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Cited by 17Mitochondrial Function and PathologyAlzheimer's disease research and treatmentsCancer-related molecular mechanisms research

The mitochondrial long non-coding RNA lncMtloop regulates mitochondrial transcription and suppresses Alzheimer’s disease

Open access
Xiong, Wandi, Xu, Kaiyu, Sun, Jacquelyne Ka-Li, Liu, Siling, Zhao, Baizhen, Shi, Jie, Herrup, Karl, Chow, Hei-Man +2 more·2024·The EMBO Journal
DOI 10.1038/s44318-024-00270-7PMC PMC11612450
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Abstract

Maintaining mitochondrial homeostasis is crucial for cell survival and organismal health, as evidenced by the links between mitochondrial dysfunction and various diseases, including Alzheimer’s disease (AD). Here, we report that lncMtDloop , a non-coding RNA of unknown function encoded within the D-loop region of the mitochondrial genome, maintains mitochondrial RNA levels and function with age. lncMtDloop expression is decreased in the brains of both human AD patients and 3xTg AD mouse models. Furthermore, lncMtDloop binds to mitochondrial transcription factor A (TFAM), facilitates TFAM recruitment to mtDNA promoters, and increases mitochondrial transcription. To allow lncMtDloop transport into mitochondria via the PNPASE-dependent trafficking pathway, we fused the 3’UTR localization sequence of mitochondrial ribosomal protein S12 (MRPS12) to its terminal end, generating a specified stem-loop structure. Introducing this allotropic lncMtDloop into AD model mice significantly improved mitochondrial function and morphology, and ameliorated AD-like pathology and behavioral deficits of AD model mice. Taken together, these data provide insights into lncMtDloop as a regulator of mitochondrial transcription and its contribution to Alzheimer’s pathogenesis

AI snapshot

Written from the paper’s full text.

TL;DR

The mitochondrial D-loop–encoded long non-coding RNA lncMtDloop binds TFAM, promotes TFAM recruitment to mtDNA promoters, and supports mitochondrial transcription. Its expression is reduced in AD patient brains and 3xTg mice, and allotropic restoration improves mitochondrial function, AD-like pathology, synaptic plasticity, and behavior in 3xTg mice.

Key findings

  • lncMtDloop (formerly AC027613.1) is a conserved, noncoding mitochondrial lncRNA from the mtDNA D-loop (chrM:15,356–16,294 bp) that localizes predominantly to mitochondria in primary hippocampal neurons and in N2a, SH-SY5Y, and Cos-7 cells.
  • lncMtDloop expression is decreased in AD brains—prefrontal cortex, hippocampal CA1, and dentate gyrus—compared with age- and sex-matched non-dementia controls (n = 8 per group by RNAscope, northern blot, and RT-qPCR), and in 12-month-old 3xTg mice (n = 6 per genotype), with decline beginning at 9–12 months; loss was neuron-specific, not seen in microglia or astrocytes.
  • lncMtDloop binds TFAM, with the lncMtDloop-D4 region important for interaction; overexpression enhanced TFAM binding to the mtDNA D-loop by ChIP, luciferase assays identified the mtDNA +200 to −400 bp segment as critical, and EMSA showed mitochondrial-extract band shifting. It promoted mtRNA transcription but not mtDNA replication.
  • An allotropic construct fusing the MRPS12 3′UTR to lncMtDloop was imported into mitochondria via PNPASE and p32; PNPASE overexpression produced a twofold increase in mitochondrial import. In 3xTg mice, systemic or hippocampal AAV delivery improved mitochondrial morphology/function, reduced Aβ plaque area/intensity and Aβ40/Aβ42, restored fEPSPs/LTP, and improved fear conditioning and Morris water maze performance.

Methods

  • In vitro and in vivo study using human postmortem brain tissue (16 case-patients from the University of Pittsburgh ADRC plus additional frozen tissue; AD vs age/sex-matched controls, n = 8 per group), rhesus macaque young (4–6 years) vs old (16–20 years) brain, WT and 3xTg mice, primary hippocampal neurons/microglia/astrocytes, and N2a, SH-SY5Y, and Cos-7 cell lines.
  • Assays included RNAscope ISH, RT-qPCR, northern blot, RNA pull-down with mass spectrometry, RIP, ChIP, luciferase reporter assays, EMSA, Seahorse OCR, cytochrome c oxidase activity, STED imaging, electron microscopy, electrophysiology, and behavioral tests; AAV9 was injected into hippocampus and AAV-PHP.eB into tail vein of 11-month-old mice, with tissue analysis 6 weeks later.
  • Statistics used GraphPad Prism 7; two-tailed Student’s t-test for two groups and one-way or two-way ANOVA with Tukey’s or Dunnett’s multiple comparisons for three or more groups; significance set at P < 0.05.

Limitations

  • Stated: the mechanisms underlying lncMtDloop import into mitochondria remain ambiguous; future studies should include in vitro transcription assays to clarify its direct role in mtDNA transcription; and other lncMtDloop-interacting partners beyond TFAM could also play a role.
  • Evident: human evidence is correlative expression analysis in postmortem tissue, not causal or therapeutic testing; the rescue experiments are in 3xTg mice and primary cultures, so human translation remains untested.
  • Evident: the title uses “lncMtloop” while the abstract and results use “lncMtDloop,” an inconsistency in nomenclature.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/s44318-024-00270-7

Cites

76 of 76 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

22 of 25 cited sources checked · 8 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    PNPASE orchestrates the import of specific nucleus-encoded RNAs into mitochondria through recognition of distinct RNA stem-loop structures.

    “PNPASE orchestrates the import of specific nucleus-encoded RNAs into the mitochondria through its recognition of distinct RNA stem-loop structures”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Wang et al, 2010 source
    • cites Wang et al, 2012a source

      Section 5.3 reports PNPASE-dependent import of specific nucleus-encoded RNAs and describes stem-loop-forming sequences in RNase P and MRP RNAs. The paper says stem-loops may facilitate PNPASE binding, but states that the mechanism linking recognition to import remains unclear; the claim presents that mechanism as established. Page numbers are unavailable in our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Premisecitation

    Allotropic expression of wild-type mtDNA-encoded genes can salvage mitochondrial functionality via mitochondrial targeting sequences and 3'UTRs.

    “In the context of allotropic expression, the genes encoded by wild-type mtDNA are transcribed within the nucleus. Consequently, resulting non-coding RNAs (ncRNAs) or proteins can be transported into the mitochondria, thereby salvaging mitochondrial functionality. This transportation is facilitated by mitochondrial targeting sequences (MTSs) and 3′ untranslated regions (3′UTRs)”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Chin et al, 2018 source

      The Summary reports that allotopically expressed wild-type mtATP6 protein can be targeted to mitochondria and functionally rescue cells with an mtATP6 mutation. The Results identify mitochondrial targeting sequences as a means of importing proteins, but the Discussion says none of the tested 3′ UTRs significantly improved mitochondrial colocalization. The cited paper therefore does not establish the sentence’s implication that both MTSs and 3′ UTRs facilitated the rescue; the supplied passages also do not support transport of non-coding RNAs. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Wang et al, 2012b source

      The Abstract and Functional Rescue section report partial restoration of mitochondrial function by importing nucleus-encoded wild-type mt-tRNAs. They identify an RP RNA-import signal and an MRPS12 3′UTR localization sequence, not a mitochondrial targeting sequence that transports proteins into mitochondria. The Results show an imported COX2 transcript translated within mitochondria, but do not show functional rescue by that protein-encoding transcript. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Premisecitation

    Accumulation of abnormal mitochondria without timely clearance indicates mitophagy dysfunction in Alzheimer's disease brain neurons.

    “Furthermore, the accumulation of abnormal mitochondria without timely clearance indicates mitophagy dysfunction within AD brain neurons (Du et al, 2010; Sorrentino et al, 2017).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Du et al, 2010

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites Sorrentino et al, 2017 source

      The Abstract reports altered mitochondrial morphology in AD, and “Evidence for a mitochondrial stress signature in AD” reports changes in mitophagy-related transcripts in human cortex. Neither passage establishes that abnormal mitochondria accumulate because clearance is delayed or that mitophagy is dysfunctional specifically in AD brain neurons; the paper instead describes induction of mitophagy-related responses. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Premisecitation

    Excessive mitochondrial fission without timely mitophagy-mediated clearance compromises mitochondrial genome integrity and nucleoid organization, leading to mtDNA loss and overall mitochondrial dysfunction.

    “Other reports have corroborated that excessive mitochondrial fission without timely mitophagy-mediated clearance compromises mitochondrial genome integrity, and nucleoid organization, leading to mtDNA loss, and overall mitochondrial dysfunction (Sabouny and Shutt, 2021).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Sabouny and Shutt, 2021 source

      The “Mitophagy and mtDNA” section says fission enables mitophagy to remove damaged or mutant mtDNA, and “Nucleoid distribution” links disturbed fission–fusion balance to altered nucleoids. But the paper does not establish that excessive fission without timely mitophagy causes the claimed chain of mtDNA loss and mitochondrial dysfunction; “Fission and mtDNA replication” instead reports mtDNA depletion when fission is blocked. Page numbers are unavailable in our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Premisecitation

    Fusion of lncMtDloop with the 3′UTR of MRPS12 facilitates its targeted localization to the mitochondrial surface.

    “Our optimization process involved the fusion of lncMtDloop with the 3′UTR of MRPS12, facilitating its targeted localization to the mitochondrial surface—a technique supported by previous research (Chin et al, 2018; Wang et al, 2012b).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Chin et al, 2018 source

      The Results state that specific 3′ UTRs have been used to direct mRNAs to the mitochondrial surface. Our copy does not identify the MRPS12 3′ UTR or test its fusion with lncMtDloop, so it supports the general rationale but not the specific construct or its claimed localization. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites Wang et al, 2012b source
  • Classified as probably not a substantial claim. 20
  • May combine two claims. 34
  • The quote only partly states this claim. 4

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The non-coding 7S RNA triggers POLRMT dimerization and subsequently regulates mitochondrial transcription.

    “A recent study indicates that the non-coding 7S RNA triggers POLRMT dimerization and subsequently regulates mitochondrial transcription through a series of in vitro transcription and transcription pulse-chase experiments. (Zhu et al, 2022).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Zhu et al, 2022 source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Mitochondrial genome homeostasis is essential for mitochondrial function, and deleterious mutations in the mitochondrial genome are implicated in metabolic disorders, aging, and neurodegenerative disorders.

    “The mitochondrial genome homeostasis is essential for mitochondrial function, and its deleterious mutations are implicated in metabolic disorders, aging, and neurodegenerative disorders (Antonyova et al, 2020; Sanchez-Contreras et al, 2023).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites Antonyova et al, 2020 source
    • cites Sanchez-Contreras et al, 2023 source

      The Introduction (page not provided) says mtDNA mutations can disrupt mitochondrial functions and induce disease, and discusses the potential for deleterious mutations to cause mitochondrial dysfunction. The paper also examines mtDNA mutations during aging. It does not specifically link those mutations to metabolic or neurodegenerative disorders; searches for those terms found only related reference titles, not a statement making the claimed links. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    PNPASE is a key player in the RNA import machinery of mammalian mitochondria.

    “PNPASE emerged as a key player in the RNA import machinery of mammalian mitochondria (Wang et al, 2010; Wang et al, 2012a).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Wang et al, 2010 source
    • cites Wang et al, 2012a source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    catRAPID predicts the binding affinity of protein-RNA pairs.

    “catRAPID, an algorithm designed to predict the binding affinity of protein–RNA pairs”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Agostini et al, 2013 source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Dysregulated mitochondrial biogenesis, altered mitochondrial dynamics, and compromised genome integrity contribute to breakdown of mitochondrial health and function and are linked to Alzheimer's disease.

    “Dysregulated mitochondrial biogenesis, alterations in mitochondrial dynamics (fusion and fission), and compromised genome integrity mechanisms collectively contribute to the breakdown of mitochondrial health and function. These factors are intricately linked to various disorders, notably AD (Baloyannis et al, 2004; Zhunina et al, 2020).”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites Baloyannis et al, 2004 source

      The Introduction links mitochondrial DNA defects and abnormal mitochondrial morphology to Alzheimer’s disease, and the Discussion links mitochondrial alterations to dysfunction. The paper does not establish dysregulated biogenesis or impaired fusion and fission as contributors to AD; fusion and fission appear only in a reference title. It discusses mtDNA defects, but not compromised genome-integrity mechanisms specifically. Page numbers were not available in our copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Zhunina et al, 2020 source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    TFAM is essential for mtDNA genome maintenance and initiates mitochondrial transcription by recruiting POLRMT and TFB2M to specific promoter regions on mtDNA.

    “TFAM is essential for mtDNA genome maintenance and initiates mitochondrial transcription by recruiting mitochondrial RNA polymerase (POLRMT) and mitochondrial transcription factor B (TFBM) to specific promoter regions on mtDNA (Hillen et al, 2017; Hillen et al, 2018).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites Hillen et al, 2017 source

      The Results section, “TFAM recruits mtRNAP to promoter DNA” (page unavailable), supports TFAM’s recruitment of POLRMT to mitochondrial promoters. The Results section, “IC structure reveals locations of TFAM, TFB2M, and DNA on mtRNAP” (page unavailable), says TFAM does not contact TFB2M, so it does not support recruitment of TFB2M by TFAM. The Introduction links transcription initiation to mitochondrial maintenance but does not establish that TFAM is essential for mtDNA genome maintenance. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites Hillen et al, 2018 source

      The “Initiation factor TFAM” section (page unavailable) says TFAM binds promoter sites and recruits mitochondrial RNA polymerase to form a pre-initiation complex; TFB2M binds afterward to facilitate DNA opening. It also says TFAM is thought to mediate mitochondrial-genome packaging, but does not establish that TFAM is essential for genome maintenance or that it recruits TFB2M. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The element within the D-loop region plays a crucial role in mediating the transition between mitochondrial DNA replication and transcription events.

    “A previous report also indicates that the element within the D-loop region plays a crucial role in mediating the transition between mitochondrial DNA replication and transcription events. (Jemt et al, 2015).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites Jemt et al, 2015 source

      The Discussion reports that conserved D-loop elements appear to prevent transcription from entering the region, and that coreTAS may also influence DNA replication. It also suggests that replication and transcription termination at coreTAS may be coordinately regulated. It does not establish that the element mediates a transition between replication and transcription events. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    p32 predominantly localizes in mitochondria and is a recognized RNA-binding protein within the mitochondrial context.

    “p32, a well-conserved eukaryotic protein that predominantly localizes in mitochondria (Barna et al, 2019; Gotoh et al, 2018), serves as a recognized RNA-binding protein within the mitochondrial context.”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites Barna et al, 2019 source
    • cites Gotoh et al, 2018 source
    • cites Jiang et al, 1999 source

      The paper’s introductory discussion says p32 localizes predominantly in the mitochondrial matrix, and the Discussion reiterates that it is mainly mitochondrial under normal conditions. The passages found do not identify p32 as an RNA-binding protein in mitochondria; they describe its association with a pre-mRNA splicing factor but note that no splicing function was established. (LLM, conf=0.85)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    3xTg-AD mice demonstrated deficiencies in nest-building, open-field exploration, and novel object recognition compared to WT controls.

    “in tasks such as nest-building (Appendix Fig. S9A,B), open-field exploration (Appendix Fig. S9C,D), and novel object recognition (Appendix Fig. S9E), the performance of 3xTg-AD mice demonstrated deficiencies when compared to WT controls, as anticipated.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Ectopic expression of lncMtDloop restored mtRNA levels without affecting mtDNA copy number and increased OXPHOS subunit protein levels.

    “Interestingly, ectopic expression of lncMtDloop notably restored mtRNA levels without affecting mtDNA copy number and further boosted OXPHOS subunit protein levels.”
    • Also stated in: § LncMtDloop is required for TFAM recruitment to initiate mitochondrial gene transcription · plain
      “Figure EV3 lncMtDloop promotes mtDNA transcription in mtDNA depletion assay, related to Fig. 3.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    lncMtDloop-FL and lncMtDloop-D4, which contain the TFAM-interacting site, significantly promoted mitochondrial genome transcription but not replication.

    “Functionally, lncMtDloop-FL and lncMtDloop-D4, which constitute the interacting site for TFAM significantly promoted mitochondrial genome transcription but not its replication (Fig. 3N,O).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Neurons from the 3xTg model exhibit an elevated frequency of peripheral fission and a reduced occurrence of midzone fission during mitochondrial division, leading to an increased presence of fragmented mitochondria compared with wild-type counterparts.

    “our findings disclosed that neurons from the 3xTg model exhibited an elevated frequency of peripheral fission instances, juxtaposed with a reduced occurrence of midzone fission during mitochondrial division. This combination ultimately led to an increased presence of fragmented mitochondria in comparison to their wild-type (WT) counterparts”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Localized hippocampal expression of AAV9-lncMtDloop-3'UTRMRPS12 effectively restored impairments in field excitatory postsynaptic potentials (fEPSPs) of the Schaffer collateral pathway and long-term potentiation (LTP) in 3xTg mice.

    “Impairments in the field excitatory postsynaptic potentials (fEPSPs) of the Schaffer collateral pathway, as well as the long-term potentiation (LTP) typically observed in 3xTg mice, were effectively restored through the specific and localized hippocampal expression of AAV9-lncMtDloop-3’UTRMRPS12 (Fig. 7J,K).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The hippocampus is the most vulnerable region to pathological changes in AD.

  • May combine two claims.

    Findingown data

    Ethidium bromide treatment for 8 weeks significantly decreased mtDNA and mtRNA copy numbers, MitoTracker signaling, and OXPHOS subunit protein levels.

    “Following EB treatment, both mtDNA and mtRNA copy numbers significantly decreased (Fig. EV3A,B), along with reduced levels of MitoTracker signaling (Fig. EV3C,D) and mitochondrial complex (OXPHOS subunit proteins) (Fig. EV3E,F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Systemic allotropic expression of lncMtDloop throughout the brain ameliorated the primary deficits observed in the Morris water maze in 3xTg mice, effectively outperforming the control group.

    “the systemic allotropic expression of lncMtDloop throughout the brain notably ameliorated the primary deficits observed in the MWM, effectively outperforming the control group (Fig. 7N–R).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The AAV-PHP.eB vector delivery system can traverse the blood-brain barrier.

  • May combine two claims.

    Findingown data

    lncMtDloop is a previously undiscovered, evolutionarily conserved lncRNA originating from the mitochondrial DNA D-loop region.

    “we have unveiled a previously undiscovered yet evolutionarily conserved lncRNA originating from the mitochondrial DNA D-loop region, aptly named lncMtDloop.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The EMSA band shifting was competitively disrupted by an unlabeled probe and reversibly enhanced by lncMtDloop overexpression.

    “Such a phenomenon could be competitively disrupted by an unlabeled probe or reversibly enhanced when lncMtDloop was overexpressed (Fig. 3M; Appendix Fig. S4).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Absence of lncMtDloop leads to deficits in neuronal firing and impairments in cognition and memory in 3xTg mice.

    “with its absence leading to deficits in neuronal firing and impairments in cognition and memory within the 3xTg mice.”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    lncMtDloop expression is reduced in aged (12-month-old) 3xTg mice compared with wild-type mice.

    “Analogous findings were replicated within aged (12-month-old) 3xTg mice—a triple transgenic AD animal model characterized by classic Aβ pathology and tauopathies—employing identical analytical methodologies (Fig. 4F–J).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Allotropic expression of lncMtDloop in AD neurons significantly elevated mtRNA expression without affecting mtDNA content.

    “Notably, this intervention resulted in a significant elevation in mtRNA expression, although mtDNA content remained unaffected (Fig. 5D,E).”
    • Also stated in: § Allotropic lncMtDloop expression reverses loss of mitochondrial homeostasis in neurons of 3xTg mice · plain
      “Interestingly, the levels of mtDNA remained unchanged following this restoration (Fig. 5F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Allotropic lncMtDloop expression substantially improved the mitochondrial fission abnormalities and Drp1/Opa1 imbalance in 3xTg neurons.

    “Nevertheless, allotropic lncMtDloop expression brought about a substantial improvement in this scenario.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    7S RNA exhibits significant accumulation in AD brains, while 12S rRNA expression shows minimal changes.

    “Interestingly, 7S RNA, a polyadenylated non-coding RNA transcribed from a region immediately downstream of the mitochondrial light strand promoter, exhibited significant accumulation in AD brains, while 12S rRNA expression showed minimal changes (Appendix Fig. S5G–I).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    Allotropic lncMtDloop expression effectively restores mtDNA transcription, bolstering mitochondrial genome integrity and respiratory function.

    “Indeed, allotropic lncMtDloop expression effectively restores mtDNA transcription, bolstering mitochondrial genome integrity and respiratory function, even as other lncMtDloop-interacting partners beyond TFAM could also play a role.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Rescuing lncMtDloop expression significantly improved both context and cued freezing time in 3xTg mice.

    “Rescuing lncMtDloop expression significantly improved both context and cued freezing time in 3xTg mice (Fig. 7L,M).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    lncMtDloop influences the preservation of mitochondrial morphology, metabolism, and mitophagy.

    “the influence of lncMtDloop on the preservation of mitochondrial morphology, metabolism, and mitophagy has been underscored”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    lncMtDloop expression is diminished in AD patient brains and 3xTg mice.

    “Given this context, lncMtDloop assumes clinical significance regarding its diminished expression in AD patient brains and 3xTg mice.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Restoring lncMtDloop directly boosts mtDNA transcription and rejuvenates mitochondrial function and dynamics within AD neurons.

    “Strikingly, restoring lncMtDloop not only directly boosts mtDNA transcription but also rejuvenates mitochondrial function and dynamics within AD neurons.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The reduction in lncMtDloop expression in Alzheimer's disease brain tissue is specific to neurons and is not present in glial cells (microglia and astrocytes).

    “Notably, the reductions in lncMtDloop observed within brain tissue were specific to neurons and not present in glial cells (microglia and astrocytes), as confirmed through multiple assay approaches (Figs. 4K–O and EV4D–I).”
    • Also stated in: § Loss of lncMtDloop found in the brains of human AD and the mouse model · plain
      “Figure EV4 Decreased expression of lncMtDloop differentially occurs in distinct neural cell types of AD, related to Fig. 4.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Among known mtDNA transcription factors, TFAM showed the highest predicted interaction score with lncMtDloop by catRAPID, and western blot, RIP, and RISH-ICF confirmed the interaction.

    “From there, TFAM, an mtDNA promoter-binding protein revealed the highest interaction scores whereas other proteins identified had lower catRAPID scores (Fig. 3C), and further experimental analyses with western blot, RIP, and RISH-ICF confirmed such prediction (Fig. 3D–G).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    During normal aging, mtRNA expression shows minimal changes, whereas diminished mtDNA transcripts are evident in 12-month-old 3xTg mice.

    “While minimal changes were observed in mtRNA expression during normal aging (Fig. 5A,B), diminished mtDNA transcripts were evident in 12-month-old 3xTg mice, which experience age-associated changes (Fig. 5C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    lncMtDloop has a pivotal regulatory role in upholding TFAM-dependent transcription of the mitochondrial genome and ensuring overall homeostasis.

    “Our data has illuminated its pivotal regulatory role in upholding TFAM-dependent transcription of the mitochondrial genome and ensuring overall homeostasis.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    lncMtDloop directly binds to TFAM, inducing mitochondrial gene transcription in a cis manner by facilitating TFAM recruitment to mtDNA D-loop region promoters.

    “Our study reveals that lncMtDloop directly binds to TFAM, inducing mitochondrial gene transcription in a cis manner by facilitating TFAM recruitment to mtDNA D-loop region promoters.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    lncMtDloop homologs differ slightly in size among human (572 bp), macaque (695 bp), and mouse (939 bp).

    “a slight size variance among the human (572 bp), macaque (695 bp), and mouse (939 bp) homologs”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Fusing the 3'UTR localization sequence of MRPS12 to the terminal end of lncMtDloop increases lncMtDloop localization to the mitochondrial surface and its enrichment in the mitochondrial fraction.

    “this allotropic expression of lncMtDloop, accompanied by the inclusion of MRPS12’s 3′UTR, indeed resulted in a heightened localization of lncMtDloop to the mitochondrial surface”
    • Also stated in: § Trafficking of allotropic lncMtDloop into mitochondria · plain
      “the incorporation of the 3′UTR element from MRPS12 led to a greater enrichment of lncMtDloop within the mitochondrial fraction”
    Quote in the paperSubstantial claim
    • Rests on an assumption: No established methodologies, including CRISPR/Cas9-based techniques and conventional siRNA technology, effectively target mtDNA sequences, mainly because nucleic acid import into mitochondria is inefficient.

  • May combine two claims.

    Findingnone given

    lncMtDloop expression is decreased in the brains of both human AD patients and 3xTg AD mouse models.

    “lncMtDloop expression is decreased in the brains of both human AD patients and 3xTg AD mouse models.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In 3xTg neurons, Drp1 protein levels are significantly increased and Opa1 protein levels are decreased.

    “Combining with western blot, we showed a significant increase of Drp1 (dynamin-related protein 1) and a decrease of Opa1 (optic atrophy 1) in 3xTg neurons (Fig. 5N–P).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Additional frozen human tissue was obtained with approval from the Neuropathology Core at Hong Kong University of Science and Technology.

    “Additional frozen tissue was a generous gift of the ADRC at Washington University in St. Louis (Grant P50-AG-05681) with approval from the Neuropathology Core (protocol #T1016) at Hong Kong University of Science and Technology.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    7S RNA and 12S rRNA were used as controls in RIP analyses.

    “7S RNA and 12S rRNA was used as control.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    lncMtDloop is likely conserved during mitochondrial evolution.

    “hinting that the lncMtDloop is likely conserved during the mitochondrial evolution”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Interpretationown data

    p32 facilitates the transportation of ectopically expressed lncMtDloop into mitochondria.

    “it is plausible that endogenous p32 could potentially facilitate the transportation of ectopically expressed lncMtDloop into mitochondria”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    lncMtDloop enhances the affinity and efficacy of TFAM interaction with the mtDNA promoter, thereby promoting transcription.

    “These findings suggest that lncMtDloop enhances the affinity and efficacy of TFAM interaction with the mtDNA promoter, thereby promoting transcription (Appendix Fig. S3D).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductown data

    VDAC1 was used as a mitochondrial quality control in RNA pull-down assays.

    “VDAC1 was used as mitochondrial quality control.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Mice were randomly assigned to the experimental groups.

    “Mice were randomly assigned to the experimental groups.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Each human case had been diagnosed neuropathologically and ranked by Braak stage.

    “Each case had been diagnosed neuropathologically and ranked by Braak stage (Appendix Table S1).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    lncMtDloop is a regulator of mitochondrial transcription and contributes to Alzheimer's pathogenesis.

    “these data provide insights into lncMtDloop as a regulator of mitochondrial transcription and its contribution to Alzheimer’s pathogenesis”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Human autopsy paraffin-embedded brain sections were obtained from sources with approval from the appropriate local regulatory authorities.

    “Human autopsy paraffin-embedded 10 μm brain sections were from the following sources with approval from the appropriate local regulatory authorities.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    In the open-field test, mice were placed into the arena by a blinded experimenter.

    “For the open-field test, mice were placed into the open-field arena (made of opaque white plastic material, 35 cm × 35 cm separated into 5 × 5 grids) by a blinded experimenter and allowed to explore the arena for 15 min.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    The allotropic lncMtDloop construct exhibits an allosteric expression pattern, effectively reinstating the expression levels of lncMtDloop.

    “These results indicate that this construct exhibits an allosteric expression pattern, effectively reinstating the expression levels of lncMtDloop”
    Quote in the paperSubstantial claim
    • Rests on an assumption: No established methodologies, including CRISPR/Cas9-based techniques and conventional siRNA technology, effectively target mtDNA sequences, mainly because nucleic acid import into mitochondria is inefficient.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Results were normalized to the control IgG RIP group.

    “Results were normalized to the control IgG RIP group.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Wells whose median OCR level did not follow the expected order (median OCR(Int3) > median OCR(Int1) > median OCR(Int2) > median OCR(Int4)) were discarded from the Seahorse analysis.

    “Wells for which the median OCR level did not follow the expected order, namely, median (OCR(Int3)) > median (OCR(Int1)) > median (OCR(Int2)) > median (OCR(Int4)), were discarded (977 wells, 10.47%).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). The quote only partly states this claim.

    Study design and conductnone given

    All animal experiments complied with the Biomedical Ethics Committee for Animal Use and Protection of Peking University.

    “All animal experiments complied with the Biomedical Ethics Committee for Animal Use and Protection of Peking University.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Contaminated wells and wells in which the cells detached were excluded from the Seahorse analysis.

    “Of note, we excluded from the analysis contaminated wells and wells in which the cells got detached (461 wells, 4.94%).”
    Quote in the paperNot a substantial claim
52 of 52

  • The paper relies on this without support.

    No established methodologies, including CRISPR/Cas9-based techniques and conventional siRNA technology, effectively target mtDNA sequences, mainly because nucleic acid import into mitochondria is inefficient.

    “To date, no established methodologies, including CRISPR/Cas9-based techniques and conventional siRNA technology, have proven effective in targeting mtDNA sequences, mainly due to the inherent inefficacy of nucleic acid import into mitochondria.”

  • The paper relies on this without support.

    The mitochondrial D-loop region is essential for mtDNA replication and transcription.

    “The mitochondrial D-loop region is essential for mtDNA replication and transcription.”

  • The paper relies on this without support.

    Persistent and prolonged exposure to additional stressors, such as pathologies linked to AD, can exacerbate mitochondrial deficiencies or intensify loss-of-function mutations in mitochondrial genes, consequently deteriorating mitochondrial function.

    “Nevertheless, persistent and prolonged exposure to additional stressors, such as pathologies linked to AD, can exacerbate these deficiencies or intensify loss-of-function mutations in mitochondrial genes, consequently deteriorating mitochondrial function.”

  • The paper relies on this without support.

    The process of mitochondrial fission plays a pivotal role in governing metabolism, proliferation, and mitophagy.

    “The process of mitochondrial fission plays a pivotal role in governing metabolism, proliferation, and mitophagy.”

  • The paper relies on this without support.

    An excess of peripheral fission events, unaccompanied by timely turnover, can result in the accumulation of impaired mitochondria, which disrupts the integrity of mitochondrial genomes and overall homeostasis.

    “Furthermore, an excess of peripheral fission events, unaccompanied by timely turnover, can result in the accumulation of impaired mitochondria. This accumulation subsequently disrupts the integrity of mitochondrial genomes and overall homeostasis.”

  • The paper relies on this without support.

    mtDNA encodes essential components of the OXPHOS complexes, which play a pivotal role in the synthesis of cellular ATP.

    “mtDNA encodes essential components of the OXPHOS complexes, which play a pivotal role in the synthesis of cellular ATP.”

  • The paper relies on this without support.

    The AAV-PHP.eB vector delivery system can traverse the blood-brain barrier.

    “This approach leveraged the AAV-PHP.eB vector delivery system, known for its ability to traverse the blood-brain barrier.”

  • The paper relies on this without support.

    The hippocampus is the most vulnerable region to pathological changes in AD.

    “Given that the hippocampus stands as the most vulnerable region to pathological changes in AD”
8 of 8

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • EMSA extract source differs between Results and Methods

    Major

    The Results say the EMSA extracts came from primary cultured neurons; the EMSA Methods say they were prepared from hippocampus tissue lysate.

  • Two identifiers given for lncMtDloop

    Minor

    The Figure 1 caption identifies lncMtDloop as AC0276613.1, whereas the Results identify the same gene as AC027613.1.

  • Human brain section thickness differs between figure and methods

    Minor

    Figure 4 specifies 15 μm paraffin sections for the human RNAscope assay, while the Methods specify 10 μm human autopsy paraffin-embedded sections.

  • Water-maze sample size is labeled as brain slices

    Minor

    The Figure 7 caption labels the samples for the mouse water-maze outcomes in panels O and P as brain slices, but labels the water-maze outcomes in panels Q and R as animals. The Methods also describe the maze test as being performed on mice.

  • EV3 OXPHOS assay is described with conflicting cells and EB treatment

    Minor

    The Results attribute the EV3E,F OXPHOS measurements to EB-treated N2a cells, but the EV3 caption describes primary cultured neurons without EB treatment.

5 of 5

Cites

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Authors
Xiong, W., Xu, K., Sun, J. K.-L., Liu, S., Zhao, B., Shi, J., Herrup, K., Chow, H.-M., Lu, L., & Li, J.
Affiliations
  • Peking University (CN)
  • Kunming Institute of Zoology (CN)
  • Chinese University of Hong Kong (HK)
  • Hackensack Meridian Health (US)
  • University of Pittsburgh (US)
Corresponding author
  • Xiong, Wandi
  • Xu, Kaiyu
  • Sun, Jacquelyne Ka-Li
ORCID
Venue
The EMBO Journal
Publisher
Springer Science and Business Media LLC
Published
2024-10-18
Volume
43
Issue
23
Pages
6001-6031
ISSN
  • 0261-4189 (ISSN-L)
  • 1460-2075
DOI
10.1038/s44318-024-00270-7
PMC
PMC11612450
OpenAlex
W4403523171
Cited by
17
References
75
Citations by year
2026: 12 · 2025: 5
FWCI
2.32
Type
journal article
Language
en
Open access
Licence
Locations
  • The EMBO Journal (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • MOST | National Natural Science Foundation of China (91649119, 92049105, 81821092, 8240460)
  • Alzheimer's Association (AARF-17-531566)
  • Ministry of Science and Technology of the People's Republic of China (2015CB755605)
  • PKU | Peking University Health Science Center (BMU2019YJ001)
  • 云南省科学技术厅 | Applied Basic Research Key Project of Yunnan Province (E039030401)
  • The Hong Kong Research Grants Council (RGC)-General Research Fund (GRF16100219, GRF16100718)
  • CUHK-Improvement on Competitiveness in Hiring New Faculties Funding Scheme (Ref. 133)
  • CUHK-School of Life Sciences Startup funding
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Keywords
long non-coding RNA, mitochondrial transcription, Alzheimer's disease, mitochondrial homeostasis, TFAM, mitochondrial DNA, D-loop, stem-loop structure, 3xTg-AD mice, mitochondrial dysfunction
MeSH terms
RNA, Mitochondrial, Alzheimer Disease, Animals, Disease Models, Animal, DNA-Binding Proteins, DNA, Mitochondrial, Humans, Mice, Transgenic, Mitochondria, Transcription Factors, Transcription, Genetic, Mitochondrial Proteins, Mice, RNA, Long Noncoding

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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-30.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-30.

Cited sources are checked by gpt-6-sol.

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.

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