Biology subjects

Cecchi, F.

Publications and source records attributed to Cecchi, F..

2 recordsLinked to original sources

bioRxiv2022

High-Field Asymmetric Waveform Ion Mobility Spectrometry and Parallel Reaction Monitoring Increases Sensitivity for Clinical Biomarker Quantitation from Formalin-Fixed, Paraffin-Embedded Tumor Biopsies

Mass spectrometry-based targeted proteomics allows objective protein quantitation of clinical biomarkers from a single section of formalin-fixed, paraffin-embedded (FFPE) tumor tissue biopsies. We combined high-field asymmetric waveform ion mobility spectrometry (FAIMS) and parallel reaction monitoring (PRM) to increase assay sensitivity. The modular nature of the FAIMS source allowed direct comparison of the performance of FAIMS-PRM to PRM. Limits of quantitation were determined by spiking synthetic peptides into a human spleen matrix. In addition, 20 clinical samples were analyzed using FAIMS-PRM and the quantitation of HER2 was compared with that obtained with the Ventana immunohistochemistry assay. FAIMS-PRM improved the overall signal-to-noise ratio over that from PRM and increased assay sensitivity in FFPE tissue analysis for four (HER2, EGFR, cMET, and KRAS) of five proteins of clinical interest. FAIMS-PRM enabled sensitive quantitation of basal HER2 expression in breast cancer samples classified as HER2 negative by immunohistochemistry. Furthermore, we determined the degree of FAIMS-dependent background reduction and showed that this correlated with an improved lower limit of quantitation with FAIMS. FAIMS-PRM is anticipated to benefit clinical trials in which multiple biomarker questions must be addressed and the availability of tumor biopsy samples is limited.

cancer biology↗

bioRxiv2020

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed.

The objective of this study was to investigate the genomic background of the Garfagnina (GRF) goat breed that faces the risk of extinction. In total, 48 goats genotyped with the Illumina CaprineSNP50 BeadChip were analyzed together with 214 goats belonging to 9 Italian breeds (~25 goats/breed) from the AdaptMap project [Argentata (ARG), Bionda dellAdamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. We estimated i) runs of homozygosity (ROH), ii) admixture ancestries and iii) traceability success via discriminant analysis on principal components (DAPC) based on cross-validation. For GRF, an excess of frequent ROH (more than 45% in the GRF samples analyzed) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), spanned between the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area was also present in DIT, while the broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis depicted the uniqueness of the GRF breed, with a small part of common ancestry shared with BIO, VSS, ARG and CCG breeds. The DAPC model resulted in a 100% assignment success. We hope this work will contribute to the efforts of preventing the GRF from extinction and to add value to all the socio-agro-economic factors related with the farming of the GRF breed.

genetics↗