Prevalence of iron deficiency and anemia in pediatric heart transplant recipients.

INTRODUCTION: The prevalence of iron deficiency and anemia in the setting of modern-day maintenance immunosuppression in pediatric heart transplant (HTx) recipients is unclear. The primary aim was to determine the prevalence of iron deficiency (serum ferritin < 30 ng/mL ± transferrin saturation < 20%) and anemia per World Health Organization diagnostic criteria and associated risk factors. METHODS: Single-center, cross-sectional analysis of 200 consecutive pediatric HTx recipients (<21 years old) from 2005 to 2021. Data were collected at 1-year post-HTx at the time of annual protocol biopsy. RESULTS: Median age at transplant was 3 years (IQR .5-12.2). The median ferritin level was 32 ng/mL with 46% having ferritin < 30 ng/mL. Median transferrin saturation (TSAT) was 22% with 47% having TSAT < 20%. Median hemoglobin was 11 g/dL with 54% having anemia. Multivariable analysis revealed lower absolute lymphocyte count, TSAT < 20%, and estimated glomerular filtration rate <75 mL/min/1.73 m2 were independently associated with anemia. Ferritin < 30 ng/mL in isolation was not associated with anemia. Ferritin < 30 ng/mL may aid in detecting absolute iron deficiency while TSAT < 20% may be useful in identifying patients with functional iron deficiency ± anemia in pediatric HTx recipients. CONCLUSION: Iron deficiency and anemia are highly prevalent in pediatric HTx recipients. Future studies are needed to assess the impact of iron deficiency, whether with or without anemia, on clinical outcomes in pediatric HTx recipients.

In Vitro and In Vivo Drug-Response Profiling Using Patient-Derived High-Grade Glioma.

BACKGROUND: Genomic profiling cannot solely predict the complexity of how tumor cells behave in their in vivo microenvironment and their susceptibility to therapies. The aim of the study was to establish a functional drug prediction model utilizing patient-derived GBM tumor samples for in vitro testing of drug efficacy followed by in vivo validation to overcome the disadvantages of a strict pharmacogenomics approach. METHODS: High-throughput in vitro pharmacologic testing of patient-derived GBM tumors cultured as 3D organoids offered a cost-effective, clinically and phenotypically relevant model, inclusive of tumor plasticity and stroma. RNAseq analysis supplemented this 128-compound screening to predict more efficacious and patient-specific drug combinations with additional tumor stemness evaluated using flow cytometry. In vivo PDX mouse models rapidly validated (50 days) and determined mutational influence alongside of drug efficacy. We present a representative GBM case of three tumors resected at initial presentation, at first recurrence without any treatment, and at a second recurrence following radiation and chemotherapy, all from the same patient. RESULTS: Molecular and in vitro screening helped identify effective drug targets against several pathways as well as synergistic drug combinations of cobimetinib and vemurafenib for this patient, supported in part by in vivo tumor growth assessment. Each tumor iteration showed significantly varying stemness and drug resistance. CONCLUSIONS: Our integrative model utilizing molecular, in vitro, and in vivo approaches provides direct evidence of a patient's tumor response drifting with treatment and time, as demonstrated by dynamic changes in their tumor profile, which may affect how one would address that drift pharmacologically.

A new member of the flavodoxin superfamily from Fusobacterium nucleatum that functions in heme trafficking and reduction of anaerobilin.

Fusobacterium nucleatum is an opportunistic oral pathogen that is associated with various cancers. To fulfill its essential need for iron, this anaerobe will express heme uptake machinery encoded at a single genetic locus. The heme uptake operon includes HmuW, a class C radical SAM-dependent methyltransferase that degrades heme anaerobically to release Fe2+ and a linear tetrapyrrole called anaerobilin. The last gene in the operon, hmuF encodes a member of the flavodoxin superfamily of proteins. We discovered that HmuF and a paralog, FldH, bind tightly to both FMN and heme. The structure of Fe3+-heme-bound FldH (1.6 Å resolution) reveals a helical cap domain appended to the ⍺/ß core of the flavodoxin fold. The cap creates a hydrophobic binding cleft that positions the heme planar to the si-face of the FMN isoalloxazine ring. The ferric heme iron is hexacoordinated to His134 and a solvent molecule. In contrast to flavodoxins, FldH and HmuF do not stabilize the FMN semiquinone but instead cycle between the FMN oxidized and hydroquinone states. We show that heme-loaded HmuF and heme-loaded FldH traffic heme to HmuW for degradation of the protoporphyrin ring. Both FldH and HmuF then catalyze multiple reductions of anaerobilin through hydride transfer from the FMN hydroquinone. The latter activity eliminates the aromaticity of anaerobilin and the electrophilic methylene group that was installed through HmuW turnover. Hence, HmuF provides a protected path for anaerobic heme catabolism, offering F. nucleatum a competitive advantage in the colonization of anoxic sites of the human body.

Differential regulation of lymphatic junctional morphology and the potential effects on cardiovascular diseases.

The lymphatic vasculature provides an essential route to drain fluid, macromolecules, and immune cells from the interstitium as lymph, returning it to the bloodstream where the thoracic duct meets the subclavian vein. To ensure functional lymphatic drainage, the lymphatic system contains a complex network of vessels which has differential regulation of unique cell-cell junctions. The lymphatic endothelial cells lining initial lymphatic vessels form permeable "button-like" junctions which allow substances to enter the vessel. Collecting lymphatic vessels form less permeable "zipper-like" junctions which retain lymph within the vessel and prevent leakage. Therefore, sections of the lymphatic bed are differentially permeable, regulated in part by its junctional morphology. In this review, we will discuss our current understanding of regulating lymphatic junctional morphology, highlighting how it relates to lymphatic permeability during development and disease. We will also discuss the effect of alterations in lymphatic permeability on efficient lymphatic flux in health and how it may affect cardiovascular diseases, with a focus on atherosclerosis.

Biphasic cell cycle defect causes impaired neurogenesis in down syndrome.

Impaired neurogenesis in Down syndrome (DS) is characterized by reduced neurons, increased glial cells, and delayed cortical lamination. However, the underlying cause for impaired neurogenesis in DS is not clear. Using both human and mouse iPSCs, we demonstrate that DS impaired neurogenesis is due to biphasic cell cycle dysregulation during the generation of neural progenitors from iPSCs named the "neurogenic stage" of neurogenesis. Upon neural induction, DS cells showed reduced proliferation during the early phase followed by increased proliferation in the late phase of the neurogenic stage compared to control cells. While reduced proliferation in the early phase causes reduced neural progenitor pool, increased proliferation in the late phase leads to delayed post mitotic neuron generation in DS. RNAseq analysis of late-phase DS progenitor cells revealed upregulation of S phase-promoting regulators, Notch, Wnt, Interferon pathways, and REST, and downregulation of several genes of the BAF chromatin remodeling complex. NFIB and POU3F4, neurogenic genes activated by the interaction of PAX6 and the BAF complex, were downregulated in DS cells. ChIPseq analysis of late-phase neural progenitors revealed aberrant PAX6 binding with reduced promoter occupancy in DS cells. Together, these data indicate that impaired neurogenesis in DS is due to biphasic cell cycle dysregulation during the neurogenic stage of neurogenesis.

Artificial Intelligence System for Automatic Quantitative Analysis and Radiology Reporting of Leg Length Radiographs.

Leg length discrepancies are common orthopedic problems with the potential for poor functional outcomes. These are frequently assessed using bilateral leg length radiographs. The objective was to determine whether an artificial intelligence (AI)-based image analysis system can accurately interpret long leg length radiographic images. We built an end-to-end system to analyze leg length radiographs and generate reports like radiologists, which involves measurement of lengths (femur, tibia, entire leg) and angles (mechanical axis and pelvic tilt), describes presence and location of orthopedic hardware, and reports laterality discrepancies. After IRB approval, a dataset of 1,726 extremities (863 images) from consecutive examinations at a tertiary referral center was retrospectively acquired and partitioned into train/validation and test sets. The training set was annotated and used to train a fasterRCNN-ResNet101 object detection convolutional neural network. A second-stage classifier using a EfficientNet-D0 model was trained to recognize the presence or absence of hardware within extracted joint image patches. The system was deployed in a custom web application that generated a preliminary radiology report. Performance of the system was evaluated using a holdout 220 image test set, annotated by 3 musculoskeletal fellowship trained radiologists. At the object detection level, the system demonstrated a recall of 0.98 and precision of 0.96 in detecting anatomic landmarks. Correlation coefficients between radiologist and AI-generated measurements for femur, tibia, and whole-leg lengths were > 0.99, with mean error of < 1%. Correlation coefficients for mechanical axis angle and pelvic tilt were 0.98 and 0.86, respectively, with mean absolute error of < 1°. AI hardware detection demonstrated an accuracy of 99.8%. Automatic quantitative and qualitative analysis of leg length radiographs using deep learning is feasible and holds potential in improving radiologist workflow.

Whole exome sequencing analysis in a couple with three children who died prematurely due to carnitine-acylcarnitine translocase deficiency.

OBJECTIVE: We investigated a strategy of exome sequencing DNA from the unaffected parents and applied a set of filtering criteria to identify genes where both partners are heterozygous for a potentially pathogenic variant. CASE REPORT: We report a non-consanguineous couple who had three daughters, all spontaneous preterm birth at 36 weeks gestation and died in the first period after birth, suspected inborn errors of metabolism. Two days after birth, the first daughter presented with difficulty breathing, cyanosis and died; the second died at 33 days old; the third daughter was isolated under special care and was taken to the mother's room, developed the same symptoms and died after 5 days. Dried blood spot testing screen of 55 congenital metabolic disorders was negative. CONCLUSION: Heterogenous variant in SLC25A20 gene was found in both parents, contributing to the delineations of the neonatal phenotypes related to SLC25A20 mutation in CACTD.

Modulations of Cardiac Functions and Pathogenesis by Reactive Oxygen Species and Natural Antioxidants.

Homeostasis in the level of reactive oxygen species (ROS) in cardiac myocytes plays a critical role in regulating their physiological functions. Disturbance of balance between generation and removal of ROS is a major cause of cardiac myocyte remodeling, dysfunction, and failure. Cardiac myocytes possess several ROS-producing pathways, such as mitochondrial electron transport chain, NADPH oxidases, and nitric oxide synthases, and have endogenous antioxidation mechanisms. Cardiac Ca2+-signaling toolkit proteins, as well as mitochondrial functions, are largely modulated by ROS under physiological and pathological conditions, thereby producing alterations in contraction, membrane conductivity, cell metabolism and cell growth and death. Mechanical stresses under hypertension, post-myocardial infarction, heart failure, and valve diseases are the main causes for stress-induced cardiac remodeling and functional failure, which are associated with ROS-induced pathogenesis. Experimental evidence demonstrates that many cardioprotective natural antioxidants, enriched in foods or herbs, exert beneficial effects on cardiac functions (Ca2+ signal, contractility and rhythm), myocytes remodeling, inflammation and death in pathological hearts. The review may provide knowledge and insight into the modulation of cardiac pathogenesis by ROS and natural antioxidants.

The CLK inhibitor SM08502 induces anti-tumor activity and reduces Wnt pathway gene expression in gastrointestinal cancer models.

The Wnt/ß-catenin signaling pathway is aberrantly activated in colorectal (CRC) and many other cancers, and novel strategies for effectively targeting it may be needed due to its complexity. In this report, SM08502, a novel small molecule in clinical development for the treatment of solid tumors, was shown to reduce Wnt pathway signaling and gene expression through potent inhibition of CDC-like kinase (CLK) activity. SM08502 inhibited serine and arginine rich splicing factor (SRSF) phosphorylation and disrupted spliceosome activity, which was associated with inhibition of Wnt pathway-related gene and protein expression. Additionally, SM08502 induced the generation of splicing variants of Wnt pathway genes, suggesting that its mechanism for inhibition of gene expression includes effects on alternative splicing. Orally administered SM08502 significantly inhibited growth of gastrointestinal tumors and decreased SRSF phosphorylation and Wnt pathway gene expression in xenograft mouse models. These data implicate CLKs in the regulation of Wnt signaling and represent a novel strategy for inhibiting Wnt pathway gene expression in cancers. SM08502 is a first-in-class CLK inhibitor being investigated in a Phase 1 clinical trial for subjects with advanced solid tumors (NCT03355066).

Neurotransmitter Switching Regulated by miRNAs Controls Changes in Social Preference.

Changes in social preference of amphibian larvae result from sustained exposure to kinship odorants. To understand the molecular and cellular mechanisms of this neuroplasticity, we investigated the effects of olfactory system activation on neurotransmitter (NT) expression in accessory olfactory bulb (AOB) interneurons during development. We show that protracted exposure to kin or non-kin odorants changes the number of dopamine (DA)- or gamma aminobutyric acid (GABA)-expressing neurons, with corresponding changes in attraction/aversion behavior. Changing the relative number of dopaminergic and GABAergic AOB interneurons or locally introducing DA or GABA receptor antagonists alters kinship preference. We then isolate AOB microRNAs (miRs) differentially regulated across these conditions. Inhibition of miR-375 and miR-200b reveals that they target Pax6 and Bcl11b to regulate the dopaminergic and GABAergic phenotypes. The results illuminate the role of NT switching governing experience-dependent social preference. VIDEO ABSTRACT.

An Anti-ß-Amyloid Vaccine for Treating Cognitive Deficits in a Mouse Model of Down Syndrome.

In Down syndrome (DS) or trisomy of chromosome 21, the ß-amyloid (Aß) peptide product of the amyloid precursor protein (APP) is present in excess. Evidence points to increased APP gene dose and Aß as playing a critical role in cognitive difficulties experienced by people with DS. Particularly, Aß is linked to the late-life emergence of dementia as associated with neuropathological markers of Alzheimer's disease (AD). At present, no treatment targets Aß-related pathogenesis in people with DS. Herein we used a vaccine containing the Aß 1-15 peptide embedded into liposomes together with the adjuvant monophosphoryl lipid A (MPLA). Ts65Dn mice, a model of DS, were immunized with the anti-Aß vaccine at 5 months of age and were examined for cognitive measures at 8 months of age. The status of basal forebrain cholinergic neurons and brain levels of APP and its proteolytic products were measured. Immunization of Ts65Dn mice resulted in robust anti-Aß IgG titers, demonstrating the ability of the vaccine to break self-tolerance. The vaccine-induced antibodies reacted with Aß without detectable binding to either APP or its C-terminal fragments. Vaccination of Ts65Dn mice resulted in a modest, but non-significant reduction in brain Aß levels relative to vehicle-treated Ts65Dn mice, resulting in similar levels of Aß as diploid (2N) mice. Importantly, vaccinated Ts65Dn mice showed resolution of memory deficits in the novel object recognition and contextual fear conditioning tests, as well as reduction of cholinergic neuron atrophy. No treatment adverse effects were observed; vaccine did not result in inflammation, cellular infiltration, or hemorrhage. These data are the first to show that an anti-Aß immunotherapeutic approach may act to target Aß-related pathology in a mouse model of DS.

Questioned validity of Gene Expression Dysregulated Domains in Down's Syndrome.

Recently, in studies examining fibroblasts obtained from the tissues of one set of monozygotic twins (i.e. fetuses derived from the same egg) discordant for trisomy 21 (Down syndrome; DS), Letourneau et al., ( )reported the presence of a defined pattern of dysregulation within specific genomic domains they referred to as Gene Expression Dysregulated Domains (GEDDs). GEDDs were described as alternating segments of increased or decreased gene expression affecting all chromosomes. Strikingly, GEDDs in fibroblasts were largely conserved in induced pluripotent cells (iPSCs) generated from the twin's fibroblasts as well as in fibroblasts from the Ts65Dn mouse model of DS. Our recent analysis failed to find GEDDs. We reexamined the human iPSCs RNAseq data from Letourneau et al., and data from this same research group published earlier examining iPSCs from the same monozygotic twins. An independent analysis of RNAseq data from Ts65Dn fibroblasts also failed to confirm presence of GEDDs. Our analysis questions the validity of GEDDs in DS.

Single Figure Publications: Towards a novel alternative format for scholarly communication.

The single figure publication is a novel, efficient format by which to communicate scholarly advances. It will serve as a forerunner of the nano-publication, a modular unit of information critical for machine-driven data aggregation and knowledge integration.

The Booly aliasing resource: a database of grouped biological identifiers.

UNLABELLED: Redundancy among sequence identifiers is a recurring problem in bioinformatics. Here, we present a rapid and efficient method of fingerprinting identifiers to ascertain whether two or more aliases are identical. A number of tools and approaches have been developed to resolve differing names for the same genes and proteins, however, these methods each have their own limitations associated with their various goals. We have taken a different approach to the aliasing problem by simplifying the way aliases are stored and curated with the objective of simultaneously achieving speed and flexibility. Our approach (Booly-hashing) is to link identifiers with their corresponding hash keys derived from unique fingerprints such as gene or protein sequences. This tool has proven invaluable for designing a new data integration platform known as Booly, and has wide applicability to situations in which a dedicated efficient aliasing system is required. Compared with other aliasing techniques, Booly-hashing methodology provides 1) reduced run time complexity, 2) increased flexibility (aliasing of other data types, e.g. pharmaceutical drugs), 3) no required assumptions regarding gene clusters or hierarchies, and 4) simplicity in data addition, updating, and maintenance. The new Booly-hashing aliasing model has been incorporated as a central component of the Booly data integration platform we have recently developed and shoud be broadly applicable to other situations in which an efficient streamlined aliasing systems is required. This aliasing tool and database, which allows users to quickly group the same genes and proteins together can be accessed at: http://booly.ucsd.edu/alias. AVAILABILITY: The database is available for free at http://booly.ucsd.edu/alias.

Booly: a new data integration platform.

BACKGROUND: Data integration is an escalating problem in bioinformatics. We have developed a web tool and warehousing system, Booly, that features a simple yet flexible data model coupled with the ability to perform powerful comparative analysis, including the use of Boolean logic to merge datasets together, and an integrated aliasing system to decipher differing names of the same gene or protein. Furthermore, Booly features a collaborative sharing system and a public repository so that users can retrieve new datasets while contributors can easily disseminate new content. RESULTS: We illustrate the uses of Booly with several examples including: the versatile creation of homebrew datasets, the integration of heterogeneous data to identify genes useful for comparing avian and mammalian brain architecture, and generation of a list of Food and Drug Administration (FDA) approved drugs with possible alternative disease targets. CONCLUSIONS: The Booly paradigm for data storage and analysis should facilitate integration between disparate biological and medical fields and result in novel discoveries that can then be validated experimentally. Booly can be accessed at http://booly.ucsd.edu.

Accentuate the negative: proteome comparisons using the negative proteome database.

The availability of complete genome sequence information for diverse organisms including model genetic organisms has ushered in a new era of protein sequence comparisons making it possible to search for commonalities among entire proteomes using the Basic Local Alignment Search Tool (BLAST). Although the identification and analysis of proteins shared by humans and model organisms has proven an invaluable tool to understanding gene function, the sets of proteins unique to a given model organism's proteome have remained largely unexplored. We have constructed a searchable database that allows biologists to identify proteins unique to a given proteome. The Negative Proteome Database (NPD) is populated with pair-wise protein sequence comparisons between each of the following proteomes: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Dictyostelium discoideum, Chlamydomonus reinhardti, Escherichia coli K12, Arabidopsis thaliana and Methanoscarcina acetivorans. Our analysis of negative proteome datasets using the NPD has thus far revealed 107 proteins in humans that may be involved in motile cilia function, 1628 potential pesticide target proteins in flies, 659 proteins shared by flies and humans that are not represented in the less neurologically complex worm proteome, and 180 nuclear encoded human disease associated proteins that are absent from the fly proteome. The NPD is the only online resource where users can quickly perform complex negative and positive comparisons of model organism proteomes. We anticipate that the NPD and the adaptable algorithm which can readily be used to duplicate this analysis on custom sets of proteomes will be an invaluable tool in the investigation of organism specific protein sets.

Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris.

Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustris encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. palustris as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.