Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway
Open accessAbstract
The autophagy-lysosomal pathway (ALP) regulates cell homeostasis and plays a crucial role in human diseases, such as lysosomal storage disorders (LSDs) and common neurodegenerative diseases. Therefore, the identification of DNA sequence variations in genes involved in this pathway and their association with human diseases would have a significant impact on health. To this aim, we developed Lysoplex, a targeted next-generation sequencing (NGS) approach, which allowed us to obtain a uniform and accurate coding sequence coverage of a comprehensive set of 891 genes involved in lysosomal, endocytic, and autophagic pathways. Lysoplex was successfully validated on 14 different types of LSDs and then used to analyze 48 mutation-unknown patients with a clinical phenotype of neuronal ceroid lipofuscinosis (NCL), a genetically heterogeneous subtype of LSD. Lysoplex allowed us to identify pathogenic mutations in 67% of patients, most of whom had been unsuccessfully analyzed by several sequencing approaches. In addition, in 3 patients, we found potential disease-causing variants in novel NCL candidate genes. We then compared the variant detection power of Lysoplex with data derived from public whole exome sequencing (WES) efforts. On average, a 50% higher number of validated amino acid changes and truncating variations per gene were identified. Overall, we identified 61 truncating sequence variations and 488 missense variations with a high probability to cause loss of function in a total of 316 genes. Interestingly, some loss-of-function variations of genes involved in the ALP pathway were found in homozygosity in the normal population, suggesting that their role is not essential. Thus, Lysoplex provided a comprehensive catalog of sequence variants in ALP genes and allows the assessment of their relevance in cell biology as well as their contribution to human disease.
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The lysosomal biogenesis list resulted from an extensive literature analysis combining data that underwent previous experimental validation.
“The “lysosomal biogenesis list” resulted instead from an extensive literature analysis, obtained by combining data that underwent previous experimental validation [15, 18, 19, 28–30].”
From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [15]
The Results section ('Generation of the ALP gene list'; page not provided) says the Lysoplex list drew on literature searches, and Materials and Methods ('Selection of Lysoplex genes'; page not provided) includes previously described lysosomal genes. But the paper also says it added genes based on bioinformatic predictions; it does not establish that the list as a whole combined previously experimentally validated data, or identify it as a distinct 'lysosomal biogenesis list.' (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe list for the evaluation of "lysosomal biogenesis" was created from literature by combining data that underwent preceding experimental validation.
“Similarly, the list for the evaluation of “lysosomal biogenesis” was created from literature by combining data that underwent preceding experimental validation [15, 18, 19, 28–30].”
From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [15]
In Results, ‘Generation of the ALP gene list’ (page unavailable), the paper says it assembled a gene list using literature searches alongside bioinformatic predictions. In Materials and Methods, ‘Selection of Lysoplex genes’ (page unavailable), it says predicted lysosomal candidates were added to that list. It does not describe a distinct ‘lysosomal biogenesis’ evaluation list or say that all combined data had undergone prior experimental validation. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe authors curated a comprehensive and up-to-date annotated gene list for the autophagy pathway by combining previously published gene lists, recent publications, and bioinformatics tools.
“herein we have curated a comprehensive and up-to-date annotated gene list for autophagy pathway, by combining previously published gene lists [15], most recent publications in the field (reported in the excel file) [8] and bioinformatics tools.”
From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [15]
The authors identified 26 targets to assess the state of lysosomal biogenesis.
“Hence, for the second sub-lists, we identified 26 targets to assess the state of lysosomal biogenesis (Fig. 2) at variance with the autophagy activation list, this sub-list has been realized by only comparing data from recent work, in which mRNA levels of lysosomal genes in response to autophagy enhancement were accurately and experimentally examined [15, 18, 19, 28–30].”
From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [15]
The Methods section (‘Selection of Lysoplex genes’; page unavailable) describes selecting genes for a DNA-variation toolkit, but does not identify 26 targets for assessing lysosomal biogenesis. Searches for ‘26 targets’ and lysosomal-gene mRNA responses found no passage establishing that claim. In the citing sentence, ‘we identified 26 targets’ also appears to describe the citing authors’ own selection, rather than a finding attributed to this paper. (LLM, conf=0.77)
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- Authors
- Di Fruscio, G., Schulz, A., De Cegli, R., Savarese, M., Mutarelli, M., Parenti, G., Banfi, S., Braulke, T., Nigro, V., & Ballabio, A.
- Affiliations
- University Medical Center Hamburg-Eppendorf (DE)
- University of Campania "Luigi Vanvitelli" (IT)
- Telethon Institute Of Genetics And Medicine (IT)
- Baylor College of Medicine (US)
- Corresponding author
- Schulz, Angela
- Ballabio, Andrea
- ORCID
- Venue
- Autophagy
- Publisher
- Informa UK Limited
- Published
- 2015-06-03
- Volume
- 11
- Issue
- 6
- Pages
- 928-938
- ISSN
- 1554-8627 (ISSN-L)
- 1554-8635
- PMC
- PMC4502703
- OpenAlex
- W1566223979
- Cited by
- 62
- References
- 101
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 7 · 2023: 3 · 2022: 6 · 2021: 7 · 2020: 7 · 2019: 2 · 2018: 7 · 2017: 6 · 2016: 8 · 2015: 1
- FWCI
- 5.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Autophagy (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca - Università degli Studi della Campania "Luigi Vanvitelli" (submittedVersion)
- Funders
- Team Sanfilippo Foundation
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Health Sciences › Medicine › Physiology › Lysosomal Storage Disorders Research
- Health Sciences › Medicine › Rheumatology › Glycogen Storage Diseases and Myoclonus
- Keywords
- autophagy-lysosome pathway, lysosomal storage disease, neuronal ceroid lipofuscinosis, targeted next-generation sequencing, loss-of-function mutations, truncating mutations, missense mutations, candidate genes, homozygosity
- MeSH terms
- Amino Acid Sequence, Autophagy, Base Sequence, DNA, Homozygote, Humans, Lysosomes, Mutation, Neuronal Ceroid-Lipofuscinoses, Lysosomal Storage Diseases
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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