Interacting Genetic Lesions of Melanoma in the Tumor Microenvironment: Defining a Viable Therapy.

Melanoma is the most aggressive form of skin cancer with an estimated 106,110 newly diagnosed cases in the United States of America in 2021 leading to an approximated 7180 melanoma-induced deaths. Cancer typically arises from an accumulation of somatic mutations and can be associated with mutagenic or carcinogenic exposure. A key characteristic of melanoma is the extensive somatic mutation rate of 16.8 mutations/Mb, which is largely attributed to UV exposure. Bearing the highest mutational load, many of them occur in key driver pathways, most commonly the BRAFV600E in the mitogen-activated protein kinase (MAPK) pathway. This driver mutation is targeted clinically with FDA-approved therapies using small molecule inhibitors of oncogenic BRAFV600E and MEK, which has greatly expanded therapeutic intervention following a melanoma diagnosis. Up until 2011, therapeutic options for metastatic melanoma were limited, and treatment typically fell under the spectrum of surgery, radiotherapy, and chemotherapy.Attributed to the extensive mutation rate, as well as having the highest number of neoepitopes, melanoma is deemed to be extremely immunogenic. However, despite this highly immunogenic nature, melanoma is notorious for inducing an immunosuppressive microenvironment which can be relieved by checkpoint inhibitor therapy. The two molecules currently approved clinically are ipilimumab and nivolumab, which target the molecules CTLA-4 and PD-1, respectively.A plethora of immunomodulatory molecules exist, many with redundant functions. Additionally, these molecules are expressed not only by immune cells but also by tumor cells within the tumor microenvironment. Tumor profiling of these cell surface checkpoint molecules is necessary to optimize a clinical response. The presence of immunomodulatory molecules in melanoma, using data from The Cancer Genome Atlas and validation of expression in two model systems, human melanoma tissues and patient-derived melanoma cells, revealed that the expression levels of B and T lymphocyte attenuator (BTLA), TIM1, and CD226, concurrently with the BRAFV600E mutation status, significantly dictated overall survival in melanoma patients. These molecules, along with herpesvirus entry mediator (HVEM) and CD160, two molecules that are a part of the HVEM/BTLA/CD160 axis, had a higher expression in human melanoma tissues when compared to normal skin melanocytes and have unique roles to play in T cell activation. New links are being uncovered between the expression of immunomodulatory molecules and the BRAFV600E genetic lesion in melanoma. Small molecule inhibitors of the MAPK pathway regulate the surface expression of this multifaceted molecule, making BTLA a promising target for immuno-oncology to be targeted in combination with small molecule inhibitors, potentially alleviating T regulatory cell activation and improving patient prognosis.

Identification of a recombinogenic major histocompatibility complex Q gene with diverse alleles.

Structural diversity enables class Ia molecules to present a diverse repertoire of peptides to the T cell receptor. This diversity is thought to be generated by recombinations between class I genes. We have found that two class Ib Q2 alleles exhibit extremely high sequence diversity, even higher than class Ia alleles. Clustered nucleotide differences between Q2b and Q2k suggest that this sequence diversity was generated by microrecombinations between Q2 genes and other class I genes. The relatively high expression of Q2b in the thymus may be significant and perhaps suggests a novel role for a Q2b product in the education and selection of the T cell repertoire.

Three spontaneous H-2Db mutants are generated by genetic micro-recombination (gene conversion) events. Impact on the H-2-restricted immune responsiveness.

Sequence analysis of the mutant Dbm13, Dbm14, and Dbm24 genes indicate that they differ from the parental Db gene by 4, 1, and 8 nucleotides, respectively. The mutant sequences substituted into Dbm13 and Dbm24 are identical to those found in the Kb gene, at the homologous positions. Thus, similar to the Kb gene, the Db gene is able to undergo micro-recombination (gene conversion) events with other class I genes. Such data suggest that micro-recombination events could be an important mechanism for the diversification of all H-2 genes. The Db mutant products share a common theme: the alterations in all occur at amino acid residues whose side chains in the homologous class I HLA-A2 molecule project into the postulated peptide antigen-binding cleft, and hence, would be expected to alter the binding of foreign or self peptides. Due to such changes, the bm14 mouse has become a nonresponder in the CTL response to Moloney murine leukemia virus (M-MuLV), as the alteration of one amino acid residue at position 70 (a Gln to His) is sufficient to entirely abrogate the cell-mediated response to the virus. On the other hand, the bm13 mouse has shifted the major part of its M-MuLV restriction to Kb, a profound alteration in CTL responsiveness due to the alteration of three amino acids (Leu to Gln at 114, Phe to Tyr at 116, and Glu to Asp at 119) in a peptide stretch of beta-pleated sheet structure lining the bottom of the antigen-binding cleft. Thus, study of these mutants reveals that, in one step, micro-recombination at the genetic level has resulted at the protein level in profound changes in the immune response to viral infection. Such a mechanism operating at the population level can be a driving force during evolution for modulating the character of CTL immunity.

Microrecombinations generate sequence diversity in the murine major histocompatibility complex: analysis of the Kbm3, Kbm4, Kbm10, and Kbm11 mutants.

The mechanism that generates spontaneous mutants of the Kb histocompatibility gene was analyzed. Nucleotide sequence analysis of four mutant genes (Kbm3, Kbm4, Kbm10, and Kbm11) revealed that each mutant K gene contains clustered, multiple nucleotide substitutions. Hybridization analyses of parental B6 genomic DNA and cloned class I genes with mutant-specific oligonucleotide probes, followed by sequence analyses, have identified major histocompatibility complex class I genes in the K, D, and Tla regions (K1, Db, and T5, respectively) that contain the exact sequences as substituted into mutant Kb genes. These data provide evidence for the hypothesis that the mutant Kb genes are generated by a microrecombination (gene conversion) mechanism that results in the transfer of small DNA segments from class I genes of all four regions of the major histocompatibility complex (K, D, Qa, and Tla) to Kb. Many of the nucleotides substituted into the mutant Kb genes were identical to those found in other naturally occurring K alleles such as Kd. Thus, we propose that the accumulation of microrecombination products within the K genes of a mouse population is responsible for the high sequence diversity among H-2 alleles.

Interaction between Kb and Q4 gene sequences generates the Kbm6 mutation.

Genetic interaction as a mechanism for the generation of mutations is suggested by recurrent, multiple nucleotide substitutions that are identical to nucleotide sequences elsewhere in the genome. We have sequenced the mutant K gene from the bm6 mouse, which is one of a series of eight closely related, yet independently occurring mutants known collectively as the "bg series." Two changes from the Kb gene are found, positioned 15 nucleotides apart: an A-to-T change and a T-to-C change in the codons corresponding to amino acids 116 and 121, resulting in Tyr-to-Phe and Cys-to-Arg substitutions, respectively. Hybridization analysis with an oligonucleotide specific for the altered Kbm6 sequence identifies one donor gene, Q4, located in the Qa region of the H-2 complex. The two altered nucleotides that differentiate Kbm6 and Kb are present in Q4 in a region where Kb and Q4 are otherwise identical for 95 nucleotides, delineating the maximum genetic transfer between the two genes. Because the Kbm6 mutation arose in an homozygous mouse these data indicate that the Q4 gene contains the only donor sequence and demonstrates that Q-region gene sequences can interact with the Kb gene to generate variant K molecules.

Introduction of a disulfide bond in the alpha 1 domain of the H-2Kb molecule confers immunogenicity to the transfected RMA-S tumors.

The use of major histocompatibility complex class I genes is an emerging approach for the immunotherapy of human cancer. The conformational stability of class I molecules is important for their immunologic recognition. We have engineered a disulfide bond in the alpha 1 domain of a murine class I molecule, Kb. The expression of the engineered, but not the wild-type, Kb molecules conferred immunogenicity to a nonimmunogenic and antigen presentation-defective tumor cell line, RMA-S. Mice that rejected the engineered Kb-transfected RMA-S cells developed a long-lived antitumor immune response. These data indicate the possibility of genetically engineering class I molecules to improve their therapeutic potential.

The H-2Kkml mutation: nucleotide sequence and comparative analysis.

Nucleotide sequence analysis of mRNA from the class I murine MHC mutant H-2Kkml has established a site of mutation to be at the codon for amino acid position 152. Complete sequence information for the nucleotides coding for amino acids 136-163 demonstrates an A----C alteration at the codon for amino acid 152, changing Asp (GAT) in Kk to Ala (GCT) in Kkml. Several other murine and human class I MHC variants have similar alterations at amino acid position 152, resulting in altered biological activity. Finally, the pH-2III pseudogene of the H-2k haplotype has a GCT codon at amino acid position 152, suggesting that the GCT codon occurring in Kkml is the result of a gene conversion event.

The H-2Kkml mutation: a single nucleotide substitution is responsible for multiple functional differences in a class I MHC molecule.

Nucleotide sequence analysis of mRNA from the H-2K locus of the CBA.M523 mouse, which has the class I murine MHC mutation H-2Kkml, has established the only alteration to be at the codon for amino acid position 152 as compared to the sequence of standard Kk from both the AKR and CBA inbred mouse lines. Complete sequence information for the nucleotides coding for amino acids 1-292, which includes all of the extracellular protein domains, demonstrated an A----C alteration in the codon for amino acid 152 as compared to the standard Kk sequence, changing Asp (GAT) in Kkml. The GCT codon occurring in Kkml may be the result of a gene conversion in Kkml. The GCT codon occurring in Kkml may be the result of a gene conversion event because a potential donor gene, the pH-2III pseudogene of H-2k, is transcribed in the CBA.M523 mouse and has a GCT codon at amino acid position 152. This sequence information obtained for Kkml also demonstrates that Kk gene transcripts from two genetically distinct inbred mouse lines, CBA and AKR, are completely identical. Finally, several other murine and human class I MHC variants have similar alterations at amino acid position 152 which result in altered biological functions. This information suggests that amino acid 152 is an important part of a T-cell-recognized antigenic determinant on MHC class I antigens.

A single amino acid substitution in the H-2Kb molecule generates a defined allogeneic epitope.

Using Mitomycin C mutagenesis and negative and positive selection with monoclonal antibodies specific for H-2Kb and H-2Kbm10, respectively, a mutant cell line clone, Mitc-182, was isolated. Direct sequencing of uncloned cDNA as well as PCR based cloning and sequencing of the H-2Kb182 transcript from this mutant revealed a single G-->T transversion resulting in the substitution of Trp167 by cysteine. Serologically, the mutant Kb182 and Kbm10 are almost identical as each has lost at least five Kb specific mAb epitopes and gained several new epitopes. Interestingly, the mutant cell line, Mitc-182, is efficiently recognized by alloreactive CTLs raised in reciprocal combinations, e.g. CB6 anti Cbm10 and Cbm10 anti CB6, indicating that Kb182 contains both Kb and Kbm10 specific epitopes. The mutation has not affected the ability of Kb182 to present Kb restricted antigenic peptides of Sendai and vesicular stomatitis viruses. In addition to underscoring the importance of amino acid residue 167 in alloreactivity, these results indicate a positive correlation between the gain of both an mAb epitope and a defined alloreactive CTL epitope.

Analysis of the H-2Kbm8 mutant: correlation of structure with function.

The gene for H-2K class I major histocompatibility antigen on the bm8 variant was cloned and the DNA sequence compared with the parental gene. Sequence analysis demonstrated that seven nucleotides were changed with respect to the parental gene sequence spanning 24 nucleotides. These changes represent an alteration of four amino acids from the parent protein. As this mutation occurred in a single generation, a potential donor gene for such a complex mutation was suggested and identified. The Q4 gene class I-like molecule has a stretch of 95 nucleotides of identity in the region of the bm8 mutation. Genomic Southern analysis of the mutant and parental DNA with a gene-specific oligonucleotide demonstrated that the potential donor gene Q4 is a likely candidate sequence for such an event. The amino acid alterations for the H-2Kbm8 mutation are discussed in consideration of hte three-dimensional structure of the characterized human class I glycoprotein.

Rejuvenated expression of H-2Kb in RMA-S cells does not affect alloreactive T cell- and natural killer cell-mediated lysis.

Reduced sensitivity to alloreactive cytotoxic lymphocytes (CTLs) and increased susceptibility to natural killer (NK) cells in vivo and in vitro are two phenotypic characteristics that have been attributed to the reduced major histocompatibility complex (MHC) ligand density on the surface of an antigen-presentation-defective cell line, RMA-S. As RMA-S exhibits both defective processing of antigenic peptides and very low class I expression, it is uncertain which is responsible for the above characteristics. In this report, we show that the phenotype cannot be reversed by increasing the number of Kb + beta 2-M complexes expressed on the cell surface. These findings emphasize the importance of association of MHC class I molecules with endogenously processed peptides for biological interaction with alloreactive CTLs and NK cells.

Anti-tumor effects of PC-SPES, an herbal formulation in prostate cancer.

Prostate cancer is the most common cancer amongst males in developed countries. Surgical removal of the prostate effectively cures the primary disease but the metastatic disease is refractory to most forms of chemotherapy. There is a clinical need to develop novel treatment strategies that exploit the mode of action of both conventional and alternative drugs/medicinal plants. We have been investigating the anti-proliferative and anti-tumor effects of an herbal preparation termed PC-SPES (patent pending, US serial number 08/697, 920) which is a refined powder of eight different medicinal plants. PC-SPES administered as a food supplement caused a dramatic decrease in prostate specific antigen levels in some prostate cancer patients with advanced disease. These preliminary clinical findings laid the foundation for a program to examine the in vitro and in vivo effects of PC-SPES, and identify the active component in this mixture so that a standardized treatment regimen can be formulated. In this communication, we report the anti-tumor effects of PC-SPES incorporated in the diet utilizing a well studied Dunning R3327 rat prostate cancer model. Dietary PC-SPES at levels of 0.05% and 0.025% did not exhibit any toxicity and no significant difference in food intake was noted at the end of six weeks. Dose dependent inhibitory effect of dietary PC-SPES was observed on both tumor incidence (P=0. 01) and rate of tumor growth when tumors were induced in syngeneic Copenhagen rats by intradermal injections of MAT-LyLu cells that are known to metastasize in the lung and lymph nodes. The number of pulmonary metastases in animals on PC-SPES that showed no primary tumor growth had no metastatic lesions in the lung, however, in animals that did not respond to PC-SPES, the number of pulmonary metastases was not significantly different from the non-treated controls. The significant anti-tumor effects of PC-SPES on MAT-LyLu induced tumorigenesis and metastasis in Copenhagen rats, in general refractory to most conventional therapy, suggests a therapeutic benefit of this herbal food supplement and may be a useful adjuvant to conventional therapeutic modalities.

Interlinking of hypoxia and estrogen in thyroid cancer progression.

Estrogen aids in neo-vascularization of various tumors during hypoxic conditions, however the role of estrogen within the hypoxic environment of thyroid cancer is not known. In a series of experimentations, using human thyroid cancer cells, we observed that estrogen and hypoxia modulate the hypoxia inducible factor-1 (HIF-1) signaling which is abrogated by the anti-estrogen fulvestrant and the HIF-1 inhibitor YC-1 (3-(5'-hydroxymethyl-2'-furyl)-1-benzylindazole). Furthermore, we found that the conditioned medium from estrogen treated thyroid cancer cells lead to enhanced migration and tubulogenesis of human umbilical vein endothelial cells (HUVECs) which is abrogated by HIF-1 inhibitor. These findings, in addition to our previous and other scientific literature data, lead us to conclude that estrogen and hypoxia are interlinked in thyroid cancer and can equally modulate epithelial-endothelial cell interactions by mediating key cellular, metabolic and molecular processes of thyroid cancer progression. We believe that the hormonal component and cellular adaptation to oxygen tension of cancer cells are functionally equivalent with a cellular transition that can be exploited clinically for a combinational approach for thyroid cancer treatment involving antiestrogens as well as anti-hypoxic agents.

Pilot study using SELDI-TOF-MS based proteomic profile for the identification of diagnostic biomarkers of thyroid proliferative diseases.

Biomarkers for thyroid cancer (TCa) lack specificity. To develop TCa specific biomarkers, SELDI-TOF-MS was used to examine the proteomic profile of biopsies obtained from papillary TCa along with adjacent normal tissue. Sixty-three potential biomarkers were categorized by univariate analysis into single biomarker candidates and segregated by multivariate analysis into normal and cancerous groups. Our studies demonstrate the sensitivity and reproducibility of this approach to detect biomarkers for TCa.

Murine major histocompatibility complex class-I mutants: molecular analysis and structure-function implications.

The class-I mutants have provided a model system for understanding the generation of diversity of the genes encoding the histocompatibility molecules K, D, and L, and the relationship of their structure to function. The complex nature of the alterations found in Kb molecules from mutant mice has been documented at the nucleic acid level for eight mutants. The clustered changes in the mutant genes are consistent with the hypothesis that genetic recombination between class-I genes generates the Kb mutants. Techniques using synthetic oligonucleotide probes to mutant DNA sequence demonstrated that other class-I genes were available as donors for interaction with the Kb gene to produce the mutations. Intriguingly, donor genes found in the K region (K1) and the D region (Db), as well as the Qa regions (Q4, Q10), were capable of the interactions. The amount of genetic transfer to Kb from other class-I donor genes may range from a potential minimum of 5 nucleotides to a potential maximum of 95 nucleotides. Genealogical analysis of several bm mutants has further indicated that at least some, if not all, of the gene interaction events generating Kb mutations occurred during mitotic amplification of the germ cells. Genetic recombination among class-I genes occurring in nature to the extent observed for the Kbm mutants could readily generate mosaic transplantation genes containing sequences derived from other class-I genes. Thus, it seems likely that genetic interaction plays a major role in the diversification and ongoing evolution of the MHC. The localization of altered amino acids in the in vivo mutant Kb molecules has directed our attention to recognition regions on the Kb product that play a major role in determining alloreactivity and H-2 associative recognition. The replacement of one or a few amino acids in either of the postulated recognition regions located in the alpha 1 domain (residues 70-90) or alpha 2 domain (residues 150-180) can have marked effects on biological function. While the majority of monoclonal antibodies recognize epitopes in one or the other recognition region, CTL recognize determinants dependent on the apparent interaction of amino acids located in both regions. These overall conclusions are supported to a large extent by studies on mutants derived from several sources, i.e. spontaneous mutants, mutagen-induced somatic variants, and products of hybrid H-2 genes. Studies of in vitro variants can provide a more refined approach for analysis of structure-function relationships through the introduction of minimal biochemical changes.(ABSTRACT TRUNCATED AT 400 WORDS)