Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans.

BACKGROUND: We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle. RESULTS: Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction. CONCLUSIONS: Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.

Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control.

BACKGROUND: Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS: We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with methylation and gene expression in internal organs. We also discover unprecedented mQTL at these regions. Genetic influences on CoRSIV methylation are extremely strong (median R2=0.76), cumulatively comprising over 70-fold more human mQTL than detected in the most powerful previous study. Moreover, mQTL beta coefficients at CoRSIVs are highly skewed (i.e., the major allele predicts higher methylation). Both surprising findings are independently validated in a cohort of 47 non-GTEx individuals. Genomic regions flanking CoRSIVs show long-range enrichments for LINE-1 and LTR transposable elements; the skewed beta coefficients may therefore reflect evolutionary selection of genetic variants that promote their methylation and silencing. Analyses of GWAS summary statistics show that mQTL polymorphisms at CoRSIVs are associated with metabolic and other classes of disease. CONCLUSIONS: A focus on systemic interindividual epigenetic variants, clearly enhanced in mQTL content, should likewise benefit studies attempting to link human epigenetic variation to the risk of disease.

Rare MYC-N11S germline mutation indicative of inherited breast cancer in a multigeneration family.

We present a case of unexplained familial breast cancer (BC) from six family members, including four affected and two unaffected women, for whom clinical genetic testing panels were inconclusive. Exome sequencing data revealed heterozygous and rare germline variants to be inherited in an autosomal dominant manner in the family, in addition to several unclassified mutations in DNA repair and cell cycle-regulating genes that were not included in the family's clinical genetic testing. A rare MYC-N11S germline mutation with conflicting interpretations of pathogenicity in the literature, and predicted to be deleterious, was present in all affected individuals. Whole exome sequencing provided a more comprehensive picture of inherited BC in this family that was missed by cancer gene panels alone.

A Critical Tiriti Analysis of the Pae Ora (Healthy Futures) Bill.

AIM: The Pae Ora (Healthy Futures) Bill is the framework for a reformed health system intended to embed Te Tiriti o Waitangi and centre equity. The Bill is informed by the Wai 2575 Health Kaupapa Waitangi Tribunal Inquiry and the Health and Disability System Review, both of which established an urgent mandate to transform the health sector. This desktop review explores to what extent the proposed Bill is likely to uphold Te Tiriti. METHODS: This paper uses Critical Tiriti Analysis to review the Pae Ora Bill. The analysis involves five phases: (i) orientation; (ii) close reading; (iii) determination; (iv) strengthening practice and (v) Maori final word. As part of that, a determination is made whether the Bill is silent, poor, fair, good or excellent in relation to the Preamble and the four articles (three written, one verbal) of te Tiriti o Waitangi (Maori text). RESULTS: The desktop analysis showed fair engagement with most of the Te Tiriti elements; but with good commitment to address equity issues. The Bill was silent in relation to wairuatanga (spirituality) and there is no evidence of Maori values informing it. CONCLUSION: The dominant Crown narrative that interprets kawanatanga as the right to govern over all peoples pervades this legislation. There are significant power sharing shifts within this Bill and these are welcomed, but whilst the Crown maintains ultimate power and authority only a partial fulfilment of Te Tiriti will be evident within the health system.

Histologically resolved small RNA maps in primary focal segmental glomerulosclerosis indicate progressive changes within glomerular and tubulointerstitial regions.

Pathological heterogeneity is common in clinical tissue specimens and complicates the interpretation of molecular data obtained from the specimen. As a typical example, a kidney biopsy specimen often contains glomeruli and tubulointerstitial regions with different levels of histological injury, including some that are histologically normal. We reasoned that the molecular profiles of kidney tissue regions with specific histological injury scores could provide new insights into kidney injury progression. Therefore, we developed a strategy to perform small RNA deep sequencing analysis for individually scored glomerular and tubulointerstitial regions in formalin-fixed, paraffin-embedded kidney needle biopsies. This approach was applied to study focal segmental glomerulosclerosis (FSGS), the leading cause of nephrotic syndrome in adults. Large numbers of small RNAs, including microRNAs, 3'-tRFs, 5'-tRFs, and mitochondrial tRFs, were differentially expressed between histologically indistinguishable tissue regions from patients with FSGS and matched healthy controls. A majority of tRFs were upregulated in FSGS. Several small RNAs were differentially expressed between tissue regions with different histological scores in FSGS. Notably, with increasing levels of histological damage, miR-21-5p was upregulated progressively and miR-192-5p was downregulated progressively in glomerular and tubulointerstitial regions, respectively. This study marks the first genome scale molecular profiling conducted in histologically characterized glomerular and tubulointerstitial regions. Thus, substantial molecular changes in histologically normal kidney regions in FSGS might contribute to initiating tissue injury or represent compensatory mechanisms. In addition, several small RNAs might contribute to subsequent progression of glomerular and tubulointerstitial injury, and histologically mapping small RNA profiles may be applied to analyze tissue specimens in any disease.

Moral distress in genetic counseling: A study of North American genetic counselors.

Moral distress is the phenomenon whereby healthcare providers experience the inability to take action or act in morally appropriate ways when encountering a morally compromising situation. The correlation of moral distress to burnout and resignation in nursing and other healthcare fields has led to increasing attention and concern among healthcare professionals to identify the sources of moral distress, as well as find ways to alleviate it. An online mix-method survey was sent to NSGC members to gain information on (1) sources of moral distress, (2) emotions involved, (3) coping strategies, and (4) suggestions to alleviate it. The ProQOL 5 scale was included to measure genetic counselor compassion satisfaction, burnout, and secondary traumatic stress. Two hundred and thirteen genetic counselors from North America completed the survey. Forty-eight percent of respondents experienced moral distress and five sources were identified. The sources were situations involving other providers, family members, professional responsibility, personal beliefs, and access. Those more likely to experience moral distress worked in a prenatal setting, were over the age of 50, and worked for more than 21 years. Genetic counselors were more likely to talk to a co-worker for support, and seek social support, address the source of the problem, and sustain self through working with patients as coping strategies. Most genetic counselors recommended talking to another genetic counselor to alleviate moral distress. Moral distress did not correlate with genetic counselor burnout, but did correlate with higher levels of secondary traumatic stress (p < 0.01). Thirty-two percent of genetic counselors considered leaving their specialty, and 23% considered leaving their profession based on their experience(s) with moral distress. Our study establishes the existence of moral distress in the genetic counseling field and supports the need for coping strategies and recommendations in order to alleviate future genetic counselor moral distress.

DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children.

PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease.

The Simpson-led health sector review: a failure to uphold te Tiriti o Waitangi.

The Health and Disability System Review (the 'Simpson Review') was an opportunity for health sector transformation, particularly in light of the recent damning WAI 2575 Waitangi Tribunal report released during the review process. There appears to have been a concerted effort to engage with the sector, an impressive Maori Expert Advisory Group and an extensive body of available scholarship documenting where improvements could be made. In this viewpoint, the authors, tangata whenua (Indigenous people of the land) and tangata Tiriti (people of te Tiriti) and health scholars and leaders undertook a high-level review of the Simpson Review report and analysed it against key elements of te Tiriti o Waitangi. The Simpson Review was an opportunity to share power, commit to Maori health and embed structural mechanisms, such as the proposed Maori health authority, to uphold te Tiriti o Waitangi. It was also an opportunity to recommit to health equity and eliminate institutional racism. We conclude that the Simpson Review did not take up these opportunities, but instead perpetuated further breaches of te Tiriti.

Addressing Structural Racism Through Constitutional Transformation and Decolonization: Insights for the New Zealand Health Sector.

In colonial states and settings, constitutional arrangements are often forged within contexts that serve to maintain structural racism against Indigenous people. In 2013 the New Zealand government initiated national conversations about the constitutional arrangements in Aotearoa. Maori (Indigenous) leadership preceded this, initiating a comprehensive engagement process among Maori in 2010, which resulted in a report by Matike Mai Aotearoa which articulated a collective Maori vision of a written constitution congruent with te Tiriti o Waitangi (the founding document of the colonial state of New Zealand) by 2040.This conceptual article explores the Matike Mai Aotearoa report on constitutional transformation as a novel means to address structural racism within the health system as a key domain within the constitutional sphere. Matike Mai suggests alternative conceptual structural formations through its focus on the kawanatanga (governance), the relational and the tino rangatiratanga (sovereignty) sphere. This framework is informed by a range of Indigenous ethical values such as tikanga (protocol), belonging, and balance that can usefully inform the redesign of the health sector.We assert that constitutional transformation and decolonization are potentially powerful ethical sources of disruption to whiteness and structural racism. We argue that, to eliminate entrenched health disparities, change processes need to be informed by the Indigenous inspirations expressed in the Matike Mai report.

From gorse to ngahere: an emerging allegory for decolonising the New Zealand health system.

Prior to colonisation, Maori had a well-developed holistic health system based on maintaining balance between people, place and spirit. The colonial imposition of British economic, religious, educational, legal, health and governance, through warfare, immigration, legislation and social coercion had a devastating effect on Maori health outcomes. With the release of the WAI 2575 Waitangi Tribunal report exposing the failings of our health system in relation to Maori health, the need to decolonise our health system becomes more pressing. A key difficulty in this work is the poverty of transformative language, concepts and frameworks in our workforce. This paper is the product of an anti-racism think tank that occurred in April 2019. While working through a system change analysis on our colonial health system, Maori and Tauiwi activists and scholars created an allegory-from gorse to ngahere. The allegory depicts the ongoing impact of the colonial health system as represented by gorse, and the possibilities of a decolonised health system represented by ngahere-a self-sustaining and flourishing native forest. Racism has a geographic specificity. The allegory we developed is a mechanism for conceptualising decolonisation for the context of Aotearoa. It serves to reinforce the different roles and responsibilities of the descendants of the colonisers and the colonised in the pursuit of decolonisation.

Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data.

BACKGROUND: The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methylated regions). Variation limited to single or small numbers of CpGs has been assumed to reflect stochastic processes. To test this, we developed software, Cluster-Based analysis of CpG methylation (CluBCpG), and explored variation in read-level CpG methylation patterns in whole genome bisulfite sequencing data. RESULTS: Analysis of both human and mouse whole genome bisulfite sequencing datasets reveals read-level signatures associated with cell type and cell type-specific biological processes. These signatures, which are mostly orthogonal to classical differentially methylated regions, are enriched at cell type-specific enhancers and allow estimation of proportional cell composition in synthetic mixtures and improved prediction of gene expression. In tandem, we developed a machine learning algorithm, Precise Read-Level Imputation of Methylation (PReLIM), to increase coverage of existing whole genome bisulfite sequencing datasets by imputing CpG methylation states on individual sequencing reads. PReLIM both improves CluBCpG coverage and performance and enables identification of novel differentially methylated regions, which we independently validate. CONCLUSIONS: Our data indicate that, rather than stochastic variation, read-level CpG methylation patterns in tissue whole genome bisulfite sequencing libraries reflect cell type. Accordingly, these new computational tools should lead to an improved understanding of epigenetic regulation by DNA methylation.

Endogenous miR-204 Protects the Kidney against Chronic Injury in Hypertension and Diabetes.

BACKGROUND: Aberrant microRNA (miRNA) expression affects biologic processes and downstream genes that are crucial to CKD initiation or progression. The miRNA miR-204-5p is highly expressed in the kidney but whether miR-204-5p plays any role in the development of chronic renal injury is unknown. METHODS: We used real-time PCR to determine levels of miR-204 in human kidney biopsies and animal models. We generated Mir204 knockout mice and used locked nucleic acid-modified anti-miR to knock down miR-204-5p in mice and rats. We used a number of physiologic, histologic, and molecular techniques to analyze the potential role of miR-204-5p in three models of renal injury. RESULTS: Kidneys of patients with hypertension, hypertensive nephrosclerosis, or diabetic nephropathy exhibited a significant decrease in miR-204-5p compared with controls. Dahl salt-sensitive rats displayed lower levels of renal miR-204-5p compared with partially protected congenic SS.13BN26 rats. Administering anti-miR-204-5p to SS.13BN26 rats exacerbated interlobular artery thickening and renal interstitial fibrosis. In a mouse model of hypertensive renal injury induced by uninephrectomy, angiotensin II, and a high-salt diet, Mir204 gene knockout significantly exacerbated albuminuria, renal interstitial fibrosis, and interlobular artery thickening, despite attenuation of hypertension. In diabetic db/db mice, administering anti-miR-204-5p exacerbated albuminuria and cortical fibrosis without influencing blood glucose levels. In all three models, inhibiting miR-204-5p or deleting Mir204 led to upregulation of protein tyrosine phosphatase SHP2, a target gene of miR-204-5p, and increased phosphorylation of signal transducer and activator of transcription 3, or STAT3, which is an injury-promoting effector of SHP2. CONCLUSIONS: These findings indicate that the highly expressed miR-204-5p plays a prominent role in safeguarding the kidneys against common causes of chronic renal injury.

Unexpected Short-Tandem-Repeat Patterns in Posttransplant Chimerism Testing: Investigation of 3 Cases with Help from Forensic Science.

Chimerism testing by short tandem repeats (STRs) is used to monitor engraftment after allogeneic hematopoietic stem cell transplantation (HSCT). Generally, STR alleles are stable and transferred from parent to child or from donor to recipient. However, 3 cases did not follow this norm. Additional work-up with help from forensic literature solved these mysteries. In case 1, the patient received HSCT from his son. The son shared STR alleles in 22/23 loci except Penta E, which was explained by repeat expansion in the son. In case 2, the patient had been in remission for 14 years after HSCT for lymphoma and developed repeat expansion in CSF1PO in granulocytes. In case 3, a pre-HSCT patient demonstrated 3 alleles, with 2 peaks taller than the third, in the FGA locus (chromosome 4). A combination of a triallelic variant and leukemia-associated trisomy 4 explained the finding. STR number variants are rare and clinically inconsequential but can overlap malignancy-associated, clinically significant changes.

Cell-free DNA donor fraction analysis in pediatric and adult heart transplant patients by multiplexed allele-specific quantitative PCR: Validation of a rapid and highly sensitive clinical test for stratification of rejection probability.

Lifelong noninvasive rejection monitoring in heart transplant patients is a critical clinical need historically poorly met in adults and unavailable for children and infants. Cell-free DNA (cfDNA) donor-specific fraction (DF), a direct marker of selective donor organ injury, is a promising analytical target. Methodological differences in sample processing and DF determination profoundly affect quality and sensitivity of cfDNA analyses, requiring specialized optimization for low cfDNA levels typical of transplant patients. Using next-generation sequencing, we previously correlated elevated DF with acute cellular and antibody-mediated rejection (ACR and AMR) in pediatric and adult heart transplant patients. However, next-generation sequencing is limited by cost, TAT, and sensitivity, leading us to clinically validate a rapid, highly sensitive, quantitative genotyping test, myTAIHEART®, addressing these limitations. To assure pre-analytical quality and consider interrelated cfDNA measures, plasma preparation was optimized and total cfDNA (TCF) concentration, DNA fragmentation, and DF quantification were validated in parallel for integration into myTAIHEART reporting. Analytical validations employed individual and reconstructed mixtures of human blood-derived genomic DNA (gDNA), cfDNA, and gDNA sheared to apoptotic length. Precision, linearity, and limits of blank/detection/quantification were established for TCF concentration, DNA fragmentation ratio, and DF determinations. For DF, multiplexed high-fidelity amplification followed by quantitative genotyping of 94 SNP targets was applied to 1168 samples to evaluate donor options in staged simulations, demonstrating DF call equivalency with/without donor genotype. Clinical validation studies using 158 matched endomyocardial biopsy-plasma pairs from 76 pediatric and adult heart transplant recipients selected a DF cutoff (0.32%) producing 100% NPV for ≥2R ACR. This supports the assay's conservative intended use of stratifying low versus increased probability of ≥2R ACR. myTAIHEART is clinically validated for heart transplant recipients ≥2 months old and ≥8 days post-transplant, expanding opportunity for noninvasive transplant rejection assessment to infants and children and to all recipients >1 week post-transplant.

Correction to: Incorporating Colorectal Cancer Genetic Risk Assessment into Gastroenterology Practice.

The original article unfortunately contained a mistake. On page 8, Table 2, the row with "POLE POLD1" has been shifted right so all the columns are not correct.

DNA methylation in AgRP neurons regulates voluntary exercise behavior in mice.

DNA methylation regulates cell type-specific gene expression. Here, in a transgenic mouse model, we show that deletion of the gene encoding DNA methyltransferase Dnmt3a in hypothalamic AgRP neurons causes a sedentary phenotype characterized by reduced voluntary exercise and increased adiposity. Whole-genome bisulfite sequencing (WGBS) and transcriptional profiling in neuronal nuclei from the arcuate nucleus of the hypothalamus (ARH) reveal differentially methylated genomic regions and reduced expression of AgRP neuron-associated genes in knockout mice. We use read-level analysis of WGBS data to infer putative ARH neural cell types affected by the knockout, and to localize promoter hypomethylation and increased expression of the growth factor Bmp7 to AgRP neurons, suggesting a role for aberrant TGF-ß signaling in the development of this phenotype. Together, these data demonstrate that DNA methylation in AgRP neurons is required for their normal epigenetic development and neuron-specific gene expression profiles, and regulates voluntary exercise behavior.

Incorporating Colorectal Cancer Genetic Risk Assessment into Gastroenterology Practice.

PURPOSE OF REVIEW: Decades have passed since the underlying molecular etiologies of the most common hereditary forms of colorectal cancer (CRC), Lynch syndrome, and familial adenomatous polyposis (FAP) were first described. With the advent of next-generation sequencing (NGS) panels, the landscape of hereditary CRC testing has changed dramatically. We review available screening strategies, novel CRC predisposition genes, and challenges and opportunities in this field. RECENT FINDINGS: Improved sensitivity and availability of NGS panel testing have greatly expanded our understanding regarding the number of CRC syndromes and their phenotypic expression. A variety of screening strategies are available to identify heritable CRC syndromes, potentially decreasing morbidity and mortality in this population. However, these screening strategies remain imperfect and present challenges regarding their implementation in clinical practice. Screening strategies include universal screening of CRC tumors for Lynch syndrome, clinical prediction algorithms, and risk assessment questionnaires. Additionally, there remains a gap in our understanding of the clinical implications of novel gene mutations of variable penetrance and unexpected NGS panel test results. Incorporation of single nucleotide polymorphisms (SNPs) may help to further refine cancer risk assessment, and the clinical introduction of RNA analysis may allow us to clarify variants of unknown significance (VUSs) and identify deep intronic mutations that would otherwise be missed. Recognition of genetic predisposition to CRC is critical for the practicing gastroenterologist. The evolving field of cancer genetics offers great challenges and opportunities for improved CRC management.

Early postnatal overnutrition accelerates aging-associated epigenetic drift in pancreatic islets.

Pancreatic islets of type 2 diabetes patients have altered DNA methylation, contributing to islet dysfunction and the onset of type 2 diabetes. The cause of these epigenetic alterations is largely unknown. We set out to test whether (i) islet DNA methylation would change with aging and (ii) early postnatal overnutrition would persistently alter DNA methylation. We performed genome-scale DNA methylation profiling in islets from postnatally over-nourished (suckled in a small litter) and control male mice at both postnatal day 21 and postnatal day 180. DNA methylation differences were validated using quantitative bisulfite pyrosequencing, and associations with expression were assessed by RT-PCR. We discovered that genomic regions that are hypermethylated in exocrine relative to endocrine pancreas tend to gain methylation in islets during aging (R 2 = 0.33, P < 0.0001). These methylation differences were inversely correlated with mRNA expression of genes relevant to ß cell function [including Rab3b (Ras-related protein Rab-3B), Cacnb3 (voltage-dependent L-type calcium channel subunit 3), Atp2a3 (sarcoplasmic/endoplasmic reticulum calcium ATPase 3) and Ins2 (insulin 2)]. Relative to control, small litter islets showed DNA methylation differences directly after weaning and in adulthood, but few of these were present at both ages. Surprisingly, we found substantial overlap of methylated loci caused by aging and small litter feeding, suggesting that the age-associated gain of DNA methylation happened much earlier in small litter islets than control islets. Our results provide the novel insights that aging-associated DNA methylation increases reflect an epigenetic drift toward the exocrine pancreas epigenome, and that early postnatal overnutrition may accelerate this process.

Genetic Variants Implicate Dual Oxidase-2 in Familial and Sporadic Nonmedullary Thyroid Cancer.

Highly penetrant hereditary thyroid cancer manifests as familial nonmedullary thyroid cancer (FNMTC), whereas low-penetrance hereditary thyroid cancer manifests as sporadic disease and is associated with common polymorphisms, including rs965513[A]. Whole-exome sequencing of an FNMTC kindred identified a novel Y1203H germline dual oxidase-2 (DUOX2) mutation. DUOX2Y1203H is enzymatically active, with increased production of reactive oxygen species. Furthermore, patients with sporadic thyroid cancer homozygous for rs965513[A] demonstrated higher DUOX2 expression than heterozygous rs965513[A/G] or homozygous rs965513[A]-negative patients. These data suggest that dysregulated hydrogen peroxide metabolism is a common mechanism by which high- and low-penetrance genetic factors increase thyroid cancer risk. SIGNIFICANCE: This study provides novel insights into the genetic and molecular mechanisms underlying familial and sporadic thyroid cancers.