Mapping a Functional Cancer Genome Atlas

Over the past decade, tremendous resources have been devoted to sequencing the genomes of patient cancers. But while the molecular portraits of cancer are now in higher resolution than ever before, it has remained challenging to derive clinically actionable insights from these data. A central issue is that tumor genome sequencing often can only tell us what mutations are present, not which ones are functionally important. Towards this end, I sought to build an improved toolkit for functional cancer genomics, with the overarching goal of creating experimental platforms that are practical, scalable, and flexible. In collaboration with several colleagues, I developed autochthonous AAV-mediated CRISPR/Cas9 screens to quantitatively interrogate the contributions of specific mutations towards tumorigenesis in the murine liver and brain. Importantly, this experimental system is well suited for studies in tumor immunology, as it preserves the native tissue microenvironment in the context of an immunocompetent host. I subsequently utilized the AAV-CRISPR tumor model to further investigate the genetic determinants of response to PD-1 checkpoint blockade immunotherapy. In addition to recovering known regulators of immunotherapy response, I found that deficiency of the histone modifier KMT2D sensitizes diverse tumor types to immune checkpoint blockade by promoting the generation of immunogenic neoantigens. I further sought to comprehensively dissect the genetic regulation of anti-tumor immunity responses from both sides of the aisle, interrogating the immune cells that react against tumors as well as the cancer cells themselves. As a foray into the roles of noncoding RNAs in anti-tumor immunity, I mapped the landscape of sdRNAs expressed in human cancers, finding numerous transcripts that are associated with signatures of anti-tumor immune infiltration and survival across multiple cancer types. My colleagues and I also performed genome-scale CRISPR screens in primary CD8+ T cells to identify genetic regulators of T cell degranulation and tumor infiltration. These studies identified that Dhx37 knockout enhances NF-kB signaling in CD8+ T cells, leading to enhanced anti-tumor function in vitro and in vivo. Using genome-scale CRISPR activation (CRISPRa) screens, I further sought to identify genes that could promote tumorigenesis in immunocompetent hosts when overexpressed. In pursuing this line of study, my colleagues and I unexpectedly found that CRISPRa could be repurposed as a new immunotherapy modality, an approach we termed MAEGI (multiplexed activation of endogenous genes as immunotherapy). By delivering CRISPRa systems through AAVs to forcibly overexpress mutated genes directly in tumors, MAEGI enhanced immune recognition of tumor neoantigens, thereby eliciting robust and long-lasting anti-tumor immunity. The CRISPR screens employed in the aforementioned studies have an important limitation, however. Cancers arise from the sequential acquisition of genetic or epigenetic alterations, and the unique combinations of these alterations can interact in complex ways. To more precisely study these genetic interactions, I established a strategy for in vivo combinatorial knockout screening using massively-parallel CRISPR-Cas12a array profiling. I applied this technique to pinpoint mutation combinations that synergistically promote lung metastasis, demonstrating the utility of this technology to dissect genetic interactions in cancer. Finally, I devised a method for programmable sequential mutagenesis by combining CRISPR-Cas12a arrays with Cre recombination cassettes. I employed this approach to model the stepwise acquisition of resistance mutations against immunotherapy, thus providing a controlled experimental system for exploring strategies to overcome immunotherapy resistance

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Promoting human rights through science (Letter)

Inspired by the work of the AAAS Science and Human Rights Coalition (AAAS is the publisher of Science), we asked young scientists this question: Describe how applications of knowledge in your field (information, methodologies, services, and/or products) could support civil, political, economic, social, or cultural rights. We received responses from scientists around the world representing a variety of fields. From those protecting health and access to health care, to those working toward a safe and sustainable environment, to those concerned with citizens' rights to the best information available, respondents passionately described the benefits that their research can bring to vulnerable people. Excerpts of their responses are printed here

Parent stem cells can serve as niches for their daughter cells.

Stem cells integrate inputs from multiple sources. Stem cell niches provide signals that promote stem cell maintenance, while differentiated daughter cells are known to provide feedback signals to regulate stem cell replication and differentiation. Recently, stem cells have been shown to regulate themselves using an autocrine mechanism. The existence of a \u27stem cell niche\u27 was first postulated by Schofield in 1978 to define local environments necessary for the maintenance of haematopoietic stem cells. Since then, an increasing body of work has focused on defining stem cell niches. Yet little is known about how progenitor cell and differentiated cell numbers and proportions are maintained. In the airway epithelium, basal cells function as stem/progenitor cells that can both self-renew and produce differentiated secretory cells and ciliated cells. Secretory cells also act as transit-amplifying cells that eventually differentiate into post-mitotic ciliated cells . Here we describe a mode of cell regulation in which adult mammalian stem/progenitor cells relay a forward signal to their own progeny. Surprisingly, this forward signal is shown to be necessary for daughter cell maintenance. Using a combination of cell ablation, lineage tracing and signalling pathway modulation, we show that airway basal stem/progenitor cells continuously supply a Notch ligand to their daughter secretory cells. Without these forward signals, the secretory progenitor cell pool fails to be maintained and secretory cells execute a terminal differentiation program and convert into ciliated cells. Thus, a parent stem/progenitor cell can serve as a functional daughter cell niche

Multimessenger search for sources of gravitational waves and high-energy neutrinos: Initial results for LIGO-Virgo and IceCube

We report the results of a multimessenger search for coincident signals from the LIGO and Virgo gravitational-wave observatories and the partially completed IceCube high-energy neutrino detector, including periods of joint operation between 2007-2010. These include parts of the 2005-2007 run and the 2009-2010 run for LIGO-Virgo, and IceCube's observation periods with 22, 59 and 79 strings. We find no significant coincident events, and use the search results to derive upper limits on the rate of joint sources for a range of source emission parameters. For the optimistic assumption of gravitational-wave emission energy of 10-2 M⊙c2 at ˜150 Hz with ˜60 ms duration, and high-energy neutrino emission of 1 051 erg comparable to the isotropic gamma-ray energy of gamma-ray bursts, we limit the source rate below 1.6 ×1 0-2 Mpc-3 yr-1 . We also examine how combining information from gravitational waves and neutrinos will aid discovery in the advanced gravitational-wave detector era.status: publishe