Article
Biochemistry & Molecular Biology
Zhiheng Deng, Huasong Ai, Maoshen Sun, Zebin Tong, Yunxiang Du, Qian Qu, Liying Zhang, Ziyu Xu, Shixian Tao, Qiang Shi, Jia-Bin Li, Man Pan, Lei Liu
Summary: This study elucidates the mechanism of H2B monoubiquitylation and highlights the critical role of nucleosomal DNA in mediating E3 ligase recognition.
Article
Biochemistry & Molecular Biology
Prajakta Tathe, K. V. S. Rammohan Chowdary, Krushna Chandra Murmu, Punit Prasad, Subbareddy Maddika
Summary: In this study, the researchers discovered that the tyrosine phosphatase SHP-1 can dephosphorylate histone H2B and plays a critical role in transcription. SHP-1 dephosphorylates H2B at tyrosine 121, promoting H2B ubiquitination and maintaining basal autophagic flux. This study reveals the importance of SHP-1-regulated modification of H2B in eukaryotic transcription.
Article
Cell Biology
Liying Wang, Zhiliang Xu, Libin Wang, Chao Liu, Huafang Wei, Ruidan Zhang, Yinghong Chen, Lina Wang, Wenwen Liu, Sai Xiao, Wei Li, Wei Li
Summary: The study reveals that RNF20 is crucial for early stage somatic cell reprogramming, with Rnf20 knockout leading to failure in reprogramming at the initial stage. The absence of RNF20 affects the transcription of MET-related genes and early pluripotency genes, ultimately hindering the establishment of a pluripotent gene network.
CELL PROLIFERATION
(2021)
Article
Biochemistry & Molecular Biology
Ikumi Ohsawa, Fuminori Kawano
Summary: This study showed that exercise training activates histone turnover in skeletal muscle fibers, leading to nucleosome loosening and enhanced gene responses to exercise.
Article
Biochemistry & Molecular Biology
Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu, Jizeng Jia
Summary: In this study, the association between transposons (TEs), chromatin states, and chromatin accessibility in Aegilops tauschii was analyzed. It was found that TEs contributed to the diverse distribution of chromatin states and affected the chromatin state and openness of potential regulatory elements. Some TE superfamilies carried active/open chromatin regions. Furthermore, the accessibility shaped by TEs was associated with the histone mark H3K9ac. These findings highlight the role of TEs in shaping the epigenetic landscape and regulating gene expression in Aegilops tauschii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Developmental Biology
Anna Torok, Martin J. G. Brown, Jordina C. Vilar, Indu Patwal, Timothy Q. DuBuc, Erwan Atcheson, Uri Frank, Sebastian G. Gornik, Andrew Flaus
Summary: Many animals use sperm nuclear basic proteins (SNBPs) to compact and stabilize sperm chromatin during spermatogenesis. Hydrozoan cnidarians and echinoid sea urchins have evolved a unique family of sperm-specific histone H2Bs (spH2Bs) to regulate sperm packaging and buoyancy. In this study, we found that the sperm chromatin of Hydractinia echinata and H. symbiolongicarpus has higher stability than somatic chromatin, with reduced accessibility to transposase Tn5 integration and endonucleases. The expression of spH2Bs in these species leads to downregulation of transcription and cell cycle arrest in embryos, without affecting nuclear density. These findings suggest that spH2Bs contribute to chromatin stability and transcriptional silencing in Hydractinia sperm, potentially playing a role in sperm buoyancy as a reproductive adaptation.
Article
Multidisciplinary Sciences
Anfeng Luo, Jingwei Kong, Jun Chen, Xue Xiao, Jie Lan, Xiaorong Li, Cuifang Liu, Peng-Ye Wang, Guohong Li, Wei Li, Ping Chen
Summary: This study reveals the mechanism of direct collaboration between ubH2B and FACT at the nucleosome level. The researchers found that ubH2B impairs nucleosome stability and recruits FACT by enhancing its binding on the nucleosome. FACT preferentially binds and deposits H2A-ubH2B dimers to form an intact nucleosome. The stable altered nucleosome state obtained by ubH2B and FACT provides a key platform for gene transcription, as shown by genome-wide and time-course ChIP-qPCR analyses.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jinlei Han, Damar Lopez-Arredondo, Guangrun Yu, Yankun Wang, Baohua Wang, Sarah Brooke Wall, Xin Zhang, Hui Fang, Alfonso Carlos Barragan-Rosillo, Xiaoping Pan, Yanqin Jiang, Jingbo Chen, Hui Zhang, Bao-Liang Zhou, Luis Herrera-Estrella, Baohong Zhang, Kai Wang
Summary: This study examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton, revealing the interplay among transposable elements, cis-regulatory elements, and histone modifications during polyploidization. These findings advance our understanding of regulatory architecture in plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Plant Sciences
Jun-Li Wang, Dong-Wei Di, Pan Luo, Li Zhang, Xiao-Feng Li, Guang-Qin Guo, Lei Wu
Summary: This review focuses on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis, demonstrating that complex signaling pathways affect gene expression and subsequently protein production.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Multidisciplinary
Si-di Xie, Ran Tian, Jun-jie Zhang, Han-mei Liu, Yang-ping Li, Yu-feng Hu, Guo-wu Yu, Yu-bi Huang, Ying-hong Liu
Summary: Chromatin accessibility plays a crucial role in gene transcriptional regulation. Using a maize kernel mutant called dek219, researchers identified the DICER-LIKE1 (DCL1) protein as an important enzyme in miRNA biogenesis that affects the expression of miRNAs and histone genes. They also found that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be involved in regulating histone gene expression. ATAC-seq experiments showed that the chromatin accessibility of dek219 is altered compared to wild type, potentially impacting the expression of crucial genes in kernel development. Analysis revealed 119 candidate genes regulated by chromatin accessibility, including some known to play a role in kernel development.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Medicine, Research & Experimental
Adam J. Ferrari, Priyanka Rawat, Hannah S. Rendulich, Akshaya Annapragada, Yasuto Kinose, Xiaoming Zhang, Kyle Devins, Anna Budina, Robert B. Scharpf, Marilyn A. Mitchell, Janos L. Tanyi, Mark A. Morgan, Lauren E. Schwartz, T. Rinda Soong, Victor E. Velculescu, Ronny Drapkin
Summary: Epigenetic aberrations, specifically the loss of histone H2B monoubiquitylation (H2Bub1), are associated with the development and progression of clear cell ovarian carcinoma (CCOC). The study identified hypermethylation of RNF40 as a likely mechanism underlying the loss of H2Bub1 in CCOC. Additionally, depletion of H2Bub1 was found to promote cell proliferation and clonogenicity in an endometriosis cell line.
Article
Physics, Multidisciplinary
Yeonghoon Kim, Ludvig Lizana, Jae-Hyung Jeon
Summary: The 3D folding and macromolecular size of chromosomes determine their transport characteristics. The fractal globule-like chromosome structure accelerates macromolecular diffusion and target search.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biotechnology & Applied Microbiology
Yanding Zhao, Yadong Dong, Wei Hong, Chongming Jiang, Kevin Yao, Chao Cheng
Summary: Chromatin accessibility is crucial for transcriptional activation of the genome, with transcription factors and histone modifications playing important roles. In this study, a two-layer model was constructed to predict chromatin accessibility by integrating DNA sequence, TF binding, and HM signals. The results showed that TF binding and HM signals accurately predicted chromatin accessibility, while the predictive power of DNA sequences was limited.
Article
Gastroenterology & Hepatology
Rongjie Ji, Jiayuan Chen, Yuyang Xie, Xudan Dou, Bo Qing, Zhiheng Liu, Yumei Lu, Lin Dang, Xu Zhu, Ying Sun, Xiangjian Zheng, Lirong Zhang, Dong Guo, Yupeng Chen
Summary: This study revealed the sex-specific epigenetic regulation of cholangiocyte state transition in polycystic liver disease (PLD). By analyzing chromatin accessibility and histone modifications, different epigenetic changes were identified during cystogenesis in male and female PLD mice. Inhibition of specific epigenetic modifying enzymes slowed cyst growth, especially in male mice. Additionally, increased H3K27ac levels were found in female PLD mice, which was associated with cyst-related gene expression. These findings provide new insights into the sex differences in PLD and suggest potential epigenetic therapeutic strategies for male PLD patients.
JOURNAL OF HEPATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Atsuki En, Kazuaki Watanabe, Dai Ayusawa, Michihiko Fujii
Summary: The thymidine analogue 5-Bromodeoxyuridine (BrdU) modulates various biological phenomena by causing destabilized nucleosome positioning and gene expression changes upon incorporation into DNA. This study reveals that the HBR domain in the histone H2B N-terminal tail is involved in the action of BrdU, and deletion of this domain leads to similar effects as BrdU. Decreased HBR domain function induces cellular senescence, suggesting its crucial role in the action of BrdU and the potential involvement of disordered nucleosome organization in the induction of cellular senescence.
Review
Biochemistry & Molecular Biology
Adam James Ferrari, Ronny Drapkin, Rajan Gogna
Summary: Cell competition allows tumor cells to outcompete adjacent less fit cells. Recent studies have identified molecular fitness fingerprint, oncogenic pathways, and cell junction stability as key factors in determining the outcome of cell competition. Understanding these features may open up possibilities for new diagnostic and therapeutic approaches in cancer treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Apoorva Tangri, Kinzie Lighty, Jagadish Loganathan, Fahmi Mesmar, Ram Podicheti, Chi Zhang, Marcin Iwanicki, Ronny Drapkin, Harikrishna Nakshatri, Sumegha Mitra
Summary: The study found that the overexpression of neuronal deubiquitinating enzyme UCHL1 in HGSOC promotes tumor growth by maintaining protein homeostasis. Inhibition of UCHL1 can reduce tumor cell proliferation and invasion, as well as decrease the metastatic growth of ovarian cancer xenografts. This indicates that UCHL1 plays a crucial role in HGSOC progression through the regulation of protein homeostasis.
MOLECULAR CANCER RESEARCH
(2021)
Article
Biology
Carter J. Barger, Linda Chee, Mustafa Albahrani, Catalina Munoz-Trujillo, Lidia Boghean, Connor Branick, Kunle Odunsi, Ronny Drapkin, Lee Zou, Adam R. Karpf
Summary: FOXM1 and RHNO1 are co-amplified and co-expressed in high-grade serous carcinoma, and their bidirectional promoter may serve as a potential therapeutic target for ovarian and other cancers. Their oncogenic properties in HGSC cells highlight the significance of targeting the FOXM1/RHNO1 gene pair in cancer therapy.
Review
Oncology
Katie Lichter, Chidinma Anakwenze Akinfenwa, Emily MacDuffie, Rohini Bhatia, Christina Small, Jennifer Croke, William Small, Junzo Chino, Daniel Petereit, Surbhi Grover
Summary: Brachytherapy is an essential component of cervical cancer treatment, but its global utilization is low and there are disparities in access. This review explores the current utilization practices and efforts to address barriers to implementation, emphasizing the need to expand access to brachytherapy for women in need worldwide.
EXPERT REVIEW OF ANTICANCER THERAPY
(2022)
Review
Oncology
Rohini K. Bhatia, Katie E. Lichter, Lavanya Gurram, Emily MacDuffie, Dorothy Lombe, Gustavo R. Sarria, Surbhi Grover
Summary: The COVID-19 pandemic has had a global impact on the use of radiation therapy for gynecologic cancers. This review explores the guidelines for using radiation therapy during the pandemic and discusses how different countries have adapted to these guidelines based on their individual resources, government restrictions, and societal norms. The article also emphasizes the importance of utilizing various fractionation schemes and technologies when resources are limited.
INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER
(2022)
Review
Oncology
Rohini Bhatia, Katie E. Lichter, Lavanya Gurram, Emily MacDuffie, Dorothy Lombe, Gustavo R. Sarria, Surbhi Grover
Summary: Gynecologic malignancies pose a disproportionate burden in low- and middle-income countries, and radiation therapy plays a crucial role in their treatment. Understanding the disease epidemiology and availability of radiation therapy infrastructure is vital to improve patient care. Different geographic regions face unique challenges, including limited access to radiation equipment, geographic barriers, and lack of specialized training. Successful examples of telemedicine and cross-cultural partnerships have helped enhance access to adequate and appropriate treatment for gynecologic malignancies.
INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER
(2022)
Article
Oncology
Ashuvinee Elangovan, Jagmohan Hooda, Laura Savariau, Susrutha Puthanmadhomnarayanan, Megan E. Yates, Jian Chen, Daniel D. Brown, Priscilla F. McAuliffe, Steffi Oesterreich, Jennifer M. Atkinson, Adrian V. Lee
Summary: No special-type breast cancer (NST) and invasive lobular carcinoma (ILC) are two major subtypes of breast cancer with significant differences in clinicopathological and molecular characteristics. Loss of E-cadherin in ILC leads to increased sensitivity to IGF1 signaling and enhanced downstream signaling. These findings suggest the importance of further exploring these targets in ILC treatment and utilizing CDH1 loss as a biomarker for patient stratification.
MOLECULAR CANCER RESEARCH
(2022)
Review
Oncology
Kristine N. Kim, Michael LaRiviere, Emily Macduffie, Caitlin A. White, Mary M. Jordan-Luft, Eleanor Anderson, Matthew Ziegler, Jacob A. Radcliff, Joshua Jones
Summary: The purpose of this review is to update our knowledge on the usage of glucocorticoids in adult cancer patients. Glucocorticoids can be highly effective in improving outcomes and quality of life in patients with cancer, mainly used for managing disease manifestations, symptoms, and complications of cancer treatment. The lowest effective dose should be used and treatment duration should be minimized. Side effects can be minimized by careful monitoring, continued assessment of benefits versus harms, and preventative measures.
PRACTICAL RADIATION ONCOLOGY
(2023)
Review
Oncology
Esha Madan, Antonio M. Palma, Vignesh Vudatha, Jose G. Trevino, Kedar Nath Natarajan, Robert A. Winn, Kyoung Jae Won, Trevor A. Graham, Ronny Drapkin, Stuart A. C. McDonald, Paul B. Fisher, Rajan Gogna
Summary: The majority of human cancers evolve through the accumulation of somatic mutations and clonal selection. The mechanisms governing clonal dynamics and selection during the early stages of tissue transformation are still unclear. Cell competition, known as "survival of the fittest" at the cellular level, can eliminate less fit cells or lead to the uncontrolled expansion of super-fit cancer cells. Recent research has highlighted the role of interclonal competition and cancer microenvironment competition in tumor progression.
Review
Biotechnology & Applied Microbiology
Ori Hassin, Moshe Oren
Summary: Mutations in the TP53 gene are common in cancer, but restoring p53 functionality has been considered impossible for a long time. However, recent years have seen promising developments in p53-based therapy, including improved strategies and novel approaches. Small molecules that protect or restore p53 function are gaining interest, along with tailored drugs for specific p53 mutants. Additionally, gene therapy and immunotherapy are being reconsidered. However, significant challenges remain.
NATURE REVIEWS DRUG DISCOVERY
(2023)
Article
Biology
Kai Doberstein, Rebecca Spivak, Hunter D. Reavis, Jagmohan Hooda, Yi Feng, Paul T. Kroeger, Sarah Stuckelberger, Gordon B. Mills, Kyle M. Devins, Lauren E. Schwartz, Marcin P. Iwanicki, Mina Fogel, Peter Altevogt, Ronny Drapkin
Summary: This research provides evidence that L1 cell adhesion molecule (L1CAM) plays a role in the dissemination of transformed fallopian tube secretory cells (FTSECs) to the ovary in the early stages of high-grade serous carcinoma (HGSC) development. L1CAM upregulates integrins and fibronectin in malignant cells and activates the AKT and ERK pathways, increasing cell survival under non-adherent conditions and facilitating ovarian colonization.
COMMUNICATIONS BIOLOGY
(2022)
Article
Oncology
Yang Wu, Zheqi Li, Abdalla M. Wedn, Allison N. Casey, Daniel Brown, Shalini Rao, Soleilmane Omarjee, Jagmohan Hooda, Jason S. Carroll, Jason Gertz, Jennifer M. Atkinson, Adrian Lee, Steffi Oesterreich
Summary: Estrogen receptor alpha (ER/ESR1) mutations are common in endocrine resistant ER-positive breast cancer. Forkhead box A1 (FOXA1) plays a role in ER-chromatin interactions and endocrine response, but its role in ESR1-mutant breast cancer is unclear. This study shows that FOXA1 redistribution is associated with transcriptomic alterations caused by ESR1 mutations and suggests targeting the retinoid X receptor (RXR) pathway as a therapeutic strategy for breast tumors with ESR1 mutation.
MOLECULAR CANCER RESEARCH
(2023)
Article
Cell Biology
Jubina Balan Venghateri, Bareket Dassa, David Morgenstern, Michal Shreberk-Shaked, Moshe Oren, Benjamin Geiger
Summary: This study investigates the involvement of YAP and TAZ, key regulators of the Hippo pathway, in invadopodia formation and matrix degradation. Knockdown or inhibition of YAP and TAZ enhances matrix degradation and invadopodia formation in multiple cancer cell lines, while overexpression suppresses these processes. Proteomic and transcriptomic analysis reveals changes in levels of key invadopodia-associated proteins. These findings suggest that YAP and TAZ act as negative regulators of invadopodia formation by reducing levels of essential invadopodia components. Understanding the molecular mechanisms of invadopodia formation in cancer invasion may lead to the identification of novel therapeutic targets.
CELL DEATH & DISEASE
(2023)
Article
Oncology
Heng Liu, Jianhuang Lin, Wei Zhou, Renyta Moses, Zhongping Dai, Andrew V. Kossenkov, Ronny Drapkin, Benjamin G. Bitler, Sergey Karakashev, Rugang Zhang
Summary: This study demonstrates that the extent of effector CD8+ T cell infiltration into tumors is influenced by a histone H3 demethylase (KDM5A) in epithelial ovarian cancer. KDM5A inhibits immune cell infiltration and antitumor immune responses by silencing genes involved in antigen processing and presentation. Inhibition of KDM5A restores gene expression in the antigen-presentation pathway and promotes antitumor immune responses mediated by CD8+ T cells.
CANCER IMMUNOLOGY RESEARCH
(2022)
Review
Medicine, Research & Experimental
Stefan M. Gysler, Ronny Drapkin
Summary: Recent cancer research has shifted focus from abnormal cell division to the complex interactions between cancer and noncancer cells in the tumor microenvironment. The recruitment of peripheral nerves to the TME by tumors has been linked to enhanced tumor growth and aggressive tumor behavior, suggesting a potential role for the peripheral nervous system in cancer development. Emerging evidence also suggests that exosomes may mediate neural regulation of the TME through cell-cell communication.
JOURNAL OF CLINICAL INVESTIGATION
(2021)