Review
Oncology
Branka Powter, Sarah A. Jeffreys, Heena Sareen, Adam Cooper, Daniel Brungs, Joseph Po, Tara Roberts, Eng-Siew Koh, Kieran F. Scott, Mila Sajinovic, Joey Y. Vessey, Paul de Souza, Therese M. Becker
Summary: TERT promoter mutations C228T and C250T are crucial in cancer, can be easily detected through liquid biopsies, and hold potential for personalized cancer therapy.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Oncology
Yuan Li, Zuhua Chen, Weiping Tao, Nan Sun, Jie He
Summary: TMS18, a novel tumor mutation score, was found to be more accurate and efficient in predicting response to immunotherapy in NSCLC compared to TMB. Combined with PD-L1, TMS18 showed improved accuracy and efficiency in predicting response to ICIs, suggesting its potential as a promising biomarker in larger cohorts.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Hanpeng Du, Haiyue Wang, Fandong Kong, Mingjian Wu, Wei Chen, Jin Lyu, Sitong Zhou, Ronghua Yang
Summary: This study identified that FREM2 gene had the highest mutation frequency in colon adenocarcinoma patients. A prognostic model based on FREM2 mutations was constructed with high prediction accuracy. Differentially expressed genes were analyzed for functional enrichment and immune infiltration. FREM2 expression was found to be highly expressed in tumor tissues. Therefore, FREM2 mutations may serve as potential prognostic markers in colorectal cancer.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Genetics & Heredity
Xiaofang Sun, Jianping Zhang, Can Xiao, Zili Ge
Summary: This study investigated the expression profiles and prognostic values of the LSM family in skin cutaneous melanoma (SKCM). The results showed that LSM2 overexpression was significantly correlated with poor overall survival in SKCM patients and the LSM family was involved in RNA splicing and degradation. LSM2 may serve as a potential poor prognosticator and immunotherapeutic target of SKCM.
BMC MEDICAL GENOMICS
(2022)
Article
Oncology
Kenji M. Fujihara, Mariana Corrales Benitez, Carlos S. Cabalag, Bonnie Z. Zhang, Hyun S. Ko, David S. Liu, Kaylene J. Simpson, Ygal Haupt, Lara Lipton, Sue Haupt, Wayne A. Phillips, Nicholas J. Clemons
Summary: This study aims to identify a robust biomarker for response to APR-246 and found that the expression of SLC7A11 is a superior determinant of sensitivity to APR-246. Therefore, SLC7A11 should be utilized as the key predictive biomarker to stratify patients for future clinical investigation of APR-246.
MOLECULAR CANCER THERAPEUTICS
(2021)
Article
Biochemical Research Methods
Zicheng Zhen, Minghao Li, Muyan Zhong, Liqun Ye, Xiaofang Ma
Summary: This study reveals the correlation of FIGNL1 expression with prognosis, promoter methylation, and immune infiltrates in KIRP, LGG, and LIHC, suggesting the potential of FIGNL1 as a prognostic biomarker for these cancers.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2022)
Article
Oncology
Xiao-Peng Duan, Ke Liu, Xiao-Dong Jiao, Bao-Dong Qin, Bing Li, Xi He, Yan Ling, Ying Wu, Shi-Qi Chen, Yuan-Sheng Zang
Summary: Tumor mutation burden (TMB) is a promising biomarker associated with immunotherapy benefit and chemotherapy outcome. This study demonstrated that TMB-high advanced gastric cancer patients had a poorer prognosis when treated with first-line chemotherapy, potentially due to downregulated metabolic activity.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
K. A. Z. U. H. I. R. O. Okamoto, K. E. I. I. C. H. I. R. O. Nakamura, J. U. N. K. O. Haraga, H. I. S. A. S. H. I. Masuyama
Summary: Investigating the molecular characteristics of metastatic lesions in addition to those of primary lesions could provide beneficial prognostic information in patients with endometrial cancer with regional lymph node metastasis. Aberrant p53 expression and inter-lesion heterogeneity are associated with worse progression-free survival in metastatic lymph nodes.
ANTICANCER RESEARCH
(2022)
Article
Medicine, General & Internal
Yuan Yuan, Weimin Ren, Jinchao Zhu, Saiyan Ji, Qingyuan Yang
Summary: Lymph node metastasis, perineural/venous invasion, TNM stage, local recurrence or distant metastasis after surgery, and the expression of Ki-67 and KRAS mutation are independent prognostic biomarkers for predicting the 2-year survival rate of CRC patients. These markers show differential prognosis in different subgroups based on age, tumor site, differentiation, histological type, lymph node metastasis, TNM stage, and recurrence/metastasis.
ANNALS OF MEDICINE
(2023)
Article
Multidisciplinary Sciences
Safayat Mahmud Khan, Tonmoy Das, Sajib Chakraborty, Abdul Matin Anamur Rashid Choudhury, Howlader Fazlul Karim, Munshi Akid Mostofa, Hasib Uddin Ahmed, Md Akmal Hossain, Florence Le Calvez-Kelm, Md Ismail Hosen, Hossain Uddin Shekhar
Summary: This study investigated the role of p53 pathway genes in bladder cancer through transcriptomics analysis. Two subtypes of bladder cancer were identified, one associated with immune-related pathways and poor prognosis, and the other associated with steroid synthesis and drug metabolism pathways and better prognosis. A signature gene set consisting of six genes was created and a risk model was developed. This study has the potential to significantly impact the development of biomarkers for bladder cancer.
Article
Otorhinolaryngology
Zao Ji, Zhiyao Fang, Xue Dong, Jia Wang, Xianyao Wan, Aihui Yan
Summary: This study identified key genes closely related to ferroptosis in laryngeal cancer (LC) through analysis of differentially expressed genes, enrichment, PPI and ROC analysis. These genes may become effective clinical diagnostic and prognostic biomarkers for LC.
EUROPEAN ARCHIVES OF OTO-RHINO-LARYNGOLOGY
(2022)
Article
Computer Science, Information Systems
Xiangyu Liu, Zhenyu Liu, Ye Yan, Kai Wang, Aodi Wang, Xiongjun Ye, Liwei Wang, Wei Wei, Bao Li, Caixia Sun, Wei He, Xuehua Zhu, Zenan Liu, Jiangang Liu, Jian Lu, Jie Tian
Summary: The rapid development of computational pathology has provided new opportunities for prognosis prediction using histopathological images. However, existing deep learning frameworks lack exploration of the relationship between images and other prognostic information, resulting in poor interpretability. This study proposes a two-step framework for prognostic prediction using whole-slide images (WSIs) and achieves good performance.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2023)
Article
Oncology
G. A. Croci, R. K. H. Au-Yeung, S. Reinke, A. M. Staiger, K. Koch, I Oschlies, J. Richter, V Poeschel, G. Held, M. Loeffler, L. Trumper, A. Rosenwald, G. Ott, R. Spang, B. Altmann, M. Ziepert, W. Klapper
Summary: The content of CD68+ macrophages is associated with poor prognosis, while SPARC-positive macrophages are associated with favorable outcomes in DLBCL patients.
ANNALS OF ONCOLOGY
(2021)
Article
Medicine, General & Internal
Xiao Zhen Zhang, Mao Jian Chen, Ping Ming Fan, Wei Jiang, Shi Xiong Liang
Summary: This study investigated the role of BTG2 in lung adenocarcinoma (LUAD) and its correlation with immune infiltration. The results showed that BTG2 expression was downregulated in LUAD and was associated with poor prognosis. Additionally, BTG2 was found to be closely related to immune infiltration, immune cell markers, chemokines, and chemokine receptors. Therefore, BTG2 may serve as a promising immune-related biomarker and molecular target for patients with LUAD.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2022)
Article
Oncology
Fabienne Frohlich, Egle Ramelyte, Patrick Turko, Andreas Dzung, Sandra N. Freiberger, Joanna Mangana, Mitchell P. Levesque, Reinhard Dummer
Summary: Although immunotherapy and targeted therapy have improved melanoma survival, some patients rapidly progress and decease within months after a stage IV diagnosis. This study aimed to find genetic alterations that predict short or long survival in melanoma patients and found that a clock-like mutational signature was associated with poor survival, while a UV mutational signature was prognostic for longer survival. These findings suggest that mutational signatures could be valuable prognostic markers for melanoma.
Article
Biochemical Research Methods
Daniel Osorio, Marieke L. Kuijjer, James J. Cai
Summary: This study introduces rPanglaoDB, an R package for downloading and merging uniformly processed scRNA-seq data to collect rare cell types by integrating multiple public datasets. By characterizing a set of 157 fibrocytes, the study demonstrates the potential and utility of rPanglaoDB in enabling the collection of rare cell types for transcriptomic profiling.
Article
Biochemistry & Molecular Biology
Marouen Ben Guebila, Camila M. Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush
Summary: Gene regulation networks play a crucial role in tissue identity, disease development, and therapeutic response. The GRAND database provides computationally-inferred gene regulatory network models and targeting scores for predicting drug effects on network structures and matching potential therapeutic drugs to disease states.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Hematology
Paul G. Kemps, Jennifer Picarsic, Benjamin H. Durham, Zofia Helias-Rodzewicz, Laura Hiemcke-Jiwa, Cor van den Bos, Marianne D. van de Wetering, Carel J. M. van Noesel, Jan A. M. van Laar, Robert M. Verdijk, Uta E. Flucke, Pancras C. W. Hogendoorn, F. J. Sherida H. Woei-A-Jin, Raf Sciot, Andreas Beilken, Friedrich Feuerhake, Martin Ebinger, Robert Mohle, Falko Fend, Antje Bornemann, Verena Wiegering, Karen Ernestus, Tina Mery, Olga Gryniewicz-Kwiatkowska, Bozenna Dembowska-Baginska, Dmitry A. Evseev, Vsevolod Potapenko, Vadim V. Baykov, Stefania Gaspari, Sabrina Rossi, Marco Gessi, Gianpiero Tamburrini, Sebastien Heritier, Jean Donadieu, Jacinthe Bonneau-Lagacherie, Claire Lamaison, Laure Farnault, Sylvie Fraitag, Marie-Laure Jullie, Julien Haroche, Matthew Collin, Jackie Allotey, Majid Madni, Kerry Turner, Susan Picton, Pasquale M. Barbaro, Alysa Poulin, Ingrid S. Tam, Dina El Demellawy, Brianna Empringham, James A. Whitlock, Aditya Raghunathan, Amy A. Swanson, Mariko Suchi, Jon M. Brandt, Nabeel R. Yaseen, Joanna L. Weinstein, Irem Eldem, Bryan A. Sisk, Vaishnavi Sridhar, Mandy Atkinson, Lucas R. Massoth, Jason L. Hornick, Sanda Alexandrescu, Kee Kiat Yeo, Kseniya Petrova-Drus, Stephen Z. Peeke, Laura S. Munoz-Arcos, Daniel G. Leino, David D. Grier, Robert Lorsbach, Somak Roy, Ashish R. Kumar, Shipra Garg, Nishant Tiwari, Kristian T. Schafernak, Michael M. Henry, Astrid G. S. van Halteren, Oussama Abla, Eli L. Diamond, Jean-Francois Emile
Summary: ALK-positive histiocytosis is a rare and poorly characterized subtype of histiocytic neoplasm. This study provides the largest analysis of ALK-positive histiocytosis to date, describing the clinicopathologic and molecular characteristics of 39 cases. The study also highlights the robust responses observed in patients treated with ALK inhibition, particularly those with neurologic involvement.
Article
Biochemistry & Molecular Biology
Ramzi Khalil, Margien G. S. Boels, Palga Group, Bernard M. van den Berg, Jan A. Bruijn, Ton J. Rabelink, Pancras C. W. Hogendoorn, Hans J. Baelde
Summary: This study investigates the effect of heterozygous germline mutations in the EXT1 and EXT2 genes on the glomerular barrier function and the endothelial glycocalyx in humans. The results show that these mutations do not lead to (micro)albuminuria, specific renal phenotype or changes to the endothelial glycocalyx in humans. These findings contribute to the understanding of the role of EXT1 and EXT2 genes in pathophysiology.
MOLECULAR GENETICS AND GENOMICS
(2022)
Letter
Biochemical Research Methods
Marouen Ben Guebila, Deborah Weighill, Camila M. Lopes-Ramos, Rebekka Burkholz, Romana T. Pop, Kalyan Palepu, Mia Shapoval, Maud Fagny, Daniel Schlauch, Kimberly Glass, Michael Altenbuchinger, Marieke L. Kuijjer, John Platig, John Quackenbush
Editorial Material
Genetics & Heredity
Maud Fagny, Kimberly Glass, Marieke L. Kuijjer
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Sofia Birkealv, Mark Harland, Larissa Satiko Alcantara Sekimoto Matsuyama, Mamun Rashid, Ishan Mehta, Jonathan P. Laye, Kerstin Haase, Tracey Mell, Vivek Iyer, Carla Daniela Robles-Espinoza, Ultan McDermott, Peter van Loo, Marieke L. Kuijjer, Patricia A. Possik, Silvya Stuchi Maria Engler, D. Timothy Bishop, Julia Newton-Bishop, David J. Adams
Summary: This study conducted sequence profiling of 524 American Joint Committee on Cancer Stage I-III primary tumors, revealing recurrent driver mutations, mutually exclusive genetic interactions, and an absence of co-occurring genetic events. By intersecting copy number calls with CRISPR screening data, the transcription factor IRF4 was identified as a melanoma-associated dependency.
JOURNAL OF PATHOLOGY
(2023)
Review
Oncology
Djoko Santoso, Mochammad Thaha, Maulana A. Empitu, Ika Nindya Kadariswantiningsih, Satriyo Dwi Suryantoro, Mutiara Rizki Haryati, Decsa Medika Hertanto, Dana Pramudya, Siprianus Ugroseno Yudho Bintoro, Nasronudin Nasronudin, Mochamad Yusuf Alsagaff, Hendri Susilo, Citrawati Dyah Kencono Wungu, Nicolaas C. Budhiparama, Pancras C. W. Hogendoorn
Summary: Osteitis fibrosa cystica (OFC) and Brown Tumours are rare bone lesions associated with chronic kidney disease. The mechanism of these conditions is not well understood, but recent literature suggests that factors such as overactivation of the renin-angiotensin-aldosterone system and chronic inflammation may contribute to their occurrence through osteoclast activation. In addition, hotspot KRAS mutations have been identified in these lesions, placing them in the spectrum of RAS-MAPK-driven neoplasms. Risk factors for OFC and Brown Tumours include age, gender, comorbidities, and certain medications. Diagnosis involves clinical symptoms of chronic bone pain and laboratory findings of hyperparathyroidism, as well as radiological imaging and histological examination.
Article
Biotechnology & Applied Microbiology
Marouen Ben Guebila, Tian Wang, Camila M. M. Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N. N. Paulson, Michael Altenbuchinger, Katherine H. H. Shutta, Abhijeet R. R. Sonawane, James Lim, Genis Calderer, David G. P. van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L. L. DeMeo, Megha Padi, John Platig, Marieke L. L. Kuijjer, Kimberly Glass, John Quackenbush
Summary: This article introduces an open-source software called NetZoo, which is used for inference and analysis of gene regulatory networks. NetZoo integrates multi-omic data from various sources and harmonizes the implementations of network methods in different computing languages and between methods to allow better integration of these tools into analytical pipelines.
Article
Physiology
Ramzi Khalil, Josephine D. D. Bonnemaijer, Reinhold Kreutz, Herman P. Spaink, Pancras C. W. Hogendoorn, Hans J. Baelde
Summary: Transmembrane protein 14A (TMEM14A) is an important protein involved in maintaining the integrity of the glomerular filtration barrier. It suppresses Bax-mediated apoptosis and its expression is increased in proteinuric renal diseases.
PHYSIOLOGICAL REPORTS
(2023)
Article
Medicine, General & Internal
Marios Marcou, Matthias Galiano, Anja Tzschoppe, Katja Sauerstein, Sven Wach, Helge Taubert, Bernd Wullich, Karin Hirsch-Koch, Hendrik Apel
Summary: Recognizing risk factors is crucial for decision-making in pediatric kidney transplantation. A retrospective study identified small body surface area (<1 m(2)) as a favorable prognostic factor for long-term graft survival, while adolescents over the age of 12 had poorer outcomes.
JOURNAL OF CLINICAL MEDICINE
(2023)
Review
Immunology
Marloes M. A. R. van Dorst, Jeremia J. Pyuza, Gyaviira Nkurunungi, Vesla I. Kullaya, Hermelijn H. Smits, Pancras C. W. Hogendoorn, Linda J. Wammes, Bart Everts, Alison M. Elliott, Simon P. Jochems, Maria Yazdanbakhsh
Summary: There is considerable variation in efficacy of vaccines across populations and geographical regions, which is influenced by multiple environmental factors. Current interventions targeting these factors have had variable success, highlighting the need for a better understanding of the immunological mechanisms involved in vaccine responses.
NATURE REVIEWS IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Cedric R. Weber, Teresa Rubio, Longlong Wang, Wei Zhang, Philippe A. Robert, Rahmad Akbar, Igor Snapkov, Jinghua Wu, Marieke L. Kuijjer, Sonia Tarazona, Ana Conesa, Geir K. Sandve, Xiao Liu, Sai T. Reddy, Victor Greiff
Summary: The similarity of immune repertoires can represent an individual's immune history. However, current understanding might be incorrect as certain immune states show highly similar immune repertoires in both healthy and diseased individuals, suggesting that immune perturbations do not cause significant changes in repertoires.
CELL REPORTS METHODS
(2022)
Article
Genetics & Heredity
Marouen Ben Guebila, Daniel C. Morgan, Kimberly Glass, Marieke L. Kuijjer, Dawn L. DeMeo, John Quackenbush
Summary: Gene regulatory network inference allows for modeling genome-scale regulatory processes. Researchers have developed a collection of tools to model various regulatory processes and improve their performance through GPU-accelerated calculations.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Oncology
Paul Kemps, Jennifer Picarsic, Benjamin H. Durham, Zofia Helias-Rodzewicz, Laura Hiemcke-Jiwa, Cor van den Bos, Marianne D. van Dewetering, Carel J. M. van Noesel, Pancras C. W. Hogendoorn, F. J. Sherida H. Woei-A-Jin, Raf Sciot, Andreas Beilken, Friedrich Feuerhake, Martin Ebinger, Robert Mohle, Falko Fend, Antje Bornemann, Verena Wiegering, Karen Ernestus, Tina Mery, Olga Gryniewicz-Kwiatkowska, Bozenna Dembowska-Baginska, Dmitry A. Evseev, Vsevolod Potapenko, Vadim V. Baykov, Stefania Gaspari, Sabrina Rossi, Marco Gessi, Gianpiero Tamburrini, Sebastien Heritier, Jacinthe Bonneau-Lagacherie, Claire Lamaison, Laure Farnault, Sylvie Fraitag, Jean Donadieu, Julien Haroche, Matthew Collin, Jackie Allotey, Majid Madni, Kerry Turner, Susan Picton, Pasquale M. Barbaro, Dina El Demellawy, Brianna Empringham, James A. Whitlock, Aditya Raghunathan, Amy A. Swanson, Mariko Suchi, Jon M. Brandt, Nabeel R. Yaseen, Joanna L. Weinstein, Irem Eldem, Bryan A. Sisk, Vaishnavi Sridha, Mandy Atkinson, Lucas R. Massoth, Jason L. Hornick, Sanda Alexandrescu, Kee Kiat Yeo, Kseniya Petrova-Drus, Stephen Z. Peeke, Laura S. Munoz-Arcos, Daniel G. Leino, David D. Grier, Robert Lorsbach, Somak Roy, Ashish R. Kumar, Shipra Garg, Nishant Tiwari, Kristian T. Schafernak, Michael M. Henry, Astrid G. S. van Halteren, Oussama Abla, Eli L. Diamond, Jean-Francois Emile
PEDIATRIC BLOOD & CANCER
(2022)