Article
Radiology, Nuclear Medicine & Medical Imaging
Han Sol Kang, Jin You Kim, Jin Joo Kim, Suk Kim, Nam Kyung Lee, Ji Won Lee, Hie Bum Suh, Lee Hwangbo, Yohan Son, Robert Grimm
Summary: Quantitative diffusion parameters derived from DKI and DWI are associated with prognostic factors for breast cancer. Moreover, DKI-derived kurtosis can help distinguish between the molecular subtypes of breast cancer.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2022)
Article
Oncology
Yanjin Qin, Feng Wu, Qilan Hu, Litong He, Min Huo, Caili Tang, Jingru Yi, Huiting Zhang, Ting Yin, Tao Ai
Summary: This study investigated the correlations between quantitative diffusion parameters and prognostic factors and molecular subtypes of breast cancer using a single fast high-resolution diffusion-weighted imaging (DWI) sequence with mono-exponential, intravoxel incoherent motion (IVIM), and diffusion kurtosis imaging (DKI) models. The results showed significant differences in the DWI-derived parameters between different subtypes and prognostic factors of breast cancer. Additionally, the morphologic characteristics obtained from high-resolution DWI were found to be able to identify the estrogen receptor status of breast cancer.
FRONTIERS IN ONCOLOGY
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Qin Li, Qin Xiao, Meng Yang, Qinghuan Chai, Yan Huang, Pu-Yeh Wu, Qingliang Niu, Yajia Gu
Summary: Histogram analysis of quantitative parameters from synthetic MRI can help evaluate intra-tumoral heterogeneity and predict prognostic factors and molecular subtypes in IDC. Higher histopathologic grade IDC showed higher values in synthetic MRI parameters. Hormone receptor status and HER2 expression status were also related to certain features of synthetic MRI parameters.
EUROPEAN JOURNAL OF RADIOLOGY
(2021)
Article
Oncology
Zeni Wu, Doratha A. Byrd, Yunhu Wan, Daniel Ansong, Joe-Nat Clegg-Lamptey, Beatrice Wiafe-Addai, Lawrence Edusei, Ernest Adjei, Nicholas Titiloye, Florence Dedey, Francis Aitpillah, Joseph Oppong, Verna Vanderpuye, Ernest Osei-Bonsu, Casey L. Dagnall, Kristine Jones, Amy Hutchinson, Belynda D. Hicks, Thomas U. Ahearn, Jianxin Shi, Rob Knight, Richard Biritwum, Joel Yarney, Seth Wiafe, Baffour Awuah, Kofi Nyarko, Jonine D. Figueroa, Rashmi Sinha, Montserrat Garcia-Closas, Louise A. Brinton, Emily Vogtmann
Summary: The oral microbiome is associated with breast cancer and nonmalignant breast disease, and its diversity is negatively correlated with the risk of these conditions. There is a strong correlation between the oral and fecal microbiome in breast cancer cases, but not in controls.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Oncology
Zelalem Desalegn, Alana Smith, Meron Yohannes, Xueyuan Cao, Endale Anberber, Yonas Bekuretsion, Mathewos Assefa, Marcus Bauer, Martina Vetter, Eva Johanna Kantelhardt, Tamrat Abebe, Athena Starlard-Davenport
Summary: Breast cancer is the leading cause of cancer mortality among women in Ethiopia, especially those of African ancestry. Recent studies have shown the role of microbial dysbiosis in the initiation, growth, and treatment outcome of breast cancer. However, there is a lack of research on the association between microbial composition and clinical factors in Ethiopian women with breast cancer. This study aims to profile the microbiome in breast tumor and adjacent tissues and identify associations between microbial composition and clinicopathological factors in Ethiopian women with breast cancer.
Article
Oncology
Jhajaira M. Araujo, Gabriel De la Cruz-Ku, Melanie Cornejo, Franco Doimi, Richard Dyer, Henry L. Gomez, Joseph A. Pinto
Summary: This study evaluated the prognostic capability of a 3-gene score in different subtypes of triple negative breast cancer (TNBC). The results showed that the score was able to predict the risk of distant recurrence in the immunomodulatory and mesenchymal stem-like subtypes. Additionally, a low score was associated with a high level of tumor-infiltrating lymphocytes.
Article
Oncology
Doratha A. Byrd, Emily Vogtmann, Zeni Wu, Yongli Han, Yunhu Wan, Joe-Nat Clegg-Lamptey, Joel Yarney, Beatrice Wiafe-Addai, Seth Wiafe, Baffour Awuah, Daniel Ansong, Kofi Nyarko, Autumn G. Hullings, Xing Hua, Thomas Ahearn, James J. Goedert, Jianxin Shi, Rob Knight, Jonine D. Figueroa, Louise A. Brinton, Montserrat Garcia-Closas, Rashmi Sinha
Summary: The gut microbiota may influence breast cancer development by regulating hormonal, metabolic and immunologic pathways. Associations between fecal bacteria and both breast cancer and nonmalignant breast disease were studied in Ghana, with findings indicating strong and similar correlations with both conditions. This suggests potential microbial mechanisms of breast disease.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Immunology
ChenWei Yu, Linlin Zhou, Qiuyu Zhang
Summary: The immunogenicity of the breast tumor microenvironment is clinically heterogeneous, with two major immune subtypes, predominant immune (PI) and low immune (LI), identified in this study. These subtypes are associated with different hormone receptor phenotypes in breast tumors, with PI subtype showing significantly improved survival compared to LI subtype. These findings highlight the potential of using immune subtypes as biomarkers for precision immunotherapy.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Genetics & Heredity
Shenting Liu, He Xu, Ying Feng, Ulf D. Kahlert, Renfei Du, Luz Angela Torres-de la Roche, Kai Xu, Wenjie Shi, Fanshuai Meng
Summary: Based on the analysis of TNBC samples, we identified two subtypes (A and B) related to oxidative stress, with subtype A showing better prognosis. Subtype A exhibited higher immune infiltration characteristics, with tumor-suppressive immune cells, HLA genes, and three immune inhibitors being more prevalent. We also developed an eight-gene signature as an independent risk factor for TNBC and validated its predictive value. Our study reveals distinct molecular clusters based on OS-related genes, providing insights into the ROS-mediated progression and crosstalk with the tumor microenvironment in TNBC, and offering a risk prognostic model for clinical treatment decisions.
FRONTIERS IN GENETICS
(2023)
Article
Immunology
Xi Cao, Yidong Zhou, Feng Mao, Yan Lin, Xingtong Zhou, Qiang Sun
Summary: This study investigated the correlation between Siglec15 and breast cancer and found that high expression of Siglec15 was associated with better prognosis, while low expression was associated with worse prognosis. Three Siglec15-related subtypes of breast cancer were identified, providing important insights into the immunological function and significance of Siglec15 in breast cancer.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Review
Oncology
Molly A. Nelson, Worapol Ngamcherdtrakul, Shiuh-Wen Luoh, Wassana Yantasee
Summary: Increased levels of total tumor-infiltrating lymphocytes (TILs) are associated with good prognosis in several breast cancer subtypes; different subtypes of TILs impact both tumor cells and immune cells in various ways; specific CD8(+) T cells and NK cells are associated with better clinical outcomes; therapeutic strategies include PD-1/PD-L1 blockade, CAR T cell therapy, and ex vivo-stimulated NK cells.
CANCER AND METASTASIS REVIEWS
(2021)
Article
Oncology
Ran Ding, Yuhan Wang, Jinyan Fan, Ziyue Tian, Shuang Wang, Xiujuan Qin, Wei Su, Yanbo Wang
Summary: This study analyzed RNA-seq data from 303 TNBC samples and identified a significant T cell depletion signature in the TNBC tumor microenvironment. It also found that some TNBC patients exhibit an immunosuppressive state and have a poor prognosis and resistance to ICB treatment. These findings can be used to construct prognostic models and study the immune mechanisms within the tumor microenvironment.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Lucie Laot, Enora Laas, Noemie Girard, Elise Dumas, Eric Daoud, Beatriz Grandal, Jean-Yves Pierga, Florence Coussy, Youlia Kirova, Elsy El-Alam, Guillaume Bataillon, Marick Lae, Florence Llouquet, Fabien Reyal, Anne-Sophie Hamy
Summary: The study found that the prognostic value of residual axillary disease after neoadjuvant chemotherapy varies by breast cancer subtype, with different subtypes showing different tolerance and prognosis for lymph node involvement.
Article
Pathology
Araceli Garcia-Martinez, Ariadna Perez-Balaguer, Fernando Ortiz-Martinez, Eloy Pomares-Navarro, Elena Sanmartin, Marta Garcia-Escolano, Yoel G. Montoyo-Pujol, Elena Castellon-Molla, Gloria Peiro
Summary: The study revealed differential activation of the Hh pathway in breast carcinoma phenotypes. SMO levels stratify patients at risk of recurrence and death in the HER2 phenotype, showing independent prognostic value and potential therapeutic significance.
PATHOLOGY RESEARCH AND PRACTICE
(2021)
Article
Immunology
Yin Xia, Linlin Zhou, Hung-Chih Yang, Chen-Wei Yu
Summary: This study aimed to analyze the immune characteristics of liver cancer and its association with patient characteristics and clinical outcomes. The results showed that high expression of myeloid-derived suppressor cells (MDSCs) is linked to a decrease in effector T cells in liver tumor progression. The CCL5-high subtype was associated with improved overall survival and disease-free survival.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Microbiology
Tyler Seckar, Xiang Lin, Dipayan Bose, Zhi Wei, Joseph Rohrbaugh, Ronald G. Collman, Erle S. Robertson
Summary: The PathoChIP technology showed high sensitivity and specificity in detecting microbial agents in samples from SARS-CoV-2 infected patients, outperforming conventional diagnostic techniques. It can detect a wide range of respiratory pathogens, aiding in differentiating causative agents of respiratory illnesses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Virology
Rajnish Kumar Singh, Dipayan Bose, Erle S. Robertson
Summary: The study shows that KSHV infection significantly affects the expression of genes related to fatty acid and amino acid metabolism, particularly under hypoxic conditions. KSHV-encoded proteins vGPCR and LANA can upregulate FABP genes, and suppressing FABPs leads to adverse effects on KSHV reactivation.
JOURNAL OF VIROLOGY
(2021)
Correction
Virology
Abhik Saha, Masanao Murakami, Pankaj Kumar, Bharat Bajaj, Karen Sims, Erle S. Robertson
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Somenath Banerjee, Dipayan Bose, Subhadip Das, Nabanita Chatterjee, Snehasish Mishra, Krishna Das Saha
Summary: In this study, the researchers investigated the generation and function of lipid droplets (LD) in Leishmania donovani infection. They found that infection with L. donovani triggers LD formation in macrophages in a time-dependent manner. The signaling molecules responsible for LD accumulation were also identified. Moreover, inhibition of phagosome maturation enhanced LD accumulation in certain strains of Leishmania. Treatment with aspirin not only reduced LD load but also improved phagolysosome biogenesis and cytokine balance. These findings suggest that manipulating LD generation could be a potential therapeutic strategy against parasite growth in the early stages of infection.
MOLECULAR IMMUNOLOGY
(2022)
Editorial Material
Cell Biology
Panpan Hou, Tian Tian, Penghui Jia, Yuxin Lin, Zibo Li, Yicheng Wang, Yu Ye, Chunmei Li, Deyin Guo
Summary: The assembly of NLRP3 inflammasomes, which play a crucial role in host defense and maintaining homeostasis, can be initiated by a variety of stimuli. Our recent work has identified CCDC50 as a negative regulator of NLRP3-mediated inflammation by inhibiting the polymerization of NLRP3 and the recruitment of PYCARD/ASC, thus suppressing the assembly of inflammasomes. Our findings demonstrate the intricate crosstalk between autophagy and inflammation.
Article
Biochemistry & Molecular Biology
Yuxin Lin, Zibo Li, Yicheng Wang, Tian Tian, Penghui Jia, Yu Ye, Miao He, Zixiao Yang, Chunmei Li, Deyin Guo, Panpan Hou
Summary: This study identifies a novel autophagy cargo receptor, CCDC50, which negatively regulates NLRP3 inflammasome assembly and the release of related inflammatory factors by degrading NLRP3. CCDC50 deficiency results in upregulation of signaling pathways associated with autoinflammatory diseases and enhances gut inflammation response.
Article
Cell Biology
Bulin Jiang, Liyuan Huang, Tian Tian, Hongling Wu, Hantao Yao, Tyler Marmo, Fangfang Song, Cui Huang
Summary: In this study, we found that IRX5 plays a crucial role in promoting adipogenesis of human bone marrow-derived mesenchymal stem cells (hMSCs) by transcriptionally regulating PGC-1 alpha and inhibiting glycolysis. This study reveals a potential target to control hMSCs fate decision and bone homeostasis.
CELL DEATH DISCOVERY
(2022)
Article
Cell Biology
Nian Ma, Juan Lu, Yonggang Pei, Erie S. Robertson
Summary: This study utilized a 3D platform to culture normal oral keratinocyte cells and investigated the molecular interactions between EBV and infected cells. The results identified multiple pathways contributing to distinct pathologies associated with EBV infection and revealed key molecules involved in the regulation of latent and lytic states.
CELL DEATH & DISEASE
(2022)
Article
Oncology
Rajnish Kumar Singh, Dipayan Bose, Erle S. Robertson
Summary: Epigenetic reprogramming of the KSHV genome occurs during hypoxia, leading to enrichment of both transcriptional activator and repressor modifications of histones. KSHV-encoded antigens contribute to the increase in modified histone proteins. Specific regions of the KSHV genome are critical for DNA replication under hypoxic conditions.
Article
Multidisciplinary Sciences
Xiang Lin, Tian Tian, Zhi Wei, Hakon Hakonarson
Summary: Single-cell multimodal sequencing technologies provide an opportunity to analyze different types of data in the same cell simultaneously. However, combining multiple data sources for clustering analysis of single-cell multimodal data remains a challenge. In this study, a novel deep learning method called scMDC is developed, which explicitly models different data sources and learns latent features for clustering analysis. The experimental results show that scMDC outperforms existing methods on single-cell multimodal datasets and has linear scalability for analyzing large datasets.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Tian Tian, Cheng Zhong, Xiang Lin, Zhi Wei, Hakon Hakonarson
Summary: In this study, a model-based deep learning approach called scDHMap is proposed to visualize the complex hierarchical structures of single-cell RNA-seq data in low-dimensional hyperbolic space. The evaluations show that scDHMap outperforms existing dimensionality-reduction methods in various analytical tasks for scRNA-seq data. Additionally, scDHMap can be extended to visualize single-cell ATAC-seq data.
Review
Virology
Hui Yu, Erle S. Robertson
Summary: Epstein-Barr virus (EBV) is the first oncogenic virus identified in humans that can establish lifelong asymptomatic persistence. It is associated with a wide range of diseases, including both benign and malignant conditions. Although there have been continuous studies on the molecular biology and diseases related to EBV for nearly 60 years, the mechanism of viral-mediated transformation and the precise role of EBV in these diseases are still major challenges that require further exploration.
Article
Cell Biology
Dipayan Bose, Xiang Lin, Le Gao, Zhi Wei, Yonggang Pei, Erle S. Robertson
Summary: This study reveals that during EBV reactivation, the downregulation of m(6)A eraser ALKBH5 leads to enhanced methylation of cellular transcripts DTX4 and TYK2, resulting in degradation of TYK2 mRNA and increased translation efficiency of DTX4 mRNA. This attenuates the IFN signaling, promoting viral lytic replication.
JOURNAL OF BIOMEDICAL SCIENCE
(2023)
Article
Microbiology
Dipayan Bose, Rajnish Kumar Singh, Erle S. Robertson
Summary: Hypoxia induces KSHV reactivation by preventing the degradation of essential cellular machinery, such as RNA Pol II, required for successful viral gene synthesis. The virus manipulates the cellular microenvironment to ensure efficient functioning of the transcription machinery during hypoxic conditions.
