Article
Biochemistry & Molecular Biology
Georgia Mitsa, Qianyu Guo, Christophe Goncalves, Samuel E. J. Preston, Vincent Lacasse, Adriana Aguilar-Mahecha, Naciba Benlimame, Mark Basik, Alan Spatz, Gerald Batist, Wilson H. Miller, Sonia del Rincon, Rene P. Zahedi, Christoph H. Borchers
Summary: The article presents a 'green' xylene-free protocol for accelerated sample preparation of FFPE tissues, enabling streamlined and reproducible quantitative proteomic profiling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Samar Ijaz Gul, Aqsa Ayoub, Syed Aoun Ali, Sharoon Hanook, Deeba Noreen Baig
Summary: The study revealed significant dysregulation in the transcriptional pattern of Pfn3 in brain tumors, suggesting a potential correlation between molecular variations in Pfn3 and the malignancy of brain tumors, similar to the role of tumor suppressor genes in other types of cancer.
Article
Chemistry, Analytical
Kenneth Weke, Sachin Kote, Jakub Faktor, Sofian Al Shboul, Naomi Uwugiaren, Paul M. Brennan, David R. Goodlett, Ted R. Hupp, Irena Dapic
Summary: Developments in quantitative proteomics and DIA methodology have enabled protein quantification in biological samples, including formalin-fixed paraffin-embedded (FFPE) tissues. In this study, a simple and precise DIA-MS workflow was established to detect and quantify immune- and glioblastoma (GBM)-relevant proteins in FFPE patient materials. The results showed successful detection and quantification of more than 1700 proteins, including GBM-relevant proteins and immune-related proteins. This strategy has great potential for routine protein quantification in FFPE tissue samples.
ANALYTICA CHIMICA ACTA
(2022)
Article
Medical Laboratory Technology
Ramanath Majumdar, Julie A. Vrana, Justin W. Koepplin, Dragana Milosevic, Anja C. Roden, Joaquin J. Garcia, Benjamin R. Kipp, Ann M. Moyer
Summary: This study developed a qualitative test for detecting SARS-CoV-2 in formalin-fixed paraffin-embedded (FFPE) tissues using droplet digital PCR (ddPCR). The results showed reliable detection of SARS-CoV-2, and the assay has broad clinical utility in various applications, including evaluation of pregnancy loss and liver transplant rejection.
CLINICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
Allison K. Miller, Cara L. Brosnahan, Anjali Pande, Cindy F. Baker, Jemma L. Geoghegan, Jane Kitson, Neil J. Gemmell, Edwina J. Dowle
Summary: Infectious diseases have a significant impact on various organisms, and understanding the interactions between hosts and pathogens is crucial for their conservation and management. The use of genomic approaches has made it easier to obtain this knowledge quickly, however, many species still face challenges in accessing appropriate samples and data. Archival materials, such as formalin-fixed paraffin-embedded tissue samples, may provide a valuable resource for studying pathogen emergence and host responses over long periods of time.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Chemistry, Analytical
Hao Chen, Yuefei Zhang, Haichao Zhou, Weiran Chen, Jiayi Peng, Yang Feng, Linyuan Fan, Jun Li, Jin Zi, Yan Ren, Qidan Li, Siqi Liu
Summary: Spatial proteomics plays an important role in the era of single-cell biology. In this study, a new routine workflow was developed for proteomic analysis of micro-FFPE tissues, allowing the construction of a spatial proteomic atlas of mouse brain, which exhibited typical characteristics of spatial-dependent protein abundance and functional enrichment.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Anne-Sofie Faarvang Thorsen, Lars Peter Schodt Riber, Lars Melholt Rasmussen, Martin Overgaard
Summary: This study developed a novel mass spectrometry (MS) assay for the quantification of matrix and cytosolic proteins in FFPE samples. The assay demonstrated its utility in pathophysiological studies of cardiovascular disease in diabetes through analysis of artery specimens from diabetic and non-diabetic patients.
JOURNAL OF PROTEOMICS
(2023)
Article
Medicine, Research & Experimental
Bradley L. Ackermann, Ryan D. Morrison, Salisha Hill, Matthew D. Westfall, Brent D. Butts, Michael D. Soper, Jeff A. Fill, Andrew E. Schade, Daniel C. Liebler, Aaron M. Gruver
Summary: MS analysis allows accurate protein quantification from stained paraffin-embedded tissue sections, providing valuable data for the assessment of clinical tissue specimens.
LABORATORY INVESTIGATION
(2023)
Article
Biochemistry & Molecular Biology
Hua Zhang, Vamsi Krishna Polavarapu, Pengwei Xing, Miao Zhao, Lucy Mathot, Linxuan Zhao, Gabriela Rosen, Fredrik J. Swartling, Tobias Sjoblom, Xingqi Chen
Summary: Archived FFPE samples are widely used for cancer research, and we developed a highly sensitive method (FFPE-ATAC) to decode chromatin accessibility in FFPE tissues. This method generates high-quality chromatin accessibility profiles and allows analysis of chromatin profiles in regions of interest from a single FFPE tissue section.
Article
Biochemical Research Methods
Hanan Schoffman, Yishai Levin, Ayelet Itzhaki-Alfia, Lea Tselekovits, Lior Gonen, Gilad Wolf Vainer, Goni Hout-Siloni, Iris Barshack, Zvi R. Cohen, Nevo Margalit, Tal Shahar
Summary: This study compared the effects of formaldehyde-fixed paraffin-embedded (FFPE) tissue blocks and fresh frozen tissue (FFT) on the quantifiable proteome. The results showed that both methods yield a similar number of proteins, but there are significant differences in the proteome composition, with FFPE specimens enriched with smaller proteins.
Article
Chemistry, Analytical
Jie Pu, Chao Xue, Shihan Huo, Qingqing Shen, Yang Qu, Xinxin Yang, Bo An, Thomas E. Angel, Zhuo Chen, John T. Mehl, Huaping Tang, Eric Yang, Timothy W. Sikorski, Jun Qu
Summary: This study extensively investigated the challenges of accurate quantification of target proteins in formalin-fixed paraffin-embedded (FFPE) tissues using liquid chromatography-mass spectrometry (LC-MS) and developed a strategy enabling precise quantification. The study demonstrated efficient recovery of target signature peptides from FFPE tissues, indicated that FFPE tissue storage mainly causes decreased immunoreactivity but not chemical degradation of proteins, and proposed a novel calibration approach for accurate quantification. The pipeline was successfully applied to measure the pharmacokinetics of monoclonal antibody (mAb) and its target in FFPE tissues, showing excellent correlation with fresh tissues.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Rory T. Steven, Marcel Niehaus, Adam J. Taylor, Ammar Nasif, Efstathios Elia, Richard J. A. Goodwin, Zoltan Takats, Josephine Bunch
Summary: Mass spectrometry imaging (MSI) is a powerful technique for providing spatially resolved atomic and molecular information from almost any sample type. Optimizing MSI methods for analysis of FFPE tissue is necessary due to the prevalence and importance of FFPE tissue storage.
ANALYTICAL CHEMISTRY
(2022)
Review
Oncology
Amin Talebi, Jean Paul Thiery, Mohammad Amin Kerachian
Summary: Chimeric transcripts are important for diagnosis and prognosis, but their identification from FFPE tissues is limited due to the reduced quality and quantity of RNA. Strategies need to be developed to overcome these limitations and maximize the potential of FFPE tissues as a source for fusion transcript identification.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Biochemical Research Methods
Pascal Steffen, Jun Li, Jason Chandra, Mahsa S. Ahadi, Anthony J. Gill, Alexander F. Engel, Mark P. Molloy
Summary: Histological risk factors for lymph node metastasis in early-stage colorectal cancers have been described, with molecular features such as effector proteins of epithelial-mesenchymal transition (EMT) showing potential for enhancing metastatic risk assessment. Proteomic and gene expression profiling were used to identify these features, suggesting a link between EMT effectors and locoregional metastasis in T1/T2 CRC. Further development is needed for routine implementation of these findings.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Pathology
Giuseppa Zannini, Gaetano Facchini, Marco De Sio, Ferdinando De Vita, Andrea Ronchi, Michele Orditura, Maria Teresa Vietri, Fortunato Ciardiello, Renato Franco, Marina Accardo, Federica Zito Marino
Summary: BRCA1 and BRCA2 are genes involved in DNA repair mechanism and their mutations increase the risk of several cancer types. FDA has approved PARP inhibitors for treating BRCA1/2 mutated ovarian, breast, pancreatic, and prostate cancer patients. Guidelines for BRCA testing vary between tumor types, and there is limited data on detecting BRCA1/2 somatic mutations in FFPE samples. This review provides an overview of BRCA mutations, testing guidelines, molecular assays, and approved PARP inhibitors for various cancers, including breast, ovarian, fallopian tube, primary peritoneal, prostate, and pancreatic cancer.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Hematology
Charlotte Pawlyn, David A. Cairns, Tom Menzies, John R. Jones, Matthew W. Jenner, Gordon Cook, Kevin D. Boyd, Mark T. Drayson, Martin F. Kaiser, Roger G. Owen, Walter Gregory, Gareth J. Morgan, Graham H. Jackson, Faith E. Davies
Summary: Autologous stem cell transplant (ASCT) is the standard of care for consolidation after induction therapy in newly diagnosed myeloma patients. While older patients may have a reduced progression-free survival after ASCT, the treatment is well tolerated regardless of age. Data from clinical trials and real-world practice suggest that ASCT can benefit selected older myeloma patients.
Letter
Hematology
David John Allsup, Zoe Craig, David Cairns, Dena Howard, Anna Hockaday, Adrian Bloor, Zarni Soe, Christopher Pepper, Valter Gattei, Antonella Zucchetto, Pauline Robbe, Ruth Clifford, Anna Schuh, Talha Munir, Andrew Rawstron, Peter Hillmen
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Meeting Abstract
Hematology
Zoe Craig, Christopher Parrish, Charlotte Pawlyn, Martin F. Kaiser, Catherine Olivier, John R. Jones, Mark T. Drayson, Roger G. Owen, Matthew W. Jenner, Gordon Cook, Walter Martin Gregory, Faith E. Davies, Gareth J. Morgan, Graham Jackson, David Cairns
Meeting Abstract
Hematology
Hannah Victoria Giles, Mark T. Drayson, Nicola Wright, Gordon Cook, Faith E. Davies, Gareth J. Morgan, Ruth M. de Tute, Roger GOwen, David Cairns, Anna Hockaday, Tom Menzies, Martin F. Kaiser, Charlotte Pawlyn, Graham Jackson, Guy Pratt
Article
Hematology
Hannah Giles, Mark A. Cook, Mark Trehane Drayson, Gordon Cook, Nicola Jane Wright, Simon John North, Stephen Harding, David A. Cairns, Anna Hockaday, Martin F. Kaiser, Paul Moss, Faith E. Davies, Gareth J. Morgan, Graham Jackson, Guy Pratt
Article
Oncology
Jessica Caro, David Cairns, Tom Menzies, Eileen Boyle, Charlotte Pawlyn, Gordon Cook, Martin Kaiser, Brian A. Walker, Roger Owen, Graham H. Jackson, Gareth J. Morgan, Jennifer Heaney, Mark Drayson, Faith E. Davies
Summary: Immunoparesis is associated with poor survival in myeloma. This study demonstrates that the etiologic cytogenetic abnormality influences the degree and clinical impact of immunoparesis in newly diagnosed patients in a large clinical trial. The depth of IgM immunoparesis can be used to further risk-stratify hyperdiploid patients for future clinical decisions.
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)
Article
Oncology
Jessica Pearce, Daniel Swinson, David Cairns, Sherena Nair, Mark Baxter, Russell Petty, Matt Seymour, Peter Hall, Galina Velikova
Summary: Frailty measures, such as GO2FS, mCFS, and G8, are significantly associated with treatment outcomes in frail patients with cancer, providing evidence for optimal care.
JOURNAL OF GERIATRIC ONCOLOGY
(2022)
Article
Oncology
Ruth M. de Tute, Charlotte Pawlyn, David A. Cairns, Faith E. Davies, Tom Menzies, Andy Rawstron, John R. Jones, Anna Hockaday, Rowena Henderson, Gordon Cook, Mark T. Drayson, Matthew W. Jenner, Martin F. Kaiser, Walter M. Gregory, Gareth J. Morgan, Graham H. Jackson, Roger G. Owen
Summary: This study found that MRD status at ASCT + 3 and ASCT + 9 is a powerful predictor of PFS and OS in patients with multiple myeloma. Lenalidomide maintenance therapy can increase the likelihood of converting from MRD-positive to MRD-negative. However, high-risk molecular features still have a negative impact on PFS and OS.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Oncology
Mattia D'Agostino, David A. Cairns, Juan Jose Lahuerta, Ruth Wester, Uta Bertsch, Anders Waage, Elena Zamagni, Maria-Victoria Mateos, Daniele Dall'Olio, Niels W. C. J. van de Donk, Graham Jackson, Serena Rocchi, Hans Salwender, Joan Blade Creixenti, Bronno van der Holt, Gastone Castellani, Francesca Bonello, Andrea Capra, Elias K. Mai, Jan Durig, Francesca Gay, Sonja Zweegman, Michele Cavo, Martin F. Kaiser, Hartmut Goldschmidt, Jesus Maria Hernandez Rivas, Alessandra Larocca, Gordon Cook, Jesus F. San-Miguel, Mario Boccadoro, Pieter Sonneveld
Summary: In this study, the Revised International Staging system (R-ISS) for intermediate-risk multiple myeloma patients was revised based on the additive value of each single risk feature.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Medicine, General & Internal
Amy Beth Coulson, Kara-Louise Royle, Charlotte Pawlyn, David A. Cairns, Anna Hockaday, Jennifer Bird, Stella Bowcock, Martin Kaiser, Ruth de Tute, Neil Rabin, Kevin Boyd, John Jones, Christopher Parrish, Hayley Gardner, David Meads, Bryony Dawkins, Catherine Olivier, Rowena Henderson, Phillip Best, Roger Owen, Matthew Jenner, Bhuvan Kishore, Mark Drayson, Graham Jackson, Gordon Cook
Summary: Multiple myeloma is a bone marrow cancer that mainly affects older people, and its incidence is increasing in an ageing population. Older, less fit patients who are ineligible for stem cell transplant have shown less improvement in patient outcomes over the last 10 years. Research is needed to improve treatment tolerability, clinical outcomes, and quality of life in this patient group.
Article
Biophysics
John A. Snowden, Sam H. Ahmedzai, Angela Cox, David A. Cairns, A. John Ashcroft, Cathy Williams, Jamie D. Cavenagh, Anna Hockaday, Julia M. Brown, Ian W. Brock, Treen C. M. Morris, Gordon Cook
Summary: The Myeloma X trial explored the relationship between genetics and patient-reported outcomes in multiple myeloma patients. The study identified several single nucleotide polymorphisms (SNPs) associated with pain and health-related quality-of-life scores. These findings support previous genome-wide association studies linking SNPs to subjective parameters in multiple myeloma.
BONE MARROW TRANSPLANTATION
(2022)
Article
Hematology
Matthew W. Jenner, Charlotte Pawlyn, Faith E. Davies, Tom Menzies, Anna Hockaday, Catherine Olivier, John R. Jones, Kamuraj Karunanithi, Jindriska Lindsay, Bhuvan Kishore, Gordon Cook, Mark T. Drayson, Martin F. Kaiser, Roger G. Owen, Walter Gregory, David A. Cairns, Gareth J. Morgan, Graham H. Jackson
Summary: Lenalidomide is an effective maintenance therapy for myeloma patients, but the addition of vorinostat did not provide additional benefits in terms of progression-free survival and overall survival compared to lenalidomide alone.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Medicine, General & Internal
Kara-Louise Royle, Amy Beth Coulson, Karthik Ramasamy, David A. Cairns, Anna Hockaday, Sergio Quezada, Mark Drayson, Martin Kaiser, Roger Owen, Holger W. Auner, Gordon Cook, David Meads, Catherine Olivier, Lorna Barnard, Rhiannon Lambkin, Andrea Paterson, Bryony Dawkins, Mike Chapman, Guy Pratt, Rakesh Popat, Graham Jackson, Ceri Bygrave, Jonathan Sive, Ruth de Tute, Andrew Chantry, Christopher Parrish, Mark Cook, Samir Asher, Kwee Yong
Summary: This study is a multicenter, risk-adapted, response-guided, open-label, randomized controlled trial for patients with multiple myeloma. It includes different treatment strategies and adjusts the treatment based on the risk profile of the patients.
Meeting Abstract
Oncology
Christopher Williams, Jake Emmerson, Andrew David Beggs, Nicholas West, John A. Bridgewater, Janet Graham, Matthew T. Seymour, Gemma Hemmings, Claire Dimbleby, Geraldine A. Murden, Alexandra Gilbert, David M. Meads, David A. Cairns, Richard Adams, Jenny F. Seligmann
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Meeting Abstract
Hematology
Talha Munir, Alexandra Pitchford, Adrian Bloor, Angus Broom, Moya Young, Ben Kennedy, Renata Walewska, Michelle Furtado, Gavin Preston, Jeff Neilson, Nicholas Pemberton, Gamal Sidra, Nicholas Morley, Kate Cwynarski, Anna Schuh, Francesco Forconi, Simona Gatto, Shankara Paneesha, Christopher Fox, Dena Howard, Anna Hockaday, David Cairns, Sharon Jackson, Natasha Greatorex, Piers E. M. Patten, David Allsup, Peter Hillmen
BRITISH JOURNAL OF HAEMATOLOGY
(2022)