Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets.

We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.

Cell reprogramming promises to make characterization of the impact of human genetic variation on health and disease experimentally tractable by enabling the bridging of genotypes to phenotypes in developmentally relevant human cell lineages. Here we apply this paradigm to two disorders caused by symmetrical copy number variations of 7q11.23, which display a striking combination of shared and symmetrically opposite phenotypes--Williams-Beuren syndrome and 7q-microduplication syndrome. Through analysis of transgene-free patient-derived induced pluripotent stem cells and their differentiated derivatives, we find that 7q11.23 dosage imbalance disrupts transcriptional circuits in disease-relevant pathways beginning in the pluripotent state. These alterations are then selectively amplified upon differentiation of the pluripotent cells into disease-relevant lineages. A considerable proportion of this transcriptional dysregulation is specifically caused by dosage imbalances in GTF2I, which encodes a key transcription factor at 7q11.23 that is associated with the LSD1 repressive chromatin complex and silences its dosage-sensitive targets.

Convergent evidence associates exposure to endocrine disrupting chemicals (EDCs) with major human diseases, even at regulation-compliant concentrations. This might be because humans are exposed to EDC mixtures, whereas chemical regulation is based on a risk assessment of individual compounds. Here, we developed a mixture-centered risk assessment strategy that integrates epidemiological and experimental evidence. We identified that exposure to an EDC mixture in early pregnancy is associated with language delay in offspring. At human-relevant concentrations, this mixture disrupted hormone-regulated and disease-relevant regulatory networks in human brain organoids and in the model organisms Xenopus leavis and Danio rerio , as well as behavioral responses. Reinterrogating epidemiological data, we found that up to 54% of the children had prenatal exposures above experimentally derived levels of concern, reaching, for the upper decile compared with the lowest decile of exposure, a 3.3 times higher risk of language delay.

Objectives: Despite the interest in scientific community, there is still poor evidence about pulsed radiofrequency (PRF) efficacy in the treatment of neuropathic pain. In order to determine whether high-voltage PRF and epidural adhesiolysis (PRF-EA) showed better results than epidural adhesiolysis alone (EA), a randomized, double-blind, comparative-effectiveness study was conducted in patients with chronic lumbosacral radiating pain and neuropathic features. Materials and Methods: A total of 41 patients were randomly allocated to 2 groups. Twenty-one patients were randomized to receive 2 cycles of 240 seconds high-voltage PRF followed by the injection of local anesthetics, hyaluronidase, and betamethasone, whereas 20 patients underwent sham stimulation followed by adhesiolysis. The treatment was delivered at the affected lumbosacral roots and patients, treating physicians and assessors were blinded to intervention. Results: A significant reduction of radiating pain was observed in mean Numeric Rating Scale score at follow-up. A change of −3.43 versus −1.75 (P=0.031) after 1 month and −3.34 versus −0.80 (P=0.005) after 6 months was reported in patients undergoing PRF-EA in comparison with EA, respectively. After 1 month, 57% of patients in the PRF-EA group experienced a pain reduction of ≥50% versus only 25% of patients allocated to EA (P=0.037). Improvement decreased to 48% in the PRF-EA group whereas only 10% of EA reported significant pain relief after 6 months (P=0.008). Discussion: High-voltage PRF of dorsal root ganglion delivered through multifunctional electrode provided significant pain relief and may be considered a valuable treatment in chronic lumbosacral radicular pain with neuropathic features.

Background Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental condition affecting almost 1% of children, and represents a major unmet medical need with no effective drug treatment available. Duplication at 7q11.23 (7Dup), encompassing 26–28 genes, is one of the best characterized ASD-causing copy number variations and offers unique translational opportunities, because the hemideletion of the same interval causes Williams–Beuren syndrome (WBS), a condition defined by hypersociability and language strengths, thereby providing a unique reference to validate treatments for the ASD symptoms. In the above-indicated interval at 7q11.23, defined as WBS critical region, several genes, such as GTF2I, BAZ1B, CLIP2 and EIF4H, emerged as critical for their role in the pathogenesis of WBS and 7Dup both from mouse models and human studies. Methods We performed a high-throughput screening of 1478 compounds, including central nervous system agents, epigenetic modulators and experimental substances, on patient-derived cortical glutamatergic neurons differentiated from our cohort of induced pluripotent stem cell lines (iPSCs), monitoring the transcriptional modulation of WBS interval genes, with a special focus on GTF2I, in light of its overriding pathogenic role. The hits identified were validated by measuring gene expression by qRT-PCR and the results were confirmed by western blotting. Results We identified and selected three histone deacetylase inhibitors (HDACi) that decreased the abnormal expression level of GTF2I in 7Dup cortical glutamatergic neurons differentiated from four genetically different iPSC lines. We confirmed this effect also at the protein level. Limitations In this study, we did not address the molecular mechanisms whereby HDAC inhibitors act on GTF2I. The lead compounds identified will now need to be advanced to further testing in additional models, including patient-derived brain organoids and mouse models recapitulating the gene imbalances of the 7q11.23 microduplication, in order to validate their efficacy in rescuing phenotypes across multiple functional layers within a translational pipeline towards clinical use. Conclusions These results represent a unique opportunity for the development of a specific class of compounds for treating 7Dup and other forms of intellectual disability and autism.

39Convergent evidence associates endocrine disrupting chemicals (EDCs) with major, 40 increasingly-prevalent human disorders. Regulation requires elucidation of EDC-41 triggered molecular events causally linked to adverse health outcomes, but two factors 42 limit their identification. First, experiments frequently use individual chemicals, whereas 43 real life entails simultaneous exposure to multiple EDCs. Second, experimental studies are seldom integrated. This drawback was exacerbated until 45 recently by lack of physiopathologically meaningful human experimental systems that 46 link epidemiological data with results from model organisms. 47 We developed a novel approach, integrating epidemiological with experimental 48 evidence. Starting from 1,874 mother-child pairs we identified mixtures of chemicals, 49 measured during early pregnancy, associated with language delay or low-birth weight in 50 offspring. These mixtures were then tested on multiple complementary in vitro and in 51 vivo models. We demonstrate that each EDC mixture, at levels found in pregnant 52 women, disrupts hormone-regulated and disease-relevant gene regulatory networks at 53 both the cellular and organismal scale. . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/206664 doi: bioRxiv preprint first posted online Oct. 23, 2017; Results 70 An integrated epidemiological-experimental design assessing the impact of EDC mixtures on human health and development 72To assess health outcomes of real-life EDC exposures we harnessed: i) the power of a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/206664 doi: bioRxiv preprint first posted online Oct. 23, 2017; 5 these EDC mixtures in concentrations corresponding to human exposure ( Figure 1b); iii) 79 paradigmatic in vivo models to determine the physiological impact of key affected 80 pathways (Figure 1c (Table 1a), assessed for their urinary or serum EDC 94 levels around the 10 th week of gestation (Table 1b). Specifically, we profiled urine levels 95 of 10 metabolites of 5 phthalates, bisphenol A (BPA) and triclosan (TCS), as well as 96 serum levels of 8 perfluorinated alkyl acids (PFAAs). 97Specific mixtures (in terms of both composition and dose) were associated with the two 98 health outcomes in a three-step procedure ( Figure 1a). First, we identified the prenatal 99 exposure to EDCs, hereafter "bad actors", that was associated with lower birth weight or 100 language delay in children by using weighted quantile sum (WQS) regression 7 . Next, we 101 . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to...

ObjectiveThe aim of this study was to investigate the therapeutic effectiveness of epidural morphine and bupivacaine in patients with chronic lumbosacral radicular neuropathic pain after the cessation of treatment.MethodsTwenty-two patients with chronic lumbosacral pain with neuropathic features were enrolled. An indwelling catheter was placed into the epidural space, and each patient received an epidural injection of morphine chlorhydrate and bupivacaine up to three times a day. The medication was administered for 4 weeks. The pain intensity score on a 0–10 numeric rating scale (NRS), the total pain rating index rank (PRIr-T), and its coefficients were evaluated before treatment and 1 month after catheter removal. P-value <0.05 was considered statistically significant.ResultsNRS and PRIr-T were significantly reduced at follow-up (P=0.001 and P=0.03, respectively), whereas the parallel evolution of the two scores (r=0.75 and P<0.001, respectively) confirmed significant pain relief lasting up to 1 month after treatment cessation. None of the four pain rating coefficients was significantly modified compared to the others in either responders or nonresponders. Successful clinical outcome (pain reduction >30% in NRS) was reached and maintained in half of the patients at follow-up.ConclusionCombined epidural morphine and bupivacaine seems to be effective in the treatment of neuropathic pain.