Ticks and tick-borne rickettsiae from dogs in El Salvador, with report of the human pathogen Rickettsia parkeri

Twelve tick species have been reported in El Salvador; however, information regarding ticks infesting domestic dogs is lacking, and pathogenic tick-borne Rickettsia species have never been reported in El Salvador. This work evaluated ticks infesting 230 dogs from ten municipalities in El Salvador from July 2019 to August 2020. A total of 1,264 ticks were collected and identified into five species: Rhipicephalus sanguineus sensu lato (s.l.), Rhipicephalus microplus, Amblyomma mixtum, Amblyomma ovale, and Amblyoma cf. parvum. The tick R. sanguineus s.l. was the most frequent species in all localities (81.3% of sampled dogs), followed by Amblyomma mixtum (13.0%), Amblyomma ovale (10.9%) and Amblyomma cf. parvum (10.4%). The overall mean intensity of tick infestation was 5.5 ticks/dog. The highest specific mean intensity value was for R. sanguineus s.l. (4.8 ticks/dog), varying from 1.6 to 2.7 ticks/dog for the three Amblyomma species. From a random sample of 288 tick specimens tested molecularly for the presence of rickettsial agents, three spotted fever group Rickettsia were detected: Rickettsia amblyommatis in 90% (36/40) A. mixtum, 46% (11/24) A. cf. parvum, 4% (7/186) R. sanguineus s.l., and 17% Amblyomma spp.; Rickettsia parkeri strain Atlantic rainforest in 4% (1/25) A. ovale; and an unnamed rickettsia agent, designated as 'Rickettsia sp. ES-A.cf.parvum', in 4% (1/24) A. cf. parvum. Our finding of R. parkeri strain Atlantic rainforest in A. ovale is highly relevant because this agent has been associated to spotted fever illness in other Latin American countries, where A. ovale is implicated as its main vector. These findings suggest that spotted fever cases caused by R. parkeri strain Atlantic rainforest could be occurring in El Salvador.

Abstract 3916: Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens

Background: The National Cancer Institute (NCI) has developed a Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) of preclinical models including patient-derived xenografts (PDX), organoids (PDOrg) and patient-derived cell cultures (PDC). Extensive clinical annotation and genomic datasets are available for these preclinical models. However, it is unclear if the molecular profiles of the corresponding patient tumors are stably propagated in these models. We have previously demonstrated that PDX models from the NCI PDMR faithfully represent the patient tumors both in terms of genomic stability and tumor heterogeneity. Here, we conduct an in-depth investigation of genomic representation of patient tumors in the PDOrgs and PDCs.

Methods: PDOrgs (n=64) and PDCs (n=94) were established from tumor fragments (i.e., initiator specimens) obtained either from patient specimens or from PDX specimens of early passage. For some models (n=19), both PDOrgs and PDCs were generated from the same tumor tissue; in fewer cases (n=4), PDCs were established from organoids derived from patient specimens. Whole Exome Sequencing and RNA-Seq were performed on all PDCs and PDOrgs, and data were compared with patient specimens or early passage PDXs.

Results: A majority of the PDOrgs and PDCs have stably inherited the genome of the corresponding patient specimens based on the following observations: (1) >87% of PDOrgs and PDCs maintained similar copy number alteration profiles compared with the initiator specimens of the preclinical model; (2) the variant allele frequency (VAF) of clinically relevant mutations remained consistent between the PDOrgs, PDCs, and the initiator specimens, with none of the PDCs or PDOrgs deviating by >15% VAF; and (3) clinically relevant biomarkers (e.g., MSI, LOH, mutational signatures etc.) are concordant amongst the PDOrgs, PDCs, and the initiator specimens. We observed that the majority of SNVs and indels present in the initiator specimens were also found in the PDOrgs and PDCs, suggesting almost all the tumor heterogeneity was preserved in these preclinical models.

Conclusions: This large and histologically diverse set of PDOrgs and PDCs from the NCI PDMR exhibited genomic stability and faithfully represented the tumor heterogeneity observed in corresponding patient specimens. These preclinical models thus represent a valuable resource for researchers interested in pre-clinical drug or other studies.

Citation Format: Biswajit Das, Yvonne A. Evrard, Li Chen, Rajesh Patidar, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm-Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Carrie A. Bonomi, Kelly M. Dougherty, Joseph P. Geraghty, Marion V. Gibson, Savanna S. Styers, Abigail J. Walke, Jenna E. Moyer, Anna Wade, Mariah L. Baldwin, Kaitlyn A. Arthur, Kevin J. Plater, Luke Stockwin, Matthew R. Murphy, Michael E. Mullendore, Dianne L. Newton, Melinda G. Hollingshead, Chris A. Karlovich, Paul M. Williams, James H. Doroshow. Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3916.

Abstract 3554: Genomic landscape of acquired uniparental disomy in NCI PDMR patient derived xenograft models

Background: Acquired Uniparental Disomy (aUPD) is relatively common in cancer. Occurrence of aUPD is more frequent in some tumor histologies (e.g., serous ovarian, colorectal) and may be relevant for choice of therapy. The Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) developed by The National Cancer Institute (NCI) includes patient-derived xenograft (PDX) models from multiple tumor histologies with different passages and lineages. The associated clinical annotation and genomic data make it possible to assess the prevalence of aUPD in the PDMR cohort and the stability of aUPD in different passages and lineages within a PDX model.

Methods: High tumor purity in the PDX specimens (after removal of mouse reads representing the stroma) enabled highly accurate assessment of loss of heterozygosity (LOH). Variants called by GATK Haplotype caller from whole exome sequencing (WES) data were used to identify segments of homozygosity using BCFtools/RoH (runs of homozygosity). The RoH segments were then intersected with the bed file for chromosome arms to get %LOH at the arm level. If %LOH on a chromosome arm was >90%, we considered the sample to have aUPD at the arm level. WES was also used to look for associations between DNA damage repair (DDR) pathway alterations and aUPD.

Results: We made the following observations: a) aUPD was observed most frequently in chr18q (75/427, 17.6%) and chr3p (69/427, 16%) of PDX models; b) aUPD was observed more frequently in certain tumor histologies, e.g., clear cell renal cell carcinoma (6/8), small cell lung cancer (3/4) and non-small cell lung cancer (25/38); c) extensive aUPD was observed in 4 PDMR models (>50% of evaluated chromosome arms in these models have aUPD); d) aUPD was not observed in some tumor histologies, i.e., synovial sarcoma, uterine endometrioid carcinoma; e) in the vast majority of PDMR models (>90%), aUPD is maintained faithfully across lineages and through multiple passaging; f) subclonal aUPD events were observed in some models across different lineages; g) significant enrichment of double strand DNA break repair (DSBR) pathway alterations was observed in PDMR models without aUPD (p=0.0007, Fisher's exact test) suggesting defects in DSBR are not associated with aUPD; and h) aUPD was rarely observed in MSI-high models (1/30) suggesting mutual exclusivity of mismatch repair (MMR) pathway defects and aUPD.

Conclusion: We observed a relatively high frequency of UPD in the PDMR models (at least 1 arm of a chromosome). UPD was more frequently observed in specific chromosomal arms. The frequency of aUPD was higher in some tumor histologies and absent in others. aUPD was stably maintained across passages and lineages, although some heterogeneity was observed. Our data suggest aUPD is not associated with defects in DSBR and MMR pathways. Preclinical drug studies using NCI PDMR models may suggest appropriate therapeutic options for cancers with aUPD.

Citation Format: Rajesh Patidar, Li Chen, Chris A. Karlovich, Biswajit Das, Yvonne A. Evrard, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Suzanne D. Borgel, John P. Carter, Jesse M. Stottlemyer, Tiffanie L. Miner, Devynn R. Breen, Emily T. Delaney, Chelsea A. McGlynn, Candace N. Mallow, Marianne Radzyminski, Shannon N. Uzelac, Sergio Y. Alcoser, Tara L. Grinnage-Pulley, Michelle A. Eugeni, Dianne L. Newton, Melinda G. Hollingshead, Paul M. Williams, James H. Doroshow. Genomic landscape of acquired uniparental disomy in NCI PDMR patient derived xenograft models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3554.

Synergies, radiation and kinetics in photo-Fenton process with UVA-LEDs

The photo-Fenton process, with UV-A LED (λ = 380-390, 390-400 and 380-400 nm) has demonstrated to be effective in the abatement of a target micropollutant, such as diphenhydramine hydrochloride (DPH). Different concentrations of iron (Fe²⁺) and H₂O₂ were tested and monitored, and the best results in DPH removal were obtained for the highest concentrations of both iron (II) and H₂O₂ (10 mg Fe²⁺/L - 150 mg H₂O₂/L). The evolution of iron and peroxide concentration was also monitored. Kinetic studies showed that dark Fenton process prevails at the beginning of the experiment, when Fe²⁺ concentration is higher. However, after these initial moments, the prevailing process is photo-Fenton and, in addition, wavelength radiation plays an important role. Concerning the effect of radiation, four LEDs (4.2 W total power) were used, emitting radiation in the wavelength range between 380-390 or 390-400 nm. Similar results were obtained in both cases in DPH removal by photo-Fenton (30 min for total elimination). However, a synergistic effect was observed when two LEDs of 380-390 nm and two LEDs of 390-400 nm were used. Total power was the same (4.2 W) in each experimental condition, but the increase in the wavelength range to 20 nm (380-400 nm) produces an increase in the rate of DPH removal, achieving its total elimination at 15 min. This fact, with the use of a simple radiation model, reveals the important role that radiation plays in the photo-Fenton process. Finally, the formed intermediates were determined and some reaction pathways were proposed.

First isolation and molecular characterization of Ehrlichia canis in Costa Rica, Central America

The present study investigated Ehrlichia species in blood samples from dogs suspected of clinical ehrlichiosis, using molecular and isolation techniques in cell culture. From a total of 310 canine blood samples analyzed by 16S rRNA nested PCR, 148 (47.7%) were positive for Ehrlichia canis. DNA from Ehrlichia chaffeensis or Ehrlichia ewingii was not detected in any sample using species-specific primers in separated reactions. Leukocytes from five PCR-positive dogs were inoculated into DH82 cells; successful isolation of E. canis was obtained in four samples. Partial sequence of the dsb gene of eight canine blood samples (including the five samples for in vitro isolation) was obtained by PCR and their analyses through BLAST showed 100% of identity with the corresponding sequence of E. canis in GenBank. This study represents the first molecular diagnosis, isolation, and molecular characterization of E. canis in dogs from Costa Rica.

Mathematical model for liquid-gas equilibrium in acetic acid fermentations

An experimental study was conducted to propose an adequate mathematical model for liquid-gas equilibrium in acetic acid fermentations. Three operation scales (laboratory, pilot plant, and industrial plant) were employed to obtain the sets of experimental data. The proposed model, based in the UNIFAC method for the estimation of activity coefficients of a solution consisting of several components, takes into account the effect of temperature. However, in the set of equations, it has been necessary to put in the degree of equilibrium (epsilon). This coefficient adequately reflects the physical conditions of fermentation equipment. The experimental and numerical results help to define the fundamental mechanisms for liquid-gas equilibrium in these systems and demonstrate the model validity in the three tested scales. It was also found that in an industrial setting, closed systems are those with lowest evaporation losses. Copyright 1998 John Wiley & Sons, Inc.