Research Briefing in 2022

Single-cell nanobody-tethered transposition followed by sequencing (scNTT-seq) is a new assay that measures the genome-wide presence of multiple histone modifications and protein–DNA binding sites at single-cell resolution. scNTT-seq generates high-resolution multimodal maps of chromatin states with high accuracy and sensitivity.

Nanobody–Tn5 transposase fusion proteins enable detection of two histone marks and open chromatin regions at the same time, with single-cell resolution.

We developed a computational method based on Strand-seq that combines nucleosome occupancy and structural variation analysis in single cells to identify the functional effects of somatic structural variants in leukemia. The method revealed the molecular consequences of somatic driver mutations and informed specific therapeutic targeting of a chromothriptic leukemic subclone.

We developed a wireless smart bandage with sensors that can detect the condition of a wound and stimulators that can deliver electric cues. Application of our device on wounds in mouse models reduced infection and accelerated wound healing.

The global microbiota contains an enormous, previously inaccessible reservoir of biodiversity that can now be captured as large DNA fragments in clone libraries. To mine cloned biodiversity more effectively, we developed a CRISPR-interference-based counter-selection interruption circuit for the high-throughput retrieval of desired clones within complex libraries.

Development is orchestrated in part by myriad chromatin-associated proteins that decorate the genome and physically coordinate in ways that are often unclear. An epigenomics technique called MulTI-Tag maps the genomic locations of different chromatin proteins in the same individual cells, helping to unveil their interactions.

The ability to target the majority of human transcription factors remains an as yet unachieved goal in chemical biology and medicine. We developed a modular, synthetic transcriptional repressor platform that recapitulates the DNA-binding properties of native basic helix-loop-helix (bHLH) domains and can block the DNA-binding functions of an important oncogenic transcription factor target, MYC.

Spatial total RNA-sequencing (STRS) combines in situ polyadenylation with existing spatial transcriptomics technologies to enable a broader view of the transcriptome in tissues. We use STRS to spatially map coding, noncoding and nonhost RNAs in models of skeletal muscle regeneration and viral myocarditis.

Cells differentiate to their final fates through sequential epigenetic and transcriptional changes. A mathematical model fit on multi-omic single-cell data yields insights into the temporal relationships between chromatin accessibility and gene expression during cell differentiation.

Post-translational modifications (PTMs) alter the structure, properties and functions of proteins in all aspects of biology. A new computational pipeline, termed protein modification integrated search engine (PROMISE), reveals the impact these modifications might have on the presentation of cancer antigens to T cells.

We integrated the pre-characterized physical model of super-resolution (SR) microscopy into a deep neural network to guide the denoising of raw images for high-quality SR image reconstruction. This approach enabled us to investigate a wide variety of fragile and rapidly evolving bioprocesses at ultrahigh spatiotemporal resolution over extended imaging times.

Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from large and complex RNA-seq studies. Technical replicates together with negative and positive control genes are key tools for carrying out this task. We show how to proceed when technical replicates are unavailable.

The addition of Cas9 target sequences to long single-stranded DNAs, combined with cocktails of small molecules to boost homology-directed repair, leads to marked enhancement of non-viral knock-in efficiency and yield in primary human T cells and other hematopoietic cell types.

The application of CRISPR–Cas13 for targeted RNA degradation is hindered by the existence of collateral effects induced by Cas13. We screened hundreds of engineered Cas13 variants using a convenient and sensitive reporter system and obtained several variants with markedly reduced collateral activity and efficient on-target activity, suitable for in vivo applications.

Porcine dermal collagen was chemically and photochemically bioengineered into an implantable tissue mimicking the human corneal extracellular matrix. The implant presents a simpler and safer method than donor cornea transplantation while delivering equivalent outcomes, and has restored vision to people with advanced keratoconus in resource-limited regions, where the burden of blindness is highest.

This study reveals a high level of behavioral heterogeneity in engineered T cells that target tumor organoids. Behavior-guided transcriptomics identified the gene signatures of T cells with highly potent serial cytotoxicity. Integration of the organoid and T cell transcriptomic data enabled the design of patient-specific combinatorial treatment to achieve an optimized response to cancer immunotherapies.

Genomic surveillance is important for pandemic preparedness. By deep sequencing of wastewater samples, we monitored the genetic dynamics of circulating SARS-CoV-2 virus variants in Austria from December 2020 to February 2022. We show how wastewater-based epidemiology enables robust quantification of viral spatiotemporal dynamics as well as the detection of emergent new variants.

Many biomedical questions demand scalable, deep, and accurate proteome analysis of small samples, including single cells. A scalable framework of multiplexed data-independent acquisition for mass spectrometry enables time saving by parallel analysis of both peptide ions and protein samples, thereby realizing multiplicative gains in throughput.

Drug combinations predicted to increase tumor cell death directly and by creating strong antitumor tumor microenvironments were identified by computational analysis of local responses to combinations of anticancer drugs delivered inside a tumor. Such predicted drug combinations were highly effective when administered systemically in mouse models of breast cancer.

Current high-throughput single-cell methods detect only a small part of the transcriptome. The workflow presented here integrates molecular analysis and droplet microfluidics to derive total transcriptomic atlases that encompass alternative splicing and non-coding transcripts in large numbers of single cells. The utility of this method is demonstrated by analysis of mouse gastrulation and early organogenesis.