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Despite the pivotal role of cytotoxic T lymphocytes (CTLs) in anti-tumor immunity, a substantial proportion of CTL-rich hepatocellular carcinoma (HCC) patients experience early relapse or immunotherapy resistance. However, spatial immune variations impacting the heterogeneous clinical outcomes of CTL-rich HCCs remain poorly understood. Here, we compared the single-cell and spatial landscapes of 20 CTL-rich HCCs with distinct prognoses using multiplexed in situ staining and validated the prognostic value of myeloid spatial patterns in a cohort of 386 patients.

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StarTrack: Mapping Cellular Fates with Inheritable Color Codes.

Methods Mol Biol

January 2025

Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain.

StarTrack is a powerful multicolor genetic tool designed to unravel cellular lineages arising from neural progenitor cells (NPCs). This innovative technique, based on retrospective clonal analysis and built upon the PiggyBac system, creates a unique and inheritable "color code" within NPCs. Through the stochastic integration of 12 distinct plasmids encoding six fluorescent proteins, StarTrack enables precise and comprehensive tracking of cellular fates and progenitor potentials.

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Multicolor Cell Lineage Tracing Using MAGIC Markers Strategies.

Methods Mol Biol

January 2025

Institute for Neuroscience of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France.

Multicolor MAGIC Markers strategies are useful lineage tracing tools to study brain development at a multicellular scale. In this chapter, we describe an in utero electroporation method to simultaneously label multiple neighboring progenitors and their respective progeny using these multicolor reporters. In utero electroporation enables the introduction of any gene of interest into embryonic neural progenitors lining the brain ventricles through a simple pipeline consisting of a micro-injection followed by the application of electrical pulses.

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A Simple Method to Analyze Context- and Tissue-Specific Cis-Regulatory Modulations of Homeotic (HOX) Genes Using ChIP.

Methods Mol Biol

January 2025

Department of Integrative Biology and Physiology, Medical School, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.

Homeobox genes (HOX), the master regulators, deploy a unique set of target genes to coordinate and orchestrate the spatiotemporal development of an organism. HOX encoded transcriptional factors regulate the expression of target genes by binding to the specific sequences on the genome. Chromatin Immunoprecipitation (ChIP) and Chromatin Immunoprecipitation with Sequencing (ChIP-Seq) are widely used to map and understand specific gene locus and global regulatory regions on the genome.

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In our previous study, we identified a Short Interspersed Nuclear Element Retrotransposon Insertion Polymorphism (SINE-RIP) within the 3' untranslated region (3'UTR) of the Phospholipase A2 Group XVI (PLA2G16) gene, which is essential in lipid metabolism. In this study, we confirmed the presence of this 280 bp SINE insertion and examined its distribution across ten distinct pig breeds using PCR and sequencing. Subsequently, RT-PCR was employed to determine its potential for co-transcription.

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