Reconstructing cell lineage trees with genomic barcoding:approaches and applications

In multicellular organisms,developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree(CLT).The reconstruction of the CLT has long been a major goal in developmental biology and other related fields.Recent technological advancements,especially those in editable genomic barcodes and single-cell high-throughput sequencing,have sparked a new wave of experimental methods for reconstructing CLTs.Here we review the existing experimental approaches to the reconstruction of CLT,which are broadly categorized as either image-based or DNA barcode-based methods.In addition,we present a summary of the related literature based on the biological insight pro-vided by the obtained CLTs.Moreover,we discuss the challenges that will arise as more and better CLT data become available in the near future.Genomic barcoding-based CLT reconstructions and analyses,due to their wide applicability and high scalability,offer the potential for novel biological discoveries,especially those related to general and systemic properties of the developmental process.

A systematic study of the determinants of protein abundance memory in cell lineage

Proteins are essential players of life activities, lntraceUular protein levels directly affect cellular functions and cell fate. Upon cell division, the proteins in the mother cell are inherited by the daughters. However, what factors and by how much they affect this epigenetic inheritance of protein abundance remains unclear. Using both computational and experimental approaches, we systematically investigated this problem. We derived an analytical expression for the dependence of protein inheritance on various factors and showed that it agreed with numerical simulations of protein production and experimental results. Our work provides a framework for quantitative studies of protein inheritance and for the potential application of protein memory manipulation.

Tumor cells undergoing direct lineage conversion to neurons: unnatural but useful?

Dear Editor, In 2011, Son et al. （2011） reported that the forced expression of selected transcription factors is sufficient to convert mouse and human fibroblasts into induced motor neurons （iMNs）. The authors used three factors （Ascll, Brn2, and Mytll） to convert fibroblasts into neuronal-like ceils. After confirming that the cells had neuronal morphology, but with absence of motor neuron markers, eight candidate transcription factors were added, which participate in various stages of motor neuron specification. As expected, a significant number of motor cells emerged with known characteristics of cultured embryonic motor neurons.

Bacteroides fragilis Supernatant Extracts Enriched in Phenylacetic Acid Induce a Cytotoxic Effect in Mammalian Cells

Bacteroides species are nearly half of the fecal flora community and some are host symbionts crucial to host nutrition and systemic immunity. Among Bacteroides species B. fragilis strains are considered to be the opportunistic ones, being the most isolated anaerobic bacteria in clinical samples. Cell-free supernatants of 65 B. fragilis strains were assayed and they were capable of inducing vacuolating phenotype on Vero cells lineage. The supernatant of the Bacteroides fragilis ATCC 23745 strain was elicited to have the strongest vacuolating effect on Vero cells monolayers and peritoneal macrophages. Some drastic cell alterations were observed, such as a general disorganization of cytoplasm and chromatin condensation, evidencing cell death. By transmission electron microscopy it was confirmed that the vacuoles observed were, in fact, swollen mitochondria. An immunocytochemical assay, TUNEL, was used to confirm this hypothesis and showed that Vero cells and peritoneal macrophages were dying by apoptotic process after exposition of B. fragilis cell-free supernatant. Physical analysis of the apoptotic factor has revealed properties similar to short-chain fatty acids. After gas chromatography and mass spectrometry analysis, phenylacetic acid (PA) was characterized as the major compound present in the most purified active fraction. We believe that the PA is responsible for the pro-apoptotic effect elicited by the supernatant of B. fragilis cultures.

Dual human iPSC-derived cardiac lineage cell-seeding extracellular matrix patches promote regeneration and long-term repair of infarcted hearts

Human pluripotent stem cell-derived cardiovascular progenitor cells (hCVPCs) and cardiomyocytes (hCMs) possess therapeutic potential for infarcted hearts;however, their efficacy needs to be enhanced. Here we tested the hypotheses that the combination of decellularized porcine small intestinal submucosal extracellular matrix (SIS-ECM) with hCVPCs, hCMs, or dual of them (Mix, 1:1) could provide better therapeutic effects than the SIS alone, and dual hCVPCs with hCMs would exert synergic effects in cardiac repair. The data showed that the SIS patch well supported the growth of hCVPCs and hCMs. Epicardially implanted SIS-hCVPC, SIS-hCM, or SIS-Mix patches at 7-day post-myocardial infarction significantly ameliorated functional worsening, ventricular dilation and scar formation at 28- and 90-day post-implantation in C57/B6 mice, whereas the SIS only mildly improved function at 90-day post-implantation. Moreover, the SIS and SIS-cell patches improved vascularization and suppressed MI-induced cardiomyocyte hypertrophy and expression of Col1 and Col3, but only the SIS-hCM and the SIS-Mix patches increased the ratio of collagen III/I fibers in the infarcted hearts. Further, the SIS-cell patches stimulated cardiomyocyte proliferation via paracrine action. Notably, the SIS-Mix had better improvements in cardiac function and structure, engraftments, and cardiomyocyte proliferation. Proteomic analysis showed distinct biological functions of exclusive proteins secreted from hCVPCs and hCMs, and more exclusive proteins secreted from co-cultivated hCVPCs and hCMs than mono-cells involving in various functional processes essential for infarct repair. These findings are the first to demonstrate the efficacy and mechanisms of mono- and dual-hCVPC- and hCM-seeding SIS-ECM for repair of infarcted hearts based on the side-by-side comparison.

Dynamic glial response and crosstalk in demyelination-remyelination and neurodegeneration processes

Multiple sclerosis is an autoimmune disease in which the immune system attacks the myelin sheath in the central nervous system.It is characterized by blood-brain barrier dysfunction throughout the course of multiple sclerosis, followed by the entry of immune cells and activation of local microglia and astrocytes.Glial cells(microglia, astrocytes, and oligodendrocyte lineage cells) are known as the important mediators of neuroinflammation, all of which play major roles in the pathogenesis of multiple sclerosis.Network communications between glial cells affect the activities of oligodendrocyte lineage cells and influence the demyelination-remyelination process.A finely balanced glial response may create a favorable lesion environment for efficient remyelination and neuroregeneration.This review focuses on glial response and neurodegeneration based on the findings from multiple sclerosis and major rodent demyelination models.In particular, glial interaction and molecular crosstalk are discussed to provide insights into the potential cell-and molecule-specific therapeutic targets to improve remyelination and neuroregeneration.

Construction of a niche-specific spinal white matter-like tissue to promote directional axon regeneration and myelination for rat spinal cord injury repair

Directional axon regeneration and remyelination are crucial for repair of spinal cord injury(SCI),but existing treatments do not effectively promote those processes.Here,we propose a strategy for construction of niche-specific spinal white matter-like tissue(WMLT)using decellularized optic nerve(DON)loaded with neurotrophin-3(NT-3)-overexpressing oligodendrocyte precursor cells.A rat model with a white matter defect in the dorsal spinal cord of the T10 segment was used.The WMLT transplantation group showed significant improvement in coordinated motor functions compared with the control groups.WMLT transplants integrated well with host spinal cord white matter,effectively addressing several barriers to directional axonal regeneration and myelination during SCI repair.In WMLT,laminin was found to promote development of oligodendroglial lineage(OL)cells by binding to laminin receptors.Interestingly,laminin could also guide linear axon regeneration via interactions with specific integrins on the axon surface.The WMLT developed here utilizes the unique microstructure and bioactive matrix of DON to create a niche rich in laminin,NT-3 and OL cells to achieve significant structural repair of SCI.Our protocol can help to promote research on repair of nerve injury and construction of neural tissues and organoids that form specific cell niches.