Genes&Diseases

语种：英文出版周期：双月刊

E-ISSN：2352-3042P-ISSN：2352-4820

主管单位：重庆市教育委员会主办单位：重庆医科大学

Genes and Diseases是本由重庆医科大学于2014年创办的双月刊，也是国内第一本分子医学与转化医学相结合的全英文综合期刊，并入选“中国科技期刊卓越行动计划”高起点新刊项目。

过刊浏览

Colorectal cancer is the third most common malignant tumor globally. The current clinical therapeutic outcome is often jeopardized by the complex pathological process that is highly heterogenous among individual patients. It becomes increasingly critical for successful treatments to have diverse valid therapeutic options in clinic, which urgently demands efficient preclinical animal model to develop new drug and screen effective and safe clinical interventions. Patient-derived xenograft (PDX) mouse models, created by implanting fresh tumor tissue into immunodeficient or humanized mice, serve as a crucial resource in translational cancer research. These models closely replicate the tissue, cellular, and genetic characteristics of the original tumors, supporting their use in precision medicine, drug discovery, biomarker research, and studies of drug resistance. However, repeated transplantation can introduce genomic instability, molecular shifts, and phenotype variability. This article explores the development, advantages, limitations, and future directions of PDX models in preclinical cancer research.

172

Metabolic diseases, associated with high morbidity and mortality rates, pose a challenge to global public health and a significant burden on society. Since the discovery of carnosinase-2(CNDP2)-mediated synthesis of lactate and phenylalanine, which subsequently forms N-Lactoyl-Phenylalanine (Lac-Phe) to inhibit food intake and obesity, the carnosine dipeptidases (CNDPs)have attracted increasing scientific interest. Although the role of CNDP in diabetic nephropathy has been extensively studied, its role in other metabolic diseases remains unclear. In this study, we have overviewed the enzymatic and other roles of CNDP proteins focusing on recent research demonstrating the regulatory roles of CNDP on various metabolic diseases. Increasing evidence indicates that carnosinase-1(CNDP1) and carnosinase-2 are crucial for the management of metabolic diseases under both physiological and pathological conditions. Moreover, interest in the pharmacological modulators of CNDP has been steadily increasing. Overall, we suggest that CNDP can be considered a promising therapeutic target for the effective treatment of metabolic diseases.

161

Lipid droplets (LDs) are dynamic organelles that store neutral lipids when energy is in excess and serve as an energy reservoir during energy deprivation. Altered hepatic lipid metabolism is a critical factor influencing the development of liver disease, such as viral hepatitis, fatty liver disease, and hepatocellular carcinoma. Perilipin 2 (PLIN2) is a protein associated with the metabolism of intracellular LDs and is closely related to the clinical outcome of liver disease. While the impact of PLIN2 on the pathogenesis of liver disease is gradually being recognized, the mechanism of action remains unclear. In this review, we highlight recent advances in the understanding of PLIN2's role in the pathogenesis of liver disease through LD biogenesis, LD contact sites, LD dynamics, and lipophagy. Furthermore, we discuss the current opportunities for PLIN2-targeted therapy for liver disease.

178

Breast cancer is the most prevalent malignancy that affects women worldwide, with approximately 70% of cases classified as hormone receptor-positive (HR+). Endocrine therapy is one of the principal treatment modalities for this patient cohort. However, a considerable proportion of tumors acquire resistance to endocrine therapeutics, resulting in reduced effectiveness as the disease progresses, but the underlying mechanisms are not fully characterized. The G protein-coupled estrogen receptor (GPER), a component of the G protein-coupled receptor family, is hypothesized to mediate estrogenic effects independently of conventional estrogen receptors. In recent years, our research group and others have demonstrated that GPER plays a crucial role in facilitating the clinical progression of HR+ breast cancer and significantly contributes to endocrine resistance. In this review, we summarize the diverse mechanisms through which GPER mediates endocrine resistance, encompassing somatic alterations, epigenetic and non-genetic variations, and modifications within the tumor microenvironment. Furthermore, we discuss GPER as a potential therapeutic target for overcoming endocrine resistance of HR+ breast cancer in future clinical applications.

151

Gene mutations, organ function degeneration, and carcinogenesis are the primary threats to human health. Gene therapy, which involves the addition, deletion, regulation, and editing of genes, as well as the development of genetic vaccines, can potentially cure genetic mutation disorders, degenerative diseases, and cancers. Ex vivo gene therapy has recently been used to treat monogenetic mutation diseases of the hematopoietic system and cancers. However, in vivo gene therapy remains inapplicable. The primary elements of in vivo gene therapy include deoxyribonucleic acid (DNA) nucleases (e.g., zinc finger nucleases, transcription activator-like effector nucleases), CRISPR-Cas system, base editors, prime editors, and delivery vectors (e.g., viral and non-viral vehicles). According to the development of DNA nucleases and delivery vectors, in vivo gene therapy can be made available for future clinical use. The current review summarizes the development of DNA nucleases and delivery vectors for in vivo gene therapy, emphasizing recent progress.

166

Mitochondria, vital organelles within cells, govern energy metabolism. They play a pivotal role in maintaining redox homeostasis and are instrumental in the initiation and transmission of cell death signals, along with the synthesis of biological macromolecules. The role of mitochondria in tumor evolution and treatment has recently been the focus of extensive research. Studies indicate that the quality and biogenesis of mitochondria, along with their structure, functions, and macromolecule synthesis relevant to it, are intimately linked to tumorigenesis and the prognostic outcomes of clinical treatments. As such, therapies targeting mitochondria offer promising avenues to augment the efficacy of tumor treatment. We summarized the inherent links between mitochondrial structure, mitochondrial genes, metabolism of mitochondrial-related biological macromolecules, and mitochondria-regulated cell death in relation to tumorigenesis and progression. Furthermore, we reviewed the latest research progress in targeting mitochondria for tumor therapy. This study suggests that targeting mitochondria could open new avenues for developing tumor therapy.

161

Protein arginine methyltransferase 5 (PRMT5) is the primary type II methyltransferase that mainly catalyzes symmetric demethylation of arginine residues in both histone and nonhistone proteins. Increasing evidence has demonstrated that PRMT5 is indispensable in tumorigenesis and acquired therapeutic resistance in multiple malignancies. This review summarizes the clinical significance of PRMT5 in solid tumors such as lung cancer, breast cancer, and glioblastoma, its role in tumor immunology, and current clinical trials of PRMT5 inhibitors, and discusses the clinical status, current dilemma, and future perspectives of PRMT5 inhibition as a novel therapeutic strategy.

159

Tumor cell invasion is the key driver of metastatic dissemination, resulting in the development and progression of metastatic tumors at secondary sites, and remains the major cause of cancer-related death. Recent studies suggest that, in addition to protease-mediated degradation and chemotaxis-stimulated migration, tumor invasion is significantly influenced by physical surroundings. How tumor cells decode information about their shape deformation under mechanical stress and adapt their dynamic behavior to escape the confined regions remains largely unknown. This review highlights recent findings that illustrate mechanical cues in confined tumor microenvironment contribute to tumor progression. We also systematically discuss the role of compression-induced deformation in cell membrane topology and cytoskeletal remodeling, as well as its biophysical mechanisms in regulating tumor invasion from a biomechanical perspective.

158

Big biological data contains a large amount of life science information, yet extracting meaningful insights from this data remains a complex challenge. The hidden Markov model (HMM), a statistical model widely utilized in machine learning, has proven effective in addressing various problems in bioinformatics. Despite its broad applicability, a more detailed and comprehensive discussion is needed regarding the specific ways in which HMMs are employed in this field. This review provides an overview of the HMM, including its fundamental concepts, the three canonical problems associated with it, and the relevant algorithms used for their resolution. The discussion emphasizes the model's significant applications in bioinformatics, particularly in areas such as transmembrane protein prediction, gene discovery, sequence alignment, CpG island detection, and copy number variation analysis. Finally, the strengths and limitations of the HMM are discussed, and its prospects in bioinformatics are predicted. HMMs can play a pivotal role in addressing complex biological problems and advancing our understanding of biological sequences and systems. This review can provide bioinformatics researchers with comprehensive information on HMM and guide their work.

155

N6-methyladenosine (m6A) is the most prolific and conserved epigenetic modification of eukaryotic RNAs and is closely associated with the transcription, cleavage, translation, and degradation of target mRNAs. Cardiovascular disease (CVD) is the leading cause of death globally, with a significant research area focusing on understanding its pathogenesis and identifying effective therapeutic strategies. Recent advances in RNA methylation have revealed that m6A RNA modifications play a critical role in the initiation and progression of CVDs, potentially offering new insights into the development of these diseases. Interactions among various components influencing m6A modification levels regulate the effects of downstream targets, either by promoting or inhibiting CVD progression. This review connects the different types of CVDs and discusses the regulatory processes and intricate interactions between m6A methyltransferases and demethylases. We suggest that m6A RNA methylation could uncover potential targets for diagnosing and treating diseases, providing a clear view of how m6A modification affects CVDs and explaining the related molecular mechanisms and biological functions.

157

N6-methyladenosine (m6A) is a critical regulator of female reproductive physiology, yet existing reviews have focused predominantly on oocytes. The objective of this review is to systematically evaluate the regulatory effects of m6A throughout the pregnancy process. This review covers aspects such as oocyte maturation, granulosa cell dynamics, endometrial receptivity, immune homeostasis, and systemic adaptations, aiming to demonstrate the comprehensive regulatory capacity of m6A in female reproduction. Dysregulated m6A modifications in infertility-associated pathologies, including endometriosis, polycystic ovary syndrome, and recurrent miscarriage, are analyzed to identify mechanistic links between an epitranscriptomic imbalance and reproductive dysfunction. The key findings indicate that m6A is involved in the entire reproductive process and precisely coordinates stage-specific molecular programs within it, whereas aberrant methylation patterns disrupt gene networks essential for fertility. Notably, m6A-modifying enzymes exhibit strong potential as diagnostic biomarkers for female reproductive disorders. The synthesis of the current evidence establishes m6A dysregulation as a convergent pathogenic mechanism in diverse infertility etiologies, suggesting that the therapeutic modulation of m6A pathways could address unmet clinical needs in reproductive medicine.

157

Colorectal cancer (CRC) is a significant health burden globally, with the third highest incidence and the second highest mortality among all types of cancer. Understanding the mechanisms underlying CRC progression is crucial for advancing therapeutic strategies. Organelles are essential components of cells and play a critical role in the initiation and progression of cancer. Over the past decades, numerous studies have demonstrated that mitochondria and the endoplasmic reticulum (ER) can communicate through signaling pathways, thereby regulating cellular homeostasis and function in both normal and cancer cells. This interaction primarily occurs through mitochondria-associated endoplasmic reticulum membranes (MAMs). MAMs, as key nodes in cancer initiation and progression, are also potential vulnerabilities of cancer cells, offering promising opportunities for cancer treatment. Recent research further emphasizes the close association between MAMs and CRC in terms of proliferation, apoptosis, and invasion. To deepen our understanding of the interactions and mechanisms between mitochondria and the ER in CRC, this review, for the first time, synthesizes the research advancements concerning the crosstalk between these organelles in CRC. It innovatively identifies potential targets associated with MAMs, aiming to uncover novel therapeutic strategies for CRC.

167

154

Epithelial‒mesenchymal transition (EMT) is a dynamic cellular process in which epithelial cells lose their characteristics and acquire mesenchymal traits, leading to enhanced migratory, invasive, and stem-like properties. EMT is a fundamental mechanism in cancer progression, including in glioblastoma (GBM), an aggressive brain tumor known for its poor prognosis and resistance to treatment. In GBM, EMT has been implicated in tumor initiation, plasticity, metastasis, and treatment resistance, making it a key factor in the pathophysiology of the disease. The process of EMT can promote tumor cell migration and invasion, facilitating the spread of cancer cells within the brain. Additionally, EMT is believed to contribute to the maintenance of cancer stem cells, which are thought to be responsible for tumor recurrence and resistance to conventional therapies. Given these multifaceted roles, understanding the molecular pathways and regulatory networks that drive EMT in GBM is critical for identifying new therapeutic targets. This review summarized the roles of EMT in GBM initiation and progression, its impact on cancer cell behavior, and the challenges of targeting EMT in therapy, highlighting potential strategies to overcome resistance and improve treatment outcomes.

170

Intra-tumoral microbes have been revealed to exist in many cancer types, attracting widespread attention. The significance of intra-tumoral microbes is becoming increasingly apparent in various aspects of human cancers, encompassing cancer initiation, progression, metastasis, diagnostic approaches, prognostic evaluations, and therapeutic interventions. Despite the considerable focus dedicated to this topic by numerous scholars, a comprehensive analysis of intra-tumoral microbiota is still lacking in human cancers. Especially, identifying specific microbial hallmarks in the occurrence and development of cancer and different cancers remains the central task for investigators. This review focuses on the identification and analysis of distinct attributes and noteworthy characteristics exhibited by intra-tumoral microbiota across various types of cancer. The potential mechanisms of intra-tumoral microbiota action, as well as the significance of the microbiome in the diagnosis and prognosis of cancer, are systematically summarized. The capacity of intra-tumoral microbes to regulate cancer treatment with a focus on the relevant microbial species, and the possibility of targeting the microbiota to improve treatment effectiveness while preventing toxicity, are specifically highlighted. Lastly, the challenges, limitations, and prospects of intra-tumoral microbes in further study and clinical application, including prognostic, diagnostic, and therapeutic applications, are discussed in cancers. This review provides a systematic summary of the specific characteristics, molecular mechanisms, therapeutic effects, and diagnostic and prognostic values of intra-tumoral microbiota in different cancers, which will help improve the diagnosis, treatment, and prognosis of tumor patients and offer new ideas for achieving precise treatment of cancer with intra-tumoral microbiota.

149

Esophageal cancer (EC), with annual global reports exceeding 570,000 fresh cases, presents a relatively prevalent concern.1 Esophageal squamous cell carcinoma (ESCC), the most prevalent histological subtype of EC, is particularly common in southern Africa and southern Asia. It constitutes 90% of EC cases in China. This disease, characterized by aggressive tumor growth, significant tumor heterogeneity, and complex oncogenic pathways, typically has a poor prognosis. Recent years have seen considerable advancements in cancer immunotherapy with the advent of immune checkpoint inhibitors (ICIs) such as cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death protein 1 (PD-1).2 Nonetheless, the absence of effective treatment strategies to surmount resistance to cancer immunotherapy precludes a large number of cancer patients from reaping its benefits or achieving enduring therapeutic results.3 Identifying new immunotherapy biomarkers or novel immunoregulatory genes could pave the way for a more tailored and durable cancer immunotherapy approach. Elevated levels of Leupaxin (LPXN) have been correlated with the evolution and progression of certain malignant tumors,4 such as prostate cancer, colon cancer, breast cancer, and osteosarcoma. However, the impact of LPXN on the progression, prognosis, and its immunomodulatory functions in ESCC remains unknown.

158

Acute myeloid leukemia (AML) is a ubiquitous hematological cancer that originates from uncontrolled proliferation of bone marrow cells and presents distinct features in the population. Despite advances in chemotherapy and hematopoietic stem cell transplantation, AML remains a major challenge in improving patient survival. B cells play an important role in the immune monitoring, tumor microenvironment and therapeutic response of AML. In one aspect, AML cells can evade immune surveillance by a variety of mechanisms, including altering the expression of surface antigens, secreting immunosuppressive factors, or inducing the activity of immunosuppressive cells, which can recognize abnormal cell motility immune surveillance by impeding the production of antibodies. On the other hand, B cells and cytokines produced by them may play a supportive role in the pathogenesis and progression of AML. Accordingly, the functions of B cells and other immune cells of AML patients may be suppressed and thus may not be effective against AML cells. Therefore, this study aims to comprehensively explore the pathogenesis of B-cell-related genes in AML patients, explore the relationship between clinical outcomes of AML patients and tumor immune microenvironment characteristics, and provide ideas for precise treatment of AML patients.

169

Calreticulin (CALR) is a pleiotropic and highly conserved molecule and is recognized as an unfolded protein response effector protein. Moreover, CALR is an endoplasmic reticulum protein involved in a range of cellular processes. CALR can be translocated from the endoplasmic reticulum to the cell surface through co-localization with protein disulfide isomerase family A member 3 (PDIA3).1 Furthermore, CALR mutations affected the spindle assembly checkpoint, leading to erroneous mitosis.2 In particular, the loss-of-function CALR mutations not only impair cellular homeostasis but also compromise both natural and therapy-driven immune surveillance, thereby promoting tumorigenesis.3 Also, CALR frameshift mutations, a primary cause of myeloproliferative neoplasms, lead to rogue interactions with the thrombopoietin receptor (TpoR).4 Type I CALR mutations, but not type II, activate the inositol-requiring enzyme 1α (IRE1α)/X-box binding protein 1 (XBP1) pathway of the unfolded protein response, driving the development of myeloproliferative neoplasms.5 In this study, we demonstrate that CALR accelerates the growth of liver cancer cells by enhancing telomere activity dependent on ARAF (A-Raf proto-oncogene, serine/threonine kinase). Therefore, these results provide a basis for research on liver cancer prevention and treatment.

167

Effective clinical genome interpretation relies on accurately distinguishing between benign and pathogenic rare variants. Current machine learning-based variant prioritization tools are trained on genome-wide data and often overlook key parameters defining gene–disease relationships. Genes that cause a specific disease or a group of related diseases are likely involved in common biological processes. We hypothesize that these genes will share more features not captured by existing genome-wide tools. Disease-specific variant classifiers have been shown to outperform genome-wide tools when specifically applied to inherited cardiac diseases, inherited retinal diseases, or primary immunodeficiencies.1 However, no tool or predictor has been specifically designed for pathogenicity prediction of missense variants in childhood cancer predisposing genes (CCPGs).

153

Complete hydatidiform mole (CHM), a typical gestational trophoblastic disease (GTD), is a consequence of abnormal fertilization.1 Historically, trophoblastic cells have been categorized based on morphological and pathological characteristics, with functional classification yet to be well-established. Genetic abnormalities in these cells have been primarily studied using standard techniques such as short tandem repeats (STR) genotyping or microarray comparative genomic hybridization (aCGH).2 Previous studies using single-cell RNA sequencing (scRNA-seq) have uncovered the transcriptomic map of normal human placental cells.3, 4, 5 However, the key genes and transcriptional characteristics of trophoblast differentiation under pathological conditions remain largely unexplored due to genetic complexity and individual heterogeneity. We performed scRNA-seq on villus tissues freshly collected from two Chinese twin-pregnancies with CHM and coexisting live fetus (CHMCF) to compare the distinct transcriptional profiles. In both patients, STR analysis revealed that the molar tissues contained only paternal STR loci, confirming their identification as androgenetic monospermic CHM (Fig. 1A). In a twin pregnancy model of CHMCF, both the CHM and live fetus have the same gestational age (i.e., the timing of trophoblast differentiation) and are exposed to the same uterine environment. This theoretically identical developmental context provides optimal conditions for a comparative study.

163

Becker muscular dystrophy (BMD) and Duchenne muscular dystrophy (DMD) are X-linked recessive muscular dystrophies caused by pathogenic dystrophin (DMD) variants.1 The prevalence of DMD and BMD in Caucasian communities was estimated to be approximately 4∼6 per 100 000 people, which was similar to the prevalence in Asian communities.2 Deletions and/or duplications of one or more canonical exons account for ∼80% of disease-causing variants in DMD. Most of the remaining ∼20% pathogenic dystrophin variants are subexonic small variants, which include small insertions and/or deletions, missense variants, nonsense variants, and canonical splice site variants. Multiplex ligation-dependent probe amplification analysis combined with genomic sequencing of all DMD canonical exons and flanking intronic sequences (referred to as the routine DNA-based techniques) can identify most exonic deletions, exonic duplications, and subexonic small variants that occur in DMD canonical exons and/or adjacent intronic sequences.1 Some rare and atypical pathogenic dystrophin variants can escape the detection of routine DNA-based techniques, which mainly consist of complex chromosomal rearrangements and deep intronic splicing-altering variants.1 Cryptic exon-activating variants are the most common type among deep intronic splicing-altering variants in DMD.1 Here, a novel deep intronic cryptic exon-activating variant in the human dystrophin gene (NM_004006.2:c.5739 + 404A > G) was identified by skeletal muscle tissue-derived dystrophin protein and mRNA analyses, genomic Sanger sequencing, and long-read whole DMD gene sequencing.

177

Gestational diabetes mellitus (GDM) is the most common pregnancy-associated complication, not only increasing the risk of other pregnancy-related pathologies, but also predisposing both mother and offspring to metabolic disorders like diabetes, obesity, and cardiovascular diseases.1 GDM is characterized by abnormal gestational hyperglycemia and insulin-regulated metabolism. Previous studies have also found some GDM-induced changes in maternal organs, including reprogrammed metabolisms in the placenta2 and chronic inflammation in adipose tissue.3 The effect of GDM on the offspring is less well-described, apart from empirical observations on long-term metabolic conditions.1 There is also some previous genomic knowledge regarding GDM-induced changes, but they are generally limited to individual genes as potential biomarkers, lacking systematic insights at a pathway level. Moreover, most aforementioned findings are from stand-alone studies, a more comprehensive overview is warranted, covering different compartments and reconciling the maternal and fetal aspects.

154

Ovarian cancer (OC) is the deadliest gynecologic malignancy, with platinum-based chemotherapy, such as carboplatin, remaining the standard first-line treatment. However, resistance to carboplatin poses a major therapeutic challenge, and its mechanisms are not fully understood.1 This study employed a novel validation-based insertional mutagenesis (VBIM) technique2 to identify genes driving carboplatin resistance in human epithelial OC cells. Our screen identified hematological and neurological expressed 1-like (HN1L/JPT2) as a novel contributor to resistance. HN1L overexpression increased resistance to carboplatin, whereas shRNA-mediated knockdown sensitized OC cells to treatment. Mechanistically, HN1L conferred resistance by activating nuclear factor κB (NF-κB) signaling. HN1L depletion also reduced anchorage-independent growth in vitro and tumorigenicity in an OC xenograft model. Immunohistochemical analysis revealed elevated HN1L expression across multiple stages of OC in both cell lines and patient tissues. Collectively, our findings identify HN1L as a previously unrecognized carboplatin resistance gene and suggest that targeting HN1L may offer a promising combination strategy with carboplatin for overcoming platinum resistance in OC.

167

The apolipoprotein E (APOE) gene, located on chromosome 19, remains the primary genetic factor associated with late-onset Alzheimer's disease.1 In European populations, the ε4 haplotype of APOE, present in approximately 14% of individuals, significantly increases Alzheimer's disease risk, while the less common ε2 haplotype (∼8%) appears to confer a protective effect.2 Despite its significance, APOE has not been genetically characterized in Latin American countries, where Alzheimer's disease-related dementia disproportionately affects individuals.3

175

Acute myeloid leukemia (AML) is a malignant disease of myeloid stem/progenitor cells, marked by the proliferation of immature myeloid cells in the bone marrow and blood, leading to anemia, bleeding, infection, fever, and organ infiltration.1 It accounts for 30% of pediatric leukemia, impacting molecular biology and chemotherapy, and most cases have a poor prognosis.2 While the exact etiology is unknown, it is related to regional factors, radiation, chemicals, alcoholism, smoking, and viral infections.3 Genetic mutations and biomarkers suggest a combination of genetics and environment.4 m6A is a common mRNA modification, but little is known about its role in AML. This study examines the genetic traits and prognosis of m6A regulators in AML, using TCGA-AML samples to explore the relationship between changes in m6A regulators and clinicopathology, thereby advancing our understanding of RNA epigenetics in AML.

173

Colorectal cancer (CRC) is one of the most common malignant tumors worldwide, and its occurrence and development are associated with a variety of factors,1 among which the roles of gut microbiota, metabolites, and ions are increasingly valued. However, the interaction relationship between intestine and intestinal microecology is complex, and it is difficult to explain the causal relationship between intestinal microbial interactions with current analytical methods. Structural equation modeling is a statistical modeling method for representing, estimating, and displaying a relationship network between variables.2,3 This method integrates factor analysis and path analysis to examine the complex relationships among multiple variables, thereby systematically elucidating the causal mechanisms underlying clinical phenomena. In this study, intestinal microbiome, metabolome, and ionome were detected in stool samples from healthy individuals and CRC patients, and multi-omics big data was used to map intestinal microecological composition. The structural equation model was used to construct the intestinal microbiome–metabolome–ionome network, and comprehensively illustrate the causal relationships among the complex and diverse influencing factors of CRC, providing a new perspective for revealing the pathogenesis of CRC.

151

Progressive pseudorheumatoid dysplasia (PPD, MIM 603400) is a rare autosomal recessive skeletal disorder that profoundly impairs joint function and diminishes quality of life. It is characterized by disproportionate short stature, extensive cartilage damage, and progressive joint enlargement symptoms typically including joint pain, stiffness, and swelling, initially affecting the interphalangeal joints before progressively involving larger joints and the spine.1 This progression often leads to severe joint contractures, spinal deformities, and gait abnormalities, significantly restricting mobility and overall well-being. The complexity of these complications highlights the critical role of genetic analysis in achieving an accurate diagnosis.2

170

Long intergenic non-coding RNAs (lincRNAs), a subclass of long non-coding RNAs (lncRNAs) that do not overlap with other genes, play pivotal roles in cancer progression.1 The hypoxic tumor microenvironment, characterized by an excess of stromal cells and extracellular matrix and insufficient vascularization, is a distinctive feature of pancreatic ductal adenocarcinoma (PDAC).2 Nevertheless, a comprehensive screening and exploration of hypoxia-regulated lincRNAs in PDAC has not yet been conducted. This study analyzed the TCGA_PAAD dataset and identified LINC00431 as a hypoxia-responsive lincRNA. LINC00431 functions as an oncogenic lincRNA by modulating the protein levels of p53 and KRAS through the E3 ligase TRAF7 (tumor necrosis factor receptor-associated factor 7) in PDAC. These findings elucidate a novel mechanism in PDAC progression mediated by LINC00431, proposing it as a potential target for therapeutic intervention in PDAC.

146

Glioblastoma multiforme (GBM) remains the most aggressive and challenging central nervous system tumor due to the heterogeneity of the tumor microenvironment, prompting suboptimal effects to immune checkpoint blockade treatments.1,2 Notably, biomolecular condensates formed via liquid–liquid phase separation (LLPS) have been implicated in cancer progression by altering the tumor microenvironment and enhancing drug resistance.3, 4, 5 Consequently, it is urgent and imperative to identify valuable differentially expressed LLPS-related genes (DELRGs) and establish a prognostic model for GBM based on LLPS to address the immunosuppressive tumor microenvironment in GBM. Therefore, our study is dedicated to elucidating the machinery of LLPS-related genes in GBM by analyzing transcriptomic and single-cell RNA sequencing data, supported by experimental validation. The workflow for the transcriptomic, clinical, and single-cell RNA sequencing data analysis of GBM patients based on LLPS-related genes is shown in Figure 1.

163

Opioid analgesics, including morphine, pose significant challenges in clinical pain management due to the development of tolerance—a phenomenon that necessitates escalating dosages to maintain analgesic efficacy while increasing risks of adverse effects and addiction.1 The mechanisms driving morphine tolerance involve neuroadaptive changes, particularly microglial activation within the pain modulatory circuitry spanning the periaqueductal gray (PAG)-rostral ventromedial medulla (RVM)-dorsal root ganglion (DRG).2,3 Notably, morphine-induced microglial activation has been shown to involve the epidermal growth factor receptor (EGFR) signaling pathway. Upon EGFR activation, microglia release pro-inflammatory cytokines that amplify nociceptive signaling, thereby critically contributing to tolerance progression.4 Emerging evidence suggests that bioactive components of Cortex Magnoliae Officinalis (Houpo), such as magnolol, effectively alleviate opioid withdrawal symptoms.5 Based on these findings, the present study aims to investigate the therapeutic potential of magnolol in mitigating chronic morphine tolerance and delineate its molecular mechanisms of action, with the ultimate goal of informing novel strategies for managing opioid tolerance.

168

Epigenetic alteration is one of the common features in cancer progression.1 N6-methyladenosine (m6A) RNA modification regulates RNA metabolism and has been implicated in the development and progression of cancers.2 In our study, we discovered that the expression of methyltransferase-like 3 (METTL3) was significantly elevated in human esophageal squamous cell carcinoma (ESCC) tissues. Ablation of METTL3 inhibited proliferation and migration and induced apoptosis in ESCC cells both in vitro and in vivo. Paclitaxel (PTX) treatment resulted in a significant up-regulation of METTL3 expression within ESCC cells. Mechanistically, METTL3 promoted ESCC development and reduced chemosensitivity to PTX through regulating the mRNA stability of apoptosis-related genes caspase 9 (CASP9) and apoptosis protein repeat-containing 3 (BIRC3). These findings reveal the molecular mechanism of METTL3 in ESCC development and progression, providing new insights for developing molecular diagnosis and therapies for this malignancy.

157

PANoptosis is a novel mode of programmed cell death and plays an important role in tumor development and metastasis.1,2 Numerous studies have shown that PANoptosis plays a crucial role in cancer,3, 4, 5 however, there is limited research to reveal the association between PANoptosis and colorectal cancer (CRC). Based on our results, a PANoptosis-related signature (PRS) was developed by a combination of 101 machine learning algorithms that could accurately predict survival outcomes in TCGA and four external validation cohorts exhibited high performance when compared with other public signatures. The PRS was highly correlated with tumor microenvironment, immunotherapy, drug sensitivity, and genomic mutation. Moreover, six and nine candidate drugs from CTRP and PRISM databases respectively were identified for the high PRS score patients. A candidate therapeutic target, elastin (ELN), was screened in CRC cell lines, and its expression and clinical value were further evaluated in the GSE132257 dataset. Furthermore, the clinical significance of ELN was evaluated through CRC tissue samples. In summary, the present study uncovered a promising application of the signature in the prognosis of CRC. The potential therapeutic target of ELN might provide direction and tailor more effective treatment for CRC.

152

Glioblastoma (GBM) and low-grade glioma (LGG) are brain tumors with distinct molecular features. GBM represents the most aggressive primary brain tumor (median survival = 15 months, 5-year overall survival rate <10%) whose heterogeneity is reflected in distinct gene expression profiles.1 Non-coding alterations compromise nearly 98% of the genome and remain largely underexplored.2 In this scenario, the Pan-Cancer Analysis of Whole Genomes project detected numerous somatic single-nucleotide variations (SNVs) in gene regulatory elements, suggesting a functional impact on gene regulation. These mutations disrupt transcription factor binding sites, leading to dysregulated transcriptional programs.3 Enhancer elements (EEs), a class of gene regulatory elements, regulate proximal and distal gene expression and can become aberrantly activated in cancer, contributing to tumor progression.3 This study identified GBM-specific EEs affected by non-coding somatic SNVs in two independent and demographically diverse GBM patient cohorts (Spain and Sweden). Computational modeling demonstrated that these SNVs disrupted transcription factor (TF) binding motifs, altering the affinity of key TFs, such as transcriptional enhancer-associated domain (TEAD), early 2 factor 1 (E2F1), and signal transducer and activator of transcription 3 (STAT3), which are known to drive GBM malignancy. Our findings emphasize the role of non-coding SNVs in reprogramming the GBM epigenetic landscape and driving tumor progression through aberrant TF activity.

156

Triple-negative breast cancer (TNBC) has a poor prognosis because of its aggressive behavior, absence of specific therapies, and high recurrence.1 The exact molecular mechanisms that drive the progression of TNBC are not yet fully understood, thus highlighting the urgent need for discovering novel potential treatment targets. With the advancement of high-throughput technologies, the identification of dysregulated genes and pathways in TNBC has become feasible. Therefore, it is integral to identify novel therapeutic targets and improve patient outcomes.

154

Acute myeloid leukemia (AML) is an aggressive hematological malignancy with a poor prognosis. Cytarabine (Ara-C), a cornerstone of AML chemotherapy, causes DNA damage.1 However, patient AML blasts can develop Ara-C resistance. Therefore, there is an urgent need to explore new targets for the treatment of AML. DNA mismatch repair (MMR) pathway genes significantly contribute to the repair process by identifying DNA damage.2 The MMR system includes several MMR proteins, such as mutL homolog 1 (MLH1), MLH3, mutS homolog 2 (MSH2), MSH3, MSH6, postmeiotic segregation increased 1 (PMS1), and PMS2. Genetic variations in MMR genes affect individuals' ability to repair chemotherapeutic agent-induced DNA damage.3 For instance, MLH1 rs1799977 AG/GG genotype displayed an increased death risk in diffuse large B-cell lymphoma.4 The GG genotype of MSH2 rs3732183 is correlated with lower recurrence risk, and the GG genotype of MLH1 rs1800734 carriers is linked with higher overall survival (OS) in oral squamous cell carcinoma.5 However, research on the prognostic relationship between MMR and AML post-chemotherapy is lacking, leading us to investigate the polymorphism of MMR pathway genes and their prognostic significance in AML.

157

Lipid metabolism abnormalities are influenced by external and internal factors. Cold hypersensitivity refers to experiencing a cold sensation when the environment is not considered cold, and is clinically closely related to dyslipidemia (see supplementary background).1 Specificity protein 1 (SP1) is a key transcriptional activator and genetic factor associated with cold sensitivity (CS),2 and it contributes to lipogenic pathways3 and regulates the autophagy process4; nonetheless, its role in lipid metabolism in CS is currently unclear. Herein, we aimed to explore the roles of SP1 gene variants associated with CS in lipid metabolism. Using Mendelian randomization, we confirmed significant genetic causality between SP1 and lipid metabolism parameters, including increased total cholesterol, low-density lipoprotein-C, and triglyceride levels, and reduced high-density lipoprotein-C levels. Variant alleles at SP1 functional polymorphisms resulted in up-regulated transcriptional activation of mechanistic target of rapamycin (mTOR) and sterol regulatory element-binding transcription factor 1 (SREBP1) and down-regulated lipophagy. We thus revealed that de novo lipogenesis and lipophagy are regulated by gene variants of SP1. These results provide insights into the diagnosis and prediction of treatment response in patients with abnormal lipid metabolism.

153

The microbiome plays a significant role in human health and disease.1 Although bulk tissue analyses have identified disease-specific microbial signatures, these studies do not capture microbial-host cell enrichments and their associations with cell-type-specific activities.2, 3, 4 Thus, we present the Single Cell Microbes Atlas (ScMicrobesAtlas, http://scmbdb.geneis.org.cn:8089), a comprehensive microbial atlas that provides single-cell resolution insights into various human diseases. To date, ScMicrobesAtlas version 1.0 integrates 318 samples from 32 single-cell RNA sequencing datasets, encompassing 21 disease types, and uncovers interactions between 611 bacterial genera and over 1.3 million human cells. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, microbial signal identification and quantification, differential expression analysis, and functional enrichment analysis (Fig. 1A). ScMicrobesAtlas facilitates the comparative analysis of microbiome composition and identifies both shared and cell-type-specific microbial enrichments across diverse cell types and disease states. Additionally, it allows users to assess gene expression alterations and pathway activities in specific cell types in response to a particular microbiome. In summary, ScMicrobesAtlas offers a valuable resource for researchers to investigate disease-microbiome associations at the single-cell resolution.

154

155

Hirschsprung's disease (HSCR) results from neural crest cell migration and differentiation issues.1 Previously, analysis was limited to bulk tissue samples, but single-cell RNA sequencing now offers microscopic insights. Our pioneering single-cell RNA sequencing analysis of colon tissue is helping unravel HSCR's origins and development. We examined 22,353 cells from wild-type (WT) and endothelin receptor type B (EDNRB) mutant mice, identifying 24 clusters comprising 15 cell types. Comparing HSCR-type and healthy colons revealed distinctions in cellular differentiation, transcriptome characteristics, and biological functions. Our goal is to fill knowledge gaps and uncover the molecular basis of HSCR, facilitating potential therapeutic advancements.

159

Periodontitis, a chronic inflammatory condition, is one of the leading causes of tooth loss globally, contributing significantly to the burden of oral diseases. Its pathogenesis involves a multifaceted interaction between microbial dysbiosis and host immune responses, where macrophages are pivotal in regulating inflammation and tissue remodeling. These immune cells exhibit dual functionality, contributing to both protective immunity and pathological responses, thus underscoring their importance in the progression of periodontitis. Recent research demonstrates that iron metabolism, a critical regulator of immune cell function, strongly influences macrophage activity and may worsen the inflammatory microenvironment of periodontitis. Nevertheless, the molecular mechanisms that link iron homeostasis with macrophage-mediated periodontal destruction are not fully understood.1

153

The skin, being the largest organ of the human body, serves a critical barrier function by preventing the intrusion of harmful external substances and minimizing moisture loss. The epidermis consists of a stratified epithelium of continuously differentiating keratinocytes (KCs), which originate from the basal layer and progressively migrate upwards to form the stratum corneum. Proper epidermal differentiation is essential for maintaining the skin’s barrier function.1 However, disruptions in this process can lead to various skin diseases, including psoriasis, atopic dermatitis (AD), and squamous cell carcinoma.2 Thus, elucidating the regulatory network that governs epidermal differentiation is crucial for understanding the pathogenesis of these skin diseases.

155

Fertilization is a fundamental biological phenomenon essential for the initiation of new life. This process encompasses sperm hyperactivation, acrosome reaction, and sperm–egg fusion, all of which are intricately controlled by Ca2+ signaling.1 The cation channel CatSper, predominantly situated in the flagellar region of mature sperm, plays a pivotal role in mediating various Ca2+-dependent physiological events crucial for sperm activation and fertility.2 In animals, the motility of sperm plays a vital role in determining reproductive efficiency and overall productivity. Sperm must undergo changes in the female to fertilize eggs, including hyperactivated motility in the tail, triggered by calcium ions entering through CatSper protein.3 In hyperactivation, sperm tail movement shifts from fast and symmetrical to slow and asymmetrical. Recent findings suggest that the transmembrane protein 249 (TMEM249) may serve as an additional component of CatSper.4

163

Pompe disease, or glycogen storage disease type II (GSD2), is a rare lysosomal storage disorder caused by biallelic pathogenic variants in the acid alpha-glucosidase gene (GAA, MIM #606800). The lysosomal enzyme acid alpha-glucosidase (GAA) hydrolyses the 1,4 and 1,6 alpha-glycosidic chemical bonds to break down glycogen into glucose. In Pompe disease, GAA deficiency leads to glycogen accumulation in lysosomes, causing cellular damage. The disease ranges from an infantile-onset form characterized by severe hypotonia, hypertrophic cardiomyopathy, and respiratory failure, often resulting in death within the first year of life, to a milder, late-onset form characterized by progressive muscle weakness, respiratory insufficiency, and significant morbidity.1

156

Triple-negative breast cancer (TNBC) remains a medical challenge due to limited therapeutics.1 Histone deacetylases (HDACs) play vital roles in chromatin remodeling and epigenetics, and their dysregulation is implicated in malignancies, including TNBC.2 HDAC inhibitors (HDACis) have shown potent anti-TNBC activity in preclinical studies.3 Unfortunately, their clinical applications are beset by drug resistance, about which little is known.4 This study systematically explored the clinical significance of HDACs and transcriptomic landscapes underlying response and resistance to HDAC1/2/3/10 selective inhibitor chidamide,5 the first approved HDACi for solid tumor treatment, in TNBC.

161

Endometrial cancer, one of the most prevalent gynecological malignancies, has been steadily increasing in incidence, with 417,000 new cases and 97,000 deaths reported worldwide in 2020.1 Its classification is crucial for effective management. Endometrial cancer is a highly heterogeneous tumor, exhibiting significant variation in clinical outcomes even within defined grades and tissue types.2 An evaluation of the five leading risk stratification systems for endometrial cancer revealed that none achieved high accuracy in predicting recurrence or metastasis, resulting in substantial treatment variations for the same patient based on differing criteria.3 Stromal stem cells were regarded as one of the primary contributors to the origin of endometrial cancer.4 These cells could initiate a vicious cycle of tumor development through extensive crosstalk with tumor cells, suggesting that tumor progression may significantly depend on alterations in cancer-associated stromal cell signaling.5 However, no attempt has been made to integrate stromal cells into the prognostic prediction model for uterine corpus endometrioid cancer (UCEC) to improve accuracy. In this study, we successfully identified stromal cell differentiation fate genes (SDFGs) and developed a novel UCEC risk stratification system based on these genes.

153

Lung adenosquamous carcinoma (LASC) is distinct from lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), exhibiting higher malignancy and poorer prognosis. However, there is limited understanding of its single-cell heterogeneity, particularly in comparison to the single-cell heterogeneity of LUAD and LUSC. Here, we analyzed single-cell transcriptomic data from 34 tissue biopsy samples derived from 8 LUAD, 6 LASC, and 6 LUSC patients, and first present a single-cell resolution atlas for these distinct non-small cell lung cancer subtypes. We found that LUSC fibroblasts had higher heterogeneity compared with those from LUAD and LASC. Insulin-like growth factor binding protein 2-positive (IGFBP2+) fibroblasts exhibited the strongest interactions with macrophages, particularly a synergistic interaction with secreted phosphoprotein 1-positive (SPP1+) macrophages. Spatial relationship and crosstalk of these two subtypes were validated using independent datasets and in vivo experiments. Our findings offer a novel perspective on the biological mechanisms of tumor microenvironment in adeno-to-squamous transition, offering potential targets for therapeutic strategies in managing this disease progression.

162

The epidermal growth factor receptor (EGFR) A859S alteration is a rare variant in non-small cell lung cancer (NSCLC) that occurs in only ∼0.01% of cases1 and has been reported in few studies.2,3 To better understand its clinical relevance, we retrospectively analyzed 66,946 NSCLC patients from our next-generation sequencing (NGS) database, identifying 36,181 with EGFR variants and 18 (0.02%) with the A859S alteration. Among these, 12 samples were collected at baseline, 3 at disease progression after first-line EGFR-TKI treatment, and 3 with unknown disease status. We aimed to characterize the mutational landscape of A859S and assess survival outcomes in advanced NSCLC patients treated with first-line EGFR-tyrosine kinase inhibitors (TKIs).

152

Hemophagocytic lymphohistiocytosis (HLH) is a rare immune disorder characterized by uncontrolled activation of cytotoxic T lymphocytes (T cells), natural killer cells (NK cells), triggering a cytokine burst, and severe systemic hyperinflammation.1 HLH can be inherited or developed from infection, autoimmune/autoinflammatory disorders, and neoplasms. The only effective treatment for familial HLH is hematopoietic stem cell transplantation. However, extensive research explores other cellular and acellular therapies. Acquired HLH can be treated by addressing its cause. The treatment of HLH includes chemotherapy, immunotherapy, steroids, antibiotics, and antiviral medications.

156

We appreciate Shen and colleagues for their insightful communication regarding the presence and localization of mesenchymal stromal cells (MSCs) in the human abdominal aortic aneurysm (AAA) wall, and for citing our work.1 As they note, identifying MSCs in the human vascular wall is challenging due to the lack of universally accepted markers. This issue is particularly evident in injured tissues like AAAs, where inflammation, oxidative stress, hypoxia, and other stress factors coexist in the atherosclerotic environment.2 Moreover, vascular wall cell plasticity and differentiation processes contribute to the loss of cellular hierarchy, such as with endothelial-to-mesenchymal transition. This process induces endothelial cells to acquire mesenchymal stem cell characteristics with pro-calcific potential,3 further complicating MSC identification.

151

Gastric signet ring cell carcinoma (GSRCC) is a distinct subtype of gastric cancer with unique epidemiological and pathogenic characteristics. However, its prognostic features and molecular landscape remain poorly understood, limiting the development of targeted therapies. In this study, we analyzed clinical data from over 10,000 patients with gastric cancer treated at Zhejiang Cancer Hospital between January 2010 and December 2019. A comprehensive proteomic analysis was conducted on 112 GSRCC patients with a signet ring cell content exceeding 70%, identifying 7322 proteins. This study established a tissue-specific peptide spectral library, representing the most extensive proteomic atlas of GSRCC to date. We identified four novel proteomic subtypes: metabolism, microenvironment dysregulation, migration, and proliferation. Furthermore, PRDX2 and DDX27 emerged as potential prognostic biomarkers, which were further validated in an independent cohort of 75 patients. Molecular profiling of 79 cases that lacked expression of established gastric cancer treatment targets and biomarkers revealed significant tumor heterogeneity. Unsupervised clustering identified three distinct proteomic clusters, with cluster 2 exhibiting the poorest prognosis. Additionally, we identified four potential drug targets, including PFAS, EIF2S3, EIF6, and NFKB2. Molecular docking analysis suggested that neratinib, a clinically approved drug, could serve as a promising therapeutic agent for GSRCC, offering new avenues for clinical intervention.

161

Patients with ovarian cancer (OC) are at high risk of developing transcoelomic metastasis in the early stages, which is strongly associated with increased mortality rates. However, the mechanism by which OC cells disseminate from the primary site and colonize distant sites remains unknown. Here, through an in vivo genome-wide CRISPR/Cas9 screen, we identified NBL1, which increased dramatically in OC patients during peritoneal metastasis, as a key factor promoting the transcoelomic metastasis of OC. Overexpression of NBL1 in OC cells greatly promotes the transcoelomic metastasis. When OC cells disseminate into the peritoneal cavity, they induce the transition of peritoneal epithelial cells to mesothelial cells, ultimately activating the Jak/Stat3 signaling pathway. Thus, we show a NBL1-mediated crosstalk between peritoneum epithelial cells and mesothelial cells that supports a metastasis-promoting process.

166

Tooth formation is a highly orchestrated process that precisely regulates the size and shape of the tooth. During typical tooth development, Hertwig's epithelial root sheath (HERS) interacts with mesenchymal cells to direct the elongation of the tooth root and the deposition of dentin and cementum, thereby contributing to the formation of a fully developed tooth root. BMP9, a member of the BMP family, plays a significant role in growth, development, and cell differentiation. However, the precise function of BMP9 in dental root development remains unclear, particularly regarding its influence on HERS and odontoblasts. In this study, we utilized a mouse molar model to investigate the role of BMP9 signaling in tooth root development. The tooth formation of Bmp9 knockout (Bmp9-KO) mice and wild-type (WT) littermates was compared. Our findings revealed that Bmp9-KO mice exhibited shorter mandibular first molar roots, wider apical foramina, and thinner dentin compared with WT mice by micro-CT and hematoxylin-eosin staining analysis. Additionally, the results of immunohistochemistry and quantitative PCR indicated that in the absence of Bmp9, odontoblast differentiation and secretory function were compromised. Furthermore, Bmp9 ablation resulted in reduced cell proliferation and increased intercellular junctions within HERS, subsequently impacting root dentin formation and apical foramen closure. This study offers new insights into the regulatory role of BMP9 signaling in odontoblast and HERS function, highlighting its significance in root development and providing potential avenues for future research in tooth root regeneration.

167

Gliomas are characterized by high mortality and disability rates. Cancer-testis antigens (CTAs) are among the most promising therapeutic targets for combating cancer. While several CTAs have been associated with the development and progression of gliomas, the role of ATPase family AAA domain-containing protein 2 (ATAD2) in this context has not been thoroughly investigated. In this study, both in vitro and in vivo experiments validated the role of ATAD2 in enhancing malignant phenotypes. The LN229 cell lines were employed for RNA-seq and proteomics to uncover downstream targets of ATAD2. Results showed that elevated ATAD2 expression was noted in glioblastoma (GBM). ATAD2 knockdown significantly reduced the proliferation, migration, and invasion capabilities of GBM cells, while its overexpression had the opposite effect. The knockdown of ATAD2 led to a decrease in subcutaneous tumor size and weight, a reduction in Ki67 expression, and an extension of survival in mice bearing intracranial in situ tumors. Mechanistically, a positive feedback loop involving ATAD2 and E2F transcription factor 1 (E2F1) was identified to enhance the transcriptional activation of pyruvate dehydrogenase kinase 1 (PDK1). Notably, the expression levels of these genes were found to be positively correlated, with patients exhibiting high levels of these genes tending to have poorer prognoses. These findings demonstrate that ATAD2 plays a pivotal role in the malignant progression of glioma and synergizes with E2F1 to promote PDK1 expression, suggesting its potential as a therapeutic target for glioma.

163

Although Chromosome 1 open reading frame 122 (C1orf122) is known to be a protein-coding gene, its biological functions and mechanisms in hepatocellular carcinoma (HCC) remain unknown. Herein, bioinformatics analysis and experimental validation revealed that, C1orf122 was overexpressed in HCC tissues and cells, and correlated strongly with a poor prognosis of HCC patients. Subsequently, we knocked down and overexpressed C1orf122 in HCC cells, confirmed that C1orf122 significantly stimulated HCC cell growth and proliferation. Furthermore, flow cytometry and WB detection confirmed that C1orf122 significantly suppressed HCC cell apoptosis. Transwell migration and wound healing assays, along with WB analysis showed that C1orf122 strongly improved HCC cell migratory capacity. Mass spectrometry (MS) and Co-Immunoprecipitation (Co-IP) assays identified serine/arginine-rich protein-specific kinase 1 (SRPK1) as a C1orf122-interacting protein. Moreover, C1orf122 significantly upregulated total SRPK1 levels and suppressed SRPK1 protein phosphorylation at the Thr601 site. Using online prediction tools, we found that mTOR was the kinase of SRPK1 phosphorylating it at the Thr601 site, and other experiments confirmed that C1orf122 mediated SRPK1 Thr601 phosphorylation in a mTOR kinase-dependent manner. The cell phenotype assays further revealed that SRPK1 strongly stimulated the PI3K/AKT/GSK3β signaling pathway to enhance cell growth and migration. It was also observed that C1orf122 significantly activated the PI3K/AKT/GSK3β signaling pathway via SRPK1. To the best of our knowledge, this is the first study to demonstrate the involvement of the C1orf122-SRPK1-PI3K/AKT/GSK3β axis in HCC growth.

174

Osteoporosis (OP) is a disease characterized by decreased bone mass and damaged architectures. The promising treatment strategy for OP is to inhibit bone resorption while promoting bone formation. MicroRNAs (miRNAs) have been shown to be associated with osteoclastogenesis and osteogenesis processes in OP. In our previous study, we discovered that miR-378 inhibits bone marrow mesenchymal stem cell (BMSC) osteogenesis and bone formation during fracture healing. However, the role of miR-378 during OP progression is not validated. In this study, we found that miR-378 transgenic (Tg) mice exhibited excessive bone loss after ovariectomy (OVX) treatment. MiR-378 increased BMSC’s osteoclastogenesis by activating both canonical and non-canonical nuclear factor kappa-light-chain-enhancer of activated B (NFκB) signaling pathway. Tumor necrosis factor receptor-associated factor 3 (Traf3) was directly regulated by miR-378 during osteoclast differentiation. miR-378 also aggravated transforming growth factor beta (TGFβ) impaired osteogenesis upon OVX treatment. Traf3 was involved in this process as well. In in vivo study, the intravenous injection of anti-miR-378 lentivirus could significantly rescue OVX induced bone loss and bone microarchitecture impairment. This study uncovered the novel role of miR-378 in OVX induced osteoporosis. The potential of developing miRNA-378 inhibitors as novel diagnostics or blockers as therapeutics for osteoporosis is worth exploring.

168

MYBPC3 mutations are the leading cause of hypertrophic cardiomyopathy. Here, to study the pathogenesis of hypertrophic cardiomyopathy, we created a MYBPC3 knockout (KO) model using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). MYBPC3-deleted hiPSC-CMs revealed the characteristics of heart failure, which exhibited increased contractility at 30 days but decreased at 40 days. Furthermore, at 40 days, it also shows abnormal calcium handling, increased ROS levels, and mitochondrial damage. Further RNA sequencing revealed that the oxidative stress pathway was aberrant, in addition to alterations linked to hypertrophic cardiomyopathy. Moreover, after adding melatonin to hiPSC-CMs at 30 days, MYBPC3-deleted hiPSC-CMs showed restored calcium handling capacity, decreased ROS levels, and improved myocardial contractility. In summary, reducing ROS can improve the phenotype of hypertrophic cardiomyopathy.

154

Previous studies have demonstrated a significant association between sialic acid binding Ig-like lectin 15 (SIGLEC15) and both the progression of malignant tumors and immune infiltration. This study comprehensively analyzed and elaborated the function and related mechanism of SIGLEC15 in breast cancer. We analyzed SIGLEC15 expression levels and predicted its functions using mRNA sequencing in a population-based dataset. Single-cell RNA sequencing was utilized to investigate the biological roles of SIGLEC15 within the tumor microenvironment (TME). Finally, we conducted both in vivo and in vitro experiments to validate the findings derived from the RNA sequencing analyses. Elevated SIGLEC15 expression was associated with favorable outcomes in breast cancer patients. Tumor cells exhibiting high SIGLEC15 expression demonstrated reduced epithelial–mesenchymal transition (EMT) tendencies compared to those with lower expression levels, potentially through the regulation of ZEB1 expression. However, anti-tumor immunity was significantly suppressed in the TME containing these tumor cells. Analysis of protein expression in patient samples revealed a negative correlation between SIGLEC15 expression and CD4, CD8 T-cell infiltration. In mouse models, tumor cells overexpressing SIGLEC15 exhibited diminished invasive and migratory capabilities. Furthermore, both in vitro and in vivo experiments confirmed that Nutlin-3a has a more pronounced inhibitory effect on breast cancer cells with elevated SIGLEC15 expression. The expression level of SIGLEC15 can serve as a biomarker to assess the malignancy of breast cancer and the degree of immune infiltration. Monitoring SIGLEC15 expression levels can facilitate more informed and personalized clinical decision-making for the treatment of breast cancer patients.

147

Despite advances in cancer treatment with targeted therapies and immunotherapies, triple-negative breast cancer (TNBC) has not significantly benefited from these developments. Although poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) are approved for breast cancer, their clinical use is largely limited to the small subset of HER2-negative patients with germline BRCA1/2 mutations, and resistance is frequently observed. Previously, we demonstrated that proton pump inhibitors (PPIs), including lansoprazole and its metabolite, 5-hydroxy lansoprazole sulfide (5HLS), reduce PARP1 expression by inhibiting fatty acid synthase (FASN), a key enzyme in de-novo lipid synthesis. We also found that PPIs synergize with DNA-damaging agents by regulating PARP1 expression and impairing non-homologous end joining (NHEJ) repair of DNA damage. These findings led to the hypothesis that PPIs synergize with PARPi independently of BRCA mutation, potentially expanding the utility of PARPi to a broader TNBC population. In this study, we show that FASN contributes to PARPi resistance, and that lansoprazole and 5HLS strongly synergize with olaparib and talazoparib in both BRCA1-mutant and wild-type TNBC cells. This synergy occurs through FASN inhibition and subsequent impairment of NHEJ repair of double-strand breaks induced by PARPi trapping. 5HLS also facilitates PARPi-induced PARP1 trapping and inhibits BRCA1 expression by inhibiting FASN, contributing to the synergy with PARPi in both BRCA1 wild-type and mutant TNBC cells. Together, these findings suggest that inhibiting FASN with PPIs creates an artificial synthetic lethality, providing a rationale for combining PPIs with PARPi to expand their utility to TNBC patients without germline BRCA1 mutations and to overcome PARPi resistance.

149

Glioblastoma (GBM) is one of the most treatment-resistant brain malignancies. Dysregulation of Wnt/β-catenin signaling might be implicated in tumorigenesis of GBM. In this study, spatial transcriptomic analysis revealed elevated expression of Wnt target genes within tumor regions compared with peritumoral tissues. Overexpression of porcupine (PORCN), an O-acyltransferase for Wnt secretion, correlated with poor prognosis of GBM patients. Treatment with Wnt-C59, a PORCN inhibitor, inhibited Wnt signaling, hindered GBM cell proliferation and invasion, and inhibited GBM stem cells' self-renewal properties in a dose-dependent manner. Moreover, using β-catenin knockout and knockdown cells, FOXM1 was identified as a downstream transcription target of Wnt/β-catenin signaling. Wnt-C59 inhibited the expression of FOXM1 in GBM cells. Furthermore, Wnt-C59 demonstrated the ability to impede tumor formation and enhance the overall survival of mice bearing GBM in a preclinical model. Notably, the combined treatment of Wnt-C59 with temozolomide further enhanced therapeutic outcomes, leading to a significant extension of overall survival in GBM-bearing mice. Mechanistically, Wnt-C59 significantly down-regulated the expression of oncogenic targets associated with Wnt/β-catenin signaling (FOXM1, cyclin D, and C-Myc) both in vitro and in orthotopic GBM models. Our findings reveal that targeting Wnt/β-catenin signaling via PORCN inhibition, especially in combination with temozolomide, offers a promising therapeutic strategy for treating GBM.

155

Resistance to chemotherapy and subsequent relapse remain the primary challenge in pediatric acute myeloid leukemia (pAML), particularly in CBFA2T3-GLIS2 (C/G) fusion-positive acute megakaryoblastic leukemia. Here we demonstrate that the C/G fusion drives extensive DNA methylation changes and oncogenic enhancer activation at cis-regulatory elements (CREs), reshaping gene expression. This multi-omics analysis reveals a distinct hypermethylation pattern at promoters of up-regulated genes in C/G+ pAML across patient samples (n = 24) and representative cell lines, notably enriched in adhesion-related, TGFβ, or Wnt signaling pathways. Hypermethylated regions adjacent to transcription start sites (TSS) maintain open chromatin with H3K27ac enrichment, supporting a mechanism of de novo chromatin looping and active transcription in a non-canonical manner. Additionally, C/G fusion binding near the DNA methyltransferase 3B (DNMT3B) promoter correlates with elevated DNMT3B expression, implicating its role in aberrant DNA methylation changes at CREs. This study elucidates the epigenetic mechanisms driving C/G+ pAML, showing how the fusion reshapes chromatin and DNA methylation landscapes by impacting the expression (and likely activity) of epigenetic modifiers like DNMT3B. Functionally, DNMT3B inhibition enhances apoptotic sensitivity to BCL2 blockade, indicating that targeting DNMT3B may overcome apoptotic resistance in C/G+ leukemic cells and offer a therapeutic strategy for this high-risk subtype.

161

Osteosarcoma (OS) is a highly aggressive tumor with a propensity for early metastasis. Current treatment methods, such as chemotherapy, often bring significant side effects, affecting patients' quality of life. Veratramine (VER), an alkaloid derived from the American lily plant, has shown potential in cancer treatment. This study looks at the effects and mechanisms of VER on osteosarcoma. VER's impact was assessed using a variety of procedures, including crystal violet staining, the CCK-8 assay, and the colony formation assay, which measured cell proliferation. Wound healing assay and transwell assay were employed to evaluate the migration and invasion of osteosarcoma cells. Hoechst33258 staining, flow cytometry, and transmission electron microscopy were used to investigate apoptosis. Protein expression was assessed using western blotting and immunofluorescence. Blood tests and hematoxylin-eosin staining were used to establish VER's in vivo safety, and its effectiveness was proven using an orthotopic tumor model. The results showed that VER greatly decreased osteosarcoma cell growth, migration, and invasion while inducing apoptosis. Animal tests confirmed these findings, confirming VER's high efficacy and safety in vivo. VER might function by inhibiting the PI3K/AKT signaling pathway. To sum up, VER shows promise in treating osteosarcoma by exhibiting significant anti-tumor activity in laboratory and animal studies, likely through the regulation of the PI3K/AKT signaling pathway.

155

Intrauterine adhesion (IUA) leads to infertility or recurrent abortion; however, its etiology and pathological mechanism remain unclear. To explore the role and mechanism of the vitamin D receptor (VDR) in the pathogenesis of IUA. We found that VDR protein expression was lower in the endometria of patients with IUA than in those of the control group. Silencing VDR in endometrial epithelial cells inhibited autophagy, promoted the epithelial–mesenchymal transition (EMT) overexpression, and increased the phosphorylation of p-MTOR, p-AKT, and p-MAPK/ERK, while its overexpression suppressed the phosphorylation of p-MTOR, p-AKT, and p-MAPK/ERK. Also, the interaction between the VDR and p62 proteins was detected. Endometrial tissue in VDR knockout mice exhibited fibrosis, reduced VDR expression, decreased ATG7, LAMP1, and LC3-II levels, and increased p62 expression; the expression of the EMT marker CDH1 decreased while that of CDH2 increased. Treatment with rapamycin reversed this process. Our data indicate that the VDR receptor is a potential marker for diagnosing and treating IUA and that vitamin D may serve as a therapeutic agent for IUA.

149