Biology subjects

Jakatdar, A.

Publications and source records attributed to Jakatdar, A..

3 recordsLinked to original sources

bioRxiv2025

Deriving longitudinal tumor phylogenies from single-cell sequencing data

Tumors evolve over time and in response to treatment, leading to changes in the proportions of clones within the tumor. Single-cell sequencing of tumor samples from multiple timepoints enables the reconstruction of clonal evolution and tracking of temporal changes in tumor composition. However, the high rates of missing data in single-cell sequencing complicate evolutionary analyses, and can lead to implausible conclusions, such as the reappearance of extinct clones. We introduce PO_SCPLOWHYLLOCHRONC_SCPLOW, an algorithm that builds a longitudinal phylogeny from cancer cells sequenced from multiple timepoints and evaluates whether the constraints on clonal proportions imposed by longitudinal sampling are well supported by the data. PO_SCPLOWHYLLOCHRONC_SCPLOW relies on a novel mathematical formulation of a longitudinal perfect phylogeny, an extension of the perfect phylogeny model that is widely used in cancer evolution. We show that PO_SCPLOWHYLLOCHRONC_SCPLOW outperforms existing phylogeny inference methods on simulated single-cell sequencing data. Applied to longitudinal single-cell DNA sequencing data from an acute myeloid leukemia (AML) patient, PO_SCPLOWHYLLOCHRONC_SCPLOW constructs a longitudinal phylogeny containing rare cancer clones that persist through multiple cycles of targeted drug treatment, a crucial finding missed by existing phylogeny inference methods. The PO_SCPLOWHYLLOCHRONC_SCPLOW statistical test supports the presence of these rare clones.

genomics↗

bioRxiv2024

Genomic evolution of pancreatic cancer at single-cell resolution

We adapted a previously developed targeted single-nucleus DNA sequencing (snDNA-seq) method and constructed a new suite of computational analysis tools to study 137,491 single-nucleus DNA libraries from 24 pancreatic cancers collected under a variety of clinical scenarios including early and late diagnoses, different metastatic sites and before- and after-treatment. We refined the mutational landscape of pancreatic cancer by capturing events missed by bulk sequencing, and validated the evolution pattern of early fixation of driver single-nucleotide variants (SNVs) followed by generation of intratumoral heterogeneity for copy number variations (CNVs). Intertumoral convergent evolution was common, including subclonal inactivation of TGF-{beta} pathway by mutating various components of it; intratumoral convergence was rarely observed, likely due to strong selective force in pancreatic cancer development. Continuous evolution was frequently seen manifesting as CNVs. In the context of non-targeted treatments, no particular pattern was found across metastases or through treatment. In six pancreatic cancers with germline BRCA2 mutation, we discovered varied timing of biallelic inactivation of BRCA2, which sculpted different evolutionary trajectories and could presumably contribute to differential response to treatment. As the first large-scale application of targeted snDNA-seq on pancreatic cancer, this work provides a sample processing and computational analysis pipeline that warrants further clinical utility.

cancer biology↗

bioRxiv2024

Mechanism of neurodegeneration mediated by clonal inflammatory microglia

Langerhans cell Histiocytosis (LCH) and Erdheim-Chester disease (ECD) are clonal myeloid disorders, associated with MAP-Kinase activating mutations and an increased risk of neurodegeneration. Surprisingly, we found pervasive PU.1+ microglia mutant clones across the brain of LCH and ECD patients with and without neurological symptoms, associated with microgliosis, reactive astrocytosis, and neuronal loss. The disease predominated in the grey nuclei of the rhombencephalon, a topography attributable to a local proliferative advantage of mutant microglia. Presence of clinical symptoms was associated with a longer evolution of the disease and a larger size of PU.1+ clones (p= 0.0003). Genetic lineage tracing of PU.1+ clones suggest a resident macrophage lineage or a bone marrow precursor origin depending on patients. Finally, a CSF1R-inhibitor depleted mutant microglia and limited neuronal loss in mice suggesting an alternative to MAPK inhibitors. These studies characterize a progressive neurodegenerative disease, caused by clonal proliferation of inflammatory microglia (CPIM), with a decade(s)-long preclinical stage of incipient disease that represent a therapeutic window for prevention of neuronal death.

immunology↗