International Journal of Drug Discovery and Pharmacology
Review Progress of 3D Organoid Technology for Preclinical Investigations: Towards Human In Vitro ... more Review Progress of 3D Organoid Technology for Preclinical Investigations: Towards Human In Vitro Models Yingjuan Liu *, Honglin Xu, Sabu Abraham, Xin Wang, and Bernard D. Keavney* Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK. * Correspondence: yingjuan.liu@manchester.ac.uk (Yingjuan Liu); bernard.keavney@manchester.ac.uk (Bernard D. Keavney) Received: 1 November 2022 Accepted: 24 November 2022 Published: 21 December 2022 : Currently, with an increased requirement for new therapeutic strategies, preclinical drug testing or screening platforms have rapidly evolved in recent years. In comparison to traditional 2D cell cultures, 3D organoids or spheroids with or without scaffolds improve the microenvironment of in vitro cultures, advancing the in vitro biological observation and enabling mechanistic studies of drug reactions in the human tissue-like environment. 3D organoids and spheroids are straightforward to...
The genome-wide promoter interactome is primarily maintained and regulated by architectural prote... more The genome-wide promoter interactome is primarily maintained and regulated by architectural proteins such as CTCF and cohesin. However, some studies suggest a role for non-coding RNAs (ncRNAs) in this process. We aimed to characterise the regulatory role of RNA-mediated promoter interactions in the control of gene expression. We integrated genome-wide datasets of RNA-chromatin and promoter-genome interactions in human embryonic stem cells (hESCs) to identify putative RNA-mediated promoter interactions. We discovered that CTCF sites were enriched in RNA-PIRs (promoter interacting regions co-localising with RNA-chromatin interaction sites) and genes interacting with RNA-PIRs containing CTCF sites showed higher expression levels. One of the long noncoding RNAs (lncRNAs) expressed in hESCs, Syntaxin 18-Antisense 1 (STX18-AS1), appeared to be involved in an insulating promoter interaction with the neighbouring gene, MSX1. By knocking down STX18-AS1, the MSX1 promoter-PIR interaction was ...
Results We demonstrated that the adult heart reverts to a hypertrabeculated state between 1 and 5... more Results We demonstrated that the adult heart reverts to a hypertrabeculated state between 1 and 5 days post-MI and repeats the process of endocardial compaction from 7-14 days. This process appears to facilitate endocardium-derived neovascularization, leading to formation of mature sub-endocardial vessels after infarction. We observed reactivation of the Notch pathway in the endocardium following MI, in keeping with its role as a key regulator of these processes in development. Using a Notch1 loss-of-function mouse model targeted by an endothelial-specific Cre, we observed impaired trabeculation with reduced sub-endocardial vessel count after disruption of Notch activity. (Figure 1) Conclusion We established that de novo vessel formation constitutes a significant component of the neovascular response and revealed that the endocardium is a major contributory source. Notch1 was identified as a key driver in this remodelling process and, moreover, our data suggest a role for Notch in driving endothelial-mesenchymal transition (EndMT) to provide smooth muscle support to newly formed vessels. Ongoing work seeks to determine whether targeting trabeculation in the adult heart will contribute to improved neovascularisation post-MI.
In the original version of the Article, the gene symbol for tissue factor pathway inhibitor was i... more In the original version of the Article, the gene symbol for tissue factor pathway inhibitor was inadvertently given as ‘TFP1’ instead of ‘TFPI’. This has now been corrected in both the PDF and HTML versions of the Article.
Long-range chromosomal interactions bring distal regulatory elements and promoters together to re... more Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-de...
Background Congenital heart disease (CHD) is the commonest birth defect. Studies estimating the p... more Background Congenital heart disease (CHD) is the commonest birth defect. Studies estimating the prevalence of CHD in school-age children could therefore contribute to quantifying unmet health needs for diagnosis and treatment, particularly in lower-income countries. Data at school age are considerably sparser, and individual studies have generally been of small size. We conducted a literature-based meta-analysis to investigate global trends over a 40-year period. Methods and results Studies reporting on CHD prevalence in school-age children (4–18 years old) from 1970 to 2017 were identified from PubMed, EMBASE, Web of Science and Google Scholar. According to the inclusion criteria, 42 studies including 2,638,475 children, reporting the prevalence of unrepaired CHDs (both pre-school diagnoses and first-time school-age diagnoses), and nine studies including 395,571 children, specifically reporting the prevalence of CHD first diagnosed at school ages, were included. Data were combined ...
Cancer pain is a common problem in clinical cancer therapy. Opioid analgesia is one of the most e... more Cancer pain is a common problem in clinical cancer therapy. Opioid analgesia is one of the most effective drugs for pain relief with satisfying performance besides the side effect of opioid-induced constipation (OIC). Acupuncture, as a Chinese traditional noninvasive intervention, has been applied to clinical cancer pain management and functional constipation therapy. However, only a few studies have adopted this treatment for OIC patients. Due to limited numbers of investigated subjects and variability of application methods, including treatment apparatus, acupoints, durations, and sessions, the interpretation of acupuncture's therapy effects from single-site randomized clinical trials (RCT) is limited. Therefore, we conducted a meta-analysis by collecting published data from Pubmed, Embase, Cochrane library, and Web of Science. Five RCTs focusing on the application of acupuncture with or without medication in OIC patients were included. An overall remission rate of 86.8% in the acupuncture-treated group was achieved, higher than the control group (78.9%; RR, 1.10, 95% CI [1.03, 1.18]). The symptom scores, reporting on defecation frequency, defecation straining, abdominal pain, defection time, and stool property, in acupuncture groups were lower than control groups with a standardized mean difference (SMD) of −2.21 [−4.15, −0.27]. The quality of life (QOL) for patients in the acupuncture treated group increased compared to the control group with reduced PAC-QOL scores (SMD, −1.02 [−1.78, −0.26]). Referring to the effects from pure acupuncture treatment (SMD, −0.43 [−0.83, −0.03]), the co-intervention of acupuncture and drugs (SMD, −1.77 [−2.51, −1.02]) improved the life quality of patients more remarkably (P < 0.05). Overall, our data confirmed the therapeutic effects of acupuncture in the treatment of OIC. The co-intervention of acupuncture with drugs improves the outcomes of OIC patients better than a single strategy. Combined therapy with both medicine and acupuncture has insightful potential for future clinical cancer patient management on constipation problems.
Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 assoc... more Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 associated with the risk of Atrial Septal Defect (ASD), which is among the commonest Congenital Heart Disease (CHD) phenotypes. Here, we identify the responsible gene in the region and elucidate disease mechanisms. Linkage disequilibrium in the region, eQTL analyses in human atrial tissues, and spatio-temporal gene expression studies in human embryonic hearts concordantly suggested the long noncoding RNA (lncRNA) STX18-AS1 as the causative gene in the region. Using CRISPR/Cas9 knockdown in HepG2 cells, STX18-AS1 was shown to regulate the expression of the key cardiac transcription factor NKX2-5 via a trans-acting effect on promoter histone methylation. Furthermore, STX18-AS1 knockdown depleted the potential of human embryonic stem cells (H9) to differentiate into cardiomyocytes, without affecting their viability and pluripotency, providing a mechanistic explanation for the clinical association.
Toxicology in vitro : an international journal published in association with BIBRA, 2016
Chlormequat chloride is the most widely used plant growth regulator in agriculture to promote stu... more Chlormequat chloride is the most widely used plant growth regulator in agriculture to promote sturdier growth of grain crops by avoidance of lodging. Therefore, human exposure to chlormequat chloride is very common, but its developmental toxicity has not been studied. Thus, we investigated the developmental toxicity of chlormequat chloride by applying rat whole embryo culture (WEC) model, limb bud micromass culture and 3T3 fibroblast cytotoxicity test. Chlormequat chloride at 150μg/ml (0.93mM) retarded the rat embryo growth without causing significant morphological malformations and at 500μg/ml (3.1mM) caused both retardation and morphological malformation of the embryos. However, the proliferation and differentiation of limb bud cells were not affected by chlormequat chloride at as high as up to 1000μg/ml (6.2mM) applied. This concentration of chlormequat chloride did not affect the cell viability as examined by 3T3 fibroblast cytotoxicity test either, suggesting that cellular toxi...
International Journal of Drug Discovery and Pharmacology
Review Progress of 3D Organoid Technology for Preclinical Investigations: Towards Human In Vitro ... more Review Progress of 3D Organoid Technology for Preclinical Investigations: Towards Human In Vitro Models Yingjuan Liu *, Honglin Xu, Sabu Abraham, Xin Wang, and Bernard D. Keavney* Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK. * Correspondence: yingjuan.liu@manchester.ac.uk (Yingjuan Liu); bernard.keavney@manchester.ac.uk (Bernard D. Keavney) Received: 1 November 2022 Accepted: 24 November 2022 Published: 21 December 2022 : Currently, with an increased requirement for new therapeutic strategies, preclinical drug testing or screening platforms have rapidly evolved in recent years. In comparison to traditional 2D cell cultures, 3D organoids or spheroids with or without scaffolds improve the microenvironment of in vitro cultures, advancing the in vitro biological observation and enabling mechanistic studies of drug reactions in the human tissue-like environment. 3D organoids and spheroids are straightforward to...
The genome-wide promoter interactome is primarily maintained and regulated by architectural prote... more The genome-wide promoter interactome is primarily maintained and regulated by architectural proteins such as CTCF and cohesin. However, some studies suggest a role for non-coding RNAs (ncRNAs) in this process. We aimed to characterise the regulatory role of RNA-mediated promoter interactions in the control of gene expression. We integrated genome-wide datasets of RNA-chromatin and promoter-genome interactions in human embryonic stem cells (hESCs) to identify putative RNA-mediated promoter interactions. We discovered that CTCF sites were enriched in RNA-PIRs (promoter interacting regions co-localising with RNA-chromatin interaction sites) and genes interacting with RNA-PIRs containing CTCF sites showed higher expression levels. One of the long noncoding RNAs (lncRNAs) expressed in hESCs, Syntaxin 18-Antisense 1 (STX18-AS1), appeared to be involved in an insulating promoter interaction with the neighbouring gene, MSX1. By knocking down STX18-AS1, the MSX1 promoter-PIR interaction was ...
Results We demonstrated that the adult heart reverts to a hypertrabeculated state between 1 and 5... more Results We demonstrated that the adult heart reverts to a hypertrabeculated state between 1 and 5 days post-MI and repeats the process of endocardial compaction from 7-14 days. This process appears to facilitate endocardium-derived neovascularization, leading to formation of mature sub-endocardial vessels after infarction. We observed reactivation of the Notch pathway in the endocardium following MI, in keeping with its role as a key regulator of these processes in development. Using a Notch1 loss-of-function mouse model targeted by an endothelial-specific Cre, we observed impaired trabeculation with reduced sub-endocardial vessel count after disruption of Notch activity. (Figure 1) Conclusion We established that de novo vessel formation constitutes a significant component of the neovascular response and revealed that the endocardium is a major contributory source. Notch1 was identified as a key driver in this remodelling process and, moreover, our data suggest a role for Notch in driving endothelial-mesenchymal transition (EndMT) to provide smooth muscle support to newly formed vessels. Ongoing work seeks to determine whether targeting trabeculation in the adult heart will contribute to improved neovascularisation post-MI.
In the original version of the Article, the gene symbol for tissue factor pathway inhibitor was i... more In the original version of the Article, the gene symbol for tissue factor pathway inhibitor was inadvertently given as ‘TFP1’ instead of ‘TFPI’. This has now been corrected in both the PDF and HTML versions of the Article.
Long-range chromosomal interactions bring distal regulatory elements and promoters together to re... more Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-de...
Background Congenital heart disease (CHD) is the commonest birth defect. Studies estimating the p... more Background Congenital heart disease (CHD) is the commonest birth defect. Studies estimating the prevalence of CHD in school-age children could therefore contribute to quantifying unmet health needs for diagnosis and treatment, particularly in lower-income countries. Data at school age are considerably sparser, and individual studies have generally been of small size. We conducted a literature-based meta-analysis to investigate global trends over a 40-year period. Methods and results Studies reporting on CHD prevalence in school-age children (4–18 years old) from 1970 to 2017 were identified from PubMed, EMBASE, Web of Science and Google Scholar. According to the inclusion criteria, 42 studies including 2,638,475 children, reporting the prevalence of unrepaired CHDs (both pre-school diagnoses and first-time school-age diagnoses), and nine studies including 395,571 children, specifically reporting the prevalence of CHD first diagnosed at school ages, were included. Data were combined ...
Cancer pain is a common problem in clinical cancer therapy. Opioid analgesia is one of the most e... more Cancer pain is a common problem in clinical cancer therapy. Opioid analgesia is one of the most effective drugs for pain relief with satisfying performance besides the side effect of opioid-induced constipation (OIC). Acupuncture, as a Chinese traditional noninvasive intervention, has been applied to clinical cancer pain management and functional constipation therapy. However, only a few studies have adopted this treatment for OIC patients. Due to limited numbers of investigated subjects and variability of application methods, including treatment apparatus, acupoints, durations, and sessions, the interpretation of acupuncture's therapy effects from single-site randomized clinical trials (RCT) is limited. Therefore, we conducted a meta-analysis by collecting published data from Pubmed, Embase, Cochrane library, and Web of Science. Five RCTs focusing on the application of acupuncture with or without medication in OIC patients were included. An overall remission rate of 86.8% in the acupuncture-treated group was achieved, higher than the control group (78.9%; RR, 1.10, 95% CI [1.03, 1.18]). The symptom scores, reporting on defecation frequency, defecation straining, abdominal pain, defection time, and stool property, in acupuncture groups were lower than control groups with a standardized mean difference (SMD) of −2.21 [−4.15, −0.27]. The quality of life (QOL) for patients in the acupuncture treated group increased compared to the control group with reduced PAC-QOL scores (SMD, −1.02 [−1.78, −0.26]). Referring to the effects from pure acupuncture treatment (SMD, −0.43 [−0.83, −0.03]), the co-intervention of acupuncture and drugs (SMD, −1.77 [−2.51, −1.02]) improved the life quality of patients more remarkably (P < 0.05). Overall, our data confirmed the therapeutic effects of acupuncture in the treatment of OIC. The co-intervention of acupuncture with drugs improves the outcomes of OIC patients better than a single strategy. Combined therapy with both medicine and acupuncture has insightful potential for future clinical cancer patient management on constipation problems.
Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 assoc... more Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 associated with the risk of Atrial Septal Defect (ASD), which is among the commonest Congenital Heart Disease (CHD) phenotypes. Here, we identify the responsible gene in the region and elucidate disease mechanisms. Linkage disequilibrium in the region, eQTL analyses in human atrial tissues, and spatio-temporal gene expression studies in human embryonic hearts concordantly suggested the long noncoding RNA (lncRNA) STX18-AS1 as the causative gene in the region. Using CRISPR/Cas9 knockdown in HepG2 cells, STX18-AS1 was shown to regulate the expression of the key cardiac transcription factor NKX2-5 via a trans-acting effect on promoter histone methylation. Furthermore, STX18-AS1 knockdown depleted the potential of human embryonic stem cells (H9) to differentiate into cardiomyocytes, without affecting their viability and pluripotency, providing a mechanistic explanation for the clinical association.
Toxicology in vitro : an international journal published in association with BIBRA, 2016
Chlormequat chloride is the most widely used plant growth regulator in agriculture to promote stu... more Chlormequat chloride is the most widely used plant growth regulator in agriculture to promote sturdier growth of grain crops by avoidance of lodging. Therefore, human exposure to chlormequat chloride is very common, but its developmental toxicity has not been studied. Thus, we investigated the developmental toxicity of chlormequat chloride by applying rat whole embryo culture (WEC) model, limb bud micromass culture and 3T3 fibroblast cytotoxicity test. Chlormequat chloride at 150μg/ml (0.93mM) retarded the rat embryo growth without causing significant morphological malformations and at 500μg/ml (3.1mM) caused both retardation and morphological malformation of the embryos. However, the proliferation and differentiation of limb bud cells were not affected by chlormequat chloride at as high as up to 1000μg/ml (6.2mM) applied. This concentration of chlormequat chloride did not affect the cell viability as examined by 3T3 fibroblast cytotoxicity test either, suggesting that cellular toxi...
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