Rissler, V. | bioRxiv Science

bioRxiv2025

The cellular state space of AML unveils novel NPM1 subtypes with distinct clinical outcomes and immune evasion properties

Acute myeloid leukemia (AML) is a genetically and cellularly heterogeneous disease. We characterized 120 AMLs using genomic and transcriptomic analyses, including single-cell RNA sequencing. Our results reveal an extensive cellular heterogeneity that distorts the bulk transcriptomic profiles. Selective examination of the transcriptional signatures of >90,000 immature AML cells identified four main clusters, thereby extending current genomic classification of AML. Notably, NPM1 mutated AML could be stratified into two novel, clinically relevant classes, with NPM1class I associated with downregulation of MHC class II and excellent survival following hematopoietic stem cell transplantation (HSCT). NPM1class II was instead associated with resistance to allogeneic T cells in an ex vivo co culture assay, and importantly, dismal survival following HSCT. These findings provide new insights into the cellular state space of AML, define new diagnostic entities, and highlight potential therapeutic intervention points. Key PointsO_LIThe bulk transcriptional profiles of AML are mainly driven by a diverse set of cellular signatures. C_LIO_LISingle cell RNA-sequencing of the most common AML subtypes reveals marked heterogeneity extending beyond current genomic classification schemes. C_LIO_LINPM1-mutated AML can be divided into two new classes, with distinct immune evasion mechanisms and survival after transplantation. C_LI

cancer biology↗

bioRxiv2019

Alterations of the pro-survival Bcl-2 protein interactome in breast cancer at the transcriptional, mutational and structural level

Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulates programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stresses, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role in homeostasis and tumorigenesis coupled with progress in their structural elucidation, has led to consider pro-survival Bcl-2 proteins as therapeutic targets.\n\nA better understanding of the transcriptomic level, mutational status and molecular mechanism underlying pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery, targeting these proteins. Here, we shed light on pro-survival Bcl-2 proteins in breast cancer by proposing a multiscale bioinformatic approach. We analyzed the changes in expression of the Bcl-2 proteins and their BH3-containing interactors, in breast cancer samples. We then studied, at the structural level, a selection of interactions, also accounting for effects induced by mutations found in the breast cancer samples. We identified the complexes between the up-regulated BCL2A1 and two down-regulated BH3-only candidates (HRK and NR4A1) as targets associated with reduced apoptosis in breast cancer samples, which could deserve future experimental validation. We predicted as damaging mutations altering protein stability L99R, M75R, along with Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.

bioinformatics↗