[The Polymorphism Analysis of HLA Class II Alleles Based on Next-Generation Sequencing and Prevention Strategy for Allele Dropout]

OBJECTIVE

To investigate the accuracy of next-generation sequencing technology (NGS) in detecting the polymorphisms of HLA-DRB1, DQB1, DQA1, DRB3, DRB4, DRB5, DPA1 and DPB1 alleles in randomly-selected unrelated healthy individuals from Shenzhen Han population, investigate the potential reason for HLA-DRB1 allele dropout in routine NGS, and establish an internal quality control system.

METHODS

NGS-based HLA class II genotyping was performed on 1 012 samples using the MiSeqDxTM platform. The suspected missed alleles indicated by the quality control software and HLA-DRB1 homozygotes were confirmed by PCR-SSOP or PCR-SBT methods.

RESULTS

A total of 139 alleles were detected, including HLA-DRB1(45), DRB3(7), DRB4(5), DRB5(7), DQA1(17), DQB1(21), DPA1(10) and DPB1(27). HLA-DRB1*09:01(17.09%),15:01(10.72%); DRB3*02:02(25.99%),03:01(10.18%); DRB4*01:03(36.46%); DRB5*01:01(15.42%); DQA1*01:02(20.01%),03:02(17.19%); DQB1*03:01(19.47%),03:03(17.98%), 05:02(11.66%), 06:01(10.67%); DPA1*02:02(54.45%), 01:03(31.18%) and DPB1*05:01(39.13%), 02:01(16.90%) alleles were the most common alleles in Shenzhen Han population (frequencies >10%). There was no statistical difference between the gene frequencies of HLA-DRB1 and DQB1 loci in our study. The HLA Common and Well-Documented Alleles in China (CWD2.4) (χ2=12.68, P >0.05). 94 cases of HLA-DRB1 homozygous samples detected by NGS were retested by PCR-SSOP or SBT method, and one case of allele dropout at HLA-DRB1 locus was found. SBT method confirmed that the allele of DRB1*04:03 was missed. The laboratory internal quality control system was established. Two cases of new alleles were detected and named by WHO Nomenclature Committee for Factors of the HLA System.

CONCLUSION

The HLA genotyping results based on NGS showed a significantly lower ambiguity rate. The HLA class II alleles exhibit genetic polymorphism in the Han population of unrelated healthy individuals in Shenzhen. The independent method based on NGS in clinical histocompatibility testing has limitations and requires internal quality control strategies to avoid allele-dropout events.

Full-length sequence of the novel HLA-A*02:1103 allele by next generation sequencing in a Chinese individual

HLA-A*02:1103 differs from HLA-A*02:01:01:01 by one nucleotide change at nucleotide 811 in exon 4 from G to A.

Characterization of the novel HLA-A*30:211 allele by next generation sequencing in a Chinese individual

HLA-A*30:211 differs from HLA-A*30:01:01:01 by one nucleotide change at nucleotide 344 in exon 3 from G to C.

The novel HLA-B*13:179 variant detected by next generation sequencing in a Chinese individual

HLA-B*13:179 differs from HLA-B*13:99 by one nucleotide substitution at position 829(A>G) in exon 4.

A single nucleotide substitution in exon 5 produced the novel allele, HLA-B*40:01:83

HLA-B*40:01:83, carrying a single nucleotide substitution in exon 5 is described.

The novel HLA-B*15:664 allele, identified by next-generation sequencing in a Chinese individual

B*15:664 differs from B*15:02:01:01 by one nucleotide change at nucleotide 755 in exon 4 from C to G.

Full-length sequence of the novel HLA-C*03:04:74 allele by next generation sequencing in a Chinese individual

C*03:04:74 differs from C*03:04:01:02 by one nucleotide change at nucleotide 1047 in exon 6 from G to A.

Identification of the novel HLA-B*46:01:33 allele by next generation sequencing in a Chinese individual

B*46:01:33 differs from B*46:01:01:01 by one nucleotide change at nucleotide 105 in exon 2 from C to T.

Full-length sequence of the novel HLA-C*03:566 allele by next-generation sequencing in a Chinese individual

HLA-C*03:566 differs from HLA-C*03:04:01:02 by one nucleotide substitution at nucleotide 92 in exon 2 from A to G.

A novel HLA-DQB1*04 variant, HLA-DQB1*04:90, identified in a Chinese Han individual

Identification of the novel HLA-DQB1*04:90 allele that differs from DQB1*04:01:01:01 at nucleotide 183 in exon 2 from A to T.

[Applied anatomical study and clinical application of the caudate lobe boundary and ductal system of the liver]

Objective: To explore the relationship between the hepatic caudate lobe boundary and the ductal system so as to guide the identification of the anatomical relationship during liver surgery. Methods: The specific parts were observed and the liver parenchyma was removed according to 41 cadaveric liver autopsy specimens. The critical relationship between the hepatic caudate lobe and other ducts was observed to explore the reticular duct structure. Results: The plane formed by the hepatic hilar plate and Arantius ligament served as the boundary between the caudate lobe and other hepatic lobes. The caudate lobe hepatic portal vein was composed of numerous small branches from its left and right branches. The portal vein adjacent to the vena cava was mainly derived from the left branch, and to a lesser extent from the right branch. Blood was drained straight from the caudate lobe vein into the inferior vena cava via the short hepatic vein. There were three or four bile duct branches in the caudate lobe. The main source of arterial blood flow were the left and right branches of the hepatic artery. An avascular zone of loose connective tissue was found between the caudate lobe and the retrohepatic inferior vena cava. Conclusion: The hepatic caudate lobe is an independent lobe. During hepatic caudate lobe surgery, the plane formed by the hepatic hilar plate and Arantius ligament can serve as the boundary between the caudate lobe and other hepatic lobes and be used for anatomical site identification. The duct system of the caudate lobe's is complicated, but it also has its own distinct regularity.

[Exclusion of HLA-C Genotype with Zero Mismatched PCR-SBT Results by Next Generation Sequencing]

OBJECTIVE

Three cases of rare alleles of HLA-C with zero mismatched PCR-SBT results were analyzed by full-length sequencing to determine the true genotypes.

METHODS

Three rare HLA-C alleles with zero mismatched PCR-SBT results were screened from clinical transplant matching samples, and the full-length sequence was detected by next-generation sequencing technology.

RESULTS

The results of PCR-SBT typing of 3 samples were: HLA-C*03:04, 12:167; HLA-C*07:291, 15:02; HLA-C*01:43, 08:16. Other alleles were not in the CWD table of common and confirmed HLA alleles in China (version 2.3) except common allele HLA-C*03:04, HLA-C*15:02. NGS full-length sequencing revealed that the HLA-C genotypes of the three samples were a combination of common alleles and novel alleles, and the three novel alleles had a base mutation in exons 6, 2, and 4, respectively. The novel allele sequences have been submitted to the Genbank database (MK629722, MK335474, MK641803), which were officially named HLA-C*03:04:74, HLA-C*15:192, HLA-C*08:01:25 by the WHO HLA Nomenclature Committee. The HLA high-resolution typing results of 3 samples were: HLA-C*03:04:74, HLA-C*12:03; HLA-C*07:02, HLA-C*15:192; HLA-C*01:02, HLA-C*08:01:25.

CONCLUSION

HLA typing results containing rare alleles should be treated cautiously, and the full-length sequence should be verified by NGS or cloning. The laboratory finally confirmed that the 3 cases of PCR-SBT zero mismatch HLA-C genotypes are the combination of common alleles and novel alleles by NGS sequencing, which provides an accurate basis for clinical transplantation matching and enriches the human HLA genetic database.

Characterization of a novel variant allele, HLA-C*03:587, identified in a Chinese Han individual

The novel HLA-C*03:587 allele differs from the closest allele C*03:03:01:01 in exon 5. This article is protected by copyright. All rights reserved.

Characterization of the novel HLA-C*01:213 allele by next-generation sequencing in a Chinese family

C*01:213 differs from C*01:02:01:01 by one nucleotide change at nucleotide 655 in exon 4 from T to G.

Discovery of the HLA-C*03:561 allele, a variant of HLA-C*03, in a Chinese individual

HLA-C*03:561 differs from HLA-C*03:02:02:01 by one nucleotide change in exon 4 at position 862 (G>A).

A novel HLA-C*15 allele, HLA-C*15:192, identified by next generation sequencing in a Chinese individual

Identification of the novel HLA-C*15:192 allele that differs from HLA-C*15:02:01:01 at one position in exon 2.

Discovery of the novel HLA-C*01:179 allele in a southern Chinese patient

One nucleotide substitution in codon 189 of HLA-C*01:02:01:01 results in a novel allele, HLA-C*01:179.

A substitution in exon 2 resulted in the novel HLA-A*30:140 variant identified in a Chinese individual

HLA-A*30:140 differs from HLA-A*30:01:01 by one nucleotide change in exon 2 at position 341 (C > A).

Characterization of the novel HLA-DQB1*03:362 allele in a Chinese family

A novel variant of HLA-DQB1*03 differs from DQB1*03:02:01:01 by one nucleotide substitution in Exon 2.

The HLA-DRB1*11:23:02 allele confirmed in a Chinese individual by next-generation sequencing

DRB1*11:23:02 differs from DRB1*11:23:01 by one nucleotide change at nucleotide 357 in exon 2 from G to A.

The full-length sequence of the novel HLA-C*08:190 allele, identified by cloning and sequencing

C*08:190 differs from C*08:01:01:01 by one nucleotide change at nucleotide 503 in exon 3 from A to G.

Identification of the novel HLA-B*46:78 allele by next generation sequencing in a Chinese individual

HLA-B*46:78 differs from HLA-B*46:01:01 by one nucleotide substitution at position 205 in exon 2.

Characterization of the novel HLA-DQB1*06:01:22 allele by next-generation sequencing

HLA-DQB1*06:01:22 differs from HLA-DQB1*06:01:01:01 by one nucleotide substitution in codon 189 in exon 4.

Identification of HLA-A*31:150 by next-generation sequencing in a Chinese Han individual

HLA-A*31:150 differs from HLA-A*31:01:02:01 in exon 2 by a single nucleotide.

HLA-C*08:01:25, a novel HLA allele, which has arisen by a silent mutation in codon 271

HLA-C*08:01:25 differs from HLA-C*08:01:01 by a single-nucleotide substitution in exon 4.

Characterization of the novel HLA-B*15:435 allele by next-generation sequencing in a Chinese family

HLA-B*15:435 has 5 nt changes from HLA-B*15:09:01 in exon 3 and 4.

Bimetallic phosphide hollow nanocubes derived from a prussian-blue-analog used as high-performance catalysts for the oxygen evolution reaction

Bimetallic phosphide (Ni_xFe_1−x)₂P hollow nanocubes were prepared from PBAs as highly active and stable OER electrocatalysts.

Determination of benzo[a]pyrene in cigarette mainstream smoke by using mid-infrared spectroscopy associated with a novel chemometric algorithm

Determination of benzo[a]pyrene (BaP) in cigarette smoke can be very important for the tobacco quality control and the assessment of its harm to human health. In this study, mid-infrared spectroscopy (MIR) coupled to chemometric algorithm (DPSO-WPT-PLS), which was based on the wavelet packet transform (WPT), discrete particle swarm optimization algorithm (DPSO) and partial least squares regression (PLS), was used to quantify harmful ingredient benzo[a]pyrene in the cigarette mainstream smoke with promising result. Furthermore, the proposed method provided better performance compared to several other chemometric models, i.e., PLS, radial basis function-based PLS (RBF-PLS), PLS with stepwise regression variable selection (Stepwise-PLS) as well as WPT-PLS with informative wavelet coefficients selected by correlation coefficient test (rtest-WPT-PLS). It can be expected that the proposed strategy could become a new effective, rapid quantitative analysis technique in analyzing the harmful ingredient BaP in cigarette mainstream smoke.

Tandem solid-phase extraction followed by HPLC-ESI/QTOF/MS/MS for rapid screening and structural identification of trace diterpenoids in flowers of Rhododendron molle

INTRODUCTION

'Naoyanghua', composed of the flowers of Rhododendron molle G. Don, is a traditional Chinese medicine that is widely known for its toxicity. Grayanane-type diterpenoids are the main active ingredients in R. molle, as well as possibly their toxicity: they are, however, difficult to isolate and analyse using common chromatographic methods, due to their small amounts and absence of conjugated groups, such as phenyl and α, β-unsaturated ketone.

OBJECTIVE

To establish a highly sensitive, selective and reliable method for the qualitative evaluation of trace diterpenoids in the flowers of R. molle by using tandem solid-phase extraction followed by high-performance liquid chromatography with electrospray ionisation quadrupole-time-of-flight mass spectrometry (HPLC-ESI/QTOF/MS/MS).

METHODS

Tandem solid phase extraction (SPE) was undertaken using a polyamide cartridge and a C18E cartridge in succession to enrich the trace diterpenoids. HPLC-ESI/QTOF/MS/MS was used to determine the fragmentation patterns of diterpenoids and to tentatively characterise their fragmentation pathways.

RESULTS

HPLC-ESI/QTOF/MS/MS detected a total of 14 diterpenoids, eight of which were identified by comparison with literature sources and six based on fragmentation analysis. Among the latter six, rhodojaponin VI-3-glucoside was tentatively identified as a new diterpenoid glycoside and rhodojaponin VII, rhodojaponin IV and rhodojaponin I were reported from R. molle for the first time.

CONCLUSION

By qualitative research of diterpenoids in this plant by HPLC-ESI/QTOF/MS/MS, a reliable methodology for the analysis of these active constituents of R. molle was established for the first time.

[Cloning and sequencing HLA-A and -B genomic DNA and analyzing polymorphism in regulatory regions in Chinese Han individuals]

In the present study, a high-resolute method for cloning and sequencing genomic full-length HLA-A and -B using 20 Chinese Han individuals was established. We detected 10 HLA-A allele sequences 4.2 kb in length and 6 HLA-B allele sequences 3.7 kb in length, and the sequences included all exons, all introns, 5'promoter, and 3'UTR of the two genes. All sixteen sequences have been submitted to GenBank and IMGT/HLA database. A*1153 is a novel allele, and the introns of B*151101 are firstly reported here. The 5'promoter and 3'UTR sequences of 5 HLA-A alleles and 2 HLA-B alleles are also firstly disclosed, and all other alleles have extended the genomic full length sequences released in IMGT/HLA database. The polymorphic structures of upper 5'promoter and downstream 3'UTR, which were uncovered in IMGT/HLA database, are firstly depicted in Chinese Han individuals. Twenty-six single nucleotide polymorphisms (SNPs) and one 3 bp-insertion/deletion (Indel) were located in the upper 5'promoter and 14 SNPs were located in the 3'UTR of HLA-A. In addition, five SNPs and one 1 bp-indel were located in the upper 5'promoter and 5 SNPs were located in the 3'UTR of HLA-B. Through analyzing the phylogenetic trees of 5'promoter, exons and 3'UTR of the two genes, we found that the evolution history of regulatory regions and exons is different between the two genes. The regulatory regions are tightly linked with exons in most of HLA-A alleles excluding A*24020101. On the contrary, recombinant events may occur frequently between regulatory regions and exons in most HLA-B alleles.

[Application value of allele frequencies in direct identification of ambiguous HLA genotypes]

This study was aimed to investigate the application value of allele frequencies in direct identification of the ambiguous HLA genotypes. The HLA-A, HLA-B and HLADRB1 loci in 658 Chinese Han donor were detected by PCR-SBT method, the ambiguous genotyping samples were identified by using high resolution PCR-SSP and heterozygous ambiguity resolution primers (HAPRs) methods. The relative probability of true genotypes was calculated by using allele frequencies and was compared with true results. The results indicated that the relative probability of true genotype > 95% in 220 HLA-A ambiguous samples, 238 HLA-B ambiguous samples and 107 HLA-DRB1 ambiguous samples were 99.5% (221/222), 95.8% (228/238) and 97.7% (104/107) respectively. As compared with phenotyping results detected by PCR-SSP and HARP methods, the matching ratios for HLA-A, HLA-B and HLA-DRB1 loci were 100% (222/222), 99.6% (237/238) and 99.1% (106/107) respectively, while the mismatch genotypes were observed only in B*3501/5501 and DRB1*1241/1504, the relative probability of them were 40.3% and 2.1% respectively. It is concluded that the detection method using allele frequencies to directly identify the ambiguous HLA genotypes in large scale PCR-SBT genotyping of donors not only can give higher accurate and reliable results, but also is a simple, rapid and cost-saving method. This method has to be used with great care in the identify-test of patient-donor pair before the transplantation.

[Identifying and sequence analysis of HLA-B*2736]

An unknown HLA-B allele which was similar to HLA-B*270401 was detected by FLOW-SSOPCR-SSP and heterozygous sequence-based typing (SBT) in Chinese Han individual. Its anomalous patterns suggested the possible presence of new allele. Amplifying exon 2-5(include intron 2-4) of the HLA-B*27 allele separately by using allele-specific primers and sequencing in both directions. Identifying the difference between the novel B*27 allele and B*270401. The sequence of novel B*27 from exon 2 to partial exon 5 is 1 815 bp. There are 10 nt changes from B*270401 in exon 3-4, at nt634where A-->C(codon130 AGC-->CGC, 130 S-->R); nt670 where A-->T (codon142 ACC-->TCC, 142 T-->S); nt683 where G-->T (codon146 TGG-->TTG, 146 W-->L); nt698 where A-->T (codon151 GAG-->GTG, 151 E-->V); nt774 where G-->C (codon176 GAG-->GAC, 176 E-->D); nt776 where C-->A (codon177 ACG-->AAG, 177 T-->K); nt781 where C-->G (codon179 CAG-->GAG, 179Q-->E); nt789 where G-->T (codon181 GCG-->GCT) resulting no coding change; nt1438 where C-->T (codon206 GGC-->GGT) resulting no coding change; nt1449 where G-->C (codon210 GGG-->GCG, 210G-->A). In IMGT/HLA database, only three alleles (B*270502/2706/2732) have sequences of introns. The same sequence in intron 2 showed homology between the novel HLA-B*27 allele and B*2706, but their homology could not be supported in intron 3-4. Comparing the sequence of the novel B*27 allele in intron 3 and 4 with B*27 group, it showed there are three mutations at nt106 C-->G, nt179 G-->A, nt536 G-->A and one deletion at nt168 in intron 3 and one mutations at nt82 T-->C in intron 4, but the sequence of the novel B*27 allele in intron 3 and 4 was all the same to B*070201. The sequence was submitted to Gen-Bank and the accession number was DQ915176. The allele has been confirmed as an extension of B*2736 by the WHO Nomenclature committee in November 2006.

[Identification and sequence analysis of a novel HLA-A * 3018 allele]

To identify HLA novel allele in Chinese Han individuals, an unknown HLA-A allele was detected by PCR-SSP and FLOW-SSO in Chinese Han individuals. Heterozygous sequence-based typing (SBT) showed that there were 3 differences compared with database in exon 2. Its anomalous patterns suggested the possible presence of either a novel A * 30 or a novel A * 24. To separate the two alleles and to determine whether the allele is novel, the HLA-A * 30 and HLA-A * 24 alleles were amplified separately by using a commercial kit for the single allele-specific sequencing strategy, and both alleles for exons 2 - 4 were sequenced according to the manufacturer' protocol. To prepare B-lymphoblastoid cell line of the novel HLA allele by using Epstein-Barr virus-infected B-lymphoblastoid cells in the peripheral blood. The results indicated that the sequencing results showed HLA-A alleles of the sample to be HLA-A * 240201 and a new A * 30 allele. The sequences of the new A*30 were identical to those of HLA-A * 300101 except for three nucleotide changes in exon 2: at nt 121 (A-->C), nt 123 (T-->C) and nt 126 (A-->G), resulting in an amino acid residue substitution from S (AGT) to R (CGC) at codon 17 and a synonymous substitution from G (GGA) to G (GGG) at codon 18. Immortalized B-lymphoblastoid cell line of the novel HLA-A * 3018 allele was achieved, the sequence of HLA-A * 3018 allele was submitted to GenBank and its accession number was DQ872509. In conclusion, the HLA-A * 3018 is a novel HLA-A allele and has been officially named HLA-A * 3018 by the WHO Nomenclature committee in August 2006 (HWS10004039).

Radial Basis Function Network-Based Transform for a Nonlinear Support Vector Machine as Optimized by a Particle Swarm Optimization Algorithm with Application to QSAR Studies

The support vector machine (SVM) has been receiving increasing interest in an area of QSAR study for its ability in function approximation and remarkable generalization performance. However, selection of support vectors and intensive optimization of kernel width of a nonlinear SVM are inclined to get trapped into local optima, leading to an increased risk of underfitting or overfitting. To overcome these problems, a new nonlinear SVM algorithm is proposed using adaptive kernel transform based on a radial basis function network (RBFN) as optimized by particle swarm optimization (PSO). The new algorithm incorporates a nonlinear transform of the original variables to feature space via a RBFN with one input and one hidden layer. Such a transform intrinsically yields a kernel transform of the original variables. A synergetic optimization of all parameters including kernel centers and kernel widths as well as SVM model coefficients using PSO enables the determination of a flexible kernel transform according to the performance of the total model. The implementation of PSO demonstrates a relatively high efficiency in convergence to a desired optimum. Applications of the proposed algorithm to QSAR studies of binding affinity of HIV-1 reverse transcriptase inhibitors and activity of 1-phenylbenzimidazoles reveal that the new algorithm provides superior performance to the backpropagation neural network and a conventional nonlinear SVM, indicating that this algorithm holds great promise in nonlinear SVM learning.

Adaptive Configuring of Radial Basis Function Network by Hybrid Particle Swarm Algorithm for QSAR Studies of Organic Compounds

The configuring of a radial basis function network (RBFN) consists of selecting the network parameters (centers and widths in RBF units and weights between the hidden and output layers) and network architecture. The issues of suboptimum and overfitting, however, often occur in RBFN configuring. This paper presented a hybrid particle swarm optimization (HPSO) algorithm to simultaneously search the optimal network structure and parameters involved in the RBFN (HPSORBFN) with an ellipsoidal Gaussian function as a basis function. The continuous version of PSO was used for parameter training, while the modified discrete PSO was employed to determine the appropriate network topology. The proposed HPSORBFN algorithm was applied to modeling the inhibitory activities of substituted bis[(acridine-4-carboxamide)propyl]methylamines to murine P388 leukemia cells and the bioactivities of COX-2 inhibitors. The results were compared with those obtained from RBFNs with the parameters optimized by continuous PSO and by conventionally RBFN training the algorithm for a fixed network topology, indicating that the HPSO was competent for RBFN configuring in that it converged quickly toward the optimal solution and avoided overfitting.

Boosting support vector regression in QSAR studies of bioactivities of chemical compounds

In this paper, boosting has been coupled with SVR to develop a new method, boosting support vector regression (BSVR). BSVR is implemented by firstly constructing a series of SVR models on the various weighted versions of the original training set and then combining the predictions from the constructed SVR models to obtain integrative results by weighted median. The proposed BSVR algorithm has been used to predict toxicities of nitrobenzenes and inhibitory potency of 1-phenyl[2H]-tetrahydro-triazine-3-one analogues as inhibitors of 5-lipoxygenase. As comparisons to this method, the multiple linear regression (MLR) and conventional support vector regression (SVR) have also been investigated. Experimental results have shown that the introduction of boosting drastically enhances the generalization performance of individual SVR model and BSVR is a well-performing technique in QSAR studies superior to multiple linear regression.

[Polymorphism of HLA-B* 40 gene family in Chinese Han population]

To investigate the allele distribution of HLA-B* 40 gene family in Chinese Han population and to study its influence on the selection of clinical transplantation donor, the HLA-B genetypes of 381 individuals randomly selected from Chinese National Marrow Donor Project were identified by PCR-SSO, and then all the HLA-B* 40 positive samples from the above population and the B* 40 homozygote samples received from another 1 270 registered donors were analyzed by PCR-SBT and PCR-SSP at high resolution. The results showed that the population of 381 registered donors was examined at HLA-B locus by using Hardy-Weinberg equilibrium, the gene frequency of HLA-B* 40 was 0.1692. Four different HLA-B* 40 alleles (B* 4001, B* 4002, B* 4003, B* 4006) were identified, and the serological specificity was B60 and B61 respectively. The relative frequency of each allele was 0.1192 for B* 4001, 0.0154 for B* 4002, 0.0038 for B* 4003, 0.0308 for B* 4006. The distribution of B* 40 homozygote revealed a certain regularity at high-resolution, B* 40XX (B* 4001 group), at low-resolution; B* 4001 at high resolution; B* 40XX (B* 4002 group), at low-resolution; B* 4002 or B* 4006 or heterozygote of both at high-resolution. It is concluded that in Chinese Han population, predominant allele in HLA-B* 40 gene family is B* 4001, the high-resolution typing may be recommended to use for the selection of clinical transplantation donor.

[Difference in HLA-A*02 allele distribution between Han populations in south and north China]

OBJECTIVE

To investigate the distributions of HLA-A*02 alleles in Han populations and compare their difference between the south and north in China.

METHODS

A total of 208 individuals from south China and 109 from north China were randomly selected from registered bone marrow donors in Chinese Han population, who were tested positive for HLA-A*02 alleles by PCR with sequence-specific primers (PCR-SSP). Genotyping of the alleles was performed using PCR-sequence-based typing (PCR-SBT).

RESULTS

Six different HLA-A*02 alleles (A*020101, A*0203, A*0205, A*0206, A*0207 and A*0210) were identified in the two Chinese Han populations, of which A*0207(37%) was the predominant allele in southerners and A*020101(48%) in the northerners. A*020101(31%), A*0203(16%) and A*0206(14%) were common alleles in the southerners in comparison with A*0206(21%) and A*0207(23%) alleles in the northerners. The overall distribution of A*02 alleles and the frequencies of A*020101, A*0203 and A*0207 in the two populations differed significantly. The heterozygosity of A*02 in the southerners and northerners was higher than 90% and 80% at the high- and low-resolution levels, respectively, and the distribution of A*02 homozygote at low-resolution level in both populations showed diversity and regularity at high-resolution level.

CONCLUSIONS

HLA-A*02 alleles possess high heterogeneity and genetic diversity in Chinese Han population with significantly different distributions in the two populations. HLA-A**020101, A*0203 and A*0207 may serve as the genetic markers for dividing Chinese Han individuals into southerners and northerners in anthropological studies.

[Experimental study on quantitative monitoring engraftment of an adult with mixed umbilical cord blood transplantation]

The purpose of this research was to monitor quantitatively and study the dynamic changes and development rules of engraftment, chimera types, as well as relative amount of donor cells after allogeneic transplantation of mixed umbilical-cord blood from two units. An adult patient with acute myeloid leukemia received two units HLA one locus mismatched unrelated umbilical cord blood transplantation (2.5 x 10(7)/kg karyocytes in umbilical cord blood unit 1, and 1.53 x 10(7)/kg karyocytes in umbilical cord blood unit 2). Nine STR loci of the blood sample before and after transplantation were determined by quantitative detecting technique with fluorescence labeling polymerase chain reaction, while the engraftment and chimera types were qualitatively evaluated by comparing differential loci between the recipient and the donors. Then the relative proportion of chimera from two units of umbilical-cord blood in the patient after transplantation was calculated according to the differential gene peak areas of two donors on 377XL DNA sequencer after fluorescence scanning, and the engraftment level and the development rules of donor cells were analyzed. In addition, the results were also compared with that of HLA loci distinct analysis for engraftment. The results showed that two umbilical cord blood units at 15 days after transplantation were engrafted simultaneously and revealed a complete chimerism of the two. The relative amounts of chimera from unit 1 vs that of unit 2 were 51.3% vs 48.7%; subsequently relative amounts of chimera from unit 1 went up to 70.0% at 30 days, and that from unit 2 declined to 30.0%. However, at 52 days, only the genotype of umbilical cord blood unit 1 was detected, so that the engraftment turned to a complete chimerism of a single donor type. The one with fewer karyocytes was rejected and the one with more karyocytes finally engrafted in long-term. It is concluded that quantitatively detecting STR chimera with fluorescence labeling polymerase chain reaction can depict precisely the engraftment level and the change course of two umbilical cord blood units. It provides an accurate and reliable experimental basis for clinical umbilical cord blood application and donor selection, and is proved to be feasible for adult transplantation by using dual unit of umbilical-cord blood with HLA one locus mismatched at the same time.

Apoptosis may be either suppressed or enhanced with strategic combinations of antineoplastic drugs or anti-IgM

A variety of drugs have been used to treat B-lymphocyte neoplasms, including both cell cycle-specific (CCS) and non-cell-cycle-specific drugs. Although the therapy for such cancers is complex and can include both types of drugs, the efficacy of these drugs in inducing cell death remains unclear. In this paper we have concentrated on specific CCS drugs and have examined their ability to induce programmed cell death (apoptosis) in Burkitt's lymphoma cell lines derived from patients. The CCS drugs chosen were hydroxyurea and aphidicolin (active in late G1, early S phase), the topoisomerase poisons camptothecin and etoposide (S, early G2 phase) and vincristine and Taxol (late G2, M phase). These choices allow comparison of two drugs with differing modes of action for each of the various phases of the cell cycle. Our results indicate that the variation in apoptosis between drugs that act at the same phase of the cell cycle is negligible. Both S/G2 and G2/M blockers are very potent at inducing apoptosis whereas G1/S blockers are ineffective in the induction of apoptosis. In addition, marked kinetic variations in the rate of apoptosis induction were observed, etoposide and camptothecin being more rapid in their action than the other agents. The order of effectiveness in inducing apoptosis on a kinetic basis was S/G2 agents >> G2/M agents >> G1/S agents. In this study we have also found that growth inhibition was induced by all the CCS agents chosen and by anti-IgM in various Burkitt's lymphoma lines. Furthermore c-myc was down-regulated under similar conditions. Since apoptosis was only selectively induced by some of the CCS agents, it implies c-myc expression is associated with growth regulation and c-myc down-regulation is an insufficient condition for the induction of apoptosis. In addition, cotreatments using the CCS and other agents revealed the following: Cotreatment using two CCS drugs which act at the same stage in the cell cycle showed either no change or only additivity to the effects seen with either agent alone. However, cotreatment with CCS drugs showed that an inhibitory effect is found between G1/S and G2/M drugs or S/G2 and G2/M drugs. No effect was found between G1/S and S/G2 drugs. Anti-IgM, which by itself was capable of inducing apoptosis, was observed to augment apoptosis induced by very low concentrations of G2/M-acting drugs but it has little effect on G1/S or the S/G2 drugs. The inhibitory effect of anti-CD40 or TNF-alpha on anti-IgM-induced apoptosis did not carry over to an effect on apoptosis induction by the CCS agents. Thus specific combinations of agents may lead to either enhancement, inhibition, or no interactive effect on apoptosis.

Anti-IgM-induced growth inhibition and apoptosis are independent of ornithine decarboxylase in Ramos cells

Ornithine decarboxylase (ODC) is a key enzyme involved in polyamine production and is thought to regulate growth and apoptosis in multiple cell systems. A potential link between ODC and growth may involve the action of an oncogene c-myc which is thought to transcriptionally regulate ODC. We have examined the involvement of ODC in anti-IgM-induced growth inhibition and apoptosis in Burkitt's lymphoma cells. Inhibitors of ODC such as difluoromethylornithine (DFMO) completely blocked ODC activity, resulting in growth inhibition but not apoptosis. Addition of putrescine, the product of ODC enzymatic action, to Ramos cells had only a minor effect on growth, did not cause apoptosis, did not augment or block anti-IgM-mediated growth inhibition and apoptosis, but did reverse DFMO-mediated growth inhibition. Anti-IgM treatment of Ramos cells, which markedly decreased c-myc mRNA and protein, caused a paradoxical increase in ODC mRNA level as well as ODC enzymatic activity and increased cellular levels of putrescine. DFMO and putrescine did not alter c-myc mRNA levels directly, nor did they have any affects on anti-IgM-mediated down-regulation of c-myc mRNA. TNF-alpha, which inhibited anti-IgM-mediated apoptosis, did not inhibit either anti-IgM or DFMO-mediated inhibition of growth. These agents were without effect on ODC activity itself or on the anti-IgM-mediated increase in ODC activity. From these studies we conclude that ODC inhibition affects growth but is unrelated to the induction of apoptosis. Both anti-IgM-mediated inhibition of growth and induction of apoptosis are independent of ODC. Thus two distinct pathways for growth regulation are present: one in which ODC and polyamines are important and the other cell surface receptor-mediated (sIg) which is independent of ODC and polyamines.