Genome-wide differential expression profiling of long non-coding RNAs in FOXA2 knockout iPSC-derived pancreatic cells

BACKGROUND

Our recent studies have demonstrated the crucial involvement of FOXA2 in the development of human pancreas. Reduction of FOXA2 expression during the differentiation of induced pluripotent stem cells (iPSCs) into pancreatic islets has been found to reduce α-and β-cell masses. However, the extent to which such changes are linked to alterations in the expression profile of long non-coding RNAs (lncRNAs) remains unraveled.

METHODS

Here, we employed our recently established FOXA2-deficient iPSCs (FOXA2-/- iPSCs) to investigate changes in lncRNA profiles and their correlation with dysregulated mRNAs during the pancreatic progenitor (PP) and pancreatic islet stages. Furthermore, we constructed co-expression networks linking significantly downregulated lncRNAs with differentially expressed pancreatic mRNAs.

RESULTS

Our results showed that 442 lncRNAs were downregulated, and 114 lncRNAs were upregulated in PPs lacking FOXA2 compared to controls. Similarly, 177 lncRNAs were downregulated, and 59 lncRNAs were upregulated in islet cells lacking FOXA2 compared to controls. At both stages, we observed a strong correlation between lncRNAs and several crucial pancreatic genes and TFs during pancreatic differentiation. Correlation analysis revealed 12 DE-lncRNAs that strongly correlated with key downregulated pancreatic genes in both PPs and islet cell stages. Selected DE-lncRNAs were validated using RT-qPCR.

CONCLUSIONS

Our data indicate that the observed defects in pancreatic islet development due to the FOXA2 loss is associated with significant alterations in the expression profile of lncRNAs. Therefore, our findings provide novel insights into the role of lncRNA and mRNA networks in regulating pancreatic islet development, which warrants further investigations. Video Abstract.

iPSC-Derived Pancreatic Progenitors Lacking FOXA2 Reveal Alterations in miRNA Expression Targeting Key Pancreatic Genes

Recently, we reported that forkhead box A2 (FOXA2) is required for the development of human pancreatic α- and β-cells. However, whether miRNAs play a role in regulating pancreatic genes during pancreatic development in the absence of FOXA2 expression is largely unknown. Here, we aimed to capture the dysregulated miRNAs and to identify their pancreatic-specific gene targets in pancreatic progenitors (PPs) derived from wild-type induced pluripotent stem cells (WT-iPSCs) and from iPSCs lacking FOXA2 (FOXA2^-/-iPSCs). To identify differentially expressed miRNAs (DEmiRs), and genes (DEGs), two different FOXA2^-/-iPSC lines were differentiated into PPs. FOXA2^-/- PPs showed a significant reduction in the expression of the main PP transcription factors (TFs) in comparison to WT-PPs. RNA sequencing analysis demonstrated significant reduction in the mRNA expression of genes involved in the development and function of exocrine and endocrine pancreas. Furthermore, miRNA profiling identified 107 downregulated and 111 upregulated DEmiRs in FOXA2^-/- PPs compared to WT-PPs. Target prediction analysis between DEmiRs and DEGs identified 92 upregulated miRNAs, predicted to target 1498 downregulated genes in FOXA2^-/- PPs. Several important pancreatic TFs essential for pancreatic development were targeted by multiple DEmiRs. Selected DEmiRs and DEGs were further validated using RT-qPCR. Our findings revealed that FOXA2 expression is crucial for pancreatic development through regulating the expression of pancreatic endocrine and exocrine genes targeted by a set of miRNAs at the pancreatic progenitor stage. These data provide novel insights of the effect of FOXA2 deficiency on miRNA-mRNA regulatory networks controlling pancreatic development and differentiation.

iPSCs derived from insulin resistant offspring of type 2 diabetic patients show increased oxidative stress and lactate secretion

Background

The genetic factors associated with insulin resistance (IR) are not well understood. Clinical studies on first-degree relatives of type 2 diabetic (T2D) patients, which have the highest genetic predisposition to T2D, have given insights into the role of IR in T2D pathogenesis. Induced pluripotent stem cells (iPSCs) are excellent tools for disease modeling as they can retain the genetic imprint of the disease. Therefore, in this study, we aimed to investigate the genetic perturbations associated with insulin resistance (IR) in the offspring of T2D parents using patient-specific iPSCs.

Methods

We generated iPSCs from IR individuals (IR-iPSCs) that were offspring of T2D parents as well as from insulin-sensitive (IS-iPSCs) individuals. We then performed transcriptomics to identify key dysregulated gene networks in the IR-iPSCs in comparison to IS-iPSCs and functionally validated them.

Results

Transcriptomics on IR-iPSCs revealed dysregulated gene networks and biological processes indicating that they carry the genetic defects associated with IR that may lead to T2D. The IR-iPSCs had increased lactate secretion and a higher phosphorylation of AKT upon stimulation with insulin. IR-iPSCs have increased cellular oxidative stress indicated by a high production of reactive oxygen species and higher susceptibility to H2O2 -induced apoptosis.

Conclusions

IR-iPSCs generated from offspring of diabetic patients confirm that oxidative stress and increased lactate secretion, associated with IR, are inherited in this population, and may place them at a high risk of T2D. Overall, our IR-iPSC model can be employed for T2D modeling and drug screening studies that target genetic perturbations associated with IR in individuals with a high risk for T2D.

Human induced pluripotent stem cell line (QBRIi013-A) derivation from a 6-year-old female diagnosed with Autism spectrum disorder (ASD) and intellectual disability (ID)

Autism spectrum disorder (ASD) is a childhood-onset neurodevelopmental disorder characterized by social interaction, behavior, and communication challenges. Here, we generated an induced pluripotent stem cell (iPSC) line, QBRIi013-A using a non-integrating Sendai virus from a 6-year-old female diagnosed with ASD and intellectual disability. The QBRIi013-A cell line was fully characterized and exhibited a pluripotency capacity and trilineage differentiation potential. Furthermore, it showed normal karyotype and genetic identity to the patient's PBMCs. Consequently, this iPSC line provides a valuable cell model in understanding the molecular mechanism underlying the complexities of ASD pathogenesis.

Long-term exposure to p-Nitrophenol induces hepatotoxicity via accelerating apoptosis and glycogen accumulation in male Japanese quails

p-Nitrophenol (PNP) is the main end product of organophosphorus insecticides and a derivative of diesel exhaust particles. In addition to its unfavorable impact on reproductive functions in both genders, it also has various harmful physiological effects including lung cancer and allergic rhinitis. The identification of the cellular readout that functions in metabolic pathway perpetuation is still far from clear. This research aimed to study the impact of chronic PNP exposure on the health condition of the liver in Japanese quails. Quails were exposed to different concentrations of PNP as follows: 0.0 (control), 0.01mg (PNP/0.01), 0.1mg (PNP/0.1), and 1mg (PNP/1) per kg of body weight for 2.5 months through oral administration. Liver and plasma samples were collected at 1.5, 2, and 2.5 months post-treatment for biochemical, histopathology, and immunohistochemistry assessment. The plasma aspartate aminotransferase (AST) level was assessed enzymatically. The livers were collected for histopathology, glycogen accumulation, proliferating cell nuclear antigen (PCNA), and apoptosis assessment. Our results revealed an irregularity in body weight due to the long-term exposure of PNP with a significant reduction in liver weight. PNP treatment caused histopathological alterations in the hepatic tissues which increased in severity by the long-term exposure. The low dose led to mild degeneration with lymphocytic infiltration, while the moderate dose has a congestion effect with some necrosis; meanwhile severe hepatocyte degeneration and RBCs hemolysis were noticed due to high dose of PNP. Glycogen accumulation increased in hepatocytes by prolonged exposure to p-Nitrophenol with the highest intensity in the group treated by the high dose. Moderate and high doses of PNP resulted in a significant increase in apoptosis and hepatocytes' proliferation at the different time points after treatment. This increase is markedly notable and maximized at 2.5 months post-treatment. The damage occurred in a time-dependent manner. These changes reflected on the plasma hepatic enzyme AST that was clearly increased at 2.5 months of exposure. Therefore, it could be concluded that PNP has profound toxic effects on the liver in cellular level. Taking into consideration the time and dose factors, both have a synergistic effect on the accumulation of glycogen, apoptosis, and cellular proliferation, highlighting the power of cellular investigation which will potentially open the door for earlier medical intervention to counteract this toxicity. Collectively, PNP could have critical hurtful effects on the health of human beings, wild animals as well as livestock.

An induced pluripotent stem cell line derived from a patient with neonatal diabetes and Fanconi-Bickel syndrome caused by a homozygous mutation in the SLC2A2 gene

Recessive mutations in the glucose transporter gene SLC2A2 (GLUT2) lead to permanent neonatal diabetes (PNDM) and Fanconi Bickel Syndrome (FBS). Here, we generated an induced pluripotent stem cell (iPSC) line, QBRIi012-A, from a 24-month-old boy with FBS and PNDM due to homozygous nonsense mutation in the SLC2A2 gene (c.901C > T). The QBRIi012-A was fully characterized using different approaches. The cell line showed normal karyotype and was able to differentiate into the three germ layers in vitro. This iPSC line provides a novel human cell model to understand the pathophysiology of FBS and diabetes associated with SLC2A2 defects.

Circulating Non-Coding RNAs as a Signature of Autism Spectrum Disorder Symptomatology

Autism spectrum disorder (ASD) is a multifaced neurodevelopmental disorder that becomes apparent during early childhood development. The complexity of ASD makes clinically diagnosing the condition difficult. Consequently, by identifying the biomarkers associated with ASD severity and combining them with clinical diagnosis, one may better factionalize within the spectrum and devise more targeted therapeutic strategies. Currently, there are no reliable biomarkers that can be used for precise ASD diagnosis. Consequently, our pilot experimental cohort was subdivided into three groups: healthy controls, individuals those that express severe symptoms of ASD, and individuals that exhibit mild symptoms of ASD. Using next-generation sequencing, we were able to identify several circulating non-coding RNAs (cir-ncRNAs) in plasma. To the best of our knowledge, this study is the first to show that miRNAs, piRNAs, snoRNAs, Y-RNAs, tRNAs, and lncRNAs are stably expressed in plasma. Our data identify cir-ncRNAs that are specific to ASD. Furthermore, several of the identified cir-ncRNAs were explicitly associated with either the severe or mild groups. Hence, our findings suggest that cir-ncRNAs have the potential to be utilized as objective diagnostic biomarkers and clinical targets.

Insulin resistance in diabetes: The promise of using induced pluripotent stem cell technology

Insulin resistance (IR) is associated with several metabolic disorders, including type 2 diabetes (T2D). The development of IR in insulin target tissues involves genetic and acquired factors. Persons at genetic risk for T2D tend to develop IR several years before glucose intolerance. Several rodent models for both IR and T2D are being used to study the disease pathogenesis; however, these models cannot recapitulate all the aspects of this complex disorder as seen in each individual. Human pluripotent stem cells (hPSCs) can overcome the hurdles faced with the classical mouse models for studying IR. Human induced pluripotent stem cells (hiPSCs) can be generated from the somatic cells of the patients without the need to destroy a human embryo. Therefore, patient-specific hiPSCs can generate cells genetically identical to IR individuals, which can help in distinguishing between genetic and acquired defects in insulin sensitivity. Combining the technologies of genome editing and hiPSCs may provide important information about the genetic factors underlying the development of different forms of IR. Further studies are required to fill the gaps in understanding the pathogenesis of IR and diabetes. In this review, we summarize the factors involved in the development of IR in the insulin-target tissues leading to diabetes. Also, we highlight the use of hPSCs to understand the mechanisms underlying the development of IR.

Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency

FOXA2 has been identified as an essential factor for pancreas development and emerging evidence supports an association between FOXA2 and diabetes. Although the role of FOXA2 during pancreatic development is well-studied in animal models, its role during human islet cell development remains unclear. Here, we generated induced pluripotent stem cells (iPSCs) from a patient with FOXA2 haploinsufficiency (FOXA2^+/- iPSCs) followed by beta-cell differentiation to understand the role of FOXA2 during pancreatic beta-cell development. Our results showed that FOXA2 haploinsufficiency resulted in aberrant expression of genes essential for the differentiation and proper functioning of beta cells. At pancreatic progenitor (PP2) and endocrine progenitor (EPs) stages, transcriptome analysis showed downregulation in genes associated with pancreatic development and diabetes and upregulation in genes associated with nervous system development and WNT signaling pathway. Knockout of FOXA2 in control iPSCs (FOXA2^-/- iPSCs) led to severe phenotypes in EPs and beta-cell stages. The expression of NGN3 and its downstream targets at EPs as well as INSUILIN and GLUCAGON at the beta-cell stage, were almost absent in the cells derived from FOXA2^-/- iPSCs. These findings indicate that FOXA2 is crucial for human pancreatic endocrine development and its defect may lead to diabetes based on FOXA2 dosage.

Keratinocytes Derived from Patient-Specific Induced Pluripotent Stem Cells Recapitulate the Genetic Signature of Psoriasis Disease

Psoriasis is characterized by hyperproliferation and defective differentiation of keratinocytes (KCs). Patients with psoriasis are at a high risk of developing diabetes and cardiovascular diseases. The debate on the genetic origin of psoriasis pathogenesis remains unresolved due to lack of suitable in vitro human models mimicking the disease phenotypes. In this study, we provide the first human induced pluripotent stem cell (iPSC) model for psoriasis carrying the genetic signature of the patients. iPSCs were generated from patients with psoriasis (PsO-iPSCs) and healthy donors (Ctr-iPSCs) and were efficiently differentiated into mature KCs. RNA sequencing of KCs derived from Ctr-iPSCs and PsO-iPSCs identified 361 commonly upregulated and 412 commonly downregulated genes. KCs derived from PsO-iPSCs showed dysregulated transcripts associated with psoriasis and KC differentiation, such as HLA-C, KLF4, chemokines, type I interferon-inducible genes, solute carrier family, IVL, DSG1, and HLA-DQA1, as well as transcripts associated with insulin resistance, such as IRS2, GDF15, GLUT10, and GLUT14. Our data suggest that the KC abnormalities are the main driver triggering psoriasis pathology and highlights the substantial contribution of genetic predisposition in the development of psoriasis and insulin resistance.

Generation of a human induced pluripotent stem cell line (QBRIi009-A) from a patient with a heterozygous deletion of FOXA2

FOXA2 is a transcription factor, playing an important role during development. We established an induced pluripotent stem cell (iPSC) line, QBRIi009-A, using non-integrating Sendai virus from a 4-year-old boy, displaying a complex clinical phenotype. Molecular karyotyping and cytogenetics confirmed a de novo proximal 20p11.2 deletion with a reciprocal translocation between the short arm of chromosome 6 and 20. The deleted region (~969 kb) contains only one gene, FOXA2. The generated hiPSC line was fully characterized for its pluripotency and its genetic identity. This iPSC line provides a useful model to study FOXA2 role during human development and in disease pathogenesis.

Differentiation of human pluripotent stem cells into two distinct NKX6.1 populations of pancreatic progenitors

BACKGROUND

The expression of a specific combination of transcription factors (TFs) in the multipotent progenitor cells (MPCs) is critical for determining pancreatic cell fate. NKX6.1 expression in PDX1⁺ MPCs is required for functional β cell generation. We have recently demonstrated the generation of a novel population of human pluripotent stem cell (hPSC)-derived MPCs that exclusively express NKX6.1, independently of PDX1 (PDX1^-/NKX6.1⁺). Therefore, the aim of this study was to characterize this novel population to elucidate its role in pancreatic development.

METHODS

The hPSCs were exposed to two differentiation protocols to generate MPCs that were analyzed using different techniques.

RESULTS

Based on the expression of PDX1 and NKX6.1, we generated three different populations of MPCs, two of them were NKX6.1⁺. One of these NKX6.1 populations coexpressed PDX1 (PDX1⁺/NKX6.1⁺) which is known to mature into functional β cells, and an additional novel population did not express PDX1 (PDX1^-/NKX6.1⁺) with an undefined role in pancreatic cell fate. This novel population was enriched using our recently established protocol, allowing their reorganization in three-dimensional (3D) structures. Since NKX6.1 induction in MPCs can direct them to endocrine and/or ductal cells in humans, we examined the coexpression of endocrine and ductal markers. We found that the expression of the pancreatic endocrine progenitor markers chromogranin A (CHGA) and neurogenin 3 (NGN3) was not detected in the NKX6.1⁺ 3D structures, while few structures were positive for NKX2.2, another endocrine progenitor marker, thereby shedding light on the origin of this novel population and its role in pancreatic endocrine development. Furthermore, SOX9 was highly expressed in the 3D structures, but cytokeratin 19, a main ductal marker, was not detected in these structures.

CONCLUSIONS

These data support the existence of two independent NKX6.1⁺ MPC populations during human pancreatic development and the novel PDX1^-/NKX6.1⁺ population may be involved in a unique trajectory to generate β cells in humans.