We developed two quantitative PCR-based assays to detect SARS-CoV-2-specific T cell immunity: qTACT and dqTACT. The assays quantify CXCL10 mRNA, after incubation of whole blood with viral peptides, as a proxy of an antigen-specific T cell response, and will allow population-level monitoring of cellular immunity to SARS-CoV-2.

Recent patents relating to CRISPR methods and compositions for gene editing and therapeutic use.

The first herpesvirus replacement gene therapy for epidermolysis bullosa, a blistering skin condition, approaches the clinic.

Recent moves of note in and around the biotech and pharma industries.

A new era of cancer immunotherapy beckons as γδ T cell trials enter final stage.

Even if Amarin prevails in its patent infringement lawsuit, its key patents on Vascepa are likely to be ruled invalid in ongoing litigation, opening the way for generic formulations.

An intensive program supplements student education and collaboration while narrowing the disconnect between rising healthcare needs and trainees with the technical expertise to tackle pandemic-related challenges.

A new study describes a microscope combining three-photon excitation and adaptive optics capable of high-resolution in vivo imaging of fine neuronal structures in the mouse cortex through the intact skull. The authors demonstrate the use of this platform to guide precise laser-mediated microsurgery and for accurate and sensitive functional calcium imaging.

Red light penetrates deep into mammalian tissues and has low phototoxicity, but few optogenetic tools that use red light have been developed. Here we present MagRed, a red light–activatable photoswitch that consists of a red light–absorbing bacterial phytochrome incorporating a mammalian endogenous chromophore, biliverdin and a photo-state-specific binder that we developed using Affibody library selection

Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy

Fast, high-throughput methods for measuring the level and duration of protective immune responses to SARS-CoV-2 are needed to anticipate the risk of breakthrough infections. Here we report the development of two quantitative PCR assays for SARS-CoV-2-specific T cell activation. The assays are rapid, internally normalized and probe-based: qTACT requires RNA extraction and dqTACT avoids sample preparation

High-resolution optical imaging deep in tissues is challenging because of optical aberrations and scattering of light caused by the complex structure of living matter. Here we present an adaptive optics three-photon microscope based on analog lock-in phase detection for focus sensing and shaping (ALPHA-FSS). ALPHA-FSS accurately measures and effectively compensates for both aberrations and scattering

Reprogramming of antibody responses in mice is achieved via adeno-associated virus delivery of SaCas9, single guide RNA (sgRNA) and a repair template targeting immunoglobulin genes.

Transplantation of B cells engineered ex vivo to secrete broadly neutralizing antibodies (bNAbs) has shown efficacy in disease models. However, clinical translation of this approach would require specialized medical centers, technically demanding protocols and major histocompatibility complex compatibility of donor cells and recipients. Here we report in vivo B cell engineering using two adeno-associated

RNA interference (RNAi) therapeutics can silence disease-causing gene transcripts, but extrahepatic delivery has been challenging. Conjugating short interfering RNAs (siRNAs) to a lipophilic alkyl chain enabled safe delivery and long-term mRNA silencing in the brain, eye and lung in animal models, thereby opening new applications for RNAi therapeutics.

Interest is growing in genome-editing tools that can insert large chunks of DNA into the genome — and avoid the double-strand breaks associated with CRISPR–Cas9 genotoxicity.

Existing technologies can map the intricate spatial distribution of biomolecules and cell types within tissues, but not in specimens that remain alive and intact. This study introduces scission-accelerated fluorophore exchange (SAFE) bioorthogonal imaging tools that enable living cells and tissues to be deeply and serially profiled, revealing their biological dynamics across both space and time.

Our multidisciplinary team used novel perfusion technology to successfully keep an injured liver graft discarded by all other centers alive for several days, allowing proper graft evaluation and repair. The graft was successfully transplanted into a sick patient, who recovered quickly and enjoyed a normal life at one-year follow up.

Genome-wide association studies in combination with single-cell genomic atlases can provide insights into the mechanisms of disease-causal genetic variation. However, identification of disease-relevant or trait-relevant cell types, states and trajectories is often hampered by sparsity and noise, particularly in the analysis of single-cell epigenomic data. To overcome these challenges, we present SCAVENGE

Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities for unique applications. However, the directed evolution and selection of mirror-image aptamers directly from large randomized l-DNA libraries has, to our knowledge, not been demonstrated previously. Here, we developed a ‘mirror-image selection’ scheme for the

Therapeutics based on short interfering RNAs (siRNAs) delivered to hepatocytes have been approved, but new delivery solutions are needed to target additional organs. Here we show that conjugation of 2′-O-hexadecyl (C16) to siRNAs enables safe, potent and durable silencing in the central nervous system (CNS), eye and lung in rodents and non-human primates with broad cell type specificity. We show that

Cells in complex organisms undergo frequent functional changes, but few methods allow comprehensive longitudinal profiling of living cells. Here we introduce scission-accelerated fluorophore exchange (SAFE), a method for multiplexed temporospatial imaging of living cells with immunofluorescence. SAFE uses a rapid bioorthogonal click chemistry to remove immunofluorescent signals from the surface of

Targeted bisulfite sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. In this study, we benchmarked five commercially available TBS platforms—three hybridization capture-based (Agilent, Roche and Illumina) and two reduced-representation-based (Diagenode and NuGen)—across 11 samples. Two samples were also compared

Are major decisions in the cell made through pairs of interacting loci (enhancers and promoters) or larger teams of cooperating regulatory elements? A new genome-wide assay and algorithm answers this question and provides a scalable technology to link new dimensions of genome structure with cellular function.

A survey of national R&D-driven health biotech sectors ranks Switzerland, Sweden and the United States as leading centers for R&D-driven biotech. John Hodgson and Deanna Schreiber-Gregory report.

Current organ preservation methods provide a narrow window (usually <12 hours) to assess, transport and implant donor grafts for human transplantation. Here we report the transplantation of a human liver discarded by all centers, which could be preserved for several days using ex situ normothermic machine perfusion. The transplanted liver exhibited normal function, with minimal reperfusion injury and

Current single-cell RNA sequencing (scRNA-seq) methods with high cellular throughputs sacrifice full-transcript coverage and often sensitivity. Here we describe Smart-seq3xpress, which miniaturizes and streamlines the Smart-seq3 protocol to substantially reduce reagent use and increase cellular throughput. Smart-seq3xpress analysis of peripheral blood mononuclear cells resulted in a granular atlas

We present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption. The FS protocol can also use unique molecular identifiers (UMIs) for molecule counting while displaying

High-order three-dimensional (3D) interactions between more than two genomic loci are common in human chromatin, but their role in gene regulation is unclear. Previous high-order 3D chromatin assays either measure distant interactions across the genome or proximal interactions at selected targets. To address this gap, we developed Pore-C, which combines chromatin conformation capture with nanopore

Protein–ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions. Here we describe a flexible machine learning method, called ProBound, that accurately defines sequence recognition in terms of equilibrium binding constants

By quantifying thousands of proteins in tumor cells in an unbiased manner, Deep Visual Proteomics uncovers mechanisms that drive tumor evolution and reveals new therapeutic targets. The method incorporates advanced microscopy, artificial intelligence and ultra-high-sensitivity proteomics to characterize individual cell identities.

Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection

Recent patents relating to methods of making and using chimeric antigen receptor (CAR)-T cells to treat cancer and other diseases.

A quarterly snapshot of job expansions, reductions and availability in the biotech and pharma sectors.

Biotech companies find success with sustainably sourced ingredients for the beauty market

An analysis of decisions related to patent eligibility by the US Court of Appeals for the Federal Circuit indicates a way to avoid rejection or invalidation of eligibility.

CRISPR base- and prime-editing pooled screens reveal the function of genetic variants at unprecedented resolution.

Recent moves of note in and around the biotech and pharma industries.

The emergency use authorizations (EUAs) of two mRNA-based severe acute respiratory syndrome coronavirus (SARS-CoV)-2 vaccines approximately 11 months after publication of the viral sequence highlights the transformative potential of this nucleic acid technology. Most clinical applications of mRNA to date have focused on vaccines for infectious disease and cancer for which low doses, low protein expression

Recollections from an extraordinary 19-year journey guiding a tiny startup with an unproven therapeutic modality into a mature drug company with marketed products and >1,600 employees in nearly 20 countries provide lessons for those seeking to create the culture and values that are core to biotech success.

Two upcoming regulatory decisions represent a tipping point for commercial gene therapy, with implications for work on existing viral vectors and the pursuit of new ones.

This year could see the first trials of therapies employing base editing that introduce precise single-nucleotide changes into patient genomes.

Artificial intelligence finds candidate peptide antibiotics in the human gut microbiome.

Deciphering the functional interactions of cells in tissues remains a major challenge. Here we describe DIALOGUE, a method to systematically uncover multicellular programs (MCPs)—combinations of coordinated cellular programs in different cell types that form higher-order functional units at the tissue level—from either spatial data or single-cell data obtained without spatial information. Tested on

Many spatially resolved transcriptomic technologies do not have single-cell resolution but measure the average gene expression for each spot from a mixture of cells of potentially heterogeneous cell types. Here, we introduce a deconvolution method, conditional autoregressive-based deconvolution (CARD), that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq)

Despite the emergence of experimental methods for simultaneous measurement of multiple omics modalities in single cells, most single-cell datasets include only one modality. A major obstacle in integrating omics data from multiple modalities is that different omics layers typically have distinct feature spaces. Here, we propose a computational framework called GLUE (graph-linked unified embedding)

We designed a protein biosensor that uses thermodynamic coupling for sensitive and rapid detection of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in serum. The biosensor is a switchable, caged luciferase–receptor-binding domain (RBD) construct that detects serum-antibody interference with the binding of virus RBD to angiotensin-converting enzyme