Biology subjects

Pecori, R.

Publications and source records attributed to Pecori, R..

5 recordsLinked to original sources

bioRxiv2025

Benchmarking Software for DDA-PASEF Immunopeptidomics

Mass spectrometry (MS) is the method of choice for high-throughput identification of immunopeptides, which are generated by intracellular proteases, unlike proteomics peptides that are typically derived from trypsin-digested proteins. Therefore, the searching space for immunopeptides is not limited by proteolytic specificity, requiring more sophisticated software algorithms to handle the increased complexity. Despite the widespread use of MS in immunopeptidomics, there is a lack of systematic evaluation of data processing software, making it challenging to identify the optimal solution. In this study, we provide a comprehensive benchmarking of the most widespread/used data-dependent acquisition (DDA)-based software platforms for immunopeptidomics: MaxQuant, FragPipe, PEAKS and MHCquant. The evaluation was conducted using data obtained from the JY cell line using the Thunder-DDA-PASEF method. We assessed each softwares ability to identify immunopeptides and compared their identification confidence. Additionally, we examined potential biases in the results and tested the impact of database size on immunopeptide identification efficiency. Our findings demonstrate that all software platforms successfully identify the most prominent subset of immunopeptides with 1% false discovery rate (FDR) control, achieving medium to high identification confidence correlations. The largest number of immunopeptides were identified using the commercial PEAKS software, which is closely followed by FragPipe, making it a viable non-commercial alternative. However, we observed that larger database sizes negatively impacted the performance of some software platforms more than others. These results provide valuable insights into the strengths and limitations of current MS data processing tools for immunopeptidomics, supporting the immunopeptidomics/MS community in determining the right choice of software.

bioinformatics↗

bioRxiv2023

Neoepitope formation through the generation of RNA-derived "editopes"

Increasing the quantity and immunogenicity of neoantigens in tumors is essential for advancing immunotherapy. However, engineering neoantigens remains challenging due to the need for precise, tumor-specific antigen modification without affecting normal cells. To tackle this challenge, we developed Short Precise-Encodable ADAR Recruiting (SPEAR) ADAR-engagers, an approach that uses short guide RNAs to engage the endogenous RNA editor ADAR1 and direct it to regions of mRNA targets known to encode MHC-presented peptides. By precisely editing adenosine-to-inosine (A-to-I) in these contexts, we effectively mutate specific epitopes into neoepitopes (which we now term "editopes"). As proof of concept, we targeted the known antigen MART-1 (Melanoma-Associated Antigen Recognized by T cells-1), and demonstrated that guided ADAR1 editing can generate immunogenic epitopes that activate T cells and promote tumor cell elimination. Building on this concept, we developed a computational pipeline to identify tumor-specific somatic mutations suitable for SPEAR-mediated editing. This strategy enables selective neoantigen generation in cancer cells, effectively increasing their apparent tumor mutational burden and potentially enhancing their susceptibility to immunotherapy.

cancer biology↗

bioRxiv2020

ADAR1 can drive Multiple Myeloma progression by acting both as an RNA editor of specific transcripts and as a DNA mutator of their cognate genes

RNA editing is an epitranscriptomic modification of emerging relevance to disease development and manifestations. ADAR1, which resides on human chromosome 1q21, is an RNA editor whose over-expression, either by interferon (IFN) induction or through gene amplification, is associated with increased editing and poor outcomes in Multiple Myeloma (MM). Here we explored the role of ADAR1 in the context of MM progression, by focusing on a group of 23 patients in the MMRF CoMMpass Study for which RNAseq and WES datasets exist for matched pre-and post-relapse samples. Our analysis reveals an acquisition of new DNA mutations on disease progression at specific loci surrounding the sites of ADAR associated (A-to-I) RNA editing. These analyses suggest that the RNA editing enzyme ADAR1 can function as a DNA mutator during Multiple Myeloma (MM) progression, and further imply that guide-targeted RNA editing has the capacity to generate specific mutational signatures at predetermined locations. This dual role of RNA editor and DNA mutator might be shared by other deaminases, such as APOBECs, so that DNA mutation might be the result of collateral damage on the genome by an editing enzyme whose primary job is to re-code the cognate transcript toward specific functional outcomes.

genomics↗

bioRxiv2019

MultiEditR: An easy validation method for detecting and quantifying RNA editing from Sanger sequencing

RNA editing is the base change that results from RNA deamination by two predominant classes of deaminases; the APOBEC family and the ADAR family. Respectively, deamination of nucleobases by these enzymes are responsible for endogenous editing of cytosine to uracil (C-to-U) and adenosine to inosine (A-to-I). RNA editing is known to play an essential role both in maintaining normal cellular function, as well as altered cellular physiology during oncogenesis and tumour progression. Analysis of RNA editing in these important processes, largely relies on RNA-seq technology for the detection and quantification of RNA editing sites. Despite the power of these technologies, multiple sources of error in detecting and measuring base editing still exist, therefore additional validation and quantification of editing through Sanger sequencing is still required for confirmation of editing. Depending on the number of RNA editing sites that are of interest, this validation step can be both expensive and time-consuming. To address this need we developed the tool MultiEditR which provides a simple, and cost-effective method of detecting and quantifying RNA editing form Sanger sequencing. We expect that MultiEditR will foster further discoveries in this rapidly expanding field.

bioinformatics↗

bioRxiv2018

Dimerisation of APOBEC1 is dispensable for its RNA editing activity

The AID/APOBECs are DNA/RNA deaminases whose mutagenic activity has been linked to cancer. Among them, APOBEC1 physiologically partakes into a complex that edits a CAA codon into UAA Stop codon in the transcript of Apolipoprotein B (APOB), a protein crucial in the transport of lipids in the blood. Catalytically inactive mutants of APOBEC1 have a dominant negative effect on its activity, as they compete for the targeting of the APOB mRNA. Here we titrate APOBEC1-mediated editing in presence of catalytically inactive chimeras and mutants of APOBEC1, and we show that APOBEC1 inability to dimerise is the main determinant for its activity. This property is especially evident in an APOBEC1 mutant (L173A G227A) with increased activity on RNA despite decreased self-interaction. Moreover, dimerisation protects APOBEC1 from degradation and regulates its availability. Considering APOBEC1 capability to target DNA, we demonstrate that increased availability of the protein due to dimerisation leads to increase in the DNA damage induced by APOBEC1. These findings demonstrate that dimerisation, a property common to other APOBECs targeting DNA, might represent another layer in the regulation of this editing enzyme. BULLET POINTSO_LIAPOBEC1 inability to dimerise is the main determinant for its activity. C_LIO_LIDimerisation protects APOBEC1 from degradation and regulates its availability. C_LIO_LIAlterations in the balance between monomeric and dimeric APOBEC1 increase DNA damage. C_LI

molecular biology↗