Article
Multidisciplinary Sciences
Ali Reza Ebadi, Ali Soleimani, Abdulbaghi Ghaderzadeh
Summary: The study introduces a new method to extract driver genes more accurately through subspace learning and unsupervised learning, showing higher predictive accuracy. By comparing p-value overlap and new driver genes, the method outperforms in identifying driver genes in cancer tumors.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Jiangti Luo, Canping Chen, Zhixian Liu, Xiaosheng Wang
Summary: Splicing abnormality resulting from somatic mutations in key splicing factor genes has been found in various cancers. This study investigates the impact of splicing factor gene mutations on clinical features, tumor progression, genomic integrity, anti-tumor immune responses, and immunotherapy response in 12 common cancer types. The results show that splicing factor gene mutations are associated with worse survival prognosis, higher mutation burden and aneuploidy levels, increased immunosuppressive signatures, and higher levels of tumor stemness, proliferation potential, and intratumor heterogeneity. However, splicing factor gene mutations are also linked to higher response rates to immune checkpoint inhibitors. Single-cell data analysis further confirms the association between splicing factor gene mutations and tumor characteristics. The findings suggest that splicing factor gene mutations can serve as prognostic factors and indicators for immunotherapy response in cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Cell Biology
Neha Rohatgi, Umesh Ghoshdastider, Probhonjon Baruah, Tanmay Kulshrestha, Anders Jacobsen Skanderup
Summary: Through a tumor transcriptome deconvolution approach, we identified fundamental differences in metabolic states of cancer and stromal cells inside tumors, including the upregulation of deoxythymidine triphosphate (dTTP) and overexpression of tryptophan catabolism rate-limiting enzymes in stroma. Furthermore, we found that oxidative phosphorylation is more upregulated in cancer cells in vivo compared to stromal cells and a large atlas of cancer cell lines, suggesting a less pronounced Warburg effect in cancer cells.
Editorial Material
Genetics & Heredity
Kirsty Minton
Summary: A study published in Nature combines single-cell RNA-sequencing data from over 1,000 tumor samples to present a pan-cancer atlas that reveals the transcriptional heterogeneity within tumors.
NATURE REVIEWS GENETICS
(2023)
Article
Multidisciplinary Sciences
Zaoke He, Tao Wu, Shixiang Wang, Jing Zhang, Xiaoqin Sun, Ziyu Tao, Xiangyu Zhao, Huimin Li, Kai Wu, Xue-Song Liu
Summary: This study identified recurrent mutations in the CDC20 gene promoter that disrupt the binding of ELK4 transcription repressor, leading to up-regulation of CDC20 transcription. The findings shed light on the detailed mechanism of CDC20 gene deregulation in human cancers and also highlight the discovery of functional noncoding genetic alterations.
Article
Oncology
Marina V. Nemtsova, Alexey I. Kalinkin, Ekaterina B. Kuznetsova, Irina V. Bure, Ekaterina A. Alekseeva, Igor I. Bykov, Tatiana V. Khorobrykh, Dmitry S. Mikhaylenko, Alexander S. Tanas, Vladimir V. Strelnikov
Summary: Epigenetic mechanisms play a crucial role in gene expression patterns, and their deregulations can affect oncogenesis and metastasis in gastric cancer. Mutations in epigenetic regulation genes, particularly in KMT2D, KMT2C, ARID1A, and CHD7, were found to be associated with reduced overall survival of patients, especially in those with metastases and signet ring cell tumors. This suggests that mutations in epigenetic regulation genes may serve as valuable clinical markers for prognosis in gastric cancer patients.
Article
Oncology
Moom R. Roosan, Isa Mambetsariev, Rebecca Pharaon, Jeremy Fricke, Angel R. Baroz, Joseph Chao, Chen Chen, Mohd W. Nasser, Ramakanth Chirravuri-Venkata, Maneesh Jain, Lynette Smith, Susan E. Yost, Karen L. Reckamp, Raju Pillai, Leonidas Arvanitis, Michelle Afkhami, Edward W. Wang, Vincent Chung, Mihaela Cristea, Marwan Fakih, Marianna Koczywas, Erminia Massarelli, Joanne Mortimer, Yuan Yuan, Surinder K. Batra, Sumanta Pal, Ravi Salgia
Summary: Cancer metastasis is a leading cause of cancer-related deaths. The study evaluated the mutational landscape of seven solid metastatic tumors and found that somatic mutations in certain gene pairs had opposite effects on overall survival. Targeted therapy usage was associated with longer progression-free survival in advanced cancer cases.
Article
Oncology
Jing Yang, Shilin Zhao, Jing Wang, Quanhu Sheng, Qi Liu, Yu Shyr
Summary: Cancer-Immu is a comprehensive platform that integrates various omics data and clinical phenotypes to explore immunogenomic connections. It provides easy access to data and helps researchers translate omics datasets into biological insights and clinical applications.
Article
Genetics & Heredity
Erin R. Bonner, Adam Dawood, Heather Gordish-Dressman, Augustine Eze, Surajit Bhattacharya, Sridevi Yadavilli, Sabine Mueller, Sebastian M. Waszak, Javad Nazarian
Summary: Recent genomic data indicates an increasing role of somatic mutations in core histone and linker histone-encoding genes in cancer. This study analyzed somatic mutations in 88 linker and core histone genes across 12,743 tumors, establishing a pan-cancer histone mutation atlas. Histone mutations were found in 11% of tumors, with higher rates in certain cancers like chondrosarcoma and pediatric high-grade glioma. Recurrent pan-cancer histone mutation hotspots were identified, and the study also examined histone gene mutations in pan-cancer cell lines. Overall, this study provides important insights into the prevalence and implications of histone gene mutations in malignant tumors.
NPJ GENOMIC MEDICINE
(2023)
Article
Multidisciplinary Sciences
Kuan-lin Huang, Adam D. Scott, Daniel Cui Zhou, Liang-Bo Wang, Amila Weerasinghe, Abdulkadir Elmas, Ruiyang Liu, Yige Wu, Michael C. Wendl, Matthew A. Wyczalkowski, Jessika Baral, Sohini Sengupta, Chin-Wen Lai, Kelly Ruggles, Samuel H. Payne, Benjamin Raphael, David Fenyo, Ken Chen, Gordon Mills, Li Ding
Summary: Advances in mass-spectrometry have led to the generation of large-scale proteomics datasets containing tens of thousands of phosphorylation sites. Using a bioinformatics tool called HotPho, researchers identified 474 hybrid clusters of phosphosites and cancer mutations on protein structures, highlighting nearly 3,000 likely functional mutations and over 1,000 cancer phosphosites for potential clinical relevance.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Yuling Lin, Yan Chen, Youjing Zeng, Shuting Zhang, Zihao Zhang, YuKun Chen, Jiawei Gong, Zhongxiong Lai
Summary: A genome-wide analysis of longan miRNA genes was conducted, and 80 miRNA precursors (pre-miRNA) were predicted. Full-length cDNA sequences of 13 longan primary miRNAs (pri-miRNAs) were amplified by RLM-RACE and SMART-RACE, revealing multiple transcription start sites (TSSs) and polymorphic downstream pre-miRNAs. Analysis of the longan miRNA gene promoter elements indicated the presence of light-responsive, stress-responsive, and hormone-responsive elements. Quantitative real-time PCR assay elucidated potential spatial and temporal expression patterns of longan pre-miRNAs during somatic embryogenesis and in different longan organs/tissues.
Article
Health Care Sciences & Services
Medi Kori, Gullu Elif Ozdemir, Kazim Yalcin Arga, Raghu Sinha
Summary: Cancer hallmark genes and proteins play important roles in regulating and driving carcinogenesis. This study analyzed transcriptome data from 12 common cancers and identified differentially interacting hallmarks of cancer proteins (DIHCP) and DIHCP-centric modules. These modules showed significant changes in interaction patterns between tumor and control phenotypes, and some of them had diagnostic and prognostic capabilities. The study also investigated the druggability of the identified DIHCPs. Overall, the study presents candidate system biomarkers that could enhance understanding of tumorigenesis and improve personalized treatment strategies for various cancers, focusing on their ten hallmark characteristics.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Sijin Cheng, Ziyi Li, Ranran Gao, Baocai Xing, Yunong Gao, Yu Yang, Shishang Qin, Lei Zhang, Hanqiang Ouyang, Peng Du, Liang Jiang, Bin Zhang, Yue Yang, Xiliang Wang, Xianwen Ren, Jin-Xin Bei, Xueda Hu, Zhaode Bu, Jiafu Ji, Zemin Zhang
Summary: This study conducted a pan-cancer analysis of single myeloid cells from 210 patients across 15 human cancer types, revealing distinct features of TIMs in different cancer types. For example, mast cells in nasopharyngeal cancer were associated with better prognosis, and pro-angiogenic TAMs showed diverse markers across different cancer types. The composition of TIMs appeared to be linked with certain features of somatic mutations and gene expressions.
Review
Medicine, General & Internal
Prerna Guleria, Radhika Srinivasan, Chanchal Rana, Shipra Agarwal
Summary: Thyroid carcinomas are rare but the most common endocrine malignancy in the pediatric population. They have distinct clinical behavior and responses to therapy due to their unique pathology and molecular characteristics. Papillary thyroid carcinoma is the most common and most studied type in children. Other types, such as follicular, poorly differentiated, and medullary carcinomas, are rarer and have limited literature. Most studies come from the West, with Japan being the primary Asian contributor. This review provides a comprehensive account of established and novel biomarkers, as well as discusses familial and syndromic associations. Current management guidelines for pediatric patients are largely based on those for adults, but understanding the molecular landscape is essential for specific diagnostic and therapeutic guidelines.
Article
Oncology
Evelien Schaafsma, Chloe M. Fugle, Xiaofeng Wang, Chao Cheng
Summary: This study provides a comprehensive investigation of HLA gene expression in a pan-cancer manner, showing strong variations among cancer types and associations with genomic and immunological features. Increased HLA gene expression is linked to prolonged survival in most cancer types and patient response to immune checkpoint blockade, especially for HLA class II expression in tumour biopsies during treatment.
BRITISH JOURNAL OF CANCER
(2021)
Article
Oncology
Malwina Suszynska, Magdalena Ratajska, Paulina Galka-Marciniak, Aleksandra Ryszkowska, Dariusz Wydra, Jaroslaw Debniak, Anna Jasiak, Bartosz Wasag, Cezary Cybulski, Piotr Kozlowski
Summary: In this study, targeted next-generation sequencing of DNA pools was used to analyze the selected genes in approximately 400 Polish ovarian cancer cases, revealing no pathogenic mutations. Mutations in BARD1, PRDM9, RCC1, and RECQL were found to not substantially contribute to the risk of ovarian cancer. Pooled sequencing is a reliable and cost-effective method for the initial screening of candidate genes for rare variants.
CANCER PREVENTION RESEARCH
(2022)
Review
Genetics & Heredity
Anjani Kumari, Saam Sedehizadeh, John David Brook, Piotr Kozlowski, Marzena Wojciechowska
Summary: The discovery of introns revolutionized the understanding of gene structure, showing their essential roles in gene expression regulation. The unique processing of introns through lariat formation demonstrates their widespread involvement in cellular structure and function. Alternative splicing is a key source of transcript diversity, with retained introns playing important roles in normal development and disease-related conditions.
Article
Multidisciplinary Sciences
Paulina Galka-Marciniak, Zuzanna Kandula, Adrian Tire, Wladyslaw Wegorek, Kinga Gwozdz-Bak, Luiza Handschuh, Maciej Giefing, Krzysztof Lewandowski, Piotr Kozlowski
Summary: Recent data shows that MIR142 is one of the most frequently mutated miRNA genes and noncoding elements in all cancers, especially in blood cancers. Mutations in MIR142 have profound consequences for lympho- and myelopoiesis, and one of its targeted genes, CD274, is elevated in many cancer types, including MPNs. However, MIR142 mutations are rare in MPNs.
SCIENTIFIC REPORTS
(2022)
Article
Hematology
Krzysztof Lewandowski, Zuzanna Kandula, Michal Gniot, Edyta Paczkowska, Paulina Maria Nawrocka, Marzena Wojtaszewska, Michal Janowski, Magdalena Mariak, Luiza Handschuh, Piotr Kozlowski
Summary: The study investigates the changes in JAK2 and PD-L1 expression levels during the progression of myeloproliferative neoplasms. It is found that JAK2V617F mutation is associated with higher PD-L1 levels, while post-ET-MF patients have lower JAK2 and PD-L1 levels. Additionally, the degree of bone marrow fibrosis is correlated with the decrease in JAK2 and PDL1 mRNA levels.
ANNALS OF HEMATOLOGY
(2022)
Article
Cell Biology
Lewandowski Krzysztof, Kopydlowska Agata, Kandula Zuzanna, Bartlomiej Sankowski, Marcin Machnicki, Baranska Marta, Gwozdz-Bak Kinga, Kubicki Tadeusz, Plotka Anna, Przysiecka Lucja, Dworacki Grzegorz, Kozlowski Piotr, Stoklosa Tomasz
Summary: 3%-14% of BCR-ABL negative MPNPh- patients have concurrent MGUS. A 50-year-old patient with type 2 CALR Lys385Asnfs*47 mutation positive essential thrombocythemia (ET) developed symptomatic multiple myeloma (MM) 13 years after ET diagnosis during PEG-INF2 alpha treatment. The origin of MM cells in MPNPh- patients remains unknown, but research suggests that mutant CALR protein may impact the function and genomic stability of myeloid cells.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2023)
Article
Microbiology
Natalia Szostak, Luiza Handschuh, Anna Samelak-Czajka, Katarzyna Tomela, Marcin Schmidt, Lukasz Pruss, Kaja Milanowska-Zabel, Piotr Kozlowski, Anna Philips
Summary: The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. Research on human gut mycobiome is rare, but recent studies have shown its significant role in human health. This study investigated the gut mycobiota of a large European population and found that diet, age, and marital status were associated with the variation in the gut fungal community.
Review
Biochemistry & Molecular Biology
Magdalena Machowska, Paulina Galka-Marciniak, Piotr Kozlowski
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that posttranscriptionally regulate gene expression. Genetic variations in miRNA genes may affect their functioning and the development of human diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Martyna O. Urbanek-Trzeciak, Piotr Kozlowski, Paulina Galka-Marciniak
Summary: The miRMut protocol is introduced to annotate mutations in miRNA genes based on WES or WGS results. It assigns mutation characteristics and provides tabular and graphical summaries for further analysis.