Generation of iPSC lines (KAIMRCi003A, KAIMRCi003B) from a Saudi patient with Dravet syndrome carrying homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A.

The most prevalent form of epileptic encephalopathy is Dravet syndrome (DRVT), which is triggered by the pathogenic variant SCN1A in 80% of cases. iPSCs with different SCN1A mutations have been constructed by several groups to model DRVT syndrome. However, no studies involving DRVT-iPSCs with rare genetic variants have been conducted. Here, we established two DRVT-iPSC lines harboring a homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A gene. Therefore, the derivation of these iPSC lines provides a unique cellular platform to dissect the molecular mechanisms underlying the cellular dysfunctions consequent to CPLX1 and SCN9A mutations.

HLA-based banking of induced pluripotent stem cells in Saudi Arabia.

BACKGROUND: Human iPSCs' derivation and use in clinical studies are transforming medicine. Yet, there is a high cost and long waiting time associated with autologous iPS-based cellular therapy, and the genetic engineering of hypo-immunogenic iPS cell lines is hampered with numerous hurdles. Therefore, it is increasingly interesting to create cell stocks based on HLA haplotype distribution in a given population. This study aimed to assess the potential of HLA-based iPS banking for the Saudi population. METHODS: In this study, we interrogated the HLA database of the Saudi Stem Cell Donor Registry (SSCDR), containing high-resolution HLA genotype data from 64,315 registered Saudi donors at the time of analysis. This database was considered to be a representative sample of the Saudi population. The most frequent HLA haplotypes in the Saudi population were determined, and an in-house developed iterative algorithm was used to identify their HLA matching percentages in the SSCDR database and cumulative coverage. Subsequently, to develop a clinically relevant protocol for iPSCs generation, and to illustrate the applicability of the concept of HLA-based banking for cell therapy purposes, the first HLA-based iPS cell line in Saudi Arabia was generated. Clinically relevant methods were employed to generate the two iPS clones from a homozygous donor for the most prevalent HLA haplotype in the Saudi population. The generated lines were then assessed for pluripotency markers, and their ability to differentiate into all three germ layers, beating cardiomyocytes, and neural progenitors was examined. Additionally, the genetic stability of the HLA-iPS cell lines was verified by comparing the mutational burden in the clones and the original blood sample, using whole-genome sequencing. The standards set by the American College of Medical Genetics and Genomics (ACMG) were used to determine the clinical significance of identified variants. RESULTS: The analysis revealed that the establishment of only 13 iPSC lines would match 30% of the Saudi population, 39 lines would attain 50% coverage, and 596 lines would be necessary for over 90% coverage. The proof-of-concept HLA-iPSCs, which cover 6.1% of the Saudi population, successfully demonstrated pluripotency and the ability to differentiate into various cell types including beating cardiomyocytes and neuronal progenitors. The comprehensive genetic analysis corroborated that all identified variants in the derived iPSCs were inherently present in the original donor sample and were classified as benign according to the standards set by the ACMG. CONCLUSIONS: Our study sets a road map for introducing iPS-based cell therapy in the Kingdom of Saudi Arabia. It underscores the pragmatic approach of HLA-based iPSC banking which circumvents the limitations of autologous iPS-based cellular therapies. The successful generation and validation of iPSC lines based on the most prevalent HLA haplotype in the Saudi population signify a promising step toward broadening the accessibility and applicability of stem cell therapies and regenerative medicine in Saudi Arabia.

Generation of myoglobin (MB)-knockout human embryonic stem cell (hESC) line (KAIMRCe002-A-1S) using CRISPR/Cas9 technology.

Myoglobin (MB) is a cytoplasmic hemoprotein that is predominantly expressed in the heart and oxidative myofibers of skeletal muscle. It has been demonstrated that MB binds to oxygen and promotes its diffusion for energy production in the mitochondria. Recently, MB was found to be expressed in different forms of malignant tumors and cancer cell lines. Further studies using gene disruption technology will enhance the understanding of MB's role in human cardiovascular biology and cancers. Here, we describe the generation of a homozygous MB knockout in human embryonic stem cells (hESC-MB-/-) via CRISPR/Cas9 to study MB function in human biology and diseases.

Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism.

The histone demethylase KDM1A is a multi-faceted regulator of vital developmental processes, including mesodermal and cardiac tube formation during gastrulation. However, it is unknown whether the fine-tuning of KDM1A splicing isoforms, already shown to regulate neuronal maturation, is crucial for the specification and maintenance of cell identity during cardiogenesis. Here, we discovered a temporal modulation of ubKDM1A and KDM1A+2a during human and mice fetal cardiac development and evaluated their impact on the regulation of cardiac differentiation. We revealed a severely impaired cardiac differentiation in KDM1A-/- hESCs that can be rescued by re-expressing ubKDM1A or catalytically impaired ubKDM1A-K661A, but not by KDM1A+2a or KDM1A+2a-K661A. Conversely, KDM1A+2a-/- hESCs give rise to functional cardiac cells, displaying increased beating amplitude and frequency and enhanced expression of critical cardiogenic markers. Our findings prove the existence of a divergent scaffolding role of KDM1A splice variants, independent of their enzymatic activity, during hESC differentiation into cardiac cells.

Pseudoautosomal Region 1 Overdosage Affects the Global Transcriptome in iPSCs From Patients With Klinefelter Syndrome and High-Grade X Chromosome Aneuploidies.

Klinefelter syndrome (KS) is the most prevalent aneuploidy in males and is characterized by a 47,XXY karyotype. Less frequently, higher grade sex chromosome aneuploidies (HGAs) can also occur. Here, using a paradigmatic cohort of KS and HGA induced pluripotent stem cells (iPSCs) carrying 49,XXXXY, 48,XXXY, and 47,XXY karyotypes, we identified the genes within the pseudoautosomal region 1 (PAR1) as the most susceptible to dosage-dependent transcriptional dysregulation and therefore potentially responsible for the progressively worsening phenotype in higher grade X aneuploidies. By contrast, the biallelically expressed non-PAR escape genes displayed high interclonal and interpatient variability in iPSCs and differentiated derivatives, suggesting that these genes could be associated with variable KS traits. By interrogating KS and HGA iPSCs at the single-cell resolution we showed that PAR1 and non-PAR escape genes are not only resilient to the X-inactive specific transcript (XIST)-mediated inactivation but also that their transcriptional regulation is disjointed from the absolute XIST expression level. Finally, we explored the transcriptional effects of X chromosome overdosage on autosomes and identified the nuclear respiratory factor 1 (NRF1) as a key regulator of the zinc finger protein X-linked (ZFX). Our study provides the first evidence of an X-dosage-sensitive autosomal transcription factor regulating an X-linked gene in low- and high-grade X aneuploidies.

Generation of an iPSC cohort of isogenic iPSC lines (46-XY and 47-XXY) from a non-mosaic Klinefelter Syndrome patient (47-XXY) (KAUSTi008-A, KAUSTi008-B, KAUSTi008-C, KAUSTi008-D, KAUSTi008-E, KAUSTi008-F, KAUSTi008-G).

Klinefelter Syndrome (KS) is the most common X chromosome aneuploidy in males characterized by highly heterogeneous clinical manifestations including a subtle cognitive impairment and multisystemic disorders such as infertility, metabolic syndrome, gynecomastia and cardiovascular diseases. To date dosage-dependent correlation studies of X-linked genes and low- and high-grade KS clinical phenotypes have not been performed. Here we generated multiple isogenic 47-XXY and 46-XY iPSC lines from one 47-XXY patient. Leveraging on a fully matched genetic background, our cohort represents a highly informative tool to study the impact of X chromosome dosage on KS pathophysiology.

Generation of two iPSC lines (KAUSTi001-A, KAUSTi002-A) from a rare high-grade Klinefelter Syndrome patient (49-XXXXY) carrying a balanced translocation t(4,11) (q35,q23).

Klinefelter Syndrome (KS) is the most common aneuploidy in humans (prevalence: 85-250 per 100,000 born males) and is characterized by one or more supernumerary X-chromosomes (47-XXY, 48-XXXY and 49-XXXXY karyotypes). KS is a multisystemic disorder associated to multiple phenotypic features including cardiac abnormalities, infertility, mental retardation, diabetes and increased cancer risk. Using a non-integrative mRNAs reprogramming approach, we generated two iPSC lines 48-XXXY and 49-XXXXY from a non-mosaic 49-XXXXY KS patient carrying a balanced translocation t(4,11) (q35,q23). These iPSC lines provide a unique cellular platform to study the molecular mechanisms underlying KS pathophysiology.

Establishment of an iPSC cohort from three unrelated 47-XXY Klinefelter Syndrome patients (KAUSTi007-A, KAUSTi007-B, KAUSTi009-A, KAUSTi009-B, KAUSTi010-A, KAUSTi010-B).

Klinefelter Syndrome (KS) is caused by the presence of a supernumerary X chromosome. Cytogenetic studies revaled that 80-90% of patients carry a 47-XXY karyotype, while 10-20% of cases are represented by mosaic 46-XY/47-XXY and high-grade aneuploidies 48-XXXY and 48-XXYY. The phenotypic traits of KS are highly variable across individuals and include cognitive dysfunction, metabolic dysregulation, osteoporosis, and cardiovascular diseases. Here, we describe the derivation of multiple 47-XXY iPSC lines from three unrelated KS patients to study the impact of supernumerary X chromosome during early development.

Derivation of two naturally isogenic iPSC lines (KAUSTi006-A and KAUSTi006-B) from a mosaic Klinefelter Syndrome patient (47-XXY/46-XY).

While Klinefelter Syndrome (KS) has a prevalence of 85-250 per 100,000 born males, patients are typically underdiagnosed due to a subtle phenotype emerging only late during puberty or adulthood. Rare cases of KS carry a mosaic phenotype 47-XXY/46-XY associated to mild phenotypic traits mostly compatible with a normal life including preserved fertility. From a genetic modeling perspective, the derivation of naturally isogenic iPSCs from mosaic patients allows the comparison of disease and healthy cells carrying a virtually identical genomic background.

Establishment of iPSC lines from a high-grade Klinefelter Syndrome patient (49-XXXXY) and two genetically matched healthy relatives (KAUSTi003-A, KAUSTi004-A, KAUSTi004-B, KAUSTi005-A, KAUSTi005-B, KAUSTi005-C).

Klinefelter Syndrome (KS) is the most frequent X chromosome aneuploidy in males. KS patients with 47-XXY, 48-XXXY and 49-XXXXY karyotypes endure inter-individual phenotypic variabilities including infertility, cardiac diseases, metabolic and psychiatric disorders. We derived iPSC lines from a high-grade 49-XXXXY KS and two healthy donors' fibroblasts. Importantly, the healthy controls XY and XX are direct relatives to KS patients, thus enabling functional comparisons of healthy and disease iPSCs with partially matched genetic backgrounds. These iPSC lines provide an unprecedented cellular tool to study KS pathophysiology at the pluripotent stage as well as during differentiation into disease relevant cell types.

Generation of iPSC lines (KAUSTi011-A, KAUSTi011-B) from a Saudi patient with epileptic encephalopathy carrying homozygous mutation in the GLP1R gene.

Glucagon-like peptide-1 receptor (GLP1R) is a seven-transmembrane-spanning helices membrane protein expressed in multiple human tissues including pancreatic islets, lung, brain, heart and central nervous system (CNS). GLP1R agonists are commonly used as antidiabetic drugs, but a neuroprotective function in neurodegenerative disorders is emerging. Here, we established two iPSC lines from a patient harboring a rare homozygous splice site variant in GLP1R (NM_002062.3; c.402 + 3delG). This patient displays severe developmental delay and epileptic encephalopathy. Therefore, the derivation of these iPSC lines constitutes a primary model to study the molecular pathology of GLP1R dysfunction and develop novel therapeutic targets.

Isolation and characterization of a Rickettsia from the ovary of a Western black-legged tick, Ixodes pacificus.

A rickettsial isolate was obtained from a partially engorged Ixodes pacificus female, which was collected from Humboldt County, California. The isolate was provisionally named Rickettsia endosymbiont Ixodes pacificus (REIP). The REIP isolate displayed the highest nucleotide sequence identity to Rickettsia species phylotype G021 in I. pacificus (99%, 99%, and 100% for ompA, 16S rRNA, and gltA, respectively), a bacterium that was previously identified in I. pacifiucs by PCR. Analysis of sequences from complete opening frames of five genes, 16S rRNA, gltA, ompA, ompB, and sca4, provided inference to the bacteria's classification among other Rickettsia species. The REIP isolate displayed 99.8%, 99.4%, 99.2%, 99.5%, and 99.6% nucleotide sequence identity for 16S rRNA, gltA, ompA, ompB, and sca4 gene, respectively, with genes of 'R. monacensis' str. IrR/Munich, indicating the REIP isolate is closely related to 'R. monacensis'. Our suggestion was further supported by phylogenetic analysis using concatenated sequences of 16S rRNA, gltA, ompA, ompB, and sca4 genes, concatenated sequences of dksA-xerC, mppA-purC, and rpmE-tRNAfMet intergenic spacer regions. Both phylogenetic trees implied that the REIP isolate is most closely related to 'R. monacensis' str. IrR/Munich. We propose the bacterium be considered as 'Rickettsia monacensis' str. Humboldt for its closest phylogenetic relative (=DSM 103975 T = ATCC TSD-94 T).