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Article ; Online: Patterns in the tapestry of chromatin-bound RB.

Sanidas, Ioannis / Lawrence, Michael S / Dyson, Nicholas J

2023 Volume 34, Issue 4, Page(s) 288–298

Abstract: The retinoblastoma protein (RB)-mediated regulation of E2F is a component of a highly conserved cell cycle machine. However, RB's tumor suppressor activity, like RB's requirement in animal development, is tissue-specific, context-specific, and sometimes ... ...

Abstract	The retinoblastoma protein (RB)-mediated regulation of E2F is a component of a highly conserved cell cycle machine. However, RB's tumor suppressor activity, like RB's requirement in animal development, is tissue-specific, context-specific, and sometimes appears uncoupled from cell proliferation. Detailed new information about RB's genomic distribution provides a new perspective on the complexity of RB function, suggesting that some of its functional specificity results from context-specific RB association with chromatin. Here we summarize recent evidence showing that RB targets different types of chromatin regulatory elements at different cell cycle stages. RB controls traditional RB/E2F targets prior to S-phase, but, when cells proliferate, RB redistributes to cell type-specific chromatin loci. We discuss the broad implications of the new data for RB research.
MeSH term(s)	Animals ; Chromatin ; E2F Transcription Factors/metabolism ; Cell Cycle/genetics ; Retinoblastoma Protein/genetics ; Retinoblastoma Protein/metabolism ; Cell Division
Chemical Substances	Chromatin ; E2F Transcription Factors ; Retinoblastoma Protein
Language	English
Publishing date	2023-08-28
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2023.07.012
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Article ; Online: APOBEC3A induces DNA gaps through PRIMPOL and confers gap-associated therapeutic vulnerability.

Kawale, Ajinkya S / Ran, Xiaojuan / Patel, Parasvi S / Saxena, Sneha / Lawrence, Michael S / Zou, Lee

Science advances

2024 Volume 10, Issue 3, Page(s) eadk2771

Abstract: Mutation signatures associated with apolipoprotein B mRNA editing catalytic polypeptide-like 3A/B (APOBEC3A/B) cytidine deaminases are prevalent across cancers, implying their roles as mutagenic drivers during tumorigenesis and tumor evolution. APOBEC3A ( ...

Abstract	Mutation signatures associated with apolipoprotein B mRNA editing catalytic polypeptide-like 3A/B (APOBEC3A/B) cytidine deaminases are prevalent across cancers, implying their roles as mutagenic drivers during tumorigenesis and tumor evolution. APOBEC3A (A3A) expression induces DNA replication stress and increases the cellular dependency on the ataxia telangiectasia and Rad3-related (ATR) kinase for survival. Nonetheless, how A3A induces DNA replication stress remains unclear. We show that A3A induces replication stress without slowing replication forks. We find that A3A induces single-stranded DNA (ssDNA) gaps through PrimPol-mediated repriming. A3A-induced ssDNA gaps are repaired by multiple pathways involving ATR, RAD51, and translesion synthesis. Both ATR inhibition and trapping of poly(ADP-ribose) polymerase (PARP) on DNA by PARP inhibitor impair the repair of A3A-induced gaps, preferentially killing A3A-expressing cells. When used in combination, PARP and ATR inhibitors selectively kill A3A-expressing cells synergistically in a manner dependent on PrimPol-generated gaps. Thus, A3A-induced replication stress arises from PrimPol-generated ssDNA gaps, which confer a therapeutic vulnerability to gap-targeted DNA repair inhibitors.
MeSH term(s)	Poly(ADP-ribose) Polymerase Inhibitors ; Proteins/metabolism ; DNA ; Cytidine Deaminase/genetics ; Cytidine Deaminase/metabolism ; DNA Replication ; DNA, Single-Stranded/genetics
Chemical Substances	APOBEC3A protein, human (EC 3.5.4.5) ; Poly(ADP-ribose) Polymerase Inhibitors ; Proteins ; DNA (9007-49-2) ; Cytidine Deaminase (EC 3.5.4.5) ; DNA, Single-Stranded
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adk2771
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Article ; Online: Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations.

Butt, Yasha / Sakhtemani, Ramin / Mohamad-Ramshan, Rukshana / Lawrence, Michael S / Bhagwat, Ashok S

Nature communications

2024 Volume 15, Issue 1, Page(s) 2369

Abstract: The APOBEC3 enzymes convert cytosines in single-stranded DNA to uracils to protect against viruses and retrotransposons but can contribute to mutations that diversify tumors. To understand the mechanism of mutagenesis, we map the uracils resulting from ... ...

Abstract	The APOBEC3 enzymes convert cytosines in single-stranded DNA to uracils to protect against viruses and retrotransposons but can contribute to mutations that diversify tumors. To understand the mechanism of mutagenesis, we map the uracils resulting from expression of APOBEC3B or its catalytic carboxy-terminal domain (CTD) in Escherichia coli. Like APOBEC3A, the uracilomes of A3B and A3B-CTD show a preference to deaminate cytosines near transcription start sites and the lagging-strand replication templates and in hairpin loops. Both biochemical activities of the enzymes and genomic uracil distribution show that A3A prefers 3 nt loops the best, while A3B prefers 4 nt loops. Reanalysis of hairpin loop mutations in human tumors finds intrinsic characteristics of both the enzymes, with a much stronger contribution from A3A. We apply Hairpin Signatures 1 and 2, which define A3A and A3B preferences respectively and are orthogonal to published methods, to evaluate their contribution to human tumor mutations.
MeSH term(s)	Humans ; Cytosine/metabolism ; Proteins/metabolism ; Mutation ; Cytidine Deaminase/metabolism ; Neoplasms/genetics ; Uracil/metabolism ; Minor Histocompatibility Antigens/metabolism
Chemical Substances	APOBEC3A protein, human (EC 3.5.4.5) ; Cytosine (8J337D1HZY) ; Proteins ; Cytidine Deaminase (EC 3.5.4.5) ; Uracil (56HH86ZVCT) ; Minor Histocompatibility Antigens ; APOBEC3B protein, human (EC 3.5.4.5)
Language	English
Publishing date	2024-03-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46231-w
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Article ; Online: Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP.

Lee, Hanjun / Sanidas, Ioannis / Dyson, Nicholas J / Lawrence, Michael S

STAR protocols

2023 Volume 4, Issue 1, Page(s) 101991

Abstract: Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins ... ...

Abstract	Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins using the bedGraph2Cluster and PanChIP algorithms. Using histone modifications as an example, bedGraph2Cluster performs clustering analysis on chromatin binding patterns of target proteins. PanChIP then compares these clusters with a reference library of chromatin binding patterns and measures the overlap in peaks, capturing the heterogeneity in chromatin binding and colocalization patterns. For complete details on the use and execution of this protocol, please refer to Sanidas et al. (2022).
MeSH term(s)	Chromatin/genetics ; Chromatin Immunoprecipitation/methods ; High-Throughput Nucleotide Sequencing/methods ; Chromatin Immunoprecipitation Sequencing/methods ; Genome
Chemical Substances	Chromatin
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101991
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Article ; Online: Revisiting the use of structural similarity index in Hi-C.

Lee, Hanjun / Blumberg, Bruce / Lawrence, Michael S / Shioda, Toshihiro

Nature genetics

2023 Volume 55, Issue 12, Page(s) 2049–2052

Language	English
Publishing date	2023-12-05
Publishing country	United States
Document type	Letter
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-023-01594-6
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Article: Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations.

Butt, Yasha / Sakhtemani, Ramin / Mohamad-Ramshan, Rukshana / Lawrence, Michael S / Bhagwat, Ashok S

bioRxiv : the preprint server for biology

2023

Abstract: The APOBEC3 family of enzymes convert cytosines in single-stranded DNA to uracils thereby causing mutations. These enzymes protect human cells against viruses and retrotransposons, but in many cancers they contribute to mutations that diversify the ... ...

Abstract	The APOBEC3 family of enzymes convert cytosines in single-stranded DNA to uracils thereby causing mutations. These enzymes protect human cells against viruses and retrotransposons, but in many cancers they contribute to mutations that diversify the tumors and help them escape anticancer drug treatments. To understand the mechanism of mutagenesis by APOBEC3B, we expressed the complete enzyme or its catalytic carboxy-terminal domain (CTD) in repair-deficient
Language	English
Publishing date	2023-08-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.01.551518
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Article ; Online: Huge whole-genome study of human metastatic cancers.

Wise, Jillian F / Lawrence, Michael S

Nature

2019 Volume 575, Issue 7781, Page(s) 60–61

MeSH term(s)	Genome, Human ; Humans ; Neoplasms/genetics
Language	English
Publishing date	2019-11-05
Publishing country	England
Document type	News ; Comment
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/d41586-019-03123-0
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Article: Single-cell transcriptomic profiling for inferring tumor origin and mechanisms of therapeutic resistance.

Lin, Maoxuan / Sade-Feldman, Moshe / Wirth, Lori / Lawrence, Michael S / Faden, Daniel L

NPJ precision oncology

2022 Volume 6, Issue 1, Page(s) 71

Abstract: Head and Neck Squamous Cell Carcinoma (HNSCC) is an aggressive epithelial cancer with poor overall response rates to checkpoint inhibitor therapy (CPI) despite CPI being the recommended treatment for recurrent or metastatic HNSCC. Mechanisms of ... ...

Abstract	Head and Neck Squamous Cell Carcinoma (HNSCC) is an aggressive epithelial cancer with poor overall response rates to checkpoint inhibitor therapy (CPI) despite CPI being the recommended treatment for recurrent or metastatic HNSCC. Mechanisms of resistance to CPI in HNSCC are poorly understood. To identify drivers of response and resistance to CPI in a unique patient who was believed to have developed three separate HNSCCs, we performed single-cell RNA-seq (scRNA-seq) profiling of two responding lesions and one progressive lesion that developed during CPI. Our results not only suggest interferon-induced APOBEC3-mediated acquired resistance as a mechanism of CPI resistance in the progressing lesion but further, that the lesion in question was actually a metastasis as opposed to a new primary tumor, highlighting the immense power of scRNA-seq as a clinical tool for inferring tumor origin and mechanisms of therapeutic resistance.
Language	English
Publishing date	2022-10-10
Publishing country	England
Document type	Journal Article
ISSN	2397-768X
ISSN	2397-768X
DOI	10.1038/s41698-022-00314-3
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Article ; Online: Human activation-induced deaminase lacks strong replicative strand bias or preference for cytosines in hairpin loops.

Sakhtemani, Ramin / Perera, Madusha L W / Hübschmann, Daniel / Siebert, Reiner / Lawrence, Michael S / Bhagwat, Ashok S

Nucleic acids research

2022 Volume 50, Issue 9, Page(s) 5145–5157

Abstract: Activation-induced deaminase (AID) is a DNA-cytosine deaminase that mediates maturation of antibodies through somatic hypermutation and class-switch recombination. While it causes mutations in immunoglobulin heavy and light chain genes and strand breaks ... ...

Abstract	Activation-induced deaminase (AID) is a DNA-cytosine deaminase that mediates maturation of antibodies through somatic hypermutation and class-switch recombination. While it causes mutations in immunoglobulin heavy and light chain genes and strand breaks in the switch regions of the immunoglobulin heavy chain gene, it largely avoids causing such damage in the rest of the genome. To help understand targeting by human AID, we expressed it in repair-deficient Escherichia coli and mapped the created uracils in the genomic DNA using uracil pull-down and sequencing, UPD-seq. We found that both AID and the human APOBEC3A preferentially target tRNA genes and transcription start sites, but do not show preference for highly transcribed genes. Unlike A3A, AID did not show a strong replicative strand bias or a preference for hairpin loops. Overlapping uracilation peaks between these enzymes contained binding sites for a protein, FIS, that helps create topological domains in the E. coli genome. To confirm whether these findings were relevant to B cells, we examined mutations from lymphoma and leukemia genomes within AID-preferred sequences. These mutations also lacked replicative strand bias or a hairpin loop preference. We propose here a model for how AID avoids causing mutations in the single-stranded DNA found within replication forks.
MeSH term(s)	Cytidine Deaminase/metabolism ; Cytosine/metabolism ; DNA/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Humans ; Immunoglobulin Class Switching ; Somatic Hypermutation, Immunoglobulin ; Uracil/metabolism
Chemical Substances	Uracil (56HH86ZVCT) ; Cytosine (8J337D1HZY) ; DNA (9007-49-2) ; AICDA (activation-induced cytidine deaminase) (EC 3.5.4.-) ; APOBEC3A protein, human (EC 3.5.4.5) ; Cytidine Deaminase (EC 3.5.4.5)
Language	English
Publishing date	2022-05-07
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac296
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Article ; Online: Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes.

Sanchez, Ambrocio / Ortega, Pedro / Sakhtemani, Ramin / Manjunath, Lavanya / Oh, Sunwoo / Bournique, Elodie / Becker, Alexandrea / Kim, Kyumin / Durfee, Cameron / Temiz, Nuri Alpay / Chen, Xiaojiang S / Harris, Reuben S / Lawrence, Michael S / Buisson, Rémi

Nature communications

2024 Volume 15, Issue 1, Page(s) 2370

Abstract: Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem- ... ...

Abstract	Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets single-stranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have not been fully established, and the specific influence of the DNA sequence on APOBEC3A and APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B also selectively targets DNA stem-loop structures, and they are distinct from those subjected to deamination by APOBEC3A. We develop Oligo-seq, an in vitro sequencing-based method to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A and APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify the structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate distinct mutation landscapes in cancer genomes, driven by their unique substrate selectivity.
MeSH term(s)	Humans ; Mutation ; Neoplasms/genetics ; Cytidine Deaminase/genetics ; Cytidine Deaminase/chemistry ; DNA ; Minor Histocompatibility Antigens/genetics ; Minor Histocompatibility Antigens/chemistry ; Cytosine ; Proteins
Chemical Substances	APOBEC3A protein, human (EC 3.5.4.5) ; Cytidine Deaminase (EC 3.5.4.5) ; DNA (9007-49-2) ; Minor Histocompatibility Antigens ; Cytosine (8J337D1HZY) ; APOBEC3B protein, human (EC 3.5.4.5) ; Proteins
Language	English
Publishing date	2024-03-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45909-5
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