# Immune microenvironment heterogeneity characterizes biologically distinct KRASmut/SPOPmut and KRASmut/PIK3CAmut mesonephric-like adenocarcinoma subtypes revealed by integrated whole-exome and transcriptomic profiling **Authors:** Jing Zeng, Qingli Li, Kemin Li, Lu Yang, Lian Xu, Wei Wang, Kaixuan Yang, Qingbo Wei, Jin Wang, Changbin Zhu, Rutie Yin PMC · DOI: 10.3389/fimmu.2025.1605227 · Frontiers in Immunology · 2025-07-16 ## TL;DR This study identifies two distinct subtypes of mesonephric-like adenocarcinoma based on genetic mutations and their immune microenvironment differences. ## Contribution The first comprehensive molecular and immune profiling of MLA subtypes defined by KRAS/SPOP and KRAS/PIK3CA mutations. ## Key findings - KRAS mutations are prevalent and co-occur with either SPOP or PIK3CA, but not both. - KRAS/SPOP mutant MLAs show reduced immune infiltration and lower IFN gene expression compared to KRAS/PIK3CA mutant MLAs. - MLAs exhibit upregulated kidney development pathways and a Th2-dominated immunosuppressive tumor microenvironment. ## Abstract This study aims to uncover the molecular biology and immune microenvironment of gynecological mesonephric-like adenocarcinoma (MLA). To determine the comprehensive characteristics of MLA, 17 patients with MLA were retrospectively enrolled in this study. Whole-exome sequencing and mRNA sequencing were performed to explore the molecular features. The biological differences between MLAs and epithelial-initiated gynecologic tumors reported in The Cancer Genome Atlas database were also analyzed. KRAS mutations (82.4%) were considered the driving mechanism and were co-mutated with PIK3CA (47.1%) and SPOP (23.5%), but their functions were mutually exclusive. In addition, pathways and genes associated with kidney development were upregulated in MLA patients. Compared with adjacent tissues and common gynecological tumors in The Cancer Genome Atlas, Th2 signature and resting mast cells account for the majority in MLAs, rendering an immunosuppressive TME. Particularly, the expression levels of IFNG, IFN6, and IFN1 KRAS_SPOP group, significantly lower than the rates found in KRAS_PIK3CA group. KRAS_SPOP mutant MLAs, exhibited reduced immune infiltration in their tumor microenvironment. This is the first study to demonstrate the comprehensive molecular characteristics of MLA and detect biologically distinct subtypes of KRAS mut/SPOP mut and KRAS mut/PIK3CA mut MLAs. ## Linked entities - **Genes:** KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845], PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) [NCBI Gene 5290], SPOP (speckle type BTB/POZ protein) [NCBI Gene 8405], IFNG (interferon gamma) [NCBI Gene 3458], IFN4 (type I interferon 4) [NCBI Gene 100021340], IFN1@ (interferon, type 1, cluster) [NCBI Gene 3438] ## Full-text entities - **Genes:** PDCD1LG2 (programmed cell death 1 ligand 2) [NCBI Gene 80380] {aka B7DC, Btdc, CD273, PD-L2, PDCD1L2, PDL2}, EPCAM (epithelial cell adhesion molecule) [NCBI Gene 4072] {aka Ber-Ep4, BerEp4, DIAR5, EGP-2, EGP314, EGP40}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, NR4A1 (nuclear receptor subfamily 4 group A member 1) [NCBI Gene 3164] {aka GFRP1, HMR, N10, NAK-1, NGFIB, NP10}, PTPN11 (protein tyrosine phosphatase non-receptor type 11) [NCBI Gene 5781] {aka BPTP3, CFC, JMML, METCDS, NS1, PTP-1D}, KIF26B (kinesin family member 26B) [NCBI Gene 55083], POU3F3 (POU class 3 homeobox 3) [NCBI Gene 5455] {aka BRN1, OTF8, SNIBFIS, brain-1, oct-8}, BMP7 (bone morphogenetic protein 7) [NCBI Gene 655] {aka OP-1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, PIK3CG (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma) [NCBI Gene 5294] {aka IMD97, PI3CG, PI3K, PI3Kgamma, PIK3, p110gamma}, SOX9 (SRY-box transcription factor 9) [NCBI Gene 6662] {aka CMD1, CMPD1, ENH13, SRA1, SRXX2, SRXY10}, SIM1 (SIM bHLH transcription factor 1) [NCBI Gene 6492] {aka bHLHe14}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, ESR1 (estrogen receptor 1) [NCBI Gene 2099] {aka ER, ESR, ESRA, ESTRR, Era, NR3A1}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, LHX1 (LIM homeobox 1) [NCBI Gene 3975] {aka LIM-1, LIM1}, GATA3 (GATA binding protein 3) [NCBI Gene 2625] {aka HDR, HDRS}, LAG3 (lymphocyte activating 3) [NCBI Gene 3902] {aka CD223}, LGR5 (leucine rich repeat containing G protein-coupled receptor 5) [NCBI Gene 8549] {aka FEX, GPR49, GPR67, GRP49, HG38}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, IRF1 (interferon regulatory factor 1) [NCBI Gene 3659] {aka IMD117, IRF-1, MAR}, CD28 (CD28 molecule) [NCBI Gene 940] {aka IMD123, Tp44}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, SIX4 (SIX homeobox 4) [NCBI Gene 51804] {aka AREC3}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, BTLA (B and T lymphocyte associated) [NCBI Gene 151888] {aka BTLA1, CD272}, PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) [NCBI Gene 5290] {aka CCM4, CLAPO, CLOVE, CWS5, HMH, MCAP}, IFN1@ (interferon, type 1, cluster) [NCBI Gene 3438] {aka IFNA}, PAX8 (paired box 8) [NCBI Gene 7849] {aka PAX-8}, PAX2 (paired box 2) [NCBI Gene 5076] {aka FSGS7, PAPRS, PAX-2}, TTF1 (transcription termination factor 1) [NCBI Gene 7270] {aka TTF-1, TTF-I}, FAP (fibroblast activation protein alpha) [NCBI Gene 2191] {aka DPPIV, FAPA, FAPalpha, SIMP}, PTEN (phosphatase and tensin homolog) [NCBI Gene 5728] {aka 10q23del, BZS, CWS1, DEC, GLM2, MHAM}, CALB2 (calbindin 2) [NCBI Gene 794] {aka CAB29, CAL2, CR}, NR0B2 (nuclear receptor subfamily 0 group B member 2) [NCBI Gene 8431] {aka SHP, SHP1}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, MME (membrane metalloendopeptidase) [NCBI Gene 4311] {aka CALLA, CD10, CMT2T, NEP, SCA43, SFE}, SPOP (speckle type BTB/POZ protein) [NCBI Gene 8405] {aka BTBD32, NEDMACE, NEDMIDF, NSDVS1, NSDVS2, TEF2}, FMN1 (formin 1) [NCBI Gene 342184] {aka FMN, LD}, CD274 (CD274 molecule) [NCBI Gene 29126] {aka ADMIO5, B7-H, B7H1, PD-L1, PDCD1L1, PDCD1LG1}, MUL1 (mitochondrial E3 ubiquitin protein ligase 1) [NCBI Gene 79594] {aka C1orf166, GIDE, MAPL, MULAN, RNF218}, HOXB7 (homeobox B7) [NCBI Gene 3217] {aka HHO.C1, HOX2, HOX2C, Hox-2.3}, SIX1 (SIX homeobox 1) [NCBI Gene 6495] {aka BOS3, DFNA23, TIP39}, EREG (epiregulin) [NCBI Gene 2069] {aka EPR, ER, Ep}, FRAS1 (Fraser extracellular matrix complex subunit 1) [NCBI Gene 80144] {aka FRASRS1}, HOXA11 (homeobox A11) [NCBI Gene 3207] {aka HOX1, HOX1I, RUSAT1}, SOX17 (SRY-box transcription factor 17) [NCBI Gene 64321] {aka PPH7, VUR3}, PGR (progesterone receptor) [NCBI Gene 5241] {aka NR3C3, PR}, MFAP5 (microfibril associated protein 5) [NCBI Gene 8076] {aka AAT9, MAGP-2, MAGP2, MFAP-5, MP25}, KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845] {aka 'C-K-RAS, C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A} - **Diseases:** endometrioid adenocarcinoma (MESH:D018269), ovarian cancer (MESH:D010051), middle renal cell carcinoma (MESH:D002292), cervical squamous cell carcinoma (MESH:D002294), renal, Mullerian, and thyroid-origin tumors (MESH:D018200), Sarcomas (MESH:D012509), colorectal cancer (MESH:D015179), ovarian and endometrial mesonephric-like tumors (MESH:D001948), EC (MESH:D016889), carcinogenesis (MESH:D063646), breast cancer (MESH:D001943), nonsmall-cell lung cancer (MESH:D002289), metastasis (MESH:D009362), gynecologic tumors (MESH:D005833), glioma (MESH:D005910), pancreatic cancer (MESH:D010190), death (MESH:D003643), ovarian (MESH:D010049), fibrosis (MESH:D005355), mesonephric duct hyperplasia (MESH:D006965), MLA (MESH:D000230), Cancer (MESH:D009369) - **Chemicals:** hematoxylin (MESH:D006416), paraffin (MESH:D010232), Alpelisib (MESH:C585539), cetuximab (MESH:D000068818), MRTX1133 (MESH:C000723088), Adagrasib (MESH:C000718190), formalin (MESH:D005557), BI-2865 (-), sotorasib (MESH:C000706028), eosin (MESH:D004801) - **Species:** Homo sapiens (human, species) [taxon 9606] - **Mutations:** D140G, E542A, H1047R, G12V, M117T, G12, E47K, E545A, M1004I, C420R, serine/threonine ## Full text _Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12307467/full.md ## Figures 6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12307467/full.md ## References 88 references — full list in the complete paper: https://tomesphere.com/paper/PMC12307467/full.md --- Source: https://tomesphere.com/paper/PMC12307467