SYSTEMATIC REVIEW article

Front. Oral Health, 25 August 2026

Sec. Oral Cancers

Volume 7 - 2026 | https://doi.org/10.3389/froh.2026.1939172

Tissue-based genomic instability markers for predicting malignant transformation in oral leukoplakia and proliferative verrucous leukoplakia: a systematic review

  • 1. Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, National University of Singapore, Singapore, Singapore

  • 2. Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden

  • 3. Department of Oral and Maxillofacial Surgery, National University Centre for Oral Health, Singapore, Singapore

  • 4. Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, Singapore

  • 5. Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital Huddinge and Karolinska Comprehensive Cancer Center, Stockholm, Sweden

Abstract

Objectives:

Although several biomarkers have been described for predicting malignant transformation in oral leukoplakias (OLs) and proliferative verrucous leukoplakias (PVLs), no systematic review has comprehensively evaluated tissue-based genomic instability markers. This review aimed to evaluate the evidence for these markers and their potential role in biomarker panel development.

Methods:

A systematic review across PubMed, Embase and Cochrane Library was performed to identify studies evaluating the differences in tissue-based genomic markers between OL and PVL patients with and without malignant transformation.

Results:

34 observational studies comprising 3,237 patients were included, and genomic aberrations were categorised into DNA-level, chromosomal, and gene-specific alterations. For studies on OLs, DNA-level and chromosomal markers for which individual studies reported associations with malignant transformation included aneuploidy, impaired DNA repair capacity, loss of heterozygosity, chromosomal instability, and copy number alterations. Multiple gene-specific alterations also showed associations (e.g., TP53, MKI67, FGFR1), but findings varied across studies. The genomic markers of PVLs differed substantially, with fewer consistent predictors found. No meta-analysis was performed as all included studies were observational.

Conclusions:

Genomic instability across multiple levels contributes to malignant transformation, and represents a promising biological framework for predicting malignant transformation for OLs. While no single marker reliably demonstrates sufficient predictive performance, the integration of complementary genomic alterations with clinical and histopathological risk factors may provide a basis for the development of robust multi-marker panels. Future prospective studies using standardised detection methods and multivariable prediction models are required before clinical implementation.

Systematic Review Registration:

identifier CRD42024585830.

1 Introduction

Oral cancer is the sixth most common cancer in the world, with an estimated incidence of more than 370,000 cases and a mortality rate of more than 177,000 individuals annually (, ). Oral squamous cell carcinoma (OSCC) accounts for more than 90% of oral cancers (), and despite advancements in surgery, radiotherapy and chemotherapy alone or in combination, lip and oral cavity cancers remain among the top global causes of death, with the largest number of increases between 2000 and 2023 (). The 5-year overall survival rate and disease-free survival rates for OSCC have remained at 60% and 50% respectively in recent years, and almost every second patient has postoperative recurrence or metastasis even after radical surgery ().

The aggressive nature and high mortality associated with OSCC underscore the necessity of early diagnosis and risk stratification. The search for early indicators invariably leads to the study of oral potentially malignant disorders (OPMDs). Oral leukoplakia (OL), one of the most common OPMDs, is defined by the World Health Organisation (WHO) as a predominantly white plaque of questionable risk, having excluded other known diseases that carry no increased risk for cancer (). It has a worldwide prevalence of 4.11% (), a malignant transformation rate of 9.8% (95% CI: 7.9–11.7), and a mean evolution time of 3.2 years. While non-homogeneous OL has four times the risk of malignant transformation compared to homogeneous OL (), the proliferative verrucous leukoplakia (PVL) subtype, defined as a progressive, persistent, and irreversible disorder characterised by the presence of multiple leukoplakias that frequently become warty, is notorious for its increased risk for malignant transformation, with a transformation rate of 45.8% reported ().

Clinical and demographic risk factors for malignant transformation include lesion size and location, female gender, betel quid or tobacco use, and exposure to nickel (). Histopathologic assessment by the presence of dysplasia has been considered (). However, the grading of dysplasia alone may not be entirely sufficient to deduce the risk of malignant transformation. A large cohort study by Hsue et al. found only 4.83% of dysplastic oral leukoplakias (OLs) subsequently progressed to OSCC, and 3.55% among non-dysplastic OLs over a mean follow-up time of 42.6 months (). Furthermore, the grading of dysplasia is subjective and requires standardisation (). Hence, the challenge lies especially in the identification of high-risk lesions with little to no dysplasia, with an ever-present clinical dilemma between wide surgical excision and surveillance needs.

Genomic instability represents a fundamental hallmark of cancer and encompasses a wide spectrum of DNA, chromosomal or gene-specific alterations. These alterations collectively reflect progressive genomic derangement preceding malignant transformation, and may provide a foundation for the development of predictive marker panels. While previous reviews have evaluated the role of biomarkers in the malignant transformation of OLs, these reviews have largely investigated a broader range of biomarkers involved in various aspects of the hallmarks of cancer, and different sample types such as tissue, saliva or serum (). Studies on genomic alterations have largely focused on specific parts of genomic instability, such as aneuploidy, loss of heterozygosity or specific genes (, ). Consequently, these prior studies provide limited insight into genomic instability as a unified biological process underlying malignant transformation or its potential utility in objective risk prediction.

To our knowledge, no systematic review has comprehensively synthesised tissue-based genomic instability markers specifically evaluated as longitudinal predictors of malignant transformation for oral leukoplakias (OLs) and proliferative verrucous leukoplakias (PVLs). This systematic review therefore aimed to evaluate the available evidence for tissue-based genomic instability markers associated with malignant transformation, and to identify promising candidates for biomarker panel development.

2 Materials and methods

This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines (

). The review was registered on PROSPERO (CRD42024585830). The review utilised the following PICOTS structure:

  • Population: Patients histologically or clinically diagnosed with oral leukoplakia (OL) or proliferative verrucous leukoplakia (PVL)

  • Intervention: Tissue-based genomic instability markers, defined as tissue-derived biomarkers reflecting genomic alterations or molecular events implicated in genomic instability and malignant transformation. This includes markers that directly measure genomic instability (i.e., DNA-level or chromosomal-level markers), and gene-specific alterations that represent downstream molecular consequences of genomic alterations

  • Comparator: Patients with lesions without genomic instability markers of interest, or with a lower or alternative level of the marker

  • Outcome: Histologically confirmed malignant transformation

  • Timing: Minimum of three months duration from initial biopsy to malignant transformation, or last follow-up for lesions without malignant transformation

  • Study Design: Randomised controlled trials, clinical trials, prospective and retrospective observational studies

2.1 Search strategy

A search was performed on 3 September 2024 and updated on 27 September 2025 and 1 August 2026 through the PubMed, Embase, and Cochrane Library databases. The search terms encompassed the following: (1) oral leukoplakia, (2) transformation or progression, and (3) genomic or genetic factors. The full search terms are shown in Supplementary Table S1. From the search results, duplicates were removed, and the articles were then screened by their titles and abstracts, followed by screening of the full-length articles for inclusion on Covidence by two team investigators (B.Q. and Y.Z.).

A manual search of the references of relevant articles was also done, and eligible articles were included. Disagreements were reconciled through discussion and mediation with a third team investigator (N.B.S.) to arrive at a consensus.

2.2 Inclusion and exclusion criteria

The following inclusion criteria were used:

  • Patients diagnosed with OL or PVL with follow-up and known outcomes of progression or non-progression to oral squamous cell carcinoma

  • Analyses of genomic changes for these patients reported

  • Full-length articles (randomised controlled trials, clinical trials, prospective and retrospective observational studies) published in English

The following exclusion criteria were applied:

  • Patients with leukoplakia outside the oral cavity

  • Patients with other potentially malignant disorders outside of oral leukoplakia

  • Patients with pre-existing oral cancer at the onset

  • Studies with no direct follow-up and reporting of the presence or absence of malignant transformations

  • Studies reporting outcomes other than malignant transformation to oral squamous cell carcinoma (e.g., carcinoma in situ, severe dysplasia)

  • Studies utilising only non-histopathological tissue samples (e.g., blood, saliva)

  • Animal studies, in vitro studies, Case series, case reports, abstracts, letters to the editor, comments or review articles

  • Articles not published in English

The inclusion and exclusion criteria set out to investigate local tissue-specific genomic instability, focusing on markers intrinsic to tissue transformation processes, rather than circulating biomarkers.

2.3 Data extraction

Data extraction was performed by two team investigators (B.Q. and Y.Z.). The following information was transferred from the articles onto a data extraction Excel spreadsheet:

  • Study characteristics: Author, Year, Study type

  • Patient characteristics: Age, Gender, Tobacco use, Alcohol use, Betel quid use,

  • Lesion characteristics: Lesion type (OL/PVL), Sample type

  • Patient/lesion sample size

  • Duration of follow-up

  • Genomic aberrations and detection method

  • Outcome: Presence or absence of malignant transformation

Discrepancies were discussed and mediated by a third team investigator (N.B.S.) until resolution was achieved before the data was compiled onto a final data extraction Excel spreadsheet. Results were subsequently grouped by the type of genomic markers the study investigated, e.g., DNA ploidy status was classified as a DNA-level alteration, while studies evaluating specific genes were classified as gene-specific alterations.

While a meta-analysis was planned to be done if possible, it was not performed due to the lack of sufficient studies for each domain and the heterogeneity of the studies' methods.

2.4 Quality assessment

Two authors (B.Q. and Y.Z.) performed the risk of bias assessment for each study independently. The Newcastle-Ottawa Scale for cohort studies was employed as part of the assessment for risk of bias for observational studies (), with 7–9 stars being considered Low risk of bias, 4–6 stars considered Unclear risk of bias, and 0–3 stars considered High risk of bias. The Risk of Bias 2 (RoB 2) tool was employed for randomised controlled trials if any were to be included (). Discrepancies were discussed with a third team investigator (N.B.S.) until a consensus was reached before the final compilation.

3 Results

A total of 1,855 records were identified through the database search, of which 34 studies fulfilled our inclusion criteria and were thus included in the review (Figure 1) (53). All studies included were observational, and none were clinical trials. A total of 3,237 patients were included, of which 3,131 patients (30 studies) presented with OL and 106 patients (five studies) presented with PVL. Of these, 622 of the OLs and 52 of the PVLs underwent malignant transformation, translating to a malignant transformation rate of 19.9% and 49.1% respectively, over a reported follow-up duration across studies of 5–300 months. A summary of the included studies' characteristics is shown in Table 1.

Figure 1

Table 1

AuthorYearCountryStudy DesignTypeSample SizeSample TypeGenomic Alteration(s)Detection MethodFollow-Up (Months)
Qurishi et al.2025Saudi ArabiaProspectiveOLTotal: 150
MT: 40
No MT: 110
Fresh frozenMicrosatellite instability, p53, cyclin D1 expressionNot specified24
Cai et al.2024ChinaRetrospectiveOLTotal: 324
MT: 47
No MT: 277
FFPECNAsWhole genome sequencing67 (34-98)
Mariz et al.2023BrazilRetrospectiveOLTotal: 30
MT: 6
No MT: 24
FFPEFGFR1 expression IHC, ISH40.1 (6-168)
Pentenero et al.2023ItalyProspectiveOL, PVLTotal (OL): 133
MT: 6
No MT: 127,
Total (PVL): 20
MT: 10
No MT: 10
FFPEDNA ploidy statusFlow cytometry72
Wils et al.2023NetherlandsRetrospectiveOLTotal: 89
MT: 25
No MT: 64
FFPECNAs, multiple gene expressions (e.g., TP53, NOTCH1)Next-Generation Sequencing12-258
Jäwert et al.2022SwedenRetrospectiveOLTotal: 28
MT: 14
No MT: 14
FFPECNAsISH35 (12-150) (MT group) 102 (50-268) (No MT group)
Monteiro et al.2022PortugalRetrospectiveOLTotal: 52
MT: 6
No MT: 46
FFPECD44v6, CD147, EGFR, p53, p63, p73, p16, podoplanin expressionIHC32.4 (2-120)
Li et al.2021ChinaRetrospectiveOLTotal: 477a
MT: 19
No MT: 458
FFPECNAsWhole genome sequencingNR
Liu et al.2021ChinaRetrospectiveOLTotal: 60
MT: 5
No MT: 55
FFPELOLA1 expression qRT-PCR38.5
Lv et al.2020ChinaRetrospectiveOLTotal: 79
MT: 30
No MT: 49
FFPEPTHLH expressionIHC5-75
Thomas et al.2020IndiaProspectiveOLTotal: 181
MT: 12
No MT: 169
FFPEDNA ploidy status, DNA telomerase activity, DNA repair capacityFlow cytometry, TRAP, MSA102
Baran et al.2019GermanyRetrospectiveOLTotal: 135
MT: 53
No MT: 82
FFPEMAGE-A expressionIHC, RT-PCR17 (MT group), 153.5 (no MT group)
Farah et al.2019AustraliaRetrospectiveOLTotal: 13
MT: 5
No MT: 8
FFPEGenomic mutations pathwaysWhole exome sequencing, qPCR, IHC16-220
Ding et al.2018ChinaRetrospectiveOLTotal: 78
MT: 19
No MT: 59
FFPENotch1 expressionIHC74.18
Upadhyaya et al.2018USARetrospectivePVLTotal: 20
MT: 9
No MT: 11
FFPEp16INK4A, p53 expressionIHC, ISH91.86
Wu et al.2018ChinaRetrospectiveOLTotal: 98
MT: 21
No MT: 77
FFPETGM3 expressionIHC, qPCR57 (13-173) (MT group)
95 (20-240) (no MT group)
Habiba et al.2017JapanRetrospectiveOLTotal: 79
MT: 37
No MT: 42
FFPEALDH1, podoplanin expressionIHC42.1 ± 34.1
Sakata et al.2017JapanRetrospectiveOLTotal: 150
MT: 23
No MT: 127
FFPESMAD4 expressionIHC34
Zhang et al.2017South KoreaRetrospectiveOLTotal: 154
MT: 22
No MT: 132
FFPEAxin2 and SNAI1 expressionIHC130
Kil et al.2016South KoreaRetrospectiveOLTotal: 27
MT: 7
No MT: 20
FFPECNVsRT-PCR43 ± 36.7 (MT group)
117.68 ± 28.8 (no MT group)
Gouvêa et al.2013BrazilRetrospectivePVLTotal: 7a
MT: 5
No MT: 2
FFPEDNA ploidy status, Ki67, Mcm2 and geminin expressionImage cytometry, IHC88.62 ± 82.26
Graveland et al.2013NetherlandsRetrospectiveOLTotal: 43
MT: 6
No MT: 37
FFPELOH, p53 expressionIHC, qPCR20.3 (11-31) (MT group)
Liu et al.2013ChinaRetrospectiveOLTotal: 141
MT: 37
No MT: 104
FFPEALDH1 and CD133 expressionIHC61.2 ± 43.2 (MT group)
67.2 ± 45.6 (no MT group)
Ries et al.2013GermanyRetrospectiveOLTotal: 98
MT: 53
No MT: 45
FFPEEGFR expressionIHC60
Siebers et al.2013NetherlandsRetrospectiveOLTotal: 102
MT: 16
No MT: 86
FFPEChromosomal instabilityImage cytometry, FISH27 (MT group)
91.5 (no MT group)
Ries et al.2012GermanyRetrospectiveOLTotal: 74
MT: 24
No MT: 50
FFPEMAGE-A expressionqPCR60
Bremmer et al.2011NetherlandsRetrospectiveOLTotal: 62
MT: 13
No MT: 49
FFPEDNA ploidy statusImage cytometry69 (10-193)
Cao et al.2011ChinaRetrospectiveOLTotal: 76
MT: 37
No MT: 39
FFPEEZH2 expressionIHC24 (MT group) 136.9 (no MT group)
Matsubara et al.2011JapanRetrospectiveOLTotal: 112
MT: 6
No MT: 106
FFPEΔNp63 expressionIHCNR
Klanrit et al.2007United KingdomRetrospectivePVLTotal: 6
MT: 6
No MT: 0
FFPEDNA ploidy statusImage cytometry144-300
Mogi et al.2003JapanRetrospectiveOLTotal: 60
MT: 13
No MT: 47
FFPEp53 expressionIHC28.6 (6-84) (MT group)
26.1 (3-90) (no MT group)
Nogami et al.2003JapanRetrospectiveOLTotal: 13
MT: 7
No MT: 6
FFPEp53, Bcl-2, Bax expression, Ki-67IHC60
Jiang et al.2001JapanRetrospectiveOLTotal: 13
MT: 13
No MT: 0
FFPELOH, microsatellite instability, fractional allelic lossPCR17.7 (2-87)
Chang et al.2000TaiwanRetrospectivePVLTotal: 53
MT: 22
No MT: 31
FFPEp53, p21WAF1 expressionIHC42

Overview of included studies.

MT, malignant transformation; FFPE  , formalin-fixed paraffin-embedded tissue samples; CNAs  , copy number alterations; IHC, immunohistochemistry; ISH, in situ hybridisation; qRT-PCR, quantitative reverse transcription polymerase chain reaction; TRAP, Telomeric Repeat Amplification Protocol (TRAP); MSA, mutagen sensitivity assay; qPCR, quantitative or real-time polymerase chain reaction; CNVs, copy number variations; LOH, loss of heterozygosity.

a

Only samples with clear information on the presence or absence of malignant transformation were included.

To align with the multifaceted nature of genomic instability, the genomic changes are classified into three major domains: DNA-level alterations, chromosomal alterations and gene-specific alterations. Details of these genomic alterations observed in the included cohorts are presented in Tables 24 for OL and Table 5 for PVL.

Table 2

StudyVariableSummary of Findings
Pentenero et al.DNA ploidy statusMTNo MTp-value
Aneuploidy presence4/6 (66.7%)33/127 (26%)0.03
High aneuploidy2/6 (33.3%)5/127 (3.9%)0.002
PPV10.8% (6−18.6)
NPV of diploid status97.9% (93.8–99.3)
Thomas et al.DNA ploidy statusMTNo MTp-value
Aneuploidy8/12 (66.7%)37/157 (23.6%)0.0035
Sensitivity66.67% (34.89–90.08)
Specificity77.30% (70.10–83.49)
PLR2.94 (1.80–4.80)
NLR0.43 (0.19–0.96)
DNA telomerase activityMTNo MTp-value
Telomerase positive10/12 (83%)91/169 (53.8%)0.0654
Sensitivity83.33% (51.59–97.9)
Specificity46.15% (38.47–53.98)
PLR1.55 (1.16–2.07)
NLR0.36 (0.10–1.29)
DNA repair capacityMTNo MTp-value
Hypersensitivity11/12 (91.6%)27/169 (15.9%)0.0001
Sensitivity91.67% (61.52 −99.79)
Specificity84.02% (77.61–89.20)
PLR5.74 (3.90–8.44)
NLR0.1 (0.02–0.65)
Farah et al.Gene mutation pathwaysDNA damage repair pathways were in the top 10 significantly enriched pathways for progressive lesions e.g., mismatch repair pathway, BRCA pathway, Fanconi anaemia pathway
Bremmer et al.DNA ploidy statusMTNo MTp-value
Abnormal DNA content7/13 (53.8%)20/49 (40.8%)
AneuploidyHR of 3.7 (1.1–13.0)0.039
Sensitivity54%
Specificity59%
PPV26%
NPV83%

Summary of DNA-level alteration findings for oral leukoplakia.

MT, malignant transformation; PPV, positive predictive value; NPV, negative predictive value; PLR, positive likelihood ratio; NLR, negative likelihood ratio.

Table 3

StudyVariableSummary of Key Findings
Graveland et al.LOH
  • -

    All OLs with MT showed LOH at 9p

  • -

    LOH at 9p sig. related to increased risk of MT (p = 0.014)

Jiang et al.LOH
  • -

    Sig. difference in LOH at 5q21–23 before and after MT (p = 0.0137)

  • -

    Other loci with high incidence in OL with MT: 5q21–23, 6p25–27, 6q21–23, and 11q23

FAL
  • -

    Mean value of FAL of 0.46 for OL with MT, 0.27 without MT

  • -

    Sig. difference in mean FAL with and without MT (p < 0.05)

MI
  • -

    No OLs showed high level MI

  • -

    MI observed after MT in 2 OLs where not present before MT

Qurishi et al.MI
  • -

    10/25 (40%) OL with MT were tested positive for MI, compared to 25/150 (16.7%) without MT

  • -

    Sig. association between expression of MI + p53 + cyclin D1 and MT (p < 0.05)

Siebers et al.Chromosomal instability
  • -

    Chromosomal instability was a stronger marker for MT

  • -

    Hazard ratio of 7.2 with image cytometry (p < 0.001)

  • -

    Hazard ratio of 6.8 with fluorescence in situ hybridisation (p < 0.001)

Cai et al.CNAsResults
  • -

    CNA score sig. higher in MT group (p < 0.001)

  • -

    CNA score predictive of MT (p < 0.001)

Significant regionsGainChromosome 3, 8, 20
LossChromosome 3, 5, 8, 9, 13
Wils et al.CNAsResults
  • -

    Presence of CNA not sig. associated with the risk of MT (p = 0.313)

  • -

    Number of CNAs sig. associated with the risk of MT (p = 0.011)

Significant regionsGain20p11
Loss3p14, 8p23, 13q12
Jäwert et al.CNAs
  • -

    Reported CNAs specific to genes

  • -

    CNAs most common in EGFR (43.5%), followed by CDKN2A (26.1%), CCND1 (26.1%), and MYC (8.3%)

  • -

    No sig. difference in loss of CDKN2A (p = 0.16)

Li et al.CNAs
  • -

    More CNAs in MT group compared to no MT (p < 0.0001)

  • -

    Sig. higher CNA score and frequency in OLs with MT (p < 0.001)

  • -

    High occurrence rates at Chromosomes 1, 2, 7, 8, 20

Kil et al.Copy number variationsResults
  • -

    6/6 (100%) of OL with MT had CNVs, compared to 6/17 (35.3%) of OL without MT (p = 0.014)

  • -

    4/6 (66.7%) of OL with MT had >3 CNVs, compared to 1/17 (5.9%) without MT (p = 0.008)

  • -

    CNV outside 3p rarely seen in OL without MT

Significant regions
  • -

    9p21 (p = 0.04)

  • -

    13q14 (p = 0.011)

Summary of chromosome-level alteration findings for oral leukoplakia.

MT, malignant transformation; LOH, loss of heterozygosity; FAL, fractional allelic loss; MI, microsatellite instability; CNAs, copy number alterations.

Table 4

StudyGeneProteinSignificant Findings
P53 Family
Qurishi et al.TP53p5318/30 (60%) p53-positive OLs had MT
Sig. association between expression of MI + p53 + cyclin D1 and MT (p < 0.05)
Wils et al.TP53p53TP53 mutation sig. associated with MT (HR 2.70, p = 0.013)
Monteiro et al.TP53p53No sig. relationship with MT-free survival (p = 0.574–0.642)
TP63p63No sig. relationship with MT-free survival (p = 0.478–0.745)
TP73p73No sig. relationship with MT-free survival (p = 0.526–0.582)
Graveland et al.TP53p53P53 mutation by sequencing sig. associated with MT (p = 0.009)
ositive P53 IHC or P53 field not sig. related to MT-free survival
Matsubara et al.TP63ΔNp63 isoformΔNp63-labelling index of OL with MT was sig. higher than without MT (49.3 vs. 34.2%, p = 0.0035)
Mogi et al.TP53p53P53 positive rates in OL with MT sig. higher than without MT (77 vs. 42%, p = 0.0120)
Nogami et al.TP53p53Many p53 positive cells seen in OL with MT, compared to a few p53 positive cells in OL without MT
Cell Cycle Regulators
Qurishi et al.CCND1Cyclin D122/45 (48.9%) cyclin D1-positive OLs had MT
Sig. association between expression of MI + p53 + cyclin D1 and MT (p < 0.05)
Wils et al.CDKN2Ap16CDKN2A mutations + loss of 9p21 were not significantly associated with MT
Monteiro et al.CDKN2Ap16No sig. relationship with MT-free survival (p = 0.081–0.126)
MKI67Ki-67Sig. higher positive Ki-67 expression in OL with MT (14.9 vs. 6.4%, p < 0.05)
Mariz et al.FGFR1FGFR1All OL with MT has high FGFR1 expression (p = 0.006)
Higher risk of MT in OL with high FGFR1 expression (HR 7.3, p = 0.016)
Cao et al.EZH2EZH2EZH2 expression strongly associated with MT-free survival in an expression level-dependent manner (p < 0.0001)
Apoptosis Regulators
Wils et al.CASP8Caspase-8Sig. association with higher MT rate (HR 16.69, p = 0.031) and shorter MT-free survival (p = 0.010)
Nogami et al.BCL2Bcl-2Weak-moderate Bcl-2 immunoreactivity in OL with MT, vs. weak immunoreactivity in OL without MT
BAXBaxWeak Bax positivity in OL with MT, vs. moderate to strong positivity in OL without MT
Oncogenic Signalling Pathways
Monteiro et al.EGFREGFRNo sig. relationship with MT-free survival (p = 0.461–0.610)
Ries et al.EGFREGFRSig. difference in EGFR expression rate in OL with and without MT (p = 0.017)
Odds ratio 4.83 for EGFR over 44.96
Wils et al.NOTCH1Notch1Associated with a longer MT-free survival, but not sig. (p = 0.149)
Ding et al.NOTCH1Notch1Sig. decreased expression in OL with MT (p = 0.001)
Sakata et al.SMAD4Smad4Low expression sig. associated with MT (p = 0.0017), sig. predictor for MT (HR 2.63, p = 0.043)
Zhang et al.AXIN2Axin-2High expression sig. associated with MT in multivariate analysis (HR 7.47, p = 0.001)
Cancer Stem Cell, Differentiation and Invasion Markers
Habiba et al.PodoplaninPodoplaninSig. higher incidence of expression in OL with MT (84 vs. 52%, p = 0.003)
Expression sig. associated with MT (HR = 2.95, p = 0.007 in univariate, HR 2.62, p = 0.039 in multivariate)
ALDH1ALDH1Sig. higher incidence of expression in OL with MT (73 vs. 50%, p = 0.037)
Expression sig. associated with MT (HR = 2.91, p = 0.005 in univariate, HR 3.02, p = 0.004 in multivariate)
Monteiro et al.PodoplaninPodoplaninHigher expression had sig. association with MT (p < 0.001)
CD44CD44v6No sig. relationship with MT-free survival (p = 0.510–0.803)
Liu et al.CD133Prominin-1Sig. higher incidence of expression in OL with MT (51.4 vs. 12.5%, p < 0.001)
Sig. higher number of CD133-positive OL had MT (59.4 vs. 16.5%, p < 0.001)
ALDH1ALDH1Sig. higher incidence of expression in OL with MT (70.3 vs. 26.9%, p < 0.001)
Sig. higher number of ALDH1-positive OL had MT (48.1 vs. 12.6%, p < 0.001)
Zhang et al.SNAI1SnailSig. higher incidence of MT in Snail-positive (p = 0.007) and high expression OL (p < 0.001)
Snail expression sig. associated with MT (HR 3.28, p = 0.007 in univariate, HR 4.41, p = 0.001 in multivariate)
Wu et al.TGM3TGase3Low levels sig. associated with increased risk of MT (p = 0.0005)
TGM3 expression is an independent predictor for MT (HR 5.045, p = 0.004)
Immune and Tumour Microenvironment
Baran et al.MAGE-AMAGE-ASig. higher positivity in OL with MT with IHC (62.5 vs. 3.5%, p = 0.001)
PPV of 93%, NPV of 74.3%, MAGE-A is a highly reliable predictor for MT (p < 0.001)
Ries et al.MAGE-AMAGE-ASig. higher positivity in OL with MT (46 vs. 0%, p = 0.00001)
Lv et al.PTHLHPTHrPPTHrP expression levels sig. associated with MT (HR 4.54, p = 0.000 in univariate, HR 3.3, p = 0.001 in multivariate)
Monteiro et al.BSGCD147No sig. relationship with MT-free survival (p = 0.586–0.779)
Others
Wils et al.NSD1NSD1Mutation sig. associated with longer MT-free survival
Liu et al.LOLA1LOLA1 lncRNAExpression sig. higher in OL with MT (p = 0.003–0.058)
Sig. higher number of OL with LOLA1 expression had MT (44.4 vs. 5.6%, p = 0.017)

Summary of gene-specific alteration findings for oral leukoplakia.

MT, malignant transformation; PPV, positive predictive value; NPV, negative predictive value; HR, hazard ratio.

Table 5

StudyVariableKey Findings
DNA-Level Alterations
Gouvêa et al.DNA ploidy statusAneuploidy presence4/5 (80%) in PVL with MT,
1/2 (50%) in PVL without MT
Klanrit et al.DNA ploidy statusAneuploidy presence5/6 (83.3%) of PVL with MT had aneuploidy prior to MT
Pentenero et al.DNA ploidy statusAneuploidy presenceNo sig. association (p = 0.329)
High aneuploidyNo sig. association (p = 0.305)
Gene-Specific Alterations
Chang et al.CDKN1A (p21)Sig. higher MT in p21 positive OL (80 vs. 32%, p = 0.002)
TP53 (p53)Sig. higher MT in p53 positive OL (93 vs. 42%, p = 0.00008)
Upadhyaya et al.TP53 (p53)<25% stained positive for p53
CDKN2A (p16)No sig. association between p16 positivity and MT (p = 0.658)
Gouvêa et al.MKI67 (Ki-67)No sig. correlation
MCM2 (Mcm2)Higher MCM2 expression sig. correlated with increasingly severe epithelial changes (p = 0.03)
GMNN (geminin)No sig. correlation

Summary of genomic alteration findings for proliferative verrucous leukoplakia.

MT, malignant transformation.

3.1 DNA-level alterations

Four studies involving 389 patients investigated the role of DNA-level alterations in the malignant transformation of OL (Table 2) (, , , ). Three studies investigated DNA ploidy status, all of which reported significant associations between aneuploidy and malignant transformation (, , ). The studies reported the presence of aneuploidy to have a poor to fair sensitivity of 54%–66.7%, specificity of 59%–77.3%, a positive predictive value (PPV) of 10.8%–26%, and a notably high negative predictive value of 83%–97.9%.

Two studies evaluated the role of damage repair capacity and pathways in the malignant transformation of OL (, ). Thomas et al. quantified DNA repair capacity using a bleomycin-induced Mutagen Sensitivity Assay (MSA) and reported a significantly increased proportion of hypersensitivity to bleomycin in OL with malignant transformation (p = 0.0001), with a sensitivity of 91.7% and a specificity of 84.0%. Farah et al. similarly found that DNA damage repair-related pathways were some of the most significantly affected pathways in patients with progressive OL.

Thomas et al. also investigated DNA telomerase activity. While a higher proportion of telomerase positivity was seen in progressive OL, the difference was not significant (p = 0.065). The authors also reported a sensitivity of 83.3% and a specificity of 46.2% for DNA telomerase activity.

3.2 Chromosomal alterations

Nine studies comprising 1,253 patients evaluated the role of structural aberrations at the chromosomal level in OL progression (Table 3) (, , , , , , , , 52). These included loss of heterozygosity (LOH), microsatellite instability, chromosomal instability, fractional allelic loss, and copy number alterations/variations. LOH was evaluated in two studies (, 52); Graveland et al. identified LOH at chromosome 9p to be significantly associated with malignant transformation, while Jiang et al. found LOH at 5q21–23 to be significantly different between progressive and non-progressive lesions. Jiang et al. also reported significant differences in mean fractional allelic loss between the two groups (p < 0.05).

Two studies evaluated the role of microsatellite instability (, 52). Jiang et al. did not report high levels of microsatellite instability in any progressive OLs. Qurishi et al. found a higher proportion of patients with microsatellite instability in progressive lesions; although statistical analyses showed a significant association with malignant transformation, these analyses were in combination with other markers (p53 and cyclin D1). Chromosomal instability was studied by Siebers et al. who reported it as a strong marker of malignant transformation, with hazard ratios of 6.8–7.2 ().

Copy number alterations (CNAs) and variations (CNVs) were investigated by five studies (, , , , ). Cai et al., Wils et al., Li et al. and Kil et al. reported significant associations between the number of CNAs/CNVs and CNA score and malignant transformation. The locations of these CNAs were highly variable between studies. Cai et al. and Wils et al. both reported significant copy number gains at chromosome 20, and losses at chromosomes 3, 8 and 13. Li et al. and Kil et al. reported different chromosomes with high occurrences of CNAs, and neither specified if these alterations were gains or losses. While Wils et al. did not find significant associations between the presence of CNAs and progression, Li et al. and Kil et al. reported a significantly higher proportion of samples with CNAs and CNVs in the progressive group over the non-progressive lesions. A full description of the regions reported to have copy number gains and losses is depicted in Table 3.

3.3 Gene expression-specific alterations

20 studies evaluated the role of gene alterations in 26 genes in the malignant transformation of OLs (Table 4). With seven studies, the p53 gene family was most commonly investigated (, , , , , 50, 51). While five studies reported p53 overexpression as being associated with malignant transformation (, , , 50, 51), two studies evaluating p53 by immunohistochemistry (IHC) did not confirm the associations between p53 expression and malignant transformation (, ). Moreover, while Monteiro et al. found no significant relationship between p63 and p73 and malignant transformation, Matsubara et al. reported a significantly higher ΔNp63-labelling index in progressed OLs (, ).

In addition to p53, the marker genes studied are classified into the following categories (

Table 4

):

  • Cell cycle regulators: Five marker genes were identified over five studies (, , , , ). Increased expression of MKI67, FGFR1 and EZH2 had significant associations with malignant transformation (, , ). While Qurishi et al. reported that 48.9% of CCND1-positive OLs progressed, no analysis of significance was reported (). No significant associations between CDKN2A mutations and malignant transformation were found (, ).

  • Apoptosis regulators: Three genes over two studies were identified (, 51). While CASP8 mutations and BAX positivity were more clearly associated with malignant transformation, differences in Bcl-2 immunoreactivity between progressed and non-progressed OLs were not as clearly defined (, 51).

  • Oncogenic signalling pathways: Four genes over six studies were identified (, , , , , ). While Monteiro et al. reported no significant relationship between EGFR expression and progression, Ries et al. instead found significantly higher EGFR expression in progressed OLs (, ). Although Wils et al. and Ding et al. both reported reduced NOTCH1 expression in OLs with malignant transformation, only Ding et al. found statistical significance (, ). Low SMAD4 and high AXIN2 expressions were also significantly associated with malignant transformation (, ).

  • Cancer stem cell, differentiation and invasion markers: Six genes were identified over five studies (, , , , ). Higher expressions of podoplanin, ALDH1, CD133 and SNAI1 and lower expressions of TGM3 were significantly associated with malignant transformation. No significant relationship was found between CD44 and progression ().

  • Immune/tumour microenvironment: Three genes were identified over four studies (, , , ). Significantly higher levels of MAGE-A positivity and PTHrP expression were both seen in OLs with malignant transformation (, , ). No significant relationship was found between BSG/CD147 and progression ().

  • Others: Wils et al. reported NSD1 mutations to be significantly associated with progression-free survival (). Liu et al. identified a novel long noncoding RNA, lncRNA oral leukoplakia progressed associated 1 or LOLA1, and reported a significant association between LOLA1 expression and malignant transformation ().

3.4 Proliferative verrucous leukoplakia

Three studies on PVLs investigated the role of DNA ploidy status on malignant transformation risk (Table 5) (, , 49). None of the studies reported significant associations between aneuploidy and malignant transformation. However, Gouvêa et al. and Klanrit et al. did report a high prevalence of aneuploidy in PVLs with malignant transformation (80%–83.3%), compared to those without (50%) in Gouvêa et al's study (, 49).

Six genes were investigated over three studies for associations with malignant transformation (, , 53). While Chang et al. reported significantly higher progression rates in P53-positive PVLs, Upadhyaya et al. instead found low levels of P53-positivity in PVLs (, 53). Increased CDKN1A and MCM2 gene expressions were reported to be significantly associated with malignant transformation, while the CDKN2A, MKI67 and GMNN genes were not.

3.5 Quality assessment

The risk of bias assessment was performed with the Newcastle-Ottawa Scale for cohort studies for all studies, as shown in Supplementary Table S2. Of the 34 studies included, 19 were found to have a Low risk of bias (7–9 stars), and 15 had an Unclear risk of bias (4–6 stars). None had a High risk of bias (0–3 stars).

4 Discussion

This systematic review, encompassing 34 studies with 3,131 oral leukoplakia (OL) patients and 106 patients with proliferative verrucous leukoplakia (PVL), confirms the presence of tissue-based genomic instability markers that are strongly associated with malignant transformation. Specifically, aberrations at the DNA, chromosomal, and gene expression levels appear sequentially or synergistically to drive progression. While no single marker was found to definitively predict malignant transformation, a combination of markers or a progression of instability can be key in identifying lesions with high malignancy risk.

4.1 DNA-level and chromosomal instability: the early drivers

Several types of DNA-level and chromosomal alterations were identified to be useful in identifying malignant transformation risk; these alterations often represent early major events that destabilise the genome. DNA ploidy status refers to the number of chromosome sets within a cell, with aneuploidy representing an abnormal number of chromosomes and DNA content. Aneuploidy is a hallmark of cancer that indicates genetic damage that drives carcinogenesis, and is an established prognostic factor in other cancers (54, 55). All studies evaluating DNA ploidy status in this review found significant associations between aneuploidy and malignant transformation. In particular, the high negative predictive value of up to 97.9% may indicate the potential use of DNA ploidy status to rule out a high malignant transformation risk and allow more conservative follow-up regimens for OL patients. However, it is insufficient as a ‘rule-in’ tool for definitive prophylactic wide excision.

The genomic instability indicated by aneuploidy is further compounded by more localised events, such as loss of heterozygosity (LOH). LOH, a mutation resulting in the loss of a copy of a DNA segment, is a common genetic event in carcinogenesis. A LOH event may result in the complete inactivation of essential genes, such as tumour suppressor genes, that favour cancer development. The two studies included in this review evaluating LOH both found significant associations between LOH and malignant transformation of OL. However, no common pattern was found between the two studies; while Graveland et al. identified associations with LOH at chromosome 9p, Jiang et al. found LOH at chromosome 5q, 6p, 6q and 11q instead.

Expanding from localised events like LOH, instability can also occur at the chromosomal level. Chromosomal instability (CIN) refers to alterations in chromosome number and structure during cell division, leading to widespread chromosomal abnormalities such as aneuploidy and LOH. It is a hallmark of cancer, with correlations with tumour stage and metastasis (56). Siebers et al. investigated the role of CIN in malignant transformation of OLs, and reported significant associations between the two, with hazard ratios of 6.8–7.2. The addition of image cytometry of in-situ hybridisation analysis for CIN may thus be indicative of high-risk OLs.

Beyond chromosomal alterations, impaired DNA repair mechanisms further exacerbate genomic instability to promote carcinogenesis. Thomas et al. utilised a bleomycin-induced mutagen sensitivity assay (MSA) to quantify the frequency of bleomycin-induced DNA breaks that indicate increased mutagen sensitivity and reduced DNA repair capacity, and reported significantly higher incidence of mutagen hypersensitivity in progressive OLs. The high sensitivity and specificity of 91.7% and 84.0% respectively may indicate its good applicability in differentiating at-risk lesions. Similarly, Farah et al. reported multiple DNA damage repair pathways to be significantly enriched in progressive OLs. This further highlights impaired DNA repair as a contributory factor to carcinogenesis, as defects in DNA repair pathways can lead directly to the accumulation of chromosomal and gene-specific aberrations.

4.2 Gene expression-specific alterations: mechanistic correlates

p53, also known as a “guardian of the genome”, is a critical tumour suppressor protein whose mutation is attributed to cancer development. Of the seven studies investigating p53, four reported significant associations between p53 mutation and malignant transformation of OL. Qurishi et al. only reported significant associations between p53, cyclin D1, and microsatellite instability coexpression and progression, while Nogami et al. did not perform any statistical analysis. Identification of p53 mutations by sequencing seems to correlate better with progression; Graveland et al. found significant associations between p53 and progression with sequencing but not immunohistochemistry (IHC), and Monteiro et al., who utilised IHC for detection, reported no significant associations. Therefore, in the consideration of p53 as a genomic marker, while sequencing incurs a higher cost than IHC, clinicians and pathologists should consider sequencing over IHC due to its potentially higher reliability in predicting malignant transformation.

Identifiable cancer stem cell markers may be good indicators of acquired malignant phenotypes that occur after the accumulation of initial genomic damage, characterised by invasion and stemness. Podoplanin and ALDH1 were identified by two studies each in this review to have significant associations with malignant transformation. As both of these markers are detected through IHC, the addition of IHC stains to include markers like podoplanin and ALDH1 may act as a simple risk stratification tool for malignant transformation risk.

While several other genes involved in cell cycle regulation (MKI67, FGFR1, EZH2), apoptosis (CASP8, BAX), oncogenic signalling pathways (NOTCH1, SMAD4, AXIN2), differentiation and invasion (SNAI1, TGM3), and stromal markers (PTHLH) were reported to be significantly associated with malignant transformation, these associations were only reported in one study each and have not yet been validated by other studies. Further studies should be conducted to investigate the applicability of these findings in other patient populations before implementation into clinical practice can be considered.

4.3 Contextualisation and clinical correlation

Dysplasia has traditionally been considered one of the key markers for predicting malignant transformation of OL (57). However, even as the current ‘gold standard’, the presence and grade of dysplasia are subjective, inconsistent and have poor specificity. While some studies in this review reported significant associations between dysplasia grade and OL progression, high malignant transformation rates of up to 31.9%–46.7% were still observed in lesions with low-grade dysplasia (, ). Furthermore, although initial univariate analyses reported dysplasia to be significantly associated with malignant transformation, multivariate analyses of several studies subsequently either indicated no or marginal associations, and instead found genomic alterations to be more independent predictors of progression (, , ). Thus, there should be strong consideration to incorporate genomic markers in conjunction with dysplasia for more robust risk evaluation, especially in lesions showing no or mild dysplasia that may, as a result, be falsely determined to be low-risk.

For translation into clinical practice, future research should not focus on identifying a single genomic marker, but on the development and validation of multi-marker genomic panels that combine the most prognostic DNA, chromosomal, and gene expression markers to provide a truly personalised risk assessment. For example, from the findings of this review, a panel combining DNA ploidy status, TP53 and podoplanin or ALDH1 is a strong candidate as a multi-marker panel, where the presence of aneuploidy, TP53 mutation and podoplanin or ALDH1 expression may help to identify a lesion where prophylactic surgery rather than surveillance should be chosen, although this requires prospective validation.

The tissue genomic profiles seen in the patients with PVLs included in this review differ greatly from those of the patients with OLs. No studies found significant associations between aneuploidy and malignant transformation. Similarly, while some gene expressions (MCM2, CDKN1A) were associated with progression, others, including TP53, showed no significant associations. This further reinforces the notion that PVL is a biologically separate entity from OL (58); with higher malignant transformation rates and few consistent clinical and histopathologic predictive factors, the management of PVLs would benefit from more aggressive early surgical intervention.

4.4 Strengths and limitations

This systematic review provides a comprehensive search and review of more than 3,200 patients over 34 studies in accordance with the PRISMA guidelines, and is registered on PROSPERO. Previous studies and reviews have focused on clinical predictors, broad biomarker inventories, or individual molecular pathways. In contrast, the present review systematically synthesises tissue-based genomic instability markers evaluated in longitudinal malignant transformation studies and integrates traditional cytogenetic markers with contemporary genomic profiling techniques to inform future biomarker panel development.

However, several limitations need to be discussed. The primary limitation lies in the heterogeneity between included studies. A wide variety of genomic alterations were studied, with few markers discussed across multiple studies. Even among markers evaluated across studies, such as p53, there were significant variations in detection methods and follow-up durations that make comparisons and meta-analyses between studies very challenging. Follow-up duration is also a key confounder for the outcome measure of malignant transformation; this lack of standardisation further limits the validity of the findings. Additionally, as not all samples of each study were successfully analysed for each genomic marker, several studies reported different sample denominators for some genomic markers compared to their reported sample size (, , ), potentially contributing to a smaller-than-anticipated sample size. Furthermore, all studies included were observational in nature, with no clinical trials. While some studies did perform analyses to account for other known risk factors such as a non-homogeneous appearance and dysplasia, the failure of many studies to control for these covariates limits the ability to determine if a genomic marker is independent of these known clinical predictors. Several included studies also originated from the same institutions or research groups (e.g., Bremmer et al., Graveland et al. and Wils et al.), and thus may have included partially overlapping patient cohorts to evaluate different genomic instability markers. These studies were retained to provide a comprehensive overview of the available literature, but this overlap should be considered when interpreting the strength of the above evidence due to potential for overrepresentation from certain populations. Finally, many gene-specific markers were evaluated in single studies and reported significant associations with malignant transformation, raising the possibility of publication or selective reporting bias, as studies with null findings may be less likely to be published. These findings should therefore be interpreted cautiously and require validation in larger, independent prospective cohorts.

It should also be noted that the malignant transformation rates reported in this review for both OL and PVL are higher than those described in previous studies. The malignant transformation rate of 19.9% for OL and 49.1% for PVL is higher than the 9.8% and 45.8% reported respectively in previous meta-analyses (, ). This is because some of the included studies follow a case-control design with the selection of only lesions with malignant transformation for analysis, hence over-representing the number of progressive lesions. Furthermore, for the PVL group, the malignant transformation rate calculated may not be accurate as the majority of samples were from one study (53), while the remaining studies contributed to only a minority of the sample size. More prospective studies with larger cohorts are warranted for the PVL group to obtain the most accurate estimation of its malignant transformation rate.

5 Conclusion

This systematic review highlights the key role of genomic alterations at the DNA, chromosomal and gene levels, and demonstrates potential for the use of some tissue-based genomic markers at each level to supplement current clinical and histopathological methods in determining the risk of malignant transformation for OL. While the results are promising, there is still a need for standardisation of detection methods (e.g., with a consensus gene panel or standardised cut-offs) and data reporting (e.g., follow-up duration) to further validate these findings.

Statements

Data availability statement

The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.

Author contributions

BQ: Data curation, Project administration, Formal analysis, Writing – review & editing, Methodology, Investigation, Writing – original draft, Conceptualization. YZ: Conceptualization, Methodology, Writing – review & editing. RN: Writing – review & editing, Project administration. NI: Data curation, Conceptualization, Supervision, Writing – review & editing. MS: Writing – review & editing, Supervision, Data curation. NS: Methodology, Data curation, Investigation, Supervision, Conceptualization, Project administration, Writing – review & editing, Resources, Writing – original draft.

Funding

The author(s) declared that financial support was not received for this work and/or its publication.

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The author MS declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Generative AI statement

The author(s) declared that generative AI was not used in the creation of this manuscript.

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Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/froh.2026.1939172/full#supplementary-material

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Summary

Keywords

carcinoma, squamous cell, genetic markers, genomic instability, leukoplakia, oral, oral cancer

Citation

Quah B, Zhang Y, Nagadia RH, Iyer NG, Sällberg Chen M and Shannon NB (2026) Tissue-based genomic instability markers for predicting malignant transformation in oral leukoplakia and proliferative verrucous leukoplakia: a systematic review. Front. Oral Health 7:1939172. doi: 10.3389/froh.2026.1939172

Received

16 July 2026

Revised

10 August 2026

Accepted

11 August 2026

Published

25 August 2026

Volume

7 - 2026

Edited by

Saman Warnakulasuriya, King's College London, United Kingdom

Reviewed by

Ovais Shafi, Jinnah Sindh Medical University, Pakistan

Haruki Sato, Chitahanto Medical Center, Japan

Updates

Copyright

*Correspondence: Nicholas Brian Shannon

Disclaimer

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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