Biochemical and immunological properties of cytokines conjugated to dendritic polymers.

Here we describe a post-translational modification of SC-63032, a variant of the species restricted, multi-lineage hematopoeitic factor human interleukin-3 (hIL-3). We have made two new dendritic polymer (polyamidoamine or PAMAM dendrimers, generation 5)-SC-63032 bioconjugates. Using two distinct chemistries (one of which is novel to this work), we achieved site-specific conjugation with respect to the amino acid in the proteins ligated to the dendrimers. In both bioconjugates, conjugated cytokine maintains its ability to bind the hIL-3 alpha receptor subunit, but is significantly (about 10-fold) less potent in inducing hIL-3 dependent in vitro cell proliferation than is the free cytokine. In vivo data indicates that conjugation decreases the immunogenicity of the conjugated cytokine modestly. In the absence of pharmacokinetic or biodistribution effects associated with the bioconjugates that increase their potency in vivo (which can only be tested in a higher primate, due to the species restriction of hIL-3 and its derivatives), these immune mitigation effects may be too small to be therapeutically significant. Though unmodified PAMAM dendrimers fail to elicit an antibody response in mice, protein conjugation to dendrimers haptenizes them, and a dendrimer-specific antibody response is produced. In toto, the principal limitation of the dendrimer-cytokine bioconjugates herein is in their reduced receptor affinity and potency in vitro. Were the in vivo potency of the bioconjugates to parallel the in vitro potency of the conjugates reported here, it is likely that particular dendrimer bioconjugates could not justify their higher costs of goods relative to the parent SC-63032 molecule, though retention of SC-63032 biological activities in conjugates suggests that other cytokine-dendrimer bioconjugates may be bioactive. This is good news to the nanotechnology community, in as much as PAMAM dendrimers are among the monodisperse polymeric nanomaterials available, and these results show that they can be used successfully in conjugates to bioactive proteins.

The function of the octamer-binding site in the DRA promoter.

The octamer binding site, which is located immediately upstream of the poorly conserved DRA TATA sequence, is important for high levels of expression of this human major histocompatibility class II gene in B cells. In this study, we demonstrate that the substitution of the DRA TATA sequence with the TATA box from the adenovirus E1b promoter removes the requirement for the octamer binding site for high levels of expression from the DRA promoter. Since only the TATA box from the E1b but not the DRA promoters binds the TATA binding protein, we conclude that the octamer binding site helps to recruit TBP to the DRA promoter.

Mapping cis-acting defects in promoters of transcriptionally silent DQA2, DQB2, and DOB genes.

Defects in promoters of the nonexpressed DQA2, DQB2, and DOB genes from the class II major histo-compatibility complex were mapped by placing Z and X boxes of these silent genes into a synthetic DRA promoter. These conserved upstream sequences confer B-cell-specific and gamma-interferon-inducible expression to the DRA gene. Since DRA promoters containing the X box from the DQA2 gene and Z boxes from DQA2, DQB2, and DOB genes were neither expressed constitutively in B cells nor inducible by gamma interferon in fibroblastic cells, these conserved upstream sequences are implicated in the transcriptional defects of these silent genes.

B-cell factor 1 is required for optimal expression of the DRA promoter in B cells.

The X box in the DRA promoter of the human histocompatibility complex is required for expression of the DRA gene in B cells. We show that a B-cell factor binds to a sequence that is clearly distinguishable from binding sites for the previously described X box binding nuclear proteins RF-X, NF-X, NF-Xc, NF-S, hXBP, and AP-1. Mutations in the DRA X box that disrupt the binding of this factor result in a lower level of gene expression, as does the presence of Id (a trans-dominant regulatory protein that negatively regulates helix-loop-helix proteins). Furthermore, this factor is recognized by antibodies directed against the helix-loop-helix protein A1, a mouse homolog of the immunoglobulin enhancer binding proteins E12/E47, and it binds to sequences in other genes that were previously shown to bind these proteins. By these criteria, this factor is BCF-1.

Isolation of the mouse cytochrome P450J (CYP2E1) cDNA and its reciprocal testosterone regulation in kidney and liver.

A hybridization probe that is homologous to the B2 short interspersed repetitive element detects an mRNA in mouse kidney and liver that is regulated by androgen. Administration of testosterone induces this mRNA in kidney and represses it in liver. The mRNA was cloned by first using the B2 probe to select 48 cDNA clones from an androgen-induced kidney library. These clones were then tested for their androgen response by hybridizing them with probes made by reverse transcription of basal and testosterone-treated kidney poly(A)+ RNA. Any homology to the B2 sequence was masked by prehybridizing the filters to an excess of non-radioactive RNA synthesized from a B2 sequence cloned into a riboprobe vector. A unique sequence was subcloned from the largest androgen-responsive cDNA clone. A radioactive riboprobe generated from the unique sequence subclone detected an androgen-responsive mRNA in Northern blots with the same electrophoretic mobility as the predominant androgen-responsive mRNA detected with the B2 homologous riboprobe. The riboprobe also detected a unique sequence in Southern blots of genomic DNA. This subclone was then used as the probe to isolate a full-length cDNA clone from a second androgen-induced kidney library. When sequenced, this full-length cDNA of an androgen-responsive, B2-containing mRNA showed strong homology to the rat and human cytochrome P450J and the rabbit cytochrome P450 3a genes (CYP2E1). It showed only weak homology to the mouse testosterone 15 alpha-hydroxylase gene (CYP2A3) which is also regulated reciprocally by androgen in kidney and liver. The sequence of mouse P450J is identical to the B2 homologous mRNA previously named B2+ mRNAx which is abundant in mouse liver.

An analysis of replacement and synonymous changes in the rodent L1 repeat family.

L1 is a family of long interspersed repetitive sequences in mammals that includes the BamHI family in rodents and the KpnI family in primates. Previous studies have shown that L1 repeats contain a long open reading frame and that the family evolves in concert. Working with 32 rodent elements for which DNA sequence is available, we used the distribution of replacement and synonymous changes to determine which L1 lineages had been expressing their reading frame. The evidence obtained is consistent with there having been a small number of L1 genes that have been expressing a functional protein. Much of the concerted evolution in L1 is accounted for by the tendency of these functioning L1 genes to continually create nonfunctional pseudogenes by reinsertion into the genome of sequences derived from their transcripts. The gain of new pseudogenes is balanced by the loss of old pseudogenes with a half-life of 2 Myr. Therefore, most of the observed L1 repeats are at a dead end with respect to either the expression of the L1 protein or the potential to elaborate further copies of themselves. However, the turnover of L1 pseudogenes is sufficient to constitute a vast flux of sequences into and then out of the flanking regions of all cellular genes. If the presence of flanking L1 pseudogenes affects the expression of other genes in even a subtle fashion, this process should represent a major source of genetic variation. A second level of concerted evolution occurs within the functional L1 sequences in a pattern that did not meet our expectations for selfish DNA. Also, in spite of the marked suppression of replacement relative to synonymous changes in functioning L1 genes, they evolve at an overall rate accelerated to the level of their own pseudogenes.

Conservation throughout mammalia and extensive protein-encoding capacity of the highly repeated DNA long interspersed sequence one.

We report an investigation of the structure, evolutionary history, and function of the highly repeated DNA family named Long Interspersed Sequence One (L1). Hybridization studies show, first, that L1 is present throughout marsupial and placental mammalian orders. Second, L1 is more homologous within these species than between them, which suggests that it has undergone concerted evolution within each mammalian lineage. Third, on the whole L1 diverges in accordance with the fossil record. This suggests that it arose in each lineage rather by inheritance from a common ancestral family, which was present in the progenitor to mammals, than by cross-species transmission. Alignment of 1.6 X 10(3) bases of primate and mouse L1 DNA sequences shows a predominance of silent mutations within aligned long open reading frames, indicating that at least this part of L1 has produced functional protein. The observation of additional long open reading frames in further unaligned DNA sequences suggests that a minimum of 3.2 X 10(3) bases or at least half of the L1 structure is a protein-coding sequence. Thus L1, which contains about 100,000 members in mouse, is by far the most repetitive family of which a subset comprises functional protein-encoding genes. The ability of the putative protein-encoding regions of mouse L1 to hybridize to L1 homologs throughout the Mammalia implies that these sequences have been subject to conservative selection upon protein function in all mammalian lineages, rather than in a few. L1 is therefore a highly repeated family of genes with both a widespread and an ancient history of function in mammals.

Tempo and mode of concerted evolution in the L1 repeat family of mice.

A 300-bp DNA sequence has been determined for 30 (10 from each of three species of mice) random isolates of a subset of the long interspersed repeat family L1. From these data we conclude that members of the L1 family are evolving in concert at the DNA sequence level in Mus domesticus, Mus caroli, and Mus platythrix. The mechanism responsible for this phenomenon may be either duplicative transposition, gene conversion, or a combination of the two. The amount of intraspecies divergence averages 4.4%, although between species base substitutions accumulate at the rate of approximately 0.85%/Myr to a maximum divergence of 9.1% between M. platythrix and both M. domesticus and M. caroli. Parsimony analysis reveals that the M. platythrix L1 family has evolved into a distinct clade in the 10-12 Myr since M. platythrix last shared a common ancestor with M. domesticus and M. caroli. The parsimony tree also provides a means to derive the average half-life of L1 sequences in the genome. The rates of gain and loss of individual copies of L1 were estimated to be approximately equal, such that approximately one-half of them turn over every 3.3 Myr.

Dispersal process associated with the L1 family of interspersed repetitive DNA sequences.

We have determined the complete nucleotide sequence for five members of the L1Md repetitive family from the beta-globin gene region of the BALB/c mouse. The five repeats are different lengths, each terminating at the 5' end at different points with respect to one another. We have analyzed the nucleotides around the endpoints of the five repeats for clues as to the mechanisms involved with the dispersal and 5' truncation of this repeat family. Each L1 member is flanked by a pair of short direct repeats. Since these direct repeats differ in length and sequence in each of the five cases, the dispersal mechanism does not involve a sequence targeted process. The sequence at the 3' end is conserved and its organization resembles the 3' end of a polyadenylated RNA, suggesting that transcripts of the repeat are involved in the dispersal process either directly or as intermediates in the generation of complementary DNA copies of the sequence. One of the L1 repeats is a recent insertion, since it is found in the Hbbd chromosome, but not in the Hbbs chromosome. This suggests a dispersal process that has been active as recently as 4 million years ago.

A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein.

DNA sequence analysis of a region contained within a large, interspersed repetitive family of mice reveals a long open reading frame. This sequence extends 978 base pairs between two stop codons, creating a reading frame that is open for 326 amino acids. The DNA sequence in this region is conserved between three distantly related Mus species, as well as between mouse and monkey, in a manner that is characteristic of regions undergoing selection for protein function.

The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end.

We have characterized a large repetitive element which has been found at seven different locations within the beta globin locus of the BALB/c mouse. This repeat has an unusual structure in that each of the different members has the same end of the element conserved while the other end terminates at a different point in each repeat member. The sequences within the repeats from the beta globin locus have homology with other repetitive families such as the MIF-1, Bam-5, R, and the BamH1 families. These were recently proposed (T. Fanning, (1983) Nucleic Acids Res. 11, 5073-5091) to be part of a structure with the same organization which we found in the globin locus. Probing plaques from a BALB/c genomic library with sequences derived from the repeats in the globin locus shows that virtually all of the repeats from this family are organized in a manner consistent with the proposed structure.

DNA sequence organization of the beta-globin complex in the BALB/c mouse.

Clones containing five non-adult beta-globin genes were isolated from a library of BALB/c DNA. Together, the newly cloned regions comprise a contiguous block of 32 kb of the mouse genome. Restriction mapping of genomic DNA established the physical linkage of these non-adult genes to the two adult beta-globin genes as well as the two adult genes to each other. Thus this entire BALB/c beta-globin complex consists of seven linked genes, all with the same transcriptional orientation, arrayed over 70 kb of DNA. The order of these genes is: 5'-epsilon y3-beta h0-beta h1-beta h2-beta h3-beta major-beta minor-3' Portions of each of the five newly identified genes have been sequenced. Only one, epsilon y3, encodes a previously described globin. beta h0 and beta h1, which are closely related, differ significantly from both adult and embryonic globins. The beta h2 sequence is more closely related to the adult genes than to the other non-adult genes. However, it is the sequence least homologous to both of these classes. The 5' half of the beta h3 gene (preceding codon 75) has an aberrant structure. The rest of this sequence is intact, resembling an adult beta-globin gene except for an inserted base at cocon 90, resulting in a frameshift. Consequently, the beta h3 sequence cannot be translated to produce a normal beta-globin.