Association of peripheral blood DNA methylation level with Alzheimer’s disease progression

Background: Identifying biomarkers associated with Alzheimer's disease (AD) progression may enable patient enrichment and improve clinical trial designs. Epigenome-wide association studies have revealed correlations between DNA methylation at cytosine-phosphate-guanine (CpG) sites and AD pathology and diagnosis. Here, we report relationships between peripheral blood DNA methylation profiles measured using Infinium® MethylationEPIC BeadChip and AD progression in participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Results: The rate of cognitive decline from initial DNA sampling visit to subsequent visits was estimated by the slopes of the modified Preclinical Alzheimer Cognitive Composite (mPACC; mPACCdigit and mPACCtrailsB) and Clinical Dementia Rating Scale Sum of Boxes (CDR-SB) plots using robust linear regression in cognitively normal (CN) participants and patients with mild cognitive impairment (MCI), respectively. In addition, diagnosis conversion status was assessed using a dichotomized endpoint. Two CpG sites were significantly associated with the slope of mPACC in CN participants (P < 5.79 × 10-8 [Bonferroni correction threshold]); cg00386386 was associated with the slope of mPACCdigit, and cg09422696 annotated to RP11-661A12.5 was associated with the slope of CDR-SB. No significant CpG sites associated with diagnosis conversion status were identified. Genes involved in cognition and learning were enriched. A total of 19, 13, and 5 differentially methylated regions (DMRs) associated with the slopes of mPACCtrailsB, mPACCdigit, and CDR-SB, respectively, were identified by both comb-p and DMRcate algorithms; these included DMRs annotated to HOXA4. Furthermore, 5 and 19 DMRs were associated with conversion status in CN and MCI participants, respectively. The most significant DMR was annotated to the AD-associated gene PM20D1 (chr1: 205,818,956 to 205,820,014 [13 probes], Sidak-corrected P = 7.74 × 10-24), which was associated with both the slope of CDR-SB and the MCI conversion status. Conclusion: Candidate CpG sites and regions in peripheral blood were identified as associated with the rate of cognitive decline in participants in the ADNI cohort. While we did not identify a single CpG site with sufficient clinical utility to be used by itself due to the observed effect size, a biosignature composed of DNA methylation changes may have utility as a prognostic biomarker for AD progression

Editorial : Women in science : Genetics

No abstract available.https://www.frontiersin.org/journals/geneticsam2023Obstetrics and Gynaecolog

CYP1B1-RMDN2 Alzheimer’s disease endophenotype locus identified for cerebral tau PET

Determining the genetic architecture of Alzheimer’s disease pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we perform a genome-wide association study of cortical tau quantified by positron emission tomography in 3046 participants from 12 independent studies. The CYP1B1-RMDN2 locus is associated with tau deposition. The most significant signal is at rs2113389, explaining 4.3% of the variation in cortical tau, while APOE4 rs429358 accounts for 3.6%. rs2113389 is associated with higher tau and faster cognitive decline. Additive effects, but no interactions, are observed between rs2113389 and diagnosis, APOE4, and amyloid beta positivity. CYP1B1 expression is upregulated in AD. rs2113389 is associated with higher CYP1B1 expression and methylation levels. Mouse model studies provide additional functional evidence for a relationship between CYP1B1 and tau deposition but not amyloid beta. These results provide insight into the genetic basis of cerebral tau deposition and support novel pathways for therapeutic development in AD

Dnmt3a is essential for hematopoietic stem cell differentiation

Loss of the de novo DNA methyltransferases Dnmt3a and Dnmt3b in embryonic stem cells obstructs differentiation; however, the role of these enzymes in somatic stem cells is largely unknown. Using conditional ablation, we show that Dnmt3a loss progressively impairs hematopoietic stem cell (HSC) differentiation over serial transplantation, while simultaneously expanding HSC numbers in the bone marrow. Dnmt3a-null HSCs show both increased and decreased methylation at distinct loci, including substantial CpG island hypermethylation. Dnmt3a-null HSCs upregulate HSC multipotency genes and downregulate differentiation factors, and their progeny exhibit global hypomethylation and incomplete repression of HSC-specific genes. These data establish Dnmt3a as a critical participant in the epigenetic silencing of HSC regulatory genes, thereby enabling efficient differentiation

Harnessing peripheral DNA methylation differences in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease

Background Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease impacting an estimated 44 million adults worldwide. The causal pathology of AD (accumulation of amyloid-beta and tau), precedes hallmark symptoms of dementia by more than a decade, necessitating development of early diagnostic markers of disease onset, particularly for new drugs that aim to modify disease processes. To evaluate differentially methylated positions (DMPs) as novel blood-based biomarkers of AD, we used a subset of 653 individuals with peripheral blood (PB) samples in the Alzheimer’s disease Neuroimaging Initiative (ADNI) consortium. The selected cohort of AD, mild cognitive impairment (MCI), and age-matched healthy controls (CN) all had imaging, genetics, transcriptomics, cerebrospinal protein markers, and comprehensive clinical records, providing a rich resource of concurrent multi-omics and phenotypic information on a well-phenotyped subset of ADNI participants. Results In this manuscript, we report cross-diagnosis differential peripheral DNA methylation in a cohort of AD, MCI, and age-matched CN individuals with longitudinal DNA methylation measurements. Epigenome-wide association studies (EWAS) were performed using a mixed model with repeated measures over time with a P value cutoff of 1 × 10−5 to test contrasts of pairwise differential peripheral methylation in AD vs CN, AD vs MCI, and MCI vs CN. The most highly significant differentially methylated loci also tracked with Mini Mental State Examination (MMSE) scores. Differentially methylated loci were enriched near brain and neurodegeneration-related genes (e.g., BDNF, BIN1, APOC1) validated using the genotype tissue expression project portal (GTex). Conclusions Our work shows that peripheral differential methylation between age-matched subjects with AD relative to healthy controls will provide opportunities to further investigate and validate differential methylation as a surrogate of disease. Given the inaccessibility of brain tissue, the PB-associated methylation marks may help identify the stage of disease and progression phenotype, information that would be central to bringing forward successful drugs for AD

On the Origin of Leukemic Species

Recent studies (Shlush et al., 2014; Corces-Zimmerman et al., 2014) have demonstrated that leukemias develop from hematopoietic stem cells that acquire preleukemic mutations, allowing clonal expansion and subsequent acquisition of mutations leading to cancer. Preleukemic cells survive chemotherapy and serve as reservoirs for disease, generating new clones and leading to relapse

Hematopoietic Stem Cell Function Is Regulated By Hormonal and Epigenetic Factors

Abstract Gender-specific hormones have been known to play a role in hematopoietic function for some time. For example, treatment with estrogens suppresses B lymphocyte production in murine bone marrow, and hormonally compromised mice undergoing hematopoietic stem cell transplantation demonstrate enhanced immune reconstitution. Furthermore, androgens have been employed as therapy for bone marrow failure syndromes. Despite these experimental observations and clinical practices, the precise molecular mechanism by which gender-specific hormones influence physiology is not understood. To test if epigenetic modifications could alter HSC function in a gender-specific manner, we compared the engraftment potential of hematopoietic stem cells (HSCs) with altered DNA methylation patterns in female versus male recipients. We used DNMT3B7 transgenic mice as the HSC source. Our laboratory demonstrated that the introduction of DNMT3B7, a truncated DNMT3B isoform commonly expressed in cancer cells, impedes normal embryonic development. Homozygous DNMT3B7 transgenic mice have developmental defects similar to the Immunodeficiency, Centromeric instability, Facial anomalies syndrome, and demonstrate lymphopenia and defective craniofacial development. These physiological defects are accompanied by global DNA hypermethylation and disruption in DNA methylation patterns (Shah MY et al, Cancer Res. 2010). Since DNMT3B7 homozygous mice fail to survive past the day of birth, we used a transplantation model to assay the effect of DNMT3B7 on hematopoiesis. We found large differences in engraftment potential when cells expressing DNMT3B7 were transplanted into female versus male recipients. Pancytopenia occurred at two weeks, with anemia and leucopenia persisting until eight weeks post-transplantation when females received DNMT3B7 homozygous cells. However, cells from wild-type (WT) embryos engrafted normally regardless of recipient gender. We also observed that oophorectomized female recipients engrafted DNMT3B7-expressing cells normally. Interestingly, we found an improved engraftment of WT cells in these oophorectomized mice, suggesting that female hormones repress hematopoiesis. In competitive transplantation experiments to determine HSC function, the CD45.1 and CD45.2 alleles were used to distinguish competitor and experimental cells respectively. We observed that DNMT3B7-expressing CD45.2+ cells were out-competed by WT CD45.1+ cells within female recipients, although there were 4-fold more transgenic cells than CD45.1+ competitor cells. Because our previous studies suggested that DNMT3B7 functions as a dominant negative isoform of Dnmt3b, we compared our results with DNMT3B7-expressing cells to those observed with competitive transplants using Dnmt3b knockout cells. Cells from WT, heterozygous Dnmt3b, and homozygous Dnmt3b knockout embryos had similar engraftment potentials in female recipients and were not out-competed by competitor WT CD45.1+ cells, similar to previous observations in a distinct Dnmt3b knockout mouse model (Challen GA et al, Nat Genet. 2011). DNMT3B7 homozygous embryos had significantly fewer numbers of HSCs than WT embryos, as assayed by the LSK (Lineage-, Sca1+, Kit+) and SLAM (CD48, CD150) set of markers. We observed a dose-response relative to DNMT3B7 content, with DNMT3B7 homozygous embryos having the fewest number of HSCs, and DNMT3B7 hemizygous embryos having intermediate numbers of HSCs compared to WT embryos. These observations point to the dual influence of epigenetics and hormones on HSC function. Our hope is that we will be able to use our understanding of the molecular basis for the influence of hormonal milieu on hematopoiesis to augment stem/progenitor cell function in patients undergoing stem cell transplantation and chemotherapy. Disclosures: No relevant conflicts of interest to declare. </jats:sec

Expression of a Truncated DNMT3B Protein, DNMT3B7, Highlights the Sensitivity of Hematopoietic Progenitor Cell Function to Hormonal Milieu.

Abstract Abstract 83 Epigenetic changes, including DNA methylation and histone modifications, alter chromatin structure and regulate gene transcription in numerous cellular processes, including stem cell differentiation, mammalian embryogenesis, genomic imprinting, X-chromosome inactivation, and in cancer cells. Our laboratory studies the molecular basis for the abnormal distribution of DNA methylation in tumors. We found that cancer cells exhibit aberrant splicing of the DNMT3B gene, which encodes one of the de novo DNA methyltransferase enzymes. Aberrant DNMT3B transcripts encode truncated proteins, some of which lack the C-terminal catalytic domain. We hypothesize that aberrant DNA methylation in cancer cells is due in part to the presence of these truncated, catalytically inactive DNMT3B proteins. To test the in vivo effects of expression of a truncated DNMT3B protein, we engineered transgenic mice to express DNMT3B7, a truncated isoform expressed in cancer cells, and tested its influence on murine hematopoiesis. Since homozygous DNMT3B7 transgenic mice die in mid-gestation or within hours of birth, we propagated transgenic fetal liver cells (FLCs) in lethally irradiated recipients to bypass the animals' developmental abnormalities. DNMT3B7 was expressed in E14.5 FLCs, and we achieved approximately 80% donor chimerism in all recipients. Cells from wild-type (WT) embryos engrafted normally regardless of recipient gender. However, pancytopenia occurred at 2 weeks, with anemia and leucopenia persisting until 8 weeks post-transplant when females received DNMT3B7 homozygous cells. Male recipients displayed normal peripheral blood counts regardless of donor cell genotype. For example, females receiving WT or hemizygous cells had hemoglobin levels of 10 g/dL, whereas those receiving homozygous cells had levels of about 6 g/dL. Anemia was not seen in male recipients, where hemoglobin levels were 11-12 g/dL across all donor genotypes. When DNMT3B7 homozygous cells were transplanted into female recipients, neutropenia and lymphopenia were observed. Normal white blood cell recovery was seen in male recipients. Additionally, thrombocytopenia was observed at 2 weeks in female recipients of homozygous DNMT3B7 transgenic cells, but the platelet count normalized in these animals by 4 weeks. In preliminary experiments to further examine the role of hormonal milieu, oophorectomized female recipients demonstrated loss of the previously observed effect. At 2 weeks, oophorectomized females transplanted with DNMT3B7 homozygous cells showed recovery of hemoglobin levels to levels around 11 g/dL, the same level seen in normal female recipients transplanted with WT or hemizygous cells. Oophorectomized females receiving homozygous cells also showed improvement in white blood cell count. This suggests that the female hormonal milieu is suppressive to DNMT3B7-expressing hematopoietic progenitor cell function, rather than male-specific hormones augmenting hematopoiesis. We hypothesize that DNMT3B7 alters the DNA methylation patterns, and consequently, the gene expression profiles of hematopoietic progenitor cells, revealing a dependence of these cells on a particular hormonal milieu in recipient animals. Preliminary gene expression profiling of DNMT3B7-expressing versus WT E14.5 fetal liver cells reveals 29 genes are differentially expressed. These genes fall into interesting gene ontogenies, including chromatin modification genes (GSG2, SUZ12), cell cycle, programmed cell death, cell differentiation and proliferation. The defective hematopoiesis seen up to 8 weeks after transplantation in female recipients of DNMT3B7-expressing progenitor cells, suggests that there is an important relationship between progenitor cell function and hormonal milieu. Our hope is that we will be able to use our understanding of the molecular basis for the influence of hormonal milieu on hematopoiesis to augment stem/progenitor cell function in patients undergoing stem cell transplantation and chemotherapy. Disclosures: No relevant conflicts of interest to declare. </jats:sec