Chromosomal localization of human leukocyte, fibroblast, and immune interferon genes by means of in situ hybridization

Interferon gamma-related gene signature based on anti-tumor immunity predicts glioma patient prognosis

Background: Glioma is the most common primary tumor of the central nervous system. The conventional glioma treatment strategies include surgical excision and chemo- and radiation-therapy. Interferon Gamma (IFN-γ) is a soluble dimer cytokine involved in immune escape of gliomas. In this study, we sought to identify IFN-γ-related genes to construct a glioma prognostic model to guide its clinical treatment. Methods: RNA sequences and clinicopathological data were downloaded from The Cancer Genome Atlas (TCGA) and the China Glioma Genome Atlas (CGGA). Using univariate Cox analysis and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm, IFN-γ-related prognostic genes were selected to construct a risk scoring model, and analyze its correlation with the clinical features. A high-precision nomogram was drawn to predict prognosis, and its performance was evaluated using calibration curve. Finally, immune cell infiltration and immune checkpoint molecule expression were analyzed to explore the tumor microenvironment characteristics associated with the risk scoring model. Results: Four out of 198 IFN-γ-related genes were selected to construct a risk score model with good predictive performance. The expression of four IFN-γ-related genes in glioma tissues was significantly increased compared to normal brain tissue (p < 0.001). Based on ROC analysis, the risk score model accurately predicted the overall survival rate of glioma patients at 1 year (AUC: The Cancer Genome Atlas 0.89, CGGA 0.59), 3 years (AUC: TCGA 0.89, CGGA 0.68), and 5 years (AUC: TCGA 0.88, CGGA 0.70). Kaplan-Meier analysis showed that the overall survival rate of the high-risk group was significantly lower than that of the low-risk group (p < 0.0001). Moreover, high-risk scores were associated with wild-type IDH1, wild-type ATRX, and 1P/19Q non-co-deletion. The nomogram predicted the survival rate of glioma patients based on the risk score and multiple clinicopathological factors such as age, sex, pathological grade, and IDH Status, among others. Risk score and infiltrating immune cells including CD8 T-cell, resting CD4 memory T-cell, regulatory T-cell (Tregs), M2 macrophages, resting NK cells, activated mast cells, and neutrophils were positively correlated (p < 0.05). In addition, risk scores closely associated with expression of immune checkpoint molecules such as PD-1, PD-L1, CTLA-4, LAG-3, TIM-3, TIGIT, CD48, CD226, and CD96. Conclusion: Our risk score model reveals that IFN-γ -associated genes are an independent prognostic factor for predicting overall survival in glioma, which is closely associated with immune cell infiltration and immune checkpoint molecule expression. This model will be helpful in predicting the effectiveness of immunotherapy and survival rate in patients with glioma.

PROPERTIES AND FUNCTIONS OF THE NOVEL TYPE I INTERFERON EPSILON

Interferon epsilon (IFNε) is a type I IFN with unusual patterns of expression and therefore, function. It is constitutively expressed by reproductive tract epithelium and regulated by hormones during estrus cycle, reproduction, and menopause and by exogenous hormones. The IFNe protein is encoded by a gene in the type I IFN locus, binds to IFNAR1 and 2 which are required for signaling via the JAK STAT pathway. Its affinity for binding receptors and transducing signals is less potent than IFNα or β subtypes in vitro. Nevertheless, in vivo experiments indicate its efficacy in regulating mucosal immune responses and protecting from bacterial and viral infections. These studies demonstrate a different mechanism of action to type I IFNs. In this organ system with dynamic fluxes in cellularity, requirement to tolerate an implanted fetus, and be protected from disease, there is co-option of a special IFN from a family of effective immunoregulators, with unique controls and modified potency to make it a safe and effective constitutive reproductive tract cytokine.

Interferon γ and Its Important Roles in Promoting and Inhibiting Spontaneous and Therapeutic Cancer Immunity

Originally identified in studies of cellular resistance to viral infection, interferon (IFN)-γ is now known to represent a distinct member of the IFN family and plays critical roles not only in orchestrating both innate and adaptive immune responses against viruses, bacteria, and tumors, but also in promoting pathologic inflammatory processes. IFN-γ production is largely restricted to T lymphocytes and natural killer (NK) cells and can ultimately lead to the generation of a polarized immune response composed of T helper (Th)1 CD4+ T cells and CD8+ cytolytic T cells. In contrast, the temporally distinct elaboration of IFN-γ in progressively growing tumors also promotes a state of adaptive resistance caused by the up-regulation of inhibitory molecules, such as programmed-death ligand 1 (PD-L1) on tumor cell targets, and additional host cells within the tumor microenvironment. This review focuses on the diverse positive and negative roles of IFN-γ in immune cell activation and differentiation leading to protective immune responses, as well as the paradoxical effects of IFN-γ within the tumor microenvironment that determine the ultimate fate of that tumor in a cancer-bearing individual.

TNF-α and IFN-γ gene variation and genetic susceptibility to type 1 diabetes and its microangiopathic complications

Background

TNF-α has accelerating role in development of type 1 diabetes. Although an immunosupressor function and leading protecting role in T1DM also has been claimed for this pro-inflammatory cytokine. Over-expression of pro-inflammatory and type 1 cytokines (Th1, like IFN-γ) drive insulitis toward the destructive form that leads to type 1 diabetes (T1DM). Among type 1 cytokines only IFN-γ has been detectable in the islet β cells. In deletion studies IFN-γ was also the only Th1 cytokine for which its ablation or blockade caused delayed or decreased incidence of T1DM.

Methods

Functional polymorphisms of TNF-α at position -308*G/A and at position +874*T/A of IFN-γ gene were employed as markers and the comparative distribution of derived genotypes/alleles were assessed in 248 British Caucasian T1DM patients and 118 healthy controls.

Results

There was no significant association between IFN-γ gene polymorphism and T1DM or the diabetic complication triad. There was a marginal association between TNF-α –308*G/A polymorphism in nephropaths (vs healthy controls) (p = 0.06), which its insignificancy may be due to survivor factor. No significant association was evident between the genotype/allele of the applied marker and T1DM or diabetic complication triad.

Conclusion

Our results are in contrast with previous reports suggesting that these polymorphisms are not related to T1DM. This study also underlines the importance of replication of association studies to confirm the previous interpretation.

Evolutionary genetic dissection of human interferons

As revealed by population genetic analyses, different human interferon genes evolved under distinct selective constraints and signatures of positive selection vary according to geographic region, suggesting that some sequence changes may have conferred an advantage by increasing resistance to viral infection.

Interferons (IFNs) are cytokines that play a key role in innate and adaptive immune responses. Despite the large number of immunological studies of these molecules, the relative contributions of the numerous IFNs to human survival remain largely unknown. Here, we evaluated the extent to which natural selection has targeted the human IFNs and their receptors, to provide insight into the mechanisms that govern host defense in the natural setting. We found that some IFN-α subtypes, such as IFN-α6, IFN-α8, IFN-α13, and IFN-α14, as well as the type II IFN-γ, have evolved under strong purifying selection, attesting to their essential and nonredundant function in immunity to infection. Conversely, selective constraints have been relaxed for other type I IFNs, particularly for IFN-α10 and IFN-ε, which have accumulated missense or nonsense mutations at high frequencies within the population, suggesting redundancy in host defense. Finally, type III IFNs display geographically restricted signatures of positive selection in European and Asian populations, indicating that genetic variation at these genes has conferred a selective advantage to the host, most likely by increasing resistance to viral infection. Our population genetic analyses show that IFNs differ widely in their biological relevance, and highlight evolutionarily important determinants of host immune responsiveness.

Interleukins, from 1 to 37, and interferon-γ: receptors, functions, and roles in diseases

Advancing our understanding of mechanisms of immune regulation in allergy, asthma, autoimmune diseases, tumor development, organ transplantation, and chronic infections could lead to effective and targeted therapies. Subsets of immune and inflammatory cells interact via ILs and IFNs; reciprocal regulation and counter balance among T(h) and regulatory T cells, as well as subsets of B cells, offer opportunities for immune interventions. Here, we review current knowledge about ILs 1 to 37 and IFN-γ. Our understanding of the effects of ILs has greatly increased since the discoveries of monocyte IL (called IL-1) and lymphocyte IL (called IL-2); more than 40 cytokines are now designated as ILs. Studies of transgenic or knockout mice with altered expression of these cytokines or their receptors and analyses of mutations and polymorphisms in human genes that encode these products have provided important information about IL and IFN functions. We discuss their signaling pathways, cellular sources, targets, roles in immune regulation and cellular networks, roles in allergy and asthma, and roles in defense against infections.

Molecular genetics of Psoriasis (Principles, technology, gene location, genetic polymorphism and gene expression)

Psoriasis is a common inflammatory skin disease with an etiology bases on both environmental and genetic factors. As is the case of many autoimmune diseases its real cause remains poorly defined. However, it is known that genetic factors contribute to disease susceptibility. The linkage analysis has been used to identify multiple loci and alleles that confer risk of the disease. Some other studies have focused upon single nucleotide polymorphisms (SNPs) for mapping of probable causal variants. Other studies, using genome-wide analytical techniques, tried to link the disease to copy number variants (CNVs) that are segments of DNA ranging in size from kilobases to megabases that vary in copy number. CNVs represent an important element of genomic polymorphism in humans and harboring dosage-sensitive genes may cause or predispose to a variety of human genetic diseases. The mechanisms giving rise to SNPs and CNVs can be considered as fundamental processes underlying gene duplications, deletions, insertions, inversions and complex combinations of rearrangements. The duplicated genes being the results of 'successful' copies are fixed and maintained in the population. Conversely, many 'unsuccessful' duplicates remain in the genome as pseudogenes. There is another form of genetic variations termed copy-neutral loss of heterozygosity (LOH) with less information about their potential impact on complex diseases. Additional studies would include associated gene expression variations with either SNPs or CNVs. Now many genetic techniques such as PCR, real time PCR, microarray and restriction fragment length analysis are available for detecting genetic polymorphisms, gene mapping and estimation of gene expression. Recently, the scientists have used these tools to define genetic signatures of disease, to understand genetic causes of disease and to characterize the effects of certain drugs on gene expression. This review highlights the principles, technology and applications on psoriasis.

Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies

BACKGROUND

The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families.

RESULTS

The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus. The IFNT, which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW. A new Type I IFN family (IFNX) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore.

CONCLUSION

In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus, thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and foregut fermentation.

Relationships between specific serum IgE, IgG, IFN-gamma level and IFN-gamma, IFNR1 polymorphisms in patients with penicillin allergy

OBJECTIVE

The findings of numerous studies have suggested that both genetic and environmental influences are involved in the pathogenesis of allergic disease and atopy. We studied the polymorphisms in the interferon (IFN)-gamma (gamma) and IFN-gamma receptor 1 (IFNR1) gene with the aim of clarifying the relationships among these polymorphisms, penicillin allergy and anti-penicillin antibodies.

METHODS

A restriction endonuclease fragment length polymorphism (RFLP)-PCR analysis and sequencing were used to study the IFNR1 and IFN-gamma polymorphisms. The presence and level of eight specific immunoglobulin (Ig)E and IgG antibodies were determined by the radioallergosorbent test (RAST) and enzyme-linked immunosorbent assay (ELISA), respectively.

RESULTS

The positive rates of specific IgE and IgG were 61.11 and 53.92%, respectively. There was no significant difference in the whole-allele of IFN-gamma distribution between patients with a penicillin allergy and control subjects. Allele 7 (18CA repeat) was significantly less frequent in the urticaria group (3.19 vs. 11.93%) than in the controls. There was no difference in IFN-gamma production among different alleles in IFN-gamma. The frequency of G/A (Val/Met) in the IFNR1 gene in allergic patients was significantly less than that in the controls (P < 0.05). There were no significant differences in the positive rate of IgE among different alleles of IFN-gamma. The same was true for the positive rate of IgG.

CONCLUSIONS

The Met/Val allele in IFNR1 gene may have a protective role in the non-penicillin allergic population. The allele 18CA repeat in IFN-gamma gene may be associated with urticaria.

Differential effects of the type I interferons alpha4, beta, and epsilon on antiviral activity and vaccine efficacy

The type I IFNs exert a range of activities that include antiviral, antiproliferative, and immunomodulatory effects. To study this further, we have constructed recombinant vaccinia viruses expressing HIV or hemagglutinin (HA) Ags along with murine type I IFNs, IFN-alpha(4) (HA-VV-IFN-alpha(4)), IFN-beta (HA-VV-IFN-beta), or IFN-epsilon (HIV-VV-IFN-epsilon), a recently discovered member of this family. Our aims were to characterize IFN-epsilon functionality as a type I IFN and also to study the biological properties of these factors toward the development of safer and more effective vector-based vaccines. HIV-VV-IFN-epsilon and HA-VV-IFN-beta grew to lower titers than did their parental controls in murine cell lines. In vivo, however, HIV-VV-IFN-epsilon growth was not attenuated, while IFN-beta demonstrated potent local antiviral activity with no replication of HA-VV-IFN-beta detected. Flow cytofluorometric analysis of B lymphocytes incubated with virally encoded IFN-epsilon showed up-regulation of activation markers CD69 and CD86, while RT-PCR of IFN-epsilon-treated cells revealed that gene expression levels of antiviral proteins were elevated, indicating the induction of an antiviral state. The use of these constructs in a poxvirus prime-boost immunization regime led to robust humoral and cellular immune responses against the encoded Ags, despite the lack of replication in the case of HA-VV-IFN-beta. Thus, coexpression of these factors may be beneficial in the design of safer vector-based vaccines. Our data also indicate that while IFN-epsilon exhibits certain biological traits similar to other type I IFNs, it may also have a specific role in mucosal immune regulation that is quite distinct.

Genes and structure of selected cytokines involved in pathogenesis of psoriasis

Psoriasis is a common skin disease involving 1-4% of human population worldwide, of strong genetic background. The following cytokines are directly involved in psoriasis: TNF, IL-1, IL-2, IL-6, IL-7, IL-8, IL-15, IL-18, IL-19, IL-20, IL-23 whereas IL-4, IL-10, IL-12 as well as IL-11, IL-17 and IFN-gamma are rather indirectly engaged. This work is a review of some genetic factors and structure of selected cytokines and receptors and their genes location.

Association of interferon-gamma and interferon regulatory factor 1 polymorphisms with asthma in a family-based association study in Taiwan

BACKGROUND

Asthma is a multi-factorial disorder caused by complex interactions between genetic and environmental factors. IFN-gamma and IFN regulatory factor 1 (IRF-1) affect Th1/Th2 cytokine balance, and influence the differentiation of Th2 cells, which influence the development of asthma.

OBJECTIVE

This study investigated CA repeats polymorphism of the IFN-gamma gene and GT repeats polymorphism of the IRF-1 gene, which may predispose individuals to asthma pathogenesis.

METHODS

In the present study, we used the transmission/disequilibrium test (TDT) to investigate the relationship between asthma and the IFN-gamma and IRF-1 polymorphisms by studying 348 subjects composed of 232 parents and 116 asthmatic children.

RESULTS

For global TDT test, IFN-gamma CA repeats and IRF-1 GT repeat polymorphisms showed a significant association with asthma in children (P=0.009 and 0.017, respectively). We demonstrated that 13 CA repeats (138 bp) of IFN-gamma gene and 11 GT repeats (306 bp) of IRF-1 gene are significantly preferentially transmitted to asthmatic children (T/NT=89/61, chi2=8.43, P<0.005 and T/NT=75/49, chi2=8.18, P<0.005, respectively). The offspring will have an increased risk of asthma when their parents transmit IFN-gamma 13 CA repeats (OR=1.83, P=0.009) and IRF1 11 GT repeats (OR=1.88, P=0.007) to them. But we observed that the IFN-gamma and IRF-1 polymorphisms are not associated with IgE concentrations.

CONCLUSION

These findings provide strong evidence of which IFN-gamma CA repeat and IRF-1 GT repeat polymorphisms influence the risk of asthma for children in Taiwan.

The gene for bovine interferon gamma (IFNG) maps to the q22-q24 bands of chromosome 5 in cattle

A approximately 700 bp bovine IFNG cDNA probe was used for the chromosomal localization of the IFNG gene in cattle using in situ hybridization technique. This locus has previously been assigned to chromosome 5 by analysis of a somatic cell hybrid panel. The in situ hybridization results obtained in the present study allow us to map the locus at the 5q22-q24 bands. Relative location of the IFNG gene and the class II cytokeratin and HOX3 gene clusters in cattle and humans is discussed.

Involvement of protein phosphatase 2A in interferon-alpha-2b-induced apoptosis in K562 human chronic myelogenous leukaemia cells

Interferon-alpha (IFN-alpha)-2b is known to have antiproliferative effects on hematological malignant cells, especially chronic myelogenous leukaemia (CML). However, it can induce cytogenetical remissions in a very small percentage of the patients. Also during interferon therapy, resistance can emerge in the CML clones. K562 is an in vitro model cell line transformed from a Ph positive CML patient. It can be induced to differentiate to granulocytic and/or monocytic lineages with certain molecules. IFN-alpha-2b generally exerts its effects on CML cells by Janus family kinases (Jak/Stat) pathway, mostly through tyrosine kinase system. However, there is almost no data on the relevance of serine/threonine (Ser/Thr) protein phosphatase (PP) system in the interferon induced signal transduction pathways. In this study, we investigated serine/threonine protein phosphatases in the IFN-alpha-2b induced K562 cytotoxicity. Trypan blue dye exclusion test and MTT assay were utilised for determining cytotoxicity. IC(50) of IFN-alpha-2b on K562 cells was found to be 600IU/ml. However, no differentiation was determined by analysis of cell surface antigen expressions. Serine/threonine protein phosphatase inhibitors calyculin A (Cal A) and okadaic acid (OKA) augmented the IFN-alpha-2b induced cytotoxicity. Apoptosis assay by the mono-oligonucleosome detection and acridine orange/propidium iodide dye revealed marked apoptosis underlying cytotoxicity. Phosphatase enzyme assay revealed a gradual increase in protein phosphatase 2A (PP2A) activity during interferon induced cytotoxicity. Conversely, immunoblots showed no change in the expression of PP2A catalytic and regulatory subunits. In conclusion, PP2A plays a role in IFN-alpha-2b induced apoptosis of K562 cells and should be investigated as a new window furthermore.

Viruses and the type I interferon antiviral system: induction and evasion

The type I interferon (IFN) system responds to viral infection and induces an "antiviral state" in cells, providing an important first line of defense against virus infection. Interaction of type I IFNs (IFN alpha and IFN beta) with their receptor induces hundreds of cellular genes. Of the proteins induced by IFN, the antiviral function of only a few is known, and their mechanisms of action are only partly understood. Additionally, although viral-encoded mechanisms that counteract specific components of the type I IFN response have been known for some time, it has recently become clear that many (if not most) viruses encode some form of IFN-antagonist. Understanding the interplay between viral-encoded IFN antagonists and the interferon response will be essential if the therapeutic potential of IFNs is to be fully exploited.

Association of IFN-gamma and IFN regulatory factor 1 polymorphisms with childhood atopic asthma

BACKGROUND

IFN-gamma and related molecules play important roles in the differentiation and function of TH2 cells.

OBJECTIVE

We sought to determine whether IFNG and related genes contribute to any susceptibility to atopic asthma, a representative TH2-dominant disorder.

METHODS

We investigated the association of IFNG (CA repeat polymorphism within the first intron), IRF1 (GT repeat polymorphism within the intron 7), IFNGR1 (Val 14 Met), and IFNGR2 (Gln 64 Arg) gene polymorphisms with atopic asthma in the Japanese child population.

RESULTS

A significant association (P =.0018) was observed between IFNG gene polymorphism and atopic asthma. The tendency was more prominent in patients with age of onset of 3 years or younger (P =.0004) or patients with a family history of allergic diseases (P =.0038). Furthermore, there was a significant association between IRF1 gene whole-allele distribution and atopic asthma (P =.044). The tendency was more prominent in patients with onset at 3 years of age or less (P =.0058). On the other hand, IFNGR1 and IFNGR2 gene polymorphisms showed no association with atopic asthma.

CONCLUSION

These results suggested that among IFNG and related genes, IFNG and IRF1 genes confer genetic susceptibility to atopic asthma in Japanese children.

Close linkage of Mdm-1, a gene amplified and overexpressed in a transformed 3T3 cell line, with gamma interferon (Ifg) on chromosome 10 of the mouse

The Mdm-1 gene was mapped to the distal end of Chromosome (Chr) 10. An extensive series of restriction fragment variants was identified among conventional and exotic inbred strains of mice. Mapping was carried out with recombinant inbred strains and an intersubspecific testcross. No recombinants were observed between Mdm-1 and the gamma interferon locus (Ifg). These two loci appear to be in linkage disequilibrium among inbred strains. Data from the testcross place Mdm-1 approximately 11 centimorgans distal to the steel (Sl) locus. Because of its extensive polymorphism, Mdm-1 is a useful genetic marker for distal Chr 10.

Insights into the biologic and molecular abnormalities in adult acute lymphocytic leukemia

The last 3 decades have seen much progress in the treatment and outcome of patients with ALL. Unfortunately, the success that has been achieved in children with ALL has not yet been translated into adult patients. Insight into the biologic and molecular abnormalities in ALL may, however, provide the necessary clues that allow a clearer understanding of the crucial differences in the behavior of ALL in different groups of patients. As the molecular basis of the disease is deciphered, new targets are discovered that may prove useful for therapeutic interventions in the future.

Biologic responses to IFN-alpha administration in humans

Although interferon-alpha (IFN-alpha) was discovered over 40 years ago, it was many years before it was registered as a therapeutic agent. Because of its unique qualities, it has been registered for both antiviral and antitumor indications. In addition to its therapeutic effects in viral diseases and cancer, IFN-alpha interferes with several important physiologic systems. It interacts with the immune system and affects several neuroendocrine and metabolic circuits. The specific mechanisms by which IFN-alpha exerts its therapeutic effects are complex, and it is very difficult to tie the biologic actions of IFN-alpha to specific clinical effects.

A novel t(11;12)(q23-24;q24) in a case of minimally-differentiated acute myeloid leukemia (AML-M0)

Acute myeloid leukemia with minimal signs of myeloid differentiation (AML-M0) is a recent addition to the FAB group classification. Chromosome data is scarce, but existing reports describe a high incidence of complex karyotypes and myelodysplastic syndrome-like chromosome alterations, while single chromosome translocations have rarely been reported. We describe the case of a 60-year-old woman diagnosed with AML-M0 with a novel translocation t(11;12)(q23-24;q24) as the sole karyotypic marker. Fluorescence in situ hybridization analysis to assess MLL gene splitting did not show rearrangement of this oncogene.

Analysis of an IFN-gamma gene (IFNG) polymorphism in multiple sclerosis in Europe: effect of population structure on association with disease

An intronic dinucleotide polymorphism in the IFN-gamma gene (IFNG) was used as a marker for testing association with multiple sclerosis (MS). Disease association was analyzed in case-control sets sampled from four geographically separate European populations (Germany, Northern Italy, Sardinia, and Sweden). Only in the Swedish was a weak disease association of the IFNG allele pattern found, mainly due to a higher frequency of IFNG allele I1 in MS patients. No evidence for association was found in the German or Northern Italian populations. These results contrast with the situation in Sardinia. We have recently reported transmission disequilibrium of IFNG allele I2 in Sardinian MS siblings not carrying the predisposing DRB1 *03 or *04 alleles (Ann. Neurol. 44, 841-842, 1998). Further analysis now shows that I2 is significantly more often transmitted to DRB1 *03-/*04- males, than to DRB1 *03-/*04- females. The odds ratio (OR) for IFNG-associated susceptibility to MS in the total Sardinian DRB1*03-/*04- group was 1.88 for I2 heterozygotes but amounted to 8.235 for I2 homozygotes, suggestive of a recessive mode of inheritance. Score test-based statistics pointed to an I2 allele dosage effect acting in susceptibility. Comparison of the IFNG allele frequencies in seven European populations (Northern Finnish, Southern Finnish, Swedish, Danish, German, Italian, and Sardinian) revealed a highly different distribution pattern. We introduced latitude as a score variable in order to test for trend in binomial proportions. This test statistic showed that for both most common alleles, I1 and I2 (compiled allele frequency about 85%), a significant opposite north-to-south trend is seen throughout Europe. This effect is primarily due to the extreme values found in the outlier populations of Finland and Sardinia. Our findings are discussed with respect to recent literature pertinent to the role of the IFNG chromosome region in autoimmune diseases.

Diaphyseal medullary stenosis with malignant fibrous histiocytoma: a hereditary bone dysplasia/cancer syndrome maps to 9p21-22

Diaphyseal medullary stenosis with malignant fibrous histiocytoma (DMS-MFH) is an autosomal dominant bone dysplasia/cancer syndrome of unknown etiology. This rare hereditary cancer syndrome is characterized by bone infarctions, cortical growth abnormalities, pathological fractures, and eventual painful debilitation. Notably, 35% of individuals with DMS develop MFH, a highly malignant bone sarcoma. A genome scan for the DMS-MFH gene locus in three unrelated families with DMS-MFH linked the syndrome to a region of approximately 3 cM on chromosome 9p21-22, with a maximal two-point LOD score of 5.49 (marker D9S171 at recombination fraction [theta].05). Interestingly, this region had previously been shown to be the site of chromosomal abnormalities in several other malignancies and contains a number of genes whose protein products are involved in growth regulation. Identification of this rare familial sarcoma-causing gene would be expected to simultaneously define the cause of the more common nonfamilial, or sporadic, form of MFH-a tumor that constitutes approximately 6% of all bone cancers and is the most frequently occurring adult soft-tissue sarcoma.

Interferon-gamma and human megakaryopoiesis

Interferon-gamma (IFN-gamma) exhibits various properties including antigrowth activity in neoplastic and normal cells and regulatory roles in immune responses and hematopoiesis, but studies of IFN-gamma effects on human megakaryopoiesis have been inconclusive. Recently we have used serum-free culture of purified CD34+ cells to demonstrate that IFN-gamma stimulates the proliferation of relatively mature megakaryocytic progenitors independently of thrombopoietin. It has been also shown that IFN-gamma stimulates the maturation of megakaryocytes, and has a significant synergism with stem cell factor in human megakaryopoiesis. Further studies are needed to clarify the in vivo effect of IFN-gamma on human megakaryopoiesis and the clinical relevance of IFN-gamma.

Mutation screening of interferon-gamma (IFNgamma) as a candidate gene for asthma

BACKGROUND

Reduced levels of interferon gamma (IFNgamma) mRNA and protein have been detected in the bronchoalveolar lavage fluid of atopic asthmatics. IFNgamma is secreted by TH1 cells while IL-4 and IL-5 are secreted by TH2 cells and an imbalance in the TH1/TH2 response may be responsible for atopic asthma. The gene for IFNgamma is located on chromosome 12; a region of the genome which has been shown in linkage studies to be associated with asthma.

OBJECTIVE

To determine if there are any mutations present in the coding exons and 5' flanking region of the IFNgamma gene in atopic asthmatic subjects compared with controls to explain the lower levels of this cytokine as an inherited, rather than acquired, factor in the asthmatic subjects.

METHODS

The four exons and 5' flanking region of the IFNgamma gene were amplified by polymerase chain reaction (PCR) from genomic DNA of 265 individuals from a Western Australian and a Venezuelan population. The PCR products were examined by single strand conformational polymorphism and heteroduplex analyses to see if there were any changes in the DNA migration patterns which would suggest the presence of a sequence variation.

RESULTS

The four exons and the 5' flanking region of the IFNgamma gene were amplified from 265 individuals from two populations. Single strand conformational polymorphism and heteroduplex analyses did not reveal any mutations in the regions examined.

CONCLUSION

The gene for IFNgamma appears to be highly conserved as no sequence variations were detected in 265 individuals. These results suggest that mutations of the IFNgamma gene are unlikely to be a significant cause of an inherited asthma diathesis.

Expression of methylthioadenosine phosphorylase cDNA in p16-, MTAP- malignant cells: restoration of methylthioadenosine phosphorylase-dependent salvage pathways and alterations of sensitivity to inhibitors of purine de novo synthesis

5'-Deoxy-5'-methylthioadenosine phosphorylase (MTAP) is involved in the salvage of adenine and methylthio moieties of 5'-deoxy-5'-methylthioadenosine, a byproduct of polyamine synthesis, to adenine nucleotides and methionine, respectively. The gene encoding MTAP, MTAP, is frequently codeleted along with the tumor suppressor gene p16 in malignant cells bearing homozygous deletions in the chromosome 9p21 region. p16-, MTAP- malignant cells have been shown to be more susceptible to the purine de novo inhibitory actions of antifolates such as methotrexate than are p16+, MTAP+ cells. To understand the underlying mechanism, we reintroduced MTAP activity into two p16-, MTAP- cell model systems, the MiaPaCa-2 and PANC-1 human pancreatic carcinoma cell lines, by transfection with MTAP cDNA. It was found that transfection with MTAP cDNA (i) restored both the MTAP-dependent adenine and methionine salvage pathways, (ii) decreased the rates of purine de novo synthesis (18-47% lower than the wild-type or sham-transfected counterparts), and (iii) decreased cellular sensitivity to the antipurine-related growth-inhibitory actions of methotrexate and azaserine. These data support the hypothesis that operation of the MTAP-dependent adenine salvage pathway renders MTAP+ cells less dependent on de novo purine synthesis and hence less susceptible than MTAP- malignant cells to the growth-inhibitory actions of agents (e.g. antifolates) whose mechanism of action in part involves the de novo purine pathway. These findings provide a theoretical basis for the relatively selective action certain antifolates may have against MTAP-deficient malignancies.

Analysis of an interferon-gamma gene (IFNG) polymorphism in Danish and Finnish insulin-dependent diabetes mellitus (IDDM) patients and control subjects. Danish Study Group of Diabetes in Childhood

A CA-repeat polymorphism within the first intron of the interferon (IFN)-gamma gene was analyzed. This polymorphism was recently demonstrated to be associated with insulin-dependent diabetes mellitus (IDDM) in Japanese subjects. We typed 266 IDDM patients and 195 control subjects of Danish Caucasoid origin. No significant differences in allele or genotype frequencies between patients and control were observed. In addition, we typed 168 IDDM and 110 control subjects of Finnish origin. A significant disease association of the studied IFN-gamma allelic pattern was found (p = 0.029). Analysis of data according to HLA-DQB1 susceptibility status did not reveal heterogeneity of risk at the IFN-gamma locus in either of the populations. Fifty-five Danish and 94 Finnish IDDM multiplex families with at least two affected siblings (660 individuals) were typed to test for transmission disequilibrium (TDT). No evidence for overall transmission disequilibrium using either an allele-wise (p = 0.42; combined data) or a genotype-wise analysis (p = 0.21; combined data) could be detected. Thus, the modest significance level observed in the Finnish case-control study and the failure to replicate it by the TDT provide little support for the hypothesis that the IFN-gamma gene microsatellite is associated with IDDM.

Inactivation of the p15INK4B and p16INK4 genes in hematologic malignancies

The recently discovered p15INK4B and p16INK4 genes encoding cell cycle regulating proteins, map to a region on chromosome 9p21 that is commonly deleted in a variety of malignant diseases. The p16INK4 gene has now been shown to be a tumor suppressor gene. It is frequently inactivated in cancer and is possibly the second most often mutated gene in human malignant disease after p53. The role of the p15INK4B and p16INK4 genes in hematologic malignancies has been the subject of intense investigation since their discovery. In this review we address the function and possible role in tumorigenesis of the p15INK4B and p16INK4 genes and discuss their significance as prognostic markers in hematologic malignancies.

Polymorphism in the interferon-alpha gene family

A pronounced genetic polymorphism of the interferon type I gene family has been assumed on the basis of RFLP analysis of the genomic region as well as the large number of sequences published compared to the number of loci. However, IFNA2 is the only locus that has been carefully analyzed concerning gene frequency, and only naturally occurring rare alleles have been found. We have extended the studies on a variation of expressed sequences by studying the IFNA1, IFNA2, IFNA10, IFNA13, IFNA14, and IFNA17 genes. Genomic white-blood-cell DNA from a population sample of blood donors and from a family material were screened by single-nucleotide primer extension (allele-specific primer extension) of PCR fragments. Because of sequence similarities, in some cases "nested" PCR was used, and, when applicable, restriction analysis or control sequencing was performed. All individuals carried the interferon-alpha 1 and interferon-alpha 13 variants but not the LeIF D variant. At the IFNA2 and IFNA14 loci only one sequence variant was found, while in the IFNA10 and IFNA17 groups two alleles were detected in each group. The IFNA10 and IFNA17 alleles segregated in families and showed a close fit to the Hardy-Weinberg equilibrium. There was a significant linkage disequilibrium between IFNA10 and IFNA17 alleles. The fact that the extent of genetic polymorphism was lower than expected suggests that a majority of the previously described gene sequences represent nonpolymorphic rare mutants that may have arisen in tumor cell lines.

Linkage mapping of the retinoic acid receptor-gamma gene to porcine chromosome 5

The porcine retinoic acid receptor-gamma gene (RARG) has been mapped by restriction fragment length polymorphism analysis to porcine chromosome 5. The placement of RARG distal to the diacylglycerol kinase gene increases the length of the existing map (PiGMaP) and adds a fifth type-I marker to this sparsely mapped chromosome. This augments the homology of pig chromosome 5 and human chromosome 12 established by previous comparative mapping.

Analysis of tumor suppressor gene on human chromosome 9 in mouse x human somatic cell hybrids

Deletions of the short arm of human chromosome 9 (9p) are common in human leukemia and solid tumors. The minimum region of overlap of these deletions, located between the interferon genes and the methylthioadenosine phosphorylase gene, is partially syntenic with a region of mouse chromosome 4 that has tumor suppressor activity. Somatic cell hybrids between tumorigenic, MTAP-deficient, mouse L cells, and MTAP-competent human cells containing either a normal copy of 9p or a 9p with a deletion involving band 9p21 were selected in culture conditions that require MTAP activity for continued growth. Somatic cell hybrids that contained a normal copy of 9p rarely formed tumors in nude mice. Cells from the rare tumors that grew had lost the normal 9p. Hybrid cells that contained a 9p with deletions formed tumors more frequently, and cells from these tumors retained the 9p deletion chromosome. These results provide evidence that a tumor suppressor gene (or genes) is located on human chromosome 9 within the region of deletion.

Hematopoietic progenitors and synergism of interferon-gamma and stem cell factor

Interferon-gamma (IFN-gamma), an immunoregulatory cytokine produced by activated T cells and natural killer cells in response to viral infection or other stimuli, is generally recognized as a suppressor of hematopoiesis. IFN-gamma inhibited in vitro colony formation by granulocyte-macrophage (GM), erythroid and multipotential progenitors. This cytokine exerted direct suppression on the proliferation process, but not on the commitment, of GM progenitors. The antiproliferative effects of IFN-gamma may, in part, result from the prolongation of the doubling time of GM progenitors. Clinically, IFN-gamma may play an important role in the pathogenesis of pancytopenia in aplastic anemia and in the hemophagocytic syndrome. However, as well as showing inhibitory effects, IFN-gamma increased the number of pure and mixed megakaryocyte colonies formed by post-5-fluorouracil treated bone marrow cells and, moreover, the addition of IFN-gamma to culture containing stem cell factor resulted in a synergistic effect on the development of both primitive hematopoietic progenitors and mature populations. These findings suggest that IFN-gamma has bifunctional activity in hematopoiesis.

Detection of allelic loss within the beta 1-interferon gene in childhood acute lymphoblastic leukemia using differential PCR

Deletion of the short arm of chromosome 9p involving the beta 1-interferon (IFN) gene has been implicated in the process of malignant transformation in lymphomas and acute lymphoblastic leukemias. Since cytogenetic analysis is frequently unsuccessful in clinical samples, we used a recently described differential PCR technique to detect losses within the beta 1-IFN gene in 86 acute leukemias. Using differential PCR, no beta 1-IFN deletion was detected in 44 acute myeloid leukemia (AML) and eight control samples. However, five of 42 acute lymphoblastic leukemia (ALL) probes (12%) exhibited loss of the beta 1-IFN gene (three common ALL, two T-ALL). Cytogenetic analysis was performed independently in three of these five cases and revealed abnormalities of chromosome 9p in two samples. Two of five T-ALL cases exhibited a loss within the beta 1-IFN gene, compared with 3/29 c-ALLs, suggesting a predominance of IFN gene loss in T-ALLs. These data indicate that PCR can be used for rapid detection of gene dosage phenomena in clinical leukemia samples.

Interferon DNA polymorphism in chronic leukemia

The interferon (IFN) system (alpha, beta and gamma IFNs) is closely related to the first line of defenses against viral and tumoral diseases. Chronic leukemic and chronic lymphoproliferative patients respond in variable degrees to therapy with exogenous IFN. Remission after treatment with IFN-alpha in hairy cell leukemia (HCL) and in chronic myelogenous leukemia (CML) have been reported by other authors. In order to determine whether there are differences in IFN-alpha and beta genes between healthy and chronic leukemic individuals and among the different chronic leukemic patients, restriction fragment length polymorphism (RFLP) analyses was performed in a panel of patients with HCL, CML and chronic lymphocytic leukemia (CLL), and in a sample of healthy individuals. A significant difference in the allelic frequencies for the IFN-beta and Sst I enzyme in Chronic leukemias, mainly of myeloid origin, compared with the healthy individuals, was found.

Recurrent cytogenetic abnormalities in squamous cell carcinomas of the head and neck region

We characterized the breakpoints, gains, and losses of chromosome material in squamous cell carcinomas of the head and neck region from 29 patients. Cell lines were karyotyped in 1/3 of cases, direct preparations or early in vitro harvests in 1/3, and both in 1/3 of cases. GTG-banding was employed in all cases, as were C-banding and RBG- and AgNOR-staining in most. Some tumors were near-diploid and others near-tetraploid, but many had mixed populations, with diploid, tetraploid, and octoploid subclones representing essentially the same karyotypic pattern. The most frequent changes were deletions. Losses affecting 3p13-p24, 5q12-q23, 8p22-p23, 9p21-p24, and 18q22-q23 ranged in frequency from 40% to 60% of tumors. Loss of the short arm of the inactive X occurred in 70% of tumors from female patients, and loss or rearrangement of the Y occurred in 74% of tumors from male patients. Loss of 18q appeared to be associated with short survival, as did the presence of multiple deletions. There was gain (2-5 extra copies) of 3q21-qter, 5p, 7p, 8q, and 11q13-q23 in 28-38% of tumors. Three tumors had an hsr involving 11q13-q21. Gain of material at 11q13 is postulated to be associated with amplification of the PRADI/CCND gene at that locus. A translocation between proximal 1p and either an acrocentric short arm or proximal 8p or 9p was observed in squamous cell carcinomas of the head and neck region but not in female genital tract tumors. No other abnormalities appeared to be site specific, suggesting a pattern of genetic evolution in squamous cell carcinoma that is independent of anatomic site.

Molecular genetics of APUDomas

It is tempting to speculate that genetic studies of the human APUDomas, particularly those of a hereditary nature, may ultimately provide valuable clues to the molecular basis of malignant transformation in cells of all types, uncover the mechanisms responsible for tumor progression, and perhaps decipher the signals important in the differentiation of normal neural crest-derived tissue. Generally, several strategies have been used in the genetic analysis of these tumors with success. These include (1) cytogenetic examination of recurring chromosomal abnormalities in hopes of pinpointing critical neighboring growth regulatory sequences important in tumor evolution, (2) identification of dominant acting oncogenes in tumor cells, (3) search for recessive inactivated suppressor genes that may regulate cell growth by analyzing tumors for loss of heterozygosity (LOH), and (4) genetic linkage studies of kindreds affected with familial APUDomas to identify and subsequently characterize the predisposition gene using a positional or functional cloning approach. The results of these strategies as they have been employed in the investigation of cutaneous malignant melanoma (CMM), the dysplastic nevus syndrome (DNS), and the multiple endocrine neoplasia (MEN) syndromes are summarized.

Interferon treatment of cutaneous T-cell lymphoma

In this report we have reviewed studies on the clinical effect of the interferon (IFN) treatment of 304 patients suffering from cutaneous T-cell lymphoma (CTCL). Intramuscular, subcutaneous or intralesional administration of recombinant IFN has been used as monotherapy or as part of combination therapy. In general, IFN has proved to be a relatively effective agent in the treatment of CTCL, and the best responses have been achieved in the early stages of the disease. In CTCL the overall response rate to IFN including complete, partial and minor responses is 70%. Neither the doses nor the routes of administration in these studies has any statistically significant influence on the clinical response to IFN treatment. Continuous low-dose IFN therapy, presumably in combination with psoralen and UVA light (PUVA), is recommended. This review concludes that the clinical stage of disease before treatment is the only known predictive parameter concerning the clinical response to IFN treatment in patients with CTCL.

Inhibition of growth, transformation, and expression of human papillomavirus type 16 E7 in human keratinocytes by alpha interferons

We used a model system of normal human keratinocytes (HKc) and HKc immortalized with human papillomavirus type 16 DNA (HKc/HPV16) to investigate the effects of alpha interferons (IFN-alpha) on the growth of HPV16-immortalized human epithelial cells, on HPV16-mediated immortalization of normal HKc, and on HPV16 gene expression. Normal HKc and HKc/HPV16 were treated with several recombinant human IFN-alpha subtypes (IFN-alpha B, IFN-alpha D, and IFN-alpha B/D). These IFN-alpha subtypes inhibited proliferation of both normal HKc and HKc/HPV16 in a dose-dependent fashion; however, although 1,000 to 10,000 U of IFN-alpha per ml were required to inhibit growth of normal HKc, HKc/HPV16 were substantially growth inhibited by 100 U/ml. In addition, 100 U of IFN-alpha B/D per ml inhibited transformation of normal HKc by HPV16 DNA. Northern (RNA) blot analysis showed no effect of IFN-alpha on the mRNA levels of the HPV16 E6 and E7 open reading frames. However, immunofluorescence studies of the HPV16 E6 and E7 proteins with anti-E6 and anti-E7 monoclonal antibodies showed significant inhibition of E7 protein expression in cells treated with IFN-alpha, whereas E6 protein expression was not altered. The inhibition of E7 protein expression in cells treated with IFN-alpha was further confirmed by Western immunoblot analysis. These results suggest that IFN-alpha may inhibit HPV16-mediated transformation of HKc and proliferation of HKc/HPV16 through an inhibition of HPV16 E7 protein expression.

Cartilage-hair hypoplasia gene assigned to chromosome 9 by linkage analysis

Cartilage-hair hypoplasia (CHH) is an autosomal recessive skeletal dysplasia of unknown pathogenesis leading to short-limbed stature. Associated features include hypoplasia of hair, abnormal cellular immunity, deficient erythrogenesis, increased risk of malignancies, Hirschsprung disease, and Diamond-Blackfan type hypoplastic anaemia. We mapped the CHH gene by linkage analysis with 5 markers to chromosome 9. Multipoint linkage analysis gives a lod score of 9.94 for a location between D9S43 and D9S50. Based on strong linkage disequilibrium the closest marker, D9S50, is likely to be less than 1 cM from the gene. No heterogeneity was observed in 14 Finnish families, nor was there evidence of reduced penetrance. These results provide a starting point for the eventual cloning and characterization of the CHH gene.

Post-transcriptional regulation of interferon-alpha 4 subtype production by lymphoblastoid cells

The constitutive production of interferon-alpha (IFN-alpha) subtypes by the lymphoblastoid cell lines, Namalwa, Daudi and Raji, was investigated using sensitive and semi-quantitative flow cytometric techniques. Further, we sought to determine whether the previously described failure of these cell lines to produce IFN-alpha-4 was a result of the deletion of the IFN A4 gene. Cytoplasmic production of IFN-alpha-2 and IFN-alpha-4 was assessed using IFN-alpha subtype-specific antipeptide antibodies and FITC-labelled secondary antibodies in indirect immunofluorescence-flow cytometry studies. The constitutive production of IFN-alpha-2 was detected in all three cell lines. Significant increases in fluorescence representing increased production of IFN-alpha-2 and possibly other IFN-alpha subtypes were detected after induction by Sendai virus. Approximately 100 per cent of cells in the Namalwa, Daudi and Raji cell populations contained IFN-alpha-2 before and after induction. However, no cells from the same cell populations contained the IFN-alpha-4 subtype. Analysis of genomic DNA isolated from the lymphoblastoid cells using the Polymerase Chain Reaction (PCR) and oligonucleotide primers specific for IFN A2 or IFN A4 confirmed the presence of the genes encoding both IFN-alpha subtypes. Furthermore, using reverse transcriptase-PCR amplification, mRNAs for both IFN-alpha-2 and IFN-alpha-4 were detected. Therefore, in contrast to some leukaemias and derived cell lines where IFN A genes have been deleted, these cell lines of B cell lineage exhibit selective expression of IFN A genes, as a result of altered transcriptional/translational control of IFN-alpha expression.

Molecular genetics of human malignant melanoma

Due to a variety of known and unknown control mechanisms, the human genome is remarkably stable when compared to most other species. The long latency periods of most solid tumors, during which the cell undergoes malignant transformation, are presumably due to this stability. The molecular basis responsible for the induction of genetic instability and the resultant biological characteristics manifest in tumor populations is not well understood. The discovery of both oncogenes and tumor suppressor genes, however, has placed the phenomenon of human genome stability on a more solid conceptual footing. These types of genes clearly place multiple barriers to oncogenic transformation, and traversing these barriers apparently requires both time and the accumulation of genetic defects that cannot be corrected. The evolution of neoplasias can, therefore, be predicted to be due to: (1) consistent and progressive loss of tumor suppressor genes; (2) gene amplification, resulting in the over-expression of proteins that aid in tumor progression; (3) gene mutation, which alters the orderly biochemistry of the normal cell; (4) genes that allow a cell like the melanocyte to escape the confining nature of the epidermis and to invade through the dermis into the circulatory and lymphatic systems in order to disseminate itself to other organs (e.g., proteolytic enzymes, enzyme inhibitors, integrins, metastases genes, chemotactic factors etc.); (5) factors, perhaps such as TGF beta 2, that may impact negatively on MHC antigens and confuse host defense mechanisms; and (6) S.O.S.-type genes, which may be expressed as a direct response to the accumulating damage in an attempt to correct the damage, but that may then become part of the problem instead of the solution. The extraordinary plasticity and instability of the genome of a melanoma cell suggests an inordinate amount of genetic flux. In addition to activating and inactivating various genes, this constant shuffling and rearranging of the genome in neoplasms such as MM may be constantly altering gene dose. Cytogenetic and molecular biological studies have been the Rosetta stone for understanding the etiological relevant genetic events in human cancers. Genetic alterations fundamental to the pathology of MM have begun to be defined. Studies designed to understand these perturbations at the biochemical and organismic level are underway.(ABSTRACT TRUNCATED AT 400 WORDS)