Semi-automatic algorithm to build finite element numerical models of the human hearing system from Micro-CT data

Finite Element modeling has been an extended methodology to build numerical model to simulate the behavior of the hearing system. Due to the complexity of the system and the difficulties to reduce the uncertainties of the geometric data, they result in computationally expensive models, sometimes generic, representative of average geometries. It makes it difficult to validate the model with direct experimental data from the same specimen or to establish a patient-oriented modeling strategy. In the present paper, a first attempt to automatize the process of model building is made. The source information is geometrical information obtained from CT of the different elements that compose the system. Importing that data, we have designed the complete procedure to build a model including tympanic membrane, ossicular chain and cavities. The methodology includes the proper coupling of all the elements and the generation of the corresponding finite element model. The whole automatic procedure is not complete, as we need to make some human-assisted decisions; however, the model development time is reduced from 4 weeks to approximately 3 days. The goal of the modeling algorithm is to build a Finite Element Model with a limited computational cost. Several tasks as contour identification or model decimation are designed and integrated in order to follow a semi-automated process that allows generating a patient-oriented model.

Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma

BACKGROUND

Cell-free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES-specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma.

METHODS

We previously performed an integrative analysis to identify ADRN and MES-specific genes (n = 373 and n = 159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples.

RESULTS

Samples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < .001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse.

CONCLUSIONS

While it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.

5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma

PURPOSE

Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high-risk neuroblastoma.

METHODS

5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunoprecipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.

RESULTS

In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found increased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.

CONCLUSION

Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma

Background

Cell free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma.

Methods

We previously performed an integrative analysis to identify ADRN and MES specific genes (n=373 and n=159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples.

Results

Samples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < 0.001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse.

Conclusions

While it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.

5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma

Neuroblastoma is the most common extra-cranial solid tumor in childhood and epigenetic dysregulation is a key driver of this embryonal disease. In cell-free DNA from neuroblastoma patients with high-risk disease, we found increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes, a finding previously described in the context of bivalent genes. As bivalent genes, defined as genes bearing both activating (H3K4me3) and repressive (H3K27me3) chromatin modifications, have been shown to play an important role in development and cancer, we investigated the potential role of bivalent genes in maintaining a de-differentiated state in neuroblastoma and their potential use as a biomarker. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogenous neuroblastoma cell lines. Through gene set variance analysis, we developed a clinically implementable bivalent signature. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in high-risk neuroblastoma patients. Thus, low expression of bivalent genes is a biomarker of ultra-high-risk disease and may represent a therapeutic opportunity in neuroblastoma.

Abstract A025: Assessing the role of bivalency in MYCN-amplified neuroblastoma

Introduction: Neuroblastoma is an embryonic pediatric cancer with a broad spectrum of clinical behavior. In aggressive neuroblastoma tumors, we previously demonstrated enrichment of 5-hydroxymethylcytosine (5-hmC), a marker of transcriptional activation, on genes targeted by the repressive Polycomb Repressive Complex 2 (PRC2). PRC2 has been shown to be a dependency of MYCN-amplified neuroblastoma. In embryonic stem cells, 5-hmC is disproportionately enriched at the transcription start sites (TSS) of bivalent genes that are characterized by the presence of both repressive and activating histone modifications (H3K27me3 and H3K4me3). Bivalent genes are postulated to be poised for rapid activation during embryogenesis. We hypothesized that bivalent genes enriched for 5-hmC at the TSS play a key role in regulating the undifferentiated phenotype of MYCN-amplified neuroblastoma. Methods: Tumor derived 5-hmC profiles were obtained previously. Nano-hmC-seal was used to generate genome-wide 5-hmC profiles in the MYCN-amplified or overexpressed SK-N-BE2, LA1-55n, LA1-5s, NBLW-N, NBLW-S, NBL-S, and MYCN-non-amplified SH-SY5Y, and SHEP cell lines. H3K27me3, H3K4me3, and H3K27ac profiles were generated in these cell lines using ChIP-Seq. KAS-Seq, a chemical pulldown of ssDNA that marks active enhancers and transcribed genes, and RNA-Seq profiling were performed. MACS2 and deepTools were used to analyze ChIP-Seq, 5-hmC, and KAS-Seq data. Results: A comparison of 5-hmC profiles derived from diagnostic tumor biopsy samples with and without MYCN-amplification demonstrated increased 5-hmC deposition on SUZ12 and EZH2 (PRC2 subunits) target genes. MYCN-amplified and MYC overexpressing cell lines but not MYCN-non-amplified lines bore a TSS specific association between 5-hmC deposition and H3K27me3 enrichment. Using the SK-N-BE2 and NBLW-N cell lines, we identified 313 genes with both H3K4me3 and H3K27me3 deposition, which we defined as bivalent, and 806 genes with only H3K27me3 deposition. Both H3K27me3-only and bivalent genes had TSS specific 5-hmC deposition, were enriched in development and differentiation pathways, and had significantly lower expression in cell lines with high MYCN expression. However, unlike H3K27me3-only genes, bivalent genes were also enriched for transcription factor biding sites of AP-2 and E2F which co-regulate MYCN. Using a publicly available dataset of 498 tumors, we found that bivalent genes were transcriptionally repressed in MYCN-amplified tumor samples. Within the cohort of 175 high-risk patients, those with lower expression of bivalent genes (N=55) had worse overall survival (OS) from diagnosis than those (N=120) with high expression (5-year OS: 27.2% vs. 52.0%; 95% CI: 17.1%-43.3% vs 42.9%-63.1%, p=0.001 by log-rank test). Conclusion: The low-level expression of bivalent genes enriched for 5-hmC at the TSS in MYCN-amplified neuroblastoma cells may represent a novel mechanism by which dedifferentiated states and aggressive phenotype is maintained in MYCN-amplified neuroblastoma.

Citation Format: Mohansrinivas Chennakesavalu, Gepoliano Chaves, Kelley Moore, Tong Wu, Ruitu Lyu, Rachel TerHaar, Alexandre Chlenski, Chuan He, Susan Cohn, Andrea Piunti, Mark Applebaum. Assessing the role of bivalency in MYCN-amplified neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A025.

Impact of Early Pandemic SARS-CoV-2 Lineages Replacement with the Variant of Concern P.1 (Gamma) in Western Bahia, Brazil

BACKGROUND

The correct understanding of the epidemiological dynamics of COVID-19, caused by the SARS-CoV-2, is essential for formulating public policies of disease containment.

METHODS

In this study, we constructed a picture of the epidemiological dynamics of COVID-19 in a Brazilian population of almost 17000 patients in 15 months. We specifically studied the fluctuations of COVID-19 cases and deaths due to COVID-19 over time according to host gender, age, viral load, and genetic variants.

RESULTS

As the main results, we observed that the numbers of COVID-19 cases and deaths due to COVID-19 fluctuated over time and that men were the most affected by deaths, as well as those of 60 or more years old. We also observed that individuals between 30- and 44-years old were the most affected by COVID-19 cases. In addition, the viral loads in the patients' nasopharynx were higher in the early symptomatic period. We found that early pandemic SARS-CoV-2 lineages were replaced by the variant of concern (VOC) P.1 (Gamma) in the second half of the study period, which led to a significant increase in the number of deaths.

CONCLUSIONS

The results presented in this study are helpful for future formulations of efficient public policies of COVID-19 containment.

First description of a multisystemic and lethal SARS-CoV-2 variant of concern P.1 (Gamma) infection in a FeLV-positive cat

BACKGROUND

Phylogenetic studies indicate bats as original hosts of SARS-CoV-2. However, it remains unclear whether other animals, including pets, are crucial in the spread and maintenance of COVID-19 worldwide.

METHODS

In this study, we analyzed the first fatal case of a SARS-CoV-2 and FeLV co-infection in an eight-year-old male cat. We carried out a clinical evaluation and several laboratory analyses.

RESULTS

As main results, we observed an animal presenting severe acute respiratory syndrome and lesions in several organs, which led to the animal's death. RT-qPCR analysis showed a SARS-CoV-2 as the causative agent. The virus was detected in several organs, indicating a multisystemic infection. The virus was found in a high load in the trachea, suggesting that the animal may have contribute to the transmission of the virus. The whole-genome sequencing revealed an infection by SARS-CoV-2 Gamma VOC (P.1), and any mutations indicating host adaptation were observed.

CONCLUSION

Our data show that FeLV-positive cats are susceptible to SARS-CoV-2 infection and raise questions about the potential of immunocompromised FeLV-positive cats to act as a reservoir for SARS-CoV-2 new variants.

Mutant Huntingtin Affects Diabetes and Alzheimer's Markers in Human and Cell Models of Huntington's Disease

A higher incidence of diabetes was observed among family members of individuals affected by Huntington's Disease with no follow-up studies investigating the genetic nature of the observation. Using a genome-wide association study (GWAS), RNA sequencing (RNA-Seq) analysis and western blotting of Rattus norvegicus and human, we were able to identify that the gene family of sortilin receptors was affected in Huntington's Disease patients. We observed that less than 5% of SNPs were of statistical significance and that sortilins and HLA/MHC gene expression or SNPs were associated with mutant huntingtin (mHTT). These results suggest that ST14A cells derived from R. norvegicus are a reliable model of HD, since sortilins were identified through analysis of the transcriptome in these cells. These findings help highlight the genes involved in mechanisms targeted by diabetes drugs, such as glucose transporters as well as proteins controlling insulin release related to mHTT. To the best of our knowledge, this is the first GWAS using RNA-Seq data from both ST14A rat HD cell model and human Huntington's Disease.

Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology

Examining the behavior of a single cell within its natural environment is valuable for understanding both the biological processes that control the function of cells and how injury or disease lead to pathological change of their function. Single-cell analysis can reveal information regarding the causes of genetic changes, and it can contribute to studies on the molecular basis of cell transformation and proliferation. By contrast, whole tissue biopsies can only yield information on a statistical average of several processes occurring in a population of different cells. Electrowetting within a nanopipette provides a nanobiopsy platform for the extraction of cellular material from single living cells. Additionally, functionalized nanopipette sensing probes can differentiate analytes based on their size, shape or charge density, making the technology uniquely suited to sensing changes in single-cell dynamics. In this review, we highlight the potential of nanopipette technology as a non-destructive analytical tool to monitor single living cells, with particular attention to integration into applications in molecular biology.

Avaliação das Propriedades Físico-Químicas de Diferentes Pastas de Hidróxido de Cálcio

O objetivo deste trabalho foi avaliar e comparar a composic,ão química e a radiopacidade de diferentes pastas de hidróxido de cálcio. Foram avaliadas treˆs pastas comerciais: Ultracal XS Hydropast e Callen. O hidróxido de cálcio PA foi utilizado como controle. Para avaliar a composição química dos materiais, uma amostra de cada pasta foi avaliada por análise termogravimétrica, e a massa de hidróxido de cálcio presente foi obtida através de cálculos estequiométricos a partir da decomposic,ão térmica de suas moléculas. Para avaliar a radiopacidade, foram analisadas 03 amostras para cada grupo. A radiopacidade foi avaliada com um sistema de radiografia digital indireta EXPRESS e equipamento de raios X FOCUS. As imagens obtidas foram analisadas quanto aos padrões do valor de cinza através do software ImageJ. Os percentuais de massa de hidróxido de cálcio obtidos para cada material foram: hidróxido de cálcio PA: 87,12% Ultracal XS: 36,38% Hydropast: 30,66% Callen: 50,54%. Os valores de escala de cinza das pastas foram de: 63,41 para o hidróxido de cálcio PA 126,35 para Ultracal XS 106,73 para Hydropast, e 72,23 para Callen. Na mesma análise, a escala de alumínio apresentou os valores: Al 1mm: 53,50 Al 4 mm:  98,06 Al 8mm:  162,14 Al 12mm: 205,4. Houve diferenc,as em todas as pastas entre a quantidade de hidróxido de cálcio informada pelo fabricante e a quantidade encontrada nas análises termogravimétricas. As pastas comerciais testadas apresentaram maior radiopacidade que o grupo controle. A Ultracal XS foi o material com maior radiopacidade, seguido da Hydropast e Callen.Palavras-chave: Hidróxido de Cálcio. Termogravimetria. Radiografia.

Metabolic and transcriptomic analysis of Huntington's disease model reveal changes in intracellular glucose levels and related genes

Huntington's Disease (HD) is a neurodegenerative disorder caused by an expansion in a CAG-tri-nucleotide repeat that introduces a poly-glutamine stretch into the huntingtin protein (mHTT). Mutant huntingtin (mHTT) has been associated with several phenotypes including mood disorders and depression. Additionally, HD patients are known to be more susceptible to type II diabetes mellitus (T2DM), and HD mice model develops diabetes. However, the mechanism and pathways that link Huntington's disease and diabetes have not been well established. Understanding the underlying mechanisms can reveal potential targets for drug development in HD. In this study, we investigated the transcriptome of mHTT cell populations alongside intracellular glucose measurements using a functionalized nanopipette. Several genes related to glucose uptake and glucose homeostasis are affected. We observed changes in intracellular glucose concentrations and identified altered transcript levels of certain genes including Sorcs1, Hh-II and Vldlr. Our data suggest that these can be used as markers for HD progression. Sorcs1 may not only have a role in glucose metabolism and trafficking but also in glutamatergic pathways affecting trafficking of synaptic components.

Helminths of hawksbill turtle (Eretmochelys imbricata) from the Pacific coast of Costa Rica

Parasitological examination of a stranded hawksbill turtle (Eretmochelys imbricata) from Pacific coast of Costa Rica revealed the presence of a rich digenean fauna including Carettacola stunkardi (Spirorchiidae), Enodiotrema reductum (Plagiorchiidae), Cricocephalus albus, Adenogaster serialis, Epi-bathra crassa, Pleurogonius lobatus, P. trigonocephalus, P. linearis, and Pyelosomum posterorchis (Pronocephalidae). All helminths except C. albus and P. lobatus represent new geographical records for Costa Rica. Carettacola stunkardi is reported for first time in an Eastern Pacific hawksbill turtle and its pathological changes are here described. Histologically, nodular lesions on the serosal surface of intestine revealed a mixed infiltrate of heterophils, lymphocytes, and histiocytes within necrotic debris. Granulomas with spirorchiid eggs were observed in the mucosa, sub-mucosa and muscular layers of stomach and intestine, gallbladder and liver.

Hypoosmotic test in equine spermatozoa

The aim of the study was to evaluate equine sperm membrane integrity using the hypoosmotic swelling (HOS) test and to correlate this test with different sperm parameters in raw and frozen thawed semen. The HOS solutions were made with fructose, sucrose, lactose and sodium citrate each at 300, 150, 100, 50 and 25 mosm. Maximum numbers of swollen spermatozoa were observed in solutions of fructose, sucrose and lactose each at 100, 50 and 25 mosm. Correlations between progressive motility, morphologically normal spermatozoa and the HOS test were r = 0.75 and r = 0.51 in raw semen and r = 0.26 and r = -0.22 in frozen-thawed semen. The correlation between HOS and percentage of intact membranes with the fluorescent stain was r = 0.32 in frozen-thawed semen. The HOS test is a simple and accessible method which could be used as a complement to routine equine semen analysis. It has the added advantages of being less susceptible to the immediate effects of cold shock and of evaluating individual spermatozoa rather than the population as a whole, as does progressive motility.