INTEGRATED SINGLE-CELL MUTATION, GENE EXPRESSION AND ISOFORM ANALYSIS TO DECONVOLVE ACUTE MYELOID LEUKEMIA HETEROGENEITY
type: CreativeWork
description: Acute myeloid leukemia (AML) is an aggressive cancer arising from the hematopoietic stem cell (HSC). As other tumor types, AMLs are characterized by multiple and interconnected levels of intra-tumor heterogeneity, including genetic (DNA mutations), phenotypic (transcriptional patterns) and ecological (interactions with host immune-cells) diversity. Emerging evidence suggest that intra-tumor heterogeneity impacts directly on leukemogenesis, disease prognosis and sensitivity/resistance to available treatments. How the different layers of intra-tumoral heterogeneity interact with each other and shape the different leukemia phenotypes at single-cell level, however, is still missing. One major limit is the lack of technologies allowing ecosystem-wide characterization of tumor samples, including the simultaneous multiomic analyses of both malignant and immune populations at single-cell level. In this work, we have developed a novel high-throughput multiomics approach to integrate gene mutation, expression and isoform information at single-cell resolution. SCM-seq (Single Cell and Molecule sequencing) combines high- throughput droplet-based scRNA-seq to Nanopore single-molecule sequencing of full- length whole transcriptome and enriched mutated transcripts. This technology allows the integration at single cell-level of expression profiles and lineage-imputation (from scRNA-seq data) with mutation burden and transcript isoform diversity (from Nanopore data). We have applied this methodology to the analysis of three AML samples sharing a mutation in a spliceosome factor, with the aim to investigate how phenotypic heterogeneity is related to genetic complexity in both the malignant and immune compartments of a coherent AML subgroup. Results showed that SCM-seq allows multiomic characterization at single-cell level with sufficiently high throughput to represent sample complexity. We identified mutations at cell-level with high sensitivity and were able to stratify groups of ce…
abstract: Acute myeloid leukemia (AML) is an aggressive cancer arising from the hematopoietic stem cell (HSC). As other tumor types, AMLs are characterized by multiple and interconnected levels of intra-tumor heterogeneity, including genetic (DNA mutations), phenotypic (transcriptional patterns) and ecological (interactions with host immune-cells) diversity. Emerging evidence suggest that intra-tumor heterogeneity impacts directly on leukemogenesis, disease prognosis and sensitivity/resistance to available treatments. How the different layers of intra-tumoral heterogeneity interact with each other and shape the different leukemia phenotypes at single-cell level, however, is still missing. One major limit is the lack of technologies allowing ecosystem-wide characterization of tumor samples, including the simultaneous multiomic analyses of both malignant and immune populations at single-cell level. In this work, we have developed a novel high-throughput multiomics approach to integrate gene mutation, expression and isoform information at single-cell resolution. SCM-seq (Single Cell and Molecule sequencing) combines high- throughput droplet-based scRNA-seq to Nanopore single-molecule sequencing of full- length whole transcriptome and enriched mutated transcripts. This technology allows the integration at single cell-level of expression profiles and lineage-imputation (from scRNA-seq data) with mutation burden and transcript isoform diversity (from Nanopore data). We have applied this methodology to the analysis of three AML samples sharing a mutation in a spliceosome factor, with the aim to investigate how phenotypic heterogeneity is related to genetic complexity in both the malignant and immune compartments of a coherent AML subgroup. Results showed that SCM-seq allows multiomic characterization at single-cell level with sufficiently high throughput to represent sample complexity. We identified mutations at cell-level with high sensitivity and were able to stratify groups of ce…
author: CAPRIOLI, CHIARA
language: eng
keywords: acute myeloid leukemia, multiomic, single-cell sequencing, Settore MED/04 - Patologia Generale
date published: 2022-12-16
date modified: 2026-07-27T20:18:43Z
provider: Università degli Studi di Milano
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Università degli Studi di Milano

PropertyValue
property ID: Handle
value: https://hdl.handle.net/2434/946325

PropertyValue
property ID: DOI
value: 10.13130/caprioli-chiara_phd2022-12-16