CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant.

Functional enhancer annotation is critical for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants. However, unbiased enhancer discovery in disease-relevant contexts remains challenging. To identify enhancers pertinent to diabetes, we conducted a CRISPR interference (CRISPRi) screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers identified, we focused on an enhancer we named ONECUT1e-664kb, ∼664 kb from the ONECUT1 promoter. Previous studies have linked ONECUT1 coding mutations to pancreatic hypoplasia and neonatal diabetes. We found that homozygous deletion of ONECUT1e-664kb in hPSCs leads to a near-complete loss of ONECUT1 expression and impaired pancreatic differentiation. ONECUT1e-664kb contains a type 2 diabetes-associated variant (rs528350911) disrupting a GATA motif. Introducing the risk variant into hPSCs reduced binding of key pancreatic transcription factors (GATA4, GATA6, and FOXA2), supporting its causal role in diabetes. This work highlights the utility of unbiased enhancer discovery in disease-relevant settings for understanding monogenic and complex disease.

CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant.

Functional enhancer annotation is a valuable first step for understanding tissue-specific transcriptional regulation and prioritizing disease-associated non-coding variants for investigation. However, unbiased enhancer discovery in physiologically relevant contexts remains a major challenge. To discover regulatory elements pertinent to diabetes, we conducted a CRISPR interference screen in the human pluripotent stem cell (hPSC) pancreatic differentiation system. Among the enhancers uncovered, we focused on a long-range enhancer ∼664 kb from the ONECUT1 promoter, since coding mutations in ONECUT1 cause pancreatic hypoplasia and neonatal diabetes. Homozygous enhancer deletion in hPSCs was associated with a near-complete loss of ONECUT1 gene expression and compromised pancreatic differentiation. This enhancer contains a confidently fine-mapped type 2 diabetes associated variant (rs528350911) which disrupts a GATA motif. Introduction of the risk variant into hPSCs revealed substantially reduced binding of key pancreatic transcription factors (GATA4, GATA6 and FOXA2) on the edited allele, accompanied by a slight reduction of ONECUT1 transcription, supporting a causal role for this risk variant in metabolic disease. This work expands our knowledge about transcriptional regulation in pancreatic development through the characterization of a long-range enhancer and highlights the utility of enhancer discovery in disease-relevant settings for understanding monogenic and complex disease.

Correction to "Carbodiimide Ring-Opening Metathesis Polymerization".

[This corrects the article DOI: 10.1021/acscentsci.3c00032.].

Carbodiimide Ring-Opening Metathesis Polymerization.

Controlled incorporation of nitrogen into macromolecular skeletons is a long-standing challenge whose resolution would enable the preparation of soft materials with the scalability of man-made plastics and functionality of Nature's proteins. Nylons and polyurethanes notwithstanding, nitrogen-rich polymer backbones remain scarce, and their synthesis typically lacks precision. Here we report a strategy that begins to address this limitation founded on a mechanistic discovery: ring-opening metathesis polymerization (ROMP) of carbodiimides followed by carbodiimide derivatization. An iridium guanidinate complex was found to initiate and catalyze ROMP of N-aryl and N-alkyl cyclic carbodiimides. Nucleophilic addition to the resulting polycarbodiimides enabled the preparation of polyureas, polythioureas, and polyguanidinates with varied architectures. This work advances the foundations of metathesis chemistry and opens the door to systematic investigations of structure-folding-property relationships in nitrogen-rich macromolecules.

Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells.

The mechanisms underlying the ability of embryonic stem cells (ESCs) to rapidly activate lineage-specific genes during differentiation remain largely unknown. Through multiple CRISPR-activation screens, we discovered human ESCs have pre-established transcriptionally competent chromatin regions (CCRs) that support lineage-specific gene expression at levels comparable to differentiated cells. CCRs reside in the same topological domains as their target genes. They lack typical enhancer-associated histone modifications but show enriched occupancy of pluripotent transcription factors, DNA demethylation factors, and histone deacetylases. TET1 and QSER1 protect CCRs from excessive DNA methylation, while HDAC1 family members prevent premature activation. This "push and pull" feature resembles bivalent domains at developmental gene promoters but involves distinct molecular mechanisms. Our study provides new insights into pluripotency regulation and cellular plasticity in development and disease. One sentence summary: We report a class of distal regulatory regions distinct from enhancers that confer human embryonic stem cells with the competence to rapidly activate the expression of lineage-specific genes.

Genetic Engineering of Immune Evasive Stem Cell-Derived Islets.

Genome editing has the potential to revolutionize many investigative and therapeutic strategies in biology and medicine. In the field of regenerative medicine, one of the leading applications of genome engineering technology is the generation of immune evasive pluripotent stem cell-derived somatic cells for transplantation. In particular, as more functional and therapeutically relevant human pluripotent stem cell-derived islets (SCDI) are produced in many labs and studied in clinical trials, there is keen interest in studying the immunogenicity of these cells and modulating allogeneic and autoimmune immune responses for therapeutic benefit. Significant experimental work has already suggested that elimination of Human Leukocytes Antigen (HLA) expression and overexpression of immunomodulatory genes can impact survival of a variety of pluripotent stem cell-derived somatic cell types. Limited work published to date focuses on stem cell-derived islets and work in a number of labs is ongoing. Rapid progress is occurring in the genome editing of human pluripotent stem cells and their progeny focused on evading destruction by the immune system in transplantation models, and while much research is still needed, there is no doubt the combined technologies of genome editing and stem cell therapy will profoundly impact transplantation medicine in the future.

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction.

The pancreas and liver arise from a common pool of progenitors. However, the underlying mechanisms that drive their lineage diversification from the foregut endoderm are not fully understood. To tackle this question, we undertook a multifactorial approach that integrated human pluripotent-stem-cell-guided differentiation, genome-scale CRISPR-Cas9 screening, single-cell analysis, genomics and proteomics. We discovered that HHEX, a transcription factor (TF) widely recognized as a key regulator of liver development, acts as a gatekeeper of pancreatic lineage specification. HHEX deletion impaired pancreatic commitment and unleashed an unexpected degree of cellular plasticity towards the liver and duodenum fates. Mechanistically, HHEX cooperates with the pioneer TFs FOXA1, FOXA2 and GATA4, shared by both pancreas and liver differentiation programmes, to promote pancreas commitment, and this cooperation restrains the shared TFs from activating alternative lineages. These findings provide a generalizable model for how gatekeeper TFs like HHEX orchestrate lineage commitment and plasticity restriction in broad developmental contexts.

Efficient Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Exhaled Breath.

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is transmitted through airborne particles in exhaled breath, causing severe respiratory disease, coronavirus disease-2019 (COVID-19), in some patients. Samples for SARS-CoV-2 testing are typically collected by nasopharyngeal swab, with the virus detected by PCR; however, patients can test positive for 3 months after infection. Without the capacity to assay SARS-CoV-2 in breath, it is not possible to understand the risk for transmission from infected individuals. To detect virus in breath, the Bubbler-a breathalyzer that reverse-transcribes RNA from SARS-CoV-2 particles into a sample-specific barcoded cDNA-was developed. In a study of 70 hospitalized patients, the Bubbler was both more predictive of lower respiratory tract involvement (abnormal chest X-ray) and less invasive than alternatives. Samples tested using the Bubbler were threefold more enriched for SARS-CoV-2 RNA than were samples from tongue swabs, implying that virus particles were being directly sampled. The barcode-enabled Bubbler was used for simultaneous diagnosis in large batches of pooled samples at a lower limit of detection of 334 genomic copies per sample. Diagnosis by sequencing can provide additional information, such as viral load and strain identity. The Bubbler was configured to sample nucleic acids in water droplets circulating in air, demonstrating its potential in environmental monitoring and the protective effect of adequate ventilation.

Evaluating Closures of Fresh Fruit and Vegetable Vendors During the COVID-19 Pandemic: Methodology and Preliminary Results Using Omnidirectional Street View Imagery.

BACKGROUND: The COVID-19 pandemic has significantly disrupted the food retail environment. However, its impact on fresh fruit and vegetable vendors remains unclear; these are often smaller, more community centered, and may lack the financial infrastructure to withstand supply and demand changes induced by such crises. OBJECTIVE: This study documents the methodology used to assess fresh fruit and vegetable vendor closures in New York City (NYC) following the start of the COVID-19 pandemic by using Google Street View, the new Apple Look Around database, and in-person checks. METHODS: In total, 6 NYC neighborhoods (in Manhattan and Brooklyn) were selected for analysis; these included two socioeconomically advantaged neighborhoods (Upper East Side, Park Slope), two socioeconomically disadvantaged neighborhoods (East Harlem, Brownsville), and two Chinese ethnic neighborhoods (Chinatown, Sunset Park). For each neighborhood, Google Street View was used to virtually walk down each street and identify vendors (stores, storefronts, street vendors, or wholesalers) that were open and active in 2019 (ie, both produce and vendor personnel were present at a location). Past vendor surveillance (when available) was used to guide these virtual walks. Each identified vendor was geotagged as a Google Maps pinpoint that research assistants then physically visited. Using the "notes" feature of Google Maps as a data collection tool, notes were made on which of three categories best described each vendor: (1) open, (2) open with a more limited setup (eg, certain sections of the vendor unit that were open and active in 2019 were missing or closed during in-person checks), or (3) closed/absent. RESULTS: Of the 135 open vendors identified in 2019 imagery data, 35% (n=47) were absent/closed and 10% (n=13) were open with more limited setups following the beginning of the COVID-19 pandemic. When comparing boroughs, 35% (28/80) of vendors in Manhattan were absent/closed, as were 35% (19/55) of vendors in Brooklyn. Although Google Street View was able to provide 2019 street view imagery data for most neighborhoods, Apple Look Around was required for 2019 imagery data for some areas of Park Slope. Past surveillance data helped to identify 3 additional established vendors in Chinatown that had been missed in street view imagery. The Google Maps "notes" feature was used by multiple research assistants simultaneously to rapidly collect observational data on mobile devices. CONCLUSIONS: The methodology employed enabled the identification of closures in the fresh fruit and vegetable retail environment and can be used to assess closures in other contexts. The use of past baseline surveillance data to aid vendor identification was valuable for identifying vendors that may have been absent or visually obstructed in the street view imagery data. Data collection using Google Maps likewise has the potential to enhance the efficiency of fieldwork in future studies.

A More Efficient Method for Synthetic Textile Fiber Analysis Using Polarized Light Microscopy.

The efficiency of conventional polarized light microscopy (PLM) methods for analyzing synthetic fiber evidence analyses is improved. Historically, using PLM for fiber identification relied on measuring refractive index. This prior PLM technology is reliable, but it is not efficient. Most fibers are optically anisotropic, having two principal refractive index values, N(High) and N(Low) . When the fiber is mounted in intermediate refractive index medium, efficiency is improved by observing the change in contrast while the polarized light's vector is rotated relative to the fiber's axis. Minimum contrast occurs when the refractive indices of the mounting medium and fiber are equal. This angle of equality is determined by orienting the fiber's highest refractive index parallel to the polarized light's electric field vector, rotating the fiber or polarizing element, observing minimum contrast and measuring the angle of equality. This method is rapid, reduces remounting fibers in different mounting media and provides a quantitative measure for fiber comparisons.