Multilocus variation—pathogenic variants in two or more disease genes—can potentially explain the underlying genetic basis for apparent phenotypic expansion in cases for which the observed clinical ...features extend beyond those reported in association with a “known” disease gene.
Analyses focused on 106 patients, 19 for whom apparent phenotypic expansion was previously attributed to variation at known disease genes. We performed a retrospective computational reanalysis of whole-exome sequencing data using stringent Variant Call File filtering criteria to determine whether molecular diagnoses involving additional disease loci might explain the observed expanded phenotypes.
Multilocus variation was identified in 31.6% (6/19) of families with phenotypic expansion and 2.3% (2/87) without phenotypic expansion. Intrafamilial clinical variability within two families was explained by multilocus variation identified in the more severely affected sibling.
Our findings underscore the role of multiple rare variants at different loci in the etiology of genetically and clinically heterogeneous cohorts. Intrafamilial phenotypic and genotypic variability allowed a dissection of genotype–phenotype relationships in two families. Our data emphasize the critical role of the clinician in diagnostic genomic analyses and demonstrate that apparent phenotypic expansion may represent blended phenotypes resulting from pathogenic variation at more than one locus.
We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher ...disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated.
Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis.
High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches).
These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.
Kisspeptins (kp) activate a receptor coupled to a Gαq subunit (GPR54 or KiSS-1R) receptor to perform a variety of functions, including inhibition of cell motility, chemotaxis, and metastasis. In this ...study we have investigated whether kp-10, the most potent member of the kisspeptin family, can modulate CXCR4 (C-X-C chemokine receptor type 4) expression and mesenchymal stem cells (MSCs) migration that may influence the development of tumors.
We compared the directional migration of MSCs treated with 10-100 or 500 nM kp-10 for 24 hours and no treated cells using an in vitro transmembrane migration assay. In addition, Chloromethylbenzamido Dialkylacarbocyanine (CM-Dil) labeled adipose-derived mesenchymal stem cells treated with 10-100 or 500 nM kp-10 and no treated cells were transfused via the tail vein to the melanoma tumor bearing C57BL/6 mice. After 24 hours, the mice were scarified, the tumors were dissected, and the tumor cell suspensions were analyzed by flow cytometry for detection of CM-Dil(+) MSCs.
We have found that kp-10 increased the MSCs migration at 100 nM, while it decreased the MSCs migration at 500 nM, both in vitro and in vivo, with a significant increase of CXCR4 expression at 100 nM kp-10 compared to the no treated cells, but it had no significant difference between the various concentrations of kp-10.
Thus, our data showed that kp-10 can differently affect MSCs migration in various concentrations, probably through different effects on CXCR4 expression in various concentrations.
Background: Bone is a tissue with high repair capacity; but, this ability dramatically is limited during irrecoverable bone and skeletal defects. Stem cell therapy is a promising approach for ...construction of bone tissue. Mesenchymal stem cells (MSCs) have been introduced as basic tools for bone tissue generation in tissue engineering. Core binding factor alpha 1 (Cbfa1) is one of the main genes involved in osteogenesis. Since relative expression of Cbfa1 in differentiated osteoblasts from adipose derived stem cells is unknown, this study aimed to evaluate the gene expression pattern of Cbfa1 in adipose derived differentiated osteoblasts in 4 different time intervals. Methods: Real-time PCR was used for studying the gene expression of Cbfa1 in human normal osteoblasts and adipose derived osteogenic osteoblasts at the days 7, 14, 21 and 28. Findings: There was a progressive increase in Cbfa1 expression over the differentiation period of adipose derived mesenchymal stem cells (ADSCs) from day 7 to day 28. Differentiated osteoblasts expressed Cbfa1 lower than native osteoblasts (P < 0.05). Conclusion: ADSCs are an attractive source for engineering a new bone tissue. According to our results, adipose derived differentiated osteoblasts express candidate gene at least on day 7 of culture. Our study indicates that longer treatment of ADSCs in osteogenic medium confer better osteoblastic properties to these cells.
There are significant limitations in repair of irrecoverable bone defects. Stem-cell therapy is a promising approach for the construction of bone tissue. Mesenchymal stem cells (MSCs) have been ...introduced as basic tools for bone tissue generation. Through MSCs, adipose-derived stem cells (ADSCs) are more interesting. Since the similarity of native osteoblasts and differentiated osteoblasts from ADSCs in terms of gene expression pattern is unknown, this study was designed to compare gene expression patterns of some genes involved in osteogenesis between human native osteoblasts and adipose-derived differentiated osteoblasts.
Realtime qRT-PCR was used for studying the gene expression of osteocalcin, osteopontin, and core binding factor alpha 1 (Cbfa1) in human native osteoblasts and adipose derived osteogenic osteoblasts at days 7, 14, 21, and 28 of differentiation.
This study demonstrated that native osteoblasts and differentiated osteoblasts, cultured in common osteogenic medium, have significant differences in gene expression levels for osteocalcin and osteopontin. Compared to native osteoblasts, these genes are expressed lower in all four groups of differentiated osteoblastic cells. We also found, there is a progressive increase in cbfa1 expression over the differentiation period of ADSCs from day 7 to day 28.
Our findings help for better assessment of adipose-derived differentiated cells as a source for cell-based therapy.
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete ...loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50% of pathogenic CNVs in different disease cohorts where 7.1-11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based ...biomarkers. However, plasma RNA analysis can unleash tremendous opportunities for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of RNA within plasma extracellular vesicles (evRNA), we successfully predicted consensus molecular subtypes in patients with metastatic colorectal cancer. Analysis of plasma evRNA also enabled monitoring of changes in transcriptomic subtype under treatment selection pressure and identification of molecular pathways associated with recurrence. This approach also revealed expressed gene fusions and neoepitopes from evRNA. These results demonstrate the feasibility of using transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to the identification of expressed fusions and neoantigens as cancer-specific therapeutic targets, sans the need for tissue-based sampling.
The development of an approach to interrogate molecular subtypes, cancer-associated pathways, and differentially expressed genes through RNA sequencing of plasma extracellular vesicles lays the foundation for liquid biopsy-based longitudinal monitoring of patient tumor transcriptomes.
Background: Micro ribonucleic acids (miRNA) are a type of ribonucleic acids with 20-24 nucleotides. They seem to have an important regulating role in cells. MiR-211 is an miRNA whose expression ...decreases in cancer cells, especially human melanoma cells. It is of high importance in suppression of tumor growth and invasion. Up to now, no study has evaluated miR-211 expression in murine melanoma cells for in vivo and in vitro conditions. We evaluated and compared the expression of miR-211 in murine melanoma cell line and melanoma tumors using real-time polymerase chain reaction (PCR). Methods: Melanoma B16F10 cell line was cultured. Subcutaneous melanoma tumors were induced by injecting this line to C57 mice. Melanoma cell line and melanoma tumors were lysed and miRNAs were extracted. After complementary deoxyribonucleic acid (cDNA) synthesis, real-time PCR of samples was performed using miR-211 primers. Data was statistically analyzed by Student’s t-test. Findings: Average expression of miR-211 in melanoma cell line was significantly higher than melanoma tumors. Conclusion: Due to the lower expression of miR-211 in murine melanoma tumors in comparison to murine melanoma cells, miRNA may be involved in invasive properties of melanoma cells in the mouse model of melanoma. Keywords: MiRNA, Murine melanoma cells, Real time polymerase chain reaction
Locus heterogeneity characterizes a variety of skeletal dysplasias often due to interacting or overlapping signaling pathways. Robinow syndrome is a skeletal disorder historically refractory to ...molecular diagnosis, potentially stemming from substantial genetic heterogeneity. All current known pathogenic variants reside in genes within the noncanonical Wnt signaling pathway including ROR2, WNT5A, and more recently, DVL1 and DVL3. However, ∼70% of autosomal-dominant Robinow syndrome cases remain molecularly unsolved. To investigate this missing heritability, we recruited 21 families with at least one family member clinically diagnosed with Robinow or Robinow-like phenotypes and performed genetic and genomic studies. In total, four families with variants in FZD2 were identified as well as three individuals from two families with biallelic variants in NXN that co-segregate with the phenotype. Importantly, both FZD2 and NXN are relevant protein partners in the WNT5A interactome, supporting their role in skeletal development. In addition to confirming that clustered –1 frameshifting variants in DVL1 and DVL3 are the main contributors to dominant Robinow syndrome, we also found likely pathogenic variants in candidate genes GPC4 and RAC3, both linked to the Wnt signaling pathway. These data support an initial hypothesis that Robinow syndrome results from perturbation of the Wnt/PCP pathway, suggest specific relevant domains of the proteins involved, and reveal key contributors in this signaling cascade during human embryonic development. Contrary to the view that non-allelic genetic heterogeneity hampers gene discovery, this study demonstrates the utility of rare disease genomic studies to parse gene function in human developmental pathways.
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