Graphical abstract

   graphic file with name fx1.jpg
   [61]Open in a new tab

Highlights

     * •
       A tumor population shows increased expression of ribosomal genes
       and elongation factors
     * •
       Longitudinal analysis of astrocytomas reveals stable tumor
       populations during recurrence
     * •
       Receptor-ligand analysis infers interactions between tumor and TAM
       subpopulations
     * •
       Compositions of TAM transcriptional states differ in
       oligodendrogliomas and astrocytomas
     __________________________________________________________________

   Blanco-Carmona et al. apply single-nucleus RNA-seq and ATAC-seq to
   profile the cellular heterogeneity in adult IDH-mutant gliomas. They
   identify a range of transcriptional states within tumor cells and
   tumor-associated macrophage subpopulations in these gliomas. Comparing
   the relative abundance of these populations sheds light on the
   distinctions between IDH-mutant glioma subtypes.

Introduction

   Diffuse gliomas exhibit recurrent mutations in the isocitrate
   dehydrogenase (IDH) gene.[62]^1 IDH-mutant gliomas are classified into
   two subtypes: oligodendrogliomas featuring chromosome arm 1p/19q
   co-deletion and astrocytomas characterized by euploid 1p/19q.[63]^2
   Intratumoral heterogeneity is a feature of IDH-mutant
   gliomas,[64]^3^,[65]^4 showcasing a hierarchy of cellular phenotypes
   wherein a neural stem cell-like population gives rise to tumor
   subpopulations resembling expression profiles of astrocytes and
   oligodendrocytes. Nevertheless, a comprehensive comparative analysis of
   transcriptional and epigenomic heterogeneity in oligodendrogliomas
   versus astrocytomas remains elusive. Furthermore, IDH-mutant gliomas
   manifest distinct activation states of tumor-associated
   microglia/macrophages (TAMs),[66]^5^,[67]^6 although it remains
   uncertain whether TAM composition differs between oligodendrogliomas
   and astrocytomas, how tumor subpopulations interact with TAMs, and to
   what extent tumor grade and recurrence influence TAM diversity.
   Therefore, analyses of tumor heterogeneity and tumor-host interactions
   are important for our understanding of IDH-mutant gliomas and their
   evolution.

   Here, we performed high-throughput single-nucleus RNA and ATAC
   sequencing (snRNA- and snATAC-seq) on primary IDH-mutant gliomas and
   snRNA-seq on a cohort of primary and recurrent astrocytoma pairs. This
   effort generated a comprehensive resource for resolving tumor diversity
   and TAM states. Our findings reaffirm previously described
   differentiation hierarchies and unveil a distinct subgroup of
   non-cycling, ribosomal-enriched stem-like tumor cells characterized by
   unique epigenetic and transcriptional signatures. We identify
   significant transcriptional differences in TAM states between
   oligodendrogliomas and astrocytomas. By mapping receptor-ligand
   interactions between tumor and TAM subpopulations, we highlight a
   notable interaction between inflammatory TAMs and astrocytic tumor
   subpopulations in astrocytomas, subsequently validated through
   immunohistochemistry in independent cohorts. Results from the clinical
   trial with vorasidenib, the brain-penetrant mutant IDH inhibitor, has
   shown promising results in patients with grade 2 IDH-mutant gliomas,
   significantly improving progression-free survival and delaying time to
   next intervention.[68]^7 Moving forward, molecular studies focused on
   higher grade and recurrent IDH-mutant gliomas may uncover molecular
   alterations suitable for targeted therapeutic strategies.

Results

Tumor metasignatures in IDH-mutant gliomas reveal the presence of a
ribosomal-enriched population

   To investigate intratumor heterogeneity in adult IDH-mutant gliomas, we
   generated snRNA-seq from 14 snap-frozen primary tissues, comprising 8
   oligodendrogliomas and 6 astrocytomas ([69]Figure 1A;
   [70]Tables S1A–S1D), encompassing 76,680 and 72,385 nuclei,
   respectively. We used a multistep approach to delineate cell types
   based on their genetic and transcriptional states. To distinguish
   nuclei as tumor or tumor microenvironment (TME)-derived, we merged,
   normalized, and clustered the datasets, assigning initial cell-type
   classifications to each cluster using literature-derived marker
   signatures.[71]^4^,[72]^8^,[73]^9^,[74]^10 This approach identified
   major cell types, including microglia, oligodendrocytes, neurons,
   astrocytes, endothelial cells, pericytes, and T cells ([75]Figures S1A
   and S1B). Using microglia and oligodendrocytes as non-malignant
   references, we inferred genome-wide copy-number alterations (CNAs) from