Five Gene Therapy Trials (The Medicine Issue)

Including first-in-human zinc finger nuclease trials & an RNA vaccine for Ebola virus.

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iGEM judging is over, so it’s back to the grind. Particular congratulations to the high school team from Lambert, Georgia who walked away with a top prize. They blew me away with their breadth of knowledge and enthusiasm — bright futures ahead.

A slew of Phase I trials were published this week, including one that used CRISPR-edited T-cells to treat children with a refractory form of B-cell leukemia, another trial for patients with adenocarcinomas, and the “first-in-human” trials for zinc finger nucleases.

First up, in Science Translational Medicine, a London-based group used CRISPR-modified T cells to treat six children with refractory CD19-positive B cell acute lymphoblastic leukemia, or B-ALL. These kids have cancer in their blood and bone marrow. B cells are a type of white blood cell that produces antibodies for the immune system and carries an antigen called CD19. Elevated levels of CD19 are often used to detect whether this cancer is present. Each of these children was aggressively treated for their leukemia, but their bone marrow still had residual cancer cells afterward.

Researchers knocked out two genes in CAR19 T cells using CRISPR-Cas9: CD52 and TRAC, which encode a short peptide found on T cell surfaces and an antigen receptor, respectively. These deletions help the engineered cells to last in the body for a longer time. Modified T cells were grown in the lab for about two weeks and then were collected in a tube. The six children were each given a short chemotherapy course to kill off their existing T cells, and then were injected with about 1.4 million of the engineered T cells per kilogram of body weight.

Two of the children had complete remission, and four died. The CAR19 T cells never expanded after infusion for two of the children, and only one child experienced treatment-related toxicity.

For the second study in Nature Communications, a new type of cancer vaccine was tested in 21 people with advanced adenocarcinomas, a type of cancer that begins in glands lining the inside of the body.

A cancer vaccine was made by packing adenovirus with a loop of DNA encoding a MUC1 antigen fused to the extracellular bit of CD40. MUC1 is a protein secreted by adenocarcinoma cells (a biomarker, basically) and CD40 probably helps to block tumors from growing. Preclinical data suggests that fusing CD40 to tumor-associated antigens can help produce an immune response against specific cancers.

Each trial participant was injected with the vaccine. Adverse effects were mild; a few allergic reactions and fevers. Although none of the patients had a partial or complete response to the vaccine, the vaccines did change each patient’s “cancer immunome,” helping to increase the proportion of cytotoxic CD8 T cells, which help protect against tumors and pathogens, and CD14+ monocytes, which are white blood cells that help mediate inflammatory responses.

And for the third study in Molecular Therapy, researchers report initial data from the first-in-human clinical study to test zinc finger nucleases for gene therapy. Zinc finger nucleases are engineered enzymes that cut DNA. They are made by fusing a DNA-binding protein to a DNA-cleavage domain. By tweaking these fused proteins, a zinc finger nuclease can be modified to target a wide range of target sequences. Patients were first dosed back in 2017 for three conditions: mucopolysaccharidoses I or II — an inherited, metabolic condition in which enzymes stop working and long sugar chains build up in cells — and hemophilia B, an inherited bleeding disorder.

Each trial was quite small; just three people were treated for mucopolysaccharidoses I, nine for type II, and one person for hemophilia B. The results were a bit disappointing. The treatments were relatively safe, but didn’t work for the person with hemophilia B (nor did the researchers sequence the genome to see if the zinc finger nucleases cut the target DNA). A couple of people with mucopolysaccharidoses had a moderate response, but there were “no clinically significant findings in either MPS I or MPS II subjects.”

Thanks for reading.

— Niko McCarty

A self-amplifying RNA vaccine protected mice against lethal doses of the Ebola virus. Two types of vaccines were tested; one carries an RNA encoding the Ebola virus’ glycoprotein, and another carries an RNA that encodes both the glycoprotein and a nucleoprotein. Companies like Chimeron Bio are already developing self-amplifying RNA vaccines, which include a replicase sequence that helps them to make many copies inside of a cell. I wasn’t able to access the full text of this paper, but I thought it sounded interesting and merits a share. Molecular Therapy (Link)


African trypanosomiasis doesn’t kill many people these days. In 2020, there were just 663 reported cases of the parasitic disease, typically in rural areas of sub-Saharan Africa. But a small number of cases doesn’t mean we should forego new diagnostics.

A new study reports a CRISPR-based diagnostic tool, called SHERLOCK4HAT, that can detect two different species of T. brucei parasites known to cause trypanosomiasis. The tool can detect just 1 parasite per microliter of blood — wet or dry — in one hour, at a cost of 2.2€ per sample. Sensitivities weren’t always great, but current diagnostics rely upon antibodies and physical observations of parasites under a microscope, which requires specially-trained staff and costs more money. eBioMedicine (Link)

A single-step reaction, using SHERLOCK4HAT, can detect 1 parasite per microliter of blood in about one hour.

Special paper can sensitively detect SARS-CoV-2 in less than one minute “directly from unprocessed saliva samples,” according to a new study that used carbon paper electrodes — the same material used in flow batteries and fuel cells — to detect a specific biomarker of viral replication, called 3CL-pro.

The paper is first coated in an antibody that binds to this biomarker. The paper also has a reactive indicator that electrochemically detects pH changes. Saliva samples carrying the virus cause a change in pH that can be detected electrochemically. The papers were tested on samples from 26 SARS-CoV-2 positive participants, as well as 24 people who had previously recovered from COVID-19. It had a sensitivity and specificity of 100% and could detect just 6.6 micrograms of virus per milliliter of saliva. Nature Communications (Link)

Oxidation peak shifts for 50 saliva samples.

The Index 🔻

(↑ = recommended article, * = open access, † = review, comment, etc. )

Basic Research

*First direct evidence for direct cell-membrane penetrations of polycationic homopoly(amino acid)s produced by bacteria. Takeuchi Y…Hamano Y. Communications Biology. Link

Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI. Liu C…Wang J. Nature Biotechnology. Link

YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Zheng Y & Nair SK. Nature Chemical Biology. Link

Structure and function of a bacterial type III-E CRISPR–Cas7-11 complex. Yu G…Zhang H. Nature Microbiology. Link

Biomanufacturing, Metabolic Engineering & Biomaterials

*Metabolic reconfiguration enables synthetic reductive metabolism in yeast. Yu T…Nielsen J. Nature Metabolism. Link

*An Inducible T7 Polymerase System for High-Level Protein Expression in Diverse Gram-Negative Bacteria. Greenwich JL, Alaklavuklar MA & Fuqua C. bioRxiv (preprint). Link

Synthesis and Concomitant Assembly of Adeno-Associated Virus-like Particles in Escherichia coli. Le DT…Müller KM. ACS Synthetic Biology. Link

*Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production. Benisch M…Khammash M. bioRxiv (preprint). Link

*Light-regulated pro-angiogenic engineered living materials. Dhakane P, Tadimarri VS & Sankaran S. bioRxiv (preprint). Link

*Overproduction of Native and Click-able Colanic Acid Slime from Engineered Escherichia coli. Sadler JC…Wallace S. bioRxiv (preprint). Link

†Design of biomass-based renewable materials for environmental remediation. Zhang W…Dai SY. Trends in Biotechnology. Link

†A review of yeast: high cell-density culture, molecular mechanisms of stress response and tolerance during fermentation. Shen D…Wu Z. FEMS Yeast Research. Link

Engineering Escherichia coli for Conversion of Dietary Isoflavones in the Gut. Kydd L, Shiveshwarkar P & Jaworski J. ACS Synthetic Biology. Link

Biosensors

A propeptide-based biosensor for the selective detection of Vibrio cholerae using an environment-sensitive fluorophore. DeColli AA…Hatzios SK. Cell Chemical Biology. Link

Sensitive genetically encoded sensors for population and subcellular imaging of cAMP in vivo. Massengill CI…Zhong H. Nature Methods. Link

Harnessing Escherichia coli’s Native Machinery for Detection of Vitamin C (Ascorbate) Deficiency. Piorino F & Styczynski MP. ACS Synthetic Biology. Link

*Revealing β-TrCP activity dynamics in live cells with a genetically encoded biosensor. Paul D…Cappell SD. Nature Communications. Link

Build-A-Cell

*Ribozyme-phenotype coupling in peptide-based coacervate protocells. Le Vay K…Mutschler H. bioRxiv (preprint). Link

Cell-Free Systems

*Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA. McFeely CAL…Hartman MCT. Nucleic Acids Research. Link

*A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans. Jaroentomeechai T…DeLisa MP. Nature Communications. Link

Computational Tools & Models

*Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data. Ciciani M…Segata N. Nature Communications. Link

*RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications. Bao X…Zuo Z. Nucleic Acids Research. Link

*PROTAC-DB 2.0: an updated database of PROTACs. Weng G…Hou T. Nucleic Acids Research. Link

Annotation of spatially resolved single-cell data with STELLAR. Brbić M…Leskovec J. Nature Methods. Link

*Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline. Mikolajewicz N…Han H. Communications Biology. Link

CRISPR, Gene Editing & Control

*License to cut: Smart RNA guides for conditional control of CRISPR-Cas9. Baccouche A…Genot AJ. bioRxiv (preprint). Link

*A doxycycline- and light-inducible Cre recombinase mouse model for optogenetic genome editing. Vizoso M…van Rheenen J. Nature Communications. Link

*Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells. Li M…Zhou T. Nature Communications. Link

DNA Sequencing, Synthesis & Assembly

*HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. Kim CY, Ma J & Lee I. Nature Communications. Link

Medicine & Diagnostics

*First-in-human in vivo genome editing via AAV-zinc finger nucleases for mucopolysaccharidosis I/II and hemophilia B. Harmatz P…Muenzer J. Molecular Therapy. Link

Phase 1 clinical trial of CRISPR-engineered CAR19 universal T cells for treatment of children with refractory B cell leukemia. Ottaviano G & the TT52 CRISPR-CAR Group. Science Translational Medicine. Link

*SHERLOCK4HAT: A CRISPR-based tool kit for diagnosis of Human African Trypanosomiasis. Sima N…Glover L. eBioMedicine. Link

*A phase I study of an adenoviral vector delivering a MUC1/CD40-ligand fusion protein in patients with advanced adenocarcinoma. Tan TJ…Toh HC. Nature Communications. Link

*Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial. Choudhary MC & the ACTIV-2/A5401 Study Team. Nature Microbiology. Link

*Optogenetic-controlled immunotherapeutic designer cells for post-surgical cancer immunotherapy. Yu Y…Ye H. Nature Communications. Link

Self-amplifying RNA vaccine protects mice against lethal Ebola virus infection. Krähling V…Sahin U. Molecular Therapy. Link

Therapeutic gene editing of T cells to correct CTLA-4 insufficiency. Fox TA…Morris EC. Science Translational Medicine. Link

*Ultrafast one-minute electronic detection of SARS-CoV-2 infection by 3CLpro enzymatic activity in untreated saliva samples. Borberg E, Granot E & Patolsky F. Nature Communications. Link

*Diagnostic efficiency of RPA/RAA integrated CRISPR-Cas technique for COVID-19: A systematic review and meta-analysis. Zhang X…Li H. PLoS One. Link

*De novo selected hACE2 mimics that integrate hotspot peptides with aptameric scaffolds for binding tolerance of SARS-CoV-2 variants. Lee M…Oh SS. Science Advances. Link

Plants

*Phytoremediation of isoproturon-contaminated sites by transgenic soybean. Kong X…Jiang J. Plant Biotechnology Journal. Link

Protein Engineering

Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs. Xu Y & Zhu TF. Science. Link

*Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics. Gavrilov M…Ha T. Nature Communications. Link

*Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro. Lee J…Jewett MC. Nature Communications. Link

In vitro evolution of ribonucleases from expanded genetic alphabets. Jerome CA…Biondi E. PNAS. Link

Tissue & Molecular Engineering

Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains. Speltz TE…Moellering RE. Nature Biotechnology. Link

AgeMTPT, a Catalyst for Peptide N-Terminal Modification. Cong Y, Scesa PD & Schmidt EW. ACS Synthetic Biology. Link

*Intermediate cells of in vitro cellular reprogramming and in vivo tissue regeneration require desmoplakin. Ha J…Kim J. Science Advances. Link

Geometric engineering of organoid culture for enhanced organogenesis in a dish. Park SE…Huh DD. Nature Methods. Link

Tools, Toolkits & Technology

Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Jiang K…Abudayyeh OO. Nature Biotechnology. Link

*Cell-specific bioorthogonal tagging of glycoproteins. Cioce A…Schumann B. Nature Communications. Link

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. Dardani I…Raj A. Nature Methods. Link

*Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing. Gunter HM…Mercer TR. Nature Communications. Link

3D-printed machines that manipulate microscopic objects using capillary forces. Zeng C…Manoharan VN. Nature. Link

HT-smFISH: a cost-effective and flexible workflow for high-throughput single-molecule RNA imaging. Safieddine A…Bertrand E. Nature Protocols. Link

*Wireless, fully implantable cardiac stimulation and recording with on-device computation for closed-loop pacing and defibrillation. Ausra J…Gutruf P. Science Advances. Link

Two-Layered Microfluidic Devices for High-Throughput Dynamic Analysis of Synthetic Gene Circuits in E. coli. Sun Y…Luo C. ACS Synthetic Biology. Link

*Synthetic Biology Toolbox, Including a Single-Plasmid CRISPR-Cas9 System to Biologically Engineer the Electrogenic, Metal-Resistant Bacterium Cupriavidus metallidurans CH34. Turco F…Kovacs K. ACS Synthetic Biology. Link

Other Interesting Stuff

A soil-inspired dynamically responsive chemical system for microbial modulation. Lin Y…Tian B. Nature Chemistry. Link

Resolution doubling in light-sheet microscopy via oblique plane structured illumination. Chen B…Fiolka RP. Nature Methods. Link

*A population-based cohort study of traffic congestion and infant growth using connected vehicle data. Willis MD…Hystad P. Science Advances. Link

*Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty. Breznau N…Żółtak T. PNAS. Link

*A model for the collective synchronization of flashing in Photinus carolinus. McCrea M, Ermentrout B & Rubin JE. Journal of the Royal Society Interface. Link

†Harnessing synthetic biology for mushroom farming. Zou G, Nielsen JB & Wei Y. Trends in Biotechnology. Link

*Peptide-DNA origami as a cryoprotectant for cell preservation. Lee C…Ahn DJ. Science Advances. Link