Investigation of Human Endogenous Retrovirus-K (ERVK) Expression and Function in Normal Placentation and Preterm Pregnancy

Background: There is a growing body of evidence indicating the importance of endogenous retrovirus (ERV) derived proteins during early development and reproduction in mammals. Recently, a protein derived from the youngest ERV in humans, ERVK (HML2), was shown to be expressed during human placentation. Since a number of highly similar ERVK proviral loci exist across the human genome, locus-specific analysis of ERVK transcription and identification of the coding sequence expressed in the human placenta is difficult. Thus, despite its activity in early human development, the native expression and function of ERVK in the human placenta remains largely uncharacterized. Results: In this study, we comprehensively examined locus-specific ERVK transcription across several human placental tissues and cell types. Through a combination of RNA-seq and siRNA knock-down analyses, we identified the expression of a single ERVK locus, ERVK11q23.3, as (1) being significantly upregulated in preterm compared to term placenta, (2) predominantly expressed by mononuclear trophoblasts, (3) capable of encoding a truncated viral-like envelope protein, and (4) contributing to the expression cytokines involved in both antiviral and anti-inflammatory innate immune responses in human placental trophoblasts and BeWo choriocarcinoma cells, respectively. Conclusions: Collectively, the results of this study highlight the utility of studying locus-specific ERVK expression, provide a thorough characterization of locus-specific ERVK transcription from human placental tissues, and indicate that altered expression of placental ERVK11q23.3 influences interferon antiviral response, which may contribute to preterm birth and other pregnancy complications.

Cells of the human intestinal tract mapped across space and time

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung’s disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.

Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation

The first lineage choice made in human embryo development separates trophectoderm from the inner cell mass, which proceeds to form the pluripotent epiblast and primitive endoderm. Trophectoderm on the other hand gives rise to the placenta. Naïve pluripotent stem cells are derived from the pluripotent epiblast of the blastocyst and offer possibilities to explore how lineage integrity is maintained. Here, we discover that Polycomb repressive complex 2 (PRC2) restricts an intrinsic capacity of naïve pluripotent stem cells to give rise to trophectoderm. Through quantitative epigenome profiling, we find that broad histone H3 lysine 27 trimethylation (H3K27me3) hypermethylation is a common feature of naïve pluripotency across species. We define a previously unappreciated, naïve-specific set of bivalent promoters, featuring PRC2-mediated H3K27me3 concomitant with H3K4me3. Naïve bivalency maintains key trophectoderm transcription factors in a transcriptionally poised state that is resolved to an active state upon depletion of H3K27me3 via inhibition of the enzymatic subunits of PRC2, EZH1/2. Conversely, primed human embryonic stem cells cannot be driven towards trophectoderm development via PRC2 inhibition. While naïve and primed hESCs share the majority of bivalent promoters, PRC2 contributes to the repression of largely non-overlapping subsets of these promoters in each state, hence H3K27me3-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development.

Primate-specific cis- and trans-regulators shape transcriptional networks during human development

The human genome contains more than 4.5 million inserts derived from transposable elements (TE), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or preimplantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins of similar evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in an equally lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.

Everyday parameters for daily temporal schedules of music in infancy

Experience-dependent change pervades early human development. Though trajectories of developmental achievements have been well charted in many domains, the episode-to-episode schedules of experiences on which they are hypothesized to depend have not. Here, we took up this issue in a domain known to be governed in part by early experiences: music. Using a corpus of longform audio recordings, we parameterized the daily temporal schedules of music encountered by 35 infants ages 6-12 months. We discovered that everyday music episodes, as well as the interstices between episodes, typically persisted less than a minute, with most daily schedules also including some very extended episodes and interstices. We also discovered that infants encountered music episodes in a bursty rhythm, rather than a periodic or random rhythm, over the day. Future theories about how infants build knowledge across multiple episodes can now be parameterized using these insights from infants’ everyday lives.

Pediatric Environmental Health

Pediatric environmental health is the academic discipline that studies how environmental exposures in early life — biological, chemical, nutritional, physical, and social—influence health and development in childhood and across the lifespan. This discipline emerged in the mid-1980s after the discovery that secondhand smoke exposure was linked to increased rates of lower respiratory illness in children. Before that, most people did not realize that smoking cigarettes harmed anyone but the smoker. When the harmful effects of secondhand exposure to tobacco smoke were uncovered, researchers began asking questions about other pollutants—could it be that other biological, chemical, physical, and social agents to which children are routinely exposed also harm their health? Children have environmental exposures that are different from and often larger than those of adults. Children also have enormous susceptibilities in early development—unique “windows of vulnerability”—to toxic exposures that have no counterpart in adult life. It is well understood that timing of exposure is critically important in early human development. The tissues and organs of embryos, fetuses, infants, and children are rapidly growing and developing. Adolescence also is a period of rapid growth. These complex and delicate developmental processes are uniquely sensitive to disruption by environmental influences. Exposures sustained during windows of early vulnerability, even to extremely low levels of toxic materials, can cause lasting damage.

Generation of human blastocyst-like structures by somatic cell reprogramming

In the human blastocyst, as development progresses, cells of the epiblast (EPI) lineage will develop into the embryo proper and amnion, whereas cells of the trophectoderm (TE) and primitive endoderm (PE) will give rise to the placenta and yolk sac, respectively1. The study of early human development relies on the use of blastocysts donated to research or cell culture systems such as pluripotent and trophoblast stem cells. Altogether, these have been seminal in shedding light on many key differentiation processes. However, simple culture systems lack the necessary complexity to adequately model the spatio-temporal/cellular and molecular dynamics occurring during the early phases of embryonic development. Currently, an in vitro model of the human blastocyst is not available. Here, we describe a protocol for the generation of an in vitro integrated model of the human blastocyst obtained by reprogramming fibroblasts, termed iBlastoids.