Article
Biochemistry & Molecular Biology
Yiyi Chen, Yujie Dong, Jie Yan, Lan Wang, Shirley Yu, Kangwei Jiao, Francois Paquet-Durand
Summary: This study systematically mapped the transcriptional changes that occur in the degenerating mouse retina at the single cell level using single-cell RNA-sequencing. The results highlight the relevance of Ca2+-signaling and metabolic pathways to hereditary photoreceptor degeneration, and suggest that metabolic changes in rd1 mutation may be regulated through the MAPK pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Adrian Dockery, Laura Whelan, Pete Humphries, G. Jane Farrar
Summary: Inherited retinal diseases (IRDs) encompass a variety of genetically diverse conditions with phenotypic variations, researchers utilize cutting-edge sequencing techniques to identify elusive causes, providing accurate diagnoses and informed prognoses for family planning and medical interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, General & Internal
Sofia Barbosa-Gouveia, Maria Eugenia Vazquez-Mosquera, Emiliano Gonzalez-Vioque, Alvaro Hermida-Ameijeiras, Paula Sanchez-Pintos, Maria Jose de Castro, Soraya Ramiro Leon, Belen Gil-Fournier, Cristina Dominguez-Gonzalez, Ana Camacho Salas, Luis Negrao, Isabel Fineza, Francisco Laranjeira, Maria Luz Couce
Summary: Neuromuscular diseases are genetically heterogeneous, making diagnosis challenging. In this study, comprehensive gene-panel analysis and next-generation sequencing were used to analyze 268 patients with suspected inherited neuromuscular disorders. The addition of genes to the panel increased the diagnostic rate exponentially, with an overall rate of 36%. Most diagnoses were muscular dystrophies/myopathies and peripheral nerve diseases. The most common causative genes were TTN, RYR1, and ANO5.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Genetics & Heredity
Kunka Kamenarova, Kalina Mihova, Nevyana Veleva, Elena Mermeklieva, Bilyana Mihaylova, Galina Dimitrova, Alexander Oscar, Iliyan Shandurkov, Sylvia Cherninkova, Radka Kaneva
Summary: This study successfully identified disease-causing mutations in 16 Bulgarian patients with different inherited retinal degenerations using a targeted NGS approach. The results demonstrate the effectiveness of this approach based on frequently mutated genes as a comprehensive and successful genetic diagnostic tool for IRDs with significant impact on patient counseling.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2022)
Review
Urology & Nephrology
Jiahui Zhang, Changming Zhang, Erzhi Gao, Qing Zhou
Summary: Recent advances in genomics have revealed the complexity of Mendelian disorders, highlighting allelic heterogeneity, locus heterogeneity, reduced penetrance, variable expressivity, modifier genes, and/or environmental factors. Precision medicine in clinical nephrology can improve the clinical diagnostic rate and treatment efficiency of kidney diseases, requiring nephrologists to have a good understanding of genetics.
Article
Biochemistry & Molecular Biology
Kirk A. J. Stephenson, Julia Zhu, Adrian Dockery, Laura Whelan, Tomas Burke, Jacqueline Turner, James J. O'Byrne, G. Jane Farrar, David J. Keegan
Summary: Inherited retinal degenerations (IRDs) are a common cause of blindness in the working age population. Genetic testing plays a crucial role in diagnosing IRDs, with first-tier panel-based next-generation sequencing having a high success rate. This study demonstrates the reassessment of patients with negative results from first-tier testing and the effectiveness of second-tier genetic testing methods. By utilizing appropriate genetic testing techniques, the overall resolution rate of previously unresolved cases was increased to 92%. First-tier testing remains the most cost-effective approach, and second-tier testing should be guided by clinical and genetic indications to achieve a genetic diagnosis in a cost-effective manner.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Qing Zhu, Xue Rui, Ya Li, Ya You, Xun-Lun Sheng, Bo Lei
Summary: The study aimed to describe the genetic and clinical features of 17 patients with ABCA4-related inherited retinal degenerations (IRDs) and define the phenotype-genotype correlations. Four novel ABCA4 variants were identified, expanding the spectrum of disease-causing variants in ABCA4 for future genetic counseling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Dabin Moon, Hye Won Park, Dongheon Surl, Dongju Won, Seung-Tae Lee, Saeam Shin, Jong Rak Choi, Jinu Han
Summary: In this study, medically or surgically actionable genes in inherited eye disease were investigated based on clinical phenotype and genomic data. The findings show that individualized management of inherited eye diseases can be achieved through genetic testing, and precision medical or surgical interventions can be provided for patients.
Article
Ophthalmology
Alireza Badiei, William A. Beltran, Gustavo D. Aguirre
Summary: This study compared the expression levels of genes and proteins involved in retinal degeneration in normal dogs and canine models of inherited retinal degeneration. The results showed increased levels of H2S and NO in affected retinas, making cells vulnerable to oxidative damage and apoptosis.
EXPERIMENTAL EYE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jie Yan, Alexander Guenter, Soumyaparna Das, Regine Muehlfriedel, Stylianos Michalakis, Kangwei Jiao, Mathias W. Seeliger, Francois Paquet-Durand
Summary: Inherited retinal degenerations (IRDs) are blinding diseases characterized by progressive loss of photoreceptors. The excessive activation of calpain and poly (ADP-ribose) polymerase (PARP) is associated with the pathology of IRDs. Inhibitors of these enzymes have shown promise in preventing photoreceptor cell death. However, the relationship between calpain and PARP in IRDs is still unclear. In this study, organotypic retinal explant cultures were used to investigate the effects of calpain inhibitors, PARP inhibitors, and voltage-gated Ca2+ channel (VGCC) inhibitors on cell death in IRD mice models. The results suggest that PARP acts upstream of calpain and both enzymes are part of the same degenerative pathway in Pde6b-dependent photoreceptor degeneration. Our findings highlight the potential of targeting PARP for therapeutic interventions in IRD-type diseases.
Article
Ophthalmology
Marta Del Pozo-Valero, Rosa Riveiro-Alvarez, Inmaculada Martin-Merida, Fiona Blanco-Kelly, Saoud Swafiri, Isabel Lorda-Sanchez, Maria Jose Trujillo-Tiebas, Ester Carreno, Belen Jimenez-Rolando, Blanca Garcia-Sandoval, Marta Corton, Almudena Avila-Fernandez, Carmen Ayuso
Summary: This study utilized next-generation sequencing technologies to analyze the genetic landscape of 1036 families diagnosed with either autosomal recessive or sporadic macular dystrophies. The study discovered the mutational spectrum and identified ABCA4 as the most commonly mutated gene. Furthermore, the study found associations between other genes and different types of dystrophies.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Clinical Neurology
Nelson Astur, Brenno Ferreira Bento Maciel, Andre Mario Doi, Marines Dalla Valle Martino, Marcela Souza Basqueira, Marcelo Wajchenberg, Mario Lenza, Delio Eulalio Martins
Summary: This study analyzed the microbiome of the intervertebral disc using next-generation sequencing (NGS) molecular test and validated it with tissue culture and clinical data. The results showed the presence of bacteria or remnant DNA in herniated discs, indicating that the disc is not sterile. However, the study did not find any evidence of infection-related Cutibacterium acnes in patients with lumbar disc herniation.
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Cell & Tissue Engineering
Ishaq A. Viringipurampeer, Anat Yanai, Vahitha S. Nizamudheen, Cheryl Y. Gregory-Evans, Kevin Gregory-Evans
Summary: Cell replacement therapy holds promise for treating neurodegenerative diseases, but challenges remain in improving cell survival and integration. Pre-treatment with PKX-001 enhances cell survival, maturation, and functional integration in vivo, showing potential for clinical application in repairing damaged retinas.
JOURNAL OF TISSUE ENGINEERING AND REGENERATIVE MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Noor D. White, Zachary A. Batz, Edward L. Braun, Michael J. Braun, Karen L. Carleton, Rebecca T. Kimball, Anand Swaroop
Summary: The study used a probe set to capture 46 genes related to avian vision, achieving high success rates and saving sequencing resources, while avoiding the issue of chimeric assembly. By applying these data, positively selected genes in the evolution of night vision and high-speed vision were identified, providing a new perspective for evolutionary research.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Claire Marchal, Nivedita Singh, Ximena Corso-Diaz, Anand Swaroop
Summary: This article presents mathematical concepts for estimating and predicting the resolution of Hi-C datasets, and introduces HiCRes, a docker pipeline, for analyzing multiple Hi-C libraries.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Ophthalmology
Nina Schneider, Yogapriya Sundaresan, Prakadeeswari Gopalakrishnan, Avigail Beryozkin, Mor Hanany, Eyal Banin, Shay Ben-Aroya, Dror Sharon
Summary: Inherited retinal diseases (IRDs) are a complex and heterogeneous group of visual impairments caused by pathogenic variants in numerous genes. The understanding of the genotype-phenotype correlations, inheritance patterns, hypomorphic alleles, and modifier genes associated with IRDs is challenging due to their unique characteristics. Advances in next-generation sequencing have facilitated the identification of novel IRD-related genes and variants. The Global Retinal Inherited Disease (GRID) dataset provides valuable information on the frequencies and complexities of pathogenic variants among 194 genes.
PROGRESS IN RETINAL AND EYE RESEARCH
(2022)
Article
Biology
Andrew J. Smith, Jayshree Advani, Daniel C. Brock, Jacob Nellissery, Jessica Gumerson, Lijin Dong, L. Aravind, Breandan Kennedy, Anand Swaroop
Summary: We identified a mitochondrial protein, GATD3A, with bacterial evolutionary affinities, that functions as a deglycase and restricts the formation of AGEs in mitochondria. GATD3A may play a role in maintaining the integrity of important biomolecules.
Article
Genetics & Heredity
Talya Millo, Antonio Rivera, Alexey Obolensky, Devora Marks-Ohana, Mingchu Xu, Yumei Li, Enosh Wilhelm, Prakadeeswari Gopalakrishnan, Menachem Gross, Boris Rosin, Mor Hanany, Andrew Webster, Anna Maria Tracewska, Robert K. Koenekoop, Rui Chen, Gavin Arno, Ora Schueler-Furman, Susanne Roosing, Eyal Banin, Dror Sharon
Summary: This study investigates the clinical and genetic aspects of solute carrier (SLC) genes in inherited retinal diseases (IRDs). Pathogenic variants in SLC genes were identified through exome sequencing data analysis. The study identifies candidate novel IRD genes, establishes the pathogenicity of SLC37A3, and provides further evidence of SLC4A7 as IRD genes. The phenotypic spectrum of SLC24A1 is extended and its association with ARRP is suggested to be more common than previously reported.
GENETICS IN MEDICINE
(2022)
Article
Ophthalmology
Rani Patal, Eyal Banin, Tomer Batash, Dror Sharon, Jaime Levy
Summary: This study analyzes the genotype-phenotype correlation in patients with retinitis pigmentosa caused by mutations in the FAM161A, DHDDS, or MAK genes using ultra-widefield fundus autofluorescence imaging. The results suggest that patients with different causative genetic mutations may present with specific ultra-widefield fundus autofluorescence patterns. This finding highlights the importance of genetic testing in guiding the diagnosis and management of retinitis pigmentosa.
GRAEFES ARCHIVE FOR CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Avigail Beryozkin, Ananya Samanta, Prakadeeswari Gopalakrishnan, Samer Khateb, Eyal Banin, Dror Sharon, Kerstin Nagel-Wolfrum
Summary: Ataluren and Gentamicin, as translational readthrough drugs, have been shown to effectively restore expression, localization, and function of the FAM161A protein in fibroblasts from retinitis pigmentosa patients. These drugs also restored ciliogenesis and cilia length, with Ataluren showing better results compared to Gentamicin.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xulong Liang, Sharda P. Yadav, Zachary A. Batz, Jacob Nellissery, Anand Swaroop
Summary: During retinal development, NRL protein specifies the fate of rod photoreceptor cells by controlling the expression of genes such as Rhodopsin. Our study reveals that protein kinase CK2 can phosphorylate Ser117 residue of NRL, thereby modulating its transcriptional regulatory activity. The regulation of NRL by CK2 highlights the intricate interdependence of transcriptional and signaling pathways in maintaining the homeostasis of rod photoreceptors.
HUMAN MOLECULAR GENETICS
(2022)
Article
Multidisciplinary Sciences
Claire Marchal, Nivedita Singh, Zachary Batz, Jayshree Advani, Catherine Jaeger, Ximena Corso-Diaz, Anand Swaroop
Summary: This study reveals the genomic regulation of the human retina using high-resolution chromatin contact maps, identifying candidate genes associated with retinal degeneration and susceptibility to eye diseases, and providing new insights into the genetic control of tissue-specific functions.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Tamar Hayman, Talya Millo, Karen Hendler, Itay Chowers, Menachem Gross, Eyal Banin, Dror Sharon
Summary: This study conducted whole exome sequencing (WES) on 491 unsolved cases of Inherited Retinal Diseases (IRDs) in Israeli and Palestinian families, identifying the genetic cause of the disease in 51% of cases, with 11% attributed to CNVs. The analysis also identified potential new genes, ESRRB and DNM1.
JOURNAL OF MEDICAL GENETICS
(2023)
Meeting Abstract
Ophthalmology
Nina Schneider, Ricky Steinberg, Johanna Valensi, Amit Eylon, Eyal Banin, Erez Levanon, Shay Ben-Aroya, Dror Sharon
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Dror Sharon, Talya Millo, Jose Antonio Rivera, Alexey Obolensky, Dvorah Marks-Ohana, Enosh Wilhelm, Prakadee Gopalakrish, Menachem Gross, Boris Rosin, Mor Hanany, Anna Maria Tracewska, Ora Schueler-Furman, Susanne Roosing, Eyal Banin
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Yogapriya Sundaresan, Maya Ross, Ron Ofri, Eyal Banin, Dror Sharon
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Meeting Abstract
Ophthalmology
Prakadeeswari Gopalakrishnan, Chen Matsevich, Eyal Banin, Dror Sharon, Avigail Beryozkin, Alexey Obolensky
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Samer Khateb, Aya Shemesh, Ashly Offenheim, Ruth Sheffer, Tamar Ben-Yosef, Itay Chowers, Rina Leibu, Britta Baumann, Bernd Wissinger, Susanne Kohl, Eyal Banin, Dror Sharon
Summary: This study aimed to investigate the clinical, genetic, and electrophysiological characteristics of a specific form of Blue Cone Monochromacy (BCM) caused by mutations in the OPN1LW/OPN1MW genes. The results showed that patients with these mutations exhibited milder symptoms, improved visual acuity, more severe myopia, and higher 30-Hz cone flicker responses compared to the typical BCM group.