Abstract A02: MEK-CDK4/6 inhibition induces plasma cell tumor infiltration and sensitizes de novo MPNSTs to immune checkpoint blockade

Malignant peripheral nerve sheath tumors (MPNSTs) are deadly, Ras-driven sarcomas that lack effective therapies. Many tumors are unresectable and toxic chemotherapies are ineffectual. The sensitivity of MPNSTs to immune checkpoint blockade (ICB) therapies is not known, although sarcomas are generally unresponsive. Patient tumor analyses comparing MPNSTs to benign precursors identified Ras effectors, MEK and CDK4/6 kinases, as rational targets for therapy. We tested the efficacy of dual MEK-CDK4/6 inhibition versus single drug therapy using preclinical MPNST models. In MPNST cells, low-dose drug combinations synergistically reactivated the retinoblastoma (RB1) tumor suppressor, induced cell death and decreased clonogenic survival. In de novo MPNSTs in immune competent mice, combination therapy caused tumors to shrink, substantially delayed resistant tumor outgrowth and improved survival relative to monotherapies. Tumor regression was associated with an immune activation gene expression profile featuring plasma cell infiltration, an event not previously observed with MEK-CDK4/6 inhibitor therapy. In other human tumor types, intratumoral plasma cells prognose better overall survival and improved response to ICB therapies. Excitingly, MEK-CDK4/6 therapy sensitized de novo MPNSTs to anti-programmed death ligand 1 (PD-L1) therapy with the combination achieving complete tumor ablation and apparent cure in 10% of mice. These findings implicate a critical role for plasma cells in mediating MPNST regression in response to kinase inhibitor therapy and sensitizing tumors to PD-L1 targeting. This novel therapeutic combination is a promising option for MPNST therapy that could improve ICB efficacy in other solid tumors.

Citation Format: Joshua Lingo, Jordan Kohlmeyer, Courtney Kaemmer, Amanda Scherer, Ellen Voigt, Michael Chimenti, Munir Tanas, Varun Monga, Ben Darbro, David Meyerholz, Rebecca Dodd, Dawn Quelle. MEK-CDK4/6 inhibition induces plasma cell tumor infiltration and sensitizes de novo MPNSTs to immune checkpoint blockade [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A02.

Genome-wide methylation analysis in long-term survivors of glioblastoma (GBM)

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Background: Identification of tumor characteristics that may be associated with survival in patients with glioblastoma (GBM) has been largely characterized by IDH mutations and MGMT promoter methylation status. However, these genetic changes and other currently available data are not sufficient to explain the longevity experienced by a subset of long-term survivors (LTS) - patients surviving longer than 3 years past diagnosis. Methods: The study identified GBM patients established and treated at University of Iowa Holden Comprehensive Cancer Center from 2007-2017 whose disease recurred after initial resection. Patients were categorized LTS if they survived > = 3 years beyond initial definitive resection; short-term survivors (STS) if less than 3 years. Pathologic specimens at initial and repeat resection underwent genome wide methylation analysis using the Infinium EPIC microarray system. Data were analyzed to identify genes that exhibited differentially methylated CpG regions. Results: Resection specimens from GBM survivors were compared to those of STS. A total of 29 samples were analyzed and compared (15 LTS and 14 STS samples). Multidimensional scaling plots identified significant differences in genomic constitution between LTS and STS specimens. Granular analysis yielded 89 differentially methylated regions significantly associated with long-term survival (adjusted p < 0.05). PTPRN2 (p = 0.000376), PTPN11 (p = 1.38E-05), and PAX6 (p = 0.000671) were found to exhibit numerous differentially methylated CpG sites between MGMT-methylated vs. unmethylated specimens. Further notable, higher levels of differentially methylated CpG shores and open-seas regions on chromosome 12 were associated with long-term survival (p = 1.89E-08). Conclusions: Our study identified multiple significant epigenetic differences that, functionally or consequentially, may be associated with extended survival in GBM patients. The implication that CpG shores, rather than islands, are associated with long-term survival raises further intriguing questions regarding the depth of epigenetic complexity in this disease. More immediately, the surprising association of multiple protein phosphatases with LTS in our study may hint at the class’ previously unspecified, yet integral, role in delaying disease progression and identify new, novel avenues for therapy.

A class-wide phylogenetic assessment of Dothideomycetes

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Molecular systematics of the marine Dothideomycetes

Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae,Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae,Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. Few marine species are reported from the Dothideomycetidae (e.g. Mycosphaerellaceae, Capnodiales), a group poorly studied at the molecular level. New marine lineages include the Testudinaceae and Manglicolaguatemalensis in the Jahnulales. Significantly, most marine Dothideomycetes are intertidal tropical species with only a few from temperate regions on salt marsh plants (Spartina species and Juncus roemerianus), and rarely totally submerged (e.g. Halotthia posidoniae and Pontoporeia biturbinata on the seagrasses Posidonia oceanica and Cymodocea nodosum). Specific attention is given to the adaptation of the Dothideomycetes to the marine milieu, new lineages of marine fungi and their host specificity.

Two assays for measuring fibrosis: reverse transcriptase-polymerase chain reaction of collagen alpha(1) (III) mRNA is an early predictor of subsequent collagen deposition while a novel serum N-terminal procollagen (III) propeptide assay reflects manifest fibrosis in carbon tetrachloride-treated rats

Using a novel quantitative reverse transcriptase-polymerase chain reaction assay, we have determined the amount of specific mRNA for procollagen alpha(1) (III) (PIIIP) in the carbon tetrachloride (CCl(4)) model of liver fibrosis in rats. After a single week of CCl(4) application, the amount of PIIIP mRNA was increased approximately 10 times over the untreated control group and continued to increase to approximately 30 times after 7 weeks of intoxication. In this model substantial fibrosis was demonstrated by computer-aided morphometry after 5 to 7 weeks of treatment. Using recombinant murine N-terminal procollagen alpha(1) (III) propeptide (PIIINP), a novel sensitive immunoassay for the measurement of circulating PIIINP in rodent sera was established. An increase in PIIINP serum levels was observed after 5 to 7 weeks of CCl(4) intoxication. Our results suggest PIIIP gene expression is an early marker of tissue fibrosis. Early PIIIP gene expression is correlated with the extent of the subsequent fibrosis. PIIIP mRNA levels increase much earlier than conventional histological examination or PIIINP levels. PIIINP measurements with our new serum assay, on the other hand, are a good noninvasive marker of manifest fibrosis but are a poor marker of fibrogenesis.

Epitope-specific monoclonal antibodies against human C-terminal procollagen alpha1(III)-propeptide

We have generated monoclonal antibodies against recombinant C-terminal human procollagen alpha1(III) propeptide (PIIICP), produced in E. coli in high yields. The monoclonal antibodies were screened for epitope specificity using recombinant truncated PIIICP. Several antibodies were identified which recognized different regions of the PIIICP molecule. The ability of the antibodies to detect PIIICP antigens in human cell line lysates and supernatants was demonstrated. As PIIICP antigens are a key marker of extracellular matrix metabolism, the monoclonal antibodies described here should be of value for clinical and basic research.

Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.

Geographical distribution and taxonomy of fungi from salt marsh Spartina

Collections were made of filamentous fungi on Spartina alterniflora, S. patens, and Spartina sp. from tidal salt marshes along the east coasts of North and South America. Buergenerula spartinae, Phaeosphaeria typharum, Phoma sp., and Stagonospora sp. were found at most of the sites sampled. All the species collected in Florida have also been reported from Rhode Island, indicating that a characteristic mycota is possibly associated with Spartina alterniflora along the east coast of the U.S.A. A compilation of all the higher filamentous fungi reported from Spartina spp. from marine habitats is included. The list has been compiled from the literature and our collections and includes 66 Ascomycetes, 5 Basidiomycetes, 29 Fungi Imperfecti, and 1 Mycelium Sterilium. Ellisiodothis inquinans and Leptosphaeria typhicola are reported for the first time from Spartina. The new name Leptosphaeria neomaritima Gessner et Kohlmeyer nom. nov. (basionym Sphaeria maritima Cooke et Plowright 1877, non S. maritima Crouan et Crouan 1867) is proposed. Leptosphaeria discors Sacc. et Ellis 1882 is made a synonym of L. obiones (Crouan et Crouan) Sacc. (basionym Pleospora obiones Crouan et Crouan 1867).

Buergenerula spartinae sp. nov., an Ascomycete from salt marsh cordgrass, Spartina alterniflora

Comparisons between the marine wood-inhabiting Ascomycete Sphaerulina pedicellata Johnson and a similar species from Spartina spp. demonstrate that the two fungi are not identical. The species from Spartina, described as Buergenerula spartinae sp. nov., is compared with the type species of the genus, B. biseptata (Rostrup) Sydow. Buergenerula spartinae is characterized by hyphopodia, periphyses, pseudoparaphyses, unitunicate, thick-walled asci with a non-amyloid, ring-like apical apparatus, and clavate, three-septate, hyaline ascospores. Sphaerulina pedicellata is considered a doubtful species.