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Article ; Online: The transcription factor code in iPSC reprogramming.

Deng, Weixian / Jacobson, Elsie C / Collier, Amanda J / Plath, Kathrin

Current opinion in genetics & development

2021 Volume 70, Page(s) 89–96

Abstract: Transcription factor (TF)-induced reprogramming of somatic cells across lineages and to induced pluripotent stem cells (iPSCs) has revealed a remarkable plasticity of differentiated cells and presents great opportunities for generating clinically ... ...

Abstract	Transcription factor (TF)-induced reprogramming of somatic cells across lineages and to induced pluripotent stem cells (iPSCs) has revealed a remarkable plasticity of differentiated cells and presents great opportunities for generating clinically relevant cell types for disease modeling and regenerative medicine. The understanding of iPSC reprogramming provides insights into the mechanisms that safeguard somatic cell identity, drive epigenetic reprogramming, and underlie cell fate specification in vivo. The combinatorial action of TFs has emerged as the key mechanism for the direct and indirect effects of reprogramming factors that induce the remodelling of the enhancer landscape. The interplay of TFs in iPSC reprogramming also yields trophectoderm- and extraembryonic endoderm-like cell populations, uncovering an intriguing plasticity of cell states and opening new avenues for exploring cell fate decisions during early embryogenesis.
MeSH term(s)	Animals ; Cellular Reprogramming ; Embryonic Development ; Epigenesis, Genetic ; Humans ; Induced Pluripotent Stem Cells/chemistry ; Induced Pluripotent Stem Cells/metabolism ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors
Language	English
Publishing date	2021-07-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2021.06.003
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Article ; Online: Neural features of sustained emotional information processing in autism spectrum disorder.

Mazefsky, Carla A / Collier, Amanda / Golt, Josh / Siegle, Greg J

Autism : the international journal of research and practice

2020 Volume 24, Issue 4, Page(s) 941–953

Abstract: Lay abstract: Many individuals with autism spectrum disorder struggle with emotions that are intense and interfering, which is referred to as emotion dysregulation. Prior research has established that individuals with autism may be more likely than ... ...

Abstract	Lay abstract: Many individuals with autism spectrum disorder struggle with emotions that are intense and interfering, which is referred to as emotion dysregulation. Prior research has established that individuals with autism may be more likely than individuals who are not autistic to have repetitive thoughts. It is possible that persistent thoughts about negative or distressing stimuli may contribute to emotion dysregulation in autism spectrum disorder. This study aimed to identify areas of the brain with evidence of persistent processing of negative information via functional magnetic resonance neuroimaging. We used a task that alternated between emotional processing of personally relevant negative words, neutral words, and a non-emotional task. Criteria were developed to define heightened and persistent emotional processing, and analyses were conducted to identify all brain regions satisfying these criteria. Participants included 25 adolescents with autism spectrum disorder and 23 typically developing adolescents who were similar to the autism spectrum disorder group in IQ, age, and gender ratios. Brain regions identified as having greater and continued processing following negative stimuli in the autism spectrum disorder group as compared with the typically developing group included the salience network and the prefrontal dorsolateral cortex. These areas have been previously implicated in emotion dysregulation outside of autism spectrum disorder. Collectively, brain activity in the identified regions was associated with parent-reported emotion dysregulation in the autism spectrum disorder group. These results help to identify a potential process in the brain associated with emotion dysregulation in autism spectrum disorder. This information may be useful for the development of treatments to decrease emotion dysregulation in autism spectrum disorder.
MeSH term(s)	Adolescent ; Autism Spectrum Disorder ; Brain/diagnostic imaging ; Cognition ; Emotions ; Female ; Humans ; Magnetic Resonance Imaging ; Male
Language	English
Publishing date	2020-02-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1338513-6
ISSN	1461-7005 ; 1362-3613
ISSN (online)	1461-7005
ISSN	1362-3613
DOI	10.1177/1362361320903137
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Article ; Online: XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells.

Dror, Iris / Chitiashvili, Tsotne / Tan, Shawn Y X / Cano, Clara T / Sahakyan, Anna / Markaki, Yolanda / Chronis, Constantinos / Collier, Amanda J / Deng, Weixian / Liang, Guohao / Sun, Yu / Afasizheva, Anna / Miller, Jarrett / Xiao, Wen / Black, Douglas L / Ding, Fangyuan / Plath, Kathrin

Cell

2024 Volume 187, Issue 1, Page(s) 110–129.e31

Abstract: X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent ... ...

Abstract	X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
MeSH term(s)	Animals ; Female ; Humans ; Male ; Mice ; Gene Silencing ; Genes, X-Linked ; RNA, Long Noncoding/genetics ; X Chromosome/genetics ; Pluripotent Stem Cells/metabolism
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.11.033
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Global Emergency Medicine: A Scoping Review of the Literature from 2022.

Hexom, Braden J / Quao, Nana Serwaa A / Bandolin, N Shakira / Bonney, Joseph / Collier, Amanda / Dyal, Jonathan / Lee, J Austin / Nicholson, Benjamin D / Rybarczyk, Megan M / Rees, Chris A / Roy, Charlotte M / Bhaskar, Nidhi / Kivlehan, Sean M

Academic emergency medicine : official journal of the Society for Academic Emergency Medicine

2023 Volume 31, Issue 1, Page(s) 71–85

Abstract: Objective: The objective was to identify the highest quality global emergency medicine (GEM) research published in 2022. The top articles are compiled in a comprehensive list of all the year's GEM articles and narrative summaries are performed on those ... ...

Abstract	Objective: The objective was to identify the highest quality global emergency medicine (GEM) research published in 2022. The top articles are compiled in a comprehensive list of all the year's GEM articles and narrative summaries are performed on those included. Methods: A systematic PubMed search was conducted to identify all GEM articles published in 2022 and included a manual supplemental screen of 11 organizational websites for gray literature (GRAY). A team of trained reviewers and editors screened all identified titles and abstracts, based on three case definition categories: disaster and humanitarian response (DHR), emergency care in resource-limited settings (ECRLS), and emergency medicine development (EMD). Articles meeting these definitions were independently scored by two reviewers using rubrics for original research (OR), review (RE) articles, and GRAY. Articles that scored in the top 5% from each category as well as the overall top 5% of articles were included for narrative summary. Results: The 2022 search identified 58,510 articles in the main review, of which 524 articles screened in for scoring, respectively, 30% and 18% increases from last year. After duplicates were removed, 36 articles were included for narrative summary. The GRAY search identified 7755 articles, of which 33 were scored and one was included for narrative summary. ECRLS remained the largest category (27; 73%), followed by DHR (7; 19%) and EMD (3; 8%). OR articles remained more common than RE articles (64% vs. 36%). Conclusions: The waning of the COVID-19 pandemic has not affected the continued growth in GEM literature. Articles related to prehospital care, mental health and resilience among patients and health care workers, streamlining pediatric infectious disease care, and disaster preparedness were featured in this year's review. The continued lack of EMD studies despite the global growth of GEM highlights a need for more scholarly dissemination of best practices.
MeSH term(s)	Child ; Humans ; Pandemics ; Global Health ; Emergency Medical Services ; Emergency Medicine ; Disasters
Language	English
Publishing date	2023-11-03
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	1329813-6
ISSN	1553-2712 ; 1069-6563
ISSN (online)	1553-2712
ISSN	1069-6563
DOI	10.1111/acem.14816
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Article ; Online: Personalized Antihypertensive Treatment Optimization With Smartphone-Enabled Remote Precision Dosing of Amlodipine During the COVID-19 Pandemic (PERSONAL-CovidBP Trial).

Journal of the American Heart Association

2024 Volume 13, Issue 4, Page(s) e030749

Abstract: Background: The objective of the PERSONAL-CovidBP (Personalised Electronic Record Supported Optimisation When Alone for Patients With Hypertension: Pilot Study for Remote Medical Management of Hypertension During the COVID-19 Pandemic) trial was to ... ...

Abstract	Background: The objective of the PERSONAL-CovidBP (Personalised Electronic Record Supported Optimisation When Alone for Patients With Hypertension: Pilot Study for Remote Medical Management of Hypertension During the COVID-19 Pandemic) trial was to assess the efficacy and safety of smartphone-enabled remote precision dosing of amlodipine to control blood pressure (BP) in participants with primary hypertension during the COVID-19 pandemic. Methods and results: This was an open-label, remote, dose titration trial using daily home self-monitoring of BP, drug dose, and side effects with linked smartphone app and telemonitoring. Participants aged ≥18 years with uncontrolled hypertension (5-7 day baseline mean ≥135 mm Hg systolic BP or ≥85 mm Hg diastolic BP) received personalized amlodipine dose titration using novel (1, 2, 3, 4, 6, 7, 8, 9 mg) and standard (5 and 10 mg) doses daily over 14 weeks. The primary outcome of the trial was mean change in systolic BP from baseline to end of treatment. A total of 205 participants were enrolled and mean BP fell from 142/87 (systolic BP/diastolic BP) to 131/81 mm Hg (a reduction of 11 (95% CI, 10-12)/7 (95% CI, 6-7) mm Hg, Conclusions: Personalized dose titration with amlodipine was safe, well tolerated, and efficacious in treating primary hypertension. The majority of participants achieved BP control on novel doses, and with personalization of dose there were no trial discontinuations due to drug intolerance. App-assisted remote clinician dose titration may better balance BP control and adverse effects and help optimize long-term care. Registration: URL: clinicaltrials.gov. Identifier: NCT04559074.
MeSH term(s)	Adolescent ; Adult ; Humans ; Amlodipine/therapeutic use ; Antihypertensive Agents/therapeutic use ; Blood Pressure ; COVID-19 ; Essential Hypertension/drug therapy ; Hypertension/diagnosis ; Hypertension/drug therapy ; Hypertension/chemically induced ; Pandemics ; Pilot Projects ; Smartphone ; Treatment Outcome
Chemical Substances	Amlodipine (1J444QC288) ; Antihypertensive Agents
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Clinical Trial ; Journal Article
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.123.030749
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Article ; Online: Identifying Human Naïve Pluripotent Stem Cells - Evaluating State-Specific Reporter Lines and Cell-Surface Markers.

Collier, Amanda J / Rugg-Gunn, Peter J

BioEssays : news and reviews in molecular, cellular and developmental biology

2018 Volume 40, Issue 5, Page(s) e1700239

Abstract: Recent reports that human pluripotent stem cells can be captured in a spectrum of states with variable properties has prompted a re-evaluation of how pluripotency is acquired and stabilised. The latest additions to the stem cell hierarchy open up ... ...

Abstract	Recent reports that human pluripotent stem cells can be captured in a spectrum of states with variable properties has prompted a re-evaluation of how pluripotency is acquired and stabilised. The latest additions to the stem cell hierarchy open up opportunities for understanding human development, reprogramming, and cell state transitions more generally. Many of the new cell lines have been collectively termed 'naïve' human pluripotent stem cells to distinguish them from the conventional 'primed' cells. Here, several transcriptional and epigenetic hallmarks of human pluripotent states in the recently described cell lines are reviewed and evaluated. Methods to derive and identify human naïve pluripotent stem cells are also discussed, with a focus on the uses and future developments of state-specific reporter cell lines and cell-surface proteins. Finally, opportunities and uncertainties in naïve stem cell biology are highlighted, and the current limitations of human naïve pluripotent stem cells considered, particularly in the context of differentiation.
MeSH term(s)	Cell Differentiation/genetics ; Cell Differentiation/physiology ; Cell Line ; Cellular Reprogramming/genetics ; Cellular Reprogramming/physiology ; Embryonic Stem Cells/cytology ; Embryonic Stem Cells/metabolism ; Epigenomics ; Humans ; Pluripotent Stem Cells/metabolism
Language	English
Publishing date	2018-03-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201700239
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Article ; Online: Species-specific regulation of XIST by the JPX/FTX orthologs.

Rosspopoff, Olga / Cazottes, Emmanuel / Huret, Christophe / Loda, Agnese / Collier, Amanda J / Casanova, Miguel / Rugg-Gunn, Peter J / Heard, Edith / Ouimette, Jean-François / Rougeulle, Claire

Nucleic acids research

2023 Volume 51, Issue 5, Page(s) 2177–2194

Abstract: X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved ... ...

Abstract	X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved concomitantly to XIST and have orthologues across all placental mammals. Here, we addressed the functional conservation of human orthologues of two such LRGs, FTX and JPX. By combining analysis of single-cell RNA-seq data from early human embryogenesis with various functional assays in matched human and mouse pluripotent stem- or differentiated post-XCI cells, we demonstrate major functional differences for these orthologues between species, independently of primary sequence conservation. While the function of FTX is not conserved in humans, JPX stands as a major regulator of XIST expression in both species. However, we show that different entities of JPX control the production of XIST at various steps depending on the species. Altogether, our study highlights the functional versatility of LRGs across evolution, and reveals that functional conservation of orthologous LRGs may involve diversified mechanisms of action. These findings represent a striking example of how the evolvability of LRGs can provide adaptative flexibility to constrained gene regulatory networks.
MeSH term(s)	Pregnancy ; Humans ; Female ; Mice ; Animals ; Placenta/metabolism ; X Chromosome Inactivation/genetics ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Mammals/genetics ; Embryo, Mammalian/metabolism
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2023-02-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad029
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Article ; Online: Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification.

von Meyenn, Ferdinand / Berrens, Rebecca V / Andrews, Simon / Santos, Fátima / Collier, Amanda J / Krueger, Felix / Osorno, Rodrigo / Dean, Wendy / Rugg-Gunn, Peter J / Reik, Wolf

Developmental cell

2022 Volume 57, Issue 23, Page(s) 2669–2671

Language	English
Publishing date	2022-12-05
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2022.11.009
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Article: Identifying Human Naïve Pluripotent Stem Cells − Evaluating State‐Specific Reporter Lines and Cell‐Surface Markers

Collier, Amanda J / Peter J. Rugg‐Gunn

BioEssays. 2018 May, v. 40, no. 5

2018

Abstract: Recent reports that human pluripotent stem cells can be captured in a spectrum of states with variable properties has prompted a re‐evaluation of how pluripotency is acquired and stabilised. The latest additions to the stem cell hierarchy open up ... ...

Abstract	Recent reports that human pluripotent stem cells can be captured in a spectrum of states with variable properties has prompted a re‐evaluation of how pluripotency is acquired and stabilised. The latest additions to the stem cell hierarchy open up opportunities for understanding human development, reprogramming, and cell state transitions more generally. Many of the new cell lines have been collectively termed ‘naïve’ human pluripotent stem cells to distinguish them from the conventional ‘primed’ cells. Here, several transcriptional and epigenetic hallmarks of human pluripotent states in the recently described cell lines are reviewed and evaluated. Methods to derive and identify human naïve pluripotent stem cells are also discussed, with a focus on the uses and future developments of state‐specific reporter cell lines and cell‐surface proteins. Finally, opportunities and uncertainties in naïve stem cell biology are highlighted, and the current limitations of human naïve pluripotent stem cells considered, particularly in the context of differentiation.
Keywords	cell lines ; epigenetics ; human development ; humans ; proteins ; stem cells ; transcription (genetics) ; uncertainty
Language	English
Dates of publication	2018-05
Size	p. e1700239.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201700239
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Article ; Online: Assessment of an education tool to improve knowledge and reduce stigma of a syringe service program (SSP) at a VA Medical Center.

Collier, Jaclyn / Coker, Elijah / Triboletti, Mark / Hooker, Jeremy / Ifeachor, Amanda P / Houck, Kelly K

Journal of the American Pharmacists Association : JAPhA

2023 Volume 64, Issue 2, Page(s) 551–556

Abstract: Background: Drug overdose deaths are a growing epidemic in the United States owing in part to inadequate support from health care systems. In response, the Veterans Health Administration (VHA) plans to implement syringe service programs (SSPs) across ... ...

Abstract	Background: Drug overdose deaths are a growing epidemic in the United States owing in part to inadequate support from health care systems. In response, the Veterans Health Administration (VHA) plans to implement syringe service programs (SSPs) across VHA medical centers. This SSP education project aims to positively affect health care staff perceptions regarding SSPs and reduce the stigma surrounding substance use. Objectives: The purpose of this research was to allow Advanced Pharmacy Practice Experience (APPE) students to implement and assess an educational program regarding SSP enactment at this institution. Furthermore, the objectives of the educational program were to address the stigma associated with substance use and provide knowledge to staff about SSPs. Practice description: Eleven complete and one abbreviated (no questionnaire) presentations were delivered by APPE students throughout the main facility and outpatient clinics, with presentations being delivered to physicians, nurses, and a range of other professions. Practice innovation: APPE students developed educational content and pre- and postsurveys that were used to assess for changes in knowledge and perception surrounding substance use and SSPs. Evaluation methods: The primary outcome was to assess individual pre- and postprogram survey responses using mean, SD, and mean change to measure the impact that the presentation had on individualized stigma. Results: A total of 104 completed surveys were analyzed in Microsoft Excel and subcategorized by profession; 10 of the 15 questions asked in the questionnaire yielded statistical significance when comparing pre- and postpresentation results (P < 0.05). Conclusions: A presentation method developed and delivered by APPE students resulted in a statistically significant change in perception and knowledge, proving to be an effective method for educating health care staff on SSPs.
MeSH term(s)	Humans ; United States ; Social Stigma ; Drug Overdose ; Substance-Related Disorders ; Educational Status ; Education, Pharmacy/methods
Language	English
Publishing date	2023-11-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2118585-2
ISSN	1544-3450 ; 1544-3191 ; 1086-5802
ISSN (online)	1544-3450
ISSN	1544-3191 ; 1086-5802
DOI	10.1016/j.japh.2023.10.035
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