The chromatin immunoprecipitation followed by sequencing (ChIP-seq) assay is an instrumental and accurate method for understanding chromatin dynamics in eukaryotic cells. It provides critical insights into the regulation of gene expression and enables identification of regulatory elements, patterns of histone modifications, and chromatin states in health and disease conditions. Although cell cultures are great models to study molecular mechanisms associated with pathologies, studying tissues provides a physiologically native environment that reflects the cellular heterogeneity and spatial organization that are missing in an in vitro model. Several ChIP-seq protocols have been published; however, performing ChIP-seq in tissues remains a challenge in many settings due to the heterogeneity of tissues, complexity of cell matrices, low input material and intricacy of chromatin fragmentation and handling. Here, we present an optimized ChIP-seq protocol for solid tissues, with a focus on colorectal cancer. In this article, we incorporate simplified and efficient procedures for tissue preparation, chromatin extraction, immunoprecipitation, and library construction. The refined protocols overcome common limitations related to tissue processing and allows for highly reproducible, sensitive, and scalable analysis of disease-relevant chromatin states in vivo. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Frozen tissues preparation Basic Protocol 2: Chromatin immunoprecipitation from tissues Basic Protocol 3: Library construction for DNA sequencing Basic Protocol 4: DNA nanoballs preparation for the DNBSEQ-G99RS sequencing platform and data quality control.

Chen et al demonstrated that regulator of G protein signaling (RGS) 4 promotes gastric cancer (GC) progression by activating the focal adhesion kinase/phosphatidyl-inositol-3-kinase/protein kinase B pathway and inducing epithelial-mesenchymal transition. Although their multilevel approach integrating clinical data, functional assays, and xenograft models demonstrated a key role for RGS4 in GC pathogenesis, several limitations should be considered. The mechanism of the RGS4-focal adhesion kinase interaction remains unclear, specifically whether it involves direct binding or intermediaries. The clinical analysis of 90 patients lacks stratification by GC subtypes or immune features, potentially limiting generalizability. Furthermore, fully validating RGS4's oncogenic role requires additional studies, including functional assays in chemotherapy-resistant and metastatic cell lines, metastasis models including orthotopic implantation and tail vein injection, and comparison with other RGS family members. Addressing these via targeted mechanistic studies and expanded clinical validation could strengthen RGS4's potential as a therapeutic target in GC.

High expression of pescadillo ribosomal biogenesis factor 1 (PES1) has been reported across multiple cancer types and is significantly associated with poor prognosis. Hu et al in their recent paper described their investigation of PES1 in gastric cancer and head and neck squamous cell carcinoma, demonstrating positive correlations between PES1 and programmed death-ligand 1 (PD-L1) expression (51.72% for PES1 and 58.62% for PD-L1), as well as associations with lymph node metastasis and tumor invasion depth. However, the relationship between PES1 and PD-L1 remains incompletely defined. To further address this gap, we analyzed The Cancer Genome Atlas gastric adenocarcinoma dataset and found a negative correlation between PES1 expression and CD8+ T cell infiltration, alongside a positive correlation with PD-L1 expression. Based on prior findings, we hypothesize that PES1 may regulate PD-L1 through the phosphatidylinositol 3-kinase/protein kinase B pathway or cellular Myc-mediated mechanisms. While these pathways require experimental validation, our observations highlight PES1 as a potential regulator of immune evasion and a promising target for cancer immunotherapy.

Hodgkin lymphoma (HL) is characterized by rare Hodgkin/Reed-Sternberg (H/RS) cells surrounded by a predominant immune infiltrate that shapes tumor biology and influences prognosis. FKBP51, an immunophilin and NF-κB/Akt modulator, is implicated in cancer progression, but its role within the HL tumor microenvironment (TME) remains unclear.

RNA epigenetic modifications critically regulate gene expression, with 5-methylcytosine (m5C) emerging as an important mark in cancer biology. NSUN2, a key m5C methyltransferase, modifies diverse RNA species, thereby influencing RNA stability, processing, export, and translation. Accumulating evidence indicates that NSUN2 promotes tumorigenesis by enhancing cell proliferation, supporting drug resistance, driving epithelial-mesenchymal transition, and reprogramming metabolic pathways. Clinically, its dysregulated expression is associated with poor prognosis and potential as a biomarker or therapeutic target. Beyond intrinsic tumor functions, NSUN2 also shapes the tumor immune microenvironment by regulating immune checkpoint molecules, cytokine networks, and immune cell activities, ultimately contributing to immune evasion and influencing immunotherapy efficacy. This review summarizes current insights into the roles and mechanisms of NSUN2 in cancer progression and immune modulation, and discusses challenges and future opportunities for therapeutic exploration.

RNA methylation modification has always been a research hotspot. RNA methylation modification can regulate processes such as transcription, translation, splicing, stability, and degradation of RNA, in which effector proteins play an important role, including 'writers', 'erasers', and 'readers'. There are various types of proteins involved in cancer progression, and in recent years, research on their mechanisms of action has been increasing, providing new ideas for targeted cancer therapy. By regulating the expression of related genes and affecting signaling pathways, protein writing plays a role in promoting or inhibiting cancer in the proliferation, invasion, migration, and metastasis of different tumors, providing direction for the treatment of malignant tumors. This article reviews the mechanisms of common RNA methylation modified writers and their prospects in targeted cancer therapy.

Pancreatic cancer (PC) is one of the deadliest malignancies due to early metastasis, therapy resistance, and a highly immunosuppressive microenvironment. Although oncogenic mutations such as KRAS and TP53 are well characterized, the role of protein tyrosine phosphatase non-receptor type 14 (PTPN14)-a Hippo-pathway regulator implicated in other cancers-remains unclear in PC. PTPN14 expression was analyzed in PC tissues and cell lines using immunohistochemistry and western blotting. Functional effects of PTPN14 knockdown or overexpression on proliferation, apoptosis, migration, and invasion were evaluated in vitro using CCK-8, flow cytometry, wound healing, and Transwell assays. Molecular mechanisms were explored via western blotting, immunofluorescence, and rescue experiments focusing on β-catenin and NF-κB signaling. In vivo, a xenograft mouse model assessed tumor growth, histopathology, apoptosis (TUNEL), Ki67 expression, and serum cytokine levels (ELISA). PTPN14 was markedly upregulated in PC tissues and cell lines. Silencing PTPN14 significantly inhibited cell proliferation, migration, and invasion, while enhancing apoptosis in vitro. Mechanistically, PTPN14 activated β-catenin and NF-κB signaling, promoting β-catenin nuclear translocation and p65 phosphorylation, with increased IL-6, TNF-α, and IL-1β secretion. In vivo, PTPN14 knockdown suppressed xenograft tumor growth, reduced Ki67 expression, enhanced apoptosis, and lowered serum pro-inflammatory cytokines. PTPN14 drives PC progression by co-activating β-catenin and NF-κB pathways and promoting a pro-tumor inflammatory milieu. These findings highlight PTPN14 as a promising therapeutic target to inhibit PC aggressiveness and inflammation-driven tumor progression.

Fusion genes represent a core molecular mechanism in the pathogenesis of acute promyelocytic leukemia (APL). In recent years, a novel type of tripartite retinoic acid receptor (RAR) fusion genes has been identified in atypical APL (aAPL), exhibiting distinct structural characteristics and pathogenic mechanisms compared to the classical bipartite fusion. This article systematically introduces relevant content in this field: it begins by outlining the long-standing scientific puzzle of inconsistent clinical resistance versus in vitro sensitivity in aAPL patients; subsequently, it describes the discovery process and structural features of tripartite fusion genes in all RARG and specific RARA-related cases, and elucidates the key molecular mechanism by which tripartite fusion leads to all-trans retinoic acid (ATRA) resistance at the protein conformational level; finally, the discovery of transposon involvement in the formation of tripartite fusions and its implications for the mechanism of fusion gene are discussed.

c-Met (also known as MET) protein is encoded by the MET proto-oncogene. In non-small cell lung cancer (NSCLC), c-Met protein overexpression (OE) drives tumorigenesis and is a therapeutic target, given recent US Food and Drug Administration approval of telisotuzumab vedotin-tllv. This retrospective analysis of tumor samples and clinical data from real-world patients with non-squamous NSCLC characterized the prevalence of c-Met protein OE, its association with messenger ribonucleic acid (mRNA) expression, MET gene amplification, programmed-death ligand 1 (PD-L1) expression, and its impact on prognosis.

Polycystic ovary syndrome (PCOS) is a complex disorder involving reproductive, endocrine, and metabolic abnormalities and is characterized by irregular menstruation, infrequent or absent ovulation, elevated androgen levels, insulin resistance (IR), and polycystic ovarian morphology (PCOM). It is the main cause of female infertility and high miscarriage rates and leads to high incidence of metabolic diseases. The pathogenesis of PCOS is complex, and IR is a crucial pathophysiological mechanism involved in multiple processes, such as ovulatory dysfunction, reproductive endocrine abnormalities, and metabolic disorders. Notably, long noncoding RNAs (lncRNAs), potential novel biomarkers and intervention targets for predicting the development of PCOS, have been shown to have a reciprocal regulatory relationship with IR in the context of PCOS therapy. A comprehensive analysis of lncRNAs and IR in PCOS is presented in this paper, highlighting the potential for mutual synergistic effects. Specifically, we discuss the mechanisms underlying lncRNAs and IR, emphasizing their ability to regulate reproductive endocrine disorders and metabolic abnormalities. Furthermore, we investigated the interactions between lncRNAs and IR in the pathogenesis, treatment, and prognosis of PCOS. We aim to provide a prospective view of the promising value of combining lncRNAs and IR in the treatment of PCOS by elucidating the roles and mutual regulatory network of lncRNAs and IR.

Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of aggressive non-Hodgkin lymphoma, contributing significantly to global health and economic challenges. Sodium-myoinositol cotransporter-1 (SMIT1) acts as an oncogene in different types of cancer. This study aimed to explore [1] the role of SMIT1 in DLBCL development, and [2] whether N6-Methyladenosine (m6A) modifications were responsible for high SMIT1 expression within DLBCL tissues.

Dermatofibroma/fibrous histiocytoma is a common tumor of the dermis, composed of myofibroblasts, dendrocytes, and macrophages with characteristic entrapment of dermal collagen fibers at the periphery of the tumor. Various subtypes of dermatofibroma, including cellular, aneurysmal, and atypical dermatofibroma, are associated with an increased risk of recurrence, especially with incomplete excision. Two cases of benign fibrous histiocytoma with recurrence and metastasis are described. Patient 1 had a cellular fibrous histiocytoma with KIRREL1::PRKCD fusion presenting as a superficial and deep soft tissue mass involving the scapula and lateral clavicle. Patient 1 subsequently developed metastasis to the chest wall and thigh. Patient 2 had a recurrent aneurysmal fibrous histiocytoma with LAMTOR1::PRKCD fusion presenting as a large shoulder mass with invasion of the clavicle and lymph node metastasis. Patient 2 developed rapid local recurrence and PET-avid pulmonary nodules, radiologically consistent with metastasis. Fibrous histiocytoma is typically a morphologically benign neoplasm that only rarely exhibits clinically aggressive behavior with multiple recurrences and metastases. Although uncommon, recognition of this entity is important so that pathologists and sarcoma oncologists can ensure accurate diagnosis, multidisciplinary management, and appropriate clinical surveillance. In addition, complex chromosomal abnormalities may serve as useful indicators of fibrous histiocytoma with the risk of aggressive clinical behavior.

RNF185 is a mitochondrial RING-type E3 ubiquitin ligase known to regulate mitochondrial homeostasis, apoptosis, and innate immune signaling through ubiquitination of substrates such as BNIP1, JWA, and cGAS. Although dysregulation of RNF185 has been reported in several cancers, its role in esophageal squamous cell carcinoma (ESCC) remains unclear. The present study aimed to investigate the function of RNF185 in ESCC progression and assess its potential as a therapeutic target.

Significant progress has been made in understanding the complex immune evasion mechanisms of triple-negative breast cancer (TNBC), paving the way for more effective immunotherapies. This review highlights key advances in elucidating the molecular basis of TNBC immune escape, including aberrant immune checkpoint expression, metabolic reprogramming, epigenetic regulation, immune evasion by associated cellular components, and clinical trials of emerging immunotherapies. Specifically, overexpression of immune checkpoint inhibitors such as PD-L1 on TNBC cells and within the tumor microenvironment (TME) plays a critical role in suppressing antitumor immunity. Secondly, TNBC cells evade immune surveillance through metabolic reprogramming. For instance, upregulated glutamine metabolism supports tumor growth and modulates the TME toward immunosuppression by limiting nutrient availability to immune cells. Competitive consumption of amino acids such as tryptophan and arginine further compromises immune cell function, promoting immune escape. Epigenetic modifications, including DNA methylation and histone modifications, are increasingly recognized as key contributors to immune evasion in TNBC. These mechanisms can silence genes involved in antigen presentation and immune activation while promoting the expression of immunosuppressive factors. Long non-coding RNAs (lncRNAs) have been identified as central regulators of immune evasion in TNBC, offering new therapeutic targets for intervention. Moreover, TNBC actively shapes its microenvironment to establish immunosuppression, including recruitment of regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and M2-polarized macrophages, which collectively inhibit effector T cell function. Building on these mechanistic insights, this review also integrates findings from clinical trials evaluating next-generation immunotherapies, including bispecific antibodies targeting PD-1/CTLA-4, LAG-3 inhibitors, and CD47-SIRPα blockers, as well as potential biomarkers. These novel combination strategies aim to overcome resistance to single-agent checkpoint inhibitors, while research explores monoclonal antibodies, bispecific antibodies, and antibody-drug conjugates (ADCs) within biomarker-driven personalized treatment frameworks. The ultimate goal is to improve survival and quality of life for TNBC patients through tailored immunotherapies.

The MKRN1 gene encodes a specialized E3 ubiquitin ligase with a zinc finger structure, is the ancestor of the MKRN gene family, and is involved in the occurrence and development of colorectal cancer, lung cancer, ovarian cancer, and other malignancies. However, its role in acute lymphoblastic leukemia (ALL) is still unknown. This study aims to explore the function of MKRN1 in ALL.

Mature T/NK-cell lymphoma is a highly heterogeneous, aggressive non-Hodgkin lymphoma. Due to the lack of specific therapeutic targets, treatment outcomes for patients with relapsed/refractory (R/R) disease are limited, and survival rates are low. Therefore, there is an urgent need to explore specific therapeutic targets and treatment strategies based on molecular mechanisms.

Anaplastic oligodendrogliomas are rare diffuse gliomas. Although radiotherapy (RT) combined with procarbazine, lomustine, and vincristine (PCV) has been the historical standard, temozolomide (TMZ) has been increasingly used.

The hypomethylating agents (HMAs) 5-azacytidine (vidaza-AZA) and 5-aza-2'-deoxycytidine (decitabine-DAC) are part of the standard of care for the treatment of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). However, the molecular events mediated by HMAs in MDS and AML are poorly understood, and the efficacy of MDS and AML treatments is still improvable. The majority of CpG dinucleotides are located at satellite repeats, and their methylation levels are known to play a fundamental role in ensuring the genomic stability of cells. HMAs are believed to act through a plethora of effects, including DNA demethylation and the consequent re-expression of aberrantly silenced genes, DNA damage due to the covalent trapping of DNA methyltransferases (DNMTs) on DNA, and endogenous retroelements (EREs) reactivation associated with the induction of a cell-intrinsic antiviral response. DNA demethylation of satellite repeats and the consequent genomic destabilization and mitotic impairment of leukemic cells are also believed to play important roles. Although the demethylating activity of HMAs on gene promoters has been extensively investigated, little is known about their effects on satellite DNA methylation during treatment, especially when the selective pressure of the treatment ends. Here, we characterized the dynamics of satellite 2 DNA methylation mediated by decitabine in a human AML cell line model (U937 cells). We demonstrate that the initial demethylation of satellite 2 repeats is followed by complete recovery after 48 h of culture. The observed regain of methylation is associated with increased expression of DNMT3B, the de novo DNMT known to target satellite 2 repeats. In the intent of deciphering the regulation of DNMT3B expression, we found that DAC significantly increased the level of H3 acetylation at the DNMT3B promoter. These preliminary data shed light on DAC-mediated methylation dynamics at satellite 2 repeats, suggesting that satellite 2 remethylation could limit the genomic-destabilizing effects mediated by HMAs in tumor cells and, thus, the future evaluation of strategies to impair this methylation regain and to improve HMAs activity against tumor cells.

Skin cutaneous melanoma (SKCM) is an aggressive malignancy with limited prognostic markers. Mitochondrial permeability transition (MPT)-driven necrosis has been implicated in tumor progression and immune regulation, yet its role in SKCM remains unclear.

DNA methylation plays a pivotal role in the pathogenesis of Acute Lymphocytic Leukemia (ALL), a hematological malignancy marked by abnormal cellular behavior and immune dysregulation. This study aimed to investigate how alterations in DNA methylation affect lysosmal function in pediatric ALL. A total of 50 blood samples were collected from children diagnosed with ALL and analyzed for biochemical markers associated with the disease. Expression levels of key DNA methylation regulators, including DNA methyltransferase 1 (DNMT1) and DNMT3, were evaluated and compared with those from healthy controls. In addition, pro-inflammatory cytokines, interleukin-6 (IL-6), interleukin-27 (IL-27), and tumor necrosis factor-alpha (TNF-α), were monitored over a six-day period prior to treatment initiation. The study also assessed the expression of lysosome-associated membrane proteins, LAMP1 and LAMP2, which are essential for lysosomal function and the degradation of autophagosomes. To determine the DNA methylation status of the promoter regions of these genes, genomic DNA underwent sodium bisulfite treatment and digestion with methylation-sensitive and methylation-dependent restriction enzymes, followed by amplification with gene-specific primers. Our results revealed a significant upregulation of DNMT1 and DNMT3 in ALL samples, along with a marked downregulation of TET1 gene expression, which is responsible for DNA demethylation. This suggests that disrupted DNA methylation dynamics may contribute to the pathogenesis of the disease. Furthermore, methylation levels within the CpG islands of the LAMP1 and LAMP2 promoter regions were substantially elevated, showing more than a seven-fold increase in ALL samples compared to healthy control blood samples. In ALL samples, the expression levels of LAMP1 and LAMP2 were significantly reduced, may due to promoter region hypermethylation, which contributes to lysosomal dysfunction. In parallel, the expression of autophagy-related genes such as ATG5 and LC3B, markers of autophagy initiation and maturation, respectively, was markedly increased, suggesting an accumulation of autophagosomes that depend on functional lysosomes for complete degradation. Additionally, elevated levels of pro-inflammatory cytokines IL-6, IL-27, and TNF-α were consistently observed in ALL patients, indicating heightened immune activation that may drive disease progression. Collectively, these findings underscore the pivotal role of DNA methylation in disrupting lysosomal function, leading to autophagosome accumulation and impaired recycling of cytoplasmic components.