Relevant Degree Programs
Affiliations to Research Centres, Institutes & Clusters
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.
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.
Complete these steps before you reach out to a faculty member!
- Familiarize yourself with program requirements. You want to learn as much as possible from the information available to you before you reach out to a faculty member. Be sure to visit the graduate degree program listing and program-specific websites.
- Check whether the program requires you to seek commitment from a supervisor prior to submitting an application. For some programs this is an essential step while others match successful applicants with faculty members within the first year of study. This is either indicated in the program profile under "Requirements" or on the program website.
- Identify specific faculty members who are conducting research in your specific area of interest.
- Establish that your research interests align with the faculty member’s research interests.
- Read up on the faculty members in the program and the research being conducted in the department.
- Familiarize yourself with their work, read their recent publications and past theses/dissertations that they supervised. Be certain that their research is indeed what you are hoping to study.
- Compose an error-free and grammatically correct email addressed to your specifically targeted faculty member, and remember to use their correct titles.
- Do not send non-specific, mass emails to everyone in the department hoping for a match.
- Address the faculty members by name. Your contact should be genuine rather than generic.
- Include a brief outline of your academic background, why you are interested in working with the faculty member, and what experience you could bring to the department. The supervision enquiry form guides you with targeted questions. Ensure to craft compelling answers to these questions.
- Highlight your achievements and why you are a top student. Faculty members receive dozens of requests from prospective students and you may have less than 30 seconds to pique someone’s interest.
- Demonstrate that you are familiar with their research:
- Convey the specific ways you are a good fit for the program.
- Convey the specific ways the program/lab/faculty member is a good fit for the research you are interested in/already conducting.
- Be enthusiastic, but don’t overdo it.
G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.
Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - Nov 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.
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.
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.
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.
- Friend and foe: β-cell Ca2+ signaling and the development of diabetes (2019)
Molecular Metabolism, 21, 1--12
- In vitro analyses of suspected arrhythmogenic thin filament variants as a cause of sudden cardiac death in infants. (2019)
Proceedings of the National Academy of Sciences of the United States of America,
- Ins2 gene bursting activity defines a mature β-cell state (2019)
- Mediator subunit MDT-15/MED15 and Nuclear Receptor HIZR-1/HNF4 cooperate to regulate toxic metal stress responses in Caenorhabditis elegans (2019)
- Neuronal PAS Domain Protein 4 Suppression of Oxygen Sensing Optimizes Metabolism during Excitation of Neuroendocrine Cells. (2018)
- Recessive mutations in ATP8A2 cause severe hypotonia, cognitive impairment, hyperkinetic movement disorders and progressive optic atrophy. (2018)
Orphanet journal of rare diseases,
- Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors. (2018)
Stem cell reports,
- The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes. (2018)
- SOX4 Allows Facultative β-Cell Proliferation Through Repression of Cdkn1a (2017)
Diabetes, 66 (8), 2213--2219
- Phosphorylation of NEUROG3 Links Endocrine Differentiation to the Cell Cycle in Pancreatic Progenitors (2017)
Developmental Cell, 41 (2), 129--142.e6
- The p300 and CBP Transcriptional Coactivators are Required for Beta Cell and Alpha Cell Proliferation (2017)
Diabetes, , db170237
- Generation of a Conditional Allele of the Transcription Factor Atonal Homolog 8 (Atoh8) (2016)
PLOS ONE, 11 (1), e0146273
- Npas4 Transcription Factor Expression Is Regulated by Calcium Signaling Pathways and Prevents Tacrolimus-induced Cytotoxicity in Pancreatic Beta Cells. (2016)
The Journal of biological chemistry,
- Reawakening the Duct Cell Progenitor? (2016)
Endocrinology, 157 (1), 52--53
- Reduced Insulin Production Relieves Endoplasmic Reticulum Stress and Induces β Cell Proliferation. (2016)
- Using CRISPR-Cas9 Genome Editing to Enhance Cell Based Therapies for the Treatment of Diabetes Mellitus (2016)
Genome Editing, , 127--147
- All-encomPASsing regulation of β-cells: PAS domain proteins in β-cell dysfunction and diabetes (2015)
Trends in Endocrinology & Metabolism, 26 (1), 49--57
- SOX4 cooperates with neurogenin 3 to regulate endocrine pancreas formation in mouse models. (2015)
- Use-dependent activation of neuronal Kv1.2 channel complexes. (2015)
The Journal of neuroscience : the official journal of the Society for Neuroscience,
- Glycoprotein 130 Receptor Signaling Mediates alpha-Cell Dysfunction in a Rodent Model of Type 2 Diabetes (2014)
Diabetes, 63 (9), 2984--2995
- Quetiapine treatment in youth is associated with decreased insulin secretion. (2014)
Journal of clinical psychopharmacology,
- TALEN/CRISPR-mediated eGFP knock-in add-on at the OCT4 locus does not impact differentiation of human embryonic stem cells towards endoderm. (2014)
- Characterization of polyhormonal insulin-producing cells derived in vitro from human embryonic stem cells. (2013)
Stem cell research,
- Identification and analysis of murine pancreatic islet enhancers. (2013)
- Npas4 Is a Novel Activity–Regulated Cytoprotective Factor in Pancreatic β-Cells (2013)
Diabetes, 62 (8), 2808--2820
- The transcription factor Atonal homolog 8 regulates Gata4 and Friend of Gata-2 during vertebrate development. (2013)
The Journal of biological chemistry,
- Maintenance of beta-Cell Maturity and Plasticity in the Adult Pancreas: Developmental Biology Concepts in Adult Physiology (2012)
Diabetes, 61 (6), 1365--1371
- Noncoding RNAs (2012)
Experimental Diabetes Research, 2012, 1--2
- Regulation of GIP and GLP1 Receptor Cell Surface Expression by N-Glycosylation and Receptor Heteromerization (2012)
PLoS ONE, 7 (3), e32675
- A mouse model for monitoring islet cell genesis and developing therapies for diabetes. (2011)
Disease models & mechanisms,
- Sequence and epigenetic determinants in the regulation of the Math6 gene by Neurogenin3. (2011)
Differentiation; research in biological diversity,
- Rfx6 directs islet formation and insulin production in mice and humans. (2010)
- Serotonin regulates pancreatic beta cell mass during pregnancy (2010)
Nature Medicine, 16 (7), 804--808
- Homeodomain transcription factor NKX2.2 functions in immature cells to control enteroendocrine differentiation and is expressed in gastrointestinal neuroendocrine tumors. (2009)
- Meta-regulation: microRNA regulation of glucose and lipid metabolism (2009)
Trends in Endocrinology & Metabolism, 20 (9), 452--459
- Identification of the bHLH factor Math6 as a novel component of the embryonic pancreas transcriptional network. (2008)
- Induction of pancreatic islet cell differentiation by the neurogenin-neuroD cascade. (2008)
Differentiation; research in biological diversity,
- Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. (2008)
- Novel glucagon receptor antagonists with improved selectivity over the glucose-dependent insulinotropic polypeptide receptor. (2008)
Journal of medicinal chemistry,
- MicroRNA expression is required for pancreatic islet cell genesis in the mouse. (2007)
- Post-translational regulation of the beta-cell specific factor Nkx6.1 (2007)
Developmental Biology, 306 (1), 365
- Reversal of islet GIP receptor down-regulation and resistance to GIP by reducing hyperglycemia in the Zucker rat. (2007)
Biochemical and biophysical research communications,
- Sox9 coordinates a transcriptional network in pancreatic progenitor cells. (2007)
Proceedings of the National Academy of Sciences of the United States of America,
- The HMG box transcription factor Sox4 contributes to the development of the endocrine pancreas. (2005)
- A novel pathway for regulation of glucose-dependent insulinotropic polypeptide (GIP) receptor expression in beta cells. (2003)
FASEB journal : official publication of the Federation of American Societies for Experimental Biology,
- Dipeptidyl Peptidase IV Inhibitor Treatment Stimulates beta-Cell Survival and Islet Neogenesis in Streptozotocin-Induced Diabetic Rats (2003)
Diabetes, 52 (3), 741--750
- Glucose-dependent insulinotropic polypeptide (GIP): development of DP IV-resistant analogues with therapeutic potential. (2003)
Advances in experimental medicine and biology,
- Glucose-dependent insulinotropic polypeptide receptor null mice exhibit compensatory changes in the enteroinsular axis. (2003)
American journal of physiology. Endocrinology and metabolism,
- Structure-activity relationships of glucose-dependent insulinotropic polypeptide (GIP). (2003)
- Defective glucose-dependent insulinotropic polypeptide receptor expression in diabetic fatty Zucker rats. (2001)
- Characterization of the Carboxyl-terminal Domain of the Rat Glucose-dependent Insulinotropic Polypeptide (GIP) Receptor (1999)
Journal of Biological Chemistry, 274 (35), 24593--24601
- Glucose-dependent insulinotropic polypeptide stimulation of lipolysis in differentiated 3T3-L1 cells: wortmannin-sensitive inhibition by insulin. (1999)
- Improved glucose tolerance in rats treated with the dipeptidyl peptidase IV (CD26) inhibitor Ile-thiazolidide (1999)
Metabolism, 48 (3), 385--389
- HIP1, a human homologue of S. cerevisiae Sla2p, interacts with membrane-associated huntingtin in the brain. (1997)