Review N°103 : Silencing stemness in T cell differentiation

Epigenetic repression is required for the generation of CD8+ effector T cells

By Amanda N. Henning,1,2 Christopher A. Klebanoff,3,4 Nicholas P. Restifo1,2

1Center for Cell-Based Therapy, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

 2Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.

3Center for Cell Engineering and Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA.

4Parker Institute for Cancer Immunotherapy, MSKCC, New York, NY 10065, USA.


Functional diversity in multicellular organisms is achieved through the differentiation of stem cells. During this process, stem cells must retain both the capacity for self-renewal and the ability to differentiate into highly specialized cell types to produce a diverse array of tissues, each with distinct functions and organization. This plasticity is achieved through alterations to the epigenome, heritable and reversible modifications to DNA and histones that affect chromatin structure and gene transcription without altering the DNA sequence itself. Alterations to the epi-genome enable cell type–specific transcriptional control that can change dynamically over the life of a cell. Such flexibility and responsiveness are instrumental in directing gene expression changes throughout cellular differentiation and lineage specification. The acquisition of more specialized functions during differentiation requires not only that the epigenome turn “on” genes involved in lineage commitment, it also necessitates that genes associated with stemness are simultaneously turned “off” (1). On page 177 of this issue, Pace et al. (2) demonstrate that this phenomenon exists in CD8+ T cells, in which epigenetic repression of stemness-associated genes by the histone methyltransferase SUV39H1 is required for T cell effector differentiation. Understanding these mechanisms addresses important questions in immunology and is applicable to cancer immunotherapy.


The CD8+ T lymphocyte compartment of the adaptive immune system has emerged as a model for developmental biology in adult mammalian cells owing to its remark-able degree of functional plasticity (3). CD8+ T cells can rapidly differentiate from a quiescent, long-lived memory state into an effector state characterized by short-lived cytotoxicity toward cancer cells or cells infected with intracellular pathogens (4). Multiple differentiation models have been proposed to account for the observed changes in CD8+ T cell subsets during an immune response. The linear differentiation model places effector T cells (Teff cells) at the end of the differentiation process after the development of multiple intermediary memory T cell subsets (3). Specialized memory T cells, including the relatively rare T memory stem cells (Tscm cells) and the more common central memory T cells (Tcm cells), have characteristics associated with conventional stem cells. This includes enhanced self-renewal, which is essential for maintaining long-term immunological memory, and the ability to reconstitute other CD8+ T cell subsets, which maintains the functional diversity of the CD8+ T cell compartment (5–7). Tscm cells have enhanced stem cell–like capabilities, whereas Tcm cells are poised to rapidly initiate an effector response. With further T cell activation, memory subsets can differentiate into Teff cells followed by terminal differentia-tion, functional senescence, and ultimately apoptosis (cell death). An alternative model suggests that naïve T cells (Tn cells) differentiate into Teff cells immediately after activation, with “dedifferentiation” into memory cells occurring after pathogen clearance (8). Because the dedifferentiation of lineage-restricted cells rarely occurs in nature outside of cancer formation (9), we and others (7) feel that the linear differentiation model is more consistent with typical patterns of cellular differentiation.


CD8+ T cell subsets can be partitioned on the basis of distinct patterns of gene expression. Multiple subset-specific transcription factors regulate gene expression through-out differentiation (4). Although transcription factors are critical mediators of gene expression programs, their activity is largely dependent on epigenetic modifications, the profiles of which can also be used to distinguish T cell subsets (10). Indeed, activating epigenetic modifications are progressively gained at Teff cell–associated gene loci after T cell activation (10, 11). Recently, characterization of repressive epigenetic modifications during differentiation, as described by Pace et al. and others (11–14), have highlighted the importance of epigenetic silencing for proper Teff cell differentiation. Specifically, epigenetic silencing of stem cell– and T cell memory–associated genes in activated T cells permits efficient Teff cell differentiation and function, such that elimination of this activity results in defective Teff cells (2, 1114).


Investigations into the repressive chromatin landscape of CD8+ T cells have focused on DNA methylation and trimethylation (me3) of specific lysine residues (K) on the histone H3 (specifically, H3K27me3 and H3K9me3). The epigenetic “writer” proteins responsible for adding these modifications include DNA methyltransferase 3A (DNMT3A), an enzyme responsible for de novo DNA methylation, and the histone methyltransferase enzymes enhancer of zeste homolog 2 (EZH2) and SUV39H1 (10). In mice, conditional ablation of Dnmt3a (12) and Ezh2 (13) in T cells and germline ablation of Suv39h1 (2) result in an altered phenotypic composition of antigen-specific CD8+ T cells after viral infection: Both the proportion and number of responding Teff cells are reduced and the frequency of memory T cells are increased. In vitro experiments using Ezh2-deficient T cells suggest selective apoptosis within the Teff cell population (14), which accounts for the equal numbers of antigen-specific memory cell subsets as well as the impaired functional efficacy of CD8+ T cells after secondary viral challenge observed in Ezh2- and Suv39h1-deficient mice (2, 13). Preserved memory T cell formation is consistent with the linear differentiation model that places memory cell development before differentiation into Teff cells. By contrast, in a model that predicts that memory T cells originate from Teff cells, one would expect numbers of memory T cells to decrease as well as Teff cells.


Transcriptional and epigenetic profiling of Dnmt3a-, Ezh2-, and Suv39h1-deficient Teff cells illustrates a common defect that is responsible for impaired Teff cell differentiation. Genes encoding master regulators of the stem and memory cell state fail to acquire repressive epigenetic modifications, leading to aberrant gene expression and differentiation (2, 12, 13). Therefore, epigenetic repression of essential stem and memory genes is required for full Teff cell differentiation (see the figure). That Teff cell differentiation is still possible with loss of any one of these epigenetic writers illustrates the functional redundancy in silencing stem and memory genes, stressing the importance of this mechanism. This mirrors the epigenetic silencing of developmental and pluripotency genes during differentiation of human embryonic stem cells (1) and further highlights transcriptional silencing of stem cell–associated genes as a hallmark of cellular differentiation.


Understanding the mechanisms of epi-genetic regulation of Teff cell differentiation has considerable implications for multiple fields, including cancer immunotherapy. Less differentiated T cell subsets, such as Tscm and Tcm cells, have enhanced proliferative potential and greater antitumor activity when transferred into both mice and humans compared with the more differentiated T effector memory cell (Tem cell) and Teff cell subsets. This is likely due to their stem cell–like properties (4, 6). Because the majority of cells currently used for T cell–based cancer immunotherapy are Teff cells, the epigenetic silencing of stem and memory genes in these cells poses a considerable therapeutic roadblock. To reacquire therapeutically beneficial stem cell–like properties, Teff cells would need to be epigenetically reprogrammed. This can be experimentally accomplished, albeit inefficiently (15). A greater understanding of the CD8+ T cell epigenome may therefore provide essential clues for how to unlock the potential of highly differentiated, tumor-antigen– specific T cells infiltrating tumors (4). Epi-genetic modifying drugs may reverse the repression of stem and memory genes in differentiated T cells and improve T cell– based immunotherapies. j    

Shutting down stem and memory genes in CD8+ T cells    

As cells differentiate, stem and memory genes pass through transitional epigenetic states, in which epigenetic modifications associated with transcriptional activation, including H3K4me3 and H3K27ac, are lost via lysine demethylases (KDMs) and histone deacetylases (HDACs). Conversely, repressive modifications such as DNA methylation, H3K27me3, and H3K9me3 are gained because of epigenetic writers, including DNMT3A, EZH2 as part of the Polycomb repressive complex 2 (PRC2), and SUV39H1. Not shown but occurring simultaneously is the acquisition of activating epigenetic modifications at effector-associated genes during T cell differentiation.

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6. C. A. Klebanoff et al., J. Clin. Invest. 126, 318 (2016).

8. B. Youngblood et al., Nature 10.1038/nature25144 (2017).

9. D. Friedmann-Morvinski, I. M. Verma, EMBO Rep. 15, 244 (2014).

11. J. G. Crompton et al., Cell Mol. Immunol. 13, 502 (2016).

Review N°100: Review of plant propagation

by Clarissien Ramongolalaina

It is not essential to learn about botany to garden well: it’s inevitable. Why is the science of plants relevant to the propagator? For the same reason that the physician needs to know about human physiology. By observing the extraordinary truths and beauty of the plant kingdom, we can recognize where to go, how to get there, what to do, and when to do it. Gardeners can discover how to capitalize on plants’ primal goal: to perpetuate themselves, by either passing on genes through seeds or by regenerating tissue, sometimes creating an entire new plant from a single leaf.

The fact that many ancient organisms still exist today is proof that the reproductive strategies that evolved over time are extremely reliable. Well before the first flowers appeared for sexual procreation, fungi reproduced asexually via fruiting bodies —mushrooms —which release billions of spores into the air. A few of these spores would settle in comfortable spots, divide as cells do, and create new beings. The spores grew into exact copies of their single parents.

Evolution and natural selection favor chance: sexual propagation, with its exchange of genetic material, increases the odds for accidental improvements. Mosses and ferns, among the earliest plants, produce spores, but unlike fungi, these plants have sex. A fern spore grows both male and female organs, and a reproductive structure called a prothallus has an aqueous film in which a male gamete (fertile reproductive cell) travels to the female. On rare occasions, however, one of the sexual partners might arrive from a neighboring plant, carried perhaps in the splash of a raindrop. The resulting hybrid —containing genes from both parents —is evolution’s dividend. The new fern may prove better able to survive environmental changes and in time dominate the species.

Gardeners need to understand fern reproduction when sowing spores to grow more plants, but recognizing the impact of hybridization reveals the achievements of natural selection. The sexual plants that evolved after ferns —the gymnosperms, such as conifers, cycads, and the ginkgo —came up with a way to exchange genetic material through the dry medium of air. The gymnosperms encased their male gametes in pollen; and even more revolutionary, they introduced the seed.

Flowers fine-tuned the delivery system, but at a great cost. Intricate and elaborate blossoms enlist the help of animals in swapping chromosomes with like flowers in distant neighborhoods. But it takes a great deal of energy to produce a fancy flower. Adaptations to environmental circumstances must be made, as well as adjustments to the independent evolution of the specific animal partner.

Some of the most recent plants that have evolved returned to the strategy utilized by earlier plants. These plants have found that the energy conserved in producing modest flowers can be directed into building large colonies of individuals in close proximity.

It is probably no coincidence that the world’s most important food crops —rice, wheat, and corn —come from the grass family, whose barely visible flowers grow in vast numbers.

The next time you husk an ear of corn look at the withered silk. Each thread is actually a pistil leading to a single kernel.”

The great food plants of the world—rice, corn, and wheat (shown)—are members of the grass family. Grasses, the most recent flowering plants to evolve, found it efficient to produce unassuming flowers in huge colonies. Airborne pollen is transmitted and received over a relatively short distance.

Fungi were once thought to be part of the botanical kingdom, because they have spores like mosses and ferns. A mushroom produces many millions of spores that are set adrift on the wind in an effective, if not economical, method of asexual reproduction: only a few find the perfect spot to grow. If all of the spores of a single fungus grew, the progeny would soon cover the earth.

Thousands of fern spores are stored in sori, seen as golden dots beneath a frond. Ferns introduced sexual reproduction, while still relying on huge numbers of spores.

In order for an ear of corn to be filled with kernels, the tips of each of its pistils—the silk—must come in contact with a grain of pollen and be fertilized.


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Review N°102: Detecting the building blocks of aromatics

Detection of benzonitrile in an interstellar cloud helps to constrain interstellar chemistry

Christine Joblin1 and José Cernicharo

1Institut de Recherche en Astrophysique et Planétologie, Université de Toulouse (UPS), CNRS, 31028 Toulouse Cedex 4, France. 2Instituto de Ciencia de Materiales de Madrid (ICMM), Consejo Superior de Investigaciones Científicas (CSIC), Molecular Astrophysics Group, Cantoblanco, 28049 Madrid, Spain. Email: 

Interstellar clouds are sites of active organic chemistry (1). Many small, gas- phase molecules are found in the dark parts of the clouds that are protected from ultraviolet (UV) photons, but these molecules photodissociate in the external

layers of the cloud that are exposed to stellar radiation (see the photo). These irradiated regions are populated by large polycyclic aromatic hydrocarbons (PAHs) with characteristic infrared (IR) emission features. These large aromatics are expected to form from benzene (C6H6), which is, however, difficult to detect because it does not have a permanent dipole moment and can only be detected via its IR absorption transitions against a strong background source (2). On page 202 of this issue, McGuire et al. (3) report the detection of benzonitrile (c-C6H5CN) with radio telescopes. Benzonitrile likely forms in the reaction of CN with benzene; from its observation, it is therefore possible to estimate the abundance of benzene itself.

Chemical models that include molecular formation and destruction processes, both in the gas phase and at the surface of dust grains, can account reasonably well for the observed abundances of a number of molecular species (4). The situation is different for large aromatics, for which no individual species have been identified, with the exception of the C60 molecule (5). Although PAHs are large molecules, they are considered by astronomers as very small dust particles. They are therefore generally thought to form in the dense and hot environments of the envelopes of evolved stars. Chemical models have been developed that are based on chemical networks in flames (6). More recently, the possibility to form PAHs at the very low temperatures of molecular clouds has been discussed (7) following the dem- onstration that the reaction CCH + C4H6  leading to benzene (C6H6) is barrierless and therefore efficient at low temperature (8).

In both hot and cold gas-phase chemistry, benzene derivatives—such as C6H4 and C6H5— that can lead to further growth toward larger aromatic species are involved. Observations of benzene-type species are therefore crucial for constraining these chemical models.

McGuire et al. were able to detect benzonitrile in a cold molecular cloud of the Taurus region thanks to an elegant spectral-stacking procedure (9) that increases the chance of detecting molecules with aromatic rings. Among the species that they searched for, only benzonitrile was identified as a promising candidate. The authors confirmed its detection after identification of individual rotational lines, including their hyperfine structure, through detailed spectroscopic work in the laboratory. The presence of a CN side group leads to a substantial dipole moment and thus facilitates detection of benzo- nitrile. Calculated benzonitrile abundances from a chemical model that includes different gas-phase reactions at low temperature are lower than those observed by a factor of four. The authors suggest that alternative mechanisms involving cosmic-ray radiation-induced chemistry at the surface of grains produce the missing benzonitrile. The mismatchbetween observations andmodels shows that, despitethe low observed abundanceof benzonitrile, its detectionremains important in constraining chemical models.

Is there any relation be-tween the detection of thefirst aromatic ring in dark clouds and the presence of PAHs, the carriers of the mid- IR aromatic emission bands, in the external UV-irradiated regions of the clouds? In addition to the gas-phase chemical reactions mentioned above, these PAHs and related species, such as C60, could be produced through UV processing of dust grains (10). Other scenarios have also been proposed. For instance, large hydrocarbons, including PAHs, could be formed by chemical processing on the surface of silicon carbide grains, a mechanism that could be efficient in the envelopes of carbon-rich red giant stars (11, 12).

It remains unclear how many of the PAHs and their precursors are synthesized in the dense and hot envelopes of evolved stars and how many arise from photo- or radiative chemistry in interstellar environments. The detection by McGuire et al. of a benzene derivative in a cold molecular cloud indicates that it can form even at very low temperatures and without UV radiation. The authors did not detect larger species with two or three cycles, but the species they selected have lower dipole moments compared to benzonitrile, which reduces the chance for their detection unless they have an anomalously large abundance.

Among the ~200 molecules detected in space, many are organic species. Studying their composition and chemical networks is key for understanding molecular complexity in protoplanetary disks surrounding young stars (13). The search for complex molecules has mainly been performed in the millimeter and submillimeter domains. The work of McGuire and collaborators (3, 14) shows the potential of centimeter-wave instruments for chemical complexity studies. This opens avenues for research at the upcoming Square Kilometer Array, which will operate in this spectral range.

Knowledge of astrochemical networks also helps in understanding the nucleation and growth of interstellar dust (including PAHs) and its role in star and planet for- mation. However, the detection of benzoni- trile in the Taurus region is not sufficient to conclude on the possibility to form PAHs in cold molecular clouds. It also remains to be shown whether the detection of benzonitrile indicates that PAHs could contain nitrogen (15). More insights into the chemistry of PAHs and related species are expected from combining data from radio and in- frared waves with the James Webb Space Telescope, due to launch in 2019. In addition to observations, guide- lines from laboratory astrophysics studies are key to progress in this area. These include spectroscopic and kinetic studies but also experimental simulations in reactors in order to provide scenarios that can explain the building of molecular complexity in cosmic conditions.    



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Review N°101 : ANDROID OS

by Andrew Farrell, MLIS


This article brie y discusses the general issues involved with mobile computing and presents a history and analysis of Google’s Android operating system. It concludes with a look at Android’s future in the growing market for mobile technology.

Prinicipal terms

ƒ application program interface (API): the code that defines how two pieces of software interact, particularly a software application and the operating system on which it runs.

ƒ immersive mode: a full-screen mode in which the status and navigation bars are hidden from view when not in use.

ƒ material Design: a comprehensive guide for visual, motion, and interaction design across Google plat- forms and devices.

ƒ multitasking: in the mobile phone environment, allowing different apps to run concurrently, much like the ability to work in multiple open windows on a PC.

ƒ multi-touch gestures: touch-screen technology that allows for different gestures to trigger the behavior of installed software.

A Force in mobile computing

Mobile computing is the fastest-growing segment of the tech market. As pricing has become more afford- able, developing nations, particularly in Africa, are the largest growing market for smartphones. With smartphones, users shop, gather information, connect via social media such as Twitter and Facebook, and communicate—one of the uses more tradition- ally associated with phones.

By far the most popular operation system running on mobile phones is Android. It has outpaced Apple’s iOS with nearly double the sales. As of 2014, more than a million Android devices were being activated daily. Since its launch in 2008, Android has far and away overtaken the competition.

Android takes off

Android came about amid a transformative moment in mobile technology. Prior to 2007, slide-out keyboards mimicked the typing experience of desktop PCs. In June of that year, Apple released its rst iPhone, forever altering the landscape of mobile phones. Apple focused on multi-touch gestures and touch-screen technology. Nearly concurrent with this, Google’s Android released its rst application program interface (API).

The original API of Google’s new operating system (OS) rst appeared in October 2008. The Android OS was rst installed on the T-Mobile G1, also known as the HTC Dream. This prototype had a very small set of preinstalled apps, and as it had a slide-out QWERTY keyboard, there were no touch- screen capabilities. It did have native multitasking, which Apple’s iOS did not yet have. Still, to compete with Apple, Google was forced to replace physical keyboards and access buttons with virtual onscreen controls. The next iteration of Android shipped with the HTC Magic and was accompanied by a virtual keyboard and a more robust app marketplace. Among the other early features that have stood the test of time are the pull-down noti cation list, home- screen widgets, and strong integration with Google’s Gmail service.

One later feature, the full-screen immersive mode, has become quite popular as it reduces distractions. First released with Android 4.4, “KitKat,” in 2013, it hides the navigation and status bars while certain apps are in use. It was retained for the release of Android 5.0, “Lollipop,” in 2015.

Android changes and Grows

Both of Google’s operating systems—Android and its cloud-based desktop OS, Chrome— are based on the free open-source OS Linux, created by engineer Linus Torvalds and rst released in 1991. Open-source software is created using publicly available source code. The open-source development of Android has allowed manufacturers to produce robust, affordable products that contribute to its widespread popularity in emerging and developing markets. This may be one reason why Android has had more than twice as many new users as its closest rival, Apple’s iOS. This strategy has kept costs down and has also helped build Android’s app marketplace, which offers more than one million native apps, many free of charge. By 2014 Android made up 54 percent of the global smartphone market.

This open-source development of Android has had one adverse effect: the phenomenon known as “forking,” which occurs primarily in China. Forking is when a private company takes the OS and creates their own products apart from native Google services such as e-mail. Google seeks to prevent this loss of control (and revenue) by not supporting these com- panies or including their apps in its marketplace. Forked versions of Android made up nearly a quarter of the global market in early 2014.

Google’s business model has always focused on a “rapid-iteration, web-style update cycle.” By contrast, rivals such as Microsoft and Apple have had a far slower, more deliberate pace due to hardware issues. One bene t of Google’s faster approach is the ability to address issues and problems in a timely manner. A drawback is the phenomenon known as “cloud rot.” As the cloud-based OS grows older, servers that were once devoted to earlier versions are repurposed. Since changes to the OS initially came every few months, apps that worked a month prior would suddenly lose functionality or become completely unusable. Later Android updates have been released on a timescale of six months or more.

Android’s Future

In 2014 alone, more than one billion devices using Android were activated. One of the biggest concerns about Android’s future is the issue of forking. Making the code available to developers at no cost has made Android a desirable and cost-effective alternative to higher-end makers such as Microsoft and Apple, but it has also made Google a target of competitors.

Another consideration for Android’s future is its inextricable link to the Chrome OS. Google plans to keep the two separate. Further, Google executives have made it clear that Chromebooks (laptops that run Chrome) and Android devices have distinct purposes. Android’s focus has been on touch-screen technology, multi-touch gesturing, and screen resolution, making it a purely mobile OS for phones, tablets, and more recently wearable devices and TVs. Meanwhile, Chrome has developed tools that are more useful in the PC and laptop environment, such as keyboard shortcuts. However, an effort to unify the appearance and functionality of Google’s different platforms and devices called Material Design was introduced in 2014. Further, Google has ensured that Android apps can be executed on Chrome through Apps Runtime on Chrome (ARC). Such implementations suggest a slow merging of the Android and Chrome user experiences.



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