Abstract

Purpose

   This study aimed to explore the role of CHAF1A in hepatocellular
   carcinoma (HCC) progression, focusing on its expression, co-expression
   genes, genomic alterations, promoter methylation, clinical relevance,
   prognostic value, and immune associations.

Methods

   CHAF1A mRNA expression was analyzed using UALCAN. Co-expression genes
   and functions were explored via LinkedOmics. Genomic alterations were
   assessed using cBioPortal. Promoter methylation and clinical
   correlations were examined using GEO datasets. Prognostic significance
   was evaluated via Kaplan-Meier analysis. Immune cell infiltration and
   checkpoint gene associations were investigated.

Results

   CHAF1A was significantly upregulated in HCC and involved in
   cancer-related pathways. Genomic alterations were prominent in T1-stage
   tumors, often linked to alcohol-related liver disease. Promoter
   methylation influenced HCC progression and prognosis. CHAF1A expression
   correlated with clinical characteristics (gender, stage, grade, etc.)
   and showed diagnostic potential (AUC = 0.795). High CHAF1A expression
   predicted poor prognosis across various subgroups and was positively
   associated with immune cell infiltration and checkpoint genes.

Conclusion

   CHAF1A plays a critical role in HCC progression, with elevated
   expression linked to poor prognosis and immune modulation. These
   findings highlight its potential as a therapeutic target for HCC.

   Keywords: CHAF1A, HCC, expression patterns, immune cell infiltration,
   gene

Graphical Abstract

   [32]graphic file with name CEG-18-25-g0001.jpg
   [33]Open in a new tab

Introduction

   Hepatocellular carcinoma (HCC), the most prevalent form of primary
   liver cancer, represents a significant global health burden,
   particularly in regions with high incidences of hepatitis B and C virus
   infections, alcohol abuse, and non-alcoholic fatty liver
   disease.[34]1,[35]2 With an annual incidence exceeding 800,000 cases
   worldwide and a five-year survival rate hovering around 18%, HCC poses
   a formidable challenge to healthcare systems and underscores the urgent
   need for better understanding of its molecular mechanisms and the
   development of more effective therapeutic strategies. HCC progression
   is a multi-step process, involving complex interactions between genetic
   alterations, epigenetic modifications, and the tumor microenvironment,
   including immune cells and factors.[36]3–5

   In recent years, research efforts have intensified to unravel the
   intricate molecular landscape of HCC, aiming to identify novel
   biomarkers and therapeutic targets.[37]6,[38]7 Among the myriad of
   genes implicated in HCC, CHAF1A (Chromatin Assembly Factor 1 Subunit A)
   has garnered significant attention due to its emerging role in cancer
   progression.[39]8,[40]9 CHAF1A, a component of the histone chaperone
   complex CAF-1, plays a pivotal role in chromatin assembly and
   epigenetic regulation, processes that are often dysregulated in cancer.
   While previous studies have hinted at CHAF1A’s involvement in various
   cancer types, including HIV-1 infection, gastric cancer, epithelial
   ovarian cancer and B cell lymphoma,[41]10–13 its specific role in HCC
   remains largely unexplored. Given the critical function of chromatin
   dynamics and epigenetic regulation in HCC development and
   progression,[42]14,[43]15 investigating the expression patterns,
   functional roles, and underlying mechanisms of CHAF1A in HCC is of
   paramount importance.

   In this study, we first analyzed the expression level of CHAF1A and its
   prognostic value in various types of human cancers, especially in HCC.
   Subsequently, genomic alterations of CHAF1A were predominantly detected
   in the early T1 stage of tumor development and expression levels were
   analyzed with clinical characteristics such as gender, tumor stage,
   grade, obesity, age, and ethnicity, which showed good sensitivity and
   specificity in the clinical diagnosis of HCC. Finally, High CHAF1A
   expression was associated with poor prognosis in HCC patients and was
   positively correlated with immune cell infiltration and immune
   checkpoint genes in HCC. Together, this study provides potential
   biomarkers and therapeutic targets for improving HCC diagnosis,
   prognosis, and treatment.

Materials and Methods

UALCAN Database

   The UALCAN platform comprehensively analyzes transcriptomic data from
   The Cancer Genome Atlas (TCGA)
   ([44]http://ualcan.path.uab.edu/index.html) (doi:
   10.1016/j.neo.2022.01.001). This database is used to study the
   expression levels of CHAF1A in relation to various clinical and
   pathological parameters of HCC (such as gender, age, tumor grade,
   cancer staging, etc), as well as its expression in various human
   tumors.

GEPIA Database

   To further confirm the expression of CHAF1A in HCC, we compared the
   expression levels of CHAF1A mRNA between normal liver tissue and HCC
   tissue using the GEPIA database (doi.org/10.1093/nar/gkx247)
   ([45]http://gepia.cancer-pku.cn/index.html) (an online analysis tool
   that can use TCGA and GTEx data for gene expression analysis).
   Meanwhile, this database is used to explore the correlation between the
   expression of CHAF1A and HCC related factors.

GEO Database

   The GEO database (doi.org/10.1093/nar/gks1193)
   ([46]https://www.ncbi.nlm.nih.gov/geo/) is a gene expression database
   created and maintained by the National Center for Biotechnology
   Information (NCBI) in the United States. Use it to screen for liver
   cancer expression data induced by various factors and visualize it
   using GraphPad Prism 6.01. Meanwhile, the data in this database can
   also be used for ROC analysis.

Human Protein Atlas Database

   The Human protein Atlas database ([47]https://www.Proteinatlas.org)
   provides immunohistochemical data on protein expression in 20 different
   types of cancer, which can be used to explore different tumor type
   specific proteins that exhibit differential expression (doi:
   10.1126/science.aay5947, doi: 10.1126/science.aan2507, doi:
   10.1126/science.aan2507). This study selected the expression results of
   CHAF1A protein detected by specific antibody CAB015186. Compare the
   expression levels of CHAF1A protein in normal and HCC tissues using
   immunohistochemistry images.

LinkedOmics Database

   LinkedOmics ([48]http://www.linkedomics.org/login.php) is a public
   portal website that contains multi omics data from all 32 TCGA cancer
   types and 10 Clinical Proteomics Tumor Analysis Alliance (CPTAC) cancer
   cohorts (doi.org/10.1093/nar/gkx1090). The web application has three
   analysis modules: LinkFinder LinkInterpreter and LinkCompare. We have
   chosen the TCGA-LIHC project for analysis, The differentially co
   expressed genes of CHAF1A were obtained from the LinkFinder module.
   Evaluate using Pearson correlation coefficient and display the results
   through heat maps and volcano maps. In addition, Gene Ontology (GO)
   andKyoto Encyclopedia of Genes and Genomes (KEGG) gene set enrichment
   analysis (GSEA) was performed using the LinkInterpreter module.

cBioPortal Database

   The cBioPortal database ([49]https://www.cbioportal.org/) is an
   international public database that includes large tumor research
   projects such as TCGA and ICGC, and integrates cancer gene data and
   clinical data. Its integrated genomic data types include somatic
   mutations, DNA copy number changes (CNA), mRNA and microRNA (miRNA)
   expression, DNA methylation, protein abundance, and phosphoprotein
   abundance (doi: 10.1126/scisignal.2004088, doi:
   10.1158/0008-5472.CAN-23-0816). Select two liver cancer datasets,
   Firehost Legacy and PanCancer Atlas, from this database, and use
   OncoPrint, Cancer Type Summary, Mutations, Comparison/Survival modules
   to analyze the mutation, amplification, and prognosis of CHAF1A in
   liver cancer tissue, exploring whether its expression abnormalities in
   liver cancer are related to its own mutations. Meanwhile, it is
   inferred that the expression stability of CHAF1A in liver cancer is
   stable.

MethSurv Database

   MethSurv ([50]https://biit.cs.ut.ee/methsurv) is a network tool for
   survival analysis based on CpG methylation patterns, with 7358
   methylation data from 25 different human cancers
   (doi.org/10.2217/epi-2017-0118). An interactive network tool for
   survival analysis was developed using the Cox proportional risk model.
   Exploring the possible methylation sites of CHAF1A and its relationship
   with the prognosis of liver cancer patients through this database, in
   order to further understand the role of CHAF1A in the occurrence and
   development of HCC.

Kaplan-Meier Database

   Kaplan Meier is a comprehensive database
   ([51]http://kmplot.com/analysis/) It can be used to evaluate the impact
   of miRNA or genes on the survival outcomes of different tumor types
   (doi. org/10.1016/j.xinn. 2024100625). Based on this database, 364,
   370, 316, and 362 samples were used to analyze the survival of CHAF1B
   expression in terms of overall survival (OS), recurrence free survival
   (RFS, also known as DFS), disease-specific survival (DSS), and
   progression free survival (PFS). In addition, the database was used to
   explore the relationship between CHAF1A and some clinical pathological
   features in HCC (gender, AJCC T-stage, race, grade, staging, alcohol
   consumption, vascular invasion, sorafenib treatment, and hepatitis
   virus).

TISCH2 Database

   Tumor Immune Single Cell Center 2 (TISCH2) is an online database
   ([52]http://tisch.comp-genomics.org) Integrated single-cell
   transcriptome profiles of approximately 2 million cells from
   76 high-quality cancer datasets (doi.org/10.1093/nar/gkac959). Use it
   to explore the distribution of CHAF1A in immune cells.

TIMER2.0 Database

   TIMER2.0 is a comprehensive software tool (doi:
   10.1158/0008-5472.CAN-17-0307) ([53]http://timer.comp-genomics.org/) to
   facilitate systematic analysis of immune infiltration in various types
   of cancer, we utilized its online analysis to investigate the
   correlation between CHAF1A and tumor immune cell infiltration, and
   selected the tumor type as LIHC. The immune cells involved include
   CD8+T cells, CD4+T cells, B cells, macrophages, neutrophils, and
   dendritic cells.

TISIDB Database

   TISIDB database ([54]http://cis.hku.hk/TISIDB) is a tumor immunoassay
   database that integrates massive tumor immunology resources (including
   TCGA pan cancer multi omics data), which can predict responses to
   immunotherapy by predicting interactions between the immune system and
   tumor tissue (doi.org/10.1093/bioinformatics/btz210). We used RNA Seq
   data from a cohort of 373 TCGA-LIHC patients obtained from the TISIDB
   database to investigate the relationship between CHAF1A expression
   levels and immune agonists, immune modulators, chemokines, and their
   receptors.

Networkanalyst

   Networkanalyze ([55]https://www.networkanalyst.ca/) Created an
   interaction network between gene miRNA and gene transcription factors
   (doi.org/10.1093/nar/gkz240). Using it to predict possible miRNAs of
   key genes and transcription factors that regulate each other, set the
   parameters as follows: organism: human; ID type: Official Gene Symbol;
   Gene TF interaction database: ENCODE and ChEA databases. Intersect the
   predicted transcription factors from the two databases. Gene miRNA
   interaction database: TarBase v8.0 database.

StarBase Database

   StarBase is a database that integrates miRNA target interactions from
   various sources ([56]http://starbase.sysu.edu.cn/)
   (doi.org/10.1093/nar/gkt1248). We used it to predict the upstream
   regulation of CHAF1A miRNA and summarized the predicted results with
   the TarBase v8.0 database. In addition, the StarBase database was used
   to predict the relationship between the expression of miRNAs shared by
   the two databases and the survival time of HCC patients.

Results

Elevated Expression of CHAF1A in Hepatocellular Carcinoma Tissues

   Utilizing the UALCAN database, we first investigated the expression
   levels of CHAF1A mRNA in various human tumor types. The results
   revealed a significant upregulation of CHAF1A expression in multiple
   tumors, including hepatocellular carcinoma (HCC), cervical squamous
   cell carcinoma, cholangiocarcinoma, and lung squamous cell carcinoma
   ([57]Figure 1A). Crucially, the GEPIA database further confirmed the
   high expression of CHAF1A in HCC tissues ([58]Figure 1B). Moreover,
   CHAF1A exhibited differential expression patterns in HCC tissues
   arising from diverse etiologies, such as hepatitis B virus (HBV),
   hepatitis C virus (HCV), and alcohol consumption ([59]Figure 1C).
   Subsequently, an assessment of CHAF1A protein levels in HCC using the
   Human Protein Atlas revealed low expression in normal liver tissues and
   high expression in HCC tissues ([60]Figure 1D). Additionally, we
   examined the correlation between CHAF1A expression and HCC-related
   genes such as TP53, AXIN1, and CTNNB1 ([61]Figure 1E). The findings
   indicated a positive correlation between CHAF1A expression and TP53
   (r=0.33, p=8.4e-11), AXIN1 (r=0.48, p=0), and CTNNB1 (r=0.28,
   p=4.1e-8), suggesting a pivotal role of CHAF1A in the development and
   progression of HCC.

Figure 1.

   [62]Figure 1
   [63]Open in a new tab

   Expression of CHAF1A in Hepatocellular Carcinoma. (A) Expression of
   CHAF1A in various tumors detected by the UALCAN database; (B)
   Expression of CHAF1A in HCC detected by the GEPIA database; (C)
   Expression patterns of CHAF1A in HCC caused by different factors; (D)
   Expression of CHAF1A protein in normal and HCC tissues; (E) Correlation
   between CHAF1A expression and HCC-related genes. *p<0.05, ***P<0.001.

Co-Expression Gene Enrichment Analysis of CHAF1A in Hepatocellular Carcinoma
Tissues

   Utilizing the LinkedOmics database, we explored the co-expression genes
   of CHAF1A and their biological functions and pathways in HCC. The
   results showed that CHAF1A positively correlated with 12,091 genes and
   negatively correlated with 7,831 genes ([64]Figure 2A). Heatmaps of the
   top 50 positively and negatively correlated genes with CHAF1A
   expression are presented in [65]Figure 2B and [66]C. Functional
   enrichment analysis revealed that these differentially expressed genes
   primarily impact biological processes such as DNA replication,
   chromosome segregation, protein activation cascade, and antibiotic
   metabolic process ([67]Figure 2D). In cellular components, they are
   primarily associated with the composition of condensed chromosomes,
   chromosomal regions, blood microparticles, and microbodies ([68]Figure
   2E). Regarding molecular functions, these genes primarily affect
   catalytic activity acting on DNA, damaged DNA binding, nucleosome
   binding, and electron transfer activity ([69]Figure 2F). KEGG pathway
   enrichment analysis indicated that they are primarily enriched in
   pathways such as cell cycle, DNA replication, and drug metabolism
   ([70]Figure 2G).

Figure 2.

   [71]Figure 2
   [72]Open in a new tab

   CHAF1A Co-expression Gene Enrichment Analysis. (A) Volcano plot of
   CHAF1 co-expression genes; (B) Heatmap of the top fifty positively
   correlated gene with CHAF1; (C) Heatmap of the top five negatively
   correlated genes with CHAF1A; (D) Biological processes; (E) Cellular
   components; (F) Molecular functions; (G) KEGG signaling pathways.

Analysis of Genomic Alterations and Stability

   Genomic strategies offer effective insights into cancer analysis. To
   assess the potential genomic-level alterations of CHAF1A in HCC, we
   analyzed its genetic alterations using the cBioPortal database. The
   results revealed that the copy number variation of CHAF1A in liver
   cancer, matched with TCGA data, was merely 1.7%, indicating its
   relative stability. The primary types of alterations were gene
   amplification, mutations, and deep deletions ([73]Figure 3A and [74]B),
   with mutations primarily occurring at amino acid positions 480, 482,
   and 790 ([75]Figure 3C). Our investigation into the impact of these
   alterations on HCC patient outcomes revealed that patients with genomic
   alterations had shorter overall survival times compared to those
   without alterations ([76]Figure 3D), suggesting an adverse prognosis
   associated with CHAF1A gene alterations. Furthermore, we observed a
   significantly higher frequency of other gene alteration events in the
   CHAF1A genetic alteration group compared to the normal group, with the
   top 10 genes being RN7SL121P, TNFAIP8L1, LRG1, MYDGF, UBXN6, SH3GL1,
   FSD1, SEMA6B, STAP2, and MPND ([77]Figure 3E). Additionally, according
   to the GISTIC database, alterations in CHAF1A, such as Shallow
   Deletion, Diploid, and Gain, were primarily observed in the T1 stage of
   tumor progression, and most patients with these alterations had various
   liver diseases caused by alcohol consumption ([78]Figure 3F and [79]G).

Figure 3.

   [80]Figure 3
   [81]Open in a new tab

   Genetic Variations of CHAF1A. (A) Copy number variations of CHAF1 in
   liver cancer; (B) Genomic alterations of CHAF1; (C) Common mutation
   sites of the CHAF1A gene; (D) Survival curve of patients with CHAF1A
   variations; (E) Genes with significant changes in the mutation group;
   (F) Relationship between tumor staging and copy number variations; (G)
   Association between risk factors for liver cancer and copy number
   status.

Methylation of Sites in the CHAF1A Promoter Region and HCC Patient Outcomes

   Alterations in the expression status of epigenetically regulated genes
   can affect cell growth, differentiation, and proliferation, thereby
   influencing tumor development. To further explore the role of CHAF1A
   epigenetics in HCC, we investigated potential methylation sites in the
   CHAF1A promoter region and their relationship with patient outcomes.
   The results suggested that the methylation sites of CHAF1A could be
   cg03006338, cg03741332, cg04346879, cg05297461, cg06727521, cg07783855,
   cg09700233, cg18804734, cg19682666, cg23811775, and cg24085258
   ([82]Figure 4A and [83]B). The relationship between methylation at
   these sites and HCC patient outcomes is depicted in [84]Figure 4C–M,
   with cg04346879 (p=0.0003) and cg23811775 (p=0.0280) standing out as
   significant and meaningful. Higher methylation levels at these two
   sites were associated with shorter survival times for patients
   ([85]Figure 4E and [86]L), suggesting that CHAF1A promoter methylation
   plays a crucial role in liver cancer progression and that the level of
   CHAF1A promoter methylation may influence the prognosis of HCC
   patients.

Figure 4.

   [87]Figure 4
   [88]Open in a new tab

   Methylation Sites in the CHAF1A Promoter and Their Prognostic
   Implications. (A–D) Depict the methylation sites, degrees of
   methylation, and related information within the DNA sequence of
   CHAF1,in (B), the red-marked sites represent the modified sites with
   significant differences. (C–M) Illustrate the correlation between the
   methylation status of the CHAF1 promoter and the prognosis of HCC
   patients.

Clinical Characteristics of CHAF1A Expression Levels

   To investigate the clinical role of CHAF1A, we leveraged the UALCAN
   online platform to assess the expression patterns of CHAF1A in HCC
   across various parameters. The results revealed that both male and
   female HCC patients exhibited higher CHAF1A expression levels compared
   to the control group, with females showing a slightly higher expression
   ([89]Figure 5A). Irrespective of tumor stage or grade, CHAF1A
   expression was significantly upregulated in HCC patients compared to
   normal counterparts ([90]Figure 5B and [91]C). Additionally, obese HCC
   patients displayed relatively high CHAF1A expression ([92]Figure 5D).
   From an age perspective, CHAF1A expression was relatively high in HCC
   patients aged 21–60 years, while it slightly declined in patients aged
   61–100 years ([93]Figure 5E). Compared to the control group, CHAF1A
   expression was significantly upregulated in HCC patients of Caucasian,
   African American, and Asian ethnicities ([94]Figure 5F). Furthermore,
   HCC patients with TP53 mutations exhibited significantly higher CHAF1A
   expression levels compared to both the normal and non-mutated groups
   ([95]Figure 5G). Subsequently, to validate the diagnostic efficacy of
   CHAF1A in HCC, ROC regression analysis was performed based on
   [96]GSE46408 and [97]GSE115018 datasets. An AUC value > 0.50 was
   considered diagnostically valuable. The results indicated an AUC value
   of 0.795 for CHAF1A, suggesting its good sensitivity and specificity in
   clinical diagnosis of HCC ([98]Figure 5H).

Figure 5.

   [99]Figure 5
   [100]Open in a new tab

   Quantitative Analysis of CHAF1A Expression in Different Patient Groups
   Using the UALCAN Database. (A–G) Expression of CHAF1A in relation to
   gender, tumor stage, tumor grade, body weight, age, race, and the
   presence of TP53 mutations; (H) ROC Diagnostic Curve for CHAF1A.

Prognostic Analysis of CHAF1A Expression

   Utilizing the Kaplan-Meier database, we explored the prognostic
   significance of CHAF1A expression in HCC patients. Our findings
   revealed that patients with high CHAF1A expression exhibited lower OS
   (HR = 1.68, P = 0.016) ([101]Figure 6A), DFS (HR = 1.5, P = 0.023)
   ([102]Figure 6B), DSS (HR = 1.76, P = 0.041) ([103]Figure 6C), and PFS
   (HR = 1.41, P = 0.024) ([104]Figure 6D) compared to those with low
   expression, all with statistical significance. This suggests that the
   upregulation of CHAF1A expression is associated with poor prognosis in
   HCC patients. Moreover, the upregulated expression of CHAF1A in HCC
   patients correlated with OS, DFS, DSS, and PFS ([105]Figure 6E–H),
   exhibiting a certain degree of correlation regardless of tumor grade,
   stage, gender, vascular invasion, ethnicity, sorafenib treatment,
   alcohol consumption, and hepatitis virus status.

Figure 6.

   [106]Figure 6
   [107]Open in a new tab

   Relationship between CHAF1A Expression and Prognosis of HCC Patients.
   (A–D) Associations between CHAF1A expression levels and patient
   outcomes, including OS, DFS, DSS, and PFS; (E–H) Correlation analysis
   between CHAF1A expression and clinicopathological parameters in HCC
   patients.

The Association of CHAF1A Expression with Immune Cell Infiltration and Immune
Factors in HCC

   Moving forward, our aim was to identify potential mechanisms underlying
   CHAF1A’s role in HCC development. Understanding the interplay between
   tumor immune cells and key genes involved in cancer progression is
   crucial for improving cancer treatment strategies. In this study, we
   conducted a correlation analysis to explore the relationship between
   CHAF1A and tumor immune cell infiltration and immune checkpoints.

   Within the HCC transcriptome dataset, we found that CHAF1A is expressed
   in various immune cells, including T cells and B cells ([108]Figure
   7A). Subsequently, we analyzed the [109]GSE140228 single-cell
   transcriptome data further, revealing that CHAF1A is primarily
   expressed in T immune cells and dendritic cells (DCs), but also
   exhibits expression in most immune cell types ([110]Figure 7B).
   Furthermore, analysis using the TIMER 2.0 database showed that CHAF1A
   expression positively correlates with cell purity and the immune
   infiltration levels of B cells (r = 0.437, p = 1.82e-17), CD8+ T cells
   (r = 0.311, p = 4.13e-9), CD4+ T cells (r = 0.355, p = 1.27e-11),
   macrophages (r = 0.382, p = 2.57e-13), neutrophils (r = 0.385, p =
   1.29e-13), and dendritic cells (r = 0.454, p = 1.15e-18) ([111]Figure
   7C). These findings may provide insights into understanding the immune
   microenvironment of hepatocellular carcinoma.

Figure 7.

   [112]Figure 7
   [113]Open in a new tab

   Relationship between CHAF1A Expression and Immune Cell Infiltration.
   (A) Heatmap of CHAF1A expression across various immune cell types in
   different datasets; (B) Distribution of CHAF1A expression in the
   [114]GSE140228 dataset; (C) Correlation plot depicting the association
   between CHAF1A expression and the infiltration of B cells, CD8+ T
   cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells.

The Association Between CHAF1A Expression and Immune Checkpoint Genes in HCC

   Next, we explored the relationship between CHAF1A expression and
   immune-related factors using the TISIDB database. The results revealed
   a correlation between CHAF1A expression in various tumors and immune
   suppressors, enhancers, and chemokines. Specifically, in HCC, CHAF1A
   expression exhibited a significant correlation with immune suppressors
   ([115]Figure 8A), such as LAG3 (r=0.196, p=1.42e-4) and KDR (r=−0.326,
   p=1.49e-10). Furthermore, CHAF1A expression also showed a notable
   association with immune agonists like MICB (r=0.296, p=5.64e-9) and
   CXCL12 (r=−0.313, p=7.83e-10) ([116]Figure 8B). More importantly, a
   strong correlation was observed between its expression and chemokines
   CCL14 (r=−4.18, p<2.2e-16) and CXCL12 (r=−0.313, p=7.83e-10)
   ([117]Figure 8C). Finally, there was a certain relationship between
   CHAF1A and chemokine receptors ([118]Figure 8D), particularly CXCR1
   (r=0.225, p=1.19e-5) and CXCR2 (r=−0.205, p=6.94e-5). In summary, these
   data suggest that CHAF1A may influence the development and progression
   of HCC by modulating immune checkpoint-related factors.

Figure 8.

   [119]Figure 8
   [120]Open in a new tab

   Relationship between CHAF1A Expression and Immune Checkpoints. (A–D)
   Depicts the correlations between CHAF1A expression and immune
   suppressors, agonists, chemokines, and their receptors.

Discussion

   HCC is a complex disease driven by multiple factors, including viral
   infections such as hepatitis B and C, aflatoxin exposure, and lifestyle
   choices. Despite advancements in treatment modalities, HCC prognosis
   remains poor, emphasizing the need for novel therapeutic targets and
   biomarkers.[121]4,[122]5 In this study, we explored the expression and
   functional significance of CHAF1A in HCC. We found that CHAF1A is
   dysregulated in HCC tissues, contributing to tumor progression and
   aggressiveness. Our data suggest that CHAF1A promoter methylation
   played a crucial role in liver cancer progression, and CHAF1A
   expression levels were associated with clinical characteristics such as
   gender, tumor stage, grade, obesity, age, and ethnicity. Furthermore,
   we uncovered that CHAF1A expression was positively correlated with
   immune cell infiltration and immune checkpoint genes in HCC, providing
   insights into the development of targeted therapies.

   CHAF1A, as a component of the histone chaperone complex CAF-1, has
   garnered significant attention in recent years for its role in
   chromatin assembly and epigenetic regulation, processes that are
   frequently dysregulated in cancer.[123]16,[124]17 Prior studies have
   implicated CHAF1A in the progression of various cancer types, including
   breast, ovarian, and lung cancers.[125]8,[126]18–20 These findings
   highlight the potential significance of CHAF1A in cancer biology and
   suggest its involvement in tumorigenesis and metastasis. However, the
   specific mechanisms underlying CHAF1A’s function in HCC remain largely
   unexplored. Our study provides a comprehensive investigation into the
   role of CHAF1A in HCC progression. The significant upregulation of
   CHAF1A expression in HCC tissues compared to normal liver tissues, as
   observed using the UALCAN and GEPIA databases, underscores its
   potential as a biomarker for HCC. Furthermore, the analysis of CHAF1A’s
   co-expression genes revealed its involvement in crucial biological
   processes such as DNA replication, chromosome segregation, and protein
   activation cascades, further emphasizing its functional importance in
   HCC.

   Genomic and genetic alterations influence the
   progression.[127]21,[128]22 Notably, our findings on genomic
   alterations in CHAF1A reveal a relatively low frequency of copy number
   variations but significant associations with patient outcomes. The
   predominance of genomic alterations in the early T1 stage of tumor
   progression, coupled with the adverse prognosis observed in patients
   with CHAF1A alterations, highlights the potential significance of these
   genetic changes in HCC initiation and progression. In addition, DNA
   methylation patterns in circulating tumor DNA hold great promise for
   minimally invasive cancer detection and classification.[129]23,[130]24
   The analysis of CHAF1A promoter methylation further underscores the
   epigenetic regulation of this gene and its impact on HCC patient
   outcomes.

   Immune cell infiltration into the tumor microenvironment is closely
   related to the therapeutic efficiency and prognosis of multiple human
   cancers.[131]25–27 The positive correlation between CHAF1A expression
   and immune cell infiltration, as well as immune checkpoint genes,
   observed in our study, suggests a potential role for CHAF1A in
   modulating the tumor microenvironment. This finding has important
   implications for the development of novel immunotherapeutic strategies
   targeting CHAF1A. By modulating CHAF1A expression, it may be possible
   to influence the immune response against HCC, thereby enhancing the
   efficacy of immunotherapy.

   In conclusion, our study provides novel insights into the role of
   CHAF1A in HCC progression, including its expression patterns, genomic
   alterations, and epigenetic regulation. The associations observed
   between CHAF1A expression and clinical characteristics, prognosis, and
   immune modulation suggest its potential as a biomarker and therapeutic
   target in HCC. However, further studies are needed to fully elucidate
   the molecular mechanisms underlying CHAF1A’s function in HCC and to
   evaluate the efficacy of CHAF1A-targeted therapies in clinical
   settings. These efforts will pave the way for the development of more
   effective diagnostic and therapeutic approaches for HCC patients.

Acknowledgments