RNAseq Analyses Identify Tumor Necrosis Factor-Mediated Inflammation as a Major Abnormality in ALS Spinal Cord

ALS is a rapidly progressive, devastating neurodegenerative illness of adults that produces disabling weakness and spasticity arising from death of lower and upper motor neurons. No meaningful therapies exist to slow ALS progression, and molecular insights into pathogenesis and progression are sorely needed. In that context, we used high-depth, next generation RNA sequencing (RNAseq, Illumina) to define gene network abnormalities in RNA samples depleted of rRNA and isolated from cervical spinal cord sections of 7 ALS and 8 CTL samples. We aligned \u3e50 million 2X150 bp paired-end sequences/sample to the hg19 human genome and applied three different algorithms (Cuffdiff2, DEseq2, EdgeR) for identification of differentially expressed genes (DEG’s). Ingenuity Pathways Analysis (IPA) and Weighted Gene Co-expression Network Analysis (WGCNA) identified inflammatory processes as significantly elevated in our ALS samples, with tumor necrosis factor (TNF) found to be a major pathway regulator (IPA) and TNFα-induced protein 2 (TNFAIP2) as a major network “hub” gene (WGCNA). Using the oPOSSUM algorithm, we analyzed transcription factors (TF) controlling expression of the nine DEG/hub genes in the ALS samples and identified TF’s involved in inflammation (NFkB, REL, NFkB1) and macrophage function (NR1H2::RXRA heterodimer). Transient expression in human iPSC-derived motor neurons of TNFAIP2 (also a DEG identified by all three algorithms) reduced cell viability and induced caspase 3/7 activation. Using high-density RNAseq, multiple algorithms for DEG identification, and an unsupervised gene co-expression network approach, we identified significant elevation of inflammatory processes in ALS spinal cord with TNF as a major regulatory molecule. Overexpression of the DEG TNFAIP2 in human motor neurons, the population most vulnerable to die in ALS, increased cell death and caspase 3/7 activation. We propose that therapies targeted to reduce inflammatory TNFα signaling may be helpful in ALS patients

The Endoplasmic Reticulum Stress Response in Neuroprogressive Diseases: Emerging Pathophysiological Role and Translational Implications

The endoplasmic reticulum (ER) is the main cellular organelle involved in protein synthesis, assembly and secretion. Accumulating evidence shows that across several neurodegenerative and neuroprogressive diseases, ER stress ensues, which is accompanied by over-activation of the unfolded protein response (UPR). Although the UPR could initially serve adaptive purposes in conditions associated with higher cellular demands and after exposure to a range of pathophysiological insults, over time the UPR may become detrimental, thus contributing to neuroprogression. Herein, we propose that immune-inflammatory, neuro-oxidative, neuro-nitrosative, as well as mitochondrial pathways may reciprocally interact with aberrations in UPR pathways. Furthermore, ER stress may contribute to a deregulation in calcium homoeostasis. The common denominator of these pathways is a decrease in neuronal resilience, synaptic dysfunction and even cell death. This review also discusses how mechanisms related to ER stress could be explored as a source for novel therapeutic targets for neurodegenerative and neuroprogressive diseases. The design of randomised controlled trials testing compounds that target aberrant UPR-related pathways within the emerging framework of precision psychiatry is warranted

Mining the human phenome using allelic scores that index biological intermediates

J. Kaprio ja M-L. Lokki työryhmien jäseniä.It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Longitudinal Study of Parents and Children, and in publicly available data from the first Wellcome Trust Case Control Consortium. We compared the explanatory ability of allelic scores in terms of their capacity to proxy for the intermediate of interest, and the extent to which they associated with disease. We found that allelic scores derived from known variants and allelic scores derived from hundreds of thousands of genetic markers explained significant portions of the variance in biological intermediates of interest, and many of these scores showed expected correlations with disease. Genome-wide allelic scores however tended to lack specificity suggesting that they should be used with caution and perhaps only to proxy biological intermediates for which there are no known individual variants. Power calculations confirm the feasibility of extending our strategy to the analysis of tens of thousands of molecular phenotypes in large genome-wide meta-analyses. We conclude that our method represents a simple way in which potentially tens of thousands of molecular phenotypes could be screened for causal relationships with disease without having to expensively measure these variables in individual disease collections.Peer reviewe

Speech Detection in Noise for Young Bilaterally Implanted Children: Is There Evidence of Binaural Benefit Over the Shadowed Ear Alone?

OBJECTIVES: To measure binaural benefit over the shadowed ear alone for young bilateral cochlear implant (CI) users. It was hypothesized that children who received bilateral CIs at a young age (<4 years), and had significant bilateral experience, would demonstrate lower detection thresholds for speech sounds in background noise in the bilateral CI over the unilateral CI condition when the added CI was ipsilateral to the noise source. DESIGN: Children receiving bilateral CIs at the Eye and Ear Hospital Clinic in Melbourne were invited to participate in a wider research project evaluating outcomes; those participating in the wider project who were bilaterally implanted by 4 years and were approximately 2 years postoperative were included in the present study. For 20 participants, detection signal to noise ratios (SNRs) were measured for speech presented from in front and noise from 90° in at least 3 of 4 device/noise conditions, namely left CI/noise right and right CI/noise left, plus bilateral CIs/noise right and bilateral CIs/noise left. RESULTS: As some participants could only complete testing in 3 conditions within the 1 test block, the unilateral versus bilateral comparison was performed for 1 CI (i.e., 1 noise direction) for 15 participants and for both CIs (i.e., noise left and noise right) for 5 participants. Group analysis indicated no significant difference in detection SNR between the unilateral and bilateral CI conditions when adding the left CI or right CI (for the overall group) or when adding the first or second CI (for the 15 participants with sequential bilateral CIs). Separate analyses indicated no significant difference in detection SNR between the unilateral and bilateral CI conditions for the majority of individuals; this occurred irrespective of whether the analysis indicated that the CI added in the bilateral condition was poorer-performing, better-performing, or not significantly different compared with the other CI. Four individuals demonstrated a significant improvement in the bilateral condition when the CI added in the bilateral condition was a better-performing (n = 1), poorer-performing (n = 2), or not significantly different CI (n = 1). There was no relationship between the detection SNR difference between each CI and the detection SNR difference between the unilateral and bilateral conditions. CONCLUSIONS: The hypothesis of a lower detection SNR in the bilateral condition was not supported by the group results or by the results for the majority of individuals. For the 4 participants who did demonstrate benefit over the shadowed ear alone, that benefit cannot be separated from the potential benefit gained as a result of the CI added in the bilateral condition being the better-performing CI for 1 of the 4. Variation in outcomes could not be related to demographic factors for this group, which was relatively homogeneous for age at bilateral CI and experience; an older, more experienced group may demonstrate greater binaural benefit in these conditions. These results can be used during counseling for families regarding postoperative expectations for young children, especially in the first 2 years

Interaural Time-Delay Sensitivity in Bilateral Cochlear Implant Users: Effects of Pulse Rate, Modulation Rate, and Place of Stimulation

Electrical interaural time delay (ITD) discrimination was measured using 300-ms bursts applied to binaural pitch matched electrodes at basal, mid, and apical locations in each ear. Six bilateral implant users, who had previously shown good ITD sensitivity at a pulse rate of 100 pulses per second (pps), were assessed. Thresholds were measured as a function of pulse rate between 100 and 1,000 Hz, as well as modulation rate over that same range for high-rate pulse trains at 6,000 pps. Results were similar for all three places of stimulation and showed decreasing ITD sensitivity as either pulse rate or modulation rate increased, although the extent of that effect varied across subjects. The results support a model comprising a common ITD mechanism for high- and low-frequency places of stimulation, which, for electrical stimulation, is rate-limited in the same way across electrodes because peripheral temporal responses are largely place invariant. Overall, ITD sensitivity was somewhat better with unmodulated pulse trains than with high-rate pulse trains modulated at matched rates, although comparisons at individual rates showed that difference to be significant only at 300 Hz. Electrodes presenting with the lowest thresholds at 600 Hz were further assessed using bursts with a ramped onset of 10 ms. The slower rise time resulted in decreased performance in four of the listeners, but not in the two best performers, indicating that those two could use ongoing cues at 600 Hz. Performance at each place was also measured using single-pulse stimuli. Comparison of those data with the unmodulated 300-ms burst thresholds showed that on average, the addition of ongoing cues beyond the onset enhanced overall ITD sensitivity at 100 and 300 Hz, but not at 600 Hz. At 1,000 Hz, the added ongoing cues actually decreased performance. That result is attributed to the introduction of ambiguous cues within the physiologically relevant range and increased dichotic firing

Neural and Behavioral Sensitivity to Interaural Time Differences Using Amplitude Modulated Tones with Mismatched Carrier Frequencies

Bilateral cochlear implantation is intended to provide the advantages of binaural hearing, including sound localization and better speech recognition in noise. In most modern implants, temporal information is carried by the envelope of pulsatile stimulation, and thresholds to interaural time differences (ITDs) are generally high compared to those obtained in normal hearing observers. One factor thought to influence ITD sensitivity is the overlap of neural populations stimulated on each side. The present study investigated the effects of acoustically stimulating bilaterally mismatched neural populations in two related paradigms: rabbit neural recordings and human psychophysical testing. The neural coding of interaural envelope timing information was measured in recordings from neurons in the inferior colliculus of the unanesthetized rabbit. Binaural beat stimuli with a 1-Hz difference in modulation frequency were presented at the best modulation frequency and intensity as the carrier frequencies at each ear were varied. Some neurons encoded envelope ITDs with carrier frequency mismatches as great as several octaves. The synchronization strength was typically nonmonotonically related to intensity. Psychophysical data showed that human listeners could also make use of binaural envelope cues for carrier mismatches of up to 2–3 octaves. Thus, the physiological and psychophysical data were broadly consistent, and suggest that bilateral cochlear implants should provide information sufficient to detect envelope ITDs even in the face of bilateral mismatch in the neural populations responding to stimulation. However, the strongly nonmonotonic synchronization to envelope ITDs suggests that the limited dynamic range with electrical stimulation may be an important consideration for ITD encoding