Harnessing orthogonal recombinases to decipher cell fate with enhanced precision

Ductal or Ngn3+ cells do not contribute to adult pancreatic islet beta-cell neogenesis in homeostasis

The adult pancreatic ducts have long been proposed to contain rare progenitors, some of which expressing Ngn3, that generate new beta cells in endocrine-islet homeostasis. Due to their postulated rarity and the lack of definitive markers, the existence or absence of ductal endocrine progenitors remains unsettled despite many studies. Genetic lineage tracing of ductal cells or Ngn3+ cells with currently available CreER drivers has been complicated by off-target labeling of pre-existing beta cells. Here, using dual-recombinase-mediated intersectional genetic strategy and newly-derived Ngn3-2A-CreER and Hnf1b-2A-CreER knock-in drivers, we succeeded in specifically labeling Ngn3-positive cells and Hnf1b-positive ductal cells without marking pre-existing beta cells. These data revealed no evidence of de novo generation of insulin-producing beta cells from ductal cells or endogenous Ngn3-positive cells in the adult pancreas during homeostasis.

ASTROCYTES AND ALCOHOL THROUGHOUT THE LIFESPAN

Evidence for involvement of astrocytes in several neurodegenerative disorders and in drug addiction has been emerging over the last two decades, but only in recent years have astrocytes been investigated for their roles in alcohol use disorder (AUD). As a result, there is a need to evaluate existing preclinical literature supporting involvement of astrocytes in the effects of alcohol exposure. Here we review emerging evidence about responses of astrocytes to alcohol, and the contributions of astrocytes to the development of AUD. We review studies of single-cell RNA sequencing with a focus on alcohol and astrocyte heterogeneity, astrocyte reactivity, and the role of astrocytes in remodeling the extracellular matrix. Effects of alcohol on astrocyte-modulated synaptic transmission are also discussed emphasizing studies never reviewed before. Since astrocytes play essential roles in brain development, we review recent research on the role of astrocytes in fetal alcohol spectrum disorders (FASD) which may also shed light on fetal development of psychiatric disorders that have a high prevalence in individuals affected by FASD. Finally, this review highlights gaps in knowledge about astrocyte biology and alcohol that need further research. Particularly, the dire need to identify astrocyte subpopulations and molecules that are susceptible to alcohol exposure and may be targets for therapeutic intervention.

Pushing the frontiers of babesiosis research: in vitro culture and gene editing

Babesiosis is a tick-borne parasitic disease that poses a significant risk to both animal and human health. A comprehensive understanding of Babesia biology necessitates the application of advanced laboratory techniques. This review explores recent advancements in gene editing technologies of Babesia, emphasizing the foundational importance of in vitro culture systems. We highlight the historical challenges encountered in establishing effective in vitro culture and discuss the need for optimizing these methods to enhance gene editing efficiency. Here, we describe recent progress in Babesia transfection, different gene manipulation systems, and the applications of gene editing. This review aims to provide essential insights and technical guidance for future studies in Babesia genetics, highlighting the transformative potential of gene manipulation in combating this important parasitic disease.

Exploring cell death pathways in oral cancer: mechanisms, therapeutic strategies, and future perspectives

Oral squamous cell carcinoma (OSCC) represents a significant global health challenge, characterized by aggressive progression and poor therapeutic response despite advances in treatment modalities. This review provides a comprehensive analysis of diverse cell death mechanisms in OSCC, encompassing traditional pathways (apoptosis, autophagy, and necrosis), newly characterized mechanisms (ferroptosis, pyroptosis, and necroptosis), and emerging pathways (cuproptosis, anoikis, parthanatos, and entosis). By examining the molecular basis of these pathways, particularly the crucial roles of p53 signaling and miRNA regulation, we highlight how their dysregulation contributes to treatment resistance and tumor progression. The review synthesizes recent evidence demonstrating the complex interplay between these ten distinct cell death mechanisms and their impact on the tumor microenvironment and immune response. We evaluate innovative therapeutic approaches that target these pathways, including novel small molecules, combination strategies, and immunomodulatory treatments that exploit specific cell death mechanisms to enhance therapeutic efficacy. Special attention is given to emerging personalized medicine strategies that consider individual tumor characteristics and cell death pathway profiles. By integrating current challenges with future research directions, this review provides a framework for developing more effective treatments that can leverage multiple cell death pathways to overcome therapy resistance and improve outcomes for oral cancer patients.

The landscape of cell lineage tracing

Cell fate changes play a crucial role in the processes of natural development, disease progression, and the efficacy of therapeutic interventions. The definition of the various types of cell fate changes, including cell expansion, differentiation, transdifferentiation, dedifferentiation, reprogramming, and state transitions, represents a complex and evolving field of research known as cell lineage tracing. This review will systematically introduce the research history and progress in this field, which can be broadly divided into two parts: prospective tracing and retrospective tracing. The initial section encompasses an array of methodologies pertaining to isotope labeling, transient fluorescent tracers, non-fluorescent transient tracers, non-fluorescent genetic markers, fluorescent protein, genetic marker delivery, genetic recombination, exogenous DNA barcodes, CRISPR-Cas9 mediated DNA barcodes, and base editor-mediated DNA barcodes. The second part of the review covers genetic mosaicism, genomic DNA alteration, TCR/BCR, DNA methylation, and mitochondrial DNA mutation. In the final section, we will address the principal challenges and prospective avenues of enquiry in the field of cell lineage tracing, with a particular focus on the sequencing techniques and mathematical models pertinent to single-cell genetic lineage tracing, and the value of pursuing a more comprehensive investigation at both the spatial and temporal levels in the study of cell lineage tracing.

Lineage tracing of pancreatic cells for mechanistic and therapeutic insights

Recent advances in lineage-tracing technologies have significantly improved our understanding of pancreatic cell biology, particularly in elucidating the ontogeny and regenerative capacity of pancreatic cells. A deeper appreciation of the mechanisms underlying pancreatic cell identity and plasticity holds the potential to inform the development of new therapeutic modalities for conditions such as diabetes and pancreatitis. With this goal in mind, here we summarize advances, challenges, and future directions in tracing pancreatic cell origins and fates using lineage-tracing technologies. Given their essential role for blood glucose regulation, we pay particular attention on the insights gained from endocrine cells, especially β-cells.

Engineered extrachromosomal oncogene amplifications promote tumorigenesis

Focal gene amplifications are among the most common cancer-associated mutations1 but have proven challenging to engineer in primary cells and model organisms. Here we describe a general strategy to engineer large (more than 1 Mbp) focal amplifications mediated by extrachromosomal DNAs (ecDNAs)2 in a spatiotemporally controlled manner in cells and in mice. By coupling ecDNA formation with expression of selectable markers, we track the dynamics of ecDNA-containing cells under physiological conditions and in the presence of specific selective pressures. We also apply this approach to generate mice harbouring Cre-inducible Myc- and Mdm2-containing ecDNAs analogous to those occurring in human cancers. We show that the engineered ecDNAs spontaneously accumulate in primary cells derived from these animals, promoting their proliferation, immortalization and transformation. Finally, we demonstrate the ability of Mdm2-containing ecDNAs to promote tumour formation in an autochthonous mouse model of hepatocellular carcinoma. These findings offer insights into the role of ecDNA-mediated gene amplifications in tumorigenesis. We anticipate that this approach will be valuable for investigating further unresolved aspects of ecDNA biology and for developing new preclinical immunocompetent mouse models of human cancers harbouring specific focal gene amplifications.

Identification of Postn+ periosteal progenitor cells with bone regenerative potential

Bone contains multiple pools of skeletal stem/progenitor cells (SSPCs), and SSPCs in periosteal compartments are known to exhibit higher regenerative potential than those in BM and endosteal compartments. However, the in vivo identity and hierarchical relationships of periosteal SSPCs (P-SSPCs) remain unclear due to a lack of reliable markers to distinguish BM SSPCs and P-SSPCs. Here, we found that periosteal mesenchymal progenitor cells (P-MPs) in periosteum can be identified based on Postn-CreERT2 expression. Postn-expressing periosteal subpopulation produces osteolineage descendants that fuel bones to maintain homeostasis and support regeneration. Notably, Postn+ P-MPs are likely derived from Gli1+ skeletal stem cells (SSCs). Ablation of Postn+ cells results in impairments in homeostatic cortical bone architecture and defects in fracture repair. Genetic deletion of Igf1r in Postn+ cells dampens bone fracture healing. In summary, our study provides a mechanistic understanding of bone regeneration through the regulation of region-specific Postn+ P-MPs.

Application of New Lineage Tracing Techniques in Cardiovascular Development and Physiology

Cardiovascular disease has been the leading cause of mortality and morbidity worldwide in the past 3 decades. Multiple cell lineages undergo dynamic alternations in gene expression, cell state determination, and cell fate conversion to contribute, adapt, and even modulate the pathophysiological processes during disease progression. There is an urgent need to understand the intricate cellular and molecular underpinnings of cardiovascular cell development in homeostasis and pathogenesis. Recent strides in lineage tracing methodologies have revolutionized our understanding of cardiovascular biology with the identification of new cellular origins, fates, plasticity, and heterogeneity within the cardiomyocyte, endothelial, and mesenchymal cell populations. In this review, we introduce the new technologies for lineage tracing of cardiovascular cells and summarize their applications in studying cardiovascular development, diseases, repair, and regeneration.

Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts

Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.

Protective fibroblastic niches in secondary lymphoid organs

Fibroblastic reticular cells (FRCs) are specialized fibroblasts of secondary lymphoid organs that provide the structural foundation of the tissue. Moreover, FRCs guide immune cells to dedicated microenvironmental niches where they provide lymphocytes and myeloid cells with homeostatic growth and differentiation factors. Inflammatory processes, including infection with pathogens, induce rapid morphological and functional adaptations that are critical for the priming and regulation of protective immune responses. However, adverse FRC reprogramming can promote immunopathological tissue damage during infection and autoimmune conditions and subvert antitumor immune responses. Here, we review recent findings on molecular pathways that regulate FRC-immune cell crosstalk in specialized niches during the generation of protective immune responses in the course of pathogen encounters. In addition, we discuss how FRCs integrate immune cell-derived signals to ensure protective immunity during infection and how therapies for inflammatory diseases and cancer can be developed through improved understanding of FRC-immune cell interactions.

Lineage Tracing Identifies Dynamic Contribution of Endothelial Cells to Cardiac Valve Mesenchyme During Development

Heart valve disease is an important cause of morbidity and mortality among cardiac patients worldwide. However, the pathogenesis of heart valve disease is not clear, and a growing body of evidence hints at the importance of the genetic basis and developmental origins of heart valve disease. Therefore, understanding the developmental mechanisms that underlie the formation of heart valves has important implications for the diagnosis, prevention, and treatment of congenital heart disease. Endothelial to mesenchymal transition is a key step in initiating cardiac valve development. The dynamic changes in the relative localization and proportion of different cell sources in the heart valve mesenchymal population are still not fully understood. Here, we used the Cdh5-CreER;R26R-tdTomato mouse line to trace endocardial cushion-derived endothelial cells to explore the dynamic contribution of these cells to each layer of the valve during valve development. This is beneficial for elaborating on the role of endocardial cells in the process of valve remodeling from a precise angle.

Immortalization and transformation of primary cells mediated by engineered ecDNAs

Focal gene amplifications are among the most common cancer-associated mutations, but their evolution and contribution to tumorigenesis have proven challenging to recapitulate in primary cells and model organisms. Here we describe a general approach to engineer large (>1 Mbp) focal amplifications mediated by extrachromosomal circular DNAs (ecDNAs, also known as "double minutes") in a spatiotemporally controlled manner in cancer cell lines and in primary cells derived from genetically engineered mice. With this strategy, ecDNA formation can be coupled with expression of fluorescent reporters or other selectable markers to enable the identification and tracking of ecDNA-containing cells. We demonstrate the feasibility of this approach by engineering MDM2-containing ecDNAs in near-diploid human cells, showing that GFP expression can be used to track ecDNA dynamics under physiological conditions or in the presence of specific selective pressures. We also apply this approach to generate mice harboring inducible Myc - and Mdm2 -containing ecDNAs analogous to those spontaneously occurring in human cancers. We show that the engineered ecDNAs rapidly accumulate in primary cells derived from these animals, promoting proliferation, immortalization, and transformation.

Perfect duet: Dual recombinases improve genetic resolution

As a powerful genetic tool, site-specific recombinases (SSRs) have been widely used in genomic manipulation to elucidate cell fate plasticity in vivo, advancing research in stem cell and regeneration medicine. However, the low resolution of conventional single-recombinase-mediated lineage tracing strategies, which rely heavily on the specificity of one marker gene, has led to controversial conclusions in many scientific questions. Therefore, different SSRs systems are combined to improve the accuracy of lineage tracing. Here we review the recent advances in dual-recombinase-mediated genetic approaches, including the development of novel genetic recombination technologies and their applications in cell differentiation, proliferation, and genetic manipulation. In comparison with the single-recombinase system, we also discuss the advantages of dual-genetic strategies in solving scientific issues as well as their technical limitations.

Constitutive and conditional gene knockout mice for the study of intervertebral disc degeneration: Current status, decision considerations, and future possibilities

There have been an increasing number of patients with degenerative disc diseases due to the aging population. In light of this, studies on the pathogenesis of intervertebral disc degeneration have become a hot topic, and gene knockout mice have become a valuable tool in this field of research. With the development of science and technology, constitutive gene knockout mice can be constructed using homologous recombination, zinc finger nuclease, transcription activator-like effector nuclease technology and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, and conditional gene knockout mice can be constructed using the Cre/LoxP system. The gene-edited mice using these techniques have been widely used in the studies on disc degeneration. This paper reviews the development process and principles of these technologies, functions of the edited genes in disc degeneration, advantages, and disadvantages of different methods and possible targets of the specific Cre recombinase in intervertebral discs. Recommendations for the choice of suitable gene-edited model mice are presented. At the same time, possible technological improvements in the future are also discussed.

Using a modified piggyBac transposon-combined Cre/loxP system to produce selectable reporter-free transgenic bovine mammary epithelial cells for somatic cell nuclear transfer

Transposon systems are widely used for genetic engineering in various model organisms. PiggyBac (PB) has recently been confirmed to have highly efficient transposition in the mouse germ line and mammalian cell lines. In this study, we used a modified PB transposon system mediated by PB transposase (PBase) mRNA carrying the human lactoferrin gene driven by bovine β-casein promoter to transfect bovine mammary epithelial cells (BMECs), and the selectable reporter in two stable transgenic BMEC clones was removed using cell-permeant Cre recombinase. These reporter-free transgenic BMECs were used as donor cells for somatic cell nuclear transfer (SCNT) and exhibited a competence of SCNT embryos similar to stable transgenic BMECs and nontransgenic BMECs. The comprehensive information from this study provided a modified approach using an altered PB transposon system mediated by PBase mRNA in vitro and combined with the Cre/loxP system to produce transgenic and selectable reporter-free donor nuclei for SCNT. Consequently, the production of safe bovine mammary bioreactors can be promoted.

Cre-loxP-mediated genetic lineage tracing: Unraveling cell fate and origin in the developing heart

The Cre-loxP-mediated genetic lineage tracing system is essential for constructing the fate mapping of single-cell progeny or cell populations. Understanding the structural hierarchy of cardiac progenitor cells facilitates unraveling cell fate and origin issues in cardiac development. Several prospective Cre-loxP-based lineage-tracing systems have been used to analyze precisely the fate determination and developmental characteristics of endocardial cells (ECs), epicardial cells, and cardiomyocytes. Therefore, emerging lineage-tracing techniques advance the study of cardiovascular-related cellular plasticity. In this review, we illustrate the principles and methods of the emerging Cre-loxP-based genetic lineage tracing technology for trajectory monitoring of distinct cell lineages in the heart. The comprehensive demonstration of the differentiation process of single-cell progeny using genetic lineage tracing technology has made outstanding contributions to cardiac development and homeostasis, providing new therapeutic strategies for tissue regeneration in congenital and cardiovascular diseases (CVDs).

Dual Cre and Dre recombinases mediate synchronized lineage tracing and cell subset ablation in vivo

Genetic technology using site-specific recombinases (SSR), such as the Cre-loxP system, has been widely employed for labelling specific cell populations and for studying their functions in vivo. To enhance the precision of cell lineage tracing and functional study, a similar SSR system termed Dre-rox has been recently used in combination with Cre-loxP. To enable more specific cell lineage tracing and ablation through dual recombinase activity, we generated two mouse lines that render Dre- or Dre+Cre-mediated recombination to excise a stop codon sequence that prevents the expression of diphtheria toxin receptor (DTR) knocked into the ubiquitously expressed and safe Rosa26 locus. Using different Dre- and Cre-expressing mouse lines, we showed that the surrogate gene reporter tdTomato and DTR were simultaneously expressed in target cells and in their descendants, and observed efficient ablation of tdTomato⁺ cells after diphtheria toxin administration. These mouse lines were used to simultaneously trace and deplete target cells of interest through the inducible expression of a reporter and DTR using dual Cre and Dre recombinases, allowing more precise and efficient study of the role of specific cell subsets within a heterogeneous population in pathophysiological conditions in vivo.