bluuebunny/crossref_metadata_2025 huggingface dataset:
TBIO-06. Study of cell free DNA extracted from CSF enables molecular classification of embryonal brain tumors
Authors: Mathieu Chicard , Iddir Yasmine , Masliah-Planchon Julien , Combaret Valérie , Saint-Charles Alexandra , Baulande Sylvain , Delattre Olivier , Waterfall Joshua , Bourdeaut Franck , Schleiermacher Gudrun
Published: June 2022

Liquid biopsies are revolutionary tools to detect tumour-specific genetic alterations in body fluids. Here, we assess whether the circulating tumor DNA (ctDNA) in Cerebral Spinal Fluid (CSF) could be used for the tumor genetic profiling of pediatric embryonal brain tumors (EBT). Cell free DNA extracted from CSF from 4-5 lumbar puncture droplets from patients with Medulloblastoma (n=18), ATRT (n=3), ETMR(n=1), FOXR2 EBT (n=2) or other pediatric EBT (n=1) (cfDNA mean quantity 48 ng/ml ; range 5.6 - 442 ng/ml) and matched genomic DNA from primary tumors were sequenced by WES (Illumina 100PE) using Nimblegen Medexome Capture. SNVs/mutations were called using GATK-UnifiedGenotyper, GATK-HaplotypeCaller and Samtools. Copy Number profiles were generated with CNVkits. 10/13 cfDNA WES yielded satisfactory depth (>10x). A mean of 466 (range 93-945) SNVs were detected in the primary tumor and 474 (range 18-922) in the CSF. A mean of 416 (range 18-872) commons SNVs were observed between the cfDNA and the primary tumor, comprising classical medulloblastoma genes such as SMO or MLL2. Interestingly, several SNVs were observed either in the tumor only (mean 50 ; range 3-115) or in CSF only (mean 58 ; range 0-148) suggesting a clonal heterogeneity. For 5 cases, Copy Number profiles were also available, allowing the detection of MYCN amplification or 19q13 miRNA cluster amplification. Altogether, we demonstrate the feasibility of WES on CSF with a low input of ctDNA. These results may pave the way for new tumor monitoring tools.
TBIO-07. Pediatric tumor classification through genome-wide methylation profiling of extracellular vesicle DNA
Authors: Ricklefs Franz , Maire Cecile , Fita Krys , Fritzsche Friederike , Kammler Gertrud , Westphal Manfred , Lamszus Katrin , Schüller Ulrich
Published: June 2022

BACKGROUND: Genome-wide methylation profiling reliably classifies pediatric central nervous system (CNS) tumors. Extracellular vesicles (EVs) are released by pediatric CNS tumor cells (pCC) and contain high molecular weight tumor DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated, whether the DNA in pCC-derived EVs reflects genome-wide tumor methylation profiles and allows tumor subtype classification. Currently, the tests are being expanded to include blood samples (n=80 patients). METHODS: DNA was isolated from EVs secreted by pediatric CNS tumor cells (pCC) as well as from the shortly cultured tumor cells and from the original tumor samples (n=4 patients). Pediatric Fibroblasts and EVs derived thereof were used as a non-tumorous control. EVs were classified by nanoparticle analysis (NTA), immunoblotting, imaging flow cytometry (IFCM and electron microscopy. Genome-wide DNA methylation profiling was performed using an 850k Illumina EPIC array and results were classified according to the DKFZ brain tumor classifier and further analysed by t-SNE and Copy number alteration analysis (CNA). RESULTS: The size range of pCC-derived EVs was 120-150 nm, as measured by NTA. The majority of secreted EVs exhibited high expression of common EV markers (i.e. CD9, CD63 and CD81), as characterized by IFCM. Genome-wide DNA methylation profiling of pCC-derived EVs correctly identified the methylation class of the original tumor (i.e. pilocytic astrocytoma, medulloblastoma). In addition, t-SNE analysis and copy number alterations matched the pattern of the parental pCC and original tumor samples. CONCLUSION: EV DNA faithfully reflects the tumor methylation class and copy number alterations present in the parental cells and the original tumor. Methylation profiling of circulating tumor EV DNA could become a useful tool to detect and classify pediatric CNS tumors.
TBIO-09. EZHIP is not expressed within the developing mouse or human brain
Authors: Talal Younes Subhi , Weaver Kristin , Collier Anderson , Herrington Betty
Published: June 2022

The protein EZHIP, first described as part of the genetic signature of group A posterior fossa ependymoma (PFA), functions in a manner analogous to the onco-histone H3K27M, itself first described in diffuse midline glioma (DMG). These two proteins modulate activity of the Polycomb repressive complex 2 (PRC2), resulting in global loss of H3K27 trimethylation. Thus, both PFA and DMG are characterized by global loss of the H3K27me3 mark, and PRC2 modulation is critical to oncogenesis of these tumors. However, the precise mechanism(s) of EZHIP and H3K27M-induced tumorigenesis is not known. One possibility is that EZHIP is expressed within the developing brain where it acts to modulate cellular development. In turn, EZHIP overexpression or H3K27M mutation could co-opt this developmental program to drive tumorigenesis. Relatedly, whether EZHIP is expressed in the cell of origin for PFA or DMG is not known. In order to evaluate these hypotheses, we defined the landscape of EZHIP expression in both murine and human developing brain. Leveraging single cell RNA sequencing databases, we show that EZHIP is not expressed within the developing mouse brain, a finding that is consistent across separate datasets. Similarly, EZHIP is not expressed in the developing murine cerebellum, where the cell of origin for PFA is located. Furthermore, we examined bulk RNA sequencing datasets of the developing human brain. Similar to our findings in the mouse brain, EZHIP is not expressed at any time point or spatial location within the developing human brain. Taken together, these data reject the above hypothesis, that EZHIP or H3K27M co-opt an endogenous PRC2 inhibitory developmental program. Similarly, these results show that EZHIP is not expressed within the cell of origin for PFA or DMG. Further studies will seek to understand the endogenous function of EZHIP by further defining its normal expression pattern and function.
TBIO-10. NGS molecular profile of paediatric brain tumours: results from 92 consecutive patients treated at Centro Hospitalar Universitário de São João
Authors: Lima Jorge , Pinheiro Jorge , Nunes Susana , Fernandes Ana Paula , Soares Paula , Machado Jose Carlos , Pereira Josue , da Costa Maria Joao Gil
Published: June 2022

AIM: Our aim was to progress in bringing molecular medicine to routine clinical practice in the setting of paediatric neuro-oncology. We have implemented a protocol between Ipatimup and Centro Hospitalar Universitário de São João for the rapid and efficient delivery of the molecular portrait of paediatric brain tumours. MATERIAL AND METHODS: We have enrolled 92 patients with the following inclusion criteria: Age 0-18 years; newly diagnosed brain tumour; previously diagnosed brain tumour, whenever it presented as rare, aggressive or refractory disease; availability of tumour material; signed informed consent. Tumour samples were centrally reviewed by expert pathologists and profiled using the Oncomine Childhood Cancer Research Assay. RESULTS: In the 92 tumours that were molecularly profiled, BRAF was the most frequently altered gene, especially in pilocytic astrocytomas, being also detected in other LGG and HGG. Other commonly mutated genes were PIK3CA and FGFR, the former in HGG and the latter in LGG. MYB and RAF1 rearrangements were also found in low grade glial/glioneuronal tumours, while HGG showed a more complex profile, with many cases harbouring multiple alterations in EGFR, PDGFRA, ATRX, H3F3A, HIST1H3B, TP53, among others. A 16-year old patient with CMMR (homozygous mutation in PMS2) developed a glioblastoma that carried nearly 5x the average number of mutations. Among the 8 medulloblastomas, 2 showed mutations in the SHH pathway (1 in PTCH1 and one in SUFU) and 2 in the WNT pathway (1 in CTNNB1 and one in APC). In the remaining cases, one ependymoma presented MYCN amplification, while no alterations were detected in 3 patients. CONCLUSIONS: This study enabled the detailed molecular study of 92 paediatric brain patients, allowing a more robust tumour classification and the identification of actionable alterations. A subset of the patients are already undergoing targeted therapy, mainly using BRAF or MEK inhibitors with generally good improvement.
THER-01. Precision brain tumor therapy by AAV-mediated oncogene editing
Authors: von Soosten Laura , Haar Janina , Frehtman Veronika , Holderbach Stefan , Belzen Julius Upmeier zu , Jendrusch Michael , Okonechnikov Konstantin , Pfister Stefan M , Grimm Dirk , Leuchs Barbara , Jones David , Kutscher Lena M , Zuckermann Marc
Published: June 2022

Pediatric high-grade glioma is a heterogeneous group of highly malignant tumors of the central nervous system, with a median overall survival of less than two years after diagnosis, demanding novel treatment options. One innovative approach is gene therapy, which has so far been hampered for cancer treatment owing to the lack of a system targeting tumor cells specifically. To overcome this limitation, we established a novel strategy for gene therapy, combining tumor cell-specific adeno-associated virus (AAV) variants with oncogene-specific CRISPR-Cas nucleases. We screened 177 different Cas9/gRNA combinations targeting the genes encoding H3K27M or BRAFV600E, and identified highly specific nucleases that edited the oncogenic allele but left the respective WT loci intact, which we validated by PCR amplicon sequencing. Next, we intravenously injected an AAV library engineered to encode its own capsid DNA into mice harboring patient-derived xenograft tumors driven by H3K27M or BRAFV600E. After 21 days, we resected neoplasms and separated mCherry-labeled tumor cells from normal surrounding cells by fluorescence-activated cell sorting. Using the DNA from tumor cells as template, we generated a second AAV library, which was utilized in another round of in vivo selection. At the end of each screen, DNA from tumor cells, surrounding cells, and control tissues (liver and spleen) was analyzed by amplicon sequencing. Strikingly, we identified multiple AAV variants that were highly and recurrently enriched in the analyzed tumor tissues. We are currently validating these variants by intravenously injecting selected, GFP-encoding AAVs to tumor-bearing mice and by subsequently analyzing their distribution throughout the aforementioned tissues. We will combine oncogene-specific nucleases with these validated AAV variants and analyze their anti-tumoral efficacy in a preclinical setting. Furthermore, we plan to adapt this approach to allografted mice, evaluating its feasibility and efficacy in syngeneic models.
THER-02. Pediatric brain tumor cultures reveal differential susceptibility to four oncolytic viruses
Authors: Vazaios Konstantinos , Stavrakaki Eftychia , Vogelezang Lisette , van den Hoogen Bernadette , Hoeben Rob C , Chiocca Antonio E , Goins William F , Hulleman Esther , Straetemans Trudy , Calkoen Friso G J , van der Lugt Jasper , Lamfers Martine L M
Published: June 2022

INTRODUCTION: New therapeutic modalities such as Oncolytic viruses (OVs) are considered possible treatment options for pediatric brain tumors (PBTs) either as monotherapy or as adjuvants to immunotherapies. OVs specifically lyse tumor cells and can induce anti-tumor immune responses. Here, we evaluate the oncolytic potency of different clinically relevant OVs against various PBT entities. METHODS: The effect of four different OVs, Reovirus (R124), Newcastle Disease virus (NDV), Adenovirus (DNX-2401) and Herpes simplex virus-1 (rQNestin 34.5v.1), was assessed on patient-derived cell cultures belonging to four different PBT entities. Cell viability 5 days after virus treatment of diffuse midline gliomas (DMG n=6), atypical teratoid rhabdoid tumors (n=4), glioblastomas (n=1) and ependymomas (n=2) was measured using Cell Titer Glo assay to demonstrate the cytotoxic potency of each virus. RESULTS: Our screenings revealed that DNX-2401, rQNestin and NDV could infect and kill the majority of cell cultures (12 out of 13, 11 out of 13 and 11 out of 13, respectively). rQNestin34.5v.1 required lower amounts of infectious particles per cell (MedianEC50: 0.65±2.7) compared to NDV (3.5±1.7) and DNX-2401 (7.5±14.5), with DMGs being more sensitive for rQNestin34.5v.1 than non-DMGs. R124 was effective in only 6 out of 13 cultures, with DMGs being more resistant with EC50 > 100 (5 out of 6) compared to non-DMG cell lines with EC50 < 8 (5 out of 7). CONCLUSION: All cell lines revealed differential susceptibility to the 4 different OVs with at least one effective OV per cell line. Further analysis of transcriptome and methylome data might uncover genes and pathways which correlate with specific OV susceptibility and provide biomarkers for response prediction. Further investigation is ongoing to interpret how differential susceptibility affects OV-induced anti-tumor immunity.
INSP-08. Cerebellar mutism syndrome: incidence, symptoms, risk factors, prognosis. Results and future perspectives from the Nordic-European study of the cerebellar mutism syndrome
Authors: Sehested Astrid , Grønbæk Jonathan , Laustsen Aske , Juhler Marianne
Published: June 2022

Cerebellar mutism syndrome (CMS) can be a devastating consequence of paediatric fossa posterior tumour surgery. This prospective observational multi-centre study was designed to investigate incidence, symptoms, risk factors and prognosis of CMS. It has been running since 2014 and is currently involving 28 centres in 10 countries. So far 600 patients have been included as of 1.2.22, and with the aim of including a total of 1000 the study is still ongoing. Analysis of the first 500 patients has described the incidence, course and associated risk factors of postoperative speech impairment (POSI). Midline location, histological diagnosis of medulloblastoma and ATRT and younger age are associated with increased risk of POSI in our cohort. Route of surgical access specifically comparing telovelar to transvermian approach does not seem to influence the risk of POSI. Second surgery is associated with a lower risk of POSI than primary surgery, whereas we found no difference in risk of cranial nerve dysfunction. Left-handedness is not associated with an increased risk of POSI. Further and ongoing analysis include language analyses of recorded patient speech samples, detailed imaging analysis and description of associations between POSI and other neurological symptoms. The results aim to facilitate pre-operative risk assessment and postoperative robust scoring methods for use in clinical trials. Presented on behalf of the CMS study group, clinicaltrials.gov: Nordic study of the cerebellar mutism syndrome.
LGG-28. Rapid symptomatic improvement for a patient treated with BRAF inhibition for BRAFV600E mutated ganglioglioma
Authors: Cantor Evan , Cochrane Anne , Morris Stephanie , Meyer Ashley , Ogle Andrea , Shatara Margaret , Cluster Andrew , Deng Mai , Abdelbaki Mohamed S , Brossier Nicole M
Published: June 2022

BACKGROUND: Biologically targeted agents such as the BRAF inhibitor dabrafenib are now used to treat progressive low-grade glioma (LGG), but the effect of these agents on the neurologic symptoms that accompany LGGs is poorly understood. CASE: A 21-year-old male was diagnosed with medullary ganglioglioma (GG) after presenting with persistent vertigo and positional headaches. Immunohistochemistry was consistent with BRAF V600E mutation and dabrafenib was started. The patient had resolution of his neurologic symptoms within 3 weeks of treatment initiation; surveillance MRI several months later demonstrated interval decrease in tumor size. The patient remained on therapy for 2 years. Several days after planned drug discontinuation the patient had re-emergence of persistent vertigo that impaired his ability to work. Repeat imaging two months later demonstrated an increase in tumor size and solid enhancement along tumor margins. He was restarted on dabrafenib. Within one week, he again had complete resolution of his vertigo. DISCUSSION: Gangliogliomas are comprised of mixed neuronal and glial components and associated with epilepsy, headache and other localizing neurologic symptoms. In this report, we describe clinical and radiographic response from single-therapy dabrafenib in a patient with BRAF V600E+ GG, along with a very rapid resolution of neurologic symptoms upon initiation of the drug and recrudescence shortly following cessation of therapy. The symptoms subsided within a week of restarting dabrafenib, suggesting a separate, more rapid mechanism of symptom reversal than decline in tumor size. BRAF mutations have been identified in both the neuronal and glial components of ganglioglioma, suggesting that dabrafenib may provide symptomatic relief via inhibition of abberant neuronal processes. CONCLUSION: BRAF inhibitors can rapidly improve neurological symptoms via a rapid, not yet fully elucidated mechanism. Kinetics of this response suggest it is independent of effects on tumor volume and the degree of compression to tissue surrounding the tumor.
The psychosocial work environment among educators during the COVID-19 pandemic
Authors: Smith P , Oudyk J , Cedillo L , Inouye K , Potter G , Mustard C
Published: June 2022

Background

The education sector has been heavily impacted by COVID-19. While the impact on school-aged children has received much attention, less attention has focused on the experiences of educators.

Aims

To compare various dimensions of the psychosocial work environment and health outcomes between educators engaged in online learning to those engaged in in-person learning in the Canadian province of Ontario.

Methods

Responses from 5438 educators engaged in either online or in-person learning were collected between 23 November and 21 December 2020; three months after the start of the 2020/21 academic year in September 2020. Psychosocial outcomes included quantitative demands, work pace, predictability, role conflicts, and social support from supervisors and co-workers; assessed using an abbreviated version of the Copenhagen Psychosocial Questionnaire. Secondary outcomes included burnout and sleep troubles. Ordinary Least-Squares regression models examined adjusted mean differences in the levels of outcomes for respondents in in-person versus online learning, after adjustment for a variety of covariates.

Results

Compared to respondents engaged in in-person learning, respondents engaged in online learning reported less predictability, higher role conflicts and less support from supervisors and co-workers. Statistically significant differences in work pace, burnout and sleep troubles were also observed across learning modes, although these differences did not exceed previously suggested thresholds for minimum important differences.

Conclusions

Important differences in the psychosocial work environment were observed between respondents engaged in in-person learning versus online learning. Addressing these differences is required, given the potential continued importance of online learning within the context of the COVID-19 pandemic and beyond.
Infection Dynamics of Potato Virus Y Isolate Combinations in Three Potato Cultivars
Authors: Mondal Shaonpius , Wintermantel William M. , Gray Stewart M.
Published: June 2022

The United States potato industry has recently experienced a strain shift; recombinant potato virus Y (PVY) strains (e.g., PVYNTN) have emerged as the predominant strains over the long dominant ordinary strain (PVYO), yet both are often found as single infections within the same field and as mixed infections within individual plants. To understand mixed infection dynamics in potato plants and in daughter tubers, three potato varieties varying for PVY resistance, ‘Red Maria’, ‘CalWhite’, and ‘Pike’, were mechanically inoculated either at the pre- or postflowering stage with all possible heterologous isolate combinations of two PVYO and two PVYNTN isolates. Virus titer was determined from leaves collected at different positions on the plant at different times, and tuber-borne infection was determined for two successive generations. PVYNTN accumulated to higher levels than PVYO at nearly all sampling time points in ‘Pike’ potato. However, both virus strains accumulated to similar amounts in ‘Red Maria’ and ‘CalWhite’ potato early in the infection when inoculated preflowering; however, PVYNTN dominated at later stages and in plants inoculated postflowering. Regardless of inoculation time, both virus strains were transmitted to daughter plants raised from the tubers for most isolate combinations. The relative titer of PVYNTN and PVYO isolates at the later stages of mother plant development was indicative of what was found in the daughter plants. Although virus titer differed among cultivars depending on their genetics and virus isolates, it did not change the strain outcome in tuber-borne infection in subsequent generations. Differential virus accumulation in these cultivars suggests isolate-specific resistance to PVY accumulation.
Gonioscopy-Assisted Transluminal Trabeculotomy Following Failed iStent Surgery
Authors: Sigona Mark , Saravanan Amrita , Pipis Spyros , Masood Imran
Published: June 2022

We describe 4 cases of eyes initially treated with phacoemulsification and iStent trabecular microbypass (Glaukos Corporation). These patients subsequently required further surgery and were successfully treated with the removal of the iStent device followed by gonioscopy-assisted transluminal trabeculotomy (GATT), using the iTrack catheter (Ellex Medical Lasers Ltd). Three of the cases had prior first-generation iStent (G1), and 1 had prior second-generation iStent (G2). This case series demonstrates that in selected cases, a further angle procedure in the form of a GATT can show efficacy and durability in the medium term. Our patients had controlled intraocular pressures (IOPs) at 1-year post-GATT: 2 on IOP-lowering therapy and 2 without any IOP-lowering medications. Three patients had transient hyphema and 2 with high IOP in the immediate postoperative period. No patients experienced a decrease in best-corrected visual acuity postoperatively. To the best of our knowledge, there is no prior literature describing this surgical strategy. This series demonstrates that GATT could potentially be an effective procedure in the case of a failed initial iStent microtrabecular bypass.
Association of Polymorphisms at the SIX1/SIX6 Locus With Normal Tension Glaucoma in a Korean Population
Authors: Shin Hye-Young , Lee Young Chun , Lee Mee Yon
Published: June 2022

Précis:

We demonstrated that SIX1/SIX6 locus polymorphism (rs10483727 and rs33912345) was significantly associated with a genetic susceptibility to NTG in a Korean population. More studies are needed to investigate whether the SIX1/SIX6 locus is associated with NTG among various ethnic populations.

Purpose:

Several previous studies have reported that the relevance of the SIX1/SIX6 locus to open angle glaucoma (OAG) in various ethnic populations. However, definitions of OAG patients were different among those studies. The relevance of the SIX1/SIX6 locus to normal tension glaucoma (NTG) in a Korean population remains uncertain. Therefore, the purpose of this study was to investigate the relationship of the SIX1/SIX6 locus with NTG in a Korean cohort.

Method:

Patients with NTG and ethnically matched healthy controls were recruited from eye clinics in Korea (210 cases and 117 controls). Four polymorphisms (rs33912345, rs12436579, rs2179970, and rs10483727) of the SIX1/SIX6 locus were genotyped for 327 subjects using a TaqMan single nucleotide polymorphism genotyping assay.

Results:

The rs33912345 polymorphism was significantly correlated with NTG in the recessive model [odds ratio (OR): 0.265; 95% confidence interval (CI): 0.078–0.898, P=0.033], but not in the allelic and dominant models (both P>0.05). The SNP rs10483727 was significantly associated with NTG in the allelic model (OR: 0.674; 95% CI: 0.464–0.979, P=0.038) and the recessive model (OR: 0.187; 95% CI: 0.058–0.602, P=0.005). Genetic association analysis of SNP rs12436579 and rs2179970 revealed no significant difference in genotype distribution between NTG cases and controls in the allelic, dominant, or recessive models (all P>0.05).

Conclusion:

The current study found that SIX1-SIX6 locus rs10483727 and rs33912345 polymorphisms were significantly associated with NTG risk in the Korean population.
Noninvasive prenatal screening using cell-free DNA
Authors: Mladenka Christine
Published: June 2022

Noninvasive prenatal screening using cell-free DNA involves analysis of a sample of maternal blood for DNA fragments of fetal chromosomes from the fetal–placental unit to detect common chromosome abnormalities, trisomy 21, trisomy 13, trisomy 18, and sex chromosomes as early as 10 weeks' gestation when the fetal fraction is usually more than 4%. It is the most sensitive and specific prenatal screening option for these conditions. Because it is a screening test, false-positive and false-negative results can occur. Positive screen results necessitate further evaluation for diagnosis to confirm a medical condition, before critical decisions regarding pregnancy are made. Professional organizations provide clinical recommendations to providers regarding prescreen and postscreen counseling and management of results.
The Selective Estrogen Receptor Modulator, Raloxifene, Is Protective Against Renal Ischemia–reperfusion Injury
Authors: Hernandez Paul , O’Brien Ciaran , Concors Seth J. , Wang Zhonglin , Ge Guanghui , Hancock Wayne W. , Levine Matthew H.
Published: June 2022

Background.

There is increasing evidence that estrogen is responsible for improved outcomes in female kidney transplant recipients. Although the exact mechanism is not yet known, estrogen appears to exert its protective effects by ameliorating ischemia–reperfusion injury (IRI). In this study, we have examined whether the beneficial effects of exogenous estrogen in renal IRI are replicated by therapy with any one of several selective estrogen receptor modulators.

Methods.

C57BL/6 adult mice underwent standardized warm renal ischemia for 28 min after being injected with the selective estrogen receptor modulators, raloxifene, lasofoxifene, tamoxifen, bazedoxifene, or control vehicle (dimethyl sulfoxide), at 16 and 1 h before IRI. Plasma concentrations of blood urea nitrogen and creatinine were assessed 24, 48, 72, and 96 h post-IRI. Tissue was collected 30 d postischemia for fibrosis analysis using Sirius Red staining.

Results.

Raloxifene treatment in female mice resulted in significantly lower blood urea nitrogen and creatinine after IRI and significantly lower fibrosis 30 d following IRI.

Conclusions.

Raloxifene is protective against both acute kidney injury and fibrosis resulting from renal IRI in a mouse model.
Pleural macrophages translocate to the lung during infection to promote improved influenza outcomes
Authors: Stumpff James P , Kim Sang Yong , Forero Adriana , Nishida Andrew , Steuerman Yael , Gat-Viks Irit , Nair Meera G , Morrison Juliet
Published: June 2022

Seasonal influenza results in 3 to 5 million cases of severe disease and 250,000 to 500,000 deaths annually. Macrophages have been implicated in both the resolution and progression of the disease, but the drivers of these outcomes are poorly understood. We probed mouse lung transcriptomic datasets using the Digital Cell Quantifier algorithm to predict immune cell subsets that correlated with mild or severe influenza A virus (IAV) infection outcomes. We identified a novel lung macrophage population that transcriptionally resembled small serosal cavity macrophages and correlated with mild disease. Until now, the study of serosal macrophage translocation in the context of infections has been neglected. Here, we show that pleural macrophages (PMs) migrate from the pleural cavity to the lung after infection with pH1N1 A/California/04/2009 IAV. We found that the depletion of PMs increased morbidity and pulmonary inflammation. There were increased proinflammatory cytokines in the pleural cavity and an influx of neutrophils within the lung. Our results show PMs are recruited to the lung during IAV infection and contribute to recovery from influenza. This study expands our knowledge of PM plasticity and provides a new source of lung macrophages independent of monocyte recruitment and local proliferation.

GRAPHICAL ABSTRACT
Recapitulating Human Ovarian Aging Using Random Walks
Authors: Johnson Joshua , Emerson John W. , Lawley Sean D.
Published: June 2022

Mechanism(s) that control whether individual human primordial ovarian follicles (PFs) remain dormant, or begin to grow, are all but unknown. One of our groups has recently shown that activation of the Integrated Stress Response (ISR) pathway can slow follicular granulosa cell proliferation by activating cell cycle checkpoints. Those data suggest that the ISR is active and fluctuates according to local conditions in dormant PFs. Because cell cycle entry of (pre)granulosa cells is required for PF growth activation (PFGA), we propose that rare ISR checkpoint resolution allows individual PFs to begin to grow. Fluctuating ISR activity within individual PFs can be described by a random process. In this paper, we model ISR activity of individual PFs by one-dimensional random walks (RWs) and monitor the rate at which simulated checkpoint resolution and thus PFGA threshold crossing occurs. We show that that the simultaneous recapitulation of i) the loss of PFs over time within simulated subjects, and ii) the timing of PF depletion in populations of simulated subjects equivalent to the distribution of the human age of natural menopause can be produced using this approach. In the RW model, the probability that individual PFs grow is influenced by regionally fluctuating conditions, that over time manifests in the known pattern of PFGA. Considered at the level of the ovary, randomness appears to be a key, purposeful feature of human ovarian aging.
Intraindividual variability in cognitive function in older people in the English Longitudinal Study of Ageing: modelling risk factors using a mixed-effects beta-binomial model
Authors: Parker Richard M.A. , Tilling Kate , Terrera Graciela Muniz , Barrett Jessica K.
Published: June 2022

Cognitive functioning in older age has a huge impact on quality of life and physical and mental health. Whilst most research in cognition in older age has focussed on mean levels, there is some evidence that individuals with cognitive functioning that varies a lot around this may have different risk factors and outcomes to those with less variable functioning. Existing approaches to investigate such intraindividual variability (IIV) typically involve deriving a summary statistic for each person from residual error around a fitted mean. However, such methods ignore sampling variability, prohibit the exploration of associations with time-varying factors, and are biased by floor and ceiling effects. To address this, we fitted a mixed-effects location scale beta-binomial model to estimate average per-trial probability and IIV in a word recall test with the English Longitudinal Study of Aging (ELSA). After adjusting for mean performance, in an analysis of 9,873 individuals observed across 7 (mean: 3.4) waves we found IIV to be greater: at older ages; with lower education; in females; with more difficulties with activities of daily living; in later cohorts; and when interviewers recorded issues which may have affected the tests. Our study identifies groups with more varying cognitive performance, which has implications for their daily functioning and care. Further work is needed to identify the impact of this for future health outcomes.
A Spatial Whole-Cell Model for Hepatitis B Viral Infection and Drug Interactions
Authors: Ghaemi Zhaleh , Nafiu Oluwadara , Tajkhorshid Emad , Gruebele Martin , Hu Jianming
Published: June 2022

Despite a vaccine, hepatitis B virus (HBV) remains a world-wide source of infections and deaths, and tackling the infection requires a multimodal approach against the virus. We develop a whole-cell computational platform combining spatial and kinetic models for the infection cycle of a virus host cell (hepatocyte) by HBV. We simulate a near complete viral infection cycle with this whole-cell platform stochastically for 10 minutes of biological time, to predict viral infection, map out virus-host as well as virus-drug interactions. We find that with an established infection, decreasing the copy number of the viral envelope proteins can shift the dominant infection pathways from secreting the capsids from the cell to re-importing the capsids back to the nucleus, resulting in higher viral DNA referred to as covalently closed circular DNA (cccDNA) copy number. This scenario can mimic the consequence of drugs designed to manipulate viral gene expression (such as siRNAs). Viral capsid mutants lead to their destabilization such that they disassemble at nuclear pore complexes, result in an increase in cccDNA copy number. However, excessive destabilization leading to cytoplasmic disassembly does not increase the cccDNA copy number. Finally, our simulations can predict the best drug dosage and timing of its administration to reduce the cccDNA copy number which is the hallmark of infection. Our adaptable computational platform can be utilized to study other viruses, more complex host-virus interactions, and identify the most central viral pathways that can be targeted by drugs or a combination of them.
Tomato brassinosteroid-signaling kinase Bsk830 is a component of flagellin signaling that regulates pre-invasion immunity
Authors: Sobol Guy , Majhi Bharat Bhusan , Pasmanik-Chor Metsada , Zhang Ning , Roberts Holly M. , Martin Gregory B. , Sessa Guido
Published: June 2022

Detection of bacterial flagellin by the tomato receptors Flagellin sensing 2 (Fls2) and Fls3 triggers activation of pattern-triggered immunity (PTI). Tomato signaling components associated or downstream of flagellin receptors are largely unknown. We investigated the involvement of tomato brassinosteroid-signaling kinase 830 (Bsk830) in PTI triggered by flagellin perception. Bsk830 localized to the plasma membrane and interacted with Fls2 and Fls3. Consistent with a role in flagellin- induced signaling, CRISPR/Cas9-generated tomato bsk830 mutants were impaired in ROS accumulation induced by the flagellin-derived flg22 and flgII-28 peptides. In addition, bsk830 mutants developed larger populations of Pseudomonas syringae pv. tomato (Pst) strain DC3000 than wild-type plants, whereas no differences were observed in plants infected with the flagellin deficient Pst DC3000ΔfliC. bsk830 mutants failed to close stomata when infected with Pst DC3000 and Pseudomonas fluorescens, and were more susceptible to Pst DC3000 than wild-type plants when inoculated by dipping, but not by vacuum-infiltration, indicating involvement of Bsk830 in pre-invasion immunity. Analysis of gene expression profiles in bsk830 mutants detected a reduced number of differentially expressed genes and altered expression of jasmonic acid (JA)-related genes. In support of deregulation of JA response in bsk830 mutants, these plants were similarly susceptible to Pst DC3000 and to the Pst DC3118 strain, which is deficient in coronatine production, and more resistant to the necrotrophic fungus Botrytis cinerea following PTI activation. These results indicate that tomato Bsk830 is required for a subset of flagellin-triggered PTI responses and support a model in which Bsk830 negatively regulates JA signaling during PTI activation.
A developmental atlas of somatosensory diversification and maturation in the dorsal root ganglia by single-cell mass cytometry
Authors: Keeler Austin B. , Van Deusen Amy L. , Cheng Irene , Williams Corey M. , Goggin Sarah M , Hirt Ashley K. , Vradenburgh Shayla A. , Fread Kristen I. , Puleo Emily A. , Jin Lucy , Deppmann Christopher D. , Zunder Eli R.
Published: June 2022

Precisely controlled development of the somatosensory system is essential for detecting pain, itch, temperature, mechanical touch, and body position. To investigate the protein-level changes that occur during somatosensory development, we performed single-cell mass cytometry on dorsal root ganglia from C57/BL6 mice, with litter replicates collected daily from E11.5 to P4. Measuring nearly 3 million cells, we quantified 30 molecularly distinct somatosensory glial and 41 distinct neuronal states across all time points. Analysis of differentiation trajectories revealed rare cells that coexpress two or more Trk receptors and overexpress stem cell markers, suggesting that these neurotrophic factor receptors play a role in cell fate specification. Comparison to previous RNA-based studies identified substantial differences between many protein/mRNA pairs, demonstrating the importance of protein-level measurements to identify functional cell states. Overall, this study demonstrates that mass cytometry is a high-throughput, scalable platform to rapidly phenotype somatosensory tissues.
Delayed recovery and host specialization may spell disaster for coral-fish mutualism
Authors: Froehlich Catheline Y.M. , Klanten O. Selma , Hing Martin L. , Dowton Mark , Wong Marian Y.L.
Published: June 2022

Mutualisms are prevalent in many ecosystems, yet little is known about how symbioses are affected by multiple disturbances. Here we show delayed recovery for 13 coral-dwelling goby fishes (genus Gobiodon) compared with their host Acropora corals following 4 consecutive cyclones and heatwaves. While corals became twice as abundant 3 years post-disturbances, their symbiotic gobies were only half as abundant relative to pre-disturbances and half of the goby species disappeared. Although goby species preferred particular coral species, surviving goby species shifted hosts to newly abundant coral species when their preferred hosts became rare. As host specialization is key for goby fitness, shifting hosts may have negative fitness consequences for gobies and corals alike and affect their survival in response to environmental changes. Our study demonstrates that mutualist partners do not respond identically to multiple disturbances, and that goby host plasticity, while potentially detrimental, may be the only possibility for early recovery.
Development and Validation of Multivariable Prediction Models of Serological Response to SARS-CoV-2 Vaccination in Kidney Transplant Recipients
Authors: Osmanodja Bilgin , Stegbauer Johannes , Kantauskaite Marta , Rump Lars Christian , Heinzel Andreas , Reindl-Schwaighofer Roman , Oberbauer Rainer , Benotmane Ilies , Caillard Sophie , Masset Christophe , Kerleau Clarisse , Blancho Gilles , Budde Klemens , Grunow Fritz , Mikhailov Michael , Schrezenmeier Eva , Ronicke Simon
Published: June 2022

Background

Repeated vaccination against SARS-CoV-2 increases serological response in kidney transplant recipients (KTR) with high interindividual variability. No decision support tool exists to predict SARS-CoV-2 vaccination response in KTR.

Methods

We developed, internally and externally validated five different multivariable prediction models of serological response after the third and fourth vaccine dose against SARS-CoV-2 in KTR. Using 27 candidate predictor variables, we applied statistical and machine learning approaches including logistic regression (LR), LASSO-regularized LR, random forest, and gradient boosted regression trees. For development and internal validation, data from 585 vaccinations were used. External validation was performed in four independent, international validation datasets comprising 191, 184, 254, and 323 vaccinations, respectively.

Findings

LASSO-regularized LR performed on the whole development dataset yielded a 23- and 11- variable model, respectively. External validation showed AUC-ROC of 0.855, 0.749, 0.828, and 0.787 for the sparser 11-variable model, yielding an overall performance 0.819.

Interpretation

An 11-variable LASSO-regularized LR model predicts vaccination response in KTR with good overall accuracy. Implemented as an online tool, it can guide decisions when choosing between different immunization strategies to improve protection against COVID-19 in KTR.
Galaxy Training: A Powerful Framework for Teaching!
Authors: Hiltemann Saskia , Rasche Helena , Gladman Simon , Hotz Hans-Rudolf , Larivière Delphine , Blankenberg Daniel , Jagtap Pratik D. , Wollmann Thomas , Bretaudeau Anthony , Goué Nadia , Griffin Timothy J. , Royaux Coline , Le Bras Yvan , Mehta Subina , Syme Anna , Coppens Frederik , Droesbeke Bert , Soranzo Nicola , Bacon Wendi , Psomopoulos Fotis , Gallardo-Alba Cristóbal , Davis John , Föll Melanie Christine , Fahrner Matthias , Doyle Maria A. , Serrano-Solano Beatriz , Fouilloux Anne , van Heusden Peter , Maier Wolfgang , Clements Dave , Heyl Florian , Grüning Björn , Batut Bérénice ,   the Galaxy Training Network
Published: June 2022

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis and stewardship are still rarely taught in life science educational programs [1], resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org); an open access, community-driven framework for the collection of FAIR training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform [2].

Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.
Inclusive fitness forces of selection in an age-structured population
Authors: Roper Mark , Green Jonathan P. , Salguero-Gómez Roberto , Bonsall Michael B.
Published: June 2022

Current evolutionary theories of senescence predict that the force of selection on survival will decline from maturity to zero at the age of last reproduction, and the force of selection on reproduction will decline monotonically from birth. These predictions rest upon the assumption that individuals within a population do not interact with one another. This assumption, however, is violated in social species, where an individual’s survival and/or reproduction may shape the fitness of other group members. In such species, it is inclusive fitness that natural selection optimises. Yet, it remains unclear how the forces of selection on survival and reproduction might be modified when inclusive fitness, rather than population growth rate, is considered the appropriate metric for fitness. Here, we derive inclusive fitness forces of selection for hypothetical populations of social species. We show that selection on survival is not always constant before maturity, and can remain above zero in post-reproductive age classes, contrary to conventional models of senescence. We also show how the trajectory of the force of selection on reproduction does not always decline monotonically from birth, as predicted by classical theory, but instead depends on the balance of benefits to direct fitness and costs to indirect fitness. Our theoretical framework provides the unique opportunity to expand our understanding of senescence across social species, with important implications to species with variable life histories.
Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection
Authors: Allgoewer Kristina , Choi Hyungwon , Vogel Christine
Published: June 2022

Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses with similar symptoms; understanding differences in their molecular impact on the host is therefore of high interest. Viruses interact with the host’s post-translational modifications, inducing changes visible in serum. As modifications are diverse and of low abundance, they typically require additional sample processing which is not feasible for large cohort studies. Therefore, we tested the potential of next-generation proteomics data in its ability to prioritize specific modifications for later targeted analysis. We re-mined published mass spectra from 122 unenriched serum samples from ZIKV and DENV patients for the presence of phosphorylated, methylated, oxidized, glycosylated/glycated, sulfated, and carboxylated peptides. We identified 272 modified peptides with significantly differential abundance in ZIKV and DENV patients. Amongst these, methionine-oxidized peptides from apolipoproteins and glycosylated peptides from immunoglobulin proteins were more abundant in ZIKV patient serum and generate hypotheses on the potential roles of the modification in the infection. The results demonstrate how data-independent acquisition techniques can help prioritize future analyses of peptide modifications.
Ensemble remodeling supports memory-updating
Authors: Mau William , Baggetta Austin M. , Dong Zhe , Sweis Brian M. , Morales-Rodriguez Denisse , Pennington Zachary T. , Francisco Taylor , Freedman David J. , Baxter Mark G. , Shuman Tristan , Cai Denise J.
Published: June 2022

Memory-updating is critical in dynamic environments because updating memories with new information promotes versatility. However, little is known about how memories are updated with new information. To study how neuronal ensembles might support memory-updating, we used a hippocampus-dependent spatial reversal task to measure hippocampal ensemble dynamics when mice switched navigational goals. Using Miniscope calcium imaging, we identified neuronal ensembles (co-active neurons) in dorsal CA1 that were spatially tuned and stable across training sessions. When reward locations were moved during a reversal session, a subset of these ensembles decreased their activation strength, correlating with memory-updating. These “remodeling” ensembles were a result of weakly-connected neurons becoming less co-active with their peers. Middle-aged mice were impaired in reversal learning, and the prevalence of their remodeling ensembles correlated with their memory-updating performance. Therefore, we have identified a mechanism where the hippocampus breaks down ensembles to support memory-updating.