Article
Microbiology
Sota Sadamoto, Yurika Mitsui, Yasuhiro Nihonyanagi, Kazuki Amemiya, Minoru Shinozaki, Somay Yamagata Murayama, Masahiro Abe, Takashi Umeyama, Naobumi Tochigi, Yoshitsugu Miyazaki, Kazutoshi Shibuya
Summary: Invasive fungal infections have high mortality rates in patients undergoing hematopoietic stem cell transplantation and are often confirmed postmortem. Use of formalin-fixed, paraffin-embedded samples is crucial for identifying fungi when autopsy confirmation is challenging. PCR, along with histopathological diagnosis, is valuable for precise identification, but has limitations in autopsy FFPE samples.
Article
Biotechnology & Applied Microbiology
Jin Sung Jang, Eileen Holicky, Julie Lau, Samantha McDonough, Mark Mutawe, Matthew J. Koster, Kenneth J. Warrington, Julie M. Cuninngham
Summary: The study demonstrates that QuantSeq 3' mRNA-Seq with PCR bias correction using UMI is suitable for gene quantification in both FF and FFPE RNAs. 3' mRNA-Seq with UMI can be applied to severely degraded RNA from FFPE tissues generating high-quality sequencing data.
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
Biochemistry & Molecular Biology
Linxuan Zhao, Pengwei Xing, Vamsi Krishna Polavarapu, Miao Zhao, Blanca Valero-Martinez, Yonglong Dang, Nagaprathyusha Maturi, Lucy Mathot, Ines Neves, Irem Yildirim, Fredrik Johansson Swartling, Tobias Sjoblom, Lene Uhrbom, Xingqi Chen
Summary: The study introduces a new method (FACT-seq) for efficient analysis of histone modifications in archived FFPE tissues, significantly improving resolution. High-quality chromatin profiles can be generated using a small number of FFPE nuclei, offering insights into epigenetic regulation in cancer and human disease.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Genetics & Heredity
Gerardo Cazzato, Concetta Caporusso, Francesca Arezzo, Antonietta Cimmino, Anna Colagrande, Vera Loizzi, Gennaro Cormio, Teresa Lettini, Eugenio Maiorano, Vincenza Sara Scarcella, Paola Tarantino, Maricla Marrone, Alessandra Stellacci, Paola Parente, Paolo Romita, Aurora De Marco, Vincenzo Venerito, Caterina Foti, Giuseppe Ingravallo, Roberta Rossi, Leonardo Resta
Summary: Advancements in pathology have shifted towards molecular and genetic studies, allowing for the implementation of targeted therapies; however, issues may arise in NGS due to damage to genetic material in fixed samples.
Article
Veterinary Sciences
Nelly O. Elshafie, Jessica Hanlon, Mays Malkawi, Ekramy E. Sayedahmed, Lynn F. Guptill, Yava L. Jones-Hall, Andrea P. Santos
Summary: Pythium insidiosum is a waterborne fungus-like organism that can cause a disease called pythiosis in dogs and other animals. This disease can lead to inflammatory lesions on the skin and gastrointestinal tract, which can be fatal if left untreated. The development of a molecular technique called nested PCR can aid in the diagnosis of this organism by specifically detecting P. insidiosum DNA in biopsy specimens. The combination of this technique with microscopic examination can increase the sensitivity of diagnosing pythiosis in dogs.
VETERINARY SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Katarina Vitosevic, Danijela Todorovic, Zivana Slovic, Tatjana Varljen, Ivana Radakovic, Dusan Radojevic, Vanja Canovic, Milos Todorovic
Summary: This study compared the quality of DNA isolated from fixed tissues and tissues embedded in paraffin blocks after fixation, finding that the fixation time and embedding time have an impact on DNA yield and integrity.
MOLECULAR BIOLOGY REPORTS
(2023)
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
Infectious Diseases
Shawn T. Clark, Yvonne C. W. Yau, Aaron Campigotto, Farhad Gharabaghi, Susan E. Richardson, Manal Tadros
Summary: In this study, we evaluated the performance of a DNA-based test for detecting fungal DNA in archived human biopsy tissues. Our results indicate that the best performance can be achieved when fungi are observed under a microscope before testing, suggesting that this test should only be used under these conditions.
Review
Biochemistry & Molecular Biology
Ekenedirichukwu N. Obi, Daniel A. Tellock, Gabriel J. Thomas, Timothy D. Veenstra
Summary: The recent developments in mass spectrometry (MS) have provided new opportunities in biomarker discovery and diagnostics, particularly in analyzing clinical samples at a deeper level. While most developments have focused on blood, there is potential in utilizing archived formalin-fixed paraffin-embedded (FFPE) tissues, which were previously considered difficult to analyze using proteomics techniques. Researchers have developed methods to extract proteins from FFPE tissues, allowing for their analysis using state-of-the-art technologies like MS and protein arrays. This review discusses the history of these developments and their current applications in identifying biomarkers and diagnosing diseases such as cancer.
Article
Biology
Masachika Ikegami, Shinji Kohsaka, Takeshi Hirose, Toshihide Ueno, Satoshi Inoue, Naoki Kanomata, Hideko Yamauchi, Taisuke Mori, Shigeki Sekine, Yoshihiro Inamoto, Yasushi Yatabe, Hiroshi Kobayashi, Sakae Tanaka, Hiroyuki Mano
Summary: The researchers developed MicroSEC, a filtering pipeline to remove sequencing artifacts from archival formalin-fixed and paraffin-embedded samples. The sensitivity and specificity of MicroSEC were confirmed to be 97% and 96% respectively using amplicon-based sequencing with 97 mutations. This tool may improve the reliability of clinical sequencing and advance cancer research using formalin-fixed, paraffin-embedded samples, which are of great interest for genomic analysis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Pathology
Rebecca Sparks, Catriona L. Halliday, Wendy Green, Sharon C-A Chen
Summary: The performance of panfungal PCR-DNA sequencing assays for diagnosing invasive fungal disease on FFPE tissue is influenced by various factors. Interpretation of positive results is challenging due to the need to differentiate colonisers and contaminants from clinically significant pathogens. A retrospective audit was conducted on 248 FFPE tissue specimens, comparing panfungal PCR results between samples with and without visualised fungal elements on histopathology. The study found limited clinical utility of panfungal PCR in FFPE tissue without visible fungal elements, suggesting that restricting the assay to histopathology positive samples aids interpretation of PCR results and conserves resources.
Article
Chemistry, Analytical
Yunxia Guo, Junjie Ma, Zhengyue Li, Kaitong Dang, Qinyu Ge, Yan Huang, Guang-zhong Wang, Xiangwei Zhao
Summary: This study investigates the effects of fixation and storage time on the nuclear transcriptome signatures of the brain. The fixation time has a greater impact on the transcriptomic profiles than the retention time of FFPE samples. The findings will guide the preparation of FFPE samples for single-nucleus RNA-seq, especially in transcriptomic studies of brain diseases.
ANALYTICA CHIMICA ACTA
(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
Endocrinology & Metabolism
Norifusa Iwahashi, Hironobu Umakoshi, Masatoshi Ogata, Tazuru Fukumoto, Hiroki Kaneko, Eriko Terada, Shunsuke Katsuhara, Naohiro Uchida, Katsuhiko Sasaki, Maki Yokomoto-Umakoshi, Yayoi Matsuda, Ryuichi Sakamoto, Yoshihiro Ogawa
Summary: This study evaluated the utility of transcriptome data from formalin-fixed paraffin-embedded (FFPE) samples in adrenocortical tumor research. The results demonstrated that FFPE samples can serve as a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors, enabling distinction of tumor types and detection of marker genes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Orthopedics
Mark Porter, Bruce Shadbolt
AMERICAN JOURNAL OF SPORTS MEDICINE
(2020)
Article
Oncology
P-T Chiou, S. Ohms, P. G. Board, J. E. Dahlstrom, D. Rangasamy, M. G. Casarotto
Summary: In contrast to hormone receptor driven breast cancer, patients with triple-negative breast cancer (TNBC) often have limited treatment options. Efavirenz, a non-nucleoside reverse transcriptase (RT) inhibitor, has shown promising anticancer effects in treating prostate and pancreatic cancers. This study demonstrates that Efavirenz can induce cell death, inhibit cell proliferation, and alter cell morphology in TNBC cell lines, with the fatty acid metabolism pathway identified as a key regulator in this process.
CLINICAL & TRANSLATIONAL ONCOLOGY
(2021)
Article
Oncology
Sabine Meessen, Nicola Currey, Zeenat Jahan, Hannah W. Parker, Mark A. Jenkins, Daniel D. Buchanan, John L. Hopper, Eva Segelov, Jane E. Dahlstrom, Maija R. J. Kohonen-Corish
Summary: EMAST is a DNA mismatch repair defect related to MSI-H and MSI-L, with potential as a valuable prognostic and predictive marker for colorectal carcinomas.
Article
Oncology
Pey-Tsyr Chiou, Stephen Ohms, Philip G. Board, Jane E. Dahlstrom, Danny Rangasamy, Marco G. Casarotto
Summary: This study explores the effects of the antiretroviral medication Efavirenz on cancer stem cells derived from multiple breast cancer cell lines, finding that it can alter CSC numbers, morphology, and gene expression. Efavirenz not only eliminates primary breast cancer cells but also induces changes in cell morphology, with potential therapeutic implications for breast CSCs.
Article
Biochemistry & Molecular Biology
Matthew F. Waters, Viviane Delghingaro-Augusto, Kiran Javed, Jane E. Dahlstrom, Gaetan Burgio, Stefan Broer, Christopher J. Nolan
Summary: The study found that knocking out the Slc6a19 gene does not prevent or delay the development of type 1 diabetes in female NOD mice.
Article
Oncology
Jenny Dunn, Robert D. McCuaig, Abel H. Y. Tan, Wen Juan Tu, Fan Wu, Kylie M. Wagstaff, Anjum Zafar, Sayed Ali, Himanshu Diwakar, Jane E. Dahlstrom, Elaine G. Bean, Jade K. Forwood, Sofiya Tsimbalyuk, Emily M. Cross, Kristine Hardy, Amanda L. Bain, Elizabeth Ahern, Riccardo Dolcetti, Roberta Mazzieri, Desmond Yip, Melissa Eastgate, Laeeq Malik, Peter Milburn, David A. Jans, Sudha Rao
Summary: The study found that a protein called nPKC-theta is enriched in circulating tumor cells (CTCs) in patients with triple-negative breast cancer (TNBC) brain metastases and immunotherapy-resistant metastatic melanoma, and is associated with poor survival in immunotherapy-resistant disease. A novel nPKC-theta inhibitor was designed to target nPKC-theta and showed potential in reducing mesenchymal cancer stem cell signatures in immunotherapy-resistant CTCs and TNBC xenografts.
Review
Hematology
Simone A. Brysland, M. Gohar Maqbool, Dipti Talaulikar, Elizabeth E. Gardiner
Summary: Waldenstrom macroglobulinemia (WM) is a rare and incurable B cell lymphoma that often leads to symptoms such as anemia, bleeding, and neurological symptoms. The bleeding phenotype in WM is complex and may involve factors such as platelet dysfunction, hyperviscosity, abnormal hematopoiesis, cryoglobulinemia, and amyloidosis. Understanding the pathophysiological mechanisms behind bleeding is important for clinical decision-making and treatment management.
THROMBOSIS AND HAEMOSTASIS
(2022)
Review
Oncology
Beatrice Sim, Jun Yen Ng, Benjamin W. Teh, Dipti Talaulikar
Summary: Acquired hypogammaglobulinemia is a common secondary immunodeficiency in hematological malignancies, and its management with immunoglobulin replacement therapy lacks sufficient evidence, particularly for newer treatments. Further research, including randomized controlled trials and observational studies, is needed to determine the optimal indications, timing, and duration of immunoglobulin replacement therapy to improve efficacy, safety, and cost-effectiveness.
LEUKEMIA & LYMPHOMA
(2023)
Article
Pathology
Caitlin Coombes, Keisuke Horikawa, Sanjiv Jain, Simon Jiang, Jun Hee Lim, Kartik Saxena, Bruce Shadbolt, Lillian Smyth, Joshua Tobin, Dipti Talaulikar
Summary: There is an association between lymphoma and autoimmune disease, and red cell autoimmunity is related to the development of DLBCL. Specific gene mutations may contribute to red cell autoimmunity in DLBCL. Overexpression of immunoglobulin gene IGHV4-34 in DLBCL may be associated with antigen-driven lymphomagenesis.
Article
Medicine, General & Internal
Dipti Talaulikar, Douglas Joshua, Joy Phoebe Ho, John Gibson, Hang Quach, Simon Gibbs, Silvia Ling, Christopher Ward, Bradley Augustson, Judith Trotman, Simon J. Harrison, Constantine S. Tam
Summary: Waldenstrom macroglobulinaemia (WM) is a B-cell malignancy characterized by IgM paraprotein, bone marrow infiltration, and MYD88 L265P mutation. Traditional treatment includes chemoimmunotherapy, but recent trials have shown the efficacy and safety of Bruton tyrosine kinase inhibitors in WM. Other agents such as BCL2 inhibitors are also being studied, and the authors provide specific recommendations based on the available evidence since 2017.
INTERNAL MEDICINE JOURNAL
(2023)
Article
Oncology
Irene Dogliotti, Cristina Jimenez, Marzia Varettoni, Dipti Talaulikar, Tina Bagratuni, Martina Ferrante, Jose Perez, Daniela Drandi, Noemi Puig, Milena Gilestro, Maria Garcia-Alvarez, Roger Owen, Wojciech Jurczak, Alessandra Tedeschi, Veronique Leblond, Efstathios Kastritis, Marie Jose Kersten, Shirley D'Sa, Michal Kascak, Wolfgang Willenbacher, Aldo M. Roccaro, Stephanie Poulain, Pierre Morel, Charalampia Kyriakou, Falko Fend, Josephine M. Vos, Meletios A. Dimopoulos, Christian Buske, Simone Ferrero, Ramon Garcia-Sanz
Summary: This paper presents consensus recommendations and laboratory requirements for the diagnosis of Waldenstrom's macroglobulinemia (WM) developed by the European Consortium of Waldenstrom's Macroglobulinemia, providing guidance for clinicians and researchers on multiparametric flow cytometry, fluorescence in situ hybridization, and molecular tests.
Article
Oncology
Dipti Talaulikar, Cecile Tomowiak, Elise Toussaint, Pierre Morel, Prashant Kapoor, Jorge J. Castillo, Alain Delmer, Eric Durot
HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA
(2023)
Review
Oncology
Kai Ping Tan, Dipti Talaulikar, Brett Scholz
Summary: Objective distress is prevalent among lymphoma patients/survivors and current processes of distress identification may be limited. This systematic review aims to comprehensively review factors contributing to distress in lymphoma patients/survivors. Consistent risk factors include younger age, relapsed disease, comorbidities, symptom burden, and treatment-related challenges. Adequate social support, adaptive adjustment, work engagement, and healthcare professionals' support may mitigate distress. More research is needed to identify significant factors and support clinicians in identifying and intervening with distressed lymphoma patients/survivors.
Article
Hematology
Adrian Minson, Nada Hamad, Pietro Di Ciaccio, Dipti Talaulikar, Matthew Ku, Sumita Ratnasingam, Chan Cheah, Costas K. Yannakou, Mark Bishton, Zi Yun Ng, Shivam Agrawal, Andrew Mcquillan, Anna Johnston, Emily Choong, Kimberly Wong, James Mcquillan, Ashley Beekman, Eliza Hawkes, Michael Dickinson
Summary: This study analyzed the treatment outcomes of 389 patients with mantle cell lymphoma and found that the rate of lymphoma-related death increased after each treatment line. Older age at diagnosis and early relapse after induction therapy were associated with a higher risk of death after second-line treatment. The results of this study support the exploration of novel therapies in earlier treatment lines.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Oncology
Thomas U. Ahearn, Haoyu Zhang, Kyriaki Michailidou, Roger L. Milne, Manjeet K. Bolla, Joe Dennis, Alison M. Dunning, Michael Lush, Qin Wang, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Kristan J. Aronson, Paul L. Auer, Annelie Augustinsson, Adinda Baten, Heiko Becher, Sabine Behrens, Javier Benitez, Marina Bermisheva, Carl Blomqvist, Stig E. Bojesen, Bernardo Bonanni, Anne-Lise Borresen-Dale, Hiltrud Brauch, Hermann Brenner, Angela Brooks-Wilson, Thomas Bruening, Barbara Burwinkel, Saundra S. Buys, Federico Canzian, Jose E. Castelao, Jenny Chang-Claude, Stephen J. Chanock, Georgia Chenevix-Trench, Christine L. Clarke, J. Margriet Collee, Angela Cox, Simon S. Cross, Kamila Czene, Mary B. Daly, Peter Devilee, Thilo Dork, Miriam Dwek, Diana M. Eccles, D. Gareth Evans, Peter A. Fasching, Jonine Figueroa, Giuseppe Floris, Manuela Gago-Dominguez, Susan M. Gapstur, Jose A. Garcia-Saenz, Mia M. Gaudet, Graham G. Giles, Mark S. Goldberg, Anna Gonzalez-Neira, Grethe I. Grenaker Alnaes, Mervi Grip, Pascal Guenel, Christopher A. Haiman, Per Hall, Ute Hamann, Elaine F. Harkness, Bernadette A. M. Heemskerk-Gerritsen, Bernd Holleczek, Antoinette Hollestelle, Maartje J. Hooning, Robert N. Hoover, John L. Hopper, Anthony Howell, Milena Jakimovska, Anna Jakubowska, Esther M. John, Michael E. Jones, Audrey Jung, Rudolf Kaaks, Saila Kauppila, Renske Keeman, Elza Khusnutdinova, Cari M. Kitahara, Yon-Dschun Ko, Stella Koutros, Vessela N. Kristensen, Ute Kruger, Katerina Kubelka-Sabit, Allison W. Kurian, Kyriacos Kyriacou, Diether Lambrechts, Derrick G. Lee, Annika Lindblom, Martha Linet, Jolanta Lissowska, Ana Llaneza, Wing-Yee Lo, Robert J. MacInnis, Arto Mannermaa, Mehdi Manoochehri, Sara Margolin, Maria Elena Martinez, Catriona McLean, Alfons Meindl, Usha Menon, Heli Nevanlinna, William G. Newman, Jesse Nodora, Kenneth Offit, Hakan Olsson, Nick Orr, Tjoung-Won Park-Simon, Alpa Patel, Julian Peto, Guillermo Pita, Dijana Plaseska-Karanfilska, Ross Prentice, Kevin Punie, Katri Pylkas, Paolo Radice, Gad Rennert, Atocha Romero, Thomas Ruediger, Emmanouil Saloustros, Sarah Sampson, Dale P. Sandler, Elinor J. Sawyer, Rita K. Schmutzler, Minouk J. Schoemaker, Ben Schottker, Mark E. Sherman, Xiao-Ou Shu, Snezhana Smichkoska, Melissa C. Southey, John J. Spinelli, Anthony J. Swerdlow, Rulla M. Tamimi, William J. Tapper, Jack A. Taylor, Lauren R. Teras, Mary Beth Terry, Diana Torres, Melissa A. Troester, Celine M. Vachon, Carolien H. M. van Deurzen, Elke M. van Veen, Philippe Wagner, Clarice R. Weinberg, Camilla Wendt, Jelle Wesseling, Robert Winqvist, Alicja Wolk, Xiaohong R. Yang, Wei Zheng, Fergus J. Couch, Jacques Simard, Peter Kraft, Douglas F. Easton, Paul D. P. Pharoah, Marjanka K. Schmidt, Montserrat Garcia-Closas, Nilanjan Chatterjee
Summary: This study identifies breast cancer susceptibility variants that are associated with tumor features and intrinsic molecular subtypes, providing insights for subtype-specific risk prediction.
BREAST CANCER RESEARCH
(2022)
