Cellular metabolic processes are catalyzed within specific compartments consisting of cytosol and different subcellular organelles. Many inherited metabolic diseases are caused by defects in genes that encode organellar proteins (commonly enzymes or transporters). These defects lead to the accumulation of metabolites that cannot be further processed or transported. The accumulation of a metabolite eventually results in organelle dysfunction, perturbation of cellular homeostasis, and organ damage. The brain is often impacted by organelle-associated metabolic disorders, including lysosomal and peroxisomal storage diseases and mitochondrial disorders.
Our laboratory is devoted to understanding the molecular and biochemical basis of organelle-associated metabolic disorders with a special focus on lysosomal storage diseases. Our goals include characterizing these metabolic disorders, understanding the impact of metabolic perturbations on organellar function and cellular homeostasis, developing tools to monitor organellar metabolism, searching for biomarkers, and designing therapies to restore normal metabolism.
We conduct our experiments using cell cultures and transgenic mouse models, employing several subcellular multi-omics, high-throughput functional genomics, and biochemical techniques. Moreover, we collaborate with clinical geneticists and scientists at prestigious hospitals and institutions (such as Johns Hopkins Aramco Healthcare, King Faisal Specialist Hospital & Research Centre, and Stanford University). This provides us with valuable opportunities to access patient samples and cells as well as engage in hands-on training utilizing state-of-the-art technologies. Our research will offer novel insights into organellar metabolism and inform the development of future therapeutics of human diseases in which organelles are implicated.
SPECIFIC RESEARCH PROJECTS
Functional characterization of proteins involved in organelle-associated metabolic disorders and syndromes
The lysosome is the primary site for the intracellular degradation of metabolic. Defects in genes that encode lysosomal or lysosomal-associated proteins can result in the abnormal build-up and subsequent storage of metabolic wastes. These defects lead to lysosomal storage diseases (LSDs), which include over 70 genetically distinct metabolic disorders. Despite the fact that the causative genes are known and most mutations have been reported, the molecular and cellular mechanisms underlying each distinct LSD remain obscure. To elucidate these mechanisms, our lab utilizes subcellular immunopurification tools and harnesses the power of multi-omics approaches such as metabolomics, proteomics, and functional genomics. Indeed, our recent discovery has been facilitated by using lysosomal immunopurification (LysoIP) from cultured cells (LysoTag cells) and animal models (LysoTag mouse) of CLN3-Batten disease in combination with untargeted metabolomics and lipidomics analyses (Laqtom, NN. et al., 2022) In addition to LSDs, our lab is interested in studying: 1) the function of the endosomal protein TBC1D24, the deficiency of which results in DOORS syndrome, and 2) the function of the ER-resident CYBC1 protein, the loss of which causes an immunodeficiency disorder of phagocytes (CGD).
Development of a method for isolating pure endoplasmic reticulum (ER) and characterizing its molecular components
ER is a metabolic compartment that is critical for protein, lipid, and glucose metabolism, as well as calcium homeostasis. It consists of a network of branching tubules extending from the outer membrane of the nuclear envelope to the plasma membrane. Therefore, it has a large and continuous lumen, which occupies more than 10% of the cell volume. The luminal micro-environment is characteristically different from the cytosol. Besides the presence of ER-related human syndromes, ER dysfunction is associated with a range of neurological disorders, such as multiple sclerosis, Parkinson's, and Huntington's diseases, but the pathogenic mechanisms remain obscure. To allow the study of the ER metabolism in health and diseases, our lab aims to develop a method utilizing magnetic immunopurification (IP) of HA-tagged ER to achieve rapid isolation of pure and intact ER that is compatible with subsequent analysis of their content. By using LC-MS, we can establish a comprehensive map of the human ER proteome, metabolome, and lipidome.
Understanding the contribution of endosomal and ER proteins to lysosome function
ER forms direct contact sites with the plasma membrane and various organelles in eukaryotic cells. The crosstalk between ER and other organelles, including lysosomes, was demonstrated by several studies. ER and lysosomes have divergent roles in cell metabolism; ER operates as a platform for anabolic reactions, whereas lysosomes for catabolic reactions. Our lab focuses on elucidating the functional interplay between ER and lysosomes in the context of metabolic disease. CLN6 is an ER-resident protein and its loss results in a lysosomal storage disease, variant late infantile neuronal ceroid lipofuscinosis (vLINCL). The precise role of CLN6 and how it regulates lysosome integrity remain unclear. By using organelle-specific immunoprecipitation and high-resolution MS, we can capture the abnormal changes in these organelles' content and gain some insights into inter-organelle communication.
Development of therapeutic strategies and biomarkers for metabolic diseases
Most metabolic and genetic disorders cause patients with these disorders to have unmet medical needs. Therefore, it is crucial to make progress in developing novel therapies and biomarkers that can be used to monitor the clinical course of patients with these disorders over time. Our lab, in collaboration with others, is interested in the following: 1) developing small molecule drugs (agonist or antagonist drugs) that target a specific gene and reverse the phenotype and 2) using an ASO-mediated exon-skipping approach that targets storage disorders at the mRNA level and edits out-of-frame transcripts to produce in-frame ones. This approach is an emerging approach to drug development for treating incurable monogenic diseases.
# Equal contribution
1. Laqtom NN. 2023. Studying lysosomal function and dysfunction using LysoIP. Nat Rev Mol Cell Biol. doi.org/10.1038/s41580-023-00619-6
2. Laqtom NN, Dong W, Medoh UN, Cangelosi AL, Dharamdasani V, Chan SH, Kunchok T, Lewis CA, Heinze I, Tang R, Grimm C, Do AND, Porter FD, Ori A, Sabatini DM, AbuRemaileh M. 2022. CLN3 is required for the clearance of glycerophosphodiesters from lysosomes. Nature. 609, 1005–11. doi.10.1038/s41586-022-05221-y
3. Armenta D, Laqtom NN#, Alchemy G, Dong W, Morrow D, Alchemy G, Poltorack C, Nathanson D, Abu-Remalieh M, Dixon SJ. 2022. Ferroptosis inhibition by lysosomal protein catabolism. Cell Chem Biol. 24:S2451-9456(22)00360-9. doi: 10.1016/j.chembiol.2022.10.006.
4. Pedram K, Laqtom NN, Shon DJ, Di Spiezio A, Riley NM, Saftig P, Abu-Remaileh M, Bertozzi, CR. 2022. Discovery of a pathway for endogenous mucin glycodomain catabolism in mammals. PNAS. 119(39):e2117105119.
5. Vest RT, Chou C-C, Zhang H, Haney MS, Li L, Laqtom NN, Chang B, Shuken S, Nguyen A, Yerra L, Yang AC, Green C, Tanga M, Abu-Remaileh M, Bassik MC, Frydman J, Luo J, WyssCoray T. 2022. Small molecule C381 targets the lysosome to reduce inflammation and ameliorate disease in models of neurodegeneration. PNAS. 119 (11) e2121609119.
6. Rogala KB, Gu X, Kedir JF, Abu-Remaileh M, Bianchi LF, Bottino AMS, Dueholm R, Niehaus A, Overwijn D, Fils AP, Zhou SX, Leary D, Laqtom NN, Brignole EJ, Sabatini DM. 2019. Structural basis for the docking of mTORC1 on the lysosomal surface. Science. 366(6464): 468–475.
7. Abu-Remaileh M, Wyant GA, Kim C, Laqtom NN, Abbasi M, Chan SH, Freinkman E, Sabatini DM. 2017. Lysosomal metabolomics reveals v-ATPase and mTOR-dependent mechanisms for the efflux of amino acids from lysosomes. Science. 358(6364):807-813.