COL4A5

Gene Summary

Gene:COL4A5; collagen, type IV, alpha 5
Aliases: ATS, ASLN, CA54
Location:Xq22
Summary:This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]
Databases:OMIM, VEGA, HGNC, Ensembl, GeneCard, Gene
Protein:collagen alpha-5(IV) chain
HPRD
Source:NCBIAccessed: 21 August, 2015

Ontology:

What does this gene/protein do?
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Pathways:What pathways are this gene/protein implicaed in?
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Cancer Overview

Research Indicators

Publications Per Year (1990-2015)
Graph generated 21 August 2015 using data from PubMed using criteria.

Literature Analysis

Mouse over the terms for more detail; many indicate links which you can click for dedicated pages about the topic.

  • Esophageal Cancer
  • DNA
  • Young Adult
  • Messenger RNA
  • Adolescents
  • Genetic Linkage
  • Gene Deletion
  • Leiomyomatosis
  • Amino Acid Sequence
  • Restriction Mapping
  • Mutation
  • Basement Membrane
  • Childhood Cancer
  • X-Ray Computed Tomography
  • Cancer Gene Expression Regulation
  • Urinary Bladder
  • Esophagus
  • Polymerase Chain Reaction
  • Nephritis, Hereditary
  • Point Mutation
  • Cloning, Molecular
  • Chromosome X
  • Sequence Homology, Nucleic Acid
  • Exons
  • Sequence Deletion
  • Muscle, Smooth
  • DNA Mutational Analysis
  • Collagen Type IV
  • Molecular Sequence Data
  • Immunohistochemistry
  • Viscera
  • Cancer RNA
  • Chromosome Mapping
  • Cancer DNA
  • Collagen
  • Leiomyoma
  • X Chromosome
  • Vulva
  • Base Sequence
Tag cloud generated 21 August, 2015 using data from PubMed, MeSH and CancerIndex

Specific Cancers (1)

Data table showing topics related to specific cancers and associated disorders. Scope includes mutations and abnormal protein expression.

Note: list is not exhaustive. Number of papers are based on searches of PubMed (click on topic title for arbitrary criteria used).

Latest Publications: COL4A5 (cancer-related)

Chao L, Yi-Sheng H, Yu C, et al.
Relevance of EGFR mutation with micropapillary pattern according to the novel IASLC/ATS/ERS lung adenocarcinoma classification and correlation with prognosis in Chinese patients.
Lung Cancer. 2014; 86(2):164-9 [PubMed] Related Publications
BACKGROUND: A new histological classification by the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) for lung adenocarcinoma (LAC) was proposed recently, in which a micropapillary pattern (MPP) was described.
OBJECTIVES: This study aimed to evaluate the clinicopathological characteristics of LAC with MPP (LAC-MPP) and to investigate the correlation between LAC-MPP and epidermal growth factor receptor (EGFR) mutation status with the prognosis in Chinese patients.
PATIENTS AND METHODS: From May 2007 and February 2012, two hundred and forty-eight patients underwent resection and pathologically confirmed LAC. We classified all cases histologically according to the IASLC/ATS/ERS classification; an MPP ratio ≥5% was considered MPP-positive. Used Pearson's chi-square test to evaluate the relationships between EGFR mutation status and MPP status with patient clinicopathological characteristics.
RESULTS: There were MPP-positive tumors (MPP ratio ≥5%) in 31.9% of cases (79/248); the MPP ratio correlated with TNM stage (p=0.001) and lymph node metastasis (p=0.03). EGFR mutation (EGFR-mut) was detected in 87 cases (34.3%); 161 cases had wild-type EGFR (EGFR-wt). EGFR mutation was present in 65% of the MPP-positive subtype. Patients with EGFR-mut tumors had significantly longer overall survival (OS) (p=0.002). OS was also significantly longer in MPP-negative EGFR-mut or EGFR-wt patients (p<0.001).
CONCLUSION: These findings indicate that EGFR-mut tumors are likelier to be MPP-positive subtypes and that MPP may be a novel potential pathological marker of poor prognosis in Chinese LAC patients.

Mehine M, Mäkinen N, Heinonen HR, et al.
Genomics of uterine leiomyomas: insights from high-throughput sequencing.
Fertil Steril. 2014; 102(3):621-9 [PubMed] Related Publications
Uterine leiomyomas are benign smooth-muscle tumors of extremely low malignant potential. Early work utilizing classical cytogenetics revealed that a subset of uterine leiomyomas harbor recurrent chromosomal rearrangements, such as translocations affecting the HMGA2 gene. Our understanding of the genetics of many tumor types has deepened remarkably with the emergence of next-generation sequencing technologies. Exome sequencing identified that the majority of leiomyomas display highly specific MED12 mutations. Further studies suggest that these MED12 hotspot mutations are also frequent in breast fibroadenomas, but not in other human tumors. Whole-genome sequencing showed that a subset of leiomyomas display complex chromosomal rearrangements resembling chromothripsis. These were formed in a single event of chromosomal breakage and random reassembly involving one or a limited number of chromosomes. Although most leiomyomas have been shown to arise independently, these studies also revealed that distinct nodules within a uterus may display identical genetic changes indicating a common clonal origin. A minority of leiomyomas were also found to display deletions within the COL4A5-COL4A6 genes, leading to upregulation of the adjacent gene IRS4. The findings derived from high-throughput sequencing combined with previous knowledge have led to an emerging molecular classification of leiomyomas, suggesting that there are several distinct pathogenic pathways involved in leiomyoma formation. The evidence points to at least 4 molecular subclasses: leiomyomas with MED12 mutation, FH inactivation, HMGA2 overexpression, and COL4A6-COL4A5 deletion. Elucidating the molecular pathogenesis of leiomyomas should be relevant for developing treatments for this very common disease.

Yanagawa N, Shiono S, Abiko M, et al.
The correlation of the International Association for the Study of Lung Cancer (IASLC)/American Thoracic Society (ATS)/European Respiratory Society (ERS) classification with prognosis and EGFR mutation in lung adenocarcinoma.
Ann Thorac Surg. 2014; 98(2):453-8 [PubMed] Related Publications
BACKGROUND: The purpose of this study was to validate the prognostic effect and the frequency of mutations in the gene expressing epidermal growth factor receptor (EGFR) in lung adenocarcinoma of Japanese patients, on the basis of the new adenocarcinoma classification proposed by the International Association for the Study of Lung Cancer, American Thoracic Society, and European Respiratory Society.
METHODS: The new classification was used to reclassify 486 adenocarcinomas. The percentage of each histopathologic subtype and the predominant pattern were determined. EGFR mutation was also investigated. The relationship between these results and clinicopathologic backgrounds was investigated statistically.
RESULTS: No patients with adenocarcinoma in situ or minimally invasive adenocarcinoma died within the follow-up periods, followed by patients with lepidic predominant. Patients with papillary or acinar predominant, or invasive mucinous adenocarcinoma, showed almost similar overall survival (OS). The patients with solid predominant and micropapillary predominant showed the worst OS. Multivariate analysis showed that the new classification was an independent predictor of OS. The frequency of EGFR mutation was adenocarcinoma in situ (62%), minimally invasive adenocarcinoma (60%), lepidic (77%), acinar (49%), papillary (50%), solid (28%), micropapillary (43%), and invasive mucinous adenocarcinoma (0%).
CONCLUSIONS: This new adenocarcinoma classification is a very useful predictive marker to plan and determine a therapeutic strategy for lung adenocarcinoma.

Nakagiri T, Sawabata N, Morii E, et al.
Evaluation of the new IASLC/ATS/ERS proposed classification of adenocarcinoma based on lepidic pattern in patients with pathological stage IA pulmonary adenocarcinoma.
Gen Thorac Cardiovasc Surg. 2014; 62(11):671-7 [PubMed] Related Publications
BACKGROUND: The International association for the study of cancer (IASLC)/American thoracic society (ATS)/European respiratory society (ERS) has established a new subclassification of lung adenocarcinoma, especially for the lepidic pattern component, formerly called bronchioloalveolar adenocarcinoma (BAC). According to the new classification, BAC has been classified into the following 4 main subtypes: adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), invasive adenocarcinoma (IA), and variants of invasive adenocarcinoma (VIA). An observational study was conducted to validate this classification in patients with pathological stage IA pulmonary adenocarcinoma.
PATIENTS AND METHODS: 147 patients treated for pathological stage IA lung adenocarcinoma by complete resection at Osaka University Medical Hospital from January 1993 to December 2002 were assessed. The tumor specimens of the cohort were classified into the 4 subgroups. In addition, these groups were compared for various prognostic factors.
RESULTS: Adenocarcinoma in situ was observed in 30 patients, MIA in 8, IA in 104, and VIA in 5 patients, with 5-year survival rates of 100, 100, 85.5, and 60.0 %, respectively. The relationship between the histological classification and K-ras mutation was significant (p < 0.001), especially when comparing the VIA group with the others (p ≪ 0.001). Ki67-labeling indices were significantly different between the AIS and IA groups (p = 0.040).
CONCLUSIONS: This study validated the proposed IASLC/ATS/ERS classification for pulmonary adenocarcinoma in patients with pathological stage IA pulmonary adenocarcinoma. The difference between AIS and IA may depend on the proliferation of the carcinoma. In addition, the difference between VIA and the other adenocarcinoma types may depend on genetic factors, especially K-ras mutations.

Wang CX, Liu B, Wang YF, et al.
Pulmonary enteric adenocarcinoma: a study of the clinicopathologic and molecular status of nine cases.
Int J Clin Exp Pathol. 2014; 7(3):1266-74 [PubMed] Free Access to Full Article Related Publications
Pulmonary enteric adenocarcinoma (PEAC), a extremely rare variant of primary invasive adenocarcinoma of the lung, was recognized by the international multidisciplinary classification of lung adenocarcinoma which was proposed by the International Association for the Study of Lung Cancer (IASLC), the American Thoracic Society (ATS), and the European Respiratory Society (ERS) published in early 2011. Histologically, PEAC is considered to be mainly composed of tall columnar cells arranged in an irregular glandular cavity or cribriform pattern with extensive central necrosis which show high resemblance to that of intestinal epithelia and colorectal carcinomas. Immunohistochemically, PEAC can not only expresses typical proteins common to lung primaries but is positive for at least one intestinal markers, such as CDX2, cytokeratin (CK) 20, MUC2, therefore, the differentiation of primary PEACs from metastatic colorectal cancers can be challenging. In this study, we report 9 cases of PEAC and a panel of immunohistochemical protein markers of CK7, CK20, thyroid transcription factor 1 (TTF-1), Napsin A, MUC2 and villin was analyzed with the comparison of 20 metastatic colorectal carcinomas (MCRs), and 20 typical primary adenocarcinomas (tPACs). As was expected, CK7 expression was documented in all 9 PEACs and 20 tPCAs while CK20 was significantly more prevalent in adenocarcinoma that originated from colorectal. Additionally, we evaluate the classical mutations of EGFR, KRAS in the 9 cases of PEACs, it turned out that all tumors were EGFR-wild and KRAS-wild types, which confirmed that PEAC has a separate phenotype from usual pulmonary adenocarcinoma.

Villa C, Cagle PT, Johnson M, et al.
Correlation of EGFR mutation status with predominant histologic subtype of adenocarcinoma according to the new lung adenocarcinoma classification of the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society.
Arch Pathol Lab Med. 2014; 138(10):1353-7 [PubMed] Related Publications
CONTEXT: Epidermal growth factor receptor (EGFR) mutations have been identified as predictors of response to EGFR tyrosine kinase inhibitors in non-small cell lung cancer.
OBJECTIVE: To investigate the relationship of EGFR mutation status to the histologic subtype of adenocarcinoma according to the new International Association for the Study of Lung Cancer (IASLC)/American Thoracic Society (ATS)/European Respiratory Society (ERS) classification.
DESIGN: We screened EGFR mutation in 200 consecutive lung adenocarcinoma resection specimens diagnosed between 2008 and 2011.
RESULTS: Among 200 lung adenocarcinomas, EGFR mutations were identified in 41 tumors (20.5%). The mean age in the EGFR-mutant group was 64.8 years and this group consisted of 78% females and 22% males. Most patients with EGFR-positive lung cancers were never-smokers (51%) as compared to 8% with EGFR-negative cancers (P < .001). The most common mutations identified in our population were deletions in exon 19 (22 patients) and L858R in exon 21 (12 patients). Five patients had double mutations. The predominant pattern of adenocarcinoma was lepidic (44%) in EGFR-mutant lung cancers as compared to 69% with acinar pattern in EGFR wild-type lung cancers (P < .001). Of 22 minimally invasive adenocarcinomas, 8 (36%) had EGFR mutations, accounting for 20% of adenocarcinomas with EGFR mutations (P < .05).
CONCLUSIONS: Based on the new IASLC/ATS/ERS classification, the predominant subtype of adenocarcinoma was lepidic (44%) in EGFR-mutant lung cancers (P < .001). However, histologic subtype should not be used to exclude patients from tyrosine kinase inhibitor therapy, since EGFR mutations are found in lung adenocarcinomas of other subtypes.

Kool MM, Galac S, Kooistra HS, Mol JA
Expression of angiogenesis-related genes in canine cortisol-secreting adrenocortical tumors.
Domest Anim Endocrinol. 2014; 47:73-82 [PubMed] Related Publications
The aim of this study was to evaluate the expression of angiogenesis-related genes in canine cortisol-secreting adrenocortical tumors (ATs). Quantitative RT-PCR analysis revealed mRNA encoding for vascular endothelial growth factor, vascular endothelial growth factor receptors 1 and 2, angiopoietin 1 and 2 (ANGPT1 and ANGPT2), the splice variant ANGPT2443, the ANGPT-receptor Tie2, and basic fibroblast growth factor in 38 canine cortisol-secreting ATs (26 carcinomas and 12 adenomas) and 15 normal adrenals. The relative expression of both ANGPT2 and ANGPT2443 was higher in adenomas (P = 0.020 for ANGPT2 and P = 0.002 for ANGPT2443) and carcinomas (P = 0.003 for ANGPT2 and P < 0.001 for ANGPT2443) compared with normal adrenals, and this enhanced expression was also detected with Western blot analysis. Immunohistochemistry indicated expression of ANGPT2 protein in AT cells and in vascular endothelial cells of carcinomas, whereas Tie2 was mainly present in the tumor vascular endothelial cells. The ANGPT2-to-ANGTPT1 ratio, a marker for a proangiogenic state, was higher in both adenomas (P = 0.020) and carcinomas (P = 0.043). With the use of the human H295R cortisol-producing adrenocortical carcinoma cell line, we were able to demonstrate that the ANGPT2 expression was stimulated by cyclic adenosine monophosphate and progesterone but not by cortisol. In conclusion, canine cortisol-secreting ATs have enhanced ANGPT2 expression with a concomitant shift toward a proangiogenic state. On the basis of this information, treatment modalities may be developed that interfere with ANGPT2 expression, including inhibition of the cyclic adenosine monophosphate/protein kinase A pathway, or of the effect of ANGPT2, by using specific ANGPT2 inhibitors.

Sá MJ, Fieremans N, de Brouwer AP, et al.
Deletion of the 5'exons of COL4A6 is not needed for the development of diffuse leiomyomatosis in patients with Alport syndrome.
J Med Genet. 2013; 50(11):745-53 [PubMed] Related Publications
BACKGROUND: Alport syndrome (AS), a hereditary type IV collagen nephropathy, is a major cause of end-stage renal disease in young people. About 85% of the cases are X-linked (ATS), due to mutations in the COL4A5 gene. Rarely, families have a contiguous gene deletion comprising at least exon 1 of COL4A5 and the first exons of COL4A6, associated with the development of diffuse leiomyomatosis (ATS-DL). We report three novel deletions identified in families with AS, one of which challenges the current concepts on genotype-phenotype correlations of ATS/ATS-DL.
METHODS: In the setting of a multicentric study aiming to describe the genetic epidemiology and molecular pathology of AS in Portugal, three novel COL4A5 deletions were identified in two families with x-linked Alport syndrome (ATS) and in one family with ATS-DL. These mutations were initially detected by PCR and Multiplex Ligation-dependent Probe Amplification, and further mapped by high-resolution X chromosome-specific oligo-array and PCR.
RESULTS: In the ATS-DL family, a COL4A5 deletion spanning exons 2 through 51, extending distally beyond COL4A5 but proximally not into COL4A6, segregated with the disease phenotype. A COL4A5 deletion encompassing exons 2 through 29 was identified in one of the ATS families. In the second ATS family, a deletion of exon 13 of COL4A5 through exon 3 of COL4A6 was detected.
CONCLUSIONS: These observations suggest that deletion of the 5' exons of COL4A6 and of the common promoter of the COL4A5 and COL4A6 genes is not essential for the development of leiomyomatosis in patients with ATS, and that COL4A5_COL4A6 deletions extending into COL4A6 exon 3 may not result in ATS-DL.

Tsuta K, Kawago M, Inoue E, et al.
The utility of the proposed IASLC/ATS/ERS lung adenocarcinoma subtypes for disease prognosis and correlation of driver gene alterations.
Lung Cancer. 2013; 81(3):371-6 [PubMed] Related Publications
BACKGROUND: The present study aimed to determine the ability of the revised International Association for the Study of Lung Cancer (IASLC)/American Thoracic Society (ATS)/European Respiratory Society (ERS) classification of lung adenocarcinoma to predict patient survivals and driver gene alterations.
PATIENTS AND METHODS: A reclassification of 904 surgically resected adenocarcinomas was performed. The results were statistically analyzed to examine the correlation between the classification and overall survival (OS) using Cox regression analyses, and integrated discrimination improvement (IDI) analyses.
RESULTS: The 5-year OS rates for adenocarcinomas in situ (AIS) or minimally invasive adenocarcinoma (MIA) were 98%. Five-year OS rates of Lepidic-, acinar-, papillary-, micropapillary-, and solid-predominant adenocarcinomas was 93%, 67%, 74%, 62%, and 58%, respectively. The IDI estimates revealed that classification of ADC into the 7 subgroups had a higher estimated (0.0175) than did the combined histological grouping (AIS + MIA, lepidic + acinar + papillary, micropapillary + solid + others) (0.0111). Epidermal growth factor receptor mutations, KRAS gene mutations, and anaplastic lymphoma kinase gene alterations were statistically prevalent in papillary-predominant (P = 0.00001), invasive mucinous (P = 0.00001), and micropapillary- and acinar-predominant (P = 0.00001) adenocarcinomas, respectively.
CONCLUSIONS: The new classification reflects disease prognosis, and was also associated with driver gene alterations.

Sousa RG, Figueiredo PC, Pinto-Marques P, et al.
An unusual cause of pseudoachalasia: the Alport syndrome-diffuse leiomyomatosis association.
Eur J Gastroenterol Hepatol. 2013; 25(11):1352-7 [PubMed] Related Publications
Alport syndrome (AS) is a hereditary disease characterized by glomerular nephropathy progressing to end-stage renal disease, frequently associated with sensorineural deafness and ocular abnormalities. Rarely, AS coexists with diffuse leiomyomatosis, a benign proliferation of smooth muscle in the gastrointestinal tract, mostly of the oesophagus, but also of the tracheobronchial tree and the female genital tract. Patients with this association have been shown to have contiguous gene deletion involving both COL4A5 and COL4A6 genes. The authors report the case of a 25-year-old man with AS and long-standing dysphagia. The patient received a renal transplant at the age of 23 because of end-stage renal disease. Clinical assessment as well as endoscopic, manometric and radiologic studies suggested the diagnosis of achalasia, which was treated by Heller's myotomy with Dor fundoplication. Postprocedure dysphagia led to an endoscopic ultrasound that showed diffuse thickening of the second layer, resulting in the hypothesis of oesophageal leiomyomatosis. The diagnosis was confirmed through histological study of endoscopic biopsies and genetic analysis.

Mehine M, Kaasinen E, Mäkinen N, et al.
Characterization of uterine leiomyomas by whole-genome sequencing.
N Engl J Med. 2013; 369(1):43-53 [PubMed] Related Publications
BACKGROUND: Uterine leiomyomas are benign but affect the health of millions of women. A better understanding of the molecular mechanisms involved may provide clues to the prevention and treatment of these lesions.
METHODS: We performed whole-genome sequencing and gene-expression profiling of 38 uterine leiomyomas and the corresponding myometrium from 30 women.
RESULTS: Identical variants observed in some separate tumor nodules suggested that these nodules have a common origin. Complex chromosomal rearrangements resembling chromothripsis were a common feature of leiomyomas. These rearrangements are best explained by a single event of multiple chromosomal breaks and random reassembly. The rearrangements created tissue-specific changes consistent with a role in the initiation of leiomyoma, such as translocations of the HMGA2 and RAD51B loci and aberrations at the COL4A5-COL4A6 locus, and occurred in the presence of normal TP53 alleles. In some cases, separate events had occurred more than once in single tumor-cell lineages.
CONCLUSIONS: Chromosome shattering and reassembly resembling chromothripsis (a single genomic event that results in focal losses and rearrangements in multiple genomic regions) is a major cause of chromosomal abnormalities in uterine leiomyomas; we propose that tumorigenesis occurs when tissue-specific tumor-promoting changes are formed through these events. Chromothripsis has previously been associated with aggressive cancer; its common occurrence in leiomyomas suggests that it also has a role in the genesis and progression of benign tumors. We observed that multiple separate tumors could be seeded from a single lineage of uterine leiomyoma cells. (Funded by the Academy of Finland Center of Excellence program and others.).

Yoshizawa A, Sumiyoshi S, Sonobe M, et al.
Validation of the IASLC/ATS/ERS lung adenocarcinoma classification for prognosis and association with EGFR and KRAS gene mutations: analysis of 440 Japanese patients.
J Thorac Oncol. 2013; 8(1):52-61 [PubMed] Related Publications
INTRODUCTION: This study aimed to validate the utility of the new histological classification proposed by the International Association for the Study of Lung Cancer (IASLC), American Thoracic Society (ATS), and European Respiratory Society (ERS) for identifying the prognostic subtypes of adenocarcinomas in Japanese patients; correlations between the classification and the presence of EGFR or KRAS mutation status were also investigated.
METHODS: We retrospectively reviewed 440 patients with lung adenocarcinoma, who underwent resection. The tumors were classified according to the IASLC/ATS/ERS classification. EGFR and KRAS mutations were detected using the established methods.
RESULTS: Five-year disease-free survival rates were: 100% for adenocarcinoma in situ (n = 20) and minimally invasive adenocarcinoma (n = 33), 93.8% for lepidic-predominant adenocarcinoma (n = 36), 88.8% for invasive mucinous adenocarcinoma (n = 10), 66.7% for papillary-predominant adenocarcinoma (n = 179), 69.7% for acinar-predominant adenocarcinoma (n = 61), 43.3% for solid-predominant adencoarcinoma (n = 78), and 0% for micropapillary-predominant adenocarcinoma (n = 19). Multivariate analysis revealed that the new classification was an independent predictor of disease-free survival. EGFR and KRAS mutations were detected in 90 cases (53.9%) and 21 cases (13.3%), respectively; EGFR mutations were significantly associated with adenocarcinoma in situ, minimally invasive adenocarcinoma, lepidic- and papillary-predominant adenocarcinoma, and KRAS mutations adenocarcinomas with mucinous tumor subtypes.
CONCLUSIONS: We found that the IASLC/ATS/ERS classification identified prognostic histologic subtypes of lung adenocarcinomas among Japanese patients. Histologic subtyping and molecular testing for EGFR and KRAS mutations can help predict patient prognosis and select those who require adjuvant chemotherapy.

Ulbrich C, Pietsch J, Grosse J, et al.
Differential gene regulation under altered gravity conditions in follicular thyroid cancer cells: relationship between the extracellular matrix and the cytoskeleton.
Cell Physiol Biochem. 2011; 28(2):185-98 [PubMed] Related Publications
Extracellular matrix proteins, adhesion molecules, and cytoskeletal proteins form a dynamic network interacting with signalling molecules as an adaptive response to altered gravity. An important issue is the exact differentiation between real microgravity responses of the cells or cellular reactions to hypergravity and/or vibrations. To determine the effects of real microgravity on human cells, we used four DLR parabolic flight campaigns and focused on the effects of short-term microgravity (22 s), hypergravity (1.8 g), and vibrations on ML-1 thyroid cancer cells. No signs of apoptosis or necrosis were detectable. Gene array analysis revealed 2,430 significantly changed transcripts. After 22 s microgravity, the F-actin and cytokeratin cytoskeleton was altered, and ACTB and KRT80 mRNAs were significantly upregulated after the first and thirty-first parabolas. The COL4A5 mRNA was downregulated under microgravity, whereas OPN and FN were significantly upregulated. Hypergravity and vibrations did not change ACTB, KRT-80 or COL4A5 mRNA. MTSS1 and LIMA1 mRNAs were downregulated/slightly upregulated under microgravity, upregulated in hypergravity and unchanged by vibrations. These data indicate that the graviresponse of ML-1 cells occurred very early, within the first few seconds. Downregulated MTSS1 and upregulated LIMA1 may be an adaptive mechanism of human cells for stabilizing the cytoskeleton under microgravity conditions.

Uliana V, Marcocci E, Mucciolo M, et al.
Alport syndrome and leiomyomatosis: the first deletion extending beyond COL4A6 intron 2.
Pediatr Nephrol. 2011; 26(5):717-24 [PubMed] Related Publications
Alport syndrome (ATS) is a nephropathy characterized by the association of progressive hematuric nephritis with ultrastructural changes of the glomerular basement membrane (thinning, thickening, and splitting), sensorineural deafness, and variable ocular abnormalities (anterior lenticonus, macular flecks, and cataracts). The most common mode of transmission is X-linked inheritance, due to COL4A5 mutations. X-linked ATS is rarely associated with diffuse leiomyomatosis (DL), a benign hypertrophy of the visceral smooth muscle in gastrointestinal, respiratory, and female reproductive tracts. The ATS-DL complex is due to deletions that encompass the 5' ends of the COL4A5 and COL4A6 genes and include the bidirectional promoter. In this paper, we described 3 ATS-DL cases, 2 familial and 1 sporadic bearing a deletion encompassing the 5'-end of both the COL4A5 and COL4A6 genes, as identified by multiplex ligation-dependent probe amplification (MLPA) analysis. The array-CGH technique allowed a better definition of deletion size, confirming that the proximal breakpoint was within COL4A6 intron 2 in 2 cases. Surprisingly, 1 case had a deletion extending proximally beyond exon 3 of COL4A6, as confirmed by qPCR analysis. This is the largest deletion reported to date that has been associated with ATS-DL and this case should lead us to reconsider the mechanisms that might be involved in the development of diffuse leiomyomatosis.

Oohashi T, Naito I, Ueki Y, et al.
Clonal overgrowth of esophageal smooth muscle cells in diffuse leiomyomatosis-Alport syndrome caused by partial deletion in COL4A5 and COL4A6 genes.
Matrix Biol. 2011; 30(1):3-8 [PubMed] Related Publications
This is a study of a patient who manifests all of the features of a diffuse leiomyomatosis-Alport syndrome (DL-ATS), and her two-year-old son who has already been diagnosed with Alport syndrome. Fourteen years ago, the patient underwent a partial esophageal resection followed by a replacement with jejunum. Recently, she underwent a surgical resection of the esophagus due to esophageal dysfunction. Genetic analyses of COL4A5 and COL4A6 on the X-chromosome were efficiently performed using the genomic DNA of her son. We have identified a novel deletion of 194-kb in length, encompassing COL4A5-COL4A6 promoters as well as nearly the entire large intron 1 of COL4A5 and intron 2 of COL4A6. To uncover the relationship of the esophagus-specific occurrence of the tumor and the expression of those genes, immunohistochemical analyses of type IV collagen α chains were conducted in the non-affected individuals. The esophageal smooth muscle-specific expression of α5(IV) and α6(IV) chains in the gastrointestinal tract was observed. Moreover, CAG repeat analysis of the androgen receptor gene and an immunohistochemical analysis in the leiomyoma revealed clonal overgrowth of the cells which received X-inactivation on the non-affected allele. These results may suggest that the dominant effect was caused by the partial deletion of the esophageal smooth muscle-specific genes, COL4A5 and COL4A6.

Chakraborty A, Mishra AK, Soni A, et al.
Vitamin D receptor gene polymorphism(s) and breast cancer risk in north Indians.
Cancer Detect Prev. 2009; 32(5-6):386-94 [PubMed] Related Publications
BACKGROUND: Vitamin D (1,25-dihydroxyVitamin D3) has shown experimentally anticarcinogenic effects and is thought to protect against breast cancer. The actions of Vitamin D are mediated via the Vitamin D receptor (VDR), and the polymorphisms at 3'UTR region of this gene are associated with the risk and progression of breast carcinoma. The current study is an attempt to examine the association of these variations with breast cancer risk in north Indians.
METHODS: A total of 160 cases and 140 control subjects were studied for the polymorphisms at 3' end of the VDR gene. A polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) method and fragment analysis was performed to determine ApaI and TaqI polymorphisms and variable length poly-A microsatellite repeats. Linkage disequilibrium (LD) was calculated for each pair of polymorphisms. Unadjusted and adjusted odds ratios for breast cancer with genotypes comprising the polymorphic sites were calculated to understand their role towards breast cancer susceptibility.
RESULTS: Patient's with long poly-A repeat showed a significant association with disease (chi 2 = 9.52, df = 2, P CONCLUSIONS: The results indicate that the VDR poly-A polymorphism is significantly associated with breast cancer risk in north Indians especially with early onset disease. Although, ApaI and TaqI did not show any significant association with the disease when analyzed in isolation, but TaqI might modulate the risk associated with L alleles. Further, understanding the functional role of these variants residing on the VDR haplotype associated with disease susceptibility may suggest novel approaches for breast cancer prevention and therapy.

Karrman K, Kjeldsen E, Lassen C, et al.
The t(X;7)(q22;q34) in paediatric T-cell acute lymphoblastic leukaemia results in overexpression of the insulin receptor substrate 4 gene through illegitimate recombination with the T-cell receptor beta locus.
Br J Haematol. 2009; 144(4):546-51 [PubMed] Related Publications
The t(X;7)(q22;q34), a translocation not previously reported in a neoplastic disorder, was identified and molecularly characterised in a paediatric T-cell acute lymphoblastic leukaemia (T-ALL), subsequently shown also to harbour a deletion of 6q, a STIL/TAL1 fusion and an activating NOTCH1 mutation. The t(X;7) was further investigated using fluorescence in situ hybridisation (FISH), real-time quantitative polymerase chain reaction (RQ-PCR) and Western blot analyses. FISH revealed a breakpoint at the T-cell receptor beta locus at 7q34 and mapped the corresponding breakpoint to Xq22.3. The latter region contains only two known genes, namely insulin receptor substrate 4 (IRS4) and collagen, type IV, alpha 5 (COL4A5), the expressions of which were analysed by the use of RQ-PCR. COL4A5 was not differentially expressed in the t(X;7)-positive sample compared to five T-ALL controls. However, a marked, 1000-fold overexpression of IRS4 was identified. Western blot analysis with a monoclonal antibody against IRS4 showed overexpression also at the protein level. Considering that forced expression of several members of the IRS family has been shown to result in increased cell proliferation, for example in haematopoietic cells, we hypothesise that the IRS4 up-regulation in T-ALL is pathogenetically important as a mitogenic stimulus.

Kato T, Shinoda J, Nakayama N, et al.
Metabolic assessment of gliomas using 11C-methionine, [18F] fluorodeoxyglucose, and 11C-choline positron-emission tomography.
AJNR Am J Neuroradiol. 2008; 29(6):1176-82 [PubMed] Related Publications
BACKGROUND AND PURPOSE: Positron-emission tomography (PET) is a useful tool in oncology. The aim of this study was to assess the metabolic activity of gliomas using (11)C-methionine (MET), [(18)F] fluorodeoxyglucose (FDG), and (11)C-choline (CHO) PET and to explore the correlation between the metabolic activity and histopathologic features.
MATERIALS AND METHODS: PET examinations were performed for 95 primary gliomas (37 grade II, 37 grade III, and 21 grade IV). We measured the tumor/normal brain uptake ratio (T/N ratio) on each PET and investigated the correlations among the tracer uptake, tumor grade, tumor type, and tumor proliferation activity. In addition, we compared the ease of visual evaluation for tumor detection.
RESULTS: All 3 of the tracers showed positive correlations with astrocytic tumor (AT) grades (II/IV and III/IV). The MET T/N ratio of oligodendroglial tumors (OTs) was significantly higher than that of ATs of the same grade. The CHO T/N ratio showed a significant positive correlation with histopathologic grade in OTs. Tumor grade and type influenced MET uptake only. MET T/N ratios of more than 2.0 were seen in 87% of all of the gliomas. All of the tracers showed significantly positive correlations with Mib-1 labeling index in ATs but not in OTs and oligoastrocytic tumors.
CONCLUSION: MET PET appears to be useful in evaluating grade, type, and proliferative activity of ATs. CHO PET may be useful in evaluating the potential malignancy of OTs. In terms of visual evaluation of tumor localization, MET PET is superior to FDG and CHO PET in all of the gliomas, due to its straightforward detection of "hot lesions".

Nagy Z, Tora L
Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation.
Oncogene. 2007; 26(37):5341-57 [PubMed] Related Publications
Transcription in eukaryotes is a tightly regulated, multistep process. Gene-specific transcriptional activators, several different co-activators and general transcription factors are necessary to access specific loci to allow precise initiation of RNA polymerase II transcription. As the dense chromatin folding of the genome does not allow the access of these sites by the huge multiprotein transcription machinery, remodelling is required to loosen up the chromatin structure for successful transcription initiation. In the present review, we summarize the recent evolution of our understanding of the function of two histone acetyl transferases (ATs) from metazoan organisms: GCN5 and PCAF. Their overall structure and the multiprotein complexes in which they are carrying out their activities are discussed. Metazoan GCN5 and PCAF are subunits of at least two types of multiprotein complexes, one having a molecular weight of 2 MDa (SPT3-TAF9-GCN5 acetyl transferase/TATA binding protein (TBP)-free-TAF complex/PCAF complexes) and a second type with about a size of 700 kDa (ATAC complex). These complexes possess global histone acetylation activity and locus-specific co-activator functions together with AT activity on non-histone substrates. Thus, their biological functions cover a wide range of tasks and render them indispensable for the normal function of cells. That deregulation of the global and/or specific AT activities of these complexes leads to the cancerous transformation of the cells highlights their importance in cellular processes. The possible effects of GCN5 and PCAF in tumorigenesis are also discussed.

Prenzel KL, Schäfer E, Stippel D, et al.
Multiple giant leiomyomas of the esophagus and stomach.
Dis Esophagus. 2006; 19(6):504-8 [PubMed] Related Publications
Leiomyomas are rare esophageal disorders, although among the benign esophageal neoplasms, they are the most common. Multiple leiomyomas are distinguished from esophageal leiomyomatosis, an extremely rare condition, which is associated with Alport syndrome, showing deletions and rearrangements of the COL4A5/COL4A6 gene. There are only a few reports of diffuse multilocular lesions. A 19-year-old man presented with upper gastrointestinal bleeding and diffuse abdominal pain. On endoscopy multiple nodules covered with intact mucosa were present, the largest tumor arising from the gastro-esophageal border infiltrating the cardia. Barium swallow demonstrated narrowing of the middle and lower esophagus with the upper third of the stomach filled by the tumor. Thorax and abdominal CT scans revealed infiltration of almost the total aboral esophagus by the tumor with compression of left and right bronchi. The infiltration reached the whole lesser curvature of the stomach. Endosonography showed multiple encapsulated nodules. Due to the extended tumor growth with infiltration of the upper third of the stomach, a total esophago-gastrectomy with reconstruction by colon interposition was performed. On histopathological examination multiple esophageal leiomyomas with infiltration of the proximal third of the stomach was shown. Immunohistochemically the tumor stained positive for desmin and sm-actin and negative for CD34 and c-kit. Genetic analysis ruled out a deletion of the COL4A5/COL4A6 locus on chromosome X that is linked with Alport syndrome-diffuse leiomyomatosis. Extended mutations in the COL4A5 gene, associated with Alport syndrome, to the COL4A6 gene, are required for the development of leiomyomatosis. In young patients with diffuse multinodular infiltration by encapsulated tumors, esophageal leiomyomatosis should be considered. If the proximal third of the stomach is infiltrated by the tumor an extended resection is necessary. Reconstruction procedures include colon interposition.

Ikeda K, Iyama K, Ishikawa N, et al.
Loss of expression of type IV collagen alpha5 and alpha6 chains in colorectal cancer associated with the hypermethylation of their promoter region.
Am J Pathol. 2006; 168(3):856-65 [PubMed] Free Access to Full Article Related Publications
Type IV collagen, a major component of the basement membrane (BM), is composed of six genetically distinct alpha(IV) chains, alpha1(IV) to alpha6(IV). Their genes are paired on three different chromosomes in a head-to-head arrangement. The alpha5(IV) gene (COL4A5) and the alpha6(IV) gene (COL4A6) are on chromosome Xq22 and are regulated by a bidirectional promoter. Loss of the alpha5(IV)/alpha6(IV) chains in epithelial BM occur in the early stage of cancer invasion. However, the regulatory mechanism of the specific loss of the alpha5(IV)/alpha6(IV) chains during cancer cell invasion is still undetermined. In the present study, we examined the expression of the alpha5(IV)/alpha6(IV) chains and the methylation profiles of the bidirectional promoter region of COL4A5/COL4A6 in colon cancer cell lines and colorectal tumor tissues. The expression of the alpha5(IV)/alpha6(IV) chains was down-regulated in colorectal cancer, and the loss of expression of the alpha5(IV)/alpha6(IV) chains was associated with the hypermethylation of their promoter region. In conclusion, the hypermethylation of the bidirectional promoter region of COL4A5/COL4A6 is one of the events that is responsible for the loss of expression of the alpha5(IV)/alpha6(IV) chains and the remodeling of the epithelial BM during cancer cell invasion.

Storlazzi CT, Wozniak A, Panagopoulos I, et al.
Rearrangement of the COL12A1 and COL4A5 genes in subungual exostosis: molecular cytogenetic delineation of the tumor-specific translocation t(X;6)(q13-14;q22).
Int J Cancer. 2006; 118(8):1972-6 [PubMed] Related Publications
Subungual exostosis is a benign bone- and cartilage-producing tumor occurring in the hands and feet of children and young adults. The recent identification of a recurrent chromosomal translocation t(X;6)(q24-q26;q15-21) in short-term-cultured tumor cells strongly suggests that subungual exostosis is a neoplastic lesion caused by rearrangement of genes in the two breakpoints. To identify the genes that are critical for neoplastic transformation, we have studied five subungual exostoses by interphase or metaphase FISH. The results of these analyses demonstrated a clustering of the breakpoints to the regions harboring the collagen genes COL12A1 and COL4A5 in chromosome bands 6q13-14 and Xq22, respectively. Furthermore, in all but one case, these two genes were shown to colocalize on the derivative chromosomes X and 6, strongly suggesting that at least one of them is consistently involved in the formation of a chimeric fusion gene or in the exchange of regulatory sequences. Because collagen molecules are important for tissue remodeling during physiologic growth and differentiation, both COL12A1 and COL4A5 constitute good candidate target genes in the pathogenesis of subungual exostosis. Further investigations on the transcript level are required to elucidate the functional outcome of the t(X;6) translocation in subungual exostoses.

Sugimoto K, Yanagida H, Yagi K, et al.
A Japanese family with Alport syndrome associated with esophageal leiomyomatosis: genetic analysis of COL4A5 to COL4A6 and immunostaining for type IV collagen subtypes.
Clin Nephrol. 2005; 64(2):144-50 [PubMed] Related Publications
BACKGROUND: In some families, X-linked Alport syndrome (AS) is associated with diffuse leiomyomatosis. We describe clinical, pathologic and molecular-genetic findings in a Japanese family with this inheritance mode of AS in association with leiomyomatosis.
PATIENT: AS was diagnosed in a one-year-old boy with recurrent aspiration pneumonia caused by esophageal stenosis from leiomyomatosis. Diagnosis was confirmed by electron microscopy coupled with type IV collagen chain subtype staining in a renal biopsy specimen. His mother, who exhibited esophageal leiomyomatosis and is heterozygous for AS, showed a discontinuous staining pattern for collagen alpha5(IV) chain along the epidermal basement membrane in a skin biopsy specimen. Genetic analysis in the boy revealed the deletion of the first two exons of COL4A6 together with deletion of the 5' end of COL4A5. Despite administration of cyclosporin A, massive proteinuria has persisted in the boy, although renal function otherwise remains normal.
CONCLUSION: Identification of an AS patient during infancy is extremely rare. Clinical manifestations, including macroscopic hematuria, cataracts and leiomyomatosis caused by the large deletion involving COL4A5 to COL4A6, led to early presentation with AS.

Thielen BK, Barker DF, Nelson RD, et al.
Deletion mapping in Alport syndrome and Alport syndrome-diffuse leiomyomatosis reveals potential mechanisms of visceral smooth muscle overgrowth.
Hum Mutat. 2003; 22(5):419 [PubMed] Related Publications
Diffuse leiomyomatosis is associated with the inherited kidney disease Alport syndrome, and characterized by visceral smooth muscle overgrowth within the respiratory, gastrointestinal and female reproductive tracts. Although partial deletions of the type IV collagen genes COL4A5 and COL4A6, paired head-to-head on chromosome Xq22, are known to cause diffuse leiomyomatosis, loss of function for type IV collagen does not explain smooth muscle overgrowth. To further clarify pathogenic mechanisms, we have characterized novel deletions in patients with Alport syndrome-diffuse leiomyomatosis or Alport syndrome alone. A 27.6-kb deletion, in a female with Alport syndrome-diffuse leiomyomatosis, is marked by the most proximal, i.e. most 5', COL4A5 breakpoint described to date. By comparing this deletion to others described here and previously, we have defined a minimal overlap region, only 4.2 kb in length and containing the COL4A5-COL4A6 proximal promoters, loss of which contributes to smooth muscle overgrowth. A novel deletion in a male with Alport syndrome alone is>1.4 Mb in length, encompassing COL4A5 and COL4A6 entirely, as well as neighboring genes. We postulate that loss of the 4.2-kb region in diffuse leiomyomatosis causes misregulation of neighboring genes, contributing to smooth muscle overgrowth. Deletion of the neighboring genes themselves may afford protection from this condition.

Anker MC, Arnemann J, Neumann K, et al.
Alport syndrome with diffuse leiomyomatosis.
Am J Med Genet A. 2003; 119A(3):381-5 [PubMed] Related Publications
Alport syndrome (AS) is a hereditary nephropathy with hematuria progressing to end-stage renal failure (ESRF), sensorineural deafness, and specific eye signs (lenticonus, macular flecks, and congenital cataracts). Inheritance is X-linked in about 85% of the cases, caused by different mutations in the COL4A5 gene. Rarely AS is seen in combination with diffuse leiomyomatosis (DL). DL is a tumorous process involving smooth muscle cells, mostly of the esophagus, but also of the tracheobronchial tree and the female genital tract. Characteristically, the patients have deletions of the 5'-end of both the COL4A5 and the COL4A6 genes, respectively. We here present a 9-year-old boy who was admitted because of a newly diagnosed sensorineural deafness. He was born with cataracts and presented symptoms of dysphagia and bronchial irritation in the first year of life. Macroscopic hematuria was first noticed at 2 years during a febrile infection. Since early childhood the boy suffered from severe constipation. Taking together these symptoms, the diagnosis of Alport syndrome with diffuse leiomyomatosis (AS-DL) has to be considered. Genetic analysis demonstrated the predicted deletion of the COL4A5/COL4A6 genes.

Jang JH
Identification and characterization of soluble isoform of fibroblast growth factor receptor 3 in human SaOS-2 osteosarcoma cells.
Biochem Biophys Res Commun. 2002; 292(2):378-82 [PubMed] Related Publications
We have previously reported the alternatively spliced transcripts of fibroblast growth factor 3 (FGFR3 ATs and MTs) derived by aberrant splicing and usage of cryptic splicing sites. Here, we describe a soluble variant of FGFR3 (FGFR3 AT-III) arising from skipping exons 8, 9, and 10 in human SaOS-2 osteosarcoma cell. This splicing event leads to the generation of an mRNA encoding a FGFR3 in which the COOH-terminal portion of the Ig-like-III domain and transmembrane domain are deleted while the remainder of the mature molecule is fused in-frame to the COOH-terminal cytoplasmic kinases domains. Sf9 cells transfected with the corresponding cDNA express the soluble form of FGFR3 AT-III into the condition medium and its secreted form was able to bind both FGF-1 and FGF-2 leading to loss of ligand binding specificity. These results indicate that the FGFR3 AT-III mRNAs are transcribed due to exon skipping with altered ligand binding specificity. These results suggest that the presence of soluble transcripts of FGFRs gene is a common feature due to mRNA splicing and this splicing plays an important role in the regulation of FGFRs function.

Mothes H, Heidet L, Arrondel C, et al.
Alport syndrome associated with diffuse leiomyomatosis: COL4A5-COL4A6 deletion associated with a mild form of Alport nephropathy.
Nephrol Dial Transplant. 2002; 17(1):70-4 [PubMed] Related Publications
BACKGROUND: The X-linked Alport syndrome (AS) is an inherited nephropathy due to mutations in the COL4A5 gene, encoding the alpha5 chain of type IV collagen, a major component of the glomerular basement membrane (GBM). Here, we report a new kindred with the rare association of X-linked AS and diffuse leiomyomatosis (DL), which is a tumourous process involving smooth muscle cells of the oesophagus, the tracheobronchial tree and, in females, the genital tract. For this syndrome, an almost constant association of large COL4A5 rearrangements with a severe juvenile form of nephropathy has been described for male patients.
METHODS: DNA rearrangement at the COL4A5-COL4A6 locus was studied in several members of this family using polymerase chain reaction and pulsed field gel electrophoresis. Furthermore, immunohistochemical staining of tumour and skin samples was performed.
RESULTS: The affected patients in this family carry a 120 kb deletion by which the COL4A5 exon 1 and COL4A6 exons 1, 1', and 2 are removed. Immunohistochemical investigation of a skin biopsy of an affected male patient confirmed the absence of both the alpha5 and the alpha6 chains of type IV collagen in the basement membrane of the skin. Surprisingly, both affected male patients had a rather mild renal phenotype.
CONCLUSIONS: This report shows that, contrary to what has been reported to date, patients suffering from AS associated with DL can be associated with a late onset renal failure (adult) form of nephropathy.

Guillem P, Delcambre F, Cohen-Solal L, et al.
Diffuse esophageal leiomyomatosis with perirectal involvement mimicking Hirschsprung disease.
Gastroenterology. 2001; 120(1):216-20 [PubMed] Related Publications
We describe a 25-year-old woman with diffuse esophageal leiomyomatosis. During childhood, achalasia was mistakenly diagnosed in this patient. Subsequently, she underwent cardiomyotomy and developed symptoms of Hirschsprung disease. These symptoms were caused by infiltration of the esophageal and rectal walls by benign muscular hypertrophy. The pseudo-Hirschsprung disorder was manifested by chronic severe constipation, with consistent manometric findings. Clitoral hypertrophy and vulvar and periurethral leiomyoma were also present. Genetic analysis demonstrating deletion of the COL4A5/COL4A6 locus and the discovery of microscopic hematuria implied that the patient could transmit both diffuse leiomyomatosis and the Alport syndrome.

Garcia-Torres R, Cruz D, Orozco L, et al.
Alport syndrome and diffuse leiomyomatosis. Clinical aspects, pathology, molecular biology and extracellular matrix studies. A synthesis.
Nephrologie. 2000; 21(1):9-12 [PubMed] Related Publications
The Alport syndrome-diffuse leiomyomatosis association can be defined as a hereditary disease of type IV collagen combining features of Alport syndrome (hematuric nephropathy, deafness and ocular abnormalities: anterior lenticonus, maculopathy) and leiomyomatosis involving oesophagus (diffuse type), tracheobronchial tree, and genitals (only in women). This entity is transmitted as an X-linked dominant trait. Mutations of both the COL4A5 and COL4A6 genes, located head to head in Xq22 encoding the alpha 5 and alpha 6(IV) chains are responsible for the abnormalities. Molecular studies have shown deletions of the 5' end of both COL4A5 and COL4A6 including the intergenic region. The breakpoint in COL4A6 is always located within intron 2. Immunohistochemistry has shown significant alterations of basement membranes in the kidney and esophageal leiomyomas. Leiomyomas lack alpha 5 and alpha 6(IV) chains, fibronectin and laminin beta 1 chains in the muscle basement membranes where they are normally expressed. The tumors also show myocyte anomalies: irregular expression of the alpha 5 integrin subunits, and disorganization of actin and desmin filaments. It is hypothesized that a third as yet unknown gene, situated within the large intron 2 in a critical 90 kb region, is responsible for the smooth muscle proliferation. Abnormalities of the basement membranes could destabilize interactions between muscular cells and the extracellular matrix.

Béroud C, Collod-Béroud G, Boileau C, et al.
UMD (Universal mutation database): a generic software to build and analyze locus-specific databases.
Hum Mutat. 2000; 15(1):86-94 [PubMed] Related Publications
The human genome is thought to contain about 80,000 genes and presently only 3,000 are known to be implicated in genetic diseases. In the near future, the entire sequence of the human genome will be available and the development of new methods for point mutation detection will lead to a huge increase in the identification of genes and their mutations associated with genetic diseases as well as cancers, which is growing in frequency in industrial states. The collection of these mutations will be critical for researchers and clinicians to establish genotype/phenotype correlations. Other fields such as molecular epidemiology will also be developed using these new data. Consequently, the future lies not in simple repositories of locus-specific mutations but in dynamic databases linked to various computerized tools for their analysis and that can be directly queried on-line. To meet this goal, we devised a generic software called UMD (Universal Mutation Database). It was developed as a generic software to create locus-specific databases (LSDBs) with the 4(th) Dimension(R) package from ACI. This software includes an optimized structure to assist and secure data entry and to allow the input of various clinical data. Thanks to the flexible structure of the UMD software, it has been successfully adapted to nine genes either involved in cancer (APC, P53, RB1, MEN1, SUR1, VHL, and WT1) or in genetic diseases (FBN1 and LDLR). Four new LSDBs are under construction (VLCAD, MCAD, KIR6, and COL4A5). Finally, the data can be transferred to core databases.

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