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A key question in human genetics and evolutionary biology is how mutations in different genes combine to alter phenotypes. Efforts to systematically map genetic interactions have mostly made use of gene deletions. However, most genetic variation consists of point mutations of diverse and difficult to predict effects. Here, by developing a new sequencing-based protein interaction assay – deepPCA – we quantified the effects of >120,000 pairs of point mutations on the formation of the AP-1 transcription factor complex between the products of the FOS and JUN proto-oncogenes. Genetic interactions are abundant both in cis (within one protein) and trans (between the two molecules) and consist of two classes – interactions driven by thermodynamics that can be predicted using a three-parameter global model, and structural interactions between proximally located residues. These results reveal how physical interactions generate quantitatively predictable genetic interactions. Proteins, the molecular workhorses of the cell, are made of small units called amino acids attached together like the links of a chain. Each protein is composed of a unique combination of amino acids, which is determined by a specific sequence of DNA called a gene. A change in a gene – a mutation – can create a variation in the protein it codes for, for instance by swapping a type of amino acid for another. Different mutations in the same gene can alter a protein in different ways. Some of these changes are harmless, but other can hinder how the protein performs its role. For example, a small change in the structure of a protein could affect how it will bind to other molecules. It is possible for people to have identical mutations in the same genes, but experience different consequences. For instance, two persons could carry the same disease-inducing mutation, but one has a severe version of the condition and the other only mild symptoms. One reason is that changes in other genes cancel out or enhance the effect of a mutation. This phenomenon is known as a genetic interaction and it remains poorly understood, especially at the molecular level. Here, Diss and Lehner developed a method, called deepPCA, to study the consequences of mutations in proteins in the laboratory. The experiments focused on two human genes which code for two proteins that normally attach to each other. Two mutations were artificially created, either one in each gene, or two in one of them. Diss and Lehner then examined how strongly the two mutated proteins could still attach to each other. By repeating this process with over 120,000 different pairs of mutations, it became possible to study how one mutation can have different effects depending on the presence of other mutations in the same protein or in the binding partner. Overall, Diss and Lehner found that genetic interactions are the result of two mechanisms. In the first one, the two mutations together cause specific structural changes that modify how proteins bind to each other. In the second one, the changes solely depend on the magnitude of the initial, thermodynamic effects of individual mutations, but not on their specific physical and chemical properties. To predict the consequences of this second type of genetic interactions, knowing the identity or the exact effects of the two mutations is not necessary. Understanding and predicting genetic interactions is important to develop personalized medicine, where treatments are tailored based on the genetic make up of an individual. This knowledge will also help to study how genes have evolved together.

Diverse mouse strains have different health and life spans, mimicking the diversity among humans. To capture conserved aging signatures, we studied long‐lived C57BL/6J and short‐lived NZO/HILtJ mouse strains by profiling transcriptomes and epigenomes of immune cells from peripheral blood and the spleen from young and old mice. Transcriptional activation of the AP‐1 transcription factor complex, particularly Fos, Junb, and Jun genes, was the most significant and conserved aging signature across tissues and strains. ATAC‐seq data analyses showed that the chromatin around these genes was more accessible with age and there were significantly more binding sites for these TFs with age across all studied tissues, targeting pro‐inflammatory molecules including Il6. Age‐related increases in binding sites of JUN and FOS factors were also conserved in human peripheral blood ATAC‐seq data. Single‐cell RNA‐seq data from the mouse aging cell atlas Tabula Muris Senis showed that the expression of these genes increased with age in B, T, NK cells, and macrophages, with macrophages from old mice expressing these molecules more abundantly than other cells. Functional data showed that upon myeloid cell activation via poly(I:C), the levels of JUN protein and its binding activity increased more significantly in spleen cells from old compared to young mice. In addition, upon activation, old cells produced more IL6 compared to young cells. In sum, we showed that the aging‐related transcriptional activation of Jun and Fos family members in AP‐1 complex is conserved across immune tissues and long‐ and short‐living mouse strains, possibly contributing to increased inflammation with age. Here we show that transcriptional activation of the AP‐1 transcription factor (TF) complex members, particularly Fos, Junb, and Jun genes, is the most significant and conserved aging signature across immune cells and tissues in both short (NZO) and long‐living (B6) mice strains. Genomic and functional data showed that chromatin accessibility levels around these genes and the binding activity of their TFs increase with age. These TFs target pro‐inflammatory molecules (e.g., Il6); therefore contributing to increased inflammation with age.

Developmental pathways that orchestrate the fleeting transition of endothelial cells into haematopoietic stem cells remain undefined. Here we demonstrate a tractable approach for fully reprogramming adult mouse endothelial cells to haematopoietic stem cells (rEC-HSCs) through transient expression of the transcription-factor-encoding genes Fosb , Gfi1 , Runx1 , and Spi1 (collectively denoted hereafter as FGRS) and vascular-niche-derived angiocrine factors. The induction phase (days 0–8) of conversion is initiated by expression of FGRS in mature endothelial cells, which results in endogenous Runx1 expression. During the specification phase (days 8–20), RUNX1 + FGRS-transduced endothelial cells commit to a haematopoietic fate, yielding rEC-HSCs that no longer require FGRS expression. The vascular niche drives a robust self-renewal and expansion phase of rEC-HSCs (days 20–28). rEC-HSCs have a transcriptome and long-term self-renewal capacity similar to those of adult haematopoietic stem cells, and can be used for clonal engraftment and serial primary and secondary multi-lineage reconstitution, including antigen-dependent adaptive immune function. Inhibition of TGFβ and CXCR7 or activation of BMP and CXCR4 signalling enhanced generation of rEC-HSCs. Pluripotency-independent conversion of endothelial cells into autologous authentic engraftable haematopoietic stem cells could aid treatment of haematological disorders. The authors reprogram in vitro endothelial cells from adult mice into engraftable haematopoietic stem cells that display single-cell and multilineage properties, are capable of long-term self-renewal and can reconstitute T cell adaptive immune function. Generating functional haematopoietic stem cells The transition pathways of endothelial cells into haematopoietic stem cells remain undefined. Shahin Rafii and colleagues reprogrammed in vitro mouse adult endothelial cells into mouse engraftable haematopoietic stem cells which display the range of functional properties expected from true haematopoietic stem cells. They use a sequential approach to express transcription factors known to participate in the induction of haematopoiesis from the embryonic endothelium, as well as an endothelial cell line that acts as the vascular niche to provide the required signals. The reprogramed cells display single-cell and multilineage properties, long-term self-renewal and reconstitute T cell adaptive immune function. Converting endothelial cells into functional and self-renewing haematopoietic stem cells could open up treatment opportunities for haematological disorders, the authors suggest. Elsewhere in this issue, George Daley and colleagues differentiated human pluripotent stem cells to the haemogenic endothelium by expressing a set of transcription factors that regulate hematopoiesis.

The transcription factor FOSL1 plays an important role in cell differentiation and tumorigenesis. Primarily, FOSL1 is crucial for the differentiation of several cell lineages, namely adipocytes, chondrocytes, and osteoblasts. In solid tumors, FOSL1 controls the progression of tumor cells through the epithelial–mesenchymal transformation. In this review, we summarize the available data on FOSL1 expression, stabilization, and degradation in the cell. We discuss how FOSL1 is integrated into the intracellular signaling mechanisms and provide a comprehensive analysis of FOSL1 influence on gene expression. We also analyze the pathological changes caused by altered Fosl1 expression in genetically modified mice. In addition, we dedicated a separate section of the review to the role of FOSL1 in human cancer. Primarily, we focus on the FOSL1 expression pattern in solid tumors, FOSL1 importance as a prognostic factor, and FOSL1 perspectives as a molecular target for anticancer therapy.

The link between contextual memory representations and locations or routes represented by hippocampal place cells during exploration remains unknown. Tanaka et al. examined spatial firing properties of neurons in hippocampal area CA1 on the basis of whether they had recently expressed the immediate-early activity-induced gene c-Fos in response to a novel context. The c-Fos–positive neurons displayed a more on-off firing pattern than the c-Fos–negative cells during context discrimination. In a contextual recognition paradigm, these results support the index theory of hippocampal function over a cognitive mapping theory. Science , this issue p. 392 Neuronal firing in the hippocampus is related to experience rather than just a representation of place. Episodic memories are encoded by a sparse population of hippocampal neurons. In mice, optogenetic manipulation of this memory engram established that these neurons are indispensable and inducing for memory recall. However, little is known about their in vivo activity or precise role in memory. We found that during memory encoding, only a fraction of CA1 place cells function as engram neurons, distinguished by firing repetitive bursts paced at the theta frequency. During memory recall, these neurons remained highly context specific, yet demonstrated preferential remapping of their place fields. These data demonstrate a dissociation of precise spatial coding and contextual indexing by distinct hippocampal ensembles and suggest that the hippocampal engram serves as an index of memory content.

Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos , Arc and Egr1 . SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo. The molecular dynamics associated with neuronal activation patterns in vivo are unclear. Lacar et al . perform single-nuclei RNA-sequencing of hippocampal neurons from mice exposed to a novel environment, and identify large-scale transcriptome changes in individual neurons associated with the experience.

KRAS mutated tumours represent a large fraction of human cancers, but the vast majority remains refractory to current clinical therapies. Thus, a deeper understanding of the molecular mechanisms triggered by KRAS oncogene may yield alternative therapeutic strategies. Here we report the identification of a common transcriptional signature across mutant KRAS cancers of distinct tissue origin that includes the transcription factor FOSL1. High FOSL1 expression identifies mutant KRAS lung and pancreatic cancer patients with the worst survival outcome. Furthermore, FOSL1 genetic inhibition is detrimental to both KRAS-driven tumour types. Mechanistically, FOSL1 links the KRAS oncogene to components of the mitotic machinery, a pathway previously postulated to function orthogonally to oncogenic KRAS. FOSL1 targets include AURKA, whose inhibition impairs viability of mutant KRAS cells. Lastly, combination of AURKA and MEK inhibitors induces a deleterious effect on mutant KRAS cells. Our findings unveil KRAS downstream effectors that provide opportunities to treat KRAS-driven cancers. KRAS-driven cancers remain refractory to current clinical therapies. In this study, the authors show that lung and pancreatic cancers expressing oncogenic KRAS can be targeted by genetic inhibition of FOSL1, which involves downregulation of genes of the mitotic machinery.

Microcystin–leucine–arginine (MC-LR) can cause male reproductive disorders. However, the underlying mechanisms are not yet fully understood. In this study, we aimed to investigate the effects of MC-LR on the integrity of blood–testis barrier (BTB) and the related molecular mechanisms. Both transepithelial electrical resistance measurement in vitro and electron microscope observation ex vivo revealed that MC-LR caused disruption of the tight junction between Sertoli cells, which was paralleled by the degradation of occludin. We observed increased expression of matrix metalloproteinase-8 (MMP-8) upon exposure to MC-LR, and confirmed that abrogation of MMP-8 activity by specific inhibitors as well as transfection with MMP-8 shRNA could abolish the degradation of occludin. Our data demonstrated that MC-LR up-regulated nuclear levels of c-Fos and c-Jun through activating ERK and JNK, and increased NF-κB levels by activating the phosphatidylinositol 3-kinase (PI3K)/AKT cascades. Enhanced binding of c-Fos and NF-κB to the promoter of MMP-8 promoted the transcription of MMP - 8 gene. Furthermore, miR-184-3p was significantly downregulated in SC following exposure to MC-LR through targeting MMP-8 expression. Together, these results confirmed that MC-LR-induced MMP-8 expression was regulated at both transcriptional and post-transcriptional levels, which was involved in MC-LR-induced degradation of occludin and BTB destruction. This work may provide new perspectives in developing new diagnosis and treatment strategies for MC-induced male infertility.

The unique oncogene duet of coexisting BRAF V600E and TERT promoter mutations are widely found to be a robust genetic background promoting human cancer aggressiveness, but the mechanism is unclear. Here, we demonstrate that the BRAF V600E/MAP kinase pathway phosphorylates and activates FOS, which in turn acts as a transcription factor to bind and activate the GABPB promoter, increasing GABPB expression and driving formation of GABPA-GABPB complex; the latter selectively binds and activates mutant TERT promoter, upregulating TERT expression. Elevated TERT functions as a strong oncoprotein, robustly promoting aggressive behaviors of cancer cells and tumor development. We thus identify a molecular mechanism for the activation of mutant TERT by the BRAF V600E/MAP kinase pathway, in which FOS as a transcriptional factor of GABPB promoter plays a key role in functionally bridging the two oncogenes in cooperatively promoting oncogenesis, providing important cancer biological and clinical implications. The mechanism of tumor progression robustly promoted by co-existing BRAF V600E and TERT promoter mutations is not known. Here, the authors show a mechanism of mutant TERT activation by BRAF V600E and MAPK pathways in which FOS, as a transcription factor of the GABPB promoter, functionally links the two oncogenes.

Bromodomain and extra terminal domain (BET) proteins function as epigenetic signaling factors that associate with acetylated histones and facilitate transcription of target genes. Inhibitors targeting the activity of BET proteins have shown potent antiproliferative effects in hematological cancers through the suppression of c-MYC and downstream target genes. However, as the epigenetic landscape of a cell varies drastically depending on lineage, transcriptional coactivators such as BETs would be expected to have different targets in cancers derived from different cells of origin, and this may influence the activity and mechanism of action of BET inhibitors. To test this hypothesis, we treated a panel of lung adenocarcinoma (LAC) cell lines with the BET inhibitor JQ1 and found that a subset is acutely susceptible to BET inhibition. In contrast to blood tumors, we show that LAC cells are inhibited by JQ1 through a mechanism independent of c-MYC down-regulation. Through gene expression profiling, we discovered that the oncogenic transcription factor FOSL1 and its targets are suppressed by JQ1 in a dose-dependant manner. Knockdown of BRD4 also decreased FOSL1 levels, and inhibition of FOSL1 phenocopied the effects of JQ1 treatment suggesting that loss of this transcription factor may be partly responsible for the cytotoxic effects of BET inhibition in LAC cells, although ectopic expression of FOSL1 alone did not rescue the phenotype. Together, these findings suggest that BET inhibitors may be useful in solid tumors and that cell-lineage-specific differences in transcriptional targets of BETs may influence the activity of inhibitors of these proteins in different cancer types.