Implementation of Quantitative Systems Pharmacology for Drug Discovery and Development
D. Lansing Taylor, PhD

It is evident that gene-gene-based interactions are main drivers for the phenotypes seen in common complex diseases. Consequently, targeting the disease phenotype may represent a complementary strategy to the target-centric approach that is now the dominant drug discovery method. Indeed, the value of phenotypic screens and their successes relative to target-focused approaches, particularly for complex diseases, has recently been demonstrated to be successful. It is becoming evident from these considerations that a deep understanding of interactions among biomolecules involved in both normal and disease states (and how particular outcomes from these interactions result in discernable phenotypes) is crucial for developing therapeutics to address complex diseases. Thus, a systems-based platform to generate quantitative representations of biological processes and discover network-level emergent properties needs to be integrated into the drug discovery process. These emergent properties are not ordinarily evident from the study of individual components and, when abnormally perturbed, form the mechanistic basis for pathological phenotypes. It appears that the developing discipline of quantitative systems pharmacology might well satisfy this need.

3D Microtissues for Upgrading Cell-Based High-Throughput Drug Testing to 3D Using Bench-Top Equipment
Yanan Du, PhD

3D microtissues (on the scale of several hundred microns) are a promising cell culture configuration, resembling functional tissue units in vivo. These microtissues are expected to upgrade in vitro cellular models from 2D to a more biomimetic 3D configuration to accelerate the pace of drug discovery. Here we present an off-the-shelf micro-scaffold array chip that enables high-throughput 3D microtissue formation, drug administration, and quantitative in situ assays entirely on the same chip. The sponge-like micro-scaffolds functioned both as absorbents (to realize parallel auto-loading of cells or drugs) and as barriers (to prevent cell loss during medium exchange via centrifugation). Rapid manual loading of cell suspensions or drugs into the 96 isolated micro-scaffolds on the chip was achieved in the timescale of several seconds. At the same time, total medium consumption was reduced to microliters. Proof-of-concept demonstration of drug cytotoxicity testing was performed on multiple cancer cells using common benchtop equipment, making it accessible to most biomedical labs with basic cell culture set-ups. Higher cellular drug resistance was constantly obtained with this platform compared to planar cultures, which was partially attributed to the malignant phenotype of cancer cells yielded by enhanced cell–matrix interactions in the micro-scaffolds. We further incorporated magnetic nanoparticles within the microcryogels to assist microtissue formation with enhanced controllability and robustness. The magnetically controllable microtissues were applied to constitute a novel, separable 3D co-culture system, realizing functional enhancement of the hepatic microtissues co-cultured with the stromal microtissues and easy purification of the hepatic microtissues for downstream drug testing. The 3D microtissue system developed here offers promising 3D cellular configuration for cell-based applications like drug testing and regenerative therapies.


Gripping Histone Acetylation with YEATS Domain
Haitao Li, PhD

The recognition of modified histones by “reader” proteins constitutes a key mechanism regulating gene expression in the chromatin context. In contrast to the great variety of readers available for histone methylation, few protein modules that recognize histone acetylation are known. Here, we show that the AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and uses a serine-lined aromatic “sandwiching” cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. ChIP-sequencing experiments revealed a strong co-localization of AF9 and H3K9 acetylation genome-wide, which is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identified the evolutionarily conserved YEATS domain (named for its five founding domain-containing proteins [Yaf9, ENL, AF9, Taf14, and Sas5]) as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.


Stuck on Repeat: Platforms To Study Repetitive DNA at Chromosome Ends
Roderick O’Sullivan, PhD

Telomeres are specialized nucleoprotein structures located at the ends of our chromosomes. The basic view is that telomeres are composed of the TTAGGG DNA sequence that is repeated over several kilobases. Telomeres are essential to cellular viability because they prevent the recognition of chromosome ends as double strand breaks. Also, telomere length strongly correlates with cell proliferative capacity. These functions are orchestrated by a specialized complex, termed shelterin. Mounting evidence suggests that telomeres of normal healthy cells and cancer cells display significant variations of shelterin abundance and harbor distinct protein compositions and chromatin architectures. It is strongly suspected that such changes in the chromatin environment of telomeres directly dictate telomere maintenance processes in cancer cells by significantly influencing telomere movement and dynamics in the nucleus. Thus, understanding the molecular basis and mechanisms of these phenomena is of major importance to our knowledge of telomere function in cancer.

However, deciphering the identity of those proteins that regulate these telomere maintenance pathways and how the chromatin structure at telomeres is reconfigured has been constrained by the technical challenge of isolating sufficient quantities of high-purity telomeric chromatin for proteomic analysis. To circumvent these major technical hurdles so that this critically important issue can be addressed, we have developed a novel approach for the capture and isolation of telomeric chromatin from human cell lines. In addition, we are developing cutting-edge molecular imaging platforms to visualize telomere dynamics in three-dimensional space within live cells. These novel approaches will be presented here.



Pluripotent Stem Cells and the Heart: What Can We Do?
Lei Yang, PhD

Recent progress in the development of pluripotent stem cells, especially induced pluripotent stem (iPS) cells, enables access to early-stage human organ-specific cells and patient-specific tissue cells. Using human embryonic stem cells, we could establish a valuable in vitro model system to recapitulate early events in human heart development, such as the early formation of human cardiovascular progenitors and commitment of human cardiovascular lineage cells. Using iPS cells derived from patients with various inherited heart diseases, we generated patient-specific cardiomyocytes as a cellular model to elucidate the molecular mechanisms of human heart diseases and for use in future screening of therapeutic compounds. We also used human iPS cell-derived multipotent cardiovascular progenitor cells to engineer three-dimensional human heart constructs by repopulating whole 3D mouse-heart scaffolds, with a long-term goal of rebuilding a whole patient-specific bio-artificial human heart for transplantation.

Study of lncRNA Functions in Stem Cell and Gene Regulation
Xiaohua Shen, PhD

Pervasive transcription in the mammalian genome produces thousands of long noncoding RNA (lncRNA) transcripts. It has been hypothesized that lncRNAs may serve as versatile modulators of diverse aspects of biology. However, the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we characterized a lncRNA located ~40 kb upstream of an ultraconserved, developmentally regulated gene cluster in embryonic stem cells (ESCs). Our work established a rigorous paradigm for the study of lncRNA functions and revealed a complex effect for the lncRNA transcripts and their genomic DNA locus in fine-tuning downstream transcription and in orchestrating ESC differentiation. Importantly, we illustrated the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions.



Recent Developments at Tsinghua University School of Medicine
Bai Lu, PhD

Dubbed the “Chinese MIT” for its renowned science and engineering programs, Tsinghua University began in 1912 as a preparatory school for students chosen to study in the United States. Dr. Lu will discuss current progress at the School of Medicine.


Big Data to Knowledge: The Center for Causal Discovery
Gregory Cooper, MD, PhD

This talk will provide an overview of the Center for Causal Discovery (CCD), which is an NIH-funded Big-Data-to-Knowledge (BD2K) Center of Excellence. The CCD is focused on developing and disseminating computational methods for causal modeling and discovery of biomedical knowledge from big data. Its aims include research, training, software dissemination, and collaborative projects with other centers and groups.



Designing Biomaterials To Interrupt Pathological Tissue Remodeling Processes
William R. Wagner, PhD

Tissue remodeling occurs in disease and following trauma, often yielding results that are dysfunctional and that may ultimately progress toward tissue failure. In the case of mechanically active soft tissues, the mechanical environment in which the damaged tissue heals influences the direction and outcome of the remodeling process. To develop biomaterial-based approaches to improve soft tissue repair, we have created degradable supports that act as scaffolds for new tissue generation or as temporary load-bearing elements during the remodeling process. Efforts have been directed at (1) the adverse ventricular remodeling process that occurs following myocardial infarction, resulting in dilated ischemic cardiomyopathy, and (2) the remodeling of veins used in arterial grafting and tissue-engineered blood vessel development. Two general types of supporting biomaterials have been developed and tested in at least one of these settings. In the first approach, thermoplastic elastomers, typified by poly(ester urethane)urea, have been synthesized and processed to form microporous elastic patches or wraps. Molecular design parameters can be selected to tune mechanical and degradation properties. In the processing steps, composites with natural materials, such as extracellular matrix digests, have been generated. A second approach has focused on the development of thermoresponsive, injectable copolymers that “set up” quickly in situ to provide mechanical support to tissues under load but degrade to become soluble over time. The application of these materials in vivo has been shown to alter remodeling patterns and facilitate tissue generation with associated functional improvements.


Advanced Diagnostic and Therapeutic Techniques for Intelligent Minimally Invasive Surgery
Hongen Liao, PhD

There have been significant advances in the field of minimally invasive and noninvasive surgeries. Rapid technical advances in medical imaging, including its growing application in therapy and invasive/interventional procedures, have attracted significant interest in the close integration of research in different areas. The use of diagnostic images as a means of navigating during surgery, in combination with the use of a positional tracking device, has been a focus of interest following advances in medical imaging and computer technology. Techniques for diagnosis and treatment have been integrated (e.g., through imaging modalities and intervention devices) and, thus, provide high-precision minimally invasive treatment. Compared with conventional diagnosis and therapy, future research on and clinical trials promoting minimally invasive surgery are expected to shift medical imaging from a primarily diagnostic modality to a therapeutic and interventional aid. Integrated diagnostic and therapeutic processes will be streamlined through the application of intraoperative medical information and robotic-assisted intervention and brought to clinical trials. This lecture will introduce the development and application of minimally invasive precision diagnostic and therapeutic techniques for intelligent medical systems based on biomedical imaging, bio-robotics, and precision and control engineering, as well as a fusional development of imaging modalities and surgical devices.



Clinical Neuroprosthetics Studies for Improving Quality of Life
Wei Wang, MD, PhD

Basic neuroscience research generated the foundational knowledge that enables us to communicate with the nervous system through neural recording and neurostimulation. Leveraging our clinical strength and rehabilitation research infrastructure, our group focuses on conducting “first-in-human” clinical trials of novel neural interface devices. This talk will review outcomes of our studies using various implantable brain electrodes over the past couple of years, demonstrating the clinical feasibility and benefits of these neural interface devices. This talk also aims to demonstrate that such pilot clinical studies are not only clinically significant but also generate valuable scientific insights and questions that complement and guide basic neuroscience research.


Cortical Processing of Chinese Phonemes and Tones
Bo Hong, PhD

A finite set of phonetic units is used in human speech, but how our brain recognizes these units from speech stream is still largely unknown. Identification of this neural mechanism may lead to the development of new types of speech-brain computer interfaces and computer-speech recognition systems. In this study, we used electrocorticography (ECoG) signals from the human cortex to decode Chinese phonetic units during continuous speech perception. By exploring the wavelet time-frequency features, we identified ECoG electrodes that have selective response to specific Chinese phonemes. Powers of gamma and high-gamma bands of ECoG signals recorded from these electrodes were further combined to separate sets of phonemes into clusters. The clustered organization largely coincided with phonological categories defined by discriminative features, similar to what has been found in English (Mesgarani et al., 2014).
These findings were incorporated into a decoding framework of Chinese phoneme-clusters and achieved consistent accuracies measured at higher than chance level. In addition to phonetic units, tonal languages like Chinese also depend on lexical tone to provide contrast in word meaning. Behavioral studies suggest that Mandarin Chinese tone is categorically perceived (Wang 1976; Xu et al. 2006). However, the neural mechanism underlying Mandarin tone perception is still poorly understood.

In this study, an oddball paradigm was designed by selecting two standard-deviant stimulus pairs with the same physical distance but different category labels among the synthesized tones with continuously varying pitch contours. Using ECoG recording over the human auditory cortex, high temporal and spatial resolution cortical neural signals were used for the first time to investigate the cortical processing of lexical tone. Here, we found different neural responses to the two standard-deviant tone pairs. The difference increased from low to high along the hierarchy of human auditory cortex. In the two-dimensional neural space, cross-category neural distance of lexical tones is selectively amplified on those high-level electrodes.

These findings support a hierarchical and categorical model of Mandarin tone perception. Although the Chinese phonemes and tones are likely processed in the same vicinity of superior temporal gyrus (STG) and superior temporal sulcus (STS), it is still a challenge to elucidate how the speech cortex integrates phonetic units with lexical tone to produce meaning for each Chinese word. The temporal structure and spatial organization of this integration will be the subject of a future study. (This work is supported by National Science Foundation of China # 61473169.)