Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants.

Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.

Ultraconserved Enhancers Are Required for Normal Development.

Non-coding "ultraconserved" regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revealed that loss of such extraordinarily constrained sequences had no immediate impact on viability. Here, we show that ultraconserved enhancers are required for normal development. Focusing on some of the longest ultraconserved sites genome wide, located near the essential neuronal transcription factor Arx, we used genome editing to create an expanded series of knockout mice lacking individual or combinations of ultraconserved enhancers. Mice with single or pairwise deletions of ultraconserved enhancers were viable and fertile but in nearly all cases showed neurological or growth abnormalities, including substantial alterations of neuron populations and structural brain defects. Our results demonstrate the functional importance of ultraconserved enhancers and indicate that remarkably strong sequence conservation likely results from fitness deficits that appear subtle in a laboratory setting.

An atlas of dynamic chromatin landscapes in mouse fetal development.

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Precise Manipulation of the Site and Stoichiometry of Capsid Modification Enables Optimization of Functional Adeno-Associated Virus Conjugates.

The ability to engineer adeno-associated virus (AAV) vectors for targeted transduction of specific cell types is critically important to fully harness their potential for human gene therapy. A promising approach to achieve this objective involves chemically attaching retargeting ligands onto the virus capsid. Site-specific incorporation of a bioorthogonal noncanonical amino acid (ncAA) into the AAV capsid proteins provides a particularly attractive strategy to introduce such modifications with exquisite precision. In this study, we show that using ncAA mutagenesis, it is possible to systematically alter the attachment site of a retargeting ligand (cyclic-RGD) on the AAV capsid to create diverse conjugate architectures and that the site of attachment heavily impacts the retargeting efficiency. We further demonstrate that the performance of these AAV conjugates is highly sensitive to the stoichiometry of capsid labeling (labels per capsid), with an intermediate labeling density providing optimal activity for cRGD-mediated retargeting. Finally, we developed a technology to more precisely control the number of attachment sites per AAV capsid by selectively incorporating an ncAA into the minor capsid proteins with high fidelity and efficiency, such that AAV conjugates with varying stoichiometry can be synthesized. Together, this platform provides unparalleled control over the site and stoichiometry of capsid modification, which will enable the development of next-generation AAV vectors tailored with desirable attributes.

Enhancer redundancy provides phenotypic robustness in mammalian development.

Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.

Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis.

Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus-assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base-pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem of M. mazei pyrrolysyl tRNA (tRNAPyl ), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell-lines for ncAA mutagenesis.

Chemical Tagging of Bioactive Amides by Cooperative Catalysis: Applications in the Syntheses of Drug Conjugates.

We disclose a practical catalytic method for arming bioactive amide-based natural products and other small-molecule drugs with various functional handles for the synthesis of drug conjugates. We demonstrate that a set of readily available Sc-based Lewis acids and N-based Brønsted bases can function cooperatively to deprotonate amide N-H bonds in polyfunctional drug molecules. An aza-Michael reaction between the resulting amidate and α,ß-unsaturated compounds produces an array of drug analogues that are equipped with an alkyne, azide, maleimide, tetrazine, or diazirine moiety under redox and pH-neutral conditions. The utility of this chemical tagging strategy is showcased through the production of drug conjugates by the click reaction between the alkyne-tagged drug derivatives and an azide-containing green fluorescent protein, nanobody, or antibody.

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. We demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.

Acceptability of prenatal diagnosis and prenatal treatment of haemophilia using cell and gene therapies within US haemophilia community.

BACKGROUND: The overall burden of disease in persons with haemophilia continues to be high despite the latest advancements in therapeutics. Clinical trials testing prenatal treatments for several genetic disorders are underway or are recruiting subjects, attesting to the much-needed change in paradigm of how patients with monogenic disorders can be treated. Here we investigate the overall attitude towards prenatal diagnosis, preferences on types of prenatal therapies for haemophilia, the level of 'acceptable' risk tolerated, and which social and moral pressures or disease personal experiences may predict willingness of individuals to consider foetal therapy in a future pregnancy. RESULTS: A multidisciplinary team designed the survey, and the study was carried out using REDCap, and publicized through the National Haemophilia Foundation. Subjects ≥18 years of age were eligible to participate in the study. We assessed participants' attitudes towards prenatal therapy and their level of 'acceptable' risk towards the procedure and therapy. The survey was completed by 67 adults, the majority females. Respondents were willing to undergo prenatal diagnosis, and their main concerns related to the well-being of the pregnant woman and the foetus regarding lasting therapeutic efficacy, side effects of the therapy, and procedural risks, but they were likely to accept a wide range of prenatal therapeutic options, particularly if the foetal therapy proved to be long-lasting and safe. CONCLUSIONS: These data demonstrate the willingness of persons with haemophilia, and the haemophilia community, to explore new treatment options beyond the currently offered approaches.

Photoredox-Catalyzed Labeling of Hydroxyindoles with Chemoselectivity (PhotoCLIC) for Site-Specific Protein Bioconjugation.

We have developed a novel visible-light-catalyzed bioconjugation reaction, PhotoCLIC, that enables chemoselective attachment of diverse aromatic amine reagents onto a site-specifically installed 5-hydroxytryptophan residue (5HTP) on full-length proteins of varied complexity. The reaction uses catalytic amounts of methylene blue and blue/red light-emitting diodes (455/650 nm) for rapid site-specific protein bioconjugation. Characterization of the PhotoCLIC product reveals a unique structure formed likely through a singlet oxygen-dependent modification of 5HTP. PhotoCLIC has a wide substrate scope and its compatibility with strain-promoted azide-alkyne click reaction, enables site-specific dual-labeling of a target protein.

Intracytoplasmic sperm injection versus conventional in-vitro fertilisation in couples with infertility in whom the male partner has normal total sperm count and motility: an open-label, randomised controlled trial.

BACKGROUND: The use of intracytoplasmic sperm injection has increased substantially worldwide, primarily in couples with non-male factor infertility. However, there is a paucity of evidence from randomised trials supporting this approach compared with conventional in-vitro fertilisation (IVF). We aimed to investigate whether intracytoplasmic sperm injection would result in a higher livebirth rate compared with conventional IVF. METHODS: This open-label, multicentre, randomised trial was done at two IVF centres in Ho Chi Minh City, Vietnam (IVFMD, My Duc Hospital and IVFAS, An Sinh Hospital). Eligible couples were aged at least 18 years and the male partner's sperm count and motility (progressive motility) were normal based on WHO 2010 criteria. Couples had to have undergone two or fewer previous conventional IVF or intracytoplasmic sperm injection attempts, have used an antagonist protocol for ovarian stimulation, and agree to have two or fewer embryos transferred. Couples were randomly assigned (1:1) to undergo either intracytoplasmic sperm injection or conventional IVF, using block randomisation with variable block size of 2, 4, or 8 and a telephone-based central randomisation method. The computer-generated randomisation list was prepared by an independent statistician who had no other involvement in the study. Embryologists and couples were not masked to study groups because of the type of interventions and differences in hospital fees, but clinicians performing embryo transfer were unaware of study group allocation. The primary outcome was livebirth after the first embryo transfer from the initiated cycle. Analyses were done on an intention-to-treat basis. The trial is registered with ClinicalTrials.gov, NCT03428919. FINDINGS: Between March 16, 2018, and Aug 12, 2019, we randomly assigned 1064 couples to intracytoplasmic sperm injection (n=532) or conventional IVF (n=532). Livebirth after the first embryo transfer from the initiated cycle occurred in 184 (35%) of 532 couples randomly assigned to intracytoplasmic sperm injection and in 166 (31%) of 532 couples randomly assigned to conventional IVF (absolute difference 3·4%, 95% CI -2·4 to 9·2; risk ratio [RR] 1·11, 95% CI 0·93 to 1·32; p=0·27). 29 (5%) couples in the intracytoplasmic sperm injection group and 34 (6%) couples in the conventional IVF group had fertilisation failure (absolute difference -0·9%, -4·0 to 2·1, RR 0·85, 95% CI 0·53 to 1·38; p=0·60). INTERPRETATION: In couples with infertility in whom the male partner has a normal total sperm count and motility, intracytoplasmic sperm injection did not improve the livebirth rate compared with conventional IVF. Our results challenge the value of the routine use of intracytoplasmic sperm injection in assisted reproduction techniques for this population. FUNDING: My Duc Hospital and Merck Sharp and Dohme.

Investigating the microbial pathogens of sexually transmitted infections among heterosexual Vietnamese men with symptomatic urethritis.

OBJECTIVE: To explore the microbial etiology of urethritis in Vietnamese men and the association with patients' characteristics, especially their sexual behaviors. METHODS: This study was conducted on 349 men who presented with symptomatic urethritis and evidence of STIs (determined by multiplex PCR tests) at the Department of Andrology and Sexual Medicine-Hanoi Medical University Hospital. All information regarding medical history, sexual activities, and symptoms of urethritis was documented. RESULTS: C. trachomatis and N. gonorrhoea remained the two most common causative pathogens, followed by an unexpectedly high prevalence of Mycoplasma and Ureaplasma species. Coinfection was significant with a rate of 40.7%. Men who had sex with female sex workers (FSWs) were more likely to be positive with N. gonorrhoea but less likely to be positive with C. trachomatis and M. genitalium than those having sex with only one romantic partner. CONCLUSIONS: Our findings suggested the important role of other microorganisms, especially M. genitalium, in the etiology of urethritis in men besides the previously well-known causes of STIs. Since the coinfection rate is quite high, targeted treatment with clear microbial evidence should be considered rather than empiric antimicrobial therapy.

Target Design of Novel Histone Deacetylase 6 Selective Inhibitors with 2-Mercaptoquinazolinone as the Cap Moiety.

Epigenetic alterations found in all human cancers are promising targets for anticancer therapy. In this sense, histone deacetylase inhibitors (HDACIs) are interesting anticancer agents that play an important role in the epigenetic regulation of cancer cells. Here, we report 15 novel hydroxamic acid-based histone deacetylase inhibitors with quinazolinone core structures. Five compounds exhibited antiproliferative activity with IC50 values of 3.4-37.8 µM. Compound 8 with a 2-mercaptoquinazolinone cap moiety displayed the highest antiproliferative efficacy against MCF-7 cells. For the HDAC6 target selectivity study, compound 8 displayed an IC50 value of 2.3 µM, which is 29.3 times higher than those of HDAC3, HDAC4, HDAC8, and HDAC11. Western blot assay proved that compound 8 strongly inhibited tubulin acetylation, a substrate of HDAC6. Compound 8 also displayed stronger inhibition activity against HDAC11 than the control drug Belinostat. The inhibitory mechanism of action of compound 8 on HDAC enzymes was then explored using molecular docking study. The data revealed a high binding affinity (-7.92 kcal/mol) of compound 8 toward HDAC6. In addition, dock pose analysis also proved that compound 8 might serve as a potent inhibitor of HDAC11.

Regulatory T cells promote remyelination in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis following human neural stem cell transplant.

Multiple sclerosis (MS) is a chronic, inflammatory autoimmune disease that affects the central nervous system (CNS) for which there is no cure. In MS, encephalitogenic T cells infiltrate the CNS causing demyelination and neuroinflammation; however, little is known about the role of regulatory T cells (Tregs) in CNS tissue repair. Transplantation of neural stem and progenitor cells (NSCs and NPCs) is a promising therapeutic strategy to promote repair through cell replacement, although recent findings suggest transplanted NSCs also instruct endogenous repair mechanisms. We have recently described that dampened neuroinflammation and increased remyelination is correlated with emergence of Tregs following human NPC transplantation in a murine viral model of immune-mediated demyelination. In the current study we utilized the prototypic murine autoimmune model of demyelination experimental autoimmune encephalomyelitis (EAE) to test the efficacy of hNSC transplantation. Eight-week-old, male EAE mice receiving an intraspinal transplant of hNSCs during the chronic phase of disease displayed remyelination, dampened neuroinflammation, and an increase in CNS CD4+CD25+FoxP3+ regulatory T cells (Tregs). Importantly, ablation of Tregs abrogated histopathological improvement. Tregs are essential for maintenance of T cell homeostasis and prevention of autoimmunity, and an emerging role for Tregs in maintenance of tissue homeostasis through interactions with stem and progenitor cells has recently been suggested. The data presented here provide direct evidence for collaboration between CNS Tregs and hNSCs promoting remyelination.

Reference Intervals of Thyroid Function Tests in First Trimester Vietnamese Pregnant Women.

BACKGROUND: Although TSH suppression by elevated ß-hCG is essentially seen during first trimester, differences in TSH reference ranges between various countries have been reported. Physiologic changes during pregnancy may also influence FT4 assays. This study aims to establish method-specific reference intervals (RIs) of TSH, FT4, and FT3 in Vietnamese, first trimester pregnant women. METHODS: This cross-sectional study was conducted at My Duc Hospital, Ho Chi Minh, Vietnam. Women with singleton pregnancies in the first trimester and conceived naturally were included. Those with a history of thyroid disease, positive thyroid-specific autoantibodies, diffuse goiter or one thyroid nodule > 10 mm in size or ≥ 2 nodules detected by ultrasound, and taking medications affecting thyroid function were excluded. Serum TSH, FT4, and FT3 were measured by chemiluminescent detection technology on the Access 2 Immunoassay System (Beckman Coulter, Inc., USA). Intra- and interassay coefficients of variations (CV) were 3.6% and 4.4% for TSH, 5.4% and 6.1% for FT4, 6.6%, and 6.0% for FT3, respectively. The 2.5th and 97.5th percentiles were used to determine RIs. RESULTS: Between August 1, 2017, to December 1, 2018, there were 876 pregnant women who fulfilled inclusion and exclusion criteria. They had a mean age of 30.1 years, an average BMI of 21.3 kg/m2, and 77.3% of them were primigravida. The RIs for TSH, FT4 and FT3 were 0.17 - 2.35 mIU/L, 0.67 - 1.11 ng/dL and 2.82 - 3.90 pg/mL, respectively. CONCLUSIONS: Established RIs for TSH, FT4, and FT3 in Vietnamese women would help to reduce the misdiagnosis of gestational thyroid disorders.

Single cell three-channel wavelength division multiplexing in visible light communication.

This paper examines the design of a prototype of a single cell three-channel visible light communication (VLC) based on wavelength division multiplexing for a radio frequency (RF)-free indoor healthcare. For a low complexity application, a single red green blue (RGB)-type white light-emitting diode (LED) and a single color sensor are adopted. An active low pass filter is utilized for robust light detection to eliminate ambient light and low frequency noise. The incoming tri-color lights are separated by an adopted color sensor and simultaneously demodulated by a receiver processor. Then, the collected data are monitored in real-time and analyzed to provide the necessary medical attention to the concerned patient.

Female Sexually Fluid (Non)identity Management Strategies at Work.

Previous research on sexual identity management at work focuses on default fixed sexual categories and related strategies such as pass or reveal. What if employees experience changes in their sexual attractions and identity? The present study pioneers in incorporating the concept of sexual fluidity into organization research in order to both complement and challenge the scholarship of sexual identity management at work. It provides empirical evidence from Vietnam that is in line with queer perspective in challenging the notion of a fixed, constructed sexual identity. Through in-depth interviews with 30 female employees experiencing sexual fluidity during their work, this study aims to investigate how they manage a sexually fluid identity in the workplace. The results show that female employees first consider or choose (non)identity1 that matches their new sexual attractions. These (non)identity choices include identity change, fluid identity, non-identity, and resisting identity. Next, strategies are utilized for managing that (non)identity at work-pass, cover, implicitly out, explicitly out, inform/educate. These strategies can be used independently or multiply (mixed/change), in which mixed strategy takes account of communication objects and situations, while change strategy relies on time. Associated individual, organizational and social factors are preliminarily mentioned, in which coworker reactions to the identity changes is a notable point (e.g., surprise, curiosity, inquiry, advice). This study also provides discussion on the construction of sexual identity as stigmatized social identity and the gap of scholarship of sexual identity management at work.

Directed Evolution of a Bacterial Leucyl tRNA in Mammalian Cells for Enhanced Noncanonical Amino Acid Mutagenesis.

The Escherichia coli leucyl-tRNA synthetase (EcLeuRS)/tRNAEcLeu pair has been engineered to genetically encode a structurally diverse group of enabling noncanonical amino acids (ncAAs) in eukaryotes, including those with bioconjugation handles, environment-sensitive fluorophores, photocaged amino acids, and native post-translational modifications. However, the scope of this toolbox in mammalian cells is limited by the poor activity of tRNAEcLeu. Here, we overcome this limitation by evolving tRNAEcLeu directly in mammalian cells by using a virus-assisted selection scheme. This directed evolution platform was optimized for higher throughput such that the entire acceptor stem of tRNAEcLeu could be simultaneously engineered, which resulted in the identification of several variants with remarkably improved efficiency for incorporating a wide range of ncAAs. The advantage of the evolved leucyl tRNAs was demonstrated by expressing ncAA mutants in mammalian cells that were challenging to express before using the wild-type tRNAEcLeu, by creating viral vectors that facilitated ncAA mutagenesis at a significantly lower dose and by creating more efficient mammalian cell lines stably expressing the ncAA-incorporation machinery.