Adaptive functions of structural variants in human brain development.

Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.

Origin of functional de novo genes in humans from "hopeful monsters".

For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.

Current and Emerging Technologies to Address the Placebo Response Challenge in CNS Clinical Trials: Promise, Pitfalls, and Pathways Forward.

Excessive placebo response rates have long been a major challenge for central nervous system (CNS) drug discovery. As CNS trials progressively shift toward digitalization, decentralization, and novel remote assessment approaches, questions are emerging about whether innovative technologies can help mitigate the placebo response. This article begins with a conceptual framework for understanding placebo response. We then critically evaluate the potential of a range of innovative technologies and associated research designs that might help mitigate the placebo response and enhance detection of treatment signals. These include technologies developed to directly address placebo response; technology-based approaches focused on recruitment, retention, and data collection with potential relevance to placebo response; and novel remote digital phenotyping technologies. Finally, we describe key scientific and regulatory considerations when evaluating and selecting innovative strategies to mitigate placebo response. While a range of technological innovations shows potential for helping to address the placebo response in CNS trials, much work remains to carefully evaluate their risks and benefits.

6mA-Sniper: Quantifying 6mA sites in eukaryotes at single-nucleotide resolution.

While N6-methyldeoxyadenine (6mA) modification is a fundamental regulation in prokaryotes, its prevalence and functions in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution, and delineate a 6mA profile in Caenorhabditis elegans with 2034 sites. Twenty-six of 39 events with Mnl I restriction endonuclease sites were verified, demonstrating the feasibility of this method. The levels of 6mA sites pinpointed by 6mA-Sniper are generally increased after Pseudomonas aeruginosa infection, but decreased in strains with the removal of METL-9, the dominant 6mA methyltransferase. The enrichment of these sites on specific motif of [GC]GAG, the selective constrains on them, and their coordinated changes with METL-9 levels thus support an active shaping of the 6mA profile by methyltransferase. Moreover, for regions marked by 6mA sites that emerged after infection, an enrichment of up-regulated genes was detected, possibly mediated through a mutual exclusive cross-talk between 6mA and H3K27me3 modification. We thus highlight 6mA regulation as a previously neglected regulator in eukaryotes.

A Human-Specific De Novo Gene Promotes Cortical Expansion and Folding.

Newly originated de novo genes have been linked to the formation and function of the human brain. However, how a specific gene originates from ancestral noncoding DNAs and becomes involved in the preexisting network for functional outcomes remains elusive. Here, a human-specific de novo gene, SP0535, is identified that is preferentially expressed in the ventricular zone of the human fetal brain and plays an important role in cortical development and function. In human embryonic stem cell-derived cortical organoids, knockout of SP0535 compromises their growth and neurogenesis. In SP0535 transgenic (TG) mice, expression of SP0535 induces fetal cortex expansion and sulci and gyri-like structure formation. The progenitors and neurons in the SP0535 TG mouse cortex tend to proliferate and differentiate in ways that are unique to humans. SP0535 TG adult mice also exhibit improved cognitive ability and working memory. Mechanistically, SP0535 interacts with the membrane protein Na+ /K+ ATPase subunit alpha-1 (ATP1A1) and releases Src from the ATP1A1-Src complex, allowing increased level of Src phosphorylation that promotes cell proliferation. Thus, SP0535 is the first proven human-specific de novo gene that promotes cortical expansion and folding, and can function through incorporating into an existing conserved molecular network.

De novo genes with an lncRNA origin encode unique human brain developmental functionality.

Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.

Comparison of Good Clinical Practice Inspection Processes for Marketing Applications Between the United States Food and Drug Administration and the European Medicines Agency.

BACKGROUND: The U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) began collaboration on Good Clinical Practice (GCP) inspections for marketing applications since 2009. The main characteristics of the GCP inspection processes between FDA and EMA were never evaluated. This is the first analysis comparing the GCP inspection processes between the two agencies. METHODS: We examined and analyzed the key characteristics of the GCP inspection processes, including the geographical distribution, inspection types and timelines from application submission to final inspection reporting for marketing applications from September 2009 through December 2015. RESULTS: Fifty-five shared applications were included for analysis. For these applications, a total of 433 GCP inspections were conducted in 47 countries. Most clinical investigator (CI) inspections were conducted in regions outside of each agency's own regulatory jurisdiction, while most sponsor/contract research organization (CRO) inspections were conducted in the U.S. by both agencies. Twenty-eight shared applications included common sites inspected by both agencies. There were 15 joint inspections conducted for seven of these applications and the remaining applications had common sites inspected by both agencies at separate times. Of the joint inspections, 73% were conducted in the U.S and 20% in the E.U. The median time from submission of an application to generation of final inspection reports was 232 days for FDA and 204 days for EMA, with no significant differences noted among applications with and without common sites. CONCLUSION: The inspection processes and timelines between the two agencies were similar, providing support for continued FDA-EMA GCP collaboration.

Descriptive Analysis of Good Clinical Practice Inspection Findings from U.S. Food and Drug Administration and European Medicines Agency.

BACKGROUND: The United States Food and Drug Administration (FDA) and European Medicines Agency (EMA) have collaborated in good clinical practice (GCP) inspections since September 2009. The two agencies operate under different regulatory frameworks for GCP oversight. No systematic assessments of GCP inspection findings have been reported. METHODS: We identified common inspections of clinical investigators, sponsors, and contract research organizations conducted by both agencies in support of marketing applications that had the same trial data submitted between 2009 and 2015. We grouped inspection findings into deficiency areas. We reviewed and compared these findings and calculated concordance rate for each deficiency area. RESULTS: Twenty-six clinical investigator sites and 23 sponsors/contract research organizations were inspected by both agencies in support of 31 marketing applications during this period. For FDA, the most common GCP findings were deficiencies related to Protocol Compliance for clinical investigator inspections and Trial Management issues for sponsor/contract research organization inspections. For EMA, deficiencies related to Documentation (including Trial Master File) were the most common findings for both clinical investigator and sponsor/contract research organization inspections. There was high concordance, of approximately 90%, for deficiencies related to Protocol Compliance for clinical investigator inspections and Trial Management for sponsor/contract research organization inspections between the two agencies. There was a concordance rate of about 70% for Documentation deficiencies for both clinical investigator and sponsor/contract research organization GCP inspections. CONCLUSION: GCP inspection findings from 49 common clinical investigator and sponsor/contract research organization inspections were comparable, providing support for continued FDA-EMA GCP collaboration.

Using Artificial Intelligence-based Methods to Address the Placebo Response in Clinical Trials.

The placebo response is a highly complex psychosocial-biological phenomenon that has challenged drug development for decades, particularly in neurological and psychiatric disease. While decades of research have aimed to understand clinical trial factors that contribute to the placebo response, a comprehensive solution to manage the placebo response in drug development has yet to emerge. Advanced data analytic techniques, such as artificial intelligence (AI), might be needed to take the next leap forward in mitigating the negative consequences of high placebo-response rates. The objective of this review was to explore the use of techniques such as AI and the sub-discipline of machine learning (ML) to address placebo response in practical ways that can positively impact drug development. This examination focused on the critical factors that should be considered in applying AI and ML to the placebo response issue, examples of how these techniques can be used, and the regulatory considerations for integrating these approaches into clinical trials.

Improve the clinical effective decision of the oral feeding readiness in preterm infants: Revise and validate the TC-POFRAS.

BACKGROUND: Currently there is limited information to guide health professionals regarding the optimal time frame to initiate safe and effective oral feedings to preterm infants. The study aims to revise and validate a streamlined version of the Traditional Chinese-Preterm Oral Feeding Readiness Assessment Scale, the TC-POFRAS®, and evaluate its construct validity in the clinical decisions regarding feeding readiness of preterm infants. METHODS: Eighty-one clinically stable preterm infants were assessed using the TC-POFRAS for oral feeding readiness. Item-total correlation analysis was used to check if any item was inconsistent with the averaged TC-POFRAS scores. Cronbach's α coefficient was used to evaluate the inter-item consistency. Exploratory factor analysis was used to determine the coherence of variables to reorganize assessment domains. The revised version of TC-POFRAS (TC-POFRAS®) was developed and a new cut-off score based on discriminant accuracy was established. RESULTS: Based on the results from statistical analysis, five items ("lips posture," "tongue posture," "biting reflex," "gag reflex," and "tongue cupping") were deleted from the original TC-POFRAS to form the TC-POFRAS®. The TC-POFRAS®'s global accuracy was 92.1%. The cut-off value of 19 was the one that presented the most optimization of sensitivity based on specificity. The TC-POFRAS® was reconstructed into corrected gestational age and five behavioral domains. CONCLUSIONS: The TC-POFRAS® is considered a valid, safe, and accurate objective instrument to assist health professionals to initiate oral feeding of preterm infants.

Tackling Challenging Data Integrity Topics in 2020: Update on Good Clinical Practice Perspectives from the US FDA and MHRA UK.

With the globalization of clinical trials, regulators have increased collaboration to evaluate the adequacy of clinical trial conduct and to optimize regulatory oversight. The 2020 joint Good Clinical Practice (GCP) symposium of the US Food and Drug Administration and the UK Medicines and Healthcare products Regulatory Agency provided the agencies' perspectives on the challenges in ensuring data quality in novel clinical trial designs and the importance of the management and documentation of protocol deviations, sponsor oversight of clinical trials, and use of electronic source data, including electronic health records. This paper summarizes considerations of both agencies on these topics, along with case examples. This paper touches upon considerations when using real-world data to support regulatory decisions. It also discusses the impact of the coronavirus disease 2019 (COVID-19) pandemic on clinical trial conduct and underscores the importance of well-designed, resilient, and adaptable systems for GCP compliance and data integrity.

Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure.

Rhesus macaque is a unique nonhuman primate model for human evolutionary and translational study, but the error-prone gene models critically limit its applications. Here, we de novo defined full-length macaque gene models based on single molecule, long-read transcriptome sequencing in four macaque tissues (frontal cortex, cerebellum, heart and testis). Overall, 8 588 227 poly(A)-bearing complementary DNA reads with a mean length of 14 106 nt were generated to compile the backbone of macaque transcripts, with the fine-scale structures further refined by RNA sequencing and cap analysis gene expression sequencing data. In total, 51 605 macaque gene models were accurately defined, covering 89.7% of macaque or 75.7% of human orthologous genes. Based on the full-length gene models, we performed a human-macaque comparative analysis on polyadenylation (PA) regulation. Using macaque and mouse as outgroup species, we identified 79 distal PA events newly originated in humans and found that the strengthening of the distal PA sites, rather than the weakening of the proximal sites, predominantly contributes to the origination of these human-specific isoforms. Notably, these isoforms are selectively constrained in general and contribute to the temporospatially specific reduction of gene expression, through the tinkering of previously existed mechanisms of nuclear retention and microRNA (miRNA) regulation. Overall, the protocol and resource highlight the application of bioinformatics in integrating multilayer genomics data to provide an intact reference for model animal studies, and the isoform switching detected may constitute a hitherto underestimated regulatory layer in shaping the human-specific transcriptome and phenotypic changes.

Transscrotal stimulation of the testes and epididymides improves urethral sperm collection in domestic cats.

Urethral catheterisation after medetomidine administration is the method of choice for semen collection in cats, but it yields variable results. This study tested whether scrotal manual stimulation can improve urethral sperm collection in domestic cats. The study was performed on 20 male cats, from which two urethral semen samples were collected, one before and one after 2min of transscrotal finger massage of the testes and epididymides. Both sperm samples were assessed for total sperm count and motility using computer-aided sperm analysis, viability and morphology (eosin-nigrosin staining). The transscrotal manual stimulation allowed a significantly higher number of spermatozoa to be obtained (P=0.0015). Viability was similar before and after the stimulation (median 92% and 90.5%), whereas the number of motile (median 60% and 70%) and morphologically normal (median 17% and 30.5%) spermatozoa was higher in the second sample (P=0.03 and P=0.002 respectively), which confirms that transscrotal massage induced the expulsion of a fresh pool of spermatozoa into the urethra. Transscrotal stimulation of the testes and epididymides significantly improves urethral semen collection in domestic cats and can be easily introduced into clinical practice.

Data Integrity in Global Clinical Trials: Discussions From Joint US Food and Drug Administration and UK Medicines and Healthcare Products Regulatory Agency Good Clinical Practice Workshop.

Good Clinical Practice (GCP) is an international ethical and scientific quality standard for designing, conducting, recording, and reporting clinical trials. Regulatory agencies conduct GCP inspections to verify the integrity of data generated in clinical trials and to assure the protection of human research subjects, in addition to ensuring that clinical trials are conducted according to the applicable regulations. The first joint GCP workshop of the US Food and Drug Administration (FDA) Center for Drug Evaluation and Research (CDER) and the United Kingdom Medicines and Healthcare products Regulatory Agency (MHRA-UK) was held in October 2018 and provided the agencies' perspectives on the importance of data quality management practices on data integrity. Regulatory perspectives on data blinding to minimize introduction of bias, and the role of audit trails in assessing data integrity in global clinical trials were discussed. This paper summarizes considerations of both agencies on these topics, along with case examples.

Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates.

BACKGROUND: Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed. RESULTS: Here, we perform a comparative editome study in human and rhesus macaque and uncover a substantial proportion of macaque A-to-I editing sites that are genomically polymorphic in some animals or encoded as non-editable nucleotides in human. The occurrence of these recent gain and loss of RNA editing through DNA point mutation is significantly more prevalent than that expected for the nearby regions. Ancestral state analyses further demonstrate that an increase in recent gain of editing events contribute to the over-representation, with G-to-A mutation site as a favorable location for the origination of robust A-to-I editing events. Population genetics analyses of the focal editing sites further reveal that a portion of these young editing events are evolutionarily significant, indicating general functional relevance for at least a fraction of these sites. CONCLUSIONS: Overall, we report a list of A-to-I editing events that recently originated through G-to-A mutations in primates, representing a valuable resource to investigate the features and evolutionary significance of A-to-I editing events at the population and species levels. The unique subset of primate editome also illuminates the general functions of RNA editing by connecting it to particular gene regulatory processes, based on the characterized outcome of a gene regulatory level in different individuals or primate species with or without these editing events.

The associations between anthropometric measurements and left ventricular structure and function: the Echo-SOL Study.

OBJECTIVE: The objective of this study is to determine associations between anthropometry and echocardiographic measures of cardiac structure and function in Hispanic/Latinos. METHODS: A total of 1,824 participants from ECHO-SOL were included. We evaluated associations between echocardiographic measures of left ventricular structure and function and anthropometric measures using multivariable-adjusted linear and logistic regression models adjusting for traditional cardiovascular risk factors. RESULTS: The mean age was 56 ± 0.17 years, 57% were women. The mean body mass index (BMI) was 30 ± 9.4 kg m-2, waist circumference (WC) was 100 ± 18 cm, and waist-to-hip ratio (WHR) was 0.93 ± 0.15. Adjusted analysis showed that 5-unit increment in BMI and 5-cm increase in WC was associated with 3.4 ± 0.6 and 1.05 ± 0.05 g m-2.7 (p < 0.05 for both) higher left ventricular (LV) mass index, respectively. Similarly, 0.1-unit increment in WHR was associated with 2.0 ± 0.16 g m-2.7 higher LV mass index (p < 0.01). WHR was associated with 0.22 ± 0.08% decrease in ejection fraction (p < 0.05). Concomitantly, 5-unit increment in BMI and WC was associated with increased odds of abnormal LV geometry (odds ratio 1.40 and 1.16, p = 0.03 and <0.01, respectively); 0.1-unit increment in WHR was associated with increased odds of abnormal LV geometry (odds ratio 1.51, p < 0.01). CONCLUSIONS: Among Hispanic/Latinos, higher anthropometric measures were associated with adverse cardiac structure and function.

PD-L1 expression, tumor mutational burden, and response to immunotherapy in patients with MET exon 14 altered lung cancers.

Background: MET exon 14 alterations are actionable oncogenic drivers. Durable responses to MET inhibitors are observed in patients with advanced MET exon 14-altered lung cancers in prospective trials. In contrast, the activity of immunotherapy, PD-L1 expression and tumor mutational burden (TMB) of these tumors and are not well characterized. Patients and methods: Patients with MET exon 14-altered lung cancers of any stage treated at two academic institutions were identified. A review of clinicopathologic and molecular features, and an analysis of response to single-agent or combination immune checkpoint inhibition were conducted. PD-L1 immunohistochemistry was carried out and TMB was calculated by estimation from targeted next-generation sequencing panels. Results: We identified 147 patients with MET exon 14-altered lung cancers. PD-L1 expression of 0%, 1%-49%, and ≥50% were 37%, 22%, and 41%, respectively, in 111 evaluable tumor samples. The median TMB of MET exon 14-altered lung cancers was lower than that of unselected non-small-cell lung cancers (NSCLCs) in both independently evaluated cohorts: 3.8 versus 5.7 mutations/megabase (P < 0.001, n = 78 versus 1769, cohort A), and 7.3 versus 11.8 mutations/megabase (P < 0.001, n = 62 versus 1100, cohort B). There was no association between PD-L1 expression and TMB (Spearman's rho=0.18, P = 0.069). In response-evaluable patients (n = 24), the objective response rate was 17% (95% CI 6% to 36%) and the median progression-free survival was 1.9 months (95% CI 1.7-2.7). Responses were not enriched in tumors with PD-L1 expression ≥50% nor high TMB. Conclusion: A substantial proportion of MET exon 14-altered lung cancers express PD-L1, but the median TMB is lower compared with unselected NSCLCs. Occasional responses to PD-1 blockade can be achieved, but overall clinical efficacy is modest.

Human exonization through differential nucleosome occupancy.

Nucleosomal modifications have been implicated in fundamental epigenetic regulation, but the roles of nucleosome occupancy in shaping changes through evolution remain to be addressed. Here we present high-resolution nucleosome occupancy profiles for multiple tissues derived from human, macaque, tree shrew, mouse, and pig. Genome-wide comparison reveals conserved nucleosome occupancy profiles across both different species and tissue types. Notably, we found significantly higher levels of nucleosome occupancy in exons than in introns, a pattern correlated with the different exon-intron GC content. We then determined whether this biased occupancy may play roles in the origination of new exons through evolution, rather than being a downstream effect of exonization, through a comparative approach to sequentially trace the order of the exonization and biased nucleosome binding. By identifying recently evolved exons in human but not in macaque using matched RNA sequencing, we found that higher exonic nucleosome occupancy also existed in macaque regions orthologous to these exons. Presumably, such biased nucleosome occupancy facilitates the origination of new exons by increasing the splice strength of the ancestral nonexonic regions through driving a local difference in GC content. These data thus support a model that sites bound by nucleosomes are more likely to evolve into exons, which we term the "nucleosome-first" model.