Abstract PO-253: Overcoming barriers to colorectal cancer screening for underserved patients: Lessons from the COVID-19 pandemic

Introduction This patient navigation initiative works to address cancer health disparities by improving education and access to screening and cancer care. This initiative includes partnerships with local Federally Qualified Health Centers (FQHCs) and primary care physicians (PCPs), primarily focused on increasing colorectal cancer (CRC) screening rates among underserved populations in Western New York (WNY) who may have low health literacy. Grounded in health services research, we aimed to improve clinical care by implementing evidence-based guidelines into practice by working directly with underserved communities in our area to improve CRC screening rates at an urban FQHC. Methods Throughout the COVID-19 pandemic, our navigators pivoted to a hybrid schedule with remote access to health systems, splitting time between our cancer center and remotely at home until allowed back on-site to work at the FQHC. Colonoscopy halted in NY between March and June 2020, resulting in scheduling challenges due to significant backlogs of cancelled procedures during the shutdown and regional hold on elective procedures. Endoscopists across WNY had reduced capacity for postponed procedures, leading to the prioritization of scheduling for symptomatic patients. Therefore, navigators focused screening efforts on widely disseminating stool-based tests to patients due for average-risk CRC screening and prioritizing patients with positive screening results to coordinate colonoscopy appointments. Results Between April 2020 through March 2021, our pre-pandemic goal was to educate 550 patients and screen 300 patients. During this timeframe, navigators provided screening education to 632 patients and screened 232 patients despite significant challenges presented by the COVID-19 pandemic. With many colonoscopy procedures being cancelled and/or rescheduled, stool-based tests were widely available and became a more common choice for patients. To date, since April 2020, navigators have educated 807 patients and have navigated 306 patients to complete CRC screening. Of those 306 patients, 234 chose to complete at-home stool-based testing. In 2020, CRC screening rates remained over 50%, exceeding national FQHC targets. This was achieved through targeted patient outreach, education, and navigation, despite significant challenges with the shutdown and the COVID-19 pandemic. Conclusions Stool-based tests paired with targeted outreach and education were an efficient tool for CRC screening during this challenging time. Navigators regularly cross-check records to be sure results are received by ordering physicians and properly coded for accurate data reporting. This is especially important for positive test results and timely follow up, which may lead to improved health outcomes. Moving forward, this paired approach may be an effective strategy for improving screening rates among hard-to-reach patient populations and patients facing substantial barriers to accessing routine medical care.

Citation Format: Kathryn M. Glaser, Christina Crabtree-Ide, Alyssa McNulty, Ellis Gomez, Nicole Donofrio, Tessa Flores, Mary E. Reid. Overcoming barriers to colorectal cancer screening for underserved patients: Lessons from the COVID-19 pandemic [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-253.

Combined effects of arsenic and Magnaporthe oryzae on rice and alleviation by silicon

While the impacts of arsenic (As) and Magnaporthe oryzae on rice have been well-studied, a dearth of knowledge exists on how rice responds to their combined stress. Moreover, increasing exogenous silicon (Si) can alleviate M. oryzae infection and As uptake, but how increasing exogenous Si affects the combined stress of M. oryzae and As is unknown. We grew three cultivars of rice that varied in their susceptibility to As and M. oryzae under low (50 μM, Si_L) and high (1500 μM, Si_H) Si with and without As (4 μM, 80/20 As (III)/As(V)) and with or without M. oryzae infection and examined the impacts of treatments on plant As and Si concentrations, severity of disease by M. oryzae, and stress via targeted gene expression. Si_H treatments generally decreased shoot As concentrations by 20-70% compared to Si_L treatments depending on cultivar and M. oryzae exposure. There was no effect of Si or As treatments on percent of leaf diseased in the As-tolerant cultivar M206, but in the As-sensitive cultivar IR66, Si_H treatment decreased percent of leaf diseased in the absence of As and had no impact when As was present. In the M. oryzae-susceptible Sariceltik, plants receiving Si_H had significantly fewer lesions than those receiving Si_L and plants with the fewest lesions were in the Si_H + As treatments. Plants that were exposed to As + M. oryzae were the most stressed when grown under Si_L, but this stress response was lowered by Si_H treatments. A separate pathogenicity assay with Sariceltik showed that in contrast to our hypothesis, As exposure decreased lesion growth, particularly under Si_H treatments, and lessened the impact of M. oryzae on rice. These results suggest that rice grown under replete Si will be able to withstand combined stressors of M. oryzae and As, but will be highly stressed under Si deficient scenarios.

Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility

Coffee leaf rust caused by the fungus Hemileia vastatrix is one of the most important leaf diseases of coffee plantations worldwide. Current knowledge of the H. vastatrix genome is limited and only a small fraction of the total fungal secretome has been identified. In order to obtain a more comprehensive understanding of its secretome, we aimed to sequence and assemble the entire H. vastatrix genome using two next-generation sequencing platforms and a hybrid assembly strategy. This resulted in a 547 Mb genome of H. vastatrix race XXXIII (Hv33), with 13,364 predicted genes that encode 13,034 putative proteins with transcriptomic support. Based on this proteome, 615 proteins contain putative secretion peptides, and lack transmembrane domains. From this putative secretome, 111 proteins were identified as candidate effectors (EHv33) unique to H. vastatrix, and a subset consisting of 17 EHv33 genes was selected for a temporal gene expression analysis during infection. Five genes were significantly induced early during an incompatible interaction, indicating their potential role as pre-haustorial effectors possibly recognized by the resistant coffee genotype. Another nine genes were significantly induced after haustorium formation in the compatible interaction. Overall, we suggest that this fungus is able to selectively mount its survival strategy with effectors that depend on the host genotype involved in the infection process.

Marker-Assisted Molecular Profiling, Deletion Mutant Analysis, and RNA-Seq Reveal a Disease Resistance Cluster Associated with Uromyces appendiculatus Infection in Common Bean Phaseolus vulgaris L

Common bean (Phaseolus vulgaris L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen Uromyces appendiculatus (Pers.) Unger can cause major loss in susceptible varieties of the common bean. The Ur-3 locus provides race specific resistance to virulent strains or races of the bean rust pathogen along with Crg, (Complements resistance gene), which is required for Ur-3-mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant “Sierra” and susceptible crg) with rust race 53 of U. appendiculatus, isolated leaf RNA at specific time points, and sequenced their transcriptomes. First, molecular markers were used to locate and identify a 250 kb deletion on chromosome 10 in mutant crg (which carries a deletion at the Crg locus). Next, we identified differential expression of several disease resistance genes between Mock Inoculated (MI) and Inoculated (I) samples of “Sierra” leaf RNA within the 250 kb delineated region. Both marker assisted molecular profiling and RNA-seq were used to identify possible transcriptomic locations of interest regarding the resistance in the common bean to race 53. Identification of differential expression among samples in disease resistance clusters in the bean genome may elucidate significant genes underlying rust resistance. Along with preserving favorable traits in the crop, the current research may also aid in global sustainability of food stocks necessary for many populations.

Generic names in Magnaporthales

The order Magnaporthales comprises about 200 species and includes the economically and scientifically important rice blast fungus and the take-all pathogen of cereals, as well as saprotrophs and endophytes. Recent advances in phylogenetic analyses of these fungi resulted in taxonomic revisions. In this paper we list the 28 currently accepted genera in Magnaporthales with their type species and available gene and genome resources. The polyphyletic Magnaporthe 1972 is proposed for suppression, and Pyricularia 1880 and Nakataea 1939 are recommended for protection as the generic names for the rice blast fungus and the rice stem rot fungus, respectively. The rationale for the recommended names is also provided. These recommendations are made by the Pyricularia/Magnaporthe Working Group established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF).

Crucial Roles of Abscisic Acid Biogenesis in Virulence of Rice Blast Fungus Magnaporthe oryzae

Rice suffers dramatic yield losses due to blast pathogen Magnaporthe oryzae. Pseudomonas chlororaphis EA105, a bacterium that was isolated from the rice rhizosphere, inhibits M. oryzae. It was shown previously that pre-treatment of rice with EA105 reduced the size of blast lesions through jasmonic acid (JA)- and ethylene (ETH)-mediated ISR. Abscisic acid (ABA) acts antagonistically toward salicylic acid (SA), JA, and ETH signaling, to impede plant defense responses. EA105 may be reducing the virulence of M. oryzae by preventing the pathogen from up-regulating the key ABA biosynthetic gene NCED3 in rice roots, as well as a β-glucosidase likely involved in activating conjugated inactive forms of ABA. However, changes in total ABA concentrations were not apparent, provoking the question of whether ABA concentration is an indicator of ABA signaling and response. In the rice-M. oryzae interaction, ABA plays a dual role in disease severity by increasing plant susceptibility and accelerating pathogenesis in the fungus itself. ABA is biosynthesized by M. oryzae. Further, exogenous ABA increased spore germination and appressoria formation, distinct from other plant growth regulators. EA105, which inhibits appressoria formation, counteracted the virulence-promoting effects of ABA on M. oryzae. The role of endogenous fungal ABA in blast disease was confirmed through the inability of a knockout mutant impaired in ABA biosynthesis to form lesions on rice. Therefore, it appears that EA105 is invoking multiple strategies in its protection of rice from blast including direct mechanisms as well as those mediated through plant signaling. ABA is a molecule that is likely implicated in both tactics.

Plant biomass degradation by fungi

Plant biomass degradation by fungi has implications for several fields of science. The enzyme systems employed by fungi for this are broadly used in various industrial sectors such as food & feed, pulp & paper, detergents, textile, wine, and more recently biofuels and biochemicals. In addition, the topic is highly relevant in the field of plant pathogenic fungi as they degrade plant biomass to either gain access to the plant or as carbon source, resulting in significant crop losses. Finally, fungi are the main degraders of plant biomass in nature and as such have an essential role in the global carbon cycle and ecology in general. In this review we provide a global view on the development of this research topic in saprobic ascomycetes and basidiomycetes and in plant pathogenic fungi and link this to the other papers of this special issue on plant biomass degradation by fungi.

Natural rice rhizospheric microbes suppress rice blast infections

BACKGROUND

The natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease.

RESULTS

Naturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by 16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70-15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice.

CONCLUSIONS

Out of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with current disease protection strategies could aid in global food security.

Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae

BACKGROUND

Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood.

RESULTS

We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.

CONCLUSION

We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.

Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae

Towards the goal of disrupting all genes in the genome of Magnaporthe oryzae and identifying their function, a collection of >55,000 random insertion lines of M. oryzae strain 70-15 were generated. All strains were screened to identify genes involved in growth rate, conidiation, pigmentation, auxotrophy, and pathogenicity. Here, we provide a description of the high throughput transformation and analysis pipeline used to create our library. Transformed lines were generated either by CaCl(2)/PEG treatment of protoplasts with DNA or by Agrobacterium tumefaciens-mediated transformation (ATMT). We describe the optimization of both approaches and compare their efficiency. ATMT was found to be a more reproducible method, resulting in predominantly single copy insertions, and its efficiency was high with up to 0.3% of conidia being transformed. The phenotypic data is accessible via a public database called MGOS and all strains are publicly available. This represents the most comprehensive insertional mutagenesis analysis of a fungal pathogen.

Fungal biology reaps the benefit of genomics

A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005.

A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005.

The genome sequence of the rice blast fungus Magnaporthe grisea

Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.

'PACLIMS': a component LIM system for high-throughput functional genomic analysis

BACKGROUND

Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.

RESULTS

The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured.

CONCLUSION

Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.

Differences between nouns and verbs after anterior temporal lobectomy

To test the claim that lesions of left anterior and middle temporal cortical structures specifically impair processing of nouns but not verbs, 56 left-hemisphere-language-dominant patients who had undergone anterior temporal lobectomy (ATL) completed tasks assessing confrontation naming of pictured objects and actions, generation of synonyms for nouns and verbs, and semantic lexical judgments about nouns and verbs. Compared with right ATL patients, left ATL patients were impaired across different tasks that assessed naming and comprehension of high-imageability as well as low-imageability nouns. These groups did not differ, however, in verb naming or comprehension on most tasks. Results are consistent with the hypothesized specialization of left temporal lobe structures for processing nouns and suggest that naming problems commonly seen after left ATL extend beyond difficulties with retrieving object names and may be related to subtle disturbances in comprehension of the meanings underlying nominal word forms.

Use of the MMPI and MMPI-2 in patients being evaluated for cardiac transplant

The MMPI and MMPI-2 have been used extensively in the study of personality correlates in various coronary populations. It has been hypothesized that personality variables are associated with various clinical outcomes, such as quality of life, morbidity, and mortality; however, no data are available in a cardiac transplant sample. This study presents descriptive MMPI and MMPI-2 data for male and female patients awaiting cardiac transplant. Analyses of differences in MMPI-2 depression scales between cardiomyopathy groups for 366 men and 99 women were performed. Significant differences were found between ischemic and nonischemic male patients.

Hemispheric asymmetries in arousal affect outcome of the intracarotid amobarbital test

Objective: To evaluate changes in arousal and their impact on memory performance during the intracarotid amobarbital test (IAT).

Methods: Along with memory measures, level of arousal was evaluated through clinical ratings and nonverbal self-ratings in epilepsy patients undergoing IAT before anterior temporal lobectomy.

Results: Irrespective of seizure focus, left-sided amobarbital injection resulted in decreased objective and subjective arousal more often than right-side injection. Impaired objective arousal was greater when the left hemisphere was injected second, because of the presumed additive effects of systemic amobarbital residual from the first injection. Decreased objective arousal was related to poorer performance on memory testing following left-hemisphere injection.

Conclusions: The IAT, as practiced in most centers, is biased, so patients with right temporal lobe seizure focus are more likely to “pass” the test, whereas patients with left seizure focus are more likely to “fail” the test. The significant impact of changes in arousal on memory testing needs to be considered when using IAT results to select patients for temporal lobectomy.

Interhemispheric memory transfer in the intracarotid amobarbital procedure

The authors examined interhemispheric memory transfer in 32 patients with lateralized temporal lobe complex partial epilepsy (15 right onsets, 17 left onsets). Visually presented verbal, nonverbal, and two types of dually encodable stimuli were displayed during amobarbital anesthesia, and recognition memory was tested with verbal and nonverbal (pointing) response modalities. No relationship was found between the material specificity of stimuli and response modality. The only significant findings were for poorer recognition memory after injection of the hemisphere contralateral to the seizure focus. Visual information presented predominantly to one hemisphere during anesthesia is available to the other hemisphere for recognition memory on clearing.