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Results for “gene expression variability”

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PubMed1992

Antigen selection in human lymphomagenesis.

Although surface immunoglobulin plays a central role in the differentiation and growth of normal B-cells, its role in the growth of human B-cell malignancies is largely a matter of conjecture. Human follicular lymphomas are attractive systems to study in part because they are clones of cells sharing many similarities with germinal center B-cells which are critically dependent on antigen selection for survival. Nucleotide sequence information was determined for the immunoglobulin heavy chain variable genes expressed by two cases of follicular lymphoma. In addition, the germ line variable gene counterparts were also cloned and sequenced from biopsy material obtained from both of these patients. Numerous mutations from germ line were present in the variable genes from both of these cases, many of which accumulated during expansion and growth of these lymphomas. Moreover, the mutations that accumulated during tumor expansion were distributed in a manner that almost certainly was dependent on positive selection presumably mediated by contact with an antigen. These data indicate that antigen selection is probably important for the growth and clonal evolution of follicular lymphomas.

Antigens, Neoplasm↗
PubMed1996

Analysis of germline and expressed T cell receptor variable region genes in Crohn's disease.

A possible role of the T cell receptor genes in the pathogenesis of Crohn's disease was investigated by 1) comparison of restriction fragment length polymorphisms at the T cell receptor beta chain locus in 64 Crohn's patients and 64 normal controls; 2) semi-quantitative polymerase chain reaction analysis of T cell receptor beta and alpha chain variable region gene expression by lamina propria lymphocytes from resected segments of diseased terminal ileum. We found no association between any of the restriction fragment length polymorphisms and Crohn's disease using polymorphic markers spanning the T cell receptor beta chain locus. Analysis of T cell receptor V beta and V alpha gene expression showed that expression of T cell receptor V region families in terminal ileum lymphocytes from patients with active Crohn's disease was indistinguishable from the lymphocytes found in normal terminal ileum. These data fail to support susceptibility to Crohn's disease being associated with the T cell beta chain antigen receptor genotype. No restricted or dominant T cell receptor variable region gene expression was found in Crohn's disease tissue, compared to normal terminal ileum.

Adult↗
PubMed2005

Integration of gene expression profiling and clinical variables to predict prostate carcinoma recurrence after radical prostatectomy.

BACKGROUND: Gene expression profiling of prostate carcinoma offers an alternative means to distinguish aggressive tumor biology and may improve the accuracy of outcome prediction for patients with prostate carcinoma treated by radical prostatectomy. METHODS: Gene expression differences between 37 recurrent and 42 nonrecurrent primary prostate tumor specimens were analyzed by oligonucleotide microarrays. Two logistic regression modeling approaches were used to predict prostate carcinoma recurrence after radical prostatectomy. One approach was based exclusively on gene expression differences between the two classes. The second approach integrated prognostic gene variables with a validated postoperative predictive model based on standard variables (nomogram). The predictive accuracy of these modeling approaches was evaluated by leave-one-out cross-validation (LOOCV) and compared with the nomogram. RESULTS: The modeling approach using gene variables alone accurately classified 59 (75%) tissue samples in LOOCV, a classification rate substantially higher than expected by chance. However, this predictive accuracy was inferior to the nomogram (concordance index, 0.75 vs. 0.84, P = 0.01). Models combining clinical and gene variables accurately classified 70 (89%) tissue samples and the predictive accuracy using this approach (concordance index, 0.89) was superior to the nomogram (P = 0.009) and models based on gene variables alone (P < 0.001). Importantly, the combined approach provided a marked improvement for patients whose nomogram-predicted likelihood of disease recurrence was in the indeterminate range (7-year disease progression-free probability, 30-70%; concordance index, 0.83 vs. 0.59, P = 0.01). CONCLUSIONS: Integration of gene expression signatures and clinical variables produced predictive models for prostate carcinoma recurrence that perform significantly better than those based on either clinical variables or gene expression information alone.

Aged↗
PubMed2006

Cross-validated bagged prediction of survival.

In this article, we show how to apply our previously proposed Deletion/Substitution/Addition algorithm in the context of right-censoring for the prediction of survival. Furthermore, we introduce how to incorporate bagging into the algorithm to obtain a cross-validated bagged estimator. The method is used for predicting the survival time of patients with diffuse large B-cell lymphoma based on gene expression variables.

Algorithms↗
PubMed1993

mu-Chain gene expression in common variable immunodeficiency.

Three patients with common variable immunodeficiency (CVID) were analyzed for translation from mu mRNA by the cell-free translation method and for expression of mu mRNA by northern blotting. In cases 1 and 2, the mu chain was not detected in the products by cell-free translation nor was mu mRNA detected by northern blotting. In case 3, mu mRNA was detected at a low level. This suggests that the disorders occur between rearrangement of the Ig genes and transcription of the C mu gene in cases 1 and 2, and that the functions of rearrangement and transcription are qualitatively preserved to a certain degree in case 3. Thus, the pathogeneses of CVID are variable and more research on regulatory mechanisms of B cell development is necessary to understand each case of CVID.

B-Lymphocytes↗
PubMed2004

Simultaneously monitoring gene expression kinetics and genetic noise in single cells by optical well arrays.

An optical fiber based well array platform was used for simultaneous, dynamic gene expression monitoring from hundreds of individual live Escherichia coli cells carrying promoter-fluorescent reporter gene fusions. High information content about gene expression kinetics and cell-to-cell gene expression variability can be collected from a single experiment. These data are invaluable for investigating gene regulation and gene networks as well as for systems biology applications.

Escherichia coli↗
PubMed1995

Mohr syndrome (oro-facial-digital syndrome II)--a familial case with different phenotypic findings.

We report on two male siblings with an oro-facial-digital syndrome. The parents and two other siblings, a boy and a girl, are unaffected. The clinical findings on the reported brothers were different. Patient 1 had typical oral, facial and digital anomalies plus hypoplastic genitalia and short limbs. Clinically he had marked hypotonia, convulsions and apneic episodes. He died shortly after birth. His brother, Patient 2, had OFD features with conductive hearing loss and normal psychomental development. He did not have syndactylous reduplication of the great toes, although the toes were disproportionately large. These two patients are classified as OFD type II-Mohr syndrome. Involvement of the central nervous system in OFD type II is noted. Different phenotypic findings could be explained as variable gene expressivity. The patients described here support the hypothesis that the clinical variability of the Mohr syndrome is even wider than previously thought.

Adult↗
PubMed2004

Combining gene expression profiles and clinical parameters for risk stratification in medulloblastomas.

PURPOSE: Stratification of risk in patients with medulloblastoma remains a challenge. As clinical parameters have been proven insufficient for accurately defining disease risk, molecular markers have become the focus of interest. Outcome predictions on the basis of microarray gene expression profiles have been the most accurate to date. We ask in a multivariate model whether clinical parameters enhance survival predictions of gene expression profiles. PATIENTS AND METHODS: In a cohort of 55 young patients (whose medulloblastoma samples have been analyzed previously for gene expression profile), associations between clinical and gene expression variables and survival were assessed using Cox proportional hazards models. Available clinical variables included age, stage (ie, the presence of disseminated disease at diagnosis), sex, histologic subtype, treatment, and status. RESULTS: Univariate analysis demonstrated expression profiles to be the only significant clinical prognostic factor (P=.03). In multivariate analysis, gene expression profiles predicted outcome independent of other criteria. Clinical criteria did not significantly contribute additional information for outcome predictions, although an exploratory analysis noted a trend for decreased survival of patients with metastases at diagnosis but favorable gene expression profile. CONCLUSION: Gene expression profiling predicts medulloblastoma outcome independent of clinical variables. These results need to be validated in a larger prospective study.

Adolescent↗
PubMed2006

Borrelia afzelii gene expression in Ixodes ricinus (Acari: Ixodidae) ticks.

Spirochetes belonging to the Borrelia burgdorferi sensu lato (s. l.) complex have evolved remarkable ability to survive in diverse ecological niches during transmission cycles between ticks and vertebrate hosts by variable gene expression. To understand the events during spirochete transmission from feeding ticks to hosts, mRNA levels of selected B. afzelii genes (bbk32, dbpA, ospA, ospC and vlsE) were measured by quantitative real-time SYBR Green PCR. B. afzelii infected Ixodes ricinus nymphs fed on laboratory BALB/c mice for 0, 24, 48, and 72 hours. The mRNA levels of the constantly expressed flagellin gene were used for the relative quantification of selected genes. Differences in gene expression profiles were observed in unfed ticks and during tick feeding. mRNA levels of bbk32 and dbpA showed distinctive decreasing patterns during the first 24 hours post-attachment, while ospC and vlsE mRNA levels increased significantly during the feeding process. In contrast, ospA levels decreased for the 48 hours of tick feeding and slightly increased by 72 hours. More detailed and comprehensive studies on regulation of gene expression in different Borellia genospecies on the vector-host interface would aid to develop effective strategies in preventing pathogen transmission.

Animals↗
PubMed1998

Cloning of 3H11 mAb variable region gene and expression of 3H11 human-mouse chimeric light Chain.

AIM:To clone mouse anti-human gastric cancer mAb(3H11) variable genes and to construct 3H11 human-mouse chimeric antibody.METHODS: The entire VH and VL genes of anti-gastric cancer mAb 3H11 were cloned by RT-PCR method from 3H11 hybridoma cells, using 5' primers for leader sequences. The 3H11 VL gene was then inserted into human-mouse chimeric light chain expression vector and transfected into murine Sp2/0 myeloma cells.RESULTS: DNA sequence analysis indicated that the cloned genes included the whole leader sequences and the mature Ig variable region encoding sequences. After gene transfection, transient expression of chimeric light chain protein was detected.CONCLUSION: DNA sequences and transient expression indicated that the cloned gene was functional. This work laid basis for constructing 3H11 human mouse chimeric antibody in the future.

Journal Article↗
PubMed2025

Tunable, proteolytic dosage control of CRISPR-Cas systems enables precise gene therapy for dosage sensitive disorders.

The ability to modulate gene expression through modular and universal genetic tools like CRISPR-Cas has greatly advanced gene therapy for therapeutics and basic science. Yet, the inherent stochasticity of delivery methods cause variation in target gene expression at the single-cell level, limiting their applicability in systems that require more precise expression. Thus, we implement a modular incoherent feedforward loop based on proteolytic cleavage of Cas to reduce gene expression variability against the variability of vector delivery. We target a genome-integrated marker and demonstrate dosage control of gene activation and repression, post-delivery tuning, and RNA-based compatibility of the system. To illustrate therapeutic relevance, we target the gene RAI1, the haploinsufficiency and triplosensitivity of which cause two autism-related syndromes. We demonstrate dosage-controlled gene activation for both human and mouse Rai1 via viral delivery to patient-derived cell lines and mouse cortical neurons. Overall, we established a robust dosage control circuit for uniform gene expression, beneficial for basic and translational research.

Journal Article↗
PubMed1996

The complete 685-kilobase DNA sequence of the human beta T cell receptor locus.

The human beta T cell receptor (TCR) locus, comprising a complex family of genes, has been sequenced. The locus contains two types of coding elements--TCR elements (65 variable gene segments and two clusters of diversity, joining, and constant segments) and eight trypsinogen genes --that constitute 4.6 percent of the DNA. Genome-wide interspersed repeats and locus-specific repeats span 30 and 47 percent, respectively, of the 685-kilobase sequence. A comparison of the germline variable elements with their approximately 300 complementary DNA counterparts reveals marked differential patterns of variable gene expression, the importance of exonuclease activity in generating TCR diversity, and the predominant tendency for only functional variable elements to be present in complementary DNA libraries.

Amino Acid Sequence↗
PubMed1995

Physiopathological investigations in a family with a history of unilateral hereditary deafness.

We examined several members of the same family with unilateral sensorineural hearing loss. The defect showed dominant inheritance. Clinical examination and auditory tests, including high-definition audiogram and otoacoustic emission recording, were done to characterize the physiopathological process of hearing loss, and to investigate possible asymptomatic auditory features in the normal ear of affected subjects and nonaffected siblings. Hypotheses as to the underlying mechanisms are discussed, eg, variable expression of bilateral isolated hereditary deafness, incomplete Klein-Waardenburg syndrome with stria vascularis anomalies and highly variable gene expression, or unilateral cochlear aplasia. The phenomenon may also be related to the delayed progressive unilateral loss in patients with bilateral hereditary deafness, involving perhaps unilateral vascular disorders or a genetically induced degeneration of cochlear cells or auditory neurons.

Adult↗
PubMed2026

Integration of methylome and transcriptome reveals age-associated signatures of stage-specific dynamics and regulatory remodeling in dogs.

Aging in mammals is characterized by widespread yet coordinated epigenetic alterations. However, integrative analyses of DNA methylation and gene expression in dogs remain largely unexplored, particularly within genetically homogeneous single-breed populations. To elucidate the molecular signatures of canine aging, we profiled the genome-wide methylome and transcriptome of clinically healthy beagle dogs representing three distinct age groups. Global methylation levels were highly conserved across individuals, yet both methylation and gene expression variability increased progressively with aging. This epigenetic drift was not stochastic but structured by genomic context, as reduced CpG-gene associations indicated a gradual loss of epigenetic control over transcription. We further observed stage-related methylation change patterns across the three age groups, including early-shift, late-shift, and progressive patterns. These groups showed partially overlapping but distinct hallmark associations, suggesting links to different age-related biological processes. Together, these findings indicate that canine epigenetic aging involves multifaceted molecular changes across adulthood and support dogs as a useful model for investigating conserved molecular signatures of aging.

Beagle dog↗
PubMed2003

cDNA microarray analysis of individual Duchenne muscular dystrophy patients.

We have developed a novel cDNA microarray encompassing 3500 genes expressed in skeletal muscle. With this system, we have performed the first study of gene expression in samples from individual patients. We analyzed muscle specimen from individuals with Duchenne muscular dystrophy to identify differences among patients. Among the variably expressed genes, we focused on the expression of the genes encoding HLA-related proteins, myosin light chains and troponin Ts as markers of muscle necrosis and regeneration. The expression patterns of these genes correlated with the severity of dystrophic changes on histological examination. Our cDNA microarray provides a new tool to investigate molecular muscle pathology.

Child, Preschool↗
PubMed1997

Differential expression of the neuroendocrine genes Hel-N1 and HuD in small-cell lung carcinoma: evidence for down-regulation of HuD in the variant phenotype.

Hel-NI and HuD belong to the elav gene family and have gained recent attention as potential neuroendocrine markers for small-cell lung carcinoma (SCLC). Members of this conserved family normally appear at different stages of neuronal maturation, raising the possibility that their expression patterns in SCLC reflect the degree of neuroendocrine differentiation. I have utilized a ribonuclease protection assay to analyze Hel-NI and HuD expression in cultured SCLC cells with high (classic phenotype) and low (variant phenotype) levels of neuroendocrine differentiation. Hel-NI was detected in both classic and variant SCLC. Although HuD was detected consistently in classic SCLC, it was low to absent in variant SCLC, indicating a significant down-regulation in that phenotype. The expression patterns of Hel-NI and HuD also were analyzed in 9 primary SCLC and 10 non-SCLC lung-tumor samples. In the majority of SCLC samples, either Hel-NI or HuD was detected exclusively or predominantly, indicating a pattern of variable gene expression similar to cultured SC LC. Neither transcript could be detected in the non-SCLC samples. These data indicate that (i) HuD mRNA expression is associated with a higher level of neuroendocrine differentiation in SCLC, (ii) Hel-NI and HuD expressions are variable in both primary and cultured SCLC and (iii) HuD and Hel-NI, in combination, are neurogenetic markers for SCLC.

Carcinoma, Non-Small-Cell Lung↗
PubMed1998

Dynamic changes in spontaneous intracellular free calcium oscillations and their relationship to prolactin gene expression in single, primary mammotropes.

Cytosolic calcium plays a critical role in the control of a number of genes, including that of the pituitary hormone PRL. Cells that secrete this hormone, termed mammotropes, display spontaneous oscillations of intracellular free calcium ([Ca2+]i) that are positively correlated to PRL release. However, the precise contribution of calcium signaling to the expression of any gene including PRL has remained obscure owing to the requirement for and lack of a strategy for monitoring both of these dynamic variables (gene expression and [Ca2+]i oscillations) in the same living cell. In the present study, we overcame this technical limitation by making real-time measurements of PRL gene expression in transfected, primary rat mammotropes previously subjected to [Ca2+]i determinations by digital imaging fluorescence microscopy of fura-2. Our results showed that the majority of mammotropes (75%) exhibited distinct oscillatory behaviors that could be subgrouped on the basis of frequency/amplitude of [Ca2+]i changes, whereas the remainder (25%) were quiescent (nonoscillatory). Interestingly, most mammotropes displayed spontaneous transitions between oscillatory and quiescent states over the course of several hours. As a consequence of this oscillatory plasticity, there was not a positive correlation between [Ca2+]i dynamics and gene expression at any point in time, as would be predicted by studies with entire populations of cells. Instead, the relationship was distinctly inverse, suggesting that dynamic changes in PRL gene expression may be regulated by temporally dissociated transitions between quiescent and oscillatory states.

Animals↗
PubMed2001

A SAGE (serial analysis of gene expression) view of breast tumor progression.

To identify molecular alterations involved in the initiation and progression of breast carcinomas, we analyzed the global gene expression profiles of normal mammary epithelial cells and in situ, invasive, and metastatic breast carcinomas using serial analysis of gene expression (SAGE). We identified sets of genes expressed only or most abundantly in a specific stage of breast tumorigenesis or in a certain subtype of tumors through the pair-wise comparison and by hierarchical clustering analysis of these eight SAGE libraries (two/stage). On the basis of these comparisons, we made the following observations: Normal mammary epithelial cells showed the most distinct and least variable gene expression profiles. Many of the genes highly expressed in normal mammary epithelium and lost in carcinomas encoded secreted proteins, cytokines, and chemokines, implicating abnormal paracrine and autocrine signaling in the initiation of breast tumorigenesis. Very few genes were universally up-regulated in all tumors regardless of their stage and histological grade, indicating a high degree of diversity at the molecular level that likely reflects the clinical heterogeneity characteristic of breast carcinomas. Tumors of different histology type and stage had very distinct gene expression patterns. No genes seemed to be specific for metastatic or for in situ carcinomas. We found that the most dramatic and consistent phenotypic change occurred at the normal-to-in situ carcinoma transition. This observation, combined with the fact that many of the genes involved encode secreted, cell-nonautonomous factors, implies that the normal epithelium-to-in situ carcinoma transition may be the most promising target for cancer prevention and treatment.

Adult↗