Ferran Reverter

Human genomics. The human transcriptome across tissues and individuals.

Expression, genetic variation, and tissues Human genomes show extensive genetic variation across individuals, but we have only just started documenting the effects of this variation on the regulation of gene expression. Furthermore, only a few tissues have been examined per genetic variant. In order to examine how genetic expression varies among tissues within individuals, the Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative genetic traits that affect gene expression and determined which of these exhibit tissue-specific expression patterns. Melé et al. measured how transcription varies among tissues, and Rivas et al. looked at how truncated protein variants affect expression across tissues. Science, this issue p. 648, p. 660, p. 666; see also p. 640 RNA expression documents patterns of human transcriptome variation across individuals and tissues. [Also see Perspective by Gibson] Transcriptional regulation and posttranscriptional processing underlie many cellular and organismal phenotypes. We used RNA sequence data generated by Genotype-Tissue Expression (GTEx) project to investigate the patterns of transcriptome variation across individuals and tissues. Tissues exhibit characteristic transcriptional signatures that show stability in postmortem samples. These signatures are dominated by a relatively small number of genes—which is most clearly seen in blood—though few are exclusive to a particular tissue and vary more across tissues than individuals. Genes exhibiting high interindividual expression variation include disease candidates associated with sex, ethnicity, and age. Primary transcription is the major driver of cellular specificity, with splicing playing mostly a complementary role; except for the brain, which exhibits a more divergent splicing program. Variation in splicing, despite its stochasticity, may play in contrast a comparatively greater role in defining individual phenotypes.

CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis

Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome during human CPC cardiac differentiation, we profiled the lncRNA transcriptome in CPCs isolated from the human fetal heart and identified 570 lncRNAs that were modulated during cardiac differentiation. Many of these were associated with active cardiac enhancer and super enhancers (SE) with their expression being correlated with proximal cardiac genes. One of the most upregulated lncRNAs was a SE-associated lncRNA that was named CARMEN, (CAR)diac (M)esoderm (E)nhancer-associated (N)oncoding RNA. CARMEN exhibits RNA-dependent enhancing activity and is upstream of the cardiac mesoderm-specifying gene regulatory network. Interestingly, CARMEN interacts with SUZ12 and EZH2, two components of the polycomb repressive complex 2 (PRC2). We demonstrate that CARMEN knockdown inhibits cardiac specification and differentiation in cardiac precursor cells independently of MIR-143 and -145 expression, two microRNAs located proximal to the enhancer sequences. Importantly, CARMEN expression was activated during pathological remodeling in the mouse and human hearts, and was necessary for maintaining cardiac identity in differentiated cardiomyocytes. This study demonstrates therefore that CARMEN is a crucial regulator of cardiac cell differentiation and homeostasis.

Chitinase 3-like 1: prognostic biomarker in clinically isolated syndromes.

Chitinase 3-like 1 (CHI3L1) has been proposed as a biomarker associated with the conversion to clinically definite multiple sclerosis in patients with clinically isolated syndromes, based on the finding of increased cerebrospinal fluid CHI3L1 levels in clinically isolated syndrome patients who later converted to multiple sclerosis compared to those who remained as clinically isolated syndrome. Here, we aimed to validate CHI3L1 as a prognostic biomarker in a large cohort of patients with clinically isolated syndrome. This is a longitudinal cohort study of clinically isolated syndrome patients with clinical, magnetic resonance imaging, and cerebrospinal fluid data prospectively acquired. A total of 813 cerebrospinal fluid samples from patients with clinically isolated syndrome were recruited from 15 European multiple sclerosis centres. Cerebrospinal fluid CHI3L1 levels were measured by enzyme-linked immunosorbent assay. Multivariable Cox regression models were used to investigate the association between cerebrospinal fluid CHI3L1 levels and time to conversion to multiple sclerosis and time to reach Expanded Disability Status Scale 3.0. CHI3L1 levels were higher in patients who converted to clinically definite multiple sclerosis compared to patients who continued as clinically isolated syndrome (P = 8.1 × 10(-11)). In the Cox regression analysis, CHI3L1 levels were a risk factor for conversion to multiple sclerosis (hazard ratio = 1.7; P = 1.1 × 10(-5) using Poser criteria; hazard ratio = 1.6; P = 3.7 × 10(-6) for McDonald criteria) independent of other covariates such as brain magnetic resonance imaging abnormalities and presence of cerebrospinal fluid oligoclonal bands, and were the only significant independent risk factor associated with the development of disability (hazard ratio = 3.8; P = 2.5 × 10(-8)). High CHI3L1 levels were associated with shorter time to multiple sclerosis (P = 3.2 × 10(-9) using Poser criteria; P = 5.6 × 10(-11) for McDonald criteria) and more rapid development of disability (P = 1.8 × 10(-10)). These findings validate cerebrospinal fluid CHI3L1 as a biomarker associated with the conversion to multiple sclerosis and development of disability and reinforce the prognostic role of CHI3L1 in patients with clinically isolated syndrome. We propose that determining cerebrospinal fluid chitinase 3-like 1 levels at the time of a clinically isolated syndrome event will help identify those patients with worse disease prognosis.

Interfacing Differential Capacitive Sensors to Microcontrollers: A Direct Approach

This paper introduces and analyzes a novel circuit to directly connect differential resistive sensors to microcontrollers without using either a signal conditioner or an analog-to-digital converter (ADC) in the signal path. This new circuit relies on measuring the discharging time of several resistance-capacitance ( RC) circuits that include the two sensor resistances. Such an operating principle makes the circuit simple, compact, low cost, low power, and accurate. The main uncertainty sources are the quantization of the discharging time measurement and the mismatch of internal resistances of the microcontroller. According to experimental results, the circuit shows errors in the range of 0.01% full-scale span (FSS), and the effective resolution can be up to 13 bits for a measuring time of 100 ms, which are very remarkable considering its simplicity.

Transcriptomics: mRNA and alternative splicing.

Transcriptomics has emerged as a powerful approach for biomarker discovery. In the present review, the two main types of high throughput transcriptomic technologies - microarrays and next generation sequencing - that can be used to identify candidate biomarkers are briefly described. Microarrays, the mainstream technology of the last decade, have provided hundreds of valuable datasets in a wide variety of diseases including multiple sclerosis (MS), in which this approach has been used to disentangle different aspects of its complex pathogenesis. RNA-seq, the current next generation sequencing approach, is expected to provide similar power as microarrays but extending their capabilities to aspects up to now more difficult to analyse such as alternative splicing and discovery of novel transcripts.

Stability and accuracy of active shielding for grounded capacitive sensors

Active shielding is commonly used to measure remote grounded capacitive sensors because it reduces the effects of both external noise/interference and parasitic capacitances of the shielded cable. However, due to active shielding, the measurement circuit can become unstable and inaccurate. This paper analyses these limitations theoretically and experimentally, and then provides guidelines for improving the performance of active shielding. One of the key points is the selection of the bandwidth of the amplifier that drives the shield of the coaxial cable. A wide bandwidth improves accuracy, but a narrow bandwidth improves stability. Therefore, there is a trade-off between stability and accuracy with respect to the bandwidth of the amplifier.

Analysis of Power Supply Interference Effects on Direct Sensor-to-Microcontroller Interfaces

Microcontrollers with embedded timers can directly measure resistive and capacitive sensors by determining the charging or discharging time of an RC circuit that includes the sensor. However, the same as classical signal conditioning circuits, these microcontroller-based interfaces are susceptible to power supply interference. This susceptibility is analyzed herein by using theoretical and experimental methods. The variability of the measurement depends on both the amplitude and frequency of the power supply interference, and also on the measurand. Experimental data obtained for a PIC microcontroller agree with the theoretical predictions. Adding a resistor to the circuit significantly improves interference rejection

A microcontroller-based interface circuit for lossy capacitive sensors

This paper introduces and analyses a low-cost microcontroller-based interface circuit for lossy capacitive sensors, i.e. sensors whose parasitic conductance (Gx) is not negligible. Such a circuit relies on a previous circuit also proposed by the authors, in which the sensor is directly connected to a microcontroller without using either a signal conditioner or an analogue-to-digital converter in the signal path. The novel circuit uses the same hardware, but it performs an additional measurement and executes a new calibration technique. As a result, the sensitivity of the circuit to Gx decreases significantly (a factor higher than ten), but not completely due to the input capacitances of the port pins of the microcontroller. Experimental results show a relative error in the capacitance measurement below 1% for Gx < 200 nS, which is quite remarkable considering the simplicity of the circuit proposed. The measurement of a commercial capacitive humidity sensor subjected to condensation (in order to have a significant value of Gx) shows the effectiveness of the circuit.

A novel interface circuit for grounded capacitive sensors with feedforward-based active shielding

This paper proposes and analyses a novel interface circuit for capacitive sensors in which one of the electrodes is grounded. The novel design makes a charge-balanced relaxation oscillator (applied so far to floating capacitive sensors) suited for the measurement of grounded capacitive sensors and applies advanced measurement techniques, such as auto-calibration and chopping. Furthermore, these techniques are combined with feedforward-based active shielding instead of the usual feedback-based one, thus avoiding instability problems. A prototype of the novel interface circuit has been implemented with discrete components and tested for sensor capacitances between 27 pF and 330 pF and for different lengths of the interconnecting cable. The nonlinearity error amounts to less than 0.1% FSS for a 10 m cable.

A low-cost microcontroller interface for low-value capacitive sensors

Microcontrollers with embedded timers can measure resistances or capacitances by determining the charging or discharging time of an RC circuit. The microcontroller-based interfaces proposed for capacitive sensors have not been analyzed in detail, and basic information such as capacitance range, stray capacitance compensation, and accuracy is not available. This paper analyzes the performance of these interfaces when measuring capacitances in the picofarad range. The effects of stray capacitances are evaluated and reduced by applying the three-signal calibration technique. For the PIC16F873 microcontroller, the absolute error achieved is below 4% FSR for 1 pF < C/sub x/ < 10 pF, and below 1.5% for 10 pF < C/sub x/ < 100 pF.