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2. Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation

Author

Fitzgerald, Rebecca C., Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Loreno, Christine, Redmond, Aisling M., Abbas, Sujath, Freeman, Adam, Smyth, Elizabeth C., O'Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Cheah, Calvin, Coles, Hannah, Millington, Curtis, Devonshire, Ginny, Eldridge, Matthew, Secrier, Maria, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H., Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O'Neill, J Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Contino, Gianmarco, Underwood, Timothy J., Walker, Robert C., Grace, Ben L., Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Chan, David, Cheong, Ed, Kumar, Bhaskar, Sreedharan, L., Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Scott, Michael, Sothi, Sharmila, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Moorthy, Krishna, Grabowska, Anna, Turkington, Richard, McManus, Damian, Coleman, Helen, Petty, Russell D., Bartlet, Freddie, O'Neill, J. Robert, Yébenes Mayordomo, Marcos, Mitulović, Goran, Al Shboul, Sofian, Bedran, Georges, Faktor, Jakub, Hernychova, Lenka, Uhrik, Lukas, Gómez-Herranz, Maria, Kocikowski, Mikołaj, Vojtěšek, Bořivoj, Arends, Mark J., Hupp, Ted, and Alfaro, Javier Antonio

Published
2024
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4. Use of a Cytosponge biomarker panel to prioritise endoscopic Barrett's oesophagus surveillance: a cross-sectional study followed by a real-world prospective pilot

Author

Pilonis, Nastazja Dagny, Killcoyne, Sarah, Tan, W Keith, O'Donovan, Maria, Malhotra, Shalini, Tripathi, Monika, Miremadi, Ahmad, Debiram-Beecham, Irene, Evans, Tara, Phillips, Rosemary, Morris, Danielle L, Vickery, Craig, Harrison, Jon, di Pietro, Massimiliano, Ortiz-Fernandez-Sordo, Jacobo, Haidry, Rehan, Kerridge, Abigail, Sasieni, Peter D, and Fitzgerald, Rebecca C

Published
2022
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5. Serial ctDNA detection using a personalized, tumor-informed assay in esophageal adenocarcinoma patients following resection

Author

Ococks, Emma, Sharma, Shruti, Tian Ng, Alvin Wei, Aleshin, Alexey, Fitzgerald, Rebecca C., Smyth, Elizabeth, Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Fidziukiewicz, Elwira, Redmond, Aisling M., Northrop, Alex, Abbas, Sujath, Smyth, Elizabeth C., O’Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Grantham, Amber, Cheah, Calvin, Coles, Hannah, Flint, Connor, Eldridge, Matthew, Secrier, Maria, Devonshire, Ginny, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H., Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O’Neill, J. Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Contino, Gianmarco, Underwood, Timothy J., Walker, Robert C., Grace, Ben L., Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Chan, David, Cheong, Ed, Kumar, Bhaskar, Sreedharan, L., Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Scott, Michael, Sothi, Sharmila, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Moorthy, Krishna, Grabowska, Anna, Turkington, Richard, McManus, Damian, Coleman, Helen, and Petty, Russell D.

Published
2021
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6. Baseline Data and Measurement Instruments Reported in Observational Studies in Inflammatory Bowel Disease: Results from a Systematic Review.

Author

Wong, Charlotte, Oostrom, Joep van, Pittet, Valerie, Bossuyt, Peter, Hanzel, Jurij, Samaan, Mark, Tripathi, Monika, Czuber-Dochan, Wladyslawa, Burisch, Johan, Leone, Salvatore, Saldaña, Roberto, Baert, Filip, Kopylov, Uri, Jaghult, Susanna, Adamina, Michel, Gecse, Krisztina, and Arebi, Naila

Abstract

Background Heterogeneity in demographic and outcomes data with corresponding measurement instruments [MIs] creates barriers to data pooling and analysis. Several core outcome sets have been developed in inflammatory bowel disease [IBD] to homogenize outcomes data. A parallel Minimum Data Set [MDS] for baseline characteristics is lacking. We conducted a systematic review to develop the first MDS. Methods A systematic review was made of observational studies from three databases [2000–2021]. Titles and abstracts were screened, full-text articles were reviewed, and data were extracted by two reviewers. Baseline data were grouped into ten domains: demographics, clinical features, disease behaviour/complications, biomarkers, endoscopy, histology, radiology, healthcare utilization and patient-reported data. Frequency of baseline data and MIs within respective domains are reported. Results From 315 included studies [600 552 subjects], most originated from Europe [196; 62%] and North America [59; 19%], and were published between 2011 and 2021 [251; 80%]. The most frequent domains were demographics [311; 98.7%] and clinical [289; 91.7%]; 224 [71.1%] studies reported on the triad of sex [306; 97.1%], age [289; 91.7%], and disease phenotype [231; 73.3%]. Few included baseline data for radiology [19; 6%], healthcare utilization [19; 6%], and histology [17; 5.4%]. Ethnicity [19; 6%], race [17; 5.4%], and alcohol/drug consumption [6; 1.9%] were the least reported demographics. From 25 MIs for clinical disease activity, the Harvey–Bradshaw Index [ n  = 53] and Mayo score [ n  = 37] were most frequently used. Conclusions Substantial variability exists in baseline population data reporting. These findings will inform a future consensus for MDS in IBD to enhance data harmonization and credibility of real-world evidence. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett's oesophagus surveillance: individual-level data analysis.

Author

Black, Emily L., Ococks, Emma, Devonshire, Ginny, Wei Tian Ng, Alvin, O'Donovan, Maria, Malhotra, Shalini, Tripathi, Monika, Miremadi, Ahmad, Freeman, Adam, Coles, Hannah, and Fitzgerald, Rebecca C.

Subjects
BARRETT'S esophagus, METAPLASIA, ESOPHAGUS, MEDICAL sciences, HUMAN genetic variation, ESOPHAGEAL cancer, SHORT bowel syndrome
Published
2024
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9. Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts

Author

Noorani, Ayesha, Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Hughes, Caitriona, Fidziukiewicz, Elwira, Bornschein, Jan, MacRae, Shona, Crawte, Jason, Contino, Gianmarco, Li, Xiaodun, Rue, Rachel de la, O’Donovan, Maria, Miremad, Ahmad, Malhotra, Shalini, Tripathi, Monika, Tavaré, Simon, Lynch, Andy G., Eldridge, Matthew, Secrier, Maria, Bower, Lawrence, Devonshire, Ginny, Perner, Juliane, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Preston, Shaun R., Oakes, Sarah, Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O’Neill, J. Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Underwood, Timothy J., Noble, Fergus, Owsley, Jack, Barr, Hugh, Shepherd, Neil, Old, Oliver, Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Zylstra, Janine, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Harden, Catherine, Bunting, David, Lewis, Mike, Cheong, Ed, Kumar, Bhaskar, Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Eneh, Victor, Igali, Laszlo, Scott, Michael, Sothi, Sharmila, Suortamo, Sari, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Grabowska, Anna, Turkington, Richard, Sawas, Tarek, Killcoyne, Sarah, Iyer, Prasad G., Wang, Kenneth K., Smyrk, Thomas C., Kisiel, John B., Qin, Yi, Ahlquist, David A., Rustgi, Anil K., Costa, Rui J., Gerstung, Moritz, Fitzgerald, Rebecca C., and Katzka, David A.

Published
2018
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12. Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

Author

Kim, Eun Na, primary, Chen, Phyllis Zixuan, additional, Bressan, Dario, additional, Tripathi, Monika, additional, Miremadi, Ahmad, additional, di Pietro, Massimiliano, additional, Coussens, Lisa M, additional, Hannon, Gregory J, additional, Fitzgerald, Rebecca C, additional, Zhuang, Lizhe, additional, and Chang, Young Hwan, additional

Published
2023
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14. Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

Author

Kim, Eun Na, Chen, Phyllis Zixuan, Bressan, Dario, Tripathi, Monika, Miremadi, Ahmad, di Pietro, Massimiliano, Coussens, Lisa M, Hannon, Gregory J, Fitzgerald, Rebecca C, Zhuang, Lizhe, and Chang, Young Hwan

Subjects
Article
Abstract

SummaryImaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for singlecell-based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dimensional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as a spatial reference and integrates small FOVs IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images, and demonstrated the advantage of the dual-modality imaging strategy.MotivationHighly multiplexed tissue imaging allows visualization of the spatially resolved expression of multiple proteins at the single-cell level. Although imaging mass cytometry (IMC) using metal isotope-conjugated antibodies has a significant advantage of low background signal and absence of autofluorescence or batch effect, it has a low resolution that hampers accurate cell segmentation and results in inaccurate feature extraction. In addition, IMC only acquires mm2-sized rectangle regions, which limits its application and efficiency when studying larger clinical samples with non-rectangle shapes. To maximize the research output of IMC, we developed the dual-modality imaging method based on a highly practical and technical improvement requiring no extra specialized equipment or agents and proposed a comprehensive computational pipeline that combines IF and IMC. The proposed method greatly improves the accuracy of cell segmentation and downstream analysis and is able to obtain whole slide image IMC to capture the comprehensive cellular landscape of large tissue sections.

Published
2023
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15. OGC P04 Spatial sampling of Barrett's oesophagus reveals that tumour heterogeneity is not a useful predictor of progression to cancer

Author

Katz-Summercorn, Annalise, primary, Peneva, Iliana, additional, Frangou, Anna, additional, Jammula, Sriganesh, additional, O'Donovan, Maria, additional, Tripathi, Monika, additional, Malhotra, Shalini, additional, di Pietro, Massimiliano, additional, Devonshire, Ginny, additional, Redmond, Aisling, additional, Wedge, David, additional, and Fitzgerald, Rebecca, additional

Published
2022
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17. Development of a Core Outcome Set for Real-world Data in Inflammatory Bowel Disease: A European Crohn’s and Colitis Organisation [ECCO] Position Paper

Author

Hanzel, Jurij, primary, Bossuyt, Peter, additional, Pittet, Valerie, additional, Samaan, Mark, additional, Tripathi, Monika, additional, Czuber-Dochan, Wladyslawa, additional, Burisch, Johan, additional, Leone, Salvatore, additional, Saldaña, Roberto, additional, Baert, Filip, additional, Kopylov, Uri, additional, Jäghult, Susanna, additional, Adamina, Michel, additional, Arebi, Naila, additional, and Gecse, Krisztina, additional

Published
2022
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18. Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma.

Author

Abbas, Sujath, Pich, Oriol, Devonshire, Ginny, Zamani, Shahriar A., Katz-Summercorn, Annalise, Killcoyne, Sarah, Cheah, Calvin, Nutzinger, Barbara, Grehan, Nicola, Lopez-Bigas, Nuria, Edwards, Paul A. W., Fidziukiewicz, Elwira, Redmond, Aisling M., Freeman, Adam, Smyth, Elizabeth C., O'Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, and Coles, Hannah

Subjects
DNA repair, BARRETT'S esophagus, ADENOCARCINOMA, NUCLEOTIDE sequencing, CARCINOGENESIS, DNA damage
Abstract

A variety of mutational processes drive cancer development, but their dynamics across the entire disease spectrum from pre-cancerous to advanced neoplasia are poorly understood. We explore the mutagenic processes shaping oesophageal adenocarcinoma tumorigenesis in 997 instances comprising distinct stages of this malignancy, from Barrett Oesophagus to primary tumours and advanced metastatic disease. The mutational landscape is dominated by the C[T > C/G]T substitution enriched signatures SBS17a/b, which are linked with TP53 mutations, increased proliferation, genomic instability and disease progression. The APOBEC mutagenesis signature is a weak but persistent signal amplified in primary tumours. We also identify prevalent alterations in DNA damage repair pathways, with homologous recombination, base and nucleotide excision repair and translesion synthesis mutated in up to 50% of the cohort, and surprisingly uncoupled from transcriptional activity. Among these, the presence of base excision repair deficiencies show remarkably poor prognosis in the cohort. In this work, we provide insights on the mutational aetiology and changes enabling the transition from pre-neoplastic to advanced oesophageal adenocarcinoma. It is critical to understand what drives the progression of oesophageal adenocarcinoma (OAC) from a pre-cancerous state. Here, the authors use whole-genome sequencing to characterise the mutational processes and drivers of OAC progression from Barrett's Oesophagus, as well as their prognostic associations. [ABSTRACT FROM AUTHOR]

Published
2023
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19. ARTIFICIAL INTELLIGENCE - BASED MULTIOPATH TRANSMISSION MODEL FOR WSN ENERGY EFFICIENCY

Author

Shan-E-Fatima and Tripathi, Monika

Subjects
Artificial Intelligence Transmission Models WSN Energy Efficiency
Abstract

This paper presents a network-coding-based transmission strategy called alternative multipath to boost the transmission reliability and energy efficiency of wireless sensor networks (AMNC). Encoded data packets are transmitted to the sink through alternative multipath from the cluster head. MATLAB 7.0 simulates WSNs energy utilization and reliability. Simulation findings show AMNC outperforms parallel multipath based on network coding. The two techniques show this. A well-defined discussion of the research subject, specific technologies, strengths and weaknesses, scopes, and problem formulation is required for any study. The ocean covers approximately two-thirds of the earths surface, therefore its hard for any economy to avoid it (i.e., country). The ocean serves as a main method of transportation, supports international trade, and is crucial for defense. In recent years, it has come to light how crucial ocean or water-routes are for enabling rapid and cost-effective transportation for the expansion of businesses. In order to realize transcontinental commercial practices and discover the true meaning of socioeconomic globalization, the role that oceanic waterways have played has been essential. On the other hand, maintaining efficient real-time environmental or auditory conditioning (also known as condition awareness) is required in order to make optimum mobility possible. Because of its exceptionally high dynamic network topology, an audio channel experiences a significant amount of network deviation as a result, it calls for a communication paradigm that is more effective in order to support the aforementioned application environment. &nbsp

Published
2022
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20. Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas

Author

Ng, Alvin Wei Tian, Contino, Gianmarco, Killcoyne, Sarah, Devonshire, Ginny, Hsu, Ray, Abbas, Sujath, Su, Jing, Redmond, Aisling M., Weaver, Jamie M.J., Eldridge, Matthew D., Tavaré, Simon, Grehan, Nicola, Nutzinger, Barbara, Fidziukiewicz, Elwira, Freeman, Adam, Smyth, Elizabeth C., O’Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Cheah, Calvin, Coles, Hannah, Flint, Connor, Eldridge, Matthew, Secrier, Maria, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H., Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O’Neill, J. Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Scott, Michael, Turkington, Richard, McManus, Damian, Coleman, Helen, Ng, Alvin Wei Tian [0000-0003-4672-0815], Devonshire, Ginny [0000-0002-1408-8176], Eldridge, Matthew D [0000-0002-5799-8911], Edwards, Paul AW [0000-0002-4789-3374], Fitzgerald, Rebecca C [0000-0002-3434-3568], Apollo - University of Cambridge Repository, Eldridge, Matthew [0000-0002-5799-8911], and Fitzgerald, Rebecca [0000-0002-3434-3568]

Subjects
Esophageal Neoplasms, Whole Genome Sequencing, Agricultural and Biological Sciences(all), 631/67/1504/1477, 45, Genome, Human, Biochemistry, Genetics and Molecular Biology(all), article, Medicine (miscellaneous), 45/22, 45/23, 631/67/69, Adenocarcinoma, General Biochemistry, Genetics and Molecular Biology, 631/67/395, 631/67/1244, Humans, General Agricultural and Biological Sciences, Histone Acetyltransferases
Abstract

Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed structural variations (SV) with a predominance of deletions, tandem duplications and inter-chromosome junctions that could be identified as LINE-1 mobile element (ME) insertions. Complex clusters of rearrangements resembling breakage-fusion-bridge cycles or extrachromosomal circular DNA accounted for 22% of complex SVs affecting known oncogenes. Counting SV events affecting known driver genes substantially increased the recurrence rates of these drivers. After excluding fragile sites, we identified 51 candidate new drivers in genomic regions disrupted by SVs, including ETV5, KAT6B and CLTC. RUNX1 was the most recurrently altered gene (24%), with many deletions inactivating the RUNT domain but preserved the reading frame, suggesting an altered protein product. These findings underscore the importance of identification of SV events in OAC with implications for targeted therapies.

Published
2022
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21. The utility of P53 immunohistochemistry in the diagnosis of Barrett's oesophagus with indefinite for dysplasia

Author

Januszewicz, Wladyslaw, primary, Pilonis, Nastazja D, additional, Sawas, Tarek, additional, Phillips, Richard, additional, O'Donovan, Maria, additional, Miremadi, Ahmad, additional, Malhotra, Shalini, additional, Tripathi, Monika, additional, Blasko, Adrienn, additional, Katzka, David A, additional, Fitzgerald, Rebecca C, additional, and Pietro, Massimiliano, additional

Published
2022
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22. Deciphering the Immune Complexity in Esophageal Adenocarcinoma and Pre-Cancerous Lesions With Sequential Multiplex Immunohistochemistry and Sparse Subspace Clustering Approach

Author

Sundaram, Srinand, primary, Kim, Eun Na, additional, Jones, Georgina M., additional, Sivagnanam, Shamilene, additional, Tripathi, Monika, additional, Miremadi, Ahmad, additional, Di Pietro, Massimiliano, additional, Coussens, Lisa M., additional, Fitzgerald, Rebecca C., additional, Chang, Young Hwan, additional, and Zhuang, Lizhe, additional

Published
2022
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23. A Narrative Systematic Review and Categorisation of Outcomes in Inflammatory Bowel Disease to Inform a Core Outcome Set for Real-world Evidence

Author

Wong, Charlotte, primary, van Oostrom, Joep, additional, Bossuyt, Peter, additional, Pittet, Valerie, additional, Hanzel, Jurij, additional, Samaan, Mark, additional, Tripathi, Monika, additional, Czuber-Dochan, Wladyslawa, additional, Burisch, Johan, additional, Leone, Salvatore, additional, Saldaña, Roberto, additional, Baert, Filip, additional, Kopylov, Uri, additional, Jaghult, Susanna, additional, Adamina, Michel, additional, Gecse, Krisztina, additional, and Arebi, Naila, additional

Published
2022
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24. EP1034: HETEROGENEITY IN REPORTED BASELINE DATA AND VARIABLES FROM OBSERVATIONAL STUDIES IN INFLAMMATORY BOWEL DISEASE: RESULTS FROM A SYSTEMATIC REVIEW

Author

Wong, Charlotte, primary, Oostrom, Joep M. van, additional, Bossuyt, Peter, additional, Pittet, Valerie, additional, Hanzel, Jurij, additional, Samaan, Mark A., additional, Tripathi, Monika, additional, Czuber-Dochan, Wladyslawa, additional, Burisch, Johan M., additional, Leone, Salvatore, additional, Saldaña, Roberto, additional, Baert, Filip J., additional, Kopylov, Uri, additional, Jaghult, Susanna, additional, Adamina, Michel, additional, Gecse, Krisztina B., additional, and Arebi, Naila, additional

Published
2022
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27. Development of a Core Outcome Set for Real-world Data in Inflammatory Bowel Disease: A European Crohn's and Colitis Organisation [ECCO] Position Paper.

Author

Hanzel, Jurij, Bossuyt, Peter, Pittet, Valerie, Samaan, Mark, Tripathi, Monika, Czuber-Dochan, Wladyslawa, Burisch, Johan, Leone, Salvatore, Saldaña, Roberto, Baert, Filip, Kopylov, Uri, Jäghult, Susanna, Adamina, Michel, Arebi, Naila, and Gecse, Krisztina

Abstract

Background and Aims The utility of real-world data is dependent on the quality and homogeneity of reporting. We aimed to develop a core outcome set for real-world studies in adult patients with inflammatory bowel disease [IBD]. Methods Candidate outcomes and outcome measures were identified and categorised in a systematic review. An international panel including patients, dietitians, epidemiologists, gastroenterologists, nurses, pathologists, radiologists, and surgeons participated in a modified Delphi consensus process. A consensus meeting was held to ratify the final core outcome set. Results A total of 26 panellists from 13 countries participated in the consensus process. A total of 271 items [130 outcomes, 141 outcome measures] in nine study domains were included in the first-round survey. Panellists agreed that real-world studies on disease activity should report clinical, endoscopic, and biomarker disease activity. A disease-specific clinical index [Harvey–Bradshaw Index, Partial Mayo Score, Simple Clinical Colitis Activity Index] should be used, rather than physician global assessment. In ulcerative colitis [UC], either the UC Endoscopic Index of Severity or the Mayo Endoscopic Score can be used, but there was no consensus on an endoscopic index for Crohn's disease, nor was there consensus on the use of the presence of ulcers. There was consensus on using faecal calprotectin and C-reactive protein. There was no consensus on the use of histology in real-world studies. Conclusions A core outcome set for real-world studies in IBD has been developed based on international multidisciplinary consensus. Its adoption will facilitate synthesis in the generation of real-world evidence. [ABSTRACT FROM AUTHOR]

Published
2023
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28. P-OGC44 Multi-omic cohort study of Barrett’s oesophagus reveals structural variation and retrotransposon activity to occur early in cancer evolution

Author

Katz-Summercorn, Annalise, primary, Jammula, Sriganesh, additional, Frangou, Anna, additional, Peneva, Iliana, additional, O'Donovan, Maria, additional, Tripathi, Monika, additional, Malhotra, Shalini, additional, Pietro, Massimiliano di, additional, Abbas, Shujath, additional, Devonshire, Ginny, additional, Januszewicz, Wladyslaw, additional, Blasko, Adrienn, additional, Nowicki-Osuch, Karol, additional, MacRae, Shona, additional, Northrop, Alex, additional, Redmond, Aisling, additional, Wedge, David, additional, and Fitzgerald, Rebecca, additional

Published
2021
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29. Narrative Systematic Review and Categorisation of Outcomes in Inflammatory Bowel Disease to Inform a Core Outcome Set for Real-world Evidence.

Author

Wong, Charlotte, Oostrom, Joep van, Bossuyt, Peter, Pittet, Valerie, Hanzel, Jurij, Samaan, Mark, Tripathi, Monika, Czuber-Dochan, Wladyslawa, Burisch, Johan, Leone, Salvatore, Saldaña, Roberto, Baert, Filip, Kopylov, Uri, Jaghult, Susanna, Adamina, Michel, Gecse, Krisztina, and Arebi, Naila

Abstract

Background Heterogeneity exists in reported outcomes and outcome measurement instruments [OMI] from observational studies. A core outcome set [COS] for observational and real-world evidence [RWE] in inflammatory bowel disease [IBD] will facilitate pooling large datasets. This systematic review describes and classifies clinical and patient-reported outcomes, for COS development. Methods The systematic review of MEDLINE, EMBASE, and CINAHL databases identified observational studies published between 2000 and 2021 using the population exposure outcome [PEO] framework. Studies meeting eligibility criteria were included. After titles and abstracts screening, full-text articles were extracted by two independent reviewers. Primary and secondary outcomes with corresponding OMI were extracted and categorised in accordance with OMERACT Filter 2.1 framework. The frequency of outcomes and OMIs are described. Results From 5854 studies, 315 were included: 129 [41%] Crohn's disease [CD], 60 [19%] ulcerative colitis [UC], and 126 [40%] inflammatory bowel disease [IBD] studies with 600 552 participants. Totals of 1632 outcomes and 1929 OMI were extracted mainly from medical therapy [181; 72%], surgical [34; 11%], and endoscopic [6; 2%] studies. Clinical and medical therapy-related safety were frequent outcome domains recorded in 194 and 100 studies. Medical therapy-related adverse events [ n = 74] and need for surgery [ n = 71] were the commonest outcomes. The most frequently reported OMI were patient or event numbers [ n = 914], Harvey-Bradshaw Index [ n = 45], and Montreal classification [ n = 42]. Conclusions There is substantial variability in outcomes reporting and OMI types. Categorised outcomes and OMI from this review will inform a Delphi consensus on a COS for future RWE in IBD. Data collection standardisation may enhance the quality of RWE applied to decision-making. [ABSTRACT FROM AUTHOR]

Published
2022
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30. ECCO Topical Review on Clinicopathological Spectrum and Differential Diagnosis of Inflammatory Bowel Disease

Author

Feakins, Roger, primary, Torres, Joana, additional, Borralho-Nunes, Paula, additional, Burisch, Johan, additional, Cúrdia Gonçalves, Tiago, additional, De Ridder, Lissy, additional, Driessen, Ann, additional, Lobatón, Triana, additional, Menchén, Luis, additional, Mookhoek, Aart, additional, Noor, Nurulamin, additional, Svrcek, Magali, additional, Villanacci, Vincenzo, additional, Zidar, Nina, additional, and Tripathi, Monika, additional

Published
2021
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31. Single-bite versus double-bite technique for mapping biopsies during endoscopic surveillance for hereditary diffuse gastric cancer: a single-centre, randomized trial

Author

Fitzgerald, Rebecca, Pappas, A, Tan, Wei Keith, Waldock, William, Richardson, Susan, Tripathi, Monika, Januszewicz, Wladyslaw, Roberts, Geoffrey, O'Donovan, Maria, Di Pietro, Massi, Fitzgerald, Rebecca [0000-0002-3434-3568], Di Pietro, Massimiliano [0000-0003-4866-7026], and Apollo - University of Cambridge Repository

Subjects
Gastrectomy, Stomach Neoplasms, Biopsy, Gastroscopy, Humans, Cadherins, Carcinoma, Signet Ring Cell
Abstract

Background and Aims Endoscopic surveillance is recommended in patients with Hereditary Diffuse Gastric Cancer (HDGC) that want to delay or refuse surgery. Since early signet ring cell carcinoma (SRCC) can be inconspicuous, current surveillance endoscopy protocol entails 30 random biopsies which are time-consuming. This study aimed to compare single and double-bite techniques in HDGC surveillance., The study has received infrastructure support from the Experimental Cancer Medicine Center and Cambridge Biomedical Research Center. AP was funded by a CRUK Multidisciplinary Project Award (C47594/A21202).

Published
2021

32. Serial circulating tumor DNA detection using a personalized, tumor-informed assay in esophageal adenocarcinoma patients following resection

Author

Ococks, Emma, Sharma, Shruti, Ng, Alvin Wei Tian, Consortium, OCCAMS, Aleshin, Alexey, Fitzgerald, Rebecca C, Smyth, Elizabeth, Edwards, Paul AW, Grehan, Nicola, Nutzinger, Barbara, Fidziukiewicz, Elwira, Redmond, Aisling M, Northrop, Alex, Abbas, Sujath, Smyth, Elizabeth C, O���Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Grantham, Amber, Cheah, Calvin, Coles, Hannah, Flint, Connor, Eldridge, Matthew, Secrier, Maria, Devonshire, Ginny, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H, Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J, Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R, Bagwan, Izhar, Save, Vicki, Skipworth, Richard JE, Hupp, Ted R, O���Neill, J Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Contino, Gianmarco, Underwood, Timothy J, Walker, Robert C, Grace, Ben L, Lagergren, Jesper, Gossage, James, Mahadeva, Ula, Davies, Andrew, Chang, Fuju, Goh, Vicky, Ciccarelli, Francesca D, Sanders, Grant, Berrisford, Richard, Chan, David, Cheong, Ed, Kumar, Bhaskar, Sreedharan, L, Parsons, Simon L, Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Scott, Michael, Sothi, Sharmila, Lishman, Suzy, Hanna, George B, Moorthy, Krishna, Peters, Christopher J, Grabowska, Anna, Turkington, Richard, McManus, Damian, Coleman, Helen, and Petty, Russell D

Subjects
Genome Integrity & Repair, Gene Expression, Genetics & Genomics, Computational & Systems Biology
Abstract

No description supplied

Published
2021
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33. ECCO topical review optimising reporting in surgery, endoscopy, and histopathology collaboration between S-ECCO, EduCom, H-ECCO

Author

Adamina, Michel, Feakins, Roger, Iacucci, Marietta, Spinelli, Antonino, Cannatelli, Rosanna, D'Hoore, Andre, Driessen, Ann, Katsanos, Konstantinos, Mookhoek, Aart, Myrelid, Par, Pellino, Gianluca, Peros, Georgios, Tontini, Gian Eugenio, Tripathi, Monika, Yanai, Henit, and Svrcek, Magali

Subjects
reporting, Science & Technology, Gastroenterology & Hepatology, LONG-TERM, inflammatory bowel disease [IBD], CHRONIC ULCERATIVE-COLITIS, Endoscopy, MAGNETIC-RESONANCE ENTEROGRAPHY, CROHNS-DISEASE, COLORECTAL-CANCER, surgery, EVIDENCE-BASED CONSENSUS, pathology, SERRATED EPITHELIAL CHANGES, Human medicine, INTRAABDOMINAL SEPTIC COMPLICATIONS, Life Sciences & Biomedicine, POUCH-ANAL ANASTOMOSIS, INFLAMMATORY-BOWEL-DISEASE
Abstract

BACKGROUND AND AIMS: Diagnosis and management of inflammatory bowel diseases [IBD] requires a lifelong multidisciplinary approach. The quality of medical reporting is crucial in this context. The present topical review addresses the need for optimised reporting in endoscopy, surgery, and histopathology. METHODS: A consensus expert panel consisting of gastroenterologists, surgeons, and pathologists, convened by the European Crohn's and Colitis Organisation, performed a systematic literature review. The following topics were covered: in endoscopy: [i] general IBD endoscopy; [ii] disease activity and surveillance; [iii] endoscopy treatment in IBD; in surgery: [iv] medical history with surgical relevance, surgical indication, and strategy; [v] operative approach; [vi] intraoperative disease description; [vii] operative steps; in pathology: [viii] macroscopic assessment and interpretation of resection specimens; [ix] IBD histology, including biopsies, surgical resections, and neoplasia; [x] IBD histology conclusion and report. Statements were developed using a Delphi methodology incorporating two consecutive rounds. Current practice positions were set when ≥ 80% of participants agreed on a recommendation. RESULTS: Thirty practice positions established a standard terminology for optimal reporting in endoscopy, surgery, and histopathology. Assessment of disease activity, surveillance recommendations, advice to surgeons for operative indication and strategies, including margins and extent of resection, and diagnostic criteria of IBD, as well as guidance for the interpretation of dysplasia and cancer, were handled. A standardised report including a core set of items to include in each specialty report, was defined. CONCLUSIONS: Interdisciplinary high-quality care requires thorough and standardised reporting across specialties. This topical review offers an actionable framework and practice recommendations to optimise reporting in endoscopy, surgery, and histopathology. ispartof: JOURNAL OF CROHNS & COLITIS vol:15 issue:7 pages:1089-1105 ispartof: location:England status: published

Published
2021

34. ID: 3523652 P53 IMMUNOHISTOCHEMISTRY REDUCES THE RATE OF INDEFINITE FOR DYSPLASIA DIAGNOSES IN BARRETT'S ESOPHAGUS ASSESSMENT AND IMPROVES THE INTEROBSERVER AGREEMENT AMONG HISTOPATHOLOGISTS

Author

Januszewicz, Wladyslaw, primary, Pilonis, Nastazja D., additional, Phillips, Richard, additional, O'Donovan, Maria, additional, Sawas, Tarek, additional, Katzka, David A., additional, Miremadi, Ahmad, additional, Malhotra, Shalini, additional, Tripathi, Monika, additional, Blasko, Adrienn, additional, Fitzgerald, Rebecca C., additional, and Di Pietro, Massimiliano, additional

Published
2021
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35. ECCO Position Paper: Harmonisation of the approach to Ulcerative Colitis Histopathology

Author

Magro, Fernando, Doherty, Glen, Peyrin-Biroulet, Laurent, Svrcek, Magali, Borralho, Paula, Walsh, Alissa, Carneiro, Fatima, Rosini, Francesca, de Hertogh, Gert, Biedermann, Luc, Pouillon, Lieven, Scharl, Michael, Tripathi, Monika, Danese, Silvio, Villanacci, Vincenzo, Feakins, Roger, and University of Zurich

Subjects
10219 Clinic for Gastroenterology and Hepatology, 610 Medicine & health
Published
2020
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36. The Utility of P53 Immunohistochemistry in the Diagnosis of Barrett's Esophagus with Indefinite for Dysplasia

Author

Januszewicz, Wladyslaw, primary, Pilonis, Nastazja Dagny, additional, Sawas, Tarek, additional, Phillips, Richard, additional, O'Donovan, Maria, additional, Miremadi, Ahmad, additional, Malhotra, Shalini, additional, Tripathi, Monika, additional, Blasko, Adrienn, additional, Katzka, David A., additional, Fitzgerald, Rebecca C., additional, and di Pietro, Massimiliano, additional

Published
2021
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37. Cytosponge-trefoil factor 3 versus usual care to identify Barrett's oesophagus in a primary care setting: a multicentre, pragmatic, randomised controlled trial

Author

Fitzgerald, Rebecca C, primary, di Pietro, Massimiliano, additional, O'Donovan, Maria, additional, Maroni, Roberta, additional, Muldrew, Beth, additional, Debiram-Beecham, Irene, additional, Gehrung, Marcel, additional, Offman, Judith, additional, Tripathi, Monika, additional, Smith, Samuel G, additional, Aigret, Benoit, additional, Walter, Fiona M, additional, Rubin, Greg, additional, Sasieni, Peter, additional, Bagewadi, Abhay, additional, Patrick, Abigail, additional, Shenoy, Achuth, additional, Redmond, Aisling, additional, Muddu, Ajay, additional, Northrop, Alex, additional, Groves, Alice, additional, Shiner, Alice, additional, Heer, Amardeep, additional, Takhar, Amrit, additional, Bowles, Amy, additional, Jarman, Andrea, additional, Wong, Angela, additional, Lucas, Angie, additional, Gibbons, Anita, additional, Dhar, Anjan, additional, Curry, Anji, additional, Lalonde, Anna, additional, Swinburn, Anna, additional, Turner, Anne, additional, Lydon, Anne-Marie, additional, Gunstone, Anthony, additional, Lee, Arlene, additional, Nambi, Arul, additional, Ariyarathenam, Arun, additional, Elden, Ashley, additional, Wilson, Ashley, additional, Donepudi, Balaji, additional, Campbell, Barbara, additional, Uszycka, Basia, additional, Bowers, Ben, additional, Coghill, Ben, additional, de Quadros, Bruno, additional, Cheah, Calvin, additional, Bratten, Carla, additional, Brown, Carly, additional, Moorbey, Chantelle, additional, Clisby, Charles, additional, Gordon, Charles, additional, Schramm, Chris, additional, Castle, Chris, additional, Newark, Chris, additional, Norris, Chrissie, additional, A'Court, Christine, additional, Graham, Claire, additional, Fletcher, Clare, additional, Grocott, Clare, additional, Rees, Colin, additional, Bakker, Corinne, additional, Paschalides, Costas, additional, Vickery, Craig, additional, Schembri, Damian, additional, Morris, Danielle, additional, Hagan, Daryl, additional, Cronk, David, additional, Goddard, David, additional, Graham, David, additional, Phillips, Dean, additional, Prabhu, Deeksha, additional, Kejariwal, Deepak, additional, Garg, Dhirendra, additional, Lonsdale, Diane, additional, Butterworth, Dianne, additional, Clements, Donna, additional, Bradman, Drew, additional, Blake, Duncan, additional, Mather, Elizabeth, additional, O'Farrell, Ewan, additional, Markowetz, Florian, additional, Adams, Fran, additional, Pesola, Francesca, additional, Forbes, Gareth, additional, Taylor, Gary, additional, Collins, Glenn, additional, Irvine, Gordon, additional, Fourie, Gysbert, additional, Doyle, Harriet, additional, Barnes, Heather, additional, Bowyer, Helen, additional, Whiting, Helen, additional, Beales, Ian, additional, Binnian, Ian, additional, Bremner, Ian, additional, Jennings, Ian, additional, Troiceanu, Ilona, additional, Modelell, Ines, additional, Emmerson, Ingrid, additional, Ortiz, Jacobo, additional, Lilley, Jacqueline, additional, Harvey, Jacquelyn, additional, Vicars, Jacqui, additional, Takhar, Jagjit, additional, Larcombe, James, additional, Bornschein, Jan, additional, Aldegather, Jehad, additional, Johnson, Jenny, additional, Ducker, Jill, additional, Skinner, Jo, additional, Dash, Joanne, additional, Walsh, Joanne, additional, Miralles, Jose, additional, Ridgway, Josephine, additional, Ince, Julia, additional, Kennedy, Julie, additional, Hampson, Kat, additional, Milne, Kate, additional, Ellerby, Katherine, additional, Priddis, Katherine, additional, Rainsbury, Kathy, additional, Powell, Kelly, additional, Gunner, Kerry, additional, Ragunath, Krish, additional, Knox, Kyle, additional, Baseley, Laura, additional, White, Lauren, additional, Lovat, Laurence, additional, Berney, Lee, additional, Crockett, Lindsay, additional, Murray, Lisa, additional, Westwood, Lisa, additional, Chalkley, Lisa, additional, Leggett, Loraine, additional, Dale, Louise, additional, Scovell, Louise, additional, Brooks, Lucy, additional, Saunders, Lucy, additional, Owen, Lydia, additional, Dilwershah, Maria, additional, Baldry, Marie, additional, Corcoran, Marie, additional, Roy, Marie, additional, Macedo, Mario, additional, Attah, Mark, additional, Anson, Mary-Jo, additional, Rutter, Matt, additional, Wallard, Matthew, additional, Gaw, Matthew, additional, Hunt, Matthew, additional, Lea-Hagerty, Megan, additional, Penacerrada, Melchizedek, additional, Bianchi, Michele, additional, Baker-Moffatt, Michelle, additional, Czajkowski, Michelle, additional, Sleeth, Michelle, additional, Brewer, Nick, additional, Wooding, Nick, additional, Todd, Nicky, additional, Millen, Nicola, additional, Zolle, Olga, additional, Whitehead, Orla, additional, Ojechi, Patrick, additional, Moore, Patrick, additional, Banim, Paul, additional, Spellar, Paula, additional, Bhandari, Pradeep, additional, Kant, Prashant, additional, Nixon, Rachel, additional, Russell, Rebecca, additional, Roberts, Rebekah, additional, Skule, Rene, additional, West, Richard, additional, Fox, Robin, additional, Beesley, Ruth, additional, Gibbins, Ruth, additional, Osborne, Ruth, additional, Thiagarajan, S, additional, Bastiman, Sally, additional, Warburton, Samantha, additional, Pai, Samir, additional, Leith-Russell, Sarah, additional, Utting, Sarah, additional, Watson, Sarah, additional, Wytrykowski, Sarah, additional, Singh, Satish, additional, Malhotra, Shalini, additional, Woods, Sharon, additional, Conway, Shaun, additional, Mateer, Sherrie, additional, Macrae, Shona, additional, Singh, Shruti, additional, Fourie, Simona, additional, Campbell, Siobhan, additional, Parslow-Williams, Siobhan, additional, Goel, Sonica, additional, Dellar, Stephen, additional, Jones, Stephen, additional, Knight, Steve, additional, Mackay-Thomas, Stuart, additional, Mukherjee, Stuti, additional, Allen, Sue, additional, Henry, Suzanne, additional, Evans, Tara, additional, Leighton, Theresa, additional, Bray, Tim, additional, Shackleton, Tom, additional, Santosh, Vanaja, additional, Glover, Vicki, additional, Chandraraj, Vijay, additional, Elson, Will, additional, Briggs, William, additional, Barron, Zoe, additional, and Khan, Zohrah, additional

Published
2020
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38. Somatic Evolution in Non-neoplastic IBD-Affected Colon

Author

Olafsson, Sigurgeir, primary, McIntyre, Rebecca E., additional, Coorens, Tim, additional, Butler, Timothy, additional, Jung, Hyunchul, additional, Robinson, Philip S., additional, Lee-Six, Henry, additional, Sanders, Mathijs A., additional, Arestang, Kenneth, additional, Dawson, Claire, additional, Tripathi, Monika, additional, Strongili, Konstantina, additional, Hooks, Yvette, additional, Stratton, Michael R., additional, Parkes, Miles, additional, Martincorena, Inigo, additional, Raine, Tim, additional, Campbell, Peter J., additional, and Anderson, Carl A., additional

Published
2020
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39. Single-bite versus double-bite technique for mapping biopsies during endoscopic surveillance for hereditary diffuse gastric cancer: a single-center, randomized trial

Author

Pappas, Apostolos, primary, Tan, Wei Keith, primary, Waldock, William, additional, Richardson, Susan, additional, Tripathi, Monika, additional, Januszewicz, Wladyslaw, additional, Roberts, Geoffrey, additional, O'Donovan, Maria, additional, Fitzgerald, Rebecca C., additional, and di Pietro, Massimiliano, additional

Published
2020
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40. ECCO Position Paper: Harmonization of the Approach to Ulcerative Colitis Histopathology

Author

Magro, Fernando, primary, Doherty, Glen, additional, Peyrin-Biroulet, Laurent, additional, Svrcek, Magali, additional, Borralho, Paula, additional, Walsh, Alissa, additional, Carneiro, Fatima, additional, Rosini, Francesca, additional, de Hertogh, Gert, additional, Biedermann, Luc, additional, Pouillon, Lieven, additional, Scharl, Michael, additional, Tripathi, Monika, additional, Danese, Silvio, additional, Villanacci, Vincenzo, additional, and Feakins, Roger, additional

Published
2020
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41. 464 MULTI-OMIC CHARACTERIZATION OF BARRETT'S ESOPHAGUS REVEALS A MOLECULAR CONTINUUM IN THE PROGRESSION TO ESOPHAGEAL ADENOCARCINOMA

Author

Katz-Summercorn, Annalise, primary, Jammula, Sriganesh, additional, Frangou, Anna, additional, Peneva, Iliana, additional, O'Donovan, Maria, additional, Tripathi, Monika, additional, Malhotra, Shalini, additional, Di Pietro, Massimiliano, additional, Abbas, Shujath, additional, Devonshire, Ginny, additional, Januszewicz, Wladyslaw, additional, Nowicki-Osuch, Karol, additional, MacRae, Shona, additional, Northrop, Alex, additional, Wedge, David C., additional, and Fitzgerald, Rebecca C., additional

Published
2020
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42. Identification of Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data

Author

Jammula, SriGanesh, primary, Katz-Summercorn, Annalise C., additional, Li, Xiaodun, additional, Linossi, Constanza, additional, Smyth, Elizabeth, additional, Killcoyne, Sarah, additional, Biasci, Daniele, additional, Subash, Vinod V., additional, Abbas, Sujath, additional, Blasko, Adrienn, additional, Devonshire, Ginny, additional, Grantham, Amber, additional, Wronowski, Filip, additional, O’Donovan, Maria, additional, Grehan, Nicola, additional, Eldridge, Matthew D., additional, Tavaré, Simon, additional, Fitzgerald, Rebecca C., additional, Noorani, Ayesha, additional, Edwards, Paul A.W., additional, Nutzinger, Barbara, additional, Hughes, Caitriona, additional, Fidziukiewicz, Elwira, additional, Bornschein, Jan, additional, MacRae, Shona, additional, Crawte, Jason, additional, Northrop, Alex, additional, Contino, Gianmarco, additional, de la Rue, Rachel, additional, Miremadi, Ahmad, additional, Malhotra, Shalini, additional, Tripathi, Monika, additional, Lynch, Andy G., additional, Eldridge, Matthew, additional, Secrier, Maria, additional, Bower, Lawrence, additional, Perner, Juliane, additional, Jammula, Sriganesh, additional, Davies, Jim, additional, Crichton, Charles, additional, Carroll, Nick, additional, Safranek, Peter, additional, Hindmarsh, Andrew, additional, Sujendran, Vijayendran, additional, Hayes, Stephen J., additional, Ang, Yeng, additional, Preston, Shaun R., additional, Oakes, Sarah, additional, Bagwan, Izhar, additional, Save, Vicki, additional, Skipworth, Richard J.E., additional, Hupp, Ted R., additional, O’Neill, J. Robert, additional, Tucker, Olga, additional, Beggs, Andrew, additional, Taniere, Philippe, additional, Puig, Sonia, additional, Underwood, Timothy J., additional, Noble, Fergus, additional, Owsley, Jack, additional, Barr, Hugh, additional, Shepherd, Neil, additional, Old, Oliver, additional, Lagergren, Jesper, additional, Gossage, James, additional, Davies, Andrew, additional, Chang, Fuju, additional, Zylstra, Janine, additional, Mahadeva, Ula, additional, Goh, Vicky, additional, Ciccarelli, Francesca D., additional, Sanders, Grant, additional, Berrisford, Richard, additional, Harden, Catherine, additional, Lewis, Mike, additional, Cheong, Ed, additional, Kumar, Bhaskar, additional, Parsons, Simon L., additional, Soomro, Irshad, additional, Kaye, Philip, additional, Saunders, John, additional, Lovat, Laurence, additional, Haidry, Rehan, additional, Igali, Laszlo, additional, Scott, Michael, additional, Sothi, Sharmila, additional, Suortamo, Sari, additional, Lishman, Suzy, additional, Hanna, George B., additional, Moorthy, Krishna, additional, Peters, Christopher J., additional, Grabowska, Anna, additional, and Turkington, Richard, additional

Published
2020
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43. ECCO Topical Review on Clinicopathological Spectrum and Differential Diagnosis of Inflammatory Bowel Disease.

Author

Feakins, Roger, Torres, Joana, Borralho-Nunes, Paula, Burisch, Johan, Gonçalves, Tiago Cúrdia, Ridder, Lissy De, Driessen, Ann, Lobatón, Triana, Menchén, Luis, Mookhoek, Aart, Noor, Nurulamin, Svrcek, Magali, Villanacci, Vincenzo, Zidar, Nina, and Tripathi, Monika

Abstract

Introduction Many diseases can imitate inflammatory bowel disease [IBD] clinically and pathologically. This review outlines the differential diagnosis of IBD and discusses morphological pointers and ancillary techniques that assist with the distinction between IBD and its mimics. Methods European Crohn's and Colitis Organisation [ECCO] Topical Reviews are the result of an expert consensus. For this review, ECCO announced an open call to its members and formed three working groups [WGs] to study clinical aspects, pathological considerations, and the value of ancillary techniques. All WGs performed a systematic literature search. Results Each WG produced a draft text and drew up provisional Current Practice Position [CPP] statements that highlighted the most important conclusions. Discussions and a preliminary voting round took place, with subsequent revision of CPP statements and text and a further meeting to agree on final statements. Conclusions Clinicians and pathologists encounter a wide variety of mimics of IBD, including infection, drug-induced disease, vascular disorders, diverticular disease, diversion proctocolitis, radiation damage, and immune disorders. Reliable distinction requires a multidisciplinary approach. [ABSTRACT FROM AUTHOR]

Published
2022
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44. Synthèse de ligands et de complexes métalliques incorporant des motifs oxyallyles

Author

Tripathi, Monika, STAR, ABES, Département de Chimie Moléculaire (DCM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Grenoble Alpes, and David Martin

Subjects
Complexes, [CHIM.OTHE] Chemical Sciences/Other, Activité redox, Catalyse, [CHIM.OTHE]Chemical Sciences/Other, Ligands, Redox activity, Catalysis
Abstract

The stabilization of transient and non-observable oxyallyl intermediates can be achieved through the introduction of electron-donating amino substituents. The resulting 1,3-di(amino)oxyallyls are redox-active and can have up to three persistent redox forms. In particular, their radical cations are even air-persistent, as the result of “enhanced” capto-dative effect. This manuscript reports our efforts for the development of redox-active metal complexes featuring oxyallyl frameworks, with a particular focus on β-diketiminate (NacNac) ligands. Indeed, metal-complexes of the latter generally decompose upon ligand-centered oxidation/reduction and the design of redox-active NacNac remains a challenge. The first chapter summarizes recent bibliography related to stabilized oxyallyl molecules and the study of redox-active ligands.The second chapter describes the direct oxidation of vinamidines with m-CPBA to afford bis-imine ketone ligands. This methodology is far simpler and easier as compared to the previously described method from the literature. The coordination chemistry of these ligands and their redox behavior were also studied.The third chapter explores an original substitution pattern on bis-imine ketones, with the introduction of electron-donating amino groups in 1,3-positions. A detailed study of the reaction of 1,3-dichloro vinamidinium salts with aniline derivatives is reported, as well as preliminary study of the metal coordination of the novel electron-rich ligand.The last chapter presents alternatives strategies and concepts, including the use of O-protected and/or bidentates ligands., Les oxyallyles sont considérés généralement comme des espèces transitoires non observables, mais peuvent être stabilisés par l’introduction de groupements aminés donneurs d’électrons. De tels 1,3-di(amino)oxyallyls sont rédox-actifs et peuvent exister sous jusqu’à trois formes redox. En particulier, leurs cations radicaux sont persistants à l’air, en raison d’un effet capto-datif «extrême». Ce manuscrit décrit nos efforts pour développer des complexes métalliques redox-actifs comportant des motifs oxyallyles, avec une attention particulière pour les ligands de type β-diketiminate (Nacnac). En effet, en général, les complexes de ces derniers se décomposent lors de d’une oxydation/réduction centrée sur le ligand et la conception de version redox-actives représente encore un défi. Le premier chapitre résume la littérature récente concernant les oxyallyles stabilisés et l’étude des ligands redox actifs.Le second chapitre décrit l’oxydation directe de vinamidines par m-CPBA pour former des ligands bis(imino)cétones. Cette approche synthétique représente une amélioration importante par rapport aux méthodologies précédemment décrites. La chimie de coordination et l’électrochimie de ces composés ont également été étudiées.Le troisième chapitre explore l’introduction d’un nouveau motif di(methyl)amino en positions 1 et 3 des bis(imino)cétones. Nous décrivons notamment une étude détaillée de la réaction des sels de 1,3-dichlorovinamidinium avec des dérivés de l’aniline, ainsi qu’une étude préliminaire de la chimie de coordination du nouveau ligand enrichi électroniquement.Le dernier chapitre expose des stratégies et des concepts alternatifs, notamment l’utilisation de ligands O-protégés et/ou bidentés.

Published
2019

46. Somatic evolution in non-neoplastic IBD-affected colon

Author

Olafsson, Sigurgeir, primary, McIntyre, Rebecca E., additional, Coorens, Tim, additional, Butler, Timothy, additional, Jung, Hyunchul, additional, Robinson, Philip, additional, Lee-Six, Henry, additional, Sanders, Mathijs A., additional, Arestang, Kenneth, additional, Dawson, Claire, additional, Tripathi, Monika, additional, Strongili, Konstantina, additional, Hooks, Yvette, additional, Stratton, Michael R., additional, Parkes, Miles, additional, Martincorena, Inigo, additional, Raine, Tim, additional, Campbell, Peter J., additional, and Anderson, Carl A., additional

Published
2019
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48. Single-bite versus double-bite technique for mapping biopsies during endoscopic surveillance for hereditary diffuse gastric cancer: a single-center, randomized trial.

Author

Pappas, Apostolos, Tan, Wei Keith, Waldock, William, Richardson, Susan, Tripathi, Monika, Januszewicz, Wladyslaw, Roberts, Geoffrey, O'Donovan, Maria, Fitzgerald, Rebecca C., and di Pietro, Massimiliano

Subjects
ADENOCARCINOMA, STOMACH tumors, RESEARCH, BIOPSY, RESEARCH methodology, MEDICAL cooperation, EVALUATION research, GASTRECTOMY, COMPARATIVE studies, RANDOMIZED controlled trials, GLYCOPROTEINS, RESEARCH funding, GASTROSCOPY
Abstract

BACKGROUND : Endoscopic surveillance is recommended in patients with hereditary diffuse gastric cancer (HDGC) who refuse or want to delay surgery. Because early signet-ring cell carcinoma (SRCC) can be inconspicuous, the current surveillance endoscopy protocol entails 30 random biopsies, which are time-consuming. This study aimed to compare single-bite and double-bite techniques in HDGC surveillance. METHODS : Between October 2017 and December 2018, consecutive patients referred for HDGC surveillance were prospectively randomized to the single- or double-bite arm. The primary outcome was the diagnostic yield for SRCC foci. Secondary outcomes were: procedural time for random biopsies; comfort score; biopsy size; and quality of specimens, the latter assessed by the presence of muscularis mucosa, crush artifact, and proportion usable for diagnostic assessment. RESULTS : 25 patients were randomized to the single-bite arm and 23 to the double-bite arm. SRCC foci were detected in three and four patients in the single- and double-bite arms, respectively (P = 0.70). The procedural time for the double-bite arm (12 minutes, interquartile range [IQR] 4) was significantly shorter than for the single-bite arm (15 minute, IQR 6; P = 0.01), but comfort scores were similar. The size of the biopsies in the double-bite arm was significantly smaller than in single-bite arm (2.5 mm vs. 3.0 mm; P < 0.001) but this did not affect the presence of muscularis mucosa (P = 0.73), artifact level (P = 0.11), and diagnostic utility (P = 0.051). CONCLUSION : For patients undergoing HDGC surveillance, the double-bite technique is significantly faster than the single-bite technique. The diagnostic yield for SRCC and the biopsy quality were similar across both groups. [ABSTRACT FROM AUTHOR]

Published
2021
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50. Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation

Author

O'Neill, J. Robert, Yébenes Mayordomo, Marcos, Mitulović, Goran, Al Shboul, Sofian, Bedran, Georges, Faktor, Jakub, Hernychova, Lenka, Uhrik, Lukas, Gómez-Herranz, Maria, Kocikowski, Mikołaj, Save, Vicki, Vojtěšek, Bořivoj, Arends, Mark J., Fitzgerald, Rebecca C., Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Loreno, Christine, Redmond, Aisling M., Abbas, Sujath, Freeman, Adam, Smyth, Elizabeth C., O'Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Cheah, Calvin, Coles, Hannah, Millington, Curtis, Devonshire, Ginny, Eldridge, Matthew, Secrier, Maria, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H., Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O'Neill, J Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Contino, Gianmarco, Underwood, Timothy J., Walker, Robert C., Grace, Ben L., Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Chan, David, Cheong, Ed, Kumar, Bhaskar, Sreedharan, L., Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Scott, Michael, Sothi, Sharmila, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Moorthy, Krishna, Grabowska, Anna, Turkington, Richard, McManus, Damian, Coleman, Helen, Petty, Russell D., Bartlet, Freddie, Hupp, Ted, and Alfaro, Javier Antonio

Abstract

Efforts to address the poor prognosis associated with esophageal adenocarcinoma (EAC) have been hampered by a lack of biomarkers to identify early disease and therapeutic targets. Despite extensive efforts to understand the somatic mutations associated with EAC over the past decade, a gap remains in understanding how the atlas of genomic aberrations in this cancer impacts the proteome and which somatic variants are of importance for the disease phenotype. We performed a quantitative proteomic analysis of 23 EACs and matched adjacent normal esophageal and gastric tissues. We explored the correlation of transcript and protein abundance using tissue-matched RNA-seq and proteomic data from seven patients and further integrated these data with a cohort of EAC RNA-seq data (n = 264 patients), EAC whole-genome sequencing (n = 454 patients), and external published datasets. We quantified protein expression from 5879 genes in EAC and patient-matched normal tissues. Several biomarker candidates with EAC-selective expression were identified, including the transmembrane protein GPA33. We further verified the EAC-enriched expression of GPA33 in an external cohort of 115 patients and confirm this as an attractive diagnostic and therapeutic target. To further extend the insights gained from our proteomic data, an integrated analysis of protein and RNA expression in EAC and normal tissues revealed several genes with poorly correlated protein and RNA abundance, suggesting posttranscriptional regulation of protein expression. These outlier genes, including SLC25A30, TAOK2, and AGMAT, only rarely demonstrated somatic mutation, suggesting post-transcriptional drivers for this EAC-specific phenotype. AGMAT was demonstrated to be overexpressed at the protein level in EAC compared to adjacent normal tissues with an EAC-selective, post-transcriptional mechanism of regulation of protein abundance proposed. Integrated analysis of proteome, transcriptome, and genome in EAC has revealed several genes with tumor-selective, posttranscriptional regulation of protein expression, which may be an exploitable vulnerability.

Published
2024
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