bims-curels 2025-12-21 papers

bims-curels

Biomed News

on Leigh syndrome

Issue of 2025–12–21
twelve papers selected by
Cure Mito Foundation

Counseling and Prognostic Challenges in Survivorship and Mortality in Primary Mitochondrial Disease: Reshaping a Once Bleak Landscape.
Current understanding of mitochondrial DNA genetic diseases and gene therapy.
Quantifying variability of mitochondrial markers in m3243A > G myopathy.
Comprehensive Iranian guidelines for the diagnosis and management of mitochondrial disorders: an evidence- and consensus-based approach.
Patient perspectives of patient engagement in medicine development: a qualitative study.
Functional Screening of NDUFAF6 Variants in Knockout Cells and Complementary Computational Analysis.
Identification of Intronic Variants in NDUFA3 as a Cause of Leigh Syndrome by Whole Genome Sequencing and RNA Sequencing.
Partial restoration of mitochondrial dysfunction by AAV-Ant1 protects from dilated cardiomyopathy in Ant1-/- plus mtDNA mutant mice.
Surrogate Endpoints in Regulatory Decision-Making.
Modeling rare genetic disease with gene-edited induced pluripotent stem cells: relevance of the starting stock line.
Two genomes, one destiny: Mitophagy at the crossroads of inheritance and disease.
Ethical Considerations for Genetic Testing and Counseling in Obstetrics and Gynecology.

Pediatr Neurol. 2025 Nov 27. pii: S0887-8994(25)00370-4. [Epub ahead of print]175 223-228

Counseling and Prognostic Challenges in Survivorship and Mortality in Primary Mitochondrial Disease: Reshaping a Once Bleak Landscape.

Ibrahim Elsharkawi, Amy Goldstein, Rebecca D Ganetzky, Eva Morava.

  Primary mitochondrial diseases comprise a clinically, genetically, and biochemically heterogenous group of disorders associated with multisystemic involvement and significant morbidity and mortality of various etiologies. To date, no disease modifying therapies have been FDA approved, and treatment is largely symptomatic and supportive. Because of the rarity of mitochondrial specialists, most patients with mitochondrial diseases are cared for by clinicians without mitochondrial-specific expertise. Therefore, these clinicians by necessity rely on existing literature or older prognostic approaches which may be discordant with modern clinical practice and evolving therapeutic strategies and outcomes. Furthermore, existing literature may be skewed to the more severe end of the spectrum as publications may disproportionately focus on the most severe or unusual cases. Prognostic, therapeutic, and palliative discussions should ideally take place in a multidisciplinary setting where shared decision making can take place between the patient, family, and clinician team. Prognosis is increasingly shaped by the unprecedented development of various therapeutic modalities and personalized medicine. We aim to highlight the multipronged challenges and considerations faced in counseling patients and caregivers and draw from our own patient cohorts and observations in contemporary mitochondrial medicine to offer additional insights and future considerations for approaching patient counseling and prognostication.

Keywords:  Leigh syndrome; MELAS; Mitochondrial disease prognosis; Mitochondrial dysfunction; Primary mitochondrial disease; Survivorship

DOI:  https://doi.org/10.1016/j.pediatrneurol.2025.11.019
Yi Chuan. 2025 Dec;47(12): 1300-1325

Current understanding of mitochondrial DNA genetic diseases and gene therapy.

Cheng Tang, Shun-Qing Xu, Han-Zeng Li.

  Mitochondria, as crucial organelles within eukaryotic cells, have their proteins and RNAs encoded by both the nuclear genome and the mitochondrial genome. They play vital roles in energy regulation, cellular metabolism, signal transduction, and various other physiological activities. Additionally, mitochondria interact with multiple organelles to collectively maintain cellular homeostasis. Mitochondria can also be transferred between cells and tissues through mechanisms such as migrasomes. Mitochondrial DNA (mtDNA) mutations often cause severe inherited rare diseases, characterized by tissue specificity, heterogeneity, multiple mutation sites, and challenges in achieving a complete cure. Gene editing of mtDNA holds promise for fundamentally curing such diseases. Traditional gene-editing nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nuclease (TALENs), as well as novel gene editors like DddA-derived cytosine base editors (DdCBEs), have been demonstrated to correct certain mtDNA mutations. However, CRISPR-based technologies-despite their superior programmability and efficiency-are currently limited due to the technical bottleneck of inefficient sgRNA delivery into mitochondria. This article systematically reviews the structure and function of mitochondria, related diseases, and the current state of mtDNA gene-editing therapies. Furthermore, it explores future directions for optimizing therapeutic tools to overcome the challenge of sgRNA delivery, thereby addressing the treatment barriers posed by pathogenic mtDNA mutations in inherited rare diseases.

Keywords:  CRISPR; mitochondria; mtDNA associated rare diseases; mtDNA editing

DOI:  https://doi.org/10.16288/j.yczz.25-032
Sci Rep. 2025 Dec 19.

Quantifying variability of mitochondrial markers in m3243A > G myopathy.

Tiago M Bernardino Gomes, Jordan B Childs, Valeria Di Leo, Charlotte Warren, Gavin Hudson, Doug M Turnbull, Conor Lawless, Amy E Vincent.

  Myopathy is a prevalent and disabling feature of mitochondrial disease, in which skeletal muscle accumulates fibres with mitochondrial dysfunction in a variable mosaic pattern. This intra-individual spatial heterogeneity, a key consideration in longitudinal assessments, remains largely uncharacterised, hindering mechanistic studies and clinical trials by obscuring or confounding findings. We quantified this variability in m.3243 A > G-related myopathy, a leading cause of adult mitochondrial disease. Post-mortem biopsies from quadriceps femoris and tibialis anterior muscles of four patients were analysed for single-fibre deficiency in oxidative phosphorylation (OXPHOS) complex I and IV, while homogenate mitochondrial DNA (mtDNA) copy number and m.3243 A > G heteroplasmy were respectively determined by quantitative PCR and pyrosequencing. Bootstrapped combinatorial analyses established thresholds for minimum meaningful change above the 97.5th percentile, while accounting for anatomical biopsy distancing. Spatial variability in the proportion of OXPHOS-deficient fibres increased with distancing; within the same muscle, this threshold was 13.8% for NDUFB8 and 9.8% for MT-CO1. Variability in mtDNA copy number modestly increased with distance, while m.3243 A > G heteroplasmy remained largely stable, with within-muscle thresholds of 1,136 copies per nucleus and 8.2%, respectively. These findings provide assay-specific thresholds and offer mechanistic and translational insights for trial design, patient monitoring, and reliable detection of disease progression or therapeutic response.

Keywords:  Heteroplasmy; M.3243A > G; Mitochondria; Mitochondrial DNA copy number; Myopathy; Oxidative phosphorylation

DOI:  https://doi.org/10.1038/s41598-025-33106-3
Orphanet J Rare Dis. 2025 Dec 19. 20(1): 623

Comprehensive Iranian guidelines for the diagnosis and management of mitochondrial disorders: an evidence- and consensus-based approach.

Setila Dalili, Noushin Rostampour, Seyedeh Tahereh Mousavi, Saeid Sadeghi Joni, Nejat Mahdieh, Afagh Hassanzadeh Rad, Seyede Tahoura Hakemzadeh, Sara Nikpour, Ali Talea, Hossein Moravvej.

  Mitochondrial disorders are a heterogeneous group of inherited metabolic diseases resulting from dysfunctions in oxidative phosphorylation. These conditions predominantly affect high-energy-demand organs such as the brain, heart, liver, and muscles, leading to diverse clinical manifestations and diagnostic challenges. This article presents the first comprehensive Iranian guideline for the diagnosis and management of mitochondrial diseases, developed through an evidence-based and consensus-driven methodology. We conducted a structured literature review across major biomedical databases from 2000 to 2023 and engaged a multidisciplinary panel of Iranian experts to establish context-specific recommendations. The guideline covers clinical presentations, laboratory biomarkers, neuroimaging features, genetic diagnostics, and treatment approaches including "cocktail therapy" and acute management protocols. It also integrates a mitochondrial disease scoring system to standardize diagnosis and provides detailed insights into safe anesthesia practices for affected individuals. Special attention is given to practical implementation in resource-limited settings. These guidelines aim to enhance diagnostic accuracy, optimize management strategies, and improve the quality of life for patients with mitochondrial disorders across Iran and similar healthcare systems.

Keywords:  Diagnosis; Genetic testing; Mitochondrial diseases

DOI:  https://doi.org/10.1186/s13023-025-04127-y
Curr Med Res Opin. 2025 Dec 20. 1-17

Patient perspectives of patient engagement in medicine development: a qualitative study.

Fatima I Auwal, Elizabeth J Clark, Caroline S Copeland, Graham R McClelland.

   INTRODUCTION: Patient engagement (PE) is increasingly recognized as an essential component of medicine development, yet there remains limited empirical evidence on its value from the patient perspective. Existing literature points to benefits such as empowerment, improved trial design, and greater acceptability, but challenges around communication, authenticity, and sustainability persist.
OBJECTIVES: This study explored the perceived value, challenges, and strategies for effective PE from the perspective of patients, carers, and patient advocates involved in medicines development.
METHODS: A qualitative study was conducted using semi-structured interviews on Microsoft Teams. Participants were recruited via LinkedIn and academic networks if they had lived experience of a health condition, caregiving responsibilities, or advocacy roles and had engaged with the pharmaceutical industry. Twenty-two interviews were conducted online between 23 April and 26 November 2024, recorded, transcribed, and analyzed using reflexive thematic analysis.
RESULTS: Six overarching themes and 23 sub-themes were identified covering participants' understanding, motivations, initiatives, value, challenges and strategies for being involved. Engagement was valued for enhancing clinical trial outcomes, personal empowerment, and community support. Challenges included structural barriers, tokenism, lack of feedback, and inconsistent practices across companies and patient organizations. Strategies to improve PE emphasized clear communication, simplification and formalization of processes, greater inclusivity, capacity building, and stronger alliances among advocacy groups. Participants also highlighted the need for fair compensation and balancing regulation with meaningful involvement.
CONCLUSIONS: Patients perceive PE as transformative when authentic, inclusive, and supported by transparent communication. Addressing structural inconsistencies, recognizing diverse patient identities, and prioritizing relational over transactional approaches are critical for embedding meaningful and sustainable PE in medicine development.

Keywords:  Patient engagement; medicine development; motivation; patients; value, challenges

DOI:  https://doi.org/10.1080/03007995.2025.2605694
J Clin Lab Anal. 2025 Dec 15. e70147

Functional Screening of NDUFAF6 Variants in Knockout Cells and Complementary Computational Analysis.

Feng Jiang, Ayumu Sugiura, Yoshihito Kishita, Kohta Nakamura, Xinju Qi, Yuxin Liu, Kei Murayama, Yasushi Okazaki.

   BACKGROUND: NDUFAF6 (NADH:ubiquinone oxidoreductase complex assembly factor 6) is a nuclear-encoded gene essential for the assembly of mitochondrial respiratory chain complex I (NADH:ubiquinone oxidoreductase), the largest and most intricate component of the oxidative phosphorylation system, and its mutations are associated with mitochondrial diseases. However, the functional consequences of many NDUFAF6 variants remain unclear.
METHODS: We selected 24 NDUFAF6 variants from published studies and our internal sequencing database. Using CRISPR-Cas9, we generated NDUFAF6 knockout HEK293FT cells and transfected them with wild-type or mutant expression vectors. Functional validation was performed using a luminescence-based ATP assay under mitochondrial stress. In silico predictions were conducted using multiple tools, and ColabFold, MitoFates, and ProtScale were used for structural modeling, mitochondrial targeting analysis, and hydrophobicity profiling.
RESULTS: Six variants (p.Pro26fs, p.Asp69Val, p.Arg113Ter, p.Leu193Ter, p.Arg303Ter, and p.Lys331Arg) failed to restore ATP levels in knockout cells, indicating a significant loss of function. Among these, p.Asp69Val and p.Arg113Ter were consistent with ClinVar classifications. However, other variants such as p.Arg303Ter and p.Lys331Arg also showed functional impairment, highlighting discrepancies between database annotations and experimental results. Most variants retained mitochondrial targeting features, though p.Pro26fs exhibited a shifted MPP cleavage site. Hydrophobicity analysis indicated structural instability in several variants.
CONCLUSIONS: Our study highlights the importance of experimental validation in improving the classification of NDUFAF6 variants. The ATP-based functional assay provides a useful and quantitative approach for assessing mitochondrial variant effects, which may complement in silico predictions and contribute to future efforts in mitochondrial disease diagnostics.

Keywords:   NDUFAF6 ; ATP assay; mitochondrial diseases; mitochondrial dysfunction; variants of uncertain significance

DOI:  https://doi.org/10.1002/jcla.70147
Neurol Genet. 2026 Feb;12(1): e200330

Identification of Intronic Variants in NDUFA3 as a Cause of Leigh Syndrome by Whole Genome Sequencing and RNA Sequencing.

Kohta Nakamura, Yoshihito Kishita, Ayumu Sugiura, Kokoro Ozaki, Yukiko Yatsuka, Naoyuki Matsumoto, Atsuko Okazaki, Holger Prokisch, Koichi Maruyama, Hiroyasu Iwasa, Kei Murayama, Hiroshi Matsumoto, Akira Ohtake, Yuichi Shiraishi, Yasushi Okazaki.

Background and Objectives: Leigh syndrome is an important manifestation of childhood-onset primary mitochondrial disease. Panel sequencing and whole exome sequencing are cost-effective for diagnosing mitochondrial diseases; however, more than half of mitochondrial disease cases remain genetically undiagnosed. This study aimed to demonstrate that combining whole genome sequencing (WGS) and RNA sequencing (RNA-seq) analyses can identify disease-causing variants that would otherwise be missed.
Methods: We performed WGS and RNA-seq on a patient with Leigh syndrome. Chromosomal phasing using Sanger sequencing of parental and patient blood samples was conducted to confirm compound heterozygous variants. RNA-seq data were analyzed for splicing abnormalities. Overexpression studies of wild-type NDUFA3 in patient-derived fibroblasts were performed to assess restoration of mitochondrial function.
Results: We discovered compound heterozygous intronic variants (c.86-16_86-15del in intron2 and c.164-362G>A in intron3) of the NDUFA3 gene. RNA-seq data analysis revealed intron retention and exonization in NDUFA3. Exonization was related to a variant involving the mobile element Alu that resulted in complex abnormal splicing events. Overexpression of wild-type NDUFA3 restored mitochondrial dysfunction in patient-derived fibroblasts, confirming NDUFA3 as a Leigh syndrome causative gene.
Discussion: This study highlights the importance of combining WGS and RNA-seq and provides new insights into detecting abnormalities in deep intronic regions, particularly those involving mobile elements, such as Alu. This approach can play a crucial role in identifying genetic variations and elucidating transcriptional control mechanisms that are not readily achieved by conventional methods, especially in the context of mobile element-induced complexities.

DOI: https://doi.org/10.1212/NXG.0000000000200330
Nat Commun. 2025 Dec 15.

Partial restoration of mitochondrial dysfunction by AAV-Ant1 protects from dilated cardiomyopathy in Ant1-/- plus mtDNA mutant mice.

Alessia Angelin, Kierstin Keller, Peiran Lu, Joseph W Guarnieri, Gabrielle A Widjaja, Rasheed Sule, Kevin Janssen, Arnold Olali, Zimu Cen, Valeria Carosi, Maina Beauplan, Deborah G Murdock, Prasanth Potluri, Liming Pei, Douglas C Wallace.

Primary mitochondrial disease (PMD) patients manifesting cardiomyopathy are twice as likely to die as other PMD patients. One PMD with cardiomyopathy is caused by null mutations in the heart-muscle isoform of the adenine nucleotide translocator (SLC25A4, ANT1) gene, with the severity of cardiomyopathy mediated by mitochondrial DNA. To optimize strategies for addressing mitochondrial cardiomyopathy, we generated an Ant1 null mouse and combined it with the ND6P25L mitochondrial DNA mutation to mimic the hypertrophic versus dilated cardiomyopathies observed in patients. Here, we transduce the neonatal Ant1-/- and Ant1-/-+ND6P25L mouse hearts with an AAV2/9-pDes-Gfp-mAnt1 cDNA vector. We show that restoration of just 10% of Ant1 gene expression was sufficient to ameliorate the cardiomyopathies in these mice. Proteomics and single-nucleus RNA sequencing reveal the reversal of dysregulated mitochondrial metabolic genes, including PGC1α, as well as cardiac contractile and extracellular matrix proteins. Hence, a modest increase in cardiac mitochondrial energetics can have profound benefits on cardiac function and is effective in treating mitochondrial cardiomyopathy.

DOI: https://doi.org/10.1038/s41467-025-67134-4
Clin Transl Sci. 2025 Dec;18(12): e70445

Surrogate Endpoints in Regulatory Decision-Making.

Linda J B Jeng, Jeffrey Siegel.

  To support approval, FDA requires substantial evidence of effectiveness that demonstrates a drug improves meaningful clinical outcomes as measured by how a patient feels, functions, or survives. Effectiveness is measured directly (e.g., by patient-reported outcome or other clinical outcome assessment) or indirectly (i.e., by use of a surrogate endpoint (SE) that predicts how a patient will feel, function, or survive). Use of biomarkers as SEs can hasten drug development for patients with unmet medical needs.

Keywords:  biomarkers; drug development; surrogate endpoints

DOI:  https://doi.org/10.1111/cts.70445
Stem Cells Transl Med. 2025 Nov 24. pii: szaf065. [Epub ahead of print]14(12):

Modeling rare genetic disease with gene-edited induced pluripotent stem cells: relevance of the starting stock line.

Ashok R Dinasarapu, Diane J Sutcliffe, Erkin Ozel, Anike Thite, Lauren Grychowski, Jasper E Visser, Ellen J Hess, Sharon M Kolk, H A Jinnah.

  Induced pluripotent stem cells (iPSCs) are commonly used to model human genetic diseases. Two main strategies are used. The first involves making iPSC lines from individual cases with a disease, and the second involves making disease-relevant gene edits in established iPSC lines. Because generating gene-edited lines is time consuming and expensive, most studies begin with one starting iPSC stock line and evaluate several gene-edited sublines. The current studies focus on gene-editing to model Lesch-Nyhan disease (LND), which is caused by mutations in the HPRT1 gene. The same pathogenic c.508C>T edit was made in four well-established stock lines, and three gene-edited lines were isolated from each. RNA sequencing (RNAseq) was, then, used to evaluate the impact of the gene edit. Gene-edited lines were compared to their corresponding stock lines, as well as to each other. An aggregate analysis of all lines combined was also conducted to determine the most robust findings across all lines. Results from gene editing were further compared with iPSC lines derived from individual cases with LND, to determine how closely findings from gene editing match results obtained with case-derived lines. There were two main findings. First, the same gene edit has a different impact on gene expression when starting with different starting stock lines. Second, the gene editing strategy does not produce the same results as the case-derived strategy. Potential explanations for these differences are addressed, along with the relevance of these two different strategies for disease modeling.

Keywords:  HPRT1; Lesch–Nyhan disease; disease modeling; human induced pluripotent stem cell; hypoxanthine-guanine phosphoribosyltransferase

DOI:  https://doi.org/10.1093/stcltm/szaf065
Cell Chem Biol. 2025 Dec 18. pii: S2451-9456(25)00390-3. [Epub ahead of print]32(12): 1439-1441

Two genomes, one destiny: Mitophagy at the crossroads of inheritance and disease.

Chih-Yao Chung, Kritarth Singh, Brigida R Pinho, Jorge M A Oliveira, Michael R Duchen.

Mechanisms ensuring mito-nuclear compatibility are poorly understood. In a recent study published in Science,1 Frison et al. found that a mouse mitochondrial DNA (mtDNA) mutation can escape mitochondrial surveillance in embryogenesis by repressing the ubiquitin-proteasome system. Inhibition of USP30 restored ubiquitin-mediated mitophagy and reduced mutant burden, suggesting a potential therapeutic target for mtDNA disorders.

DOI: https://doi.org/10.1016/j.chembiol.2025.11.010
Obstet Gynecol. 2026 Jan 01. 147(1): e16-e23

Ethical Considerations for Genetic Testing and Counseling in Obstetrics and Gynecology.

Given the increasing availability and complexity of genetic testing, it is imperative that practicing obstetrician-gynecologists and other health care professionals maintain a firm comprehension of the benefits, limitations, and risks of genetic testing offered in their practices. The use of genetic testing has the potential to improve the care of patients and their families; however, the nuances and possible implications of test results can be challenging to interpret and effectively communicate, highlighting the importance of appropriate pretest and posttest counseling as well as expert consultation, when applicable. The challenges for practicing obstetrician-gynecologists often are compounded by severe limitations in time, limited expertise with new testing or rare results, and potentially limited scientific literacy among patients. This document seeks to explore the ethical considerations obstetricians and gynecologists should consider when offering genetic testing in their practices.

DOI: https://doi.org/10.1097/AOG.0000000000006131