhibition of NFAT1 decreased the microglial neuroinflammation, thereby ameliorating neurodegeneration and α-syn neuropathology in vivo. Furthermore, the comprehensive in vivo transcriptomic analysis of the microglia revealed that the inhibition of NFAT1 restored their mobility and phagocytic abilities via upregulations of related genes. Our study proposes that the inhibition of NFAT1 redirects the excessively activated microglia to active healthy microglia, thereby reducing synucleinopathy neurotoxicity.

Lung cancer, particularly non-small-cell lung cancer (NSCLC), remains a leading cause of cancer-related mortality worldwide. Recent studies have implicated pyrroline-5-carboxylate reductase 1 (PYCR1), a key enzyme in proline biosynthesis, in cancer progression, yet its specific role in lung cancer remains unclear. Here we demonstrate that PYCR1 plays a critical role in NSCLC progression through its functional association with the epidermal growth factor receptor (EGFR) and Toll-like receptor (TLR) signaling pathways. An analysis of patient datasets revealed that PYCR1 is upregulated in NSCLC tissues, with the enrichment of cancer-associated pathways in PYCR1-upregulated patients. Functional studies in PYCR1-knockout (PYCR1-KO) lung cancer cells generated via CRISPR-Cas9 showed reduced cell proliferation, migration, colony formation and tumor spheroid growth both in vitro and in vivo. Mechanistically, PYCR1 stabilizes EGFR by forming a complex with EGFR and USP11, thereby enhancing EGFR deubiquitination and stability. In addition, PYCR1 promotes TLR signaling by interacting with key downstream molecules, including TRAF6, TAK1, ECSIT and TAB2, facilitating their ubiquitination and NF-κB activation. The loss of PYCR1 attenuates EGFR- and TLR-induced signaling cascades, resulting in reduced activation of AKT, TAK1 and NF-κB. Importantly, treatment with PYCR1-IN-1, a selective PYCR1 inhibitor, significantly suppressed EGFR- and TLR-induced tumor spheroid growth in multiple lung cancer cell lines, underscoring PYCR1's potential as a therapeutic target. Collectively, our findings establish PYCR1 as a critical regulator of EGFR and TLR signaling pathways, driving lung cancer progression. Targeting PYCR1 with pharmacological inhibitors such as PYCR1-IN-1 offers a promising strategy for combating EGFR- and TLR-driven NSCLC progression.

In recent years, cryo-electron microscopy structures of ion channels in complex with G proteins have been resolved, providing insights into the molecular mechanisms underlying the crosstalk between G protein-coupled receptors (GPCRs) and ion channels. Downstream signaling initiated by GPCR activation can indirectly modulate ion channel activity. Alternatively, the direct binding of Gα or Gβγ subunits to ion channels can directly regulate their ion conduction activity. Recent cryo-electron microscopy structures, such as TRPC5-Gα, GIRK-Gβγ and TRPM3-Gβγ, have elucidated these direct interactions and advanced our understanding of how Gα or Gβγ subunits activated by GPCRs modulate ion channel activity. In addition, the structure of the TRPV4-RhoA complex has revealed that small G proteins can also directly modulate ion channels. Understanding the physiological roles of these complexes will be critical for their potential use as pharmacological targets. Here we summarize the current knowledge of the interactions between ion channels and G proteins.