Verified Rigor RecordRigor Reviewed

Rigor-Reviewed Manuscript

Selective Molecular Alterations in the Autophagy Pathway in Patients with Lewy Body Disease and in Models of α-Synucleinopathy · 10.1371/journal.pone.0009313

Name: Verified Rigor Record — Selective Molecular Alterations in the Autophagy Pathway in Patients with Lewy Body Disease and in Models of α-Synucleinopathy · 10.1371/journal.pone.0009313
Item: Selective Molecular Alterations in the Autophagy Pathway in Patients with Lewy Body Disease and in Models of α-Synucleinopathy · 10.1371/journal.pone.0009313
Rating: 75
Author: Αlpha¹

Paper source

Read full text

Αlpha¹ Editorial

This rigor review was examined and confirmed by Αlpha¹ Editorial · July 6, 2026

Αlpha¹ Rigor Review

Rigor Reviewed

WARN

Warnings to address · Mixed Methods

Eight dimensions — click a segment for details

Critical

High-priority

Model-reported confidence: highReviewer agreement: moderateEngine: 7.6.0Source: full text

Not verified in this report

No reported statistical tests were found to recompute.
No data or code availability links were detected to verify.

This Αlpha¹ Rigor Review uses AI Rigor Reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

The paper presents a plausible and well-motivated scientific premise linking autophagy dysfunction to DLB pathology, with adequate ethics approvals and a clear rationale. However, critical rigor gaps in study design (missing randomization, power analysis, and incomplete blinding), statistical reporting (no exact p-values, effect sizes, or assumption checks), data availability (no data statement or repository), and key resource identification (missing catalog numbers, RRIDs, cell line authentication) substantially limit the reproducibility and interpretability of the reported findings.

This evaluation synthesizes three independent reviewers who scored all eight dimensions, plus a copyedit pass and verification components (citations, statistics, preregistration, integrity, claim audit). The statistics component covered 0 recomputable tests because the paper reports only threshold p-values without test statistics or degrees of freedom; thus no mathematical verification was possible. The review is based on a full-text manuscript.

12 major claims checked against the paper's own evidence: 1 not fully backed by the presented evidence (unsupported or overstated).

3 integrity concerns flagged (0 high).

Rigor

Eight Dimensions3 pass · 4 warn · 1 fail

12 major claims1 overstated11 supported

The introduction cites multiple prior studies linking autophagy impairment to α-synuclein pathology and highlights that specific molecular components dysregulated in DLB were unknown. The rationale for focusing on mTor and Atg7 is logically derived from prior evidence, and the discussion explicitly acknowledges that the mechanisms through which these alterations occur are not completely clear, indicating a balanced acknowledgment of limitations. All three sub-criteria (prior_work_cited, premise_rationale, limitations_addressed) are reported adequately.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 95% conf

The study clearly establishes its scientific foundation by citing prior work on autophagy in neurodegeneration, providing a logical rationale for investigating mTor and Atg7 in DLB, and addressing unresolved questions from prior research.

Evidence

direct quote[Introduction, paragraph 1 and 2]

“Recent evidence suggests that impairment of lysosomal pathways (i.e. autophagy) involved in α-synuclein clearance might play an important role.”

direct quote[Abstract, Introduction]

“For this reason, we sought to examine the expression levels of members of the autophagy pathway in brains of patients with DLB and Alzheimer's Disease (AD) and in α-synuclein transgenic mice.”

direct quote[Discussion, paragraph 1]

“However it was unclear which molecular components of the autophagy pathway might be dysregulated in the brains of patients with DLB/PD and in α-syn tg models.”

PASSReviewer 2· 90% conf

The study provides a strong scientific premise by citing extensive prior research on α-synuclein accumulation, lysosomal pathways, and autophagy in neurodegenerative diseases, particularly DLB and PD. It clearly establishes the rationale for investigating specific autophagy components.

Evidence

direct quote[Introduction, paragraph 1]

“Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common causes of dementia and movement disorders in the elderly , .”

direct quote[Introduction, paragraph 4]

“Taken together, these lines of evidence suggest that in DLB and PD, specific molecular defects in the autophagy pathway might play a role in the pathogenesis of these disorders.”

direct quote[Introduction, paragraph 4]

“In this context, the main objective of the present study was to investigate alterations in components of the autophagy pathway in DLB and in a-syn tg models.”

PASSReviewer 3· 95% conf

The paper clearly establishes the scientific premise linking autophagy dysfunction to α-synuclein pathology in Lewy body disease, citing prior work and outlining a logical rationale.

Evidence

direct quote[Introduction, paragraphs 1–5]

“Impaired clearance of the α-syn aggregates might play an important role in the pathogenesis of PD and DLB , . Among the lysosomal pathways involved, the autophagy signaling cascade has emerged as a key mechanism for the removal of α-syn aggregates.”

direct quote[Introduction, final paragraph]

“the main objective of the present study was to investigate alterations in components of the autophagy pathway in DLB and in a-syn tg models.”

direct quote[Discussion, paragraph 1]

“However it was unclear which molecular components of the autophagy pathway might be dysregulated in the brains of patients with DLB/PD and in α-syn tg models.”

The human tissue component is observational and lacks a pre-specified analysis plan; blinding is mentioned for code-breaking after analysis but not for investigators during data collection. Power analysis is absent. Inclusion/exclusion criteria are provided for human cases via clinico-pathological definitions, and controls are appropriate. Biological vs. technical replication is not explicitly distinguished. The in vitro experiments state triplicates, but independence is unclearly defined. Randomization is not applicable to the human cohort. The animal experiments mention blind-coded sections for neurodegeneration analysis but not for other analyses.

Sub-criteria

controlsADEQUATE

power analysisNOT REPORTED

blinding levelsINADEQUATE

outlier handlingNOT REPORTED

randomization unitN/A

inclusion exclusionADEQUATE

randomization methodN/A

replicate distinctionNOT REPORTED

independent replicationNOT REPORTED

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 85% conf

The study fails to report key design elements such as randomization, blinding for most analyses, a priori power analysis, replicate distinction, outlier handling, and independent replication, though inclusion/exclusion criteria and controls are adequate.

Evidence

direct quote[Materials and Methods, Cases and Neuropathological Evaluation]

“All cases met the Consortium to Establish a Registry for AD (CERAD) and National Institute of Aging (NIA) criteria for diagnosis and displayed neuritic plaques and tangle formation in the neocortex and limbic system.”

direct quote[Materials and Methods, Analysis of Neurodegeneration]

“The immunolabeled blind-coded sections were imaged with the LSCM (MRC1024, Bio-Rad) and analyzed with the Image 1.43 program (NIH)”

direct quote[Materials and Methods, α-Synuclein Transgenic Mice and Treatments]

“For western blot and immunocytochemical studies levels of components of the autophagy pathway were compared to littermate non tg controls and to an APP tg model (line J9M) of AD-like pathology.”

WARNReviewer 2· 70% conf

The study design for animal and cell culture experiments includes controls and distinguishes replicates, but lacks explicit reporting of randomization methods, blinding levels, and power analysis. The human tissue analysis is observational and appropriately described.

Evidence

direct quote[Materials and Methods, Analysis of Neurodegeneration]

“To evaluate the integrity of the dendritic system, blind-coded 40µm-thick vibratome sections from mouse brains fixed in 4% PFA were immunolabeled with the mouse monoclonal antibody against microtubule associated protein 2 (MAP2) (dendritic marker, 1∶40, Millipore), as previously described .”

direct quote[Materials and Methods, a-Synuclein Transgenic Mice and Treatments]

“For western blot and immunocytochemical studies levels of components of the autophagy pathway were compared to littermate non tg controls and to an APP tg model (line J9M) of AD-like pathology.”

direct quote[Materials and Methods, Cases and Neuropathological Evaluation]

“The study included a total of 24 cases (); of them, 6 were non-demented controls, 12 were DLB cases and the other 6 were AD cases.”

WARNReviewer 3· 85% conf

The study design is descriptive for human tissue and interventional for animal/cell models, but several key elements (blinding, power analysis, replication distinction) are inadequately reported.

Evidence

direct quote[Materials and Methods, Statistical Analysis]

“All experiments were conducted in triplicate on blind-coded samples. After the results were obtained, the code was broken and data were analyzed”

absence[Materials and Methods]

No power analysis is reported.

direct quote[Materials and Methods, Cases and Neuropathological Evaluation]

“cases were subdivided into: 1) non-demented age-matched controls, 2) AD cases, and 3) DLB cases. All cases met the Consortium to Establish a Registry for AD (CERAD) and National Institute of Aging (NIA) criteria for diagnosis”

For human cases, age, gender, brain weight, PMT, and disease duration are provided. For mice, the species (heterozygous tg mice, Line D, expressing human wildtype α-syn under PDGFβ promoter) and control strains (littermate non tg, APP tg model line J9M) are specified. The cell line (rat neuroblastoma B103) is also identified.

Sub-criteria

demographicsADEQUATE

sex reportedADEQUATE

sex justifiedN/A

age weight healthADEQUATE

housing conditionsNOT REPORTED

species strain sourceADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

Human biological variables (sex, age, health status) are partially reported, but mouse sex, strain background, and housing conditions are not reported, resulting in inadequate coverage of applicable sub-criteria.

Evidence

direct quote[Table 1, Cases and Neuropathological Evaluation]

“Diagnosis N = Mean Age (yrs) Mean brain weight Gender M/F ... Control 6 79.8±2 1150±115 4/2 ... AD 6 81±1 1058±97 3/3 ... DLB 12 82.7±2 1074±119 4/8”

direct quote[Materials and Methods, α-Synuclein Transgenic Mice and Treatments]

“heterozygous tg mice (Line D) expressing human wildtype α-syn under the regulatory control of the PDGFβ promoter were used.”

absence[Materials and Methods, α-Synuclein Transgenic Mice and Treatments]

Mouse sex is not reported.

PASSReviewer 2· 90% conf

Biological variables for human subjects, animal models, and cell lines are adequately reported, including demographics, species, strain, and source.

Evidence

direct quote[Table 1]

“Diagnosis N = Mean Age (yrs) Mean brain weight Gender M/F Mean PMT (hrs) Mean Duration (yrs) Blessed score Frontal cortex Amyloid Plaques (0.1sq mm) Temporal cortex Lewy bodies (0.1sq mm) Control 6 79.8±2 1150±115 4/2 6.5±2 NA 0–1 0 0 AD 6 81±1 1058±97 3/3 8±1 12.8±1 19–33 50 0 DLB 12 82.7±2 1074±119 4/8 7.2±1.5 9.8± 5–32 33 12±2”

direct quote[Materials and Methods, a-Synuclein Transgenic Mice and Treatments]

“For this study, heterozygous tg mice (Line D) expressing human wildtype α-syn under the regulatory control of the PDGFβ promoter were used.”

direct quote[Materials and Methods, Cell Culture and Treatments]

“For in vitro experiments we used the previously described rat neuroblastoma cell line B103 .”

PASSReviewer 3· 90% conf

Human demographics, age, sex, postmortem interval, and diagnostic criteria are well reported; animal models are described in detail.

Evidence

direct quote[Materials and Methods, Table 1]

“Table 1 Summary of clinico-pathological characteristics. Diagnosis N = Mean Age (yrs) Mean brain weight Gender M/F Mean PMT (hrs) Mean Duration (yrs)”

direct quote[Materials and Methods, α-Synuclein Transgenic Mice and Treatments]

“heterozygous tg mice (Line D) expressing human wildtype α-syn under the regulatory control of the PDGFβ promoter were used.”

absence[Materials and Methods]

Housing conditions for mice are not described.

The study reports approval by the UCSD Institutional Review Board for human studies, with written informed consent obtained. Animal studies were approved by the UCSD Institutional Animal Care and Use Committee, adhering to good animal practice and NIH guidelines.

Sub-criteria

iacuc statementADEQUATE

informed consentADEQUATE

irb ethics statementADEQUATE

regulatory complianceADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 95% conf

Ethical approvals are adequately reported: human tissue use was approved by a named IRB (UCSD) with informed consent, and animal procedures were approved by a named IACUC (UCSD), with regulatory compliance stated.

Evidence