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Article ; Online: Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters.

Ceschi, Silvia / Berselli, Michele / Cozzaglio, Marta / Giantin, Mery / Toppo, Stefano / Spolaore, Barbara / Sissi, Claudia

Nucleic acids research

2022 Volume 50, Issue 3, Page(s) 1370–1381

Abstract: G-quadruplex (G4) structures that can form at guanine-rich genomic sites, including telomeres and gene promoters, are actively involved in genome maintenance, replication, and transcription, through finely tuned interactions with protein networks. In the ...

Abstract	G-quadruplex (G4) structures that can form at guanine-rich genomic sites, including telomeres and gene promoters, are actively involved in genome maintenance, replication, and transcription, through finely tuned interactions with protein networks. In the present study, we identified the intermediate filament protein Vimentin as a binder with nanomolar affinity for those G-rich sequences that give rise to at least two adjacent G4 units, named G4 repeats. This interaction is supported by the N-terminal domains of soluble Vimentin tetramers. The selectivity of Vimentin for G4 repeats versus individual G4s provides an unprecedented result. Based on GO enrichment analysis performed on genes having putative G4 repeats within their core promoters, we suggest that Vimentin recruitment at these sites may contribute to the regulation of gene expression during cell development and migration, possibly by reshaping the local higher-order genome topology, as already reported for lamin B.
MeSH term(s)	G-Quadruplexes ; Guanine/chemistry ; Intermediate Filaments ; Promoter Regions, Genetic ; Telomere/metabolism ; Vimentin/metabolism
Chemical Substances	Vimentin ; Guanine (5Z93L87A1R)
Language	English
Publishing date	2022-01-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab1274
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Article ; Online: Chromoscope: interactive multiscale visualization for structural variation in human genomes.

L'Yi, Sehi / Maziec, Dominika / Stevens, Victoria / Manz, Trevor / Veit, Alexander / Berselli, Michele / Park, Peter J / Głodzik, Dominik / Gehlenborg, Nils

Nature methods

2023 Volume 20, Issue 12, Page(s) 1834–1835

Language	English
Publishing date	2023-11-01
Publishing country	United States
Document type	Letter
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-023-02056-x
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Article ; Online: QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable.

Berselli, Michele / Lavezzo, Enrico / Toppo, Stefano

Bioinformatics (Oxford, England)

2019 Volume 36, Issue 2, Page(s) 393–399

Abstract: Motivation: G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: ... ...

Abstract	Motivation: G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE. Results: QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS, respectively). While its assessment versus known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2 and hTERT. Availability and implementation: QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	DNA ; G-Quadruplexes ; Humans ; Nucleic Acid Conformation ; RNA ; Sequence Analysis, DNA
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2019-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz569
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Article: Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations.

Nadimpalli Kobren, Shilpa / Moldovan, Mikhail A / Reimers, Rebecca / Traviglia, Daniel / Li, Xinyun / Barnum, Danielle / Veit, Alexander / Willett, Julian / Berselli, Michele / Ronchetti, William / Sherwood, Richard / Krier, Joel / Kohane, Isaac S / Sunyaev, Shamil R

bioRxiv : the preprint server for biology

2024

Abstract: Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients. The increasing sizes of ultra-rare, "N-of-1" disease cohorts internationally newly enables cohort-wide analyses for ... ...

Abstract	Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients. The increasing sizes of ultra-rare, "N-of-1" disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.
Language	English
Publishing date	2024-02-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.13.580158
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Article ; Online: NeSSie: a tool for the identification of approximate DNA sequence symmetries.

Berselli, Michele / Lavezzo, Enrico / Toppo, Stefano

Bioinformatics (Oxford, England)

2018 Volume 34, Issue 14, Page(s) 2503–2505

Abstract: Motivation: Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, ...

Abstract	Motivation: Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures. Results: We developed NeSSie, an easily customizable C/C++ 64-bit library and tool, based on dynamic programming, to quickly scan for perfect and degenerate DNA palindromes, mirrors and potential triplex forming patterns. In addition, the tool computes linguistic complexity and Shannon entropy measures to verify the repetitive nature of the DNA regions enriched in these motifs. As a case study, the analysis of the Mycobacterium bovis genome is presented. Availability and implementation: http://www.medcomp.medicina.unipd.it/main_site/doku.php? id=nessie and https://github.com/B3rse/nessie. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	DNA/chemistry ; DNA/metabolism ; Genome ; Genome, Bacterial ; Genomics/methods ; Mycobacterium bovis/genetics ; Nucleic Acid Conformation ; Sequence Analysis, DNA/methods ; Software
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2018-03-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty142
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Article: NeSSie: a tool for the identification of approximate DNA sequence symmetries

Berselli, Michele / Hancock, John / Lavezzo, Enrico / Toppo, Stefano

Bioinformatics. 2018 July 15, v. 34, no. 14

2018

Abstract: Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform ... ...

Abstract	Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures. We developed NeSSie, an easily customizable C/C++ 64-bit library and tool, based on dynamic programming, to quickly scan for perfect and degenerate DNA palindromes, mirrors and potential triplex forming patterns. In addition, the tool computes linguistic complexity and Shannon entropy measures to verify the repetitive nature of the DNA regions enriched in these motifs. As a case study, the analysis of the Mycobacterium bovis genome is presented. http://www.medcomp.medicina.unipd.it/main_site/doku.php? id=nessie and https://github.com/B3rse/nessie Supplementary data are available at Bioinformatics online.
Keywords	bioinformatics ; case studies ; DNA ; dynamic programming ; entropy ; genes ; genomics ; Mycobacterium bovis ; nucleotide sequences
Language	English
Dates of publication	2018-0715
Size	p. 2503-2505.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4811 ; 1367-4803
ISSN (online)	1460-2059 ; 1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty142
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Article ; Online: Universal screening to identify Lynch syndrome: two years of experience in a Northern Italian Center.

Chiaravalli, A M / Carnevali, I / Sahnane, N / Leoni, E / Furlan, D / Berselli, M / Sessa, F / Tibiletti, M G

European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)

2019 Volume 29, Issue 4, Page(s) 281–288

Abstract: Lynch syndrome is caused by germline mutations of genes affecting the mismatch repair proteins MLH1, MSH2, MSH6 or PMS2. Identification of Lynch syndrome patients using germline molecular testing in colorectal cancer (CRC) affected patients and in their ... ...

Abstract	Lynch syndrome is caused by germline mutations of genes affecting the mismatch repair proteins MLH1, MSH2, MSH6 or PMS2. Identification of Lynch syndrome patients using germline molecular testing in colorectal cancer (CRC) affected patients and in their healthy relatives is a cost-effective model of cancer prevention. Several studies demonstrate that universal tumor testing using immunohistochemical (IHC) analysis of CRC samples is the most efficient approach to identifying patients affected by Lynch syndrome. We studied a cohort of 352 consecutive CRCs for MSH2, MLH1, MSH6 and PMS2 protein expression using universal IHC screening. IHC mismatch repair (MMR) defects were identified in 70 out of 352 cases (19.8%) including six CRCs MSH2/MSH6 defective, two CRCs, respectively, MSH6 and PMS2 defective, 58 CRCs MLH1/PMS2 defective and four CRCs showing atypical MMR pattern. MLH1 promoter methylation and V600E BRAF mutation analysis were investigated on 61 CRCs. Cancer genetic counseling was offered to all 68 patients affected by MMR defective CRCs and 25 patients opted in to this service (36.8% compliance). Pathogenetic variants of MSH2 genes were identified in two cases (55 and 79 years old). Universal screening based on an IHC approach showed a Lynch syndrome incidence of 1/173. The protocol recommended by regional law improved patient compliance. This study demonstrates that the IHC approach for both MMR deficiency and V600E BRAF mutation detections is the most efficient approach for Lynch syndrome screening in the Italian population.
Language	English
Publishing date	2019-10-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1137033-6
ISSN	1473-5709 ; 0959-8278
ISSN (online)	1473-5709
ISSN	0959-8278
DOI	10.1097/CEJ.0000000000000543
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Article ; Online: BamSnap: a lightweight viewer for sequencing reads in BAM files.

Kwon, Minseok / Lee, Soohyun / Berselli, Michele / Chu, Chong / Park, Peter J

Bioinformatics (Oxford, England)

2020 Volume 37, Issue 2, Page(s) 263–264

Abstract: Summary: Despite the improvement in variant detection algorithms, visual inspection of the read-level data remains an essential step for accurate identification of variants in genome analysis. We developed BamSnap, an efficient BAM file viewer utilizing ...

Abstract	Summary: Despite the improvement in variant detection algorithms, visual inspection of the read-level data remains an essential step for accurate identification of variants in genome analysis. We developed BamSnap, an efficient BAM file viewer utilizing a graphics library and BAM indexing. In contrast to existing viewers, BamSnap can generate high-quality snapshots rapidly, with customized tracks and layout. As an example, we produced read-level images at 1000 genomic loci for >2500 whole-genomes. Availability and implementation: BamSnap is freely available at https://github.com/parklab/bamsnap. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2020-12-31
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa1101
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Article ; Online: Open versus laparoscopic gastrectomy for advanced gastric cancer: a propensity score matching analysis of survival in a western population-on behalf of the Italian Research Group for Gastric Cancer.

Lombardi, Pietro Maria / Bernasconi, D / Baiocchi, G L / Berselli, M / Biondi, A / Castoro, C / Catarci, M / Degiuli, M / Fumagalli Romario, U / Giacopuzzi, S / Marchesi, F / Marrelli, D / Mazzola, M / Molfino, S / Olmi, S / Rausei, S / Rosa, F / Rosati, R / Roviello, F /

Santi, S / Solaini, L / Staderini, F / Viganò, J / Ferrari, G

Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association

2022 Volume 25, Issue 6, Page(s) 1105–1116

Abstract: Background: Oncologic outcomes after laparoscopic gastrectomy for advanced gastric cancer in the West have been poorly investigated. The aim of the present study was to compare survival outcomes in patients undergoing curative-intent laparoscopic and ... ...

Abstract	Background: Oncologic outcomes after laparoscopic gastrectomy for advanced gastric cancer in the West have been poorly investigated. The aim of the present study was to compare survival outcomes in patients undergoing curative-intent laparoscopic and open gastrectomy for advanced gastric cancer in several centres belonging to the Italian Research Group for Gastric Cancer. Methods: Data of patients operated between 2015 and 2018 were retrospectively analysed. Propensity Score Matching was performed to balance baseline characteristics of patients undergoing laparoscopic and open gastrectomy. The primary endpoint was 3-year overall survival. Secondary endpoints were 3-year disease-free survival and short-term outcomes. Multivariable regression analyses for survival were conducted. Results: Data were retrieved from 20 centres. Of the 717 patients included, 438 patients were correctly matched, 219 per group. The 3-year overall survival was 73.6% and 68.7% in the laparoscopic and open group, respectively (p = 0.40). When compared with open gastrectomy, laparoscopic gastrectomy showed comparable 3-year disease-free survival (62.8%, vs 58.9%, p = 0.40), higher rate of return to intended oncologic treatment (56.9% vs 40.2%, p = 0.001), similar 30-day morbidity/mortality. Prognostic factors for survival were ASA Score ≥ 3, age-adjusted Charlson Comorbidity Index ≥ 5, lymph node ratio ≥ 0.15, p/ypTNM Stage III and return to intended oncologic treatment. Conclusions: Laparoscopic gastrectomy for advanced gastric cancer offers similar rates of survival when compared to open gastrectomy, with higher rates of return to intended oncologic treatment. ASA score, age-adjusted Charlson Comorbidity Index, lymph node ratio, return to intended oncologic treatment and p/ypTNM Stage, but not surgical approach, are prognostic factors for survival.
MeSH term(s)	Humans ; Stomach Neoplasms/pathology ; Propensity Score ; Retrospective Studies ; Adenocarcinoma/pathology ; Treatment Outcome ; Gastrectomy/adverse effects ; Laparoscopy/adverse effects
Language	English
Publishing date	2022-07-21
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1463526-4
ISSN	1436-3305 ; 1436-3291
ISSN (online)	1436-3305
ISSN	1436-3291
DOI	10.1007/s10120-022-01321-w
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Article: Oligometastatic Gastric Cancer: Clinical Data from the Meta-Gastro Prospective Register of the Italian Research Group on Gastric Cancer.

Bencivenga, Maria / Ministrini, Silvia / Morgagni, Paolo / Mura, Gianni / Marrelli, Daniele / Milandri, Carlo / Mazzei, Maria Antonietta / Berselli, Mattia / Monti, Manlio / Graziosi, Luigina / Reddavid, Rossella / Rosa, Fausto / Solaini, Leonardo / Donini, Annibale / Fumagalli Romario, Uberto / Roviello, Franco / de Manzoni, Giovanni / Tiberio, Guido Alberto Massimo

Cancers

2023 Volume 16, Issue 1

Abstract: Background: Interest in the field of metastatic gastric cancer has grown in recent years, and the identification of oligometastatic patients plays a critical role as it consents to their inclusion in multimodal treatment strategies, which include ... ...

Abstract	Background: Interest in the field of metastatic gastric cancer has grown in recent years, and the identification of oligometastatic patients plays a critical role as it consents to their inclusion in multimodal treatment strategies, which include systemic therapy but also surgery with curative intent. To collect sound clinical data on this subject, The Italian Research Group on Gastric Cancer developed a prospective multicentric observational register of metastatic gastric cancer patients called META-GASTRO. Methods: Data on 383 patients in Meta-Gastro were mined to help our understanding of oligometastatic, according to its double definition: quantitative/anatomical and dynamic. Results: the quantitative/anatomical definition applies to single-site metastases independently from the metastatic site ( Conclusions: META-GASTRO supports the two-fold definition of oligometastatic gastric cancer: the quantitative/anatomical one, which accounts for 30% of our population, and the dynamic one, observed in 16% of our cases.
Language	English
Publishing date	2023-12-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers16010170
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