# Distinct mutational signature and clonal evolution in constitutional mismatch repair deficiency-associated high-grade gliomas

**Authors:** Chang Li, E. Zeynep Erson-Omay, Yavuz Koksal, Ekrem Unal, Buket Kara, Kaya Bilguvar, Yahya Paksoy, Nimetullah Alper Durmus, Ali Kurtsoy, Huseyin Per, John Rosendahl Østergaard, Murat Günel, Ahmet Okay Çağlayan

PMC · DOI: 10.1016/j.isci.2026.115029 · iScience · 2026-02-14

## TL;DR

This study explores the genetic patterns and tumor evolution in a rare type of brain cancer linked to a genetic disorder, finding distinct differences between subgroups that affect patient outcomes.

## Contribution

The study identifies distinct mutational signatures and clonal evolution patterns in CMMRD-associated high-grade gliomas, particularly between MSH6 and PMS2 subgroups.

## Key findings

- MSH6 and PMS2 subgroups show unique mutational signatures (SBS6 and SBS21) linked to prognosis.
- Clonal evolution reveals early POLE/POLD1 events and survival of the founding clone during tumor recurrence.
- Patients with CMMRD-associated gliomas have early onset and poor prognosis.

## Abstract

Constitutional mismatch repair deficiency (CMMRD) is a rare cancer-predisposing syndrome. Recent studies have advanced our understanding of the genomic and epigenomic features of this disease, however, the mutational signatures and clonal evolution of CMMRD-associated high-grade gliomas (HGGs) requires further investigation. Herein, we analyzed the mutational signature and clonal evolution of 25 CMMRD-associated HGGs. Germline biallelic mutations in MSH6 (56.0%), PMS2 (36.0%), MLH1 (8.0%) were identified. Patients showed early onset (5.8 ± 4.2 years) and poor prognosis (progression-free survival 16 ± 18.0 months). Notably, we identified distinct mutational signatures, evolution pattern and clinical outcome between MSH6 and PMS2 subgroups, showing enriched SBS6 and SBSS21, respectively, which were found to correlate with prognosis. Clonal evolution model indicated early POLE/POLD1 events and survival of founding clone during tumor recurrence. These findings provide valuable insights into the genomic landscape and clinical outcomes of CMMRD-associated HGGs, emphasizing the critical role of mutational signature and tumor evolution in tumorigenesis and patient prognosis.

•CMMRD-associated gliomas show distinct mutational and evolutionary profiles•MSH6 and PMS2 subgroups show unique mutational signatures associated with prognosis•Clonal evolution model shows early POLE/POLD1 events and survival of founding clone

CMMRD-associated gliomas show distinct mutational and evolutionary profiles

MSH6 and PMS2 subgroups show unique mutational signatures associated with prognosis

Clonal evolution model shows early POLE/POLD1 events and survival of founding clone

Molecular biology; cancer

## Linked entities

- **Genes:** MSH6 (mutS homolog 6) [NCBI Gene 2956], PMS2 (PMS1 homolog 2, mismatch repair system component) [NCBI Gene 5395], MLH1 (mutL homolog 1) [NCBI Gene 4292], POLE (DNA polymerase epsilon, catalytic subunit) [NCBI Gene 5426], POLD1 (DNA polymerase delta 1, catalytic subunit) [NCBI Gene 5424]

## Full-text entities

- **Genes:** LAMA5 (laminin subunit alpha 5) [NCBI Gene 3911] {aka BBDS2, NPHS26}, PTPN11 (protein tyrosine phosphatase non-receptor type 11) [NCBI Gene 5781] {aka BPTP3, CFC, JMML, METCDS, NS1, PTP-1D}, MSH6 (mutS homolog 6) [NCBI Gene 2956] {aka GTBP, GTMBP, HNPCC5, HSAP, LYNCH5, MMRCS3}, PDGFRA (platelet derived growth factor receptor alpha) [NCBI Gene 5156] {aka CD140A, PDGFR-2, PDGFR2}, IDH2 (isocitrate dehydrogenase (NADP(+)) 2) [NCBI Gene 3418] {aka D2HGA2, ICD-M, IDH, IDH-2, IDHM, IDP}, OBSCN (obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF) [NCBI Gene 84033] {aka ARHGEF30, RHABDO1, UNC89}, FAT1 (FAT atypical cadherin 1) [NCBI Gene 2195] {aka CDHF7, CDHR8, FAT, ME5, hFat1}, DNAH11 (dynein axonemal heavy chain 11) [NCBI Gene 8701] {aka CILD7, DNAHBL, DNAHC11, DNHBL, DPL11}, PMS2 (PMS1 homolog 2, mismatch repair system component) [NCBI Gene 5395] {aka HNPCC4, LYNCH4, MLH4, MMRCS4, PMS-2, PMSL2}, LRP2 (LDL receptor related protein 2) [NCBI Gene 4036] {aka DBS, GP330, LRP-2}, PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) [NCBI Gene 5290] {aka CCM4, CLAPO, CLOVE, CWS5, HMH, MCAP}, DYNC1H1 (dynein cytoplasmic 1 heavy chain 1) [NCBI Gene 1778] {aka CDCBM13, CMT2O, DHC1, DHC1a, DNCH1, DNCL}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, NES (nestin) [NCBI Gene 10763] {aka Nbla00170}, ABCA13 (ATP binding cassette subfamily A member 13) [NCBI Gene 154664], PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, IDH1 (isocitrate dehydrogenase (NADP(+)) 1) [NCBI Gene 3417] {aka HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC}, SPHKAP (SPHK1 interactor, AKAP domain containing) [NCBI Gene 80309] {aka SKIP}, RYR3 (ryanodine receptor 3) [NCBI Gene 6263] {aka CMYO20, CMYP20, RYR-3}, CDKN2B (cyclin dependent kinase inhibitor 2B) [NCBI Gene 1030] {aka CDK4I, INK4B, MTS2, P15, TP15, p15INK4b}, CIC (capicua transcriptional repressor) [NCBI Gene 23152] {aka MRD45}, MUC16 (mucin 16, cell surface associated) [NCBI Gene 94025] {aka CA125}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, NEB (nebulin) [NCBI Gene 4703] {aka AMC6, NEB177D, NEM2}, DST (dystonin) [NCBI Gene 667] {aka BP240, BPA, BPAG1, CATX-15, CATX15, CMYO29}, NF1 (neurofibromin 1) [NCBI Gene 4763] {aka NFNS, VRNF, WSS}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, PIK3R1 (phosphoinositide-3-kinase regulatory subunit 1) [NCBI Gene 5295] {aka AGM7, GRB1, IMD36, p85, p85-ALPHA, p85alpha}, TTN (titin) [NCBI Gene 7273] {aka CMD1G, CMH9, CMPD4, CMYO5, CMYP5, EOMFC}, TERT (telomerase reverse transcriptase) [NCBI Gene 7015] {aka CMM9, DKCA2, DKCB4, EST2, PFBMFT1, TCS1}, MSH2 (mutS homolog 2) [NCBI Gene 4436] {aka COCA1, FCC1, HNPCC, HNPCC1, LCFS2, LYNCH1}, MLH1 (mutL homolog 1) [NCBI Gene 4292] {aka COCA2, FCC2, HNPCC, HNPCC2, LYNCH2, MLH-1}, SSPOP (SCO-spondin, pseudogene) [NCBI Gene 23145] {aka SSPO}, COL1A2 (collagen type I alpha 2 chain) [NCBI Gene 1278] {aka EDSARTH2, EDSCV, OI4}, BRAF (B-Raf proto-oncogene, serine/threonine kinase) [NCBI Gene 673] {aka B-RAF1, B-raf, BRAF-1, BRAF1, NS7, RAFB1}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, IFIT5 (interferon induced protein with tetratricopeptide repeats 5) [NCBI Gene 24138] {aka ISG58, P58, RI58}, PIGM (phosphatidylinositol glycan anchor biosynthesis class M) [NCBI Gene 93183] {aka GPI-MT-I}, MGMT (O-6-methylguanine-DNA methyltransferase) [NCBI Gene 4255], RYR1 (ryanodine receptor 1) [NCBI Gene 6261] {aka CCO, CMYO1A, CMYO1B, CMYP1A, CMYP1B, KDS}, SMARCB1 (SWI/SNF related BAF chromatin remodeling complex subunit B1) [NCBI Gene 6598] {aka BAF47, CSS3, INI-1, INI1, MRD15, PPP1R144}, MEGF8 (multiple EGF like domains 8) [NCBI Gene 1954] {aka C19orf49, CRPT2, EGFL4, SBP1}, FLT1 (fms related receptor tyrosine kinase 1) [NCBI Gene 2321] {aka FLT, FLT-1, VEGFR-1, VEGFR1}, RB1 (RB transcriptional corepressor 1) [NCBI Gene 5925] {aka OSRC, PPP1R130, RB, p105-Rb, p110-RB1, pRb}, ATRX (ATRX chromatin remodeler) [NCBI Gene 546] {aka JMS, MRX52, RAD54, RAD54L, XH2, XNP}, POLD1 (DNA polymerase delta 1, catalytic subunit) [NCBI Gene 5424] {aka CDC2, CRCS10, IMD120, MDPL, POLD}, H3-3A (H3.3 histone A) [NCBI Gene 3020] {aka BRYLIB1, H3.3A, H3F3, H3F3A}, SPATA2 (spermatogenesis associated 2) [NCBI Gene 9825] {aka PD1, PPP1R145, tamo}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}
- **Diseases:** glioblastoma (MESH:D005909), anaplastic astrocytoma (MESH:D001254), brain cancers (MESH:D001932), necrotic (MESH:D009336), HGGs (MESH:D008228), CNS tumors (MESH:D016543), replication repair deficiency (MESH:D049914), Primary (MESH:D010538), Lynch (MESH:D003123), OS (MESH:C567932), SBS (MESH:D012640), embryonal tumors (MESH:D009373), ASCN (MESH:D000080888), tumorigenesis (MESH:D063646), Constitutional mismatch repair deficiency (MESH:C536928), CNS cancers (MESH:D009369), autosomal recessive inherited cancer predisposition syndrome (MESH:D009386), RRD syndromes (MESH:D013577), inflammatory (MESH:D007249), GBM (MESH:D005910)
- **Chemicals:** etoposide (MESH:D005047), TMZ (MESH:D000077204), alkylating (-), H&amp;E (MESH:D006371), 5-methylcytosine (MESH:D044503), thymine (MESH:D013941)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** chrX: 284,212-2,726,273, p.R1331X, C>A, C>T, C90Y, c.285 + 6C>T, p.V411L, G106D, R190H, p.S964Y, p.E978G, p.R847W, R440C, R502W, p.F134V, p.R680C, p. A692V, R156H, p.P286R, V1772F, p.A915V, G365S
- **Cell lines:** NG2504-1 — Homo sapiens (Human), Down syndrome, Finite cell line (CVCL_L976)

## Full text

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## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12964222/full.md

## References

75 references — full list in the complete paper: https://tomesphere.com/paper/PMC12964222/full.md

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Source: https://tomesphere.com/paper/PMC12964222