Biology subjects

Nam, A. S.

Publications and source records attributed to Nam, A. S..

5 recordsLinked to original sources

bioRxiv2026

Targeted sequencing of mutations via RNA-templated gap filling of oligonucleotides for single-cell RNA-seq

We describe a method for targeted sequencing of expressed mutations in single cells. The approach exploits the reverse transcriptase and nick translation activities of the Bst DNA polymerase (Full Length) from Bacillus stearothermophilus (BstFL) to perform an RNA-templated gap filling and ligation between flanking probes. Integrated with probe-based single cell RNAseq workflows, it enables simultaneous whole transcriptomic and multiplexed mutation profiling from the same cell, overcoming key limitations of mutation detection in existing scRNA-seq approaches.

molecular biology↗

bioRxiv2022

Type 1 interferon remodels normal and neoplastic hematopoiesis in human

Inflammation perturbs evolutionary dynamics of hematopoietic stem cell (HSC) clones in clonal hematopoiesis and myeloid neoplasms. We studied HSCs, progenitors and immune cells from patients with myeloproliferative neoplasm (MPN) at baseline and following interferon- (IFN) treatment, the only MPN therapy to deplete clonal stem cells. We focused on essential thrombocythemia, an informative model of early-phase neoplastic hematopoiesis. We integrated somatic genotyping, transcriptomes, immunophenotyping, and chromatin accessibility across single cells. IFN simultaneously activated HSCs into two polarized states, a lymphoid progenitor expansion associated with an anti-inflammatory state and an IFN-specific inflammatory granulocytic progenitor (IGP) state derived directly from HSCs. The augmented lymphoid differentiation balanced the typical MPN-induced myeloid bias, associated with normalized blood counts. Clonal fitness upon IFN exposure was due to resistance of clonal stem cells to differentiate into IGPs. These results support a paradigm wherein inflammation perturbs clonal dynamics by HSC induction into the precipitous IGP differentiation program. One-Sentence SummaryInflammation accelerates clonal evolution by driving stem cell differentiation into an alternate interferon--induced progenitor state.

cancer biology↗

bioRxiv2022

Using the Dynamic Forward Scattering Signal for Optical Coherence Tomography based Blood Flow Quantification

To our knowledge, all existing optical coherence tomography approaches for quantifying blood flow, whether Doppler-based or decorrelation-based, analyze light that is back-scattered by moving red blood cells (RBCs). This work investigates the potential advantages of basing these measurements on light that is forward-scattered by RBCs, i.e., by looking at the signals back-scattered from below the vessel. We show experimentally that this results in a flowmetry measure that is insensitive to vessel orientation for vessels that are approximately orthogonal to the imaging beam. We further provide proof-of-principle demonstrations that DFS can be used to measure flow in human retinal and choroidal vessels.

bioengineering↗

bioRxiv2022

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Somatic mutations in cancer genes have been ubiquitously detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, mutated and wildtype cells are morphologically and phenotypically similar, limiting the ability to link genotypes with cellular phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing the mutation with transcriptomes and methylomes in stem and progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations resulted in myeloid over lymphoid bias, and in expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate. We observed dysregulated expression of lineage and leukemia stem cell markers. DNMT3A R882 led to preferential hypomethylation of polycomb repressive complex 2 targets and a specific sequence motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A R882 mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics pave the road to defining the downstream consequences of mutations that drive human clonal mosaicism.

cancer biology↗

bioRxiv2018

High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations

Defining the transcriptomic identity of clonally related malignant cells is challenging in the absence of cell surface markers that distinguish cancer clones from one another or from admixed non-neoplastic cells. While single-cell methods have been devised to capture both the transcriptome and genotype, these methods are not compatible with droplet-based single-cell transcriptomics, limiting their throughput. To overcome this limitation, we present single-cell Genotyping of Transcriptomes (GoT), which integrates cDNA genotyping with high-throughput droplet-based single-cell RNA-seq. We further demonstrate that multiplexed GoT can interrogate multiple genotypes for distinguishing subclonal transcriptomic identity. We apply GoT to 26,039 CD34+ cells across six patients with myeloid neoplasms, in which the complex process of hematopoiesis is corrupted by CALR-mutated stem and progenitor cells. We define high-resolution maps of malignant versus normal hematopoietic progenitors, and show that while mutant cells are comingled with wildtype cells throughout the hematopoietic progenitor landscape, their frequency increases with differentiation. We identify the unfolded protein response as a predominant outcome of CALR mutations, with significant cell identity dependency. Furthermore, we identify that CALR mutations lead to NF-{kappa}B pathway upregulation specifically in uncommitted early stem cells. Collectively, GoT provides high-throughput linkage of single-cell genotypes with transcriptomes and reveals that the transcriptional output of somatic mutations is heavily dependent on the native cell identity.

cancer biology↗