Polymorphic short tandem repeats make widespread contributions to blood and serum traits

Short tandem repeats (STRs) are genomic regions consisting of repeated sequences of 1-6 bp in succession. Single-nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) do not fully capture STR effects. To study these effects, we imputed 445,720 STRs into genotype arrays from 408,153 White British UK Biobank participants and tested for association with 44 blood phenotypes. Using two fine-mapping methods, we identify 119 candidate causal STR-trait associations and estimate that STRs account for 5.2%-7.6% of causal variants identifiable from GWASs for these traits. These are among the strongest associations for multiple phenotypes, including a coding CTG repeat associated with apolipoprotein B levels, a promoter CGG repeat with platelet traits, and an intronic poly(A) repeat with mean platelet volume. Our study suggests that STRs make widespread contributions to complex traits, provides stringently selected candidate causal STRs, and demonstrates the need to consider a more complete view of genetic variation in GWASs.

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice

Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1-6 bp. We leveraged whole-genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate genome-wide patterns of new mutations arising during parent-to-offspring transmission at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and performed quantitative trait locus (QTL) analyses for each of these phenotypes. We identified a locus on Chromosome 13 at which strains inheriting the C57BL/6J (B) haplotype have a higher rate of STR expansions than those inheriting the DBA/2J (D) haplotype. The strongest candidate gene in this locus is Msh3, a known modifier of STR stability in cancer and at pathogenic repeat expansions in mice and humans, as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5' end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion. The rate of expansion covaries positively with Msh3 expression-with higher expression from the B haplotype. Finally, detailed analysis of mutation patterns showed that strains carrying the B allele have higher expansion rates, but slightly lower overall total mutation rates, compared with those with the D allele, particularly at tetranucleotide repeats. Our results suggest an important role for inherited variants in Msh3 in modulating genome-wide patterns of germline mutations at STRs.

Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1

Combination of immunofluorescence, Western blot, and ChIP-seq revealed the interplay between HDAC2, HDAC3, and SIRT1 in H3K9 deacetylation during mitosis of mammalian cells.

Histone acetylation levels are reduced during mitosis. To study the mitotic regulation of H3K9ac, we used an array of inhibitors targeting specific histone deacetylases. We evaluated the involvement of the targeted enzymes in regulating H3K9ac during all mitotic stages by immunofluorescence and immunoblots. We identified HDAC2, HDAC3, and SIRT1 as modulators of H3K9ac mitotic levels. HDAC2 inhibition increased H3K9ac levels in prophase, whereas HDAC3 or SIRT1 inhibition increased H3K9ac levels in metaphase. Next, we performed ChIP-seq on mitotic-arrested cells following targeted inhibition of these histone deacetylases. We found that both HDAC2 and HDAC3 have a similar impact on H3K9ac, and inhibiting either of these two HDACs substantially increases the levels of this histone acetylation in promoters, enhancers, and insulators. Altogether, our results support a model in which H3K9 deacetylation is a stepwise process—at prophase, HDAC2 modulates most transcription-associated H3K9ac-marked loci, and at metaphase, HDAC3 maintains the reduced acetylation, whereas SIRT1 potentially regulates H3K9ac by impacting HAT activity.

The Use of Base Editing Technology to Characterize Single Nucleotide Variants

Single nucleotide variants (SNVs) represent the most common type of polymorphism in the human genome. However, in many cases the phenotypic impacts of such variants are not well understood. Intriguingly, while some SNVs cause debilitating diseases, other variants in the same gene may have no, or limited, impact. The mechanisms underlying these complex patterns are difficult to study at scale. Additionally, current data and research is mainly focused on European populations, and the mechanisms underlying genetic traits in other populations are poorly studied. Novel technologies may be able to mitigate this disparity and improve the applicability of personalized healthcare to underserved populations. In this review we discuss base editing technologies and their potential to accelerate progress in this field, particularly in combination with single-cell RNA sequencing. We further explore how base editing screens can help link SNVs to distinct disease phenotypes. We then highlight several studies that take advantage of single-cell RNA sequencing and CRISPR screens to emphasize the current limitations and future potential of this technique. Lastly, we consider the use of such approaches to potentially accelerate the study of genetic mechanisms in non-European populations.

Missing heritability may be hiding in repeats

[Figure: see text].

Early COVID-19 therapy with azithromycin plus nitazoxanide, ivermectin or hydroxychloroquine in outpatient settings significantly improved COVID-19 outcomes compared to known outcomes in untreated patients

In a prospective observational study (pre-AndroCoV Trial), the use of nitazoxanide, ivermectin and hydroxychloroquine demonstrated unexpected improvements in COVID-19 outcomes when compared to untreated patients. The apparent yet likely positive results raised ethical concerns on the employment of further full placebo controlled studies in early-stage COVID-19. The present analysis aimed to elucidate, through a comparative analysis with two control groups, whether full placebo-control randomized clinical trials (RCTs) on early-stage COVID-19 are still ethically acceptable. The Active group (AG) consisted of patients enrolled in the Pre-AndroCoV-Trial (n = 585). Control Group 1 (CG1) consisted of a retrospectively obtained group of untreated patients of the same population (n = 137), and Control Group 2 (CG2) resulted from a precise prediction of clinical outcomes based on a thorough and structured review of indexed articles and official statements. Patients were matched for sex, age, comorbidities and disease severity at baseline. Compared to CG1 and CG2, AG showed reduction of 31.5-36.5% in viral shedding (p < 0.0001), 70-85% in disease duration (p < 0.0001), and 100% in respiratory complications, hospitalization, mechanical ventilation, deaths and post-COVID manifestations (p < 0.0001 for all). For every 1000 confirmed cases for COVID-19, at least 70 hospitalizations, 50 mechanical ventilations and five deaths were prevented. Benefits from the combination of early COVID-19 detection and early pharmacological approaches were consistent and overwhelming when compared to untreated groups, which, together with the well-established safety profile of the drug combinations tested in the Pre-AndroCoV Trial, precluded our study from continuing employing full placebo in early COVID-19.

A flexible ChIP-sequencing simulation toolkit

Background

A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this challenge, but existing frameworks are either too cumbersome to apply genome-wide or unable to model a number of important experimental conditions in ChIP-seq.

Results

We present ChIPs, a toolkit for rapidly simulating ChIP-seq data using statistical models of key experimental steps. We demonstrate how ChIPs can be used for a range of applications, including benchmarking analysis tools and evaluating the impact of various experimental parameters. ChIPs is implemented as a standalone command-line program written in C++ and is available from https://github.com/gymreklab/chips.

Conclusions

ChIPs is an efficient ChIP-seq simulation framework that generates realistic datasets over a flexible range of experimental conditions. It can serve as an important component in various ChIP-seq analyses where ground truth data are needed.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04097-5.

Erosive pustular dermatosis of the scalp: a multicentre study

BACKGROUND

Erosive pustular dermatosis of the scalp (EPDS) is characterized by crusted erosions or superficial ulcerations that lead to scarring alopecia.

OBJECTIVES AND METHODS

We performed a multicentre retrospective clinical study including 56 patients (29 females and 27 males, mean age 62.7) with a confirmed EPDS in order to describe epidemiology, clinical findings and therapeutic choices of this disease.

RESULTS

Mechanical/chemical trauma was reported in 28.6%, a previous infection in 10.7%, a previous cryotherapy in 5.4% androgenetic alopecia in 48.2% and severe actinic damage in 25%. Trichoscopy showed absence of follicular ostia, tufted and broken hair, crusts, serous exudate, dilated vessels, pustules and hyperkeratosis. Histopathology revealed three different features, depending on the disease duration. The most prescribed therapy was topical steroids (62.5%), followed by the combination of topical steroids and topical tacrolimus (8.9%), systemic steroids (7.1%) and topical tacrolimus (5.4%). A reduction of inflammatory signs was observed in 28 patients (50%) treated with topical steroids and in all three patients treated with topical tacrolimus.

CONCLUSION

The relatively high number of patients collected allowed us to identify a better diagnostic approach, using trichoscopy and a more effective therapeutic strategy, with high-potency steroids or tacrolimus, which should be considered as first-line treatment.

H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration

Deciphering the genetic and epigenetic regulation of cardiomyocyte proliferation in organisms that are capable of robust cardiac renewal, such as zebrafish, represents an attractive inroad towards regenerating the human heart. Using integrated high-throughput transcriptional and chromatin analyses, we have identified a strong association between H3K27me3 deposition and reduced sarcomere and cytoskeletal gene expression in proliferative cardiomyocytes following cardiac injury in zebrafish. To move beyond an association, we generated an inducible transgenic strain expressing a mutant version of histone 3, H3.3K27M, that inhibits H3K27me3 catalysis in cardiomyocytes during the regenerative window. Hearts comprising H3.3K27M-expressing cardiomyocytes fail to regenerate, with wound edge cells showing heightened expression of structural genes and prominent sarcomeres. Although cell cycle re-entry was unperturbed, cytokinesis and wound invasion were significantly compromised. Collectively, our study identifies H3K27me3-mediated silencing of structural genes as requisite for zebrafish heart regeneration and suggests that repression of similar structural components in the border zone of an infarcted human heart might improve its regenerative capacity.

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing

Transcriptional regulation in eukaryotes occurs at promoter-proximal regions wherein transcriptionally engaged RNA polymerase II (Pol II) pauses before proceeding toward productive elongation. The role of chromatin in pausing remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 binds to Pol II and prevents the release of the negative elongation factor (NELF), thus stabilizing Pol II promoter-proximal pausing. Genetic depletion of SIRT6 or its chromatin deficiency upon glucose deprivation causes intragenic enrichment of acetylated histone H3 at lysines 9 (H3K9ac) and 56 (H3K56ac), activation of cyclin-dependent kinase 9 (CDK9)-that phosphorylates NELF and the carboxyl terminal domain of Pol II-and enrichment of the positive transcription elongation factors MYC, BRD4, PAF1, and the super elongation factors AFF4 and ELL2. These events lead to increased expression of genes involved in metabolism, protein synthesis, and embryonic development. Our results identified SIRT6 as a Pol II promoter-proximal pausing-dedicated histone deacetylase.

Identification of the sulfotransferase iso-enzyme primarily responsible for the bio-activation of topical minoxidil

Pattern hair loss (i.e., androgenetic alopecia) is a common condition afflicting approximately fifty percent of men and women by the age of fifty. Currently, topical minoxidil is the only US FDA approved drug for the treatment of pattern hair loss in men and women.

Low-dose daily aspirin reduces topical minoxidil efficacy in androgenetic alopecia patients

Topical minoxidil is the only US FDA approved OTC drug for the treatment of androgenetic alopecia (AGA). Minoxidil is a pro-drug converted into its active form, minoxidil sulfate, by the sulfotransferase enzymes in the outer root sheath of hair follicles. Previously, we demonstrated that sulfotransferase activity in hair follicles predicts response to topical minoxidil in the treatment of AGA. In the human liver, sulfotransferase activity is significantly inhibited by salicylic acid. Low-dose OTC aspirin (75-81 mg), a derivative of salicylic acid, is used by millions of people daily for the prevention of coronary heart disease and cancer. It is not known whether oral aspirin inhibits sulfotransferase activity in hair follicles, potentially affecting minoxidil response in AGA patients. In the present study, we determined the follicular sulfotransferase enzymatic activity following 14 days of oral aspirin administration. In our cohort of 24 subjects, 50% were initially predicted to be responders to minoxidil. However, following 14 days of aspirin administration, only 27% of the subjects were predicted to respond to topical minoxidil. To the best of our knowledge, this is the first study to report the effect of low-dose daily aspirin use on the efficacy of topical minoxidil.

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns

Mitosis encompasses key molecular changes including chromatin condensation, nuclear envelope breakdown, and reduced transcription levels. Immediately after mitosis, the interphase chromatin structure is reestablished and transcription resumes. The reestablishment of the interphase chromatin is probably achieved by "bookmarking," i.e., the retention of at least partial information during mitosis. To gain a deeper understanding of the contribution of histone modifications to the mitotic bookmarking process, we merged proteomics, immunofluorescence, and ChIP-seq approaches. We focused on key histone modifications and employed HeLa-S3 cells as a model system. Generally, in spite of the general hypoacetylation observed during mitosis, we observed a global concordance between the genomic organization of histone modifications in interphase and mitosis, suggesting that the epigenomic landscape may serve as a component of the mitotic bookmarking process. Next, we investigated the nucleosome that enters nucleosome depleted regions (NDRs) during mitosis. We observed that in ∼60% of the NDRs, the entering nucleosome is distinct from the surrounding highly acetylated nucleosomes and appears to have either low levels of acetylation or high levels of phosphorylation in adjacent residues (since adjacent phosphorylation may interfere with the ability to detect acetylation). Inhibition of histone deacetylases (HDACs) by the small molecule TSA reverts this pattern, suggesting that these nucleosomes are specifically deacetylated during mitosis. Altogether, by merging multiple approaches, our study provides evidence to support a model where histone modifications may play a role in mitotic bookmarking and uncovers new insights into the deposition of nucleosomes during mitosis.

The effect of topical minoxidil treatment on follicular sulfotransferase enzymatic activity

Minoxidil is the only US FDA-approved topical drug for the treatment of female and male pattern hair loss. Previously, it was demonstrated that topical minoxidil is metabolized to its active metabolite, minoxidil sulfate, by sulfotransferase enzymes located in the outer root sheath of hair follicles. The expression of sulfotransferase in the scalp varies greatly between individuals, and this difference in expression explains the varied response to minoxidil treatment. Previously, we have demonstrated the clinical utility of detecting sulfotransferase in plucked hair follicles to predict minoxidil response in pattern hair loss patients. Typically, exogenous exposure to substrates affects the expression of the enzymatic system responsible for their metabolism. For example, Phase I metabolizing enzymes, such as the cytochrome P450 family of enzymes, are known to be up-regulated in the presence of xenobiotic substrates. However, it is not known if Phase II metabolizing enzymes, such as the sulfotransferase family of enzymes, are similarly affected by the presence of substrates. In this study, we recruited 120 subjects and analyzed their sulfotransferase enzymatic activity before and after treatment with topical minoxidil. Adjusting the results for biologic (within subject) variability, we discovered that the sulfotransferase enzymatic system expression is stable over the course of minoxidil treatment. To the best of our knowledge, this is the first study to demonstrate the stability of sulfotransferase, a Phase II metabolizing enzyme, over the course of minoxidil treatment.

Social selection favours offspring prone to the development of androgenetic alopecia

In recent years, dermatologists have observed an increase in the incidence of male androgenetic alopecia (AGA). In a survey of 41 dermatologists, 88% reported an increase in incidence of AGA in men younger than 30 years. This phenomenon has no apparent explanation. However, due to the strong genetic inheritance component of AGA, a social or environmental factor which favours the inheritance of genes that increase the risk of developing AGA is suspected. To date, the strongest predictor of AGA in men has been the length of the CAG repeat located in the androgen receptor gene (AR gene) on the X chromosome. The same genetic variant in women is associated with ovulation at a later age, higher antral follicle count, and lower risk for premature ovarian failure. This led us to theorize that, due to social pressure to conceive later in life, women carriers of the short CAG repeat in the AR gene would have a selective advantage to conceive later in life and would thus favour male offspring exhibiting AGA.

Mechanism of action of minoxidil in the treatment of androgenetic alopecia is likely mediated by mitochondrial adenosine triphosphate synthase-induced stem cell differentiation

Topical minoxidil is the only topical drug approved by the US Food and Drug Administration (FDA) for the treatment of androgenetic alopecia. However, the exact mechanism by which minoxidil stimulates anagen phase and promotes hair growth is not fully understood. In the late telegen phase of the hair follicle growth cycle, stem cells located in the bulge region differentiate and re-enter anagen phase, a period of growth lasting 2-6 years. In androgenetic alopecia, the anagen phase is shortened and a progressive miniaturization of hair follicles occurs, eventually leading to hair loss. Several studies have demonstrated that minoxidil increases the amount of intracellular Ca2+, which has been shown to up-regulate the enzyme adenosine triphosphate (ATP) synthase. A recent study demonstrated that ATP synthase, independent of its role in ATP synthesis, promotes stem cell differentiation. As such, we propose that minoxidil induced Ca2+ influx can increase stem cell differentiation and may be a key factor in the mechanism by which minoxidil facilitates hair growth. Based on our theory, we provide a roadmap for the development of a new class of drugs for the treatment of androgenetic alopecia.

Potential risk of developing herpes simplex encephalitis in patients treated with sildenafil following primary exposure to genital herpes

Herpes simplex encephalitis (HSE) is associated with significant mortality and morbidity. As a consequence of HSE, up to 75% of infected individuals die or experience irreversible neurological damage. While the pathogenesis of the disease is unknown, it is traditionally hypothesized that the viral infection occurs by neuronal transmission directly from peripheral sites. Non-neuronal modes of infection have generally been overlooked as the brain is protected by the blood-brain-barrier (BBB). The BBB poses an effective barrier to pathogens as well as to drugs such as chemotherapies. In the pursuit to deliver chemotherapeutic agents to the brain, several studies demonstrated that phosphodiesterase type 5 (PDE5) inhibitors, such as sildenafil, may increase the permeability of the BBB enabling successful delivery of chemotherapeutic agents to the brain. In this communication, we report a case of HSE infection in a 62-year-old man, which we suspect was facilitated by the use of sildenafil during a primary genital herpes simple virus (HSV) infection. Due to large number of patients treated with PDE5 inhibitors for erectile dysfunction and the high incidence of genital HSV infection in the general population, a larger study should examine the potential risk of developing HSE in patients treated with PDE5 inhibitors.

Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences

Avoiding biases in next generation sequencing (NGS) library preparation is crucial for obtaining reliable sequencing data. Recently, a new library preparation method has been introduced which has eliminated the need for the ligation step. This method, termed SMART (switching mechanism at the 5' end of the RNA transcript), is based on template switching reverse transcription. To date, there has been no systematic analysis of the additional biases introduced by this method. We analysed the genomic distribution of sequenced reads prepared from genomic DNA using the SMART methodology and found a strong bias toward long (≥12bp) poly dA/dT containing genomic loci. This bias is unique to the SMART-based library preparation and does not appear when libraries are prepared with conventional ligation based methods. Although this bias is obvious only when performing paired end sequencing, it affects single end sequenced samples as well. Our analysis demonstrates that sequenced reads originating from SMART-DNA libraries are heavily skewed toward genomic poly dA/dT tracts. This bias needs to be considered when deciding to use SMART based technology for library preparation.

Melanin of the nipple areola complex

Biological pigments or biochromes are ubiquitous in animals, plants, and simpler organisms such as fungi and bacteria. They serve a wide spectrum of functions from photosynthesis, camouflage, mimicry, photo protection from the environment to attracting mates. The human female nipple areola complex (NAC) is a highly-pigmented area. Currently, the prevailing theory as to the evolution of the pigmented human NAC is based on infant recognition of breast feeding latching zone; however, due to the protruding shape of the nipple and surrounding breast, the authors of this letter believe that the evolutionary advantage of the pigmented NAC has a direct physiological function, namely the initiation of involution at the end of the infant lactation period.

Abstract B16: Loss of SIRT6 reactivates the RNA-binding protein Lin28b to drive pancreatic cancer

Chromatin remodeling proteins are frequently dysregulated in human cancer; however, little is known about how they control tumorigenesis. The NAD+ dependent histone deacetylase Sirtuin 6 (SIRT6) is a nutrient sensor that reprograms the epigenome in response to nutrient stress and shows reduced expression in human pancreatic ductal adenocarcinoma (PDAC) relative to normal tissue. Thus, we aimed to determine the role of SIRT6 in PDAC and to determine how the loss of this chromatin modifier could influence PDAC formation, progression and metastasis.

Here, we uncover an epigenetic program mediated by SIRT6 that is critical for the suppression of PDAC. We demonstrate that SIRT6 inactivation cooperates with oncogenic KRAS to greatly accelerate the development of lethal pancreatic tumors regardless of p53 status. In addition to developing PDAC and high-grade pancreatic intraepithelial neoplasia (PanIN) at an earlier age, SIRT6-deficient tumors had a greater propensity to metastasize to the lung, compared to their SIRT6 wild-type (WT) counterparts. Through genome-wide profiling of SIRT6 WT and knock-out (KO) PDAC cell lines, we identified the oncofetal RNA-binding protein Lin28b as a target of Sirt6-mediated transcriptional repression. Loss of SIRT6 in both murine and human PDAC cell lines resulted in hyperacetylation of histone 3 lysine 9 and lysine 56 at the Lin28b promoter, MYC recruitment, and pronounced induction of Lin28b expression. Knocking down Lin28b resulted in potent suppression of cell proliferation and tumor sphere formation in Sirt6null/low murine and human cell lines, while murine and human Sirt6WT/high PDAC lines were completely insensitive to the same treatment. Functionally, Lin28b binds to and induces the degradation of the let-7 family of microRNA, thus resulting in increased expression of let-7 target genes such as the IGF2BPs and HMGA2, which have been correlated with increased agressiveness and metastasis in pancreatic tumors. Furthermore, Gene Set Enrichment Analysis (GSEA) comparing PDAC tumors and cell lines with high versus low expression of LIN28B revealed that LIN28Bhigh tumors were strongly enriched for the expression of let-7 targets. Finally, either loss of SIRT6 or the reactivation of Lin28b or the let-7 target genes IGF2BP3 and HMGA2 correlated with a worse overall survival in human PDAC patients.

Thus, our critical findings define SIRT6 as a tumor suppressor in PDAC, working as a transcriptional repressor of the oncofetal RNA-binding protein Lin28b. We demonstrate that loss of Sirt6 creates a permissive hyperacetylated chromatin state, allowing for MYC-dependent transactivation of Lin28b. This work not only provides new insights into the epigenetic mechanisms governing the reactivation of oncofetal proteins in cancer but also demonstrates that this pathway is well-conserved in human PDAC, where reduced SIRT6 expression defines a specific subset of tumors which may benefit from novel therapeutic approaches aimed at targeting components of the LIN28B/let-7 pathway.

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section PR09 of the Conference Proceedings.

Citation Format: Sita Kugel, Carlos Sebastián, Julien Fitamant, Kenneth N. Ross, Supriya K. Saha, Esha Jain, Adrianne Gladden, Kshitij S. Arora, Yasutaka Kato, Miguel N. Rivera, Sridhar Ramaswamy, Ruslan I. Sadreyev, Alon Goren, Vikram Deshpande, Nabeel Bardeesy, Raul Mostoslavsky.{Authors}. Loss of SIRT6 reactivates the RNA-binding protein Lin28b to drive pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B16.

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq

Background

The robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance between lots and need to be validated with each new lot. In contrast, monoclonal antibody lots are renewable and provide consistent performance. To increase ChIP-seq standardization, we investigated whether monoclonal antibodies could replace polyclonal antibodies. We compared monoclonal antibodies that target five key histone modifications (H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3) to their polyclonal counterparts in both human and mouse cells.

Results

Overall performance was highly similar for four monoclonal/polyclonal pairs, including when we used two distinct lots of the same monoclonal antibody. In contrast, the binding patterns for H3K27ac differed substantially between polyclonal and monoclonal antibodies. However, this was most likely due to the distinct immunogen used rather than the clonality of the antibody.

Conclusions

Altogether, we found that monoclonal antibodies as a class perform equivalently to polyclonal antibodies for the detection of histone post-translational modifications in both human and mouse. Accordingly, we recommend the use of monoclonal antibodies in ChIP-seq experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-016-0100-6) contains supplementary material, which is available to authorized users.

Minoxidil dose response study in female pattern hair loss patients determined to be non-responders to 5% topical minoxidil

Topical minoxidil is the only US FDA approved drug for the treatment of female pattern hair loss (FPHL). 5% minoxidil foam is only effective at re-growing hair in a minority of women (approximately 40%). Thus, the majority of FPHL patients remain untreated. Previously, we demonstrated that nonresponders to 5% minoxidil have low metabolism of minoxidil in hair follicles. As such, we hypothesized that increasing the dosage of topical minoxidil to low metabolizers would increase the number of responders without increasing the incidence of adverse events. In this study, we recruited FPHL subjects that were identified as non-responders to 5% topical minoxidil utilizing the previously validated assay for minoxidil response. Subjects were treated for 12 weeks with a novel 15% topical minoxidil solution. At 12 weeks, 60% of subjects achieved a clinically significant response based on target area hair counts (>13.7% from baseline), as well as significant improvement in global photographic assessment. None of the subjects experienced significant hemodynamic changes or any other adverse events. To the best of our knowledge, this is the first study to demonstrate the potentially beneficial effect of a higher dosage of minoxidil in FPHL subjects who fail to respond to 5% minoxidil.

Abstract 2656: Loss of SIRT6 reactivates the oncofetal RNA-binding protein Lin28b to drive pancreatic cancer

Chromatin remodeling proteins are frequently dysregulated in human cancer, however little is known about how they control tumorigenesis. The NAD+-dependent histone deacetylase Sirtuin 6 (SIRT6) is a nutrient sensor that reprograms the epigenome in response to nutrient stress and shows reduced expression in human pancreatic ductal adenocarcinoma (PDAC) relative to normal tissue. Thus, we aimed to determine the role of SIRT6 in PDAC and to determine how the loss of this chromatin modifier could influence PDAC formation, progression and metastasis.

Here, we uncover an epigenetic program mediated by SIRT6 that is critical for suppression of PDAC. We demonstrate that SIRT6 inactivation cooperates with oncogenic KRAS to greatly accelerate the development of lethal pancreatic tumors regardless of p53 status. In addition to developing PDAC and high-grade pancreatic intraepithelial neoplasia (PanIN) at an earlier age, SIRT6-deficient tumors had a greater propensity to metastasize to the lung, compared to their SIRT6 wild-type (WT) counterparts. Through genome-wide profiling of SIRT6 WT and knock-out (KO) PDAC cell lines, we identified the oncofetal RNA-binding protein Lin28b as a target of Sirt6-mediated transcriptional repression. Loss of SIRT6 in both murine and human PDAC cell lines resulted in hyperacetylation of histone 3 lysine 9 and lysine 56 at the Lin28b promoter, MYC recruitment, and pronounced induction of Lin28b expression. Knocking down Lin28b resulted in potent suppression of cell proliferation and tumor sphere formation in Sirt6null/low murine and human cell lines, while murine and human Sirt6WT/high PDAC lines were completely insensitive to the same treatment. Functionally, Lin28b binds to and induces the degradation of the let-7 family of microRNA, thus resulting in increased expression of let-7 target genes such as the Igf2bps, which have been correlated with increased agressiveness and metastasis in pancreatic tumors. Furthermore, Gene Set Enrichment Analysis (GSEA) comparing PDAC tumors and cell lines with high versus low expression of LIN28B revealed that LIN28Bhigh tumors were strongly enriched for the expression of let-7 targets.

Thus, our critical findings define SIRT6 as a tumor suppressor in PDAC, working as a transcriptional repressor of the oncofetal RNA-binding protein Lin28b. We demonstrate that loss of Sirt6 creates a permissive hyperacetylated chromatin state, allowing for MYC-dependent transactivation of Lin28b. This work not only provides new insights into the epigenetic mechanisms governing the reactivation of oncofetal proteins in cancer but also demonstrates that this pathway is well-conserved in human PDAC, where reduced SIRT6 expression defines a specific subset of tumors which may benefit from novel therapeutic approaches aimed at targeting components of the LIN28B/let-7 pathway.

Citation Format: Sita Kugel, Carlos Sebastián, Julien Fitamant, Kenneth N. Ross, Supriya K. Saha, Alon Goren, Sridhar Ramaswamy, Vikram Deshpande, Nabeel Bardeesy, Raul Mostoslavsky. Loss of SIRT6 reactivates the oncofetal RNA-binding protein Lin28b to drive pancreatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2656.

SIRT6 Suppresses Pancreatic Cancer through Control of Lin28b

Chromatin remodeling proteins are frequently dysregulated in human cancer, yet little is known about how they control tumorigenesis. Here, we uncover an epigenetic program mediated by the NAD(+)-dependent histone deacetylase Sirtuin 6 (SIRT6) that is critical for suppression of pancreatic ductal adenocarcinoma (PDAC), one of the most lethal malignancies. SIRT6 inactivation accelerates PDAC progression and metastasis via upregulation of Lin28b, a negative regulator of the let-7 microRNA. SIRT6 loss results in histone hyperacetylation at the Lin28b promoter, Myc recruitment, and pronounced induction of Lin28b and downstream let-7 target genes, HMGA2, IGF2BP1, and IGF2BP3. This epigenetic program defines a distinct subset with a poor prognosis, representing 30%-40% of human PDAC, characterized by reduced SIRT6 expression and an exquisite dependence on Lin28b for tumor growth. Thus, we identify SIRT6 as an important PDAC tumor suppressor and uncover the Lin28b pathway as a potential therapeutic target in a molecularly defined PDAC subset. PAPERCLIP.

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

Angiocentric gliomas are pediatric low-grade gliomas (PLGGs) without known recurrent genetic drivers. We performed genomic analysis of new and published data from 249 PLGGs including 19 Angiocentric Gliomas. We identified MYB-QKI fusions as a specific and single candidate driver event in Angiocentric Gliomas. In vitro and in vivo functional studies show MYB-QKI rearrangements promote tumorigenesis through three mechanisms: MYB activation by truncation, enhancer translocation driving aberrant MYB-QKI expression, and hemizygous loss of the tumor suppressor QKI. This represents the first example of a single driver rearrangement simultaneously transforming cells via three genetic and epigenetic mechanisms in a tumor.

Potential benefits of diagnosis and treatment on health outcomes among elderly people with symptoms of overactive bladder

OBJECTIVES

This study examined potential benefits of diagnosing and treating elderly adults with overactive bladder (OAB) symptoms.

METHODS

Data were analysed from the OAB Re-Contact Study (N = 2750), a cross-sectional, self-reported Internet survey. Elderly respondents (65+ years old) with OAB were identified according to current medication use to control OAB symptoms or by scores > 14 (men) or > 16 (women) on the OAB Awareness Tool. Treated were those currently using prescription medication and never treated were those who never used prescription medication for OAB. Outcome measures included health-related quality of life, activity impairment, OAB-related severity and symptoms, and healthcare resource use (e.g. hospitalisations). Generalised linear models predicted health outcomes as a function of diagnosis or treatment, adjusting for covariates.

RESULTS

Diagnosed vs. not diagnosed elderly respondents had higher mental component summary (MCS) scores and SF-6D health utilities, and less activity impairment. Treated vs. never treated elderly respondents had higher MCS and SF-6D health utilities, less activity impairment, fewer OAB symptoms, lower OAB Awareness Tool scores, and lower odds of having bladder problems or incontinence. There were no significant differences in healthcare resource use. Further analysis by age group (middle-aged vs. elderly respondents) revealed significantly greater diagnosis- and treatment-related benefits on MCS (2.93 and 4.49 points more, respectively) and activity impairment (1.24 and 1.37 times as much, respectively) among elderly respondents.

CONCLUSIONS

Diagnosis and treatment were each associated with a lower health burden for elderly adults with OAB symptoms. These findings highlighted the importance of diagnosis and treatment in alleviating OAB symptoms and their impact on health outcomes.

Doppler laser imaging predicts response to topical minoxidil in the treatment of female pattern hair loss

Topical minoxidil is the only drug approved by the US FDA for the treatment of female pattern hair loss. Unfortunately, following 16 weeks of daily application, less than 40% of patients regrow hair. Several studies have demonstrated that sulfotransferase enzyme activity in plucked hair follicles predicts topical minoxidil response in female pattern hair loss patients. However, due to patients’ discomfort with the procedure, and the time required to perform the enzymatic assay it would be ideal to develop a rapid, non-invasive test for sulfotransferase enzyme activity. Minoxidil is a pro-drug converted to its active form, minoxidil sulfate, by sulfotransferase enzymes in the outer root sheath of hair. Minoxidil sulfate is the active form required for both the promotion of hair regrowth and the vasodilatory effects of minoxidil. We thus hypothesized that laser Doppler velocimetry measurement of scalp blood perfusion subsequent to the application of topical minoxidil would correlate with sulfotransferase enzyme activity in plucked hair follicles. In this study, plucked hair follicles from female pattern hair loss patients were analyzed for sulfotransferase enzyme activity. Additionally, laser Doppler velocimetry was used to measure the change in scalp perfusion at 15, 30, 45, and 60 minutes, after the application of minoxidil. In agreement with our hypothesis, we discovered a correlation (r=1.0) between the change in scalp perfusion within 60 minutes after topical minoxidil application and sulfotransferase enzyme activity in plucked hairs. To our knowledge, this is the first study demonstrating the feasibility of using laser Doppler imaging as a rapid, non-invasive diagnostic test to predict topical minoxidil response in the treatment of female pattern hair loss.

Oct1 and OCA-B are selectively required for CD4 memory T cell function

Shakya et al. identify the transcription factor Oct1 and its cofactor OCA-B as central mediators for generating memory T cell responses in mice.

Epigenetic changes are crucial for the generation of immunological memory. Failure to generate or maintain these changes will result in poor memory responses. Similarly, augmenting or stabilizing the correct epigenetic states offers a potential method of enhancing memory. Yet the transcription factors that regulate these processes are poorly defined. We find that the transcription factor Oct1 and its cofactor OCA-B are selectively required for the in vivo generation of CD4⁺ memory T cells. More importantly, the memory cells that are formed do not respond properly to antigen reencounter. In vitro, both proteins are required to maintain a poised state at the Il2 target locus in resting but previously stimulated CD4⁺ T cells. OCA-B is also required for the robust reexpression of multiple other genes including Ifng. ChIPseq identifies ∼50 differentially expressed direct Oct1 and OCA-B targets. We identify an underlying mechanism involving OCA-B recruitment of the histone lysine demethylase Jmjd1a to targets such as Il2, Ifng, and Zbtb32. The findings pinpoint Oct1 and OCA-B as central mediators of CD4⁺ T cell memory.

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

Chromatin profiling provides a versatile means to investigate functional genomic elements and their regulation. However, current methods yield ensemble profiles that are insensitive to cell-to-cell variation. Here we combine microfluidics, DNA barcoding and sequencing to collect chromatin data at single-cell resolution. We demonstrate the utility of the technology by assaying thousands of individual cells, and using the data to deconvolute a mixture of ES cells, fibroblasts and hematopoietic progenitors into high-quality chromatin state maps for each cell type. The data from each single cell is sparse, comprising on the order of 1000 unique reads. However, by assaying thousands of ES cells, we identify a spectrum of sub-populations defined by differences in chromatin signatures of pluripotency and differentiation priming. We corroborate these findings by comparison to orthogonal single-cell gene expression data. Our method for single-cell analysis reveals aspects of epigenetic heterogeneity not captured by transcriptional analysis alone.

Burden of smoking among adults with COPD, chronic bronchitis, and emphysema in urban China

OBJECTIVE

Tobacco, widely used in China, poses a major risk for chronic obstructive pulmonary disease (COPD). This study assessed health outcomes of COPD-diagnosed smokers vs. never smokers and examined treatment patterns of patients attempting to quit smoking in urban China.

METHODS

National Health and Wellness Survey (NHWS) 2010 and 2012 China data were analysed. Respondents self-reporting diagnosis with COPD, chronic bronchitis, or emphysema were categorised: quit attempters (current smokers 'trying to quit' or non-smokers 'in the process of quitting'), smokers (including quit attempters) and those who never smoked. Respondents reported smoking cessation treatment utilisation; health status: SF-36v2-based scores and SF-6D health utilities; Work Productivity and Activity Impairment questionnaire-based metrics; and resource utilisation. Regression modelling assessed health outcomes, controlling for covariates.

RESULTS

Among 1421 (3.6%) diagnosed respondents, 51.6% never smoked and 35.5% smoked (of whom, 43.8% were attempting to quit). After adjustments, smokers vs. never smokers had significantly lower health utilities, lower mental/physical health status and greater absenteeism, presenteeism, overall work impairment, activity impairment, emergency room visits, hospitalisations and provider visits. Quit attempters were diagnosed an average 6.9 years (SD = 7.7) previously, with 25.3% reporting moderate/severe COPD. Most-reported main causes of COPD were: smoking (57.5%), illnesses/conditions (53.8%) and pollutants (44.3%). Among quit attempters, 82.8% smoked currently. Use of prescription cessation treatments was reported by 12.7%.

CONCLUSIONS

Smokers experienced poorer health outcomes, reinforcing importance of prevention in mitigating disease burden. Among quit attempters, few reported using prescription cessation treatments. Given the high burden imposed by smoking in China, effective interventions may be beneficial.

The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine

How embryonic stem cells (ESCs) commit to specific cell lineages and yield all cell types of a fully formed organism remains a major question. ESC differentiation is accompanied by large-scale histone and DNA modifications, but the relations between these epigenetic categories are not understood. Here we demonstrate the interplay between the histone deacetylase sirtuin 6 (SIRT6) and the ten-eleven translocation enzymes (TETs). SIRT6 targets acetylated histone H3 at Lys 9 and 56 (H3K9ac and H3K56ac), while TETs convert 5-methylcytosine into 5-hydroxymethylcytosine (5hmC). ESCs derived from Sirt6 knockout (S6KO) mice are skewed towards neuroectoderm development. This phenotype involves derepression of OCT4, SOX2 and NANOG, which causes an upregulation of TET-dependent production of 5hmC. Genome-wide analysis revealed neural genes marked with 5hmC in S6KO ESCs, thereby implicating TET enzymes in the neuroectoderm-skewed differentiation phenotype. We demonstrate that SIRT6 functions as a chromatin regulator safeguarding the balance between pluripotency and differentiation through Tet-mediated production of 5hmC.

Optimization of transcription factor binding map accuracy utilizing knockout-mouse models

Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify 'hyper ChIPable regions' as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.