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Article ; Online: scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities.

Kim, Yong-Il / O'Rourke, Rebecca / Sagerström, Charles G

2023 Volume 12

Abstract: Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form has not been fully established. ...

Abstract	Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form has not been fully established. Here, we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium that represent prospective rhombomere r2/r3 (possibly including r1), r4, and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires the resolution of mixed transcription and chromatin states.
MeSH term(s)	Animals ; Zebrafish/genetics ; Prospective Studies ; Zebrafish Proteins/metabolism ; Rhombencephalon ; Chromatin/metabolism
Chemical Substances	Zebrafish Proteins ; Chromatin
Language	English
Publishing date	2023-11-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.87772
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities.

Kim, Yong-Il / O'Rourke, Rebecca / Sagerström, Charles G

bioRxiv : the preprint server for biology

2023

Abstract	Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual mature rhombomeres requires resolution of mixed transcription and chromatin states.
Language	English
Publishing date	2023-01-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.27.525932
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Article ; Online: Single cell sequencing of the mouse anterior palate reveals mesenchymal heterogeneity.

Ozekin, Yunus H / O'Rourke, Rebecca / Bates, Emily Anne

Developmental dynamics : an official publication of the American Association of Anatomists

2023 Volume 252, Issue 6, Page(s) 713–727

Abstract: Background: Cleft palate is one of the most prevalent birth defects. Mice are useful for studying palate development because of their morphological and genetic similarities to humans. In mice, palate development occurs between embryonic days (E)11.5 to ... ...

Abstract	Background: Cleft palate is one of the most prevalent birth defects. Mice are useful for studying palate development because of their morphological and genetic similarities to humans. In mice, palate development occurs between embryonic days (E)11.5 to 15.5. Single cell transcriptional profiles of palate cell populations have been a valuable resource for the craniofacial research community, but we lack a single cell transcriptional profile for anterior palate at E13.5, at the transition from proliferation to shelf elevation. Results: A detailed single cell RNA sequencing analysis reveals heterogeneity in expression profiles of the cell populations of the E13.5 anterior palate. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA FISH) reveals epithelial populations segregate into layers. Mesenchymal populations spatially segregate into four domains. One of these mesenchymal populations expresses ligands and receptors distinct from the rest of the mesenchyme, suggesting that these cells have a unique function. RNA velocity analysis shows two terminal cell states that contribute to either the proximal or distal palatal regions emerge from a single progenitor pool. Conclusion: This single cell resolution expression data and detailed analysis from E13.5 anterior palate provides a powerful resource for mechanistic insight into secondary palate morphogenesis for the craniofacial research community.
MeSH term(s)	Humans ; Mice ; Animals ; In Situ Hybridization, Fluorescence ; Palate ; Cleft Palate/metabolism ; Morphogenesis/genetics ; RNA/metabolism ; Mesoderm ; Gene Expression Regulation, Developmental
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1102541-4
ISSN	1097-0177 ; 1058-8388
ISSN (online)	1097-0177
ISSN	1058-8388
DOI	10.1002/dvdy.573
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Article ; Online: Professionalism development and assessment in the pre-registration pharmacist placement in England: transformative moments and maturation periods.

Ireland, Helen / Sowter, Julie / O'Rourke, Rebecca

The International journal of pharmacy practice

2022 Volume 30, Issue 4, Page(s) 367–376

Abstract: Objectives: Development of new patient-facing roles for pharmacists and reports of poor patient care in the UK has led to questions concerning how pharmacists develop professionalism. This study explored how professionalism is developed and assessed ... ...

Abstract	Objectives: Development of new patient-facing roles for pharmacists and reports of poor patient care in the UK has led to questions concerning how pharmacists develop professionalism. This study explored how professionalism is developed and assessed during the post-graduation year in practice or pre-registration placement. The perspectives of two staff at the professional regulator UK (General Pharmaceutical Council), eight service users, seven pre-registration trainees, and 12 pre-registration tutors were recruited. Methods: An interpretative paradigm was adopted. Data collection involved a semi-structured group interview, focus groups and a qualitative e-questionnaire. An inductive reasoning approach informed data analysis and interpretation. Key findings: All groups provided insights into examples of transformative moments which potentiated professionalism development, the first being awarding the 'pre-registration trainee' title. All groups reported that contact with patients and trainee reflection aided professionalism maturation from a 'self-centred student' to becoming a 'responsible professional' where more than 'doing' is demanded. Furthermore, tutors stated the rate of professionalism development was affected by the sector of training and its opportunities for patient contact. Tutors felt they alone, not the registration exam, assessed professionalism using a variety of assessment approaches. Importantly, no tutors reported patient involvement in the assessment of trainees' professionalism, yet service users expected to be involved. Conclusions: Transformative moments and maturation periods during pre-registration training develop professionalism and enable trainees to 'become' a pharmacist. Careful planning of placements to optimise professionalism development across pharmacy sectors and consistent patient involvement in assessing trainee professionalism is recommended.
MeSH term(s)	Education, Pharmacy ; England ; Humans ; Pharmacists ; Pharmacy ; Professionalism
Language	English
Publishing date	2022-05-31
Publishing country	England
Document type	Journal Article
ZDB-ID	1087040-4
ISSN	2042-7174 ; 0961-7671
ISSN (online)	2042-7174
ISSN	0961-7671
DOI	10.1093/ijpp/riac042
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Article ; Online: Bulk and single-cell transcriptome datasets of the mouse fetal and adult rete ovarii and surrounding tissues.

Anbarci, Dilara N / O'Rourke, Rebecca / Xiang, Yu / Peters, Derek T / Capel, Blanche / McKey, Jennifer

Scientific data

2024 Volume 11, Issue 1, Page(s) 383

Abstract: The rete ovarii (RO) is an epithelial structure that arises during development in close proximity to the ovary and persists throughout adulthood. However, the functional significance of the RO remains elusive, and it is absent from recent discussions of ... ...

Abstract	The rete ovarii (RO) is an epithelial structure that arises during development in close proximity to the ovary and persists throughout adulthood. However, the functional significance of the RO remains elusive, and it is absent from recent discussions of female reproductive anatomy. The RO comprises three regions: the intraovarian rete within the ovary, the extraovarian rete in the periovarian tissue, and the connecting rete linking the two. We hypothesize that the RO plays a pivotal role in ovarian homeostasis and responses to physiological changes. To begin to uncover the nature and function of RO cells, we conducted transcriptomic profiling of the RO. This study presents three datasets, and reports our analysis and quality control approaches for bulk, single-cell, and nucleus-level transcriptomics of the fetal and adult RO tissues using the Pax8-rtTA; Tre-H2B-GFP mouse line, where all RO regions express nuclear GFP. The integration and rigorous validation of these datasets will advance our understanding of the RO's roles in ovarian development, female maturation, and adult female fertility.
MeSH term(s)	Animals ; Female ; Mice ; Fetus ; Gene Expression Profiling ; Ovary/embryology ; Ovary/growth & development ; Transcriptome
Language	English
Publishing date	2024-04-13
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-024-03227-x
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Article: Recognising the elephant in the room: Foundation doctors and anticipatory care planning.

Chapman, Helen / Jassam, Miriam / O'Rourke, Rebecca / Anthony, Rebecca

Future healthcare journal

2021 Volume 8, Issue 1, Page(s) e179–e182

Abstract: Anticipatory/advance care planning (ACP) conversations are often known to be challenging and should be undertaken sensitively. A qualitative service evaluation was undertaken with the elderly care department at The Leeds Teaching Hospitals NHS Trust by ... ...

Abstract	Anticipatory/advance care planning (ACP) conversations are often known to be challenging and should be undertaken sensitively. A qualitative service evaluation was undertaken with the elderly care department at The Leeds Teaching Hospitals NHS Trust by medical students to explore the thoughts and experiences of foundation doctors. ACP discussions include consideration of future treatment options and preferences; however, foundation doctors were not confident to discuss issues beyond resuscitation status. The key themes identified include understanding of and confidence in ACP, variation across specialty and medical educational needs. The analysis highlights a further need for qualitative research into prevalent attitudes towards ACP discussions across the range of specialties.
Language	English
Publishing date	2021-03-29
Publishing country	England
Document type	Journal Article
ZDB-ID	3016427-8
ISSN	2514-6653 ; 2514-6645
ISSN (online)	2514-6653
ISSN	2514-6645
DOI	10.7861/fhj.2020-0200
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Article: Leptomeningeal Neural Organoid (LMNO) Fusions as Models to Study Meninges-Brain Signaling.

Jones, Hannah E / Robertson, Gabriella L / Romero-Morales, Alejandra / O'Rourke, Rebecca / Siegenthaler, Julie A / Gama, Vivian

Research square

2023

Abstract: Neural organoids derived from human induced pluripotent stem cells (iPSCs) provide a model to study the earliest stages of human brain development, including neurogenesis, neural differentiation, and synaptogenesis. However, neural organoids lack ... ...

Abstract	Neural organoids derived from human induced pluripotent stem cells (iPSCs) provide a model to study the earliest stages of human brain development, including neurogenesis, neural differentiation, and synaptogenesis. However, neural organoids lack supportive tissues and some non-neural cell types that are key regulators of brain development. Neural organoids have instead been co-cultured with non-neural structures and cell types to promote their maturation and model interactions with neuronal cells. One structure that does not form
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3694849/v1
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Article: Leptomeningeal Neural Organoid (LMNO) Fusions as Models to Study Meninges-Brain Signaling.

Jones, Hannah E / Robertson, Gabriella L / Romero-Morales, Alejandra / O'Rourke, Rebecca / Siegenthaler, Julie A / Gama, Vivian

bioRxiv : the preprint server for biology

2023

Abstract	Neural organoids derived from human induced pluripotent stem cells (iPSCs) provide a model to study the earliest stages of human brain development, including neurogenesis, neural differentiation, and synaptogenesis. However, neural organoids lack supportive tissues and some non-neural cell types that are key regulators of brain development. Neural organoids have instead been co-cultured with non-neural structures and cell types to promote their maturation and model interactions with neuronal cells. One structure that does not form
Language	English
Publishing date	2023-12-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.01.569648
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Article: Transcriptome analysis of the mouse fetal and adult rete ovarii and surrounding tissues.

Anbarci, Dilara N / O'Rourke, Rebecca / Xiang, Yu / Peters, Derek T / Capel, Blanche / McKey, Jennifer

bioRxiv : the preprint server for biology

2023

Abstract: The rete ovarii (RO) is an epithelial structure that arises during fetal development in close proximity to the ovary and persists throughout adulthood in mice. However, the functional significance of the RO remains elusive, and it has been absent from ... ...

Abstract	The rete ovarii (RO) is an epithelial structure that arises during fetal development in close proximity to the ovary and persists throughout adulthood in mice. However, the functional significance of the RO remains elusive, and it has been absent from recent discussions of female reproductive anatomy. The RO comprises three distinct regions: the intraovarian rete (IOR) within the ovary, the extraovarian rete (EOR) in the periovarian tissue, and the connecting rete (CR) linking the EOR and IOR. We hypothesize that the RO plays a pivotal role in maintaining ovarian homeostasis and responding to physiological changes. To uncover the nature and function of RO cells, we conducted transcriptome analysis, encompassing bulk, single-cell, and nucleus-level sequencing of both fetal and adult RO tissues using the
Language	English
Publishing date	2023-11-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.06.565717
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Article: Temporal single-cell transcriptomes of zebrafish spinal cord pMN progenitors reveal distinct neuronal and glial progenitor populations

Scott, Kayt / O'Rourke, Rebecca / Winkler, Caitlin C. / Kearns, Christina A. / Appel, Bruce

Developmental biology. 2021 Nov., v. 479

2021

Abstract: Ventral spinal cord progenitor cells, which express the basic helix loop helix transcription factor Olig2, sequentially produce motor neurons and oligodendrocyte precursor cells (OPCs). Following specification some OPCs differentiate as myelinating ... ...

Abstract	Ventral spinal cord progenitor cells, which express the basic helix loop helix transcription factor Olig2, sequentially produce motor neurons and oligodendrocyte precursor cells (OPCs). Following specification some OPCs differentiate as myelinating oligodendrocytes while others persist as OPCs. Though a considerable amount of work has described the molecular profiles that define motor neurons, OPCs, and oligodendrocytes, less is known about the progenitors that produce them. To identify the developmental origins and transcriptional profiles of motor neurons and OPCs, we performed single-cell RNA sequencing on isolated pMN cells from embryonic zebrafish trunk tissue at stages that encompassed motor neurogenesis, OPC specification, and initiation of oligodendrocyte differentiation. Downstream analyses revealed two distinct pMN progenitor populations: one that appears to produce neurons and one that appears to produce OPCs. This latter population, called Pre-OPCs, is marked by expression of GS Homeobox 2 (gsx2), a gene that encodes a homeobox transcription factor. Using fluorescent in situ hybridizations, we identified gsx2-expressing Pre-OPCs in the spinal cord prior to expression of canonical OPC marker genes. Our data therefore reveal heterogeneous gene expression profiles among pMN progenitors, supporting prior fate mapping evidence.
Keywords	Danio rerio ; RNA ; fluorescence ; gene expression ; genes ; neurogenesis ; oligodendroglia ; spinal cord ; transcription (genetics) ; transcription factors ; transcriptome
Language	English
Dates of publication	2021-11
Size	p. 37-50.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2021.07.010
Database	NAL-Catalogue (AGRICOLA)

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