Article
Chemistry, Medicinal
Yi Yuan, Dingqiang Fu, Yan Xu, Xuyang Wang, Xiongfei Deng, Shan Zhou, Feng Du, Xin Cui, Yun Deng, Zhuo Tang
Summary: This study describes a novel Pt(IV) prodrug, AP1, that targets the BER protein APE1 and induces DNA damage response and apoptosis in cancer cells. AP1 shows strong inhibitory effects on malignant cells, including cisplatin-resistant cells, with minimal toxicity to normal cells. It can also directly inhibit the activity of APE1 and interrupt miRNA processing, leading to the upregulation of the tumor suppressor PTEN.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Zhouyiyuan Xue, Bruce Demple
Summary: Apurinic/apyrimidinic endonuclease 1/redox effector-1 (Ape1/Ref-1) is an important enzyme in mammalian cells that plays a key role in DNA repair and transcription factor activation. Recent studies have shown that APEX1 knockout cell lines are more sensitive to the inhibitors Compound 3 and APX2009, suggesting off-target effects of these inhibitors.
Article
Genetics & Heredity
Heike Katrin Schreier, Rahel Stefanie Wiehe, Miria Ricchetti, Lisa Wiesmueller
Summary: This study identifies the role of polymerase zeta (POLZ) in maintaining mitochondrial DNA (mtDNA) under conditions of oxidative stress. POLZ knockdown leads to mtDNA accumulation and requires the activity of the base excision repair enzyme APE1. Additionally, POLZ is involved in the formation of mtDNA deletions independently of reactive oxygen species. These findings highlight the significance of POLZ in mtDNA turnover, particularly in the presence of oxidative stress.
Article
Biochemistry & Molecular Biology
Anatoly A. Bulygin, Olga S. Fedorova, Nikita A. Kuznetsov
Summary: AP endonucleases are crucial DNA repair enzymes that exhibit broad substrate specificity for repairing AP sites and various damaged bases. A computational study on several homologous APE1-like endonucleases revealed that amino acid residues in the active site and the damage recognition loop significantly affect catalytic complex formation and the efficiency of cleaving different damaged nucleotides.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Anatoly A. Bulygin, Victoria N. Syryamina, Aleksandra A. Kuznetsova, Darya S. Novopashina, Sergei A. Dzuba, Nikita A. Kuznetsov
Summary: This study investigated the molecular events in the process of damage recognition by Apurinic/apyrimidinic endonuclease 1 (APE1) through DEER spectroscopy and kinetic analysis. The results showed that specific mutants of APE1 had higher activity in recognizing and repairing damaged DNA, revealing the factors that affect its substrate specificity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Cynthia J. Burrows, Shereen A. Howpay Manage, Aaron M. Fleming, Hsiao-Nung Chen
Summary: This study quantitatively investigated cysteine oxidation to sulfenic acid in APE1 and how this modified form affects APE1's binding to the NEIL3 gene promoter G4; the results suggest that cysteine oxidation can enhance G4 binding but reduce endonuclease activity in APE1, potentially triggering a switch from base excision repair to transcriptional modulation.
ACS CHEMICAL BIOLOGY
(2022)
Review
Cell Biology
Mansour Akbari, Hilde Loge Nilsen, Nicola Pietro Montaldo
Summary: Mitochondria are essential for cellular energy production and play a crucial role in organismal development and normal function. Understanding the mechanisms of mtDNA maintenance and transcription can provide insights into the pathogenesis of various diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiaoying Wei, Zhishuo Wang, Caroline Hinson, Kun Yang
Summary: The study found that human tyrosyl-DNA phosphodiesterase 1 (TDP1), AP endonuclease 1 (APE1), and three-prime repair exonuclease 1 (TREX1) can repair 3'-PUA-protein crosslinks, providing new repair pathways for maintaining genome integrity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Shereen A. Howpay Manage, Aaron M. Fleming, Hsiao-Nung Chen, Cynthia J. Burrows
Summary: This study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and demonstrates how this modification affects APE1's function towards the NEIL3 gene promoter G4. The research suggests that cysteine oxidation to sulfenic acid enhances APE1's affinity for G4 during oxidative stress, but attenuates its endonuclease activity.
ACS CHEMICAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Susan E. Tsutakawa, Altaf H. Sarker
Summary: The canonical role of DNA glycosylase is in repairing global base damage, but it also plays a role in epigenetic gene regulation, immune response modulation, replication, and transcription. In this issue of Structure, Eckenroth et al. (2020) reveal the structure of NEIL2 glycosylase, showing that its catalytic domain flexibility sets it apart from other glycosylases and implies novel regulatory mechanisms.
Article
Biochemistry & Molecular Biology
Adib Behrouzi, Hanyu Xia, Eric L. Thompson, Mark R. Kelley, Jill C. Fehrenbacher
Summary: Cisplatin-induced neurotoxicity is a common complication of anti-cancer treatment. Inhibition of OGG1 and APE1 endonuclease activity exacerbates oxidative DNA damage and neurotoxicity in sensory neurons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Inga R. Grin, Daria V. Petrova, Anton V. Endutkin, Chunquan Ma, Bing Yu, Haiying Li, Dmitry O. Zharkov
Summary: Base excision DNA repair is an important pathway in safeguarding the genome of plants, and understanding their repair mechanisms is crucial for developing new crop varieties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Jiahui Zhu, Lexin Liu, Xiaodi Ma, Xinyu Cao, Yu Chen, Xiangping Qu, Ming Ji, Huijun Liu, Chi Liu, Xiaoqun Qin, Yang Xiang
Summary: The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Oxidative stress, especially DNA stimulation, plays a crucial role in pulmonary fibrosis. DNA damage is important in the initiation of IPF and DNA repair systems targeting damage are crucial for lung cell survival. However, existing research has not focused on the role of DNA damage and repair pathways in IPF.
Article
Biochemistry & Molecular Biology
Ashan P. Wettasinghe, Melodee O. Seifi, Marco Bravo, Austen C. Adams, Aman Patel, Monica Lou, Dimithree Kahanda, Hao-Che Peng, Allison L. Stelling, Li Fan, Jason D. Slinker
Summary: DNA helicase activity is crucial for various DNA metabolic processes. This study investigates the binding and activity of helicases StXPB2 and AfXPB, revealing a concentration-dependent activity for AfXPB and a crossover between fast molecular wrench and slower conventional helicase modes. The AfXPB-Bax1 complex inhibits rapid activity, while the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations.
Review
Biochemistry & Molecular Biology
Yuliya Krasikova, Nadejda Rechkunova, Olga Lavrik
Summary: Nucleotide excision repair (NER) is a versatile DNA repair pathway that is linked to neurological degeneration in patients with Xeroderma pigmentosum. Xeroderma pigmentosum patients typically have a high sensitivity to ultraviolet light due to DNA repair defects, leading to multiple skin and eye cancers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Swati Bajaj, Sk. Kayum Alam, Kumar Singha Roy, Arindam Datta, Somsubhra Nath, Susanta Roychoudhury
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Biochemistry & Molecular Biology
Shrabasti Roychoudhury, Somsubhra Nath, Heyu Song, Muralidhar L. Hegde, Larry J. Bellot, Anil K. Mantha, Shiladitya Sengupta, Sutapa Ray, Amarnath Natarajan, Kishor K. Bhakat
MOLECULAR AND CELLULAR BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Chunying Yang, Shiladitya Sengupta, Pavana M. Hegde, Joy Mitra, Shuai Jiang, Brooke Holey, Altaf H. Sarker, Miaw-Sheue Tsai, Muralidhar L. Hegde, Sankar Mitra
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Arijit Dutta, Bradley Eckelmann, Sanjay Adhikari, Kazi Mokim Ahmed, Shiladitya Sengupta, Arvind Pandey, Pavana M. Hegde, Miaw-Sheue Tsai, John A. Tainer, Michael Weinfeld, Muralidhar L. Hegde, Sankar Mitra
NUCLEIC ACIDS RESEARCH
(2017)
Article
Neurosciences
Velmarini Vasquez, Joy Mitra, Pavana M. Hegde, Arvind Pandey, Shiladitya Sengupta, Sankar Mitra, K. S. Rao, Muralidhar L. Hegde
JOURNAL OF ALZHEIMERS DISEASE
(2017)
Article
Genetics & Heredity
Shiladitya Sengupta, Chunying Yang, Muralidhar L. Hegde, Pavana M. Hegde, Joy Mitra, Arvind Pandey, Arijit Dutta, Abdul Tayyeb Datarwala, Kishor K. Bhakat, Sankar Mitra
Review
Oncology
Suryendu Saha, Samya Dey, Somsubhra Nath
Summary: This article discusses the role of steroid hormone receptors in cell cycle regulation, with a focus on their interaction with breast cancer.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Samya Dey, Debmalya Bhattacharyya, Partha Pratim Gupta, Somsubhra Nath
Summary: This study examined the features and long-term outcomes of Ph+ve leukemia cases from a tertiary cancer care center in Eastern India, focusing on CML and ALL cases. The research found that the OS and PFS in CML cases are significantly affected by the phase of disease at time of detection, and the use of non-TKI treatment before TKI commencement leads to a decrease in both survival rates.
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2021)
Article
Multidisciplinary Sciences
Debmalya Sengupta, Souradeep Banerjee, Pramiti Mukhopadhyay, Ritabrata Mitra, Tamohan Chaudhuri, Abhijit Sarkar, Gautam Bhattacharjee, Somsubhra Nath, Susanta Roychoudhury, Samsiddhi Bhattacharjee, Mainak Sengupta
Summary: The study conducted a meta-analysis of genetic associations with lung cancer in the Indian subcontinent, identifying significant correlations between certain genes and lung cancer risk, particularly in smokers, with specific associations noted for different subtypes of lung cancer.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Sangeeta Ghuwalewala, Dishari Ghatak, Sumit Das, Stuti Roy, Pijush Das, Ramesh Butti, Mahadeo Gorain, Somsubhra Nath, Gopal C. Kundu, Susanta Roychoudhury
Summary: The study found an elevated expression of miR-146a in the CD44(high)CD24(low) population within OSCC cells and primary HNSCC tumors. Over-expression of miR-146a enhances stemness phenotype by stabilizing beta-catenin and resulting in loss of E-cadherin and CD24. CD24 is identified as a novel functional target of miR-146a, and mechanistic analysis reveals that higher CD24 levels inhibit AKT phosphorylation leading to beta-catenin degradation.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Stuti Roy, Suryendu Saha, Debanil Dhar, Puja Chakraborty, Kumar Singha Roy, Chitranjan Mukherjee, Arnab Gupta, Samir Bhattacharyya, Anup Roy, Sanghamitra Sengupta, Susanta Roychoudhury, Somsubhra Nath
Summary: This study reveals the role of CUEDC2 in breast cancer, especially in endocrine resistance and mitotic progression. Upregulation of CUEDC2 renders ERα+ve tumors behave similarly to HR-ve tumors with an increase in aneuploidy. Furthermore, CUEDC2 is identified as a potential prognostic marker and therapeutic target in breast cancer management.
CANCER GENE THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Puja Chakraborty, Ratnadip Paul, Abhishek Chowdhury, Nayonika Mukherjee, Somsubhra Nath, Susanta Roychoudhury
Summary: This study investigates the role of histone ubiquitylation in transcription regulation, particularly the mono-ubiquitylation of histone 2B by RING finger motif-containing ubiquitin ligases. The study shows that the anaphase-promoting complex/cyclosome (APC/C), along with its adapter protein Cdc20, catalyses the mono-ubiquitylation of Lysine-120 on the UBCH10 promoter. The study also uncovers a cell-cycle-specific pattern of this modification and suggests a crosstalk between acetylation and ubiquitylation in UBCH10 trans-regulation.
Article
Multidisciplinary Sciences
Debmalya Sengupta, Pramiti Mukhopadhyay, Souradeep Banerjee, Kausik Ganguly, Prateek Mascharak, Noyonika Mukherjee, Sangeeta Mitra, Samsiddhi Bhattacharjee, Ritabrata Mitra, Abhijit Sarkar, Tamohan Chaudhuri, Gautam Bhattacharjee, Somsubhra Nath, Susanta Roychoudhury, Mainak Sengupta
Summary: This study aims to identify the cis-regulatory variants of genes that modulate lung cancer risk among tobacco smokers and alter chemotherapy responses. By analyzing various datasets, the researchers found 22 cis-eQTLs of 14 genes, which predictably alter the binding of transcription factors expressed in lung tissue. They also discovered an association between certain cis-eQTLs and lung cancer risk in a case-control study. Additionally, the study revealed that the risk alleles of these variants significantly decreased patient survival.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Somsubhra Nath, Shrabasti Roychoudhury, Matthew J. Kling, Heyu Song, Pranjal Biswas, Ashima Shukla, Hamid Band, Shantaram Joshi, Kishor K. Bhakat
CELLULAR SIGNALLING
(2017)