Missionbio

Clonal heterogeneity in acute myeloid leukemia (AML) can drive drug resistance because different clones may respond variably to treatments. Studying the evolution of these clones under the influence of therapeutic selective pressures is important for designing strategies to overcome drug resistance. Here, we used single-cell proteogenomic analysis to monitor the clonal evolution and differentiation of isocitrate dehydrogenase (*IDH*)–mutated AML in patient-derived xenografts (PDX) treated with IDH inhibitors alone or in combination with other antileukemic therapies. Furthermore, we generated mixed PDX models by coengrafting ≥2 leukemic samples into the same animal and used single-cell DNA sequencing to deconvolute their clonal composition. Using these models, we tracked clonal evolution under selective pressure from IDH inhibitors and combination therapies, identifying an association between *WT1* mutations and ivosidenib (IDH1 inhibitor) monotherapy resistance, as well as an antagonism between ivosidenib and enasidenib (IDH2 inhibitor) when tested in *IDH1*-mutated cells. Our findings demonstrate how single-cell proteogenomic analysis of PDX models can illuminate drug resistance mechanisms and inform therapeutic strategies.


Single-cell proteogenomic analysis of clonal evolution in PDX models of AML treated with IDH inhibitors

Aromatase inhibitors (AIs) are used sequentially to treat ER+ breast cancer, yet resistance limits benefit. This session integrates WES from 11 patients across three treatment timepoints (Neoletexe trial) with single-cell DNA sequencing validation to reconstruct subclonal architectures. We’ll connect rising cancer cell fraction trajectories with reduced response, contrast exemestane- vs. letrozole-resistant clones, and highlight clinically actionable alterations—spanning PI3K/AKT/mTOR, CDK4/6, DNA repair, and immune checkpoint pathways.


Clonal selection meets single-cell DNA sequencing: unveiling hormonal adaptation and AI resistance in ER+ breast cancer

Acute myeloid leukemia (AML) remains one of the most heterogeneous hematologic malignancies, both at the genetic and phenotypic levels. Despite initial responses to therapy, relapse is frequent and largely driven by a rare population of leukemic stem cells (LSC), which persist in up to 70–80% of AML cases and act as a reservoir for disease propagation and resistance. Traditional bulk approaches have provided key insights into AML biology but inherently obscure the cellular diversity that shapes disease evolution and therapeutic escape.

Here, we leveraged single-cell proteogenomics to dissect the heterogeneity of LSC at unprecedented resolution. By combining high-dimensional genotyping with a custom-designed antibody panel, we were able to simultaneously capture mutational landscapes and phenotypic profiles of stem and progenitor compartments. This approach uncovered unexpected subclonal architectures, revealed co-existing immunophenotypic states within genetically defined clones, and highlighted rare but clinically relevant LSC subsets that would have been invisible using conventional methods.

Our work illustrates how single-cell proteogenomics can bridge the gap between genotype and phenotype in AML, offering a powerful framework to better understand LSC biology, monitor minimal residual disease, and ultimately inform precision therapeutic strategies.


Dissecting leukemic stem cells at single-cell resolution: A proteogenomic approach

See how **single-cell DNA + DNA methylation + surface protein** profiling with **scTAM-seq (on Tapestri)** dissects treatment response in **MDS/AML** using **sequential patient bone-marrow samples** collected during targeted therapy.

*   **Multi-omic resolution, one assay:** scTAM-seq simultaneously profiles **somatic mutations, methylation, and protein** at single-cell resolution.
*   **Sharper cell typing:** Integrating **scTAM-seq + ADT-seq** improves **cell-type identification**, resolving subtle hematopoietic populations.
*   **Track clonal evolution:** Combining **scTAM-seq with single-cell genotyping** maps **clonal architecture** and **evolution under therapy** across **sequential samples**.

**Rethinking response metrics:** Understand **clinical response** that can occur **independent of changes in mutant allelic burden**, and implications for disease monitoring.


Deconvolution of clonal dynamics with scTAM-seq

Recent advances in single-cell profiling and targeted therapy are reshaping acute myeloid leukemia (AML) management. In this webinar, we will present results from a randomized trial of CXCR4 inhibition in AML, integrating single-cell MRD analysis and biomarker stratification. We will explore how molecular heterogeneity and CXCR4 expression inform therapeutic response and relapse risk, highlighting new opportunities for personalized patient care.


Single-Cell MRD Profiling in AML Identifies CXCR4 Expression as a Predictor of Motixafortide Response

Genetic variants,both coding and noncoding,can profoundly influence gene regulation and disease progression. Yet, systematically linking genetic variants to functional consequences with single-cell resolution remains a major challenge.

In this webinar, **Dr. Dominik Lindenhofer (EMBL Heidelberg)** will present his pioneering work on **single-cell DNA–RNA sequencing (SDR-seq)**, a breakthrough method developed to simultaneously detect hundreds of genomic variants and transcripts within the same cell. By applying SDR-seq to induced pluripotent stem cells and B cell lymphoma samples, Dr. Lindenhofer demonstrates how coding and noncoding genetic variants influence gene expression and tumorigenic signaling. SDR-seq has major clinical applications because it can help pinpoint how specific genetic variants alter gene expression to guide more precise diagnostics and targeted therapeutic strategies through single-cell analysis.


Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing

Myeloproliferative neoplasms (MPNs) driven by mutCALR present a clear therapeutic target, yet validating the *in vivo* mechanism of action (MOA) of new drugs like INCA033989 is a major challenge. Traditional bulk sequencing is critically insufficient, as it masks heterogeneous responses and cannot resolve the drug's effect on specific hematopoietic lineages. To overcome this, the deployment of a single-cell multiomic assay was essential. By combining scDNA-seq and immunophenotyping, clinical phase 1 studies (NCT05936359, NCT06034002) provided the first definitive, cell-type-specific evidence of INCA033989's activity. It uniquely demonstrated a profound, selective eradication of mutCALR+ hematopoietic stem/progenitor (HSPC) and myeloid populations, an insight impossible to gain from bulk analysis. This single-cell validation, which also captured the expansion of wild-type (WT) cells, confirms the INCA033989 mechanism of action (MOA) and highlights the necessity of single-cell multiomic assays for developing modern targeted therapies.


Biomarkers in the ERA of precision medicine: Characterizing MOA for targeted therapies using single-cell multiomics in the clinic

Hyper-IgM 1 (HIGM1) is an X-linked combined immunodeficiency that is caused by a *CD40LG* mutation that impairs communication between active CD4+ T cells and effector immune cells. This results in an average lifespan of individuals with HIGM1 to be 25 years on average. Therefore, a one-size-fits-all, long-range corrective gene editing strategy is a viable therapeutic option for this cohort of individuals.

Safety requirements of gene corrected cell and gene therapies are currently under definition by regulatory agencies, and precise characterization of gene editing outcomes at the single-cell level play an important role in IND submissions. To help cure individuals with HIGM1 and inform regulatory agencies, Daniele Canarutto, M.D., Ph.D. and team developed a scalable, GMP-compliant gene therapy that utilizes CRISPR/Cas9, a corrective homology directed repair (HDR) template coupled to a selector, and an integrase-defective lentiviral vectors (IDLV) delivery system.

In this live session, Daniele will show how the adoption of a single-cell DNA sequencing (scDNA-seq) platform, coupled with their gene editing protocol and expected gene editing outcomes, enabled the rigorous validation of their gene therapy for HIGM1. The team successfully completed their preclinical safety evaluation using a custom scDNA-seq amplicon panel covering the X-chromosome, nuclease target, and donor template for characterization of gene editing outcomes.

Results of their preclinical safety evaluation using the custom scDNA-seq assays demonstrated how unsupervised clustering distinguishes precise HDR from on-target concatemers. Crucially, Daniele will show how using scDNA-seq assays confirmed the mutual exclusivity of donor integration and wild-type loci validating targeted integration and ruling out large deletions or off-targets to support their first-in-human trials.


Single-cell DNA sequencing provides a comprehensive assessment of genomic editing outcomes of gene-corrected CD4 T-cells for treating Hyper IgM1 supporting the start of clinical trial