Clinical, molecular, and drug resistance epidemiology of HIV in Jordan, 2019-2021: a national study

BACKGROUND

Limited epidemiologic studies have been conducted in Jordan describing the HIV epidemic. This study aimed to address this gap to inform HIV prevention and control.

METHODS

A nationally-representative cross-sectional study was conducted among adults living with HIV in Jordan. Laboratory testing included HIV viral load and next-generation-sequencing-based clinical genotype. Log-binomial regression estimated risk ratios (RRs) and 95% confidence intervals (CIs).

RESULTS

Among 231 (70%) participants, most were male (184/80%), and from Jordan (217/94%). Among 188 treatment-experienced-participants (>6 months), 165 (88%) were virally suppressed. High level resistance was most frequent against nucleoside reverse transcriptase inhibitor (13/81%), and integrase-strand transfer inhibitor (INSTI) (10/62%) drugs among viremic (≥1,000 HIV copies/mL) treatment-experienced participants with drug resistant mutations (DRMs, n=16). Common HIV subtypes (n=43) were B (6/14%), A1 (5/12%), and CRF01_AE (5/12%); additionally, novel recombinant forms were detected. In multivariate analysis, independently higher risk for late diagnosis (n=49) was observed with diagnosis through blood donation (vs check-up: RR 2·20, 95%CI 1·16-4·17) and earlier time-period of diagnosis (1986-2014 vs 2015-2021: RR 2·87, 95%CI 1·46-5·62).

CONCLUSIONS

Late diagnosis and INSTI resistance endanger national HIV prevention and treatment in Jordan - high-level resistance to INSTI suggests therapeutic drug monitoring is needed for treatment efficacy, and conservation of treatment options.

Alpha Calcitonin Gene-related Peptide, Neuropeptide Y, and Substance P as Biomarkers for Diagnosis and Disease Activity and Severity in Multiple Sclerosis

BACKGROUND

Alpha calcitonin gene-related peptide (aCGRP), neuropeptide Y (NPY), and substance P (SP) are neuropeptides that have emerged recently as potent immunomodulatory factors with potential as novel biomarkers and therapeutic targets in multiple sclerosis (MS).

OBJECTIVE

The study aimed to detect serum levels of aCGRP, NPY, and SP in MS patients versus healthy controls and their association with disease activity and severity.

METHODS

Serum levels were measured in MS patients and age and sex-matched healthy controls using ELISA.

RESULTS

We included 67 MS patients: 61 relapsing-remitting MS (RR-MS) and 6 progressive MS (PR-MS), and 67 healthy controls. Serum NPY level was found to be lower in MS patients than in healthy controls (p < 0.001). Serum aCGRP level was higher in PR-MS compared to RR-MS (p = 0.007) and healthy controls (p = 0.001), and it positively correlated with EDSS (r = 0.270, p = 0.028). Serum NPY level was significantly higher in RR-MS and PR-MS than in healthy controls (p < 0.001 and p = 0.001, respectively), and it was lower in patients with mild or moderate/severe disease than in healthy controls (p < 0.001). Significant inverse correlations were found between SP level and MS disease duration (r = -0.279, p = 0.022) and duration of current DMT (r = -0.315, p = 0.042).

CONCLUSION

Lower serum levels of NPY were revealed in MS patients compared to healthy controls. Since serum levels of aCGRP are significantly associated with disease activity and severity, it is a potential disease progression marker.

Cytomegalovirus and Epstein-Barr Virus Co-infection in a Patient With Chronic Granulomatous Disease Co-existing With Familial Mediterranean Fever and Early-Onset Inflammatory Bowel Disease: A Case Report

The association between primary immunodeficiencies and autoinflammatory disorders has been popularized over the past decade. In this report, we illustrated the co-infection of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) in a three-year-old Jordanian male patient with an extremely rare variant of the CYBB gene (c.125C>G, p.Thr42Arg) associated with chronic granulomatous disease (CGD) coexisting with familial Mediterranean fever (FMF). CGD and FMF co-existence induced early-onset inflammatory bowel disease mainly resembling Crohn's disease.

MicroRNA profiling in dogs undergoing induced ischemic heart infarction: An experimental study

Background and Aim

MicroRNAs (miRNAs) play an important role in various biological functions. According to many studies, miRNA expression is tissue-specific, strongly controlled throughout embryogenesis, and over- or under-expressed in numerous disorders, including cardiovascular pathologies. This study aimed to screen, characterize, and profile many induced biomarkers (miRNAs) in dog serum before and after experimentally inducing a regional myocardial infarction (MI) by occluding the coronary arteries under general anesthesia.

Materials and Methods

A preclinical experimental animal study recruited 12 healthy canine dogs. The selected canine dogs were anesthetized with 1 mg/kg xylazine and 15 mg/kg ketamine before undergoing femoral arterial catheterization under fluoroscopic supervision. Commercial assay kits were used to purify total RNA and miRNA before the occlusion and 2 h after the occlusion according to the manufacturer's guidelines, and the samples were stored in RNase/DNase-free water at -80°C. Data were analyzed by GraphPad Prism 5.0 software (GraphPad Prism, San Diego, CA) SPSS, and GenEx software (www.multid.se) or (REST V3).

Results

Among 325 transcribed genes, 20 were identified in 2 h. After MI, 14 biomarkers were negative, indicating downregulation, and 6 (3-F08, 3-B10, 4-A11, 1-A06, 2-E01, 3-F10) were positive, indicating upregulation. Polymerase chain reaction assay results showed a normalized fold-change in gene expression in the test sample. Fold values >1 represented a biologically significant change.

Conclusion

Profiling of miRNAs before and after MI in a dog model revealed upregulation of six previously unidentified biomarkers (3-F08, 3-B10, 4-A11, 1-A06, 2-E01, and 3-F10), indicating various miRNA regulatory patterns.

A Novel ANO1 Gene Variant is Associated with Intestinal Dysmotility Syndrome Masquerading as Hirschsprung Disease: A Case Report

Anoctamin 1 (ANO1)-related intestinal dysmotility syndrome (OMIM: 620045) is an extremely rare disorder with only 2 cases reported in the medical literature. We present the clinical scenario of a 2-month-old male infant that presented to our center with diarrhea, vomiting, and abdominal distension. Routine investigations did not yield a clear diagnosis. Whole-exome sequencing showed a novel homozygous nonsense ANO1 pathogenic variant (c.1273G>T) with a protein alternation of p.Glu425Ter that fits the patient's phenotype. Sanger sequencing revealed the same ANO1 variant in both parents in a heterozygous form confirming an autosomal recessive mode of inheritance. The patient experienced multiple bouts of diarrhea-related metabolic acidosis, dehydration, and severe electrolyte imbalances that required intensive care unit monitoring. The patient was managed conservatively and being followed regularly in an outpatient setting.

Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions

Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.

Significance of serum VIP and PACAP in multiple sclerosis: an exploratory case-control study

BACKGROUND

Multiple sclerosis (MS) is a chronic inflammatory neurodegenerative disease of the central nervous system. Vasoactive and intestinal peptide (VIP) and pituitary adenylate cyclase-activating peptide (PACAP) are neuropeptides that play roles in anti-inflammation and neuroprotection in MS. In this study, we aimed to determine the serum levels of VIP and PACAP in MS patients versus healthy controls and to correlate them with demographics and clinical characteristics.

METHODS

Serum samples were collected from MS patients (n = 145) and healthy controls (n = 73) to measure serum levels VIP and PACAP.

RESULTS

VIP serum levels were lower in MS patients than healthy controls (p < 0.001). Serum PACAP levels were the same among the two groups. Gender-based analysis showed that VIP levels were lower in healthy females (1238.840 pg/ml) than healthy males (3300.105 pg/ml; p < 0.001), and PACAP serum levels were significantly lower in male MS patients (48,516.214 fg/ml) than female MS patients (62,466.400 fg/ml; p = 0.029). ROC curve suggested that serum VIP level can discriminate patients with MS from healthy controls. Relapsing-remitting MS, progressive-MS, and clinically isolated syndrome groups were different in age, MS disease duration, EDSS score, and VIP levels (p < 0.05). MS disease type and history of previous relapses in the preceding 24 months predicted serum VIP levels, while gender predicted PACAP levels.

CONCLUSION

VIP serum levels are decreased in MS patients and can be used to differentiate between MS patients and healthy controls. Further studies with larger sample sizes are required to investigate VIP as a marker to reflect MS disease progression.

Characterizing and Profiling microRNAs in Dogs Undergoing Induced Ischemic Brain Stroke After Middle Cerebral Artery Occlusion Under Fluoroscopic Guidance

Purpose

Ischemic stroke of the brain is still considered one of the most common causes of disability and death in developed and developing countries in human beings despite advances in medicine and technology. This study was conducted to characterize and profile tens of induced biomarkers (microRNAs) after experimentally inducing regional ischemic stroke of the brain by occluding the middle cerebral artery under fluoroscopic guidance using an autologous blood clot.

Patient and Methods

A total of six healthy dogs were recruited for this study. The microRNAs were profiled in the blood and urine before and after occluding the middle cerebral artery using genetic techniques.

Results

The very highly expressed genes were comprised within cluster A, followed by cluster D in both 24 and 48-hour brain samples. Clusters B and C revealed down-regulated genes, while miRNAs remained up-regulated in the 24-hour samples merely in cluster F. Upregulated genes at 48 hours of reperfusion were included in cluster E. On the other hand, changes were observed after a day on the cluster G genes. Exclusive upregulation was notified after 2 days due to the changes in mIR-138. The normalized gene expression in the test sample is witnessed through Fold-Change, which divides the control sample’s normalized gene expression. Moreover, fold-change has emerged as a significant approach for representing fold-regulation.

Conclusion

The microRNAs expression in blood and urine may have a potential role in the diagnosis, prognosis, and assessment of therapy associated with cerebral artery occlusion under fluoroscopic guidance.

Horizontal gaze palsy and progressive scoliosis with two novel ROBO3 gene mutations in two Jordanian families

BACKGROUND

Horizontal gaze palsy and progressive scoliosis (HGPPS) is a rare autosomal recessive disorder due to mutations in ROBO3 gene. Patients have characteristic clinical and imaging findings. We report six patients from two families with this disorder with two novel mutations.

MATERIALS AND METHODS

One patient from a non-consanguineous family and five patients from extended consanguineous families were clinically and radiologically examined. Blood samples from the patients and their parents were obtained and all the coding exons and flanking intronic sequences of the ROBO3 gene were amplified and subjected to bidirectional DNA sequencing.

RESULTS

All six patients had the characteristic clinical and radiological findings of HGPPS. Genetic testing showed two novel mutations including frame-shift and nonsense.

CONCLUSION

Two novel mutations in the ROBO3 gene were identified in two Jordanian families with six affected individuals. To our knowledge, this is the first molecular study of HGPPS in Jordan.

The effect of combined treatment with sodium phenylbutyrate and cisplatin, erlotinib, or gefitinib on resistant NSCLC cells

Background

Chemotherapy resistance is the main cause of the marginal clinical benefit of platinum-based chemotherapy and tyrosine kinase inhibitors in advanced non-small-cell lung cancer (NSCLC). Thus, the identification of new therapeutic agents that can enhance the sensitivity of these drugs is of clinical importance. Histone deacetylase inhibitors (HDACIs) are emerging as new promising agents with strong antiproliferative effects against different types of cancers. This study investigates the synergistic potential of sodium phenylbutyrate (NaPB) added on top of standard chemotherapy used against NSCLC.

Objective

The objective of this study was to evaluate the ability of NaPB to overcome the resistance of NSCLC cell lines to cisplatin, gefitinib, and erlotinib.

Methods

MTT cell proliferation assay was used to measure the anticancer effects of cisplatin, erlotinib, or gefitinib alone or combined with various concentrations of NaPB against A549, Calu1, and H1650 NSCLC cell lines. Synergism was estimated by measuring synergy value (R), which is equal to the ratio of IC₅₀ of each primary drug alone divided by combination IC₅₀s. Student’s t-test analysis was used to evaluate the potential differences between IC₅₀ values. ANOVA followed by Tukey’s post hoc was used to evaluate the potential differences among monotherapy and combination treatment groups. Analyses were performed using R 3.3.2 software. P-value <0.05 was considered to be statistically significant.

Results

NaPB was shown to inhibit the growth of A549, Calu1, and H1650 cell lines in a dose-dependent manner (IC₅₀ 10, 8.53, and 4.53 mM, respectively). Furthermore, the addition of NaPB along with cisplatin, erlotinib, or gefitinib to A549, Calu1, and H1650 cell lines resulted in a synergistic antiproliferative effect against the three NSCLC cell lines (R>1.6, P-value <0.05), thus suggesting that NaPB can potentiate the effect of cisplatin, erlotinib, and gefitinib on A549, Calu1, and H1650 cell lines.

Conclusion

Current results suggest a potential role of NaPB as a sensitizing agent in NSCLC.

Molecular analysis of LPIN1 in Jordanian patients with rhabdomyolysis

Recessive mutations in LPIN1, which encodes a phosphatidate phosphatase enzyme, are a frequent cause of severe rhabdomyolysis in childhood. Hence, we sequenced the 19 coding exons of the gene in eight patients with recurrent hereditary myoglobinuria from four unrelated families in Jordan. The long-term goal is to facilitate molecular genetic diagnosis without the need for invasive procedures such as muscle biopsies. Three different mutations were detected, including the novel missense mutation c.2395G>C (Gly799Arg), which was found in two families. The two other mutations, c.2174G>A (Arg725His) and c.1162C>T (Arg388X), have been previously identified, and were found to cosegregate with the disease phenotype in the other two families. Intriguingly, patients homozygous for Arg725His were also homozygous for the c.1828C>T (Pro610Ser) polymorphism, and were exercise-intolerant between myoglobinuria episodes. Notably, patients homozygous for Arg388X were also homozygous for the c.2250G>C silent variant (Gly750Gly). Taken together, the data provide family-based evidence linking hereditary myoglobinuria to pathogenic variations in the C-terminal lipin domain of the enzyme. This finding highlights the functional significance of this domain in the absence of structural information. This is the first analysis of LPIN1 in myoglobinuria patients of Jordanian origin, and the fourth such analysis worldwide.

•

LPIN1 mutations were cataloged in families with hereditary myoglobinuria.

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A novel missense Gly799Arg mutation was identified.

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Arg725His, the only other known missense mutation, was confirmed to be pathogenic.

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Arg388X, a known nonsense mutation, was the most common among Arabic patients.

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Patients exercise-intolerant between myoglobinuria episodes have a second mutation.

Two novel mutations of FBN1 in Jordanian patients with Marfan syndrome

Marfan syndrome is an autosomal dominant inheritance disorder with a 1/5000-live-birth prevalence. More than 3000 mutations have been characterized thus far in the FBN1 gene. The goal of this study is to facilitate Marfan syndrome diagnosis in Jordanian patients using a molecular genetic testing. All of the 65 coding exons and flanking intronic sequences of the FBN1 gene were amplified using polymerase chain reaction and were subjected to sequencing in five unrelated Jordanian patients suspected of having Marfan syndrome. Four different mutations were identified, including two novel mutations: the c.1553dupG frame-shift (p.Tyr519Ilefs*14) and the c.6650G>A (p.Cys2217Tyr) missense mutations. Two other missense mutations, c.2243G>A (p.Cys748Tyr) and c.2432G>A (p.Cys811Tyr), have been previously detected. Patient number five was heterozygous for the synonymous substitution variant c.1875T>C (p.Asn625Asn; rs#25458). Additionally, eight variants in the intronic sequence of the FBN1 gene were identified, of which the c.2168-46A>G mutation was a new variant. The data provide molecular-based evidence linking Marfan syndrome to pathogenic mutations in the FBN1 gene among Jordanians for the first time. Thus, our results will contribute to the better management of the disease using molecular tools and will help in genetic counseling of the patients' families.

Custom genotyping for substance addiction susceptibility genes in Jordanians of Arab descent

Background

Both environmental and genetic factors contribute to individual susceptibility to initiation of substance use and vulnerability to addiction. Determining genetic risk factors can make an important contribution to understanding the processes leading to addiction. In order to identify gene(s) and mechanisms associated with substance addiction, a custom platform array search for a genetic association in a case/control of homogenous Jordanian Arab population was undertaken. Patients meeting the DSM-VI criteria for substance dependence (n = 220) and entering eight week treatment program at two Jordanian Drug Rehabilitation Centres were genotyped. In addition, 240 healthy controls were also genotyped. The sequenom MassARRAY system (iPLEX GOLD) was used to genotype 49 single nucleotide polymorphisms (SNPs) within 8 genes (DRD1, DRD2, DRD3, DRD4, DRD5, BDNF, SLC6A3 and COMT).

Results

This study revealed six new associations involving SNPs within DRD2 gene on chromosome 11. These six SNPs within the DRD2 were found to be most strongly associated with substance addiction in the Jordanian Arabic sample. The strongest statistical evidence for these new association signals were from rs1799732 in the C/−C promoter and rs1125394 in A/G intron 1 regions of DRD2, with the overall estimate of effects returning an odds ratio of 3.37 (χ2 (2, N = 460) = 21, p-value = 0.000026) and 1.78 (χ2 (2, N = 460) = 8, p-value = 0.001), respectively. It has been suggested that DRD2, dopamine receptor D2, plays an important role in dopamine secretion and the signal pathways of dopaminergic reward and drug addiction.

Conclusion

This study is the first to show a genetic link to substance addiction in a Jordanian population of Arab descent. These findings may contribute to our understanding of drug addiction mechanisms in Middle Eastern populations and how to manage or dictate therapy for individuals. Comparative analysis with different ethnic groups could assist further improving our understanding of these mechanisms.

Mu opioid receptor (OPRM1) as a predictor of treatment outcome in opiate-dependent individuals of Arab descent

BACKGROUND

A number of research studies on the genetics of opiate dependence have focused on the μ-opioid receptor (OPRM1), which is a primary target for opiates. This study aims to identify genetic polymorphisms within the OPRM1 gene involved in response to the biopsychosocial treatment in opiate-dependent individuals of Arab descent.

METHODS

Unrelated Jordanian Nationals of Arab descent (N = 183) with opiate dependence were selected for this study. These individuals, all males, met the DSM-IV criteria for opiate dependence and were undergoing a voluntary 8-week treatment program at a Jordanian Drug Rehabilitation Centre. All individuals were genotyped for 22 single nucleotide polymorphisms (SNPs) within the OPRM1 gene using the Sequenom MassARRAY(®) system (iPLEX GOLD). Statistical analyses were carried out using the R package.

RESULTS

Patients receiving biopsychosocial treatment showed that there was a significant difference in their OPRM1 SNPs' genotyping distribution between good, moderate, and poor responders to the treatment at two sites (rs6912029 [G-172T], and rs12205732 [G-1510A], P < 0.05, Fisher's exact test).

CONCLUSION

This study is the first report of an association between the OPRM1 G-172T and G-1510A polymorphisms and treatment response for opiate dependence. Specifically, this study demonstrated that the OPRM1 GG-172 and GG-1510 genotypes were more frequent among patients who were nonresponders to the biopsychosocial treatment. However, further pharmacogenetic studies in a larger cohort of opiate-dependent patients of Arab descent are needed to confirm these findings and identify individuals with increased chance of relapse.

Association of interleukin-10 gene promoter polymorphisms with chronic and aggressive periodontitis

OBJECTIVE

Interleukin-10 gene promoter polymorphisms have been associated with interleukin-10 decreased production, thereby playing a role in the pathogenesis of periodontitis. This study aimed to investigate whether interleukin-10 single nucleotide polymorphisms at positions -1087(G/A) and -597(C/A) are associated with generalised chronic periodontitis and localised aggressive periodontitis.

METHODS

Genomic DNA samples were isolated from 276 unrelated Jordanian participants. Subjects were categorised into 86 periodontally healthy controls, 105 chronic periodontitis patients and 85 localised aggressive periodontitis patients. Genotype frequencies were calculated, and differences were determined using Pearson chi-squared test, and odds ratio and 95% confidence intervals were included.

RESULTS

The frequencies of the -1087A and -597A alleles were significantly more common in chronic periodontitis patients than controls. The A-positive allele genotypes (GA, AA) at position -1087 and A-positive allele genotypes (CA, AA) at position -597 appeared to increase the risk of having chronic periodontitis. No significant differences were observed in the genotype frequencies between localised aggressive periodontitis patients and controls.

CONCLUSIONS

These findings indicate the possible use of interleukin-10 single nucleotide polymorphisms as genetic markers in chronic periodontitis patients and further emphasise the molecular differences between chronic periodontitis and aggressive periodontitis.

Characterization of surface proteins of Cronobacter muytjensii using monoclonal antibodies and MALDI-TOF Mass spectrometry

BACKGROUND

Cronobacter spp. is a newly emerging pathogen that causes meningitis in infants and other diseases in elderly and immunocompromised individuals. This study was undertaken to investigate surface antigenic determinants in Cronobacter spp. using monoclonal antibodies (MAbs) and MALDI-TOF Mass spectrometry.

RESULTS

Spleenocytes from mice that were immunized with heat-killed (20 min, 80°C) Cronobacter cells were fused with SP2 myeloma cells. Five desirable MAbs (A1, B5, 2C2, C5 and A4) were selected. MAbs A1, B5, 2C2 and C5 were of IgG2a isotype while A4 was an IgM. Specificity of the MAbs was determined by using immunoblotting with outer membrane protein preparations (OMPs) extracted from 12 Cronobacter and 6 non-Cronobacter bacteria. All MAbs recognized proteins with molecular weight ranging between 36 and 49 kDa except for one isolate (44) in which no OMPs were detected. In addition, MAbs recognized two bands (38-41 kDa) in four of the non-Cronobacter bacteria. Most of the proteins recognized by the MAbs were identified by MALDI-TOF peptide sequencing and appeared to be heterogeneous with the identities of some of them are still unknown. All MAbs recognized the same epitope as determined by an additive Index ELISA with their epitopes appeared to be conformational rather than sequential. Further, none of the MAbs recognized purified LPS from Cronobacter spp. Specificity of the MAbs toward OMPs was further confirmed by transmission electron microscopy.

CONCLUSIONS

Results obtained in this study highlight the immunological cross-reactivity among Cronobacter OMPs and their Enterobacteriaceae counterparts. Nevertheless, the identity of the identified proteins appeared to be different as inferred from the MALDI-TOF sequencing and identification.

Transcriptome analysis of mouse stem cells and early embryos

Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

250,000 EST sequences from oocytes, blastocysts, and embryonic and adult stem cells contribute to the annotation of the mouse genome and suggest genes that contribute to the unique features of these developmental stages and cell types

Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity

Large-scale gene expression profiling was performed on embryo-derived stem cell lines to identify molecular signatures of pluripotency and lineage specificity. Analysis of pluripotent embryonic stem (ES) cells, extraembryonic-restricted trophoblast stem (TS) cells, and terminally-differentiated mouse embryo fibroblast (MEF) cells identified expression profiles unique to each cell type, as well as genes common only to ES and TS cells. Whereas most of the MEF-specific genes had been characterized previously, the majority (67%) of the ES-specific genes were novel and did not include known differentiated cell markers. Comparison with microarray data from embryonic material demonstrated that ES-specific genes were underrepresented in all stages sampled, whereas TS-specific genes included known placental markers. Investigation of four novel TS-specific genes showed trophoblast-restricted expression in cell lines and in vivo, whereas one uncharacterized ES-specific gene, Esg-1, was found to be exclusively associated with pluripotency. We suggest that pluripotency requires a set of genes not expressed in other cell types, whereas lineage-restricted stem cells, like TS cells, express genes predictive of their differentiated lineage.

Genomic organization and promoter regulation of human cytochrome c oxidase subunit VII heart/muscle isoform (COX7AH)

We have isolated and characterized the human gene (COX7AH) for the contractile muscle isoform of cytochrome c oxidase (COX) subunit VIIa. This subunit is one of the 10 nuclear encoded subunits of the 13-subunit holoenzyme that carries out the terminal step in the electron transport chain. Using transient transfection assays, we have located a 5'-flanking region sufficient to direct high level, skeletal myotube-specific reporter gene expression. This 792 bp basal promoter, which contains the single transcription start but no canonical TATA or CCAAT boxes, contains one MEF2 site, three E boxes, and an Sp1 site that show binding to their cognate factors, and are all required for full expression. Mutation and transactivation analysis suggest that there is functional interaction between these binding sites.

Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray

cDNA microarray technology has been increasingly used to monitor global gene expression patterns in various tissues and cell types. However, applications to mammalian development have been hampered by the lack of appropriate cDNA collections, particularly for early developmental stages. To overcome this problem, a PCR-based cDNA library construction method was used to derive 52,374 expressed sequence tags from pre- and peri-implantation embryos, embryonic day (E) 12.5 female gonad/mesonephros, and newborn ovary. From these cDNA collections, a microarray representing 15,264 unique genes (78% novel and 22% known) was assembled. In initial applications, the divergence of placental and embryonic gene expression profiles was assessed. At stage E12.5 of development, based on triplicate experiments, 720 genes (6.5%) displayed statistically significant differences in expression between placenta and embryo. Among 289 more highly expressed in placenta, 61 placenta-specific genes encoded, for example, a novel prolactin-like protein. The number of genes highly expressed (and frequently specific) for placenta has thereby been increased 5-fold over the total previously reported, illustrating the potential of the microarrays for tissue-specific gene discovery and analysis of mammalian developmental programs.

Transcriptional regulation of mammalian cytochrome c oxidase genes

The cytochrome c oxidase (COX) holoenzyme is a 13-subunit complex that carries out the terminal step in the electron transport chain. Three of the subunits, which contain the electron transfer function, are coded by mitochondrial DNA and the other ten subunits by nuclear DNA. Since the holoenzyme contains equivalent amounts of each subunit, we and others have examined transcriptional regulation of COX nuclear subunits to explore whether there is a common basis for co-regulation. Each gene is seen to have a unique pattern of recognition by regulatory factors; although some factors bind to more than one gene, not all COX genes seem to be regulated by the same set of factors. Current information about the COX promoters that have been examined is summarized, and the relation of promoter regulation to coordinate gene expression is discussed.

Tissue-specific expression and mapping of the Cox7ah gene in mouse

We have isolated and examined the gene for the heart isoform of cytochrome c oxidase subunit VIIa (COX VIIa-H) in mouse, an isoform gene previously thought to be lacking in rodents. Interspecies amino acid comparisons indicate that mouse COX VIIa-H protein displays 82.5 and 70.9% identity with the bovine and human heart isoforms of COX VIIa, but only 53.7% identity with the paralogous mouse liver isoform (COX VIIa-L). Expression in adult mouse tissues is limited to heart and skeletal muscle, as found in other species. In the early mouse embryo, Cox7al was the exclusive isoform expressed and Cox7ah mRNA was not detectable until day 17 postcoitum. That the mouse Cox7ah gene characterized in this study is orthologous to the human COX7AH gene was also suggested by its mapping to mouse chromosome 7, to a conserved region syntenic with the human chromosome location of COX7AH, 19q13.1. As a result, all three COX heart isoform genes in mouse group to chromosome 7. Interestingly, mapping of the mouse Cox7al to chromosome 9 suggests a new syntenic region between the mouse and the human genomes.

Molecular evolution of cytochrome c oxidase: rate variation among subunit VIa isoforms

Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We examined relative evolutionary rates for the COX6A heart (H) and liver (L) isoform genes along the length of the molecule, specifically in relation to the tissue-specific function(s) of the two isoforms. Nonsynonymous (amino acid replacement) substitutions in the COX6AH gene occurred more frequently than in the ubiquitously expressed COX6AL gene. Maximum-parsimony analysis and sequence divergences from reconstructed ancestral sequences revealed that after the ancestral COX6A gene duplicated to yield the genes for the H and L isoforms, the sequences encoding the mitochondrial matrix region of the COX VIa protein experienced an elevated rate of nonsynonymous substitutions relative to synonymous substitutions. This is expected for relaxed selective constraints after gene duplication followed by purifying selection to preserve the replacements with tissue-specific functions.