Whole Genome Analysis Nets New Lewy Body Dementia Gene

Whole-genome sequencing detects single nucleotide variants but tends to miss larger changes, such as deletions, insertions, duplications, and inversions. Using a new machine-learning method to analyze WGS data, researchers led by Sonja Scholz at the National Institute of Neurological Disorders and Stroke in Bethesda, Maryland, found a whopping 160,000 such structural variants in the human genome. In the May 4 Cell Genomics, they reported that one common structural variant, a deletion in the TPCN1 gene, associated with Lewy body dementia. A separate analysis netted 160 rare structural changes among 50 genes linked to neurodegenerative diseases, including LBD and FTD/ALS. All the variants can be found in a publicly available dataset.

  • Whole-genome sequencing found 160,000 structural variants.
  • Most are common; one tracks with LBD.
  • One hundred and sixty rare structural variants found in risk genes for LBD and FTD/ALS.

“This tour de force is the first study assessing the association of structural variants with different types of dementia and is a huge resource to the field,” said Céline Bellenguez and Jean-Charles Lambert at Université de Lille, France. Peter Nelson, University of Kentucky, Lexington, noted that there had not yet been a good GWAS on structural variants in non-Alzheimer’s disease pathology. “This type of analysis constitutes an important new paradigm in genomic investigation,” he told Alzforum.

Co-first authors Karri Kaivola of NINDS, Ruth Chia and Jinhui Ding of the National Institute on Aging, Bethesda, analyzed whole-genome sequencing data from about 2,600 people with LBD, 2,600 with FTD/ALS, and 4,100 controls. Most were in their early- to mid-70s and of European ancestry. The effort involved more than 50 authors from three consortia. It was co-led by Bryan Traynor and Raphael Gibbs at the NIA, Clifton Dalgard of the Uniformed Services University of the Health Sciences, Bethesda, and Owen Ross at the Mayo Clinic, Jacksonville, Florida.

To map structural variants (SVs), the scientists used the Genome Analysis Toolkit’s Structural Variant pipeline. GATK-SV uses machine learning to combine five different SV detection algorithms to better detect variants in short-read WGS data (Abel et al., 2020). Short-read sequencing identifies snippets of DNA, usually a few hundred base pairs long, then pieces together overlapping segments to reconstitute the genome.

All Shapes and Sizes. In FTD/ALS, the five main types of structural gene variant—deletions (red), duplications (blue), insertions (purple), inversions (orange), and complex variants (green)—range from 50 base pairs to 1 million. An almost identical pattern and distribution occurred for SVs in LBD cases. [Courtesy of Kaivola et al., Cell Genomics, 2023.]

The GATK-SV analysis unearthed almost 151,000 structural variants (SVs) among LBD cases and controls and 159,000 in the FTD/ALS cohort (see image above). On average, each person had about 880 in his or her genome. “We were intrigued to see how common structural variants are in the human genome, many of which have never been catalogued before, and little is known about the role of these variants in human health and disease,” Scholz wrote to Alzforum.

For both LBD and FTD/ALS cases, half the SVs were deletions, one-fifth were duplications, one-sixth were insertions, and the rest were made up of inversions, complex SVs, and unresolved structural changes.

Of the nearly 160,000 SVs, 96 percent were rare, with an allele frequency below 1 percent. Curious if any fell within known neurodegenerative risk genes, the researchers scanned 50 such genes, including APP, PSEN1, PSEN2, GBA, and SOD1. Among them, they detected 83 exonic SVs in LBD cases and 81 in people with FTD/ALS. For example, one person with LBD carried the duplication in the α-synuclein gene that is known to cause Parkinson's disease. Two FTD/ALS cases carried rare deletions in CHCHD10 or FIG4, genes known to cause the diseases if both alleles contain missense mutations. “This study demonstrates the utility of using short-read WGS for structural variant discovery and sheds light on the role of structural variants,” wrote Vivek Swarup, University of California, Irvine (comment below).

SV GWAS. Only C9ORF72 and MAPT variants were genome-wide significant for FTD/ALS (top). For LBD, a TPCN1 variant met the threshold (bottom). [Courtesy of Kaivola et al., Cell Genomics, 2023.]

Four percent of SVs were common, namely 4,700 from the FTD/ALS cohort and 4,900 from the LBD cohort. When the scientists queried which ones appeared more frequently in cases than controls, they found two known causal variants for FTD/ALS—the hexanucleotide repeat expansion in C9ORF72, and a 673 kilobase inversion in MAPT (see image above). “Seeing these as signals in our FTD/ALS cohort served as proof of principle and confirmed that the GATK-SV pipeline is working,” said Scholz.

However, for LBD, out popped a 309-base-pair deletion within intron 2 of TPCN1, which had not previously been linked to the disease. This gene encodes two-pore segment channel 1, an ion channel within the endolysosomal membranes of neurons and glia.

Scientists debate whether TPCN1 releases calcium or sodium ions from the organelles and what the channel responds to, be it voltage changes, phosphatidylinositol, or the small molecule NAADP (Patel et al., 2023; Patel et al., 2022; Feng et al., 2022; Wang and Zhu, 2023). The TPCN1 deletion occurred in 7 percent of LBD cases. Prior research has implicated dysfunctional endolysosomal trafficking in the pathogenesis of LBD, making TPCN1 a plausible new risk gene, Scholz noted.

Others agreed. “These genetic findings further support the importance of the endosomal/lysosomal system in neurodegeneration, likely related to dysregulated calcium signaling and autophagy defects,” wrote Ilya Bezprozvanny, University of Texas Southwestern Medical Center, Dallas. He recently reported such calcium/autophagy dysfunction in Alzheimer’s disease (Mar 2023 news).

In a recent GWAS, Bellenguez and Lambert linked AD to an SNP within TPCN1, rs6489896. It lies 36 kilobases away from the deletion, suggesting the gene might be important in multiple related diseases (Apr 2022 news). “The exciting work [by Kaivola and colleagues pits] endolysosomal deficits as a common mechanistic link between shared phenotypes in LBD and Alzheimer’s disease,” wrote Grace (Beth) Stutzmann and Sarah Mustaly, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois (comment below).

Nelson and colleagues had found a trend, if not a statistically significant association, for the same TPCN1 SNP with limbic-predominant age-related TDP-43 neuropathologic changes (LATE-NC; Katsumata et al., 2022). The SNP did not associated with Parkinson’s disease, however (Nalls et al., 2019). “We didn’t see this SNP associated with Lewy bodies in our study either, which might be why it is not associated with PD,” Nelson told Alzforum.

While TPCN1 has not been linked to AD pathology, TPCN2 has. In human cells with faulty or no presenilin, it becomes overactive, causing lysosome alkalization and poor amyloid clearance (Tong et al., 2021; Neely Kayala et al., 2012). 

Searching the Genotype-Tissue Expression (GTEx) database for gene-expression changes in brain tissue linked to the rs6489896 SNP in TPCN1, Kaivola and colleagues saw decreased expression of the nearby gene RITA1 in excitatory neurons. RITA1 encodes a tubulin-binding protein that tamps down Notch signaling, which controls cell differentiation and intracellular protein trafficking. Notch is also cleaved by γ-secretase, the protease that uses presenilin to chop up amyloid precursor protein. Less RITA1 might mean more Notch signaling and dysregulated protein handling in neurons. To Scholz, this data suggests that LBD risk may not only be driven by TPCN1 but possibly a combination of genes within this locus.

Scholz plans to expand this analysis to include more participants, especially those with diverse ancestry, and incorporate multi-omics and cell biology data to learn how the TPCN1 deletion relates to LBD risk.—Chelsea Weidman Burke

Comments

  1. The main takeaway from this study is the identification and characterization of structural variants in non-Alzheimer's dementias, specifically Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). By applying a multi-algorithm pipeline (GATK-SV) to short-read whole-genome sequence data, the researchers were able to identify a novel risk locus for LBD, a deletion in TPCN1, and confirm known structural variants at the C9ORF72 and MAPT loci associated with FTD/ALS. They also discovered rare pathogenic structural variants in both LBD and FTD/ALS.

    One surprising finding was the association of a 309-base-pair deletion in TPCN1 with LBD. TPCN1 encodes an ion channel expressed in neuronal and glial endo-lysosomal membranes. This deletion may have potential implications for Alzheimer's disease, as a suggestive association between the intronic TPCN1 variant rs6489896 and Alzheimer's disease was reported in a recent GWAS. The TPCN1 locus did not correlate with Parkinson's disease, indicating that the deletion might not be specific to LBD. The study also identified rare structural variants in neurodegenerative disease genes, such as SNCA duplications in Parkinson's disease and LBD, and OPTN deletions in FTD and ALS.

    The results of this study highlight the value of studying structural variants in understanding the underlying pathogenesis of non-Alzheimer's dementia. The researchers have also provided an interactive resource that can be investigated by other researchers for new insights into these dementias. However, there are limitations to the study, stemming from the inherent difficulty of calling structural variants from short-read whole-genome sequencing data. Despite these challenges, this study demonstrates the utility of using short-read whole-genome sequencing for structural variant discovery and sheds light on the role of structural variants in non-Alzheimer's dementias.

    View all comments by Vivek Swarup

  2. This is a very interesting finding, though I’ll note that TPC1 two-pore channels are not voltage-gated calcium channels; the reference [34] in the paper is outdated. Rather, they are PI(3,5)P2-activated Na+ channels that function mainly in endosomes, see ref [37] in the paper and see also a more recent review article that describes their function (Wang et al., 2023). 

    Overall, these genetic findings further support the importance of the endosomal/lysosomal system in neurodegeneration. The likely mechanism is related to autophagic defects. We recently published a connection between dysregulated calcium signaling and autophagy defects in AD as discussed on Alzforum (Mar 2023 news). 

    In the case of Lewy body dementia and frontotemporal dementia/amyotrophic lateral sclerosis examined by Kaivola, their discovery of the TPC1 locus points to a more direct connection with dysfunction of the endosomal/lysosomal/autophagy pathway.

    References:

    Wang Q, Zhu MX. NAADP-Dependent TPC Current. Handb Exp Pharmacol. 2023;278:35-56. PubMed.

    View all comments by Ilya Bezprozvanny

  3. This is exciting work that continues to show endo-lysosomal deficits in neurodegenerative diseases and serves as a common mechanistic link between shared phenotypes in LBD and AD. TPCN1 encodes the two-pore channels (TPC) which are present on endo-lysosomal vesicles. Release of Ca2+ from lysosomal stores via TPC channels plays a role in autophagy-degradation, lysosomal acidification and proteolysis, vesicle fusion, etc., all of which are important in reducing misfolded and damaged proteins.

    In LBD, the deletion of TPCN1 would therefore likely have downstream consequences on protein clearance and increased cellular stress. Recent work by Tong et al., 2022, claimed that inhibition of TPC in cells expressing mutant PSEN1 restored the reduced lysosomal Ca2+ release and acidified lysosomes, thereby rescuing autophagy. This work was similar to that of Ralph Nixon’s group (Lee et al., 2010, 2015) where they showed that regulating the hyperactive TRPML1 (another lysosomal Ca2+ efflux channel) restored lysosomal acidic pH and calcium release, as well as autophagic clearance. Therefore, TPC loss can disrupt calcium and proton balance, the electrochemical gradient of the lysosomes, and its downstream function.

    Other channels, including the vacuolar-ATPase (vATPase), maintain this gradient as well. Cytosolic rise in Ca2+ concentrations is present in early stages of Alzheimer’s and disrupts the vATPase function and lysosomal acidification (Mustaly-Kalimi et al., 2022), which can have downstream effects on TPC and lysosomal Ca2+ regulation.

    In this paper, the authors also suggested that TPCN1 deletion could disrupt RITA1 and notch signaling. This is interesting, as disruption in notch signaling is thought to play a role in vascular damage in AD. Therefore, there is a  possible link between endo-lysosomal disruption and neurovascular-related dementia (Kapoor and Nation, 2020). 

    References:

    Kapoor A, Nation DA. Role of Notch signaling in neurovascular aging and Alzheimer's disease. Semin Cell Dev Biol. 2020 Dec 28; PubMed.

    Lee JH, McBrayer MK, Wolfe DM, Haslett LJ, Kumar A, Sato Y, Lie PP, Mohan P, Coffey EE, Kompella U, Mitchell CH, Lloyd-Evans E, Nixon RA. Presenilin 1 Maintains Lysosomal Ca(2+) Homeostasis via TRPML1 by Regulating vATPase-Mediated Lysosome Acidification. Cell Rep. 2015 Sep 1;12(9):1430-44. Epub 2015 Aug 20 PubMed.

    Lee JH, Yu WH, Kumar A, Lee S, Mohan PS, Peterhoff CM, Wolfe DM, Martinez-Vicente M, Massey AC, Sovak G, Uchiyama Y, Westaway D, Cuervo AM, Nixon RA. Lysosomal proteolysis and autophagy require presenilin 1 and are disrupted by Alzheimer-related PS1 mutations. Cell. 2010 Jun 25;141(7):1146-58. PubMed.

    Mustaly-Kalimi S, Gallegos W, Marr RA, Gilman-Sachs A, Peterson DA, Sekler I, Stutzmann GE. Protein mishandling and impaired lysosomal proteolysis generated through calcium dysregulation in Alzheimer's disease. Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2211999119. Epub 2022 Nov 28 PubMed.

    Tong BC, Wu AJ, Huang AS, Dong R, Malampati S, Iyaswamy A, Krishnamoorthi S, Sreenivasmurthy SG, Zhu Z, Su C, Liu J, Song J, Lu JH, Tan J, Pan W, Li M, Cheung KH. Lysosomal TPCN (two pore segment channel) inhibition ameliorates beta-amyloid pathology and mitigates memory impairment in Alzheimer disease. Autophagy. 2021 Jul 27;:1-19. PubMed.

    View all comments by Sarah Mustaly View all comments by Grace Stutzmann

Make a Comment

To make a comment you must login or register.

References

News Citations

  1. Could Calming Overactive Ryanodine Receptor Restore Autophagy?
  2. Paper Alert: Massive GWAS Meta-Analysis Published

Paper Citations

  1. Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, NHGRI Centers for Common Disease Genomics, Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020 Jul;583(7814):83-89. Epub 2020 May 27 PubMed.
  2. Patel S, Zissimopoulos S, Marchant JS. Endo-Lysosomal Two-Pore Channels and Their Protein Partners. Handb Exp Pharmacol. 2023;278:199-214. PubMed.
  3. Patel S, Yuan Y, Gunaratne GS, Rahman T, Marchant JS. Activation of endo-lysosomal two-pore channels by NAADP and PI(3,5)P2. Five things to know. Cell Calcium. 2022 May;103:102543. Epub 2022 Jan 25 PubMed.
  4. Feng X, Xiong J, Cai W, Tian JB, Zhu MX. The Three Two-Pore Channel Subtypes from Rabbit Exhibit Distinct Sensitivity to Phosphoinositides, Voltage, and Extracytosolic pH. Cells. 2022 Jun 23;11(13) PubMed.
  5. Wang Q, Zhu MX. NAADP-Dependent TPC Current. Handb Exp Pharmacol. 2023;278:35-56. PubMed.
  6. Katsumata Y, Shade LM, Hohman TJ, Schneider JA, Bennett DA, Farfel JM, Alzheimer’s Disease Genetics Consortium, Kukull WA, Fardo DW, Nelson PT. Multiple gene variants linked to Alzheimer's-type clinical dementia via GWAS are also associated with non-Alzheimer's neuropathologic entities. Neurobiol Dis. 2022 Nov;174:105880. Epub 2022 Sep 30 PubMed.
  7. Nalls MA, Blauwendraat C, Vallerga CL, Heilbron K, Bandres-Ciga S, Chang D, Tan M, Kia DA, Noyce AJ, Xue A, Bras J, Young E, von Coelln R, Simón-Sánchez J, Schulte C, Sharma M, Krohn L, Pihlstrøm L, Siitonen A, Iwaki H, Leonard H, Faghri F, Gibbs JR, Hernandez DG, Scholz SW, Botia JA, Martinez M, Corvol JC, Lesage S, Jankovic J, Shulman LM, Sutherland M, Tienari P, Majamaa K, Toft M, Andreassen OA, Bangale T, Brice A, Yang J, Gan-Or Z, Gasser T, Heutink P, Shulman JM, Wood NW, Hinds DA, Hardy JA, Morris HR, Gratten J, Visscher PM, Graham RR, Singleton AB, 23andMe Research Team, System Genomics of Parkinson's Disease Consortium, International Parkinson's Disease Genomics Consortium. Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet Neurol. 2019 Dec;18(12):1091-1102. PubMed.
  8. Tong BC, Wu AJ, Huang AS, Dong R, Malampati S, Iyaswamy A, Krishnamoorthi S, Sreenivasmurthy SG, Zhu Z, Su C, Liu J, Song J, Lu JH, Tan J, Pan W, Li M, Cheung KH. Lysosomal TPCN (two pore segment channel) inhibition ameliorates beta-amyloid pathology and mitigates memory impairment in Alzheimer disease. Autophagy. 2021 Jul 27;:1-19. PubMed.
  9. Neely Kayala KM, Dickinson GD, Minassian A, Walls KC, Green KN, Laferla FM. Presenilin-null cells have altered two-pore calcium channel expression and lysosomal calcium: implications for lysosomal function. Brain Res. 2012 Dec 13;1489:8-16. PubMed.

External Citations

  1. publicly available dataset

Further Reading

No Available Further Reading

Primary Papers

  1. Kaivola K, Chia R, Ding J, Rasheed M, Fujita M, Menon V, Walton RL, Collins RL, Billingsley K, Brand H, Talkowski M, Zhao X, Dewan R, Stark A, Ray A, Solaiman S, Alvarez Jerez P, Malik L, Dawson TM, Rosenthal LS, Albert MS, Pletnikova O, Troncoso JC, Masellis M, Keith J, Black SE, Ferrucci L, Resnick SM, Tanaka T. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias. https://doi.org/10.1016/j.xgen.2023.100316 Cell Genomics

Annotate

To make an annotation you must Login or Register.