BER: Base Excision Repair

CSC: Cancer Stem Cell

CTLA-4: Cytotoxic T-Lymphocyte-Associated Protein 4

DC: Dendritic Cell

DC1: YTHDC1

DC2: YTHDC2

DF: YTHDF Protein Family

DF1: YTHDF1

DF2: YTHDF2

DF3: YTHDF3

DSB: Double-Strand Break

ECM: Extracellular Matrix

EGFR: Epidermal Growth Factor Receptor

EMT: Epithelial-Mesenchymal Transition

FA: Fanconi Anemia DNA Repair Pathway

FDA: Food and Drug Administration

FTO: Fat Mass And Obesity-Associated Protein

HIF: Hypoxia-Inducible Factor

HIF-1α: Hypoxia-Inducible Factor 1 α Subunit

HIF-1β: Hypoxia-Inducible Factor 1 β Subunit

HNSCC: Head And Neck Squamous Cell Carcinoma

HPV: Human Papillomavirus

HR: Homologous Recombination

HRE: Hypoxia Response Element

ICL: Interstrand Crosslinks

IL-10: Interleukin-10

LSCC: Laryngeal Squamous Cell Carcinoma

M1: M1-Polarised Macrophages

M2: M2-Polarized Macrophages

m³U: 3-Methyluridine

m⁶A: N6-Methyladenosine

MDSC: Myeloid-Derived Suppressor Cell

MHC I: Major Histocompatibility Complex Class I

MHC II: Major Histocompatibility Complex Class II

MHC: Major Histocompatibility Complex

MRP: Multidrug Resistance Protein

ncRNA: non-coding RNA

NER: Nucleotide Excision Repair

NHEJ: Non-Homologous End Joining

NK: Natural Killer Cell

NPC: Nasopharyngeal Carcinoma

OPSCC: Oropharyngeal Squamous Cell Carcinoma

ORR: Overall Response Rates

OSCC: Oral Squamous Cell Carcinoma

P-bodies: RNA processing bodies

PD-1: Programmed Death Protein 1

PDH: Prolyl Hydroxylase

PD-L1: Programmed Death-Ligand 1

pVHL: Von Hippel-Lindau Protein

R/M: Reccurent/Metastatic

Rb: Retinoblastoma Protein

ROS: Reactive Oxygen Species

shRNA: Short hairpin RNA

snRNA: Small Nuclear RNA

SNSCC: Sinonasal Squamous Cell Carcinoma

SRSF: Serine/Arginine-Rich Splicing Factor

SSB: Single-Strand Break

TCA: Tricarboxylic Acid

TGF-β: Transforming Growth Factor Beta

TIL: Tumor Infiltrating Lymphocyte

TLR: Toll-Like Receptor

TME: Tumor Microenvironment

Treg: Regulatory T Cell

Head and neck squamous cell carcinoma, the sixth most common cancer worldwide, develops from mucosal epithelium of tongue, oral cavity, pharynx or larynx. The principal risk factors of HNSCC are tobacco use, alcohol consumption and human papillomavirus (HPV) infection. HNSCC of oral cavity and larynx are linked to tobacco and alcohol exposure, whereas oropharyngeal HNSCC is predominantly correlated with HPV infection (Jiang et al., 2024[41]). Among the oncogenic HPV types, HPV-16 and HPV-18 are chiefly implicated in HNSCC, with HPV-16 responsible for almost 60 % of oropharyngeal cancers (Galati et al., 2024[26], Johnson et al., 2020[42]).

The survival rate for HNSCC is approximately 40-50 % despite the development of various treatments, including surgery, chemo-/radio-/immunotherapy. The poor prognosis of patients is caused by late diagnosis, as T4 is the most common stage at diagnosis for oral and oropharyngeal cancer (Gormley et al., 2022[30]).

Over the years there has been an increase of HPV-positive HNSCC, particularly among young people and those not using tobacco and alcohol (Deschler et al., 2014[13]). HPV-negative HNSCC is much more common in the older population not abstaining from such substances (Farsi et al., 2017[21]). The increased incidence of HPV-positive HNSCC among younger, non-smoking and non-drinking individuals indicates another important risk factor for HNSCC that is sexual transmission of HPV. Oral sex is a key mode of HPV transmission and the changing sexual behaviour of recent decades has contributed to HNSCC (Shah et al., 2017[81]).

Epidemiological analyses of the U.S. population from 1992 to 2015 have demonstrated a significant increase in the incidence of oropharyngeal squamous cell carcinoma (OPSCC), particularly among white males, with an annual increase of 3.8 %. This rising trend has been characterized as a virus-associated epidemic primarily affecting younger individuals, with projections estimating approximately 30,000 new cases per year by 2029. Notably, the highest incidence rate has been observed among individuals born before 1955, with a 5.3 % annual increase (Tota et al., 2019[91]).

This demographic trend is largely attributed to historically lower awareness of safe sexual practices in these cohorts, primarily due to the lack of comprehensive sex education in the pre-HIV era, which facilitated the transmission of HPV. As the population continues to age, the burden of OPSCC is expected to shift towards older white males. This shift underscores the need for treatment strategies that are better tailored to the health status and comorbidities of an ageing patient population (Tota et al., 2019[91]).

Over the next two decades, a significant increase in HPV-positive HNSCC is anticipated, particularly in developed regions such as Europe, North America, Australia, New Zealand (de Martel et al., 2017[12]). The change in demographic profile points to the increased importance of HPV vaccination and public awareness programmes to reduce the increasing number of HPV-dependent cancers. Current HPV-16 and HPV-18 vaccines as a prevention for cervical cancer are able to potentially reduce the incidence of HPV-positive HNSCC; however, differences in the risk factor profiles and pathogenesis mechanisms of the two diseases indicate the need for novel diagnostic and therapeutic strategies (Olsson et al., 2007[66]).

HPV-positive HNSCC patients have a better response to treatment (radio-,chemotherapy), and higher overall survival rates (Li et al., 2018[48]). Data showed a significant increase in three-year overall survival rates of 82.4 % in HPV-positive compared to 57.1 % in HPV-negative HNSCC patients (Ang et al., 2010[1]). HPV status has become a key factor in the treatment stratification of HNSCC. The better prognosis for patients affected by HPV-positive HNSCC has led to the development of new treatment regimens, improving quality of life by reducing treatment-related toxicity (Wang et al., 2019[95]). The inclusion of HPV status in the disease staging system and treatment guidelines has resulted in increased accuracy of prognosis and clinical decision-making (Lewis et al., 2018[46]). Better treatment response and prognosis of HPV-positive HNSCC have been attributed to several factors. Firstly, stronger protection from the immune system may be caused by patients' healthier lifestyles, as they are less likely to be heavy smokers or alcohol abusers (Deschler et al., 2014[13]). Furthermore, the presence of HPV may trigger an enhanced immune response resulting in a better prognosis (Chakravarthy et al., 2016[7], Wang et al., 2019[95]). Thirdly, the characteristics of HPV-positive tumors, i.e. less aggressiveness and greater sensitivity to radiotherapy, translate into better patient outcomes (Mirghani et al., 2015[59]).

Human papillomaviruses are highly epitheliotropic DNA viruses, which targets the multilayered keratocyte regions in order to replicate (Speel, 2017[87]). The viral genome encodes two genes (L1 and L2) necessary for infection and six genes (E1-E7) involved in viral replication, regulation, and HPV-related cellular transformation (Pinkiewicz et al., 2022[73]). The oncogenic potential of HPV-driven cancers primarily stems from the viral proteins E6 and E7, which disrupt crucial tumor suppressor pathways (Williams et al., 2011[105]). E6 facilitates the degradation of p53, a key regulator of DNA damage response and apoptosis, by recruiting the cellular ubiquitin ligase E6AP (Mijit et al., 2020[57]). The loss of p53 function allows cells with genetic abnormalities to continue dividing rather than undergoing programmed cell death. E7 protein, on the other hand, targets the retinoblastoma (Rb) protein for degradation, leading to unchecked activation of E2F transcription factors, which drive the cell cycle forward regardless of regulatory signals (McLaughlin-Drubin and Münger, 2009[56]). Together, these alterations result in uncontrolled cellular proliferation, increased genomic instability, and a weakened ability to undergo cell cycle arrest in response to damage (Figure 2(Fig. 2)).

The expression of cyclin D1, protein encoded by CCND1 gene, involved in cell cycle regulation is a key distinction between HPV-positive and HPV-negative tumors. In HPV-negative cancers, Rb function is not disrupted by viral oncoproteins leading to CCND1 overexpression and excessive cell cycle progression and enhanced tumor growth. By contrast, HPV-positive tumors are characterized by CCND1 inhibition through E7-mediated Rb inactivation (Farah, 2021[20]). Additionally, HPV-negative tumors frequently exhibit mutations in the CDKN2A gene, which encodes, a protein that normally inhibits cyclin-dependent kinases and restricts cell cycle progression. In HPV-positive cancers, p16 is paradoxically overexpressed as a compensatory response to E7-mediated Rb degradation, constituting p16 as a useful biomarker for distinguishing HPV-related tumors (Farah, 2021[20]).

Beyond cell cycle deregulation, HPV-positive tumors also develop sophisticated mechanisms to evade immune detection. By suppressing the expression of major histocompatibility complex (MHC) molecules, HPV-positive tumors reduce their visibility to the host immune system (Westrich et al., 2017[103]). Additionally, increased expression of the immune checkpoint programmed death-ligand 1 (PD-L1) protein inhibits T-cell activation, allowing cancer cells to persist and evade immune surveillance (Lim et al., 2019[51]). These features explain why HPV-positive tumors tend to respond better to immune checkpoint inhibitors, such as anti- programmed death protein 1 (PD-1) and anti-PD-L1 therapies, which aim to restore the patients' immune system's ability to recognize and destroy cancer cells.

The differences in genomic landscape of HPV-positive and HPV-negative HNSCC emphasize the diverse nature of those tumors. HPV-negative HNSCC genetic alterations frequently involve direct mutations in the TP53 gene. More than 70 % of HPV-negative HNSCCs harbor TP53 mutations, leading to the loss of p53 function and contributing to aggressive tumor behavior and poorer treatment responses. In contrast, HPV-positive HNSCC rarely exhibit TP53 mutations since p53 is already functionally inactivated by viral protein E6 (Mountzios et al., 2014[61]). Instead, they frequently harbor mutations in the PIK3CA gene, which encodes a critical regulator of the PI3K/AKT/mTOR signaling pathway. This pathway plays a central role in cell survival, metabolism, and tumor progression, making PIK3CA a promising target for therapeutic intervention in HPV-driven malignancies (Lim et al., 2019[51], Mountzios et al., 2014[61]).

The presence of these distinct genetic alterations significantly influences treatment responses and therapeutic strategies. HPV-positive tumors, characterized by lower mutational burdens and immune evasion mechanisms, tend to be more sensitive to radiation therapy and immune checkpoint blockade. In contrast, HPV-negative tumors, with frequent TP53 mutations, CCND1 amplification, and epidermal growth factor receptor (EGFR) overexpression, are often more resistant to standard therapies and may require combination treatments involving chemotherapy, EGFR inhibitors, or targeted molecular agents (Chung et al., 2015[11], Farah, 2021[20], Mountzios et al., 2014[61], Shi et al., 2023[82]). The growing understanding of these molecular distinctions continues to shape personalized treatment approaches, highlighting the importance of tailoring therapies based on the underlying genetic and viral characteristics of each tumor.

Hypoxia is a characteristic feature observed in up to 90 % of solid tumors, including HNSCC, and is recognized as a hallmark of cancer (Chen et al., 2023[9]). The tumor microenvironment (TME) in solid malignancies is composed of heterogeneous populations, including cancer cells, immune cells, cancer stem cells (CSCs), fibroblasts, extracellular matrix (ECM) components, and blood and lymphatic vessels. This complex structure leads to uneven oxygen distribution, particularly in the tumor core, where high cellular density and metabolic demand exceed the oxygen supply provided by dysfunctional vasculature (Emami Nejad et al., 2021[19]).

Cellular adaptation to hypoxia is largely governed by hypoxia-inducible factors (HIFs), heterodimeric transcription factors consisting of an oxygen-regulated α-subunit (commonly HIF-1α) and a constitutively expressed β-subunit (HIF-1β) (Chen et al., 2023[9]). Under normoxic conditions, HIF-1α is hydroxylated by prolyl hydroxylases (PHD1-3) and targeted for ubiquitin-mediated degradation via the von Hippel-Lindau (pVHL) protein (Ostapowicz et al., 2024[67]). Under hypoxic or iron-depleted conditions, HIF-1α is stabilized, translocates to the nucleus, and dimerizes with HIF-1β. The active complex binds to hypoxia response elements (HREs) in target gene promoters, activating pathways that promote cellular adaptation to low oxygen (Ostapowicz et al., 2024[67]).

HIF-1α directly upregulates genes involved in angiogenesis, such as VEGF, SDF1, and ANGPT2, which promote the formation of abnormal, leaky blood vessels that further impair oxygen and drug delivery (Rey and Semenza, 2010[75]). Interestingly, VEGF expression is significantly lower in HPV-positive HNSCC than in HPV-negative tumors, suggesting that HPV status may influence the angiogenic profile of HNSCC (Baruah et al., 2015[4]).

Hypoxia also reprograms cellular metabolism by promoting anaerobic glycolysis, known as the Warburg effect (Icard et al., 2018[38]). HIF-1α upregulates GLUT1, enhancing glucose uptake, and several glycolytic enzymes including PDK1, LDHA, and PKM. PDK1 inhibits PDH, blocking pyruvate conversion to acetyl-CoA and entry into the tricarboxylic acid (TCA) cycle, thereby promoting glycolysis. LDHA converts pyruvate to lactate, contributing to extracellular acidosis, while PKM2 facilitates metabolic adaptation favoring proliferation and survival (Wicks and Semenza, 2022[104]).

CSCs phenotype is also considered to be maintained by hypoxia conditions. HNSCC stem-like cells are characterized by upregulation of stemness markers including OCT3, OCT4, SOX2 and NANOG (Johnson et al., 2020[42]), which expression promotes invasiveness in HNSCC cells (Emami Nejad et al., 2021[19]). Furthermore, stem-like phenotype is strongly linked to epithelial-mesenchymal transition (EMT) characterized by loss of cell-cell interactions, gaining mesenchymal cell features, detachment from primary tumor or remodeling ECM (Emami Nejad et al., 2021[19]). HIF1 induces expression of SNAIL and TWIST transcription factors that promote EMT through E-cadherin downregulation (Johnson et al., 2020[42]). Therefore, loss of E-cadherin has been linked to increased metastasis in HNSCC (Peltanova et al., 2019[72]). Altogether, weak extracellular interactions and additional vessels are a great opportunity for cancer cells migration and metastasis, highlighting the role of hypoxia signaling in tumor progression.

Therapeutically, hypoxia reduces the effectiveness of radiotherapy by limiting oxygen availability for the formation of DNA-damaging reactive oxygen species (ROS) and promoting DNA repair mechanisms (Chen et al., 2023[9]). It also contributes to chemoresistance through several mechanisms: HIF-1α induces MDR1 expression, encoding P-glycoprotein that actively effluxes drugs from cancer cells; lactate accumulation lowers extracellular pH, impairing the activity of pH-sensitive drugs (e.g., anthracyclines); and poorly perfused tumor vessels prevent efficient drug delivery (Kopecka et al., 2021[45]). Moreover, the lack of oxygen directly diminishes the cytotoxic efficacy of drugs like cisplatin and 5-fluorouracil (Rohwer et al., 2010[77]).

Hypoxia also impairs anti-tumor immune responses. HIF-1α upregulates immune checkpoints such as PD-L1, PD-1, and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) on tumor and immune cells, respectively, leading to immune evasion (Hill et al., 2022[32]). Furthermore, the hypoxic, acidic TME favors recruitment of immunosuppressive cells including M2-polarized macrophages (M2), myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs), while limiting the infiltration and activity of CD8⁺ T cells, which are essential for effective anti-tumor immunity (Kopecka et al., 2021[45]).

Clinically, increased HIF-1α expression correlates with poor prognosis, higher mortality, and resistance to radiotherapy in HNSCC patients (Semenza, 2007[80]). Paradoxically, studies have shown that HIF-1α protein levels are higher in HPV-positive oropharyngeal HNSCC cell lines compared to HPV-negative lines derived from the oral cavity, under both normoxic and hypoxic conditions (Knuth et al., 2017[44]). This contradicts the generally favorable outcomes associated with HPV-positive HNSCC. Additional studies, such as those involving sinonasal squamous cell carcinoma (SNSCC), have failed to show consistent correlations between HPV status and HIF-1α, VEGF, or GLUT1 expression, suggesting that the impact of HPV on hypoxia signaling may be tumor subtype-specific (Vinciguerra et al., 2023[92]).

Overall, hypoxia-driven HIF-1α signaling is a central mediator of tumor progression, treatment resistance, and immune evasion in HNSCC. Its interplay with HPV infection and m⁶A RNA methylation warrants further investigation as a potential target for improving therapy outcomes in this disease.

The regulation of mRNA fate through dynamic m⁶A modification involves a coordinated interplay between methyltransferases, demethylases, and reader proteins operating across nuclear and cytoplasmic compartments (Figure 3(Fig. 3)).

RNA methylation is a critical mechanism involved in the regulation of genes and cellular processes, significantly influencing cancer biology (Sun et al., 2019[89]). The mechanisms regulating RNA methylation in the presence of HPV are mainly driven by the viral oncoproteins E6 and E7 (Zheng et al., 2022[120]). These proteins are able to interact with the cellular machinery to modify the epigenetic landscape. The HPV E6 protein affects the activity of methyltransferases (Hsu et al., 2012[34]). As a result of methyltransferases activity, the stability, splicing and translation of various mRNA molecules may be altered, resulting in induction of oncogenic processes in HPV-positive HNSCC (Maity and Das, 2016[54]). The E7 protein, as a result of targeting RB and interfering with cell cycle regulation, indirectly causes an effect on RNA methylation by altering the expression of regulatory genes responsible for RNA processing and modification (Fu et al., 2014[25], Slebos et al., 1994[85]).

Overexpression of METTL3 or reduced activity of ALKBH5 has been linked to enhanced mRNA methylation, resulting in the stabilization of transcripts involved in cell proliferation and survival. Conversely, loss of m⁶A modifications may impair the proper degradation of oncogenic mRNAs or disrupt cellular differentiation (Wang et al., 2014[98]). In oral squamous cell carcinoma (OSCC), both METTL3 and METTL14 are significantly overexpressed in cancerous tissues compared to normal oral tissues, with higher expression levels correlated with advanced tumor stages and poorer histopathological differentiation. This dysregulation results in an altered mRNA methylation status, affecting the stability and translation of key oncogenes and tumor suppressor genes. In vitro experiments show that silencing METTL3 and METTL14 in OSCC cell lines inhibits cell proliferation, further supporting their role in tumor growth. Additionally, overexpression of these enzymes is associated with shorter overall survival in OSCC patients, positioning METTL3 and METTL14 as independent prognostic markers (Wang et al., 2016[97], Wu et al., 2022[108]).

Distinct patterns of m⁶A methylation are present in HPV-positive tumors, which correlate with specific gene expression profiles and clinical outcomes. Altered m⁶A methylation in HPV-positive HNSCC leads to increased proliferation and resistance to apoptosis of tumour cells (Ban et al., 2020[3]). Writer METTL14 and eraser ALKBH5 collaboratively modulate m⁶A levels on transcripts that control key processes including cell cycle progression, EMT, and angiogenesis. Additionally, hypoxia disrupts the balance of m⁶A machinery by altering the expression of METTL14, ALKBH5, and the m⁶A reader YTHDF3, leading to reduced m⁶A methylation and aberrant gene expression. This disruption contribute to uncontrolled tumor growth, invasion, and angiogenesis (Panneerdoss et al., 2018[69]).

In the case of HPV-positive HNSCC, an immune-invasive phenotype is noticeable, resulting in part from modifications of RNA methylation in immune-related genes. This regulation may translate into altered cytokine production, immune cell infiltration and expression of immune checkpoints, affecting the overall immune landscape of the tumor (Feng et al., 2021[23], Yi et al., 2020[111]).

Recent studies have demonstrated that RNA methylation, particularly m⁶A, plays a significant role in modulating the immune response and the efficacy of immunotherapy. m⁶A modification in mRNA can influence the expression of immune checkpoint molecules and the presentation of neoantigens, thereby affecting tumor recognition by the immune system. Moreover, m⁶A methylation directly and indirectly regulates T cell development, homeostasis, and differentiation. For example, methylation of IL-17 mRNA in T cells promotes its translation and leads to increased IL-17 expression. In DC, the presence of m⁶A enhances DC activation and boosts their ability to stimulate T cell responses. Interestingly, a high abundance of RNA modifications such as m⁶A, m⁵C, and 2-O-methylation has been shown to suppress DC activation under necrosis-like conditions. The cross-presentation of tumor antigens and the capacity of DCs to activate T cells is enhanced when the m⁶A RNA reader YTHDF1 is deleted (Zhang et al., 2022[113]).

Upregulation of METTL3 promotes polarization of macrophages toward the M1 (antitumor) phenotype while inhibiting M2 polarization, which is associated with tumor progression (Zhang et al., 2022[113]). m⁶A-methylated RNAs also suppress activation of the innate immune system via the TLR pathway. Additionally, the expression of type I interferons, key modulators of antiviral and antitumor immunity, is regulated by m⁶A machinery: METTL14 upregulates their expression, while the demethylase ALKBH5 downregulates it (Rubio et al., 2018[79]).

In HNSCC, the expression of the m⁶A reader YTHDC2 correlates with infiltration of CD4+ T cell subsets (Li et al., 2020[50]), and elevated PD-L1 expression has been linked with m⁶A RNA methylation levels (Yi et al., 2020[111]). These findings underscore the epigenetic role of m⁶A in shaping the immune microenvironment of tumors.

Considering the high impact of m⁶A RNA methylation in modulating immune cells activity it is fair to allow for this process as one of the key epigenetic components influencing the immune response to cancer and its treatment. Moreover, it opens up possibilities in the context of new targeted therapies and monitoring the effects of treatment.

To date, there are some studies highlight m⁶A RNA methylation role in anti-cancer therapy response. Overexpression of YTHDF2 gene reduces sensitivity of tumor to cisplatin in colorectal cancer. Upregulation of METTL3 in tumors is associated with tamoxifen resistance and tumor progression. In glioblastoma, temozolmide resistance is mediated in m⁶A- dependent manner. M⁶A RNA methylation related enzymes METTL3, FTO or ALKBH5 affect tumor cells metabolism, thereby causing a resistance to radiotherapy (Zhang et al., 2022[113]). In melanoma, knockdown of FTO resulted in increased PD-1 expression and reversed tumor resistance to anti-PD-1 treatment. What is more, combining PD-L1 checkpoint inhibition and YTHDF1 deletion, indolent tumor progression through stimulation of CD8+ T cells function (Zhang et al., 2022[113]).

Recent clinical trials based on HPV-dependent HNSCC have primarily aimed to optimize treatment by balancing efficacy with minimizing toxicity. Key studies have explored de-escalation strategies in definitive therapy, including reduced-dose radiotherapy and chemotherapy regimens, to address the unique biology and favorable prognosis of HPV-positive tumors. Many clinical trials are focusing on combining immunotherapy with traditional treatments. Novel approaches, including therapeutic HPV-targeted vaccines and agents that enhance the tumor microenvironment, are also under active investigation. These trials reflect a growing emphasis on tailoring interventions to the distinct clinical profile of HPV-related HNSCC. A summary of the latest actively conducted clinical trials is presented in Table 1(Tab. 1).

Growing evidences highlights the critical role of m⁶A RNA methylation in cancer development and progression, positioning it as a potential biomarker for diagnosis, prognosis, and personalized treatment strategies. Unfortunately, there are only few data concerning epigenetic changes in RNA as a biomarker for HNSCC as a response to treatment and patient prognosis. Worth mentioning is the work by Zhao et al. focusing on a bioinformatic search for RNA methylation regulatory signatures in the prediction and prognosis of head and neck squamous cell carcinoma using TCGA data (Zhao and Cui, 2019[117]).

In rectal cancer, m⁶A RNA methylation regulators expression have been linked to disease prognosis (Zhuang et al., 2020[122]). In lung cancer, research by Muraoka et al. suggested that m⁶A RNA methylation of miR-34b/c could serve as both a diagnostic and prognostic marker for malignant pleural mesothelioma, an aggressive lung-related malignancy (Muraoka et al., 2013[62]).

Meanwhile, another study identified five m⁶A regulators-HNRNPA2B1, HNRNPC, KIAA1429/VIRMA, RBM15, and METTL3-as key players in determining survival rates in lung adenocarcinoma patients (Wang et al., 2021[94]).

A study conducted in 2019 by focused on, using transcriptomic data from TCGA to analyze the correlation between m⁶A-associated risk signatures and patient outcomes. Chen et al. findings based on transcriptomic TCGA data revealed that bladder cancer patients may be classified by significant differences in survival based on the expression of FTO, YTHDC1, and WTAP genes (Chen et al., 2019[8]).

More recently, Hou et al. developed a prognostic model based on m⁶A RNA methylation regulators for papillary thyroid carcinoma. This model, which incorporated RBM15, KIAA1429, and FTO expression, was validated as an effective predictor of overall survival in thyroid cancer patients, further cementing the role of RNA methylation in cancer prognosis (Hou et al., 2019[33]).

With the increasing availability of RNA methylation profiling techniques, above/presented findings highlight the clinical potential of epitranscriptomic markers in precision oncology, offering new avenues for early cancer detection, risk assessment, and tailored therapeutic interventions. Furthermore, a better understanding of the role of m⁶A RNA methylation in HPV-positive HNSCC could result in the development of new biomarkers for early detection and prognosis (Minor et al., 2012[58], Misawa et al., 2020[60]).

Recent advances in cancer research highlight the potential of targeting HPV oncoproteins and m⁶A RNA methylation pathways as innovative therapeutic strategies. One of the most promising approaches in HPV-related cancers involves direct inhibiting the viral oncoproteins that sustain malignant cell growth. Strategies such as monoclonal antibodies and small-molecule inhibitors aim to disrupt E6/E7 interactions with host proteins, restoring tumor suppressor activity and reducing cancer cell proliferation (Ni et al., 2025[64]). Another promising avenue is RNA-based therapeutics, including short hairpin RNAs (shRNAs) and CRISPR-Cas9-based gene editing, that inhibit E6/E7 expression and trigger apoptosis in HPV-positive cancer cells (Folliero et al., 2023[24]). Additionally, emerging research suggests that immune checkpoint inhibitors targeting PD-L1 in HPV-driven tumors may enhance immune responses, allowing for better recognition and elimination of cancer cells (Li et al., 2024[49]). Furthermore, therapeutic HPV vaccines that elicit immune responses against E6 and E7 peptides have demonstrated significant preclinical potential (Folliero et al., 2023[24]).

Beyond HPV oncoproteins, another promising target in cancer therapy is m⁶A RNA methylation related regulators. Inhibiting selected m⁶A writers, erasers and readers has been shown to increase sensitivity to chemotherapy and immunotherapy, suggesting that m⁶A modulation could enhance current treatment approaches (Pulliero et al., 2024[74]). Additionally, the combination of m⁶A inhibitors with DNA methylation drugs has been explored as a strategy to reprogram gene expression and reverse cancer-associated epigenetic changes (Durzynska et al., 2017[17]).

Further studies highlighted the role of non-coding RNAs (ncRNAs) in regulating both HPV oncoproteins and m⁶A RNA methylation pathways. Certain lncRNAs interact with E6 and E7 proteins, influencing cancer cell metabolism and immune evasion, making them potential therapeutic targets (Ghiani and Chiocca, 2022[29]). Targeting these RNA molecules using mRNA-based drugs or antisense oligonucleotides could provide a novel way to correct epitranscriptomic imbalances in cancer cells.

Combining HPV oncoprotein inhibition and m⁶A RNA methylation modulation is a promising frontier in precision oncology. These targeted strategies not only disrupt key oncogenic pathways but also offer potential solutions to therapy resistance, which remains a major challenge in cancer treatment.

This review underscores the complex interplay between hypoxia, m⁶A RNA methylation, and HPV infection in shaping both the oncogenic landscape and therapeutic resistance in HNSCC. Each of these factors-acting individually or in synergy-modulates cellular metabolism, immune surveillance, and response to treatment.

Hypoxia contributes to tumor progression and immune evasion by stabilizing HIF-1α, altering m⁶A regulatory enzyme expression, and promoting resistance to radiotherapy and chemotherapy. At the same time, m⁶A RNA methylation dynamically regulates gene expression involved in DNA repair, immune checkpoint presentation, and treatment response. Dysregulation of m⁶A machinery can promote oncogenic pathways and mediate adaptive resistance to cisplatin, temozolomide, and even immune checkpoint inhibitors.

HPV-driven tumors represent a biologically distinct subset of HNSCC, characterized by viral antigen expression, altered immune microenvironments, and differential regulation of m⁶A-related enzymes. Notably, HPV-positive tumors exhibit greater immunogenicity and often demonstrate improved clinical responses to immunotherapy and radiation-outcomes that may be partially mediated by epitranscriptomic modifications.

Taken together, these insights reveal that hypoxia, m⁶A methylation, and HPV infection are not only biomarkers of tumor behavior but also active participants in therapy resistance. Targeting these intertwined mechanisms could lead to novel, more effective combination strategies-incorporating immunotherapy, epigenetic modulation, and hypoxia-directed interventions-for patients with both HPV-positive and HPV-negative HNSCC.