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M G Tilanus

Publications and source records attributed to M G Tilanus.

At least 55 records · Page 3Linked to original sources
PubMed1996

A computerized method to predict the discriminatory properties for class II sequencing based typing.

Accurate identification of alleles or groups of alleles is obtained using DNA techniques for HLA class II typing. In PCR-SSP and PCR-SSO the typing resolution is dependent on the location of the amplification primers and the number of oligonucleotide probes used for hybridization. These primers are developed based upon the known allele sequences. However, the number of published allele sequences increases rapidly. Periodic reconsideration of the discriminatory properties of the methods used is necessary and often leads to the addition of primers, and an increase of ambiguous genotypes. SBT is a high-resolution class II typing method which utilizes the second exon sequence at all positions for typing. Using a generic amplification and sequencing approach, a limited number of ambiguous heterozygotes can be expected. However, the number of ambiguities is dependent on the location of the primers. These ambiguities can be solved by the use of group-specific primers in either the amplification or sequencing reaction. To identify the applicability of a SBT approach with respect to typing resolution, it is important to identify these ambiguities and develop strategies to solve them. We developed software that predicts the ambiguous heterozygotes, and analyzes their sequences for group specific primers, solving these ambiguities. The location of the primers is considered as well as the use of generic vs group-specific amplification or sequencing reactions. Allele sequences of all class II genes, as accepted by the WHO nomenclature committee for factors of the HLA system and submitted to the EMBL/Genbank databases, are analyzed to define the allelic discrimination level of HLA-DQB1, -DQA1, -DFB1, -DPA1, -DRB1, -DRB3, -DRB4, and -DRB5.

Alleles↗
PubMed1996

Sequenase sequence profiles used for HLA-DPB1 sequencing-based typing.

Sequencing-based HLA typing (SBT) is a PCR based high resolution HLA typing method in which polymorphic regions of the gene are sequenced and directly used for typing. Currently, for class II SBT, alleles are identified by comparison of the exon 2 sequence with their corresponding allele sequence library. Routine SBT requires reliable identification of heterozygosity, and automated assignment of the alleles. In sequencing strategies different enzymes can be used for primer extension. The most characteristic difference between sequences obtained by two protocols using Sequenaseregistered, or Taq-cycle sequencing, respectively, is a difference in incorporation of nucleotides in the primer extension leading to different sequence profiles. In Taq-cycling sequencing variable nucleotide incorporation results in irregular, but reproducible peak patterns, whereas Sequenase incorporates nucleotides in nearly equal amounts, resulting in more even peak patterns. In a previously published multi-center study we evaluated HLA-DPB1 SBT using Taq-cycle sequencing, and showed that typing can reliably be performed, considering the specific sequence profiles. In this study the applicability of Sequenase for HLA-DPB1 SBT was tested. A panel of samples were typed by SBT at five test sites which participate in the Sequencing Based Typing component of the 12th International Histocompatibility Workshop. The panel represents the existing polymorphism at all known polymorphic positions of exon 2, both in homozygous and heterozygous combinations. The assignment of homozygosity and heterozygosity was validated by Multi-Sequence Analysis, performing cluster analysis of chromatographic data of all sequences at each position. Sequence characteristics were examined and considered for appropriate assignment. Data reveals that Sequenase sequencing can also reliably be used for HLA-DPB1 typing.

Bacteriophage T7↗
PubMed1996

Six newly identified HLA-DRB alleles: DRB1*1121, *1419, *1420, *1421, DRB3*0203 and DRB5*0103.

Seven samples with irregular PCR-SSO hybridization patterns, observed during routine HLA-DRB typing, were studied in more detail. Group-specific amplification, followed by hybridization with relevant SSOs strengthened the suggestion that these samples contained new DRB alleles. DRB exon 2 segments were amplified, cloned and sequenced and revealed: DRB1*1121 [MUL] is similar to DRB1*1102 in which codon 85 changed from GTT(V) into GTC(A); DRB1*1419 [AKKAL] is similar to DRB1*1402 with codon 71 changed from AGG(R) into AAG(K); DRB1*1420 [OND-52971] is a DRB1*1406 with codon 37 changed from AAC(N) into TTC(F); DRB1*1421 [TGI] is similar to DRB1*1417 with codon 71 changed from AGG(R) into AAG(K); DRB3*0203 [POS] is similar to DRB3*0202 in which codons 37-38 are changed from TAC GCG(YA) into TCC GTC(SV); DRB5*0103 was found in two unrelated individuals of Oriental origin [IND-24 and IND-59] and is similar to DRB5*0102 in which codon 71 AGG(R) changed into ACG(T). This particular sequence variation at position 71 has not yet been described. The new DRB sequences were confirmed using the sequencing based typing technique. Low resolution PCR-SSP typing failed to amplify two of the DRB1*14 variants, whereas high resolution PCR-SSP resulted in aberrant patterns. Class II alloantisera identify the codon 71 changes in DRB1*1419 and *1421 with respect to the MC1 ('DR1+DR4') epitope.

Alleles↗
PubMed1996

Molecular test for the detection of tumor cells in blood and sentinel nodes of melanoma patients.

Lymph node metastasis dramatically decreases the 5-year survival of melanoma patients. The so-called sentinel node surgery offers a therapeutic approach to resect the first draining lymph node. This technique enables accurate staging of melanoma patients in an early stage of the disease. Detection of a sentinel node metastasis is a strong argument for local lymphadenectomy. To improve the detection of micrometastasis in sentinel nodes of melanoma patients, molecular biological techniques were used. The exclusively melanocyte-specific tyrosinase transcript was amplified by reverse transcription followed by polymerase chain reaction (RT-PCR). In sentinel node examination, the detection of tyrosinase-positive cells by RT-PCR was compared with routine immunohistochemistry. From 16 patients, a total of 28 lymph nodes were tested. The lymph nodes were derived after lymphadenectomy (4 patients) and after sentinel node resection (12 patients with melanoma stage I). By using RT-PCR we could detect 100 tumor cells in a background of 10(8) peripheral blood mononuclear cells. The negative controls were all negative for tyrosinase. Cryostat sections of lymph nodes for mRNA isolation were alternated with sections for immunohistochemistry. By using tyrosinase RT-PCR, we detected 6 additional positive sentinel nodes in patients with melanoma stage I. Furthermore, the tyrosinase RT-PCR enabled us to design a blood test for circulating melanoma cells. Therefore, mRNA was directly isolated from whole blood of 23 blood samples, of which 3 samples were positive for tyrosinase. The present study demonstrates the possibility of a simple and rapid blood test for melanoma patients that has not been available until now. Furthermore, the detection of micrometastasis in sentinel nodes by tyrosinase RT-PCR dramatically increases the accuracy of melanoma staging.

Base Sequence↗
PubMed1996

Complete donor T cell chimerism is accomplished in patients transplanted with bone marrow grafts containing a fixed low number of T cells.

T cell depletion of the bone marrow graft, the most effective method to prevent severe graft-versus-host disease (GVHD) after allogeneic bone marrow transplantation (BMT), has resulted in approximately three times more relapses of the disease post-transplant than after non-T cell-depleted BMT. It has been hypothesized that this is caused by the development of mixed T cell chimerism, often observed after T cell depleted BMT, whereas non-T cell-depleted BMT generally results in complete donor T cell chimerism. In order to find an approach of T cell depletion which may avoid the high relapse rate but prevent severe GVHD, we gave marrow recipients a partial T cell-depleted marrow graft containing 1 x 10(5) donor T cells/kg recipient's weight. To investigate whether our approach results in complete donor T cell chimerism, we analyzed post-transplant the origin of purified T cells in 56 patients with hematologic malignancies, including 15 patients at the time they relapsed. The T cells were studied for being of host or donor origin by amplification of four loci of variable number of tandem repeats (VNTR) by PCR. From 6 months post-BMT, all 45 patients who could be analyzed in remission (five had died and six had relapsed within 6 months) had T cells that were exclusively of donor origin. Furthermore, the T cells of 15 patients who had relapsed post-BMT were also exclusively of donor origin. Severe GVHD was never observed. Thus, this approach seems to combine the favorable aspects of both T cell-depleted and non-T cell-depleted BMT.

Adolescent↗
PubMed1996

HLA-DRB1*04 high resolution typing.

High resolution typing for HLA-DR4 is required to identify the individual subtypes. In this study a panel of DR4-positive samples was typed by both sequencing-based typing (SBT) and oligohybridization (PCR sequence-specific oligonucleotide; PCR-SSO). SBT reveals the highest resolution; moreover, ambiguous DRB1*04 allelic combinations can be resolved by a selective amplification of the individual alleles and subsequent sequencing. An extended DR4-specific PCR-SSO makes high resolution typing possible; however, an additional protocol is required to resolve ambiguities.

Alleles↗
PubMed1995

Novel HLA-DPB1 alleles detected in the Ethiopian population.

The number of identified HLA-DPB1 alleles increased rapidly by application of DNA-based typing techniques. PCR-SSO typing indicated the presence of possible new HLA-DPB1 variants in the Ethiopian population. The use of the SBT technique, which considers polymorphic as well as constant regions in the second exon of HLA genes, allowed direct identification of two new allelic variants. Moreover, a recently identified HLA-DPA1 variant was also present in this population. The newly defined allelic HLA-DPB1 sequences found in five individuals of the Ethiopian population were confirmed by cloning and subsequent sequencing of the cloned DNA. One of the new alleles was shown to segregate in a family and was also present in unrelated individuals. Both new DPB1 alleles represent new combinations of existing polymorphism in the hypervariable regions. In different populations the frequency of these new HLA-DP variants remains to be determined.

Alleles↗
PubMed1995

Transforming growth factor-alpha and epidermal growth factor expression in the exocrine pancreas of azaserine-treated rats: modulation by cholecystokinin or a low fat, high fiber (caloric restricted) diet.

Expression of transforming growth factor-alpha (TGF-alpha) and epidermal growth factor (EGF) was studied in normal pancreatic tissue and in (pre)neoplastic pancreatic lesions of azaserine-treated rats. They were given either a low fat, high fiber (low caloric) diet, to inhibit carcinogenesis, or a low fat diet combined with injections of the cholecystokinin analog caerulein to enhance carcinogenesis. The control groups, maintained on a low fat diet, were injected with azaserine or were not treated at all. Autopsy was performed at 6 and 15 months after the last azaserine injection. After both 6 and 15 months immunohistochemistry revealed a weak expression of EGF and TGF-alpha peptides in the acinar cells, and a stronger expression in the ductular and centroacinar cells. TGF-alpha peptide expression was reduced in both putative preneoplastic and neoplastic acinar cell lesions, but no differences in EGF peptide expression were observed between the various stages of exocrine pancreatic carcinogenesis. After 16 months an increase in TGF-alpha mRNA due to treatment with azaserine was detected by semi-quantitative PCR in total pancreatic homogenates, whereas EGF mRNA expression had decreased. TGF-alpha mRNA levels in macroscopically isolated tumors were significantly lower, but EGF mRNA levels were significantly higher, than in total pancreatic homogenates from azaserine-treated rats. Furthermore, EGF and TGF-alpha mRNA levels in isolated tumors did not differ significantly from mRNA levels in non-carcinogen-treated rats. Neither with immunohistochemistry nor with PCR were differences in EGF or TGF-alpha expression observed due to either inhibition or stimulation of carcinogenesis. It is concluded that putative preneoplastic acinar cell lesions induced in rat pancreas by azaserine may develop into acinar adenocarcinomas independently of TGF-alpha and EGF. The results suggest involvement of these growth factors at the early stage of the carcinogenic process, during the initiation of normal acinar cells into putative preneoplastic cells. However, modulation of azaserine-induced pancreatic carcinogenesis by cholecystokinin or a low fat, high fiber (caloric restricted) diet appeared not to be regulated by EGF or TGF-alpha.

Animals↗
PubMed1995

Serology versus PCR-SSP in typing for HLA-DR and HLA-DQ: a practical evaluation.

In this study, serological HLA-DR and -DQ typing results were compared to typing results obtained with sequence-specific primers in the polymerase chain reaction (PCR-SSP). HLA-DR typing was performed on a random caucasian population consisting of 31 patients and 73 healthy individuals. Considering HLA-DR1-10, differences in typing results were found in 3 out of 73 healthy individuals and 8 out of 31 patients. When HLA-DR1-16 alleles were taken into account, differences in typing results were found in 11 out of 31 patients and 14 out of 73 healthy individuals. Typing results of PCR-SSP, different from that of serology, were all confirmed by sequencing-based typing of HLA-DRB1 alleles. HLA-DQ1-3 typings were performed on 40 individuals consisting of 17 patients and 23 healthy individuals. Differences in typing results were found in 5 out of 17 patients and 1 out of 23 healthy individuals. From the results of this study it can be concluded that serology is a reliable technique, when restricted to identification of HLA-DR1-10 and HLA-DQ1-3 antigens in healthy individuals. By PCR-SSP, however, reliable HLA-DR1-16 and -DQ1-3 typings can be obtained both in patients and healthy individuals.

HLA-DQ Antigens↗
PubMed1995

Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism.

An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the--corrected--DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1995

An evaluation of a multicenter study on HLA-DPB1 typing using solid-phase Taq-cycle sequencing chemistry.

In HLA Class II genes, polymorphism is mainly located in the second exon. Most DNA based typing methods are confined to the identification of specific sequence motifs in the second exon. In contrast, Sequencing Based Typing (SBT) elucidates the entire exon 2 sequence for typing. Comparison of the obtained exon 2 sequence with an allele sequence library results in allele assignment. We tested the applicability of SBT using a protocol for amplification followed by solid phase Taq-cycle sequencing for HLA-DPB1 typing. A panel of 32 samples were typed by SBT at five test sites which are participating in the Sequencing Based Typing component of the 12th International Histocompatibility Workshop. The panel represents the existing polymorphism at all known polymorphic positions of exon 2, both in homozygous and heterozygous combinations. In this multicenter study we focused on the reliability of analyzing heterozygous sequences for HLA typing. A multi-sequence analysis approach, Polall, was developed to evaluate sequences obtained. The assignment of homozygosity and heterozygosity was validated by cluster analysis of chromatographic data of all sequences. Sequence characteristics were examined and considered for appropriate assignment. Differences in sequence characteristics that occurred between the test sites are considered in detail. The evaluation of data of 5 test sites reveals that Taq-cycle sequencing can reliably be performed for HLA-DPB1 SBT.

DNA-Directed DNA Polymerase↗