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RARB-related syndromic microphthalmia

Asta Literature Retrieval: Pathophysiology and clinical mechanisms of RARB-related syndromic microphthalmia. Core disease mechanisms, molecular...

2026-07-30
Asta MONDO:0014229 Model: Asta Scientific Corpus Retrieval 19 citations

Asta Literature Retrieval: Pathophysiology and clinical mechanisms of RARB-related syndromic microphthalmia. Core disease mechanisms, molecular...

This report is retrieval-only and is generated directly from Asta results.

  • Papers retrieved: 19
  • Snippets retrieved: 20

Relevant Papers

[1] Molecular Genetics of Bartter Syndrome: Bridging Genotype–Phenotype Correlations and Precision Therapeutics

  • Authors: Lina Zhu, Yang Li, Yiyao Bao
  • Year: 2026
  • Venue: Current Issues in Molecular Biology
  • URL: https://www.semanticscholar.org/paper/a5e1ddccfa7d333834c4d32be123c71bfd573f83
  • DOI: 10.3390/cimb48040422
  • PMID: 42042082
  • PMCID: 13114623
  • Summary: A comprehensive framework to provide a comprehensive framework to facilitate precise diagnosis and individualized treatment strategies, ultimately advancing precision medicine in the management of Bartter syndrome is provided.
  • Evidence snippets:
  • Snippet 1 (score: 0.424) > Molecular genetic research on Bartter syndrome has made remarkable strides, elucidating the principal BS genes SLC12A1, KCNJ1, CLCNKB, BSND, and MAGED2 and their corresponding protein defects, thereby refining the molecular framework of disease classification while separating CaSR-associated Bartter-like disease from the core canonical BS spectrum. This progress has significantly deepened our understanding of the underlying pathophysiology and provided an essential framework for correlating genotypes with clinical phenotypes. However, the intricate relationship between genetic mutations and clinical manifestations remains complex and multifaceted, reflecting the profound heterogeneity of the syndrome. Addressing these diagnostic challenges and refining disease classification beyond traditional clinical criteria requires an integrative approach that seamlessly balances high-throughput sequencing technologies with rigorous functional studies. > The mechanisms by which these genetic mutations lead to protein dysfunction are diverse, encompassing critical defects in protein expression, impaired membrane localization, and direct functional impairments. Notably, aberrant protein folding, endoplasmic reticulum-associated degradation (ERAD), and splicing abnormalities have emerged as critical pathogenic pathways. These mechanistic insights not only enhance our fundamental understanding of the disease but also highlight highly promising therapeutic targets. While current treatments remain predominantly symptomatic, focusing primarily on managing electrolyte imbalances and associated complications, they inherently fail to address the underlying molecular defects driving the disease. > The precise identification of specific molecular defects opens innovative avenues for the development of targeted interventions aimed at correcting or compensating for specific protein abnormalities. For instance, molecular chaperones that assist in protein folding, agents that modulate aberrant splicing, and future gene-based strategies represent important experimental directions for mechanism-based therapy. Consequently, the future of Bartter syndrome management may increasingly move toward precision medicine tailored to the molecular pathology of individual patients. However, the transition from concept to clinical implementation will require substantial additional functional, translational, and trial-level evidence. Such mechanism-based strategies promise not only to alleviate clinical symptoms but to fundamentally modify disease progression, thereby drastically improving long-term prognosis and quality of life for patients.

[2] Animal and cellular models of microphthalmia

  • Authors: Philippa Harding, D. Cunha, M. Moosajee
  • Year: 2021
  • Venue: Therapeutic Advances in Rare Disease
  • URL: https://www.semanticscholar.org/paper/4d2e4dcc85cec0b36a5e8dc218ea73bed92976b1
  • DOI: 10.1177/2633004021997447
  • PMID: 37181112
  • PMCID: 10032472
  • Citations: 12
  • Influential citations: 1
  • Summary: By understanding the causes of microphthalmia, researchers can develop treatments to prevent or reduce the severity of this condition and establish genotype–phenotype correlations to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling.
  • Evidence snippets:
  • Snippet 1 (score: 0.419) > Converting genomic annotations from animal models to humans can be misleading, due to divergence in genetic regulation of eye development. Evidence from human cellular studies can therefore be more practical for identifying and validating novel candidates. Generation of transcriptomic and epigenomic data from humanderived 3D microphthalmic models could provide datasets from which pathway components and disease mechanisms can be identified, providing both validation for putative genetic causes found in patients as well as resources to discover new genes to screen in microphthalmic cohorts by next-generation sequencing. To date, few 3D cellular disease models have been generated, but as protocols grow more efficient, and multi-omic technologies become more affordable, cellular modelling could become an effective strategy for detecting molecular causes of microphthalmia. > Modelling environmental causes of microphthalmia in cells. The effect of exogenous chemicals on cellular function can be quickly investigated in 2D cell culture, due to efficient diffusion of compounds. Retinoic acid treatment of ARPE-19 cells induced dose-dependent increase in RARβ mRNA and protein within 24 h, which was inhibited by treatment with antagonist LE135. 331 tilising more complex 3D models, toxins and potential treatments can be applied directly to mature human ocular tissues without bioavailability and drug metabolism issues, allowing greater understanding of effect on ocular development and its regulation. Importantly, using journals.sagepub.com/home/trd Therapeutic Advances in Rare Disease 2 patient-derived cells can shed light on the effects of environmental factors on different genetic backgrounds and particular modifiers, leading to more precise clinical advice and care.
  • Snippet 2 (score: 0.408) > Microphthalmia is a rare developmental eye disorder affecting 1 in 7000 births. It is defined as a small (axial length ⩾2 standard deviations below the age-adjusted mean) underdeveloped eye, caused by disruption of ocular development through genetic or environmental factors in the first trimester of pregnancy. Clinical phenotypic heterogeneity exists amongst patients with varying levels of severity, and associated ocular and systemic features. Up to 11% of blind children are reported to have microphthalmia, yet currently no treatments are available. By identifying the aetiology of microphthalmia and understanding how the mechanisms of eye development are disrupted, we can gain a better understanding of the pathogenesis. Animal models, mainly mouse, zebrafish and Xenopus, have provided extensive information on the genetic regulation of oculogenesis, and how perturbation of these pathways leads to microphthalmia. However, differences exist between species, hence cellular models, such as patient-derived induced pluripotent stem cell (iPSC) optic vesicles, are now being used to provide greater insights into the human disease process. Progress in 3D cellular modelling techniques has enhanced the ability of researchers to study interactions of different cell types during eye development. Through improved molecular knowledge of microphthalmia, preventative or postnatal therapies may be developed, together with establishing genotype–phenotype correlations in order to provide patients with the appropriate prognosis, multidisciplinary care and informed genetic counselling. This review summarises some key discoveries from animal and cellular models of microphthalmia and discusses how innovative new models can be used to further our understanding in the future. Plain language summary Animal and Cellular Models of the Eye Disorder, Microphthalmia (Small Eye) Microphthalmia, meaning a small, underdeveloped eye, is a rare disorder that children are born with. Genetic changes or variations in the environment during the first 3 months of pregnancy can disrupt early development of the eye, resulting in microphthalmia. Up to 11% of blind children have microphthalmia, yet currently no treatments are available. By understanding the genes necessary for eye development, we can determine how disruption by genetic changes or environmental factors can cause this condition. This helps us understand why microphthalmia

[3] Visualization of automatically combined disease maps and pathway diagrams for rare diseases

  • Authors: P. Gawron, D. Hoksza, Janet Piñero, M. Peña-Chilet, M. Esteban-Medina et al.
  • Year: 2023
  • Venue: Frontiers in Bioinformatics
  • URL: https://www.semanticscholar.org/paper/e056afeedddf14232c07099779301bdb7244a93d
  • DOI: 10.3389/fbinf.2023.1101505
  • PMID: 37502697
  • PMCID: 10369067
  • Citations: 2
  • Summary: This work allows for an ad-hoc construction of molecular diagrams combined from different sources, preserving their layout and graphical style, but integrating them into a single resource, to reduce time consuming tasks of prototyping of a molecular disease map.
  • Evidence snippets:
  • Snippet 1 (score: 0.402) > Retinitis pigmentosa (RP) is a rare genetic disorder that causes the progressive degeneration of the retina photoreceptor cells (rod and cones). The heterogeneity of RP makes it not a single entity but rather a group of disorders, meaning that it can be caused by mutations in many different genes (Ayuso and Millan, 2010). Several cellular pathways have been implicated in the degeneration of photoreceptor cells in RP, including phototransduction, cell survival and metabolism, and vesicle trafficking (Ferrari et al., 2011). The phototransduction pathway is responsible for converting light into electrical signals, and mutations in genes such as RHO, RP1, and RDS that encode phototransduction proteins can lead to decreased visual sensitivity and progressive vision loss (Mannu, 2014). In the cell survival and metabolism pathway, which is responsible for maintaining the health of retinal cells including photoreceptor cells, mutations in genes like PRPF31 (Frontiers, 2021) and PRPH2 (Chakraborty et al., 2020) can cause increased cell death, abnormal disk formation, photoreceptor cell death, and retinal dysfunction. Protein trafficking within the photoreceptors is key to maintaining the overall retinal homeostasis. Mutations in genes encoding vesicle trafficking proteins can result in cellular dysfunction and increased cell death (Bales and Gross, 2016). The constructed RP Map from our workflow highlights the molecular mechanisms involved in RP pathophysiology. As we can see in the WikiPathways section on the middle-left, pathways describing processes involved in ciliopathies, with enrichment of gene variants associated with RP. The dysfunction of photoreceptors cilia proteins can result in various symptoms such as retinal degeneration and other pleiotropic phenotypes (Adams et al., 2007). Other key molecular mechanisms captured by the Reactome section, at the bottom-right side of the map, are Visual phototransduction, which is a well-defined hallmark process affected by RP (Ferrari et al., 2011), and Cell surface interactions at the vascular wall.

[4] CHM/REP1 Transcript Expression and Loss of Visual Function in Patients Affected by Choroideremia.

  • Authors: V. Di Iorio, G. Esposito, F. De Falco, Rosa Boccia, Tiziana Fioretti et al.
  • Year: 2019
  • Venue: Investigative ophthalmology & visual science
  • URL: https://www.semanticscholar.org/paper/e9dbb73f87a3e872a0f9d42b948f10b47245e3c8
  • DOI: 10.1167/iovs.18-25501
  • PMID: 30995293
  • Citations: 17
  • Summary: Analysis of morphological and functional parameters in choroideremia patients showed a slow disease progression, particularly in the first decades of life, and reevaluation of clinical and molecular data suggests exploring the genotype-phenotype relationship based on CHM/REP1 transcript expression.
  • Evidence snippets:
  • Snippet 1 (score: 0.402) > Functional studies showed that efficiency of the REP1-mediated prenylation is higher than Rab escort protein 2, 5 supporting the evidence that Rab escort protein 2 alone is not able to replace the total loss of CHM/ REP1 function in CHM patients. Despite the characterization of the genetic basis of the disease, until now no studies have established the correlation between mechanisms of vision loss associated with CHM and the genotypic pattern. A study by Freund et al. 6 supported the fact that the rare CHM/REP1 pathogenic missense variants do not seem to cause a milder phenotype when compared with whole gene deletions or to the most common type of CHM/REP1 pathogenic variants (i.e., those leading to putative truncated proteins), thereby indicating that there are no genotype-phenotype correlations in males affected by CHM. > To date, few reports scanned the longitudinal study of the natural history of CHM. Some studies investigated the clinical evolution of the disease in terms of visual acuity 7,8 ; other studies reported both clinical and genetic analyses, focusing on visual impairment and visual field constriction 6 and on electrophysiological variability. 9 Because clinical studies evaluating the effect of experimental treatments for CHM are underway, the accurate description of the disease course in genetically characterized CHM patients is warranted. 10,11 nowledge regarding CHM natural evolution and any genotype correlation could drive the selection of subjects to be enrolled in clinical trials as well as the outcomes of experimental therapy on disease progression. To this end, the present study aims to track disease progression during a long-term follow-up period in a cohort of patients with complete clinical and molecular diagnoses of CHM and to unveil any new phenotype-genotype correlations.

[5] Subretinal fibrosis in neovascular age-related macular degeneration: current concepts, therapeutic avenues, and future perspectives

  • Authors: Louis Tenbrock, Julian Wolf, Stefaniya K Boneva, A. Schlecht, H. Agostini et al.
  • Year: 2021
  • Venue: Cell and Tissue Research
  • URL: https://www.semanticscholar.org/paper/9653e7c50b745b52fc7018e2a8c7552deb2c739a
  • DOI: 10.1007/s00441-021-03514-8
  • PMID: 34477966
  • PMCID: 8975778
  • Citations: 125
  • Influential citations: 4
  • Summary: This review provides an overview of subretinal fibrosis in neovascular AMD, by summarizing its clinical manifestations, exploring the current understanding of the underlying cellular and molecular mechanisms and discussing potential therapeutic approaches to inhibit sub retinal Fibrosis in the future.
  • Evidence snippets:
  • Snippet 1 (score: 0.400) > However, there are challenging hurdles that need to be overcome before treatment can be translated into clinical practice. Although considerable progress has been made in recent years, our understanding of the molecular and cellular mechanisms needs to be further enhanced. Continued scientific studies on human CNV membranes exploiting single-cell proteomics, single-cell RNA sequencing, and systems biology approaches will be necessary to define the cell types involved and the signalling pathways activated in them. Single-cell RNA sequencing approaches, for example, can reveal the mRNA expression profile of complex and rare cell populations in MNV, uncover regulatory relationships between genes, and track the trajectories of distinct cell lineages in disease progression (Hwang et al. 2018). These studies can be complemented by proteomic studies, e.g. by mass spectrometry, on MNV tissues, which will allow further delineation of the mechanisms involved in the diseases and identification of new biomarkers or drug targets. In addition, systems biology approaches will be valuable to integrate genomic, transcriptomic, proteomic, pharmacological, and clinical data from patients with nAMD into mathematical models that may predict disease onset and progression, identify biomarkers, and eventually unravel disease-causing mechanisms (Handa et al. 2019). However, as human MNV membranes are no longer surgically extracted in clinical practice, these single cell analyses will be difficult to accomplish. Therefore, further efforts should be made to establish novel and optimised animal models that resemble the human situation and the clinical picture of AMD even more closely and may thus be available for the preclinical evaluation of potential future therapeutic approaches. Another difficult obstacle will be the design of effective clinical trials with well-defined clinical endpoints. For this purpose, predictive serum markers, improved imaging techniques or other clinical features that can serve to accurately monitor the course of subretinal fibrosis in a quantitative manner are needed. In addition, the search for genetic factors, such as single nucleotide polymorphisms (SNPs), should continue to determine the individual relative risk of developing fibrosis.

[6] Identification of 13 novel USH2A mutations in Chinese retinitis pigmentosa and Usher syndrome patients by targeted next-generation sequencing

  • Authors: Ling-hui Qu, Xin Jin, Y. Long, Jia-yun Ren, Chuang-huang Weng et al.
  • Year: 2020
  • Venue: Bioscience Reports
  • URL: https://www.semanticscholar.org/paper/a82d96818d129b6a03065b51851df3a190f4d706
  • DOI: 10.1042/BSR20193536
  • PMID: 31904091
  • PMCID: 6974426
  • Citations: 5
  • Summary: These findings provide a basis for investigating genotype–phenotype relationships in Chinese USH II and RP patients and for clarifying the pathophysiology and molecular mechanisms of the diseases associated with USH2A mutations.
  • Evidence snippets:
  • Snippet 1 (score: 0.397) > Abstract Background: The USH2A gene encodes usherin, a basement membrane protein that is involved in the development and homeostasis of the inner ear and retina. Mutations in USH2A are linked to Usher syndrome type II (USH II) and non-syndromic retinitis pigmentosa (RP). Molecular diagnosis can provide insight into the pathogenesis of these diseases, facilitate clinical diagnosis, and identify individuals who can most benefit from gene or cell replacement therapy. Here, we report 21 pathogenic mutations in the USH2A gene identified in 11 Chinese families by using the targeted next-generation sequencing (NGS) technology. Methods: In all, 11 unrelated Chinese families were enrolled, and NGS was performed to identify mutations in the USH2A gene. Variant analysis, Sanger validation, and segregation tests were utilized to validate the disease-causing mutations in these families. Results: We identified 21 pathogenic mutations, of which 13, including 5 associated with non-syndromic RP and 8 with USH II, have not been previously reported. The novel variants segregated with disease phenotype in the affected families and were absent from the control subjects. In general, visual impairment and retinopathy were consistent between the USH II and non-syndromic RP patients with USH2A mutations. Conclusions: These findings provide a basis for investigating genotype–phenotype relationships in Chinese USH II and RP patients and for clarifying the pathophysiology and molecular mechanisms of the diseases associated with USH2A mutations.

[7] Identification of biomarkers and immune microenvironment associated with pterygium through bioinformatics and machine learning

  • Authors: Li-Wei Zhang, Ji Yang, Hua Jiang, Xiu-Qiang Yang, Ya-Nan Chen et al.
  • Year: 2024
  • Venue: Frontiers in Molecular Biosciences
  • URL: https://www.semanticscholar.org/paper/1dfcbb05c1d5dd83452fc12b72917422400a2fa7
  • DOI: 10.3389/fmolb.2024.1524517
  • PMID: 39722894
  • PMCID: 11668640
  • Citations: 7
  • Summary: The identification of pivotal feature gene KRT10 and NGEF provide valuable insights into the molecular mechanisms underlying pterygium progression, and key miRNAs and candidate drugs targeting these feature genes are identified.
  • Evidence snippets:
  • Snippet 1 (score: 0.392) > Current research on pterygium has largely focused on its clinical manifestations and surgical management. However, the molecular mechanisms underlying pterygium development remain poorly understood, creating a gap in knowledge that could inform future therapeutic strategies. In addition, there are also immune inflammation, cell proliferation and apoptosis disorders and lipid metabolism disorders and other related mechanisms involved in the development of pterygium (Shahraki et al., 2021;Chalkia et al., 2019;Kalogeropoulos et al., 2020;Rubeshkumar et al., 2020). Recent studies have highlighted the importance of inflammatory processes in pterygium pathology, revealing that the disease is associated with a heightened inflammatory response and altered immune cell infiltration within the conjunctival tissue (Labbé et al., 2010). This suggests that targeting inflammatory pathways may offer new avenues for intervention. > Currently, there is a lack of consensus regarding the risk factors and clear molecular mechanisms underlying pterygium. Our study aims to contribute to a deeper understanding of pterygium by exploring these risk factors and potential molecular mechanisms. High-throughput RNA sequencing technologies have emerged as powerful tools for investigating gene expression profiles associated with various diseases, including pterygium. Studies employing RNA sequencing have demonstrated significant differences in gene expression between pterygium and normal conjunctival tissues, providing insights into the molecular pathways involved in pterygium development (Yoon et al., 2023). Furthermore, machine learning techniques such as random forests (RF) and support vector machines (SVM) have been applied to identify key gene signatures associated with pterygium, enhancing the predictive power of genomic data (Uddin et al., 2019). Figure 1 depicts our research protocol. > Therefore, an in-depth exploration of the molecular mechanisms underlying pterygium pathogenesis holds significant importance for disease prevention, treatment, and the identification of potential drug targets. Given the complexity and uncertainty surrounding the risk factors and molecular mechanisms of pterygium, we aim to screen for differentially expressed genes in pterygium and bulbar conjunctiva tissues through transcriptomics research. Additionally, we seek to identify module gene sets associated with the pterygium phenotype and analyze their biological functions.

[8] Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome

  • Authors: S. Otsuji, Y. Nishio, M. Tsujita, M. Rio, C. Huber et al.
  • Year: 2022
  • Venue: Journal of Medical Genetics
  • URL: https://www.semanticscholar.org/paper/5bfb9432a8e6160de9c68b2c40ed8f99c56835b3
  • DOI: 10.1136/jmg-2022-108602
  • PMID: 36113987
  • PMCID: 10086474
  • Citations: 22
  • Influential citations: 1
  • Summary: VPS35L-associated RSS is a distinct clinical entity with diverse phenotype and severity, with a possible molecular mechanism of hypercholesterolaemia, and new insight is provided into the essential and distinctive role of Retriever in human development.
  • Evidence snippets:
  • Snippet 1 (score: 0.391) > ][10][11][12] We previously reported siblings with biallelic loss-of-function variants in VPS35L, which is listed as the third responsible gene for RSS (MIM619135). The siblings showed overlapping phenotypes that were similar to 3C syndrome, including the triad of RSS, as well as global developmental delay, skeletal malformation and ophthalmological malformation. That said, they exhibited a more severe disease condition compared with patients with RSS that had WASHC5 or CCDC22 pathogenic variants. The elder girl died in the infantile period due to sudden cardiac arrest while the younger boy presented with a variety of severe complications, including short stature (−6 SD), microphthalmia, coloboma, proteinuria, severe global developmental delay and skeletal malformation that included vertebral body hypoossification, breast bone aplasia, shortened ulnae with radial bowing, short limbs and chondrodysplasia punctata. > To better understand the clinical manifestations of VPS35Lassociated RSS, more clinical information is required. While impairment of cell surface protein recycling and the subsequent reduction of protein expression level is likely to be a molecular cause of the observed clinical phenotypes, the underlying molecular mechanisms in these patients have not been well investigated. In this study, we sought to understand the clinical features of patients with VPS35L variants, and to uncover the molecular dysfunction in VPS35L and the Retriever complex that leads to human disorders.

[9] New therapeutic targets in rare genetic skeletal diseases

  • Authors: M. Briggs, Peter A. Bell, M. Wright, K. A. Pirog
  • Year: 2015
  • Venue: Expert Opinion on Orphan Drugs
  • URL: https://www.semanticscholar.org/paper/1363107f71ae6d2d60abca471cddf3da5d13644b
  • DOI: 10.1517/21678707.2015.1083853
  • PMID: 26635999
  • PMCID: 4643203
  • Citations: 39
  • Influential citations: 1
  • Summary: An overview of disease mechanisms that are shared amongst groups of different GSDs and potential therapeutic approaches that are under investigation are described to generate critical mass for the identification and validation of novel therapeutic targets and biomarkers.
  • Evidence snippets:
  • Snippet 1 (score: 0.391) > However, emerging knowledge suggests that the primary genetic defect may be less important than the cells' response to the expression of the mutant gene product [107]. Moreover, the largely overlooked response of a cell (i.e. chondrocyte) to the abnormal extracellular environment is also important for disease progression as illustrated by several GSDs discussed in this review. > It is important that 'omics'-based approaches and technologies are systematically applied to the study of rare GSDs so that definitive reference profiles and disease signatures are generated for each phenotype. These can then be used in a Systems Biology approach to identify both common and dissimilar pathological signatures and disease mechanisms. This approach is entirely dependent upon relevant in vitro and in vivo models (and also novel 'disease-mechanism phenocopies' [107]) for testing new diagnostic and prognostic tools and for determining the molecular mechanisms that underpin the pathophysiology so that effective therapeutic treatments can be developed and validated. This approach will eventually lead to personalized treatments and care strategies centred on shared disease mechanisms with the use of relevant biomarkers to monitor the efficacy of treatment and disease progression. > It is vital that all relevant stakeholders are involved from the outset in defining the appropriate outcomes of any potential therapeutic regime. The perceptions of a successful therapy can differ widely between the clinical academic community and the relevant patient-support groups and it is vital that there is engagement on all these issues. > In summary, the identification of causative genes and mutations for GSDs over the last 20 years, coupled with the generation and in-depth analysis of a plethora of relevant cell and mouse models, has derived new knowledge on disease mechanisms and suggested potential therapeutic targets. The fast-evolving hypothesis that clinically disparate diseases can share common disease mechanisms is a powerful concept that will generate critical mass for the identification and validation of novel therapeutic targets and biomarkers.

[10] Human Dermal Fibroblast: A Promising Cellular Model to Study Biological Mechanisms of Major Depression and Antidepressant Drug Response

  • Authors: P. Mesdom, R. Colle, É. Lebigot, S. Trabado, Eric Deflesselle et al.
  • Year: 2020
  • Venue: Current Neuropharmacology
  • URL: https://www.semanticscholar.org/paper/79368e365458486de96794333613c12a6063bf54
  • DOI: 10.2174/1570159X17666191021141057
  • PMID: 31631822
  • PMCID: 7327943
  • Citations: 15
  • Summary: This review highlights the great and still underused potential of HDF, which stands out as a very promising tool in the understanding of MDD and AD mechanisms of action.
  • Evidence snippets:
  • Snippet 1 (score: 0.391) > Background: Human dermal fibroblasts (HDF) can be used as a cellular model relatively easily and without genetic engineering. Therefore, HDF represent an interesting tool to study several human diseases including psychiatric disorders. Despite major depressive disorder (MDD) being the second cause of disability in the world, the efficacy of antidepressant drug (AD) treatment is not sufficient and the underlying mechanisms of MDD and the mechanisms of action of AD are poorly understood. Objective The aim of this review is to highlight the potential of HDF in the study of cellular mechanisms involved in MDD pathophysiology and in the action of AD response. Methods The first part is a systematic review following PRISMA guidelines on the use of HDF in MDD research. The second part reports the mechanisms and molecules both present in HDF and relevant regarding MDD pathophysiology and AD mechanisms of action. Results HDFs from MDD patients have been investigated in a relatively small number of works and most of them focused on the adrenergic pathway and metabolism-related gene expression as compared to HDF from healthy controls. The second part listed an important number of papers demonstrating the presence of many molecular processes in HDF, involved in MDD and AD mechanisms of action. Conclusion The imbalance in the number of papers between the two parts highlights the great and still underused potential of HDF, which stands out as a very promising tool in our understanding of MDD and AD mechanisms of action

[11] Transcriptional profiling of Hutchinson-Gilford progeria patients identifies primary target pathways of progerin

  • Authors: Sandra Vidak, Sohyoung Kim, Tom Misteli
  • Year: 2026
  • Venue: Nucleus
  • URL: https://www.semanticscholar.org/paper/4bd99b0875508364d8672b6da5a50d024d485a53
  • DOI: 10.1080/19491034.2025.2611484
  • PMID: 41489464
  • PMCID: 12773485
  • Citations: 1
  • Summary: To probe the clinical relevance of previously implicated cellular pathways and to address the extent of gene expression heterogeneity between patients, transcriptomic analysis of a comprehensive set of HGPS patients finds misexpression of several cellular pathways, including multiple signaling pathways, the UPR and mesodermal cell fate specification.
  • Evidence snippets:
  • Snippet 1 (score: 0.391) > Oxidative stress represents another key pathogenic mechanism in HGPS, as impaired NRF2 activity or increased reactive oxygen species (ROS) levels are sufficient to recapitulate HGPSassociated phenotypes [17,32,60]. Collectively, these findings underscore the multifactorial nature of HGPS pathogenesis, implicating interconnected signaling cascades involved in inflammation, oxidative stress, proteostasis, and vascular remodeling. Reassuringly, our findings indicate that many of the major pathways that have been described to contribute to HGPS phenotypes in mouse and cellular disease models are also misregulated in progeria patients, and targeting these pathways may provide therapeutic avenues to mitigate disease severity and improve outcomes in HGPS. > Although individuals with HGPS typically exhibit a characteristic set of clinical features, such as craniofacial abnormalities, growth retardation, and cardiovascular complications, there is notable variability in the age of onset, severity, and progression of symptoms between patients [7,9]. At the cellular level, HGPS is associated with several hallmark abnormalities, including nuclear envelope defects, decreased expression of several nuclear proteins and epigenetic marks, mitochondrial dysfunction, and increased cellular senescence [1,11,30,31,61]. These cellular phenotypes also exhibit considerable variation between patients, possibly contributing to differences in clinical outcomes. Our results indicate that even though some degree of transcriptional heterogeneity between the individual patients exists, the majority of patients exhibit misregulation of a set of shared pathways, suggesting that these pathways are universal driver mechanisms in HGPS. Further work is needed to understand the molecular and genetic factors that underlie inter-individual variability in disease expression and progression. > A limitation of pathway analysis of HGPS patient samples is to distinguish the pathways which are directly targeted by the disease-causing progerin protein and the emergence of adaptive secondary response pathways during progression of the disease in patients during their lifetime. The same caveat applies to the use of cell-based models used in the study of HGPS disease mechanisms.

[12] 18O-assisted dynamic metabolomics for individualized diagnostics and treatment of human diseases

  • Authors: E. Nemutlu, Song Zhang, N. Juranic, A. Terzic, S. Macura et al.
  • Year: 2012
  • Venue: Croatian Medical Journal
  • URL: https://www.semanticscholar.org/paper/880f053c7f060db4b990e447d0a22c4b69372ddb
  • DOI: 10.3325/cmj.2012.53.529
  • PMID: 23275318
  • PMCID: 3541579
  • Citations: 30
  • Summary: The potential use of dynamic phosphometabolomic platform for disease diagnostics currently under development at Mayo Clinic is described and discussed briefly.
  • Evidence snippets:
  • Snippet 1 (score: 0.388) > Living cells represent an integrated and interacting network of genes, transcripts, proteins, small signaling molecules, and metabolites that define cellular phenotype and function. Traditionally the focus of biomedical research was on individual genes, single protein targets, single metabolites, and metabolic or signaling pathways. This "molecular reductionist" paradigm was based on the assumption that identifying genetic variations and molecular components would lead to discovery of cures for human diseases. However, most of diseases are complex and multi-factorial and the disease phenotype is determined by the alterations of multiple genes, pathways, proteins and metabolites (at cellular, tissue, and organismal levels). Therefore, an integrated "omics" approach is more viable direction for uncovering alterations in metabolic networks, disease mechanisms, and mechanisms of drug effects. > Recent advent of large-scale metabolomics and fluxomic (metabolite dynamics and metabolic flux analysis) completed the "omics revolution" (Figure 1), where genomics, transcriptomics, proteomics, metabolomics, and fluxomics all together complement phenotype determination of living organism. Such integrated "omics" cascades provide a framework for advances in system and network biology, integrative physiology, and system medicine as well as system pharmacology and regenerative medicine. Noteworthy is the "reverse omic" approach or "metabolomicsinformed pharmacogenomics, " where discovery of specific metabolite changes have led to discovery of genetic alterations (2). Therefore, bringing new "omics" technologies to clinical practice will improve disease diagnostics and treatment by targeting drugs and procedures for each unique transcriptomic and metabolomic profiles.

[13] Proteogenomic characterization of MiT family translocation renal cell carcinoma

  • Authors: Y. Qu, Xiaohui Wu, Aihetaimujiang Anwaier, Jinwen Feng, Wenhao Xu et al.
  • Year: 2022
  • Venue: Nature Communications
  • URL: https://www.semanticscholar.org/paper/988de9f78d8ccfd7f0630a61c9c0fe14b53b18ba
  • DOI: 10.1038/s41467-022-34460-w
  • PMID: 36470859
  • PMCID: 9722939
  • Citations: 47
  • Influential citations: 6
  • Summary: The comprehensive proteogenomic analysis of tRCC tumors and normal adjacent tissues reveals dysregulation of DNA repair, mTOR signalling and metabolic processes and identifies mTOR signaling pathway as a potential therapeutic target.
  • Evidence snippets:
  • Snippet 1 (score: 0.386) > Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare type of kidney cancer, which is not well characterized. Here we show the comprehensive proteogenomic analysis of tRCC tumors and normal adjacent tissues to elucidate the molecular landscape of this disease. Our study reveals that defective DNA repair plays an important role in tRCC carcinogenesis and progression. Metabolic processes are markedly dysregulated at both the mRNA and protein levels. Proteomic and phosphoproteome data identify mTOR signaling pathway as a potential therapeutic target. Moreover, molecular subtyping and immune infiltration analysis characterize the inter-tumoral heterogeneity of tRCC. Multi-omic integration reveals the dysregulation of cellular processes affected by genomic alterations, including oxidative phosphorylation, autophagy, transcription factor activity, and proteasome function. This study represents a comprehensive proteogenomic analysis of tRCC, providing valuable insights into its biological mechanisms, disease diagnosis, and prognostication. The molecular landscape of microphthalmia transcription factor family translocation renal cell carcinoma tumours remain to be characterised. Here, the authors perform proteogenomic analysis and reveal dysregulation of DNA repair, mTOR signalling and metabolic processes.

[14] Serum metabolomics identified specific lipid compounds which may serve as markers of disease progression in patients with Alström and Bardet-Biedl syndromes

  • Authors: Krzysztof Jeziorny, Karolina Pietrowska, Julia Siemińska, E. Zmysłowska-Polakowska, A. Kretowski et al.
  • Year: 2023
  • Venue: Frontiers in Molecular Biosciences
  • URL: https://www.semanticscholar.org/paper/1a1d29801c10582356f9813c445fa88ea892e855
  • DOI: 10.3389/fmolb.2023.1251905
  • PMID: 38028552
  • PMCID: 10657895
  • Citations: 5
  • Summary: Patients with ALMS/BBS have altered lipid metabolism compared to controls or obese subjects, and as the disease progresses, they show elevated levels of lipid oxidation products, which may suggest increased oxidative stress.
  • Evidence snippets:
  • Snippet 1 (score: 0.385) > To date, no precise therapy has been found to inhibit the development of all components of both syndromes, and treatment is only symptomatic or targeted at particular disorders, including those of a central origin (Haws et al., 2020;Haws et al., 2021). > Due to the progressive nature of the observed symptoms, leading to shortened life expectancy of patients, it seems reasonable to look for markers of progression of ALMS and BBS syndromes. One of the promising methods may be metabolomics. > Metabolomics is a relatively new technology that enables the evaluation of metabolites-small molecules formed during metabolism, the precise identification of which provides insight into biological processes. This allows a better understanding of cellular mechanisms and links them to the phenotype of patients. > Metabolomics is gaining popularity and there are more and more attempts to demonstrate its usefulness in understanding the pathophysiology of diseases, especially rare diseases (Zmyslowska et al., 2017;Zacchia et al., 2020). > The aim of the study was to identify serum metabolites characteristic to ALMS and BBS and to correlate the identified compounds with clinical parameters and diseases progression.

[15] Changes in Serum Proteomic Profiles at Different Stages of Pregnancy Toxemia in Goats

  • Authors: M. Uzti̇mür, C. N. Ünal, Gurler Akpinar
  • Year: 2025
  • Venue: Journal of Veterinary Internal Medicine
  • URL: https://www.semanticscholar.org/paper/4b9c488b5dbd65d7b26fd2ad9aed70e8c4b59942
  • DOI: 10.1111/jvim.70139
  • PMID: 40492724
  • PMCID: 12150350
  • Citations: 2
  • Summary: Understanding the serum proteome profiles of goats with pregnancy toxemia might help identify the proteomes and pathways responsible for the development of this disease and improve diagnosis and treatment.
  • Evidence snippets:
  • Snippet 1 (score: 0.383) > The pathophysiology and progression of this disease are not fully understood. > Traditional biomedical research has focused on the analysis of single genes, proteins, metabolites, or metabolic pathways in diseases. This molecular reductionist approach is based on the assumption that identifying genetic variations and molecular components will lead to new treatments for diseases [13][14][15][16]. However, many diseases are complex and multifactorial, and in order to determine the phenotype of such diseases, it is necessary to understand the changes that occur in more than one gene, pathway, protein, or metabolite at the cellular, tissue, and organismal levels [17][18][19]. Therefore, in recent years, proteomics, as one field of multi-omics technologies, has helped in evaluating the complex pathogenetic mechanisms of different diseases from a broad perspective and has made substantial contributions [20,21]. In veterinary medicine, proteomic analysis of metabolic diseases such as ketosis [16], hypocalcemia [22], and fatty liver [23] in dairy cows has contributed valuable insights for the definition of new pathophysiological pathways and new diagnosis and treatment protocols for these diseases. The proteomic approach can contribute importantly to a broad and detailed understanding of the changes that occur at the organismal level associated with the increase in BHBA concentration in goats with pregnancy toxemia. Our aim was to evaluate the serum protein profiles of goats with SPT or CPT using proteomic techniques to determine the proteomic profiles of these animals and to identify the relevant pathophysiological mechanisms.

[16] Pathogenic mechanisms of RPGR mutations in X-linked retinitis pigmentosa: integrating clinical pedigree and single-cell transcriptomics

  • Authors: Xinrong Wang, Yuyang Bai, Xiaoyan Zuo, Xiaoying Lei, Xue Wang et al.
  • Year: 2026
  • Venue: Frontiers in Genetics
  • URL: https://www.semanticscholar.org/paper/e2019f566179365cdd1206cee7da5b63bf62dafb
  • DOI: 10.3389/fgene.2026.1814462
  • PMID: 42306097
  • PMCID: 13268601
  • Summary: Findings expand the RPGR mutation spectrum, provide mechanistic insights into XLRP pathogenesis, and have implications for genetic counseling and targeted therapy through the integrated analysis of clinical data and single-cell transcriptomics.
  • Evidence snippets:
  • Snippet 1 (score: 0.382) > Purpose This study aims to identify pathogenic retinitis pigmentosa GTPase regulator (RPGR) mutations in a Chinese pedigree with X-linked retinitis pigmentosa (XLRP) and elucidate the cellular and molecular mechanisms underlying RPGR-associated photoreceptor degeneration through the integrated analysis of clinical data and single-cell transcriptomics. Methods A three-generation Chinese XLRP pedigree was enrolled for comprehensive ophthalmic examinations, including BCVA, OCT, FAF, and ERG. Whole-exome sequencing was performed on the proband to identify the pathogenic variants, followed by Sanger sequencing for validation in family members. To analyze the downstream molecular mechanisms, we analyzed a public single-cell RNA sequencing dataset (SRP535874) of RPGR mutant retinal organoids across four developmental time-points (D40–D200). Bioinformatics analyses included cell clustering, differential expression analysis, GO/KEGG enrichment, protein–protein interaction (PPI) network construction, and pseudotime trajectory analysis. Results A hemizygous frameshift mutation (c.2476_2477del; p.R826Gfs*8) in the ORF15 region of RPGR was identified in the proband and confirmed in his two sons by Sanger sequencing. Clinical examinations revealed severe retinal degeneration in the affected male, intermediate phenotype in female carriers, and early-stage changes in the young affected male. Single-cell transcriptomic analysis of RPGR mutant retinal organoids revealed a paradoxical increase in photoreceptor transcriptional activity at late developmental stages (D150 and D200) despite the loss of the outer retinal structure in the patients, which may reflect aberrant differentiation and impaired functional maturation of photoreceptor precursors. Differential expression analysis showed upregulation of the stress-response genes and downregulation of phototransduction and ciliary transport genes. GO and KEGG enrichment analyses implicated disrupted ribosome biogenesis, RNA metabolism, ubiquitin-mediated proteolysis, and neurodegenerative disease pathways. PPI network analysis indicated decoupling of the core “ciliary transport

[17] The first review on prenatal drug exposure and ocular malformation occurrence

  • Authors: C. Dubucs, Julie Plaisancié, Monique Courtade-Saidi, C. Damase-Michel
  • Year: 2024
  • Venue: Frontiers in Pediatrics
  • URL: https://www.semanticscholar.org/paper/f7e30022de8ac515f86699136a59135674fc5b4c
  • DOI: 10.3389/fped.2024.1379875
  • PMID: 39296666
  • PMCID: 11408236
  • Citations: 6
  • Summary: The role of medications described in the genesis of ocular malformations is explored and the role that has been little evaluated and probably still underestimated is reviewed, especially since several studies have shown the wide exposure of pregnant women to medication.
  • Evidence snippets:
  • Snippet 1 (score: 0.380) > It has been suggested that Möebius syndrome may be due to vascular disruption of the subclavian artery during early embryonic development as previously discussed (158). Indeed, cases of infants with Möebius syndrome were reported following maternal antenatal splenic rupture and hypotension with Misoprostol exposition. Reduced vascular supply can also be seen in medications with a vasoconstrictive effect such as norepinephrine which can have a possible developmental effect due to ischemia (143). Furthermore, this mechanism of vascular disruption could explain asymmetric or unilateral defect particularly frequent in colobomas and microphthalmia. > Moreover, specific pathways such as retinoic acid (RA) signalling are of particular interest in eye development. RA is a biologically active metabolite of vitamin A that serves as a signalling molecule which plays multiple roles during eye development. The link between maternal vitamin A deficiency and fetal ocular defects such as microphthalmia has been known for a long time (49). RA signalling is required for interactions between the optic vesicle and lens placode and supports normal development of the retina and the optic nerve through its involvement in the periocular mesenchyme derived from neural crest cells. RA coordinates these actions by regulating specific receptors activities, RARα/β/γ and RXRα/β/γ. Inactivation of RARα/β/γ receptors in the periocular mesenchyme stops anterior eye segment formation. A review by Cvekl et al. summarizes genetic knowledge on RA signalling (159). These findings are concordant with the broad spectrum of ocular malformations in RA embryopathy such as microphthalmia, optic nerve hypoplasia and coloboma in a similar way as pathogenic variants in STRA6 (MIM610745) or RARB (MIM180220) genes, both of which are responsible of dysregulation in the RA pathway and therefore involved in syndromic microphthalmia (i.e., PDAC). Knowledge on genetic bases is fundamental to better understand the molecular aspects involved in the processes of teratogenesis with similar pathways of genes and protein dysfunction caused by specific drug exposure.

[18] ‘Breast Cancer Resistance Likelihood and Personalized Treatment Through Integrated Multiomics’

  • Authors: S. Mehmood, M. Faheem, Hammad Ismail, S. M. Farhat, Mahwish Ali et al.
  • Year: 2022
  • Venue: Frontiers in Molecular Biosciences
  • URL: https://www.semanticscholar.org/paper/c542ec176c594aeddb3790bb3d10767598b86ae4
  • DOI: 10.3389/fmolb.2022.783494
  • PMID: 35495618
  • PMCID: 9048735
  • Citations: 21
  • Influential citations: 2
  • Summary: This review has summarized therapeutic resistance associated with BC and the techniques used for its management, and identifies the biomarkers of disease progression and treatment progress by collective characterization and quantification of pools of biological molecules within and among the cancerous cells.
  • Evidence snippets:
  • Snippet 1 (score: 0.379) > Breast cancer is a very complex and heterogeneous disorder with unique molecular and morphological features relative to a disease which involves only a single gene or protein in a simple signaling pathway contributing toward the progression of disease in an independent and autonomous manner (Organization 2019). Various studies had represented BC heterogeneity through the differential response of the same type of BC patients to treatment and risk of developing side effects. One of the major clinical complications in the treatment of breast carcinoma patients is the development of therapeutic resistance (Luque-Bolivar et al., 2020). Recently drug resistance in BC treatment is not properly addressed, rather to focus on molecular pathways deeply; an alternative strategy of using a different drug is commonly applied. In order to reduce the adverse effects of BC treatment including drug resistance, a profound understanding of the molecular mechanism of the disease and the response to the drug is needed. Multidrug resistance (MDR) and consequent relapse on therapy are prevalent issues related to breast carcinoma as our understanding is incomplete related to the molecular mechanism of breast carcinoma disease (Waks and Winer, 2019a). Therefore, elucidating the molecular mechanisms involved in drug resistance is critical. For the management of breast cancers, the treatment decision not only depends on the Treatment with exemestane alone or in combination with an mTOR inhibitor such as everolimus (Carlini et al., 2007Chin et al., 2007Geisler et al., 2008Bahrami et al. (2020) ER+/ HER2- assessment of prognosis factors but also on the evaluation of pathological and clinical factors. Integrated data assessments of these multiple factors of breast carcinoma through multiomics can provide significant insight and hope for making therapeutic decisions (Parsons and Francavilla 2020). Major BC treatment strategies rely on the tumor subtype, immunohistochemical evaluation of prognostic elements, and seek new genetic markers to improve the diagnostic strategies and to enhance treatment outcomes with minimal side effects.

[19] Dual inheritance patterns: a spectrum of non-syndromic inherited retinal disease phenotypes with varying molecular mechanisms.

  • Authors: Lara K Holtes, Suzanne E. de Bruijn, Frans P. M. Cremers, S. Roosing
  • Year: 2024
  • Venue: Progress in retinal and eye research
  • URL: https://www.semanticscholar.org/paper/86f66fd5a9b46872bcd38fce72afea48db306090
  • DOI: 10.1016/j.preteyeres.2024.101308
  • PMID: 39486507
  • Citations: 10
  • Summary: This review aims to determine whether the molecular mechanisms behind the dual inheritance of each IRD-associated gene is well established, not yet properly understood, or if the association is questionable.
  • Evidence snippets:
  • Snippet 1 (score: 0.379) > Additionally, risk calculations may be incorrect if the carrier status of a partner is unknown as illustrated by the example of the family with both AD an AR conditions due to variants in RP1 (Buckley et al., 2022). A genetic diagnosis also permits patients to be enrolled in relevant gene or variant-based clinical trials. The genes discussed in this review demonstrate that different molecular mechanisms can underlie disease caused by variants in the same gene. This indicates that different therapeutic strategies will be required per gene and may direct future research into therapies for IRDs. > In conclusion, the occurrence of dual inheritance in IRD-associated genes is responsible for a spectrum of IRD phenotypes with varying molecular mechanisms depending on the variant type, variant location, protein structure, and protein function. L.K. Holtes et al. Progress in Retinal and Eye Research 104 (2025) 101308

Notes

  • This provider combines search_papers_by_relevance with snippet_search.
  • No synthesis or second-stage model call is performed.