The global obesity epidemic has emerged as a major driver of cancer incidence and mortality, with accumulating evidence highlighting the gut-adipose-tumor axis as a critical mediator of obesity-related carcinogenesis. The gut-adipose-tumor axis is a tripartite communication network, wherein the intestinal microbiome, adipose tissue, and tumor microenvironment engage in dynamic bidirectional crosstalk that alters cancer susceptibility and progression. This review synthesizes current understanding of the epidemiology, pathophysiology, therapeutic implications, and future directions of this axis. Obesity-induced gut dysbiosis leads to systemic dissemination of pro-inflammatory microbial products and metabolites. These gut-derived signals profoundly influence adipose tissue homeostasis, exacerbating chronic low-grade inflammation, promoting macrophage infiltration and polarization, and disrupting adipokine secretion patterns. Dysfunctional adipose tissue generates cancer-promoting mediators and metabolic perturbations. The convergence of gut-derived and adipose-derived signals creates a systemic pro-carcinogenic environment that reshapes the tumor microenvironment through multiple mechanisms. Understanding the gut-adipose-tumor axis as an integrated biological system offers opportunities for cancer prevention and treatment. This is of significant importance for exploring the mechanisms of obesity-related carcinogenesis and developing new therapeutic approaches for obesity-related cancers.

Diabetic wounds constitute a significant global health challenge, affecting millions of individuals worldwide and imposing a substantial burden on healthcare systems. This review explores the complex pathophysiology of diabetic wound healing and discusses innovative interventions aimed at addressing this critical clinical problem. The impaired healing process in diabetic wounds is characterized by a multitude of interrelated factors, including cellular dysfunction, altered inflammatory responses, oxidative stress, the formation of advanced glycation end-products, and neurovascular abnormalities. Fibroblasts, keratinocytes, and endothelial cells demonstrate diminished proliferation and migration capabilities, while immune cells exhibit dysregulated responses, which contribute to a persistent inflammatory state. Complications associated with diabetes, such as neuropathy and vascular insufficiency, further exacerbate the wound healing process. Recent advancements in wound care strategies have opened new avenues for enhancing diabetic wound healing. These advancements encompass the development of advanced dressings and biomaterials, growth factor therapies, cell-based interventions, and gene therapy approaches. The integration of diverse treatment modalities, coupled with the management of systemic metabolic abnormalities, offers significant promise for improving outcomes in diabetic wound care. Future research should focus on optimizing combination therapies, developing personalized treatment algorithms, and conducting large-scale clinical trials to establish the most effective and safest interventions for diabetic wound healing.

The sensory quality of pork constitutes a complex phenotype that arises from the interplay between genetic factors and environmental conditions. As a local pig breed in China, Tibetan pigs (TPs) are known for their high-quality meat. However, their slow growth rate and low production efficiency limit their large-scale breeding. We have used Duroc as a hybrid sire to improve TP. Our study found that TPs have higher intramuscular fat content and higher levels of monounsaturated fatty acids. Duroc × Tibetan crossbred pigs (DZs) not only retain the paternal high productivity but also inherit the superior meat quality of the maternal parent. Transcriptome analysis identified IL6, GPX1, GPX3, AOX1, ALDH7A1, PTGS2, NFKBIA, ADIPOQ and PPARG as being involved in affecting meat quality. Metabolomic analysis found that betaine, carnosine, L-carnitine, and lysophosphatidylcholine were important components that affect meat quality. Joint analysis further reveals that the expression of ATF4, DGKB, GNMT, and ADSL genes is closely related to arachidonic acid, lysophosphatidylcholine, betaines, and hypoxanthine, ultimately affecting the quality of the meat. By comprehensively analyzing the carcass and meat quality traits, genes and metabolites affecting meat quality traits, this study provides new evidence for improving pork quality and guiding breeding strategies.

The CRISPR/Cas9 system has emerged as a transformative tool in genome editing, playing a pivotal role in enabling precise genetic engineering. Achieving high on-target efficiency while minimizing off-target activity is critical for translating CRISPR/Cas9 into reliable experimental and therapeutic applications. Conventional off-target detection methods are labor-intensive and cost-prohibitive, limiting their scalability. The integration of artificial intelligence has markedly reduced detection costs and substantially increased throughput. Early shallow learning models in the CRISPR/Cas9 domain, although effective in basic classification tasks, exhibited limited feature representation and poor generalization. With advances in algorithms and computational power, deep learning architectures have significantly improved off-target prediction accuracy. However, a critical blind spot remains, most current models operate predominantly at the sequence level, overlooking the downstream functional consequences of genome edits. This review summarizes the current landscape of AI-driven CRISPR/Cas9 prediction methods and proposes a forward-looking “three-layer framework” that integrates molecular, cellular, and tissue dimensions. By linking nucleotide-level edits to protein alterations, cellular functional changes, and tissue-specific responses, this framework aims to bridge the gap between sequence-based predictions and phenotypic outcomes, thereby advancing the precision and translational potential of CRISPR/Cas9 technologies. Not applicable.

With the rapid development of gene editing technology, its application in breast cancer has gradually become the focus of research. This article reviews the application of gene editing technology in the treatment of breast cancer, and discusses its challenges and future development directions. The key application areas of gene editing technology in the treatment of breast cancer will be outlined, including the discovery of new therapeutic targets and the development of drugs related to the pathway. Gene editing technology has played an important role in the discovery of new therapeutic targets. Through the use of gene editing technology, breast cancer-related genes are systematically edited to regulate key regulatory factors on related pathways or key tumor suppressor genes such as FOXC1 and BRCA, and the results are analyzed in cell or animal experiments, and the target is obtained from the experimental results, which provides important clues for the development of new drugs. This approach provides an innovative way to find more effective treatment strategies and inhibit tumor growth. In addition, gene editing technology has also promoted the personalization of breast cancer treatment. By analyzing a patient's genomic information, researchers can pinpoint key genetic mutations in a patient's tumor and design personalized treatments. This personalized treatment approach is expected to improve the therapeutic effect and reduce adverse reactions. Finally, the application of gene editing technology also provides support for the development of breast cancer immunotherapy. By editing immune cells to make them more potent against tumors, researchers are trying to develop more effective immunotherapies to bring new treatment options to breast cancer patients.

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a clinical-pathological syndrome primarily characterized by excessive accumulation of fat in hepatocytes, independent of alcohol consumption and other well-established hepatotoxic agents. Mitochondrial dysfunction is widely acknowledged as a pivotal factor in the pathogenesis of various diseases, including cardiovascular diseases, cancer, neurodegenerative disorders, and metabolic diseases such as obesity and obesity-associated MAFLD. Mitochondria are dynamic cellular organelles capable of modifying their functions and structures to accommodate the metabolic demands of cells. In the context of MAFLD, the excess production of reactive oxygen species induces oxidative stress, leading to mitochondrial dysfunction, which subsequently promotes metabolic disorders, fat accumulation, and the infiltration of inflammatory cells in liver and adipose tissue. This review aims to systematically analyze the role of mitochondria-targeted therapies in MAFLD, evaluate current therapeutic strategies, and explore future directions in this rapidly evolving field. We specifically focus on the molecular mechanisms underlying mitochondrial dysfunction, emerging therapeutic approaches, and their clinical implications. This is of significant importance for the development of new therapeutic approaches for these metabolic disorders.

Genome editing with the CRISPR/Cas9 system has revolutionized life and medical sciences, particularly in treating monogenic genetic diseases by enabling long-term therapeutic effects from a single intervention. However, the CRISPR/Cas9 system can tolerate mismatches and DNA/RNA bulges at target sites, leading to unintended off-target effects that pose challenges for gene-editing therapy development. Existing high-throughput detection and in silico prediction methods are often limited to specifically designed single guide RNAs (sgRNAs) and perform poorly on unseen sequences. To address these limitations, we introduce CCLMoff, a deep learning framework for off-target prediction that incorporates a pretrained RNA language model from RNAcentral. CCLMoff captures mutual sequence information between sgRNAs and target sites and is trained on a comprehensive, updated dataset. This approach enables accurate off-target identification and strong generalization across diverse NGS-based detection datasets. Model interpretation reveals the biological importance of the seed region, underscoring CCLMoff's analytical capabilities. The development of CCLMoff lays the foundation for a comprehensive, end-to-end sgRNA design platform, enhancing both the precision and efficiency of CRISPR/Cas9-based therapeutics. CCLMoff is a versatile tool and is publicly available at github.com/duwa2/CCLMoff .

Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique fat metabolism pattern due to long-term adaptation to harsh environments. This makes it an excellent genetic and physiological model for investigating fat deposition characteristics. Adipose tissue from different body regions displays varying morphologies, cytokines, and adipokines. This study aimed to examine adipose tissue deposition characteristics in different parts of Tibetan pigs and provide additional data to explore the underlying mechanisms of differential fat deposition. Methods: Our research identified significant differences in the morphology and gene expression patterns between subcutaneous fat (abdominal fat [AF] and back fat [BF]) and intramuscular fat (IMF) in Tibetan pigs. Results: Histological observations revealed that subcutaneous fat cells were significantly larger in area and diameter compared to IMF cells. The transcriptomic analysis further identified differentially expressed genes (DEGs) between subcutaneous fat and IMF, with a total of 65 DEGs in BF vs. IMF and 347 DEGs in AF vs. IMF, including 25 DEGs common to both comparisons. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these genes were significantly associated with lipid metabolism-related signaling pathways, such as the Wnt, mTOR, and PI3K-Akt signaling pathways. Several DEGs, including DDAH1, ADRA1B, SLCO3A1, and THBS3, may be linked to the differences in fat deposition in different parts of Tibetan pigs, thereby affecting meat quality and nutritional value. Conclusions: These findings provide new insights into the unique fat distribution and deposition characteristics of Tibetan pigs and establish a foundation for breeding strategies aimed at improving pork quality.

A chromosome-level genome assembly of Bohadschia ocellata, a member of the Holothuriidae family, was constructed through the integration of MGI DNBSEQ-T7 short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C genomic scaffolding technology. After optimization to eliminate redundant sequences, the genome assembly was precisely anchored to 23 chromosomes, resulting in a total size of 909.18 Mb. The N50 of its contig and scaffold sequences were 12.00 Mb and 38.97 Mb, respectively, confirming that the assembly was highly continuous. According to Merqury and BUSCO evaluations, the genome assembly reached a QV of 64.44 and completeness of 94.40%. From this assembly, 31,277 protein-coding genes were identified, which were 98.10% complete based on BUSCO assessment of the predicted proteome. Functional annotations were obtained from at least one database for more than 99% of these genes. This high-quality B. ocellata genome assembly from the current study could offer valuable information for further genetic and evolutionary studies of this sea cucumber species.

The aim of this study is to investigate the physiological characteristics and regulatory mechanisms of porcine intramuscular fat (IMF), subcutaneous fat (take back fat (BF), for example), and visceral fat (take perienteric fat (PF), for example) to address the challenge of optimizing meat quality without excessive fat deposition. Many improved breed pigs have fast growth rates, high lean meat rates, and low subcutaneous fat deposits, but they also have low IMF content, resulting in poor meat quality. There is usually a positive correlation between intramuscular fat and subcutaneous fat deposits. This study selected eight-month-old female Tibetan pigs as experimental subjects. After slaughter, fat samples were collected. Histological differences in adipocyte morphology were observed via hematoxylin–eosin (HE) staining of tissue sections, and phenotypic characteristics of different adipose tissues were analyzed through fatty acid composition determination. Transcriptome sequencing and untargeted metabolomics were employed to perform pairwise comparisons between different fatty tissues to identify differentially expressed genes and metabolites. A siRNA interference model was constructed and combined with Oil Red O staining and lipid droplet optical density measurement to investigate the regulatory role of WNT16 in adipocyte differentiation. Comparative analysis of phenotypic and fatty acid composition differences in adipocytes from different locations revealed that IMF adipocytes have significantly smaller areas and diameters compared to other fat depots and contain higher levels of monounsaturated fatty acids. Integrated transcriptomic and metabolomic analyses identified differential expression of WNT16 and L-tyrosine, both of which are involved in the melanogenesis pathway. Functional validation showed that inhibiting WNT16 in porcine preadipocytes downregulated adipogenic regulators and reduced lipid droplet accumulation. This cross-level regulatory mechanism of “phenotype detection–multi-omics analysis–gene function research” highlighted WNT16 as a potential key regulator of site-specific fat deposition, providing new molecular targets for optimizing meat quality through nutritional regulation and genetic modification.

Gene edited pigs have extensive and important application value in the fields of agriculture and biomedicine. With the increasing demand in medical research and agricultural markets, more and more application scenarios require gene edited pigs to possess two or even more advantageous phenotypes simultaneously. The current production of multi gene edited pigs is inefficient, time-consuming, and costly, and there is an urgent need to develop efficient and accurate multi gene editing application technologies. The polycistronic tRNA-gRNA-processing system (PTG), developed based on endogenous tRNA self-processing systems, has been shown to exhibit efficient multi gene editing in plants. This study aims to combine a PTG strategy with multiple gRNA production functions with an adenine base editor (ABE) to test its feasibility for efficient and precise multi gene base editing in pig cells. The results indicate that the PTG based integrated ABE plasmid can perform efficient base editing at multiple gene loci in pig cells. And while the gene editing efficiency was significantly improved, no indel and sgRNA dependent off target effects caused by DSB were detected. This work permit will provide a solid foundation for the production of multi gene edited pigs with agricultural and medical applications.

Activation of the induced receptor for advanced glycation end products (RAGE) leads to initiation of NF- κ B and MAP kinase signaling pathways, resulting in propagation and perpetuation of inflammation. RAGE-knockout animals are less susceptible to acute inflammation and carcinogen-induced tumor development. We have reported that most forms of tumor cell death result in release of the RAGE ligand, high-mobility group protein 1 (HMGB1). We now report a novel role for RAGE in the tumor cell response to stress. Targeted knockdown of RAGE in the tumor cell, leads to increased apoptosis, diminished autophagy and decreased tumor cell survival . In contrast, overexpression of RAGE is associated with enhanced autophagy, diminished apoptosis and greater tumor cell viability. RAGE limits apoptosis through a p53-dependent mitochondrial pathway. Moreover, RAGE-sustained autophagy is associated with decreased phosphorylation of mammalian target of rapamycin (mTOR) and increased Beclin-1/VPS34 autophagosome formation. These findings show that the inflammatory receptor, RAGE, has a heretofore unrecognized role in the tumor cell response to stress. Furthermore, these studies establish a direct link between inflammatory mediators in the tumor microenvironment and resistance to programmed cell death. Our data suggest that targeted inhibition of RAGE or its ligands may serve as novel targets to enhance current cancer therapies.

Ferroptosis is an iron-dependent and regulated form of cell death, characterized by lipid peroxidation and oxidative stress. The progressive development of pulmonary fibrosis (PF) is closely linked to the ferroptosis pathway. Although the underlying mechanisms remain incompletely defined, this field has drawn intense research attention. Notable progress has been made in identifying ferroptosis-related metabolic pathways and key targets during PF development. In this review, we first summarize the basic regulation of iron metabolism in the human lung, iron metabolic imbalance, and the activation of ferroptosis. Second, we focus on elaborating the mechanistic connections between ferroptosis and PF, encompassing the clinical features, pathological manifestations, and core pathogenic mechanisms of PF, as well as the interplay between ferroptosis and 3 specific cell types in PF: alveolar epithelial cells, macrophages, and fibroblasts. Third, the research progress in the pharmacotherapy of PF is categorized into 3 categories: drugs already approved for PF and those under clinical trials; ferroptosis-targeted therapeutic strategies, including inhibitors, natural compounds, gene therapy, and combination strategies. This review, grounded in key metabolic pathways and therapeutic targets, systematically explores the complex relationships among iron metabolic disorders, ferroptosis, and PF progression. Our aim is to provide a theoretical and practical foundation for ferroptosis-targeted PF treatment.

Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in sea cucumber remains limited. Methods: We searched the genomes of sea cucumber Holothuria leucospilota for genes encoding RIPKs and MLKL, performed phylogenetic tree, motif and functional domain analyses, and examined tissue distribution and embryonic development patterns using qPCR. Results: RIPK5 (Hl-RIPK5), RIPK7 (Hl-RIPK7) and MLKL (Hl-MLKL) were identified in sea cucumber H. leucospilota. Hl-RIPK5 and Hl-RIPK7 were mainly expressed in coelomocytes, suggesting that they play a role in innate immunity, whereas Hl-MLKL exhibited relatively low expression across tissues. During embryonic development, Hl-MLKL was highly expressed from the 2-cell stage to the morula stage, while Hl-RIPK5 and Hl-RIPK7 were primarily expressed after the morula stage, indicating different roles in embryonic development. In primary coelomocytes, Hl-RIPK5 transcriptional activity was significantly depressed by LPS, poly(I:C), or pathogen Vibrio harveyi. Hl-RIPK7 expression levels were unchanged following the same challenges. Hl-MLKL mRNA levels were significantly decreased with poly(I:C) or V. harveyi, but did not change with LPS. Conclusions: These findings provide valuable insights into the evolutionary tree and characterization of RIPK and MLKL genes in sea cucumber, contributing to the broader understanding of the RIPK gene family and MLKL in ancient echinoderms.

Cuproptosis is a new pattern of Cu-dependent cell death distinct from classic cell death pathways and characterized by aberrant lipoylated protein aggregation in TCA cycle, Fe-S cluster protein loss, HSP70 elevation, proteotoxic and oxidative stress aggravation. Previous studies on Cu homeostasis and Cu-induced cell death provide a great basis for the discovery of cuproptosis. It has gradually gathered enormous research interests and large progress has been achieved in revealing the metabolic pathways and key targets of cuproptosis, due to its role in mediating some genetic, neurodegenerative, cardiovascular and tumoral diseases. In terms of the key targets in cuproptosis metabolic pathways, they can be categorized into three types: oxidative stress, mitochondrial respiration, ubiquitin-proteasome system. And strategies for developing cuproptosis inducers and inhibitors involved in these targets have been continuously improved. Briefly, based on the essential cuproptosis targets and metabolic pathways, this paper classifies some relevant inducers and inhibitors including small molecule compounds, transcription factors and ncRNAs with the overview of principle, scientific and medical application, in order to provide reference for the cuproptosis study and target therapy in the future.

Varying from other identified cell death pathways, cuproptosis is a new type of regulated cell death characterized by excess Cu ions, abnormal aggregation of lipoylated proteins in TCA cycle, loss of Fe-S cluster proteins, upregulation of HSP70, leading to proteotoxic and oxidative stress. Cuproptosis is highly concerned by scientific community and as the field of cuproptosis further develops, remarkable progress has been made in the verification and mechanism of cuproptosis, and methods used to detect cuproptosis have been continuously improved. According to the characteristic changes of cuproptosis, techniques based on cell death verification, Cu content, morphology, molecular biology of protein levels of cuproptosis-related molecules and biochemical pathways of cuproptosis-related enzyme activity and metabolites of oxidative stress, lipoic acid, TCA cycle, Fe-S cluster proteins, oxidative phosphorylation, cell respiration intensity have been subject to cuproptosis verification and research. In order to further deepen the understanding of detecting cuproptosis, the principle and application of common cuproptosis detection methods are reviewed and categorized in cellular phenomena and molecular mechanism in terms of cell death, Cu content, morphology, molecular biology, biochemical pathways with a flow chart. All the indicating results have been displayed in response to the markers of cuproptosis, their advantages and limitations are summaried, and comparison of cuproptosis and ferroptosis detection is performed in this study. Our collection of methods for cuproptosis detection will provide a great basis for cuproptosis verification and research in the future.

[Objective]In mammals,Toll-like receptors and antimicrobial peptide genes are important components of the innate immune system,which play a crucial role in fighting against pathogen attacks.The study was conducted to explore the expression differences of Toll-like receptor and antimicrobial peptide genes between different immune organs or tissues in Tibetan pigs and Duroc-Landrace-Yorkshire pigs,with an aim to reveal the potential contribution of these genes to disease resistance and immune response and provide theoretical support for the screening of molecular markers for disease resistance.[Method]The mRNA abundance of Toll-like receptors genes(TLR1-TLR9)and two types of antimicrobial peptide genes(PBD-1 and PR-39)in lungs,mesenteric lymph nodes,inguinal lymph nodes,submandibular lymph nodes and spleens of 6-month-old Tibetan and Duroc-Landrace-Yorkshire pigs were detected by qPCR.[Result]The mRNA expression of Toll-like receptors and antimicrobial peptide genes in most of the immune organs or tissues of Tibetan pigs was significantly higher than that of Duroc-Landrace-Yorkshire pigs.Among them,the mRNA expression of TLR1 and TLR2 in lungs was increased by about 50%,and PR-39 was increased by 2.6 times;the expression of TLR4 in mesenteric lymph nodes was increased by 40%,and the expression of TLR1 and PR-39 was increased by 88%and 3 times,respectively.In the inguinal lymph nodes,the expression of TLR1 and TLR2 was increased by about 2 times,and the expression of TLR9 and PR-39 was increased by 70%,especially,the expression of PR-39 increasing by 7 times;The expression of TLR1,TLR2,TLR4 and TLR7 in submandibular lymph nodes was increased by more than 2 times,and the expression of PR-39 was increased by nearly 7 times,which was similar to that in inguinal lymph nodes;the expression of TLR1 in the spleen rose by 3.5 times,which was similar to that in submandibular lymph nodes.The expression of TLR4 and TLR9 increased by about 50%,and the expression of PR-39 increased by 2.5 times.[Conclusion]Tibetan pigs show higher expression levels of Toll-like receptors and antimicrobial peptide genes in multiple immune organs or tissues compared to Duroc-Landrace-Yorkshire pigs.It is implied that Tibetan pigs may possess stronger innate immunity and be able to generate more effective local or systemic immune responses against pathogenic microbial infections.The results of this study provide important theoretical support for the identification of disease resistance molecular markers and are expected to provide a scientific basis for further improvement of disease resistance in Tibetan pigs and other pig breeds.

Adipose tissue, an indispensable organ, fulfils the pivotal role of energy storage and metabolism and is instrumental in maintaining the dynamic equilibrium of energy and health of the organism. Adipocyte hypertrophy and adipocyte hyperplasia (adipogenesis) are the two primary mechanisms of fat deposition. Mature adipocytes are obtained by differentiating mesenchymal stem cells into preadipocytes and redifferentiation. However, the mechanisms orchestrating adipogenesis remain unclear. Autophagy, an alternative cell death pathway that sustains intracellular energy homeostasis through the degradation of cellular components, is implicated in regulating adipogenesis. Furthermore, adipose tissue functions as an endocrine organ, producing various cytokines, and certain inflammatory factors, in turn, modulate autophagy and adipogenesis. Additionally, autophagy influences intracellular redox homeostasis by regulating reactive oxygen species, which play pivotal roles in adipogenesis. There is a growing interest in exploring the involvement of autophagy, inflammation, and oxidative stress in adipogenesis. The present manuscript reviews the impact of autophagy, oxidative stress, and inflammation on the regulation of adipogenesis and, for the first time, discusses their interactions during adipogenesis. An integrated analysis of the role of autophagy, inflammation and oxidative stress will contribute to elucidating the mechanisms of adipogenesis and expediting the exploration of molecular targets for treating obesity-related metabolic disorders.