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1.
Cell ; 175(2): 372-386.e17, 2018 10 04.
Article in English | MEDLINE | ID: mdl-30270042

ABSTRACT

Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD.


Subject(s)
Inflammatory Bowel Diseases/physiopathology , Mesoderm/physiology , Animals , Cell Proliferation , Colitis/genetics , Colitis/physiopathology , Colon/physiology , Epithelial Cells/metabolism , Fibroblasts/physiology , Genetic Heterogeneity , Homeostasis , Humans , Inflammation , Intestinal Mucosa/immunology , Intestinal Mucosa/physiology , Intestines/immunology , Intestines/physiology , Mesenchymal Stem Cells/physiology , Mesoderm/metabolism , Mice , Mice, Inbred C57BL , Myofibroblasts , Pericytes , RAW 264.7 Cells , SOXD Transcription Factors/physiology , Single-Cell Analysis/methods , Thromboplastin/physiology , Tumor Necrosis Factor Ligand Superfamily Member 14/genetics , Wnt Signaling Pathway/physiology
2.
Immunity ; 50(4): 1029-1031, 2019 04 16.
Article in English | MEDLINE | ID: mdl-30995495

ABSTRACT

Genome-wide association studies in ulcerative colitis point to a role for FcγRIIA, a receptor for IgG. Castro-Dopico et al. (2019) find a profound induction of anti-commensal IgG in the colonic mucosa of UC patients and outline a pathway whereby FcγR activation by IgG triggers IL-1ß production, type 17 immunity, and the exacerbation of inflammation.


Subject(s)
Colitis, Ulcerative , Colitis , Colon , Genome-Wide Association Study , Humans , Immunoglobulin G , Inflammation , Intestinal Mucosa
3.
Nature ; 567(7746): 49-55, 2019 03.
Article in English | MEDLINE | ID: mdl-30814735

ABSTRACT

The colonic epithelium facilitates host-microorganism interactions to control mucosal immunity, coordinate nutrient recycling and form a mucus barrier. Breakdown of the epithelial barrier underpins inflammatory bowel disease (IBD). However, the specific contributions of each epithelial-cell subtype to this process are unknown. Here we profile single colonic epithelial cells from patients with IBD and unaffected controls. We identify previously unknown cellular subtypes, including gradients of progenitor cells, colonocytes and goblet cells within intestinal crypts. At the top of the crypts, we find a previously unknown absorptive cell, expressing the proton channel OTOP2 and the satiety peptide uroguanylin, that senses pH and is dysregulated in inflammation and cancer. In IBD, we observe a positional remodelling of goblet cells that coincides with downregulation of WFDC2-an antiprotease molecule that we find to be expressed by goblet cells and that inhibits bacterial growth. In vivo, WFDC2 preserves the integrity of tight junctions between epithelial cells and prevents invasion by commensal bacteria and mucosal inflammation. We delineate markers and transcriptional states, identify a colonic epithelial cell and uncover fundamental determinants of barrier breakdown in IBD.


Subject(s)
Colon/cytology , Colon/pathology , Epithelial Cells/classification , Epithelial Cells/cytology , Health , Inflammatory Bowel Diseases/pathology , Ion Channels/metabolism , Animals , Biomarkers/analysis , Colitis, Ulcerative/genetics , Colitis, Ulcerative/microbiology , Colitis, Ulcerative/pathology , Colon/microbiology , Epithelial Cells/microbiology , Epithelial Cells/pathology , Genetic Predisposition to Disease/genetics , Goblet Cells/cytology , Goblet Cells/metabolism , Goblet Cells/pathology , Humans , Hydrogen-Ion Concentration , Inflammatory Bowel Diseases/genetics , Inflammatory Bowel Diseases/microbiology , Intestinal Mucosa/metabolism , Intestinal Mucosa/microbiology , Intestinal Mucosa/pathology , Male , Mice , Natriuretic Peptides/metabolism , Proteins/metabolism , Single-Cell Analysis , Stem Cells/cytology , Stem Cells/metabolism , Stem Cells/pathology , Tight Junctions/metabolism , Transcription, Genetic , WAP Four-Disulfide Core Domain Protein 2
4.
Mod Pathol ; : 100543, 2024 Jun 17.
Article in English | MEDLINE | ID: mdl-38897453

ABSTRACT

Gastrointestinal (GI) tract involvement by Langerhans cell histiocytosis (LCH) is rare and its clinicopathologic characteristics have only been described in case reports and small series. We reviewed hematoxylin and eosin- and CD1a, S100, and Langerin immunohistochemical-stained slides from 47 patients with well-documented demographic and clinical findings. Our cases included 8 children and 39 adults, with a mean follow-up of 63 months. All pediatric patients had concurrent multisystem LCH, presented with GI symptoms, and showed non-polypoid lesions. Seven (88%) showed multifocal GI disease, including five with multiple GI organ involvement. All sampled lesions from children exhibited infiltrative growth. More than half had died of the disease or manifested persistent LCH at last follow-up. Twenty-five of 39 (64%) adults had LCH involving only the GI tract (single-system), with the remaining 14 (36%) exhibiting multi-system disease. Adult single-system GI LCH was typically encountered incidentally on screening/surveillance endoscopy (72%). Most exhibited isolated colorectal involvement (88%) as a solitary polyp (92%), with a well-demarcated/noninfiltrative growth pattern (70%), and excellent prognosis (100%). In comparison, adult patients with multi-system LCH more frequently presented with GI symptoms (92%, P<0.001), non-colorectal GI site involvement (50%, P=0.02), multifocal GI lesions (43%, P=0.005), non-polypoid lesions (71%, P<0.001), infiltrative histologic growth pattern (78%, P=0.04), and persistent disease (57%, P<0.001). Adult multi-system LCH patients appear to exhibit similar clinicopathologic features to those of pediatric patients. These results demonstrate that adults with single-system LCH involving the GI tract have an excellent prognosis, while multi-system LCH occurring at any age carries an unfavorable prognosis. High-risk features of GI LCH include pediatric age, GI symptomatology, non-colorectal GI involvement, multifocal GI disease, non-polypoid lesions, and infiltrative growth pattern.

5.
Am J Otolaryngol ; 45(1): 104088, 2024.
Article in English | MEDLINE | ID: mdl-37832329

ABSTRACT

PURPOSE: To determine if an endoscopic otologic and rhinologic examination performed by a patient and interpreted remotely by an otolaryngologist is non-inferior to in-person examination, and to assess the feasibility of this system for telemedical visits. MATERIALS AND METHODS: Twenty healthy subjects performed a self-examination of their ears and nose using a commercially available endoscope under remote guidance by an otolaryngology provider over Zoom. This same provider and another otolaryngologist also performed separate, in-person examinations of each subject and rated their findings. Finally, both providers blindly reviewed a video recording of each virtual exam four weeks later and rated their findings. Subjects were surveyed about their experience. Interrater reliability was calculated using Cohen's kappa coefficients and the ability to detect different anatomic structures and features by in-person vs. virtual examination was compared using Wilcoxon tests and Chi-squared proportion tests. RESULTS: The subjects' average age was 30 (SD 11.5) years. Interrater reliability was excellent; kappa coefficients were 0.72 and 0.81 (p < 0.001) for virtual and in-person exams, respectively. Of the 3 anatomic structures within the ear exam, none showed a difference in detectability between virtual and in-person exams. Of the 12 structures in the nasal exam, 3 were better visualized in-person and 9 showed no difference. Subject satisfaction was excellent; the average likelihood of recommending this virtual technology to peers (1-10) was 8.65 (SD 1.4). CONCLUSIONS: Patient self-examination of the ears and nose using a portable endoscope may be an effective strategy for obtaining valuable data during telemedical otolaryngology visits.


Subject(s)
Otolaryngology , Humans , Adult , Reproducibility of Results , Otolaryngologists , Physical Examination , Video Recording
6.
Cancer Cell Int ; 23(1): 165, 2023 Aug 11.
Article in English | MEDLINE | ID: mdl-37568162

ABSTRACT

BACKGROUND: Breast malignancies are the predominant cancer-related cause of death in women. New methods of diagnosis, prognosis and treatment are necessary. Previously, we identified the breast cancer cell surface protein ADAM8 as a marker of poor survival, and a driver of Triple-Negative Breast Cancer (TNBC) growth and spread. Immunohistochemistry (IHC) with a research-only anti-ADAM8 antibody revealed 34.0% of TNBCs (17/50) expressed ADAM8. To identify those patients who could benefit from future ADAM8-based interventions, new clinical tests are needed. Here, we report on the preclinical development of a highly specific IHC assay for detection of ADAM8-positive breast tumors. METHODS: Formalin-fixed paraffin-embedded sections of ADAM8-positive breast cell lines and patient-derived xenograft tumors were used in IHC to identify a lead antibody, appropriate staining conditions and controls. Patient breast cancer samples (n = 490) were used to validate the assay. Cox proportional hazards models assessed association between survival and ADAM8 expression. RESULTS: ADAM8 staining conditions were optimized, a lead anti-human ADAM8 monoclonal IHC antibody (ADP2) identified, and a breast staining/scoring control cell line microarray (CCM) generated expressing a range of ADAM8 levels. Assay specificity, reproducibility, and appropriateness of the CCM for scoring tumor samples were demonstrated. Consistent with earlier findings, 36.1% (22/61) of patient TNBCs expressed ADAM8. Overall, 33.9% (166/490) of the breast cancer population was ADAM8-positive, including Hormone Receptor (HR) and Human Epidermal Growth Factor Receptor-2 (HER2) positive cancers, which were tested for the first time. For the most prevalent HR-positive/HER2-negative subtype, high ADAM8 expression identified patients at risk of poor survival. CONCLUSIONS: Our studies show ADAM8 is widely expressed in breast cancer and provide support for both a diagnostic and prognostic value of the ADP2 IHC assay. As ADAM8 has been implicated in multiple solid malignancies, continued development of this assay may have broad impact on cancer management.

7.
PLoS Genet ; 14(4): e1007352, 2018 04.
Article in English | MEDLINE | ID: mdl-29684080

ABSTRACT

Patients with heritable cancer syndromes characterized by germline PTEN mutations (termed PTEN hamartoma tumor syndrome, PHTS) benefit from PTEN-enabled cancer risk assessment and clinical management. PTEN-wildtype patients (~50%) remain at increased risk of developing certain cancers. Existence of germline mutations in other known cancer susceptibility genes has not been explored in these patients, with implications for different medical management. We conducted a 4-year multicenter prospective study of incident patients with features of Cowden/Cowden-like (CS/CS-like) and Bannayan-Riley-Ruvalcaba syndromes (BRRS) without PTEN mutations. Exome sequencing and targeted analysis were performed including 59 clinically actionable genes from the American College of Medical Genetics and Genomics (ACMG) and 24 additional genes associated with inherited cancer syndromes. Pathogenic or likely pathogenic cancer susceptibility gene alterations were found in 7 of the 87 (8%) CS/CS-like and BRRS patients and included MUTYH, RET, TSC2, BRCA1, BRCA2, ERCC2 and HRAS. We found classic phenotypes associated with the identified genes in 5 of the 7 (71.4%) patients. Variant positive patients were enriched for the presence of second malignant neoplasms compared to patients without identified variants (OR = 6.101, 95% CI 1.143-35.98, p = 0.035). Germline variant spectrum and frequencies were compared to The Cancer Genome Atlas (TCGA), including 6 apparently sporadic cancers associated with PHTS. With comparable overall prevalence of germline variants, the spectrum of mutated genes was different in our patients compared to TCGA. Intriguingly, we also found notable enrichment of variants of uncertain significance (VUS) in our patients (OR = 2.3, 95% CI 1.5-3.5, p = 0.0002). Our data suggest that only a small subset of PTEN-wildtype CS/CS-like and BRRS patients could be accounted for by germline variants in some of the known cancer-related genes. Thus, the existence of alterations in other and more likely non-classic cancer-associated genes is plausible, reflecting the complexity of these heterogeneous hereditary cancer syndromes.


Subject(s)
Germ-Line Mutation , Hamartoma Syndrome, Multiple/genetics , Oncogenes , PTEN Phosphohydrolase/genetics , Adolescent , Adult , Aged , Child , Child, Preschool , DNA Glycosylases/genetics , DNA Mutational Analysis , Female , Genes, BRCA1 , Genes, BRCA2 , Genetic Predisposition to Disease , Genetic Variation , Humans , Infant , Male , Middle Aged , Neoplasms, Multiple Primary/genetics , Prospective Studies , Proto-Oncogene Proteins c-ret/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Tuberous Sclerosis Complex 2 Protein , Tumor Suppressor Proteins/genetics , Exome Sequencing , Xeroderma Pigmentosum Group D Protein/genetics , Young Adult
8.
N Engl J Med ; 387(5): 452-458, 2022 08 04.
Article in English | MEDLINE | ID: mdl-35921455
9.
Environ Sci Technol ; 53(6): 3166-3176, 2019 03 19.
Article in English | MEDLINE | ID: mdl-30763514

ABSTRACT

Anaerobic biological secondary treatment has the potential to substantially reduce the energy cost and footprint of wastewater treatment. However, for utilities seeking to meet future water demand through potable reuse, the compatibility of anaerobically treated secondary effluent with potable reuse trains has not been evaluated. This study characterized the effects of different combinations of chloramines, ozone, and biological activated carbon (BAC), applied as pretreatments to mitigate organic chemical fouling of reverse osmosis (RO) membranes, and the production of 43 disinfection byproducts (DBPs). The study employed effluent from a pilot-scale anaerobic reactor and soluble microbial products (SMPs) generated from a synthetic wastewater. Ozonation alone minimized RO flux decline by rendering the dissolved organic carbon (DOC) more hydrophilic. When combined with chloramination, ozone addition after chloramines maintained a higher RO flux. BAC treatment was ineffective for reducing the pressure and energy requirements for a set permeate flux. Regardless of pretreatment method prior to RO, the total DBP concentrations were <14 µg/L upstream of RO. After treatment by RO, the UV/hydrogen peroxide advanced oxidation process, and chloramination, the total DBP concentrations were ≤5 µg/L. When DBP concentrations were weighted by metrics of toxic potency, the total DBP calculated toxicity was 4-fold lower than observed previously in full-scale potable reuse facilities receiving aerobically treated secondary effluent. The RO fouling and DBP formation behavior of anaerobic SMPs were similar to that of the pilot-scale anaerobic effluent. The results of this study are promising, but more research is needed to evaluate whether anaerobic effluent is suitable as an influent to potable reuse trains.


Subject(s)
Disinfection , Water Purification , Anaerobiosis , Chloramines , Filtration
10.
J Pediatr Gastroenterol Nutr ; 68(1): 50-55, 2019 01.
Article in English | MEDLINE | ID: mdl-30074576

ABSTRACT

OBJECTIVES: No formal comparative effectiveness studies have been conducted to evaluate the effect of eosinophilic esophagitis (EoE) treatment choice on long-term growth in pediatric patients. Long-term studies of inhaled corticoid steroids in asthma, however, suggest possible effects on linear growth. The aim of this study was to compare longitudinal, anthropometric growth in children with EoE according to treatment approach. METHODS: We conducted a retrospective, multicenter cohort study of anthropometric growth (height and body mass index [BMI] z scores) in pediatric (<18 years of age) patients newly diagnosed with EoE across 5 clinical sites between 2005 and 2014. We compared differences in growth according to treatment approach over a 12-month period. Modification by sex and age was examined and sensitivity analyses were conducted to assess robustness of results given study assumptions. RESULTS: In the 409 patients identified, the mean age and proportion male differed by treatment (P =  < 0.01 and P = 0.04, respectively). Baseline growth measures were associated with slight impairment of height at diagnosis (median baseline height z score of -0.1 [interquartile range -0.9, 0.8]). In general, treatment approach was not associated with any significant increase or decrease in expected growth over a 12-month period. Subtle decrease in linear growth was observed with treatment using a combined elemental and topical steroid (Δ height z score [adjusted]: -0.04; 95% confidence interval [CI]: -0.08, -0.01). Differences in linear growth differed by sex (P for interaction <0.01). For elemental formula in combination with topical steroids, only girls exhibited a significant decline in linear growth (Δ height z score [adjusted]: -0.24; 95% CI: -0.32, -0.17). A slight reduction in BMI was observed for patients treated with a combination of elemental diet and dietary elimination (Δ BMI z score [adjusted]: -0.07; 95% CI: -0.13, -0.01). CONCLUSIONS: Treatment of EoE, in general, is not associated with major anthropometric growth changes in most pediatric patients. Slight linear growth impairment was observed for topical steroid treatment, and sex differences in growth by treatment approach were observed. Future prospective studies should evaluate the effect of treatment on optimal growth and development and over a longer period of follow-up.


Subject(s)
Adrenal Cortex Hormones/adverse effects , Body Height/drug effects , Body Weight/drug effects , Eosinophilic Esophagitis/drug therapy , Eosinophilic Esophagitis/physiopathology , Administration, Topical , Adolescent , Adrenal Cortex Hormones/administration & dosage , Anthropometry , Child , Child Development/drug effects , Child, Preschool , Comparative Effectiveness Research , Female , Humans , Longitudinal Studies , Male , Retrospective Studies , Sex Factors , Treatment Outcome
12.
South Med J ; 111(6): 328-332, 2018 06.
Article in English | MEDLINE | ID: mdl-29863219

ABSTRACT

OBJECTIVES: Differences in the initial management of pediatric eosinophilic esophagitis (EoE) by practice setting have not been well characterized. We aimed to characterize these differences for sites in the Carolinas EoE Collaborative (CEoEC), a multicenter network of academic and community practices. METHODS: We performed a retrospective cohort study of pediatric EoE patients at five CEoEC sites: University of North Carolina (UNC) Hospital, Charlotte Asthma and Allergy Specialists, Greenville Health Systems, Wake Forest Baptist Medical Center, and the Medical University of South Carolina Hospital. Cases of EoE were defined by consensus guidelines. Data were extracted from electronic medical records. We tested for differences among sites and used a multinomial model (polytomous regression) to assess associations between treatment and site, adjusting on patient factors. RESULTS: We identified 464 children with EoE across the CEoEC sites. The median age was highest at Wake Forest (11.4 years), the median eosinophil count was highest at UNC (69 eos/hpf), and UNC had the most male patients (82%). UNC used topical steroids for initial treatment in 86% of cases, compared with <1% in Greenville (P < 0.01). Greenville used dietary elimination more frequently than UNC (81% vs 2%, P < 0.01). Differences in treatment approach held after adjusting for potential baseline confounders. There was no significant association between patient factors and initial treatment approach. CONCLUSIONS: Significant differences in EoE patient factors and treatment approaches were identified across CEoEC sites and were not explained by patient or practice factors. This suggests that institutional or provider preferences drive initial treatment approaches, and that more data are needed to drive best practice decisions.


Subject(s)
Eosinophilic Esophagitis/diagnosis , Practice Patterns, Physicians'/statistics & numerical data , Research Design/trends , Adolescent , Child , Child, Preschool , Cohort Studies , Electronic Health Records , Eosinophilic Esophagitis/epidemiology , Female , Humans , Male , North Carolina/epidemiology , Retrospective Studies , South Carolina/epidemiology
13.
J Allergy Clin Immunol ; 139(2): 607-620.e15, 2017 02.
Article in English | MEDLINE | ID: mdl-27477328

ABSTRACT

BACKGROUND: Patients with heterozygous germline mutations in phosphatase and tensin homolog deleted on chromosome 10 (PTEN) experience autoimmunity and lymphoid hyperplasia. OBJECTIVES: Because regulation of the phosphoinositide 3-kinase (PI3K) pathway is critical for maintaining regulatory T (Treg) cell functions, we investigate Treg cells in patients with heterozygous germline PTEN mutations (PTEN hamartoma tumor syndrome [PHTS]). METHODS: Patients with PHTS were assessed for immunologic conditions, lymphocyte subsets, forkhead box P3 (FOXP3)+ Treg cell levels, and phenotype. To determine the functional importance of phosphatases that control the PI3K pathway, we assessed Treg cell induction in vitro, mitochondrial depolarization, and recruitment of PTEN to the immunologic synapse. RESULTS: Autoimmunity and peripheral lymphoid hyperplasia were found in 43% of 79 patients with PHTS. Immune dysregulation in patients with PHTS included lymphopenia, CD4+ T-cell reduction, and changes in T- and B-cell subsets. Although total CD4+FOXP3+ Treg cell numbers are reduced, frequencies are maintained in the blood and intestine. Despite pathogenic PTEN mutations, the FOXP3+ T cells are phenotypically normal. We show that the phosphatase PH domain leucine-rich repeat protein phosphatase (PHLPP) downstream of PTEN is highly expressed in normal human Treg cells and provides complementary phosphatase activity. PHLPP is indispensable for the differentiation of induced Treg cells in vitro and Treg cell mitochondrial fitness. PTEN and PHLPP form a phosphatase network that is polarized at the immunologic synapse. CONCLUSION: Heterozygous loss of function of PTEN in human subjects has a significant effect on T- and B-cell immunity. Assembly of the PTEN-PHLPP phosphatase network allows coordinated phosphatase activities at the site of T-cell receptor activation, which is important for limiting PI3K hyperactivation in Treg cells despite PTEN haploinsufficiency.


Subject(s)
B-Lymphocytes/physiology , Hamartoma Syndrome, Multiple/immunology , Immunological Synapses/metabolism , Lymphocyte Subsets/physiology , Nuclear Proteins/metabolism , PTEN Phosphohydrolase/metabolism , Phosphoprotein Phosphatases/metabolism , T-Lymphocytes, Regulatory/physiology , Adolescent , Adult , Aged , Autoimmunity , Cells, Cultured , Child , Forkhead Transcription Factors/metabolism , Hamartoma Syndrome, Multiple/genetics , Humans , Hyperplasia , Male , Membrane Potential, Mitochondrial , Middle Aged , Mutation/genetics , PTEN Phosphohydrolase/genetics , Protein Binding , Protein Transport , Signal Transduction , Young Adult
14.
Hum Mutat ; 38(10): 1372-1377, 2017 10.
Article in English | MEDLINE | ID: mdl-28677221

ABSTRACT

Germline mutations in the tumor-suppressor gene PTEN predispose to subsets of Cowden syndrome (CS), Bannayan-Riley-Ruvalcaba syndrome, and autism. Evidence-based classification of PTEN variants as either deleterious or benign is urgently needed for accurate molecular diagnosis and gene-informed genetic counseling. We studied 34 different germline PTEN intronic variants from 61 CS patients, characterized their PTEN mRNA processing, and analyzed PTEN expression and downstream readouts of P-AKT and P-ERK1/2. While we found that many mutations near splice junctions result in exon skipping, we also identified the presence of cryptic splicing that resulted in premature termination or a shift in isoform usage. PTEN protein expression is significantly lower in the group with splicing changes while P-AKT, but not P-ERK1/2, is significantly increased. Our observations of these PTEN intronic variants should contribute to the determination of pathogenicity of PTEN intronic variants and aid in genetic counseling.


Subject(s)
Alternative Splicing/genetics , Hamartoma Syndrome, Multiple/genetics , PTEN Phosphohydrolase/genetics , Pathology, Molecular , Adolescent , Adult , Aged , Child , Child, Preschool , Female , Gene Expression Regulation/genetics , Germ-Line Mutation/genetics , Hamartoma Syndrome, Multiple/physiopathology , Humans , MAP Kinase Signaling System/genetics , Male , Middle Aged , Protein Isoforms/genetics , Proto-Oncogene Proteins c-akt/genetics , RNA Splice Sites/genetics , Young Adult
17.
BMC Bioinformatics ; 16: 338, 2015 Oct 23.
Article in English | MEDLINE | ID: mdl-26493399

ABSTRACT

BACKGROUND: The entire collection of genetic information resides within the chromosomes, which themselves reside within almost every cell nucleus of eukaryotic organisms. Each individual chromosome is found to have its own preferred three-dimensional (3D) structure independent of the other chromosomes. The structure of each chromosome plays vital roles in controlling certain genome operations, including gene interaction and gene regulation. As a result, knowing the structure of chromosomes assists in the understanding of how the genome functions. Fortunately, the 3D structure of chromosomes proves possible to construct through computational methods via contact data recorded from the chromosome. We developed a unique computational approach based on optimization procedures known as adaptation, simulated annealing, and genetic algorithm to construct 3D models of human chromosomes, using chromosomal contact data. RESULTS: Our models were evaluated using a percentage-based scoring function. Analysis of the scores of the final 3D models demonstrated their effective construction from our computational approach. Specifically, the models resulting from our approach yielded an average score of 80.41%, with a high of 91%, across models for all chromosomes of a normal human B-cell. Comparisons made with other methods affirmed the effectiveness of our strategy. Particularly, juxtaposition with models generated through the publicly available method Markov chain Monte Carlo 5C (MCMC5C) illustrated the outperformance of our approach, as seen through a higher average score for all chromosomes. Our methodology was further validated using two consistency checking techniques known as convergence testing and robustness checking, which both proved successful. CONCLUSIONS: The pursuit of constructing accurate 3D chromosomal structures is fueled by the benefits revealed by the findings as well as any possible future areas of study that arise. This motivation has led to the development of our computational methodology. The implementation of our approach proved effective in constructing 3D chromosome models and proved consistent with, and more effective than, some other methods thereby achieving our goal of creating a tool to help advance certain research efforts. The source code, test data, test results, and documentation of our method, Gen3D, are available at our sourceforge site at: http://sourceforge.net/projects/gen3d/.


Subject(s)
Chromosomes, Human/genetics , Genome/genetics , B-Lymphocytes , Humans , Models, Theoretical , Sequence Alignment , Templates, Genetic
18.
Gastroenterology ; 146(4): 1028-39, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24417819

ABSTRACT

BACKGROUND & AIMS: Very early onset inflammatory bowel diseases (VEOIBD), including infant disorders, are a diverse group of diseases found in children younger than 6 years of age. They have been associated with several gene variants. Our aim was to identify the genes that cause VEOIBD. METHODS: We performed whole exome sequencing of DNA from 1 infant with severe enterocolitis and her parents. Candidate gene mutations were validated in 40 pediatric patients and functional studies were carried out using intestinal samples and human intestinal cell lines. RESULTS: We identified compound heterozygote mutations in the Tetratricopeptide repeat domain 7 (TTC7A) gene in an infant from non-consanguineous parents with severe exfoliative apoptotic enterocolitis; we also detected TTC7A mutations in 2 unrelated families, each with 2 affected siblings. TTC7A interacts with EFR3 homolog B to regulate phosphatidylinositol 4-kinase at the plasma membrane. Functional studies demonstrated that TTC7A is expressed in human enterocytes. The mutations we identified in TTC7A result in either mislocalization or reduced expression of TTC7A. Phosphatidylinositol 4-kinase was found to co-immunoprecipitate with TTC7A; the identified TTC7A mutations reduced this binding. Knockdown of TTC7A in human intestinal-like cell lines reduced their adhesion, increased apoptosis, and decreased production of phosphatidylinositol 4-phosphate. CONCLUSIONS: In a genetic analysis, we identified loss of function mutations in TTC7A in 5 infants with VEOIBD. Functional studies demonstrated that the mutations cause defects in enterocytes and T cells that lead to severe apoptotic enterocolitis. Defects in the phosphatidylinositol 4-kinase-TTC7A-EFR3 homolog B pathway are involved in the pathogenesis of VEOIBD.


Subject(s)
Inflammatory Bowel Diseases/genetics , Mutation , Proteins/genetics , 1-Phosphatidylinositol 4-Kinase/metabolism , Age of Onset , Apoptosis , Cell Adhesion , Cell Line , Child, Preschool , DNA Mutational Analysis , Enterocolitis/genetics , Enterocytes/metabolism , Enterocytes/pathology , Exome , Female , Genetic Association Studies , Genetic Predisposition to Disease , Heterozygote , Humans , Infant , Infant, Newborn , Inflammatory Bowel Diseases/diagnosis , Inflammatory Bowel Diseases/metabolism , Inflammatory Bowel Diseases/pathology , Inflammatory Bowel Diseases/therapy , Intestinal Atresia/genetics , Lymphocytes/metabolism , Lymphocytes/pathology , Male , Pedigree , Phenotype , Prognosis , Protein Binding , Proteins/metabolism , RNA Interference , Severity of Illness Index , Signal Transduction , Transfection
19.
Int J Cancer ; 135(5): 1238-46, 2014 Sep 01.
Article in English | MEDLINE | ID: mdl-24474587

ABSTRACT

Oncolytic vaccinia virus has been shown to induce a profound, rapid and tumor-specific vascular collapse in both preclinical models and clinical studies; however, a complete examination of the kinetics and levels of collapse and revascularization has not been described previously. Contrast-enhanced ultrasound was used to follow tumor perfusion levels in mouse tumor models at times after vaccinia therapy. It was observed that revascularization after viral therapy was dramatically delayed and did not occur until after viral clearance. This indicated that oncolytic vaccinia may possess a previously undescribed antiangiogenic potential that might synergize with the reported anti-vascular effects. Despite a rapid loss of perfusion and widespread hypoxia within the tumor, it was observed that VEGF levels in the tumor were suppressed throughout the period of active viral infection. Although tumor vasculature could eventually reform after the viral therapy was cleared in mouse models, anti-tumor effects could be significantly enhanced through additional combination with anti-VEGF therapies. This was initially examined using a gene therapy approach (Ad-Flk1-Fc) to target VEGF directly, demonstrating that the timing of application of the antiangiogenic therapy was critical. However, it is also known that oncolytic vaccinia sensitizes tumors to tyrosine kinase inhibitors (TKI) in the clinic through an unknown mechanism. It is possible this phenomenon may be mediated through the antiangiogenic effects of the TKIs. This was modeled in mouse tumors using sunitinib in combination with oncolytic vaccinia. It was observed that prevention of angiogenesis mediated by oncolytic vaccinia can be utilized to enhance the TKI therapy.


Subject(s)
Neoplasms/therapy , Neovascularization, Pathologic/therapy , Oncolytic Virotherapy/methods , Oncolytic Viruses , Vaccinia virus , Vascular Endothelial Growth Factor A/antagonists & inhibitors , Angiogenesis Inhibitors/therapeutic use , Animals , Cell Line, Tumor , Drug Resistance, Neoplasm , Enzyme Inhibitors/therapeutic use , Genetic Therapy , Humans , Indoles/therapeutic use , Mice , Mice, Inbred BALB C , Mice, Nude , Neoplasms/blood supply , Neoplasms/drug therapy , Protein-Tyrosine Kinases/antagonists & inhibitors , Pyrroles/therapeutic use , Sunitinib , Vascular Endothelial Growth Factor A/genetics
20.
Mol Ther ; 21(1): 167-74, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23281444

ABSTRACT

Genetic therapies, including transfected immune cells and viral vectors, continue to show clinical responses as systemically deliverable and targeted therapeutics, with the first such approaches having been approved for cancer treatment. The majority of these employ cytokine transgenes. However, expression of cytokines early after systemic delivery can result in increased toxicity and nonspecific induction of the immune response. In addition, premature immune-mediated clearance of the therapy may result, especially for viral-based approaches. Here, it was initially verified that cytokine (interleukin (IL)2) or chemokine (CCL5) expression from a systemically delivered oncolytic virus resulted in reduced oncolytic activity and suboptimal immune activation, while IL2 also resulted in increased toxicity. However, all these limitations could be overcome through incorporation of exogenous regulation of cytokine or chemokine transgene function through fusion of a small and externally controllable destabilizing domain to the protein of interest. Regulation allowed an initial phase without cytokine function, permitting enhanced delivery and oncolytic activity before activation of cytokine function and a subsequent phase of enhanced and tumor-targeted immunotherapeutic activity. As a result of this exogenous regulation of cytokine function, both oncolytic and immune-mediated mechanisms of action were optimized, greatly enhancing therapeutic activity, while toxicity was significantly reduced.


Subject(s)
Cytokines/physiology , Genetic Therapy , Neoplasms/therapy , Animals , Cytokines/metabolism , Female , Humans , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Oncolytic Virotherapy , Transgenes , Vaccinia virus/metabolism , Vaccinia virus/physiology , Virus Replication
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