Neil Robertson

• PhD
• Bioinformatician at Mayo Clinic - Rochester

Background Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging ?clock?, a robust biomarker of aging. However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised. To fill this knowledge gap, we defined ag...

Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as...

Robertson et al. report that age-related clonal haemopoiesis (ARCH) is associated with overall accelerated ageing as measured by epigenetic clocks, which are based on methylation status. ARCH is driven by somatic mutations in healthy individuals and confers an increased risk for age-related disease such as haematological cancers and atherosclerosis...

Cellular senescence is a potent tumor suppressor mechanism but also contributes to aging and aging-related diseases. Senescence is characterized by a stable cell cycle arrest and a complex proinflammatory secretome, termed the senescence-associated secretory phenotype (SASP). We recently discovered that cytoplasmic chromatin fragments (CCFs), extru...

Clonal hematopoiesis of indeterminate potential (CHIP) increases rapidly in prevalence beyond age 60 and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in hematopoietic stem and progenitor cells (HSPCs). Because mutations in HSPCs often drive leukemia, we hypothesized t...

Clonal hematopoiesis (CH) is characterized by expanding blood cell clones carrying somatic mutations in healthy aged individuals and is associated with various age-related diseases and all-cause mortality. While CH mutations affect diverse genes associated with myeloid malignancies, their mechanisms of expansion and disease associations remain poor...

The prevalence of clonal hematopoiesis of indeterminate potential (CHIP) in healthy individuals increases rapidly from age 60 onwards and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in stem cells that are also drivers of myeloid malignancies. We previously reported g...

Aberrant expression of stem-cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example of the recurrently activated "stemness" network in AML, we screened for chromatin regulators that sustain its expression. We dep...

Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline o...

Aberrant expression of stem-cell-associated genes is a common feature in acute myeloid leukemia (AML) and is linked to leukemic self-renewal and therapy resistance. Using AF10-rearranged leukemia as a prototypical example displaying a recurrent “ stemness ” network activated in AML, we screened for chromatin regulators that sustain aberrant activat...

Several leukemia-associated oncoproteins activate transcriptional circuits resembling a stem-like state in acute myeloid leukemia (AML). This activation of “stemness” genes is achieved by enlisting the activity of specialized components of the epigenetic machinery. We sought to comprehensively map epigenetic regulators critical for perpetuating the...

Introduction: CHIP is associated with inflammation, atherogenesis and poor outcomes in patients with HFrEF. Although inflammation may be important in the pathophysiology of HFpEF, CHIP has not previously been assessed in patients with HFpEF. We examined the prevalence of CHIP and its associated clinical characteristics in patients with HFpEF or HFr...

Several leukemia-associated oncoproteins activate transcriptional circuits resembling a stem-like state in acute myeloid leukemia (AML). This activation of “stemness” genes such as the clustered homeobox (HOX) genes, TALE domain proteins MEIS1, PBX1/3, and the Polycomb group gene BMI1 is achieved by enlisting the activity of specialized components...

Characterising associations between the methylome, proteome and phenome may provide insight into biological pathways governing brain health. Here, we report an integrated DNA methylation and phenotypic study of the circulating proteome in relation to brain health. Methylome-wide association studies of 4058 plasma proteins are performed (N = 774), i...

Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline and targeted depletion of senescent cells in vivo ameliorates many age-related phenotyp...

Histone chaperone HIRA is thought to play a role in both early development and aging, but little is known about connections between the two processes. Here, we explore this relationship using a lineage-specific knockout mouse model, TyrCre::Hira fl/fl , in which HIRA is deficient in the pigmentary system consisting of embryonic melanoblasts, postna...

Background Once bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Without the use of a visualisation and interpretation pipeline this step can be time consuming and laborious, and is often completed...

Clonal Haematopoiesis (CH) exponentially increases with age, with 18-20% of individuals over age 90 presenting somatic mutations in leukaemic driver genes. One of those mutations can be found in the tyrosine kinase Janus 2 (JAK2V617F). Patients with Polycythaemia Vera (PV), a subgroup of Myeloproliferative Neoplasms considered as pre-neoplastic and...

Clonal haemopoiesis of indeterminate potential (CHIP) in healthy individuals was initially observed through an increased skewing in X chromosome inactivation and occurs from age 60 onwards with up to 20% of 90 year olds being CHIP carriers. More recently, several groups reported that CHIP is driven by somatic mutations (Genovese et al, 2014), with...

The prevalence of clonal haematopoiesis of indeterminate potential (CHIP) in healthy individuals increases rapidly from age 60 onwards and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in stem cells that are also drivers of myeloid malignancies. Since mutations in stem...

Acute myeloid leukemia (AML) is a typically lethal molecularly heterogeneous disease, with few broad-spectrum therapeutic targets. Unusually, most AML retain wild-type TP53 , encoding the pro-apoptotic tumor suppressor p53. MDM2 inhibitors (MDM2i), which activate wild-type p53, and BET inhibitors (BETi), targeting the BET-family co-activator BRD4,...

The aberrant and constitutive activation of the HOXA cluster genes and the their-co-factor MEIS1 (HOX/MEIS) is a recurrent feature in several types of myeloid and lymphoid leukemias. Aberrant HOX/MEIS expression has been shown to drive limitless leukemia stem cell self-renewal and is therefore an attractive target for therapy in acute myeloid leuke...

Acute Myeloid Leukemia (AML) is a typically-lethal molecularly heterogeneous disease, with few broad-spectrum therapeutic targets. Unusually compared to many other cancers, over 90% of AML patients retain wild type TP53, encoding pro-apoptotic tumor suppressor p53. However, wild-type p53 functions are frequently suppressed by MDM2, an E3 ubiquitin...

Acute Myeloid Leukemia (AML) is a typically-lethal molecularly heterogeneous disease, with few broad-spectrum therapeutic targets. Unusually, most AML retain wild-type TP53 , encoding the pro-apoptotic tumor suppressor p53. MDM2 inhibitors (MDM2i), which activate wild-type p53, and BET inhibitors (BETi), targeting the BET-family co-activator BRD4,...

p>Acute Myeloid Leukemia (AML) is a typically-lethal molecularly heterogeneous disease, with few broad-spectrum therapeutic targets. Unusually, over 90% of AML patients retain wild type TP53 , encoding pro-apoptotic tumor suppressor p53. However, wild-type p53 functions are frequently suppressed by MDM2, an E3 ubiquitin ligase that targets p53 for...

Acute Myeloid Leukemia (AML) is a typically-lethal molecularly heterogeneous disease, with few broad-spectrum therapeutic targets. Unusually, over 90% of AML patients retain wild type TP53, encoding pro-apoptotic tumor suppressor p53. However, wild-type p53 functions are frequently suppressed by MDM2, an E3 ubiquitin ligase that targets p53 for pro...

Clonal haematopoiesis of indeterminate potential (CHIP) is widespread in the elderly. CHIP is driven by somatic mutations in leukaemia driver genes, such as Janus Kinase 2 (JAK2), Tet methylcytosine dioxygenase 2 (TET2), ASXL Transcriptional Regulator 1 (ASXL1) and DNA (cytosine-5)-methyltransferase 3A (DNMT3A), leading to reduced diversity of the...

Cell‐based therapeutics, such as in vitro manufactured red blood cells (mRBCs), are different to traditional biopharmaceutical products (the final product being the cells themselves as opposed to biological molecules such as proteins) and that presents a challenge of developing new robust and economically feasible manufacturing processes, especiall...

Approximately 10% of human colorectal cancer (CRC) are associated with activated BRAFV600E mutation, typically in absence of APC mutation and often associated with a CpG island methylator (CIMP) phenotype. To protect from cancer, normal intestinal epithelial cells respond to oncogenic BRAFV600E by activation of intrinsic p53 and p16-dependent tumor...

Overcoming cellular growth restriction, including the evasion of cellular senescence, is a hallmark of cancer. We report that PAK4 is overexpressed in all human breast cancer subtypes and associated with poor patient outcome. In mice, MMTV-PAK4 overexpression promotes spontaneous mammary cancer, while PAK4 gene depletion delays MMTV-PyMT driven tum...

Age-related clonal haemopoiesis (ARCH) in healthy individuals was initially observed through an increased skewing in X chromosome inactivation 1. More recently, several groups reported that ARCH is driven by somatic mutations 2,3. The most prevalent ARCH mutations are in the DNMT3A and TET2 genes, previously described as drivers of myeloid malignan...

Age-related clonal haemopoiesis (ARCH) in healthy individuals was initially observed through an increased skewing in X chromosome inactivation. More recently, several groups reported that ARCH is driven by somatic mutations. The most prevalent ARCH mutations are in the DNMT3A and TET2 genes, previously described as drivers of myeloid malignancies....

Drug resistance and relapse remain key challenges in pancreatic cancer. Here, we have used RNA sequencing (RNA-seq), chromatin immunoprecipitation (ChIP)-seq, and genome-wide CRISPR analysis to map the molecular dependencies of pancreatic cancer stem cells, highly therapy-resistant cells that preferentially drive tumorigenesis and progression. This...

Host innate immune defences play a critical role in restricting the intracellular propagation and pathogenesis of invading viral pathogens. Here we show that the histone H3.3 chaperone HIRA (histone cell cycle regulator) associates with promyelocytic leukaemia nuclear bodies (PML-NBs) to stimulate the induction of innate immune defences against her...

HIRA monoclonal antibody (mAb) validation. HFt cells were stably transduced to express non-targeting control (shCtrl), Daxx- (shDaxx; secondary control), or HIRA- targeting (shHIRA; clones F2-F4) shRNAs. (A) Western blot analysis of the expression levels of HIRA (anti-HIRA mAb 04–1488, Millipore) in whole cell lysates derived from shCtrl, shDaxx, o...

HIRA is not recruited to PML-NBs in mock infected or uninfected cells on the periphery of a developing WT HSV-1 plaque. Representative confocal microscopy images for quantitated data presented in Fig 2C. Wide-field images showing the nuclear localization of HIRA (red) and PML (cyan) in cells mock infected or in close proximity to a developing WT HS...

IFN-β induced HIRA localization at PML-NBs is cell-type dependent. Representative confocal microscopy images for quantitated data presented in Fig 3G. Primary (MRC5, HFs, IMR-90), immortalized (MRC5t, HFt, RPE, HaCat), or carcinoma (U2OS, SAOS, HeLa, A549) cells were (A) mock treated or (B) stimulated with IFN-β (100 IU/ml) for 24 h (as indicated)....

HIRA depletion minimally effects ISG expression following IFN-β stimulation. HFt cells were stably transduced to express non-targeting control (shCtrl) or HIRA -targeting (shHIRA) shRNAs. Cells were treated with IFN-β (100 IU/ml) for 9 or 17 h (as indicated). (A) qRT-PCR quantitation of Mx1, ISG54, ISG15, and OAS1 mRNA levels in IFN-β stimulated sh...

HIRA is recruited to PML-NBs in non-productively infected cells on the periphery of a developing ICP0-null mutant HSV-1 plaque. Split channel confocal microscopy images for data presented in Fig 2A. Wide-field images showing the nuclear localization of HIRA (red) and PML (cyan) in cells in close proximity to a developing ICP0-null mutant HSV-1 plaq...

Inhibition of GSK-3α/β stimulates cell proliferation following release from cell cycle arrest. HFt cells were seeded into 48-well plates and incubated in medium containing low serum (1% FBS) for 24 h to induce cell cycle arrest. Cells were released from starvation into medium containing high serum (10% FBS), 1 μM EdC, and either DMSO (carrier contr...

Pathway analysis of IFN-β stimulated or HSV-1 infected HFt shCtrl and shHIRA cells. Reactome (https://reactome.org/) pathway analysis of high confidence transcriptome changes (FDR Q-value ≤ 0.0001, ≥ log2 fold change) identified following IFN-β (IFNb; 100 IU/ml) or HSV-1 (WT or ΔICP0 HSV-1, annotated WT and dICP0 HSV-1; MOI 1 PFU/cell) treatment of...

Differentially downregulated immune genes between IFN-β stimulated or HSV-1 infected HFt shCtrl and shHIRA cells. Differential downregulated immune system genes identified by Reactome (https://reactome.org/) pathway analysis of treated (t) HFt shCtrl and shHIRA cells (as described in S4 Table). shHIRA (t)/shCtrl (t). (XLSX)

Pathway analysis of untreated HFt shCtrl and shHIRA cells. Reactome (https://reactome.org/) pathway analysis of high confidence transcriptome changes (FDR Q-value ≤ 0.0001, ≥ log2 fold change) identified between untreated (no treatment; nt) HFt shCtrl and shHIRA cells. shHIRA (nt)/shCtrl (nt). (XLSX)

Pathway analysis of IFN-β stimulated or HSV-1 infected HFt shCtrl and shHIRA cells. Reactome (https://reactome.org/) pathway analysis of high confidence transcriptome changes (FDR Q-value ≤ 0.0001, ≥ log2 fold change) identified following IFN-β (IFNb; 100 IU/ml) or HSV-1 (WT or ΔICP0 HSV-1, annotated WT and dICP0 HSV-1; MOI 1 PFU/cell) treatment of...

HIRA recruitment to PML-NBs in cells at the periphery of a developing ΔICP0 HSV-1 plaques is JAK-dependent. Representative confocal microscopy images for quantitated data presented in Fig 2D. Wide-field images showing the nuclear localization of HIRA (red) and PML (cyan) in cells in close proximity to a developing ΔICP0 HSV-1 plaque-edge (eYFP.ICP4...

IFN-β induced HIRA localization at PML-NBs is Sp100 dependent. (A, B) Representative confocal microscopy images for quantitated data presented in Fig 4D. HFt cells were stably transduced to express non-targeting control (shCtrl) or Sp100-targeting (shSp100) shRNAs. Cells were mock treated or stimulated with IFN-β (100 IU/ml) for 24 h (as indicated)...

ICP0 disrupts HIRA localization to input or nascent vDNA. HFt cells were mock infected or infected with 3 PFU/cell of pre-labelled (HSV-1EdC or ΔICP0EdC) or pulse-labelled (0.5 μM EdC upon overlay) WT or ΔICP0 HSV-1 in the presence 50 μM acycloguanasine (ACG; to enable the visualization of input pre-labelled EdC viral genomes following the onset of...

Pathway analysis of IFN-β stimulated or HSV-1 infected HFt shCtrl cells. Reactome (https://reactome.org/) pathway analysis of high confidence transcriptome changes (FDR Q-value ≤ 0.0001, ≥ log2 fold change) identified following IFN-β (IFNb; 100 IU/ml) or HSV-1 (WT or ΔICP0 HSV-1, annotated WT and dICP0 HSV-1; MOI 1 PFU/cell) treatment of HFt shCtrl...

Relative fold ISG transcriptome changes in HFt shCtrl and shHIRA cells following IFN-β stimulation or HSV-1 infection. Relative fold ISG transcriptome [84] changes (FDR Q-value < 0.05) identified following IFN-β (IFNb; 100 IU/ml) or HSV-1 infection (WT or ΔICP0 HSV-1, annotated WT HSV1 and dICP0 HSV-1; MOI 1 PFU/cell) treatment. Conditions: shHIRA...

HIRA ChIP-seq alignment statistic and ISG enrichment analysis. Mapped input control and HIRA ChIP-seq reads in untreated (neg.) or IFN-β treated (2000 IU/ml; Pos.) IMR-90 shCtrl and shPML cells (as indicated). Relative HIRA enrichment levels on 49 similarly sized interferon stimulated or non-interferon stimulated coding genes in mock (no treatment,...

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Ageing is the biggest risk factor for cardiovascular disease. Cellular senescence, a process driven in part by telomere shortening, has been implicated in age-related tissue dysfunction. Here, we address the question of how senescence is induced in rarely dividing/post-mitotic cardiomyocytes and investigate whether clearance of senescent cells atte...

In 2016, there will be approximately 19,950 new cases of Acute Myeloid Leukaemia (AML) in the United States. After diagnosis, five-year survival is currently ~26%, with available therapeutic approaches. Therefore, there remains a critical requirement for novel therapies for AML. Bromodomain and extra-terminal domain inhibitors (BETi) are emerging a...

Ageing is the biggest risk factor for cardiovascular health and is associated with increased incidence of cardiovascular disease. Cellular senescence, a process driven in part by telomere shortening, has been implicated in age-related tissue dysfunction. Here, we address the question of how senescence is induced in rarely dividing/post-mitotic card...

Numerous mechanisms to support cells under conditions of transient nutrient starvation have been described. Several functions of the tumor-suppressor protein p53 can contribute to the adaptation of cells to metabolic stress and help cancer cell survival under nutrient-limiting conditions. We show here that p53 promotes the expression of SLC1A3, an...

Introduction Cancer cells are frequently exposed to nutrient and oxygen limited environments, resulting from poor vascularisation in the developing tumour mass, and there is a growing interest in understanding the metabolic plasticity that supports cancer cell survival and proliferation under these conditions. Glutamine is the most abundant amino a...

Background Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammali...

Background Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although H4K20me3 abundance increases during cellular senescence, a stable proliferation arrest and tumor suppressor process, triggered by diverse molecular cues, including activated...