Francis Lynn

Associate Professor

Research Interests

ß-cell development
ß-cell biology
Human pluripotent stem cells
transcriptional regulation

Relevant Thesis-Based Degree Programs

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Francis Lynn completed his PhD in Ray Pederson's laboratory at UBC where he became interested in beta cells, diabetes and gene regulation. Postdoctoral studies with Michael German in San Francisco piqued his interest in beta cell development and small RNA biology.

His group is interested in understanding the mechanisms that regulate the formation of islet β-cells from pancreatic stem or progenitor cells during solid organ formation. They focus on the gene regulatory networks at play in the progenitor cells and how these networks change during differentiation to mature endocrine cells and in the long-term maintenance of the β-cell. They believe that a greater understanding of these genetic mechanisms and pathways will refine cell-based approaches for preventing and reversing the β-cell deterioration and loss that occur with diabetes.


Doctoral students
Postdoctoral Fellows
Any time / year round

Research in the Lynn lab is targeted at understanding the insulin-producing pancreatic β-cell, how it fails during diabetes mellitus and how we can make surrogate cells to cure diabetes. We use a variety of models to study the regulatory pathways important for embryonic β-cell genesis and function. The current focus of research in the lab is understanding how DNA-binding transcription factors regulate β-cell formation and function, how they are reguated post-translationally and how they prevent β-cell dysfunction and diabetes. We currently have positions available for graduate students and postdoctoral scholars interested in studying the regulation of pancreatic β-cell development and function. Please contact me personally by e-mail with a cover letter outlining your interests, why you would like to join my lab, and please include your vita. Experience in cell and developmental biology, molecular biology or stem cell biology is preferred. More important are curiosity and passion about stem and developmental biology, and a talent for independent research, supported by a strong publication record.

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Graduate Student Supervision

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Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

Activity-regulated genes in pancreatic islets and neurons of the arcuate nucleus (2023)

Both pancreatic islets and hypothalamic arcuate nucleus neurons are critical for energy homeostasis and depend on activity-regulated genes to respond to stimuli. NPAS4 is one such gene that is expressed in both sites and is important for proper function of islets and neurons. The overall goals of my thesis are to profile activity-regulated genes in pancreatic islets and arcuate nucleus neurons, and characterize the functional role of NPAS4 in arcuate nucleus neurons in order to reveal novel mechanisms in cells important in energy homeostasis. To identify calcium-dependent activity-regulated genes in human islet cell types, I used single cell RNA sequencing on islets that had experimentally induced or inhibited intracellular calcium signalling. In addition to identifying activity-regulated genes in each islet cell type, I found that beta cells with the most calcium-regulated genes expressed the marker PCDH7 and had enhanced glucose-stimulated insulin secretion. In order to study the role of NPAS4 in the arcuate nucleus, I first determined that Npas4 mRNA was expressed and was induced in AgRP and POMC neurons in the arcuate nucleus in response to peripheral nutrient and endocrine stimuli. Next, I characterized mice with NPAS4 knockout in either AgRP or POMC neurons, with or without high-fat diet, and found that mice with POMC-specific NPAS4 knockout gained less body weight on high-fat diet due to an early reduction in food intake. To determine the molecular mechanism behind this phenotype, I performed single cell RNA sequencing on arcuate nuclei from fasted and refed NPAS4 knockout and control mice fed high-fat diet. I found that the POMC neurons with NPAS4 knockout had reduced Pomc expression, increased feeding-regulated genes, and reduced inhibitory GABAergic synapse genes, which could explain the reduced body weight over time. Future experiments would involve assessing electrophysiological changes in POMC neurons from NPAS4 knockout mice to confirm functional alterations as a result of reduced inhibitory synapses. Overall, this thesis shows the importance of activity-regulated genes in both pancreatic islets and arcuate nucleus neurons, and shows a novel role of the transcription factor NPAS4 in POMC neurons in regulating energy homeostasis.

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Exploring the function and regulation of histone H3 lysine 4 trimethylation in mature beta cells (2022)

Aims:Insufficient insulin release by β-cells is the primary etiology in type 2 diabetes and coincides with impaired expression of genes essential for β-cell function, but drivers of gene expression dysregulation are not well resolved. Alterations to the genome-wide enrichment and organization of chromatin post-translational modifications may promote gene expression dysregulation. Here, I investigate the role of H3K4me3 in mature β-cells and how its organization in chromatin is linked to the unique β-cell gene transcriptome in health and diabetes. I further test how its enrichment is altered by external challenges in the form of type 2 diabetes-like stresses or perturbation of one carbon metabolism.Methods:To study the functional importance of H3K4me3 in mature β-cells, we depleted H3K4me3 in β-cells of mature mice using an inducible Dpy30 deletion model under control of the Pdx1 or Ins1 promoter and performed a panel of metabolic, transcriptomic, and epigenetic tests. We compared H3K4me3 enrichment patterns with gene expression changes that occur in islets in a mouse model of type 2 diabetes and in human type 2 diabetes. We then examined the metabolic and transcriptomic consequences of folic acid restriction in mouse islets.Results:H3K4me3 contributes to gene expression in mature β-cells. H3K4me3 contributes to H3K27ac levels and, in the absence of H3K4me3, promoter-associated H3K4me1 is partially sufficient to maintain expression. H3K4me3 peak breadth is correlated with gene expression dysregulation in type 2 diabetes in mice and humans. Using a genetic mouse model to impair the methyltransferase activity of trithorax group complexes, we find that reduction of H3K4me3 reduces insulin production and glucose-responsiveness and increases transcriptional entropy. H3K4me3 in mouse β-cells is particularly required for the expression of genes that are dysregulated in a mouse model of type 2 diabetes. While locus-specific alterations are observed, global enrichment of H3K4me3 in islets is robust against external disruption of glucose homeostasis and one-carbon metabolism.Conclusions/interpretation:Overall, this thesis shows that H3K4me3 contributes to expression of genes essential for β-cell identity and function in mature β-cells and implicates dysregulation of H3K4me3 as a factor contributing to β-cell dysfunction in type 2 diabetes by altering gene expression patterns.

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Investigating the role of transcriptional coactivator MED15 in beta cell maturation (2020)

The Mediator complex, a coregulator required for RNA pol II activity, interacts with specific transcription factors through its distinct subunits. These interactions promote the expression of defined gene sets both during development and for tissue homeostasis. Transcriptional regulatory networks are critical for the development and function of pancreatic β-cells. To date, few studies examining how transcription factors interact with co-activators, such a Mediator, have been performed in the pancreas. Tail module subunit MED15 is highly expressed in nascent β-cells and required for lipid metabolism, various stress responses, and TGF-β signalling, all of which are important for β-cell function. As such, we hypothesized that MED15 plays a role in β-cells. We found MED15 to be expressed during mouse pancreatogenesis and in mature β-cells. Expression of MED15 was impaired in human T2D islets suggesting it is important for mature β-cell function. After generating a β-cell specific knockout mouse (IM15KO), we observed defects in maturation as assessed by loss of β-cell maturation markers UCN3, MAFA, and GLUT2. In agreement with reduced GLUT2 expression, IM15KO cells had impaired glucose uptake and reduced glucose-stimulated insulin secretion, the hallmark process of β-cell maturation. ChIP-seq analysis determined that MED15 is bound to key GSIS related genes and Co-IP found transcription factors NEUROD1 and NKX6-1 to bind MED15. As the pancreas contains among the highest levels of Zn²⁺ in the body, we also found a role for MED15 in heavy metal stress response. Through this thesis, I provide evidence of the importance of Mediator in β-cell maturation and demonstrate an additional layer of control that modulates transcription factor function. A greater understanding of how Mediator and MED15 regulate β-cell maturation could help refine the generation of cell-based therapies for diabetes.

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The role of Npas4 and Rgs2 in the regulation of pancreatic ?-cell function (2019)

Pancreatic β-cells regulate systemic glycemia by releasing the glucose-lowering hormone insulin. Diabetes, a chronic metabolic disease characterized by insulin insufficiency, is linked to β-cell dysfunction with perturbed calcium homeostasis. The activity-induced, calcium-dependent transcription factor, NPAS4, reduced insulin secretion and promoted β-cell health, in part through its target gene, the GTPase-activating protein RGS2. Because our mechanistic understanding of this process remains incomplete, studying the normal physiology of calcium-dependent β-cell function may uncover new avenues for the treatment or prevention of diabetes. The overall goal of my thesis was to establish whether activity-induced NPAS4 and RGS2 expression could optimize β-cell function. Initially, I uncovered a role for CaMKII, calcineurin, and PKB in membrane depolarization-induced Npas4 mRNA and protein expression in MIN6 cells and mouse islets. Calcineurin inhibition and concurrent loss of NPAS4 showed cytotoxic increases in cleaved caspase 3 expression, which was reversed by adenovirally reinstating NPAS4 in MIN6 cells. Co-immunoprecipitation studies in MIN6 cells then uncovered competition between NPAS4 and a related transcription factor, HIF1α, for the shared heterodimerization partner, ARNT. Accordingly, HIF1α target gene expression was lower in human and mouse islets overexpressing Npas4, and higher in β-cell-specific Npas4 knockout mouse islets (N4KO). Because excessive HIF1α signalling compromises β-cell function by switching energy production from oxidative phosphorylation to anaerobic glycolysis, I examined whether N4KO mice developed functional defects. Indeed, N4KO islets showed lower oxygen consumption rate, and HFD-fed N4KO mice developed mild glucose intolerance. To understand how NPAS4 may counteract these defects, I identified shared DNA binding sites of NPAS4 and ARNT in MIN6 cells using ChIP-Seq. Among the shared sites, I observed NPAS4 and ARNT binding near Rgs2, corroborating an earlier study. I then demonstrated that RGS2 is a negative regulator of glucose-stimulated insulin secretion (GSIS), because Rgs2-overexpressing MIN6 cells and mouse islets showed reduced GSIS, due to lower calcium influx and oxygen consumption, whereas Rgs2 knockout cells exhibited increased GSIS. In sum, I demonstrated that NPAS4 and its target gene, RGS2, are important regulators of β-cell function. This suggests that these two factors could be promising therapeutic targets to promote β-cell health and optimize insulin secretion in diabetes.

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The cell cycle regulates mouse and human pancreas development (2018)

Diabetes is caused by a loss or dysfunction of insulin-producing pancreatic beta-cells. A potential treatment for diabetes is to replace these cells through transplantation. As there is a shortage of donor tissue, efforts to generate an unlimited source of functional insulin-producing beta-cells from human embryonic stem cells (hESCs) are ongoing. During pancreas development, proliferating pancreatic progenitors activate Neurog3, exit the cell cycle, and differentiate. The overarching goal of this thesis was to understand the role of the cell cycle in regulating Neurog3 expression and endocrine cell fate. First, the length of each cell cycle phase of pancreatic progenitors was measured using cumulative EdU labelling, determining an increase in G1 length in Pdx1+ progenitors from 4.5±0.4 to 7.2±0.8 hours between embryonic day (E)11.5 and E13.5. Next, two mouse models were used to show that cell cycle lengthening within pancreatic progenitors stimulates endocrine differentiation. Kras heterozygous loss-of-function mice have increased endocrine cell genesis that was correlated with an increase in progenitor cell cycle length. Ectopic expression of the cyclin-dependent kinase inhibitor Cdkn1b in Sox9+ progenitor cells resulted in a 2.7-fold increase in the number of Neurog3+ cells. As Cdkn1b is an inhibitor of G1-S cyclin-dependent kinases (Cdks), the effect of directly inhibiting Cdk2, Cdk4 and Cdk6 on endocrine differentiation was investigated. Treating embryonic pancreata, ex vivo, for 24 hours with Cdk inhibitors resulted in a 3-fold increase in the number of Neurog3+ cells. To investigate the consequences of CDK inhibition on human endocrine differentiation, a NEUROG3-2A-eGFP (N5-5) knock-in reporter CyT49 hESC line was generated using CRISPR-Cas9. CDK inhibition increased the number of GFP+ endocrine progenitor cells 1.7-fold. These findings suggest that G1 lengthening is required for normal mouse and human organogenesis and that cyclin-dependent kinases act directly to reduce Neurog3 protein. In the final chapter, single-cell transcriptomics was used to profile the gene expression and cell populations present during mouse and human endocrine development. In conclusion, these studies show that progenitor cell-cycle G1 lengthening, through its actions on stabilization of Neurog3, is an essential determinant of normal endocrine cell genesis.

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The Roles of SOX4 and MED15 in the Development and Maintenance of Pancreatic ?-cells (2017)

Pancreatic beta-cells (β-cells) are essential for the maintenance of blood glucose homeostasis, as the primary insulin-secreting cells of the body. During embryogenesis, β-cells differentiate from pancreatic progenitor cells, and following birth, these cells re-enter the cell-cycle and proliferate to maintain a sufficient adult population of β-cells. Transcription factors (TFs) such as neurogenin3 (Neurog3) are essential for endocrine cell specification within the pancreas, while other TFs are required in adult β-cells to maintain their function. Despite the identification of many TFs throughout β-cell development, how TFs regulate the transition between cell states, and how these TFs engage the RNA Polymerase II holoenzyme to regulate transcription is unknown. To address these questions, this thesis examines the role of Sry-related HMG-box 4 (SOX4) and Mediator 15 (MED15) in β-cell development and the adult β-cell state.Work in this thesis has established that in mice, SOX4 is expressed in pancreatic progenitor cells and cooperates with NEUROG3 to activate Neurog3 expression. This demonstrated a requirement for SOX4 in endocrine progenitor cell specification. SOX4 continued to be expressed in endocrine specified cells, and was essential for Neurod1 and Pax4 induction, TFs required for β-cell specification. High-fat diet (HFD)-fed mice with inducible SOX4 deletion in β-cells also exhibited glucose intolerance, due to decreased β-cell mass and replication rate. Loss of Sox4 led to the upregulation of the cell-cycle inhibitor Cdkn1a, a gene that prevents G1-S cell-cycle transition. Additionally, Med15 deletion in pancreatic progenitors demonstrated reduced NEUROG3 expression, and reduced endocrine cell numbers. MED15 deletion following endocrine specification also led to reduced β-cell numbers. Finally, Ins1-Cre facilitated deletion of MED15 in β-cells revealed that its function varied depending on cell-state, with compromised β-cell function if expression is lost during β-cell maturation. These data are the first to determine when SOX4 is required for pancreatic endocrine specification in mice and which targets are directly regulated by SOX4. In addition, the first known in-vivo role for MED15 in mammals is identified, demonstrating that it is an indispensable factor for β-cell differentiation and function. Collectively, these findings contribute to the understanding of how TFs regulate β-cell states.

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The role of NPAS4 in glucose homeostasis (2016)

Type 2 diabetes is characterized by hyperglycemia associated with reduced insulin secretion from pancreatic beta cells and impaired insulin sensitivity at peripheral target tissues. There is a growing body of evidence that supports the importance of bHLH-PAS domain transcription factors in promoting beta cell function. With the recent identification of neuronal PAS domain protein 4 (NPAS4) within the central nervous system, studies were undertaken to determine whether NPAS4 is expressed in beta cells, how its expression is regulated in response to changing environmental signals and uncover the functional significance of NPAS4 in the maintenance of glucose homeostasis. Together, experiments within this thesis demonstrate that NPAS4 is expressed within the pancreatic beta cell and is rapidly upregulated in response to membrane depolarization and calcium influx. Further, this induction was impaired in a mouse model of beta cell dysfunction and within islets from individuals with T2D. Overexpression studies performed in vitro identified NPAS4 as a novel negative regulator of insulin expression and GLP-1 potentiated insulin secretion. Furthermore, NPAS4 protected beta cells from maladaptive cellular pathways that promote cell dysfunction and death; including endoplasmic reticulum stress and activation of HIF1α. Finally, the characterization of three different Npas4 mouse knockout models suggests that continued NPAS4 expression in the beta cell is required to maintain differentiation status and cellular function. An independent role for NPAS4 in the maintenance of glucose homeostasis was also discovered in other Pdx1-Cre expressing cells, likely within the hypothalamus. Together, the data suggest beta cells induce NPAS4 expression during periods of cellular activity and acts as a protective factor to protect cells in order to promote the maintenance of euglycemia.

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Master's Student Supervision

Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

Truncated CD19 as a selection marker for the isolation of stem cell derived β-cells (2023)

Stem cell-derived β-cells (SCβ-cell) are a renewable and scalable alternative to cadaveric islet transplants as a cell replacement therapy for type 1 diabetes (T1D). However, heterogeneity within SCβ-cell cultures remains problematic for graft safety and function. Magnetic selection of SCβ-cells expressing a unique cell surface marker may help deplete undesirable cell types and facilitate functional maturation. This is study, I explored CD19 as a potential cell surface marker for the enrichment of insulin-expressing SCβ-cells. Using CRISPR/Cas9 technology, I created a knock-in add-on of CD19-mScarlet downstream of the insulin coding sequence in human embryonic stem cells (hESCs). I established reproducible SCβ-cell surface expression of CD19-mScarlet. Importantly, I developed and optimized a magnetic sorting protocol for CD19-mScarlet-expressing cells, forming enriched SCβ-cell clusters with improved glucose-stimulated c-peptide secretion. This strategy holds promise to facilitate large-scale production of functional SCβ-cells for T1D disease modeling and cell replacement therapy.

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