PD Functional Genomics

Study Rationale: Genetic mutations that lead to the activation of the enzyme LRRK2 are a major cause of inherited Parkinson’s disease. Team Alessi aims to combine the complementary expertise of its four research laboratories to perform fundamental, state-of-the-art experimentation to better comprehend the biology that is controlled by LRRK2. Team Alessi’s goal is to gain a much better understanding of LRRK2-driven Parkinson’s disease, hopefully providing a foundation for the development of future therapies.

Hypothesis: LRRK2 targets and modifies a set of enzymes known as Rab GTPases, triggering new biological events by creating new protein: protein interactions. Team Alessi aims to decipher what controls the activity of LRRK2 and to explore, in precise molecular detail, how this enzyme affects three major cellular structures (cilia, lysosomes, and mitochondria) implicated in Parkinson’s disease.

Study Design: Team Alessi showed that mutant LRRK2 triggers a series of molecular changes that cause new sets of proteins to interact. Team Alessi’s goal is to use a combination of state-of-the-art approaches to understand the consequences of these new interactions on the biology of three important subcellular compartments: primary cilia, lysosomes, and mitochondria.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Team Alessi’s findings will provide novel, fundamental information of relevance to understanding the origin and progression of Parkinson’s that they hope will lead to new ideas to better diagnose, treat, and even prevent this malady in the future.

Study Rationale: Geneticists have made great progress in identifying gene mutations that either cause Parkinson’s or increase disease risk. The critical next step is to determine how some of these mutations perturb the function of brain cells involved in Parkinson’s disease. By advancing knowledge of these processes, Team De Camilli’s research will help to identify new opportunities for reversing the vulnerabilities that cause the disease.

Hypothesis: Team De Camilli hypothesizes that the functions of multiple Parkinson’s disease genes converge on common biochemical pathways involving endocytic organelles and/or mitochondria within vulnerable cell types.

Study Design: Team De Camilli will use a comprehensive cell biology tool kit including cutting-edge biochemistry, structural biology, microscopy at different scales, and genome editing tools to elucidate the function of selected Parkinson’s disease genes and the effects produced by their dysfunction both in cellular models in vitro and in mouse and rat models. By defining the molecular and cellular networks in which the products of these genes operate, Team De Camilli hopes to identify strategies for reversing the cellular vulnerabilities that cause Parkinson’s disease or increase disease risk.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Similar to assembling the pieces of a puzzle, the project has the potential to reveal interconnections between the functions of distinct Parkinson’s disease genes, thus helping to build an understanding of Parkinson’s disease cell biology. This is a critical step towards the development of therapeutic strategies to make neurons resistant to the dysfunctions that cause Parkinson’s disease.

Study Rationale: The progression of Parkinson’s disease is very variable, with some individuals having a rapid course and others having a longer and more benign course. Team Hardy believes that by understanding the genetics and the mechanistic basis of this variability, they will be able to design therapies to slow Parkinson’s progression. Team Hardy has already found that GBA mutations lead to a rapid disease course and that LRRK2, linked to familial forms of Parkinson’s, influences the course of parkinsonism in another disease: progressive supranuclear palsy. They will test whether modulating these enzymes influences the course of pathology spread in a pre-clinical model of progression as a validation of this approach to disease treatment.

Hypothesis: Team Hardy wants to find and understand the genes that are involved in Parkinson’s progression and test whether modulating them pharmacologically influences disease progression.

Study Design: Through genetic analysis, Team Hardy will find genes that influence the progression of parkinsonism, and then assess the mechanisms by which they affect disease development. They have already found that GBA and LRRK2 influence clinical rates of decline so Team Hardy will test, in a mouse model of pathology progression, whether inhibiting these enzymes influences pathology spread and thereby develop a relevant platform to test drugs for slowing disease progression.

Impact on Diagnosis/Treatment of Parkinson’s Disease: This research will impact Parkinson’s care in three ways. First, by understanding the genetics of rate of decline, these data can be factored into clinical trial design and possibly more generally into clinical practice. Second, the identification of pathways involved in disease progression is likely to reveal further drug targets. And thirdly, the testing of GBA and LRRK2 inhibitors in a mouse model of disease progression will test this as a valid approach to treatment development.

Study Rationale: Abnormal protein aggregation and prion-like aggregate spreading are hallmarks of the degenerative cascades of sporadic and familial Parkinson’s disease (PD) and can damage cells, including neurons. Multiple mechanisms of aggregate toxicity have been implicated in cellular PD pathology, and PD risk alleles may have the potential to illuminate additional underlying biological mechanisms.

Hypothesis: Parkinson’s disease, at the molecular level, results from the failure of cellular quality control (QC) mechanisms, and finding ways to maintain (or augment) QC capacity will provide new therapeutic strategies for PD and possibly other neurodegenerative disorders.

Study Design: Using powerful molecular visualization and discovery tools in disease-relevant cells, Team Harper will elucidate how individual types of protein aggregates linked with PD strains (including patient-derived aggregates) alter cellular pathways, including effects on cell survival and function. Team Harper will also use genetic approaches to understand what cellular proteins promote the processing of PD-related aggregates.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Team Harper’s expectation is that this work will identify those critical cellular functions that are disrupted by protein aggregates and will help define how mutations alter the underlying mechanisms of dysfunctional proteostasis.

Study Rationale: Mitochondria are tiny power-generating stations within all cells, including neurons. They are vital energy producers, but when things go wrong, they can spew toxic materials and sicken or kill neurons. The clean-up crew for mitochondria gone wrong is called “mitophagy” (as in “eating mitochondria”) and is directed by two proteins called PINK1 and parkin. Studies of Parkinson’s disease have taught researchers that PINK1, parkin and mitophagy are very important in preventing disease.

Hypothesis: The purpose of this project is to figure out how PINK1, parkin and mitophagy work together to prevent disease. Once Team Hurley knows how they work together, they hope to figure out how to make them work faster and better, so that they can prevent Parkinson’s disease from ever starting.

Study Design: Team Hurley thinks of PINK1, parkin and the proteins of mitophagy as nanomachines. They call their type of research “mechanistic” because it seeks to understand how these machines work. Team Hurley relies heavily on the most powerful light and electron microscopes available, and they also use genome engineering of stem cells to make versions of neurons that are easier to study.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Team Hurley’s dream is to understand PINK1, parkin, and mitophagy so well that they can build a computerized description of the pathway that will be able to predict which drugs and treatments will help the mitochondrial clean-up crew enough to prevent or cure disease.

Study Rationale: Several genes are known to be associated with Parkinson’s disease, although how they impact the disease process is not fully understood. Team Kirik will use stem cells from patients in whom the genetic cause is known and perform mechanistic studies to elucidate the interactions between three key genes and how they impact the function of cells in the brain.

Hypothesis: This project will provide new insights into the role specific gene mutations play in the development of disease features in cell types known to be affected in Parkinson’s disease.

Study Design: Stem cells generated from patients with neurological disease, including Parkinson’s disease, provide a tool for researchers to study and understand mechanisms underlying the disease. One limitation of this approach is that the cells are maintained in culture dishes in the laboratory in an artificial environment that does not closely model that of the disease. This project proposes a unique approach involving the transplantation of the human cells into mice in order to study them in the living brain and thus reveal new insights into disease mechanisms.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Researchers’ ability to design better treatments for Parkinson’s is directly related to the level of understanding on the basic biological processes governing the initiation of the disease process and how the disease progresses from that point onward. This information is critical in efforts to intervene with the disease process.

Study Rationale: While aging is the greatest risk factor for the development of Parkinson’s disease (PD), how aging promotes PD is not fully understood. Examining the role of cellular senescence (deterioration of function), a major driver of aging, in PD represents a completely novel approach to understanding disease pathophysiology and may lead to new therapeutic approaches.

Hypothesis: Senescence and PD-linked gene mutations have reciprocal pathological interactions where (i) senescence causes PD-relevant neuropathology; (ii) PD-linked mutant genes (alpha-synuclein, LRRK2, Vps35) cause premature senescence; and (iii) senescence participates in neuropathology caused by PD-linked genes.

Study Design: First, Team Lee will use novel mouse models of premature senescence to test whether premature senescence in specific cell types causes PD-like neuropathology. Second, they will combine mouse models of senescence and familial PD to test whether senescence participates in neuropathology caused by mutant PD-linked genes. Specifically, Team Lee will determine if pathology in a PD mouse model causes premature senescence and whether removing senescent cells from brain can prevent PD pathology. Finally, Team Lee will perform gene expression analysis of PD brains and mouse brains, at a single-cell level, to gain high-resolution insights about cellular processes that link aging and PD pathology.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Team Lee’s results will support the use of senolytics (drugs that selectively kill senescent cells and are currently in Phase II clinical trials) as novel disease-modifying therapies for PD. In addition, Team Lee’s studies may identify new biomarkers of senescence in PD.

Study Rationale: Leucine Rich Repeat Kinase 2 (LRRK2) is the most commonly mutated gene in inherited forms of Parkinson’s disease (PD). The LRRK2 gene codes for a protein kinase, an enzyme that adds chemical groups to other proteins to change their activity inside cells. However, researchers currently do not understand how LRRK2 normally works and why its malfunction causes PD. Importantly, LRRK2 has also been shown to function abnormally in PD patients that have the sporadic form of the disease, making LRRK2 one of the most promising targets for drug development.

Hypothesis: Team Reck-Peterson recently discovered that chains of the LRRK2 protein can wrap around cellular highways called “microtubules”. Their work suggests that LRRK2 blocks the cellular machines that move on these highways. Team Reck-Peterson will explore the idea that mutations in LRRK2 cause PD by acting as roadblocks that change the normal transport of chemical information inside cells. They will test additional ideas that arise from the experiments they perform.

Study Design: The collaborative team includes experts in cryo-electron microscopy (Cryo-EM), cryo-electron tomography (Cryo-ET), small molecule synthesis, proteomics, and single-molecule and live-cell imaging. The team will use their expertise to solve structures of multiple conformations and variants of LRRK2 to manipulate these different pools of LRRK2 and understand their cellular functions. Team Reck-Peterson will determine how LRRK2 binds to microtubules and affects microtubule-based motors. They will also identify the protein interaction landscape of LRRK2 and test emergent cellular hypotheses resulting from this work, including whether LRRK2 regulates the transport of chemical information on microtubules.

Impact on Diagnosis/Treatment of Parkinson’s Disease: A major barrier to developing LRRK2-based PD therapy has been the lack of a blueprint of LRRK2’s three-dimensional shape, alone or interacting with other molecules it comes into contact with inside human cells. Team Reck-Peterson expects that the work will reveal what LRRK2 looks like, what it does in cells, and why its malfunction causes PD. The work will be critical for the design of drugs targeting LRRK2.

Study Rationale: Parkinson’s disease can have multiple complex causes, including genetic and environmental, that are not fully understood. Team Rio will combine modern genetic and human stem cell-based approaches to determine how heritable genetic changes affect Parkinson’s disease predisposition. By identifying how even small genetic changes can compound the risk of developing Parkinson’s disease, Team Rio hopes to identify new ways to detect and treat the disease in the future.

Hypothesis: Team Rio hypothesizes that combining complex human cell culture models such as 3-dimensional brain organoids with sophisticated genome-scale functional analysis will allow the team to elucidate how diverse genetic factors interact and contribute to the risk of developing Parkinson’s disease, thereby informing the development of early detection diagnostics and advanced treatment options.

Study Design: Team Rio will genetically engineer human embryonic stem cells to model the genetic alterations known to increase risk for Parkinson’s disease and turn those cells into disease-relevant cell types such as dopamine neurons. By profiling the gene expression changes caused by these known Parkinson’s disease risk variants, the team will decipher the key molecular signatures that contribute to Parkinson’s disease. Once identified, the team will confirm these genetic signatures in patient samples and validate their effects in animal models.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Elucidating how Parkinson’s disease genetic risk variants affect cell biology has promise to identify disease-specific biomarkers and novel treatment options.

Study Rationale: Genome-wide association studies (GWAS) have unequivocally linked thousands of noncoding variants in ninety independent GWAS signals to susceptibility for common, genetically complex Parkinson’s disease (PD) that affects more than 7 million people around the world. Why have these breakthroughs not uncovered the mechanism(s) of PD? Researchers do not know how disease-associated variants cause neurodegeneration and why they impair some brain cells but not others. Team Scherzer’s research will tackle the critical task of clarifying the precise mechanisms through which this wealth of genetic variation regulates onset and progression of PD.

Hypothesis: Team Scherzer hypothesizes that most GWAS variants function through cell-, space-, and stage-dependent gene-regulatory mechanisms.

Study Design: Here Team Scherzer will develop a molecular atlas of PD that reveals how GWAS/familial genetics control proximal disease mechanisms in five dimensions: brain cells (1D), brain space (3D), and disease stage (1D). The team will reveal how genetic variants modulate mechanisms in specific brain cells in specific topographic locations of midbrain and cortex during the progression of neuropathology from healthy brains to prodromal to symptomatic disease. Massively parallel analysis of hundreds of thousands of single human brain cells with genetic transcriptomics, high-resolution spatial transcriptomics, and fine-mapping of causal alleles with allelic imbalance in human brains will be combined with the prodigious power of cell- and stage-specific mechanistic analyses in brain of Drosophila avatars and in vitro in human pluripotent stem cells.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Team Scherzer’s collaborative and integrative project will translate the complex human genetics of PD into a dynamic, five-dimensional view of proximal cellular mechanisms. It will begin to reveal how single nucleotide variation in a person’s universal DNA code regulates gene activity (without changing protein sequence) in situ in billions of physiologically specialized neurons and glia cells, and determines, how, when, which, and where brain cells are destined to malfunction.

Study Rationale: Why do some people develop Parkinson’s disease (PD) while others do not? Although many genetic risk factors have been identified, researchers still cannot confidently answer this question, or explain how certain cells in the brain go from being healthy early in life to diseased in old age. Clearly, numerous complex factors are involved, and a systematic investigation of the key cellular and molecular players is necessary to understand and effectively treat this disease.

Hypothesis: Team Studer hypothesizes that single genetic factors are insufficient to cause PD — rather, that it is triggered by a combination of genetics, age-related factors, and their effects in different brain cells.

Study Design: Here, Team Studer proposes to dissect the genetic, age-related, and cell-type-specific factors that lead to PD using a collection of genetically diverse stem cells derived from patients. Using advanced methods pioneered by the team, they will convert these stem cells into the different types of brain cells implicated in PD — neurons, microglia, and astrocytes — allowing the team to investigate how genetic risk factors, the aging process, and these different cell types interact to trigger disease. Team Studer will assess how various combinations of these factors disrupt the function of brain cells using detailed molecular studies, microscopy, genetic manipulations, and biochemical measurements — building a computational network model of the factors that cause PD.

Impact on Diagnosis/Treatment of Parkinson’s Disease: This richer, fully human cell model of PD will provide an entirely new level of understanding of how the interplay between genetics, different brain cells, and aging shapes individual disease risk, enabling early diagnosis, prediction of therapeutic targets that could halt or reverse the disease, and stratification of patients into therapeutically meaningful subgroups.

Study Rationale: Mutations in the genes ATP13A2 (PARK9) and ATP10B trigger Parkinson’s disease (PD) and cause dysfunction of lysosomes, the recycling compartments of the cell. Team Vangheluwe explained these defects by impaired transport of polyamines and glucosylceramide out of the lysosome, respectively. Polyamines are cell protective agents, whereas the levels of the lipid glucosylceramide are controlled by GBA1, the major genetic risk factor of PD. However, there is a clear knowledge gap regarding the biology of polyamine and glucosylceramide transport systems in neurons and their supporting cells of the brain, and how an impaired polyamine and glucosylceramide distribution in these cells leads to neurodegeneration.

Hypothesis: Team Vangheluwe hypothesizes that an impaired polyamine and glucosylceramide transport activity causes toxic accumulation of these substances in lysosomes and leads to a shortage elsewhere in the cell. Together, this may cause lysosomal and mitochondrial dysfunction, and lead to α-synuclein toxicity, three major hallmarks of PD.

Study Design: First, Team Vangheluwe will investigate the molecular architecture of polyamine and glucosylceramide transporters and identify mechanisms to modulate their activity. Second, the team will examine how these transporters influence the intracellular distribution of polyamine and glucosylceramide, and how this affects the cross-talk between lysosomes and mitochondria. Third, they will investigate how dysfunctional polyamine and glucosylceramide transporters affect other PD pathways, such as mitophagy, GBA1 and alpha-synuclein aggregation, and whether the modulation of these transporters can be validated as therapeutic approach for PD. Finally, Team Vangheluwe will collect evidence for disturbed polyamine and glucosylceramide transport in PD patients.

Impact on Diagnosis/Treatment of Parkinson’s Disease: Team Vangheluwe will validate the neuroprotective effect of polyamine and glucosylceramide transporters and investigate their potential to reverse α-synuclein and GBA1 pathology. This may offer new therapeutic strategies that correct aberrant lysosomal and mitochondrial dysfunction in Parkinson’s disease. The team will analyze whether alterations in the polyamine and glucosylceramide levels together may be considered as biomarkers for PD.

Study Rationale: Parkinson’s disease (PD) is a disorder that not only affects the function of the brain, but also of the gut, which are both complex tissues composed of functionally diverse types of cells that need to cooperate for organ function. Around 90 regions of the DNA that we inherit from our parents, show differences between people with and without PD. Furthermore, as we develop and age, new, non-inherited DNA mutations may also be acquired in part of our body cells. How such inherited and newly acquired DNA variants function in increasing the risk of developing PD remains however largely unknown.

Hypothesis: Team Voet hypothesizes that these DNA variants can increase or decrease the activity of key (un)known genes in particular types of cells of the brain and the gut, which in turn increases the risk of developing PD.

Study Design: Team Voet will use the expertise of their consortium in analyzing single cells to study the brain and gut from individuals who lived with and without PD. Specifically, gene expression profiling of over 4,500,000 single cells will allow the team to discover the genes of which the expression is altered by the DNA variants, and importantly, also in which type of brain and/or gut cells the expression of the gene is disturbed. Team Voet will next analyze how these DNA variants change the functioning of these specific cell types, by using their existing models of the fruitfly, and of cultured human nerve and immune gut cells.

Impact on Diagnosis/Treatment of Parkinson’s Disease: This study will provide crucial mechanistic insights into how faults in our DNA change the functioning of specific cells in our brains and guts, and thus cause a predisposition to PD.

Study Rationale: To determine the molecular and cellular process that lead to PD, a powerful approach is to single out and study the cells where the disease originates. To achieve this goal, Team Wood uses alpha-synuclein oligomers as a cellular biomarker to identify the right cells. The team will then apply state-of-the-art genomic and genetic analyses to identify genes and proteins that form the disease pathways. Team Wood can then determine the difference between cause and effect by using human cell models derived from induced pluripotent stem cells.

Hypothesis: Team Wood hypothesizes that alpha-synuclein oligomers can be used as cellular biomarkers to identify the specific cells where the disease processes begin, thus making their targeted study possible.

Study Design: By detecting the presence of alpha-synuclein oligomers, Team Wood will identify neuronal and non-neuronal cells in the human brain at different stages of disease, which the team will then study using state of the art single cell genomic and transcriptomic methods. This will allow the team to build a comprehensive and detailed picture of the genes and molecular processes that underlie the disease, which the team will then prioritize using network theory and their knowledge of the current and emerging genetic factors. Using a human model system (iPSC), Team Wood will be able to distinguish cause and effect and deliver new targets for therapeutics, diagnostics, and biomarkers of disease.

Impact on Diagnosis/Treatment of Parkinson’s Disease: This interdisciplinary program, combining physical chemistry, computational modeling, genetics, and neurobiology, will allow researchers to much more fully understand the reasons behind why some cells succumb and others resist the pathological processes. Team Wood findings will offer opportunities for accurate markers of disease status, progression, and validated targets for biopharma to develop novel therapies.