A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues.

Comparative genomic studies in primates have the potential to reveal the genetic and mechanistic basis for human specific traits. These studies may also help us better understand inter-species phenotypic differences that are clinically relevant. Unfortunately, the obvious limitation on sample collection and experimentation in humans and non-human apes severely restrict our ability to perform dynamic comparative studies in primates. Induced pluripotent stem cells (iPSCs), and their corresponding differentiated cells, may provide a suitable alternative system for dynamic comparative studies. Yet, to effectively use iPSCs and differentiated cells for comparative studies, one must characterize the extent to which these systems faithfully represent biological processes in primary tissues. To do so, we compared gene expression data from primary adult heart tissue and iPSC-derived cardiomyocytes from multiple human and chimpanzee individuals. We determined that gene expression in cultured cardiomyocytes from both human and chimpanzee is most similar to that of adult hearts compared to other adult tissues. Using a comparative framework, we found that 50% of gene regulatory differences between human and chimpanzee hearts are also observed between species in cultured cardiomyocytes; conversely, inter-species regulatory differences seen in cardiomyocytes are found significantly more often in hearts than in other primary tissues. Our work provides a detailed description of the utility and limitation of differentiated cardiomyocytes as a system for comparative functional genomic studies in primates.

A comparative study of endoderm differentiation in humans and chimpanzees.

BACKGROUND: There is substantial interest in the evolutionary forces that shaped the regulatory framework in early human development. Progress in this area has been slow because it is difficult to obtain relevant biological samples. Induced pluripotent stem cells (iPSCs) may provide the ability to establish in vitro models of early human and non-human primate developmental stages. RESULTS: Using matched iPSC panels from humans and chimpanzees, we comparatively characterize gene regulatory changes through a four-day time course differentiation of iPSCs into primary streak, endoderm progenitors, and definitive endoderm. As might be expected, we find that differentiation stage is the major driver of variation in gene expression levels, followed by species. We identify thousands of differentially expressed genes between humans and chimpanzees in each differentiation stage. Yet, when we consider gene-specific dynamic regulatory trajectories throughout the time course, we find that at least 75% of genes, including nearly all known endoderm developmental markers, have similar trajectories in the two species. Interestingly, we observe a marked reduction of both intra- and inter-species variation in gene expression levels in primitive streak samples compared to the iPSCs, with a recovery of regulatory variation in endoderm progenitors. CONCLUSIONS: The reduction of variation in gene expression levels at a specific developmental stage, paired with overall high degree of conservation of temporal gene regulation, is consistent with the dynamics of a conserved developmental process.

[Results to 4-year follow-up of the treatment of the cervical stenosis by corpectomy, titanium mesh cage and anterior plate fixation]. / Resultados a 4 años de seguimiento del tratamiento del conducto cervical estrecho mediante corpectomía, malla de titanio y fijación anterior con placa.

BACKGROUND: Cervical spondylotic myelopathy is caused by cervical stenosis. Several techniques have been described for the treatment of multilevel disease, such as the anterior corpectomy with titanium mesh cage and anterior cervical plate placement, which has the advantage of performing a wider decompression and using the same bone as graft. However, it has caused controversy since the collapse of the mesh cage continues being a major limitation of this procedure. MATERIAL AND METHOD: A prospective 4-year follow-up study was conducted in 7 patients diagnosed with cervical stenosis, who were treated surgically by one level corpectomy with titanium mesh cage and anterior cervical plate placement, evaluating them by radiographs and clinical scales. RESULTS: 7 patients, 5 women and 2 males were studied. The most common level was C5 corpectomy (n=4). The Neck Disability Index (NDI) preoperative average was 30.01±24.32 and 4-year postoperative 16.90±32.05, with p=0.801. The preoperative and 4-year postoperative Nürick was 3.28± 48 and 3.14±1.21 respectively, with p=0.766. Preoperative lordosis was 14.42±8.03 and 4-year postoperative 17±11.67 degrees, with p=0.660. The immediate postoperative and 4-year postoperative subsidence was 2.69±2.8 and 6.11±1.61 millimeters respectively, with p=0.0001. CONCLUSIONS: Despite the small sample, the subsidence of the mesh cage is common in this procedure. No statistically significant changes were observed in the lordosis or Nürick scale and NDI.

Integrated analyses of gene expression and genetic association studies in a founder population.

Genome-wide association studies (GWASs) have become a standard tool for dissecting genetic contributions to disease risk. However, these studies typically require extraordinarily large sample sizes to be adequately powered. Strategies that incorporate functional information alongside genetic associations have proved successful in increasing GWAS power. Following this paradigm, we present the results of 20 different genetic association studies for quantitative traits related to complex diseases, conducted in the Hutterites of South Dakota. To boost the power of these association studies, we collected RNA-sequencing data from lymphoblastoid cell lines for 431 Hutterite individuals. We then used Sherlock, a tool that integrates GWAS and expression quantitative trait locus (eQTL) data, to identify weak GWAS signals that are also supported by eQTL data. Using this approach, we found novel associations with quantitative phenotypes related to cardiovascular disease, including carotid intima-media thickness, left atrial volume index, monocyte count and serum YKL-40 levels.

[Clinical presentation of a dorsal epidural arachnoid cyst after an epidural anesthesia]. / Presentación clínica de quiste aracnoideo epidural dorsal posterior a anestesia epidural.

BACKGROUND: Arachnoid cysts are dural diverticula with liquid content similar to cerebrospinal fluid, with 1% occurring in the spinal cord. They locate mainly in the dorsal region of the thoracic spine, and are unusual causes of spinal cord compression. CLINICAL CASE: The case is presented of a previously healthy 15-year-old boy, with a 20-month history of spastic paraparesis that started apparently after epidural block for ankle osteosynthesis. There was decreased sensitivity and strength of the pelvic limbs and gradually presented with anaesthesia from T12 to L4 dermatomes, L5 and S1 bilateral hypoaesthesia and 4+/5 bilateral strength, in the L2 root and 2+/5 in L3, L4, L5, S1, hyperreflexia, Babinski and clonus, but with no alteration in the sacral reflexes. In the magnetic resonance it was diagnosed as an extradural arachnoid cyst from T6 to T9. The patient underwent a T6 to T10 laminotomy, cyst resection, dural defect suture, and laminoplasty. One year after surgery, the patient had recovered sensitivity, improvement of muscle strength up to 4+/5 in L2 to S1, and normal reflexes. CONCLUSIONS: After the anaesthetic procedure, increased pressure and volume changes within the cyst could cause compression of the spinal cord, leading to symptoms. Despite being a long-term compression, the patient showed noticeable improvement.

[Spinal osteochondroma: diagnostic imaging and treatment. Case reports]. / Osteocondroma espinal: diagnóstico por imagen y tratamiento. Reporte de casos.

BACKGROUND: Osteochondromas are benign bony tumours, with only 1 to 4% being located in the spine. It occurs more frequently in the cervical spine, with C2 being the vertebra most affected. The neurological presentation is slow due to the growth characteristics of the tumour. Computed axial tomography is the reference method for diagnosis. Surgical management is indicated for patients with neurological impairment or pain. CLINICAL CASE: The first case presents a 21-year-old male with osteochondroma located in the spinous processes of L2, L3 and L4. The second case is a 20-year-old female with multiple osteochondromatosis with tumours at the right lateral mass of C1, with extension to C2 and tumours on the spinous processes of C5 and C7. Both patients presented with painful symptoms, which were resolved after surgical resection of the tumours. CONCLUSIONS: The rarity of these conditions, relevance of a clinical-radiographic diagnosis, and considerations required for surgical treatment are discussed here.

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.

Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.

[Profile of the patient with failed back surgery syndrome in the National Institute of Rehabilitation. Comparative analysis]. / Perfil del paciente con síndrome de columna multioperada en el Instituto Nacional de Rehabilitación. Análisis comparativo.

BACKGROUND: Failed back surgery syndrome is a complication of spine surgery that leads to chronic pain and disability, often with disastrous emotional consequences to the patient. AIM: To compare the profile of patients whose first surgery was performed in our hospital versus a group that underwent first spine surgery in a different centre. METHODS: Retrospective study with 65 patients; 18 formed group I (first spine surgery performed in our institution), and 47 patients in group II (first surgery performed in another hospital). Background, demographic, clinical features and functional status were compared. In group I the majority of the cases had a previous diagnosis of lumbar stenosis (group I 44.4% vs group II 25.5% p = 0.22), whereas disk herniation was the main diagnosis in group II (group I 22.2% vs group II 61.7% p = 0.001). The main cause of the syndrome in group I was technical error during surgery (61.1%), while in group II this cause represented only 6.3% (p=.001). Among the patients of this latter group, misdiagnosis was highly prevalent (57.4%), against no cases in group I (p=.001). The preoperative functional status between both groups and their recovery in the immediate postoperative period was similar (p = 0.68). CONCLUSIONS: This study suggests that the diagnostic and treatment standards are different between healthcare centres, specifically between academic centres vs. private practice.

Influence of depression symptoms on patient expectations and clinical outcomes in the surgical management of spinal stenosis.

OBJECT: This prospective cohort study was designed to determine the influence of depressive symptoms on patient expectations and the clinical outcomes of the surgical management of lumbar spinal stenosis. METHODS: Patients with an age > 45 years, a diagnosis of lumbar spinal stenosis at one level, and an indication for decompressive surgery were included in this study. Data for all of the following parameters were recorded: age, sex, highest level of education, and employment status. Depression symptoms (Beck Depression Inventory), disability (Oswestry Disability Index), and back and leg pain (visual analog scale) were assessed before surgery and at 12 months thereafter. The reasons for surgery and patient expectations (North American Spine Society lumbar spine questionnaire) were noted before surgery. The global effectiveness of surgery (Likert scale) was assessed at the 1-year follow-up. RESULTS: Fifty-eight patients were divided into two groups based on the presence (Group 1) or absence (Group 2) of depressive symptoms preoperatively; each group comprised 29 patients. Demographic data were similar in both groups before surgery. The main reason to undergo surgery was "fear of a worse situation" in 34% of the patients in Group 1 and "to reduce pain" in 24% of the patients in Group 2. The most prevalent expectation was to improve my social life and my mental health in both groups. Surgery had a relieving effect on the depressive symptoms in 14 patients (48%). Thus, in the postoperative period, the number of patients who were free of depressive symptoms was 43 compared with the 15 who were depressed (p = 0.001). The 15 patients with persistent depression symptoms after surgery had a worse clinical outcome compared with the 43 patients free of depression symptoms at the 1-year follow-up in terms of severe back pain (20% vs. 0%, respectively), severe leg pain (40% vs. 2.3%, respectively), and severe disability (53% vs. 9.3%, respectively). Only 33% of patients with persistent depression symptoms after surgery chose the option "surgery helped a lot" compared with 76% of patients without depression symptoms. Moreover, in terms of expectations regarding improvement in back pain, leg pain, walking capacity, independence, physical duties, and social activities, fewer patients were "completely satisfied" in the group with persistent depression symptoms after surgery. CONCLUSIONS: Surgery for spinal stenosis had a relieving effect on preoperative depression symptoms at the 1-year follow-up. The persistence of depressive symptoms after surgery correlated with a worse clinical outcome and a higher rate of unmet expectations. Screening measures to detect and treat depression symptoms in the perioperative period could lead to better clinical results and increased patient satisfaction.

Association of the C-type lectin-like domain family-16A (CLEC16A) gene polymorphisms with acute coronary syndrome in Mexican patients.

The CLEC16A gene has an important role in the immune activation and regulation inflammatory. This gene encodes to C-type lectin domain that is involved in the recognition of DAMPS. The aim of this study was assess the CLEC16A gene polymorphisms in the risk of developing ACS in a group of patients. Four rs12708716, rs12917716, rs6498142 and rs9925481 (positions 146529 A>G, 155804 G>C, 47905 C>G and 64135 C>T, respectively) single nucleotide polymorphisms of CLEC16A gene were analyzed by TaqMan assays in a group of 452 patients with ACS and 456 healthy controls. The analysis was performed on the total group of individuals and then in groups of men and women separately. Under co-dominant model adjusted by cardiovascular risk factors the rs12708716 (146529 A>G) and rs12917716 (155804 G>C) polymorphisms were significantly associated with decrease risk of ACS in men (OR=0.16, PCo-dom=0.027 and OR=0.37, PCo-dom=0.016, respectively). In summary, our data suggests that two polymorphisms of the CLEC16A gene play an important role in the developing of ACS in men.

Association of the suppressor of cytokine signaling 1 (SOCS1) gene polymorphisms with acute coronary syndrome in Mexican patients.

Recent studies provide evidence on the emerging role of the SOCS1 gene in the development and progression of atherosclerotic lesions. This gene encodes for the suppressor of the cytokine signaling-1 protein that interacts directly with the Janus kinases that are essential intracellular mediators of the immune cytokine action. The aim of this study was to test for associations between SOCS1 gene single nucleotide polymorphisms (SNPs) and the risk of developing acute coronary syndromes (ACS) in a group of Mexicans patients. Four SNPs [-3969 C>T (rs243327), -1656 G>A (rs243330), -820 G>T (rs33977706) and +1125 G>C (rs33932899)] of SOCS1 gene were determined for TaqMan genotyping assays in a group of 447 patients with ACS and 622 healthy controls. Under heterozygous model, the -3969 C>T (rs243327) SNP was associated with increased risk of ACS (OR=1.45, P(Het)=0.021). On the other hand, under co-dominant and heterozygous models, the -1656 G/A (rs243330) SNP was associated with increased risk of ACS (OR=1.47, P(Co-dom)=0.038 and OR=1.50, P(Het)=0.013, respectively). Moreover, under co-dominant, dominant, and heterozygous models, the -820T/G (rs33977706) SNP was associated with increased risk of ACS (OR=1.59, P(Co-dom)=0.03, OR=1.48, P(Dom)=0.028 and OR=1.61, P(Het)=0.01). Finally, under co-dominant and heterozygous models, the +1125 G/C (rs33932899) SNP was associated with increased risk of ACS (OR=1.54, P(Co-dom)=0.006, OR=1.58, P(Het)=0.012, respectively). Models were adjusted for gender, age, body index mass, dyslipidemia, alcohol consumption, and smoking. In summary, our data suggests that the four studied polymorphisms of the SOCS1 gene play an important role as susceptibility markers for developing ACS.

Association of the interleukin 15 (IL-15) gene polymorphisms with the risk of developing ulcerative colitis in Mexican individuals.

Interleukin 15 (IL-15) is a Th1-related cytokine that triggers inflammatory cell recruitment with implications for pathogenesis in ulcerative colitis. The IL-15 gene is located within a 35 kb region of the q28-31 locus of chromosome 4. In the present work, the role of IL-15 gene polymorphisms as susceptibility markers for UC was evaluated. Seven polymorphisms of IL-15 (rs3806798, rs10833, rs4956403, rs2254514, rs2857261, rs10519613, and rs1057972) were genotyped by 5' exonuclease TaqMan genotyping assays in a group of 199 Mexican patients with UC and 698 Mexican Mestizo healthy unrelated individuals. UC patients and healthy controls showed similar distribution of the rs3806798, rs10833, rs4956403, rs2857261, rs10519613, and rs1057972 polymorphisms. The rs2254514 polymorphism was significantly associated with decreased risk of UC as compared to controls under both dominant and additive models (OR 0.62, Pdom = 0.014 and OR 0.65, Padd = 0.02). The rs2254514 CC genotype was associated with young age at diagnosis <40 years (P = 0.03; OR 3.67). Five polymorphisms (rs1051613, rs2254514, rs2857261, rs1057972, and rs10833) were in strong linkage disequilibrium and were included in six haplotypes: H1 (ACAAC), H2 (CCGTC), H3 (CTAAT), H4 (CCAAT), H5 (CTAAC), and H6 (CCAAC). UC patients showed an increased frequency of the H6 haplotype (P = 0.005; OR 3.2) and a decreased frequency of the H5 haplotype (P = 0.031; OR 0.40). These results suggest that the IL-15 rs2254514 polymorphism might have an important role in the development of UC in the Mexican population. We were able to distinguish one risk and one protective uncommon haplotype for the development of UC.

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.

Recent genome-wide association studies (GWAS) have identified a number of novel genetic associations with complex human diseases. In spite of these successes, results from GWAS generally explain only a small proportion of disease heritability, an observation termed the 'missing heritability problem'. Several sources for the missing heritability have been proposed, including the contribution of many common variants with small individual effect sizes, which cannot be reliably found using the standard GWAS approach. The goal of our study was to explore a complimentary approach, which combines GWAS results with functional data in order to identify novel genetic associations with small effect sizes. To do so, we conducted a GWAS for lymphocyte count, a physiologic quantitative trait associated with asthma, in 462 Hutterites. In parallel, we performed a genome-wide gene expression study in lymphoblastoid cell lines from 96 Hutterites. We found significant support for genetic associations using the GWAS data when we considered variants near the 193 genes whose expression levels across individuals were most correlated with lymphocyte counts. Interestingly, these variants are also enriched with signatures of an association with asthma susceptibility, an observation we were able to replicate. The associated loci include genes previously implicated in asthma susceptibility as well as novel candidate genes enriched for functions related to T cell receptor signaling and adenosine triphosphate synthesis. Our results, therefore, establish a new set of asthma susceptibility candidate genes. More generally, our observations support the notion that many loci of small effects influence variation in lymphocyte count and asthma susceptibility.

Expression quantitative trait loci detected in cell lines are often present in primary tissues.

Expression quantitative trait loci (eQTL) mapping is a powerful tool for identifying genetic regulatory variation. However, at present, most eQTLs in humans were identified using gene expression data from cell lines, and it remains unknown whether these eQTLs also have a regulatory function in other expression contexts, such as human primary tissues. Here we investigate this question using a targeted strategy. Specifically, we selected a subset of large-effect eQTLs identified in the HapMap lymphoblastoid cell lines, and examined the association of these eQTLs with gene expression levels across individuals in five human primary tissues (heart, kidney, liver, lung and testes). We show that genotypes at the eQTLs we selected are often predictive of variation in gene expression levels in one or more of the five primary tissues. The genotype effects in the primary tissues are consistently in the same direction as the effects inferred in the cell lines. Additionally, a number of the eQTLs we tested are found in more than one of the tissues. Our results indicate that functional studies in cell lines may uncover a substantial amount of genetic variation that affects gene expression levels in human primary tissues.