Gamma interferon and 5-azacytidine cause transcriptional elevation of class I major histocompatibility complex gene expression in K562 leukemia cells in the absence of differentiation

Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance

Only a subset of cancer patients respond to T-cell checkpoint inhibitors, highlighting the need for alternative immunotherapeutics. We performed CRISPR-Cas9 screens in a leukemia cell line to identify perturbations that enhance natural killer effector functions. Our screens defined critical components of the tumor-immune synapse and highlighted the importance of cancer cell interferon-γ signaling in modulating NK activity. Surprisingly, disrupting the ubiquitin ligase substrate adaptor DCAF15 strongly sensitized cancer cells to NK-mediated clearance. DCAF15 disruption induced an inflamed state in leukemic cells, including increased expression of lymphocyte costimulatory molecules. Proteomic and biochemical analysis revealed that cohesin complex members were endogenous client substrates of DCAF15. Genetic disruption of DCAF15 was phenocopied by treatment with indisulam, an anticancer drug that functions through DCAF15 engagement. In AML patients, reduced DCAF15 expression was associated with improved survival. These findings suggest that DCAF15 inhibition may have useful immunomodulatory properties in the treatment of myeloid neoplasms.

The human immune system can recognize and kill cancer cells growing in the body. Certain immune cells recognize mutated proteins on the surface of cancer cells known as antigens, and this ability can be enhanced by drugs. These so-called immunotherapies can be effective to treat several cancer types, but only some patients benefit from them. This is because cancer cells often stop presenting antigens on their surface, thus hiding from the immune response.

Natural killer cells are a type of immune cell that does not rely on antigen presentation to recognize cancer cells. Scientists are now trying to develop drugs to increase the effectiveness with which natural killer cells attack cancer.

Pech et al. used cells from a human leukemia, a type of blood cancer, to look for proteins that made these cells more vulnerable to natural killer cells. The main experiment, in which every single protein in the cancer cells was deleted one by one, revealed that a protein called DCAF15 changes how cancer and natural killer cells interact. Leukemia cells lacking DCAF15 could be attacked by natural killer cells much more easily because the cancer cells exhibited inflammation-like symptoms that stimulated the immune response. DCAF15 is part of a family of ‘adaptors’ that that provide specificity to the cellular machinery that controls proliferation, the recycling of proteins and DNA repair.

Inhibiting DCAF15 with a drug also made natural killer cells more efficient at eliminating leukemia cells. Patients with leukemia whose cancer cells make little DCAF15 protein have a better chance of survival, suggesting that this process may already be happening in some patients.

Together these data indicate that targeting DCAF15 in leukemia patients may help natural killer cells attack cancer cells. Future research is needed to see if a similar process takes place in other cancer types.

Large-scale ex vivo expansion and characterization of natural killer cells for clinical applications

BACKGROUND AIMS

Interest in natural killer (NK) cell-based immunotherapy has resurged since new protocols for the purification and expansion of large numbers of clinical-grade cells have become available.

METHODS

We have successfully adapted a previously described NK expansion method that uses K562 cells expressing interleukin (IL)-15 and 4-1 BB Ligand (BBL) (K562-mb15-41BBL) to grow NK cells in novel gas-permeable static cell culture flasks (G-Rex).

RESULTS

Using this system we produced up to 19 × 10(9) functional NK cells from unseparated apheresis products, starting with 15 × 10(7) CD3(-) CD56 (+) NK cells, within 8-10 days of culture. The G-Rex yielded a higher fold expansion of NK cells than conventional gas-permeable bags and required no cell manipulation or feeding during the culture period. We also showed that K562-mb15-41BBL cells up-regulated surface HLA class I antigen expression upon stimulation with the supernatants from NK cultures and stimulated alloreactive CD8 (+) T cells within the NK cultures. However, these CD3 (+) T cells could be removed successfully using the CliniMACS system. We describe our optimized NK cell cryopreservation method and show that the NK cells are viable and functional even after 12 months of cryopreservation.

CONCLUSIONS

We have successfully developed a static culture protocol for large-scale expansion of NK cells in the gas permeable G-Rex system under good manufacturing practice (GMP) conditions. This strategy is currently being used to produce NK cells for cancer immunotherapy.

Impaired cell surface expression of HLA-B antigens on mesenchymal stem cells and muscle cell progenitors

HLA class-I expression is weak in embryonic stem cells but increases rapidly during lineage progression. It is unknown whether all three classical HLA class-I antigens follow the same developmental program. In the present study, we investigated allele-specific expression of HLA-A, -B, and -C at the mRNA and protein levels on human mesenchymal stem cells from bone marrow and adipose tissue as well as striated muscle satellite cells and lymphocytes. Using multicolour flow cytometry, we found high cell surface expression of HLA-A on all stem cells and PBMC examined. Surprisingly, HLA-B was either undetectable or very weakly expressed on all stem cells protecting them from complement-dependent cytotoxicity (CDC) using relevant human anti-B and anti-Cw sera. IFNgamma stimulation for 48-72 h was required to induce full HLA-B protein expression. Quantitative real-time RT-PCR showed that IFNgamma induced a 9-42 fold increase of all six HLA-A,-B,-C gene transcripts. Interestingly, prior to stimulation, gene transcripts for all but two alleles were present in similar amounts suggesting that post-transcriptional mechanisms regulate the constitutive expression of HLA-A,-B, and -C. Locus-restricted expression of HLA-A, -B and -C challenges our current understanding of the function of these molecules as regulators of CD8(+) T-cell and NK-cell function and should lead to further inquiries into their expression on other cell types.

A GATA factor mediates cell type-restricted induction of HLA-E gene transcription by gamma interferon

The human major histocompatibility complex (MHC) class Ib gene, HLA-E, codes for the major ligand of the inhibitory receptor NK-G-2A, which is present on most natural killer (NK) cells and some CD8(+) cytotoxic T lymphocytes. We have previously shown that gamma interferon (IFN-gamma) induction of HLA-E gene transcription is mediated through a distinct IFN-gamma-responsive element, the IFN response region (IRR), in all cell types studied. We have now identified and characterized a cell type-restricted enhancer of IFN-gamma-mediated induction of HLA-E gene transcription, designated the upstream interferon response region (UIRR), which is located immediately upstream of the IRR. The UIRR mediates a three- to eightfold enhancement of IFN-gamma induction of HLA-E transcription in some cell lines but not in others, and it functions only in the presence of an adjacent IRR. The UIRR contains a variant GATA binding site (AGATAC) that is critical to both IFN-gamma responsiveness and to the formation of a specific binding complex containing GATA-1 in K562 cell nuclear extracts. The binding of GATA-1 to this site in response to IFN-gamma was confirmed in vivo in a chromatin immunoprecipitation assay. Forced expression of GATA-1 in nonexpressing U937 cells resulted in a four- to fivefold enhancement of the IFN-gamma response from HLA-E promoter constructs containing a wild-type but not a GATA-1 mutant UIRR sequence and increased the IFN-gamma response of the endogenous HLA-E gene. Knockdown of GATA-1 expression in K562 cells resulted in a approximately 4-fold decrease in the IFN-gamma response of the endogenous HLA-E gene, consistent with loss of the increase in IFN-gamma response of HLA-E promoter-driven constructs containing the UIRR in wild-type K562 cells. Coexpression of wild-type and mutant adenovirus E1a proteins that sequester p300/CBP eliminated IFN-gamma-mediated enhancement through the UIRR, but only partially reduced induction through the IRR, implicating p300/CBP binding to Stat-1alpha at the IRR in the recruitment of GATA-1 to mediate the cooperation between the UIRR and IRR. We propose that the GATA-1 transcription factor represents a cell type-restricted mediator of IFN-gamma induction of the HLA-E gene.

Potential role of NF-kB and RXR beta like proteins in interferon induced HLA class I and beta globin gene transcription in K562 erythroleukaemia cells

Positive effects of biological response modifiers on cancer cells are usually measured using markers for increased immunogenicity as well as those for increased differentiation of the cells. An increase in levels of HLA class I antigens and the adult (beta) globin molecules are two such markers that may be used to assess the effect of modulators like interferons on the K562 erythroleukaemia cell line. Although interferon mediated up regulation of gene expression is thought to be primarily regulated by binding of proteins to the Interferon responsive cis elements in the promoters of IFN responsive genes, recent evidence has shown the induction of other transcriptional activators in response to IFN treatment. We present evidence for one such instance wherein up regulation of HLA class I and beta globin gene transcription are accompanied by induction of binding activities similar to RXR beta and kB proteins in K562 cells.

Intronic and flanking sequences are required to silence enhancement of an embryonic beta-type globin gene

In the course of studying regulatory elements that affect avian embryonic rho-globin gene expression, the multipotential hematopoietic cell line K562 was transiently transfected with various rho-globin gene constructs containing or lacking an avian erythroid enhancer element. Enhanced levels of rho gene expression were seen from those constructs containing an enhancer element and minimal 5' or 3' flanking rho sequences but were not seen from enhancer-containing constructs that included extensive 5' and 3' flanking sequences. Deletion analysis localized 5' and 3' "enhancer-silencing elements" to -2140 to -2000 and +1865 to +2180 relative to the mRNA cap site. A third element required for enhancer silencing was identified within the second intron of the rho gene. The treatment of K562 cells with hemin, which induces erythroid differentiation, partially alleviated the enhancer-silencing effect. The silencer elements were able to block enhancement from a murine erythroid enhancer, but not from a nonerythroid enhancer. Electrophoretic mobility shift assays demonstrated that the transcription factor YY1 is able to bind both the 5' and 3' enhancer silencer elements; a point mutation of the single overlapping YY1/NF-Y binding site in the 3' element completely abolished the enhancer-silencing effect. These results demonstrate a complex enhancer silencer that requires 5' flanking, intronic, and 3' flanking sequences for a single regulatory effect on a eukaryotic gene.

5'-flanking sequences mediate butyrate stimulation of embryonic globin gene expression in adult erythroid cells

A stable transfection assay was used to test the mechanism by which embryonic globin gene transcription is stimulated in adult erythroid cells exposed to butyric acid and its analogs. To test the appropriate expression and inducibility of chicken globin genes in murine erythroleukemia (MEL) cells, an adult chicken beta-globin gene construct was stably transfected. The chicken beta-globin gene was found to be coregulated with the endogenous adult mouse alpha-globin gene following induction of erythroid differentiation of the transfected MEL cells by incubation with either 2% dimethyl sulfoxide (DMSO) or 1 mM sodium butyrate (NaB). In contrast, a stably transfected embryonic chicken beta-type globin gene, rho, was downregulated during DMSO-induced MEL cell differentiation. However, incubation with NaB, which induces MEL cell differentiation, or alpha-amino butyrate, which does not induce differentiation of MEL cells, resulted in markedly increased levels of transcription from the stably transfected rho gene. Analysis of histone modification showed that induction of rho gene expression was not correlated with increased bulk histone acetylation. A region of 5'-flanking sequence extending from -569 to -725 bp upstream of the rho gene cap site was found to be required for both downregulation of rho gene expression during DMSO-induced differentiation and upregulation by treatment with NaB or alpha-amino butyrate. These data are support for a novel mechanism by which butyrate compounds can alter cellular gene expression through specific DNA sequences. The results reported here are also evidence that 5'-flanking sequences are involved in the suppression of embryonic globin gene expression in terminally differentiated adult erythroid cells.

5'-flanking sequences mediate butyrate stimulation of embryonic globin gene expression in adult erythroid cells

A stable transfection assay was used to test the mechanism by which embryonic globin gene transcription is stimulated in adult erythroid cells exposed to butyric acid and its analogs. To test the appropriate expression and inducibility of chicken globin genes in murine erythroleukemia (MEL) cells, an adult chicken beta-globin gene construct was stably transfected. The chicken beta-globin gene was found to be coregulated with the endogenous adult mouse alpha-globin gene following induction of erythroid differentiation of the transfected MEL cells by incubation with either 2% dimethyl sulfoxide (DMSO) or 1 mM sodium butyrate (NaB). In contrast, a stably transfected embryonic chicken beta-type globin gene, rho, was downregulated during DMSO-induced MEL cell differentiation. However, incubation with NaB, which induces MEL cell differentiation, or alpha-amino butyrate, which does not induce differentiation of MEL cells, resulted in markedly increased levels of transcription from the stably transfected rho gene. Analysis of histone modification showed that induction of rho gene expression was not correlated with increased bulk histone acetylation. A region of 5'-flanking sequence extending from -569 to -725 bp upstream of the rho gene cap site was found to be required for both downregulation of rho gene expression during DMSO-induced differentiation and upregulation by treatment with NaB or alpha-amino butyrate. These data are support for a novel mechanism by which butyrate compounds can alter cellular gene expression through specific DNA sequences. The results reported here are also evidence that 5'-flanking sequences are involved in the suppression of embryonic globin gene expression in terminally differentiated adult erythroid cells.

Down regulation of poliovirus receptor RNA in HeLa cells resistant to poliovirus infection

A line of HeLa cells (SOFIA) was previously isolated that is resistant to poliovirus infection and does not express functional virus binding sites at the cell surface. The expression of the poliovirus receptor (PVR) gene in SOFIA cells was examined to determine the molecular basis for the failure of these cells to express PVRs. Southern blot analysis of genomic DNA revealed that the PVR gene in SOFIA cells did not contain gross alterations. However, PVR transcripts were not detected in Northern (RNA) blot analysis of SOFIA cell RNA. In vitro nuclear run-on analysis showed that transcription of PVR-specific RNA was reduced in SOFIA cells. Treatment of SOFIA cells with 5-azacytidine restored susceptibility to poliovirus infection, which correlated with the appearance of PVRs at the cell surface, as detected with anti-PVR monoclonal antibody D171. PVR RNA was detected in clones derived from 5-azacytidine-treated SOFIA cells. SOFIA cells were converted to poliovirus sensitivity at a rate of 5 to 7%, suggesting that down regulation of PVR expression involved few cellular targets. Resistance of SOFIA cells to poliovirus infection therefore appears to result from down regulation of PVR RNA, leading to lack of PVR expression at the cell surface. Methylation may play a role in regulating the expression of the PVR gene, which is not essential for survival of HeLa cells.

Developmental characterization and chromosomal mapping of the 5-azacytidine-sensitive fluF locus of Aspergillus nidulans

In Aspergillus nidulans, a fungus that possesses negligible, if any, levels of methylation in its genome, low concentrations of 5-azacytidine (5-AC) convert a high percentage of the cell population to fluffy phenotypic variants through a heritable modification of a single nuclear gene (M. Tamame, F. Antequera, J. R. Villanueva, and T. Santos, Mol. Cell. Biol. 3:2287-2297, 1983). This new 5-AC-altered locus, designated here fluF1, was mapped as the closest marker to the centromere that has been identified so far on the right arm of chromosome VIII. Of all mutagens tested, only 5-AC induced the fluffy phenotype with a significant frequency. Furthermore, we determined that the wild-type, dominant allele of the fluF gene was primarily accessible to modification by 5-AC at the initial stages of fungal vegetative growth. These results indicated that 5-AC does not act through random mutagenic action but, rather, that fluF constitutes a specific target for this drug during a well-defined period of fungal development. Alteration of fluF by 5-AC resulted in a dramatic modification of the developmental program of A. nidulans. The resulting fluffy clones were characterized by massive, uncontrolled proliferation of undifferentiated hyphae, a drastic delay in the onset of asexual differentiation (conidiation), and colonies with an invasive nature. These features are reminiscent of the malignant properties of tumor cells. We propose that the locus fluF plays a primary role in the control of cell proliferation in A. nidulans and that its alteration by 5-AC produces pleiotropic modifications of the developmental program of this fungus.

Developmental characterization and chromosomal mapping of the 5-azacytidine-sensitive fluF locus of Aspergillus nidulans

In Aspergillus nidulans, a fungus that possesses negligible, if any, levels of methylation in its genome, low concentrations of 5-azacytidine (5-AC) convert a high percentage of the cell population to fluffy phenotypic variants through a heritable modification of a single nuclear gene (M. Tamame, F. Antequera, J. R. Villanueva, and T. Santos, Mol. Cell. Biol. 3:2287-2297, 1983). This new 5-AC-altered locus, designated here fluF1, was mapped as the closest marker to the centromere that has been identified so far on the right arm of chromosome VIII. Of all mutagens tested, only 5-AC induced the fluffy phenotype with a significant frequency. Furthermore, we determined that the wild-type, dominant allele of the fluF gene was primarily accessible to modification by 5-AC at the initial stages of fungal vegetative growth. These results indicated that 5-AC does not act through random mutagenic action but, rather, that fluF constitutes a specific target for this drug during a well-defined period of fungal development. Alteration of fluF by 5-AC resulted in a dramatic modification of the developmental program of A. nidulans. The resulting fluffy clones were characterized by massive, uncontrolled proliferation of undifferentiated hyphae, a drastic delay in the onset of asexual differentiation (conidiation), and colonies with an invasive nature. These features are reminiscent of the malignant properties of tumor cells. We propose that the locus fluF plays a primary role in the control of cell proliferation in A. nidulans and that its alteration by 5-AC produces pleiotropic modifications of the developmental program of this fungus.

Induction of phagocyte cytochrome b heavy chain gene expression by interferon gamma

Phagocytic cells, such as macrophages and polymorphonuclear leukocytes, produce a "respiratory burst" in which oxygen is reduced to superoxide and other active oxygen species responsible for many of the microbicidal, tumoricidal, and inflammatory activities of these cells. Interferon gamma has been shown to augment phagocyte superoxide production, but the molecular mechanisms underlying this effect have remained unknown. Recently a key component of the oxidase, phagocyte cytochrome b, has been characterized as a heterodimer of a 91-kDa glycoprotein and a 22-kDa polypeptide. The present studies examined the effects of human recombinant interferon gamma on the expression of the genes for these components of the cytochrome b. In vitro treatment with interferon gamma substantially increases the level of phagocyte cytochrome b heavy chain gene transcripts in normal polymorphonuclear leukocytes, normal monocyte-derived macrophages, and the monocytic leukemia cell line THP-1. Light chain gene transcripts are less affected. In monocyte-derived macrophages and THP-1 cells, the enhanced expression of the heavy chain gene appears in large part attributable to increased rates of transcription. Treatment of monocyte-derived macrophages with human recombinant interferon alpha (a down-regulator of the respiratory burst) decreased the heavy chain transcript levels; interferon beta produced no detectable change. These findings demonstrate the responsiveness of one essential component of the phagocyte oxidase system to activation by interferon gamma and provide a rationale for its use to augment phagocytic function in chronic granulomatous disease.

Clonal analysis of the malignant properties of B16 melanoma cells treated with the DNA hypomethylating agent 5-azacytidine

The role of DNA methylation in the generation of tumor cell variants with altered growth behavior has been investigated. Cultures of the clonally heterogeneous B16 melanoma cell line and a clonal population (B16-CL) derived from it were treated with the DNA hypomethylating agent, 5-azacytidine (5-Aza-CR). The tumorigenic and metastatic properties of (sub)clones isolated from these cultures before and after drug treatment were assayed by injection via multiple routes into syngeneic C57BL/6 mice using a range of cell doses. The rate of tumor growth was monitored following intrafootpad (i.f.p.) injection and the tumor incidence was calculated from the frequency of tumor formation at i.f.p. and supraclavicular subcutaneous (s.c.) sites. Formation of both spontaneous (i.f.p., s.c. inoculations) and experimental (intravenous (i.v.) inoculation) metastatic potential was also investigated. The most consistent effect of 5-Aza-CR was the introduction of heterogeneity with respect to the tumorigenic phenotype. The effect of 5-Aza-CR treatment on metastatic behavior was variable. The majority of tumor cell variants that arose following 5-Aza-CR treatment displayed decreased malignant potential and reduced DNA methylation levels relative to untreated control cells, but the correlation was not absolute. The decreases in DNA methylation levels induced by 5-Aza-CR were unstable and began to rebound within 1 week of drug treatment. The results of the current study indicate that although 5-Aza-CR can introduce significant shifts in the malignant properties of treated cells, the direction and magnitude of the induced alterations are not predictable and are influenced by a variety of experimental parameters including the starting tumor cell population, route of tumor cell inoculation, and the drug treatment protocol. In addition, because DNA methylation levels can rebound rapidly (days) it is difficult to correlate changes in this parameter with the observed alterations in malignancy, which can only be assessed in long-term biological assays (weeks).

Negative and positive regulation of human leukocyte antigen class I gene transcription in K562 leukemia cells

The mechanism of transcriptional activation of human leukocyte antigen class I genes by gamma interferon and 5-azacytidine was studied in K562 human leukemia cells. Nuclear run-on transcription assays with various protein and RNA synthesis inhibitors yield evidence for both stimulation of a positive regulatory factor and inhibition of an mRNA that codes for a labile repressor. A novel mechanism is proposed to explain how 5-azacytidine can activate repressed genes without affecting DNA methylation.

Negative and positive regulation of human leukocyte antigen class I gene transcription in K562 leukemia cells

The mechanism of transcriptional activation of human leukocyte antigen class I genes by gamma interferon and 5-azacytidine was studied in K562 human leukemia cells. Nuclear run-on transcription assays with various protein and RNA synthesis inhibitors yield evidence for both stimulation of a positive regulatory factor and inhibition of an mRNA that codes for a labile repressor. A novel mechanism is proposed to explain how 5-azacytidine can activate repressed genes without affecting DNA methylation.