Transkriptomska razčlenitev napredovalih primarnih tumorjev endometrija glede na status popravljanja neujemanja Transcriptomic stratification of advanced primary endometrial tumors by mismatch repair status

Povzetek

Ozadje: Rak endometrija (EC) je eden najpogostejših ginekoloških rakov v razvitih državah in ima slabo prognozo pri napredovali bolezni. Uvedba dopolnilnega zdravljenja z imunoterapijo je občutno izboljšala preživetje bolnic z napredovalim EC s pomanjkljivim popravljanjem neujemanja pri podvajanju DNA (MMRd), za katerega je značilna visoka mikrosatelitska nestabilnost (MSI-H). Se pa pri več kot dveh tretjinah bolnic razvijejo tumorji z ohranjenim popravljanjem neujemanja (MMRp), ki so mikrosatelitsko stabilni (MSS) in se na imunoterapijo slabo odzivajo. To kaže na veliko klinično potrebo po razvoju novih pristopov za zdravljenje bolnic z napredovalim EC, ki so MMRp-MSS. Metode: Prosto dostopne klinične in transkriptomske podatke iz kohorte TCGA-UCEC smo prenesli z uporabo knjižnice TCGABiolinks v okolju R Studio. Vključene so bile bolnice s primarnim EC v napredovalem stadiju ter razpoložljivimi kliničnimi in transkriptomskimi podatki. Razlike v izražanju genov glede na status MMR smo analizirali z uporabo knjižnice DESeq2. Za oceno povezav med ravnmi različno izraženih genov in specifičnim preživetjem (DSS) smo v podskupini MMRp-MSS uporabili Coxove modele sorazmernih tveganj. V osnovni analizi smo primerjali tumorje tipa MMRp-MSS s tumorji tipa MMRd-MSI-H. Pri tem smo MSS tumorje molekularnih podtipov POLEmut, TP53alt ter tumorje z nespecifičnim molekularnim profilom (NSMP) razvrstili v skupino MMRp-MSS. V podanalizi pa smo primerjavo ponovili po izključitvi POLEmut tumorjev iz skupine MMRp-MSS (MMRp-MSS (brez POLEmut) proti MMRd-MSI-H). Rezultati: Od 545 bolnic z EC je bila pri 139 bolnicah prisotna napredovala bolezen (27 tipa MMRd-MSI-H, 112 tipa MMRp- MSS). Med podskupinama s tumorji tipa MMRp-MSS in tipa MMRd-MSI-H ni bilo pomembnih razlik v preživetju. Analiza sprememb v izražanju genov (|kratna razlika v izražanju| > 2, prilagojeni p < 0,01) je pokazala 974 genov. Od tega je bilo 268 genov pomembno povezanih z DSS v skupini s tumorjem tipa MMRp-MSS. Z daljšim preživetjem je bilo povezano večje izražanje genov, povezanih z aktivacijo imunskega sistema in zaviranjem signalne poti Wnt. Nasprotno pa je večje izražanje genov, vključenih v onkogeno signalizacijo, izogibanje imunskemu sistemu, nevronsko diferenciacijo ter preoblikovanje zunajceličnega matriksa, napovedovalo slabši izid. Podanaliza, v kateri smo primerjali MMRp-MSS (brez POLEmut) proti MMRd-MSI-H, je pokazala povsem primerljive rezultate: tudi v tej analizi ni bilo razlik v preživetju med skupinama, obenem pa so bili opaženi podobni vzorci diferencialnega izražanja genov ter enaka funkcionalna vozlišča, povezana s preživetjem, kot v osnovni primerjavi MMRp-MSS proti MMRd-MSI-H. Zaključki: Napredovali EC tipa MMRp-MSS se na ravni transkriptoma razlikuje od napredovalih tumorjev tipa MMRd-MSI- -H. V tumorjih tipa MMRp-MSS smo identificirali izražanje naborov genov, povezanih s prognozo. Te ugotovitve izpostavljajo možne terapevtske tarče za to podskupino EC z visokim tveganjem in podpirajo razvoj strategij zdravljenja, prilagojenih molekularnemu podtipu.    

Abstract (Eng)

Background: Endometrial cancer (EC) is one of the most common gynaecological malignancies in developed countries and has a poor prognosis in advanced disease. The introduction of adjuvant treatment with immunotherapy has significantly improved survival in patients with advanced EC with deficient mismatch repair (MMRd), which is characterized by high microsatellite instability (MSI-H). However, more than two‑thirds of patients develop tumours with proficient mismatch repair (MMRp), which are microsatellite stable (MSS) and respond poorly to immunotherapy. This highlights a substantial clinical need for the development of new therapeutic approaches for patients with advanced EC who are MMRp-MSS. Methods: Clinical and transcriptomic data from the TCGA-UCEC cohort were downloaded using the TCGABiolinks package in RStudio. Patients with primary, advanced-stage EC and available clinical, molecular, and transcriptomic data were included. Differential gene expression according to MMR status was performed using DESeq2. Cox proportional hazards models were fitted to evaluate associations between levels of differentially expressed genes and disease-specific survival (DSS) in the MMRp-MSS subgroup. In the primary analysis, we compared MMRp-MSS tumours with MMRd-MSI-H tumours. In this analysis, MSS tumours belonging to the POLEmut, TP53alt, and nonspecific molecular profile (NSMP) subtypes were classified as MMRp-MSS. In the subanalysis, we repeated the comparison after excluding POLEmut tumours from the MMRp-MSS group (MMRp-MSS excluding POLEmut vs. MMRd-MSI-H). Results: Of the 545 patients with EC, 139 had advanced disease (27 with MMRd-MSI-H tumours and 112 with MMRp-MSS tumours). There were no significant differences in survival between the MMRp-MSS and MMRd-MSI-H subgroups. Differential gene expression analysis (|fold change| > 2, adjusted p < 0.01) identified 974 genes. Of these, 268 genes were significantly associated with DSS within the MMRp-MSS tumour group. Higher expression of genes involved in immune system activation and inhibition of the Wnt signalling pathway was associated with longer survival. In contrast, higher expression of genes involved in oncogenic signalling, immune evasion, neuronal differentiation, and extracellular matrix remodelling predicted poorer outcomes. The subanalysis comparing MMRp-MSS (excluding POLEmut) with MMRd-MSI-H showed fully comparable results: again, no survival differences were observed between the groups, and similar patterns of differential gene expression and the same functional survival‑related hubs emerged as in the primary comparison of MMRp-MSS versus MMRd-MSI-H. Conclusions: Advanced MMRp-MSS ECs are transcriptionally distinct from advanced MMRd-MSI-H tumours. Within MMRp-MSS tumours, we identified gene expression programs associated with prognosis. These findings highlight potential therapeutic targets for this high-risk subgroup and support the development of molecular subtype-adjusted treatment strategies.