Project description:We introduce CALIPERS, a Fluorescence Ubiquitin Cell Cycle Indicator enabling cell cycle-aware phenotyping based on multiplexed live-cell imaging. We validate CALIPERS in three- and four-color reporter lines (HaCaT) and human induced pluripotent stem cells (WTC-11), co-expressing genetically encoded structural and functional fluorescent sensors. To exemplify the broad applications of CALIPERS, we show cell cycle-aware phenotyping in live-cell imaging applications ranging from proliferation and migration to cardiac-specific maturation and drug testing.
2026-06-25 | GSE281528 | GEO
Project description:Genetically encoded fluorescent reporter for polyamines
Project description:Understanding the complex effects of genetic perturbations on cellular state and fitness in human pluripotent stem cells (hPSCs) has been challenging using traditional pooled screening techniques which typically rely on unidimensional phenotypic readouts. Here, we use barcoded open reading frame (ORF) overexpression libraries with a coupled single-cell RNA sequencing (scRNA-seq) and fitness screening approach, a technique we call SEUSS (ScalablE fUnctional Screening by Sequencing), to establish a comprehensive assaying platform. Using this system, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs), and assayed the impact of TF overexpression on fitness and transcriptomic cell state across multiple media conditions. We further leveraged the versatility of the ORF library approach to systematically assay mutant gene libraries and also whole gene families. From the transcriptomic responses, we built genetic co-perturbation networks to identify key altered gene modules. Strikingly, we found that KLF4 and SNAI2 have opposing effects on the pluripotency gene module, highlighting the power of our method to characterize the effects of genetic perturbations. From the fitness responses, we identified ETV2 as a driver of reprogramming towards an endothelial-like state.
Project description:Mammalian cells can be directed towards specific fates by overexpression of transcription factors (TFs). However, discovering and optimizing which TFs in combination produce a state of interest remains challenging. Here, we develop a scalable screening platform that addresses this challenge by combining high-MOI pooled delivery of barcoded TF ORFs, data augmentation, targeted cell enrichments, and single-cell transcriptomic readouts. As proof of principle, we apply the platform to optimize the generation of hematopoietic stem and progenitor-like cells (HSPCs) from human embryonic stem cells. Our data demonstrate technical performance across a range of key metrics and reveal a richly structured reprogramming fitness landscape over millions of TF combinations. In silico optimization of HSPC-similarity metrics over this landscape revealed two TF combinations that demonstrate superior potency in generating naïve multipotent hematopoietic progenitors relative to gold-standard controls. This study demonstrates a powerful approach for data-driven cell fate engineering using complex combinatorial perturbations.
2026-07-12 | GSE328457 | GEO
Project description:A Genetically Encoded Device for Transcriptome Storage
Project description:International guidelines recommend deciding the treatment of colorectal lesions based on the estimated histology by endoscopic optical diagnosis. However, the theoretical and practical knowledge on optical diagnosis is not widely expanded
The mail goal of this randomised controlled trial is to compare the pooled sensitivity of optical diagnosis for predicting deep submucosal invasion in large non-pedunculated polyps > 20 mm assessed in routine colonoscopies of gastroenterologists attending a e-learning module (intervention group) vs gastroenterologists who do not (control group)
The main questions the study aims to answer are:
* Is the pooled sensitivity of optical diagnosis for predicting deep submucosal invasion in large non-pedunculated polyps assessed in routine colonoscopies increased in those gastroenterologists participating in the e-learning module?
* Is the pooled diagnostic accuracy of optical diagnosis for predicting deep sm invasion in large non-pedunculated polyps ≥ 20 mm assessed in routine colonoscopies increased in those gastroenterologists participating in the e-learning module?
* In lesions with submucosal invasion, is the en bloc and complete resection rate (R0) increased in those gastroenterologists participating in the e-learning module?
* In lesions referred to surgery, is the pooled benign polyps rate decreased in those gastroenterologists participating in the e-learning module?
* In lesions treated with advanced en bloc procedures (ESD, TAMIS, fullthickness resection), is the pooled rate of histology with high-grade dysplasia, intramucosal cancer or submucosal invasion increased in those gastroenterologists participating in the e-learning module?
* In lesions treated with piecemeal endoscopic resection, is the pooled rate of histology with high-grade dysplasia, intramucosal cancer or submucosal invasion decreased in those gastroenterologists participating in the e-learning module?
* Is the diagnostic accuracy for predicting deep submucosal invasion in a test with pictures increased after participating in the e-learning module?
The participants (or subjects of study) are gastroenterologists. They will be randomised to do the e-learning course (intervention group) or not (control group).
Researchers will compare clinical outcomes of gastroenterologists participating in the e-learning module vs gastroenterologists not participating in the e-learning module to see if:
* the pooled sensitivity of optical diagnosis for predicting deep submucosal invasion in large non-pedunculated polyps > 20 mm assessed in routine colonoscopies is increased.
* the pooled diagnostic accuracy of optical diagnosis for predicting deep sm invasion in large non-pedunculated polyps > 20 mm is increased.
* the en bloc and complete resection rate (R0) is increased in lesions with submucosal invasion.
* the pooled benign polyps rate decreased in lesions referred to surgery.
* the pooled rate of histology with high-grade dysplasia, intramucosal cancer or submucosal invasion increased in lesions treated with advanced en bloc procedures (ESD, TAMIS, fullthickness resection).
* the pooled rate of histology with high-grade dysplasia, intramucosal cancer or submucosal invasion decreased in lesions treated with piecemeal endoscopic resection.
* the diagnostic accuracy for predicting deep submucosal invasion in a test with pictures after participating is increased.