Fumiaki Nakajima

HLA-haplotype banking and iPS cells.

739 collaboration of many laboratories and requires a precision in the communication that cannot be afforded without formality. This does not mean that ambiguity has no place in biology. It means that we need to be formal about ambiguity. modeling is nondeterminism. This does not mean that biology does not need to be more formal. The way of communicating results of experiments and mechanistic ideas needs to become more formal. The development of better models requires the there are fundamental boundaries to what computers can do, or it may be feasible only with limited precision. On the other hand, a computational model prescribes explicitly for every state the possible next states of the model. Although modern compilers are extremely complex and include many optimizations, we cannot compare them with programs like Matlab and Mathematica. Undergraduate students can easily program a basic compiler from a high-level language to machine code. The translation is a straightforward change of each high-level step into several instructions of machine code. By contrast, Matlab and Mathematica include very sophisticated algorithms. They make powerful tools available to people that do not need to understand them, but to say that they resemble compilers that take a highlevel programming language and produce machine code is taking it one step too far. Indeed, there is an entire sub-discipline of computer science, called the semantics of programming languages, which studies deep relationships and differences between mathematical (or ‘denotational’) and computational (or ‘operational’) models. Hunt et al. go on to say that the real dichotomy between mathematical and computational models is one of usage rather than formalism. It is not a coincidence that mathematical models are used mainly for understanding relations between variables and computational models for understanding interactions between components. Every modeling approach has its strengths and drawbacks. This underlines our point that there is a real dichotomy between the two approaches. It is entirely correct that both mathematical and computational models are constructed using formal language, and that most models can be made nondeterministic, stochastic, hierarchical, etc. But it is also true, as Hunt et al. point out, that many such models would become too complex to be developed and analyzed. The question is not what a modeling framework can do in principle, but what it is best at: for which situations is it an intuitive fit, and for which problems does it offer strong analytical and computational support. As to their statement, “We speculate that increasingly useful computational analogs will be those that have been constructed using the more relaxed formalisms, such as partially ordered sets (of objects), which are capable of managing ambiguity,” we completely agree. This is exactly why we have emphasized that a major strength of computational HLA-haplotype banking and iPS cells

Human Leukocyte Antigen Matching Estimations in a Hypothetical Bank of Human Embryonic Stem Cell Lines in the Japanese Population for Use in Cell Transplantation Therapy

Human embryonic stem (hES) cell lines are of great potential in cell transplantation therapy. However, recipients of such allogeneic transplants probably need treatment with immunosuppressants. Recently, Taylor et al. [Lancet 2005;366:2019–2025] proposed banking of hES cell lines and estimated the required number of hES cell lines for beneficial human leukocyte antigen (HLA) matching in the U.K. population. Here, we carried out such an estimation in the Japanese population. We calculated the proportion of patients who can find at least one HLA‐matched donor at three loci of HLA‐A, ‐B, and ‐DR. With a bank of hES cell lines from 170 randomly selected donated embryos, 80% of patients were expected to find at least one hES cell line with a single mismatch at one HLA locus or a better match. Furthermore, 80% of patients are expected to find at least one donor with complete matching at the three HLA loci if parthenogenetic homozygous hES cell lines are established from 55 randomly selected donated oocytes. The relatively low ethnic diversity of the Japanese population may have resulted in a high success rate in beneficial matching. Moreover, parthenogenetic hES cell lines can greatly reduce the number required for a higher degree of HLA matching.

Cord blood transplantation from HLA‐mismatched unrelated donors as a treatment for children with haematological malignancies

Factors influencing the outcome for 39 children with haematological malignancy who were subjected to a cord blood transplantation (CBT) from genotypically HLA‐mismatched unrelated donors were analysed. This retrospective study included 21 children with acute lymphoblastic leukaemia, 15 with acute myelogenous leukaemia and one each with chronic myelogenous leukaemia, refractory anaemia with myelodysplastic syndrome (MDS) and juvenile myelomonocytic leukaemia (JMML). Those subjected to CBT during the first or second complete remission (CR) and MDS without blasts were assigned to the standard‐risk (SR) group (n = 16). Patients in third or subsequent remission, relapse or partial remission with refractory leukaemia at the time of CBT were considered to be in advanced phase, and placed in the high‐risk (HR) group (n = 11). JMML and the second CR after a relapse (n = 8), or bone marrow failure after a rejection (n = 3), following haematopoietic stem cell transplantation (HSCT) in the first CR were included in the high‐risk group. Kaplan–Meier estimates for neutrophil and platelet recovery were 83·7 ± 12·2 at d 60 and 55·4 ± 16·6% at d 100 respectively. The incidence of grades II–VI acute graft‐versus‐host disease was 58·5 ± 16·8%. The Kaplan–Meier estimate for 3‐year event‐free survival (EFS) was 49·2 ± 16·6. From multivariate analysis, the most important factor influencing EFS was disease status at CBT: SR patients had a 3‐year EFS of 75·0 ± 21·6%, compared with 29·6 ± 20·6% for those with HR disease (P = 0·013, RR 4·746, 95% CI 1·382–16·298). These data confirm that HLA‐mismatched, unrelated CBT is a feasible procedure to cure a significant proportion of children with leukaemia, especially if conducted in a favourable phase of the disease.

Both HLA-B*1301 and B*1302 exist in Asian populations and are associated with different haplotypes.

A B13 split antigen was newly identified with three alloantisera in Japanese, and two B13 split antigens were found in a Thai family. To confirm the variation of B13 and understand the correspondence between the serologic splits and the published B13 alleles, B*1301 and B*1302, we determined the sequences of genes coding for these B13 splits. The common Japanese B13 allele was found to be B*1301, whereas another split antigen was shown to be coded by B*1302. Two B13 variants identified in a Thai individual corresponded to B*1301 and B*1302. Moreover, 57 B13-positive samples from several ethnic groups were examined using the PCR-SSO method. Differing from previous reports, both B*1301 and B*1302 were found in samples from Asian populations. These two alleles were separately associated with different antigens: HLA-B*1301 exhibited a strong association with A2, Cw10, DR12, and DQ7 antigens, whereas HLA-B*1302 was strongly associated with A30, Cw6, DR7, and DQ2 antigens. In addition, applying the PCR-SSCP method, B*1301 and B*1302 could also be simply distinguished from each other.

The Influence of HLA Genotyping Compatibility on Clinical Outcome after Cord Blood Transplantation from Unrelated Donors

We performed retrospective DNA typing of class I (A, B, Cw) and class II (DRB1, DQB1, DPB1) HLA alleles in 27 unrelated cord blood transplantation (CBT) cases donated from a single cord blood bank (Kanagawa Cord Blood Bank). The influence of HLA genotype matching on clinical outcome was evaluated. From Coxs model, we found that incompatibility of two or more HLA alleles between the donor and recipient of an unrelated CBT was suggested to be a risk factor for a worse event-free survival (EFS) (p = 0.04; RR, 4.06; 95% CI, 1.06-15.61). Furthermore, mismatches including HLA-DRB1 alleles had an adverse effect on EFS (p = 0.04; RR, 4.91; 95% CI, 1.01-24.02). For definite conclusions on the role of HLA allele typing in unrelated CBT, more accumulation of data and analysis will be required.

A new HLA-C allele, CWl403, associated with HLA-B44 in Japanese

An allele encoding an HLA-C antigen, tentatively called CX44, associated with HLA-B44 was identified as a new member of the Cw14 group, Cw*1403. The nucleotide sequence of Cw*1403 was closest to that of Cw*1401: five bases were different between the two alleles, in which three bases in Cw*1403 (two in exon 3 and one in exon 4) were the same as those of most HLA-C alleles. Two substitutions from guanine to adenine were found in the new allele, both of which are in exon 2, one at position 134 (61 of exon 2) and the other at position 201 (128 of exon 2). The former nucleotide substitution leads to the substitution of amino acid residue 21 from Arg to His, and the other substitution was synonymous. The former substitution was shared with Cw2, 3, 5, 13, and 15 alleles, and the latter was shared with Cw2, 4, 5, 8, 12, 13, 15 and 16 alleles. The other seven unrelated Japanese samples with CX44 were analyzed by a PCR-SSO method. It was confirmed that all the seven samples have the same substitutions as the sequenced allele, and the allele demonstrates a strong association with A33, B44, DR13, and DQ1, which are known to form a common haplotype in Japanese and Koreans.

A new B18 Sequence (B∗1802) from Asian individuals

A new HLA-B18 allele (B*1802) derived from a Thai individual was sequenced. Comparison of this B18 nucleotide sequence with the published B*1801 sequence indicated that this Asian B18 allele has a nucleotide sequence different from that of B*1801. Three nucleotide changes were observed in exon 3, in which two substitutions at codon 97, AGG in B*1801 to AAT in the B*1802, result in an amino acid change from arginine to asparagine. The residue 97Asn has also been described in some B27 subtypes. A silent mutation was also observed at codon 99, TAC in B*1801 to TAT in the B*1802. This sequence has been reported in many class I alleles published so far. Moreover, 18 HLA-B18-positive samples were examined by the PCR-SSO method using specific probes for B*1801 and B*1802. The results demonstrated that three Asian samples possess B*1802 and share HLA-Cw7, DR12, and DQ7.

Unrelated cord blood transplantation for second hemopoietic stem cell transplantation

Background : The Kanagawa Cord Blood Bank (KCBB) reports the treatment of 12 patients who received umbilical cord blood transplantation (CBT) from unrelated donors as their second hemopoietic stem cell transplantation (HSCT).

Identification of the gene encoding a novel HLA-B39 subtype Two amino acid substitutions on the β-sheet out of the peptide-binding floor form a novel serological epitope

Serological analysis suggests the existence of a novel HLA-B39 subtype (HLA-B39N) in the Japanese population. To identify this novel allele, a gene encoding HLA-B39N was cloned and the exons were sequenced. A gene encoding HLA-B39N (B*3904) and B*39011 differs by two nucleotide substitutions at codons 11 and 12 whereas B*3904 and B*39013 differ by three nucleotide substitutions at codons 11, 12, and 312. One nucleotide difference at codon 11 produces a change from serine in B*3901 to alanine in B*3904 whereas another difference at codon 12 changes valine in B*3901 to methionine in B*3904. The residues 11 and 12 are located on the beta-sheet out of the peptide-binding floor and are completely buried in the molecule. These results suggest that the substitutions at these residues alter the conformation of other residues forming epitopes of alloantibodies. Analysis of HLA-B*3901 genes in the Japanese population showed that both B*39011 and B*39013 were observed in the Japanese population. The present study suggests that B*3904 may have evolved from B*39011 rather than B*39013.

Two novel null HLA-A alleles with identical exon 4 nonsense mutations: HLA-A*24:183N and A*02:356N

HLA-A*24:183N, A*02:356N, and A*02:15N share the same stop codon at the same position in exon 4.