Inducing somatic cells into pluripotent stem cells is an important platform to study the mechanism of early embryonic development

CORN 2.0 - Condition Orientated Regulatory Networks 2.0

Gene regulation is a fundamental process that allows organisms to adapt to their environment and increase complexity through the action of nucleic acid-binding proteins (NBPs), such as transcription factors (TFs), which regulate specific sets of genes under distinct conditions. These regulatory interactions form transcriptional regulatory networks (TRNs), which can be further broken down into transcriptional regulatory sub-networks (TRSNs) centered around individual TFs. TRSNs are more stable and practical for analysis, making them ideal for studying gene regulation under specific conditions. Condition-Oriented Regulatory Networks (CORN, https://qinlab.sysu.edu.cn/corn/home) is a comprehensive library of condition-based TRSNs, including those induced by natural compounds, small molecules, drug treatments, and gene perturbations. CORN 2.0 represents a significant update, associating 7540 specific conditions with 71934 TRSNs across 52 human cell lines, involving 542 transcription factors (TFs). Notably, CORN 2.0 includes 1550 natural compound-triggered TRSNs, providing a valuable resource for studying the pharmacological effects of natural products. This study demonstrates the utility of CORN in three key areas: personalized medicine, induced pluripotency transitions, and natural compound-associated pharmacology. By linking specific conditions to their corresponding TRSNs, CORN enables researchers to explore how gene regulatory networks are altered under various conditions, offering insights into disease mechanisms and potential therapeutic interventions.

The occurrence and development of induced pluripotent stem cells

The ectopic expression of four transcription factors, Oct3/4, Sox2, Klf4, and c-Myc (OSKM), known as "Yamanaka factors," can reprogram or stimulate the production of induced pluripotent stem cells (iPSCs). Although OSKM is still the gold standard, there are multiple ways to reprogram cells into iPSCs. In recent years, significant progress has been made in improving the efficiency of this technology. Ten years after the first report was published, human pluripotent stem cells have gradually been applied in clinical settings, including disease modeling, cell therapy, new drug development, and cell derivation. Here, we provide a review of the discovery of iPSCs and their applications in disease and development.

Transcriptional regulation of cancer stem cell: regulatory factors elucidation and cancer treatment strategies

Cancer stem cells (CSCs) were first discovered in the 1990s, revealing the mysteries of cancer origin, migration, recurrence and drug-resistance from a new perspective. The expression of pluripotent genes and complex signal regulatory networks are significant features of CSC, also act as core factors to affect the characteristics of CSC. Transcription is a necessary link to regulate the phenotype and potential of CSC, involving chromatin environment, nucleosome occupancy, histone modification, transcription factor (TF) availability and cis-regulatory elements, which suffer from ambient pressure. Especially, the expression and activity of pluripotent TFs are deeply affected by both internal and external factors, which is the foundation of CSC transcriptional regulation in the current research framework. Growing evidence indicates that regulating epigenetic modifications to alter cancer stemness is effective, and some special promoters and enhancers can serve as targets to influence the properties of CSC. Clarifying the factors that regulate CSC transcription will assist us directly target key stem genes and TFs, or hinder CSC transcription through environmental and other related factors, in order to achieve the goal of inhibiting CSC and tumors. This paper comprehensively reviews the traditional aspects of transcriptional regulation, and explores the progress and insights of the impact on CSC transcription and status through tumor microenvironment (TME), hypoxia, metabolism and new meaningful regulatory factors in conjunction with the latest research. Finally, we present opinions on omnidirectional targeting CSCs transcription to eliminate CSCs and address tumor resistance.

Challenges and Considerations of Preclinical Development for iPSC-Based Myogenic Cell Therapy

Cell therapies derived from induced pluripotent stem cells (iPSCs) offer a promising avenue in the field of regenerative medicine due to iPSCs' expandability, immune compatibility, and pluripotent potential. An increasing number of preclinical and clinical trials have been carried out, exploring the application of iPSC-based therapies for challenging diseases, such as muscular dystrophies. The unique syncytial nature of skeletal muscle allows stem/progenitor cells to integrate, forming new myonuclei and restoring the expression of genes affected by myopathies. This characteristic makes genome-editing techniques especially attractive in these therapies. With genetic modification and iPSC lineage specification methodologies, immune-compatible healthy iPSC-derived muscle cells can be manufactured to reverse the progression of muscle diseases or facilitate tissue regeneration. Despite this exciting advancement, much of the development of iPSC-based therapies for muscle diseases and tissue regeneration is limited to academic settings, with no successful clinical translation reported. The unknown differentiation process in vivo, potential tumorigenicity, and epigenetic abnormality of transplanted cells are preventing their clinical application. In this review, we give an overview on preclinical development of iPSC-derived myogenic cell transplantation therapies including processes related to iPSC-derived myogenic cells such as differentiation, scaling-up, delivery, and cGMP compliance. And we discuss the potential challenges of each step of clinical translation. Additionally, preclinical model systems for testing myogenic cells intended for clinical applications are described.

Ageing Skeletal Muscle: The Ubiquitous Muscle Stem Cell

In 1999, in a review by Beardsley, the potential of adult stem cells, in repair and regeneration was heralded (Beardsley Sci Am 281:30-31, 1999). Since then, the field of regenerative medicine has grown exponentially, with the capability of restoring or regenerating the function of damaged, diseased or aged human tissues being an underpinning motivation. If successful, stem cell therapies offer the potential to treat, for example degenerative diseases. In the subsequent 20 years, extensive progress has been made in the arena of adult stem cells (for a recent review see (Zakrzewski et al. Stem Cell Res Ther 10:68, 2019)). Prior to the growth of the adult stem cell research arena, much focus had been placed on the potential of embryonic stem cells (ESCs). The first research revealing the potential of these cells was published in 1981, when scientists reported the ability of cultured stem cells from murine embryos, to not only self-renew, but to also become all cells of the three germ layers of the developing embryo (Evans and Kaufman Nature 292:154-156, 1981), (Martin Proc Natl Acad Sci U S A 78:7634-7638, 1981). It took almost 20 years, following these discoveries, for this technology to translate to human ESCs, using donated human embryos. In 1998, Thomson et al. reported the creation of the first human embryonic cell line (Thomson et al. Science 282:1145-1147, 1998). However, research utilising human ESCs was hampered by ethical and religious constraints and indeed in 2001 George W. Bush restricted US research funding to human ESCs, which had already been banked. The contentious nature of this arena perhaps facilitated the use of and the research potential for adult stem cells. It is beyond the scope of this review to focus on ESCs, although their potential for enhancing our understanding of human development is huge (for a recent review see (Cyranoski Nature 555:428-430, 2018)). Rather, although ESCs and their epigenetic regulation will be introduced for background understanding, the focus will be on stem cells more generally, the role of epigenetics in stem cell fate, skeletal muscle, skeletal muscle stem cells, the impact of ageing on muscle wasting and the mechanisms underpinning loss, with a focus on epigenetic adaptation.

Oncofetal proteins and cancer stem cells

Cancer stem cells (CSCs) are considered as a small population of cells with stem-like properties within the tumor bulk, and are largely responsible for tumor recurrence, metastasis, and therapy resistance. CSCs share critical features with embryonic stem cells (ESCs). The pluripotent transcription factors (TFs) and developmental signaling pathways of ESCs are invariably hijacked by CSCs termed ‘oncofetal drivers’ in many cancers, which are rarely detectable in adult tissues. The unique expression pattern makes oncofetal proteins ideal therapeutic targets in cancer treatment. Therefore, elucidation of oncofetal drivers in cancers is critical for the development of effective CSCs-directed therapy. In this review, we summarize the common pluripotent TFs such as OCT4, SOX2, NANOG, KLF4, MYC, SALL4, and FOXM1, as well as the development signaling including Wnt/β-catenin, Hedgehog (Hh), Hippo, Notch, and TGF-β pathways of ESCs and CSCs. We also describe the newly identified oncofetal proteins that drive the self-renewal, plasticity, and therapy-resistance of CSCs. Finally, we explore how the clinical implementation of targeting oncofetal drivers, including small-molecule inhibitors, vaccines, antibodies, and CAR-T (chimeric antigen receptor T cell) can facilitate the development of CSCs-directed therapy.