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A Roadmap to Cure Cancer: Combining CRISPR genome editing with cancer network editing

Authors:
Eric Werner at Oxford Advanced Research Foundation
Eric Werner
  • Oxford Advanced Research Foundation
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Abstract and Figures

Genome editing technology(1-6) combined with Werner’s network theory of cancer(7) opens up a new pathway to cure cancer not by surgery, radiation, drugs or immunotherapy but by genome editing of cancer networks. There exists a precise step-by-step protocol to cure cancer. The cancer cells genome is digitized. Then it is translated into the formal CAD-genome. The cancer networks in the CAD-genome are analyzed using cancer-CAD software to find all cancer networks. The cancer networks are then edited out and replaced, transforming the cancer network nodes into cancer-free network nodes. Next transformed cancer-free nodes are synthesized into natural molecular DNA nodes. Using CRISPR-like genome editing, the molecular cancer-free DNA nodes replace the molecular DNA cancer network nodes. The result is a cancer free genome. Using viral vectors it is possible to target the cancer cells in the whole organism. The cancer cells have been transformed into cancer free cells. The cancer is cured not with external methods such as surgery, radiation, drugs and immunotherapy, but with internal DNA editing of cancer networks within the cancer cells. Additionally, the cancer cure protocol is adaptable to immunotherapy. Combine cancer network editing in coordination with T-cell editing to force cancer cells to emit unique signals that their co- engineered T-cells can recognize. Under this method transformed cancer cells cooperate with co-adapted T-cells to insure the cancer cells’ self-destruction.
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Content uploaded by Eric Werner
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All content in this area was uploaded by Eric Werner on Dec 10, 2017
Content may be subject to copyright.
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History of genome codes
Watson and Crick decoded the alphabet of DNA(18, 19),
Nirenberg and Khorana deciphered the genetic triplet
code for proteins(20, 21), still others like Davidson and
Carroll decoded protein based, gene regulatory networks
(GRNs)(22-25), Werner showed GRNs cannot generate
complex embryological development and hence are not
the only source of control of cancer(16, 26). The next
step is to decode the higher-level network control code of
cancer and, more generally, of multicellular life residing
in the so-called non-coding DNA in genomes(9, 13, 14,
16).
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... In short it allows a person with less than a high school education to edit genomes of any animal or plant. Indeed, high school students are now using this technology to do experiments that previously research scientists could only dream about [6,15,4,8] 2 CRISPR for curing cancer and for creating a cancer bomb My research has focused on the wonderful potential of applying CRISPR-like genome network editing to cure cancer [23,22,25,26,24]. It is based on the new cancer network paradigm [20] which goes to the core of how cancer cells are controlled. ...
The Coming CRISPR Wars: Or why genome editing can be more dangerous than nuclear weapons
Preprint
Full-text available
  • Jan 2019
While CRISPR-Cas genome editing technology has been heralded as a great advancement for science, human health, bioengineering and medicine, there is a potential dark side of CRISPR genome editing that may be a greater danger to humanity than nuclear weapons. We present some of the more obvious potential military and bioterrorism applications of CRISPR and related genome editing technology. CRISPR weapons have significant advantages over conventional nuclear weapons. The balance of power based on mutual assured destruction cannot be maintained once CRISPR weapons enter the international arena. Disturbingly, because of the easy entrance to the technology, it opens the door for small organizations and countries to enter the international arms arena. The simplicity and ease of development of such weapons makes it essential that CRISPR genome editing technology be carefully applied and regulated.
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... Genome editing technology (1)(2)(3)(4)(5)(6) combined with Werner's network theory of cancer (7) opens up a new pathway to cure cancer by induced cancer cell suicide. We adapt the Cancer Cure Protocol (8)(9)(10)(11)(12)(13) to design a different protocol that stops cancer by inserting into or modifying links in the cancer network that activate the cell death (apoptosis) pathway. The edit to stop cancer growth depends on the architecture of the cancer network. ...
A Cancer Cell Suicide Protocol -Using cancer-CAD and CRISPR to edit cancer cell networks to induce cancer cell apoptosis
Preprint
Full-text available
  • Jul 2018
Genome editing technology(1-6) combined with Werner's network theory of cancer(7) opens up a new pathway to cure cancer by induced cancer cell suicide. We adapt the Cancer Cure Protocol(8-13) to design a different protocol that stops cancer by inserting into or modifying links in the cancer network that activate the cell death (apoptosis) pathway. The edit to stop cancer growth depends on the architecture of the cancer network. Different network link transformations have different effects depending on the cancer network link architecture. The ability to visualize the cancer network and simulate the dynamic effects of network edits in virtual space-time helps tremendously in understanding how the cancer cell is controlled and how to stop its proliferation. In cancer-CAD software, aspects of these edits can be automated with algorithms that suggest therapeutic network link edits automatically. The user can choose between various possible network edits by observing their effects on tumor growth in the simulation. Once an optimal network transformation is found, the edits can be synthesized and implemented in live cancer cells using CRISPR or analogous molecular genome editing technologies.
View
... Any cancer can be halted by changing the cancer network back into a healthy non-cancerous one [39] 4 . Thus network transformations cause cancer and can also stop cancer. ...
A Roadmap to Create Synthetic Multicellular Life: Applications: Protocols to cure cancer, tissue regeneration, network-designed heterosis-hybrid vigor
Preprint
Full-text available
  • Dec 2017
A synthetic living cell has been created with a designed genome and booted up to start di- viding. Scientists have designed a genome on the computer then generated the molecular DNA and inserted it into a cell replacing its own previous genome. They then jump-started it with a spark and it began to divide. The technology uses a bacterial genome and a bac- terial cell. Bacteria are single celled organisms. We, however, are multicellular creatures. A method is presented to design and synthesize multicellular life. Through rapid recent developments in biotechnology this method has become a pragmatically and technologi- cally feasible. A step-by-step roadmap is presented to create synthetic multicellular life. Except for one, all the steps in the roadmap have been technologically realized. The steps that require wet-lab work been been achieved. The one remaining step requires intense software and hardware research. Application of the technology: Network designed het- erosis (hybrid vigor) for food production. Tissue regeneration using designed stem cell networks. A meta-protocol is presented for curing cancer by editing cancer networks us- ing multicellular-CAD software in combination with CRISPR-like genome editing. This opens a path to cure cancer without surgery, drugs or radiation by digital and molec- ular genome editing using multicellular-CAD software together with CRISPR-Cas style genome editing. Unfortunately, ignorant use of CRISPR could also create cancers. New regulations of are called for
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The Internet of Life Chapter 1: Universal nonrandom network protocols govern development and evolution of all bilaterians
Preprint
Full-text available
  • Feb 2020
All diploid sexual organisms have two distinct haploid genomes, one from each parent. There is the male derived haploid genome and the female derived haploid genome. Each genome contains a distinct developmental control network that directs the development of the embryo to an adult. Run separately, independent of the influence of the other network, the each haploid genome produces a morphologically different organism. The interrelationship of the male and female haploid genome networks is governed by an interaction protocol that determines which parental network is in control in any given cell at any given point in development. The protocol consists of two interacting half-protocols, one for each parental hap-loid genome. The full interaction protocol is itself a higher-level, meta-network, or internetwork between the two lower-level, parental developmental control networks. Computer simulations show that if the interaction protocol is random then there is a loss of bilateral symmetry in the generated organism. Therefore, for all bilaterally symmetric organisms, the interaction protocol between the two parental genomes cannot be random. This implies that a nonrandom ur-protocol must have evolved with the first diploid bilaterians in the Precambrian more than 570 million years ago. Nonrandom protocols partition the embryo and adult into dynamic sections that are variably controlled by one or the other parental haploid genome network. Developmental networks and their meta-network protocols provide fundamentally new insights into embryonic and post-embryonic development, developmental pathologies, animal and plant hybrids, heterosis, and evolutionary dynamics.
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Viral Black Widow Protocols for Cancer Immunotherapy: Matching cancer cell signals with oncolytic virus receptors for complete and consistent cancer eradication
Preprint
Full-text available
  • Aug 2018
The great and unresolved challenge of cancer immunotherapy is the possibility of severe, life threatening side effects. A new coordinated set of protocols creates a communication system between cancer cells and oncolytic viruses that avoids such immunotherapeutic side effects. A meta-protocol or method coordinates two protocols, a protocol for cancer network signal editing and a protocol for virus receptor editing. This meta-protocol integrates the two protocols to insure signal-receptor matching of cancer cell signals and virus receptors. Together coordinated protocols produce an engineered cooperative cell-to-virus communication system between designed oncolytic viruses and edited cancer cells. The result is that edited cancer cells emit unique "kill me!" signals to designed oncolytic virus receivers which then kill the cancer cells. Side effects are eliminated because the "kill me!" signal is unique to cancer cells and the designed oncolytic viruses have receptors that only react to this unique cancer signal while ignoring all other cells. The combination of the three protocols is called the Viral Black Widow Protocol (VBWP). It is a shotgun marriage between oncolytic viruses and cancer cells after which the oncolytic viruses destroy their partner cancer cells. Using cancer-CAD-CRISPR network editing, a gene activation link is inserted into the cancer network such that the cancer cell expresses a unique external signal recognized by the co-designed receptors of oncolytic viruses. The unique signal indicates the cell is a cancer cell. In coordination, oncolytic viruses are edited to only attack the cells that emit the unique cancer signal. Moreover, since the Viral Black Widow Protocol and the T-cell Black Widow Protocol(1) can be co-designed to respond to the same unique cancer signal, the two therapies can be used in combination. This synergy of viral and T-cell Black Widow protocols enables a powerful immunotherapy for cancer eradication.
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The Black Widow Protocol for Coordinated Cancer Immunotherapy Co-editing cancer cells and T-cells for minimal immunotherapeutic side effects 12
Preprint
Full-text available
  • Jul 2018
One of the main problems with immunotherapy of cancer is the possibility of severe life threatening side effects. Under a new paradigm (the Cancer Network Paradigm) of how cancer works side effects can be avoided by two coordinated protocols that combine cancer network editing with T-cell network editing. A third meta-protocol integrates the two protocols. Together these protocols produce an engineered cooperative multi-cellular communication system between designed T-cells and edited cancer cells. The result is that edited cancer cells emit unique “kill me!” signals to obliging T-cells. Side effects are eliminated because the “kill me!” signal is unique to cancer cells and the designed T-cells only react to this one unique signal ignoring all other cells. The combination of the three protocols is called the Black Widow Immunotherapy Protocol (BWIP) or simply the Black Widow Protocol. The result of the coordinated protocols is a marriage between T-cells and cancer cells after which the T-cells destroy their partner cancer cells. Using cancer network editing, a gene activation link is inserted into the cancer network such that it produces a unique external signal to T-cells to indicate the cell is a cancer cell. In coordination, T-cells are edited to only attack the cells that emit the unique cancer signal. Black Widow coordinated cancer network immunotherapy forces cancer cells to emit unique signals that their co-engineered T-cells can recognize. Under this method transformed cancer cells cooperate with co-adapted T-cells to insure the cancer cells’ destruction. Unlike normal T-cell immunotherapy, there should be no side effects since co-engineered T-cells only kill co-edited cancer cells leaving all other cells alone. The Black Widow Protocol can be transformed to co-edited cancer cells and oncolytic viruses creating Viral Black Widow Protocols.
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One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9
Article
Full-text available
  • Aug 2016
Bacteria are indispensable for the study of fundamental molecular biology processes due to their relatively simple gene and genome architecture. The ability to engineer bacterial chromosomes is quintessential for understanding gene functions. Here we demonstrate the engineering of the small-ribosomal subunit (16S) RNA of Mycoplasma mycoides, by combining the CRISPR/Cas9 system and the yeast recombination machinery. We cloned the entire genome of M. mycoides in yeast and used constitutively expressed Cas9 together with in vitro transcribed guide-RNAs to introduce engineered 16S rRNA genes. By testing the function of the engineered 16S rRNA genes through genome transplantation, we observed surprising resilience of this gene to addition of genetic elements or helix substitutions with phylogenetically-distant bacteria. While this system could be further used to study the function of the 16S rRNA, one could envision the “simple” M. mycoides genome being used in this setting to study other genetic structures and functions to answer fundamental questions of life.
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Stem Cells: The Good, the Bad and the Ugly
Article
Full-text available
  • Aug 2016
Cancer stem cells are controlled by developmental networks that are often topologically indistinguishable from normal, healthy stem cells. The question is why cancer stem cells can be both phenotypically distinct and have morphological effects so different from normal stem cells. The difference between cancer stem cells and normal stem cells lies not in differences their network architecture, but rather in the spatial-temporal locality of their activation in the genome and the resulting expression in the body. The metastatic potential cancer stem cells is not based primarily on their network divergence from normal stem cells, but on non-network based genetic changes that enable the evolution of gene-based phenotypic properties of the cell that permit its escape and travel to other parts of the body. Stem cell network theory allows the precise prediction of stem cell behavioral dynamics and a mathematical description of stem cell proliferation for both normal and cancer stem cells. It indicates that the best therapeutic approach is to tackle the highest order stem cells first, otherwise spontaneous remission of so called cured cancers will always be a danger. Stem cell networks point to a pathway to new methods to diagnose and cure not only stem cell cancers but cancers generally.
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Stem Cell Networks
Article
Full-text available
  • Jul 2016
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem cell networks based on their network architecture. Each stem cell network has a unique topology and semantics and developmental dynamics that result in distinct phenotypes. We show that the ideal growth dynamics of multicellular systems generated by stem cell networks have mathematical properties related to the coefficients of Pascal's Triangle. The relationship to cancer stem cells and their control networks is indicated. The theory lays the foundation for a new research paradigm for understanding and investigating stem cells. The theory of stem cell networks implies that new methods for generating and controlling stem cells will become possible.
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A Genomic Regulatory Network for Development
Article
Full-text available
  • Mar 2002
Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.
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Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage
Article
Full-text available
  • Jan 2016
CRISPR Cas9 molecular scissors The CRISPR-associated (Cas) protein Cas9 is a molecular scissor for cutting DNA. The first step in the cutting reaction is the RNA-guided unwinding of the DNA double helix. Jiang et al. determined the structures of Cas9 bound to DNA unwound by the targeting RNA (see the Perspective by Chen and Bailey). Cas9 bends the DNA to allow guide RNA infiltration into the double helix. The two separated DNA strands, one bound to RNA, are subsequently positioned in the dual active sites of the protein for cutting. Science , this issue p. 867 ; see also p. 811
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New CRISPR–Cas systems from uncultivated microbes
Article
  • Dec 2016
CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA(1,2). Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences(3,4). The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research(5). However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms(6,7). Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet identified. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in E. coli. Interrogation of environmental microbial communities combined with in vivo experiments allows access to an unprecedented diversity of genomes whose content will expand the repertoire of microbe-based biotechnologies.
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Exploring the potential of genome editing CRISPR-Cas9 technology
Article
  • Nov 2016
CRISPR-Cas9 is an RNA-mediated adaptive immune system that protects bacteria and archaea from viruses or plasmids. Herein we discuss the recent development of CRISPR-Cas9 into a key technology for genome editing, targeting, and regulation in a wide range of organisms and cell types. It requires a custom designed single guide-RNA (sgRNA), a Cas9 endonuclease, and PAM sequences in the target region. The sgRNA-Cas9 complex binds to its target and creates a double-strand break (DSB) that can be repaired by non-homologous end joining (NHEJ) or by the homology-directed repair (HDR) pathway, modifying or permanently replacing the genomic target sequence. Additionally, we highlight recent advances in the repurposing of CRISPR-Cas9 for repression, activation, and loci imaging. In this review, we underline the current progress and the future potential of the CRISPR-Cas9 system towards biomedical, therapeutic, industrial, and biotechnological applications.
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DNA Targeting by a Minimal CRISPR RNA-Guided Cascade
Article
  • Sep 2016
Bacteria employ surveillance complexes guided by CRISPR (clustered, regularly interspaced, short palindromic repeats) RNAs (crRNAs) to target foreign nucleic acids for destruction. Although most type I and type III CRISPR systems require four or more distinct proteins to form multi-subunit surveillance complexes, the type I-C systems use just three proteins to achieve crRNA maturation and double-stranded DNA target recognition. We show that each protein plays multiple functional and structural roles: Cas5c cleaves pre-crRNAs and recruits Cas7 to position the RNA guide for DNA binding and unwinding by Cas8c. Cryoelectron microscopy reconstructions of free and DNA-bound forms of the Cascade/I-C surveillance complex reveal conformational changes that enable R-loop formation with distinct positioning of each DNA strand. This streamlined type I-C system explains how CRISPR pathways can evolve compact structures that retain full functionality as RNA-guided DNA capture platforms.
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Microbiome Therapeutics – Advances and Challenges
Article
  • May 2016
The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota.
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Gene regulatory networks for development
Article
  • Apr 2005
The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways. This program is executed by cis-regulatory DNAs (e.g., enhancers and silencers) that control gene expression. The regulatory inputs and functional outputs of developmental control genes constitute network-like architectures. In this PNAS Special Feature are assembled papers on developmental gene regulatory networks governing the formation of various tissues and organs in nematodes, flies, sea urchins, frogs, and mammals. Here, we survey salient points of these networks, by using as reference those governing specification of the endomesoderm in sea urchin embryos and dorsal-ventral patterning in the Drosophila embryo.
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