bims-numges Biomed News
on Nucleotide metabolism and genome stability
Issue of 2022‒01‒09
eighteen papers selected by
Sean Rudd
Karolinska Institutet
  1. Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs.
  2. DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol.
  3. A purine metabolic checkpoint that prevents autoimmunity and autoinflammation.
  4. Targeting DNA repair pathway in cancer: Mechanisms and clinical application.
  5. Proline-serine-threonine-repeat region of MDC1 mediates Chk1 phosphorylation and the DNA double-strand break repair.
  6. The Rad5 helicase and RING domains contribute to genome stability through their independent catalytic activities.
  7. The roles of RNA helicases in DNA damage repair and tumorigenesis reveal precision therapeutic strategies.
  8. DNA Damage and Repair Deficiency in ALS/FTD-Associated Neurodegeneration: From Molecular Mechanisms to Therapeutic Implication.
  9. Perspectives on PARP Inhibitor Combinations for Ovarian Cancer.
  10. RRM2 expression in different molecular subtypes of breast cancer and its prognostic significance.
  11. Nek4 regulates mitochondrial respiration and morphology.
  12. High expression of uracil DNA glycosylase determines C to T substitution in human pluripotent stem cells.
  13. AMPK-PERK axis represses oxidative metabolism and enhances apoptotic priming of mitochondria in acute myeloid leukemia.
  14. Landscape of homologous recombination deficiencies in solid tumours: analyses of two independent genomic datasets.
  15. Repurposing the Damage Repair Protein Methyl Guanine Methyl Transferase as a Ligand Inducible Fusion Degron.
  16. Pharmacological CDK4/6 inhibition reveals a p53-dependent senescent state with restricted toxicity.
  17. RB1 loss in castration-resistant prostate cancer confers vulnerability to LSD1 inhibition.
  18. SAMHD1 Mutations and Expression in Mantle Cell Lymphoma Patients.
  1. Nature. 2022 Jan 05.
    Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs.
    Shikang Liang, Sherine E Thomas, Amanda K Chaplin, Steven W Hardwick, Dimitri Y Chirgadze, Tom L Blundell.
      The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) has a central role in non-homologous end joining, one of the two main pathways that detect and repair DNA double-strand breaks (DSBs) in humans1,2. DNA-PKcs is of great importance in repairing pathological DSBs, making DNA-PKcs inhibitors attractive therapeutic agents for cancer in combination with DSB-inducing radiotherapy and chemotherapy3. Many of the selective inhibitors of DNA-PKcs that have been developed exhibit potential as treatment for various cancers4. Here we report cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs natively purified from HeLa cell nuclear extracts, in complex with adenosine-5'-(γ-thio)-triphosphate (ATPγS) and four inhibitors (wortmannin, NU7441, AZD7648 and M3814), including drug candidates undergoing clinical trials. The structures reveal molecular details of ATP binding at the active site before catalysis and provide insights into the modes of action and specificities of the competitive inhibitors. Of note, binding of the ligands causes movement of the PIKK regulatory domain (PRD), revealing a connection between the p-loop and PRD conformations. Electrophoretic mobility shift assay and cryo-EM studies on the DNA-dependent protein kinase holoenzyme further show that ligand binding does not have a negative allosteric or inhibitory effect on assembly of the holoenzyme complex and that inhibitors function through direct competition with ATP. Overall, the structures described in this study should greatly assist future efforts in rational drug design targeting DNA-PKcs, demonstrating the potential of cryo-EM in structure-guided drug development for large and challenging targets.
    DOI:  https://doi.org/10.1038/s41586-021-04274-9
  2. J Am Chem Soc. 2022 Jan 03.
    DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol.
    Feng Tang, Jun Yuan, Bi-Feng Yuan, Yinsheng Wang.
      Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesions in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2'-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol, and its subsequent deamination also yields Tg. However, Tg's distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach capitalizes on the specificity of a bifunctional DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in the human genome, where dual ablation of NTHL1 and NEIL1, the major DNA glycosylases responsible for Tg repair, led to pronounced increases in the number of Tg peaks. In addition, Tg is depleted in genomic regions associated with active transcription but enriched at nucleosome-binding sites, especially at heterochromatin sites marked with H3K9me2. Collectively, we developed a DPC-Seq method for highly efficient enrichment of Tg-containing DNA and for genome-wide mapping of Tg in human cells. Our work offers a robust tool for future functional studies of Tg in DNA, and we envision that the method can also be adapted for mapping other modified nucleosides in genomic DNA in the future.
    DOI:  https://doi.org/10.1021/jacs.1c10490
  3. Cell Metab. 2022 Jan 04. pii: S1550-4131(21)00628-8. [Epub ahead of print]34(1): 106-124.e10
    A purine metabolic checkpoint that prevents autoimmunity and autoinflammation.
    Svetlana Saveljeva, Gavin W Sewell, Katharina Ramshorn, M Zaeem Cader, James A West, Simon Clare, Lea-Maxie Haag, Rodrigo Pereira de Almeida Rodrigues, Lukas W Unger, Ana Belén Iglesias-Romero, Lorraine M Holland, Christophe Bourges, Muhammad N Md-Ibrahim, James O Jones, Richard S Blumberg, James C Lee, Nicole C Kaneider, Trevor D Lawley, Allan Bradley, Gordon Dougan, Arthur Kaser.
      Still's disease, the paradigm of autoinflammation-cum-autoimmunity, predisposes for a cytokine storm with excessive T lymphocyte activation upon viral infection. Loss of function of the purine nucleoside enzyme FAMIN is the sole known cause for monogenic Still's disease. Here we discovered that a FAMIN-enabled purine metabolon in dendritic cells (DCs) restrains CD4+ and CD8+ T cell priming. DCs with absent FAMIN activity prime for enhanced antigen-specific cytotoxicity, IFNγ secretion, and T cell expansion, resulting in excessive influenza A virus-specific responses. Enhanced priming is already manifest with hypomorphic FAMIN-I254V, for which ∼6% of mankind is homozygous. FAMIN controls membrane trafficking and restrains antigen presentation in an NADH/NAD+-dependent manner by balancing flux through adenine-guanine nucleotide interconversion cycles. FAMIN additionally converts hypoxanthine into inosine, which DCs release to dampen T cell activation. Compromised FAMIN consequently enhances immunosurveillance of syngeneic tumors. FAMIN is a biochemical checkpoint that protects against excessive antiviral T cell responses, autoimmunity, and autoinflammation.
    Keywords:  NADH/NAD(+) reductive stress; T cell priming; autoimmunity; dendritic cells; membrane trafficking; purine nucleotide cycle
    DOI:  https://doi.org/10.1016/j.cmet.2021.12.009
  4. MedComm (2020). 2021 Dec;2(4): 654-691
    Targeting DNA repair pathway in cancer: Mechanisms and clinical application.
    Manni Wang, Siyuan Chen, Danyi Ao.
      Over the last decades, the growing understanding on DNA damage response (DDR) pathways has broadened the therapeutic landscape in oncology. It is becoming increasingly clear that the genomic instability of cells resulted from deficient DNA damage response contributes to the occurrence of cancer. One the other hand, these defects could also be exploited as a therapeutic opportunity, which is preferentially more deleterious in tumor cells than in normal cells. An expanding repertoire of DDR-targeting agents has rapidly expanded to inhibitors of multiple members involved in DDR pathways, including PARP, ATM, ATR, CHK1, WEE1, and DNA-PK. In this review, we sought to summarize the complex network of DNA repair machinery in cancer cells and discuss the underlying mechanism for the application of DDR inhibitors in cancer. With the past preclinical evidence and ongoing clinical trials, we also provide an overview of the history and current landscape of DDR inhibitors in cancer treatment, with special focus on the combination of DDR-targeted therapies with other cancer treatment strategies.
    Keywords:  DNA damage response; PARP; cancer; combination therapy
    DOI:  https://doi.org/10.1002/mco2.103
  5. Int J Biochem Cell Biol. 2021 Dec 30. pii: S1357-2725(21)00233-8. [Epub ahead of print] 106152
    Proline-serine-threonine-repeat region of MDC1 mediates Chk1 phosphorylation and the DNA double-strand break repair.
    Seung Ho Choi, Kyoungjoo Cho, Eun Seon Kim, Hae Yong Yoo.
      MDC1, a mediator of DNA damage response, recruits other repair proteins on double-strand break (DSB) sites. MDC1 is necessary for activating checkpoint kinases Chk1 and Chk2. It is unclear whether Chk1 interacts with MDC1. MDC1 also comprises many discrete domains. The role of the proline-serine-threonine (PST)-repeat domain of MDC1 in the DNA damage response is unclear. Here, we showed that MDC1 directly binds Chk1 through this PST-repeat region. Phosphorylation of Chk1 by ionizing radiation (IR) also required this PST-repeat domain. Degradation of intact MDC1 was accelerated depending on the PST-repeat domain after IR exposure. In the IR damage response, the PST-repeat-deleted MDC1 levels remained elevated with slow degradation. This abnormal regulation of MDC1 was F-box- and WD40 repeat-containing 7 (FBXW7)-dependent. The mutation of lysine 1413 within the PST-repeat of MDC1 deregulated MDC1 with or without damage. K1413R mutant and PST-deleted MDC1 displayed reduced ability to repair the damaged genome post-IR exposure. These results provide that the PST domain of MDC1 is involved in Chk1 and DNA repair activation. The findings suggest new insights into how MDC1 connects the checkpoint and DNA repair in the DNA damage response.
    Keywords:  Chk1; DNA repair; FBXW7; MDC1; PST-repeat
    DOI:  https://doi.org/10.1016/j.biocel.2021.106152
  6. J Mol Biol. 2022 Jan 03. pii: S0022-2836(21)00679-3. [Epub ahead of print] 167437
    The Rad5 helicase and RING domains contribute to genome stability through their independent catalytic activities.
    Robert Toth, David Balogh, Lajos Pinter, Gabor Jaksa, Bence Szeplaki, Alexandra Graf, Zsuzsanna Gyorfy, Marton Zs Enyedi, Erno Kiss, Lajos Haracska, Ildiko Unk.
      Genomic stability is compromised by DNA damage that obstructs replication. Rad5 plays a prominent role in DNA damage bypass processes that evolved to ensure the continuation of stalled replication. Like its human orthologs, the HLTF and SHPRH tumor suppressors, yeast Rad5 has a RING domain that supports ubiquitin ligase activity promoting PCNA polyubiquitylation and a helicase domain that in the case of HLTF and Rad5 was shown to exhibit an ATPase-linked replication fork reversal activity. The RING domain is embedded in the helicase domain, confusing their separate investigation and the understanding of the exact role of Rad5 in DNA damage bypass. Particularly, it is still debated whether the helicase domain plays a catalytic or a non-enzymatic role during error-free damage bypass and whether it facilitates a function separately from the RING domain. In this study, through in vivo and in vitro characterization of domain-specific mutants, we delineate the contributions of the two domains to Rad5 function. Yeast genetic experiments and whole-genome sequencing complemented with biochemical assays demonstrate that the ubiquitin ligase and the ATPase-linked activities of Rad5 exhibit independent catalytic activities in facilitating separate pathways during error-free lesion bypass. Our results also provide important insights into the mutagenic role of Rad5 and indicate its tripartite contribution to DNA damage tolerance.
    Keywords:  DNA damage tolerance; Rad5; enzyme assay; mutagenesis; yeast genetics
    DOI:  https://doi.org/10.1016/j.jmb.2021.167437
  7. Cancer Res. 2022 Jan 05. pii: canres.2187.2021. [Epub ahead of print]
    The roles of RNA helicases in DNA damage repair and tumorigenesis reveal precision therapeutic strategies.
    Jinru Xie, Ming Wen, Jiao Zhang, Zheng Wang, Meng Wang, Yanfang Qiu, Wenchao Zhao, Fang Zhu, Mianfeng Yao, Zhuo-Xian Rong, Wenfeng Hu, Qian Pei, Xiaoxiang Sun, Jinchen Li, Zhiyong Mao, Lunquan Sun, Rong Tan.
      DEAD-box RNA helicases belong to a large group of RNA processing factors and play vital roles unwinding RNA helices and in ribosomal RNA biogenesis. Emerging evidence indicates that RNA helicases are associated with genome stability, yet the mechanisms behind this association remain poorly understood. In this study, we performed a comprehensive analysis of RNA helicases using multiplatform proteogenomic databases. Over 50% (28/49) of detected RNA helicases were highly expressed in multiple tumor tissues, and more than 60% (17/28) of tumor-associated members were directly involved in DNA damage repair (DDR). Analysis of repair dynamics revealed that these RNA helicases are engaged in an extensively broad range of DDR pathways. Among these factors is DDX21, which was prominently upregulated in colorectal cancer. The high expression of DDX21 gave rise to frequent chromosome exchange and increased genome fragmentation. Mechanistically, aberrantly high expression of DDX21 triggered inappropriate repair processes by delaying homologous recombination repair and increasing replication stress, leading to genome instability and tumorigenesis. Treatment with distinct chemotherapeutic drugs caused higher lethality to cancer cells with genome fragility induced by DDX21, providing a perspective for treatment of tumors with high DDX21 expression. This study revealed the role of RNA helicases in DNA damage and their associations with cancer, which could expand therapeutic strategies and improve precision treatments for cancer patients with high expression of RNA helicases.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2187
  8. Front Mol Neurosci. 2021 ;14 784361
    DNA Damage and Repair Deficiency in ALS/FTD-Associated Neurodegeneration: From Molecular Mechanisms to Therapeutic Implication.
    Haibo Wang, Manohar Kodavati, Gavin W Britz, Muralidhar L Hegde.
      Emerging studies reveal that neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), are commonly linked to DNA damage accumulation and repair deficiency. Neurons are particularly vulnerable to DNA damage due to their high metabolic activity, relying primarily on oxidative phosphorylation, which leads to increased reactive oxygen species (ROS) generation and subsequent DNA damage. Efficient and timely repair of such damage is critical for guarding the integrity of genomic DNA and for cell survival. Several genes predominantly associated with RNA/DNA metabolism have been implicated in both ALS and FTD, suggesting that the two diseases share a common underlying pathology with varied clinical manifestations. Recent studies reveal that many of the gene products, including RNA/DNA binding proteins (RBPs) TDP-43 and FUS are involved in diverse DNA repair pathways. A key question in the etiology of the ALS/FTD spectrum of neurodegeneration is the mechanisms and pathways involved in genome instability caused by dysfunctions/mutations of those RBP genes and their consequences in the central nervous system. The understanding of such converging molecular mechanisms provides insights into the underlying etiology of the rapidly progressing neurodegeneration in ALS/FTD, while also revealing novel DNA repair target avenues for therapeutic development. In this review, we summarize the common mechanisms of neurodegeneration in ALS and FTD, with a particular emphasis on the DNA repair defects induced by ALS/FTD causative genes. We also highlight the consequences of DNA repair defects in ALS/FTD and the therapeutic potential of DNA damage repair-targeted amelioration of neurodegeneration.
    Keywords:  DNA damage; DNA repair deficiency; FUS; amyotrophic lateral sclerosis; frontotemporal dementia
    DOI:  https://doi.org/10.3389/fnmol.2021.784361
  9. Front Oncol. 2021 ;11 754524
    Perspectives on PARP Inhibitor Combinations for Ovarian Cancer.
    Renata Colombo Bonadio, Maria Del Pilar Estevez-Diz.
      Poly (ADP-ribose) polymerase (PARP) inhibitors constitute an important treatment option for ovarian cancer nowadays. The magnitude of benefit from PARP inhibitors is influenced by the homologous recombination status, with greater benefit observed in patients with BRCA mutated or BRCA wild-type homologous recombination deficient (HRD) tumors. Although some PARP inhibitor activity has been shown in homologous recombination proficient (HRP) ovarian tumors, its clinical relevance as a single agent is unsatisfactory in this population. Furthermore, even HRD tumors present primary or secondary resistance to PARP inhibitors. Strategies to overcome treatment resistance, as well as to enhance PARP inhibitors' efficacy in HRP tumors, are highly warranted. Diverse combinations are being studied with this aim, including combinations with antiangiogenics, immunotherapy, and other targeted therapies. This review discusses the rationale for developing therapy combinations with PARP inhibitors, the current knowledge, and the future perspectives on this issue.
    Keywords:  DNA repair; PARP inhibitor; combinations; homologous recombination; ovarian cancer
    DOI:  https://doi.org/10.3389/fonc.2021.754524
  10. Diagn Pathol. 2022 Jan 05. 17(1): 1
    RRM2 expression in different molecular subtypes of breast cancer and its prognostic significance.
    Manar Ahmed Abdel-Rahman, Mena Mahfouz, Hany Onsy Habashy.
      BACKGROUND: Breast cancer is one of the most common types of cancer. Ribonucleotide reductase (RNR) is a heterodimeric tetramer consisting of two Ribonucleoside-diphosphate reductase large subunits (RRM1) and two Ribonucleoside-diphosphate reductase small subunits (RRM2). RRM2 is the building subunit of RNR that is important for synthesis of Deoxynucleoside triphosphate (dNTP) during S phase of cell cycle during DNA replication. RRM2 is associated with poor prognosis in lung and colorectal cancer. In breast cancer, increased RRM2 protein level is strongly correlated with large tumour size, positive lymph node and relapse. In this study, we aimed to study expression of RRM2 in breast cancer and to correlate it with different clinicopathological parameters in Egyptian women.MATERIAL AND METHODS: This study was performed by investigating RRM2 protein expression in breast cancer and correlating the results with other clinicopathological variables using immunohistochemistry and tissue microarrays.
    RESULTS: About 77% of cases were RRM2 positive. High Ki67 was observed in cases with high RRM2 score. The majority of non-luminal cases expressed RRM2, however this was statistically insignificant. In ER positive group, RRM2 expression was associated with shorter disease free survival with borderline significance.
    CONCLUSION: RRM2 protein expression can help in evaluating outcome of breast cancer patients and could be a potential therapeutic target.
    Keywords:  Breast cancer; Expression; Prognosis; RRM2
    DOI:  https://doi.org/10.1186/s13000-021-01174-4
  11. FEBS J. 2022 Jan 05.
    Nek4 regulates mitochondrial respiration and morphology.
    Fernanda Luisa Basei, Camila de Castro Ferezin, Ana Luisa Rodrigues de Oliveira, Juan Pablo Muñoz, Antonio Zorzano, Jörg Kobarg.
      Nek4 is a serine/threonine kinase which has been implicated in primary cilia stabilization, DNA damage response, autophagy and epithelial-to-mesenchymal transition. The role of Nek4 in cancer cell survival and chemotherapy resistance has also been shown. However, the precise mechanisms by which Nek4 operates remain to be elucidated. Here, we show that Nek4 overexpression activates mitochondrial respiration coupled to ATP production, which is paralleled by increased mitochondrial membrane potential, and resistance to mitochondrial DNA damage. Congruently, Nek4 depletion reduced mitochondrial respiration and mtDNA integrity. Nek4 deficiency caused mitochondrial elongation, probably via reduced activity of the fission protein DRP1. In Nek4 overexpressing cells the increase in mitochondrial fission was concomitant to enhanced phosphorylation of DRP1 and Erk1/2 proteins, and the effects on mitochondrial respiration were abolished in the presence of a DRP1 inhibitor. This study shows Nek4 as a novel regulator of mitochondrial function that may explain the joint appearance of high mitochondrial respiration and mitochondrial fragmentation.
    Keywords:  DRP1; Nek4; fission; mitochondrial function
    DOI:  https://doi.org/10.1111/febs.16343
  12. Mol Ther Nucleic Acids. 2022 Mar 08. 27 175-183
    High expression of uracil DNA glycosylase determines C to T substitution in human pluripotent stem cells.
    Ju-Chan Park, Hyeon-Ki Jang, Jumee Kim, Jun Hee Han, Youngri Jung, Keuntae Kim, Sangsu Bae, Hyuk-Jin Cha.
      Precise genome editing of human pluripotent stem cells (hPSCs) is crucial not only for basic science but also for biomedical applications such as ex vivo stem cell therapy and genetic disease modeling. However, hPSCs have unique cellular properties compared to somatic cells. For instance, hPSCs are extremely susceptible to DNA damage, and therefore Cas9-mediated DNA double-strand breaks (DSB) induce p53-dependent cell death, resulting in low Cas9 editing efficiency. Unlike Cas9 nucleases, base editors including cytosine base editor (CBE) and adenine base editor (ABE) can efficiently substitute single nucleotides without generating DSBs at target sites. Here, we found that the editing efficiency of CBE was significantly lower than that of ABE in human embryonic stem cells (hESCs), which are associated with high expression of DNA glycosylases, the key component of the base excision repair pathway. Sequential depletion of DNA glycosylases revealed that high expression of uracil DNA glycosylase (UNG) not only resulted in low editing efficiency but also affected CBE product purity (i.e., C to T) in hESCs. Therefore, additional suppression of UNG via transient knockdown would also improve C to T base substitutions in hESCs. These data suggest that the unique cellular characteristics of hPSCs could determine the efficiency of precise genome editing.
    Keywords:  ABE; BER; Base editors; CBE; Diseaes model; UGI; UNG; human embryonic stem cells; human pluripotent stem cells
    DOI:  https://doi.org/10.1016/j.omtn.2021.11.023
  13. Cell Rep. 2022 Jan 04. pii: S2211-1247(21)01701-0. [Epub ahead of print]38(1): 110197
    AMPK-PERK axis represses oxidative metabolism and enhances apoptotic priming of mitochondria in acute myeloid leukemia.
    Adrien Grenier, Laury Poulain, Johanna Mondesir, Arnaud Jacquel, Claudie Bosc, Lucille Stuani, Sarah Mouche, Clement Larrue, Ambrine Sahal, Rudy Birsen, Victoria Ghesquier, Justine Decroocq, Fetta Mazed, Mireille Lambert, Mamy Andrianteranagna, Benoit Viollet, Patrick Auberger, Andrew A Lane, Pierre Sujobert, Didier Bouscary, Jean-Emmanuel Sarry, Jerome Tamburini.
      AMP-activated protein kinase (AMPK) regulates the balance between cellular anabolism and catabolism dependent on energy resources to maintain proliferation and survival. Small-compound AMPK activators show anti-cancer activity in preclinical models. Using the direct AMPK activator GSK621, we show that the unfolded protein response (UPR) is activated by AMPK in acute myeloid leukemia (AML) cells. Mechanistically, the UPR effector protein kinase RNA-like ER kinase (PERK) represses oxidative phosphorylation, tricarboxylic acid (TCA) cycle, and pyrimidine biosynthesis and primes the mitochondrial membrane to apoptotic signals in an AMPK-dependent manner. Accordingly, in vitro and in vivo studies reveal synergy between the direct AMPK activator GSK621 and the Bcl-2 inhibitor venetoclax. Thus, selective AMPK-activating compounds kill AML cells by rewiring mitochondrial metabolism that primes mitochondria to apoptosis by BH3 mimetics, holding therapeutic promise in AML.
    Keywords:  AML; AMPK; GSK621; PERK; mitochondrial apoptosis; unfolded protein response; venetoclax
    DOI:  https://doi.org/10.1016/j.celrep.2021.110197
  14. BMC Cancer. 2022 Jan 03. 22(1): 13
    Landscape of homologous recombination deficiencies in solid tumours: analyses of two independent genomic datasets.
    Zhongwu Lai, Matthew Brosnan, Ethan S Sokol, Mingchao Xie, Jonathan R Dry, Elizabeth A Harrington, J Carl Barrett, Darren Hodgson.
      BACKGROUND: DNA repair deficiencies are characteristic of cancer and homologous recombination deficiency (HRD) is the most common. HRD sensitizes tumour cells to PARP inhibitors so it is important to understand the landscape of HRD across different solid tumour types.METHODS: Germline and somatic BRCA mutations in breast and ovarian cancers were evaluated using sequencing data from The Cancer Genome Atlas (TCGA) database. Secondly, a larger independent genomic dataset was analysed to validate the TCGA results and determine the frequency of germline and somatic mutations across 15 different candidate homologous recombination repair (HRR) genes, and their relationship with the genetic events of bi-allelic loss, loss of heterozygosity (LOH) and tumour mutation burden (TMB).
    RESULTS: Approximately one-third of breast and ovarian cancer BRCA mutations were somatic. These showed a similar degree of bi-allelic loss and clinical outcomes to germline mutations, identifying potentially 50% more patients that may benefit from precision treatments. HRR mutations were present in sizable proportions in all tumour types analysed and were associated with high TMB and LOH scores. We also identified numerous BRCA reversion mutations across all tumour types.
    CONCLUSIONS: Our results will facilitate future research into the efficacy of precision oncology treatments, including PARP and immune checkpoint inhibitors.
    Keywords:  Breast; Genomic loss of heterozygosity; Germline; Homologous recombination deficiency; Homologous recombination repair; Immune checkpoint inhibitors; Loss of function; Ovarian; PARP inhibitors; Somatic; cancer
    DOI:  https://doi.org/10.1186/s12885-021-09082-y
  15. ACS Chem Biol. 2022 Jan 04.
    Repurposing the Damage Repair Protein Methyl Guanine Methyl Transferase as a Ligand Inducible Fusion Degron.
    Gosia M Murawska, Caspar Vogel, Max Jan, Xinyan Lu, Matthias Schild, Mikolaj Slabicki, Charles Zou, Saule Zhanybekova, Manisha Manojkumar, Georg Petzold, Peter Kaiser, Nicolas Thomä, Benjamin Ebert, Dennis Gillingham.
      We successfully repurpose the DNA repair protein methylguanine methyltransferase (MGMT) as an inducible degron for protein fusions. MGMT is a suicide protein that removes alkyl groups from the O6 position of guanine (O6G) and is thereafter quickly degraded by the ubiquitin proteasome pathway (UPP). Starting with MGMT pseudosubstrates (benzylguanine and lomeguatrib), we first demonstrate that these lead to potent MGMT depletion while affecting little else in the proteome. We then show that fusion proteins of MGMT undergo rapid UPP-dependent degradation in response to pseudosubstrates. Mechanistic studies confirm the involvement of the UPP, while revealing that at least two E3 ligase classes can degrade MGMT depending on cell-line and expression type (native or ectopic). We also demonstrate the technique's versatility with two clinically relevant examples: degradation of KRASG12C and a chimeric antigen receptor.
    DOI:  https://doi.org/10.1021/acschembio.1c00771
  16. EMBO J. 2022 Jan 05. e108946
    Pharmacological CDK4/6 inhibition reveals a p53-dependent senescent state with restricted toxicity.
    Boshi Wang, Marta Varela-Eirin, Simone M Brandenburg, Alejandra Hernandez-Segura, Thijmen van Vliet, Elisabeth M Jongbloed, Saskia M Wilting, Naoko Ohtani, Agnes Jager, Marco Demaria.
      Cellular senescence is a state of stable growth arrest and a desired outcome of tumor suppressive interventions. Treatment with many anti-cancer drugs can cause premature senescence of non-malignant cells. These therapy-induced senescent cells can have pro-tumorigenic and pro-disease functions via activation of an inflammatory secretory phenotype (SASP). Inhibitors of cyclin-dependent kinases 4/6 (CDK4/6i) have recently proven to restrain tumor growth by activating a senescence-like program in cancer cells. However, the physiological consequence of exposing the whole organism to pharmacological CDK4/6i remains poorly characterized. Here, we show that exposure to CDK4/6i induces non-malignant cells to enter a premature state of senescence dependent on p53. We observe in mice and breast cancer patients that the CDK4/6i-induced senescent program activates only a partial SASP enriched in p53 targets but lacking pro-inflammatory and NF-κB-driven components. We find that CDK4/6i-induced senescent cells do not acquire pro-tumorigenic and detrimental properties but retain the ability to promote paracrine senescence and undergo clearance. Our results demonstrate that SASP composition is exquisitely stress-dependent and a predictor for the biological functions of different senescence subsets.
    Keywords:  CDK4/6 inhibitors; SASP; cellular senescence; chemotherapy; p53
    DOI:  https://doi.org/10.15252/embj.2021108946
  17. Oncogene. 2022 Jan 03.
    RB1 loss in castration-resistant prostate cancer confers vulnerability to LSD1 inhibition.
    Wanting Han, Mingyu Liu, Dong Han, Muqing Li, Anthia A Toure, Zifeng Wang, Anna Besschetnova, Susan Patalano, Jill A Macoska, Shuai Gao, Housheng Hansen He, Changmeng Cai.
      Genomic loss of RB1 is a common alteration in castration-resistant prostate cancer (CRPC) and is associated with poor patient outcomes. RB1 loss is also a critical event that promotes the neuroendocrine transdifferentiation of prostate cancer (PCa) induced by the androgen receptor (AR) signaling inhibition (ARSi). The loss of Rb protein disrupts the Rb-E2F repressor complex and thus hyperactivates E2F transcription activators. While the impact of Rb inactivation on PCa progression and linage plasticity has been previously studied, there is a pressing need to fully understand underlying mechanisms and identify vulnerabilities that can be therapeutically targeted in Rb-deficient CRPC. Using an integrated cistromic and transcriptomic analysis, we have characterized Rb activities in multiple CRPC models by identifying Rb-directly regulated genes and revealed that Rb has distinct binding sites and targets in CRPC with different genomic backgrounds. Significantly, we show that E2F1 chromatin binding and transcription activity in Rb-deficient CRPC are highly dependent on LSD1/KDM1A, and that Rb inactivation sensitizes CRPC tumor to the LSD1 inhibitor treatment. These results provide new molecular insights into Rb activity in PCa progression and suggest that targeting LSD1 activity with small molecule inhibitors may be a potential treatment strategy to treat Rb-deficient CRPC.
    DOI:  https://doi.org/10.1038/s41388-021-02135-3
  18. Front Oncol. 2021 ;11 763151
    SAMHD1 Mutations and Expression in Mantle Cell Lymphoma Patients.
    Tao Wang, Wenqin Yue, Gusheng Tang, Mingyu Ye, Jiechen Yu, Bin Liu, Lijuan Jiao, Xuefei Liu, Shuyi Yin, Jie Chen, Lei Gao, Jianmin Yang, Miaoxia He.
      SAMHD1 (sterile alpha motif domain and histidine-aspartate domain-containing protein 1) is a deoxynucleoside triphosphate triphosphohydrolase regulating innate immune and modulating DNA damage signaling. It plays an important role in the development of some tumors. SAMHD1 was also reported as a barrier to cytarabine, a common chemotherapy drug for mantle cell lymphoma (MCL), and as a biomarker of grim prognosis for acute myelocytic leukemia (AML) patients. However, SAMHD1 expression and function in MCL have not been well-defined. In the present study, we evaluated SAMHD1 expression by immunohistochemistry and its gene structure by Sanger sequencing in MCL. Our results showed that SAMHD1 was positive in 36 (62.1%) patients. Importantly, SAMHD1-positive patients were associated with lower chemotherapy response rate (p = 0.023) and shorter overall survival (p = 0.039) than SAMHD1-negative cases. These results suggest that SAMHD1 is an adverse biomarker for MCL patients, which is due to the high expression of SAMHD1 and rapid cell proliferation. These findings were confirmed in an in vitro study using the siRNA technique. Silencing the SAMHD1 gene in the MCL cell line Jeko-1 significantly decreased cell proliferation and increased cell apoptosis. The MCL cell line with SAMHD1 knockdown showed lower Ki-67 proliferation index, higher caspase-3, and higher sensitivity to cytarabine. Furthermore, for the first time, four previously unreported missense mutations (S302Y, Y432C, E449G, and R451H) in exon 8 and exon 12 of the SAMHD1 gene were discovered by sequencing. The mutations had not been found to corelate with SAMHD1 protein expression detected by immunohistochemistry. The biological functions of this mutated SAMHD1 remain to be investigated.
    Keywords:  SAMHD1; cytarabine resistance; gene silencing; immunohistochemistry; mantle cell lymphoma; mutations; patient risk stratification; prognosis
    DOI:  https://doi.org/10.3389/fonc.2021.763151
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