Muir–Torre Syndrome Associated With a Cryptic Intronic MSH2 Variant Identified via Whole‐Genome Sequencing: A Case Report

ABSTRACT

Tumors exhibiting mismatch repair deficiency without detectable germline mutations via standard multigene panel testing are often classified as Lynch‐like syndrome. In the present report, we describe the case of a 47‐year‐old man presenting with synchronous axillary sebaceous carcinoma and colonic medullary carcinoma. Although initial germline multigene panel testing failed to identify pathogenic variants, a high degree of pathological suspicion for Muir–Torre syndrome remained. Immunohistochemistry revealed a concordant loss of MSH2 and MSH6 expression in both the extraocular sebaceous carcinoma and the colonic medullary carcinoma. This identical protein‐loss pattern detected across anatomically distinct tumors served as decisive pathological evidence of an underlying germline defect rather than independent biallelic somatic mutations. Consequently, whole‐genome sequencing was performed to resolve the discrepancy between the pathological findings and multigene panel testing results, successfully identifying a germline intronic MSH2 variant (NM_000251.3:c.2459‐12A>G). Subsequent RNA analysis confirmed aberrant splicing with an 11‐bp insertion. In conclusion, the present case illustrates that concordant mismatch repair protein loss across multiple tumors provides compelling morphological evidence to guide pathologists in reconsidering negative panel results and pursuing comprehensive genomic investigation to identify pathogenic intronic variants.

Pathological suspicion persisted despite negative multigene panel testing in a patient with synchronous sebaceous and colonic tumors showing concordant MSH2/MSH6 loss. Whole‐genome sequencing identified a cryptic intronic MSH2 variant (c.2459‐12A>G), and RNA analysis confirmed aberrant splicing with protein truncation. This case highlights the value of pathology‐guided comprehensive genomic testing for resolving Lynch‐like presentations and establishing Muir–Torre syndrome.

Abbreviations

ACMG/AMP

American College of Medical Genetics and Genomics and the Association for Molecular Pathology

IHC

immunohistochemistry

LLS

lynch‐like syndrome

LS

lynch syndrome

MGPT

multigene panel sequencing

MMR

mismatch repair

MTS

Muir–Torre syndrome

WGS

whole‐genome sequencing

1. Introduction

Lynch syndrome (LS) is caused by pathogenic germline variants in DNA mismatch repair (MMR) genes [1]. Clinically, tumors exhibiting MMR deficiency without identifiable germline variants are often classified as Lynch‐like syndrome (LLS) [2, 3]. However, LLS is a genetically heterogeneous category that likely encompasses undiagnosed LS cases in which pathogenic variants remain undetected via conventional multigene panel testing (MGPT) [4].

Pathologically, certain morphological phenotypes serve as critical “red flags” for a germline etiology [5]. For example, Muir–Torre syndrome (MTS), an LS subtype, is classically associated with extraocular sebaceous neoplasms [6, 7]. Periocular sebaceous carcinoma is more prevalent, whereas extraocular presentations are exceedingly rare; however, they carry a profound biological correlation with mismatch repair deficiency [8]. Given that the incidence of sebaceous neoplasms is significantly higher in Asian populations than in Western cohorts, recognizing these extraocular signals as critical “red flags” for MTS is crucial for early screening and comprehensive systemic evaluation [9, 10]. Notably, the identification of an identical pattern of MSH2/MSH6 loss across anatomically distinct tumors provides pathologists with compelling evidence of an underlying germline defect, rather than coincidental somatic events [11]. When such pathological findings strongly correlate with the clinical presentation of MTS, they should promote reconsideration of negative MGPT results and warrant more exhaustive genomic investigations [12].

In the present report, we present the case of a 47‐year‐old man presenting with synchronous axillary sebaceous carcinoma and colonic medullary carcinoma. Despite an initial negative MGPT and a provisional LLS classification, the persistent pathological conviction based on concordant MMR protein loss led to the implementation of whole‐genome sequencing (WGS), which successfully identified a pathogenic germline intronic MSH2 variant [11, 13]. This case underscores the pivotal role of pathological evaluation in identifying pathogenic variants missed by standard screening and ensuring an accurate diagnosis of hereditary cancer syndromes [14].

2. Case Presentation

2.1. Clinical Summary

A 47‐year‐old man presented with a 6‐month history of a gradually enlarging, palpable mass in the left axilla. The lesion was surgically excised, and a diagnosis of extraocular sebaceous carcinoma was rendered. Given the extraocular location of the tumor in a relatively young patient and the immunohistochemical (IHC) loss of MSH2 and MSH6 expression, MTS was strongly suspected. Given that such cutaneous neoplasms are established clinical markers that frequently precede or occur concurrently with internal malignancies, a comprehensive systemic evaluation was initiated to screen for synchronous visceral tumors. Subsequent contrast‐enhanced computed tomography and colonoscopy identified an ulcerated Type 2 tumor in the ascending colon. Accordingly, the patient underwent a laparoscopic right hemicolectomy. Histopathologically, the colorectal tumor was confirmed as medullary carcinoma (pT3N0M0, Stage IIa, UICC TNM 9th edition), and IHC revealed an identical pattern of MSH2 and MSH6 loss to that observed in the axillary tumor.

The family history of the patient was highly suggestive of a hereditary cancer syndrome, as his father had colorectal and gastric cancers, and both his paternal uncle and grandfather had brain tumors (Figure 1). The occurrence of synchronous mismatch repair‐deficient malignancies in a 47‐year‐old patient, combined with this robust pedigree, fulfilled several clinical indicators within the Revised Bethesda Guidelines for LS screening. However, MGPT targeting 31 cancer‐susceptibility genes, including all major mismatch repair genes, failed to identify any pathogenic variants. Consequently, the case was provisionally classified as LLS. Despite this negative genomic result, the pathognomonic clinical presentation and the perfect concordance of the IHC profiles provided a persistent pathological conviction that a germline etiology, likely Muir–Torre syndrome, had been overlooked by conventional exonic screening.

Figure 1.

Family pedigree. This pedigree represents a 47‐year‐old man diagnosed with Lynch syndrome through this study. The arrow indicates the proband is designated by the arrow, circles denote females, squares denote males, and diagonal slashes indicate deceased individuals. Current age/age at death of individuals (indicated as d.) and age at diagnosis (indicated as dx.) are listed below each symbol.

2.2. Pathological Findings

Histopathological examination of the excised left axillary tumor revealed a solid neoplasm with an expansive, lobulated growth pattern confined to the dermis, with no connection to the overlying epidermis (Figure 2a). The tumor primarily comprised atypical cells characterized by distinct sebocytic differentiation, featuring abundant, finely vacuolated (foamy) cytoplasm and scalloped nuclei (Figure 2b). Marked nuclear pleomorphism, prominent nucleoli, and mitotic activity, including atypical forms, were conspicuous. IHC analysis demonstrated strong cytoplasmic positivity for adipophilin and diffuse nuclear expression of androgen receptor, further confirming the diagnosis of extraocular sebaceous carcinoma.

Figure 2.

Histopathologic and immunohistochemical findings of the axillary sebaceous carcinoma. (a) Low‐power view depicting a lobulated, solid dermal tumor with an expansive growth pattern (hematoxylin and eosin [H&E]). (b) High‐power view demonstrating atypical cells with abundant, finely vacuolated cytoplasm and scalloped nuclei, characteristic of sebocytic differentiation (H&E). (c) Immunohistochemistry for mismatch repair (MMR) proteins. The tumor cells exhibit a complete loss of MSH2 and MSH6 expression, whereas infiltrating lymphocytes and adjacent fibroblasts serve as internal positive controls.

IHC evaluation of MMR proteins, with nuclear expression preserved in over 10% of tumor cells, revealed a complete loss of nuclear MSH2 and MSH6 expression in the malignant cells, whereas MLH1 and PMS2 expressions were retained (Figure 2c). This pattern established that the total loss of MSH2 and MSH6, which form a functional heterodimer, was an authentic reflection of MMR deficiency rather than a technical artifact.

The synchronous ascending colon tumor exhibited classic morphological features of medullary carcinoma, including poorly differentiated epithelial cells arranged in syncytial sheets and nests with broad, pushing borders (Figure 3a). Glandular formation was absent, and the tumor was characterized by prominent nucleoli and abundant, finely granular cytoplasm. Notably, dense tumor‐infiltrating lymphocytes and a peritumoral Crohn's‐like lymphocytic reaction were quantitatively prominent (Figure 3b). This pronounced host immune reaction was consistent with the elevated neoantigen burden characteristic of MMR‐deficient status. Moreover, IHC of the colorectal tumor revealed an identical MMR expression pattern to the axillary tumor: loss of MSH2/MSH6 and preserved MLH1/PMS2 expression (Figure 3c).

Figure 3.

Histopathologic and immunohistochemical findings of the colon tumor. (a) Low‐power view depicting the tumor structure with a lack of conspicuous glandular formation (hematoxylin and eosin [H&E]). (b) High‐power view highlighting classic medullary carcinoma features, including syncytial sheets, prominent intraepithelial lymphocytic infiltration, and poorly differentiated epithelial cells (H&E). (c) Immunohistochemistry for MMR proteins. Concordant with the axillary tumor, the colon tumor demonstrates a total loss of MSH2 and MSH6 nuclear expression, with preserved internal controls.

The identification of concordant MMR deficiency across two histologically distinct “LS‐signature” tumors strongly indicated a constitutive germline defect. This clinical suspicion persisted despite initial negative results from MGPT, which had provisionally categorized the case as LLS. To resolve this clinico‐pathological discordance, WGS was performed to investigate cryptic deep intronic variants, identifying a single nucleotide substitution in MSH2 intron 14 (c.2459−12A>G) (Figure 4a). Functional validation via RNA‐based splicing analysis demonstrated that this variant leads to a novel splice acceptor site, resulting in an 11‐bp intronic insertion (r.2458_2459insATTTCTTATAG) into the mRNA (Figure 4b–d). This insertion causes a frameshift and a premature stop codon, rendering the transcript susceptible to nonsense‐mediated mRNA decay. Accordingly, the variant was classified as pathogenic (PVS1, PS3, PM2) following ACMG/AMP guidelines, establishing a definitive diagnosis of LS‐associated MTS.

Figure 4.

Molecular analysis of the MSH2 intronic variant. (A) Whole‐genome sequencing identified a single nucleotide substitution in MSH2 intron 14 (NM_000251.3:c.2459‐12A>G). This variant is predicted to activate a cryptic splice acceptor site, resulting in aberrant splicing. (B) Sanger sequencing of reverse‐transcription polymerase chain reaction products from peripheral blood identifies an aberrant splicing pattern at the exon 14–15 junction, with overlapping signals indicative of intronic insertion. (C and D) Sanger sequencing of cloned cDNA using the T‐Vector pMD20. (C) Normal sequence. (D) Sequence depicting an 11‐bp intronic insertion (r.2458_2459insATTTCTTATAG) into the mRNA, leading to a frameshift.

3. Discussion

The present case illustrates a diagnostically instructive scenario in which pathological evaluation played a decisive role in identifying the underlying cause of MMR deficiency [12, 14]. The coexistence of extraocular sebaceous carcinoma and synchronous medullary carcinoma of the colon, combined with the concordant loss of MSH2 and MSH6 expression in both tumors, strongly suggested LS‐associated MTS [6, 7]. Importantly, this diagnostic conviction was established based on tumor morphology and IHC findings before any molecular confirmation. The identification of an extraocular sebaceous carcinoma in a relatively young patient serves as a critical “red flag” for MTS, as these cutaneous lesions frequently precede internal malignancies [7, 8]. In such scenarios, the pathological recognition of MSH2/MSH6 loss should strongly prompt consideration of systematic visceral screening, prioritizing the detection of synchronous tumors over a mere metastatic workup, as in the present case [14, 15].

Tumors classified as LLS represent a heterogeneous category defined by MMR deficiency in the absence of MLH1 promoter hypermethylation or identifiable germline pathogenic variants [2, 3]. While this category is clinically used to manage risk, it inevitably serves as a “diagnostic dustbin” for cases where causative genetic alterations remain undetected through conventional testing [4, 16]. In the present case, the pathological features were fundamentally irreconcilable with a provisional diagnosis of LLS. Extraocular sebaceous carcinoma is a clinical hallmark of MTS, with MMR deficiency relevant in cases with non‐head‐and‐neck presentations [8]. Furthermore, the selective and identical loss of MSH2/MSH6 expression across two anatomically distinct organs is a pathognomonic signal for germline MSH2 alterations, as coincidental biallelic somatic mutations in both tumors are statistically highly implausible [11, 17].

Standard MGPT is currently the first‐line approach for germline evaluation; however, it is inherently limited by its focus on coding exons and flanking splice sites [13]. This limitation renders MGPT unable to detect deep intronic variants that induce aberrant splicing [18]. In our case, the negative MGPT result did not negate the pathological impression but rather highlighted a discrepancy that warranted further investigation. The identified variant (c.2459‐12A>G) is not novel and has been documented in ClinVar with multiple submissions classified as pathogenic or likely pathogenic; it is also registered in dbSNP as rs267608012. In addition, this variant has been reported to be absent from large population databases, supporting its rarity [13]. Functionally, this variant generates an aberrant splice acceptor site, leading to an 11‐bp insertion and subsequent protein truncation, as confirmed by transcriptomic analysis [13]. This technical limitation demonstrates the vital role of deep intronic analysis in cases where clinical findings remain discordant with panel results [11, 13]. Guided by this persistent suspicion, WGS successfully identified the variant in our case, validating a hypothesis rigorously formulated based on pathological evidence [12]. More broadly, this case supports the possibility that deep intronic or other noncoding MMR variants may account for a subset of unresolved LLS cases, particularly when strong clinicopathological evidence persists despite negative standard MGPT results [11, 13, 18].

The present case underscores a fundamental diagnostic principle: pathological evaluation remains the important guide for genetic testing strategies [12, 14]. When morphological features, such as the syncytial growth of medullary carcinoma, and IHC profiles are highly suggestive of a specific hereditary defect, discordant molecular results should prompt a reconsideration of the testing scope rather than the abandonment of the pathological diagnosis [5, 7]. In practical terms, actionable indicators for considering escalation from negative MGPT to WGS include an MTS phenotype, such as extraocular sebaceous carcinoma, concordant loss of the same MMR proteins across anatomically or histologically distinct tumors, and additional clinical clues such as young onset, suggestive family history, or other LS‐associated malignancies. For patients provisionally diagnosed with LLS, a careful reappraisal of tumor pathology, IHC patterns, and relevant clinical features is essential to identify those who require more comprehensive genomic analyses [4, 16]. If WGS identifies a candidate variant, RNA‐based splicing analysis may then be added for novel variants, variants of uncertain significance, or atypical splice‐site variants, whereas it may not be necessary when pathogenicity is already well established in curated databases such as ClinVar and supported by other evidence. The practical use of WGS and RNA‐based analysis should also take into account local availability, cost, tissue accessibility, and institutional expertise.

Furthermore, the reclassification of our case from LLS to definitive LS/MTS carries profound, life‐saving implications for the patient's family. This definitive diagnosis enables targeted cascade testing for relatives and dictates a rigorous surveillance protocol for colorectal, gastric, and genitourinary malignancies [1, 19]. Such systematic monitoring can significantly reduce cancer‐related mortality in LS families by detecting pre‐malignant lesions or early‐stage cancers when they are most treatable [1, 20]. In this context, the insistence of the pathologist on comprehensive testing directly contributes to the primary prevention of future malignancies across multiple generations [1].

In conclusion, this case demonstrates that comprehensive pathological assessment serves as a diagnostic compass in the era of genomic medicine. The integration of morphology, IHC, and targeted comprehensive molecular analysis is vital for the precise diagnosis of LS‐related conditions, ensuring that patients and their families receive appropriate genetic counseling and life‐saving cancer surveillance [12, 13].

Author Contributions

Keisuke Noda: conception and design of the study, drafting the manuscript and figures, and genomic and transcriptomic analyses. Hirokazu Kurohama: pathological evaluation and critical revision of the manuscript. Katsuya Matsuda, Akira Kinoshita, and Hiroyuki Mishima: genomic and transcriptomic analyses. Megumi Matsumoto and Riko Matsuda: genetic counseling and provision of information to the patient. Nozomi Ueki and Masao Kishikawa: pathological evaluation. Masahiro Nakashima: pathological evaluation, critical revision, and final approval of the manuscript. Takashi Nonaka: clinical management and surgical intervention. Koh‐ichiro Yoshiura: genomic and transcriptomic analyses, and critical revision and final approval of the manuscript. Katsuya Matsuda and Kiyonori Miura: critical revision and final approval of the manuscript. All authors provided final approval of the version to be published and agree to be accountable for all aspects of the work.

Ethics Statement

This study was conducted according to the ethical standards of the Nagasaki University Graduate School of Biomedical Sciences. The approval number was 20111102‐12.

Consent

Written informed consent was obtained from the patient for the publication of this case report.

Conflicts of Interest

The authors declare no conflicts of interest.

Data Availability Statement

The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.