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INTRODUCTION: This retrospective study measured gene expression using RNA-seq of blastocoel fluid-conditioned media from euploid embryos with known implantation status to identify genes associated with implantation outcomes. METHODS: Blastocoel fluid-conditioned media was obtained after biopsy (ploidy status via NextGen sequencing) of intracytoplasmic sperm injection-generated day 5 blastocysts. Media used for RNA-seq were from 10 euploid blastocysts with known implantation outcomes. RNA was extracted, libraries were prepared, NextSeq500 sequencing was performed, and then sequences were aligned to the human genome. After quality control, the total gene count was 15,284. DESeq2 was used to test for differential gene expression. Raw read counts were normalized and variance stabilizing transformations were applied across samples. Log fold change shrinkage methods were used for gene visualization and rankings. Wald test statistic was used to compare implantation outcomes. Adjusted false-discovery rate P value of <.05 was considered statistically significant for differential expressed genes. RESULTS: Several genes were identified in this analysis revealing differential expression when comparing implantation outcomes. Of interest were two mitochondrial genes (DNAJC19 and MT-TK) and the NOA1 (required for mitochondrial function) with higher expression in media from embryos resulting in successful implantation. CONCLUSION: This study implicates mitochondrial function as a key player during preimplantation development that may affect implantation outcomes. DNAJC19 acts to bring proteins into the mitochondrial matrix, MT-TK encodes a mitochondrial tRNA, and NOA1 is a GTP binding protein residing in the mitochondria. The media samples in this study were collected from euploid blastocysts; therefore, gene expression differences detected represent potential molecular markers for predicting implantation success. [ABSTRACT FROM AUTHOR]

Chronic kidney disease is a progressive, incurable condition that involves a gradual loss of kidney function. While there are no non-invasive biomarkers available to determine whether individuals are susceptible to developing chronic kidney disease, small RNAs within urinary exosomes have recently emerged as a potential candidate to use for assessing renal function. Ultracentrifugation is the gold standard for urinary exosome isolation. However, extravesicular small RNA contamination can occur when isolating exosomes from biological fluids using ultracentrifugation, which may lead to misidentifying the presence of certain small RNA species in human urinary exosomes. Therefore, we characterized human urinary exosomal preparations isolated by ultracentrifugation alone, or via ultracentrifugation followed by size exclusion chromatography (SEC) column-purification. Using nanoparticle tracking analysis, we identified SEC fractions containing robust amounts of exosome-sized particles, that we further characterized using immunoblotting. When compared to exosomal preparations isolated by ultracentrifugation only, SEC fractionated exosomal preparations showed higher levels of the exosome-positive marker CD81. Moreover, while the exosome-negative marker calnexin was undetectable in SEC fractionated exosomal preparations, we did observe calnexin detection in the exosomal preparations isolated by ultracentrifugation alone, which implies contamination in these preparations. Lastly, we imaged SEC fractionated exosomal preparations using transmission electron microscopy to confirm these preparations contained human urinary exosomes. Our results indicate that combining ultracentrifugation and SEC column-purification exosome isolation strategies is a powerful approach for collecting contaminant-free human urinary exosomes and should be considered when exosomes devoid of contamination are needed for downstream applications. [ABSTRACT FROM AUTHOR]

Simple Summary: We investigated the influence of autophagy-related variants in modulating Multiple Myeloma (MM) risk through a meta-analysis of germline genetic data on 234 autophagy-related genes from three independent study populations including 13,387 subjects of European ancestry (6863 MM patients and 6524 controls) and examined the functional mechanisms behind the observed associations. We identified SNPs within the six CD46, IKBKE, PARK2, ULK4, ATG5, and CDKN2A loci associated with MM risk and observed that their effect on disease risk was mediated by specific subsets of immune cells, as well as vitamin D3-, MCP-2-, and IL20-dependent mechanisms. Multiple myeloma (MM) arises following malignant proliferation of plasma cells in the bone marrow, that secrete high amounts of specific monoclonal immunoglobulins or light chains, resulting in the massive production of unfolded or misfolded proteins. Autophagy can have a dual role in tumorigenesis, by eliminating these abnormal proteins to avoid cancer development, but also ensuring MM cell survival and promoting resistance to treatments. To date no studies have determined the impact of genetic variation in autophagy-related genes on MM risk. We performed meta-analysis of germline genetic data on 234 autophagy-related genes from three independent study populations including 13,387 subjects of European ancestry (6863 MM patients and 6524 controls) and examined correlations of statistically significant single nucleotide polymorphisms (SNPs; p < 1 × 10−9) with immune responses in whole blood, peripheral blood mononuclear cells (PBMCs), and monocyte-derived macrophages (MDM) from a large population of healthy donors from the Human Functional Genomic Project (HFGP). We identified SNPs in six loci, CD46, IKBKE, PARK2, ULK4, ATG5, and CDKN2A associated with MM risk (p = 4.47 × 10−4−5.79 × 10−14). Mechanistically, we found that the ULK4rs6599175 SNP correlated with circulating concentrations of vitamin D3 (p = 4.0 × 10−4), whereas the IKBKErs17433804 SNP correlated with the number of transitional CD24+CD38+ B cells (p = 4.8 × 10−4) and circulating serum concentrations of Monocyte Chemoattractant Protein (MCP)-2 (p = 3.6 × 10−4). We also found that the CD46rs1142469 SNP correlated with numbers of CD19+ B cells, CD19+CD3− B cells, CD5+IgD− cells, IgM− cells, IgD−IgM− cells, and CD4−CD8− PBMCs (p = 4.9 × 10−4−8.6 × 10−4) and circulating concentrations of interleukin (IL)-20 (p = 0.00082). Finally, we observed that the CDKN2Ars2811710 SNP correlated with levels of CD4+EMCD45RO+CD27− cells (p = 9.3 × 10−4). These results suggest that genetic variants within these six loci influence MM risk through the modulation of specific subsets of immune cells, as well as vitamin D3−, MCP-2−, and IL20-dependent pathways. [ABSTRACT FROM AUTHOR]

Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults worldwide. Although genome-wide association studies (GWAS) have uncovered the germline genetic component underlying CLL susceptibility, the potential use of GWAS-identified risk variants to predict disease progression and patient survival remains unexplored. Here, we evaluated whether 41 GWAS-identified risk variants for CLL could influence overall survival (OS) and disease progression, defined as time to first treatment (TTFT) in a cohort of 1039 CLL cases ascertained through the CRuCIAL consortium. Although this is the largest study assessing the effect of GWAS-identified susceptibility variants for CLL on OS, we only found a weak association of ten single nucleotide polymorphisms (SNPs) with OS (p < 0.05) that did not remain significant after correction for multiple testing. In line with these results, polygenic risk scores (PRSs) built with these SNPs in the CRuCIAL cohort showed a modest association with OS and a low capacity to predict patient survival, with an area under the receiver operating characteristic curve (AUROC) of 0.57. Similarly, seven SNPs were associated with TTFT (p < 0.05); however, these did not reach the multiple testing significance threshold, and the meta-analysis with previous published data did not confirm any of the associations. As expected, PRSs built with these SNPs showed reduced accuracy in prediction of disease progression (AUROC = 0.62). These results suggest that susceptibility variants for CLL do not impact overall survival and disease progression in CLL patients. [ABSTRACT FROM AUTHOR]

The early detection of chronic kidney disease (CKD) is key to reducing the burden of disease and rising costs of care. This need has spurred interest in finding new biomarkers for CKD. Ideal bi-omarkers for CKD should be: easy to measure; stable; reliably detected, even when interfering substances are present; site-specific based on the type of injury (tubules vs. glomeruli); and its changes in concentration should correlate with disease risk or outcome. Currently, no single can-didate biomarker fulfills these criteria effectively, and the mechanisms underlying kidney fibrosis are not fully understood; however, there is growing evidence in support of microRNA-mediated pro-cesses. Specifically, urinary exosomal microRNAs may serve as biomarkers for kidney fibrosis. In-creasing incidences of obesity and the recognition of obesity-associated CKD have increased interest in the interplay of obesity and CKD. In this review, we provide: (1) an overview of the current scope of CKD biomarkers within obese individuals to elucidate the genetic pathways unique to obesi-ty-related CKD; (2) a review of microRNA expression in obese individuals with kidney fibrosis in the presence of comorbidities, such as diabetes mellitus and hypertension; (3) a review of thera-peutic processes, such as diet and exercise, that may influence miR-expression in obesity-associated CKD; (4) a review of the technical aspects of urinary exosome isolation; and (5) future areas of research. [ABSTRACT FROM AUTHOR]

Although survival outcomes have significantly improved, up to 40% of patients die within 1 year of HLA-matched unrelated-donor blood and marrow transplantation (BMT). To identify non-HLA genetic contributors to mortality after BMT, we performed the first exome-wide association study in the DISCOVeRY-BMT cohorts using the Illumina HumanExome BeadChip. This study includes 2473 patients with acute myeloid leukemia, acute lymphoblastic leukemia, or myelodysplastic syndrome and 2221 10/10 HLA-matched donors treated from 2000 to 2011. Single-variant and gene-level analyses were performed on overall survival (OS), transplantation-related mortality (TRM), and disease-related mortality (DRM). Genotype mismatches between recipients and donors in a rare nonsynonymous variant of testis-expressed gene TEX38 significantly increased risk of TRM, which was more dramatic when either the recipient or donor was female. Using the SKAT-O test to evaluate gene-level effects, variant genotypes of OR51D1 in recipients were significantly associated with OS and TRM. In donors, 4 (ALPP, EMID1, SLC44A5, LRP1), 1 (HHAT), and 2 genes (LYZL4, NT5E) were significantly associated with OS, TRM, and DRM, respectively. Inspection of NT5E crystal structures showed 4 of the associated variants affected the enzyme structure and likely decreased the catalytic efficiency of the enzyme. Further confirmation of these findings and additional functional studies may provide individualized risk prediction and prognosis, as well as alternative donor selection strategies. [ABSTRACT FROM AUTHOR]

Genetic abnormalities can predispose patients to develop acute myeloid leukemia (AML), aplastic anemia (AA) and myelodysplastic syndrome (MDS). These mutations are more often seen in pediatric patients so genetic screening is more routinely performed in that population. Recent algorithms propose screening in adolescent and young adults (AYAs) with AML/AA/MDS. However, this is not routine practice in community hospitals where most AYAs are treated. Discovery of familial genetic abnormalities can impact donor choice in patients undergoing allogeneic stem cell transplant and treatment/screening in family members. The goal of this study is to determine the rate of genetic screening in AYAs with AML/AA/MDS based on recently proposed screening algorithms in a community hospital setting. Patients with AML/AA/MDS aged ≤50 years treated at Prisma Health Upstate (2015 to 2019) were included in this retrospective study. While the AYA population is typically defined as ages 18-39, we included patients up to age 50 given screening recommendations from some centers. Charts were reviewed to determine rates of genetic screening based on published algorithms from M.D. Anderson Cancer Center. We compared rates of screening in pediatric and AYA patients and documentation of pertinent family history. Thirty-nine patients (12 pediatric, median age: 9 years; 27 AYA, median age: 33 years) diagnosed with AML (n=19)/MDS (n=6)/AA (n=14) were included in the study. Genetic screening was performed in 8/12 (67%) pediatric patients and 8/27 (30%) in AYAs (P <0.05). The rate of detection of positive genetic abnormalities in the 16 screened patients was 25% (AYAs: 2 RUNX1 and 1 FANCM mutations; pediatric: 1 CEBPA mutation). Relevant family histories were performed in 10 of 39 patients (7 AYA vs 3 pediatric), but only 1/10 included age of diagnosis of the affected family member. Screening for hereditary predispositions to hematologic malignancies in AYAs is underperformed despite recent evidence suggesting otherwise. We report low rates of screening in our community hospital where transplant is a treatment option for AYAs with MDS/AA/AML. In addition to donor considerations, predisposition syndromes can affect treatment toxicities, conditioning regimens, and screening of family members. Our results, despite the small sample size, indicate a high detection rate of genetic abnormalities and need for improving focused family history documentation. Based on our findings, we will implement an institution wide genetic screening protocol for AYAs with MDS/AA/AML. [ABSTRACT FROM AUTHOR]