Abstract Following extensive liver resections, diminished liver regeneration impairs the maintenance or restoration of sufficient functional liver mass. Currently, effective therapies to restore liver regeneration are lacking, rendering liver transplantation the sole treatment option for end-stage liver disease. Therefore, it is imperative to elucidate the regulatory mechanisms underlying liver regeneration. In this study, we employed a multi-omics approach integrating Hi-C, RNA-seq, and ATAC-seq to dissect the early regulatory mechanisms of liver regeneration in rats and mice. Our results indicate that immune and inflammatory processes are markedly enriched during the early phase of regeneration, accompanied by upregulation of glucocorticoids (GCs) and their receptor (GR). First, the expression dynamics of the GC-related circadian gene Nr1d1 and its regulatory network—including Nfκbiα, Arntl, Clock, and Rora—align with chromatin reorganization, leading us to propose that the GC–GR–Nr1d1 axis is involved in maintaining liver homeostasis. Second, the GR-regulated FoxO family is significantly enriched, and the FoxO-associated gene Klf2 exhibits coordinated changes in expression, chromatin accessibility, and chromatin structure. Functional experiments demonstrate that Klf2 negatively regulates hepatocyte proliferation. Hence, we propose the GC–GR–FoxOs–Klf2 axis acts as a checkpoint in hepatocyte proliferation, preventing premature activation of proliferation- and cell cycle-related genes and ensuring orderly and efficient liver regeneration. Our findings on the role of GCs in liver regeneration may further support their future therapeutic application in liver diseases such as liver fibrosis, alcoholic cirrhosis, and hepatocellular carcinoma (HCC).

Cancer is a global health issue with a high mortality rate, and early detection significantly improves patient survival rates. Currently, the primary methods for cancer detection include imaging examination and tissue biopsy. However, due to technical limitations, early detection can result in invasiveness, false positives, and other complications for patients. Therefore, there is an urgent need for new cancer biomarkers to address these challenges and enhance the accuracy and non-invasiveness of detection. With advances in molecular biology, nucleic acid biomarkers have become invaluable for early cancer diagnosis, prognosis assessment, and therapeutic monitoring. Epigenetic biomarkers, such as DNA methylation and non-coding RNA, play a crucial role in tumorigenesis by regulating related gene expression. However, although they offer significant potential for early warning, the complexity of the detection process coupled with tissue specificity makes the interpretation of results challenging. Liquid biopsy, such as circulating tumor DNA (ctDNA), provide a non-invasive method for dynamic tumor monitoring. However, its applicability is limited due to low sensitivity and high cost. Combining these two approaches can help address their individual shortcomings. CtDNA methylation enhances screening specificity, while multimodal strategies are expected to overcome the limitations of single techniques. The purpose of this review is to explore the role of cancer nucleic acid markers in cancer diagnosis and prognosis, examine their molecular mechanisms, and evaluate the advantages and limitations of these markers. Additionally, it will discuss biomarkers related to the tumor microenvironment and immune response, and their interactions with nucleic acids.

BackgroundBrucella spp., facultative intracellular pathogens that cause brucellosis, drive pathogenesis by invading host cells and establishing intracellular persistence. While their molecular mechanisms are well-characterized, how Brucella induces chromatin restructuring in host cells remains poorly understood, representing a critical gap in host-pathogen interaction research.MethodsUsing an established in vitro infection model of Brucella-infected RAW264.7 murine macrophages, we integrated Hi-C, ATAC-seq, and RNA-seq to generate multi-omics datasets. Multidimensional comparative genomics approaches were employed to systematically map infection-induced changes in host chromatin architecture and functional genomic organization.ResultsOur findings unveiled substantial alterations in the host chromatin architecture, characterized by a reduction in B-B compartment regions interactions, an increase in A-B compartment interactions, and diminished long-range chromatin contacts. Crucially, Brucella reshaped chromatin compartmentalization, activating interferon-stimulated genes (ISGs) in regions transitioning from compartment B to A. Enhanced sub-TADs interactions within ISG clusters further facilitated their coordinated expression. Additionally, infection remodeled chromatin loop structures, strengthening interactions linked to immune-related gene activation.ConclusionThese results demonstrate that host cells undergo substantial chromatin remodeling during acute Brucella infection as a defense mechanism against pathogen invasion. Our findings provide critical insights into host-pathogen interactions and suggest potential epigenetic targets for managing brucellosis.

AbstractDNA lesions are linked to cancer, aging, and various diseases. The recognition and sequencing of special DNA lesions are of great interest but highly challenging. In this paper, an unnatural‐base‐pair‐promoting method for sequencing highly mutagenic ethenodeoxycytidine (εC) DNA lesions that occurred frequently is developed. First, a promising unnatural base pair of dεC–dNaM to recognize εC lesions is identified, and then a conversion PCR is developed to site‐precise transfer dεC–dNaM to dTPT3–dNaM for convenient Sanger sequencing. The low sequence dependence of this method and its capacity for the enrichment of dεC in the abundance of as low as 1.6 × 10–6 nucleotides is also validated. Importantly, the current method can be smoothly applied for recognition, amplification, enrichment, and sequencing of the real biological samples in which εC lesions are generated in vitro or in vivo, thus offering the first sequencing methodology of εC lesions at single‐base resolution. Owing to its simple operations and no destruction of inherent structures of DNA, the unnatural‐base‐pair strategy may provide a new platform to produce general tools for the sequencing of DNA lesions that are hardly sequenced by traditional strategies.

Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) are key downstream effectors of the Hippo pathway that regulate organ size, tissue homeostasis, and cancer development. YAP/TAZ play crucial regulatory roles in organ growth, cell proliferation, cell renewal, and regeneration. Mechanistically, YAP/TAZ influence the occurrence and progression of liver regeneration (LR) through various signaling pathways, including Notch, Wnt/β-catenin, TGF-β/Smad. While the activation of YAP/TAZ can promote the regeneration of damaged liver tissue, their mechanisms of action may differ under various LR conditions. Furthermore, excessive activation of YAP/TAZ may also lead to severe liver damage, manifesting as alcoholic hepatitis, liver fibrosis, and even liver cancer. Here, we review the role and mechanisms of YAP/TAZ in LR and liver disease, highlighting the potential for advancements in clinical diagnosis and treatment targeting YAP/TAZ in these contexts.

目的 了解大鼠肝再生(LR)0h、6 h和72h时骨髓瘤基因(MYC)及其mRNA相互作用的微小RNA(miRNA)和环状RNA(circRNA)调节肝细胞周期启动及终止的途径与方式.方法 按Higgins等方法制备大鼠2/3肝切除(PH)模型,按Smedsrod等方法分离肝细胞,用大规模定量检测技术测定大鼠肝再生中肝细胞的mRNA、miRNA和circRNA[合称内源竞争RNA(ceRNA)]表达变化,用Cytoscape 3.2软件构建ceRNA 的相互作用网,用ceRNA综合分析等方法解析它们的表达相关性和作用相关性.结果 在PH后肝细胞周期启动0～6h间的0h和6 h 时,MYC mRNA 的比值为 0.15±0.03 和 2.36±0.2,miR-134-5p 为 3.22±0.61 和 0.08±0.02,circRNA_12112 为0.68±0.21和13.35±3.53.同时,PH后0 h时,MYC促进的细胞周期启动相关基因Ras关联域家族成员1(RASSF1)、细胞周期蛋白依赖性激酶2(CDK2)、超氧化物歧化酶2(SOD2)表达下调,抑制的细胞周期启动相关基因嵌套蛋白(NES)、雷达21黏附复合物成分(RAD21)、CUE域包含2(CUEDC2)未发生有意义表达变化.PH后6 h时,MYC促进的细胞周期启动相关基因SOD2表达上调,抑制的细胞周期启动相关基因NES、RAD21、CUEDC2表达下调.相反,在细胞周期终止,即PH后72 h时,MYC mRNA的比值为0.30±0.10,miR-880-3p为0.54±0.01,circRNA_09599为0.54±0.16.同时,MYC促进的细胞周期终止相关基因肝细胞生长因子(HGF)表达上调,抑制的细胞周期终止相关基因MET原癌基因受体酪氨酸激酶(MET)和细胞周期蛋白依赖性激酶抑制剂1A(CDKN1A)表达下调.结论 上述circRNA抑制的miRNA、miRNA抑制的MYC mRNA以及MYC调节的细胞周期启动及终止相关基因的表达相关性和作用相关性有利于PH后6 h时肝细胞处于细胞周期启动状态和PH后72 h时肝细胞处于细胞周期终止状态.

Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehyde-assisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome. Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.

Liver fibrosis is caused by chronic hepatic injury and may lead to cirrhosis, and even hepatocellular carcinoma. When hepatic stellate cells (HSCs) are activated by liver injury, they transdifferentiate into myofibroblasts, which secrete extracellular matrix proteins that generate the fibrous scar. Therefore, it is extremely urgent to find safe and effective drugs for HSCs activation treatment to prevent liver against fibrosis. Here, we reported that PDZ and LIM domain protein 1 (PDLIM1), a highly conserved cytoskeleton organization regulator, was significantly up-regulated in fibrotic liver tissues and TGF-β-treated HSC-T6 cells. Through transcriptome analysis, we found that knockdown of PDLIM1 resulted in a significant downregulation of genes related to inflammation and immune-related pathways in HSC-T6 cells. Moreover, PDLIM1 knockdown significantly inhibited the activation of HSC-T6 cells and the trans-differentiation of HSC-T6 cells into myofibroblasts. Mechanistically, PDLIM1 is involved in the regulation of TGF-β-mediated signaling pathways in HSCs activation. Thus, targeting PDLIM1 may provide an alternative method to suppress HSCs activation during liver injury. CCCTC-binding factor (CTCF), a master regulator of genome architecture, is upregulated during HSCs activation. PDLIM1 knockdown also indirectly reduced CTCF protein expression, however, CTCF binding to chromatin was not significantly altered by CUT&Tag analysis. We speculate that CTCF may cooperate with PDLIM1 to activate HSCs in other ways. Our results suggest that PDLIM1 can accelerate the activation of HSCs and liver fibrosis progression and could be a potential biomarker for monitoring response to anti-fibrotic therapy.

The liver possesses a unique regenerative ability to restore its original mass, in this regard, partial hepatectomy (PHx) and partial liver transplantation (PLTx) can be executed smoothly and safely, which has important implications for the treatment of liver disease. Liver regeneration (LR) can be the very complicated procedure that involves multiple cytokines and transcription factors that interact with each other to activate different signaling pathways. Activation of these pathways can drive the LR process, which can be divided into three stages, namely, the initiation, progression, and termination stages. Therefore, it is important to investigate the pathways involved in LR to elucidate the mechanism of LR. This study reviews the latest research on the key signaling pathways in the different stages of LR.

RNA species act as architectural scaffolds for nuclear structures including chromatin in eukaryotic cells. However, the composition and dynamics of tightly bound chromatin-associated RNAs during mitosis remains elusive. Here we report the identification of chromatin-enriched RNA (cheRNAs) by biochemical nuclear fractionation coupled with RNA sequencing in both interphase and mitotic phase of A549 and HeLa-S3 cell lines. We showthat highly abundant cheRNAs, mostly small noncoding RNAs, are largely maintained in mitotic chromatin, and constitute a substantial part of chromatin RNA throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific and might be involved in chromatin accessibility and epigenetic memory of gene expression control. Therefore, we reveal an unexpected set of cell type-nonspecific mitotic retained chromatin-enriched RNAs. We anticipate that the landscape of RNA composition of chromatin both in interphase and mitotic phase would help understanding structure and function of chromatin.

Additional file 9: TableS2. All peaks of ZNF143.

Mesangial proliferative glomerulonephritis (MesPGN) is a common renal disease that lacks effective drug intervention. Aconiti Lateralis Radix (Fuzi), a natural Chinese medical herb, is found with significant therapeutic effects on various diseases in the clinic. However, its effects on MesPGN have not been reported. This study is aimed to discuss the therapeutic effects of the aqueous extract of Aconiti Lateralis Radix (ALR) and the polysaccharides of Aconiti Lateralis Radix (PALR) on MesPGN as well as the underlying mechanism. In this study, we, firstly, studied the anti-MesPGN mechanism of ALR and PALR. ALR and PALR inhibit the proliferation of the mesangial cells through the PI3K/AKT/mTOR pathway, induce the G0/G1 phase of block and apoptosis, inhibit the activity of Cyclin E and CDK2, increase the expression of Bax, cleaved caspase-8/caspase-8, and cleaved caspase-3/caspase-3 proteins, and effectively inhibit the growth of the mesangial cells. Overall, our data suggest that ALR and PALR may be potential candidates for MesPGN and that PALR is more effective than ALR.

Mitochondria are generally considered the powerhouse of the cell, a small subcellular organelle that produces most of the cellular energy in the form of adenosine triphosphate (ATP). In addition, mitochondria are involved in various biological functions, such as biosynthesis, lipid metabolism, oxidative phosphorylation, cell signal transduction, and apoptosis. Mitochondrial dysfunction is manifested in different aspects, like increased mitochondrial reactive oxygen species (ROS), mitochondrial DNA (mtDNA) damage, adenosine triphosphate (ATP) synthesis disorder, abnormal mitophagy, as well as changes in mitochondrial morphology and structure. Mitochondrial dysfunction is related to the occurrence and development of various chronic liver diseases, including hepatocellular carcinoma (HCC), viral hepatitis, drug-induced liver injury (DILI), alcoholic fatty liver (AFL), and non-alcoholic fatty liver (NAFL). In this review, we summarize and discuss the role and mechanisms of mitochondrial dysfunction in chronic liver disease, focusing on and discussing some of the latest studies on mitochondria and chronic liver disease.

目的:分析多层螺旋CT(MSCT)灌注成像对前列腺增生(BPH)与前列腺癌(PCa)的鉴别诊断价值.方法:选取医院收治的60例经病理学证实的前列腺病变患者,依据病理学诊断结果将其分为BPH组(32例)和PCa组(28例),所有患者均行MSCT灌注成像扫描,测定比较两组患者血流量(BF)、血容量(BV)、平均通过时间(MTT)及表面通透性(PS)等灌注参数值变化.结果:BPH组患者灌注成像扫描图像表现为中央带明显增大,呈高灌注,中央带与外周带界限清楚,且部分患者累及中央带及外围带,呈均匀高灌注;PCa组患者灌注成像扫描图像表现均呈高灌注和早期强化,BV、BF及PS病变组织为红至黄色,MTT为绿至蓝色;相对血容量(rBV)、相对血流量(rBF)及PS值均显著高于BPH组,差异有统计学意义(t=8.295,t=15.522,t=13.614;P<0.05),两组MTT值比较差异无统计学意义.结论:MSCT灌注成像能够反映BPH和PCa不同强化过程,为前列腺疾病诊断和鉴别诊断提供依据.

MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) about 22 nucleotides in size, which play an important role in gene regulation and are involved in almost all major cellular physiological processes. In recent years, the abnormal expression of miRNAs has been shown to be associated with human diseases including cancer. In the past ten years, the link between miRNAs and various cancers has been extensively studied, and the abnormal expression of miRNAs has been reported in various malignant tumors, such as lung cancer, gastric cancer, colorectal cancer, liver cancer, breast cancer, and prostate cancer. Due to the high malignancy grade of these cancers, it is more necessary to develop the related diagnostic and prognostic methods. According to the study of miRNAs, many potential cancer biomarkers have been proposed for the diagnosis and prognosis of diseases, especially cancer, thus providing a new theoretical basis and perspective for cancer screening. The use of miRNAs as biomarkers for diagnosis or prognosis of cancer has the advantages of being less invasive to patients, with better accuracy and lower price. In view of the important clinical significance of miRNAs in human cancer research, this article reviewed the research status of miRNAs in the above-mentioned cancers in 2021, especially in terms of diagnosis and prognosis, and provided some new perspectives and theoretical basis for the diagnosis and treatment of cancers.

Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit significant phenotypic changes under simulated microgravity (SMG), including enhanced biofilm formation and cellulose synthesis, which may be evoked by changes in gene expression patterns. It is well known that prokaryotic cells genomic DNA can be hierarchically organized into different higher-order three-dimensional structures, which can highly influence gene expression. It is remain elusive whether phenotypic changes induced by SMG in the subpopulations of K. pneumoniae are driven by genome higher-order structural changes. Here, we investigated the above-mentioned issue using the wild-type (WT) K. pneumoniae (WT was used as a control strain and continuously cultivated for 2 weeks under standard culture conditions of normal gravity) and two previous identified subpopulations (M1 and M2) obtained after 2 weeks of continuous incubation in a SMG device. By the combination of genome-wide chromosome conformation capture (Hi-C), RNA-seq and whole-genome methylation (WGS) analyses, we found that the along with the global chromosome interactions change, the compacting extent of M1, M2 subpopulations were much looser under SMG and even with an increase in active, open chromosome regions. In addition, transcriptome data showed that most differentially expressed genes (DEGs) were upregulated, whereas a few DEGs were downregulated in M1 and M2. The functions of both types DEGs were mainly associated with membrane fractions. Additionally, WGS analysis revealed that methylation levels were lower in M1 and M2. Using combined analysis of multi-omics data, we discovered that most upregulated DEGs were significantly enriched in the boundary regions of the variable chromosomal interaction domains (CIDs), in which genes regulating biofilm formation were mainly located. These results suggest that K. pneumoniae may regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes in response to altered gravity.

乔成林教授认为肾囊肿因阳虚血瘀、痰瘀互阻而致,以"治水必先温通"学术思想为指导,立"温阳活血"之法,创"温阳活血"方,疗效显著,为临床肾囊肿的治疗提供了参考.

Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However, the exact biological role of ZNF143 in liver regeneration and normal liver cell proliferation has not yet been investigated. In our study, we constructed a stable rat liver cell line (BRL-3A) overexpressing ZNF143 and then integrated RNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag) data to identify the mechanism underlying differential gene expression. Our results show that ZNF143 expression is upregulated during the proliferation phase of liver regeneration after 2/3 partial hepatectomy (PH). The cell counting kit-8 (CCK-8) assay, EdU staining and RNA-seq data analyses revealed that ZNF143 overexpression (OE) significantly inhibited BRL-3A cell proliferation and cell cycle progression. We then performed CUT&Tag assays and found that approximately 10% of ZNF143-binding sites (BSs) were significantly changed genome-wide by ZNF143 OE. However, CCCTC-binding factor (CTCF) binding to chromatin was not affected. Interestingly, the integration analysis of RNA-seq and CUT&Tag data showed that some of genes affected by ZNF143 differential BSs are in the center of each gene regulation module. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes are critical in the maintenance of cell identity. These results indicated that the expression level of ZNF143 in the liver is important for the maintenance of cell identity. ZNF143 plays different roles in HCC and normal liver cells and may be considered as a potential therapeutic target in liver disease.

microRNAs (miRNAs) are critically involved in liver regeneration (LR). miR-125a-5p (miR-125a) is a tumor-suppressing miRNA, but its role in LR has not been studied. Our previous studies have proved that miR-125a was related to LR at the initiation phase, while the mechanism hepatocyte proliferation triggered by miR-125a in LR has been rarely evaluated. Herein, we mainly studied the molecular mechanism of miR-125a in triggering hepatocyte proliferation and the proliferation stage of LR. Firstly, a striking reduction of miR-125a was found at 24 h as well as 30 h following partial hepatectomy (PH) in rat liver tissue by miRNAs expression profiles as well as qRT-PCR analysis. Furthermore, in vitro, upregulation of miR-125a decreased proliferation as well as G(1)/S conversion, which promoted hepatocytes apoptosis. STAT3 was the target of miR-125a. In vivo, upregulation of miR-125a by tail vein injection of agomir inhibited LR index. Upregulation of miR-125a inhibited LR index and hepatocytes proliferation by STAT3/p-STAT3/JUN/BCL2 axis. In summary, these current discoveries indicated that miR-125a inhibited hepatocytes proliferation as well as LR by targeting STAT3 and via acting on the STAT3/p-STAT3/JUN/BCL2 axis.

目的 了解大鼠肝再生启动阶段CCAAT增强子结合蛋白3(CEBPβ)mRNA、miR-369-3p和mo-Rmdn2_0006调节肝细胞处于G0期还是G1期的途径和方法.方法 按Higgins等方法制备大鼠2/3肝切除(PH)模型,按Smedsrod等方法分离肝细胞,用大规模定量分析技术检测大鼠肝再生中肝细胞竞争性内源RNA(ceRNA)表达的变化,用Cytoscape 3.2软件构建ceRNA的相互作用网络,用ceRNA综合分析等方法解析它们表达的相关性和作用相关性.结果 PH后0h和6h时,CEBP3 mRNA的比值为1.11±0.11和2.57±0.10,miR-136-3p为0.70±0.22和0.28±0.03,rno-Rmdn2_0006为1.26±0.34和2.62±0.70.CEBPp促进的G0期相关基因生长停滞和DNA损伤诱导型β(GADD45β)为0.12±0.09和2.50±0.44,细胞周期蛋白依赖性激酶抑制剂1A(CDKN1A)为0.39±0.07和0.93±0.15,抑制的G0期相关基因细胞周期蛋白依赖性激酶2相关蛋白2(CDK2AP2)为2.55±0.42和0.74±0.11,信号转导子和转录激活因子1(STAT1)为2.57±0.13和1.32±0.13.CEBPβ促进的G1期相关基因ETS变异转录因子6(ETV6)为0.77±0.05和2.22±0.68,血红蛋白加氧酶1(HMOX1)为1.05±0.21和4.57±0.88,丝裂原活化蛋白激酶14(MAPK14)为1.01±0.15和2.01±0.32,硫氧还蛋白相互作用蛋白(TXNIP)为1.03±0.07和2.50±0.19,抑制的G1期相关基因红细胞衍生核因子2样蛋白2(NFE2L2)为0.66±0.09和0.35±0.05.结论 PH后0h时,CEBPβ mRNA未上调,有利于CEBPβ抑制的G0期相关基因表达和肝细胞处于G0期.相反,PH后6h时,rno-Rmdn2_0006和miR-369-3p通过相互作用解除了后者对CEBPp mRNA的抑制,有利于CEBPp形成,有利于CEBPβ促进的G1期相关基因表达和肝细胞处于G1期.