Article
Multidisciplinary Sciences
Connor Stashko, Mary-Kate Hayward, Jason J. Northey, Neil Pearson, Alastair J. Ironside, Johnathon N. Lakins, Roger Oria, Marie-Anne Goyette, Lakyn Mayo, Hege G. Russnes, E. Shelley Hwang, Matthew L. Kutys, Kornelia Polyak, Valerie M. Weaver
Summary: Intratumor heterogeneity is associated with poor patient outcome, and stromal stiffening accompanies cancer. It is unclear whether cancers exhibit stiffness heterogeneity and its link to tumor cell heterogeneity. A new method called Spatially Transformed Inferential Force Map (STIFMap) has been developed to measure stiffness heterogeneity in human breast tumors, allowing the quantification of stromal stiffness experienced by each cell and visual registration with tumor progression biomarkers.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tomasz M. Grzywa, Agnieszka A. Koppolu, Wiktor Paskal, Klaudia Klicka, Malgorzata Rydzanicz, Jaroslaw Wejman, Rafal Ploski, Pawel K. Wlodarski
Summary: Melanoma tumors are highly heterogeneous, which leads to challenges in diagnosis and treatment failures. This study revealed significant differences in genetic mutations between high and low proliferation compartments of melanoma tumors, highlighting the functional role of genetic heterogeneity in melanoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Leonardo Pellegrina, Fabio Vandin
Summary: The study presents a new algorithm, MASTRO, for discovering significantly conserved evolutionary trajectories in cancer. The algorithm is applied to lung cancer and acute myeloid leukemia data, confirming and extending previous findings.
Article
Multidisciplinary Sciences
Zhi-Nan Xia, Jing-Gen Wu, Wen-Hao Yao, Yu-Yang Meng, Wen-Gang Jian, Teng-Da Wang, Wei Xue, Yi-Peng Yu, Li-Cheng Cai, Xing-Yuan Wang, Peng Zhang, Zhi-Yuan Li, Hao Zhou, Zhi-Cheng Jiang, Jia-Yu Zhou, Cheng Zhang
Summary: This study analyzes single-cell and bulk RNA sequencing data to explore the correlation between the tumor microenvironment, clinical outcomes, and immunotherapeutic responses in renal cell carcinoma (RCC). It identifies distinct differentiation trajectories and molecular subtypes of ccRCC, and constructs a prognostic risk signature and a nomogram for predicting patient prognosis. The study highlights the importance of ccRCC cell differentiation and TME evolution in predicting clinical outcomes and potential immunotherapeutic responses, and provides an accurate method for prognosis prediction.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Cameron Herberts, Matti Annala, Joonatan Sipola, Sarah W. S. Ng, Xinyi E. Chen, Anssi Nurminen, Olga Korhonen, Kevin Beja, Elena Schonlau, Cecily Q. Bernales, Elie Ritch, Jack V. W. Bacon, Nathan A. Lack, Matti Nykter, Rahul Aggarwal, Eric J. Small, Martin E. Gleave, David A. Quigley, Felix Y. Feng, Kim N. Chi, Alexander W. Wyatt
Summary: This study performed whole-genome sequencing of plasma and synchronous metastases in patients with aggressive prostate cancer, revealing multiple dominant populations in ctDNA and shifts in mutational processes. They found that AR augmentation is the dominant genomic driver of acquired treatment resistance.
Article
Chemistry, Multidisciplinary
Soon-Chan Kim, Ji Won Park, Ha-Young Seo, Minjung Kim, Jae-Hyeon Park, Ga-Hye Kim, Ja Oh Lee, Young-Kyoung Shin, Jeong Mo Bae, Bon-Kyoung Koo, Seung-Yong Jeong, Ja-Lok Ku
Summary: The study reveals the widespread subregional heterogeneity within single tumors, leading to varied drug responses, emphasizing the importance of understanding the molecular heterogeneity of each tumor and targeting common somatic driver mutations positioned in all tumor subregional clones.
Article
Oncology
Jiahuai Wen, Liping Ren, Wenxia Li, Junhong Li, Lezhen Huang, Zhongyu Yuan, Qianjun Chen
Summary: This study aimed to explore the influence of different malignant lesions on subsequent treatment and to classify advanced breast cancer (ABC) patients for precise prognosis prediction. The results showed that ABC patients can be classified into homogeneous progression-disease (Hom-PD) group and heterogeneous progression-disease (Heter-PD) group based on the disease progression mode after first-line treatment. The classification model provides important information for predicting prognosis and making rational treatment decisions for ABC patients.
ANNALS OF TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Madeline E. McCarthy, Caitlin M. Anglin, Heather A. Peer, Sevanna A. Boleman, Stephanie R. Klaubert, Marc R. Birtwistle
Summary: This study presents a novel method for fluorescence multiplexing using MuSIC probes, which can effectively increase the multiplexing capacity. Different MuSIC probes were successfully attached to separate batches of antibodies, and the feasibility of the method was validated through spectral flow cytometry experiments. This approach has potential applications in cell-type profiling, tissue heterogeneity studies, clinical research, biomedical studies, and drug discovery.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Oncology
Hiroyasu Aoki, Satoshi Ueha, Shigeyuki Shichino, Haru Ogiwara, Kohei Shitara, Manami Shimomura, Toshihiro Suzuki, Tetsuya Nakatsura, Makiko Yamashita, Shigehisa Kitano, Sakiko Kuroda, Masashi Wakabayashi, Makoto Kurachi, Satoru Ito, Toshihiko Doi, Kouji Matsushima
Summary: Transient depletion of CD4(+) cells leads to replacement of T-cell clones in the blood, which is associated with the extent of CD4(+) T-cell depletion and an increase in CD8(+) T-cell count. This clonal replacement of the TCR repertoire is linked to the expansion of tumor-reactive T-cell clones and antitumor responses.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Computer Science, Information Systems
Qi Yang, Ziran Cao, Yaling Jiang, Hanbo Sun, Xiaokang Gu, Fei Xie, Fei Miao, Gang Gao
Summary: This study proposes a semi-supervised GIST detection method based on self-training and a new selection criterion to ensure the quality of pseudo-labels. The pseudo-labeled data is mixed with labeled data after linear mixing and added to the training set. The improved Faster RCNN with the multiscale module and the feature enhancement module is introduced for better GIST detection.
Article
Genetics & Heredity
Joshua T. Lange, John C. Rose, Celine Y. Chen, Yuriy Pichugin, Liangqi Xie, Jun Tang, King L. Hung, Kathryn E. Yost, Quanming Shi, Marcella L. Erb, Utkrisht Rajkumar, Sihan Wu, Sabine Taschner-Mandl, Marie Bernkopf, Charles Swanton, Zhe Liu, Weini Huang, Howard Y. Chang, Vineet Bafna, Anton G. Henssen, Benjamin Werner, Paul S. Mischel
Summary: Random segregation of extrachromosomal DNA contributes to intratumoral heterogeneity and facilitates the rapid adaptation of human tumor cells to anticancer drugs. Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Through theoretical models, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, it is shown that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment.
Review
Oncology
M. Julia Lostes-Bardaji, David Garcia-Illescas, Claudia Valverde, Cesar Serrano
Summary: GIST serves as a paradigm for targeted inhibition of oncogenic driver mutations in cancer, with Ripretinib emerging as a new standard of care for advanced, multi-resistant GIST patients. This recent approval by the FDA marks a major breakthrough in sarcoma drug development after nearly a decade without new treatment approvals in GIST.
THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Hamed Ishaq Khouja, Ibraheem Mohammed Ashankyty, Leena Hussein Bajrai, P. K. Praveen Kumar, Mohammad Amjad Kamal, Ahmad Firoz, Mohammad Mobashir
Summary: This study collected gene expression data from different stages of renal cell carcinoma and used computational methods to analyze them. It found that certain pathways and genes showed significant changes in renal cell carcinoma, and these differentially expressed genes may play important roles in survival.
SCIENTIFIC REPORTS
(2022)
Article
Engineering, Biomedical
Chun Liu, Miao Li, Zhao-Xia Dong, Dong Jiang, Xiaojing Li, Shuibin Lin, Demeng Chen, Xuenong Zou, Xing-Ding Zhang, Gary D. Luker
Summary: The study showed that breast cancer cells behave differently in environments with different stiffness: cells tend to proliferate in soft environments and migrate in stiff environments. Breast cancer cells switch metabolic pathways and gene expression in response to varying environmental stiffness.
ACTA BIOMATERIALIA
(2021)
Review
Oncology
Paul David, Anke Mittelstaedt, Dina Kouhestani, Anna Anthuber, Christoph Kahlert, Kai Sohn, Georg F. Weber
Summary: Gastrointestinal (GI) cancers have a significant impact on global cancer-related mortality. Liquid biopsies (LBs) are currently being researched as a non-invasive and low-risk method for early cancer detection. LB involves the analysis of tumor-specific components in biological fluids like blood, urine, and saliva, such as circulating tumor DNA (ctDNA), extracellular vesicles (EVs), and circulating tumor cells (CTCs). LBs offer a unique approach for cancer assessment at all stages of treatment, from screening to prognosis to multidisciplinary therapies. This review provides insights into the current status and applications of LBs in early detection and monitoring of GI cancers.
Article
Hematology
Ebba Sohlberg, Aline Pfefferle, Eivind Heggernes Ask, Astrid Tschan-Plessl, Benedikt Jacobs, Herman Netskar, Susanne Lorenz, Minoru Kanaya, Mizuha Kosugi-Kanaya, Stephan Meinke, Anette Mortberg, Petter Hoglund, Mikael Sundin, Goran Carlsson, Jan Palmblad, Karl-Johan Malmberg
Summary: This study examines the NK cell repertoires in patients with neutropenia and finds that a subgroup of patients show severely disrupted NK cell homeostasis, characterized by increased frequencies of immature NK cells and a lack of mature NK cells. These immature NK cells exhibit characteristics of proliferation and exhaustion and display weakened responses to tumor target cells.
Article
Biotechnology & Applied Microbiology
Heidi M. Namlos, Magne Skarn, Deeqa Ahmed, Iwona Grad, Kim Andresen, Stine H. Kresse, Else Munthe, Massimo Serra, Katia Scotlandi, Antonio Llombart-Bosch, Ola Myklebost, Guro E. Lind, Leonardo A. Meza-Zepeda
Summary: miR-486-5p is an epigenetically regulated miRNA in osteosarcoma, playing a significant role in the biology of the disease.
Article
Medicine, Research & Experimental
Aslaug Helland, Hege G. Russnes, Gro Live Fagereng, Khalid Al-Shibli, Yvonne Andersson, Thomas Berg, Line Bjorge, Egil Blix, Bodil Bjerkehagen, Sigmund Brabrand, Marte Gronlie Cameron, Astrid Dalhaug, Dalia Dietzel, Tom Donnem, Espen Enerly, Asmund Flobak, Sverre Fluge, Bjornar Gilje, Bjorn Tore Gjertsen, Bjorn Henning Gronberg, Kari Gronas, Tormod Guren, Hanne Hamre, Ase Haug, Daniel Heinrich, Geir Olav Hjortland, Eivind Hovig, Randi Hovland, Ann-Charlotte Iversen, Emiel Janssen, Jon Amund Kyte, Hedda von der Lippe Gythfeldt, Ragnhild Lothe, Jo-Asmund Lund, Leonardo Meza-Zepeda, Monica Cheng Munthe-Kaas, Olav Toai Duc Nguyen, Pitt Niehusmann, Hilde Katarina NilsenPuco, Anne Hansen Ree, Tonje Boyum Riste, Karin Semb, Eli Sihn Samdal Steinskog, Andreas Stensvold, Pal Suhrke, Oyvind Tennoe, Geir E. Tjonnfjord, Liv Jorunn Vassbotn, Eline Aas, Kristine Aasebo, Kjetil Tasken, Sigbjorn Smeland
Summary: Personalized cancer care based on tumour molecular characteristics has revolutionized treatment approaches and brought hope to many patients. The implementation of emerging technologies in molecular diagnostics, publicly funded in Norway, allows for comprehensive genomic profiling of tumours, offering more cancer patients the possibility of receiving precision cancer drugs through the national infrastructure called IMPRESS-Norway.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Oncology
Kristine Misund, Davine Hofste Op Bruinink, Eivind Coward, Remco M. Hoogenboezem, Even Holth Rustad, Mathijs A. Sanders, Morten Rye, Anne-Marit Sponaas, Bronno van der Holt, Sonja Zweegman, Eivind Hovig, Leonardo A. Meza-Zepeda, Anders Sundan, Ola Myklebost, Pieter Sonneveld, Anders Waage
Summary: We investigated the genomic and transcriptomic changes in multiple myeloma patients before and after treatment. The study discovered changes in clonal composition and increased single-nucleotide variants. It also found alterations in specific genes and pathways, such as RAS genes, amp1q21, and TP53, and identified increased expression of potentially targetable genes in late-stage disease.
Article
Genetics & Heredity
Andreas Venizelos, Christina Engebrethsen, Wei Deng, Jurgen Geisler, Stephanie Geisler, Gjertrud T. Iversen, Turid Aas, Hildegunn S. Aase, Manouchehr Seyedzadeh, Eli Sihn Steinskog, Ola Myklebost, Sigve Nakken, Daniel Vodak, Eivind Hovig, Leonardo A. Meza-Zepeda, Per E. Lonning, Stian Knappskog, Hans P. Eikesdal
Summary: Subclonal composition of treatment-naive breast cancers undergoes profound changes during neoadjuvant chemotherapy with epirubicin and docetaxel monotherapy, while early truncal mutations and major subclones generally persist through treatment. Tumor mutational burden decreases during neoadjuvant therapy.
Article
Multidisciplinary Sciences
Mandy L. Ballinger, Swetansu Pattnaik, Piyushkumar A. Mundra, Milita Zaheed, Emma Rath, Peter Priestley, Jonathan Baber, Isabelle Ray-Coquard, Nicholas Isambert, Sylvain Causeret, Winette T. A. van der Graaf, Ajay Puri, Florence Duffaud, Axel Le Cesne, Beatrice Seddon, Coonoor Chandrasekar, Joshua D. Schiffman, Andrew S. Brohl, Paul A. James, Jean-Emmanuel Kurtz, Nicolas Penel, Ola Myklebost, Leonardo A. Meza-Zepeda, Hilda Pickett, Maya Kansara, Nicola Waddell, Olga Kondrashova, John Pearson, Andrew P. Barbour, Shuai Li, Tuong L. Nguyen, Diane Fatkin, Robert M. Graham, Eleni Giannoulatou, Melissa J. Green, Warren Kaplan, Shyamsundar Ravishankar, Joseph Copty, Joseph E. Powell, Edwin Cuppen, Kristel van Eijk, Jan Veldink, Jin-Hee Ahn, Jeong Eun Kim, R. Lor Randall, Kathy Tucker, Ian Judson, Rajiv Sarin, Thomas Ludwig, Emmanuelle Genin, Jean-Francois Deleuze, Michelle Haber, Glenn Marshall, Murray J. Cairns, Jean-Yves Blay, David M. Thomas
Summary: Cancer genetics has focused on epithelial malignancies, but this study explores specific pathways related to sarcomas, rare malignancies derived from embryonic mesoderm. Germline sequencing of sporadic cases and healthy controls reveals two sarcoma-specific pathways involved in mitotic and telomere functions. Centrosome gene variants are linked to specific tumors, while heritable defects in the shelterin complex increase susceptibility to sarcomas, melanomas, and thyroid cancers. These findings highlight the role of heritable defects in mitotic and telomere biology in sarcoma risk.
Article
Health Care Sciences & Services
Martina Ruscelli, Thais Maloberti, Angelo Gianluca Corradini, Francesca Rosini, Giulia Querzoli, Marco Grillini, Annalisa Altimari, Elisa Gruppioni, Viviana Sanza, Alessia Costantino, Riccardo Ciudino, Matteo Errani, Alessia Papapietro, Sara Coluccelli, Daniela Turchetti, Martina Ferioli, Susanna Giunchi, Giulia Dondi, Marco Tesei, Gloria Ravegnini, Francesca Abbati, Daniela Rubino, Claudio Zamagni, Emanuela D'Angelo, Pierandrea De Iaco, Donatella Santini, Claudio Ceccarelli, Anna Myriam Perrone, Giovanni Tallini, Dario de Biase, Antonio De Leo
Summary: This study aims to evaluate the impact of integrated molecular and pathologic risk stratification in the clinical practice of endometrial carcinoma (EC). It found that molecular classes and risk groups were correlated with disease-free survival. The study supports the prognostic importance of EC molecular classification and the essential role of histopathologic assessment in patients' management.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Oncology
Heidi Maria Namlos, Ksenia Khelik, Sigve Nakken, Daniel Vodak, Eivind Hovig, Ola Myklebost, Kjetil Boye, Leonardo A. Meza-Zepeda
Summary: Patients with localised, high-risk gastrointestinal stromal tumours (GIST) who receive adjuvant imatinib treatment may still relapse within 3 years. Current risk classification methods are not accurate in predicting poor outcomes after standard treatment. This study aimed to identify genomic and transcriptomic profiles associated with disease relapse and a more aggressive phenotype. The findings suggest that increased chromosomal instability is an intrinsic feature for metastasizing tumours and could serve as a novel prognostic biomarker for high-risk GIST.
MOLECULAR ONCOLOGY
(2023)
Article
Medicine, General & Internal
Maren Holand, Kaja C. G. Berg, Ina A. Eilertsen, Bodil Bjerkehagen, Matthias Kolberg, Kjetil Boye, Ole Christian Lingjaerde, Tormod K. Guren, Nils Mandahl, Eva van den Berg, Emanuela Palmerini, Sigbjorn Smeland, Piero Picci, Fredrik Mertens, Anita Sveen, Ragnhild A. Lothe
Summary: MPNSTs were classified into two transcriptomic subtypes: immune active type with sustained immune signals and favorable prognosis, and immune deficient type with aggressive disease course, PRC2 loss, and expression of potential therapeutic targets. Copy number-based proliferative transcriptomic signatures were associated with patient prognosis.
Article
Oncology
Camelia Alexandra Coada, Miriam Santoro, Vladislav Zybin, Marco Di Stanislao, Giulia Paolani, Cecilia Modolon, Stella Di Costanzo, Lucia Genovesi, Marco Tesei, Antonio De Leo, Gloria Ravegnini, Dario De Biase, Alessio Giuseppe Morganti, Luigi Lovato, Pierandrea De Iaco, Lidia Strigari, Anna Myriam Perrone
Summary: This study investigated the potential of radiomic features extracted from pre-surgical CT scans to predict disease-free survival (DFS) in endometrial cancer (EC) patients. Machine learning models achieved high sensitivities and specificities in both training and test sets, showing promise for predicting EC recurrence.
Article
Biochemistry & Molecular Biology
Eirik Hoye, Bastian Fromm, Paul H. M. Boettger, Diana Domanska, Annette Torgunrud, Christin Lund-Andersen, Torveig Weum Abrahamsen, Asmund Avdem Fretland, Vegar J. Dagenborg, Susanne Lorenz, Bjorn Edwin, Eivind Hovig, Kjersti Flatmark
Summary: This study identifies reliable miRNAs associated with metastatic progression in colorectal cancer using next-generation sequencing datasets. The identified miRNAs provide a good starting point for further research on the role of miRNAs in metastatic progression.
Meeting Abstract
Biotechnology & Applied Microbiology
Ganna Reint, Zhuokun Li, Kornel Labun, Salla Keskitalo, Inkeri Soppa, Katariina Mamia, Eero Tolo, Monika Szymanska, Leonardo Meza-Zepeda, Susanne Lorenz, Artur Cieslar-Pobuda, Xian Hu, Diana Bordin, Judith Staerk, Eivind Valen, Bernhard Schmierer, Markku Varjosalo, Jussi Taipale, Emma Haapaniemi