Stomach adenocarcinoma is a cancer resulting from the malignant transformation of somatic cells in gastric glands. It is one of the most prevalent gastrointestinal cancers, with an estimated annual incidence of over 1 million cases worldwide (Smyth et al., 2020). Unfortunately, due to its frequently advanced stage upon diagnosis, mortality rates associated with gastric cancer remain high. However, although the cancer incidence rate is decreasing in most countries, clinicians predict an increase in cancer cases in the future due to the aging population. Therefore, researching new molecular targets and pathways is crucial for providing innovative insights into the diagnosis, treatment, and prognosis of STAD.
FASTKD1 is a member of the FASTK family, which includes six members: FASTK, the original member, and its homologs, FAST Kinase Domains 1–5 (FASTKD1-5). These FASTK family proteins are found exclusively in vertebrates and have widespread expression in mitochondria across multiple body tissues. They have a vital role in preserving and stabilizing mitochondria, emerging as critical regulators of post-transcriptional gene expression within these organelles (Boehm et al., 2017). FASTKD1 is situated on chromosome 2q31.1 and is expressed in the mitochondrial matrix. It features an amino-terminal mitochondrial targeting signal (MTS) and a C-terminal region with three conserved domains, FAST1, FAST2, and RAP (Marshall et al., 2019). FASTKD1 controls the ND3 domain within mitochondria and may possibly participate in processes associated with RNA stability. Furthermore, FASTKD1 operates as a protective factor against reactive oxygen species (ROS)-induced oxidative stress and cell death, although the exact mechanism of this protection is currently unknown (Simarro et al., 2010). Additionally, FASTKD1 alters mitochondrial dynamics in a CypD-independent manner and impacts processes such as autophagy/mitophagy and caspase-3 activation (Marshall et al., 2019). However, limited research has examined the role of FASTKD1 in carcinogenesis.
In this study, we analyzed XENA-TCGA and GEO datasets to observe the significant expression levels of FASTKD1 in various tumors, including STAD. The elevated expression of FASTKD1 in STAD tissue was confirmed through IHC staining. In addition, our study has found that increased levels of FASTKD1 expression provide a diagnosis of STAD and are strongly linked to unfavorable prognosis and clinical features in STAD patients. For instance, administering anti-reflux therapy can significantly reduce the expression of FASTKD1 in STAD patients. Our GO and KEGG enrichment analysis revealed that the co-expressed genes of FASTKD1 are active in a variety of biological processes, such as nuclear chromosome segregation, chromosomal regions, catalytic activity (specifically acting on RNA), ATPase activity, cell cycle, and spliceosome pathways. Several studies have demonstrated the significant involvement of the aforementioned biological functions in the initiation and progression of tumors. Proper segregation of nuclear chromosomes is crucial to maintaining genomic stability during cell division, errors in this process can lead to aneuploidy, a condition in which cells have an abnormal number of chromosomes, which is often observed in cancer cells. Aneuploidy contributes to genomic instability, promotes tumorigenesis, and enables the acquisition of genetic alterations that propel tumor progression (Klaasen et al., 2022). Structural variations, amplifications, deletions, and rearrangements in particular chromosomal regions are associated with different types of tumors, these changes bring about alterations in gene dosage, disruption of regulatory elements, and activation or inactivation of oncogenes and tumor suppressor genes, found within these regions. These alterations lead to uncontrolled growth and survival of cells and promote the development and progression of tumors (Wang et al., 2022). Catalytic activity specifically acting on RNA includes enzymes involved in processing, modification, and degradation, dysregulation of these enzymatic activities can affect critical cellular processes, including the stability, translation, and splicing of mRNA. Aberrant RNA metabolism is frequently observed in cancer cells and can lead to altered gene expression patterns that promote tumor cell growth and survival (Barbieri & Kouzarides, 2020). ATPase activity is crucial to multiple cellular processes, such as DNA repair, chromatin remodeling, and protein folding, dysregulated ATPase activity in cancer is associated with defects in DNA damage response and repair mechanisms, compromised chromatin structure, and altered protein homeostasis, these disruptions contribute to genomic instability, a hallmark of cancer, and promote tumor progression (Chang et al., 2017). The cell cycle is precisely regulated to guarantee precise DNA replication and cell division, excessive cell proliferation and accumulation of genetic abnormalities can be caused by the checkpoint's dysregulation, dysregulation of the cell cycle is a hallmark of cancer, contributing to uncontrolled cell growth, genomic instability, and tumor progression (Sun et al., 2021). The spliceosome is a sophisticated molecular apparatus responsible for RNA splicing, a key process in the regulation of gene expression, dysregulation of splicing events can lead to the production of abnormal isoforms with oncogenic properties, disruptions in spliceosome components or splicing factors have been reported in numerous cancers and profoundly affect essential cellular processes including cell growth, survival and metastasis, thereby contributing to tumor progression (Bowling et al., 2021). The enrichment analysis using GSEA pathways revealed that the differentially expressed genes associated with FASTKD1 were enriched in these pathways, including retinoblastoma gene in cancer, activation of ATR in response to replicative stress, resolution of D-loop structures, PLK1 pathway, homologous DNA pairing and strand exchange, nuclear pore complex (NPC) disassembly. These cellular processes and pathways play a critical role in the initiation and progression of cancer. A complete understanding of their dysregulation and functional implications provides valuable insights into the underlying mechanisms of STAD. The retinoblastoma pathway in cancer involves the central role of the RB1 gene in regulating cell cycle progression and inhibiting tumorigenesis, disruptions of RB1, caused by mutations or inactivation, can significantly contribute to the development of various cancers (Dimaras et al., 2015). Activation of ATR in response to replication stress is one pathway that highlights the role of ATR proteins in response to DNA replication stress, ATR plays a critical role in maintaining genomic integrity by initiating signaling pathways involved in the DNA damage response, leading to cell cycle arrest and DNA repair (Ma et al., 2020). The association between D-loop resolution and homologous recombination suggests a DNA repair mechanism responsible for the accurate repair of DNA double-strand breaks, accurate D-loop resolution plays a critical role in maintaining genome stability and preventing the accumulation of genetic abnormalities (Yang et al., 2020). PLK1 is a critical regulator of cell division and exerts its influence at multiple stages of mitosis, including mitotic entry, spindle assembly, chromosome segregation, and cytokinesis, disruption of PLK1 activity has been reported in several cancer types and is associated with aberrant cell division, chromosomal instability, and tumor progression (Iliaki et al., 2021). Homologous DNA pairing and strand exchange is a pathway that highlights the critical steps in DNA repair by homologous recombination, specifically, this pathway highlights the importance of homologous DNA pairing and subsequent strand exchange events, dysregulation of these complex processes can lead to genomic instability and increase the risk of tumorigenesis (Zelensky et al., 2014). The nuclear pore complex (NPC) disassembly pathway sheds light on the process of NPC disassembly during mitosis to facilitate accurate chromosome segregation, dysregulation of NPC disassembly disrupts normal cell division and contributes to chromosomal instability, a common feature observed in cancer cells (Kutay et al., 2021). The intricate relationship between these biological processes and pathways suggests their potential involvement in the biological functions and mechanisms associated with FASTKD1 in STAD. Further investigation of these pathways promises to provide valuable insights into the role of FASTKD1 in the development and progression of STAD.
The assessment of immune infiltration of tumor cells has become increasingly important in cancer research and clinical practice. Understanding the composition and functional properties of the immune infiltrate can assist in identifying potential therapeutic targets and developing immunotherapies. Our investigation provides valuable insights into the interplay between FASTKD1 and the immune microenvironment in the context of STAD. Our results indicate a negative correlation between the expression level of FASTKD1 in STAD and the presence of several immune cell types. Specifically, we observed a negative correlation between FASTKD1 expression and the infiltration of CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells. These results suggest that FASTKD1 may play a role in modulating the tumor immune microenvironment in STAD by potentially affecting the abundance or activity of these immune cell populations (Chen et al., 2022). We also found that CNVs in FASTKD1 have an impact on the levels of infiltrating immune cells in STAD. We observe that changes in FASTKD1 CNV are associated with changes in the abundance of B cells, CD4+ T cells, macrophages, neutrophils and dendritic cells within the tumor microenvironment. In our study, we found that the prevalent copy number alterations associated with FASTKD1 in STAD are characterized by two patterns: arm level deletion and arm level gain. Arm level deletion is a genomic alteration commonly observed in various tumor types, including STAD. It is characterized by the loss of genetic material spanning an entire chromosomal arm. The loss of genetic material from an entire chromosomal arm can result in the inactivation or loss of multiple genes located within that region. These genes may include tumor suppressor genes (TSGs), which normally help regulate cell growth and prevent tumor formation (Roy et al., 2016). Arm gain is often associated with amplification of oncogenes, genes that promote tumor growth when abnormally activated or amplified. The increased copy number of these oncogenes leads to increased expression or functional activity, which drives tumor proliferation and survival (Truty et al., 2019). These findings suggest a potential role for FASTKD1 CNV in modulating the composition of immune cells and potentially influencing the immune response in STAD. In the context of disease, CNVs have been implicated in a variety of conditions, including developmental disorders, neurodegenerative diseases, and several types of cancer. In cancer, CNVs may contribute to tumorigenesis by affecting oncogenes or tumor suppressor genes, disrupting key signaling pathways, or altering the genomic stability of cancer cells (DeVries et al., 2022; Malhotra & Sebat, 2012). By comparing groups with elevated and low FASTKD1 expression, we can examine the differential immune cell composition between the two groups. The analysis aims to uncover potential differences in the abundance of various immune cell subtypes, including but not limited to T cells (including CD8+ T cells and CD4+ T cells), B cells, natural killer cells, macrophages, neutrophils, dendritic cells, and other identifiable immune cell populations. We also observed a significant correlation between macrophage infiltration and survival in STAD patients. This finding suggests that the presence or abundance of macrophages in the tumor microenvironment plays a role in determining patient outcome (Xia et al., 2020). We also found that FASTKD1 expression was negatively correlated with most immune infiltration markers in the TIMER and GEPIA databases. This finding suggests that as FASTKD1 expression increases, the expression or abundance of immune cell infiltration markers tends to decrease. It is possible that FASTKD1 directly or indirectly affects the release of immunosuppressive factors or alters the expression of chemokines that drive immune cell migration. A comprehensive analysis to investigate the relationship between FASTKD1 expression and changes in the immune cell landscape within STAD tumors may provide valuable insights into the potential role of FASTKD1 in influencing the immune microenvironment.
N6-methyladenosine (m6A) modification is a common and reversible RNA modification that plays an important role in post-transcriptional gene regulation. In recent years, extensive research has been conducted to understand the functional significance of m6A modification and its impact on various biological processes. In our study, a significant correlation was observed between the expression levels of FASTKD1 and two genes, namely YTHDF1 and LRPPRC. YTHDF1 is a member of the YTH domain family of RNA-binding proteins that specifically recognizes and binds to m6A-modified mRNA. As an m6A reader, YTHDF1 plays a role in the regulation of RNA metabolism and translation. It promotes translation efficiency by interacting with the translation initiation machinery and recruiting ribosomes to m6A-modified transcripts. YTHDF1 also influences mRNA decay processes, where it can either stabilize or promote degradation of m6A-modified transcripts, depending on the context (Hu et al., 2021). LRPPRC is a versatile protein involved in several cellular processes, including mitochondrial function and RNA metabolism, and has been implicated in the stabilization and maintenance of mitochondrial transcripts as well as the post-transcriptional regulation of nuclear-encoded mRNAs. It interacts with specific RNA targets, including those involved in oxidative phosphorylation and mitochondrial biogenesis, to regulate their processing, stability, or translation (Cui et al., 2019; Wei et al., 2021). Our study found a significant correlation between FASTKD1 expression and both YTHDF1 and LRPPRC. This correlation suggests a possible relationship between FASTKD1 and these two genes in the context of post-transcriptional gene regulation. Further investigation is required to determine the nature and functional implications of these correlations, such as whether FASTKD1 directly interacts with YTHDF1 and LRPPRC or whether they share a common regulatory pathway or mechanism.
In conclusion, our study demonstrated that FASTKD1 is upregulated in STAD and shows associations with clinical characteristics and survival prognoses of STAD patients. Furthermore, we investigated the interaction between FASTKD1, immune infiltration and m6A modification. Our results indicate that FASTKD1 is a promising independent diagnostic and prognostic marker for STAD and suggest potential targets for future molecularly targeted therapies.