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1.
Mol Metab ; 79: 101851, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38081412

ABSTRACT

OBJECTIVE: The bioactive sphingolipid metabolites ceramide and sphingosine-1-phosphate (S1P) accumulate with overnutrition and have been implicated in non-alcoholic steatohepatitis (NASH) development. ORMDL3, a negative regulator of the rate-limiting step in ceramide biosynthesis, has been identified as an obesity-related gene. Therefore, we assessed the role of ORMDL3 in diet-induced obesity and development of NASH. METHODS: Globally overexpressing Ormdl3-Flag transgenic mice (ORMDL3TG) were fed a western high-fat, carbohydrate and cholesterol enriched diet, with high fructose-glucose drinking water. Physiological, biochemical and sphingolipidomic analyses were employed to measure the effect of ORMDL3 overexpression on NASH development. RESULTS: ORMDL3TG male but not female mice fed a western high-fat diet and sugar water had exacerbated adipocyte hypertrophy together with increased severity of white adipose inflammation and fibrosis. Hepatic steatosis, dyslipidemia, impaired glucose homeostasis, hyperinsulinemia, and insulin resistance were significantly more severe only in obese ORMDL3TG male mice that accompanied dramatic liver fibrosis, inflammation, and formation of hepatic crown-like structures, which are unique features of human and murine NASH. Obesogenic diet induces ORMDL expression in male mice but reduces it in females. Mechanistically, overexpression of Ormdl3 lowered the levels of S1P and ceramides only in obese female mice and antithetically increased them in tissues of obese males. ORMDL3TG male mice exhibited a much greater induction of the UPR, propagating ER stress that contributed to their early development of NASH. CONCLUSIONS: This study uncovered a previously unrecognized role for ORMDL3 in sexual dimorphism important for the development and progression of NASH.


Subject(s)
Non-alcoholic Fatty Liver Disease , Animals , Female , Humans , Male , Mice , Ceramides , Diet, High-Fat/adverse effects , Glucose , Inflammation , Membrane Proteins/genetics , Mice, Transgenic , Non-alcoholic Fatty Liver Disease/metabolism , Obesity , Sex Characteristics
2.
Int J Mol Sci ; 24(20)2023 Oct 11.
Article in English | MEDLINE | ID: mdl-37894760

ABSTRACT

Diabetic cardiomyopathy is a critical diabetes-mediated co-morbidity characterized by cardiac dysfunction and heart failure, without predisposing hypertensive or atherosclerotic conditions. Metabolic insulin resistance, promoting hyperglycemia and hyperlipidemia, is the primary cause of diabetes-related disorders, but ambiguous tissue-specific insulin sensitivity has shed light on the importance of identifying a unified target paradigm for both the glycemic and non-glycemic context of type 2 diabetes (T2D). Several studies have indicated hyperactivation of the mammalian target of rapamycin (mTOR), specifically complex 1 (mTORC1), as a critical mediator of T2D pathophysiology by promoting insulin resistance, hyperlipidemia, inflammation, vasoconstriction, and stress. Moreover, mTORC1 inhibitors like rapamycin and their analogs have shown significant benefits in diabetes and related cardiac dysfunction. Recently, FDA-approved anti-hyperglycemic sodium-glucose co-transporter 2 inhibitors (SGLT2is) have gained therapeutic popularity for T2D and diabetic cardiomyopathy, even acknowledging the absence of SGLT2 channels in the heart. Recent studies have proposed SGLT2-independent drug mechanisms to ascertain their cardioprotective benefits by regulating sodium homeostasis and mimicking energy deprivation. In this review, we systematically discuss the role of mTORC1 as a unified, eminent target to treat T2D-mediated cardiac dysfunction and scrutinize whether SGLT2is can target mTORC1 signaling to benefit patients with diabetic cardiomyopathy. Further studies are warranted to establish the underlying cardioprotective mechanisms of SGLT2is under diabetic conditions, with selective inhibition of cardiac mTORC1 but the concomitant activation of mTORC2 (mTOR complex 2) signaling.


Subject(s)
Diabetes Mellitus, Type 2 , Diabetic Cardiomyopathies , Hyperlipidemias , Insulin Resistance , Sodium-Glucose Transporter 2 Inhibitors , Humans , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/drug therapy , Diabetes Mellitus, Type 2/metabolism , Sodium-Glucose Transporter 2 Inhibitors/pharmacology , Sodium-Glucose Transporter 2 Inhibitors/therapeutic use , Diabetic Cardiomyopathies/metabolism , Mechanistic Target of Rapamycin Complex 1/metabolism , Sodium-Glucose Transporter 2 , Mechanistic Target of Rapamycin Complex 2/metabolism , Sodium/metabolism , Hyperlipidemias/drug therapy
3.
FASEB J ; 37(3): e22799, 2023 03.
Article in English | MEDLINE | ID: mdl-36753412

ABSTRACT

Genome-wide association studies have linked the ORM (yeast)-like protein isoform 3 (ORMDL3) to asthma severity. Although ORMDL3 is a member of a family that negatively regulates serine palmitoyltransferase (SPT) and thus biosynthesis of sphingolipids, it is still unclear whether ORMDL3 and altered sphingolipid synthesis are causally related to non-Th2 severe asthma associated with a predominant neutrophil inflammation and high interleukin-17 (IL-17) levels. Here, we examined the effects of ORMDL3 overexpression in a preclinical mouse model of allergic lung inflammation that is predominantly neutrophilic and recapitulates many of the clinical features of severe human asthma. ORMDL3 overexpression reduced lung and circulating levels of dihydrosphingosine, the product of SPT. However, the most prominent effect on sphingolipid levels was reduction of circulating S1P. The LPS/OVA challenge increased markers of Th17 inflammation with a predominant infiltration of neutrophils into the lung. A significant decrease of neutrophil infiltration was observed in the Ormdl3 transgenic mice challenged with LPS/OVA compared to the wild type and concomitant decrease in IL-17, that plays a key role in the pathogenesis of neutrophilic asthma. LPS decreased survival of murine neutrophils, which was prevented by co-treatment with S1P. Moreover, S1P potentiated LPS-induced chemotaxis of neutrophil, suggesting that S1P can regulate neutrophil survival and recruitment following LPS airway inflammation. Our findings reveal a novel connection between ORMDL3 overexpression, circulating levels of S1P, IL-17 and neutrophil recruitment into the lung, and questions the potential involvement of ORMDL3 in the pathology, leading to development of severe neutrophilic asthma.


Subject(s)
Asthma , Interleukin-17 , Membrane Proteins , Animals , Humans , Mice , Asthma/metabolism , Genome-Wide Association Study , Inflammation/metabolism , Interleukin-17/genetics , Interleukin-17/therapeutic use , Lipopolysaccharides , Membrane Proteins/metabolism , Mice, Transgenic , Sphingolipids/metabolism
4.
Adv Biol Regul ; 87: 100925, 2023 01.
Article in English | MEDLINE | ID: mdl-36706611

ABSTRACT

Hepatocellular carcinoma (HCC) is the third leading cause of cancer related deaths worldwide and its incidence is increasing due to endemic obesity and the growing burden of non-alcoholic steatohepatitis (NASH) associated liver cancer. Although much is known about the clinical and histological pathology of NASH-driven HCC in humans, its etiology remains unclear and there is a lack of reliable biomarkers and limited effective therapies. Progress has been hampered by the scarcity of standardized animal models that recapitulate the gradual progression of NASH towards HCC observed in humans. Here we review existing mouse models and their suitability for studying NASH-driven HCC with special emphasis on a preclinical model that we recently developed that faithfully mimics all the clinical endpoints of progression of the human disease. Moreover, it is highly translatable, allows the use of gene-targeted mice, and is suitable for gaining knowledge of how NASH progresses to HCC and development of new targets for treatment.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Non-alcoholic Fatty Liver Disease , Humans , Animals , Mice , Biomarkers , Disease Models, Animal
5.
Cancer Res ; 83(4): 553-567, 2023 02 15.
Article in English | MEDLINE | ID: mdl-36541910

ABSTRACT

Reciprocal interactions between breast cancer cells and the tumor microenvironment (TME) are important for cancer progression and metastasis. We report here that the deletion or inhibition of sphingosine kinase 2 (SphK2), which produces sphingosine-1-phosphate (S1P), markedly suppresses syngeneic breast tumor growth and lung metastasis in mice by creating a hostile microenvironment for tumor growth and invasion. SphK2 deficiency decreased S1P and concomitantly increased ceramides, including C16-ceramide, in stromal fibroblasts. Ceramide accumulation suppressed activation of cancer-associated fibroblasts (CAF) by upregulating stromal p53, which restrained production of tumor-promoting factors to reprogram the TME and to restrict breast cancer establishment. Ablation of p53 in SphK2-deficient fibroblasts reversed these effects, enabled CAF activation and promoted tumor growth and invasion. These data uncovered a novel role of SphK2 in regulating non-cell-autonomous functions of p53 in stromal fibroblasts and their transition to tumor-promoting CAFs, paving the way for the development of a strategy to target the TME and to enhance therapeutic efficacy. SIGNIFICANCE: Sphingosine kinase 2 (SphK2) facilitates the activation of stromal fibroblasts to tumor-promoting cancer-associated fibroblasts by suppressing host p53 activity, revealing SphK2 as a potential target to reprogram the TME.


Subject(s)
Cancer-Associated Fibroblasts , Mammary Neoplasms, Animal , Phosphotransferases (Alcohol Group Acceptor) , Tumor Microenvironment , Animals , Mice , Cancer-Associated Fibroblasts/metabolism , Fibroblasts/metabolism , Lung Neoplasms/pathology , Lung Neoplasms/secondary , Mammary Neoplasms, Animal/metabolism , Mammary Neoplasms, Animal/pathology , Phosphotransferases (Alcohol Group Acceptor)/genetics , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Tumor Microenvironment/physiology , Tumor Suppressor Protein p53/genetics
6.
Proc Natl Acad Sci U S A ; 119(39): e2204396119, 2022 09 27.
Article in English | MEDLINE | ID: mdl-36122218

ABSTRACT

Membrane contact sites (MCS), close membrane apposition between organelles, are platforms for interorganellar transfer of lipids including cholesterol, regulation of lipid homeostasis, and co-ordination of endocytic trafficking. Sphingosine kinases (SphKs), two isoenzymes that phosphorylate sphingosine to the bioactive sphingosine-1-phosphate (S1P), have been implicated in endocytic trafficking. However, the physiological functions of SphKs in regulation of membrane dynamics, lipid trafficking and MCS are not known. Here, we report that deletion of SphKs decreased S1P with concomitant increases in its precursors sphingosine and ceramide, and markedly reduced endoplasmic reticulum (ER) contacts with late endocytic organelles. Expression of enzymatically active SphK1, but not catalytically inactive, rescued the deficit of these MCS. Although free cholesterol accumulated in late endocytic organelles in SphK null cells, surprisingly however, cholesterol transport to the ER was not reduced. Importantly, deletion of SphKs promoted recruitment of the ER-resident cholesterol transfer protein Aster-B (also called GRAMD1B) to the plasma membrane (PM), consistent with higher accessible cholesterol and ceramide at the PM, to facilitate cholesterol transfer from the PM to the ER. In addition, ceramide enhanced in vitro binding of the Aster-B GRAM domain to phosphatidylserine and cholesterol liposomes. Our study revealed a previously unknown role for SphKs and sphingolipid metabolites in governing diverse MCS between the ER network and late endocytic organelles versus the PM to control the movement of cholesterol between distinct cell membranes.


Subject(s)
Phosphatidylserines , Sphingosine , Ceramides/metabolism , Cholesterol/metabolism , Endoplasmic Reticulum/metabolism , Isoenzymes/metabolism , Liposomes/metabolism , Lysophospholipids , Phosphatidylserines/metabolism , Sphingolipids/metabolism , Sphingosine/analogs & derivatives , Sphingosine/metabolism
7.
FASEB J ; 36(7): e22372, 2022 07.
Article in English | MEDLINE | ID: mdl-35639028

ABSTRACT

Non-alcoholic steatohepatitis (NASH) results from the accumulation of excessive liver lipids leading to hepatocellular injury, inflammation, and fibrosis that greatly increase the risk for hepatocellular carcinoma (HCC). Despite the well-characterized clinical and histological pathology for NASH-driven HCC in humans, its etiology remains unclear and there is a deficiency in pre-clinical models that recapitulate the progression of the human disease. Therefore, we developed a new mouse model amenable to genetic manipulations and gene targeting that mimics the gradual NASH to HCC progression observed in humans. C57BL/6NJ mice were fed a Western high-fat diet and sugar water (HFD/SW) and monitored for effects on metabolism, liver histology, tumor development, and liver transcriptome for up to 54 weeks. Chronic HFD/SW feeding led to significantly increased weight gain, serum and liver lipid levels, liver injury, and glucose intolerance. Hepatic pathology progressed and mice developed hepatocellular ballooning, inflammation, and worse fibrosis was apparent at 16 weeks, greatly increased through 32 weeks, and remained elevated at 54 weeks. Importantly, hepatocellular cancer spontaneously developed in 75% of mice on HFD/SW, half of which were HCC, whereas none of the mice on the chow diet developed HCC. Chronic HFD/SW induced molecular markers of de novo lipogenesis, endoplasmic reticulum stress, inflammation, and accumulation of p62, all of which also participate in the human pathology. Moreover, transcriptome analysis revealed activation of HCC-related genes and signatures associated with poor prognosis of human HCC. Overall, we have identified a new preclinical model that recapitulates known hallmarks of NASH-driven HCC that can be utilized for future molecular mechanistic studies of this disease.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Non-alcoholic Fatty Liver Disease , Animals , Carcinoma, Hepatocellular/metabolism , Diet, Western/adverse effects , Fibrosis , Inflammation/complications , Liver Neoplasms/metabolism , Mice , Mice, Inbred C57BL , Non-alcoholic Fatty Liver Disease/metabolism
8.
Methods Mol Biol ; 2455: 163-179, 2022.
Article in English | MEDLINE | ID: mdl-35212994

ABSTRACT

Non-alcoholic steatohepatitis (NASH) is a major cause of chronic liver disease that can ultimately lead to cirrhosis and hepatocellular carcinoma. Although NASH is associated with excessive liver lipid accumulation, hepatocyte injury, inflammation, and fibrosis, its etiology remains incompletely understood. These can be characterized by determining transcriptional changes in specific genes previously found to be involved in these processes. As an inherently multifaceted disease, studies of NASH often require unbiased examination of major genes and pathways to identify the mechanisms involved in this disorder. To address this need, quantitative approaches such as mRNA-sequencing have been developed for the global assessment of gene expression. Here, we describe a protocol for bulk mRNA-sequencing that can be utilized for both liver samples and specific cell types isolated from the liver. This approach provides an important resource to further understand the molecular changes that occur during the development of NASH that can be utilized to design better therapeutic treatments.


Subject(s)
Liver Neoplasms , Non-alcoholic Fatty Liver Disease , Humans , Liver/metabolism , Liver Cirrhosis/pathology , Liver Neoplasms/pathology , Non-alcoholic Fatty Liver Disease/genetics , Non-alcoholic Fatty Liver Disease/metabolism , RNA, Messenger/genetics
9.
Hist Psychol ; 25(1): 1-2, 2022 02.
Article in English | MEDLINE | ID: mdl-35113634

ABSTRACT

Now in its 25th year, the journal has become an important institution within the discipline since an article of the editor's (on Aristotle's theory of mind) was the first to appear on its pages in back in 1998. It is the editor's aim to build the journal in ways that serve the community of historians of psychology even better than it has over the past quarter of a century. First, the editor intended to follow and expand even further the previous editor's impressive efforts to have the journal reflect the diversity of its disciplinary community. Second, the editor also hopes to encourage innovative practitioners of the historiographic craft-especially digital researchers-to look to the journal as a friendly outlet. Third, in sympathy with APA's adoption of the Transparency and Openness Promotion (TOP) guidelines, the editor will work with authors to ensure that the sources of their historical claims are as clear as possible. Finally, please allow the editor to personally invite you, the reader, to assist me in supporting and enriching this journal. (PsycInfo Database Record (c) 2022 APA, all rights reserved).


Subject(s)
Periodicals as Topic
10.
Cell Metab ; 33(7): 1293-1306, 2021 07 06.
Article in English | MEDLINE | ID: mdl-34233172

ABSTRACT

The bioactive sphingolipid metabolites ceramide and sphingosine-1-phosphate (S1P) are a recent addition to the lipids accumulated in obesity and have emerged as important molecular players in metabolic diseases. Here we summarize evidence that dysregulation of sphingolipid metabolism correlates with pathogenesis of metabolic diseases in humans. This review discusses the current understanding of how ceramide regulates signaling and metabolic pathways to exacerbate metabolic diseases and the Janus faces for its further metabolite S1P, the kinases that produce it, and the multifaceted and at times opposing actions of S1P receptors in various tissues. Gaps and limitations in current knowledge are highlighted together with the need to further decipher the full array of their actions in tissue dysfunction underlying metabolic pathologies, pointing out prospects to move this young field of research toward the development of effective therapeutics.


Subject(s)
Metabolic Diseases/etiology , Sphingolipids/physiology , Animals , Humans , Lipid Metabolism/physiology , Metabolic Diseases/metabolism , Metabolic Diseases/pathology , Metabolic Networks and Pathways/physiology , Obesity/etiology , Obesity/metabolism , Obesity/pathology , Sphingolipids/metabolism
11.
J Lipid Res ; 62: 100082, 2021.
Article in English | MEDLINE | ID: mdl-33939982

ABSTRACT

The serine palmitoyltransferase (SPT) complex catalyzes the rate-limiting step in the de novo biosynthesis of ceramides, the precursors of sphingolipids. The mammalian ORMDL isoforms (ORMDL1-3) are negative regulators of SPT. However, the roles of individual ORMDL isoforms are unclear. Using siRNA against individual ORMDLs, only single siORMDL3 had modest effects on dihydroceramide and ceramide levels, whereas downregulation of all three ORMDLs induced more pronounced increases. With the CRISPR/Cas9-based genome-editing strategy, we established stable single ORMDL3 KO (ORMDL3-KO) and ORMDL1/2/3 triple-KO (ORMDL-TKO) cell lines to further understand the roles of ORMDL proteins in sphingolipid biosynthesis. While ORMDL3-KO modestly increased dihydroceramide and ceramide levels, ORMDL-TKO cells had dramatic increases in the accumulation of these sphingolipid precursors. SPT activity was increased only in ORMDL-TKO cells. In addition, ORMDL-TKO but not ORMDL3-KO dramatically increased levels of galactosylceramides, glucosylceramides, and lactosylceramides, the elevated N-acyl chain distributions of which broadly correlated with the increases in ceramide species. Surprisingly, although C16:0 is the major sphingomyelin species, it was only increased in ORMDL3-KO, whereas all other N-acyl chain sphingomyelin species were significantly increased in ORMDL-TKO cells. Analysis of sphingoid bases revealed that although sphingosine was only increased 2-fold in ORMDL-TKO cells, levels of dihydrosphingosine, dihydrosphingosine-1-phosphate, and sphingosine-1-phosphate were hugely increased in ORMDL-TKO cells and not in ORMDL3-KO cells. Thus, ORMDL proteins may have a complex, multifaceted role in the biosynthesis and regulation of cellular sphingolipids.


Subject(s)
CRISPR-Cas Systems
12.
Dev Cell ; 54(4): 529-547.e12, 2020 08 24.
Article in English | MEDLINE | ID: mdl-32504559

ABSTRACT

Spermatogenesis is a highly regulated process that produces sperm to transmit genetic information to the next generation. Although extensively studied in mice, our current understanding of primate spermatogenesis is limited to populations defined by state-specific markers from rodent data. As between-species differences have been reported in the duration and differentiation hierarchy of this process, it remains unclear how molecular markers and cell states are conserved or have diverged from mice to man. To address this challenge, we employ single-cell RNA sequencing to identify transcriptional signatures of major germ and somatic cell types of the testes in human, macaque, and mice. This approach reveals similarities and differences in expression throughout spermatogenesis, including the stem/progenitor pool of spermatogonia, markers of differentiation, potential regulators of meiosis, RNA turnover during spermatid differentiation, and germ cell-soma communication. These datasets provide a rich foundation for future targeted mechanistic studies of primate germ cell development and in vitro gametogenesis.


Subject(s)
Cell Differentiation/genetics , Single-Cell Analysis , Spermatogenesis/genetics , Testis/growth & development , Animals , Gene Expression Regulation, Developmental/genetics , Humans , Macaca/genetics , Macaca/growth & development , Male , Meiosis/genetics , Mice , Sequence Analysis, RNA , Spermatogonia/cytology , Testis/metabolism
13.
Hist Psychol ; 22(4): 369-372, 2019 11.
Article in English | MEDLINE | ID: mdl-31633371

ABSTRACT

Look at any introductory psychology book that covers psychoanalysis, and you are likely to find an image of an iceberg floating in the sea. The image serves as an illustrative metaphor for Freud's theory of the mind: Only a fragment of our ideas and feelings are conscious or "visible" to us, while the vast bulk of our mental content is unconscious or "invisible" to everyday introspection. A simple Internet search of the terms "Freud iceberg" will bring forth hundreds of examples. The problem is that Freud never mentioned the iceberg in his published writings. It is a metaphor that has become ubiquitous in (English-language) writings about Freudian theory, but that does not find its source in his work. So the question is, where did it come from? Much attention has been directed to a passage in Ernest Jones's biography of Freud. Many have taken this to mean that the Freudian iceberg metaphor derives directly from Fechner. Jones encouraged this interpretation, quoting Freud on being "open to the ideas of G. T. Fechner and following that thinker upon many important points." The iceberg metaphor of mind has another source with a solid connection to Freud: Granville Stanley Hall. Hall was one of the founders of American psychology. The mystery of the Freudian iceberg is not completely resolved, but we have made considerable progress. The mystery that remains is why Hall believed the metaphor's origin to lay somewhere in Fechner's writings. (PsycINFO Database Record (c) 2019 APA, all rights reserved).


Subject(s)
Freudian Theory/history , Metaphor , History, 20th Century , Humans , Psychoanalysis/education , Psychoanalysis/history
14.
Hist Psychol ; 21(4): 374-379, 2018 11.
Article in English | MEDLINE | ID: mdl-30421949

ABSTRACT

The articles authored by Flis and van Eck (2018) and by Burman (2018) serve as fine examples of the ways in which digital historical methods can illuminate aspects of psychology's past that would probably not be possible otherwise. This success, however, presents no reason to think that digital history is some kind of threat to conventional historiography or that former aims to replace the latter. The two can work complementarily-so closely, in fact, that it sometimes becomes difficult to know which of the two one is practicing at any given moment. Multiple skill sets need not define the historian as being a particular "kind": They just enable any historian to do his or her work more completely than before. (PsycINFO Database Record (c) 2018 APA, all rights reserved).


Subject(s)
Historiography , Archives
15.
Proc Natl Acad Sci U S A ; 115(29): 7611-7616, 2018 07 17.
Article in English | MEDLINE | ID: mdl-29967166

ABSTRACT

Brain "inflammaging," a low-grade and chronic inflammation, is a major hallmark for aging-related neurodegenerative diseases. Here, by profiling H3K27ac and gene expression patterns in human and mouse brains, we found that age-related up-regulated (Age-Up) and down-regulated (Age-Down) genes have distinct H3K27ac patterns. Although both groups show promoter H3K27ac, the Age-Up genes, enriched for inflammation-related functions, are additionally marked by broad H3K27ac distribution over their gene bodies, which is progressively reduced during aging. Age-related gene expression changes can be predicted by gene-body H3K27ac level. Contrary to the presumed transcription activation function of promoter H3K27ac, we found that broad gene-body hyper H3K27ac suppresses overexpression of inflammaging genes. Altogether, our findings revealed opposite regulations by H3K27ac of Age-Up and Age-Down genes and a mode of broad gene-body H3K27ac in repressing transcription.


Subject(s)
Aging/metabolism , Brain/metabolism , Histones/metabolism , Promoter Regions, Genetic , Transcription, Genetic , Transcriptome , Acetylation , Aging/genetics , Animals , Gene Expression Profiling , Histones/genetics , Humans , Inflammation/genetics , Inflammation/metabolism , Mice
16.
Nat Commun ; 8(1): 1856, 2017 11 30.
Article in English | MEDLINE | ID: mdl-29187729

ABSTRACT

Single-cell RNA sequencing (scRNA-seq) is a powerful method for dissecting intercellular heterogeneity during development. Conventional trajectory analysis provides only a pseudotime of development, and often discards cell-cycle events as confounding factors. Here using matched cell population RNA-seq (cpRNA-seq) as a reference, we developed an "iCpSc" package for integrative analysis of cpRNA-seq and scRNA-seq data. By generating a computational model for reference "biological differentiation time" using cell population data and applying it to single-cell data, we unbiasedly associated cell-cycle checkpoints to the internal molecular timer of single cells. Through inferring a network flow from cpRNA-seq to scRNA-seq data, we predicted a role of M phase in controlling the speed of neural differentiation of mouse embryonic stem cells, and validated it through gene knockout (KO) experiments. By linking temporally matched cpRNA-seq and scRNA-seq data, our approach provides an effective and unbiased approach for identifying developmental trajectory and timing-related regulatory events.


Subject(s)
Mouse Embryonic Stem Cells/physiology , Single-Cell Analysis/methods , Transcriptome , Animals , CRISPR-Cas Systems , Cell Cycle/genetics , Cell Differentiation , Cell Division/genetics , Computational Biology/methods , Gene Regulatory Networks , High-Throughput Nucleotide Sequencing/methods , Mice , Mice, Knockout , Mouse Embryonic Stem Cells/cytology , Proto-Oncogene Proteins c-fyn/genetics , Sequence Analysis, RNA/methods , Smad1 Protein/genetics , Tumor Suppressor Protein p53/genetics
17.
Am Psychol ; 72(8): 722-736, 2017 Nov.
Article in English | MEDLINE | ID: mdl-29172576

ABSTRACT

The American Psychological Association (APA) began 125 years ago as a small club of a few dozen members in the parlor of its founder, G. Stanley Hall. In the decades since, it has faced many difficulties and even a few existential crises. Originally a scientific society, it spent the decades between the world wars figuring out how to accommodate the growing community of applied psychologists while still retaining and enhancing its scientific reputation. After World War II, with an expanded mandate, it developed formal training models for clinical psychologists and became an important player in legal cases pertaining to civil rights and other social justice issues. With practitioners taking an ever-greater role in the governance of the organization in the late 1970s, and the financial viability of the association in doubt in the 1980s, many psychological scientists felt the need to create a separate organization for themselves. The 1990s and early 2000s brought more challenges: declining divisional memberships; a legal dispute over fees with practitioners; and a serious upheaval over the APA Board of Directors' cooperation with governmental defense and intelligence agencies during the "war on terror." These clashes appear to have precipitated a decline in the association's membership for the first time in its history. The APA has faced many storms over its century-and-a-quarter, but has, thus far, always ultimately found a way forward for itself, for its members, and for the wider discipline of psychology. (PsycINFO Database Record


Subject(s)
Psychology/history , Societies, Scientific/history , History, 20th Century , History, 21st Century
18.
Cell Rep ; 18(12): 2957-2968, 2017 03 21.
Article in English | MEDLINE | ID: mdl-28329687

ABSTRACT

Dietary interventions dramatically affect metabolic disease and lifespan in various aging models. Here, we profiled liver microRNA (miRNA), coding, and long non-coding RNA (lncRNA) expression by high-throughput deep sequencing in mice across multiple energy intake and expenditure interventions. Strikingly, three dietary intervention network design patterns were uncovered: (1) lifespan-extending interventions largely repressed the expression of miRNAs, lncRNAs, and transposable elements; (2) protein-coding mRNAs with expression positively correlated with long lifespan are highly targeted by miRNAs; and (3) miRNA-targeting interactions mainly target chromatin-related functions. We experimentally validated miR-34a, miR-107, and miR-212-3p targeting of the chromatin remodeler Chd1 and further demonstrate that Chd1 knockdown mimics high-fat diet and aging-induced gene expression changes and activation of transposons. Our findings demonstrate lifespan-extending diets repress miRNA-chromatin remodeler interactions and safeguard against deregulated transcription induced by aging and lifespan shortening diets, events linked by microRNA, chromatin, and ncRNA crosstalk.


Subject(s)
Chromatin/genetics , Diet , Gene Regulatory Networks , RNA, Long Noncoding/genetics , Animals , Base Sequence , DNA Transposable Elements/genetics , DNA-Binding Proteins/metabolism , Diet, High-Fat , Gene Expression Profiling , Gene Expression Regulation , Gene Knockdown Techniques , Liver/physiology , Longevity/genetics , Male , Mice, Inbred C57BL , MicroRNAs/genetics , MicroRNAs/metabolism , RNA, Long Noncoding/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Repetitive Sequences, Nucleic Acid/genetics
19.
Am J Psychol ; 130(1): 105-119, 2017.
Article in English | MEDLINE | ID: mdl-29508961

ABSTRACT

What is the relationship between being highly prolific in the realm of publication and being remembered as a great psychologist of the past? In this study, the PsycINFO database was used to identify the historical figures who wrote the most journal articles during the half-century from 1890 to 1939. Although a number of the 10 most prolific authors are widely remembered for their influence on the discipline today-E. L. Thorndike, Karl Pearson, E. B. Titchener, Henri Pi6ron-the majority are mostly forgotten. The data were also separated into the 5 distinct decades. Once again, a mixture of eminent and obscure individuals made appearances. Most striking, perhaps, was the great increase in articles published over the course of the half-century-approximately doubling each decade-and the enormous turnover in who was most prolific, decade over decade. In total, 100 distinct individuals appeared across just 5 lists of about 25 names each.


Subject(s)
Bibliographies as Topic , Biomedical Research/statistics & numerical data , Psychology/statistics & numerical data , Biomedical Research/history , History, 19th Century , History, 20th Century , Humans , Psychology/history
20.
Hist Psychol ; 20(1): 72-91, 2017 02.
Article in English | MEDLINE | ID: mdl-27560130

ABSTRACT

Recent research has used networks of scholarly journal articles to investigate the intellectual structure of the discipline of psychology from the later 1880s to the early 1920s. Here, instead, we examined the networks of philosophical journals that were closely aligned with psychology-The Monist, Philosophical Review, and The Journal of Philosophy, Psychology, and Scientific Methods-between 1890 and 1913. We discovered that, although the first 2 of these journals published a great deal of psychologically relevant material up to 1903, material of that sort seemed to evaporate after the launch of the third journal in 1904. It was not so much that material migrated from the old journals to the new one. It was rather that the new journal was able to attract new trends in American philosophical psychology, while interest in traditional approaches seemed to dry up. The result was that psychology moved into a new and expansive era, while America philosophy was left somewhat destabilized as it attempted to reconfigure its disciplinary identity. (PsycINFO Database Record


Subject(s)
Bibliometrics/history , Periodicals as Topic/history , Philosophy/history , Psychology/history , History, 19th Century , History, 20th Century , United States
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