101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Abstract PD3-04: Complete pathologic response rate to neoadjuvant chemotherapy increases with increasing HER2 ratio in HER2 over-expressing breast cancer: Analysis of the National cancer database (NCDB)

Background: HER2-positive (HER2+) breast cancer is an aggressive subtype that overexpresses human epidermal growth factor receptor 2 promoting cancer cell growth. Monoclonal antibodies targeting the HER2 receptor have improved survival for this patient population, and current NCCN guidelines recommend consideration of neoadjuvant anti-HER2 therapy (NAC) in Stage 2 & 3 HER2+ breast cancer. Pathologic complete response (pCR) to NAC has correlated with longer disease free survival in multiple trials.

Per ASCO-CAP guidelines tumors are considered HER2+ if HER2 copy number≥ 6/cell, HER2/CEP17 ratio≥ 2, or ratio<2 & HER2 copy number ≥6/cell. We hypothesize that patients with higher HER2 ratios will have higher rates of pCR after NAC.

Methods: The National Cancer Database is supported by the American College of Surgeons and the American Cancer Society containing de-identified patient treatment data from over 1,500 US facilities. We performed a retrospective review comparing pCR rates after NAC based on HER2 ratio. Patients were excluded if they were HER2 negative, did not undergo NAC, or if the HER2 ratio was not recorded. Chi-squared and Fisher's exact test were used to compare pCR versus partial response between deciles of HER2 ratios.

Results: The NCDB included 237,118 patients with HER2 equivocal or HER2+ breast tumors. 29,291 of these patients underwent NAC, and HER2 ratios were recorded in 14,597 of the NAC cases. The majority (98%) of included cases were from 2010-2014. A pCR was noted in 9,752 patients and 11,402 patients had a partial response. No response was observed in 1,735 patients and 6,402 patients had a response but the degree was not recorded.

HER2 ratios were significantly different between pCR vs. partial response groups, p <0.001. We identified a direct relationship between increasing HER2 ratio and response to NAC. For ratios 2-2.9, 23.6% achieved pCR and 44.7% had a partial response. For ratio of 5-5.9, 40.7% achieved pCR and even higher rates of pCR were noted for ratios 8-8.9; 49.5% achieved pCR. While both estrogen receptor (ER) positive and ER negative tumors demonstrated this trend, ER negative tumors had higher rates of pCR (ER negative pCR range 37.6% to 59.4% vs ER positive pCR range 16.9% to 42.3%, p<0.01).

Conclusion: Contrary to current dogma, not all HER2+ tumors respond similarly to NAC. We demonstrate a linear relationship between HER2 ratio and pCR in over 14,000 patients. Those with HER2 ratios ≥5.0 were more likely to achieve pCR compared to patients with ratio ≤4.9. The NCDB reflects current clinical practice across the country not restricted to confines of clinical trials, and in this population higher HER2 ratios are predictive of pCR after NAC.

Response to NAC by Her2 Ratio- Complete vs Partial Response  Response to NAC   p ValueHER2 Ratio Complete Response- pCR (N) Partial Response (N)   1.00- 1.99141819.5%343047.2%<0.01 2.00- 2.9951423.6%97444.7%<0.01 3.00- 3.9928328.7%41942.4%<0.01 4.00- 4.9926533.2%30638.2%<0.01 5.00- 5.9929940.7%24333.1%<0.01 6.00- 6.9929241.0%25435.5%<0.01 7.00- 7.9924746.2%17432.5%<0.01 8.00- 8.9918749.5%12132.0%<0.01 9.00- 9.87 and greater44143.9%31431.3%<0.01TOTAL 394627.0%623542.7%<0.01

Citation Format: Greenwell K, Hussain L, Ho C, Dunki-Jacobs E, Lee D, Bramlage M, Bills G, Mehta A, Jones J, Jackson A, Wexelman B. Complete pathologic response rate to neoadjuvant chemotherapy increases with increasing HER2 ratio in HER2 over-expressing breast cancer: Analysis of the National cancer database (NCDB) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD3-04.

The discovery of moriniafungin, a novel sordarin derivative produced by Morinia pestalozzioides

A novel sordarin derivative, moriniafungin (1), containing a 2-hydroxysebacic acid residue linked to C-3' of the sordarose residue of sordarin through a 1,3-dioxolan-4-one ring was isolated from the fungus Morinia pestalozzioides. Isolation of moriniafungin employed a highly specific bioassay consisting of a panel of Saccharomyces cerevisiae strains containing chimeric eEF2 for Candida glabrata, Candida krusei, Candida lusitaniae, Crytpococcus neoformans, and Aspergillus fumigatus as well as wild type and human eEF2. Moriniafungin exhibited an MIC of 6 microg/mL versus Candida albicans and IC(50)'s ranging from 0.9 to 70 microg/mL against a panel of clinically relevant Candida strains. Moriniafungin was shown to inhibit in vitro translation in the chimeric S. cerevisae strains at levels consistent with the observed IC(50). Moriniafungin has the broadest antifungal spectrum and most potent activity of any natural sordarin analog identified to date.

Discovery of novel antifungal (1,3)-beta-D-glucan synthase inhibitors

The increasing incidence of life-threatening fungal infections has driven the search for new, broad-spectrum fungicidal agents that can be used for treatment and prophylaxis in immunocompromised patients. Natural-product inhibitors of cell wall (1,3)-beta-D-glucan synthase such as lipopeptide pneumocandins and echinocandins as well as the glycolipid papulacandins have been evaluated as potential therapeutics for the last two decades. As a result, MK-0991 (caspofungin acetate; Cancidas), a semisynthetic analogue of pneumocandin B(o), is being developed as a broad-spectrum parenteral agent for the treatment of aspergillosis and candidiasis. This and other lipopeptide antifungal agents have limited oral bioavailability. Thus, we have sought new chemical structures with the mode of action of lipopeptide antifungal agents but with the potential for oral absorption. Results of natural-product screening by a series of newly developed methods has led to the identification of four acidic terpenoid (1,3)-beta-D-glucan synthase inhibitors. Of the four compounds, the in vitro antifungal activity of one, enfumafungin, is comparable to that of L-733560, a close analogue of MK-0991. Like the lipopeptides, enfumafungin specifically inhibits glucan synthesis in whole cells and in (1,3)-beta-D-glucan synthase assays, alters the morphologies of yeasts and molds, and produces a unique response in Saccharomyces cerevisiae strains with point mutations in FKS1, the gene which encodes the large subunit of glucan synthase.

Hyalodendrosides A and B, antifungal triterpenoid glycosides from a lignicolous hyphomycete, Hyalodendron species

Two antifungal triterpenoid glycosides, hyalodendrosides A and B (1 and 2), were isolated from a solid matrix fermentation of a lignicolous hyphomycete, Hyalodendron sp. Their structures were determined based upon extensive examination of spectral parameters, particularly NMR and MS data. Both compounds have beta-linked glucose moieties. Compounds 1 and 2 show weak to moderate antifungal activity against some clinically relevant fungi.

Production of a family of kinase-inhibiting lactones from fungal fermentations

During the course of our screening for natural products from fungi, extracts of several cultures were found to make a family of related resorcylic acid lactone compounds, which are potent inhibitors of MEK kinase. Comparative and empirical studies of fermentation conditions improved the titers of the compounds of interest. Striking changes in the ratios and amounts of the major and minor compounds in some cases were achieved by manipulations of media composition.

L-696,474, a novel cytochalasin as an inhibitor of HIV-1 protease. II. Isolation and structure

A novel HIV-1 protease inhibitor, L-696,474 (C30H39NO4, 477), was isolated from the fermentations of the fungus Hypoxylon fragiforme (ATCC 20995, MF5511) and purified by silica gel chromatography followed by crystallization. Spectroscopic studies have shown the competitive inhibitor L-696,474 to be a novel cytochalasin. Two related novel cytochalasins were also isolated and had no effect on the enzyme.

L-687,781, a new member of the papulacandin family of beta-1,3-D-glucan synthesis inhibitors. I. Fermentation, isolation, and biological activity

A new beta-1,3-D-glucan synthesis inhibitor, L-687,781 is produced by the cultivation of Dictyochaeta simplex ATCC 20960. L-687,781 exhibits potent in vitro antifungal activity as well as anti-Pneumocystis activity in a rat model.