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Publications (10 of 24) Show all publications
Andréasson, M., Donzel, M., Abrahamsson, A., Berner, A., Doimo, M., Quiroga, A., . . . Chorell, E. (2024). Exploring the dispersion and electrostatic components in arene-arene interactions between ligands and G4 DNA to develop G4-ligands. Journal of Medicinal Chemistry, 67(3), 2202-2219
Open this publication in new window or tab >>Exploring the dispersion and electrostatic components in arene-arene interactions between ligands and G4 DNA to develop G4-ligands
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2024 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 67, no 3, p. 2202-2219Article in journal (Refereed) Published
Abstract [en]

G-Quadruplex (G4) DNA structures are important regulatory elements in central biological processes. Small molecules that selectively bind and stabilize G4 structures have therapeutic potential, and there are currently >1000 known G4 ligands. Despite this, only two G4 ligands ever made it to clinical trials. In this work, we synthesized several heterocyclic G4 ligands and studied their interactions with G4s (e.g., G4s from the c-MYC, c-KIT, and BCL-2 promoters) using biochemical assays. We further studied the effect of selected compounds on cell viability, the effect on the number of G4s in cells, and their pharmacokinetic properties. This identified potent G4 ligands with suitable properties and further revealed that the dispersion component in arene-arene interactions in combination with electron-deficient electrostatics is central for the ligand to bind with the G4 efficiently. The presented design strategy can be applied in the further development of G4-ligands with suitable properties to explore G4s as therapeutic targets.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2024
National Category
Medicinal Chemistry
Identifiers
urn:nbn:se:umu:diva-220319 (URN)10.1021/acs.jmedchem.3c02127 (DOI)38241609 (PubMedID)2-s2.0-85183093324 (Scopus ID)
Funder
The Kempe Foundations, JCK-3159The Kempe Foundations, SMK-1632Swedish Research Council, 2017-05235Swedish Research Council, 2021-04805Knut and Alice Wallenberg Foundation
Available from: 2024-02-13 Created: 2024-02-13 Last updated: 2024-02-13Bibliographically approved
Doimo, M., Chaudhari, N., Abrahamsson, S., L'Hôte, V., Nguyen, T. V. H., Berner, A., . . . Wanrooij, S. (2023). Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Research, 51(14), 7392-7408
Open this publication in new window or tab >>Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells
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2023 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 51, no 14, p. 7392-7408Article in journal (Refereed) Published
Abstract [en]

Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.

Place, publisher, year, edition, pages
Oxford University Press, 2023
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-214069 (URN)10.1093/nar/gkad535 (DOI)001030190900001 ()37351621 (PubMedID)2-s2.0-85168980694 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, VR-MH 2018-0278Swedish Research Council, VR-NT 2017-05235The Kempe Foundations, SMK-1632Wenner-Gren FoundationsEU, Horizon 2020, 751474Swedish Foundation for Strategic Research, RIF14-0081
Available from: 2023-09-05 Created: 2023-09-05 Last updated: 2023-09-05Bibliographically approved
Berner, A., Das, R. N., Bhuma, N., Golebiewska, J., Abrahamsson, A., Andréasson, M., . . . Chorell, E. (2023). G4-ligand-conjugated oligonucleotides mediate selective binding and stabilization of individual G4 DNA structures. Journal of the American Chemical Society, 146(10), 6926-6935
Open this publication in new window or tab >>G4-ligand-conjugated oligonucleotides mediate selective binding and stabilization of individual G4 DNA structures
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2023 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 146, no 10, p. 6926-6935Article in journal (Refereed) Published
Abstract [en]

G-quadruplex (G4) DNA structures are prevalent secondary DNA structures implicated in fundamental cellular functions, such as replication and transcription. Furthermore, G4 structures are directly correlated to human diseases such as cancer and have been highlighted as promising therapeutic targets for their ability to regulate disease-causing genes, e.g., oncogenes. Small molecules that bind and stabilize these structures are thus valuable from a therapeutic perspective and helpful in studying the biological functions of the G4 structures. However, there are hundreds of thousands of G4 DNA motifs in the human genome, and a long-standing problem in the field is how to achieve specificity among these different G4 structures. Here, we developed a strategy to selectively target an individual G4 DNA structure. The strategy is based on a ligand that binds and stabilizes G4s without selectivity, conjugated to a guide oligonucleotide, that specifically directs the G4-Ligand-conjugated oligo (GL-O) to the single target G4 structure. By employing various biophysical and biochemical techniques, we show that the developed method enables the targeting of a unique, specific G4 structure without impacting other off-target G4 formations. Considering the vast amount of G4s in the human genome, this represents a promising strategy to study the presence and functions of individual G4s but may also hold potential as a future therapeutic modality.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-222294 (URN)10.1021/jacs.3c14408 (DOI)001179314400001 ()38430200 (PubMedID)2-s2.0-85186374110 (Scopus ID)
Funder
The Kempe Foundations, JCK-3159The Kempe Foundations, SMK-1632The Kempe Foundations, SMK21-0059Swedish Research Council, 2017-05235Swedish Research Council, 2021-04805Swedish Research Council, 2018-0278Cancerforskningsfonden i Norrland, AMP19-968Knut and Alice Wallenberg Foundation, SMK21-0059
Available from: 2024-03-20 Created: 2024-03-20 Last updated: 2024-03-20Bibliographically approved
Akhunzianov, A. A., Nesterova, A. I., Wanrooij, S., Filina, Y. V., Rizvanov, A. A. & Miftakhova, R. R. (2023). Unravelling the Therapeutic Potential of Antibiotics in Hypoxia in a Breast Cancer MCF-7 Cell Line Model. International Journal of Molecular Sciences, 24(14), Article ID 11540.
Open this publication in new window or tab >>Unravelling the Therapeutic Potential of Antibiotics in Hypoxia in a Breast Cancer MCF-7 Cell Line Model
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2023 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 24, no 14, article id 11540Article in journal (Refereed) Published
Abstract [en]

Antibiotics inhibit breast cancer stem cells (CSCs) by suppressing mitochondrial biogenesis. However, the effectiveness of antibiotics in clinical settings is inconsistent. This inconsistency raises the question of whether the tumor microenvironment, particularly hypoxia, plays a role in the response to antibiotics. Therefore, the goal of this study was to evaluate the effectiveness of five commonly used antibiotics for inhibiting CSCs under hypoxia using an MCF-7 cell line model. We assessed the number of CSCs through the mammosphere formation assay and aldehyde dehydrogenase (ALDH)-bright cell count. Additionally, we examined the impact of antibiotics on the mitochondrial stress response and membrane potential. Furthermore, we analyzed the levels of proteins associated with therapeutic resistance. There was no significant difference in the number of CSCs between cells cultured under normoxic and hypoxic conditions. However, hypoxia did affect the rate of CSC inhibition by antibiotics. Specifically, azithromycin was unable to inhibit sphere formation in hypoxia. Erythromycin and doxycycline did not reduce the ratio of ALDH-bright cells, despite decreasing the number of mammospheres. Furthermore, treatment with chloramphenicol, doxycycline, and tetracycline led to the overexpression of the breast cancer resistance protein. Our findings suggest that hypoxia may weaken the inhibitory effects of antibiotics on the breast cancer model.

Place, publisher, year, edition, pages
MDPI, 2023
Keywords
antibiotics, breast cancer, cancer stem cells, hypoxia, mitochondria
National Category
Cancer and Oncology Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-212713 (URN)10.3390/ijms241411540 (DOI)001038566100001 ()37511298 (PubMedID)2-s2.0-85165983164 (Scopus ID)
Available from: 2023-08-15 Created: 2023-08-15 Last updated: 2023-08-15Bibliographically approved
Prasad, B., Doimo, M., Andréasson, M., L'Hôte, V., Chorell, E. & Wanrooij, S. (2022). A complementary chemical probe approach towards customized studies of G-quadruplex DNA structures in live cells. Chemical Science, 13(8), 2347-2354
Open this publication in new window or tab >>A complementary chemical probe approach towards customized studies of G-quadruplex DNA structures in live cells
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2022 (English)In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 13, no 8, p. 2347-2354Article in journal (Refereed) Published
Abstract [en]

G-quadruplex (G4) DNA structures are implicated in central biological processes and are considered promising therapeutic targets because of their links to human diseases such as cancer. However, functional details of how, when, and why G4 DNA structures form in vivo are largely missing leaving a knowledge gap that requires tailored chemical biology studies in relevant live-cell model systems. Towards this end, we developed a synthetic platform to generate complementary chemical probes centered around one of the most effective and selective G4 stabilizing compounds, Phen-DC3. We used a structure-based design and substantial synthetic devlopments to equip Phen-DC3 with an amine in a position that does not interfere with G4 interactions. We next used this reactive handle to conjugate a BODIPY fluorophore to Phen-DC3. This generated a fluorescent derivative with retained G4 selectivity, G4 stabilization, and cellular effect that revealed the localization and function of Phen-DC3 in human cells. To increase cellular uptake, a second chemical probe with a conjugated cell-penetrating peptide was prepared using the same amine-substituted Phen-DC3 derivative. The cell-penetrating peptide conjugation, while retaining G4 selectivity and stabilization, increased nuclear localization and cellular effects, showcasing the potential of this method to modulate and direct cellular uptake e.g. as delivery vehicles. The applied approach to generate multiple tailored biochemical tools based on the same core structure can thus be used to advance the studies of G4 biology to uncover molecular details and therapeutic approaches. This journal is

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2022
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-193064 (URN)10.1039/d1sc05816a (DOI)000751956900001 ()2-s2.0-85125772577 (Scopus ID)
Funder
Swedish Research Council, VR-NT 2017-05235The Kempe Foundations, SMK-1632Knut and Alice Wallenberg Foundation, VR-MH 2018-0278EU, Horizon 2020, 751474
Available from: 2022-03-21 Created: 2022-03-21 Last updated: 2023-03-24Bibliographically approved
Inatomi, T., Matsuda, S., Ishiuchi, T., Do, Y., Nakayama, M., Abe, S., . . . Kang, D. (2022). TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication. Biochimica et Biophysica Acta. Molecular Cell Research, 1869(1), Article ID 119167.
Open this publication in new window or tab >>TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication
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2022 (English)In: Biochimica et Biophysica Acta. Molecular Cell Research, ISSN 0167-4889, E-ISSN 1879-2596, Vol. 1869, no 1, article id 119167Article in journal (Refereed) Published
Abstract [en]

Two classes of replication intermediates have been observed from mitochondrial DNA (mtDNA) in many mammalian tissue and cells with two-dimensional agarose gel electrophoresis. One is assigned to leading-strand synthesis in the absence of synchronous lagging-strand synthesis (strand-asynchronous replication), and the other has properties of coupled leading- and lagging-strand synthesis (strand-coupled replication). While strand-asynchronous replication is primed by long noncoding RNA synthesized from a defined transcription initiation site, little is known about the commencement of strand-coupled replication. To investigate it, we attempted to abolish strand-asynchronous replication in cultured human cybrid cells by knocking out the components of the transcription initiation complexes, mitochondrial transcription factor B2 (TFB2M/mtTFB2) and mitochondrial RNA polymerase (POLRMT/mtRNAP). Unexpectedly, removal of either protein resulted in complete mtDNA loss, demonstrating for the first time that TFB2M and POLRMT are indispensable for the maintenance of human mtDNA. Moreover, a lack of TFB2M could not be compensated for by mitochondrial transcription factor B1 (TFB1M/mtTFB1). These findings indicate that TFB2M and POLRMT are crucial for the priming of not only strand-asynchronous but also strand-coupled replication, providing deeper insights into the molecular basis of mtDNA replication initiation.

Place, publisher, year, edition, pages
Elsevier, 2022
Keywords
Mitochondrial DNA, Mitochondrial RNA polymerase, Mitochondrial transcription factor, Replication initiation, Strand-asynchronous replication, Strand-coupled replication
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-189547 (URN)10.1016/j.bbamcr.2021.119167 (DOI)000717326400004 ()2-s2.0-85118485501 (Scopus ID)
Available from: 2021-11-16 Created: 2021-11-16 Last updated: 2023-09-05Bibliographically approved
Kasho, K., Stojkovic, G., Velázquez-Ruiz, C., Martínez-Jiménez, M. I., Doimo, M., Laurent, T., . . . Wanrooij, S. (2021). A unique arginine cluster in PolDIP2 enhances nucleotide binding and DNA synthesis by PrimPol. Nucleic Acids Research, 49(4), 2179-2191
Open this publication in new window or tab >>A unique arginine cluster in PolDIP2 enhances nucleotide binding and DNA synthesis by PrimPol
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2021 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 49, no 4, p. 2179-2191Article in journal (Refereed) Published
Abstract [en]

Replication forks often stall at damaged DNA. To overcome these obstructions and complete the DNA duplication in a timely fashion, replication can be restarted downstream of the DNA lesion. In mammalian cells, this repriming of replication can be achieved through the activities of primase and polymerase PrimPol. PrimPol is stimulated in DNA synthesis through interaction with PolDIP2, however the exact mechanism of this PolDIP2-dependent stimulation is still unclear. Here, we show that PrimPol uses a flexible loop to interact with the C-terminal ApaG-like domain of PolDIP2, and that this contact is essential for PrimPol's enhanced processivity. PolDIP2 increases primer-template and dNTP binding affinities of PrimPol, which concomitantly enhances its nucleotide incorporation efficiency. This stimulation is dependent on a unique arginine cluster in PolDIP2. Since the polymerase activity of PrimPol alone is very limited, this mechanism, where the affinity for dNTPs gets increased by PolDIP2 binding, might be critical for the in vivo function of PrimPol in tolerating DNA lesions at physiological nucleotide concentrations.

Place, publisher, year, edition, pages
Oxford University Press, 2021
National Category
Biochemistry and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-181802 (URN)10.1093/nar/gkab049 (DOI)000637321900030 ()2-s2.0-85102403658 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilThe Kempe Foundations
Available from: 2021-03-30 Created: 2021-03-30 Last updated: 2023-09-05Bibliographically approved
Kasho, K., Krasauskas, L., Smirnovas, V., Stojkovic, G., Morozova-Roche, L. & Wanrooij, S. (2021). Human polymerase δ-interacting protein 2 (Poldip2) inhibits the formation of human tau oligomers and fibrils. International Journal of Molecular Sciences, 22(11), Article ID 5768.
Open this publication in new window or tab >>Human polymerase δ-interacting protein 2 (Poldip2) inhibits the formation of human tau oligomers and fibrils
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2021 (English)In: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 22, no 11, article id 5768Article in journal (Refereed) Published
Abstract [en]

A central characteristic of Alzheimer’s disease (AD) and other tauopathies is the accumulation of aggregated and misfolded Tau deposits in the brain. Tau-targeting therapies for AD have been unsuccessful in patients to date. Here we show that human polymerase δ-interacting protein 2 (PolDIP2) interacts with Tau. With a set of complementary methods, including thioflavin-T-based aggregation kinetic assays, Tau oligomer-specific dot-blot analysis, and single oligomer/fibril analysis by atomic force microscopy, we demonstrate that PolDIP2 inhibits Tau aggregation and amyloid fibril growth in vitro. The identification of PolDIP2 as a potential regulator of cellular Tau aggregation should be considered for future Tau-targeting therapeutics.

Place, publisher, year, edition, pages
MDPI, 2021
Keywords
Amyloid, PolDIP2, Tau
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-184124 (URN)10.3390/ijms22115768 (DOI)000660157600001 ()2-s2.0-85106658099 (Scopus ID)
Funder
Swedish Research Council, 2018-02781Knut and Alice Wallenberg Foundation, 2019.0307The Kempe Foundations, JCK-1831
Available from: 2021-06-10 Created: 2021-06-10 Last updated: 2023-09-05Bibliographically approved
Calvo, P. A., Martínez-Jiménez, M. I., Díaz, M., Stojkovic, G., Kasho, K., Guerra, S., . . . Blanco, L. (2021). Motif WFYY of human PrimPol is crucial to stabilize the incoming 3'-nucleotide during replication fork restart. Nucleic Acids Research, 49(14), 8199-8213
Open this publication in new window or tab >>Motif WFYY of human PrimPol is crucial to stabilize the incoming 3'-nucleotide during replication fork restart
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2021 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 49, no 14, p. 8199-8213Article in journal (Refereed) Published
Abstract [en]

PrimPol is the second primase in human cells, the first with the ability to start DNA chains with dNTPs. PrimPol contributes to DNA damage tolerance by restarting DNA synthesis beyond stalling lesions, acting as a TLS primase. Multiple alignment of eukaryotic PrimPols allowed us to identify a highly conserved motif, WxxY near the invariant motif A, which contains two active site metal ligands in all members of the archeo-eukaryotic primase (AEP) superfamily. In vivo and in vitro analysis of single variants of the WFYY motif of human PrimPol demonstrated that the invariant Trp87 and Tyr90 residues are essential for both primase and polymerase activities, mainly due to their crucial role in binding incoming nucleotides. Accordingly, the human variant F88L, altering the WFYY motif, displayed reduced binding of incoming nucleotides, affecting its primase/polymerase activities especially during TLS reactions on UV-damaged DNA. Conversely, the Y89D mutation initially associated with High Myopia did not affect the ability to rescue stalled replication forks in human cells. Collectively, our data suggest that the WFYY motif has a fundamental role in stabilizing the incoming 3'-nucleotide, an essential requisite for both its primase and TLS abilities during replication fork restart.

Place, publisher, year, edition, pages
Oxford University Press, 2021
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-187693 (URN)10.1093/nar/gkab634 (DOI)000692599800034 ()34302490 (PubMedID)2-s2.0-85114351923 (Scopus ID)
Available from: 2021-09-23 Created: 2021-09-23 Last updated: 2021-09-23Bibliographically approved
Doimo, M., Pfeiffer, A., Wanrooij, P. H. & Wanrooij, S. (2020). MtDNA replication, maintenance, and nucleoid organization. In: Giuseppe Gasparre; Anna Maria Porcelli (Ed.), The human mitochondrial genome: from basic biology to disease (pp. 3-33). Academic Press
Open this publication in new window or tab >>MtDNA replication, maintenance, and nucleoid organization
2020 (English)In: The human mitochondrial genome: from basic biology to disease / [ed] Giuseppe Gasparre; Anna Maria Porcelli, Academic Press, 2020, p. 3-33Chapter in book (Refereed)
Abstract [en]

Part of the genetic information in human cells resides in the mitochondria. Faithful maintenance of mitochondrial deoxyribonucleic acid (mtDNA) is crucial for the oxidative phosphorylation system that produces the majority of the cellular ATP, and therefore to life. This chapter provides an introduction into the characteristics of human mtDNA and summarizes the processes and factors required for the replication and maintenance of this small but essential genome. We also describe the organization of mtDNA in specialized nucleoprotein structures called nucleoids. Where applicable, we refer to human disease states that are caused by defects in the described factors or processes.

Place, publisher, year, edition, pages
Academic Press, 2020
Keywords
Mitochondrial DNA, mtDNA
National Category
Biochemistry and Molecular Biology Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-182657 (URN)10.1016/B978-0-12-819656-4.00001-2 (DOI)2-s2.0-85124853615 (Scopus ID)9780128196564 (ISBN)
Available from: 2021-04-29 Created: 2021-04-29 Last updated: 2022-02-28Bibliographically approved
Projects
The role of mitochondrial DNA double strand break repair in human disease and normal aging. [2011-02419_VR]; Umeå UniversityThe mechanisms underlying mitochondrial DNA deletion formation in human disease. [2018-02781_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-6126-4382

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