Article
Urology & Nephrology
Daniel J. Schaid, Shannon K. McDonnell, Liesel M. FitzGerald, Lissa DeRycke, Zachary Fogarty, Graham G. Giles, Robert J. MacInnis, Melissa C. Southey, Tu Nguyen-Dumont, Geraldine Cancel-Tassin, Oliver Cussenot, Alice S. Whittemore, Weiva Sieh, Nilah Monnier Ioannidis, Chih-Lin Hsieh, Janet L. Stanford, Johanna Schleutker, Cheryl D. Cropp, John Carpten, Josef Hoegel, Rosalind Eeles, Zsofia Kote-Jarai, Michael J. Ackerman, Christopher J. Klein, Diptasri Mandal, Kathleen A. Cooney, Joan E. Bailey-Wilson, Brian Helfand, William J. Catalona, Fredrick Wiklund, Shaun Riska, Saurabh Bahetti, Melissa C. Larson, Lisa Cannon Albright, Craig Teerlink, Jianfeng Xu, William Isaacs, Elaine A. Ostrander, Stephen N. Thibodeau
Summary: This study uses a two-stage design to identify new genetic variants associated with prostate cancer (PCa) in individuals with a family history of the disease or with a more aggressive form of PCa. The research detected 11 known genes associated with PCa and 10 novel genes, most of which are primarily linked to aggressive PCa risk.
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
Oncology
Hafdis T. Helgadottir, Jessada Thutkawkorapin, Anna Rohlin, Margareta Nordling, Kristina Lagerstedt-Robinson, Annika Lindblom
Summary: Identifying pathogenic variants remains challenging despite a strong history of CRC within families. Some rare high-risk mutations may cumulatively contribute to the occurrence of CRC in these families.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Biology
Chunbao Xie, Ling Zhong, Jiangrong Luo, Ji Luo, Yingmiao Wu, Shuai Zheng, Lingxi Jiang, Jianbo Zhang, Yi Shi
Summary: This study explored the clinical significance of mutated genes in multiple myeloma (MM) in the Chinese population. The mutations and low expression of BCL6, BIRC3, HLA-DQA1, and VCAN were found to be correlated with poor prognosis and immune cell infiltration in MM. This study is the first to reveal the spectrum of mutations in the Chinese population.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Genetics & Heredity
Anshita Goel, Douglas G. Ward, Boris Noyvert, Minghao Yu, Naheema S. Gordon, Ben Abbotts, John K. Colbourne, Stephen Kissane, Nicholas D. James, Maurice P. Zeegers, Kar Keung Cheng, Jean-Baptiste Cazier, Celina M. Whalley, Andrew D. Beggs, Claire Palles, Roland Arnold, Richard T. Bryan
Summary: Through whole-exome and transcriptome sequencing, it was found that NMIBC can be classified into different expression subtypes, with amplifications of ARNT and ERBB2 being significant indicators of worse PFS across all NMIBCs, and high APOBEC mutagenesis and high tumor mutation burden potentially indicating better PFS in G3pT1 NMIBCs; in G3pT1 NMIBCs, downregulated interferon-alpha and gamma response pathways were significantly associated with worse PFS.
Article
Oncology
Jung Yong Hong, Hee Jin Cho, Kum-Hee Yun, Young Han Lee, Seung Hyun Kim, Wooyeol Baek, Sang Kyum Kim, Yurimi Lee, Yoon-La Choi, Minsuk Kwon, Hyo Song Kim, Jeeyun Lee
Summary: This study investigated the molecular determinants of pazopanib response in refractory soft tissue sarcoma patients. It identified CDK4 amplification as a predictor of poor response and shorter progression-free survival. Additionally, the combination of pazopanib and durvalumab showed efficacy in patients with high immune/stromal cell infiltration and increased CD19 expression.
CANCER RESEARCH AND TREATMENT
(2023)
Article
Biochemistry & Molecular Biology
Sum-Fu Chiang, Heng-Hsuan Huang, Wen-Sy Tsai, Bertrand Chin-Ming Tan, Chia-Yu Yang, Po-Jung Huang, Ian Yi-Feng Chang, Jiarong Lin, Pei-Shan Lu, En Chin, Yu-Hao Liu, Jau-Song Yu, Jy-Ming Chiang, Hsin-Yuan Hung, Jeng-Fu You, Hsuan Liu
Summary: This study found that patients with mutated APC have better overall and recurrence-free survival in stage III CRC.
BIOMEDICAL JOURNAL
(2022)
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
Oncology
Alexander Mustea, Damian J. Ralser, Eva Egger, Ulrike Ziehm, Sonia Vivas, Stephan Brock, David Jackson, Mateja Condic, Christian Meisel, Lucia Otten, Anna Laib, Miguel Cubas Cordova, Rahel Hartmann, Martin A. Stein, Dominique Koensgen, Matthias B. Stope
Summary: This study successfully determined the four TCGA EC molecular subtypes using a single-method whole-exome sequencing approach provided by MH Guide, and compared their prognostic value with the TCGA classification. The results showed high concordance between the two approaches in terms of prognostic significance. This suggests that the MH Guide approach can reliably reproduce the multi-method-based TCGA EC molecular subtypes and represents a promising diagnostic tool.
Article
Oncology
Ryul Kim, Jung Yong Hong, Jeeyun Lee, Ghee Young Kwon, Byong Chang Jeong, Se Hoon Park
Summary: This study explores the genomic and transcriptomic characteristics of bladder cancer (BC) and investigates the impact of immune checkpoint inhibitors (ICI) on its treatment. The results show that a subset of patients express PD-L1 and have a higher tumor mutational burden. Furthermore, immune-responsive pathways and the CTLA4 pathway are enriched in PD-L1 positive BC. The study provides a theoretical basis for the application of dual checkpoint inhibition in bladder cancer treatment.
CANCER RESEARCH AND TREATMENT
(2022)
Article
Biochemistry & Molecular Biology
Byeong Hee Kang, Woon Ji Kim, Sreeparna Chowdhury, Chang Yeok Moon, Sehee Kang, Seong-Hoon Kim, Sung-Hwan Jo, Tae-Hwan Jun, Kyung Do Kim, Bo-Keun Ha
Summary: This study identified genes related to salt stress in cowpea by comparing germplasms with contrasting salt tolerance. The results provide useful information for the development of molecular markers in cowpea breeding programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Ippokratis Messaritakis, Eleni Psaroudaki, Konstantinos Vogiatzoglou, Maria Sfakianaki, Pantelis Topalis, Ioannis Iliopoulos, Dimitrios Mavroudis, John Tsiaoussis, Nikolaos Gouvas, Maria Tzardi, John Souglakos
Summary: This study investigated the molecular profiles of stage III CRC patients and found that mutations in specific genes are associated with patient outcomes. These mutations may serve as prognostic biomarkers and provide improved treatment options.
Article
Gastroenterology & Hepatology
Keming Yang, Yin Cao, Carino Gurjao, Yang Liu, Chuan-Guo Guo, Chun-Han Lo, Xiaoyu Zong, David Drew, Connor Geraghty, Elizabeth Prezioso, Matt Moore, Craig Williams, Tom Riley, Melissa Saul, Shuji Ogino, Marios Giannakis, Adam Bass, Robert E. Schoen, Andrew T. Chan
Summary: This study compared the characteristics of interval colorectal cancers (CRCs) and screen-detected CRCs. The results showed that interval CRCs had a higher risk of death compared to screen-detected CRCs, and this increased risk couldn't be explained by clinical prognostic factors. However, no significant differences in mutational features were found between interval and screen-detected CRCs.
Article
Oncology
E. Pleasance, A. Bohm, L. M. Williamson, J. M. T. Nelson, Y. Shen, M. Bonakdar, E. Titmuss, V Csizmok, K. Wee, S. Hosseinzadeh, C. J. Grisdale, C. Reisle, G. A. Taylor, E. Lewis, M. R. Jones, D. Bleile, S. Sadeghi, W. Zhang, A. Davies, B. Pellegrini, T. Wong, R. Bowlby, S. K. Chan, K. L. Mungall, E. Chuah, A. J. Mungall, R. A. Moore, Y. Zhao, B. Deol, A. Fisic, A. Fok, D. A. Regier, D. Weymann, D. F. Schaeffer, S. Young, S. Yip, K. Schrader, N. Levasseur, S. K. Taylor, X. Feng, A. Tinker, K. J. Savage, S. Chia, K. Gelmon, S. Sun, H. Lim, D. J. Renouf, S. J. M. Jones, M. A. Marra, J. Laskin
Summary: This study demonstrates the importance of comprehensive whole-genome and transcriptome sequencing and analysis in guiding personalized cancer therapy, resulting in positive clinical benefits for a significant proportion of patients.
ANNALS OF ONCOLOGY
(2022)
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)
Review
Oncology
Amit Kumar Agrawal, Vanita Noronha, Vijay Patil, Nandini Menon, Akhil Kapoor, Anuradha Chougule, Pratik Chandrani, Kumar Prabhash
Summary: Thyroid cancer treatment involves surgery and radioactive iodine therapy, with systemic therapy needed for refractory cases. Targeting oncogenic drivers in thyroid cancer cells has shown effectiveness, but challenges such as high treatment cost and lack of testing for driver mutations still exist. Further research is needed to identify oncogenic targets and corresponding agents in thyroid cancers.
INDIAN JOURNAL OF SURGICAL ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lipi Das, Shashank Shekhar, Pratik Chandrani, Ashok K. Varma
Summary: This study constructed a model structure of the pre-secretory isoform of clusterin (CLU) and predicted the impact of mutations on protein structure and function. By analyzing the conservation and pathogenicity of mutations, 11 mutations with the highest structural and functional significance were identified.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Oncology
Vichitra Behel, Anuradha Chougule, Vanita Noronha, Vijay Maruti Patil, Nandini Menon, Ajaykumar Singh, Sunil Chopade, Rajiv Kumar, Srushti Shah, Sucheta More, Shripad Dinanath Banavali, Pratik Chandrani, Kumar Prabhash
Summary: This study assessed the potential of cell-free DNA (cfDNA)-based epidermal growth factor receptor (EGFR) mutation testing as a disease monitoring tool in patients with non-small cell lung cancer (NSCLC). The results showed that clearance of plasma-ctDNA post first-line treatment initiation is associated with significantly longer survival in patients with EGFR-mutant NSCLC.
CLINICAL LUNG CANCER
(2022)
Article
Hematology
Pawan Upadhyay, Jeremy Beales, Nakul M. Shah, Agata Gruszczynska, Christopher A. Miller, Allegra A. Petti, Sai Mukund Ramakrishnan, Daniel C. Link, Timothy J. Ley, John S. Welch
Summary: The molecular events responsible for decitabine responses in myelodysplastic syndrome and acute myeloid leukemia patients remain poorly understood. In vivo treatment with decitabine induced global, reversible hypomethylation after 10 days, associated with interferon-induced pathways, expression of endogenous retroviral elements, and inhibition of erythroid-related transcripts. Clinical responses were not correlated with epigenetic or transcriptional signatures, but global hypomethylation by decitabine and reversal of erythroid-related pathways at relapse were observed.
EXPERIMENTAL HEMATOLOGY
(2022)
Letter
Oncology
Tejpal Gupta, Guncha Maheshwari, Sadhana Kannan, Sudhir Nair, Jai Prakash Agarwal
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Medicine, General & Internal
Anuradha Chougule, Vinita Jagtap, Ankita Nikam, Shrutikaa Kale, Kavya Nambiar, Priyanka Bagayatkar, Pratik Chandrani, Rajiv Kaushal, Vanita Noronha, Vijay Patil, Shripad Banavali, Kumar Prabhash
Summary: The advancements in next-generation sequencing (NGS) have revolutionized precision medicine, but there is currently a lack of standardized validation criteria for diagnostic accreditation. Strict quality control of DNA and RNA before, during, and after library preparation is crucial to ensure reliable NGS results. This study aims to establish a benchmark in QC metrics for FFPE samples to guide molecular diagnostic laboratories.
Letter
Oncology
Vanita Noronha, Anuradha Chougule, Pratik Chandrani, Rajiv Kumar Kaushal, Vijay Maruti Patil, Nandini Menon, Akhil Kapoor, Sunil Chopade, Ajaykumar Singh, Omshree Shetty, Amit Dutt, Shripad Banavali, Kumar Prabhash
Article
Medical Laboratory Technology
Bharat Rekhi, Leslie Dodd, Bhaskar Dharavath, Amit Dutt
Summary: This study presents one of the first documentations of cytomorphological features of two rare cases of spindle cell/sclerosing rhabdomyosarcoma (RMS). The differential diagnoses and treatment-related implications are discussed.
DIAGNOSTIC CYTOPATHOLOGY
(2022)
Article
Oncology
Asim Joshi, Ashwin Butle, Supriya Hait, Rohit Mishra, Vaishakhi Trivedi, Rahul Thorat, Anuradha Choughule, Vanita Noronha, Kumar Prabhash, Amit Dutt
Summary: This study found that osimertinib showed significant benefit in lung cancer patients with low allele frequency of EGFR T790M mutation, and its therapeutic effect was confirmed through experiments.
TRANSLATIONAL ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Aditi Sahu, Kivanc Kose, Lukas Kraehenbuehl, Candice Byers, Aliya Holland, Teguru Tembo, Anthony Santella, Anabel Alfonso, Madison Li, Miguel Cordova, Melissa Gill, Christi Fox, Salvador Gonzalez, Piyush Kumar, Amber Weiching Wang, Nicholas Kurtansky, Pratik Chandrani, Shen Yin, Paras Mehta, Cristian Navarrete-Dechent, Gary Peterson, Kimeil King, Stephen Dusza, Ning Yang, Shuaitong Liu, William Phillips, Pascale Guitera, Anthony Rossi, Allan Halpern, Liang Deng, Melissa Pulitzer, Ashfaq Marghoob, Chih-Shan Jason Chen, Taha Merghoub, Milind Rajadhyaksha
Summary: The response to immunotherapies is unpredictable and variable. Traditional pathology-based phenotyping of tumors is unable to accurately predict treatment response to immunotherapy. Researchers have developed a non-invasive in vivo imaging technique using reflectance confocal microscopy to combine inflammation profiles with vascular features, allowing for dynamic cellular-level phenotyping of the tumor immune microenvironment. This approach provides a more reliable predictor of response to immune therapy in skin cancer patients.
NATURE COMMUNICATIONS
(2022)
Review
Oncology
Shilpa S. Chapadgaonkar, Srashti S. Bajpai, Mukul S. Godbole
Summary: The gut microbiome plays a significant role in the incidence and treatment of breast cancer, particularly in the metabolism of estrogen and progesterone. Further research is needed to understand the mechanisms of action and improve the composition of the gut microbiome for better survival outcomes in breast cancer patients.
Article
Oncology
Neelima Yadav, Roma Sunder, Sanket Desai, Bhasker Dharavath, Pratik Chandrani, Mukul Godbole, Amit Dutt
Summary: This study reveals that breast cancer exhibits a downregulation of non-coding RNA (DSCAM-AS1) in response to progesterone treatment, and knockdown of DSCAM-AS1 mimics the effect of progesterone in impeding cell migration and invasion in breast cancer cells. Additionally, DSCAM-AS1 mediates the effect of progesterone by binding to miR-130a and regulating the expression of ESR1.
BREAST CANCER RESEARCH
(2022)
Article
Mathematical & Computational Biology
Sanket Desai, Rohit Mishra, Suhail Ahmad, Supriya Hait, Asim Joshi, Amit Dutt
Summary: This article discusses the impact of the lack of Indian-specific reference germline variation resources on identifying true cancer-associated somatic variants among Indian cancer patients, and the method and results of generating the TMC-SNPdb 2.0 database by integrating different studies.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Biochemistry & Molecular Biology
Sanket Desai, Bhasker Dharavath, Sujith Manavalan, Aishwarya Rane, Archana Kumari Redhu, Roma Sunder, Ashwin Butle, Rohit Mishra, Asim Joshi, Trupti Togar, Shruti Apte, Pratyusha Bala, Pratik Chandrani, Supriya Chopra, Murali Dharan Bashyam, Anirban Banerjee, Kumar Prabhash, Sudhir Nair, Amit Dutt
Summary: This study provides a comprehensive analysis of infectious pathogens in various types of tumors, revealing known cancer-associated pathogens as well as a significant prevalence of Fusobacterium in head and neck tumors. The Fusobacterium-high subgroup of head and neck tumors is mutually exclusive to human papillomavirus, and exhibits characteristics such as overexpression of inflammation-related miRNAs, elevated innate immune cell fraction, and nodal metastases. A higher burden of Fusobacterium is associated with poor survival, nodal metastases, and extracapsular spread in tongue tumors, defining a distinct subgroup of head and neck cancer.