Dispersion of the ras family of transforming genes to four different chromosomes in man

A Beautiful Life: High Risk-High Payoff in Genetic Science

This narrative is a personal view of adventures in genetic science and society that have blessed my life and career across five decades. The advances I enjoyed and the lessons I learned derive from educational training, substantial collaboration, and growing up in the genomics age. I parse the stories into six research disciplines my students, fellows, and colleagues have entered and, in some cases, made an important difference. The first is comparative genetics, where evolutionary inference is applied to genome organization, from building gene maps in the 1970s to building whole genome sequences today. The second area tracks the progression of molecular evolutionary advances and applications to resolve the hierarchical relationship among living species in the silence of prehistory. The third endeavor outlines the birth and maturation of genetic studies and application to species conservation. The fourth theme discusses how emerging viruses studied in a genomic sense opened our eyes to host-pathogen interaction and interdependence. The fifth research emphasis outlines the population genetic-based search and discovery of human restriction genes that influence the epidemiological outcome of abrupt outbreaks, notably HIV-AIDS and several cancers. Finally, the last arena explored illustrates how genetic individualization in human and animals has improved forensic evidence in capital crimes. Each discipline has intuitive and technological overlaps, and each has benefitted from the contribution of genetic and genomic principles I learned so long ago from Drosophila. The journey continues.

MicroRNA: An emerging therapeutic target and intervention tool

MicroRNAs (miRNAs) are a class of short non-coding RNAs with posttranscriptional regulatory functions. To date, more than 600 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs. Accumulating evidence has linked the dysregulated expression patterns of miRNAs to a variety of diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases and viral infections. MiRNAs provide its particular layer of network for gene regulation, thus possessing the great potential both as a novel class of therapeutic targets and as a powerful intervention tool. In this regard, synthetic RNAs that contain the binding sites of miRNA have been shown to work as a “decoy” or “miRNA sponge” to inhibit the function of specific miRNAs. On the other hand, miRNA expression vectors have been used to restore or overexpress specific miRNAs to achieve a long-term effect. Further, double-stranded miRNA mimetics for transient replacement have been experimentally validated. Endogenous precursor miRNAs have also been used as scaffolds for the induction of RNA interference. This article reviews the recent progress on this emerging technology as a powerful tool for gene regulation studies and particularly as a rationale strategy for design of therapeutics.

Characterization and chromosomal localization of a new protein disulfide isomerase, PDIp, highly expressed in human pancreas

Protein disulfide isomerase (PDI) catalyzes protein folding and thiol-disulfide interchange reactions. The enzyme is localized in the lumen of endoplasmic reticulum (ER) and is abundant in secretory cells of various tissues. In this study we describe the isolation and characterization from human pancreas of a new protein, PDIp, that is structurally and functionally related to PDIs. PDIp cDNA is 1,659 bp in length and predicts a protein with an open reading frame of 511 amino acids. PDIp amino acid sequence shows 46% identity and 66% similarity to that of human PDI. PDIp possesses two thioredoxin-like active sites (WCGHCQ and WCTHCK) and an endoplasmic reticulum retention signal sequence, KEEL, at the carboxyl terminus. Northern analysis of normal human tissues and various human tumor cell lines revealed PDIp mRNA (2.0 kb) expression only in the normal pancreas. Recombinant PDIp protein catalyzed reductive cleavage of insulin and renaturation of reduced RNaseA. Somatic cell genetics and fluorescence in situ hybridization localized the PDIp gene to the short arm of human chromosome 16. It is concluded that PDIp is a new member of the PDI family and is highly expressed in human pancreas.

Polymorphisms in the 3' untranslated region of the I kappa B/MAD-3 (NFKBI) gene located on chromosome 14

The NF-kappa B transcription factor regulates the expression of a number of genes, including immune function and growth control loci, and several viruses. For example, the long terminal repeat of the human immunodeficiency virus contains NF-kappa B binding sites. NF-kappa B activity in the nucleus is regulated by a cellular inhibitory protein I kappa B. To analyze the potential role of these genes in genetic disease we have mapped the NF-kappa B (NFKB2) and I kappa B/MAD-3 (NFKBI) loci in a panel of somatic cell hybrids to chromosomes 4 and 14, respectively. Amplification of the 3' untranslated region of NFKBI allows the detection of three independent polymorphisms within 410 bp. In combination these polymorphisms were informative in 27 of 36 CEPH families and allowed the gene to be placed onto the linkage map of chromosome 14, between the D14S32 and D14S42 markers.

Emergence of the keratinocyte growth factor multigene family during the great ape radiation

The structural gene for human keratinocyte growth factor (KGF), a member of the fibroblast growth factor family, consists of three coding exons and two introns typical of other fibroblast growth factor loci. A portion of the KGF gene, located on chromosome 15, is amplified to approximately 16 copies in the human genome, and these highly related copies (which consist of exon 2, exon 3, the intron between them, and a 3' noncoding segment of the KGF transcript) are dispersed to multiple human chromosomes. The KGF-like sequences are transcriptionally active, differentially regulated in various tissues, and composed of three distinct classes of coding sequences that are 5% divergent from each other and from the authentic KGF sequence. Multiple copies of KGF-like genes were also discovered in the genomic DNAs of chimpanzee and gorilla but were not found in lesser apes (gibbon), Old World monkeys (African green monkey and macaques), mice, or chickens. The pattern of evolutionary occurrence suggests that a primordial KGF gene was amplified and chromosomally dispersed subsequent to the divergence of orangutan from African apes but before the trichotomous divergence of human, chimpanzee, and gorilla 5-8 million years ago. The appearance of a transcriptionally active and chromosomally dispersed multigene KGF family may have implications in the evolution of the great apes and humans.

Localization of the gene for a third G protein beta-subunit to mouse chromosome 6 near Raf-1

The large family of signal transducing proteins known as G proteins are heterotrimers that dissociate into an independent alpha-subunit and beta gamma-subunit complex after ligand binding or other stimulation. For G alpha, at least 30 distinct sequences representing 10 different classes have been identified. On the other hand, cDNAs for only three G beta-subunit genes have been isolated so far. All three of the G beta genes have been chromosomally mapped in the human, but only two in the mouse. Using a human retinal cDNA for the third G protein beta-subunit, we have mapped the corresponding gene, termed Gnb-3, to mouse Chromosome 6 with somatic cell hybrids and have positioned it distal to but near the marker Raf-1 by analysis of the progeny of three genetic crosses.

Monocyte-derived neutrophil chemotactic factor (MDNCF/IL-8) resides in a gene cluster along with several other members of the platelet factor 4 gene superfamily

Monocyte-derived neutrophil chemotactic factor (MDNCF/IL-8, suggested gene symbol IL8) is a cytokine that chemoattracts and activates neutrophils. Using a panel of human-rodent cell hybrids that preferentially segregate human chromosomes and in situ hybridization, the MDNCF/IL-8 gene was placed on the human gene map at position 4q12-q21. This is the same location where at least three other members (platelet factor 4, melanoma growth stimulatory activity, and interferon-gamma induced factor) of the platelet factor 4 gene super-family reside. In addition, a restriction fragment length polymorphism was identified using MDNCF as a probe in screening genomic DNA digested with HindIII from unrelated individuals.

Biclonal chromosome evolution of chronic myelomonocytic leukemia in a child

A monosomy 7 was first detected in a 6-month-old boy with a chronic myelomonocytic leukemia. After etoposide treatment, relapse occurred after 29 months, with transformation of the disease into an acute myeloblastic leukemia. After bone marrow transplantations, two abnormal clones were found in marrow cells: 45,XY,-7,del(12)(p11p12)(66%), and 45,XY,-7,t(3;12)(q26;p12)(33%). Several karyotypic studies performed until the terminal phase exhibited the persistence of these two clones in the same proportion, although both independently acquired additional and often similar anomalies. The clone with t(3;12) acquired der(7),der(11),der(17),der(8),der(10),-5,-20, and the clone with del(12p), del(5q),der(4),der(8),der(10),der(17),-5,-20. The anomalies in 12p12 appear to represent an important although secondary event of the neoplastic process. The other anomalies may correspond to either those of a secondary acute nonlymphocytic leukemia, since they occurred after treatment by etoposide and alkylating agents, or to the natural evolution of myelomonocytic leukemia.

Chromosome mapping of the human ras-related rab3A gene to 19p13.2

The rab genes belong to one of the three main branches of the ras super family. The encoded rab proteins share 38 to 75% amino acid identity with the yeast YPT1 and SEC4 proteins. We used the human rab3A cDNA to map the corresponding gene on human chromosomes by chromosome sorting and in situ hybridization. Both techniques allowed the assignment of the rab3A gene to chromosome 19 with a regional localization on 19p13.2 obtained by in situ hybridization.

Chromosomal localization of DBL oncogene sequences

The DBL oncogene was generated by rearrangements involving three discontinuous regions of the human genome. Analyses of panels of human X rodent somatic cell hybrids demonstrated that the DBL proto-oncogene located on the X chromosome (just proximal or distal to bands q26-27.2) underwent recombination at its 5' and 3' ends with sequences derived from chromosomes 3 (p13q-ter) and 16 (p13-q22), respectively. DBL was localized to chromosome Xq27-q28 by in situ hybridization. Another oncogene, MCF2, was previously shown to contain sequences derived from Xq27 as well. Comparison of the restriction maps and nucleotide sequences of genomic and cDNA clones representing the chromosome X-specific sequences of the DBL oncogene and MCF2, taken together with their chromosomal localization, indicates that these oncogenes were derived from the same genetic locus.

The t(11;14)(p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts, including Ttg-1, a gene encoding a potential zinc finger protein

Interchromosomal translocations within lymphoid neoplasms frequently involve the antigen receptor genes. We cloned the breakpoints of the t(11;14)(p15;q11) in a CD3-negative T-cell acute lymphoblastic leukemia cell line (RPMI 8402) in order to identify new genes potentially involved in T-cell neoplasia. An extensive comparison of both breakpoints and their germ line counterparts indicated that an inadvertant recombinase-mediated break at chromosome segment 11p15 recombined with the delta T-cell receptor at 14q11. The derivative 11 breakpoint resembles a coding joint in which 11p15 rather than a variable region was introduced 5' to a D delta 1 D delta 2 J delta 1 intermediate rearrangement. Conversely, the derivative 14 breakpoint corresponds to a signal joint between the 5' heptamer-spacer-nonamer recombinational signal of D delta 1 and an isolated heptamer at 11p15. Multiple, apparently distinct transcripts were found flanking both breakpoints of 8402. RNAs of 3.5, 4.4, 1.4, and 8.0 kilobases originating from either side of the derivative 14 breakpoint were highly expressed in 8402 compared with other cells. This suggests that this translocation deregulated multiple genes and provides the opportunity to assess any multifactorial contribution they may have to malignancy. We cloned and sequenced several cDNAs representing the 1.4-kilobase transcript (termed Ttg-1 [T-cell translocation gene 1]) from an 8402 library. The predicted protein of 156 amino acids contained two internal repeats which could potentially form zinc fingers.

Chromosomal localization of nucleic acid-binding proteins by affinity mapping: assignment of the IRE-binding protein gene to human chromosome 9

Three human mRNAs are regulated post-transcriptionally by iron via iron-responsive elements (IREs) contained in each mRNA. A cytoplasmic protein (IRE-BP) binds to these cis-acting elements and mediates the translational regulation of ferritin H- and L-chain mRNA and the iron-dependent stability of transferrin receptor (TfR) mRNA. We have taken advantage of the different mobilities of the human and rodent IRE/IRE-BP complexes on non-denaturing polyacrylamide gels to determine the chromosomal localization of the gene encoding the IRE-BP. Utilizing a panel of 34 different human/rodent hybrid cell lines we have assigned the IRE-BP gene to human chromosome 9. This new technique based on nucleic acid/protein interaction may allow determination of the chromosomal localization of other RNA- or DNA-binding proteins.

Human gene for proliferating cell nuclear antigen has pseudogenes and localizes to chromosome 20

We have isolated from a human genomic library a pseudogene of the proliferating cell nuclear antigen (PCNA) gene. Its sequence shows a 78% similarity with the human PCNA/cDNA. The PCNA gene is located on human chromosome 20, while the pseudogene maps to chromosome region Xpter in equilibrium Xq13. An additional locus detected by the full-length PCNA cDNA, but not by intron probes, segregates concordantly with chromosome region 6p12 in equilibrium 6pter and probably represents a second pseudogene.

The t(11;14)(p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts, including Ttg-1, a gene encoding a potential zinc finger protein

Interchromosomal translocations within lymphoid neoplasms frequently involve the antigen receptor genes. We cloned the breakpoints of the t(11;14)(p15;q11) in a CD3-negative T-cell acute lymphoblastic leukemia cell line (RPMI 8402) in order to identify new genes potentially involved in T-cell neoplasia. An extensive comparison of both breakpoints and their germ line counterparts indicated that an inadvertant recombinase-mediated break at chromosome segment 11p15 recombined with the delta T-cell receptor at 14q11. The derivative 11 breakpoint resembles a coding joint in which 11p15 rather than a variable region was introduced 5' to a D delta 1 D delta 2 J delta 1 intermediate rearrangement. Conversely, the derivative 14 breakpoint corresponds to a signal joint between the 5' heptamer-spacer-nonamer recombinational signal of D delta 1 and an isolated heptamer at 11p15. Multiple, apparently distinct transcripts were found flanking both breakpoints of 8402. RNAs of 3.5, 4.4, 1.4, and 8.0 kilobases originating from either side of the derivative 14 breakpoint were highly expressed in 8402 compared with other cells. This suggests that this translocation deregulated multiple genes and provides the opportunity to assess any multifactorial contribution they may have to malignancy. We cloned and sequenced several cDNAs representing the 1.4-kilobase transcript (termed Ttg-1 [T-cell translocation gene 1]) from an 8402 library. The predicted protein of 156 amino acids contained two internal repeats which could potentially form zinc fingers.

The GLI-Kruppel family of human genes

Previous characterization of GLI, a gene found to be amplified and expressed in a subset of human brain tumors, revealed the presence of five tandem zinc fingers related to those of Krüppel (Kr), a Drosophila segmentation gene of the gap class. We have used the GLI cDNA as a molecular probe to isolate related sequences from the human genome. Partial characterization of six related loci, including sequence determination, expression studies, and chromosome localization, revealed that each locus could encode a separate finger protein. The predicted proteins all had similar H-C links, i.e., a conserved stretch of 9 amino acids connecting the C-terminal histidine of one finger to the N-terminal cysteine of the next. On the basis of amino acid sequence and intron-exon organization, the genes could be placed into one of two subgroups: the GLI subgroup (with the consensus finger amino acid sequence [Y/F]XCX3GCX3[F/Y]X5LX2HX3-4H[T/S]GEKP) or the Kr subgroup (with the consensus finger amino acid sequence [Y/F]XCX2CX3FX5LX2HXRXHTGEKP). Unlike GLI or Kr, most of the newly isolated genes were expressed in many adult tissues. The predicted proteins probably control the expression of other genes and, by analogy with Kr and GLI, may be important in human development, tissue-specific differentiation, or neoplasia.

Molecular cloning and chromosomal localization of the human T-cell receptor zeta chain: distinction from the molecular CD3 complex

The T-cell antigen receptor (TCR) is a multisubunit receptor complex specific to T cells subserving both antigen recognition and signal transduction functions. The zeta chain of the TCR is a component of all surface receptor complexes. This chain was first identified in murine T cells by virtue of the fact that it coimmunoprecipitates with the TCR complex using antibodies directed against either the clone-specific subunits or invariant CD3 subunits of the receptor. Recently, we have isolated a cDNA encoding the murine zeta. Using this as a probe, we have now isolated cDNAs encoding the human zeta. Sequence analysis of cDNAs encoding human and murine zeta reveals that it is a highly conserved protein. In addition to amino acid homology, there is remarkable interspecies conservation in the nucleotide sequence of the 5' and 3' untranslated regions of the zeta mRNA. The previously characterized invariant delta, epsilon, and gamma chains of the TCR, referred to as the CD3 complex, share significant sequence and structural homology with each other and are all located within 300 kilobases of each other on human chromosome 11 (11q23). zeta has no sequence similarity to the CD3 chains and the localization of the human zeta gene to the centromeric region of chromosome 1 underscores the fact that it is a distinct genetic component of the TCR.

The GLI-Kruppel family of human genes

Previous characterization of GLI, a gene found to be amplified and expressed in a subset of human brain tumors, revealed the presence of five tandem zinc fingers related to those of Krüppel (Kr), a Drosophila segmentation gene of the gap class. We have used the GLI cDNA as a molecular probe to isolate related sequences from the human genome. Partial characterization of six related loci, including sequence determination, expression studies, and chromosome localization, revealed that each locus could encode a separate finger protein. The predicted proteins all had similar H-C links, i.e., a conserved stretch of 9 amino acids connecting the C-terminal histidine of one finger to the N-terminal cysteine of the next. On the basis of amino acid sequence and intron-exon organization, the genes could be placed into one of two subgroups: the GLI subgroup (with the consensus finger amino acid sequence [Y/F]XCX3GCX3[F/Y]X5LX2HX3-4H[T/S]GEKP) or the Kr subgroup (with the consensus finger amino acid sequence [Y/F]XCX2CX3FX5LX2HXRXHTGEKP). Unlike GLI or Kr, most of the newly isolated genes were expressed in many adult tissues. The predicted proteins probably control the expression of other genes and, by analogy with Kr and GLI, may be important in human development, tissue-specific differentiation, or neoplasia.

The cytogenetics of childhood leukemia: clinical and biologic implications

Cytogenetic studies have revealed a broad spectrum of abnormalities in the chromosomal make-up of human leukemic cells. These abnormalities are acquired during the process of malignant transformation within the neoplastic clone and reflect the genetic lesions and ablations that have occurred. Because cytogenetic abnormalities are tightly linked to the molecular events that lead to leukemogenesis, it is not surprising that these features correlate with immunophenotypic and morphologic features of the leukemic cells, as well as with the clinical characteristics of children at diagnosis and their responsiveness to therapy. Molecular analysis of the disordered structure or disrupted regulation of genes located at critical chromosomal breakpoints in leukemic cells should continue to provide important insight into normal and aberrant hematopoietic cell function.

The ras-related ral gene maps to chromosome 7p15-22

Human cDNAs coding for the new protein ral that shares 50% homology with the ras proteins have been recently isolated. A 600-bp fragment carrying mainly the coding region was used to localize the ral gene by hybridization with sorted chromosomes and in situ hybridization. Direct molecular hybridization on sorted chromosomes using a single laser illumination allowed the assignment of the ral gene to a region of the flow karyotype containing chromosomes 7, 8 and X. With dual laser analysis ral was assigned to the fraction containing chromosome 7. In the 331 human metaphases hybridized with the 3H-labelled insert, the silver grain distribution showed a unique major signal on chromosome 7p15-22.

Chromosomal localization of the human interleukin 1 alpha (IL-1 alpha) gene

The human interleukin 1 alpha gene was assigned to chromosome 2 using Southern transfer analysis of human-rodent somatic cell hybrid DNAs. The gene was regionally localized to 2q12-21 using in situ hybridization to metaphase chromosomes. These results indicate that the IL-1 alpha gene maps to the same general region on the long arm of chromosome 2 as the IL-1 beta gene, which has been previously assigned.

The kappa-deleting element. Germline and rearranged, duplicated and dispersed forms

Human light chain genes are used in a kappa before lambda order. Accompanying this hierarchy is the rearrangement of a kappa-deleting element (Kde) which eliminates the kappa locus before lambda gene rearrangement. In approximately 60% of rearrangements the Kde recombines at a conserved heptamer within the J kappa-C kappa intron. We demonstrated that aberrant V/J rearrangements possessing apparent "N" nucleotides existed 5' to the J kappa-Kde rearrangements. This suggests that the Kde may selectively eliminate nonfunctional V/J alleles. A kappa-producing cell that displayed the unusual finding of lambda gene rearrangement demonstrated a rearranged Kde. This rearrangement was a V kappa/Kde recombination and the heptamer-11 bp spacer-nonamer flanking the V kappa is the target site of the Kde 40% of the time. The mouse possesses a counterpart to the Kde (recombining sequence [RS]) and the highly conserved regions surround the heptamer-spacer-nonamer signals. No complete protein product was predicted from the germline Kde near its break-point and no consistent fusion product was predicted from either the V/Kde or V/J-Kde rearrangements. A distal portion of the Kde is duplicated and is present at 2q11 as well as 2p11. The evolutionary conservation of the kappa-elimination event, the duplication and maintenance of the Kde indicates that it has a function. A portion of the Kde may still prove to encode a trans-acting factor that directly affects lambda rearrangement. A certain role for the Kde is its site-specific rearrangement, which destroys ineffective kappa genes and sets the stage for lambda gene utilization.

Ki-ras-2 in acute lymphoblastic leukemia cells with chromosome change at 12p12

Cytogenetic and molecular investigations were performed on a pre-B-lymphoblastic acute leukemic cell line (NALM-6). The NALM-6 cells contained a del(5)(q32) and an ins(12)(p12;?), chromosomal material of unknown origin being inserted between subbands 12p12.1 and 12p12.2. Chromosomal in situ hybridization using a 3.0-kb c-Ki-ras-2 probe showed a significant accumulation of grains on the proximal portion of the inserted chromosomal material (12p12.1), as well as on the normal chromosome #12 with a peak at 12p11p12. The signal intensity obtained after hybridization of the c-Ki-ras-2 specific probe to the NALM-6 cells DNA is comparable with the intensity of the signal after hybridization of the same probe with the control cell line (MC/B) DNA. The findings indicate that the c-Ki-ras-2 gene is neither amplified nor transposed in the NALM-6 cells.

Increase in copy number of N-myc in retinoblastomas in comparison with chromosome abnormality

N-myc oncogene amplification was studied in tumor tissue DNA from Japanese retinoblastoma patients, taking into consideration their uni- or bilateral disease form, their family history, and any chromosome abnormalities. Of the 23 cases examined, seven (30%) showed a 1.9- to 2.3-fold amplification of N-myc. No correlation was found between N-myc amplification and either tumor form or family history. Two of three cases having double minute bodies in their tumors showed N-myc amplification. In two tumors with 13q deletions, one produced in the host with constitutional 13q--abnormality showed no N-myc amplification, and the other one produced in the host with normal karyotype showed an N-myc amplification. These results indicate N-myc amplification is independent of the known genetic background in retinoblastoma patients.

Cancer-associated lactate dehydrogenase is a tyrosylphosphorylated form of human LDH-A, skeletal muscle isoenzyme

Cancer-associated lactate dehydrogenase is a tyrosylphosphorylated form of human skeletal muscle isoenzyme, since the partial amino acid sequences of human liver LDH-K/A protein were found to be identical with the known primary structure of human LDH-A isoenzyme and the LDH-A isoenzymes from human placenta and bovine muscle were shown to be tyrosylphosphorylated. This tyrosylphosphorylated LDH-K/A protein was also found to be complexed with 21 kD, 30 kD, and 56 kD proteins.

Partial structure of the human alpha 2(IV) collagen chain and chromosomal localization of the gene (COL4A2)

We have isolated a 2.1-kb cDNA clone from a human placental library encoding part of the alpha 2 chain of collagen IV, a major structural protein of basement membranes. The DNA sequence encodes 446 amino acids in the triple-helical domain plus the 227 amino acids of the carboxy-terminal globular domain. The latter structure is composed of two homologous subdomains and is highly conserved between the alpha 1 and alpha 2 chains. The triple-helical domain contained seven interruptions of the Gly-X-Y repeat and these interruptions were in general larger than their counterparts in the alpha 1 chain. DNA from human rodent hybrid cell lines was analyzed under conditions in which there was no cross-hybridization of the alpha 2(IV) cDNA probe with the gene for the alpha 1(IV) collagen chain. An EcoRI fragment characteristic of the alpha 2 chain had a concordance of 0.97 with chromosome 13. This result was confirmed and extended with in situ localization of the gene at 13q34. Since the alpha 1(IV) gene has previously been localized to 13q34, the two type IV collagen genes reside in the same chromosome region (13q34), possibly in a gene cluster. The presence of the genes for type IV collagen chains on chromosome 13 excludes a primary role for these genes in adult polycystic kidney disease and X-linked forms of hereditary nephritis.

The molecular genetics of human chromosome 6

Chromosome 6 contains several clinically important markers as well as classical enzyme loci, proto-oncogenes, and a growing number of anonymous DNA restriction fragment length polymorphisms (RFLPs). It is also of unique interest because of the location of the major histocompatibility complex (MHC) on the short arm, at 6p21.3. The MHC is one of the most detailed areas of the human genetic map to date and many important diseases, some of a suspected autoimmune aetiology, are associated with it.

Cytogenetic evaluation of human endothelial cell cultures

Cytogenetic evaluation of serially subcultivated human endothelial cells revealed significant differences between cultures derived from fetal umbilical cords and cultures derived from various vessel sites in adults. A rapid increase in the prevalence of polyploid cells, to levels of 100% in many cases, was detected in human umbilical vein endothelial cell cultures but not in endothelial cell cultures from adult vessels. Because the development of polyploidy has been viewed as one signpost of in vitro senescence, it may be that these in vitro observations of high levels of polyploidy are a reflection of the fact that umbilical tissue is at the end of its in vivo developmental lifespan when studied. Consistent karyotypic alterations also were observed in two clones from adult human abdominal aorta, even though these cultures exhibited low percentages of polyploid cells. Cultures of one clone exhibited a trisomy of chromosome 11, on which there are at least three onc gene loci, and a deletion of chromosome 13 through band q14. A loss of band 13q14 is a prezygotic chromosomal lesion known to predispose to retinoblastoma. In the other clone, two cell populations were observed, and each displayed a chromosomal abnormality. A trisomy of the long arm of chromosome 2 was noted in one cell population via a marker chromosome involving 2 and 14. The other cell population exhibited an abnormality of chromosome 2. Neither of these karyotypic alterations was detected in the parent culture from which the clones were derived. The results reported in this study have both practical and theoretical implications. The high incidence of polyploidy in serially cultivated umbilical cultures as well as the occurrence of chromosomal changes in umbilical and aortic cultures testify to the need for cytogenetic monitoring of cell cultures even though they are derived from presumably normal tissue. Cytogenetic changes in the endothelium may be important in atherogenesis and other pathologic states. The conversion of diploid endothelial cells into polyploid endothelial cells may provide a convenient model cell system for studying mechanisms of the development of polyploidy in cells and their relationship to in vitro senescence.

The molecular genetics of human non-Hodgkin's lymphoma

There is increasing evidence to implicate oncogenes in the etiology of Burkitt's and non-Burkitt's non-Hodgkin's lymphoma. Some of these oncogenes have been identified because of their location at common breakpoints, some because they have been found by transfection assays to be activated, and some because they have been shown to be expressed in non-Hodgkin's lymphomas. So far there is no consistent pattern of involvement between specific oncogenes and specific subtypes of non-Hodgkin's lymphoma. This may be because more than one oncogene is necessary for transformation.

The interleukin 3 gene is located on human chromosome 5 and is deleted in myeloid leukemias with a deletion of 5q

The gene IL-3 encodes interleukin 3, a hematopoietic colony-stimulating factor (CSF) that is capable of supporting the proliferation of a broad range of hematopoietic cell types. By using somatic cell hybrids and in situ chromosomal hybridization, we localized this gene to human chromosome 5 at bands q23-31, a chromosomal region that is frequently deleted [del(5q)] in patients with myeloid disorders. By in situ hybridization, IL-3 was found to be deleted in the 5q-chromosome of one patient with refractory anemia who had a del(5)(q15q33.3), of three patients with refractory anemia (two patients) or acute nonlymphocytic leukemia (ANLL) de novo who had a similar distal breakpoint [del(5)(q13q33.3)], and of a fifth patient, with therapy-related ANLL, who had a similar distal breakpoint in band q33 [del(5)(q14q33.3)]. Southern blot analysis of somatic cell hybrids retaining the normal or the deleted chromosome 5 from two patients with the refractory anemia 5q- syndrome indicated that IL-3 sequences were absent form the hybrids retaining the deleted chromosome 5 but not from hybrids that had a cytologically normal chromosome 5. Thus, a small segment of chromosome 5 contains IL-3, GM-CSF (the gene encoding granulocyte-macrophage-CSF), CSF-1 (the gene encoding macrophage-CSF), and FMS (the human c-fms protooncogene, which encodes the CSF-1 receptor). Our findings and earlier results indicating that GM-CSF, CSF-1, and FMS were deleted in the 5q-chromosome, suggest that loss of IL-3 or of other CSF genes may play an important role in the pathogenesis of hematologic disorders associated with a del(5q).

Molecular analysis of integrated human papillomavirus 16 sequences in the cervical cancer cell line SiHa

Human papillomavirus (HPV) 16 is frequently found integrated into cervical cancer cell genomes and these integrations are thought to play a role in tumorigenesis. To investigate the mechanisms of HPV integration and its effect on transcription and chromosomal sequence organization, we have cloned and analyzed the HPV16 integration from the cervical cancer cell line SiHa. Restriction analyses and Southern blotting indicated that approximately 95% of an HPV16 genome was integrated without gross rearrangement. Sequence analysis of the cellular-viral DNA junctions revealed that integration had occurred within the E2 and E4 ORFs where 251 bp of viral sequence was deleted. One viral terminus occurred within sequences of an Alu repeat and a 4-bp homology was present at the site of recombination. Using unique cellular flanking DNA probes, a 4.8-kb deletion of cellular sequences was detected at the site of viral integration. The chromosomal location of the viral integration and cellular deletion were mapped to chromosome 13 using a rodent X human somatic cell hybrid panel. Northern blot analysis using viral subgenomic and 3' cellular probes revealed transcription from the 3' portion of integrated HPV16 (E6, E7, E1) and flanking cellular sequences. The observation of viral-cell transcripts and chromosomal deletions associated with HPV integration may indicate that such events are part of a multistep mechanism leading to the development of cervical cancer.

Cytogenetic methodologies for gene mapping and comparative analyses in mammalian cell culture systems

Presented here are the detailed methods employed in our laboratory for gene mapping and cytogenetic analyses in human beings, in the domestic cat, and in other mammalian species. Induced in the procedures are: 1) establishment of primary fibroblast and lymphoid cell cultures; 2) heterologous cell fusion for production of rapidly proliferating cell hybrids; 3) cellular transformation of primary fibroblasts using an oncogenic retrovirus; 4) cell synchronization for high-resolution banding of promethaphase chromosomes; 5) chromosome-banding procedures, including G-banding, alkaline G-11, and Q-banding; and 6) in situ hybridization of radiolabeled molecular clones to metaphase chromosomes for regional gene localization.

A-raf oncogene localizes on mouse X chromosome to region some 10-17 centimorgans proximal to hypoxanthine phosphoribosyltransferase gene

The localization of the A-raf cellular oncogene on the mouse X chromosome has been determined using Xbal-restricted DNAs prepared from progeny of an interspecies backcross between the B6.CBA.R1 and the Spe/Pas mouse strains. This localization to the proximal part of the mouse X chromosome has been confirmed by the use of somatic cell hybrids, carrying partially deleted X chromosomes and suggests that the A-raf oncogene localizes to a region lying some 10-17 centimorgans proximal to the hypoxanthine phosphoribosyltransferase (Hprt) gene between the locus DXPas4 and the locus DXPas7 defined by the cross-reacting human X chromosome-specific probe DXS32 (M2C). This localization on the mouse X chromosome is compatible with the presence of the A-raf oncogene on the short arm of the human X chromosome between the centromere and Xp21.

Isolation of a human genomic fragment, co-amplified with c-Ki-ras, that affects plasmid supercoiling in E. coli

Amplification of cellular proto-oncogenes has been implicated in the development of human malignancies. A library was constructed from genomic DNA extracted from a lung tumour, previously shown to carry an amplified c-Ki-ras 2 gene. Using a v-Ki-ras probe, a fragment with ras homology was isolated and shown to be amplified in the original tumour DNA to the same level as c-Ki-ras. Studies with human hamster hybrids demonstrated that it is normally located on human chromosome 12 (as is c-Ki-ras). The restriction map of the fragment is different from that of the known Ha, Ki or N-ras genes and its sequence shows evolutionary conservation, as demonstrated by hybridisation to the genomic DNA of several mammalian species. A pUC19 subclone (pK42), carrying a 1.3kb insert, shows supercoil heterogeneity in plasmid preparations, as does a second compatible plasmid introduced into the same bacterial host with pK42. It appears therefore that the subclone is encoding a product that affects DNA topoisomerase activity in E. coli.

Identification of an amplified, highly expressed gene in a human glioma

A gene, termed gli, was identified that is amplified more than 50-fold in a malignant glioma. The gene is expressed at high levels in the original tumor and its derived cell line and is located at chromosome 12 position (q13 to q14.3). The gli gene is a member of a select group of cellular genes that are genetically altered in primary human tumors.

Constitutional translocation t(3;6)(p14;p11) in a family with hematologic malignancies

We describe a family with an inherited constitutional balanced translocation t(3;6)(p14;p11) and hematologic malignancies. Of two proven translocation carriers, one had acute myeloid leukemia and the other had myelofibrosis. A third member who had died of acute leukemia was a possible translocation carrier (chromosome analysis had not been performed). Five healthy translocation carriers were detected. Neither the translocation nor additional hematologic malignancies were found outside the nuclear family. It could not be definitely clarified if this constitutional translocation predisposes to hematologic malignancies. Breakpoint 3p14 has previously been implicated in recurrent cancer-associated rearrangements but 6p11 has not. We suggest that other investigators look for involvement of these breakpoints in cancer patients.

Structure of the human and murine R-ras genes, novel genes closely related to ras proto-oncogenes

The human R-ras gene was isolated by low-stringency hybridization with a v-H-ras probe. The predicted 218 amino acid R-ras protein has an amino-terminal extension of 26 residues compared with H-ras p21, and shows 55% amino acid identity; conserved domains include the p21 GTP-binding site and the carboxy-terminal membrane localization sequence. R-ras has at least six exons, with the position of the first intron conserved relative to the Drosophila ras64B and Dictyostelium ras genes; there is no similarity in the exon-intron structure of the R-ras gene and of the mammalian H-, K-, and N-ras proto-oncogenes. Cloned mouse R-ras cDNAs exhibit 88% nucleotide and 94.5% predicted amino acid identity to human R-ras. Human R-ras was localized to chromosome 19, a site different from ras p21 genes. Mouse R-ras is syntenic with c-H-ras on chromosome 7.

Chromosomal assignment of c-MEL, a human transforming oncogene, to chromosome 19 (p13.2-q13.2)

The human malignant melanoma cell line NK14 contains a novel transforming gene which was identified using DNA transfection into NIH3T3 cells (1). This gene has been assigned to chromosome 19p13.2-q13.2 using human-mouse and human-hamster somatic cell hybrids.

Two new cell lines from B-prolymphocytic leukaemia: characterization by morphology, immunological markers, karyotype and Ig gene rearrangement

Leukaemic cells from 2 patients with B-prolymphocytic leukaemia were immortalized in vitro by means of Epstein-Barr virus and phorbol-ester TPA. The resulting cell lines, named JVM-2 and JVM-3, have been growing continuously in liquid culture for more than one year. JVM-2 is characterized cytogenetically by t(11;14)(q13; q32), and JVM-3 by trisomy 12. The immunoglobulin (Ig) heavy- and light-chain genes showed the same pattern of rearrangement in both lines as in the original prolymphocytes from each case. The cells from these lines showed a spectrum of morphological and immunological features corresponding to different stages of B-cell maturation. The expression of Ig, IgM-lambda in JVM-2 and IgMD-K in JVM-3, changed from a predominantly membrane pattern in the original cells to a cytoplasmic one in the cell lines. By comparison with their original progenitors, the cells from both lines showed reduced reactivity with the monoclonal antibody (MAb) FMC7, and increased expression of the antigens recognized by the MAbs OKT10, alpha-Tac, FMC53 and Ki-I. The availability of cell lines from this rare type of lymphoid leukaemia offers a potential tool for the study of molecular events associated with the expression of Ig and other antigens by neoplastic cells.

Cloning, characterization, expression, and chromosomal localization of a human ferritin heavy-chain gene

A genomic phage clone containing a full-length copy of a functional human gene for ferritin heavy chain has been isolated. The gene consists of four exons spanning approximately 3 kilobases and has been localized to chromosome 11. The functionality of the gene was demonstrated by the fact that both transient transfectants and stable transformants of murine fibroblasts actively transcribe human ferritin heavy-chain mRNA.

Genetic characterization of human c-rel sequences

We isolated and sequenced a human genomic-DNA segment that is homologous to a portion of v-rel, the transforming gene of reticuloendotheliosis virus (strain T). We also localized the human rel sequences to human chromosome 2 by screening a panel of rodent X human somatic-cell hybrids with the newly described human rel segment.

The ral gene: a new ras related gene isolated by the use of a synthetic probe

We synthesized a set of 20-mer oligonucleotides corresponding to a sequence of seven amino acids strictly conserved in all the different ras proteins, from yeast to man, as well as in rho and YPT, two proteins distantly related to p21 ras (approximately 30% amino acid homology). This oligonucleotide probe was used to search for new members of the ras family. We describe here a new ras related gene named ral, isolated from a cDNA library of immortalized simian B-lymphocytes. The ral gene codes for a 206 amino acid protein of expected mol. wt 23.5 kd that shares greater than 50% homology with H-ras, K-ras or N-ras. The GTP binding regions of p21 ras and a C-terminal cysteine involved in membrane anchoring are also present in ral; this strongly suggests that ral is a GTP binding protein with membrane localization. Furthermore, several external regions of p21 ras presumably involved in the interaction with effector, receptor and/or regulatory proteins are highly homologous to the corresponding regions in ral. Therefore some of the proteins that interact with ral might be identical or closely related to those interacting with p21 ras.

Amplification and chromosomal dispersion of human endogenous retroviral sequences

Endogenous retroviral sequences in humans have undergone amplification events involving both viral and flanking cellular sequences. We cloned members of an amplified family of full-length endogenous retroviral sequences. Genomic blotting, employing a flanking cellular DNA probe derived from a member of this family, revealed a similar array of reactive bands in both humans and chimpanzees, indicating that an amplification event involving retroviral and associated cellular DNA sequences occurred before the evolutionary separation of these two primates. Southern analyses of restricted somatic cell hybrid DNA preparations suggested that endogenous retroviral segments are widely dispersed in the human genome and that amplification and dispersion events may be linked.

Human endothelial cell growth factor: cloning, nucleotide sequence, and chromosome localization

Several of the endothelial cell polypeptide mitogens that have been described probably play a role in blood vessel homeostasis. Two overlapping complementary DNA clones encoding human endothelial cell growth factor (ECGF) were isolated from a human brain stem complementary DNA library. Southern blot analysis suggested that there is a single copy of the ECGF gene and that it maps to human chromosome 5 at bands 5q31.3 to 33.2 A 4.8-kilobase messenger RNA was present in human brain stem messenger RNA. The complete amino acid sequence of human ECGF was deduced from the nucleic acid sequence of these clones; it encompasses all the well-characterized acidic endothelial cell polypeptide mitogens described by several laboratories. The ECGF-encoding open reading frame is flanked by translation stop codons and provides no signal peptide or internal hydrophobic domain for the secretion of ECGF. This property is shared by human interleukin-1, which is approximately 30 percent homologous to ECGF.