bims-numges 2022-02-06 papers

bims-numges

Biomed News

on Nucleotide metabolism and genome stability

Issue of 2022‒02‒06
33 papers selected by
Sean Rudd
Karolinska Institutet

Targeting purine synthesis in ASS1-expressing tumors enhances the response to immune checkpoint inhibitors.
Sonic hedgehog accelerates DNA replication to cause replication stress promoting cancer initiation in medulloblastoma.
Chemotherapy and mismatch repair deficiency cooperate to fuel TP53 mutagenesis and ALL relapse.
Anti-tumoural activity of the G-quadruplex ligand pyridostatin against BRCA1/2-deficient tumours.
Oligomerization of DNA replication regulatory protein RADX is essential to maintain replication fork stability.
Crosstalk between different DNA repair pathways for DNA double strand break repairs.
Cohesin in DNA damage response and double-strand break repair.
The CIP2A-TOPBP1 axis safeguards chromosome stability and is a synthetic lethal target for BRCA-mutated cancer.
RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair.
DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling.
Parental histone deposition on the replicated strands promotes error-free DNA damage tolerance and regulates drug resistance.
Eukaryotic stress-induced mutagenesis is limited by a local control of translesion synthesis.
Beyond PARP1: The Potential of Other Members of the Poly (ADP-Ribose) Polymerase Family in DNA Repair and Cancer Therapeutics.
Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability.
The toposiomerase IIIalpha-RMI1-RMI2 complex orients human Bloom's syndrome helicase for efficient disruption of D-loops.
Diversity upon diversity: linking DNA double-strand break repair to blood cancer health disparities.
Characterization of adenine phosphoribosyltransferase (APRT) activity in Trypanosoma brucei brucei: Only one of the two isoforms is kinetically active.
Genomic patterns of transcription-replication interactions in mouse primary B cells.
Post-translational regulation of Tyrosyl-DNA phosphodiesterase (TDP1 and TDP2) for the repair of the trapped topoisomerase-DNA covalent complex.
Protein production, kinetic and biophysical characterization of three human dihydroorotate dehydrogenase mutants associated with Miller syndrome.
Polθ inhibitors unchained.
Functional Domain Mapping of Werner Interacting Protein 1 (WRNIP1).
Positive Feedback Regulation of Poly(ADP-ribose) Polymerase 1 and the DNA-PK Catalytic Subunit Affects the Sensitivity of Nasopharyngeal Carcinoma to Etoposide.
Super-sonic speed of DNA synthesis in medulloblastoma.
BMI1 nuclear location is critical for RAD51-dependent response to replication stress and drives chemoresistance in breast cancer stem cells.
Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia.
ASS1igning purine dependency to cancer.
APOBEC3A drives deaminase domain-independent chromosomal instability to promote pancreatic cancer metastasis.
Paradoxical role of the major DNA repair protein, OGG1, in action-at-a-distance mutation induction by 8-oxo-7,8-dihydroguanine.
SPARCLE, a p53-induced lncRNA, controls apoptosis after genotoxic stress by promoting PARP-1 cleavage.
Effect of Thymidine Phosphorylase Gene Demethylation on Sensitivity to 5-Fluorouracil in Colorectal Cancer Cells.
Aldolase B suppresses hepatocellular carcinogenesis by inhibiting G6PD and pentose phosphate pathways.
Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor.

Nat Cancer. 2020 Sep;1(9): 894-908

Targeting purine synthesis in ASS1-expressing tumors enhances the response to immune checkpoint inhibitors.

Rom Keshet, Joo Sang Lee, Lital Adler, Muhammed Iraqi, Yarden Ariav, Lisha Qiu Jin Lim, Shaul Lerner, Shiran Rabinovich, Roni Oren, Rotem Katzir, Hila Weiss Tishler, Noa Stettner, Omer Goldman, Hadas Landesman, Sivan Galai, Yael Kuperman, Yuri Kuznetsov, Alexander Brandis, Tevi Mehlman, Sergey Malitsky, Maxim Itkin, S Eleonore Koehler, Yongmei Zhao, Keyur Talsania, Tsai-Wei Shen, Nir Peled, Igor Ulitsky, Angel Porgador, Eytan Ruppin, Ayelet Erez.

Argininosuccinate synthase (ASS1) downregulation in different tumors has been shown to support cell proliferation and yet, in several common cancer subsets ASS1 expression associates with poor patient prognosis. Here we demonstrate that ASS1 expression under glucose deprivation is induced by c-MYC, providing survival benefit by increasing nitric oxide synthesis and activating the gluconeogenic enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase by S-nitrosylation. The resulting increased flux through gluconeogenesis enhances serine, glycine and subsequently purine synthesis. Notably, high ASS1-expressing breast cancer mice do not respond to immune checkpoint inhibitors and patients with breast cancer with high ASS1 have more metastases. We further find that inhibiting purine synthesis increases pyrimidine to purine ratio, elevates expression of the immunoproteasome and significantly enhances the response of autologous primary CD8+ T cells to anti-PD-1. These results suggest that treating patients with high-ASS1 cancers with purine synthesis inhibition is beneficial and may also sensitize them to immune checkpoint inhibition therapy.

DOI: https://doi.org/10.1038/s43018-020-0106-7
Nat Cancer. 2020 Aug;1(8): 840-854

Sonic hedgehog accelerates DNA replication to cause replication stress promoting cancer initiation in medulloblastoma.

Lukas Tamayo-Orrego, David Gallo, Frédéric Racicot, Amandine Bemmo, Sushmetha Mohan, Brandon Ho, Samer Salameh, Trang Hoang, Andrew P Jackson, Grant W Brown, Frédéric Charron.

The mechanisms generating cancer-initiating mutations are not well understood. Sonic hedgehog (SHH) pathway activation is frequent in medulloblastoma (MB), with PTCH1 mutations being a common initiating event. Here we investigated the role of the developmental mitogen SHH in initiating carcinogenesis in the cells of origin: granule cell progenitors (GCPs). We delineate a molecular mechanism for tumor initiation in MB. Exposure of GCPs to Shh causes a distinct form of DNA replication stress, increasing both origin firing and fork velocity. Shh promotes DNA helicase loading and activation, with increased Cdc7-dependent origin firing. The S-phase duration is reduced and hyper-recombination occurs, causing copy number neutral loss of heterozygosity-a frequent event at the PTCH1/ptch1 locus. Moreover, Cdc7 inhibition to attenuate origin firing reduces recombination and preneoplastic tumor formation in mice. Therefore, tissue-specific replication stress induced by Shh promotes loss of heterozygosity, which in tumor-prone Ptch1+/- GCPs results in loss of this tumor suppressor-an early cancer-initiating event.

DOI: https://doi.org/10.1038/s43018-020-0094-7
Nat Cancer. 2021 Aug;2(8): 819-834

Chemotherapy and mismatch repair deficiency cooperate to fuel TP53 mutagenesis and ALL relapse.

Fan Yang, Samuel W Brady, Chao Tang, Huiying Sun, Lijuan Du, Malwine J Barz, Xiaotu Ma, Yao Chen, Houshun Fang, Xiaomeng Li, Pandurang Kolekar, Omkar Pathak, Jiaoyang Cai, Lixia Ding, Tianyi Wang, Arend von Stackelberg, Shuhong Shen, Cornelia Eckert, Jeffery M Klco, Hongzhuan Chen, Caiwen Duan, Yu Liu, Hui Li, Benshang Li, Renate Kirschner-Schwabe, Jinghui Zhang, Bin-Bing S Zhou.

Chemotherapy is a standard treatment for pediatric acute lymphoblastic leukemia (ALL), which sometimes relapses with chemoresistant features. However, whether acquired drug-resistance mutations in relapsed ALL pre-exist or are induced by treatment remains unknown. Here we provide direct evidence of a specific mechanism by which chemotherapy induces drug-resistance-associated mutations leading to relapse. Using genomic and functional analysis of relapsed ALL we show that thiopurine treatment in mismatch repair (MMR)-deficient leukemias induces hotspot TP53 R248Q mutations through a specific mutational signature (thio-dMMR). Clonal evolution analysis reveals sequential MMR inactivation followed by TP53 mutation in some patients with ALL. Acquired TP53 R248Q mutations are associated with on-treatment relapse, poor treatment response and resistance to multiple chemotherapeutic agents, which could be reversed by pharmacological p53 reactivation. Our findings indicate that TP53 R248Q in relapsed ALL originates through synergistic mutagenesis from thiopurine treatment and MMR deficiency and suggest strategies to prevent or treat TP53-mutant relapse.

DOI: https://doi.org/10.1038/s43018-021-00230-8
EMBO Mol Med. 2022 Feb 02. e14501

Anti-tumoural activity of the G-quadruplex ligand pyridostatin against BRCA1/2-deficient tumours.

Florian J Groelly, Manuela Porru, Jutta Zimmer, Hugo Benainous, Yanti De Visser, Anastasiya A Kosova, Serena Di Vito, Violeta Serra, Anderson Ryan, Carlo Leonetti, Alejandra Bruna, Annamaria Biroccio, Madalena Tarsounas.

  The cells with compromised BRCA1 or BRCA2 (BRCA1/2) function accumulate stalled replication forks, which leads to replication-associated DNA damage and genomic instability, a signature of BRCA1/2-mutated tumours. Targeted therapies against BRCA1/2-mutated tumours exploit this vulnerability by introducing additional DNA lesions. Because homologous recombination (HR) repair is abrogated in the absence of BRCA1 or BRCA2, these lesions are specifically lethal to tumour cells, but not to the healthy tissue. Ligands that bind and stabilise G-quadruplexes (G4s) have recently emerged as a class of compounds that selectively eliminate the cells and tumours lacking BRCA1 or BRCA2. Pyridostatin is a small molecule that binds G4s and is specifically toxic to BRCA1/2-deficient cells in vitro. However, its in vivo potential has not yet been evaluated. Here, we demonstrate that pyridostatin exhibits a high specific activity against BRCA1/2-deficient tumours, including patient-derived xenograft tumours that have acquired PARP inhibitor (PARPi) resistance. Mechanistically, we demonstrate that pyridostatin disrupts replication leading to DNA double-stranded breaks (DSBs) that can be repaired in the absence of BRCA1/2 by canonical non-homologous end joining (C-NHEJ). Consistent with this, chemical inhibitors of DNA-PKcs, a core component of C-NHEJ kinase activity, act synergistically with pyridostatin in eliminating BRCA1/2-deficient cells and tumours. Furthermore, we demonstrate that pyridostatin triggers cGAS/STING-dependent innate immune responses when BRCA1 or BRCA2 is abrogated. Paclitaxel, a drug routinely used in cancer chemotherapy, potentiates the in vivo toxicity of pyridostatin. Overall, our results demonstrate that pyridostatin is a compound suitable for further therapeutic development, alone or in combination with paclitaxel and DNA-PKcs inhibitors, for the benefit of cancer patients carrying BRCA1/2 mutations.

Keywords:  BRCA1; BRCA2; DNA damage responses; G-quadruplex ligands; pyridostatin

DOI:  https://doi.org/10.15252/emmm.202114501
J Biol Chem. 2022 Feb 01. pii: S0021-9258(22)00112-0. [Epub ahead of print] 101672

Oligomerization of DNA replication regulatory protein RADX is essential to maintain replication fork stability.

Taha Mohamed, Madison B Adolph, David Cortez.

  Genome integrity requires complete and accurate DNA replication every cell division cycle. Replication stress poses obstacles to this process that must be overcome to prevent replication fork collapse. An important regulator of replication fork stability is the RAD51 protein, which promotes replication fork reversal and protects nascent DNA strands from nuclease-mediated degradation. Many regulatory proteins control these RAD51 activities, including RADX, which binds both single-stranded DNA and RAD51 at replication forks to ensure that fork reversal is confined to stalled forks. Many single-stranded DNA binding proteins function as hetero- or homo-oligomers. In this study we addressed whether this is also the case for RADX. Using biochemical and genetic approaches we found that RADX acts as a homo-oligomer to control replication fork stability. RADX oligomerizes using at least two different interaction surfaces, including one mapped to a C-terminal region. We demonstrate that mutations in this region prevent oligomerization and prevent RADX function in cells, and that addition of a heterologous dimerization domain to the oligomerization mutants restored their ability to regulate replication. Taken together, our results demonstrate that like many single-stranded DNA binding proteins, oligomerization is essential for RADX-mediated regulation of genome stability.

Keywords:  DNA combing; DNA repair; DNA replication; RAD51; RADX; RPA; cxorf57; dimerization; fork protection; fork reversal; genome stability; recombinase

DOI:  https://doi.org/10.1016/j.jbc.2022.101672
Mutat Res Genet Toxicol Environ Mutagen. 2022 Jan;pii: S1383-5718(21)00129-7. [Epub ahead of print]873 503438

Crosstalk between different DNA repair pathways for DNA double strand break repairs.

Jung-Min Oh, Kyungjae Myung.

  DNA double strand breaks (DSBs) are the most threatening type of DNA lesions and must be repaired properly in order to inhibit severe diseases and cell death. There are four major repair pathways for DSBs: non-homologous end joining (NHEJ), homologous recombination (HR), single strand annealing (SSA) and alternative end joining (alt-EJ). Cells choose repair pathway depending on the cell cycle phase and the length of 3' end of the DNA when DSBs are generated. Blunt and short regions of the 5' or 3' overhang DNA are repaired by NHEJ, which uses direct ligation or limited resection processing of the broken DNA end. In contrast, HR, SSA and alt-EJ use the resected DNA generated by the MRN (MRE11-RAD50-NBS1) complex and C-terminal binding protein interacting protein (CtIP) activated during the S and G2 phases. Here, we review recent findings on each repair pathway and the choice of repair mechanism and highlight the role of mismatch repair (MMR) protein in HR.

Keywords:  DNA double strand break repair; DNA end resection; HR; MMEJ; NHEJ

DOI:  https://doi.org/10.1016/j.mrgentox.2021.503438
Crit Rev Biochem Mol Biol. 2022 Feb 03. 1-18

Cohesin in DNA damage response and double-strand break repair.

Wenya Hou, Yan Li, Jiaxin Zhang, Yisui Xia, Xueting Wang, Hongxiang Chen, Huiqiang Lou.

  Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.

Keywords:  Chromatin; DNA damage response (DDR); DNA damage-induced cohesion; double-strand break (DSB); sister chromatid cohesion

DOI:  https://doi.org/10.1080/10409238.2022.2027336
Nat Cancer. 2021 Dec;2(12): 1357-1371

The CIP2A-TOPBP1 axis safeguards chromosome stability and is a synthetic lethal target for BRCA-mutated cancer.

Salomé Adam, Silvia Emma Rossi, Nathalie Moatti, Mara De Marco Zompit, Yibo Xue, Timothy F Ng, Alejandro Álvarez-Quilón, Jessica Desjardins, Vivek Bhaskaran, Giovanni Martino, Dheva Setiaputra, Sylvie M Noordermeer, Toshiro K Ohsumi, Nicole Hustedt, Rachel K Szilard, Natasha Chaudhary, Meagan Munro, Artur Veloso, Henrique Melo, Shou Yun Yin, Robert Papp, Jordan T F Young, Michael Zinda, Manuel Stucki, Daniel Durocher.

BRCA1/2-mutated cancer cells adapt to the genome instability caused by their deficiency in homologous recombination (HR). Identification of these adaptive mechanisms may provide therapeutic strategies to target tumors caused by the loss of these genes. In the present study, we report genome-scale CRISPR-Cas9 synthetic lethality screens in isogenic pairs of BRCA1- and BRCA2-deficient cells and identify CIP2A as an essential gene in BRCA1- and BRCA2-mutated cells. CIP2A is cytoplasmic in interphase but, in mitosis, accumulates at DNA lesions as part of a complex with TOPBP1, a multifunctional genome stability factor. Unlike PARP inhibition, CIP2A deficiency does not cause accumulation of replication-associated DNA lesions that require HR for their repair. In BRCA-deficient cells, the CIP2A-TOPBP1 complex prevents lethal mis-segregation of acentric chromosomes that arises from impaired DNA synthesis. Finally, physical disruption of the CIP2A-TOPBP1 complex is highly deleterious in BRCA-deficient tumors, indicating that CIP2A represents an attractive synthetic lethal therapeutic target for BRCA1- and BRCA2-mutated cancers.

DOI: https://doi.org/10.1038/s43018-021-00266-w
Cell Rep. 2022 Feb 01. pii: S2211-1247(22)00051-1. [Epub ahead of print]38(5): 110335

RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair.

Takaaki Yasuhara, Reona Kato, Motohiro Yamauchi, Yuki Uchihara, Lee Zou, Kiyoshi Miyagawa, Atsushi Shibata.

  Single-stranded DNA (ssDNA) arising as an intermediate of cellular processes on DNA is a potential vulnerability of the genome unless it is appropriately protected. Recent evidence suggests that R-loops, consisting of ssDNA and DNA-RNA hybrids, can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. However, how the vulnerability of ssDNA in R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops, chromosome translocations, and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end joining dependent on BRCA1, Polθ, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.

Keywords:  Double-strand break; R-loop; RAP80; Transcription-associated DSB repair

DOI:  https://doi.org/10.1016/j.celrep.2022.110335
Front Genet. 2021 ;12 821543

DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling.

Leonhard Andreas Karl, Martina Peritore, Lorenzo Galanti, Boris Pfander.

  DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.

Keywords:  DNA end resection; DNA repair; cell cycle; double strand break; genome stability; nucleosome remodeling

DOI:  https://doi.org/10.3389/fgene.2021.821543
Genes Dev. 2022 Feb 03.

Parental histone deposition on the replicated strands promotes error-free DNA damage tolerance and regulates drug resistance.

Valeria Dolce, Sabrina Dusi, Michele Giannattasio, Chinnu Rose Joseph, Marco Fumasoni, Dana Branzei.

  Ctf4 is a conserved replisome component with multiple roles in DNA metabolism. To investigate connections between Ctf4-mediated processes involved in drug resistance, we conducted a suppressor screen of ctf4Δ sensitivity to the methylating agent MMS. We uncovered that mutations in Dpb3 and Dpb4 components of polymerase ε result in the development of drug resistance in ctf4Δ via their histone-binding function. Alleviated sensitivity to MMS of the double mutants was not associated with rescue of ctf4Δ defects in sister chromatid cohesion, replication fork architecture, or template switching, which ensures error-free replication in the presence of genotoxic stress. Strikingly, the improved viability depended on translesion synthesis (TLS) polymerase-mediated mutagenesis, which was drastically increased in ctf4 dpb3 double mutants. Importantly, mutations in Mcm2-Ctf4-Polα and Dpb3-Dpb4 axes of parental (H3-H4)2 deposition on lagging and leading strands invariably resulted in reduced error-free DNA damage tolerance through gap filling by template switch recombination. Overall, we uncovered a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.

Keywords:  DNA damage tolerance; Dpb3–Dpb4; Mcm2–Ctf4–Polα; histone deposition; mutagenesis; recombination; replication fork

DOI:  https://doi.org/10.1101/gad.349207.121
Nucleic Acids Res. 2022 Feb 01. pii: gkac044. [Epub ahead of print]

Eukaryotic stress-induced mutagenesis is limited by a local control of translesion synthesis.

Katarzyna H Masłowska, Florencia Villafañez, Luisa Laureti, Shigenori Iwai, Vincent Pagès.

The DNA damage response (DDR) preserves the genetic integrity of the cell by sensing and repairing damages after a genotoxic stress. Translesion Synthesis (TLS), an error-prone DNA damage tolerance pathway, is controlled by PCNA ubiquitination. In this work, we raise the question whether TLS is controlled locally or globally. Using a recently developed method that allows to follow the bypass of a single lesion inserted into the yeast genome, we show that (i) TLS is controlled locally at each individual lesion by PCNA ubiquitination, (ii) a single lesion is enough to induce PCNA ubiquitination and (iii) PCNA ubiquitination is imperative for TLS to occur. More importantly, we show that the activation of the DDR that follows a genotoxic stress does not increase TLS at individual lesions. We conclude that unlike the SOS response in bacteria, the eukaryotic DDR does not promote TLS and mutagenesis.

DOI: https://doi.org/10.1093/nar/gkac044
Front Cell Dev Biol. 2021 ;9 801200

Beyond PARP1: The Potential of Other Members of the Poly (ADP-Ribose) Polymerase Family in DNA Repair and Cancer Therapeutics.

Iain A Richard, Joshua T Burgess, Kenneth J O'Byrne, Emma Bolderson.

  The proteins within the Poly-ADP Ribose Polymerase (PARP) family encompass a diverse and integral set of cellular functions. PARP1 and PARP2 have been extensively studied for their roles in DNA repair and as targets for cancer therapeutics. Several PARP inhibitors (PARPi) have been approved for clinical use, however, while their efficacy is promising, tumours readily develop PARPi resistance. Many other members of the PARP protein family share catalytic domain homology with PARP1/2, however, these proteins are comparatively understudied, particularly in the context of DNA damage repair and tumourigenesis. This review explores the functions of PARP4,6-16 and discusses the current knowledge of the potential roles these proteins may play in DNA damage repair and as targets for cancer therapeutics.

Keywords:  DNA damage; DNA repair; PARP; cancer; genomic stability; tumourigenesis

DOI:  https://doi.org/10.3389/fcell.2021.801200
Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2109093119. [Epub ahead of print]119(6):

Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability.

Charlotte Hodson, Jason K K Low, Sylvie van Twest, Samuel E Jones, Paolo Swuec, Vincent Murphy, Kaima Tsukada, Matthew Fawkes, Rohan Bythell-Douglas, Adelina Davies, Jessica K Holien, Julienne J O'Rourke, Benjamin L Parker, Astrid Glaser, Michael W Parker, Joel P Mackay, Andrew N Blackford, Alessandro Costa, Andrew J Deans.

  The RecQ-like helicase BLM cooperates with topoisomerase IIIα, RMI1, and RMI2 in a heterotetrameric complex (the "Bloom syndrome complex") for dissolution of double Holliday junctions, key intermediates in homologous recombination. Mutations in any component of the Bloom syndrome complex can cause genome instability and a highly cancer-prone disorder called Bloom syndrome. Some heterozygous carriers are also predisposed to breast cancer. To understand how the activities of BLM helicase and topoisomerase IIIα are coupled, we purified the active four-subunit complex. Chemical cross-linking and mass spectrometry revealed a unique architecture that links the helicase and topoisomerase domains. Using biochemical experiments, we demonstrated dimerization mediated by the N terminus of BLM with a 2:2:2:2 stoichiometry within the Bloom syndrome complex. We identified mutations that independently abrogate dimerization or association of BLM with RMI1, and we show that both are dysfunctional for dissolution using in vitro assays and cause genome instability and synthetic lethal interactions with GEN1/MUS81 in cells. Truncated BLM can also inhibit the activity of full-length BLM in mixed dimers, suggesting a putative mechanism of dominant-negative action in carriers of BLM truncation alleles. Our results identify critical molecular determinants of Bloom syndrome complex assembly required for double Holliday junction dissolution and maintenance of genome stability.

Keywords:   helicase; Bloom’s complex; cross-link mass spectrometry; genome stability; topoisomerase

DOI:  https://doi.org/10.1073/pnas.2109093119
Nat Commun. 2022 Feb 03. 13(1): 654

The toposiomerase IIIalpha-RMI1-RMI2 complex orients human Bloom's syndrome helicase for efficient disruption of D-loops.

Gábor M Harami, János Pálinkás, Yeonee Seol, Zoltán J Kovács, Máté Gyimesi, Hajnalka Harami-Papp, Keir C Neuman, Mihály Kovács.

Homologous recombination (HR) is a ubiquitous and efficient process that serves the repair of severe forms of DNA damage and the generation of genetic diversity during meiosis. HR can proceed via multiple pathways with different outcomes that may aid or impair genome stability and faithful inheritance, underscoring the importance of HR quality control. Human Bloom's syndrome (BLM, RecQ family) helicase plays central roles in HR pathway selection and quality control via unexplored molecular mechanisms. Here we show that BLM's multi-domain structural architecture supports a balance between stabilization and disruption of displacement loops (D-loops), early HR intermediates that are key targets for HR regulation. We find that this balance is markedly shifted toward efficient D-loop disruption by the presence of BLM's interaction partners Topoisomerase IIIα-RMI1-RMI2, which have been shown to be involved in multiple steps of HR-based DNA repair. Our results point to a mechanism whereby BLM can differentially process D-loops and support HR control depending on cellular regulatory mechanisms.

DOI: https://doi.org/10.1038/s41467-022-28208-9
Trends Cancer. 2022 Jan 27. pii: S2405-8033(22)00003-6. [Epub ahead of print]

Diversity upon diversity: linking DNA double-strand break repair to blood cancer health disparities.

Jason N Sterrenberg, Melissa L Folkerts, Valeria Rangel, Sarah Eugenie Lee, Nicholas R Pannunzio.

  Chromosomal translocations arising from aberrant repair of multiple DNA double-strand breaks (DSBs) are a defining characteristic of many cancers. DSBs are an essential part of physiological processes in antibody-producing B cells. The B cell environment is poised to generate genome instability leading to translocations relevant to the pathology of blood cancers. These are a diverse set of cancers, but limited data from under-represented groups have pointed to health disparities associated with each. We focus on the DSBs that occur in developing B cells and propose the most likely mechanism behind the formation of translocations. We also highlight specific cancers in which these rearrangements occur and address the growing concern of health disparities associated with them.

Keywords:  B cells; DNA repair; V(D)J recombination; cancer health disparities; chromosomal translocations; non-homologous end joining

DOI:  https://doi.org/10.1016/j.trecan.2022.01.003
PLoS Negl Trop Dis. 2022 Feb 01. 16(2): e0009926

Characterization of adenine phosphoribosyltransferase (APRT) activity in Trypanosoma brucei brucei: Only one of the two isoforms is kinetically active.

Kayla Glockzin, Thomas D Meek, Ardala Katzfuss.

Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a Neglected Tropical Disease endemic to 36 African countries, with approximately 70 million people currently at risk for infection. Current therapeutics are suboptimal due to toxicity, adverse side effects, and emerging resistance. Thus, both effective and affordable treatments are urgently needed. The causative agent of HAT is the protozoan Trypanosoma brucei ssp. Annotation of its genome confirms previous observations that T. brucei is a purine auxotroph. Incapable of de novo purine synthesis, these protozoan parasites rely on purine phosphoribosyltransferases to salvage purines from their hosts for the synthesis of purine monophosphates. Complete and accurate genome annotations in combination with the identification and characterization of the catalytic activity of purine salvage enzymes enables the development of target-specific therapies in addition to providing a deeper understanding of purine metabolism in T. brucei. In trypanosomes, purine phosphoribosyltransferases represent promising drug targets due to their essential and central role in purine salvage. Enzymes involved in adenine and adenosine salvage, such as adenine phosphoribosyltransferases (APRTs, EC 2.4.2.7), are of particular interest for their potential role in the activation of adenine and adenosine-based pro-drugs. Analysis of the T. brucei genome shows two putative aprt genes: APRT1 (Tb927.7.1780) and APRT2 (Tb927.7.1790). Here we report studies of the catalytic activity of each putative APRT, revealing that of the two T. brucei putative APRTs, only APRT1 is kinetically active, thereby signifying a genomic misannotation of Tb927.7.1790 (putative APRT2). Reliable genome annotation is necessary to establish potential drug targets and identify enzymes involved in adenine and adenosine-based prodrug activation.

DOI: https://doi.org/10.1371/journal.pntd.0009926
Nucleic Acids Res. 2022 Jan 31. pii: gkac035. [Epub ahead of print]

Genomic patterns of transcription-replication interactions in mouse primary B cells.

Commodore P St Germain, Hongchang Zhao, Vrishti Sinha, Lionel A Sanz, Frédéric Chédin, Jacqueline H Barlow.

Conflicts between transcription and replication machinery are a potent source of replication stress and genome instability; however, no technique currently exists to identify endogenous genomic locations prone to transcription-replication interactions. Here, we report a novel method to identify genomic loci prone to transcription-replication interactions termed transcription-replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1009 unique transcription-replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. TRIs are highly enriched at transcription start sites and map to early replicating regions. TRIs exhibit enhanced Replication Protein A association and TRI-associated genes exhibit higher replication fork termination than control transcription start sites, two marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.

DOI: https://doi.org/10.1093/nar/gkac035
DNA Repair (Amst). 2022 Jan 24. pii: S1568-7864(22)00006-4. [Epub ahead of print]111 103277

Post-translational regulation of Tyrosyl-DNA phosphodiesterase (TDP1 and TDP2) for the repair of the trapped topoisomerase-DNA covalent complex.

Sangheeta Bhattacharjee, Ishita Rehman, Souvik Nandy, Benu Brata Das.

  DNA topoisomerases are essential enzymes that regulate DNA topology, the transmission of genetic materials, and gene expressions both in the nucleus and mitochondria. Trapped topoisomerases (Top1 and Top2) in covalent complexes with DNA (Topoisomerase cleavage complexes; Topcc) are detrimental DNA lesions that perturb active genome integrity and trigger cell death. Comprehensive research on the recently discovered enzymes TDP1 and TDP2 exemplify their spectacular role in repairing trapped Topcc as well as in a myriad of diverse DNA lesions. Posttranslational modifications (PTMs), play critical roles in regulating the optimal function of the DNA Damage Response (DDR) proteins. This review summarizes the mechanistic aspects of DNA damage induced by trapped Topcc during transcription and their role in human diseases. We have also highlighted the pivotal role of PTMs in fine-tuning the intricate and multilayered regulatory processes of TDP1 and TDP2 molecular networks for the repair of trapped Topcc.

Keywords:  Active genome; DNA repair; Neurological diseases; Post translational modification; TDP1; TDP2; Topoisomerase 1; Topoisomerase 2

DOI:  https://doi.org/10.1016/j.dnarep.2022.103277
Nucleosides Nucleotides Nucleic Acids. 2022 Jan 30. 1-19

Protein production, kinetic and biophysical characterization of three human dihydroorotate dehydrogenase mutants associated with Miller syndrome.

Juan Manuel Orozco Rodriguez, Ewa Krupinska, Hanna Wacklin-Knecht, Wolfgang Knecht.

  Miller syndrome is a rare Mendelian disorder caused by mutations in the gene encoding human dihydroorotate dehydrogenase (DHODH). Human DHODH, a Class II DHODH, is an integral protein of the inner mitochondrial membrane (IMM) catalyzing the fourth step of the de novo pyrimidine biosynthesis pathway. Here we present a summary of the state of knowledge regarding Miller syndrome in the absence of any current review on the topic. We then describe the production and characterization of three distinct DHODH missense mutations (G19E, E52G, R135C) associated with Miller syndrome by means of enzyme kinetics and biophysical techniques. These human DHODH mutants were produced both in E. coli and in insect cells using the baculovirus expression vector system. We can show that the effects of these mutations differ from each other and the wild-type enzyme with respect to decreased enzymatic activity, decreased protein stability and probably disturbance of the correct import into the IMM. In addition, our results show that the N-terminus of human DHODH is not only a structural element necessary for correct mitochondrial import and location of DHODH on the outer side of the IMM, but also influences thermal stability, enzymatic activity and affects the kinetic parameters.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.2023749 .

Keywords:  BEVS; Mendelian disorders; Pyrimidine biosynthesis; mitochondrial proteins; ubiquinone

DOI:  https://doi.org/10.1080/15257770.2021.2023749
Nat Cancer. 2021 Jun;2(6): 581-583

Polθ inhibitors unchained.

Thomas Helleday.

DOI: https://doi.org/10.1038/s43018-021-00225-5
Biol Pharm Bull. 2022 ;45(2): 200-206

Functional Domain Mapping of Werner Interacting Protein 1 (WRNIP1).

Akari Yoshimura, Tatsuya Sakakihara, Takemi Enomoto, Masayuki Seki.

  Werner helicase-interacting protein 1 (WRNIP1) belongs to the AAA+ ATPase family and is conserved from Escherichia coli to human. In addition to an ATPase domain in the middle region of WRNIP1, WRNIP1 contains a ubiquitin-binding zinc-finger (UBZ) domain and two leucine zipper motifs in the N-terminal and C-terminal regions, respectively. Here, we report that the UBZ domain of WRNIP1 is responsible for the reduced levels of UV-induced proliferating cell nuclear antigen (PCNA) monoubiquitylation in POLH-disrupted (polymerase η (Polη)-deficient) cells, and that the ATPase domain of WRNIP1 is involved in regulating the level of the PrimPol protein. The suppression of UV sensitivity of Polη-deficient cells by deletion of WRNIP1 was abolished by expression of the mutant WRNIP1 lacking the UBZ domain or ATPase domain, but not by the mutant lacking the leucine zipper domain in WRNIP1/POLH double-disrupted cells. The leucine zipper domain of WRNIP1 was required for its interaction with RAD18, a key factor in TLS (DNA translesion synthesis), and DNA polymerase δ catalytic subunit, POLD1. On the basis of these findings, we discuss the possible role of WRNIP1 in TLS.

Keywords:  Polδ; PrimPol; RAD18; Werner helicase–interacting protein 1 (WRNIP1); polymerase η (Polη); translesion synthesis (TLS)

DOI:  https://doi.org/10.1248/bpb.b21-00718
ACS Omega. 2022 Jan 25. 7(3): 2571-2582

Positive Feedback Regulation of Poly(ADP-ribose) Polymerase 1 and the DNA-PK Catalytic Subunit Affects the Sensitivity of Nasopharyngeal Carcinoma to Etoposide.

Lingyu Zhang, Yingting Zhuang, Guihui Tu, Ding Li, Yingjuan Fan, Shengnan Ye, Jianhua Xu, Ming Zheng, Ying Wu, Lixian Wu.

Etoposide (VP-16) is used for the treatment of various cancers, including nasopharyngeal carcinoma (NPC); however, cancers develop resistance to this agent by promoting DNA repair. The DNA-PK (DNA-PKcs) catalytic subunit and poly(ADP-ribose) polymerase 1 (PARP1) mediate acquired resistance and poor survival in NPC cells exposed to DNA damaging agents. DNA repair can alter the sensitivity of NPC cells to DNA damaging agents, and these two enzymes function concomitantly in response to DNA damage in vivo. Therefore, we explored the relationship between DNA-PKcs and PARP1, which may affect NPC cell survival by regulating DNA repair after VP-16 treatment. We performed quantitative real-time polymerase chain reaction, western blotting, and enzyme-linked immunoassays and found that DNA-PKcs knockdown downregulated the PARP1 and PAR expression. Conversely, PARP1 knockdown reduced DNA-PKcs activity, indicating the mutual regulation between DNA-PKcs and PARP1 in VP-16-induced DNA repair. Moreover, a combination treatment with olaparib (a PARP1 inhibitor) and NU7441 (a DNA-PKcs inhibitor) sensitized NPC cells to VP-16 in vitro and in vivo, suggesting that the combined treatment of olaparib, NU7441, and a DNA-damaging agent may be a successful treatment regimen in patients with NPC.

DOI: https://doi.org/10.1021/acsomega.1c04379
Nat Cancer. 2020 Aug;1(8): 758-760

Super-sonic speed of DNA synthesis in medulloblastoma.

Apolinar Maya-Mendoza, Jiri Bartek.

DOI: https://doi.org/10.1038/s43018-020-0105-8
Cell Death Dis. 2022 Feb 02. 13(2): 96

BMI1 nuclear location is critical for RAD51-dependent response to replication stress and drives chemoresistance in breast cancer stem cells.

Violette Azzoni, Julien Wicinski, Manon Macario, Martin Castagné, Pascal Finetti, Katerina Ambrosova, Célia D Rouault, Arnaud Sergé, Anne Farina, Emilie Agavnian, Sergiu Coslet, Emmanuelle Josselin, Arnaud Guille, José Adelaide, Emmanouil Zacharioudakis, Rémy Castellano, Francois Bertucci, Daniel Birnbaum, Raphael Rodriguez, Emmanuelle Charafe-Jauffret, Christophe Ginestier.

Replication stress (RS) has a pivotal role in tumor initiation, progression, or therapeutic resistance. In this study, we depicted the mechanism of breast cancer stem cells' (bCSCs) response to RS and its clinical implication. We demonstrated that bCSCs present a limited level of RS compared with non-bCSCs in patient samples. We described for the first time that the spatial nuclear location of BMI1 protein triggers RS response in breast cancers. Hence, in bCSCs, BMI1 is rapidly located to stalled replication forks to recruit RAD51 and activate homologous-recombination machinery, whereas in non-bCSCs BMI1 is trapped on demethylated 1q12 megasatellites precluding effective RS response. We further demonstrated that BMI1/RAD51 axis activation is necessary to prevent cisplatin-induced DNA damage and that treatment of patient-derived xenografts with a RAD51 inhibitor sensitizes tumor-initiating cells to cisplatin. The comprehensive view of replicative-stress response in bCSC has profound implications for understanding and improving therapeutic resistance.

DOI: https://doi.org/10.1038/s41419-022-04538-w
Nat Cancer. 2021 Nov;2(11): 1204-1223

Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia.

Claudie Bosc, Estelle Saland, Aurélie Bousard, Noémie Gadaud, Marie Sabatier, Guillaume Cognet, Thomas Farge, Emeline Boet, Mathilde Gotanègre, Nesrine Aroua, Pierre-Luc Mouchel, Nathaniel Polley, Clément Larrue, Eléonore Kaphan, Muriel Picard, Ambrine Sahal, Latifa Jarrou, Marie Tosolini, Florian Rambow, Florence Cabon, Nathalie Nicot, Laura Poillet-Perez, Yujue Wang, Xiaoyang Su, Quentin Fovez, Jérôme Kluza, Rafael José Argüello, Céline Mazzotti, Hervé Avet-Loiseau, François Vergez, Jérôme Tamburini, Jean-Jacques Fournié, Ing S Tiong, Andrew H Wei, Tony Kaoma, Jean-Christophe Marine, Christian Récher, Lucille Stuani, Carine Joffre, Jean-Emmanuel Sarry.

Therapy resistance represents a major clinical challenge in acute myeloid leukemia (AML). Here we define a 'MitoScore' signature, which identifies high mitochondrial oxidative phosphorylation in vivo and in patients with AML. Primary AML cells with cytarabine (AraC) resistance and a high MitoScore relied on mitochondrial Bcl2 and were highly sensitive to venetoclax (VEN) + AraC (but not to VEN + azacytidine). Single-cell transcriptomics of VEN + AraC-residual cell populations revealed adaptive resistance associated with changes in oxidative phosphorylation, electron transport chain complex and the TP53 pathway. Accordingly, treatment of VEN + AraC-resistant AML cells with electron transport chain complex inhibitors, pyruvate dehydrogenase inhibitors or mitochondrial ClpP protease agonists substantially delayed relapse following VEN + AraC. These findings highlight the central role of mitochondrial adaptation during AML therapy and provide a scientific rationale for alternating VEN + azacytidine with VEN + AraC in patients with a high MitoScore and to target mitochondrial metabolism to enhance the sensitivity of AML cells to currently approved therapies.

DOI: https://doi.org/10.1038/s43018-021-00264-y
Nat Cancer. 2020 Sep;1(9): 862-863

ASS1igning purine dependency to cancer.

Elodie Villa, Issam Ben-Sahra.

DOI: https://doi.org/10.1038/s43018-020-00117-0
Nat Cancer. 2021 Dec;2(12): 1338-1356

APOBEC3A drives deaminase domain-independent chromosomal instability to promote pancreatic cancer metastasis.

Sonja M Wörmann, Amy Zhang, Fredrik I Thege, Robert W Cowan, Dhwani N Rupani, Runsheng Wang, Sara L Manning, Chris Gates, Weisheng Wu, Rena Levin-Klein, Kimal I Rajapakshe, Meifang Yu, Asha S Multani, Ya'an Kang, Cullen M Taniguchi, Katharina Schlacher, Melena D Bellin, Matthew H G Katz, Michael P Kim, Jason B Fleming, Steven Gallinger, Ravikanth Maddipati, Reuben S Harris, Faiyaz Notta, Susan R Ross, Anirban Maitra, Andrew D Rhim.

Despite efforts in understanding its underlying mechanisms, the etiology of chromosomal instability (CIN) remains unclear for many tumor types. Here, we identify CIN initiation as a previously undescribed function for APOBEC3A (A3A), a cytidine deaminase upregulated across cancer types. Using genetic mouse models of pancreatic ductal adenocarcinoma (PDA) and genomics analyses in human tumor cells we show that A3A-induced CIN leads to aggressive tumors characterized by enhanced early dissemination and metastasis in a STING-dependent manner and independently of the canonical deaminase functions of A3A. We show that A3A upregulation recapitulates numerous copy number alterations commonly observed in patients with PDA, including co-deletions in DNA repair pathway genes, which in turn render these tumors susceptible to poly (ADP-ribose) polymerase inhibition. Overall, our results demonstrate that A3A plays an unexpected role in PDA as a specific driver of CIN, with significant effects on disease progression and treatment.

DOI: https://doi.org/10.1038/s43018-021-00268-8
DNA Repair (Amst). 2022 Jan 22. pii: S1568-7864(22)00005-2. [Epub ahead of print]111 103276

Paradoxical role of the major DNA repair protein, OGG1, in action-at-a-distance mutation induction by 8-oxo-7,8-dihydroguanine.

Tetsuya Suzuki, Yudai Zaima, Yoshihiro Fujikawa, Ruriko Fukushima, Hiroyuki Kamiya.

  Oxidatively damaged bases induce mutations and are involved in cancer initiation. 8-Oxo-7,8-dihydroguanine (G°, 8-hydroxyguanine) is an abundant oxidized base that induces targeted G:C→T:A transversions in human cells, as well as untargeted base substitution (action-at-a-distance) mutations of the G bases of 5'-GpA-3' dinucleotides. The action-at-a-distance mutations become more frequent than the targeted transversions when the amount of Werner syndrome (WRN) protein is decreased. In this study, OGG1, the major DNA glycosylase for the damaged base, and WRN were knocked down in isolation and in combination in human U2OS cells, and a shuttle plasmid carrying G° was introduced into the knockdown cells. Interestingly, fewer action-at-a-distance mutations were observed in the WRN plus OGG1 double knockdown cells, as compared to the WRN single knockdown cells. These results indicated the paradoxical role of OGG1, as an accelerator of the action-at-a-distance mutations by the oxidized guanine base.

Keywords:  8-Hydroxyguanine; 8-Oxo-7,8-dihydroguanine; APOBEC3; Action-at-a-distance mutation; OGG1; Werner syndrome protein

DOI:  https://doi.org/10.1016/j.dnarep.2022.103276
Mol Cell. 2022 Jan 27. pii: S1097-2765(22)00001-6. [Epub ahead of print]

SPARCLE, a p53-induced lncRNA, controls apoptosis after genotoxic stress by promoting PARP-1 cleavage.

Karla F Meza-Sosa, Rui Miao, Francisco Navarro, Zhibin Zhang, Ying Zhang, Jun Jacob Hu, Corrine Corrina R Hartford, Xiao Ling Li, Gustavo Pedraza-Alva, Leonor Pérez-Martínez, Ashish Lal, Hao Wu, Judy Lieberman.

  p53, master transcriptional regulator of the genotoxic stress response, controls cell-cycle arrest and apoptosis following DNA damage. Here, we identify a p53-induced lncRNA suicidal PARP-1 cleavage enhancer (SPARCLE) adjacent to miR-34b/c required for p53-mediated apoptosis. SPARCLE is a ∼770-nt, nuclear lncRNA induced 1 day after DNA damage. Despite low expression (<16 copies/cell), SPARCLE deletion increases DNA repair and reduces DNA-damage-induced apoptosis as much as p53 deficiency, while its overexpression restores apoptosis in p53-deficient cells. SPARCLE does not alter gene expression. SPARCLE binds to PARP-1 with nanomolar affinity and causes apoptosis by acting as a caspase-3 cofactor for PARP-1 cleavage, which separates PARP-1's N-terminal (NT) DNA-binding domain from its catalytic domains. NT-PARP-1 inhibits DNA repair. Expressing NT-PARP-1 in SPARCLE-deficient cells increases unrepaired DNA damage and restores apoptosis after DNA damage. Thus, SPARCLE enhances p53-induced apoptosis by promoting PARP-1 cleavage, which interferes with DNA-damage repair.

Keywords:  PARP-1; apoptosis; genotoxic stress; lncRNA; miR-34; p53

DOI:  https://doi.org/10.1016/j.molcel.2022.01.001
Anticancer Res. 2022 Feb;42(2): 837-844

Effect of Thymidine Phosphorylase Gene Demethylation on Sensitivity to 5-Fluorouracil in Colorectal Cancer Cells.

Muneyuki Koyama, Erika Osada, Nubutake Akiyama, Ken Eto, Yoshinobu Manome.

  BACKGROUND/AIM: Chemotherapy is used for recurrent and metastatic colorectal cancer, but the response rate of 5-fluorouracil (5-FU), the standard treatment for colorectal cancer, is low. We hypothesized that thymidine phosphorylase (TYMP) expression, a rate-limiting activating enzyme of 5-FU, is regulated by methylation of the gene promoter region, and demethylation of TYMP would increase sensitivity to 5-FU.MATERIALS AND METHODS: HCT116 colon cancer cells were treated with 5-aza-2'-deoxycytidine, a demethylating agent, and changes in TYMP transcription and sensitivity to 5-FU were evaluated.
RESULTS: TYMP expression increased over 54-fold in HCT116 transfected with TYMP. The cytotoxicity of 5-FU increased up to 5.5-fold. In comparison, in HCT116 treated with 5-aza-2'-deoxycytidine, TYMP expression increased 5.8-fold. However, the cytotoxicity of 5-FU remained unchanged.
CONCLUSION: Demethylating agent alone did not promote the cytotoxicity of 5-FU against colorectal cancer. To further increase the sensitivity to 5-FU, combination with adjuvant therapy focusing on metabolic pathways other than the TYMP pathway appear necessary.

Keywords:  5-fluorouracil; Colorectal cancer; inhibitor of methylation; thymidine phosphorylase

DOI:  https://doi.org/10.21873/anticanres.15541
Nat Cancer. 2020 Jul;1(7): 735-747

Aldolase B suppresses hepatocellular carcinogenesis by inhibiting G6PD and pentose phosphate pathways.

Min Li, Xuxiao He, Weixing Guo, Hongming Yu, Shicheng Zhang, Ningning Wang, Guijun Liu, Rina Sa, Xia Shen, Yabo Jiang, Yufu Tang, Yujuan Zhuo, Chunzhao Yin, Qiaochu Tu, Nan Li, Xiaoqun Nie, Yu Li, Zhimin Hu, Hanwen Zhu, Jianping Ding, Zi Li, Te Liu, Fan Zhang, He Zhou, Shengxian Li, Jiang Yue, Zheng Yan, Shuqun Cheng, Yongzhen Tao, Huiyong Yin.

Metabolic reprogramming is a core hallmark of cancer but it remains poorly defined in hepatocellular carcinogenesis (HCC). Here we show that hepatic aldolase B (Aldob) suppresses HCC by directly binding and inhibiting the rate-limiting enzyme in the pentose phosphate pathway, glucose-6-phosphate dehydrogenase (G6PD). A stage-dependent decrease of Aldob and increase of G6PD in human tumors are correlated with poor prognosis for patients with HCC. Global or liver-specific Aldob knockout promotes tumorigenesis in mice through enhancing G6PD activity and pentose phosphate pathway metabolism, whereas pharmacological inhibition or genetic knockdown of G6PD suppresses HCC. Consistently, restoration of Aldob in Aldob knockout mice attenuates tumorigenesis. We further demonstrate that Aldob potentiates p53-mediated inhibition of G6PD in an Aldob-G6PD-p53 complex. This scaffolding effect is independent of Aldob enzymatic activity. Together, our study reveals a new mode of metabolic reprogramming in HCC due to the loss of Aldob, suggesting a potential therapeutic strategy for HCC treatment.

DOI: https://doi.org/10.1038/s43018-020-0086-7
Cell Discov. 2022 Feb 01. 8(1): 6

Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor.

Zunpeng Liu, Wei Li, Lingling Geng, Liang Sun, Qiaoran Wang, Yang Yu, Pengze Yan, Chuqian Liang, Jie Ren, Moshi Song, Qian Zhao, Jinghui Lei, Yusheng Cai, Jiaming Li, Kaowen Yan, Zeming Wu, Qun Chu, Jingyi Li, Si Wang, Chunyi Li, Jing-Dong J Han, Reyna Hernandez-Benitez, Ng Shyh-Chang, Juan Carlos Izpisua Belmonte, Weiqi Zhang, Jing Qu, Guang-Hui Liu.

Regenerative capacity declines throughout evolution and with age. In this study, we asked whether metabolic programs underlying regenerative capability might be conserved across species, and if so, whether such metabolic drivers might be harnessed to promote tissue repair. To this end, we conducted metabolomic analyses in two vertebrate organ regeneration models: the axolotl limb blastema and antler stem cells. To further reveal why young individuals have higher regenerative capacity than the elderly, we also constructed metabolic profiles for primate juvenile and aged tissues, as well as young and aged human stem cells. In joint analyses, we uncovered that active pyrimidine metabolism and fatty acid metabolism correlated with higher regenerative capacity. Furthermore, we identified a set of regeneration-related metabolite effectors conserved across species. One such metabolite is uridine, a pyrimidine nucleoside, which can rejuvenate aged human stem cells and promote regeneration of various tissues in vivo. These observations will open new avenues for metabolic intervention in tissue repair and regeneration.

DOI: https://doi.org/10.1038/s41421-021-00361-3