rediscover your scientific aspirations · 2019. 4. 25. · your scientific aspirations...
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The advent of genome editing tools such as the CRISPR/Cas9 system has given scientists an affordable, accessible, and relatively simple method to alter genes. Yet precisely controlling protein expression
:;<=��;��:<��:�<�������=�::<�����:=�����=�����:=���:� ���=��immense importance in the context of expressed therapeutic proteins, such as prescription medications. Controlling protein expression in other species, such as mosquitoes, may even ���<����<�;�<�����<����:�������<���:;��� ���������:�����viruses, dengue fever, and other mosquito-borne illnesses.
��<���� �����=������=������<�:==���;������<�<���;���effects, as evidenced by the wide range of CRISPR applications already being used. ìCRISPR systems are amazing resources �=<������������:==���:=�������:���������������������Jamie Cate, professor in the departments of molecular and cell biology and biochemistry at the University of California, Berkeley. ìI see the present as the biological equivalent of the :<����:=<�<��=��:=���=<��=��:�<����
Other molecular tools are evolving alongsideóand sometimes interacting withóCRISPR systems to broaden the scope and increase the potency and versatility of controls =��<=:�����<���=����<:�������� �������=<����������<��shedding their limitations and gaining programmability. Molecular switches are becoming multifaceted, enabling �<��:�<������:���������:�����<�:=����<���=�����:��������churn out greater yields of complex biological therapeutics than ever before. One thing is certainóas molecular controls become increasingly sophisticated, their myriad uses continue to expand.
�" ������ ���� ���#"� �"� ����������������:;=��;�:!����=��<����:==��������:;��"�#$%�&"��'����:���;���
=����=�����<��(�� ���������:;��<���<����:��=<���<=:=����<���)����:��=:��*%�+,����������)��:���:<����=��:;���:��������:����:���-;��%�+��������������(������������=<�:;��"��'��� ������=�:��<����������������<���(�:����=���:���*����%�+������������=���!:����:���:<����=�������<�����:����:���=���������:=�(���<��:��,��.�����;�=��:;���������<��=<�(=���:����������at the ��"������# � ���� � ��#"�� �#����#�#������� "� ��#������#��� ��"������!��������::��:���:=������=���"�#$%��� ��genome editing tool that would remove this constraint, and offer �=<����<��:�:��(���<�::�����:����:;=�:���%�+�����������
�;�=!����(������=�������<:������<��:<�:=���� ����*��1,����:���(�����=��%���=������<�=���:��<=:����<=��:;���<�;��=��Pyrococcus furiosus����<= �<�=:��*������������,���<=(���-;��platform surpasses traditional type II restriction enzymesó�=������<�����=<��:;�:�������������:�<����������:���*1,��
2�������<�������<��:���������:������(�<�=���<:������<��:<�:=���� �������:;����<������������������:���������������:� �������=����<��������:;������������������:����=���:���=����������<=:����%���=������:�=������������=<�:�<��:������������������3�=�(����:<���������4������������says Zhao. ìThis system can be multiplexed, in that the same <=:�������(���=������:;����:��������������=<�:�<��:�������<����:�������:���=������
/�������:;�������������;=��%���=��;�<��:=���:��:;�����:�������(��<=�<������:=���:��<:����������;�<�����=:;�<������:������:;�:�%���=�;����=���<�<��=��:=������������*:�������56�(�����<�,�:;����=�:<��:=����<��:<�:=���� �����*�;�;�:�������<��=�� ��7�:=�8�(�����<�,9����=���<�<��=��:=������������� ���:��=<��� ����:=������������������������:���0�� ��<��=����<:������<��:<�:=���� ������%���=���������<�:���������������=���<��:� ��������;�����::���������;�;��������(������:����::��;��������<�����:��:=��:;�<�
�;�=!����(�������<�:=�����:������:��;�=�=����2������=������=�����%���=&��1�(������<��:���=������:;=��:=���=���large, natural-product biosynthetic gene clusters for discovery of novel natural products that can potentially be used
Upcoming features
����� ���������������������� � ��������� �� �� �����is increasingly important as a pharmaceutical production mechanism for biological therapeutics. The ability to direct the ultimate nature of proteins depends largely on the degree of ��������� � ���� ������ ��� ���� ����������������� �������������������� ������� ������������������� ���� �����new next-generation expression systems is revitalizing protein expression protocols.��������������
DNA/RNA: Improving ChIP Assays—December 7 Next-Gen Sequencing: RNA Seq—February 22 Multiphoton Microscopy—March 22
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Protein expression, revisited
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may be more suitable ìin clinical therapeutic genome editing in situ, or gene drives in which environmentally compatible control is paramount,î says Tsai. %&'(����(����'���'������� �(�����(�����&���(�������&������
and was developed by a Swiss collaboration headed by Tom Ward, director of NCCR (National Centre of Competence in Research) Molecular Systems Engineering, a multidisciplinary initiative comprising researchers at the University of Basel and ETH Zurich (Swiss Federal Institute of Technology). Wardís lab took a modular �����&�����'����'���&�&��(������&' ������'����(��������(��-�'�&������ �(�������(�����&�������&�(��(�&���'�������'���(���&�Matileís lab in the Department of Organic Chemistry at the Univer-sity of Geneva, and a synthetic gene-switch module produced by Martin Fusseneggerís lab in the Department of Biosystems Science and Engineering at ETH Zurich. �����&� �������&�(��(�&�����������'������(���&���(������
��(���'�&������&(��������� �(�'(������&���(�������&���&(�'������'��&��'�������������������'&��&(����(����&������(������������-tion that uncages a hormone. The synthetic gene-switch module detects the newly uncaged hormone and responds by turning on ��������'&�'��(��� '����&(��&���('�������������������&��� �(�����(���(�&���'&�����&����'(�����(�'&�'����(�������&���(�������&������������������
Now that the collaboration has established proof-of-concept for their system (4), they are actively pursuing biomedical applications (��(��&�����&(���(�&�� �(�����'�(���'(��&!�'���������������'(��&���������������&��������(��(��&�������������(����(�&����"��-�'&���&�����������'#������������'&�(���������'����&���&���cell lines,î says Ward. ìWe could use this protein to accumulate the ��(��������(���'�&�������(����'&�(���������'���&�����'���&�������$�(������(������(�&���'&�'&��� ��&�(�����(��������(���'�&-�������&���('����'&���&���������
Next-generation expression systems%�#�&����&��'������'&(�'��'����&����������'&��������'�
����&��&��(���'��'�(&�(�����'����'(��&���������'&����(�����%��������&��(������''���'��������� ����('���������&� ���'�'���������&��(���&���������'&����(�����������&�&��(��(�'&��"���&(����(����(�&�������������'&����(��������������&�"��&����
as antibiotics and anticancer drugs,î says Zhao. His newly formed company, Modular Bioscience,� ��������6��� �4�6!��use in medical diagnostics, such as liquid biopsies, and single-nucleotide polymorphism and pathogen detection.4567�����"#� "����6��7���4��65�7����67��5���6��7�����7�-
rium Marinitoga piezophila (MpAgo) is in the crosshairs of Cateís lab, which focuses on protein-translation mechanisms and regu-lation (2). ìOur goal was to make an RNA-targeting technology 7��7� ��6������76�����6���"$4���6�6����5����5�������������Cate. They wanted to target RNA using an RNA-guided protein, as an alternative to labeling RNAs with covalent tags. 6�7�676��������������4�����%���5��7������������6����7�!��
team, found the main challenge was ìhow to load the guide RNA into MpAgo inside cells,î says Cate. She solved this problem by ��������5�������"$4&��67��5�6��������'"$ �(��5���7�6��7��5���5��7���"$ ���5�������������������57���%���5��7���65��7��7����6����7�65�6��7���)*�5��67����6��7��������"$4�����7����5����������6����������"$ �� �7����������5�7��76�7����������6����-��57����"$4�7����7���+�7����6����7����6������"$ ����6 ������������7����5���5��������5�7����7 ��5�"$4����7��7���differing by only one nucleotide.��7��������7���76�����6���7�����6���7���6����5����7�5��"$4��
��5��,�4�6�"$ ������������6�7�������76����,�4�6��6��"$4�7����7�5���5����5������76�����6������5�"$4���6�6�����������5������5���5����67�6������������57�������������-�����MpAgo is derived from bacteria, its use for therapeutic purposes is unlikelyóbut Cate hopes to apply this system to gain insight into how endogenous human Argonautes work.
Molecular switches.���5�7����56��6���������7����6���"#� "/���0���56���
editing, the search is on for ways to make the system induc-�������6�7��7����7�5���5����7�5���65�6��6����7�������7������4�United Kingdomñbased collaboration between Yu-Hsuan Tsai from Cardiff University �5��457�65�� �������6��7���University of Bath�����������5� �7����6���5�������"#� "�� �7��'3(�� ����6��switches had drawbacks, such as leakiness of editing activity in the absence of signal, or a reliance on antibiotic use, which can increase the risk of antibiotic resistance. ìWe envisaged the use 6���5���7�������565�����6�6��������56�����17��72� 6�����������these problems,î says Tsai. ������5�� ����!����6���������5�7��6�������5��65�76������
����56�����5��7����76��5���7���������5����#5�������5����5���6��������6�������������������5�����7�����5�7��6�������5���7�5����766���7�7��7�������7�����������65�6�����0�'7����5�������3�����for genome editing) dependent on the presence of lysine de-����7����%���'-6(�������565�5�7�������56���������������6��7����purpose because it is cheap, safe, readily obtainable, and easy to administer to cells or whole animals. �����������������6 ���7��7�7��������5��6��%���'-6(�����7���
in genomic editing, while in its absence no genomic editing oc-���������������6��������5�� ����!��� �7�������������5����7�to the difference in strategies: ìOur approach controls the trans-��7�65�6��7����57�65������0���67��5�� ������������6����7�6���1��2��6�77��5���7�65���657�6����������6���7�5��7����7���7��6��translated protein by different stimuli,î says Tsai.
Future applications of their work include gene drives, which virtually ensure that all progeny will inherit genetic changes that rapidly spread throughout a population of animals (in herds of livestock, for instance). Because the effect is inducible, its power �5�����6����������657�6�����������5� ���5�������"#� "�� �7�� IM
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Next-gen expression systems may see further
record expression levels with the incorporation of
genome editing tools like CRISPR/Cas9.
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hamster ovary (CHO) cell lines. However, the limitations of CHO cellsósuch as high cost and comparatively slow doubling timesómake the next-gen systems worth considering for expressing new biopharmaceuticals, especially to help reduce the costs of important medicines.
For example, the SoluPro protein expression platform from AbSci can generate soluble, properly folded proteins at extremely high titers, currently 4g/L of full-length antibody and >20g/L of other complex products, using Escherichia coli expression. Typically, some human proteins canít be expressed in E. coli, and require mammalian cell lines for proper folding. AbSciís technology includes two innovations that make it possible to produce such proteins in E. coli, while taking advantage of the simplicity and lower costs of this expression system.
One creation is a semioxidized cytoplasm that produces <=>?�>�����<?>����>������=����< �����=>�<�����=�?���=���������traditionally is limited by inclusion body formation, is desirable ����?<�������<�<���������>�����������������������������>�<���places no restrictions on protein size, and achieves dramatically shorter production cycles of one to two days, compared to secretion-based expression systems,î says Sean McClain, AbSciís founder and CEO. The second innovation is SoluProís dual inducible promoters, which can be independently controlled. This ����>�<���?������=���=������=�?���=������<����=����������=������best protein-folding and titer.������=>?��=�<�<����<����>�����=��=��>���=>���=����<�
overcomes a large majority of the limitations found with traditional E. coli�����<<�=����<��<����>��� �� ����!��<?���<<�?>>��produced novel antibody scaffolds as well as IgG1 and IgG4 molecules where effector function is not desirable.î Many of these novel antibody scaffolds, which are gaining increasing traction in development pipelines, are challenging to produce in CHO ��>>< ���"������<����>���=�?<���=�����<��������=��=�?����������������=�������=���<����=>�<�����>?�������<�����<��#��$������������<��>>����>�%��?<�=���=����<������=������?>��<�������=�?��<���������=>?��=��<�����>>��<?������=����?����?�����������>�������<��< Dyadic offers another next-gen expression platform, the
fungal-based C1 gene expression system. Dyadicís scientists took advantage of a serendipitous mutation that resulted in a several &''��=>��������<������=������=�?���!����=�������>�����=?<�Myceliophthora thermophila fungus (which the company
�����������&�������������������=>��?>����==><����=��?�������fungus into a recombinant expression host). They are currently focused on biomedical efforts, applying the C1 expression platform to making biologic vaccines and drugs more affordable ��������<<��>� ���=?����>�����=?<��?��?<�����<=?�����=�����in nature they are natural secreters (C1 has a 2-hour doubling time, compared to about 20 hours for CHO cells). They also use �������<�����������������������<�������������!=��<����������for viral inactivation required for CHO cells.
Today, biosimilars are being produced ineffectively by cell lines such as CHO cells, according to Dyadicís CEO Mark Emalfarb. (=��!����<��<�)��>������� �������=�?���?��=�*��=�+�����<��=���������������=���������������������������=��=���(,��������=<�<�$�<��=�������=%�������=������!���������?<�����(,��=�?���!��� ��And because C1 secretes its product into the media, the down-stream protein harvesting steps are also simpler than those in oth-er systemsófor example, E. coli requires lysing of cells and purify-ing product from cell fractions, adding more complexity and cost. -������<��&�>���=�����������>���=�?��<��?>>�>�������=�=�>=��>�
antibodies, antibody heavy and light chains, Fc-fusion proteins, #��<�.������������������������</����<�����������=���<������!��-����< �� �������><=�����01�<�$!��?<�>��������>�<%���������������=-������>>���=���=��������<�=��!������<�����������=��������?>���=�����<<����������>���<��<�)��>���� �� ���!�����!����<��������01��now, so less is lost in downstream processing.î
Dyadic is also engineering C1 to produce human-like glycosylation in different forms, to allow pharmaceutical �=�����<��=��!�>?�������� ��2�>����(,���>><���&���>><�����monoclonal cells,î explains Matthew Jones, Dyadicís chief �=�������>�=����� ���&���<�����=������>��=��=�?����=���consistent, more homogeneous glycostructures for companies to evaluate, to test which ones may work better.î A recently announced collaboration with the biopharmaceutical company ���=��"!����<�-�?�<��>����3��(���>>�<�?�������?<��=�������&�technology to express different types of therapeutic compounds, such as vaccines and protein-based biologics.
Both E. coli- and yeast-based expression systems share other advantages, such as not requiring the expensive viral clearance steps needed in CHO cells. In addition, the lower costs of next-gen expression systems can in turn lower drug prices, while allowing ��?�����?����?���<��=�������������=���������4�������������!���<�manufacturers to produce drugs with lower prices and make them available to the public. Both McClain and Emalfarb hope their companiesí technologies will encourage manufacturers to market ��?�<�����������==���=��<=�������?���=��=������<���=����>���<?����<�������5?�����!������<�������=<��>�<<��?���=��������
None of this would be possible without the genetic tools that �����<<�����<<�=��<�<���< �"<�<������<�<������!��������=���=><�over genomes, the number of expression products will soar. For example, next-gen expression systems may see further record expression levels with the incorporation of genome editing tools like CRISPR/Cas9. As these tools continue to grow in <=��<������=�������������<��=�������<���>>��=����?���=�������<�4and may transform biomedicine in the process.
References1. B. Enghiad, H. Zhao, ACS Synth. Biol. 6��6+*76+6�.*'&6/ 2. A. Lapinaite, J. A. Doudna, J. H. D. Cate, Proc. Natl. Acad. Sci. U.S.A. 115, � 889:78868�.*'&:/ ;3. T. Suzuki et al., Sci. Rep. 8��&''+&�.*'&:/ 4. Y. Okamoto et al., Nature Comm. 9, 1943 (2018).
Caitlin Smith is a freelance science writer in Portland, Oregon.
Featured participants
AbSci
www.absci.com
Cardiff Universitywww.cardiff.ac.uk
Carl R. Woese Institute for Genomic Biology,University of Illinois at Urbana-Champaignwww.igb.illinois.edu
Dyadicwww.dyadic.com
ETH Zurich
www.ethz.ch/en.html
Modular Bioscience
modbiosci.com
NCCR Molecular Systems Engineeringwww.nccr-mse.ch/en/home
University of Baselwww.unibas.ch/en.html
University of Bathwww.bath.ac.uk
University of California, Berkeleywww.berkeley.edu
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