Genomic Reprogramming and Regeneration Precision DNA Repair Therapy System

Abstract

A therapy system for genomic reprogramming and DNA repair, including: a gene identification module configured to detect and isolate regenerative genes from planarian neoblasts, such as Smedwi-1, Smedwi-2 and β-catenin, which are responsible for cell regeneration and pluripotency; a gene adaptation unit configured to perform codon optimization and regulatory sequence modification of isolated regenerative genes for compatibility with human DNA, including the incorporation of human-specific promoters, enhancers, and terminators; a selective nucleopathy module configured with CRISPR-Cas9-based mechanisms and custom-designed guide RNAs, whereby the module selectively identifies, targets and removes mutated or damaged DNA in target cells while preserving healthy DNA; a DNA delivery unit configured to transfer the adapted regenerative genes into human stem cells, utilizing gene transfer techniques such as viral vectors, electroporation, or lipid-based nanoparticles for efficient gene integration; a genetic switch control system configured with programmable genetic kill switches for the selective activation and deactivation of regenerative genes, whereby the system enables controlled gene expression to prevent unwanted cell proliferation and tumor formation; a biopolymer scaffold support configured to provide a structural scaffold at the target site to facilitate the delivery of modified stem cells or regenerative genes and to promote cell growth and tissue integration; and an interface for hyperbaric oxygen therapy that increases cell metabolism, improves the accuracy of DNA repair and promotes tissue regeneration in synergy with regeneration and DNA repair processes.

Description

FIELD OF THE INVENTION

[0001] The present invention relates to systems and methods for advanced genomic reprogramming and regenerative precision DNA repair therapy (AGRPT). Specifically, it involves the integration of genetically modified regenerative genes adapted from planarian neoblasts with advanced DNA repair and delivery mechanisms in human cells to enable precise DNA repair and cell regeneration. BACKGROUND OF THE INVENTION

[0002] The field of regenerative medicine is seeking solutions to repair and regenerate damaged tissue through modern gene therapy, stem cell treatments, and tissue engineering. In nature, organisms such as planarians exhibit remarkable regenerative abilities and are capable of regrowing entire body structures using pluripotent stem cells (neoblasts) and specific regenerative genes such as Smedwi-1 and β-catenin. Planarian neoblasts retain their pluripotency and respond to positional signals to differentiate into specific cell types. This enables complex tissue regeneration, including muscle, nerve, and organ structures.

[0003] In humans, the inherent regenerative capacity is limited, particularly in cases of extensive tissue damage, genetic mutations, or DNA alterations due to disease or environmental factors such as radiation. While valuable in regenerative medicine, human stem cells lack the full regenerative capabilities observed in organisms such as planarians. Genetic disorders such as cystic fibrosis, sickle cell anemia, and neurodegenerative diseases such as Huntington's disease are often the result of mutations that disrupt cellular function and DNA integrity. While promising, conventional genome editing approaches face the challenge of specifically repairing specific DNA sequences without causing unwanted effects or side effects such as tumor formation.

[0004] This invention overcomes the limitations of existing therapies by introducing a system that harnesses the regenerative power of planarian-derived genes adapted for human cells. By isolating and optimizing specific planarian genes, such as Smedwi-2, for human compatibility, the invention enables targeted DNA repair through CRISPR-based selective nucleopathy, which selectively removes only mutated or damaged DNA. The system also incorporates a genetic switch control module designed to regulate regenerative gene expression to prevent uncontrolled cell growth. Furthermore, a biopolymer scaffold enables targeted delivery and supports tissue-specific regeneration and cellular integration. An interface for hyperbaric oxygen therapy is included to enhance cellular repair processes and tissue regrowth.

[0005] By integrating selective nucleopathy, regenerative gene therapy, controlled gene expression, and advanced delivery systems, this invention represents a breakthrough in precision medicine for DNA repair and regenerative therapy, paving the way for the treatment of a wide range of genetic and degenerative diseases with unprecedented accuracy and efficacy.

[0006] Therefore, there is a need to develop a therapeutic system for genome reprogramming and DNA repair. The technical advances disclosed by the present invention overcome the limitations and disadvantages of existing and conventional systems and methods. SUMMARY OF THE INVENTION

[0007] The present invention relates to systems and methods for advanced genomic reprogramming and regenerative precision DNA repair therapy (AGRPT). Specifically, it involves the integration of genetically modified regenerative genes adapted from planarian neoblasts with advanced DNA repair and delivery mechanisms in human cells to enable precise DNA repair and cell regeneration.

[0008] In one embodiment, a system for genomic reprogramming and DNA repair therapy is provided. The system comprises a gene identification module configured to detect and isolate regenerative genes from planarian neoblasts, such as Smedwi-1, Smedwi-2, and β-catenin, which are responsible for cell regeneration and pluripotency; a gene adaptation unit configured to perform codon optimization and regulatory sequence modification of isolated regenerative genes for compatibility with human DNA, including the incorporation of human-specific promoters, enhancers, and terminators; a selective nucleopathy module configured with CRISPR-Cas9-based mechanisms and custom-designed guide RNAs, wherein the module selectively identifies, targets, and removes mutated or damaged DNA in target cells while preserving healthy DNA.a DNA delivery unit configured to transfer the customized regenerative genes into human stem cells using gene transfer techniques such as viral vectors, electroporation, or lipid-based nanoparticles for efficient gene integration; a genetic switch control system equipped with programmable genetic kill switches for selectively activating and deactivating regenerative genes, enabling controlled gene expression to prevent unwanted cell proliferation and tumor formation; a biopolymer scaffold support configured to provide a structural scaffold at the target site to facilitate the delivery of modified stem cells or regenerative genes and promote cell growth and tissue integration;and a hyperbaric oxygen therapy interface configured to increase cellular metabolism, improve the accuracy of DNA repair, and promote tissue regeneration in synergy with the regeneration and DNA repair processes.;

[0009] To further clarify the advantages and features of the present invention, a more detailed description of the invention will be given with reference to specific embodiments thereof, which are illustrated in the accompanying drawings. It should be noted that these drawings represent only typical embodiments of the invention and are therefore not to be considered limiting its scope. The invention will be described and explained in additional detail and in greater detail with reference to the accompanying drawings. SHORT DESCRIPTION OF THE FIGURE

[0010] These and other features, aspects, and advantages of the present invention will become more readily understood when the following detailed description is read with reference to the accompanying drawings, in which like characters represent like parts throughout. Fig. 1 shows a block diagram of a system for genomic reprogramming and DNA repair therapy according to an embodiment of the present invention.

[0011] Furthermore, those skilled in the art will appreciate that elements in the drawing are illustrated for convenience and may not necessarily be drawn to scale. Furthermore, with respect to the construction of the device, one or more components of the device may be represented in the drawing by conventional symbols, and the drawing may show only the specific details relevant to understanding the embodiments of the present disclosure in order not to clutter the drawing with details that would be readily apparent to those skilled in the art who would benefit from the description herein. DETAILED DESCRIPTION:

[0012] To facilitate an understanding of the principles of the invention, reference will now be made to the embodiment illustrated in the drawings and described in specific language. It is to be understood, however, that no limitation on the scope of the invention is intended thereby, since such changes and further modifications of the illustrated system, and such further applications of the principles of the invention as illustrated therein, are contemplated as would normally occur to one skilled in the art to which the invention pertains.

[0013] It will be understood by one skilled in the art that the foregoing general description and the following detailed description are exemplary and explanatory of the invention and are not intended to be limiting thereof.

[0014] References in this specification to "one aspect," "another aspect," or similar expressions mean that a particular feature, structure, or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Therefore, the occurrences of the terms "in one embodiment," "in another embodiment," and similar expressions throughout this specification may or may not all refer to the same embodiment.

[0015] The terms "comprises," "comprising," or other variations thereof are intended to cover non-exclusive inclusion, such that a process or method comprising a list of steps not only includes those steps, but may also include other steps not expressly listed or inherent in such process or method. Likewise, one or more devices or subsystems or elements or structures or components preceded by "comprises...a" does not preclude, without further limitation, the existence of other devices or other subsystems or other elements or other structures or other components or additional devices or additional subsystems or additional elements or additional structures or additional components.

[0016] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The system, methods, and examples provided herein are for illustrative purposes only and should not be considered limiting.

[0017] Embodiments of the present invention will be described in detail below with reference to the accompanying drawings.

[0018] Fig.Figure 1 shows a block diagram of a system for genomic reprogramming and DNA repair therapy according to an embodiment of the present invention. The system 100 comprises a system for genomic reprogramming and DNA repair therapy including a gene identification module 102 configured to detect and isolate regenerative genes from planarian neoblasts, such as Smedwi-1, Smedwi-2, and β-catenin, which are responsible for cell regeneration and pluripotency; a gene adaptation unit 104 configured to perform codon optimization and regulatory sequence modification of isolated regenerative genes for compatibility with human DNA, including the incorporation of human-specific promoters, enhancers, and terminators;a selective nucleopathy module 106 configured with CRISPR-Cas9-based mechanisms and customized guide RNAs, wherein the module selectively identifies, targets, and removes mutated or damaged DNA in target cells while preserving healthy DNA; a DNA delivery unit 108 configured to transfer the customized regenerative genes into human stem cells, using gene transfer techniques such as viral vectors, electroporation, or lipid-based nanoparticles for efficient gene integration; a genetic switch control system 110 configured with programmable genetic kill switches for selectively activating and deactivating regenerative genes, wherein the system enables controlled gene expression to prevent unwanted cell proliferation and tumor formation;a biopolymer scaffold support 112 configured to provide a structural scaffold at the target site to facilitate the delivery of modified stem cells or regenerative genes and promote cell growth and tissue integration; and a hyperbaric oxygen therapy interface 114 configured to increase cellular metabolism, improve DNA repair fidelity, and promote tissue regeneration in synergy with the regeneration and DNA repair processes.

[0019] In another embodiment, the gene identification module further comprises a sequencing processor for mapping the coding sequences of isolated genes using next-generation sequencing (NGS) techniques with sequence alignment tools for comparing identified genes with human homologs to assess compatibility.

[0020] In another embodiment, the gene adaptation unit further comprises a codon optimization processor for analyzing and replacing non-preferred codons from the isolated planarian genes with human-preferred codons; a regulatory sequence integration module configured to integrate human-compatible promoter and enhancer sequences, such as CMV or EF-1α promoters, thereby enabling effective transcriptional regulation in human cells.

[0021] In another embodiment, the selective nucleopathy module further comprises a guide RNA synthesis unit configured to design and produce specific guide RNAs for identifying and targeting mutated DNA sequences in human cells; and a DNA excision mechanism that uses Cas9 or other site-specific nucleases to create double-strand breaks at the target sites, thereby facilitating the selective removal of altered DNA while preserving unaltered regions.

[0022] In another embodiment, the DNA delivery unit comprises a vector selection module configured to select and implement optimal delivery vectors based on patient-specific genetic and cellular profiles, including viral vectors, lipid nanoparticles, or electroporation techniques for gene insertion; a stem cell integration component that enables the transfection of human stem cells with customized regenerative genes for delivery to the target tissue site.

[0023] In another embodiment, the genetic switch control system further comprises a plurality of kill switches designed to activate or deactivate gene expression in response to specific molecular signals, such as the presence of doxycycline in tet-on / tet-off systems; an expression control module configured to switch the activation of regenerative genes depending on the cellular context and location.

[0024] In another embodiment, the present invention aims to genetically engineer these regenerative abilities of planarian neoblasts and transfer them into human cells, particularly for DNA repair or tissue regeneration. Humans do not naturally possess neoblasts like planarians, but we do possess stem cells and repair mechanisms. The goal would be to extract and manipulate specific genes from planarian neoblasts and integrate them into human cells to replicate healthy DNA and use it to regrow / regenerate damaged tissue and nerves.

[0025] In one embodiment, the invention comprises the identification and isolation of specific regenerative genes from planarian neoblasts, such as Smedwi-1, Smedwi-2, and β-catenin, which are essential for pluripotency and regeneration. This process involves the extraction of DNA from planarians by standard methods, including phenol-chloroform extraction or gel electrophoresis, followed by amplification of the target genes using polymerase chain reaction (PCR) to ensure sufficient quantities for further studies. Next-generation sequencing (NGS) is then used to map the complete coding sequences of these genes, and tools such as the Basic Local Alignment Search Tool (BLAST) compare them to human genes to identify possible homologies and the modifications required for compatibility.

[0026] Analyzing homology between species highlights similarities and differences in DNA sequences. This reveals which regions of planarian genes function effectively in human cells and which may need to be modified. For example, Smedwi-2, which is responsible for regeneration in planarians, may share similarities with human genes such as PIWIL1, which provides insight into which conserved regions retain their regenerative functionality and which aberrant regions may need to be adapted.

[0027] BLAST helps quantify the degree of sequence similarity between planarian genes and human genes, for example, by identifying a 60% match between Smedwi-2 and PIWIL1, while highlighting differences in regulatory sequences or exons. This homology analysis involves several steps: First, BLAST is used to search for planarian gene sequences in the human genome; conserved regions critical for function are identified, and divergent areas that may be incompatible with human cells are analyzed. Adaptations, such as targeted mutagenesis, alter the structure of the gene to ensure compatibility with human splicing mechanisms and enable efficient processing of modified planarian genes in human cells.

[0028] To further adapt these genes to human expression, a genetic engineering technique is used to modify the regulatory and promoter regions to enable correct expression in human cells. Codon optimization, a crucial step, involves altering the gene's DNA sequence to conform to human codon preferences without altering the protein structure. Both planarians and humans use the same set of 20 amino acids, but their genetic code may prefer different codons for each amino acid. For example, while the TTA codon codes for leucine in both species, human cells may prefer CTG for efficient translation.Tools such as GeneOptimizer or the Java Codon Adaptation Tool (JCAT) analyze and optimize codon usage by replacing rare codons in human cells with more frequently used ones, ensuring that the amino acid sequence remains unchanged. After identifying and adapting codons that are rarely used in human cells, the gene is synthesized using gene synthesis services from providers such as IDT or ThermoFisher.

[0029] The invention also modifies regulatory sequences that control gene expression in human cells. Promoters, enhancers, and terminators vary between organisms, meaning that planarian regulatory elements may be less effective in human cells. For example, the planarian promoter for Smedwi-2 lacks transcription factor binding sites required for robust human expression. To overcome this problem, the invention replaces planarian promoters with human-compatible options such as EF-1α (elongation factor 1-alpha) or the CMV (cytomegalovirus) promoter, which are well-suited to driving strong gene expression in mammalian cells. Through these modifications, the invention ensures that the genetically modified planarian genes can function effectively in the human cellular environment.

[0030] In one embodiment, the invention modifies regulatory sequences to enable planarian genes to function effectively in human cells. The process begins with the identification of human-compatible promoters such as CMV or EF-1α, which are well-characterized in mammalian systems for promoting high levels of gene expression. Next, untranslated regions (5' UTRs) adjacent to the promoter are altered to optimize translation efficiency and ensure that gene expression reaches the desired level in human cells. Human-specific enhancer sequences such as HSF1 are also incorporated to further improve gene expression efficiency. Additionally, planarian terminators are replaced with mammalian terminators such as SV40 to ensure proper transcription termination in the human cellular environment.This process of adapting mismatched regions is collectively referred to as genetic manipulation and aims to make the planarian gene functional in human cells.

[0031] To achieve these genetic alterations, targeted mutation is used to introduce specific nucleotide changes and adapt the planarian regulatory elements to match the binding sites of human transcription factors. CRISPR-Cas9 technology can also edit the gene directly at the DNA level, ensuring precise modifications. Alternatively, the entire gene, including optimized and altered regions, can be synthesized from scratch. For example, if the exon-intron structure of the Smedwi-2 gene differs from that of the human PIWIL1 gene, synthetic intron sequences compatible with human splicing mechanisms can replace the aberrant regions.By implementing these adaptations, the invention leverages the specificity of planarian cell regeneration and applies it to human tissue repair and DNA regeneration to create targeted gene constructs. This approach helps prevent unwanted effects and minimize the risk of abnormalities and tumor formation.

[0032] In one embodiment, the invention utilizes positional information to guide human stem cells in tissue regeneration. Although human biology lacks the comprehensive regenerative capabilities of planarians, molecular signaling pathways such as the Wnt / Notum gradient can be introduced to tell genetically engineered stem cells where and what to regenerate. By employing positional markers, stem cells can be modified to "know" their specific location in the body and regenerate the target tissue or organ. This includes adapting the Wnt signaling pathway, which is essential for human embryogenesis and tissue repair, to provide positional cues. For example, graded Wnt signaling pathways can control stem cell positional signals.Signals can help establish the proximal-distal axis in limb regeneration and ensure that regenerated tissue develops in the correct location and orientation.

[0033] Furthermore, localized genetic switches are being developed to control the activation of these regenerative pathways, thus ensuring safety and ethical compliance by preventing abnormal growth or tumor formation. These genetic switches can turn genes on or off in response to molecular signals, such as the selective activation of the Wnt pathway in specific regions, to restore regeneration specificity in human tissues.

[0034] While humans lack natural neoblasts, pluripotent stem cells or induced pluripotent stem cells (iPSCs) can mimic neoblast-like behavior. These cells are genetically modified to carry planarian-like regenerative genes, allowing for enhanced tissue repair. They can be programmed to respond to signals such as Wnt, BMP, and FGF to regenerate specific tissues at the correct locations. Synthetic positional signals such as engineered gradients of Wnt / Notum are also employed to instruct stem cells on the site and function of regeneration, enabling precise tissue repair.

[0035] The application of the principle of regeneration specificity also extends to DNA repair. By focusing only on the replication of the required DNA segments, the invention avoids errors or the risk of excessive growth, such as cancer. Selective nucleopathy is combined with regenerative processes to repair specific DNA segments based on positional information. This approach can, for example, detect signals of DNA damage, such as oxidative stress or tumor-related mutations, and direct repair to these areas. Through CRISPR-assisted nucleopathy, the system targets specific genomic regions and replaces damaged DNA with healthy DNA derived from the patient's stem cells.

[0036] To insert these modified regenerative genes into human cells, the invention utilizes modern genome editing techniques. CRISPR / Cas9 enables precise genome editing by targeting specific loci where guide RNA (gRNA) instructs Cas9 to introduce a double-strand break, allowing the insertion of new planarian genes. Other delivery methods include viral vectors such as lentiviruses or adenoviruses, which can integrate the genetic material into the cell genome or maintain it externally, as well as electroporation or lipofection, which use electrical pulses or lipid carriers, respectively, to deliver neoblast genes into human stem cells.

[0037] After gene integration, tests confirm the successful expression of planarian genes and compliance with selective nucleopathy. Techniques such as qPCR and Western blotting validate gene transcription into mRNA and protein translation, while fluorescent labeling (e.g., with GFP) provides visual confirmation of gene expression in human cells. Functional tests assess the regenerative capacity of these modified cells, including their differentiation potential and the ability to repair damaged DNA based on the positional information encoded in the genes.

[0038] To address potential ethical and safety concerns, measures have been taken to avoid immune reactions to non-human gene products. Gene modifications minimize differences from human genes and thus reduce immune triggers, while the controlled expression of regenerative genes through genetic switches mitigates the risk of tumor formation. The Tet-On / Tet-Off system is used as a tetracycline-responsive genetic switch, allowing gene expression to be switched on or off with tetracycline or doxycycline. This provides a precise mechanism to activate the regenerative process only when needed, ensuring that tissue repair occurs safely, specifically, and in a controlled manner, preventing unintended cell proliferation or infection during gene therapy.

[0039] This approach not only improves the success rate but also reduces overall costs compared to conventional cancer therapies such as chemotherapy and radiation, while providing a permanent cure rather than a temporary remission. With continued refinements and clinical trials, this reprogenetic therapy could redefine how we approach genetic diseases and cancer treatment.

[0040] The drawings and the foregoing description provide examples of embodiments. Those skilled in the art will recognize that one or more of the described elements may well be combined into a single functional element. Alternatively, certain elements may be separated into multiple functional elements. Elements from one embodiment may be added to another embodiment. For example, orders of the processes described herein may be changed and are not limited to the manner described herein. Furthermore, the actions of any flowchart need not be implemented in the order shown; nor do all actions necessarily need to be performed. Also, those actions that are not dependent on other actions may be performed in parallel with the other actions. The scope of the embodiments is in no way limited by these specific examples.Numerous variations, whether explicitly stated in the specification or not, such as differences in structure, dimensions, and material use, are possible. The scope of the embodiments is at least as broad as indicated in the following claims.

[0041] Advantages, other benefits, and solutions to problems have been described above with reference to specific embodiments. However, the advantages, benefits, solutions to problems, and any components that may cause an advantage or solution to occur or become more apparent are not to be construed as a critical, required, or essential feature or component of any or all of the claims. REFERENCE 100 A system for genomic reprogramming and DNA repair therapy 102 Gene identification module 104 Gene adaptation unit 106 Selective Nucleopathy Module 108 DNA delivery unit 110 Genetic switch control system 112 biopolymer scaffolds 114 Interface for Hyperbaric Oxygen Therapy

Claims

[1] A therapeutic system for genomic reprogramming and DNA repair, comprising: a gene identification module configured to detect and isolate regenerative genes from planarian neoblasts, such as Smedwi-1, Smedwi-2 and β-catenin, which are responsible for cell regeneration and pluripotency; a gene adaptation unit configured to perform codon optimization and regulatory sequence modification of isolated regenerative genes for compatibility with human DNA, including the incorporation of human-specific promoters, enhancers, and terminators; a selective nucleopathy module configured with CRISPR-Cas9-based mechanisms and tailor-made guide RNAs, whereby the module selectively identifies, targets and removes mutated or damaged DNA in target cells while preserving healthy DNA; a DNA delivery unit configured to transfer the customized regenerative genes into human stem cells using gene transfer techniques such as viral vectors, electroporation, or lipid-based nanoparticles for efficient gene integration; a genetic switch control system configured with programmable genetic kill switches for selectively activating and deactivating regenerative genes, the system enabling controlled gene expression to prevent unwanted cell proliferation and tumorigenesis; a biopolymer scaffold support configured to provide a structural scaffold at the target site to facilitate the delivery of modified stem cells or regenerative genes and promote cell growth and tissue integration; and a hyperbaric oxygen therapy interface that increases cellular metabolism, improves the accuracy of DNA repair, and promotes tissue regeneration in synergy with the regeneration and DNA repair processes. [2] The system of claim 1, wherein the gene identification module further comprises: a sequencing processor for mapping the coding sequences of isolated genes using next-generation sequencing (NGS) techniques, with sequence alignment tools for comparing identified genes with human homologs to assess compatibility. [3] The system of claim 1, wherein the gene adaptation unit further comprises: a codon optimization processor for analyzing and replacing non-preferred codons from the isolated planarian genes with human-preferred codons; a regulatory sequence integration module configured to incorporate human-compatible promoter and enhancer sequences such as CMV or EF-1α promoters, thus enabling effective transcriptional regulation in human cells. [4] The system of claim 1, wherein the selective nucleopathy module further comprises: a guide RNA synthesis unit configured to develop and produce specific guide RNAs for identifying and targeting mutated DNA sequences in human cells; a DNA excision mechanism that uses Cas9 or other site-specific nucleases to create double-strand breaks at targeted sites, thus enabling the selective removal of altered DNA while preserving unaltered regions. [5] The system of claim 1, wherein the DNA delivery unit comprises: a vector selection module configured to select and implement optimal delivery vectors based on patient-specific genetic and cellular profiles, including viral vectors, lipid nanoparticles, or electroporation techniques for gene insertion; a stem cell integration component that enables the transfection of human stem cells with adapted regenerative genes for delivery into the target tissue. [6] The system of claim 1, wherein the genetic switch control system further comprises: a variety of kill switches designed to activate or deactivate gene expression in response to specific molecular signals, such as the presence of doxycycline in tet-on / tet-off systems; an expression control module configured to switch the activation of regenerative genes depending on the cellular context and location.

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