Article
Cell Biology
Amanda J. Craig, Maruhen A. Datsch Silveira, Lichun Ma, Mahler Revsine, Limin Wang, Sophia Heinrich, Zachary Rae, Allison Ruchinskas, Kimia Dadkhah, Whitney Do, Shay Behrens, Farid R. Mehrabadi, Dana A. Dominguez, Marshonna Forgues, Anuradha Budhu, Jittiporn Chaisaingmongkol, Jonathan M. Hernandez, Jeremy L. Davis, Bao Tran, Jens U. Marquardt, Mathuros Ruchirawat, Michael Kelly, Tim F. Greten, Xin W. Wang
Summary: This study utilized single-cell technology to analyze the transcription regulatory elements in PLC patients at the genome-wide level. The enrichment levels of transcription factor motifs strongly discriminate between HCC and iCCA tumors, and POU factors are associated with prognostic features in iCCA. These findings provide insights into the development and selection of subtype-specific therapeutics for PLC.
Article
Oncology
Chih-Hao Chang, Arthur Chun-Chieh Shih, Ya-Hsuan Chang, Hsuan-Yu Chen, Ying-Ting Chao, Yi-Chiung Hsu
Summary: The study found that high expression of PD1 and PDL1 is associated with favorable outcomes in early-stage lung cancer but adverse outcomes in late-stage lung cancer. The expression levels of PD1 and PDL1 can serve as potential prognostic factors for predicting patient outcomes in lung cancer.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Aurora Savino, Niccolo De Marzo, Paolo Provero, Valeria Poli
Summary: Gene expression profiling is crucial for cancer research, but technical biases, sample heterogeneity, and small sample sizes can lead to difficulties in reproducibility. Combining multiple datasets helps reduce artifacts and improve statistical power for discovering clinically relevant markers. The database created in this study offers a valuable resource for the research community.
Review
Medicine, General & Internal
Guorong Yao, Jian Qiu, Fengjia Zhu, Xiaoxie Wang
Summary: This study compared the disease-free and overall survivals of cervical cancer patients with different histopathological subtypes treated with definitive radiotherapy or concurrent chemoradiotherapy. The results showed poorer outcomes for patients with adenocarcinoma/adenosquamous carcinoma compared to those with squamous cell carcinoma.
FRONTIERS IN MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Fawad Ali, Arifullah Khan, Syed Aun Muhammad, Syed Qamar Abbas, Syed Shams ul Hassan, Simona Bungau
Summary: This study investigates the genetic variations of hypertension and identifies potential genes and target proteins related to the disease. By analyzing publicly available datasets and using various analytical methods, the study identifies differentially expressed genes and their functional roles in hypertension. The study also explores miRNA targets and important gene signatures associated with the disease. Furthermore, molecular docking and simulation studies are conducted to identify potential drug targets for hypertension. The findings highlight the value of systems genetics in identifying drug targets and improving the understanding and treatment of hypertension.
Article
Oncology
Anna Plotkin, Ekaterina Olkhov-Mitsel, Sharon Nofech-Mozes, Bojana Djordjevic, Jelena Mirkovic, Madeline Fitzpatrick, Adriana Krizova, Nicole J. Look Hong
Summary: This study evaluated the costs associated with four approaches to classifying endometrial cancer and found that histomolecular classification had the highest cost. Therefore, informed decision-making is needed when implementing molecular classification in clinical practice.
GYNECOLOGIC ONCOLOGY
(2023)
Article
Oncology
Fazlur Rahman Talukdar, Sheila C. Soares Lima, Rita Khoueiry, Ruhina Shirin Laskar, Cyrille Cuenin, Bruna Pereira Sorroche, Anne-Claire Boisson, Behnoush Abedi-Ardekani, Christine Carreira, Diana Menya, Charles P. Dzamalala, Mathewos Assefa, Abraham Aseffa, Vera Miranda-Goncalves, Carmen Jeronimo, Rui M. Henrique, Ramin Shakeri, Reza Malekzadeh, Nagla Gasmelseed, Mona Ellaithi, Nitin Gangane, Daniel R. S. Middleton, Florence Le Calvez-Kelm, Akram Ghantous, Maria Leon Roux, Joachim Schuz, Valerie McCormack, M. Iqbal Parker, Luis Felipe Ribeiro Pinto, Zdenko Herceg
Summary: This study investigated tumor-specific DNA methylation in ESCC cases from high-incidence countries, identifying thousands of differentially methylated positions and regions, particularly in gene regions associated with transcription activation. Prioritized genes for replication showed consistent methylation differences and downregulation in tumors. The study highlights the potential of these DNA methylation events as tumor-specific markers for further biomarker discovery.
Article
Biochemistry & Molecular Biology
Oxana (Sachenkova) Lundstrom, Max Adriaan Verbiest, Feifei Xia, Helyaneh Ziaei Jam, Inti Zlobec, Maria Anisimova, Melissa Gymrek
Summary: Short tandem repeats (STRs), consisting of repeated one to six nucleotide motifs, have been shown to influence various traits in humans. However, the study of STRs has been limited due to technical challenges. Recent advancements in genome-wide analysis tools have enabled large-scale analysis of STR variations in populations.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Amit Katiyar, Gurvinder Kaur, Lata Rani, Lingaraja Jena, Harpreet Singh, Lalit Kumar, Atul Sharma, Punit Kaur, Ritu Gupta
Summary: Multiple myeloma is a complex plasma cell malignancy with diverse clinical phenotypes and molecular heterogeneity where differentially expressed genes and miRNAs may play a role in disease pathogenesis and treatment response. A genome-wide meta-analysis identified unique putative signatures for MM compared to normal plasma cells, with potential for guiding personalized therapy. Further investigation is needed to establish and translate the prognostic potential of these signatures for MM.
SCIENTIFIC REPORTS
(2021)
Review
Biodiversity Conservation
Alan B. Franklin, Katie M. Dugger, Damon B. Lesmeister, Raymond J. Davis, J. David Wiens, Gary C. White, James D. Nichols, James E. Hines, Charles B. Yackulic, Carl J. Schwarz, Steven H. Ackers, L. Steven Andrews, Larissa L. Bailey, Robin Bown, Jesse Burgher, Kenneth P. Burnham, Peter C. Carlson, Tara Chestnut, Mary M. Conner, Krista E. Herter, Eric D. Forsman, Elizabeth M. Glenn, Scott A. Gremel, Keith A. Hamm, Dale R. Herter, J. Mark Higley, Rob B. Horn, Julianna M. Jenkins, William L. Kendall, David W. Lamphear, Christopher McCafferty, Trent L. McDonald, Janice A. Reid, Jeremy T. Rockweit, David C. Simon, Stan G. Sovern, James K. Swingle, Heather Wise
Summary: The northern spotted owl populations in older coniferous forests in the Pacific Northwest are declining annually by 6-9% due to competition with barred owls and habitat loss. Barred owl presence on spotted owl territories is the primary factor negatively affecting survival rates, recruitment, and population change. Failure to address the negative effects of barred owls and preserve habitat may lead to potential extirpation of northern spotted owls.
BIOLOGICAL CONSERVATION
(2021)
Article
Biochemical Research Methods
Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie
Summary: Many complex diseases lack safe and effective therapeutics due to their polygenic nature and a lack of validated drug targets. We have developed a deep learning framework called PortalCG to predict ligands for understudied proteins, surpassing existing methods and achieving unprecedented accuracy. This approach offers new opportunities for drug discovery and could provide safe and effective therapeutics for currently incurable diseases.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Yasser Mohseni Behbahani, Elodie Laine, Alessandra Carbone
Summary: In this study, a novel and efficient deep learning framework called Deep Local Analysis (DLA) is introduced. DLA accurately predicts the binding affinity change for protein complexes by deconstructing protein interfaces into small residue-centered cubes and using 3D convolutions. It achieves a high generalization capability and can be applied to various tasks beyond mutation effects prediction.
Article
Genetics & Heredity
Meghana Manjunath, Snehal Nirgude, Anisha Mhatre, Sai G. Vemuri, Mallika Nataraj, Jayanti Thumsi, Bibha Choudhary
Summary: Breast cancer is one of the leading causes of cancer-associated death in women. Despite progress in treatment, drug resistance and recurrence still impact patient survival. This study aimed to identify lncRNA and mRNA signatures in Indian breast cancer patients using RNA-seq. The analysis revealed a gene set that could segregate the different molecular subtypes of breast cancer. Survival analysis showed that menopausal status, tumor grade, and hormone status significantly affected the risk of mortality due to breast cancer.
FRONTIERS IN GENETICS
(2022)
Review
Oncology
Alberto Martini, Daniele Raggi, Giuseppe Fallara, Luigi Nocera, Julianne G. Schultz, Federico Belladelli, Laura Marandino, Andrea Salonia, Alberto Briganti, Francesco Montorsi, Thomas Powles, Andrea Necchi
Summary: This study compared the efficacy of first-line immune checkpoint inhibition with chemotherapy in overall population, cisplatin-ineligible patients, and PD-L1-high patients, and found no overall survival benefit for patients in any of these groups.
CANCER TREATMENT REVIEWS
(2022)
Article
Multidisciplinary Sciences
Arzoo Ahad, Roohi Aslam, Alvina Gul, Rabia Amir, Faiza Munir, Tuba Sharf Batool, Mahnoor Ilyas, Muhammad Sarwar, Muhammad Azhar Nadeem, Faheem Shehzad Baloch, Sajid Fiaz, Muhammad Abu Bakar Zia
Summary: This study investigated the evolutionary characteristics, conservation, and gene expression of bZIP, BBR, and BZR transcription factors in wheat, suggesting a common lineage relationship and high conservation among these genes in cereals. The results provide new insights for future research on the functional properties of these genes in wheat.
Article
Oncology
Jin Cheon Kim, Jong Hwan Kim, Ye Jin Ha, Chan Wook Kim, Ka Hee Tak, Yong Sik Yoon, Yi Hong Kwon, Seon Ae Roh, Dong-Hyung Cho, Seon-Kyu Kim, Seon-Young Kim, Yong Sung Kim
Summary: Genomic analysis based on the revised Bethesda guidelines and additional criteria revealed specific somatic alterations related to colorectal cancer subtypes, such as location, early onset, and MSI status. Certain gene mutations were associated with gastric cancer in CRC pedigrees, while further validation is required for surveillance strategies in suspected individuals.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
A-Yeong Yang, Eun-Bee Choi, Mi So Park, Seon-Kyu Kim, Min-Seok Park, Mi-Young Kim
Summary: The cooperative roles of PARP1 and PRC2 in BRCA-proficient TNBC have been shown to accelerate tumor growth, mainly by altering the tumor microenvironment to promote cellular proliferation. Mechanistically, dual depletion of PARP1 and PRC2 activates the NF-kappa B pathway, enhancing responsiveness to external stimuli.
Article
Biochemistry & Molecular Biology
Seon-Kyu Kim, Seong-Hwan Park, Yeong Uk Kim, Young Joon Byun, Xuan-Mei Piao, Pildu Jeong, Kyeong Kim, Hee Youn Lee, Sung Pil Seo, Ho Won Kang, Won Tae Kim, Yong-June Kim, Sang-Cheol Lee, Sung-Kwon Moon, Yung Hyun Choi, Wun-Jae Kim, Seon-Young Kim, Seok Joong Yun
Summary: A molecular signature, MSP888, has been identified for Non-muscle-invasive bladder cancer (NMIBC) that can predict heterogeneity and responses to Bacillus Calmette-Guerin (BCG) therapy. This signature includes three distinct molecular subtypes, with DP.BCG+ related to progression and response to BCG treatment, and REC.BCG+ related to recurrence and response to BCG treatment. These findings enhance understanding of NMIBC prognosis and the effectiveness of BCG therapy, potentially improving clinical practice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Dong Hyuck Bae, Hee-Jin Kim, Byoung-Ha Yoon, Jong-Lyul Park, Mirang Kim, Seon-Kyu Kim, Seon-Young Kim, Sang-Il Lee, Kyu-Sang Song, Yong Sung Kim
Summary: Epigenetic changes in chromatin, such as hypomethylation of the STK31 promoter, are associated with gastric carcinogenesis. Upregulation of STK31 promotes the proliferation and migration of gastric cancer cells and may predict a shorter survival time for patients with gastric cancer.
Article
Oncology
Jong-Lyul Park, Seon-Kyu Kim, Sora Jeon, Chan-Kwon Jung, Yong-Sung Kim
Summary: Thyroid nodules are commonly benign, but molecular markers such as miRNAs can help differentiate thyroid cancer from benign tumors and predict the risk of recurrence. High expression levels of specific miRNAs, such as miR-136, miR-21, and miR-127, are associated with poor clinicopathological features and recurrent or persistent disease in patients with thyroid cancer. These miRNAs can serve as diagnostic and prognostic markers for thyroid nodules, aiding in risk stratification and treatment decisions.
Article
Oncology
Sung Gwe Ahn, Seon-Kyu Kim, Jonathan H. Shepherd, Yoon Jin Cha, Soong June Bae, Chungyeul Kim, Joon Jeong, Charles M. Perou
Summary: The SP142 PD-L1 assay is a companion diagnostic for atezolizumab in metastatic triple-negative breast cancer (TNBC). Through studying 149 TNBC samples, it was found that PD-L1-positive TNBC samples had higher levels of CD8+ T cells, stromal tumor-infiltrating lymphocytes, and immunomodulatory TNBCtype compared to PD-L1-negative samples. The SP142-guided gene expression signature consisting of 94 immune-related genes was associated with improved response and survival in multiple TNBC cohorts.
BREAST CANCER RESEARCH AND TREATMENT
(2021)
Article
Oncology
Chan Wook Kim, Ye Jin HA, Ka Hee Tak, Seon Ae Roh, Seon-Kyu Kim, Seon-Young Kim, Yong Sung Kim, Dong-Hyung Cho, Jin Cheon Kim
Summary: This study found that CEA, CKS2, OAS2, and ATG5 in preoperative serum were independent risk factors for recurrence in stage II and III colorectal cancer. The combination of these serum biomarkers effectively predicted tumor recurrence in patients.
ANTICANCER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sahar Waseem, Sudeep Kumar, Kanghoon Lee, Byoung-Ha Yoon, Mirang Kim, Hail Kim, Keesook Lee
Summary: PRMT1 is crucial for male fertility in mice, as its deficiency leads to impaired repair pathway of DNA double-strand breaks in male germ cells. This study provides new insight into the role of PRMT1-mediated asymmetric demethylation in mouse spermatogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Jin C. Kim, Ye J. Ha, In J. Park, Chan W. Kim, Yong S. Yoon, Jong L. Lee, Ka H. Tak, Dong-Hyung Cho, Seong H. Park, Seon-Kyu Kim, Seon-Young Kim, Yong S. Kim
Summary: The study revealed different immune microenvironments in mCRC patients with hepatic metastasis, pulmonary metastasis, or concurrent hepatic and pulmonary metastasis. Through RNA analysis and validation of gene expressions in the primary CRC samples, candidate genes associated with different metastasis patterns were identified. These findings help in identifying immune-related site-specific markers of mCRC.
JOURNAL OF SURGICAL ONCOLOGY
(2021)
Article
Otorhinolaryngology
Seung-Jin Park, Yea Eun Kang, Jeong-Hwan Kim, Jong-Lyul Park, Seon-Kyu Kim, Seung-Woo Baek, In Sun Chu, Shinae Yi, Seong Eun Lee, Young Joo Park, Eun-Jae Jung, Jin Man Kim, Hye Mi Ko, Je-Ryong Kim, Seung-Nam Jung, Ho-Ryun Won, Jae Won Chang, Bon Seok Koo, Seon-Young Kim
Summary: This study investigated the transcriptomic characteristics of advanced papillary thyroid cancer, revealing associations with immune-escape signaling, specific fusion genes, and a novel molecular biomarker for recurrence.
CLINICAL AND EXPERIMENTAL OTORHINOLARYNGOLOGY
(2022)
Article
Cell Biology
Hyun Ahm Sohn, Dong Chul Lee, Anna Park, Minho Kang, Byoung-Ha Yoon, Chul-Ho Lee, Yong-Hoon Kim, Kyoung-Jin Oh, Cha Yeon Kim, Seong-Hwan Park, Han Koo, Hyoung-Chin Kim, Won Kee Yoon, Dae-Sik Lim, Daesoo Kim, Kyung Chan Park, Young Il Yeom
Summary: NDRG3 plays an important role in the regulation of liver cell metabolism, and its loss of function leads to excessive glycogen accumulation, hypoglycemia, elevated liver triglyceride content, and perturbation of the methionine cycle. These findings suggest therapeutic potential for regulating NDRG3 in disorders related to metabolic pathways.
Article
Biochemistry & Molecular Biology
Xuan-Mei Piao, Seon-Kyu Kim, Young Joon Byun, Chuang-Ming Zheng, Ho Won Kang, Won Tae Kim, Yong-June Kim, Sang-Cheol Lee, Wun-Jae Kim, Sung-Kwon Moon, Yung Hyun Choi, Seok Joong Yun
Summary: This study compared the utility of different risk assessments in NMIBC patients and found that the molecular signature-based subtype predictor (MSP888) had independent predictive value for NMIBC progression, especially in patients without intravesical BCG immunotherapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Kwangho Kim, Tae Young Ryu, Eunsun Jung, Tae-Su Han, Jinkwon Lee, Seon-Kyu Kim, Yu Na Roh, Moo-Seung Lee, Cho-Rok Jung, Jung Hwa Lim, Ryuji Hamamoto, Hye Won Lee, Keun Hur, Mi-Young Son, Dae-Soo Kim, Hyun-Soo Cho
Summary: A protein called SMYD2 has been identified as a potential target for novel therapies for non-small-cell lung cancer (NSCLC) due to its role in promoting cancer spread. In laboratory experiments, inhibiting SMYD2 production in lung cancer cells hindered the process of metastasis. This discovery could lead to new treatment options for this form of lung cancer.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Mijin Park, Byul Moon, Jong-Hwan Kim, Seung-Jin Park, Seon-Kyu Kim, Kihyun Park, Jaehoon Kim, Seon-Young Kim, Jeong-Hoon Kim, Jung-Ae Kim
Summary: This study found that SETD5 expression is associated with poor prognosis of HCC, and depletion of SETD5 can reduce HCC cell proliferation and invasion, induce cell death, downregulate interferon-mediated inflammatory response, as well as decrease glycolysis activity in HCC cells, ultimately inhibiting tumor growth in xenograft mouse models.
MOLECULES AND CELLS
(2022)
Article
Biochemistry & Molecular Biology
Yong-Soon Park, Jong-Seok Park, Soohyun Lee, Sung-Hee Jung, Seon-Kyu Kim, Choong-Min Ryu
Summary: The study revealed a complex interaction between the marine bacterial pathogen V. vulnificus and the land plant Arabidopsis thaliana. The pathogen actively modulates its virulence factors and potential host immune regulators.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
