Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

From extrachromosomal DNA to neo-peptides, the broad reprogramming of the cancer genome leads to the emergence of molecules that are specific to the cancer state. We recently described orphan non-coding RNAs (oncRNAs) as a class of cancer-specific small RNAs with the potential to play functional roles in breast cancer progression1. Here, we report a systematic and comprehensive search to identify, annotate, and characterize cancer-emergent oncRNAs across 32 tumor types. We also leverage large-scale in vivo genetic screens in xenografted mice to functionally identify driver oncRNAs in multiple tumor types. We have not only discovered a large repertoire of oncRNAs, but also found that their presence and absence represent a digital molecular barcode that faithfully captures the types and subtypes of cancer. Importantly, we discovered that this molecular barcode is partially accessible from the cell-free space as some oncRNAs are secreted by cancer cells. In a large retrospective study across 192 breast cancer patients, we showed that oncRNAs can be reliably detected in the blood and that changes in the cell-free oncRNA burden captures both short-term and long-term clinical outcomes upon completion of a neoadjuvant chemotherapy regimen. Together, our findings establish oncRNAs as an emergent class of cancer-specific non-coding RNAs with potential roles in tumor progression and clinical utility in liquid biopsies and disease monitoring.

Neural correlates of processing active and passive sentences: proficiency-dependent event-related potential evidence in Chinese English foreign language learners.

We explored whether and to what extent the neural mechanisms of second language sentence processing resemble those of native speakers by investigating the temporal dynamics of syntactic processing in terms of active or passive voice in reading English sentences by Chinese English Foreign Language (EFL) learners with high or low English proficiency. Participants were divided into two groups based on their proficiency levels in English. Three types of sentences (active, passive and ungrammatical) were presented to participants when their event-related potential responses were recorded at the verbs and the final words. The results showed that high-proficiency participants exhibited a greater anterior negativity at the verb position for ungrammatical sentences compared to active sentences. Furthermore, passive sentences elicited a larger frontal positivity than active sentences at the final word position. Additionally, greater P600 effects were observed for both passive and ungrammatical sentences than active sentences at the final word. The low-proficiency group exhibited a greater anterior negativity at the verb (but not the final word) position. In conclusion, these findings emphasize the role of proficiency as a modulating factor in the processing of English active and passive sentences among Chinese EFL learners. Furthermore, the processing of English active and passive sentences by these learners can be conceptualized as a three-stage process: prediction, correction and integration, representing the underlying cognitive mechanisms. This study provides novel insights into the understanding of the cognitive mechanism involved in second language sentence processing.

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.

Large-scale sequencing efforts of thousands of tumor samples have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of germline and somatic variants occur within non-coding portions of the genome. These genomic regions do not directly encode for specific proteins, but can play key roles in cancer progression, for example by driving aberrant gene expression control. Here, we designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Application of this approach to whole-genome sequencing (WGS) data from a large cohort of metastatic castration-resistant prostate cancer (mCRPC) revealed a large set of recurrently mutated regions. We used (i) in silico prioritization of functional non-coding mutations, (ii) massively parallel reporter assays, and (iii) in vivo CRISPR-interference (CRISPRi) screens in xenografted mice to systematically identify and validate driver regulatory regions that drive mCRPC. We discovered that one of these enhancer regions, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. We found that both SF3A1 and CCDC157 are promoters of tumor growth in xenograft models of prostate cancer. We nominated a number of transcription factors, including SOX6, to be responsible for higher expression of SF3A1 and CCDC157. Collectively, we have established and confirmed an integrative computational and experimental approach that enables the systematic detection of non-coding regulatory regions that drive the progression of human cancers.

An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus.

Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis; however, its effects on cancer progression remain poorly understood. Here, to address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed dedicated regression-based methods to analyse ribosome profiling and alternative polyadenylation data, and identified heterogeneous nuclear ribonucleoprotein C (HNRNPC) as a translational controller of a specific mRNA regulon. We found that HNRNPC is downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3' untranslated region lengthening and, subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. In addition, the reduced expression of HNRNPC and its regulon is associated with the worse prognosis in breast cancer patient cohorts.

Epitope alteration by small molecules and applications in drug discovery.

Small molecules and antibodies are normally considered separately in drug discovery, except in the case of covalent conjugates. We unexpectedly discovered several small molecules that could inhibit or enhance antibody-epitope interactions which opens new possibilities in drug discovery and therapeutic modulation of auto-antibodies. We first discovered a small molecule, CRANAD-17, that enhanced the binding of an antibody to amyloid beta (Aß), one of the major hallmarks of Alzheimer's disease, by stable triplex formation. Next, we found several small molecules that altered antibody-epitope interactions of tau and PD-L1 proteins, demonstrating the generality of this phenomenon. We report a new screening technology for ligand discovery, screening platform based on epitope alteration for drug discovery (SPEED), which is label-free for both the antibody and small molecule. SPEED, applied to an Aß antibody, led to the discovery of a small molecule, GNF5837, that inhibits Aß aggregation and another, obatoclax, that binds Aß plaques and can serve as a fluorescent reporter in brain slices of AD mice. We also found a small molecule that altered the binding between Aß and auto-antibodies from AD patient serum. SPEED reveals the sensitivity of antibody-epitope interactions to perturbation by small molecules and will have multiple applications in biotechnology and drug discovery.

Effects of shank mass manipulation on sprinting techniques.

The purpose of this study was to determine the effects of shank mass manipulation on the sprinting technique in maximal-speed sprinting. Sixteen well-trained male athletes sprinted with and without an additional 15% of shank mass attached to the shank centre of mass. Kinematic data were collected using a 12-camera motion analysis system and analysed using linear regression analyses with categorical variables and paired t-tests. The sprinting speed (p < 0.01), knee flexion angle at landing (p = 0.028), and maximum hip flexion angular velocity (p = 0.029) decreased; contact time (p < 0.01) increased; and step length, step frequency, and other analysed technique measures of maximal-speed sprinting were unchanged (p ≥ 0.12) with shank mass manipulation, compare with no manipulation. The relationships of sprinting speed with critical linear and angular kinematics at landing, take-off and swing in maximal-speed sprinting were not affected by the shank mass manipulation. These results suggest that 15% shank mass manipulation does not change the sprinting technique of well-trained male athletes in maximal-speed sprinting. This supports the use of shank mass manipulation as a training method for well-trained sprinters; however, a change in correlations between sprinting speed and technique measures should be considered during such training.

Long-Lasting Bioluminescence Imaging of the Fibroblast Activation Protein by an Amphiphilic Block Copolymer-Based Probe.

Long-term specific tracing of the fibroblast activation protein (FAP) has been of great importance because it is heavily expressed by stromal fibroblasts of multiple diseases, and several disorders associated with FAP are chronical. Bioluminescence (BL) imaging has its advantages to detect FAP in vivo since no external excitation is required, but the current FAP-responsive BL probe was constructed by covalently masking the firefly luciferase substrate and easily secreted out from the animal, resulting in transient BL imaging of FAP. To circumvent this problem, a peptide-linked amphiphilic block copolymer-based probe (PABC) was developed and applied to the long-lasting BL image of FAP in vivo. For this purpose, an amphiphilic block copolymer containing an FAP-responsive peptide was fabricated to self-assemble into micelles, which act as a depot to load amounts of d-luciferin for constructing the BL probe. Upon reaction with FAP, the micelle would be destroyed to release the internal d-luciferin for BL emission by a luciferase-catalyzed reaction. By virtue of the high loading capability of micelles, the FAP was determined from 0.5 to 10 ng/mL with a detection limit of 0.105 ng/mL, and the high sensitivity makes the PABC capable of distinguishing cancer cells from normal ones. Importantly, compared with free d-luciferin, PABC can be used to persistently image the FAP in living cells and in vivo. This characteristic of long-lasting specific tracing of the FAP makes us envision that this BL probe could be used for screening of FAP inhibitors and diagnosing various FAP-related diseases in future.

Effects of Combining High-Definition Transcranial Direct Current Stimulation with Short-Foot Exercise on Chronic Ankle Instability: A Pilot Randomized and Double-Blinded Study.

(1) Background: Balance decline is highly prevalent in people suffering from chronic ankle instability (CAI). The control of balance depends upon multiple neurophysiologic systems including the activation of cortical brain regions (e.g., the primary sensorimotor cortex). The excitability of this region, however, is diminished in people with CAI. In this pilot double-blinded randomized controlled trial, we tested the effects of high-definition transcranial direct current stimulation (HD-tDCS) designed to facilitate the excitability of M1 and S1 in combination with short-foot exercise (SFE) training on proprioception and dynamic balance performance in individuals with CAI. (2) Methods: Thirty young adults completed baseline assessments including the Active Movement Extent Discrimination Apparatus (AMEDA), Joint Position Reproduction (JPR) test, Y-balance test, and the Sensory Organization Test (SOT). They were then randomized to receive a four-week intervention of SFE in combination with tDCS (i.e., HD-tDCS+SFE) or sham (i.e., control) stimulation. Baseline assessments were repeated once-weekly throughout the intervention and during a two-week follow-up period. (3) Results: Twenty-eight participants completed this study. Blinding procedures were successful and no adverse events were reported. As compared to the control group, the HD-tDCS+SFE group exhibited significant improvements in the JPR test, the Y balance test, and the SOT at different time points. No group by time interaction was observed in AMEDA test performance. (4) Conclusions: HD-tDCS combined with SFE may improve dynamic balance and proprioception in CAI. Larger, more definitive trials with extended follow-up are warranted.

Turn-on chemiluminescence probes and dual-amplification of signal for detection of amyloid beta species in vivo.

Turn-on fluorescence imaging is routinely studied; however, turn-on chemiluminescence has been rarely explored for in vivo imaging. Herein, we report the design and validation of chemiluminescence probe ADLumin-1 as a turn-on probe for amyloid beta (Aß) species. Two-photon imaging indicates that ADLumin-1 can efficiently cross the blood-brain barrier and provides excellent contrast for Aß plaques and cerebral amyloid angiopathy. In vivo brain imaging shows that the chemiluminescence signal of ADLumin-1 from 5-month-old transgenic 5xFAD mice is 1.80-fold higher than that from the age-matched wild-type mice. Moreover, we demonstrate that it is feasible to further dually-amplify signal via chemiluminescence resonance energy transfer (DAS-CRET) using two non-conjugated smart probes (ADLumin-1 and CRANAD-3) in solutions, brain homogenates, and in vivo whole brain imaging. Our results show that DAS-CRET can provide a 2.25-fold margin between 5-month-old 5xFAD mice and wild type mice. We believe that our strategy could be extended to other aggregating-prone proteins.

Non-Invasive Brain Stimulation: Augmenting the Training and Performance Potential in Esports Players.

During the last two decades, esports, a highly competitive sporting activity, has gained increasing popularity. Both performance and competition in esports require players to have fine motor skills and physical and cognitive abilities in controlling and manipulating digital activities in a virtual environment. While strategies for building and improving skills and abilities are crucial for successful gaming performance, few effective training approaches exist in the fast-growing area of competitive esports. In this paper, we describe a non-invasive brain stimulation (NIBS) approach and highlight the relevance and potential areas for research while being cognizant of various technical, safety, and ethical issues related to NIBS when applied to esports.

Do Surface Slope and Posture Influence Lower Extremity Joint Kinetics during Cycling?

The purpose of this study was to investigate the effects of surface slope and body posture (i.e., seated and standing) on lower extremity joint kinetics during cycling. Fourteen participants cycled at 250 watts power in three cycling conditions: level seated, uphill seated and uphill standing at a 14% slope. A motion analysis system and custom instrumented pedal were used to collect the data of fifteen consecutive cycles of kinematics and pedal reaction force. One crank cycle was equally divided into four phases (90° for each phase). A two-factor repeated measures MANOVA was used to examine the effects of the slope and posture on the selected variables. Results showed that both slope and posture influenced joint moments and mechanical work in the hip, knee and ankle joints (p < 0.05). Specifically, the relative contribution of the knee joint to the total mechanical work increased when the body posture changed from a seated position to a standing position. In conclusion, both surface slope and body posture significantly influenced the lower extremity joint kinetics during cycling. Besides the hip joint, the knee joint also played the role as the power source during uphill standing cycling in the early downstroke phase. Therefore, adopting a standing posture for more power output during uphill cycling is recommended, but not for long periods, in view of the risk of knee injury.

In Vivo Imaging of Hypoxia Associated with Inflammatory Bowel Disease by a Cytoplasmic Protein-Powered Fluorescence Cascade Amplifier.

Accurate and sensitive imaging of hypoxia associated with inflammatory bowel disease (IBD) is significant for the precise diagnosis and treatment of this disease, but it remains a challenge for traditional hypoxia-activatable fluorescence probes because of a more moderate hypoxic state during IBD than under other pathological conditions. To address this issue, herein, we designed a hypoxia-activatable and cytoplasmic protein-powered fluorescence cascade amplifier, named HCFA, to image hypoxia associated with IBD in vivo. In our design, a 4-aminobenzoic acid (azo)-modified mesoporous silica nanoparticle (MSN) was used as a container to load black hole quencher 2 (BHQ2) and cytoplasmic protein-binding squarylium dye (SQ); then, the ß-cyclodextrin polymer (ß-CDP) combined with azo through a host-guest interaction to form HCFA. Upon passive stagnation in the inflamed tissue of IBD, the azo band would be cleaved under a hypoxic microenvironment, and SQ was released to activate the fluorescence of HCFA. Moreover, the unconstrained SQ can bind with cytoplasmic protein to exhibit drastic fluorescence intensity enhancement, realizing the fluorescence signal amplification for imaging of hypoxia. When one takes advantage of the large load capacity of MSN and the unique property of SQ, HCFA can sense oxygen levels in the range of 0% to 10%. Meanwhile, the fluorescence imaging results demonstrate that HCFA can sensitively distinguish different levels of cellular hypoxia and monitor the variations of hypoxia in vivo, highlighting HCFA as a promising tool for the detection of hypoxia associated with IBD.

Biomechanical Insights Into Differences Between the Mid-Acceleration and Maximum Velocity Phases of Sprinting.

Yu, J, Sun, Y, Yang, C, Wang, D, Yin, K, Herzog, W, and Liu, Y. Biomechanical insights into differences between the mid-acceleration and maximum velocity phases of sprinting. J Strength Cond Res 30(7): 1906-1916, 2016-Investigating the differences between distinct phases of sprint running may increase the knowledge about the specific physical abilities needed for different phases of sprinting. Differences between the mid-acceleration and maximum velocity phases of sprint running have not yet been adequately investigated. Twenty male sprinters performed maximum-effort sprint runs, and measurements were made at 12 m from start for the mid-acceleration phase and at 40 m from the start for the maximum velocity phase. Kinematic data and ground reaction forces (GRFs) were collected at a rate of 200 and 1000 Hz, respectively. Intersegmental dynamics analysis was performed to investigate the interaction of muscle torque (MUS) with other passive torques. The peak horizontal braking force was significantly lower for the acceleration compared with that for the maximal velocity phase, whereas the peak horizontal propulsive force was similar for both phases. The peak MUS at the hip and knee joints for the braking phase was significantly smaller in the acceleration phase than in the maximum velocity phase. In conclusion, compared with the maximum velocity phase, the lower horizontal braking force was the primary cause for the increase in running velocity during the mid-acceleration phase. The force produced by lower limb muscles required to counteract external torques caused by the horizontal braking force in the braking phase was smaller during the acceleration phase than the maximum velocity phase. Therefore, training aimed at reducing the horizontal braking force might be more important than increasing the force produced by the lower limb muscles for success of the mid-acceleration phase.