Recurrent chromosomal and epigenetic alterations in oral squamous cell carcinoma and its putative premalignant condition oral lichen planus

Universal penalized regression (Elastic-net) model with differentially methylated promoters for oral cancer prediction

BACKGROUND

DNA methylation showed notable potential to act as a diagnostic marker in many cancers. Many studies proposed DNA methylation biomarker in OSCC detection, while most of these studies are limited to specific cohorts or geographical location. However, the generalizability of DNA methylation as a diagnostic marker in oral cancer across different geographical locations is yet to be investigated.

METHODS

We used genome-wide methylation data from 384 oral cavity cancer and normal tissues from TCGA HNSCC and eastern India. The common differentially methylated CpGs in these two cohorts were used to develop an Elastic-net model that can be used for the diagnosis of OSCC. The model was validated using 812 HNSCC and normal samples from different anatomical sites of oral cavity from seven countries. Droplet Digital PCR of methyl-sensitive restriction enzyme digested DNA (ddMSRE) was used for quantification of methylation and validation of the model with 22 OSCC and 22 contralateral normal samples. Additionally, pyrosequencing was used to validate the model using 46 OSCC and 25 adjacent normal and 21 contralateral normal tissue samples.

RESULTS

With ddMSRE, our model showed 91% sensitivity, 100% specificity, and 95% accuracy in classifying OSCC from the contralateral normal tissues. Validation of the model with pyrosequencing also showed 96% sensitivity, 91% specificity, and 93% accuracy for classifying the OSCC from contralateral normal samples, while in case of adjacent normal samples we found similar sensitivity but with 20% specificity, suggesting the presence of early disease methylation signature at the adjacent normal samples. Methylation array data of HNSCC and normal tissues from different geographical locations and different anatomical sites showed comparable sensitivity, specificity, and accuracy in detecting oral cavity cancer with across. Similar results were also observed for different stages of oral cavity cancer.

CONCLUSIONS

Our model identified crucial genomic regions affected by DNA methylation in OSCC and showed similar accuracy in detecting oral cancer across different geographical locations. The high specificity of this model in classifying contralateral normal samples from the oral cancer compared to the adjacent normal samples suggested applicability of the model in early detection.

DNA methylation and its potential roles in common oral diseases

Oral diseases are among the most common diseases worldwide and are associated with systemic illnesses, and the rising occurrence of oral diseases significantly impacts the quality of life for many individuals. It is crucial to detect and treat these conditions early to prevent them from advancing. DNA methylation is a fundamental epigenetic process that contributes to a variety of diseases including various oral diseases. Taking advantage of its reversibility, DNA methylation becomes a viable therapeutic target by regulating various cellular processes. Understanding the potential role of this DNA alteration in oral diseases can provide significant advances and more opportunities for diagnosis and therapy. This article will review the biology of DNA methylation, and then mainly discuss the key findings on DNA methylation in oral cancer, periodontitis, endodontic disease, oral mucosal disease, and clefts of the lip and/or palate in the background of studies on global DNA methylation and gene-specific DNA methylation.

An improved epigenetic counter to track mitotic age in normal and precancerous tissues

The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.

Oral Lichen Planus: An Updated Review of Etiopathogenesis, Clinical Presentation, and Management

Lichen planus (LP) is a chronic idiopathic immune-mediated inflammatory condition. LP is a heterogeneous disease with varied clinical presentations having different natural history, prognosis, sequelae, and outcomes. It can affect skin, hair, nails, and mucosae. Mucosal LP (including oral LP) tends to be persistent and resistant to treatment, compared to cutaneous LP. Oral LP (OLP) is broadly divided into two main categories: hyperkeratotic (usually asymptomatic) and erosive (commonly symptomatic). It can present with symptoms including odynophagia, dysphagia, dysgeusia, and sensitivity to hot spicy foods. Apart from the superficial epidermal changes, which vary with the type of clinical presentation, histopathologically oral LP shows a unifying similar and consistent feature of a lichenoid interface dermatitis. Recently, researchers have highlighted the critical role played by IL-17 in the pathogenesis of OLP. World Health Organization has categorized oral LP as one of the oral potentially malignant disorders (OPMD), albeit with a low risk of malignant transformation. Also, in the last couple of years there have been various reports on the usage of newer drugs like anti-IL17, anti-IL12/23, anti-IL 23, PDE4 inhibitors, and JAK inhibitors in the management of refractory OLP. The principal aim of treatment still remains to resolve the symptoms, prolong the symptoms free period, and reduce the risk of potential malignant transformation. We have described many new revelations made in recent times regarding the etiopathogenesis, associated conditions as well as management of OLP. Thus, the objective of this review is to present a comprehensive up-to-date knowledge including the recent advances made regarding OLP.

Mechanisms underlying sex bias in oral immune-mediated conditions, an insight

The predilection for women in systemic autoimmune diseases is well established. However, this sex bias in oral autoimmune diseases has been classically reported from an epidemiological perspective without any elaborate attempts to unveil the underlying mechanisms. The unique nature of the oral environment is likely to impose a combination of systemic and local factors that ultimately result in the sex bias in autoimmune diseases of the oral cavity. Variations of immune responses, target organ vulnerability, endocrine and genetic factors, sex chromosomes and modes of parental inheritance are potential systemic factors, while the oral microbiome, oral tolerance, saliva, and oral epithelial stem cells may account for local contributing factors. This review will discuss the preponderance of women in oral immune-mediated diseases, the potential systemic and local mechanisms underlying this predominance and highlight the crucial need for further research in this area.

Is OLP potentially malignant? A clue from ZNF582 methylation

OBJECTIVE

Whether oral lichen planus (OLP) was potentially malignant remains controversial. Here, we examined associations of ZNF582 methylation (ZNF582^m ) with OLP lesions, dysplastic features and squamous cell carcinoma (OSCC).

MATERIALS AND METHODS

This is a case-control study. ZNF582^m was evaluated in both lesion and adjacent normal sites of 42 dysplasia, 90 OSCC and 43 OLP patients, whereas ZNF582^m was evaluated only in one mucosal site of 45 normal controls. High-risk habits affecting ZNF582^m such as betel nut chewing and cigarette smoking were also compared in those groups.

RESULTS

OLP lesions showed significantly lower ZNF582^m than those of dysplasia and OSCC. At adjacent normal mucosa, ZNF582^m increased from patients of OLP, dysplasia, to OSCC. In addition, ZNF582^m at adjacent normal sites in OLP patients was comparable to normal mucosa in control group. Dysplasia/OSCC patients with high-risk habits exhibited significantly higher ZNF582^m than those without high-risk habits. However, ZNF582^m in OLP patients was not affected by those high-risk habits.

CONCLUSIONS

OLP is unlikely to be potentially malignant based on ZNF582^m levels. ZNF582^m may also be a potential biomarker for distinguishing OLP from true dysplastic features and OSCC, and for monitoring the malignant transformation of OLP, potentially malignant disorders with dysplastic features and OSCC.

Integrated analysis reveals common DNA methylation patterns of alcohol-associated cancers: A pan-cancer analysis

Background: The role of alcohol in carcinogenesis has received increasing attention in recent years. Evidence shows its impacts on various aspects, including epigenetics alteration. The DNA methylation patterns underlying alcohol-associated cancers are not fully understood. Methods: We investigated the aberrant DNA methylation patterns in four alcohol-associated cancers based on the Illumina HumanMethylation450 BeadChip. Pearson coefficient correlations were identified between differential methylated CpG probes and annotated genes. Transcriptional factor motifs were enriched and clustered using MEME Suite, and a regulatory network was constructed. Results: In each cancer, differential methylated probes (DMPs) were identified, and 172 hypermethylated and 21 hypomethylated pan-cancer DMPs (PDMPs) were examined further. Annotated genes significantly regulated by PDMPs were investigated and enriched in transcriptional misregulation in cancers. The CpG island chr19:58220189-58220517 was hypermethylated in all four cancers and silenced in the transcription factor ZNF154. Various biological effects were exerted by 33 hypermethylated and seven hypomethylated transcriptional factor motifs grouped into five clusters. Eleven pan-cancer DMPs were identified to be associated with clinical outcomes in the four alcohol-associated cancers, which might provide a potential point of view for clinical outcome prediction. Conclusion: This study provides an integrated insight into DNA methylation patterns in alcohol-associated cancers and reveals the corresponding features, influences, and potential mechanisms.

Oral Lichen Planus and Mutated TP53-A Road to Cancer?

The malignant potential of oral lichen planus (OLP) has been discussed and disputed for decades. The lesions are often characterized by strong expression of the TP53 protein in the basal layer of the mucosa. In 2002, we reported the presence of TP53 mutations in nine out of 27 OLP lesions tested. At follow-up in 2009, one case of oral squamous cell cancer (OSCC) had occurred in a different site six years later. In contrast, in another case, TP53 mutation persisted for years without malignant transformation. In a longitudinal study of eight selected patients with OSCC or different pre-malignant lesions, it was concluded that TP53 mutations could occur early or late in the development of OSCC. A follow-up in the present, almost 20 years later, revealed that one further case of OSCC had occurred in a TP53-mutated case of OLP, 21 years after the first sample was taken, again in a different site. With this second case, this small study now points towards a risk of developing OSCC in TP53-mutated OLP lesions. A review of recent literature indicates a growing consensus that OLP should be regarded as a potentially pre-malignant lesion. Several protein markers have been studied, but none proved useful for prediction of malignant progression. The great majority of published studies are retrospective, and it has been suggested that multi-centre prospective studies will be needed to reach a definitive answer on the malignant potential of OLP, and particularly, to identify contributing factors. Screening for TP53 mutations could help to identify the subgroup of OLP patients that is truly at risk of developing oral cancer.

[Mucosal lichen planus-a diagnostic and therapeutic challenge]

Mucosal lichen planus (MLP) is a chronic inflammatory disease of the mucosa. This condition can affect the mouth, esophagus, pharynx, genitalia, anus, and conjunctiva. This disease shows a tendency to chronicity with phases of relapses for a duration of 3-10 years. It presents with varying morphologies including lacy or fern-like, slightly raised striae, erosions, erythema, and atrophy. The pathophysiology is not yet fully understood and is dominated by the classic band-like lymphocytic infiltrate along the dermoepidermal junction. MLP is very challenging to treat, since the clinical course entails frequent relapses and shows resistance to therapy. The most commonly used local treatments are topical corticosteroids or calcineurin inhibitors. In addition to systemic glucocorticosteroids and traditional systemic drugs such as oral retinoids or methotrexate, emerging anti-inflammatory therapies such as Janus kinase inhibitors and biologics may be promising and are currently being evaluated in clinical trials.

Digesting the Role of JAK-STAT and Cytokine Signaling in Oral and Gastric Cancers

When small proteins such as cytokines bind to their associated receptors on the plasma membrane, they can activate multiple internal signaling cascades allowing information from one cell to affect another. Frequently the signaling cascade leads to a change in gene expression that can affect cell functions such as proliferation, differentiation and homeostasis. The Janus kinase-signal transducer and activator of transcription (JAK-STAT) and the tumor necrosis factor receptor (TNFR) are the pivotal mechanisms employed for such communication. When deregulated, the JAK-STAT and the TNF receptor signaling pathways can induce chronic inflammatory phenotypes by promoting more cytokine production. Furthermore, these signaling pathways can promote replication, survival and metastasis of cancer cells. This review will summarize the essentials of the JAK/STAT and TNF signaling pathways and their regulation and the molecular mechanisms that lead to the dysregulation of the JAK-STAT pathway. The consequences of dysregulation, as ascertained from founding work in haematopoietic malignancies to more recent research in solid oral-gastrointestinal cancers, will also be discussed. Finally, this review will highlight the development and future of therapeutic applications which modulate the JAK-STAT or the TNF signaling pathways in cancers.

Whole-Exome Sequencing of Transforming Oral Lichen Planus Reveals Mutations in DNA Damage Repair and Apoptosis Pathway Genes

BACKGROUND

Oral lichen planus confers a 1% risk of transformation to oral squamous cell carcinoma. While prior exome sequencing studies have identified multiple genetic mutations in oral squamous cell carcinoma, mutational analyses of lichen planus-derived OSCC are lacking. We sought to clarify genomic events associated with oral lichen planus transformation.

METHODS

Using rigorous diagnostic criteria, we retrospectively identified patients with non-transforming oral lichen planus (i.e. known to be non-transforming with 5 years of clinical follow-up; n=17), transforming oral lichen planus (tissue marginal to oral squamous cell carcinoma, n=9), or oral squamous cell carcinoma arising in lichen planus (n=17). Gene mutational profiles derived from whole-exome sequencing on fixed mucosal specimens were compared amongst the groups.

RESULTS

The four most frequently mutated genes in transforming oral lichen planus and oral squamous cell carcinoma (TP53, CELSR1, CASP8 and KMT2D) identified 12/17 (71%) of oral squamous cell carcinomas and 5/9 (56%) of transforming oral lichen planus but were absent in non-transforming oral lichen planus. These findings suggest alterations in DNA damage response and apoptosis pathways underlie lichen planus-related oral squamous cell carcinoma transformation and are supported by mutational signatures indicative of DNA damage. We identified other known oral squamous cell carcinoma mutations (TRRAP, OBSCN, LRP2) but also previously unreported mutations (TENM3 and ASH1L) in lichen planus-associated oral squamous cell carcinomas.

CONCLUSIONS

This study characterized patterns of mutational events present in oral lichen planus associated with squamous cell carcinoma, and in squamous cell carcinoma associated with oral lichen planus, but not in non-transforming oral lichen planus.

Integrative Multi-Omics Analysis Reveals Candidate Biomarkers for Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most common types of cancer worldwide. Due to the lack of early detection and treatment, the survival rate of OSCC remains poor and the incidence of OSCC has not decreased during the past decades. To explore potential biomarkers and therapeutic targets for OSCC, we analyzed differentially expressed genes (DEGs) associated with OSCC using RNA sequencing technology. Methylation-regulated and differentially expressed genes (MeDEGs) of OSCC were further identified via an integrative approach by examining publicly available methylomic datasets together with our transcriptomic data. Protein-protein interaction (PPI) networks of MeDEGs were constructed and highly connected hub MeDEGs were identified from these PPI networks. Subsequently, expression and survival analyses of hub genes were performed using The Cancer Genome Atlas (TCGA) database and the Gene Expression Profiling Interactive Analysis (GEPIA) online tool. A total of 56 upregulated MeDEGs and 170 downregulated MeDEGs were identified in OSCC. Eleven hub genes with high degree of connectivity were picked out from the PPI networks constructed by those MeDEGs. Among them, the expression level of four hub genes (CTLA4, CDSN, ACTN2, and MYH11) were found to be significantly changed in the head and neck squamous carcinoma (HNSC) patients. Three hypomethylated hub genes (CTLA4, GPR29, and TNFSF11) and one hypermethylated hub gene (ISL1) were found to be significantly associated with overall survival (OS) of HNSC patients. Therefore, these hub genes may serve as potential DNA methylation biomarkers and therapeutic targets of OSCC.

Elevation of Serum SSCCAII in Cutaneous and Oral Lichen Planus: Missing Link for Hidden Carcinogenic Potential?

Context:

Lichen planus (LP) is an immune mediated inflammatory condition. SCCAII is a useful biomarker reflecting Th17 type inflammation. It is also a tumour marker, especially for Squamous cell carcinoma (SCC) Mechanism of carcinogenesis in LP is still unknown. Chronic inflammation may facilitate the development of cellular clones in the epidermis.

Aims:

Estimation of serum level of SCCA II in patients with cutaneous and oral LP (OLP) to detect its role in LP pathogenesis, and to reveal the missing link in understanding mechanism of carcinogenesis in LP.

Methods and Material:

A case control study, where 100 subjects were included; 80 LP patients (40 cutaneous & 40 oral) and 20 apparently healthy controls. We obtained an informed written consent from each subject prior the participation. Cutaneous and oral LP were diagnosed clinically, SCCA II level was measured by ELISA technique.

Statistical analysis used:

Statistical analysis was done using SPSS vs.25. (IBM, Armonk, New York, United states). Numerical data was summarized as means and standard deviations or medians and ranges.

Results:

Median SSCCAII level was significantly higher in LP cases compared to controls (P < 0.001) and was significantly higher in patients with OLP compared to patients with cutaneous LP (P ≤ 0.001). Post hoc analysis revealed that median SSCCAII was significantly higher in patients with ulcerative type compared to both reticular type and others. It was also significantly higher in patients with actinic type compared to both hypertrophic type and classic type. Median SSCCAII was significantly higher in patients with ulcerative OLP compared to actinic LP (P < 0.001).

Conclusions:

Our study revealed that serum SCCAII level was higher in patients with cutaneous and OLP. This might be linked to the pathogenesis of LP, especially actinic and erosive OLP. SCCAII level could facilitate the screening and early detection of patients at risk, a potential alarm to launch accurate assessment and continue follow up of cutaneous as well as O LP patients.

Identification of HPV16-p16INK4a mediated methylation in oral potentially malignant disorder

To evaluate the possible involvement of epigenetic modulation by HPV16-p16^INK4a in oral potentially malignant disorder (OPMD). We generated DNA-methylation profiles, according to p16^INK4a expression and HPV16 genotype (positive or negative), of OPMD samples and p16^INK4a-HPV16 negative samples (used as control), using reduced-representation bisulphite sequencing (RRBS-Seq- Illumina) technology. Twelve samples, four for each group, as follows: 1) p16^INK4a+ HPV16+; 2) p16^INK4a+ HPV16-; 3) p16^INK4a- HPV16-, were analysed in triplicate for DNA-methylation profiles. Fifty-four per cent of DMRs were hypermethylated and 46% were hypomethylated. An increase in methylation of loci in OPMD was independent of the presence of HPV. The hypermethylated genes in HPV+ samples were associated with signalling pathways such as NICD traffics to nucleus, signalling by NOTCH1 (p = 0.008), Interferon-gamma (p = 0.008) and Interleukin-6 signalling (p = 0.027). The hypomethylated genes in HPV infection were associated with TRAF3-dependent IRF activation pathway (p = 0.002), RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways (p = 0.005), TRAF6 mediated IRF7 activation (p = 0.009), TRIF-mediated TLR3/TLR4 signalling (p = 0.011) and MyD88-independent cascade release of apoptotic factors (p = 0.011). Protein association analysis of DMRs in OPMD revealed 19 genes involved in the cell cycle regulation, immune system, and focal adhesion. Aberrantly methylated loci in OPMD were observed in p16^INK4a positive samples which suggests that a shift in global methylation status may be important for cancer progression. The results suggest that HPV infection in OPMD induces modulation of genes related to the immune system and regulation of the cellular cycle.

Insights Into Lung Cancer Immune-Based Biology, Prevention, and Treatment

Lung cancer is the number one cause of cancer-related deaths. The malignancy is characterized by dismal prognosis and poor clinical outcome mostly due to advanced-stage at diagnosis, thereby inflicting a heavy burden on public health worldwide. Recent breakthroughs in immunotherapy have greatly benefited a subset of lung cancer patients, and more importantly, they are undauntedly bringing forth a paradigm shift in the drugs approved for cancer treatment, by introducing "tumor-type agnostic therapies". Yet, and to fulfill immunotherapy's potential of personalized cancer treatment, demarcating the immune and genomic landscape of cancers at their earliest possible stages will be crucial to identify ideal targets for early treatment and to predict how a particular patient will fare with immunotherapy. Recent genomic surveys of premalignant lung cancer have shed light on early alterations in the evolution of lung cancer. More recently, the advent of immunogenomic technologies has provided prodigious opportunities to study the multidimensional landscape of lung tumors as well as their microenvironment at the molecular, genomic, and cellular resolution. In this review, we will summarize the current state of immune-based therapies for cancer, with a focus on lung malignancy, and highlight learning outcomes from clinical and preclinical studies investigating the naïve immune biology of lung cancer. The review also collates immunogenomic-based evidence from seminal reports which collectively warrant future investigations of premalignancy, the tumor-adjacent normal-appearing lung tissue, pulmonary inflammatory conditions such as chronic obstructive pulmonary disease, as well as systemic microbiome imbalance. Such future directions enable novel insights into the evolution of lung cancers and, thus, can provide a low-hanging fruit of targets for early immune-based treatment of this fatal malignancy.