High temperature stress response is not sexually dimorphic at the whole-body level and is dependent on androgens to induce sex reversal

The understanding of the molecular and endocrine mechanisms behind environmentally-induced sex reversal in fish is of great importance in the context of predicting the potential effects of climate change, especially increasing temperature. Here, we demonstrate the global effects of high temperature on genome-wide transcription in medaka (Oryzias latipes) during early development. Interestingly, data analysis did not show sexual dimorphic changes, demonstrating that thermal stress is not dependent on genotypic sex. Additionally, our results revealed significant changes in several pathways under high temperature, such as stress response from brain, steroid biosynthesis, epigenetic mechanisms, and thyroid hormone biosynthesis, among others. These microarray data raised the question of what the exact molecular and hormonal mechanisms of action are for female-to-male sex reversal under high temperatures in fish. Complementary gene expression analysis revealed that androgen-related genes increase in females (XX) experiencing high water temperature. To test the involvement of androgens in thermal-induced sex reversal, an androgen antagonist was used to treat XX medaka under a high-temperature setup. Data clearly demonstrated failure of female-to-male sex reversal when androgen action is inhibited, corroborating the importance of androgens in environmentally-induced sex reversal.

Machine Learning Predictions of Block Copolymer Self-Assembly

Directed self-assembly of block copolymers is a key enabler for nanofabrication of devices with sub-10 nm feature sizes, allowing patterning far below the resolution limit of conventional photolithography. Among all the process steps involved in block copolymer self-assembly, solvent annealing plays a dominant role in determining the film morphology and pattern quality, yet the interplay of the multiple parameters during solvent annealing, including the initial thickness, swelling, time, and solvent ratio, makes it difficult to predict and control the resultant self-assembled pattern. Here, machine learning tools are applied to analyze the solvent annealing process and predict the effect of process parameters on morphology and defectivity. Two neural networks are constructed and trained, yielding accurate prediction of the final morphology in agreement with experimental data. A ridge regression model is constructed to identify the critical parameters that determine the quality of line/space patterns. These results illustrate the potential of machine learning to inform nanomanufacturing processes.

Functional analysis of an R311C variant of Ca2+ -calmodulin-dependent protein kinase kinase-2 (CaMKK2) found as a de novo mutation in a patient with bipolar disorder

OBJECTIVES

Loss-of-function mutations in the gene encoding the calcium-calmodulin (Ca²⁺ -CaM)-dependent protein kinase kinase-2 (CaMKK2) enzyme are linked to bipolar disorder. Recently, a de novo arginine to cysteine (R311C) mutation in CaMKK2 was identified from a whole exome sequencing study of bipolar patients and their unaffected parents. The aim of the present study was to determine the functional consequences of the R311C mutation on CaMKK2 activity and regulation by Ca²⁺ -CaM.

METHODS

The effects of the R311C mutation on CaMKK2 activity and Ca²⁺ -CaM activation were examined using a radiolabeled adenosine triphosphate (ATP) kinase assay. We performed immunoblot analysis to determine whether the R311C mutation impacts threonine-85 (T85) autophosphorylation, an activating phosphorylation site on CaMKK2 that has also been implicated in bipolar disorder. We also expressed the R311C mutant in CaMKK2 knockout HAP1 cells and used immunoblot analysis and an MTS reduction assay to study its effects on Ca²⁺ -dependent downstream signaling and cell viability, respectively.

RESULTS

The R311C mutation maps to the conserved HRD motif within the catalytic loop of CaMKK2 and caused a marked reduction in kinase activity and Ca²⁺ -CaM activation. The R311C mutation virtually abolished T85 autophosphorylation in response to Ca²⁺ -CaM and exerted a dominant-negative effect in cells as it impaired the ability of wild-type CaMKK2 to initiate downstream signaling and maintain cell viability.

CONCLUSIONS

The highly disruptive, loss-of-function impact of the de novo R311C mutation in human CaMKK2 provides a compelling functional rationale for being considered a potential rare monogenic cause of bipolar disorder.

PIK3R2/Pik3r2 Activating Mutations Result in Brain Overgrowth and EEG Changes

OBJECTIVE

Mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) complex have been associated with a broad spectrum of brain and organ overgrowth syndromes. For example, mutations in phosphatidylinositol-3-kinase regulatory subunit 2 (PIK3R2) have been identified in human patients with megalencephaly polymicrogyria polydactyly hydrocephalus (MPPH) syndrome, which includes brain overgrowth. To better understand the pathogenesis of PIK3R2-related mutations, we have developed and characterized a murine model.

METHODS

We generated a knock-in mouse model for the most common human PIK3R2 mutation, p.G373R (p.G367R in mice) using CRISPR/Cas9. The mouse phenotypes, including brain size, seizure activity, cortical lamination, cell proliferation/size/density, interneuron migration, and PI3K pathway activation, were analyzed using standard methodologies. For human patients with PIK3R2 mutations, clinical data (occipitofrontal circumference [OFC] and epilepsy) were retrospectively obtained from our clinical records (published / unpublished).

RESULTS

The PI3K-AKT pathway was hyperactivated in these mice, confirming the p.G367R mutation is an activating mutation in vivo. Similar to human patients with PIK3R2 mutations, these mice have enlarged brains. We found cell size to be increased but not cell numbers. The embryonic brain showed mild defects in cortical lamination, although not observed in the mature brain. Furthermore, electroencephalogram (EEG) recordings from mutant mice showed background slowing and rare seizures, again similar to our observations in human patients.

INTERPRETATION

We have generated a PIK3R2 mouse model that exhibits megalencephaly and EEG changes, both of which overlap with human patients. Our data provide novel insight into the pathogenesis of the human disease caused by PIK3R2 p.G373R mutation. We anticipate this model will be valuable in testing therapeutic options for human patients with MPPH. ANN NEUROL 2020;88:1077-1094.

miR‑7/SP1/TP53BP1 axis may play a pivotal role in NSCLC radiosensitivity

MicroRNA‑7 (miR‑7) has been identified as a tumor suppressor in non‑small cell lung cancer (NSCLC) and a radiosensitivity regulator. Numerous studies have revealed that specific protein 1 (SP1) plays a critical role in the tumorigenesis of various types of cancers and regulates radiosensitivity and tumor suppressor p53‑binding protein 1 (TP53BP1), which plays an essential role in DNA repair. However, it is not clear whether miR‑7 has a regulatory effect on SP1 and TP53BP1 in NSCLC. In the present study it was revealed that miR‑7 directly binds to the 3'UTR of SP1, thereby suppressing SP1 expression to regulate radiosensitivity. Overexpression of miR‑7 and SP1 and knockdown of miR‑7 and SP1 were performed using lentiviral transfection. Protein and mRNA abundance of SP1 and TP53BP1 were determined using western blotting and RT‑qPCR, respectively, while miR‑7 binding to SP1 was validated using a luciferase reporter assay. Biological function analysis indicated that miR‑7 negatively regulated SP1 and inhibited cell proliferation, migration, and invasion when combined with radiation. It was also revealed that the expression of TP53BP1 was positively regulated by SP1 or negatively regulated by miR‑7. In conclusion, SP1 was a target of miR‑7, and the decreased expression of SP1 resulting from miR‑7 overexpression in NSCLC was vital for improving radiosensitivity in NSCLC cells. Moreover, SP1 expression was detected in 95 paired NSCLC and adjacent normal tissues, and it was determined that SP1 was significantly upregulated in NSCLC tissues and that its upregulation was correlated with the degree of tissue differentiation. Thus, SP1 and/or miR‑7 may be potential molecular targets in NSCLC radiotherapy.

The saccharibacterium TM7x elicits differential responses across its host range

Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into "permissive" and "nonpermissive" based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.

Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis

Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. Here, we undertake joint profiling of the transcriptome and DNA methylome of individual oocytes from reproductively young and old mice undergoing natural ovulation. We find reduced complexity as well as increased variance in the transcriptome of oocytes from aged females. This transcriptome heterogeneity is reflected in the identification of discrete sub‐populations. Oocytes with a transcriptome characteristic of immature chromatin configuration (NSN) clustered into two groups: one with reduced developmental competence, as indicated by lower expression of maternal effect genes, and one with a young‐like transcriptome. Oocytes from older females had on average reduced CpG methylation, but the characteristic bimodal methylation landscape of the oocyte was preserved. Germline differentially methylated regions of imprinted genes were appropriately methylated irrespective of age. For the majority of differentially expressed transcripts, the absence of correlated methylation changes suggests a post‐transcriptional basis for most age‐related effects on the transcriptome. However, we did find differences in gene body methylation at which there were corresponding changes in gene expression, indicating age‐related effects on transcription that translate into methylation differences. Interestingly, oocytes varied in expression and methylation of these genes, which could contribute to variable competence of oocytes or penetrance of maternal age‐related phenotypes in offspring.

Epigenetic Mechanisms in Leukemias and Lymphomas

Although we are just beginning to understand the mechanisms that regulate the epigenome, aberrant epigenetic programming has already emerged as a hallmark of hematologic malignancies including acute myeloid leukemia (AML) and B-cell lymphomas. Although these diseases arise from the hematopoietic system, the epigenetic mechanisms that drive these malignancies are quite different. Yet, in all of these tumors, somatic mutations in transcription factors and epigenetic modifiers are the most commonly mutated set of genes and result in multilayered disruption of the epigenome. Myeloid and lymphoid neoplasms generally manifest epigenetic allele diversity, which contributes to tumor cell population fitness regardless of the underlying genetics. Epigenetic therapies are emerging as one of the most promising new approaches for these patients. However, effective targeting of the epigenome must consider the need to restore the various layers of epigenetic marks, appropriate biological end points, and specificity of therapeutic agents to truly realize the potential of this modality.

Methionine oxidation within the prion protein

Prion diseases are characterized by the self-templated misfolding of the cellular prion protein (PrPC) into infectious aggregates (PrPSc). The detailed molecular basis of the misfolding and aggregation of PrPC remains incompletely understood. It is believed that the transient misfolding of PrPC into partially structured intermediates precedes the formation of insoluble protein aggregates and is a critical component of the prion misfolding pathway. A number of environmental factors have been shown to induce the destabilization of PrPC and promote its initial misfolding. Recently, oxidative stress and reactive oxygen species (ROS) have emerged as one possible mechanism by which the destabilization of PrPC can be induced under physiological conditions. Methionine residues are uniquely vulnerable to oxidation by ROS and the formation of methionine sulfoxides leads to the misfolding and subsequent aggregation of PrPC. Here, we provide a review of the evidence for the oxidation of methionine residues in PrPC and its potential role in the formation of pathogenic prion aggregates.

Sex-specific plasticity across generations I: Maternal and paternal effects on sons and daughters

Intergenerational plasticity or parental effects-when parental environments alter the phenotype of future generations-can influence how organisms cope with environmental change. An intriguing, underexplored possibility is that sex-of both the parent and the offspring-plays an important role in driving the evolution of intergenerational plasticity in both adaptive and non-adaptive ways. Here, we evaluate the potential for sex-specific parental effects in a freshwater population of three-spined sticklebacks Gasterosteus aculeatus by independently and jointly manipulating maternal and paternal experiences and separately evaluating their phenotypic effects in sons versus daughters. We tested the adaptive hypothesis that daughters are more responsive to cues from their mother, whereas sons are more responsive to cues from their father. We exposed mothers, fathers or both parents to visual cues of predation risk and measured offspring antipredator traits and brain gene expression. Predator-exposed fathers produced sons that were more risk-prone, whereas predator-exposed mothers produced more anxious sons and daughters. Furthermore, maternal and paternal effects on offspring survival were non-additive: offspring with a predator-exposed father, but not two predator-exposed parents, had lower survival against live predators. There were also strong sex-specific effects on brain gene expression: exposing mothers versus fathers to predation risk activated different transcriptional profiles in their offspring, and sons and daughters strongly differed in the ways in which their brain gene expression profiles were influenced by parental experience. We found little evidence to support the hypothesis that offspring prioritize their same-sex parent's experience. Parental effects varied with both the sex of the parent and the offspring in complicated and non-additive ways. Failing to account for these sex-specific patterns (e.g. by pooling sons and daughters) would have underestimated the magnitude of parental effects. Altogether, these results draw attention to the potential for sex to influence patterns of intergenerational plasticity and raise new questions about the interface between intergenerational plasticity and sex-specific selective pressures, sexual conflict and sexual selection.

N6-methyladenosine mRNA methylation of PIK3CB regulates AKT signalling to promote PTEN-deficient pancreatic cancer progression

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide. Thus far, most drugs have failed to significantly improve patient survival. N⁶-methyladenosine (m⁶A) plays an important role in the progression of PDAC, but its aberrant regulation driven by germline variants in human diseases remains unclear.

DESIGN

We first performed an exome-wide association analysis in 518 PDAC patients with overall survival and replicated in an independent population containing 552 PDAC patients. Then, a series of biochemical experiments in vitro and in vivo were conducted to investigate potential mechanisms of the candidate variant and its target gene PIK3CB underlying the PDAC progression. Moreover, the PIK3CB-selective inhibitor KIN-193 was used to block PDAC tumour growth.

RESULTS

We identified a missense variant rs142933486 in PIK3CB that is significantly associated with the overall survival of PDAC by reducing the PIK3CB m⁶A level, which facilitated its mRNA and protein expression levels mediated by the m⁶A 'writer' complex (METTL13/METTL14/WTAP) and the m⁶A 'reader' YTHDF2. The upregulation of PIK3CB is widely found in PDAC tumour tissues and significantly correlated with the poor prognosis of PDAC, especially in PTEN-deficient patients. We further demonstrated that PIK3CB overexpression substantially enhanced the proliferation and migration abilities of PTEN-deficient PDAC cells and activated AKT signalling pathway. Remarkably, KIN-193, a PIK3CB-selective inhibitor, is shown to serve as an effective anticancer agent for blocking PTEN-deficient PDAC.

CONCLUSIONS

These findings demonstrate aberrant m⁶A homoeostasis as an oncogenic mechanism in PDAC and highlight the potential of PIK3CB as a therapeutic target for this disease.

Microbiome-based interventions: therapeutic strategies in cancer immunotherapy

The composition of the commensal microbiota has recently emerged as a key element influencing the efficacy of cancer treatments. It has become apparent that the interplay between the microbiome and immune system within the host influences the response to immunotherapy, particularly immune checkpoint inhibitor therapy. Identifying the key components of the gut microbiota that influence this response is paramount for designing therapeutic interventions to enhance the response to cancer therapy. This review will discuss strategies being considered to modulate the gut microbiota, including fecal microbiota transplantation, administration of defined bacterial isolates as well as bacterial consortia, supplementation with probiotics, and lifestyle modifications such as dietary changes. Understanding the influence of the complex variables of the human microbiota on the effectiveness of cancer therapy will help drive the clinical design of microbial-based interventions in the field of oncology.

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Manipulation of the gut microbiome can influence the therapeutic efficacy of immune checkpoint inhibitors.

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Clinical studies are currently exploring therapeutic methods to modulate commensal bacteria.

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Strategies to modulate the microbiome include fecal microbiota transplantation, defined bacterial isolates and dietary manipulation.

Genome-wide investigation of proline transporter (ProT) gene family in tomato: Bioinformatics and expression analyses in response to drought stress

Proline has various functions in plants, such as growth, development and stress response to biotic and abiotic factors. Therefore, proline accumulation and transport are vital for crop production in higher quality and quantity. The present study addresses genome-wide identification and bioinformatics analyses of tomato (Solanum lycopersicum) proline transporter (ProT) genes and their expression profiles under drought stress. The analyses indicated four novel ProT genes (SlProTs) in the tomato genome and their protein lengths ranged from 439 to 452 amino acid residues. All SlProTs contained a PF01490 (transmembrane amino acid transporter protein) domain and seven exons, and they had a basic pI. The phylogeny analysis proved that monocot-dicot divergence was not present and the SlProT proteins were distinct from the ProT proteins in monocots and Arabidopsis. Based on the digital expression analysis, SlProT1 and SlProT2 genes seemed to be more active than the others in response to abiotic stress conditions. However, detected by RT-qPCR, the expression levels of all SlProT genes under drought stress were similar. The promotor analyses of SlProT genes revealed that they contained many transcription factors binding sites in cis-elements, such as MYB, Dof, Hox, bZIP, bHLH, AP2/ERF and WRKY. Finally, our findings could contribute to the understanding of SlProT genes and proline metabolism in plants.

Genomic prediction of maize microphenotypes provides insights for optimizing selection and mining diversity

Effective evaluation of millions of crop genetic stocks is an essential component of exploiting genetic diversity to achieve global food security. By leveraging genomics and data analytics, genomic prediction is a promising strategy to efficiently explore the potential of these gene banks by starting with phenotyping a small designed subset. Reliable genomic predictions have enhanced selection of many macroscopic phenotypes in plants and animals. However, the use of genomicprediction strategies for analysis of microscopic phenotypes is limited. Here, we exploited the power of genomic prediction for eight maize traits related to the shoot apical meristem (SAM), the microscopic stem cell niche that generates all the above-ground organs of the plant. With 435 713 genomewide single-nucleotide polymorphisms (SNPs), we predicted SAM morphology traits for 2687 diverse maize inbreds based on a model trained from 369 inbreds. An empirical validation experiment with 488 inbreds obtained a prediction accuracy of 0.37-0.57 across eight traits. In addition, we show that a significantly higher prediction accuracy was achieved by leveraging the U value (upper bound for reliability) that quantifies the genomic relationships of the validation set with the training set. Our findings suggest that double selection considering both prediction and reliability can be implemented in choosing selection candidates for phenotyping when exploring new diversity is desired. In this case, individuals with less extreme predicted values and moderate reliability values can be considered. Our study expands the turbocharging gene banks via genomic prediction from the macrophenotypes into the microphenotypic space.

Chromosome reciprocal translocations have accompanied subspecies evolution in bananas

Chromosome rearrangements and the way that they impact genetic differentiation and speciation have long raised questions from evolutionary biologists. They are also a major concern for breeders because of their bearing on chromosome recombination. Banana is a major crop that derives from inter(sub)specific hybridizations between various once geographically isolated Musa species and subspecies. We sequenced 155 accessions, including banana cultivars and representatives of Musa diversity, and genotyped-by-sequencing 1059 individuals from 11 progenies. We precisely characterized six large reciprocal translocations and showed that they emerged in different (sub)species of Musa acuminata, the main contributor to currently cultivated bananas. Most diploid and triploid cultivars analyzed were structurally heterozygous for 1 to 4 M. acuminata translocations, highlighting their complex origin. We showed that all translocations induced a recombination reduction of variable intensity and extent depending on the translocations, involving only the breakpoint regions, a chromosome arm, or an entire chromosome. The translocated chromosomes were found preferentially transmitted in many cases. We explore and discuss the possible mechanisms involved in this preferential transmission and its impact on translocation colonization.

Resurrecting the ancient glow of the fireflies

The color of firefly bioluminescence is determined by the structure of luciferase. Firefly luciferase genes have been isolated from more than 30 species, producing light ranging in color from green to orange-yellow. Here, we reconstructed seven ancestral firefly luciferase genes, characterized the enzymatic properties of the recombinant proteins, and determined the crystal structures of the gene from ancestral Lampyridae. Results showed that the synthetic luciferase for the last common firefly ancestor exhibited green light caused by a spatial constraint on the luciferin molecule in enzyme, while fatty acyl-CoA synthetic activity, an original function of firefly luciferase, was diminished in exchange. All known firefly species are bioluminescent in the larvae, with a common ancestor arising approximately 100 million years ago. Combined, our findings propose that, within the mid-Cretaceous forest, the common ancestor of fireflies evolved green light luciferase via trade-off of the original function, which was likely aposematic warning display against nocturnal predation.

Haloferax volcanii-a model archaeon for studying DNA replication and repair

The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.

The relation between mitogen activated protein kinase (MAPK) pathway and different genes expression in patients with beta Thalassemia

BACKGROUND

β-thalassemia is an inherited hemoglobinopathy resulting in quantitative changes in the β-globin chain. Understanding the molecular basis of that disorder requires studying the expression of genes controlling the pathways that affect the erythropoietic homeostasis especially the MAPK pathway. The MAPKs are a family of serine/threonine kinases that play an essential role in connecting cell-surface receptors to DNA in the nucleus of the cell.

AIM

to study the effect of expression of GNAI2, DUSP5 and ARRB1 genes on MAPK signaling pathway in pediatric patients with beta thalassemia.

METHODS

Forty children with beta thalassemia major (TM), forty children with beta thalassemia intermedia (TI) and forty age and gender matched healthy controls were enrolled in this study. Detection of GNAI2, DUSP5 and ARRB1 mRNA expression was done by real time polymerase chain reaction (RT-PCR).

RESULTS

revealed increased expression of ARRB1 (Arrestin Beta 1) gene, and decreased expression of both GNAI2 (Guanine nucleotide-binding protein G (i) subunit alpha-2) and DUSP5 (Dual specificity protein phosphatase 5) genes in both patient groups than control groups respectively.

CONCLUSIONS

Change in the rate of expression of ARRB1, GNAI2 and DUSP5 may have a role in the pathogenesis of abnormal hematopoiesis in cases of β thalassemia through affecting the MAPK pathway.

Framework for identifying drug repurposing candidates from observational healthcare data

OBJECTIVE

Observational medical databases, such as electronic health records and insurance claims, track the healthcare trajectory of millions of individuals. These databases provide real-world longitudinal information on large cohorts of patients and their medication prescription history. We present an easy-to-customize framework that systematically analyzes such databases to identify new indications for on-market prescription drugs.

MATERIALS AND METHODS

Our framework provides an interface for defining study design parameters and extracting patient cohorts, disease-related outcomes, and potential confounders in observational databases. It then applies causal inference methodology to emulate hundreds of randomized controlled trials (RCTs) for prescribed drugs, while adjusting for confounding and selection biases. After correcting for multiple testing, it outputs the estimated effects and their statistical significance in each database.

RESULTS

We demonstrate the utility of the framework in a case study of Parkinson's disease (PD) and evaluate the effect of 259 drugs on various PD progression measures in two observational medical databases, covering more than 150 million patients. The results of these emulated trials reveal remarkable agreement between the two databases for the most promising candidates.

DISCUSSION

Estimating drug effects from observational data is challenging due to data biases and noise. To tackle this challenge, we integrate causal inference methodology with domain knowledge and compare the estimated effects in two separate databases.

CONCLUSION

Our framework enables systematic search for drug repurposing candidates by emulating RCTs using observational data. The high level of agreement between separate databases strongly supports the identified effects.

Massively parallel techniques for cataloguing the regulome of the human brain

Complex brain disorders are highly heritable and arise from a complex polygenic risk architecture. Many disease-associated loci are found in non-coding regions that house regulatory elements. These elements influence the transcription of target genes-many of which demonstrate cell-type-specific expression patterns-and thereby affect phenotypically relevant molecular pathways. Thus, cell-type-specificity must be considered when prioritizing candidate risk loci, variants and target genes. This Review discusses the use of high-throughput assays in human induced pluripotent stem cell-based neurodevelopmental models to probe genetic risk in a cell-type- and patient-specific manner. The application of massively parallel reporter assays in human induced pluripotent stem cells can characterize the human regulome and test the transcriptional responses of putative regulatory elements. Parallel CRISPR-based screens can further functionally dissect this genetic regulatory architecture. The integration of these emerging technologies could decode genetic risk into medically actionable information, thereby improving genetic diagnosis and identifying novel points of therapeutic intervention.

A Journey Through Myeloma Evolution: From the Normal Plasma Cell to Disease Complexity

The knowledge of cancer origin and the subsequent tracking of disease evolution represent unmet needs that will soon be within clinical reach. This will provide the opportunity to improve patient's stratification and to personalize treatments based on cancer biology along its life history. In this review, we focus on the molecular pathogenesis of multiple myeloma (MM), a hematologic malignancy with a well-known multi-stage disease course, where such approach can sooner translate into a clinical benefit. We describe novel insights into modes and timing of disease initiation. We dissect the biology of the preclinical and pre-malignant phases, elucidating how knowledge of the genomics of the disease and the composition of the microenvironment allow stratification of patients based on risk of disease progression. Then, we explore cell-intrinsic and cell-extrinsic drivers of MM evolution to symptomatic disease. Finally, we discuss how this may relate to the development of refractory disease after treatment. By integrating an evolutionary view of myeloma biology with the recent acquisitions on its clonal heterogeneity, we envision a way to drive the clinical management of the disease based on its detailed biological features more than surrogates of disease burden.

Identification of Neuropsychiatric Copy Number Variants in a Health Care System Population

IMPORTANCE

Population screening for medically relevant genomic variants that cause diseases such as hereditary cancer and cardiovascular disorders is increasing to facilitate early disease detection or prevention. Neuropsychiatric disorders (NPDs) are common, complex disorders with clear genetic causes; yet, access to genetic diagnosis is limited. We explored whether inclusion of NPD in population-based genomic screening programs is warranted by assessing 3 key factors: prevalence, penetrance, and personal utility.

OBJECTIVE

To evaluate the suitability of including pathogenic copy number variants (CNVs) associated with NPD in population screening by determining their prevalence and penetrance and exploring the personal utility of disclosing results.

DESIGN, SETTING, AND PARTICIPANTS

In this cohort study, the frequency of 31 NPD CNVs was determined in patient-participants via exome data. Associated clinical phenotypes were assessed using linked electronic health records. Nine CNVs were selected for disclosure by licensed genetic counselors, and participants' psychosocial reactions were evaluated using a mixed-methods approach. A primarily adult population receiving medical care at Geisinger, a large integrated health care system in the United States with the only population-based genomic screening program approved for medically relevant results disclosure, was included. The cohort was identified from the Geisinger MyCode Community Health Initiative. Exome and linked electronic health record data were available for this cohort, which was recruited from February 2007 to April 2017. Data were collected for the qualitative analysis April 2017 through February 2018. Analysis began February 2018 and ended December 2019.

MAIN OUTCOMES AND MEASURES

The planned outcomes of this study include (1) prevalence estimate of NPD-associated CNVs in an unselected health care system population; (2) penetrance estimate of NPD diagnoses in CNV-positive individuals; and (3) qualitative themes that describe participants' responses to receiving NPD-associated genomic results.

RESULTS

Of 90 595 participants with CNV data, a pathogenic CNV was identified in 708 (0.8%; 436 women [61.6%]; mean [SD] age, 50.04 [18.74] years). Seventy percent (n = 494) had at least 1 associated clinical symptom. Of these, 28.8% (204) of CNV-positive individuals had an NPD code in their electronic health record, compared with 13.3% (11 835 of 89 887) of CNV-negative individuals (odds ratio, 2.21; 95% CI, 1.86-2.61; P < .001); 66.4% (470) of CNV-positive individuals had a history of depression and anxiety compared with 54.6% (49 118 of 89 887) of CNV-negative individuals (odds ratio, 1.53; 95% CI, 1.31-1.80; P < .001). 16p13.11 (71 [0.078%]) and 22q11.2 (108 [0.119%]) were the most prevalent deletions and duplications, respectively. Only 5.8% of individuals (41 of 708) had a previously known genetic diagnosis. Results disclosure was completed for 141 individuals. Positive participant responses included poignant reactions to learning a medical reason for lifelong cognitive and psychiatric disabilities.

CONCLUSIONS AND RELEVANCE

This study informs critical factors central to the development of population-based genomic screening programs and supports the inclusion of NPD in future designs to promote equitable access to clinically useful genomic information.

How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean Tolpis succulenta (Asteraceae)

Genome-wide genotyping and Bayesian inference method (BORICE) were employed to estimate outcrossing rates and paternity in two small plant populations of Tolpis succulenta (Asteraceae) on Graciosa island in the Azores. These two known extant populations of T. succulenta on Graciosa have recently evolved self-compatibility. Despite the expectation that selfing would occur at an appreciable rate (self-incompatible populations of the same species show low but nonzero selfing), high outcrossing was found in progeny arrays from maternal plants in both populations. This is inconsistent with an immediate transition to high selfing following the breakdown of a genetic incompatibility system. This finding is surprising given the small population sizes and the recent colonization of an island from self-incompatible colonists of T. succulenta from another island in the Azores, and a potential paucity of pollinators, all factors selecting for selfing through reproductive assurance. The self-compatible lineage(s) likely have high inbreeding depression (ID) that effectively halts the evolution of increased selfing, but this remains to be determined. Like their progeny, all maternal plants in both populations are fully outbred, which is consistent with but not proof of high ID. High multiple paternity was found in both populations, which may be due in part to the abundant pollinators observed during the flowering season.

Using common genetic variation to examine phenotypic expression and risk prediction in 22q11.2 deletion syndrome

The 22q11.2 deletion syndrome (22q11DS) is associated with a 20-25% risk of schizophrenia. In a cohort of 962 individuals with 22q11DS, we examined the shared genetic basis between schizophrenia and schizophrenia-related early trajectory phenotypes: sub-threshold symptoms of psychosis, low baseline intellectual functioning and cognitive decline. We studied the association of these phenotypes with two polygenic scores, derived for schizophrenia and intelligence, and evaluated their use for individual risk prediction in 22q11DS. Polygenic scores were not only associated with schizophrenia and baseline intelligence quotient (IQ), respectively, but schizophrenia polygenic score was also significantly associated with cognitive (verbal IQ) decline and nominally associated with sub-threshold psychosis. Furthermore, in comparing the tail-end deciles of the schizophrenia and IQ polygenic score distributions, 33% versus 9% of individuals with 22q11DS had schizophrenia, and 63% versus 24% of individuals had intellectual disability. Collectively, these data show a shared genetic basis for schizophrenia and schizophrenia-related phenotypes and also highlight the future potential of polygenic scores for risk stratification among individuals with highly, but incompletely, penetrant genetic variants.

Advanced in developmental organic and inorganic nanomaterial: a review

With the unique properties such as high surface area to volume ratio, stability, inertness, ease of functionalization, as well as novel optical, electrical, and magnetic behaviors, nanomaterials have a wide range of applications in various fields with the common types including nanotubes, dendrimers, quantum dots, and fullerenes. With the aim of providing useful insights to help future development of efficient and commercially viable technology for large-scale production, this review focused on the science and applications of inorganic and organic nanomaterials, emphasizing on their synthesis, processing, characterization, and applications on different fields. The applications of nanomaterials on imaging, cell and gene delivery, biosensor, cancer treatment, therapy, and others were discussed in depth. Last but not least, the future prospects and challenges in nanoscience and nanotechnology were also explored.

BDE-47 exposure modulates cellular responses, oxidative stress and biotransformation related-genes in Mytilus galloprovincialis

Polybrominated diphenyl ethers (PBDEs) are flame retardants, characterized by elevated stability in the marine environment, where are accumulated by organisms, inducing a wide panel of negative effects. In this study, some biochemical patterns related to toxicity, biotransformation and oxidative stress, were studied in the marine model system, Mytilus galloprovincialis, exposed to BDE-47. Mussels were fed with microalgae, previously treated with increasing concentrations of PBDEs (maximum dose 100 ng L-1 of BDE-47 per day). After 15 days of treatment, mussels were fed with the same diet without BDE-47, for additional 15 days. Gills and digestive glands were analyzed at T 0, at 15 and 30 days. Histopathological lesions were assessed in digestive glands of contaminated mussels, while expression of genes, related to cell cycle, multidrug resistance, oxidative stress and detoxification was evaluated on both gills and digestive glands. After 15 days, BDE-47 exposure significantly affected the cell activity in digestive gland and, at 30 days, only mussels exposed to the lower doses showed a certain recovery. Regarding the gene expression, both gills and digestive glands showed a significant down-regulation of the target genes at 15 days, although most of them were up-regulated at 30 days in digestive gland. The results on BDE-47 accumulation in mussels revealed a dose-dependent concentration in tissues, which remained elevated after further 15 days of depuration. This trend supports the responses of the biomarkers, indicating that exposure, at environmentally realistic concentrations of BDE-47, strongly modulates oxidative stress and related patterns of gene expression, suggesting concerns for long-term effect in the biota.

Cystic fibrosis microbiome: analysis of nasal middle meatus and sputum in different lung disease stages

BACKGROUND: Culture independent methods of molecular detection of microbiome have shown the polymicrobial nature of respiratory infections in cystic fibrosis, with pathogenic agents undetectable in conventional culture methods. Composition and diversity of the airway microbiome are still poorly understood. METHODOLOGY: This study evaluated the airway microbiome in 31 adult cystic fibrosis patients via the analysis of 16S rRNA se- quences by next generation sequencing. RESULTS: Staphylococcus, Streptococcus and Corynebacterium were the most abundant genera in the middle meatus, and Pseudo- monas, Haemophilus and Prevotella were the most abundant in sputum. In patients with advanced disease (FEV1< 50%), there was an increase in the prevalence of Pseudomonas in both sample types when studied separately. In each patient, in a paired analysis, the sputum and middle meatus showed similar microbiome composition in mild or moderate disease (FEV1≥ 50%). In patients with severe lung disease, the relative abundance of Pseudomonas had a positive correlation in both collection sites. CONCLUSIONS: This is the first Brazilian study to evaluate the airway microbiome in cystic fibrosis patients. Our findings agree with those in the international literature and indicate the role of Pseudomonas in the sputum and middle meatus in patients with advanced disease.

Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness

Influenza viruses have an error-prone polymerase complex that facilitates a mutagenic environment. Antigenic mutants swiftly arise from this environment with the capacity to persist in both humans and economically important livestock even in the face of vaccination. Furthermore, influenza viruses can adjust the antigenicity of the haemagglutinin (HA) protein, the primary influenza immunogen, using one of four molecular mechanisms. Two prominent mechanisms are: (1) enhancing binding avidity of HA toward cellular receptors to outcompete antibody binding and (2) amino acid substitutions that introduce an N-linked glycan on HA that sterically block antibody binding. In this study we investigate the impact that adsorptive mutation and N-linked glycosylation have on receptor-binding, viral fitness, and antigenicity. We utilize the H9N2 A/chicken/Pakistan/SKP-827/16 virus which naturally contains HA residue T180 that we have previously shown to be an adsorptive mutant relative to virus with T180A. We find that the addition of N-linked glycans can be beneficial or deleterious to virus replication depending on the background receptor binding avidity. We also find that in some cases, an N-linked glycan can trump the effect of an avidity enhancing substitution with respect to antigenicity. Taken together these data shed light on a potential route to the generation of a virus which is "fit" and able to overcome vaccine pressure.

Downregulation of miR-4755-5p promotes fluoride-induced osteoblast activation via tageting Cyclin D1

BACKGROUND

Endemic fluorosis remains a major public health issue in many countries. Fluoride can cause abnormalities in osteoblast proliferation and activation, leading to skeletal fluorosis. However, its detailed molecular mechanism remains unclear. Based on a previous study, the aim of this study is to explore the role of miRNA in osteoblast activation of skeletal fluorosis via targeting of Cyclin D1.

METHODS

A population study of coal-burning fluorosis and in vitro experiments were performed in this study. Urine fluoride (UF) concentrations of the participants were determined using a national standardized ion selective electrode approach. Based on our previous miRNA sequence results, bioinformatic analysis was used to predict miR-4755-5p targeting Cyclin D1. Quantitative real-time PCR (qRT-PCR) was used to verify the expression of miR-4755-5p. The expression of Cyclin D1 mRNA was detected by qRT-PCR. The expression of Cyclin D1 protein was detected by enzyme-linked immunosorbent assay (ELISA) and Western blotting, respectively. Cell viability was detected by CCK-8 method. The distribution of the cell cycle was analyzed by flow cytometry. The alkaline phosphatase (ALP) activity and bone Gla protein (BGP) content were detected by micronutrient enzymes standard method and ELISA. The target binding between miR-4755-5p and Cyclin D1 was verified using dual-luciferase reporter assay.

RESULTS

In the fluoride-exposed population, the results showed that with the increase in UF content, the expression of miR-4755-5p decreased gradually, while the mRNA transcription and protein expression of Cyclin D1 increased gradually. The relative miR-4755-5p expression showed a negative correlation with Cyclin D1 expression. Subsequently, in human osteoblasts treated with sodium fluoride (NaF), the results also showed that NaF caused low expression of miR-4755-5p and increased expression of Cyclin D1. Further, the results of miR-4755-5p mimic transfection confirmed that under the action of NaF, miR-4755-5p overexpression reduced Cyclin D1 protein expression within osteoblasts and further inhibited cell proliferation and activation. Simultaneously, luciferase reporter assays verified that Cyclin D1 was the miR-4755-5p direct target.

CONCLUSION

The results demonstrate that fluoride exposure induced the downregulation of miR-4755-5p and downregulated miR-4755-5p promoted fluoride-induced osteoblast activation by increasing Cyclin D1 protein expression. This study sheds new light on biomarkers and potential treatment for endemic fluorosis.

Systematic characterization and prediction of coenzyme A-associated proteins using sequence and network information

Coenzyme A-associated proteins (CAPs) are a category of functionally important proteins involved in multiple biological processes through interactions with coenzyme A (CoA). To date, unfortunately, the specific differences between CAPs and other proteins have yet to be systemically investigated. Moreover, there are no computational methods that can be used specifically to predict these proteins. Herein, we characterized CAPs from multifaceted viewpoints and revealed their specific preferences. Compared with other proteins, CAPs were more likely to possess binding regions for CoA and its derivatives, were evolutionarily highly conserved, exhibited ordered and hydrophobic structural conformations, and tended to be densely located in protein-protein interaction networks. Based on these biological insights, we built seven classifiers using predicted CoA-binding residue distributions, word embedding vectors, remote homolog numbers, evolutionary conservation, amino acid composition, predicted structural features and network properties. These classifiers could effectively identify CAPs in Homo sapiens, Mus musculus and Arabidopsis thaliana. The complementarity among the individual classifiers prompted us to build a two-layer stacking model named CAPE for improving prediction performance. We applied CAPE to identify some high-confidence candidates in the three species, which were tightly associated with the known functions of CAPs. Finally, we extended our algorithm to cross-species prediction, thereby developing a generic CAP prediction model. In summary, this work provides a comprehensive survey and an effective predictor for CAPs, which can help uncover the interplay between CoA and functionally relevant proteins.

ENPP4 overexpression is associated with no recovery from Barrett's esophagus

Early diagnosis and treatment of precancerous conditions of the esophagus is important to improve overall survival. Barrett's esophagus is the most common precancerous condition of the esophagus, and patients with Barrett's esophagus may develop tumor, maintain a precancerous condition, or recover. We analyzed miRNA and mRNA expression profiles from esophageal adenocarcinoma tissue and normal esophageal tissue in GEO database. We identified DEGs and DE_miRNAs from GEO2R online tools and used Venn software were used to detect the common DEGs and DE_miRNAs. We used Enrichr, an online bioinformatic tool, to perform the gene ontology (GO) analysis including BP, MF, and CC. We analyzed Mirdb.tsv, mirtarbase.tsv, and targetscan.tsv files and identified miRNA targeting genes. We analysed the data of RNA sequencing expression retrieved from the GEPIA website on the basis of thousands of samples from the GTEx projects and TCGA. There were three miRNA (has-mir-205, has-mir-203, has-mir-18) and one DEG (ENPP4) that were associated with the recovery from Barrett's esophagus. ENPP4 promotes coagulation, hemostasis, wound healing, and participates in neutrophil degranulation, neutrophil immune activation and its mediated immunity, contributes to the composition of some membrane particles and tertiary particles, and is related to nucleotide diphosphatase activity. ENPP4 overexpression was not conducive to Barrett's esophagus recovery.

TWAS pathway method greatly enhances the number of leads for uncovering the molecular underpinnings of psychiatric disorders

Genetic signal detection in genome-wide association studies (GWAS) is enhanced by pooling small signals from multiple Single Nucleotide Polymorphism (SNP), for example, across genes and pathways. Because genes are believed to influence traits via gene expression, it is of interest to combine information from expression Quantitative Trait Loci (eQTLs) in a gene or genes in the same pathway. Such methods, widely referred to as transcriptomic wide association studies (TWAS), already exist for gene analysis. Due to the possibility of eliminating most of the confounding effects of linkage disequilibrium (LD) from TWAS gene statistics, pathway TWAS methods would be very useful in uncovering the true molecular basis of psychiatric disorders. However, such methods are not yet available for arbitrarily large pathways/gene sets. This is possibly due to the quadratic (as a function of the number of SNPs) computational burden for computing LD across large chromosomal regions. To overcome this obstacle, we propose JEPEGMIX2-P, a novel TWAS pathway method that (a) has a linear computational burden, (b) uses a large and diverse reference panel (33 K subjects), (c) is competitive (adjusts for background enrichment in gene TWAS statistics), and (d) is applicable as-is to ethnically mixed-cohorts. To underline its potential for increasing the power to uncover genetic signals over the commonly used nontranscriptomics methods, for example, MAGMA, we applied JEPEGMIX2-P to summary statistics of most large meta-analyses from Psychiatric Genetics Consortium (PGC). While our work is just the very first step toward clinical translation of psychiatric disorders, PGC anorexia results suggest a possible avenue for treatment.

Eukaryote-conserved histone post-translational modification landscape in Giardia duodenalis revealed by mass spectrometry

Diarrheal disease caused by Giardia duodenalis is highly prevalent, causing over 200 million cases globally each year. The processes that drive parasite virulence, host immune evasion and transmission involve coordinated gene expression and have been linked to epigenetic regulation. Epigenetic regulatory systems are eukaryote-conserved, including in deep branching excavates such as Giardia, with several studies already implicating histone post-translational modifications in regulation of its pathogenesis and life cycle. However, further insights into Giardia chromatin dynamics have been hindered by a lack of site-specific knowledge of histone modifications. Using mass spectrometry, we have provided the first known molecular map of histone methylation, acetylation and phosphorylation modifications in Giardia core histones. We have identified over 50 previously unreported histone modifications including sites with established roles in epigenetic regulation, and co-occurring modifications indicative of post-translational modification crosstalk. These demonstrate conserved histone modifications in Giardia which are equivalent to many other eukaryotes, and suggest that similar epigenetic mechanisms are in place in this parasite. Further, we used sequence, domain and structural homology to annotate putative histone enzyme networks in Giardia, highlighting representative chromatin modifiers which appear sufficient for identified sites, particularly those from H3 and H4 variants. This study is to our knowledge the first and most comprehensive, complete and accurate view of Giardia histone post-translational modifications to date, and a substantial step towards understanding their associations in parasite development and virulence.

Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley

Meiotic recombination rates vary considerably between species, populations and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in the case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and utilize variation in meiotic recombination rates. We investigated recombination rate variation in a large intraspecific hybrid population (named HEB-25) derived from a cross between domesticated barley and 25 wild barley accessions. We observed quantitative variation in total crossover number with a maximum of a 1.4-fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis-specific α-kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome-wide recombination rate variation shapes patterns of introgression. The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis, resulting in reduced crossover suppression across pericentromeric regions. Local and genome-wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag.

Nanoparticles-assisted delivery of antiviral-siRNA as inhalable treatment for human respiratory viruses: A candidate approach against SARS-COV-2

The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has challenged healthcare structures across the globe. Although a few therapies are approved by FDA, the search for better treatment options is continuously on rise. Clinical management includes infection prevention and supportive care such as supplemental oxygen and mechanical ventilatory support. Given the urgent nature of the pandemic and the number of companies and researchers developing COVID-19 related therapies, FDA has created an emergency program to move potential treatments with already approved drugs to patients as quickly as possible in parallel to the development of new drugs that must first pass the clinical trials. In this manuscript, we have reviewed the available literature on the use of sequence-specific degradation of viral genome using short-interfering RNA (siRNA) suggesting it as a possible treatment against SARS-CoV-2. Delivery of siRNA can be promoted by the use of FDA approved lipids, polymers or lipid-polymer hybrids. These nanoparticulate systems can be engineered to exhibit increased targetability and formulated as inhalable aerosols.

An aberrant DNA methylation signature for predicting hepatocellular carcinoma

Background

By the time they are clinically diagnosed, patients with hepatocellular carcinoma (HCC) are often at the advanced stage. DNA methylation has become a useful predictor of prognosis for cancer patients. Research on DNA methylation as a biomarker for assessing the risk of occurrence in HCC patients is limited. The purpose of this study was to develop an efficient methylation site model for predicting survival in patients with HCC.

Methods

DNA methylation and gene expression profile data were extracted from The Cancer Genome Atlas (TCGA) database. Markers of DNA-methylated site in two subsets (the training subset and the test subset) were identified using a random survival forest algorithm and Cox proportional hazards regression. Then, Gene Ontology annotations were applied to investigate the functions of DNA methylation signatures.

Results

A total of 37 hub genes containing 713 methylated sites were identified among the differentially methylated genes (DMGs) and differentially expressed genes (DEGs). Finally, seven methylation sites (cg12824782, cg24871714, cg18683774, cg22796509, cg19450025, cg10474350, and cg06511917) were identified. In the training group and the test group, the area under the curve predicting the survival of patients with HCC was 0.750 and 0.742, respectively. The seven methylation sites signature could be used to divide the patients in the training group into high- and low-risk subgroups [overall survival (OS): 2.81 vs. 2.11 years; log-rank test, P<0.05]. Then, the prediction ability of the model was validated in the test dataset through risk stratification (OS: 2.04 vs. 2.88 years; log-rank test, P<0.05). Functional analysis demonstrated that these signature genes were related to the activity of DNA-binding transcription activator, RNA polymerase II distal enhancer sequence-specific DNA binding, and enhancer sequence-specific DNA binding.

Conclusions

The results of this study showed that the signature is useful for predicting the survival of HCC patients and thus, can facilitate treatment-related decision-making.

Photoperiod-induced changes in hypothalamic de novo DNA methyltransferase expression are independent of triiodothyronine in female Siberian hamsters (Phodopus sungorus)

Many temperate zone animals engage in seasonal reproductive physiology and behavior as a strategy to maximise the propagation of the species. The hypothalamus integrates environmental cues and hormonal signalling to optimize the timing of reproduction. Recent work has revealed that epigenetic modifications, such as DNA methylation, vary across seasonal reproductive states. Multiple hormones act in the hypothalamus to permit or inhibit reproductive physiology, and the increase in thyroid hormone triiodothyronine (T₃) has been implicated in the initiation of breeding in many species. The objective of this study was to examine the effect of T₃ on the photoperiod-dependent regulation of reproductive physiology and hypothalamic DNA methyltransferase enzyme expression in female Siberian hamsters (Phodopus sungorus). We tested the hypothesis that T₃ in short days (SD) would stimulate hypothalamic Rfrp3 and de novo DNA methyltransferase (Dnmt) expression in female Siberian hamsters. 10 weeks of SD lengths induced a decrease in body and uterine mass. Hamsters maintained in SD were found to express lower levels of GnRH, Rfrp3, Dnmt3a and Dnmt3b. Two weeks of daily T₃ injections did not affect body mass, uterine mass, Gnrh, Rfrp3, Dnmt3a or Dnmt3b expression in neuroendocrine tissues. SD significantly lowered Tshβ mRNA expression and T3 reduced Tshβ in LD hamsters. Our data indicate sex-dependent effects of T₃ for the neuroendocrine regulation of seasonal reproduction in hamsters.

Haldane's rule in the placenta: Sex-biased misregulation of the Kcnq1 imprinting cluster in hybrid mice

Hybrid phenotypes that contribute to postzygotic reproductive isolation often exhibit pronounced asymmetry, both between reciprocal crosses and between the sexes in accordance with Haldane's rule. Inviability in mammalian hybrids is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted gene (IGs) is the leading candidate mechanism. However, direct evidence for the involvement of IGs in hybrid growth dysplasia is limited. We used transcriptome and reduced representation bisulfite sequencing to conduct the first genome-scale assessment of the contribution of IGs to parent-of-origin placental growth dysplasia in the cross between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus). IGs with transgressive expression and methylation were concentrated in the Kcnq1 cluster, which contains causal genes for prenatal growth abnormalities in mice and humans. Hypermethylation of the cluster's imprinting control region, and consequent misexpression of the genes Phlda2 and Ascl2, is a strong candidate mechanism for transgressive placental undergrowth. Transgressive placental and gene regulatory phenotypes, including expression and methylation in the Kcnq1 cluster, were more extreme in hybrid males. Although consistent with Haldane's rule, male-biased defects are unexpected in rodent placenta because the X-chromosome is effectively hemizygous in both sexes. In search of an explanation, we found evidence of leaky imprinted (paternal) X-chromosome inactivation in hybrid female placenta, an epigenetic disturbance that may buffer females from the effects of X-linked incompatibilities to which males are fully exposed. Sex differences in chromatin structure on the X and sex-biased maternal effects are nonmutually exclusive alternative explanations for adherence to Haldane's rule in hybrid placenta. The results of this study contribute to understanding the genetic basis of hybrid inviability in mammals, and the role of IGs in speciation.

Interpretation of Maturity-Onset Diabetes of the Young Genetic Variants Based on American College of Medical Genetics and Genomics Criteria: Machine-Learning Model Development

Background

Maturity-onset diabetes of the young (MODY) is a group of dominantly inherited monogenic diabetes, with HNF4A-MODY, GCK-MODY, and HNF1A-MODY as the three most common forms based on the causal genes. Molecular diagnosis of MODY is important for precise treatment. Although a DNA variant causing MODY can be assessed based on the criteria of the American College of Medical Genetics and Genomics (ACMG) guidelines, gene-specific assessment of disease-causing mutations is important to differentiate among MODY subtypes. As the ACMG criteria were not originally designed for machine-learning algorithms, they are not true independent variables.

Objective

The aim of this study was to develop machine-learning models for interpretation of DNA variants and MODY diagnosis using the ACMG criteria.

Methods

We applied machine-learning models for interpretation of DNA variants in MODY genes defined by the ACMG criteria based on the Human Gene Mutation Database (HGMD) and ClinVar database.

Results

With a machine-learning procedure, we found that the weight matrix of the ACMG criteria was significantly different between the three MODY genes HNF1A, HNF4A, and GCK. The models showed high predictive abilities with accuracy over 95%.

Conclusions

Our results highlight the need for applying different weights of the ACMG criteria in relation to different MODY genes for accurate functional classification. As proof of principle, we applied the ACMG criteria as feature vectors in a machine-learning model and obtained a precision-based result.

Long noncoding RNA HAND2-AS1 reduced the viability of hepatocellular carcinoma via targeting microRNA-300/SOCS5 axis

BACKGROUND

Hepatocellular carcinoma (HCC) is one of the most prevalent human cancers with high mortality. Long non-coding RNA heart and neural crest derivatives expressed 2 anti-sense 1 (HAND2-AS1) is down-regulated in several cancers including HCC, yet the precise mechanisms how HAND2-AS1 regulates cell survival in HCC remains poorly understood.

METHODS

The expression levels of HAND2-AS1 and miR-300 were measured using quantitative real-time PCR. The protein levels of suppressor of cytokine signaling 5 (SOCS5), Bcl-2, Bax and cleaved caspase-3 were determined by Western blot. Cell viability and cell proliferation were assessed using cell counting kit-8 and clone formation assay, respectively. Cell apoptosis was detected using flow cytometry. The interactions between HAND2-AS1 and miR-300, miR-300 and SOCS5 were validated using luciferase reporter assay.

RESULTS

HAND2-AS1 was down-regulated in HCC tissues and cell lines, and the expression level of HAND2-AS1 was positively correlated to patient survival. HAND2-AS1 over-expression reduced viability and proliferation in HCC cells. Elevated HAND2-AS1 level induced apoptosis in HCC cells, accompanied with increased Bax and cleaved caspase-3 levels and decreased Bcl-2 level. We also validated that HAND2-AS1 acted as a sponge of miR-300, and there was a negative correlation between expression levels of HAND2-AS1 and miR-300 in HCC tissues. Furthermore, we found that SOCS5 was a downstream target of miR-300. In addition, miR-300 mimics abolished HAND2-AS1-mediated inhibition of cell viability and proliferation. miR-300 mimics also reversed the HAND2-AS1-induced apoptosis in HCC cells.

CONCLUSION

lncRNA HAND2-AS1 inhibits proliferation in HCC through regulating miR-300/SOCS5 axis.

Deep Profiling Identifies Selection of Nonsynonymous Amino Acid Substitutions in HIV-1 Envelope During Early Infection

Understanding the evolutionary dynamics of the viruses within an individual at or near the moment of transmission can provide critical inputs for the design of an effective vaccine for HIV infection. In this study, high-throughput sequencing technology was employed to analyze the evolutionary rate in viruses obtained at a single time point from drug-naive recently infected infants and adults in the chronic stage of disease. Gene-wise nonsynonymous (pN) and synonymous (pS) mutation rates were estimated and compared between the two groups. Significant differences were observed in the evolutionary rates between viruses in the early and late stages of infection. Higher rates of adaptive mutations in the HIV-1 envelope gene (env) were found in the chronic viruses as compared with those in the early stages of HIV infection. Conversely, percentage of nonsynonymous substitutions in env was found to be higher in recently transmitted viruses. In addition, a positive correlation was found between mutation and the evolutionary rate, and infectivity titer in recent infection. Despite the small sample size, the study identified useful information about viral evolution on transmission-associated bottlenecks. The effect of intraindividual HIV-1 evolution at the population level was highly contemporary, and the higher percentage of nonsynonymous substitutions seen in env during recent HIV-1 infection has suggested a pattern of convergent evolution leading to a positive selection for survival fitness and disease progression.

RNA sequencing analyses reveal differentially expressed genes and pathways as Notch2 targets in B-cell lymphoma

Splenic marginal zone lymphoma (SMZL) is a low grade, indolent B-cell neoplasm that comprises approximately 10% of all lymphoma. Notch2, a pivotal gene for marginal zone differentiation is found to be mutated in SMZL. Deregulated Notch2 signaling has been involved in tumorigenesis and also in B-cell malignancies. However the role of Notch2 and the downstream pathways that it influences for development of B-cell lymphoma remains unclear. In recent years, RNA sequencing (RNA-Seq) has become a functional and convincing technology for profiling gene expression and to discover new genes and transcripts that are involved in disease development in a single experiment. In the present study, using transcriptome sequencing approach, we have identified key genes and pathways that are probably the underlying cause in the development of B-cell lymphoma. We have identified a total of 15,083 differentially expressed genes (DEGs) and 1067 differentially expressed transcripts (DETs) between control and Notch2 knockdown B cells. Gene Ontology (GO) term enrichment and pathway analysis were applied for the identification of key genes and pathways involved in development of B-cell lymphoma. In addition, intermediate genes of top canonical pathways such as PI3K/AKT and NF-kB were found to be downregulated with Notch2 knockdown, indicating that these pathways could be the putative downstream effectors through which Notch2 mediates its oncogenic effects. Taken collectively, the identified crop of genes and pathways may be considered as targets for the treatment of B-cell lymphoma.

A Multi-Model Pipeline for Translational Intracerebral Haemorrhage Research

Apart from acute and chronic blood pressure lowering, we have no specific medications to prevent intracerebral haemorrhage (ICH) or improve outcomes once bleeding has occurred. One reason for this may be related to particular limitations associated with the current pre-clinical models of ICH, leading to a failure to translate into the clinic. It would seem that a breakdown in the 'drug development pipeline' currently exists for translational ICH research which needs to be urgently addressed. Here, we review the most commonly used pre-clinical models of ICH and discuss their advantages and disadvantages in the context of translational studies. We propose that to increase our chances of successfully identifying new therapeutics for ICH, a bi-directional, 2- or 3-pronged approach using more than one model species/system could be useful for confirming key pre-clinical observations. Furthermore, we highlight that post-mortem/ex-vivo ICH patient material is a precious and underused resource which could play an essential role in the verification of experimental results prior to consideration for further clinical investigation. Embracing multidisciplinary collaboration between pre-clinical and clinical ICH research groups will be essential to ensure the success of this type of approach in the future.

RegulomePA: a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1

We present RegulomePA, a database that contains biological information on regulatory interactions between transcription factors (TFs), sigma factor (SFs) and target genes in Pseudomonas aeruginosa PAO1. RegulomePA consists of 4827 regulatory interactions between 2831 nodes, which represent the interactions of TFs and SFs with their target genes, from the total of predicted RegulomePA including 27.27% of the TFs, 54.16% of SFs and 50.8% of the total genes. Each entry in the database corresponds to one node in the network and provides comprehensive details about the gene and its regulatory interactions such as gene description, nucleotide sequence, genome-strand position and links to other databases as well as the type of regulation it exerts or to which it is being subject (repression or activation), the associated experimental evidence and references, and topological information. Additionally, RegulomePA provides a way to recover information on the regulatory circuits of the network to which a gene pertains and also makes available the source codes to analyze the topology of any other regulatory network. The database will be updated yearly, by our team, with the contributions from ourselves and users, since the users are provided with an interactive platform where they can add interactions to the regulatory network feeding it with their respective references. Database URL: www.regulome.pcyt.unam.mx.