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GeneWerk: precision analyses for humans

Gene therapy approaches are increasingly being used for treating life-threatening diseases in humans. GeneWerk GmbH, a spin-off of the DKFZ and the NCT in Heidelberg, offers customised, high-resolution molecular and bioinformatic analyses that ensure the efficacy and safety of gene therapy and immunotherapy studies.

Gene therapy is considered one of the great beacons of hope for the treatment of incurable diseases. Viral vectors are already frequently used for transferring genes into human cells to treat life-threatening genetic defects. The number of clinical gene therapy trials worldwide is growing rapidly. Therapeutic results are extremely promising. However, in order to exclude severe adverse effects caused by gene therapy, viral gene shuttles need to undergo safety checks and resulting modifications in the cells need to be analysed. GeneWerk GmbH, a spin-off of the German Cancer Research Center (DKFZ) and the National Center for Tumour Diseases (NCT) based in the Heidelberg Technology Park, has unique expertise in determining the safety of viral gene therapy vectors. The company uses highly-efficient molecular analysis systems.

Glossary

  • Desoxyribonucleic acid (DNA) is a double-stranded, helical macromolecule encoding the genetic information of an organism.
  • An expression vector is a kind of ferry for genes, which allows the introduction of a specific gene into a host cell (e.g. E. coli, yeast cells). Furthermore, it contains all the necessary regulatory elements for the transformation of that gene into the protein.
  • A gene is a hereditary unit which has effects on the traits and thus on the phenotype of an organism. Part on the DNA which contains genetic information for the synthesis of a protein or functional RNA (e.g. tRNA).
  • Gene therapy is the attempt to cure a disease through the introduction of a gene into the body. a) Somatic gene therapy: somatic cells b) Germ cell therapy (banned in Germany) leads to inheritable alterations.
  • In a biological context, insertion often means the introduction of DNA fragments into another DNA molecule.
  • Being lytic is the feature of a bacteriophage leading to the destruction (lysis) of the host cell upon infection.
  • PCR or Polymerase Chain Reaction is a biomolecular method to amplify short DNA fragments in an easy way. Therefore, merely the DNA template, an enzyme named DNA polymerase which catalyses the amplification, short complementary oligonucleotides, which serve as starting point for the polymerase and the components of the DNA, which are called desoxynucleosidtriphosphates are needed. The amplification is controlled by several cycles of temperature changes.
  • Receptors are molecules which are often located on the surface of cells and which are capable of binding with an exactly defined molecule – their ligand. The meeting of ligand and receptors can lead to a sequence of reactions in the cell.
  • Ribonucleic acid (abbr. RNA) is a normally single-stranded nucleic acid, which is very similar to DNA. It also consists of a sugar-phosphate backbone and a sequence of four bases. However, the sugar is a ribose and instead of thymine, RNA contains uracil. RNA has got various forms and functions; e.g. it serves as template during protein synthesis and it also constitutes the genome of RNA viruses.
  • Genetic sequences are successions of the bases adenine, thymine, guanine, and cytosine on the DNA (or uracil instead of thymine in the case of RNA).
  • The somatic gene therapy is used to compensate gene defects. Therefore, the correct form of the mutated gene is transferred into somatic cells.
  • Transcription in a biological context is the process of transcription from DNA into RNA. In this processes, a single-stranded RNA molecule is synthesized on the basis of the double-stranded DNA with the help of an enzyme named RNA-polymerase.
  • Translation in a biological context is the process in which the base sequence of mRNA is translated into the amino acid sequence of a protein. This process takes place in the ribosomes. Based on a single mRNA molecule, many protein molecules can be synthesised.
  • A vector is a DNA vehicle that is able to replicate autonomously in the cell and with which foreign DNA can be introduced into a cell. Vectors (plasmid, phage, or virus) are important tools in genetic engineering for the cloning of recombinant DNA.
  • A virus is an infectious particle (no cell!) consisting of a protein envelope and a genome (DNA or RNA). To be able to reproduce it depends entirely on the metabolism of living cells of host organisms (e.g., bacteria for phages, liver cells for Hepatitis A-virus).
  • Biopharmaka are Drugs, which are produced with the help of biological systems.
  • Stem cells are cells from the embryo, fetus or adult that that have the ability to divide for indefinite periods in culture and give rise to specialized cells. In Germany it is illegal to extract the stem cells from embryos.
  • Oncology is the science that deals with cancer. In a more restrictive meaning, oncology is a sector of medicine that attends to the prevention, diagnostics, therapy and aftercare of malignant diseases.
  • A tumour is a swelling of a tissue caused by abnormal cell growth, which can be benign or malignant. Benign tumours are local swellings, whereas malign tumours may seed off and spread into other tissues, causing secondary growths (metastases).
  • Biochemistry is the study of the chemical processes in living organisms. Therefore it touches the studies of chemistry and biology as well as physiology.
  • Validation is the process of verifying a thesis or a method of resolution in relation to the problem that should be solved.
  • Molecular biology deals with the structure, biosynthesis and function of DNA and RNA and their interaction with each other and with proteins. Molecular data can lead to an improved understanding of the reasons for diseases and can help to improve the mode of action of drugs.
  • Haematopoiesis is the process of the generation and maturation of blood cells. This process takes place in the red bone marrow in the human body, where the haematopoietic stem cells are located. The decision which type of blood cell (e.g. platelets, red or white blood cells) develops from the blood stem cells mainly depends on the growth factors that are present during maturation.
  • Computer tomography (CT) is a imaging technique to display the structures within the body. Therefore, radiograms are taken from different directions and are analysed by a computer to get a three-dimensional image.
  • T-Lymphocytes (also called: T-cells) are important cells of the immune defence (white blood cells), which recognize foreign particles (antigens) when they are bound to the surface of other cells. Together with the B-lymphocytes, T-lymphocytes participate in the aquired immune response, which means that they are able to respond specifically to a certain pathogen.
  • Molecular means: at the level of molecules.
  • Biomolecules which can bind active agents are called targets. They can be receptors, enzymes or ion channels. If agent and target interact with each other the term agent-target-specific effect is used. The identification of targets is very important in biomedical and pharmaceutical research because a specific interaction can help to understand basic biomolecular processes. This is essential to identify new points of application.

Precision biology for humans

Prof. Dr. Christof von Kalle © NCT
Dr. Annette Deichmann © GeneWerk GmbH
Dr. Manfred Schmidt © GeneWerk GmbH

GeneWerk GmbH was founded by Prof. Dr. Christof von Kalle, Dr. Manfred Schmidt and Dr. Annette Deichmann in July 2014. Schmidt and Deichmann are the owners and directors of the company, in which the DKFZ is also directly involved. Oncologist and haematologist Christof von Kalle, director of the Department of Translational Oncology at the NCT and DKFZ and managing director of the NCT, is an internationally renowned scientist in the fields of stem cell research, mutation analysis and gene transfer. He is closely associated with the company as advisor.

Before molecular biologist Manfred Schmidt was involved in founding the company, he had already made a name for himself mainly through the further development of complex PCR technologies into analytical tools. Such tools can be used to check the insertion of viral DNA into the host genome with the utmost precision, right down to single-cell level. As head of the Molecular and Gene Therapy research group in the Department of Translational Oncology at NCT and DKFZ, Schmidt was involved in the most successful gene therapy studies in the world aimed at treating immunodeficiencies. Schmidt's role in the studies was monitoring the clonal composition of blood-forming cells, as knowledge of the expansion of a specific cellular clone provides information on the risk for later haematopoietic cancers. 

Biologist Annette Deichmann has been involved in research in the fields of microbiology, biochemistry and human genetics at universities in Germany and abroad. She had some experience in industrial research before becoming involved in scientific project management as coordinator in von Kalle’s research department. She is still involved in the scientific side of these research projects.

GeneWerk’s team has many years of experience in integration-site analysis, high-throughput sequencing, whole-genome sequencing and bioinformatics, and caters for its customers' needs with a broad range of highly sensitive molecular methods. The company motto is “Precision biology for humans”, and it develops innovative research concepts and analysis platforms to ensure efficacy and safety in new gene therapy and immunotherapy studies. The creativity of the company’s own technological developments is apparent, for example, in what is known as “non-restrictive linear amplification-mediated PCR” (nrLAM-PCR). This technique provides a way to precisely analyse the insertion sites of viruses that are integrated as vectors in human cells, thus counteracting the risk of tumorigenesis induced by the vector systems.

GeneWerk products

Schematic of nrLAM-PCR (non-restrictive linear amplification-mediated polymerase chain reaction) compared with LAM-PCR (abbreviations: LTR, long termination repeat; dsDNA, double-strand DNA; ssDNA, single-strand DNA). © GeneWerk GmbH

In addition to nrLAM-PCR, GeneWerk also offers a method known as target enrichment sequencing (TES), which can also be used for amplifying sequences of interest.

The company also offers the following standard analyses:

  • Immune-repertoire analyses involving the sequencing of the hypervariable region of T-cell receptors; these analyses can be used to determine the clonal and functional status of a T-cell population. In the near future, the company will also offer similar analyses for B-cell receptors, which will help determine a person’s immune status and antigen recognition capacity.
  • Quantitative PCR (qPCR) for the simultaneous amplification and quantification of DNA or RNA fragments.
  • (Off)-target analyses for genome editing, i.e., the analysis of nonspecific genome sequence modifications outside the target site using designer nucleases such as zinc finger nucleases, transcription activator-like effector nucleases (TALEN) and CRISPR/Cas9.
  • Specific bioinformatics and data management programmes for next-generation sequencing projects, whole-genome analyses, modelling and computer simulations.

Acquired data are subsequently analysed with bioinformatics methods by GeneWerk’s highly qualified staff according to clients’ individual requirements. High quality standards and the continuous optimisation of the analytical processes make it possible to deliver reproducible data within a relatively short time. The company is currently working on a new IT infrastructure in order to fulfil client requirements and efficiently evaluate the huge amounts of data. In addition, company certification is also on the cards. This upcoming certification and the company's broad range of validated analysis services mean that GeneWerk is also targeting the customers of the major international biopharmaceutical companies. Such potential customers are increasingly involved in gene therapy as a promising option for treating cancer and other incurable diseases.

Reference:

Christof von Kalle, Annette Deichmann, Manfred Schmidt: Vector integration and tumorigenesis. Human Gene Therapy, June 2014, DOI: 10.1089/hum.2014.2525

Website address: https://www.gesundheitsindustrie-bw.de/en/article/news/genewerk-precision-analyses-for-humans/