Article
Biochemistry & Molecular Biology
Yaxuan Liu, Hafdis T. Helgadottir, Pedram Kharaziha, Jungmin Choi, Francesc Lopez-Giraldez, Shrikant M. Mane, Veronica Hoiom, Carl Christofer Juhlin, Catharina Larsson, Svetlana Bajalica-Lagercrantz
Summary: This study aimed to identify new predisposing genes for hereditary breast cancer (HBC) using whole-exome sequencing, but no pathogenic variants in known hereditary cancer-related genes were found. Further analysis suggested that a combination of low- and intermediate-genetic-risk variants might contribute to breast cancer susceptibility in these families.
Review
Biotechnology & Applied Microbiology
Iuliia Branco, Altino Choupina
Summary: This paragraph highlights the importance of bioinformatics in understanding gene function and protein diseases or functions, as well as its role in providing scientists with the right means to explain biological processes, diseases, and the discovery of new medications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Onur Erdogan, Seyma Colakoglu Ozkaya, Can Erzik, Kaya Bilguvar, Kazim Yalcin Arga, Fatih Bayrakli
Summary: Precision/personalized medicine in oncology, particularly in glioblastoma, holds great promise for improving treatment options and outcomes for patients through molecular profiling and personalized reporting.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Genetics & Heredity
Debao Li, Lei Lei, Jinsong Wang, Bo Tang, Jiuling Wang, Rui Dong, Wenjiong Shi, Guo Liu, Tingting Zhao, Yuzhang Wu, Yi Zhang
Summary: We analyzed the whole exome sequencing data of 125 patients and identified 14 main mutant genes in hepatocellular carcinoma (HCC). TP53 and LRP1B mutations were found to be related to prognosis. A prognostic risk model based on 11 genes was proposed for TP53 wild-type HCC patients, which showed significant transcriptome changes and the potential for predicting HCC immunotherapy. AM580 was identified as a potential therapeutic option for high-risk TP53 wild-type HCC patients through the CMap database.
FRONTIERS IN GENETICS
(2023)
Article
Biochemical Research Methods
Andrea Binatti, Silvia Bresolin, Stefania Bortoluzzi, Alessandro Coppe
Summary: iWhale is a customizable pipeline based on Docker and SCons, which reliably detects somatic variants using three complementary callers and allows users to prioritize variants and genes according to different criteria. Its easy-to-use tool can run on multiple operating systems.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Alexander Seryakov, Zaynab Magomedova, Maria Suntsova, Anastasia Prokofieva, Elizaveta Rabushko, Alexander Glusker, Lyudmila Makovskaia, Marianna Zolotovskaia, Anton Buzdin, Maxim Sorokin
Summary: Uterine leiomyosarcoma is a rare malignant tumor with few effective treatment options. RNA sequencing and bioinformatic analysis suggested regorafenib as a potential targeted treatment with promising results in a case study. Additionally, a novel cancer fusion transcript was discovered, highlighting the potential of RNA sequencing in enhancing oncological patient management.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Chenyue Zhang, Kai Wang, Wenjie Liu, Jiamao Lin, Zhenxiang Li, Hui Wang, Chenglong Zhao, Yanhua Chen, Shuangxiu Wu, Airong Yang, Jiayan Wu, Haiyong Wang
Summary: This study describes the genomic and immunological landscape of Chinese mucinous pulmonary adenocarcinoma (MPA) and compares it with classical lung adenocarcinoma (LUAD). It is found that MPA has distinct genomic alterations and a more complex genomic profile compared to LUAD. Mutations in specific pathways are associated with survival outcomes, and mutations in immune-related genes also affect prognosis.
FRONTIERS IN ONCOLOGY
(2022)
Article
Medical Laboratory Technology
Yingdi Liu, Yanling Teng, Zhuo Li, Jingyi Cui, Desheng Liang, Lingqian Wu
Summary: By reanalyzing whole-exome sequencing data with updated algorithms and databases, optimizing processes and strategies, the diagnostic yield can be improved and missed diagnoses reduced.
CLINICA CHIMICA ACTA
(2021)
Article
Oncology
Migle Gabrielaite, Mathias Husted Torp, Malthe Sebro Rasmussen, Sergio Andreu-Sanchez, Filipe Garrett Vieira, Christina Bligaard Pedersen, Savvas Kinalis, Majbritt Busk Madsen, Miyako Kodama, Guel Sude Demircan, Arman Simonyan, Christina Westmose Yde, Lars Ronn Olsen, Rasmus L. Marvig, Olga ostrup, Maria Rossing, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Summary: Copy-number variations (CNVs) have significant clinical implications for various diseases and cancers, but detecting relevant CNVs accurately remains challenging. Our study found diverse performance levels among different CNV calling tools, suggesting that combining the best tools could be a potential solution.
Article
Biochemistry & Molecular Biology
Cristina Tous, Carmen Munoz-Redondo, Nereida Bravo-Gil, Angela Gavilan, Raquel Maria Fernandez, Juan Antinolo, Elena Navarro-Gonzalez, Guillermo Antinolo, Salud Borrego
Summary: Thyroid carcinoma (TC) can be classified into medullary (MTC) and non-medullary (NMTC). This study aimed to identify susceptibility genes for familial NMTC and non-RET MTC using whole exome sequencing. Rare candidate segregating variants were found in 12 families, with enriched biological processes related to cell proliferation, differentiation, survival, and adhesion. These findings provide insights into molecular mechanisms underlying familial forms of MTC and NMTC, which may contribute to early detection, tailored therapies, and patient management.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Eva Tosco-Herrera, Adrian Munoz-Barrera, David Jaspez, Luis A. Rubio-Rodriguez, Alejandro Mendoza-Alvarez, Hector Rodriguez-Perez, Jonathan Jou, Antonio Inigo-Campos, Almudena Corrales, Laura Ciuffreda, Francisco Martinez-Bugallo, Carol Prieto-Morin, Victor Garcia-Olivares, Rafaela Gonzalez-Montelongo, Jose Miguel Lorenzo-Salazar, Itahisa Marcelino-Rodriguez, Carlos Flores
Summary: This study assessed the performance of different tools in prioritizing germline causal variants in whole-exome sequencing (WES) data. Exomiser performed best in the top first rankings, while LIRICAL led in the top fifth rankings. Xrare had the highest diagnostic yield based on the more conservative top 10th rankings.
Article
Biology
Gaber Bergant, Ales Maver, Borut Peterlin
Summary: This study demonstrates the impact of whole-genome sequencing in diagnosing patients with rare genetic disorders who remained undiagnosed after whole-exome sequencing, uncovering a variety of causative genetic variants that may remain undetected using other methods.
Article
Cell Biology
Yi Yang, Xiaodong Gu, Zhenyang Li, Chuang Zheng, Zihao Wang, Minwei Zhou, Zongyou Chen, Mengzhen Li, Dongbing Li, Jianbin Xiang
Summary: The study identified specific genes and signaling pathways in locally recurrent rectal cancer (LRRC) through whole-exome sequencing and bioinformatics analysis, highlighting the potential importance of gene variants in the Wnt signaling pathway for LRRC development. Additionally, certain genes showed significantly higher expression levels in rectal cancer tissues compared to normal tissues.
Article
Oncology
Lucas W. Thornblade, Paul Wong, Daneng Li, Susanne G. Warner, Sue Chang, Mustafa Raoof, Jonathan Kessler, Arya Amini, James Lin, Vincent Chung, Gagandeep Singh, Yuman Fong, Laleh G. Melstrom
Summary: Cholangiocarcinomas are rare cancers with potentially targetable mutations, and a third of patients undergoing resection in the past decade have had tumor genomic profiling, with 89% harboring targetable mutations. While targeted therapies were identified in most sequenced tumors, only 4% of patients received these therapies, highlighting the potential for precision medicine in the future care of cholangiocarcinoma.
Article
Psychiatry
Jan Haavik
Summary: ADHD is a common behavioral syndrome with a heritability of 70-80%. Risk variants for ADHD are distributed across a wide range of allele frequencies and relative risks and are shared with other neuropsychiatric disorders and neurometabolic diseases. Individualized treatments and genome-guided therapies are crucial for managing ADHD.
FRONTIERS IN PSYCHIATRY
(2022)
Article
Dermatology
Nabanita Mukherjee, Chiara R. Dart, Carol M. Amato, Adam Honig-Frand, James R. Lambert, Karoline A. Lambert, William A. Robinson, Richard P. Tobin, Martin D. McCarter, Kasey L. Couts, Mayumi Fujita, David A. Norris, Yiqun G. Shellman
Summary: Uveal melanoma (UM) has a distinct expression profile of BCL2 family members compared to other cancer types, making them susceptible to BCL2 homologous 3 mimetics. UM is more sensitive to MCL1 inhibitor (MCL1i), and overexpression of BFL1 or knockdown of PUMA can increase UM resistance to MCL1i. Combination therapy of MCL1i with BCL2 inhibitor synergistically inhibits UM initiating cells expansion.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Heather M. Brechbuhl, Mengyu Xie, Etana G. Kopin, Amy L. Han, Kiran Vinod-Paul, Jaime Hagen, Susan Edgerton, Philip Owens, Sharon Sams, Anthony Elias, Carol A. Sartorius, Aik-Choon Tan, Peter Kabos
Summary: The tumor microenvironment plays a crucial role in response and resistance to endocrine therapy in ER-positive breast cancer. The study found that neoadjuvant endocrine therapy alters TME composition, promoting the expansion of less favorable TASC(CDCP1) population associated with TME remodeling and increased immune infiltration supportive of tumor progression.
MOLECULAR CARCINOGENESIS
(2022)
Article
Multidisciplinary Sciences
Marco Napoli, Sarah J. Wu, Bethanie L. Gore, Hussein Abbas, Kyubum Lee, Rahul Checker, Shilpa Dhar, Kimal Rajapakshe, Aik Choon Tan, Min Gyu Lee, Cristian Coarfa, Elsa R. Flores
Summary: Distinct lung stem cells regulated by increment Np63 play a role in the development of both lung adenocarcinoma and squamous cell carcinoma through the regulation of a common landscape of enhancer-associated genes, including BCL9L.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Ahmad A. Tarhini, Sandra J. Lee, Aik-Choon Tan, Issam M. El Naqa, F. Stephen Hodi, Lisa H. Butterfield, William A. LaFramboise, Walter J. Storkus, Arivarasan D. Karunamurthy, Jose R. Conejo-Garcia, Patrick Hwu, Howard Streicher, Vernon K. Sondak, John M. Kirkwood
Summary: Melanoma of unknown primary (MUP) has a significantly better prognosis and shows evidence of significantly enhanced immune activation within the tumor microenvironment and the circulation in high-risk melanoma patients.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Biology
Alyssa Obermayer, Li Dong, Qianqian Hu, Michael Golden, Jerald D. D. Noble, Paulo Rodriguez, Timothy J. J. Robinson, Mingxiang Teng, Aik-Choon Tan, Timothy I. I. Shaw
Summary: This paper presents a R Shiny framework called DRPPM-EASY for integrative multi-omics analysis of cancer datasets. The framework provides a user-friendly interface for exploring and integrating various omics data, reducing the need for computational experience. By analyzing transcriptomic and proteomic data, the authors identified cancer cell proliferative features associated with USP7 gene knockout and disruption of protein degradation and spliceosome. Additionally, they developed an extension called DRPPM-EASY-CCLE with preloaded cancer cell line data for sample querying and phenotype assignment.
Article
Medicine, Research & Experimental
Mariam Saad, Sandra J. Lee, Aik Choon Tan, Issam M. El Naqa, F. Stephen Hodi, Lisa H. Butterfield, William A. LaFramboise, Walter Storkus, Arivarasan D. Karunamurthy, Jose Conejo-Garcia, Patrick Hwu, Howard Streicher, Vernon K. Sondak, John M. Kirkwood, Ahmad A. Tarhini
Summary: This study found that female patients had better clinical response when receiving ipilimumab and high-dose IFN alpha as adjuvant therapy, and they showed stronger immune activation in the tumor microenvironment and circulation.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Samuel Coleman, Mengyu Xie, Ahmad A. Tarhini, Aik Choon Tan
Summary: Immunotherapy has made significant advancements in the treatment of melanoma, but there is still a need for predictive biomarkers to select patients for immune checkpoint inhibitors (ICIs) therapy. This study evaluated previously published predictive biomarkers based on gene expression signatures and found that biomarkers related to IFN-gamma-responsive genes, T and B cell markers, and chemokines in the tumor immune microenvironment can predict the response to ICIs. The study also showed that these biomarkers are more predictive in on-treatment samples compared to pretreatment samples in metastatic melanoma.
MOLECULAR CARCINOGENESIS
(2023)
Article
Cell Biology
Devin M. Boe, Holly J. Hulsebus, Kevin M. Najarro, Juliet E. Mullen, Hyunmin Kim, Aik Choon Tan, Rachel H. McMahan, Elizabeth J. Kovacs
Summary: As individuals age, alveolar macrophages (AMs) in the lower airways undergo various changes in phenotype and function, exhibiting characteristics of cellular senescence and reduced response to physiological stressors. These age-related alterations, potentially involving glucocorticoid-regulated genes, could interfere with AMs' responses to stressors and contribute to their dysfunction during healthy aging.
JOURNAL OF LEUKOCYTE BIOLOGY
(2022)
Article
Cell Biology
Zachary J. Thompson, Jamie K. Teer, Jiannong Li, Zhihua Chen, Eric A. Welsh, Yonghong Zhang, Noura Ayoubi, Zeynep Eroglu, Aik Choon Tan, Keiran S. M. Smalley, Yian Ann Chen
Summary: DRepMel is a Shiny app developed to provide rational combination treatment predictions for melanoma patients using a multi-omics drug repurposing computational approach. It offers robust predictions based on whole exome sequencing and RNA-seq data, and also identifies potential treatment effects on the tumor microenvironment using single-cell RNA-seq data.
Article
Biochemistry & Molecular Biology
Christopher M. Clements, Beat Vogeli, Yiqun G. Shellman, Morkos A. Henen
Summary: This study characterized the structural features and dynamics of the SAM1 domain in SASH1 using various biophysical techniques. It was found that SAM1 primarily exists as a less compact monomer with a minor oligomer. NMR experiments revealed the presence of both a disordered monomer and a more structured oligomer in solution, and specific mutations increased its oligomerization. This study provides important evidence and framework for further understanding the mechanism of SAM domain oligomerization.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Review
Oncology
Christopher M. Clements, Morkos A. Henen, Beat Voegeli, Yiqun G. Shellman
Summary: SAM domains play critical roles in various interactions relevant to tumorigenesis or metastasis of cancers, making them attractive targets for cancer therapies. This review focuses on the recent findings of SAM domains in proteins containing multiple SAM domains. It discusses the complexity of interactions and oligomerization arrangements due to intrinsic disorder of SAM domains and additional SAM domains in these proteins. The review also highlights the similarities among these proteins in their effects on cancer cell behaviors and their involvement in receptor-mediated signaling and neurology-related functions or diseases.
Article
Genetics & Heredity
Min Hu, Samuel Coleman, Muhammad Zaki Hidayatullah Fadlullah, Daniel Spakowicz, Christine H. Chung, Aik Choon Tan
Summary: Patients with human papillomavirus-negative head and neck squamous cell carcinoma (HPV-negative HNSCC) have worse outcomes than HPV-positive HNSCC. In our study, we found that microbial signatures can distinguish Hypoxia/Immune phenotypes similar to gene expression signatures in molecularly classified tumor groups. Additionally, we identified three highly-correlated microbes that are crucial for immunotherapy response in immune processes. The co-abundance of these three microbes significantly affects the survival of patients in a molecularly heterogenous group.
Meeting Abstract
Oncology
Ahmad A. Tarhini, Aik Choon Tan, Mengyu Xie, Issam El Naqa, Payman Ghasemi Saghand, Donghai Dai, James Lin Chen, Aakrosh Ratan, Martin McCarter, John D. Carpten, Howard Colman, Alexandra Ikeguchi, Abhishek Tripathi, Igor Puzanov, Susanne M. Arnold, Michelle L. Churchman, Patrick Hwu, Jose Conejo-Garcia, William S. Dalton, George J. Weiner
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Meeting Abstract
Oncology
Payman Ghasemi Saghand, Issam El Naqa, Aik Choon Tan, Mengyu Xie, Donghai Dai, James Lin Chen, Aakrosh Ratan, Martin McCarter, John D. Carpten, Harsh Shah, Alexandra Ikeguchi, Abhishek Tripathi, Igor Puzanov, Susanne M. Arnold, Michelle L. Churchman, Patrick Hwu, Jose Conejo-Garcia, William S. Dalton, George J. Weiner, Ahmad A. Tarhini
JOURNAL OF CLINICAL ONCOLOGY
(2022)