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LncRNA MALAT1 acts as an oncogene in multiple myeloma through sponging miR-509-5p to modulate FOXP1 expression · 10.18632/oncotarget.21957

Name: Verified Rigor Record — LncRNA MALAT1 acts as an oncogene in multiple myeloma through sponging miR-509-5p to modulate FOXP1 expression · 10.18632/oncotarget.21957
Item: LncRNA MALAT1 acts as an oncogene in multiple myeloma through sponging miR-509-5p to modulate FOXP1 expression · 10.18632/oncotarget.21957
Rating: 63
Author: Αlpha¹

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Αlpha¹ Editorial

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

Αlpha¹ Rigor Review

Rigor Reviewed

WARN

Warnings to address · Interventional Study

Eight dimensions — click a segment for details

Critical

High-priority

Model-reported confidence: moderateReviewer 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's scientific premise is sound, and the methods are described in enough detail for replication. However, the study suffers from critical reporting gaps: statistical analysis lacks exact p-values, effect sizes, and assumption verification; study design elements like randomization, blinding, and power analysis are absent; data and code are not deposited; and one cited reference is retracted. The conclusions overstate the clinical applicability of the findings.

Eight dimensions were evaluated based on the full-text manuscript. No dimension was not applicable. The three independent reviewers largely converged; divergence on study design (warn vs. fail) and biological variables (warn vs. fail) were resolved by weighing the combined evidence. The statistics verification component was non-contributory because only threshold p-values were reported, preventing recomputation. A retracted citation was identified by the citation checker.

12 major claims checked against the paper's own evidence: 4 not fully backed by the presented evidence (unsupported or overstated).

5 integrity concerns flagged (1 high).

Rigor

Eight Dimensions1 pass · 5 warn · 2 fail

12 major claims4 overstated1 partial7 supported

The paper cites prior studies showing MALAT1's role in multiple myeloma and other cancers, and clearly states that the underlying mechanism remains unclear, providing a logical rationale for the study.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The paper establishes a clear scientific premise by citing prior work on MALAT1's role in multiple myeloma and other cancers, and provides a rationale for investigating the underlying mechanism.

Evidence

direct quote[Introduction, paragraph 2]

“Previous studies showed that Metastasis associated lung adenocarcinoma transcript 1(MALAT1) acted as an oncogene in Multiple Myeloma (MM). However, the underlying mechanism of MALAT1 in MM remains unclear.”

direct quote[Introduction, last paragraph]

“However, the functional role and underlying mechanism of MALAT1 in MM remains unclear.”

absence[Introduction]

Limitations of prior research are not explicitly discussed

PASSReviewer 2· 90% conf

The scientific premise is adequately established. Prior work on MALAT1 in MM is cited, and the rationale for investigating the ceRNA mechanism is clear. However, the paper does not explicitly discuss how it addresses limitations of prior studies.

Evidence

direct quote[Introduction, paragraph 4]

“Liu et al showed that down-regulation of MALAT1 inhibited proliferation and induced apoptosis in MM. Furthermore, Cho et al showed that lncRNA MALAT1 was overexpressed in MM and might serve as a marker to predict disease progression.”

direct quote[Introduction, paragraph 4]

“However, the underlying mechanism of MALAT1 in MM remains unclear.”

absence[Introduction]

Limitations of prior work are not specifically addressed.

PASSReviewer 3· 95% conf

The scientific premise is well-established with adequate citations and rationale.

Evidence

direct quote[Introduction, paragraphs 2-4]

“Previous studies showed that Metastasis associated lung adenocarcinoma transcript 1(MALAT1) acted as an oncogene in Multiple Myeloma (MM).”

direct quote[Abstract]

“However, the underlying mechanism of MALAT1 in MM remains unclear.”

direct quote[Introduction, last sentence]

“However, the functional role and underlying mechanism of MALAT1 in MM remains unclear.”

The paper does not mention randomization for animal assignment or in vitro experiments. Blinding is not described. No a priori power analysis or sample size calculation is provided. Inclusion/exclusion criteria for patient samples are not stated. Outlier handling is omitted. Replicate distinction is only stated as 'each experiment was repeated at least three times' without defining biological vs technical replication. Positive/negative controls are present (sh-NC, normal plasma cells). No independent replication is reported.

Sub-criteria

controlsADEQUATE

power analysisNOT REPORTED

blinding levelsNOT REPORTED

outlier handlingNOT REPORTED

randomization unitNOT REPORTED

inclusion exclusionNOT REPORTED

randomization methodNOT REPORTED

replicate distinctionINADEQUATE

independent replicationNOT REPORTED

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

The study design has adequate elements for cell line and xenograft experiments, but lacks several key rigor components such as randomization, blinding, power analysis, and clearly defined inclusion/exclusion criteria.

Evidence

absence[Tumor xenograft formation assay]

No randomization method reported for xenograft experiment

absence[Materials and Methods]

Blinding is not described for any experiment

direct quote[Plasmid construction and transfection]

“miR-509-5p mimics, miR-509-5p inhibitor, lentiviruses short hairpin (shRNA) directed against MALAT1 (sh-MALAT1) and the empty lentiviral vector (sh-NC) were chemically synthesized”

FAILReviewer 2· 95% conf

The study design lacks fundamental rigor elements. No randomization, blinding, power analysis, inclusion/exclusion criteria, or outlier handling are reported. Only controls and replicate distinction are partially addressed.

Evidence

absence[Methods, Tumor xenograft formation assay]

No randomization method is described for animal or cell experiments.

absence[Methods]

Blinding is not mentioned.

direct quote[Methods, Statistical analyses]

“Each experiment was repeated at least three times.”

FAILReviewer 3· 85% conf

Many key design elements are missing: no randomization, blinding, power analysis, replication, or outlier handling.

Evidence

absence[Materials and Methods, Cell culture and transfection]

No randomization method described for in vivo or in vitro experiments.

absence[Materials and Methods]

No blinding described.

direct quote[Materials and Methods, Statistical analyses]

“Each experiment was repeated at least three times.”

For the xenograft model, the paper reports using male athymic BALB/c mice, 5-week-old, with no weight information. For human samples (37 MM patients, 19 controls), no demographics (e.g., age, sex, comorbidities) are provided. Housing conditions for mice (light cycle, temperature, enrichment) are not described. The single-sex animal study (male only) is not justified.

Sub-criteria

demographicsNOT REPORTED

sex reportedINADEQUATE

sex justifiedNOT REPORTED

age weight healthINADEQUATE

housing conditionsNOT REPORTED

species strain sourceADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The paper reports sex (male mice) and species/strain (BALB/c), but lacks age/weight details for mice beyond '5-week-old,' and does not provide demographics for human patients beyond sample size.

Evidence

direct quote[Tumor xenograft formation assay]

“Male athymic BALB/c mice, 5-week-old, were purchased from the Shanghai Experimental Animal Center of the Chinese Academy of Sciences.”

direct quote[Tumor xenograft formation assay]

“Male athymic BALB/c mice, 5-week-old”

absence[Primary MM samples]

No demographics provided for human patients

WARNReviewer 2· 85% conf

Biological variable reporting is incomplete. Sex is reported for mice, species source is adequate, but age is partially reported, weight and health status are missing, housing conditions are absent, and human demographics are not reported. The use of only male mice is not justified.

Evidence

direct quote[Methods, Tumor xenograft formation assay]

“Male athymic BALB/c mice, 5-week-old”

paraphrase[Methods, Tumor xenograft formation assay]

“Only age (5-week-old) is given; no weight or health status mentioned.”

absence[Methods, Tumor xenograft formation assay]

No housing conditions (light cycle, temperature, enrichment) are described.

FAILReviewer 3· 80% conf

Biological variables are poorly reported: sex, age, and health status for humans are missing; housing conditions for mice are absent.

Evidence

absence[Materials and Methods, Primary MM samples]

Human sample demographics not reported.

direct quote[Materials and Methods, Tumor xenograft formation assay]

“Male athymic BALB/c mice, 5-week-old, were purchased from the Shanghai Experimental Animal Center of the Chinese Academy of Sciences.”

absence[Materials and Methods]

No justification for using only male mice.

The human study was approved by the Ethics Committee of The First People's Hospital of Shangqiu and written informed consent was obtained. Animal procedures were described as being in accordance with the NIH Guide for the Care and Use of Laboratory Animals, but no specific IACUC committee or protocol number is provided. Since animal research is involved, a named IACUC approval is expected but missing.

Sub-criteria

iacuc statementNOT REPORTED

informed consentADEQUATE

irb ethics statementADEQUATE

regulatory complianceADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

The paper includes ethics approval for human samples and animal studies, but the human ethics statement lacks a protocol number, and the animal welfare statement does not name a specific IACUC body.

Evidence

direct quote[Primary MM samples]

“The study was approved by the Ethics Committee of The First People's Hospital of Shangqiu and performed in accordance with the Declaration of Helsinki (2000).”

direct quote[Tumor xenograft formation assay]

“All procedures were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.”

direct quote[Primary MM samples]

“Written informed consent obtained from all patients.”

WARNReviewer 2· 90% conf

Ethical approvals are partially reported. Human research has a named ethics committee and informed consent. Animal research lacks a named IACUC approval, only a general compliance statement. Regulatory compliance is stated.

Evidence

direct quote[Methods, Primary MM samples]

“The study was approved by the Ethics Committee of The First People's Hospital of Shangqiu”

direct quote[Methods, Primary MM samples]

“Written informed consent obtained from all patients.”

direct quote[Methods, Tumor xenograft formation assay]

“All procedures were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.”

WARNReviewer 3· 90% conf

Ethical approvals are described but the animal welfare statement lacks a specific IACUC name and protocol number.

Evidence

direct quote[Materials and Methods, Primary MM samples]

“The study was approved by the Ethics Committee of The First People's Hospital of Shangqiu and performed in accordance with the Declaration of Helsinki (2000).”

direct quote[Materials and Methods, Primary MM samples]

“Written informed consent obtained from all patients.”

direct quote[Materials and Methods, Tumor xenograft formation assay]

“All procedures were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.”

Cell lines are sourced from ATCC (Manassas). The antibody for FOXP1 (ab16645, Abcam) is identified with a catalog number. Reagents such as Lipofectamine 2000, TRIzol, and kits are named with vendors but without catalog numbers. Software (SPSS 18.0, CELL Quest 3.0) is named but without version numbers or RRIDs. Primer sequences are provided. No RRIDs are reported.

Sub-criteria

mycoplasma testingNOT REPORTED

reagents identifiedINADEQUATE

organisms identifiedADEQUATE

antibodies identifiedINADEQUATE

cell line authenticationINADEQUATE

software tools identifiedINADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

Key resources are partially identified: cell lines are from ATCC, antibodies and reagents are named with vendors, but catalog numbers, RRIDs, and validation data are incomplete, and software tools lack version numbers.

Evidence

direct quote[Cell lines and cell culture]

“We obtained MM cell lines (MM.1S, OPM-2, NCI-H929, U266, and RPMI-8226) and normal plasma cells (nPCs) from the American Type Culture Collection (ATCC, Manassas).”

direct quote[Western blot analysis]

“Blots were incubated with primary antibodies at 4°C overnight (FOXP1; ab16645, Abcam)”

direct quote[Statistical analyses]

“Statistical analysis was carried out by the SPSS 18.0.”

WARNReviewer 2· 80% conf

Key resource identification is incomplete. The FOXP1 antibody is identified with catalog number, but the Ki-67 antibody is not. Cell lines are sourced but not authenticated. Mycoplasma testing is not reported. Organisms, reagents, and software are adequately identified.

Evidence

direct quote[Methods, Western blot analysis vs Immunohistochemistry]

“FOXP1; ab16645, Abcam”

direct quote[Methods, Cell lines and cell culture]

“We obtained MM cell lines (MM.1S, OPM-2, NCI-H929, U266, and RPMI-8226) and normal plasma cells (nPCs) from the American Type Culture Collection (ATCC, Manassas).”

absence[Methods, Cell culture]

Mycoplasma testing is not mentioned.

WARNReviewer 3· 80% conf

Key resources are partially identified; cell line authentication and mycoplasma testing are missing, and antibody details are incomplete.

Evidence

direct quote[Materials and Methods, Western blot analysis]

“(FOXP1; ab16645, Abcam)”

direct quote[Materials and Methods, Cell lines and cell culture]

“We obtained MM cell lines (MM.1S, OPM-2, NCI-H929, U266, and RPMI-8226) and normal plasma cells (nPCs) from the American Type Culture Collection (ATCC, Manassas).”

absence[Materials and Methods]

Mycoplasma testing not mentioned.

Student's t-test or one-way ANOVA are named and software (SPSS 18.0) is identified. However, exact p-values are not given, assumptions are not verified, effect sizes and confidence intervals are absent, and data are shown as bar graphs with error bars but no individual data points.

Sub-criteria

tests namedADEQUATE

exact p valuesINADEQUATE

effect sizes ciNOT REPORTED

data presentationINADEQUATE

software identifiedADEQUATE

assumptions verifiedNOT REPORTED

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 75% conf

Statistical tests are named (Student's t-test, one-way ANOVA), but assumptions (normality, variance) are not verified, exact p-values are not reported (only 'P<0.05'), and effect sizes or confidence intervals are absent.

Evidence

direct quote[Statistical analyses]

“The quantitative data between groups was compared and analyzed by Student's t-test or one-way ANOVA.”

direct quote[Throughout Results]

“P<0.05”

absence[Results and figure legends]

No effect sizes or confidence intervals reported

FAILReviewer 2· 90% conf

Statistical analysis reporting is severely inadequate. Only the test names and software are given. Assumptions, exact p-values, effect sizes, and confidence intervals are not reported. Data presentation is adequate (SD defined, n stated).

Evidence

direct quote[Methods, Statistical analyses]

“The quantitative data between groups was compared and analyzed by Student's t-test or one-way ANOVA.”

direct quote[Throughout Results]

“P<0.05; P<0.01”

absence[Results]

Effect sizes and confidence intervals are not reported.

WARNReviewer 3· 85% conf

Statistical tests are named but most reporting is inadequate: only p-value thresholds, no effect sizes, no assumption checks, and data presentation lacks individual points.

Evidence

direct quote[Materials and Methods, Statistical analyses]

“The quantitative data between groups was compared and analyzed by Student's t-test or one-way ANOVA.”

direct quote[Results]

“** P<0.01; * P < 0.05.”

absence[Results]

No effect sizes or confidence intervals reported.

The paper does not include a data availability statement, and no data or code has been deposited in any public repository.

Sub-criteria

code sharingNOT REPORTED

accession numbersNOT REPORTED

repository depositNOT REPORTED

data availability statementNOT REPORTED

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 90% conf

No data availability statement is provided, data are not deposited in any repository, and custom code is not shared, despite the study generating primary data from patient samples and experiments.

Evidence

absence[Entire paper]

No data availability statement found

absence[Entire paper]

No repository deposit or accession numbers

absence[Entire paper]

No code sharing mentioned

FAILReviewer 2· 90% conf

No data or code availability is reported. There is no data availability statement, no repository deposition, and no code sharing. Given the study generated primary data (qRT-PCR, etc.), a data availability statement is expected but absent.

Evidence

absence[Entire paper]

No data availability statement is present.

FAILReviewer 3· 95% conf

No data availability statement, repository deposit, accession numbers, or code sharing are provided.

Evidence

absence[Entire manuscript]

No data availability statement anywhere in the paper.

absence[Entire manuscript]

No repository deposit or accession numbers.

absence[Entire manuscript]

No code sharing mentioned.

The Materials and Methods section provides detailed protocols for qRT-PCR, cell proliferation, colony formation, flow cytometry, luciferase reporter, RIP, western blot, and xenograft assays, enabling replication. No reporting checklist (e.g., ARRIVE) is referenced. The discussion does not explicitly discuss limitations of the study. Conclusions state that MALAT1 'could act as a novel diagnostic marker and therapeutic target,' which is common but somewhat overstated for a preclinical association study.

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedNOT REPORTED

conclusions proportionalINADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

Methods are described in sufficient detail for replication, and a conflicts of interest statement is provided, but no reporting guideline is referenced, limitations are not discussed, and conclusions are somewhat overstated relative to the in vitro and xenograft evidence.

Evidence

direct quote[Quantitative real time-PCR (qRT-PCR)]

“QRT-PCR reactions were performed using the following parameters: 95°C for 2 min followed by 40 cycles of 95°C, 15 s, and 60°C.”

absence[Entire paper]

No reporting guideline referenced

direct quote[CONFLICTS OF INTEREST]

“The authors have no actual or potential conflicts of interest to declare”

WARNReviewer 2· 85% conf

Reporting completeness is mixed. Methods are detailed enough for replication, and all outcomes appear reported. However, the paper does not follow a reporting guideline, lacks a limitations discussion, overclaims clinical applicability, and does not mention funding sources.

Evidence

direct quote[Methods]

“The primer sequences used are as follows: MALAT1 forward 5′-AAAGCAAGGTCTCCCCACAAG-3′, reverse 5′-GGTCTGTGCTAGATCAAAAGGC-3′;”

absence[Methods]

No reporting guideline is mentioned.

direct quote[Discussion, final paragraph]

“our data indicated that MALAT1 could serve as a potential therapeutic target for the treatment of MM patients.”

WARNReviewer 3· 85% conf

Methods are described adequately, but reporting lacks a limitations section, adherence to a reporting guideline, and complete funding information.

Evidence

direct quote[Materials and Methods]

“MALAT1 forward 5′-AAAGCAAGGTCTCCCCACAAG-3′, reverse 5′-GGTCTGTGCTAGATCAAAAGGC-3′”

absence[Discussion]

No limitations section or discussion of biases.

direct quote[After Discussion]

“The authors have no actual or potential conflicts of interest to declare.”

24 copyedit issues flagged (7 major): mostly typo, clarity, consistency.

Checked 30 references: 25 verified — 1 retracted, 4 not checked.

Αlpha¹ Rigor Action ItemsFinal pass before journal submission

This paper is ALREADY PUBLISHED. Post-publication, the missing rigor elements (no randomization, blinding, power analysis; threshold-only p-values; no data availability; a retracted citation) and overstated conclusions warrant a reader's caution. An erratum or, more likely, a formal correction should address the retracted citation and data availability. The statistical reporting is insufficient for a reader to independently verify any reported finding.

1.
HIGHother
Remove or replace the retracted reference: Long Noncoding RNA CRNDE Promotes Multiple Myeloma Cell Growth by Suppressing miR-451 (DOI: 10.3727/096504017x14886679715637) — cite a non-retracted source or justify retention.
Citing a retracted paper undermines the integrity of the reference list and may mislead readers about the state of the evidence.
2.
HIGHstatistics
Replace all threshold p-values (e.g., P<0.05, P<0.01) with exact p-values (e.g., P=0.023) throughout the Results section and figure legends.
Exact p-values are the standard for transparent reporting and are necessary for readers to assess the strength of evidence.
3.
HIGHdata code
Add a data availability statement (e.g., 'The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request') and deposit primary data (qRT-PCR, sequencing, tumor volume) in a public repository (e.g., GEO) with an accession number.
No data availability statement or repository deposit undermines reproducibility and is a fundamental reporting requirement for a data-generating study.
4.
HIGHreporting
Add a Limitations paragraph in the Discussion addressing small sample size (n=37), lack of external validation, single animal model, potential off-target effects, and the single-sex (male-only) mouse study without justification.
The current Discussion overstates clinical applicability without acknowledging these limitations, which is a common reviewer objection.
5.
HIGHstatistics
Include effect sizes (e.g., Cohen's d, fold-change with CI) alongside p-values for key comparisons, and add a statement on how normality and equal-variance assumptions were verified.
Effect sizes communicate practical significance, and assumption checks ensure the chosen test is appropriate.
6.
HIGHrigor
Describe the randomization method used for assigning mice to treatment groups and state whether tumor measurement and IHC scoring were performed by a blinded assessor.
Lack of randomization and blinding is a major source of bias in preclinical animal studies; these details are required by ARRIVE guidelines.
7.
HIGHreporting
Temper the conclusion that 'MALAT1 could serve as a novel diagnostic marker and therapeutic target for MM' to reflect that the data are preclinical and require clinical validation.
The claim exceeds the evidence from in vitro and xenograft studies; readers may be misled about clinical readiness.
8.
HIGHreporting
Reference a reporting guideline (e.g., ARRIVE for animal experiments) and state compliance in the Methods.
Reporting guidelines improve completeness and reproducibility; their absence is a notable gap.
9.
MEDIUMrigor
For the xenograft experiment, report housing conditions (light/dark cycle, temperature, humidity, enrichment) and provide a justification for using only male mice.
Housing conditions affect animal physiology and reproducibility; single-sex designs need scientific justification.
10.
MEDIUMrigor
Report inclusion/exclusion criteria for patient samples (e.g., newly diagnosed vs. relapsed, age range, prior treatment) and demographic characteristics (age, sex, race).
Without these details, readers cannot assess generalizability or potential confounding.
11.
MEDIUMethics
Include the IACUC protocol number and committee name for the animal study rather than only citing the NIH Guide.
A specific protocol number is standard for ethical reporting of animal research.
12.
MEDIUMrigor
Clarify whether the 'at least three times' replication refers to biological or technical replicates, and report independent replication (e.g., separate experiments on different days).
Ambiguity about replication type undermines confidence in the reproducibility of results.
13.
MEDIUMother
Provide catalog numbers and RRIDs for all antibodies (especially Ki-67, Ago2), reagents (kits, Lipofectamine), and software versions.
Incomplete identification of key resources hinders reproducibility.
14.
MEDIUMother
State whether cell lines were authenticated (e.g., STR profiling) and tested for mycoplasma.
Misidentified or contaminated cell lines are a known source of irreproducibility.
15.
MEDIUMcopyedit
Correct the garbled title block (extraneous numbers and dates), ensure the title reads cleanly as 'LncRNA MALAT1 acts as an oncogene in multiple myeloma through sponging miR-509-5p to modulate FOXP1 expression'.
The title block appears corrupted, which affects discoverability and professional presentation.
16.
MEDIUMcopyedit
Correct the inconsistency between Abstract (G1/S arrest) and Results (G0/G1 arrest) regarding cell cycle phase; unify to one description.
Internal contradictions reduce reader confidence in the data.
17.
MEDIUMcopyedit
Correct the typo 'miR-509-3p' to 'miR-509-5p' in Figure 5 legend.
Incorrect strand designation is confusing and suggests a possible error in interpretation.
18.
MEDIUMcopyedit
Fix the repeated typo 'sh-MATAT1' (should be 'sh-MALAT1') throughout the Results and Figure 3 legend.
Typos in gene names suggest carelessness and can cause confusion.
19.
MEDIUMcopyedit
Reformat the references in a standard style (e.g., Vancouver) with proper punctuation and line breaks; ensure all references include volume and page numbers.
The current references are run together without formatting, hindering readability and verification.
20.
LOWcopyedit
Fix the subject-verb agreement error 'data was compared' to 'data were compared' in Statistical analyses.
Correct grammar improves professional presentation.

Full text (32,877 chars)Analyzed: Jul 6, 2026

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