Transcriptional Profiling of Laser Capture Microdissected Subpopulations of the Osteoblast Lineage Provides Insight Into the Early Response to Sclerostin Antibody in Rats

Fruit development proceeds from cell division to expansion, maturation, and ripening. Expansion is critical for size, yield, and quality; however, this period of development has received little attention. We used 454-pyrosequencing to develop a cucumber (Cucumis sativus) fruit transcriptome, identify highly expressed transcripts, and characterize key functions during exponential fruit growth. The resulting 187,406 expressed sequence tags (ESTs) were assembled into 13,878 contigs. Quantitative real-time polymerase chain reaction (qRT-PCR) verification of differentially expressed genes from fruit of different ages, and high correlation in transcript frequency between replicates, indicated that number of reads/contig reflects transcript abundance. Putative homologs were identified in Arabidopsis thaliana for 89% of the contigs represented by at least 10 ESTs; another 4% had homologs in other species. The remainder had homologs only in cucurbit species. The most highly expressed contigs were strongly enriched for growth (aquaporins, vacuolar ATPase, phloem proteins, tubulins, actins, cell wall-associated, and hormone-related), lipid, latex, and defense-related homologs. These results provide a resource for gene expression analysis in cucumber, profile gene expression in rapidly growing fruit, and shed insight into an important, but poorly characterized, developmental stage influencing fruit yield and quality.

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MR Spectroscopic Imaging Predicts Early Response to Anti-Angiogenic Therapy in Recurrent Glioblastoma

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab060 ◽

2021 ◽

Author(s):

Pratik Talati ◽

Mohamed El-Abtah ◽

Daniel Kim ◽

Jorg Dietrich ◽

Melanie Fu ◽

...

Keyword(s):

Patient Outcomes ◽

Early Response ◽

Recurrent Glioblastoma ◽

Time Points ◽

Angiogenic Therapy ◽

Longitudinal Mri ◽

Early Failures ◽

Assess Treatment Response ◽

Insight Into ◽

Mr Spectroscopic Imaging

Abstract Background Determining failure to anti-angiogenic therapy in recurrent GBM (rGBM) remains a challenge. The purpose of the study was to assess treatment response to bevacizumab-based therapy in patients with rGBM using MR spectroscopy (MRS). Methods We performed longitudinal MRI/MRS in 33 patients with rGBM to investigate whether changes in N-acetylaspartate (NAA)/Choline (Cho) and Lactate (Lac)/NAA from baseline to subsequent time points after treatment can predict early failures to bevacizumab-based therapies. Results After stratifying based on 9 month survival, longer-term survivors had increased NAA/Cho and decreased Lac/NAA levels compared to shorter-term survivors. ROC analyses for intratumoral NAA/Cho correlated with survival at 1 day, 2 weeks, 8 weeks, and 16 weeks. Intratumoral Lac/NAA ROC analyses were predictive of survival at all time points tested. At the 8 week time point, 88% of patients with decreased NAA/Cho did not survive 9 months; furthermore, 90% of individuals with an increased Lac/NAA from baseline did not survive at 9 months. No other metabolic ratios tested significantly predicted survival. Conclusions Changes in metabolic levels of tumoral NAA/Cho and Lac/NAA can serve as early biomarkers for predicting treatment failure to anti-angiogenic therapy as soon as 1 day after bevacizumab-based therapy. The addition of MRS to conventional MR methods can provide better insight into how anti-angiogenic therapy affects tumor microenvironment and predict patient outcomes.

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Extensive phylogenies of human development reveal variable embryonic patterns

10.1101/2020.11.25.397828 ◽

2020 ◽

Author(s):

Tim H. H. Coorens ◽

Luiza Moore ◽

Philip S. Robinson ◽

Rashesh Sanghvi ◽

Joseph Christopher ◽

...

Keyword(s):

Progenitor Cell ◽

Spatial Effect ◽

Lineage Tracing ◽

Substantial Variation ◽

Normal Tissues ◽

Multiple Organs ◽

Naturally Occurring ◽

Adult Body ◽

Laser Capture ◽

Laser Capture Microdissected

ABSTRACTStarting from the zygote, all cells in the developing and adult human body continuously acquire mutations. A mutation shared between two different cells implies a shared progenitor cell and can thus be used as a naturally occurring marker for lineage tracing. Here, we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissected samples from multiple organs. Early embryonic progenitor cells inferred from the phylogenies often contribute in different proportions to the adult body and the extent of this asymmetry is variable between individuals, with ratios between the first two reconstructed cells ranging from 56:44 to 92:8. Asymmetries also pervade subsequent cell generations and can differ between tissues in the same individual. The phylogenies also resolve the spatial embryonic origins and patterning of tissues, revealing a spatial effect in the development of the human brain. Supplemented by data on eleven men, we timed the split between soma and germline, with the earliest observed segregation occurring at the first cell divisions. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.

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Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-promoting stromal components

10.1101/783621 ◽

2019 ◽

Author(s):

Parisa Amini ◽

Sina Nassiri ◽

Alexandra Malbon ◽

Enni Markkanen

Keyword(s):

Screening Method ◽

Malignant Tumours ◽

Differential Abundance ◽

Naturally Occurring ◽

Mammary Tumours ◽

Ffpe Specimen ◽

Summary Statement ◽

Benign Tumours ◽

Laser Capture ◽

Laser Capture Microdissected

AbstractThe importance of cancer-associated stroma (CAS) for initiation and progression of cancer is well accepted. However, as stromal changes in benign forms of naturally occurring tumours are poorly understood, it remains unclear how CAS from benign and malignant tumours compare. Spontaneous canine mammary tumours are viewed as excellent models of human mammary carcinomas (mCA). We have recently reported highly conserved stromal reprogramming between canine and human mCA based on transcriptome analysis of laser-capture-microdissected FFPE specimen. To identify stromal changes between benign and malignant mammary tumours, we have analysed CAS and matched normal stroma from 13 canine mammary adenomas and compared them to 15 canine mCA. Our analyses revealed distinct stromal reprogramming even in small benign tumours. While similarities in stromal reprogramming exist, the CAS signature clearly distinguished adenomas from mCA, suggesting that it may reliably discriminate between benign and malignant tumours. We identified strongly discriminatory genes and found strong differential enrichment in several hallmark signalling pathways between benign and malignant CAS. The distinction between CAS from adenoma and mCA was further substantiated by differential abundance in cellular composition. Finally, to determine key players in CAS reprograming between adenomas and mCA, a network-based gene screening method identified modules of co-expressing genes with distinct expression profile in benign and malignant CAS, and revealed several hub genes as potential molecular drivers in CAS. Given the relevance of canine CAS as a model for the human disease, our approach identifies potential stromal drivers of tumour malignancy with implications for human mCA.Summary statementRNAsequencing-based analysis of stromal reprogramming between benign and malignant naturally occurring canine mammary tumours identifies potential molecular drivers in cancer-associated stroma that support tumour growth and malignancy.

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