In 1900, Adami speculated that a sequence of context-independent energetic and structural changes governed the reversion of differentiated cells to a proliferative, regenerative state. Accordingly, we show here that differentiated cells in diverse organs become proliferative via a shared program. Metaplasia-inducing injury caused both gastric chief and pancreatic acinar cells to decrease mTORC1 activity and massively upregulate lysosomes/autophagosomes; then increase damage associated metaplastic genes such as ; and finally reactivate mTORC1 and re-enter the cell cycle. Blocking mTORC1 permitted autophagy and metaplastic gene induction but blocked cell cycle re-entry at S-phase. In kidney and liver regeneration and in human gastric metaplasia, mTORC1 also correlated with proliferation. In lysosome-defective mice, both metaplasia-associated gene expression changes and mTORC1-mediated proliferation were deficient in pancreas and stomach. Our findings indicate differentiated cells become proliferative using a sequential program with intervening checkpoints: (i) differentiated cell structure degradation; (ii) metaplasia- or progenitor-associated gene induction; (iii) cell cycle re-entry. We propose this program, which we term "paligenosis", is a fundamental process, like apoptosis, available to differentiated cells to fuel regeneration following injury.

We hypothesized that basic helix-loop-helix (bHLH) MIST1 (BHLHA15) is a "scaling factor" that universally establishes secretory morphology in cells that perform regulated secretion. Here, we show that targeted deletion of MIST1 caused dismantling of the secretory apparatus of diverse exocrine cells. Parietal cells (PCs), whose function is to pump acid into the stomach, normally lack MIST1 and do not perform regulated secretion. Forced expression of MIST1 in PCs caused them to expand their apical cytoplasm, rearrange mitochondrial/lysosome trafficking, and generate large secretory granules. Mist1 induced a cohort of genes regulated by MIST1 in multiple organs but did not affect PC function. MIST1 bound CATATG/CAGCTG E boxes in the first intron of genes that regulate autophagosome/lysosomal degradation, mitochondrial trafficking, and amino acid metabolism. Similar alterations in cell architecture and gene expression were also caused by ectopically inducing MIST1 in vivo in hepatocytes. Thus, MIST1 is a scaling factor necessary and sufficient by itself to induce and maintain secretory cell architecture. Our results indicate that, whereas mature cell types in each organ may have unique developmental origins, cells performing similar physiological functions throughout the body share similar transcription factor-mediated architectural "blueprints."

Essentially all cells contain a variety of spatially restricted regions that are important for carrying out specialized functions. Often, these regions contain specialized transcriptomes that facilitate these functions by providing transcripts for localized translation. These transcripts play a functional role in maintaining cell physiology by enabling a quick response to changes in the cellular environment. Here, we review how RNA molecules are trafficked within cells, with a focus on the subcellular locations to which they are trafficked, mechanisms that regulate their transport and clinical disorders associated with misregulation of the process. K E Y W O R D SRNA binding protein, RNA cis-element, RNA localization, RNA transport, zipcode

Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.

The transcription factor, X-box-binding protein-1 (XBP1), controls the development and maintenance of the endoplasmic reticulum (ER) in multiple secretory cell lineages. We show here that Hepatocyte Nuclear Factor 4␣ (HNF4␣) directly induces XBP1 expression. Mutations in HNF4␣ cause Mature-Onset Diabetes of the Young I (MODYI), a subset of diabetes characterized by diminished GSIS. In mouse models, cell lines, and ex vivo islets, using dominant negative and human-disease-allele point mutants or knock-out and knockdown models, we show that disruption of HNF4␣ caused decreased expression of XBP1 and reduced cellular ER networks. GSIS depends on ER Ca 2؉ signaling; we show that diminished XBP1 and/or HNF4␣ in ␤-cells led to impaired ER Ca 2؉ homeostasis. Restoring XBP1 expression was sufficient to completely rescue GSIS in HNF4␣-deficient ␤-cells. Our findings uncover a transcriptional relationship between HNF4␣ and Xbp1 with potentially broader implications about MODYI and the importance of transcription factor signaling in the regulation of secretion.Cells use transcription factors to regulate expression of gene cohorts that coordinate response to stress, determine specific developmental fates, and scale intracellular architecture during development and disease(1, 2). When the biosynthetic load of a cell is increased and misfolded proteins accumulate in the endoplasmic reticulum (ER), 2 the volume and composition of the ER is altered to facilitate the synthesis and processing of nascent polypeptides via the unfolded protein response (UPR) pathway. One of the principal components of the UPR is the transcription factor X-box-binding protein 1 (XBP1), which is canonically activated via IRE1 splicing of the XBP1 transcript during ER stress (3, 4). However, XBP1 also establishes and maintains the subcellular machinery for synthesizing large quantities of protein during the normal development of professional secretory cells (2, 5). While the majority of genes activated by XBP1 are involved in ER biogenesis, up to 40% of its targets are not directly linked to the ER-stress response (6), further supporting its functions outside the UPR. In addition, the increased XBP1 that coordinates the scaling up of the secretory apparatus during development and homeostasis of dedicated secretory cells does not seem to require activation of the UPR (7). How XBP1 is induced and maintained during differentiation of secretory cells even in the absence of substantial ER stress is unclear, but a potential alternative mechanism is that Xbp1 may also be transcriptionally regulated. Hepatocyte Nuclear Factor 4-alpha (HNF4␣) is a highly conserved transcription factor responsible for orchestrating the early development and maintenance of multiple adult organs. As a master developmental regulator, HNF4␣ likely acts upstream of the factors that establish the extensive cellular machinery required in professional secretory cell lineages within those organs. Despite overlapping expression and function, no direct relationship between HNF4␣ and Xbp1 h...

The optimal markers for human spermatogonial stem cells (SSCs) are not known. Among the genes recently linked to SSCs in mice and other animals are the basic helix-loop-helix transcription factor ID4 and the orphan G-protein coupled receptor GPR125. While ID4 and GPR125 are considered putative markers for SSCs, they have not been evaluated for co-expression in human tissue. Further, neither the size nor the character of the human spermatogonial populations that express ID4 and GPR125, respectively, are known. A major barrier to addressing these questions is the availability of healthy adult testis tissue from donors with no known reproductive health problems. To overcome this obstacle, we have employed healthy testicular tissue from a novel set of organ donors (n=16; aged 17-68 years) who were undergoing post-mortem clinical organ procurement. Using immunolabeling, we found that ID4 and GPR125 are expressed on partially overlapping spermatogonial populations and are more broadly expressed in the normal adult human testis. Additionally, we found that expression of ID4 remained stable during aging. These findings suggest that ID4 and GPR125 could be efficacious for identifying previously unrecognized human spermatogonial subpopulations in conjunction with other putative human stem cell markers, both in younger and older donors.

Alternative polyadenylation (APA) is a widespread and conserved regulatory mechanism that generates diverse 3′ ends on mRNA. APA patterns are often tissue specific and play an important role in cellular processes such as cell proliferation, differentiation, and response to stress. Many APA sites are found in 3′ UTRs, generating mRNA isoforms with different 3′ UTR contents. These alternate 3′ UTR isoforms can change how the transcript is regulated, affecting its stability and translation. Since the subcellular localization of a transcript is often regulated by 3′ UTR sequences, this implies that APA can also change transcript location. However, this connection between APA and RNA localization has only recently been explored. In this review, we discuss the role of APA in mRNA localization across distinct subcellular compartments. We also discuss current challenges and future advancements that will aid our understanding of how APA affects RNA localization and molecular mechanisms that drive these processes.

The gastric epithelium is often exposed to injurious elements and failure of appropriate healing predisposes to ulcers, hemorrhage, and ultimately cancer. We examined the gastric function of CD36, a protein linked to disease and homeostasis. We used the tamoxifen model of gastric injury in mice null for Cd36 (Cd36−/−), with Cd36 deletion in parietal cells (PC-Cd36−/−) or in endothelial cells (EC-Cd36−/−). CD36 expresses on corpus ECs, on PC basolateral membranes, and in gastrin and ghrelin cells. Stomachs of Cd36−/− mice have altered gland organization and secretion, more fibronectin, and inflammation. Tissue respiration and mitochondrial efficiency are reduced. Phospholipids increased and triglycerides decreased. Mucosal repair after injury is impaired in Cd36−/− and EC-Cd36−/−, not in PC-Cd36−/− mice, and is due to defect of progenitor differentiation to PCs, not of progenitor proliferation or mature PC dysfunction. Relevance to humans is explored in the Vanderbilt BioVu using PrediXcan that links genetically-determined gene expression to clinical phenotypes, which associates low CD36 mRNA with gastritis, gastric ulcer, and gastro-intestinal hemorrhage. A CD36 variant predicted to disrupt an enhancer site associates (p < 10−17) to death from gastro-intestinal hemorrhage in the UK Biobank. The findings support role of CD36 in gastric tissue repair, and its deletion associated with chronic diseases that can predispose to malignancy.