04-11-2023. Dr. Eran Agmon, along with a diverse team of cell modelers from prestigious institutions including the Allen Institute for Cell Science, University of Washington, Stanford University, and University of Richmond, have collaboratively published a paper that advocates for the development of next-generation virtual cells. The paper highlights the potential of these dynamic 3D models in consolidating vast cellular information, facilitating a more comprehensive understanding of cellular behaviors, and fostering collaborative breakthroughs in cell science research.

 Johnson, G. T., Agmon, E., Akamatsu, M., Lundberg, E., Lyons, B., Ouyang, W., … & Horwitz, R. (2023). Building the next generation of virtual cells to understand cellular biology. Biophysical Journal.

https://www.cell.com/biophysj/pdf/S0006-3495(23)00236-9.pdf

02-21-23. Adipose tissue development impacts many metabolic functions and adipocyte dysregulation contributes to conditions such as obesity, diabetes, and coronary artery disease. Full characterization and interpretation of the molecular changes and regulatory factors that drive differentiation, such as adipogenesis, and responses to stimuli will someday permit selectively steering diseased cells within a human body toward desired phenotypes. Our understanding of the transcriptional responses to hormones, drugs, cytokines, stimuli, and genetic intervention is needed to ultimately realize this future. In this study, the Guertin lab presents a novel approach to constructing gene regulatory networks that incorporates kinetic chromatin accessibility (ATAC-seq) and nascent transcription (PRO-seq) data. Prior characterizations of the transcriptional network driving adipogenesis overlooked essential transcription factors, genes, and regulatory elements that act transiently. Traditional gene regulatory networks lack mechanistic details about individual relationships between regulatory elements and genes. Moreover, they do not account for temporal relationships that are needed to define a regulatory hierarchy that prioritizes key regulatory factors. The networks from this work are designed so that one can easily identify key regulatory transcription factors or regulatory element hubs, determine a set of target genes for specific transcription factors, assess transcription factor cooperativity, and develop testable hypotheses.

This work found that Twist2 is a novel regulator of adipogenesis, an observation that was overlooked previously because TWIST2 acts transiently. This finding highlights the power of this relatively unbiased methodology to articulate novel hypotheses and implicate new factors that inform upon developmental processes. The network provides a wealth of information about regulatory relationships between enhancers and genes. To validate their work, TWIST2 knockout mice were found to have deficiencies in fat storage.

What is perhaps most exciting to the developmental biology and system biology fields is that these networks are constructed using only ATAC-seq and PRO-seq data. Unlike other molecular genomics assays, these two assays can theoretically be performed in any cell type and organism with a reference genome—no species-specific or factor-specific reagents are needed. To facilitate the adoption of this methodology, the Guertin lab provided an analysis vignette on GitHub that contains a step-by-step procedure for generating and interpreting these networks. This network inference framework is a powerful and general approach for interpreting complex biological phenomena and can be applied to a wide range of cellular processes.

03-02-2023. Congratulations to the Yu lab for their publication, Efficient end-to-end learning for cell segmentation with machine generated weak annotations. The article focuses on cell segmentation models trained with weak annotations that can be programmably or semi-programmably produced from experimental data. It provides an efficient means of performing single-cell segmentation for microscopy image analysis.

03-01-23. The Guertin lab characterized the normal physiological role of the protein ANKLE1 in red blood cell development and how increased expression of Ankle1 leads to an increased risk of developing breast cancer.

Background: GWAS analyses have identified thousands of regions associated with physiological phenotypes and disease risk phenotypes. Integrative GWAS and eQTL analyses can often hone in on the candidate causal genes within the region by looking for colocalization of GWAS and eQTL variants. The genotyping revolution allows geneticists to keep identifying more associated loci with smaller and smaller effect sizes, but characterizing the causal genes and mechanisms by which the genes manifest as organismal phenotypes lags substantially behind. The chr19p13.1 locus was first identified over 10 years ago as a locus that contributes to the risk of breast and ovarian cancer. The wrong genes were thought to be the causal genes for over six years, but integration with eQTL analysis repeatedly and convincingly pointed to ANKLE1 as the causal gene. There are only a handful of rigorous publications that have explored the molecular, cellular, and physiological functions of ANKLE1, but none of these studies explore the role of ANKLE1 in breast cancer biology. ANKLE1 is primarily expressed in hematopoietic tissues of vertebrates, but ANKLE1-deficient mice are viable without any detectable phenotype in hematopoiesis.

This latest work finds that the developmental role of ANKLE1 is to cleave the mitochondrial genome during erythropoiesis. Drs. Przanowski and Guertin also determined how ectopic expression of ANKLE1 confers breast cancer risk. The publication in Communications Biology reports that ectopic expression of ANKLE1 in breast epithelial spheroids cleaves mitochondrial DNA to induce mitophagy and trigger a shift in metabolism to glycolysis. These metabolic changes cause resistance to apoptosis in TP53 negative cells. Two recent GWASs quantified mitochondria DNA abundance and found that genetic variants with the ANKLE1 locus contribute to mitochondrial DNA abundance. This publication provides a direct mechanistic link between the overlapping GWAS signal for breast cancer risk and mitochondrial DNA copy number.

03-01-2023. Congratulations to Ann Cowan, Peter Setlow, and other collaborators for their work on Bacillus subtilis. The article, entitled Expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide looks at sporulation in B. subtilis and used VCell modeling to analyze the characteristics of the spore membrane in cells with mutations in genes related to germination.