Yamanaka Factors Research Articles

CELL REJUVENATION AND DISEASE

Abstract Aging is characterized by the functional decline of tissues and organs and the increased risk of aging-associated disorders. Different rejuvenating interventions have been proposed to delay aging and the onset of age-associated decline and disease to extend healthspan and lifespan. These interventions include metabolic manipulation, heterochronic parabiosis, pharmaceutical administration and senescent cell ablation. As disease and aging are associated with altered epigenetic mechanisms of gene regulation, such as DNA methylation, histone modification and chromatin remodelling, and non-coding RNAs, the manipulation of these mechanisms might be central to the effectiveness of treating disease as well as age-delaying interventions. I will discuss some of the epigenetic changes that occur during disease and aging and how partial reprogramming by the Yamanaka factors might be a potential avenue to restore cell health and resilience through cellular rejuvenation programming to reverse disease, injury, and the disabilities that can occur throughout life.

Brain reboot: Enhancing neurogenesis and resilience

In this issue of Cell Stem Cell, Shen etal. investigate invivo transient expression of Yamanaka factors (YFs) during embryogenesis and an adult mouse model of Alzheimer's disease (AD)-associated amyloidosis. These studies demonstrate that transient induction of YFs may be capable of enhancing neurogenesis and offer resilience against neurodegeneration.

Research progress on reprogramming induction of small molecules

Abstract. In the fields of medicine and biology, tissue and organ transplantation is a key area of research for scientists. In order to meet the increasing demand for tissue and organ transplantation, the artificial induction of various types of tissue and organs has gradually become a research hotspot today. The gradual reprogramming of cells can generate transplanted organs without rejection reactions and enable low-cost testing of drug effects on the human body, which has broad prospects in medicine. At present, a large amount of research has been conducted on inducing organ transplantation through recoding, and a large amount of literature has been accumulated in preclinical studies, including the mechanisms and principles of its occurrence. There have been many attempts in inducing organ development in vitro, but there is no systematic summary and analysis of the relevant content. This article reviews the research progress of reprogramming to generate iPS, from the transfer of Yamanaka factors to the induction of small molecule reprogramming. Then, considering the current difficulty in screening new highly efficient inducible small molecules, this article used a reprogramming related protein.

Myc 9aaTAD activation domain binds to mediator of transcription with superior high affinity

The overexpression of MYC genes is frequently found in many human cancers, including adult and pediatric malignant brain tumors. Targeting MYC genes continues to be challenging due to their undruggable nature. Using our prediction algorithm, the nine-amino-acid activation domain (9aaTAD) has been identified in all four Yamanaka factors, including c-Myc. The predicted activation function was experimentally demonstrated for all these short peptides in transactivation assay. We generated a set of c-Myc constructs (1–108, 69–108 and 98–108) in the N-terminal regions and tested their ability to initiate transcription in one hybrid assay. The presence and absence of 9aaTAD (region 100–108) in the constructs strongly correlated with their activation functions (5-, 3- and 67-times respectively). Surprisingly, we observed co-activation function of the myc region 69–103, called here acetyl-TAD, previously described by Faiola et al. (Mol Cell Biol 25:10220–10234, 2005) and characterized in this study as a new domain collaborating with the 9aaTAD. We discovered strong interactions on a nanomolar scale between the Myc-9aaTAD activation domains and the KIX domain of CBP coactivator. We showed conservation of the 9aaTADs in the MYC family. In summary for the c-Myc oncogene, the acetyl-TAD and the 9aaTAD domains jointly mediated activation function. The c-Myc protein is largely intrinsically disordered and therefore difficult to target with small-molecule inhibitors. For the c-Myc driven tumors, the strong c-Myc interaction with the KIX domain represents a promising druggable target.

Stemness of Cancer: A Study of Triple-negative Breast Cancer From a Neuroscience Perspective.

Stemness, giving cancer cells massive plasticity enabling them to survive in dynamic (e.g. hypoxic) environments and become resistant to treatment, especially chemotherapy, is an important property of aggressive tumours. Here, we review some essentials of cancer stemness focusing on triple-negative breast cancer (TNBC), the most aggressive form of all breast cancers. TNBC cells express a range of genes and mechanisms associated with stemness, including the fundamental four "Yamanaka factors". Most of the evidence concerns the transcription factor / oncogene c-Myc and an interesting case is the expression of the neonatal splice variant of voltage-gated sodium channel subtype Nav1.5. On the whole, measures that reduce the stemness make cancer cells less aggressive, reducing their invasive/metastatic potential and increasing/restoring their chemosensitivity. Such measures include gene silencing techniques, epigenetic therapies as well as novel approaches like optogenetics aiming to modulate the plasma membrane voltage. Indeed, simply hyperpolarizing their membrane potential can make stem cells differentiate. Finally, we give an overview of the clinical aspects and exploitation of cancer/TNBC stemness, including diagnostics and therapeutics. In particular, personalised mRNA-based therapies and mechanistically meaningful combinations are promising and the emerging discipline of 'cancer neuroscience' is providing novel insights to both fundamental issues and clinical applications.

Dermal Papilla Cells: From Basic Research to Translational Applications.

As an appendage of the skin, hair protects against ultraviolet radiation and mechanical damage and regulates body temperature. It also reflects an individual's health status and serves as an important method of expressing personality. Hair loss and graying are significant psychosocial burdens for many people. Hair is produced from hair follicles, which are exclusively controlled by the dermal papilla (DP) at their base. The dermal papilla cells (DPCs) comprise a cluster of specialized mesenchymal cells that induce the formation of hair follicles during early embryonic development through interaction with epithelial precursor cells. They continue to regulate the growth cycle, color, size, and type of hair after the hair follicle matures by secreting various factors. DPCs possess stem cell characteristics and can be cultured and expanded in vitro. DPCs express numerous stemness-related factors, enabling them to be reprogrammed into induced pluripotent stem cells (iPSCs) using only two, or even one, Yamanaka factor. DPCs are an important source of skin-derived precursors (SKPs). When combined with epithelial stem cells, they can reconstitute skin and hair follicles, participating in the regeneration of the dermis, including the DP and dermal sheath. When implanted between the epidermis and dermis, DPCs can induce the formation of new hair follicles on hairless skin. Subcutaneous injection of DPCs and their exosomes can promote hair growth. This review summarizes the in vivo functions of the DP; highlights the potential of DPCs in cell therapy, particularly for the treatment of hair loss; and discusses the challenges and recent advances in the field, from basic research to translational applications.

Expansion of the neocortex and protection from neurodegeneration by in vivo transient reprogramming

Yamanaka factors (YFs) can reverse some aging features in mammalian tissues, but their effects on the brain remain largely unexplored. Here, we induced YFs in the mouse brain in a controlled spatiotemporal manner in two different scenarios: brain development and adult stages in the context of neurodegeneration. Embryonic induction of YFs perturbed cell identity of both progenitors and neurons, but transient and low-level expression is tolerated by these cells. Under these conditions, YF induction led to progenitor expansion, an increased number of upper cortical neurons and glia, and enhanced motor and social behavior in adult mice. Additionally, controlled YF induction is tolerated by principal neurons in the adult dorsal hippocampus and prevented the development of several hallmarks of Alzheimer's disease, including cognitive decline and altered molecular signatures, in the 5xFAD mouse model. These results highlight the powerful impact of YFs on neural proliferation and their potential use in brain disorders.

Application prospects of urine-derived stem cells in neurological and musculoskeletal diseases.

Urine-derived stem cells (USCs) are derived from urine and harbor the potential of proliferation and multidirectional differentiation. Moreover, USCs could be reprogrammed into pluripotent stem cells [namely urine-derived induced pluripotent stem cells (UiPSCs)] through transcription factors, such as octamer binding transcription factor 4, sex determining region Y-box 2, kruppel-like factor 4, myelocytomatosis oncogene, and Nanog homeobox and protein lin-28, in which the first four are known as Yamanaka factors. Mounting evidence supports that USCs and UiPSCs possess high potential of neurogenic, myogenic, and osteogenic differentiation, indicating that they may play a crucial role in the treatment of neurological and musculoskeletal diseases. Therefore, we summarized the origin and physiological characteristics of USCs and UiPSCs and their therapeutic application in neurological and musculoskeletal disorders in this review, which not only contributes to deepen our understanding of hallmarks of USCs and UiPSCs but also provides the theoretical basis for the treatment of neurological and musculoskeletal disorders with USCs and UiPSCs.

Regulation of proliferative potential: insights into key signaling cascades and te-lomerase functions

Cell proliferation is a fundamental biological process that underpins tissue growth, repair, and regeneration, playing a pivotal role in both normal physiology and pathological conditions. The ability of cells to proliferate is intricately controlled by regulatory networks comprising transcription factors, signaling pathways, and telomerase activity. This review delves into the molecular mechanisms that govern cell proliferation, focusing on the critical signaling cascades – PI3K/Akt, MAPK, Wnt/β-catenin, and NF-κB – which orchestrate cell cycle progression and mediate cellular responses to external stimuli. Dysregulation of these pathways is linked to numerous disorders, including cancer, where unchecked proliferation drives disease progression. Special emphasis is placed on Yamanaka factors (OCT4, SOX2, KLF4, c-MYC, NANOG, and LIN28), which are instrumental in maintaining cellular pluripotency and promoting a high proliferative potential. These factors not only reprogram somatic cells into induced pluripotent stem cells (iPSCs) but also enhance regenerative capabilities, making them indispensable tools for tissue engineering and regenerative medicine. Their interaction with core signaling pathways and their ability to influence gene networks highlight their multifaceted roles in cellular biology. Telomerase, a ribonucleoprotein traditionally recognized for its function in telomere maintenance, is revisited in this review for its non-canonical roles. Emerging evidence indicates that telomerase modulates gene expression and interacts with signaling pathways to influence proliferation. These insights expand our understanding of telomerase beyond its established role in genomic stability, positioning it as a key regulator in cellular proliferation and potential therapeutic target. This review synthesizes current knowledge on these mechanisms, emphasizing their interconnectedness and translational potential. By highlighting advances in our understanding of proliferative regulation, the article underscores the therapeutic opportunities in leveraging these pathways for regenerative medicine, tissue engineering, and oncology. The ability to modulate proliferation through targeted interventions offers promise for addressing unmet clinical needs, advancing personalized medicine, and enhancing outcomes in tissue repair and cancer therapies. As research continues to uncover novel roles and interactions within these networks, the potential for developing innovative strategies to control proliferation remains vast, heralding a new era in biomedical science.

Generation of footprint-free human induced pluripotent stem cell line (SCIKFi001-B) from cGMP grade umbilical cord-derived mesenchymal stem cells (UC-MSCs) using episomal-plasmid based reprogramming approach

UCMSCs were reprogrammed to iPSCs using Yamanaka factor bearing episomal plasmids. SCIKFi001-B exhibited pluripotency, had typical iPSC morphology and didn’t retain any residual episomal plasmid. Although karyotyping showed chromosomal translocation, this abnormality seemed to have little impact on the functionality of SCIKFi001-B since it retained its ability to differentiate to three-germ layer. While karyotypic abnormality might negate use in therapeutic and clinical settings, this line remained a valuable educational tool for iPS cell culture techniques. Finally, our study highlighted the importance of routine karyotyping on iPSC lines as abnormal karyotypes oftentimes bear no discernible effect on cell morphology nor functionality.

Viral-mediated Oct4 overexpression and inhibition of Notch signaling synergistically induce neurogenic competence in mammalian Müller glia.

Retinal Müller glia in cold-blooded vertebrates can reprogram into neurogenic progenitors to replace neurons lost to injury, but mammals lack this ability. While recent studies have shown that transgenic overexpression of neurogenic bHLH factors and glial-specific disruption of NFI family transcription factors and Notch signaling induce neurogenic competence in mammalian Müller glia, induction of neurogenesis in wildtype glia has thus far proven elusive. Here we report that viral-mediated overexpression of the pluripotency factor Oct4 ( Pou5f1 ) induces transdifferentiation of wildtype mouse Müller glia into bipolar neurons and stimulates this process synergistically in parallel with Notch loss of function. Single cell multiomic analysis shows that Oct4 overexpression leads to widespread changes in gene expression and chromatin accessibility, inducing activity of both the neurogenic transcription factor Rfx4 and the Yamanaka factors Sox2 and Klf4. This study demonstrates that viral-mediated overexpression of Oct4 induces neurogenic competence in wildtype retinal Müller glia, identifying mechanisms that could be used in cell-based therapies for treating retinal dystrophies.

Genetic and Epigenetic Interactions Involved in Senescence of Stem Cells.

Cellular senescence is a permanent condition of cell cycle arrest caused by a progressive shortening of telomeres defined as replicative senescence. Stem cells may also undergo an accelerated senescence response known as premature senescence, distinct from telomere shortening, as a response to different stress agents. Various treatment protocols have been developed based on epigenetic changes in cells throughout senescence, using different drugs and antioxidants, senolytic vaccines, or the reprogramming of somatic senescent cells using Yamanaka factors. Even with all the recent advancements, it is still unknown how different epigenetic modifications interact with genetic profiles and how other factors such as microbiota physiological conditions, psychological states, and diet influence the interaction between genetic and epigenetic pathways. The aim of this review is to highlight the new epigenetic modifications that are involved in stem cell senescence. Here, we review recent senescence-related epigenetic alterations such as DNA methylation, chromatin remodeling, histone modification, RNA modification, and non-coding RNA regulation outlining new possible targets for the therapy of aging-related diseases. The advantages and disadvantages of the animal models used in the study of cellular senescence are also briefly presented.

Transglutaminase 2 Regulates HSF1 Gene Expression in the Acute Phase of Fish Optic Nerve Regeneration.

Fish retinal ganglion cells (RGCs) can regenerate after optic nerve lesions (ONLs). We previously reported that heat shock factor 1 (HSF1) and Yamanaka factors increased in the zebrafish retina 0.5-24 h after ONLs, and they led to cell survival and the transformation of neuro-stem cells. We also showed that retinoic acid (RA) signaling and transglutaminase 2 (TG2) were activated in the fish retina, performing neurite outgrowth 5-30 days after ONLs. In this study, we found that RA signaling and TG2 increased within 0.5 h in the zebrafish retina after ONLs. We examined their interaction with the TG2-specific morpholino and inhibitor due to the significantly close initiation time of TG2 and HSF1. The inhibition of TG2 led to the complete suppression of HSF1 expression. Furthermore, the results of a ChIP assay with an anti-TG2 antibody evidenced significant anti-TG2 immunoprecipitation of HSF1 genome DNA after ONLs. The inhibition of TG2 also suppressed Yamanaka factors' gene expression. This rapid increase in TG2 expression occurred 30 min after the ONLs, and RA signaling occurred 15 min before this change. The present study demonstrates that TG2 regulates Yamanaka factors via HSF1 signals in the acute phase of fish optic nerve regeneration.

Delaying Brain Aging or Decreasing Tau Levels as Strategies to Prevent Alzheimer's Disease: In Memoriam of Mark A. Smith.

Aging is the main risk for neurodegenerative disorders like Alzheimer's disease. In this short review, I will comment on how delaying brain aging through the addition of Yamanaka Factors or small compounds that bind to the folate receptor alpha, which promote the expression of the Yamanaka Factors or by the decrease tau levels in brain cells from older subjects could serve as strategies to prevent Alzheimer's disease.

In vivo cyclic overexpression of Yamanaka factors restricted to neurons reverses age-associated phenotypes and enhances memory performance

In recent years, there has been success in partially reprogramming peripheral organ cells using cyclic Yamanaka transcription factor (YF) expression, resulting in the reversal of age-related pathologies. In the case of the brain, the effects of partial reprogramming are scarcely known, and only some of its effects have been observed through the widespread expression of YF. This study is the first to exclusively partially reprogram a specific subpopulation of neurons in the cerebral cortex of aged mice. The in vivo model demonstrate that YF expression in postmitotic neurons does not dedifferentiate them, and it avoids deleterious effects observed with YF expression in other cell types. Additionally, our study demonstrates that only cyclic, not continuous, expression of YF result in a noteworthy enhancement of cognitive function in adult mice. This enhancement is closely tied to increased neuronal activation in regions related to memory processes, reversed aging-related epigenetic markers and to increased plasticity, induced by the reorganization of the extracellular matrix. These findings support the therapeutic potential of targeted partial reprogramming of neurons in addressing age-associated phenotypes and neurodegenerative diseases correlated with aging.

Male-pronuclei-specific granulin facilitates somatic cells reprogramming via mitigating excessive cell proliferation and enhancing lysosomal function.

Critical reprogramming factors resided predominantly in the oocyte or male pronucleus can enhance the efficiency or the quality of induced pluripotent stem cells (iPSCs) induction. However, few reprogramming factors exist in the male pronucleus had been verified. Here, we demonstrated that granulin (Grn), a factor enriched specifically in male pronucleus, can significantly improve the generation of iPSCs from mouse fibroblasts. Grn is highly expressed on Day 1, Day 3, Day 14 of reprogramming induced by four Yamanaka factors and functions at the initial stage of reprogramming. Transcriptome analysis indicates that Grn can promote the expression of lysosome-related genes, while inhibit the expression of genes involved in DNA replication and cell cycle at the early reprogramming stage. Further verification determined that Grn suppressed cell proliferation due to the arrest of cell cycle at G2/M phase. Moreover, ectopic Grn can enhance the lysosomes abundance and rescue the efficiency reduction of reprogramming resulted from lysosomal protease inhibition. Taken together, we conclude that Grn serves as an activator for somatic cell reprogramming through mitigating cell hyperproliferation and promoting the function of lysosomes.

RETINOBLASTOMA CELLS OVEREXPRESSING THE MRPS18-2 PROTEIN COULD BE DIFFERENTIATED in vitro

The mitochondrial ribosomal protein MRPS18-2 is involved in cell cycle regulation through its interaction with the retinoblastoma-associated protein, RB. Earlier we have shown that this protein plays an important role in homeostasis of normal and tumor cells, embryogenesis, and in the maintenance of cell stemness. We also found that the MRPS18-2 protein is transactivated by a transcription factor KLF4, one of the Yamanaka factors, inducing cell pluripotency. The aim of the present work was to study the functional consequences of overexpression of the MRPS18-2 and RB proteins in the retinoblastoma cell line (WERI RB 27), concerning putative directed differentiation in vitro. Methods. Direct multipotent differentiation was conducted with cocktails of chemicals for osteogenic, chondrogenic, and adipogenic lineages. Ca+2 ions were stained with Alizarin Red, triglycerides – with Oil Red O, and glycosaminoglycans - with Alcian blue. Results. Parental cells WERI RB-27 did not differentiate upon treatment with any of chemical cocktails, cells remained in suspension and did not change morphology. At the same time, cells that overexpressed MRPS18-2 have demonstrated their differentiation ability into osteo-, chondro-, and adipo-lineages. Conclusions. Thus, we have shown that overexpression of the MRPS18-2 protein in WERI RB 27 cells leads to changes in cell morphology and to ability of the directed multipotent differentiation in vitro. Hence, the MRPS18-2 protein plays a significant role in cancerogenesis and cell stemness.

Generation of two lymphoblastoid-derived induced pluripotent stem cell (iPSC) lines from patients with phenylketonuria

We employed a Sendai virus-based reprogramming method to transform human lymphoblastoid cell lines (LCL) derived from two individuals diagnosed with phenylketonuria (PKU) into induced pluripotent stem cells (iPSC). This reprogramming process involved the expression of the four Yamanaka factors: KLF4, OCT4, SOX2, and C-MYC. The resulting patient-specific iPSCs exhibited a normal karyotype and expressed endogenous pluripotent markers NANOG and OCT-4. Notably, these iPSCs demonstrated strong differentiation capabilities, giving rise to cell populations representing the ectoderm, endoderm, and mesoderm germ layers.

Abstract 4342: Breast cancer multi-omic single cell profiling identifies key progressive disease markers

Abstract Breast cancer is one of the most diagnosed cancers and has a complex tumor microenvironment (TME). Breast tumors are subtyped by receptor expression, and all have a high degree of cellular heterogeneity. We analyzed tumors from 8 individuals with early-stage breast cancer. The patients had either triple negative breast (TNBC) or an estrogen receptor (ER) positive cancer. The tumors and normal adjacent tissue were profiled by single-nuclei gene expression (GEX) and ATAC data using the 10X multi-ome methodology. Gene set analysis identified specific epithelial clusters associated with the estrogen early/late response, epithelial mesenchymal transition, and several key cytokine pathways. From those epithelial cells, a subset highly proliferative in nature emerged. It consists of both ER positive and TNBC tumor types enriched for specific DNA transcriptional motifs including those for stem cell (Yamanaka) factors and other cellular proliferation motifs. GEX proliferation markers such as MKi-67 were also highly expressed. Overlaying GEX and ATAC data, it was possible to filter the numerous differentially expressed genes and peaks into a subset of genes specific to progressive breast cancer within the proliferative cluster. Those genes included ESRP1, POP4, CCNE1, and AAMDC all of which are associated with progressive breast cancer. To further elucidate the complexity of the TME, we examined clusters of fibroblasts from our dataset. A difference in cancer associated fibroblast marker gene expression was related to the level of ER expression expressed in the tumor epithelium. In general, ER-low tumor fibroblasts had higher expression of immune cancer associated fibroblasts (iCAFs) markers while ER-positive and TNBC tumors had greater expression of extracellular matrix associated markers (emCAFs). Specific clusters were enriched for emCAFs and iCAFs representing another critical part of the TME. In conclusion, using a multi-modal single-cell approach to the TME allowed the identification of an aggressive cluster of epithelial cells marked by genes for cellular proliferation and noted therapeutic targets while also characterizing other critical TME components especially, CAFs. Citation Format: Hugh Russell, Manisha Rao, Grant Duclos, Rogelio Aguilar, Nick Barkas, Megan Callahan, Ojasvi Chaudhary, Peter Gathungu, Chris Rands, Varsha Shankarappa, Daniel Stetson, Asaf Rotem, Maurizio Scaltriti, Brian Dougherty. Breast cancer multi-omic single cell profiling identifies key progressive disease markers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4342.

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.