Recent efforts have attempted to describe the population structure of common chimpanzee, focusing on four subspecies: Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii. However, few studies have pursued the effects of natural selection in shaping their response to pathogens and reproduction. Whey acidic protein (WAP) four-disulfide core domain (WFDC) genes and neighboring semenogelin (SEMG) genes encode proteins with combined roles in immunity and fertility. They display a strikingly high rate of amino acid replacement (dN/dS), indicative of adaptive pressures during primate evolution. In human populations, three signals of selection at the WFDC locus were described, possibly influencing the proteolytic profile and antimicrobial activities of the male reproductive tract. To evaluate the patterns of genomic variation and selection at the WFDC locus in chimpanzees, we sequenced 17 WFDC genes and 47 autosomal pseudogenes in 68 chimpanzees (15 P. t. troglodytes, 22 P. t. verus, and 31 P. t. ellioti). We found a clear differentiation of P. t. verus and estimated the divergence of P. t. troglodytes and P. t. ellioti subspecies in 0.173 Myr; further, at the WFDC locus we identified a signature of strong selective constraints common to the three subspecies in WFDC6—a recent paralog of the epididymal protease inhibitor EPPIN. Overall, chimpanzees and humans do not display similar footprints of selection across the WFDC locus, possibly due to different selective pressures between the two species related to immune response and reproductive biology.
WFDC; natural selection; chimpanzees; serine protease inhibitor; reproduction; innate immunity
The authors examined the frequency and onset of 10 bedside physical signs and their diagnostic performance for impending death. They identified highly specific physical signs associated with death within 3 days among cancer patients.
The physical signs of impending death have not been well characterized in cancer patients. A better understanding of these signs may improve the ability of clinicians to diagnose impending death. We examined the frequency and onset of 10 bedside physical signs and their diagnostic performance for impending death.
We systematically documented 10 physical signs every 12 hours from admission to death or discharge in 357 consecutive patients with advanced cancer admitted to two acute palliative care units. We examined the frequency and median onset of each sign from death backward and calculated their likelihood ratios (LRs) associated with death within 3 days.
In total, 203 of 357 patients (52 of 151 in the U.S., 151 of 206 in Brazil) died. Decreased level of consciousness, Palliative Performance Scale ≤20%, and dysphagia of liquids appeared at high frequency and >3 days before death and had low specificity (<90%) and positive LR (<5) for impending death. In contrast, apnea periods, Cheyne-Stokes breathing, death rattle, peripheral cyanosis, pulselessness of radial artery, respiration with mandibular movement, and decreased urine output occurred mostly in the last 3 days of life and at lower frequency. Five of these signs had high specificity (>95%) and positive LRs for death within 3 days, including pulselessness of radial artery (positive LR: 15.6; 95% confidence interval [CI]: 13.7–17.4), respiration with mandibular movement (positive LR: 10; 95% CI: 9.1–10.9), decreased urine output (positive LR: 15.2; 95% CI: 13.4–17.1), Cheyne-Stokes breathing (positive LR: 12.4; 95% CI: 10.8–13.9), and death rattle (positive LR: 9; 95% CI: 8.1–9.8).
We identified highly specific physical signs associated with death within 3 days among cancer patients.
Death; Diagnosis; Neoplasms; Palliative care; Physical examination; Sensitivity; Signs; Specificity
Endometrial cancer (EC) is the 8th leading cause of cancer death amongst American women. Most ECs are endometrioid, serous, or clear cell carcinomas, or an admixture of histologies. Serous and clear ECs are clinically aggressive tumors for which alternative therapeutic approaches are needed. The purpose of this study was to search for somatic mutations in the tyrosine kinome of serous and clear cell ECs, because mutated kinases can point to potential therapeutic targets.
In a mutation discovery screen, we PCR amplified and Sanger sequenced the exons encoding the catalytic domains of 86 tyrosine kinases from 24 serous, 11 clear cell, and 5 mixed histology ECs. For somatically mutated genes, we next sequenced the remaining coding exons from the 40 discovery screen tumors and sequenced all coding exons from another 72 ECs (10 clear cell, 21 serous, 41 endometrioid). We assessed the copy number of mutated kinases in this cohort of 112 tumors using quantitative real time PCR, and we used immunoblotting to measure expression of these kinases in endometrial cancer cell lines.
Overall, we identified somatic mutations in TNK2 (tyrosine kinase non-receptor, 2) and DDR1 (discoidin domain receptor tyrosine kinase 1) in 5.3% (6 of 112) and 2.7% (3 of 112) of ECs. Copy number gains of TNK2 and DDR1 were identified in another 4.5% and 0.9% of 112 cases respectively. Immunoblotting confirmed TNK2 and DDR1 expression in endometrial cancer cell lines. Three of five missense mutations in TNK2 and one of two missense mutations in DDR1 are predicted to impact protein function by two or more in silico algorithms. The TNK2P761Rfs*72 frameshift mutation was recurrent in EC, and the DDR1R570Q missense mutation was recurrent across tumor types.
This is the first study to systematically search for mutations in the tyrosine kinome in clear cell endometrial tumors. Our findings indicate that high-frequency somatic mutations in the catalytic domains of the tyrosine kinome are rare in clear cell ECs. We uncovered ten new mutations in TNK2 and DDR1 within serous and endometrioid ECs, thus providing novel insights into the mutation spectrum of each gene in EC.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2407-14-884) contains supplementary material, which is available to authorized users.
Endometrial; Cancer; Mutation; TNK2; ACK1; DDR1; Copy number; Tyrosine kinase; Tyrosine kinome
The extraction of mechanically separated meat has emerged as an attractive process. However, it increases the incorporation of oxygen and, consequently, of flavors due to rancidity. Thus, preservatives must be added. The objective of this study was to evaluate the shelf life of minced tilapia to replace synthetic preservatives with Hijiki and Nori seaweeds extracts. The application of the extracts had no effect on the chemical composition of the minced tilapia. The seaweed extracts had inhibitory effect on total volatile base nitrogen. The minced tilapia complied with the microbiological standard set by Brazilin law. The panelists detected no differences in the rancid aroma and only minor differences were detected in the color of the products. It can be concluded that the minced tilapia with added seaweed extracts were within quality standards during frozen storage.
Altered production of β-amyloid (Aβ) from the amyloid precursor protein (APP) is closely associated with Alzheimer’s disease (AD). APP has a number of homo- and hetero-dimerizing domains, and studies have suggested that dimerization of β-secretase derived APP carboxyl terminal fragment (CTFβ, C99) impairs processive cleavage by γ-secretase increasing production of long Aβs (e.g., Aβ1-42, 43). Other studies report that APP CTFβ dimers are not γ-secretase substrates. We revisited this issue due to observations made with an artificial APP mutant referred to as 3xK-APP, which contains three lysine residues at the border of the APP ectodomain and transmembrane domain (TMD). This mutant, which dramatically increases production of long Aβ, was found to form SDS-stable APP dimers, once again suggesting a mechanistic link between dimerization and increased production of long Aβ. To further evaluate how multimerization of substrate affects both initial γ-secretase cleavage and subsequent processivity, we generated recombinant wild type- (WT) and 3xK-C100 substrates, isolated monomeric, dimeric and trimeric forms of these proteins, and evaluated both ε-cleavage site utilization and Aβ production. These show that multimerization significantly impedes γ-secretase cleavage, irrespective of substrate sequence. Further, the monomeric form of the 3xK-C100 mutant increased long Aβ production without altering the initial ε-cleavage utilization. These data confirm and extend previous studies showing that dimeric substrates are not efficient γ-secretase substrates, and demonstrate that primary sequence determinants within APP substrate alter γ-secretase processivity.
Recently mutations in ubiquilin-2 were identified in patients with amyotrophic lateral sclerosis (ALS) and ALS/dementia providing direct evidence for the importance of this protein in neurodegenerative diseases. Histological studies have suggested that ubiquilin-1/-2 are associated with various pathological inclusions including Lewy bodies in Parkinson’s disease, neurofibrillary tangles in Alzheimer’s disease, polyQ inclusions in expansion repeat diseases and various proteinopathies associated with ALS and frontotemporal dementia. Using specific ubiquilin-2 antibodies and a series of transgenic mouse models of proteinopathies associated with neurodegenerative disease, we show that ubiquilin-2 preferentially associates with huntingtin polyQ expansion aggregates compared to α-synuclein, tau and several other types of protein inclusions. These results were confirmed by similar findings for ubiquilin-1 and -2 in human brain tissue sections, where accumulation was observed in huntingtin inclusions, but only infrequently in other types of protein inclusions. In cultured cells, ubiquilin-2 associates with huntingtin/polyQ aggregates, but this is not compromised by disease-causing mutations. Although ubiquilin proteins can function as chaperones to shuttle proteins for degradation, there is persistent co-localization between ubiquilin-2 and polyQ aggregated proteins during disease progression in the N586-82Q-C63 Huntington’s disease mouse model. Thus, the co-localization of ubiquilin-2 with the huntingtin aggregates does not appear to facilitate aggregate removal.
Huntington’s disease; inclusions; ubiquilin; transgenic mice
Unraveling pyramidal cell structure is crucial to understanding cortical circuit computations. Although it is well known that pyramidal cell branching structure differs in the various cortical areas, the principles that determine the geometric shapes of these cells are not fully understood. Here we analyzed and modeled with a von Mises distribution the branching angles in 3D reconstructed basal dendritic arbors of hundreds of intracellularly injected cortical pyramidal cells in seven different cortical regions of the frontal, parietal, and occipital cortex of the mouse. We found that, despite the differences in the structure of the pyramidal cells in these distinct functional and cytoarchitectonic cortical areas, there are common design principles that govern the geometry of dendritic branching angles of pyramidal cells in all cortical areas.
Cancer-related-fatigue (CRF) is common in advanced cancer. The primary objective of the study was to compare the effects of methylphenidate (MP) with those of placebo (PL) on CRF as measured using the Functional Assessment of Chronic Illness Therapy–Fatigue (FACIT-F) fatigue subscale. The effect of a combined intervention including MP plus a nursing telephone intervention (NTI) was also assessed.
Patients and Methods
Patients with advanced cancer with a fatigue score of ≥ 4 out of 10 on the Edmonton Symptom Assessment Scale (ESAS) were randomly assigned to one of the following four groups: MP+NTI, PL+NTI, MP + control telephone intervention (CTI), and PL+CTI. Methylphenidate dose was 5 mg every 2 hours as needed up to 20 mg per day. The primary end point was the median difference in FACIT-F fatigue at day 15. Secondary outcomes included anxiety, depression, and sleep.
One hundred forty-one patients were evaluable. Median FACIT-F fatigue scores improved from baseline to day 15 in all groups: MP+NTI (median score, 4.5; P = .005), PL+NTI (median score, 8.0; P < .001), MP+CTI (median score, 7.0; P = .004), and PL+CTI (median score, 5.0; P = .03). However, there were no significant differences in the median improvement in FACIT-F fatigue between the MP and PL groups (5.5 v 6.0, respectively; P = .69) and among all four groups (P = .16). Fatigue (P < .001), nausea (P = .01), depression (P = .02), anxiety (P = .01), drowsiness (P < .001), appetite (P = .009), sleep (P < .001), and feeling of well-being (P < .001), as measured by the ESAS, significantly improved in patients who received NTI. Grade ≥ 3 adverse events did not differ between MP and PL (40 of 93 patients v 29 of 97 patients, respectively; P = .06).
MP and NTI alone or combined were not superior to placebo in improving CRF.
Code status discussions are important in cancer care. The best modality for such discussions has not been established. Our objective was to determine the impact of a physician ending a code status discussion with a question (autonomy approach) versus a recommendation (beneficence approach) on patients' do-not-resuscitate (DNR) preference.
Patients in a supportive care clinic watched two videos showing a physician-patient discussion regarding code status. Both videos were identical except for the ending: one ended with the physician asking for the patient's code status preference and the other with the physician recommending DNR. Patients were randomly assigned to watch the videos in different sequences. The main outcome was the proportion of patients choosing DNR for the video patient.
78 patients completed the study. 74% chose DNR after the question video, 73% after the recommendation video. Median physician compassion score was very high and not different for both videos. 30/30 patients who had chosen DNR for themselves and 30/48 patients who had not chosen DNR for themselves chose DNR for the video patient (100% v/s 62%). Age (OR=1.1/year) and white ethnicity (OR=9.43) predicted DNR choice for the video patient.
Ending DNR discussions with a question or a recommendation did not impact DNR choice or perception of physician compassion. Therefore, both approaches are clinically appropriate. All patients who chose DNR for themselves and most patients who did not choose DNR for themselves chose DNR for the video patient. Age and race predicted DNR choice.
Code status; advanced cancer; communication; patient preferences
Early-onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD) is a myopathic disorder associated with mutations in MEGF10. By novel analysis of SNP array hybridization and exome sequence coverage, we diagnosed a 10-year old girl with EMARDD following identification of a novel homozygous deletion of exon 7 in MEGF10. In contrast to previously reported EMARDD patients, her weakness was more prominent proximally than distally, and involved her legs more than her arms. MRI of her pelvis and thighs showed muscle atrophy and fatty replacement. Ultrasound of several muscle groups revealed dense homogenous increases in echogenicity. Cloning and sequencing of the deletion breakpoint identified features suggesting the mutation arose by fork stalling and template switching. These findings constitute the first genomic deletion causing EMARDD, expand the clinical phenotype, and provide new insight into the pattern and histology of its muscular pathology.
EMARDD; MEGF10; SNP array; exome sequencing; deletion analysis; myopathy
To determine if edentulism, controlling for other known factors, is associated with subjective self-report health status (SRH) in Mexican adults.
We examined the SRH of 13 966 individuals 35 years and older, using data from the National Survey of Performance Assessment, a cross-sectional study that is part of the technical collaboration between the Ministry of Health of Mexico and the World Health Organization, which used the survey instrument and sampling strategies developed by WHO for the World Health Survey. Sociodemographic, socioeconomic, medical, and behavioral variables were collected using questionnaires. Self-reported health was our dependent variable. Data on edentulism were available from 20 of the 32 Mexican states. A polynomial logistic regression model adjusted for complex sampling was generated.
In the SRH, 58.2% reported their health status as very good/good, 33.8% said they had a moderate health status, and 8.0% reported that their health was bad/very bad. The association between edentulism and SRH was modified by age and was significant only for bad/very bad SRH. Higher odds of reporting moderate health or poor/very poor health were found in women, people with lower socio-economic status and with physical disabilities, those who were not physically active, or those who were underweight or obese, those who had any chronic disease, and those who used alcohol.
The association of edentulism with a self-report of a poor health status (poor/very poor) was higher in young people than in adults. The results suggest socioeconomic inequalities in SRH. Inequality was further confirmed among people who had a general health condition or a disability.
Self-Reported Health; Oral Health; Edentulism; Socioeconomic Inequalities
The whey acidic protein (WAP) four-disulfide core domain (WFDC) locus located on human chromosome 20q13 spans 19 genes with WAP and/or Kunitz domains. These genes participate in antimicrobial, immune, and tissue homoeostasis activities. Neighboring SEMG genes encode seminal proteins Semenogelin 1 and 2 (SEMG1 and SEMG2). WFDC and SEMG genes have a strikingly high rate of amino acid replacement (dN/dS), indicative of responses to adaptive pressures during vertebrate evolution. To better understand the selection pressures acting on WFDC genes in human populations, we resequenced 18 genes and 54 noncoding segments in 71 European (CEU), African (YRI), and Asian (CHB + JPT) individuals. Overall, we identified 484 single-nucleotide polymorphisms (SNPs), including 65 coding variants (of which 49 are nonsynonymous differences). Using classic neutrality tests, we confirmed the signature of short-term balancing selection on WFDC8 in Europeans and a signature of positive selection spanning genes PI3, SEMG1, SEMG2, and SLPI. Associated with the latter signal, we identified an unusually homogeneous-derived 100-kb haplotype with a frequency of 88% in Asian populations. A putative candidate variant targeted by selection is Thr56Ser in SEMG1, which may alter the proteolytic profile of SEMG1 and antimicrobial activities of semen. All the well-characterized genes residing in the WDFC locus encode proteins that appear to have a role in immunity and/or fertility, two processes that are often associated with adaptive evolution. This study provides further evidence that the WFDC and SEMG loci have been under strong adaptive pressure within the short timescale of modern humans.
WFDC; semenogelins; natural selection; innate immunity; serine protease inhibitors; reproduction
A systematic classification and accepted nomenclature of neuron types is much needed but is currently lacking. This article describes a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria. Using Bayesian analysis and clustering algorithms on the resulting data, we investigated the suitability of several anatomical terms and neuron names for cortical GABAergic interneurons. Moreover, we show that supervised classification models could automatically categorize interneurons in agreement with experts’ assignments. These results demonstrate a practical and objective approach to the naming, characterization and classification of neurons based on community consensus.
Oral diseases are a major burden on individuals and health systems. The aim of this study was to determine whether consumption of tobacco and alcohol were associated with the prevalence of oral/dental problems in Mexican adults. Using data from the National Performance Evaluation Survey 2003, a cross-sectional study part of the World Health Survey, dental information from a representative sample of Mexico (n = 22,229, N = 51,155,740) was used to document self-reported oral/dental problems in the 12 months prior to the survey. Questionnaires were used to collect information related to sociodemographic, socioeconomic, and other risk factors. Three models were generated for each age group (18–30, 31–45 and 46–98 years). The prevalence of oral/dental conditions was 25.7%. Adjusting for sex, schooling, socioeconomic position, diabetes, and self-reported health, those who used tobacco (sometimes or daily) (OR = 1.15, p = 0.070; OR = 1.24, p < 0.01; and OR = 1.16, p < 0.05, for each age group respectively) or alcohol (moderate or high) (OR = 1.26, p < 0.001; OR = 1.18, p < 0.01 and OR = 1.30, p < 0.001, for each age group respectively) had a higher risk of reporting oral/dental problems. Because tobacco and alcohol use were associated with self-reported oral/dental problems in one out of four adults, it appears advisable to ascertain how direct is such link; more direct effects would lend greater weight to adopting measures to reduce consumption of tobacco and alcohol for the specific purpose of improving oral health.
oral health; epidemiology; smoking; alcohol; adults
Standardization of mesenchymal stromal cells (MSCs) manufacturing is urgently needed to enable translational activities and ultimately facilitate comparison of clinical trial results. In this work we describe the adaptation of a proprietary method for isolation of a specific umbilical cord tissue-derived population of MSCs, herein designated by its registered trademark as UCX®, towards the production of an advanced therapy medicinal product (ATMP).
The adaptation focused on different stages of production, from cell isolation steps to cell culturing and cryopreservation. The origin and quality of materials and reagents were considered and steps for avoiding microbiological and endotoxin contamination of the final cell product were implemented. Cell isolation efficiency, MSCs surface markers and genetic profiles, originating from the use of different medium supplements, were compared. The ATMP-compliant UCX® product was also cryopreserved avoiding the use of dimethyl sulfoxide, an added benefit for the use of these cells as an ATMP. Cells were analyzed for expansion capacity and longevity. The final cell product was further characterized by flow cytometry, differentiation potential, and tested for contaminants at various passages. Finally, genetic stability and immune properties were also analyzed.
The isolation efficiency of UCX® was not affected by the introduction of clinical grade enzymes. Furthermore, isolation efficiencies and phenotype analyses revealed advantages in the use of human serum in cell culture as opposed to human platelet lysate. Initial decontamination of the tissue followed by the use of mycoplasma- and endotoxin-free materials and reagents in cell isolation and subsequent culture, enabled the removal of antibiotics during cell expansion. UCX®-ATMP maintained a significant expansion potential of 2.5 population doublings per week up to passage 15 (P15). They were also efficiently cryopreserved in a DMSO-free cryoprotectant medium with approximately 100% recovery and 98% viability post-thaw. Additionally, UCX®-ATMP were genetically stable upon expansion (up to P15) and maintained their immunomodulatory properties.
We have successfully adapted a method to consistently isolate, expand and cryopreserve a well-characterized population of human umbilical cord tissue-derived MSCs (UCX®), in order to obtain a cell product that is compliant with cell therapy. Here, we present quality and safety data that support the use of the UCX® as an ATMP, according to existing international guidelines.
Among the plethora of cells under investigation to restore a functional myocardium, mesenchymal stromal cells (MSCs) have been granted considerable interest. However, whereas the beneficial effects of bone marrow MSCs (BM-MSCs) in the context of the diseased heart are widely reported, data are still scarce on MSCs from the umbilical cord matrix (UCM-MSCs). Herein we report on the effect of UCM-MSC transplantation to the infarcted murine heart, seconded by the dissection of the molecular mechanisms at play.
Human umbilical cord tissue-derived MSCs (UCX®), obtained by using a proprietary technology developed by ECBio, were delivered via intramyocardial injection to C57BL/6 females subjected to permanent ligation of the left descending coronary artery. Moreover, medium produced by cultured UCX® preconditioned under normoxia (CM) or hypoxia (CMH) was collected for subsequent in vitro assays.
Evaluation of the effects upon intramyocardial transplantation shows that UCX® preserved cardiac function and attenuated cardiac remodeling subsequent to myocardial infarction (MI). UCX® further led to increased capillary density and decreased apoptosis in the injured tissue. In vitro, UCX®-conditioned medium displayed (a) proangiogenic activity by promoting the formation of capillary-like structures by human umbilical vein endothelial cells (HUVECs), and (b) antiapoptotic activity in HL-1 cardiomyocytes subjected to hypoxia. Moreover, in adult murine cardiac Sca-1+ progenitor cells (CPCs), conditioned medium enhanced mitogenic activity while activating a gene program characteristic of cardiomyogenic differentiation.
UCX® preserve cardiac function after intramyocardial transplantation in a MI murine model. The cardioprotective effects of UCX® were attributed to paracrine mechanisms that appear to enhance angiogenesis, limit the extent of the apoptosis, augment proliferation, and activate a pool of resident CPCs. Overall, these results suggest that UCX® should be considered an alternative cell source when designing new therapeutic approaches to treat MI.
Background music can be used to distract from ordinary sounds and improve wellbeing in patient care areas. Little is known about individuals' attitudes and beliefs about music versus ordinary sound in this setting.
To assess the preferences of patients, caregivers and healthcare providers regarding background music or ordinary sound in outpatient and inpatient care areas, and to explore their attitudes and perceptions towards music in general.
All participants were exposed to background music in outpatient or inpatient clinical settings. 99 consecutive patients, 101 caregivers and 65 out of 70 eligible healthcare providers (93%) completed a survey about music attitudes and preferences. The primary outcome was a preference for background music over ordinary sound in patient care areas.
Preference for background music was high and similar across groups (70 patients (71%), 71 caregivers (71%) and 46 providers (71%), p=0.58). The three groups had very low disapproval for background music in patient care areas (10%, 9% and 12%, respectively; p=0.91). Black ethnicity independently predicted lower preference for background music (OR: 0.47, 95%CI: 0.23, 0.98). Patients, caregivers and providers reported recent use of music for themselves for the purpose of enjoyment (69%, 80% and 86% respectively p=0.02). Age, gender, religion and education level significantly predicted preferences for specific music styles.
Background music in patient care areas was preferred to ordinary sound by patients, caregivers and providers. Demographics of the population are strong determinants of music style preferences.
While the unique metabolic activities of malignant tissues as potential targets for cancer therapeutics has been the subject of several recent reviews, the role of cholesterol metabolism in this context is yet to be fully explored. Cholesterol is an essential component of mammalian cell membranes as well as a precursor of bile acids and steroid hormones. The hypothesis that cancer cells need excess cholesterol and intermediates of the cholesterol biosynthesis pathway to maintain a high level of proliferation is well accepted, however the mechanisms by which malignant cells and tissues reprogram cholesterol synthesis, uptake and efflux are yet to be fully elucidated as potential therapeutic targets. High and low density plasma lipoproteins are the likely major suppliers of cholesterol to cancer cells and tumors, potentially via receptor mediated mechanisms. This review is primarily focused on the role(s) of lipoproteins in carcinogenesis, and their future roles as drug delivery vehicles for targeted cancer chemotherapy.
cholesterol metabolism; lipoprotein transport; carcinogenesis; drug delivery system; SR-B1 receptor
We previously reported a human-specific gene conversion of
SIGLEC11 by an adjacent paralogous pseudogene
(SIGLEC16P), generating a uniquely human form of the Siglec-11 protein,
which is expressed in the human brain. Here, we show that Siglec-11 is expressed
exclusively in microglia in all human brains studied—a finding of potential
relevance to brain evolution, as microglia modulate neuronal survival, and Siglec-11
recruits SHP-1, a tyrosine phosphatase that modulates microglial biology. Following the
recent finding of a functional SIGLEC16 allele in human populations,
further analysis of the human SIGLEC11 and
SIGLEC16/P sequences revealed an unusual series of
gene conversion events between two loci. Two tandem and likely simultaneous gene
conversions occurred from SIGLEC16P to SIGLEC11 with a
potentially deleterious intervening short segment happening to be excluded. One of the
conversion events also changed the 5′ untranslated sequence, altering predicted
transcription factor binding sites. Both of the gene conversions have been dated to
∼1–1.2 Ma, after the emergence of the genus Homo, but prior to
the emergence of the common ancestor of Denisovans and modern humans about 800,000 years
ago, thus suggesting involvement in later stages of hominin brain evolution. In keeping
with this, recombinant soluble Siglec-11 binds ligands in the human brain. We also address
a second-round more recent gene conversion from SIGLEC11 to
SIGLEC16, with the latter showing an allele frequency of
∼0.1–0.3 in a worldwide population study. Initial pseudogenization of
SIGLEC16 was estimated to occur at least 3 Ma, which thus preceded the
gene conversion of SIGLEC11 by SIGLEC16P. As gene
conversion usually disrupts the converted gene, the fact that ORFs of
hSIGLEC11 and hSIGLEC16 have been maintained after an
unusual series of very complex gene conversion events suggests that these events may have
been subject to hominin-specific selection forces.
pseudogene; gene conversion; human evolution; human brain; microglia
To utilize high-throughput sequencing to determine the etiology of juvenile-onset neurodegeneration in a 19-year-old woman with progressive motor and cognitive decline.
Exome sequencing identified an initial list of 133,555 variants in the proband's family, which were filtered using segregation analysis, presence in dbSNP, and an empirically derived gene exclusion list. The filtered list comprised 52 genes: 21 homozygous variants and 31 compound heterozygous variants. These variants were subsequently scrutinized with predicted pathogenicity programs and for association with appropriate clinical syndromes.
Exome sequencing data identified 2 GLB1 variants (c.602G>A, p.R201H; c.785G>T, p.G262V). β-Galactosidase enzyme analysis prior to our evaluation was reported as normal; however, subsequent testing was consistent with juvenile-onset GM1-gangliosidosis. Urine oligosaccharide analysis was positive for multiple oligosaccharides with terminal galactose residues.
We describe a patient with juvenile-onset neurodegeneration that had eluded diagnosis for over a decade. GM1-gangliosidosis had previously been excluded from consideration, but was subsequently identified as the correct diagnosis using exome sequencing. Exome sequencing can evaluate genes not previously associated with neurodegeneration, as well as most known neurodegeneration-associated genes. Our results demonstrate the utility of “agnostic” exome sequencing to evaluate patients with undiagnosed disorders, without prejudice from prior testing results.
Adeno-associated virus (AAV) mediated gene expression is a powerful tool for gene therapy and preclinical studies. A comprehensive analysis of CNS cell type tropism, expression levels and biodistribution of different capsid serotypes has not yet been undertaken in neonatal rodents. Our previous studies show that intracerebroventricular injection with AAV2/1 on neonatal day P0 results in widespread CNS expression but the biodistribution is limited if injected beyond neonatal day P1. To extend these observations we explored the effect of timing of injection on tropism and biodistribution of six commonly used pseudotyped AAVs delivered in the cerebral ventricles of neonatal mice. We demonstrate that AAV2/8 and 2/9 resulted in the most widespread biodistribution in the brain. Most serotypes showed varying biodistribution depending on the day of injection. Injection on neonatal day P0 resulted in mostly neuronal transduction, whereas administration in later periods of development (24–84 hours postnatal) resulted in more non-neuronal transduction. AAV2/5 showed widespread transduction of astrocytes irrespective of the time of injection. None of the serotypes tested showed any microglial transduction. This study demonstrates that both capsid serotype and timing of injection influence the regional and cell-type distribution of AAV in neonatal rodents, and emphasizes the utility of pseudotyped AAV vectors for translational gene therapy paradigms.
The 13C-isotopomer enrichment of hepatic cytosolic acetyl-CoA of overnight-fed mice whose drinking water was supplemented with [U-13C]fructose, and [1-13C]glucose and p-amino benzoic acid (PABA) was quantified by 13C NMR analysis of urinary N-acetyl-PABA. Four mice were given normal chow plus drinking water supplemented with 5% [1-13C]glucose, 2.5% [U-13C]fructose, and 2.5% fructose (Solution 1) overnight. Four were given chow and water containing 17.5% [1-13C]glucose, 8.75% [U-13C]fructose and 8.75% fructose (Solution 2). PABA (0.25%) was present in both studies. Urinary N-acetyl-PABA was analyzed by 13C NMR. In addition to [2-13C]- and [1,2-13C]acetyl isotopomers from catabolism of [U-13C]fructose and [1-13C]glucose to acetyl-CoA, [1-13C]acetyl was also found indicating pyruvate recycling activity. This precluded precise estimates of [1-13C]glucose contribution to acetyl-CoA while that of [U-13C]fructose was unaffected. The fructose contribution to acetyl-CoA from Solutions 1 and 2 was 4.0 ± 0.4% and 10.6 ± 0.6%, respectively, indicating that it contributed to a minor fraction of lipogenic acetyl-CoA under these conditions.
Most endometrial cancers can be classified histologically as endometrioid, serous, or clear cell. Non-endometrioid endometrial cancers (NEECs; serous and clear cell) are the most clinically aggressive of the three major histotypes and are characterized by aneuploidy, a feature of chromosome instability. The genetic alterations that underlie chromosome instability in endometrial cancer are poorly understood. In the present study, we used Sanger sequencing to search for nucleotide variants in the coding exons and splice junctions of 21 candidate chromosome instability genes, including 19 genes implicated in sister chromatid cohesion, from 24 primary, microsatellite-stable NEECs. Somatic mutations were verified by sequencing matched normal DNAs. We subsequently resequenced mutated genes from 41 additional NEECs as well as 42 endometrioid ECs (EECs). We uncovered nonsynonymous somatic mutations in ESCO1, CHTF18, and MRE11A in, respectively, 3.7% (4 of 107), 1.9% (2 of 107), and 1.9% (2 of 107) of endometrial tumors. Overall, 7.7% (5 of 65) of NEECs and 2.4% (1 of 42) of EECs had somatically mutated one or more of the three genes. A subset of mutations are predicted to impact protein function. The co-occurrence of somatic mutations in ESCO1 and CHTF18 was statistically significant (P = 0.0011, two-tailed Fisher's exact test). This is the first report of somatic mutations within ESCO1 and CHTF18 in endometrial tumors and of MRE11A mutations in microsatellite-stable endometrial tumors. Our findings warrant future studies to determine whether these mutations are driver events that contribute to the pathogenesis of endometrial cancer.
Genomic technologies, such as whole-exome sequencing, are a powerful tool in genetic research. Such testing yields a great deal of incidental medical information, or medical information not related to the primary research target. We describe the management of incidental medical information derived from whole-exome sequencing in the research context. We performed whole-exome sequencing on a monozygotic twin pair in which only 1 child was affected with congenital anomalies and applied an institutional review board–approved algorithm to determine what genetic information would be returned. Whole-exome sequencing identified 79 525 genetic variants in the twins. Here, we focus on novel variants. After filtering artifacts and excluding known single nucleotide polymorphisms and variants not predicted to be pathogenic, the twins had 32 novel variants in 32 genes that were felt to be likely to be associated with human disease. Eighteen of these novel variants were associated with recessive disease and 18 were associated with dominantly manifesting conditions (variants in some genes were potentially associated with both recessive and dominant conditions), but only 1 variant ultimately met our institutional review board–approved criteria for return of information to the research participants.
whole-exome sequencing; incidental medical information
Genetic studies have established a causative role for α-synuclein (αS) in Parkinson’s disease (PD), and the presence of αS aggregates in the form of Lewy body (LB) and Lewy neurite (LN) protein inclusions are defining pathological features of PD. Recent data has established that extracellular αS aggregates can induce intracellular αS pathologies supporting the hypothesis that αS pathology can spread via a “prion-like” self-templating mechanism.
Here we investigated the potential for conformational templating of αS intracellular aggregates by seeding using recombinant wild-type and PD-linked mutant (A53T and E46K) αS in primary mixed neuronal-glial cultures. We find that wild-type and A53T αS fibrils predominantly seed flame-like inclusions in both neurons and astrocytes of mixed primary cultures; whereas the structurally distinct E46K fibrils seed punctate, rounded inclusions. Notably, these differences in seeded inclusion formation in these cultures reflect differences in inclusion pathology seen in transgenic mice expressing the A53T or E46K αS mutants. We further show that the inclusion morphology is dictated primarily by the seed applied rather than the form of αS expressed. We also provide initial evidence that αS inclusion pathology can be passaged in primary astrocyte cultures.
These studies establish for the first time that αS aggregation in cultured cells can occur by a morphological self-templating mechanism.
α-Synuclein; Parkinson’s disease; Self-templating; Amyloid; Prion