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Article ; Online: Machine Learning Methods in the 3D Analysis of Histopathological Data.

Kedziora, Katarzyna M

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

2023 Volume 29, Issue Supplement_1, Page(s) 969

Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	1385710-1
ISSN	1435-8115 ; 1431-9276
ISSN (online)	1435-8115
ISSN	1431-9276
DOI	10.1093/micmic/ozad067.484
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Article ; Online: Cell Cycle Mapping Using Multiplexed Immunofluorescence.

Kedziora, Katarzyna M / Stallaert, Wayne

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2740, Page(s) 243–262

Abstract: The development of technologies that allow measurement of the cell cycle at the single-cell level has revealed novel insights into the mechanisms that regulate cell cycle commitment and progression through DNA replication and cell division. These studies ...

Abstract	The development of technologies that allow measurement of the cell cycle at the single-cell level has revealed novel insights into the mechanisms that regulate cell cycle commitment and progression through DNA replication and cell division. These studies have also provided evidence of heterogeneity in cell cycle regulation among individual cells, even within a genetically identical population. Cell cycle mapping combines highly multiplexed imaging with manifold learning to visualize the diversity of "paths" that cells can take through the proliferative cell cycle or into various states of cell cycle arrest. In this chapter, we describe a general protocol of the experimental and computational components of cell cycle mapping. We also provide a comprehensive guide for the design and analysis of experiments, discussing key considerations in detail (e.g., antibody library preparation, analysis strategies, etc.) that may vary depending on the research question being addressed.
MeSH term(s)	Cell Cycle/physiology ; Cell Division ; DNA Replication ; Cell Cycle Checkpoints ; Fluorescent Antibody Technique
Language	English
Publishing date	2024-02-23
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3557-5_15
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Article ; Online: The consequences of differential origin licensing dynamics in distinct chromatin environments.

Mei, Liu / Kedziora, Katarzyna M / Song, Eun-Ah / Purvis, Jeremy E / Cook, Jeanette Gowen

Nucleic acids research

2022 Volume 50, Issue 17, Page(s) 9601–9620

Abstract: Eukaryotic chromosomes contain regions of varying accessibility, yet DNA replication factors must access all regions. The first replication step is loading MCM complexes to license replication origins during the G1 cell cycle phase. It is not yet known ... ...

Abstract	Eukaryotic chromosomes contain regions of varying accessibility, yet DNA replication factors must access all regions. The first replication step is loading MCM complexes to license replication origins during the G1 cell cycle phase. It is not yet known how mammalian MCM complexes are adequately distributed to both accessible euchromatin regions and less accessible heterochromatin regions. To address this question, we combined time-lapse live-cell imaging with immunofluorescence imaging of single human cells to quantify the relative rates of MCM loading in euchromatin and heterochromatin throughout G1. We report here that MCM loading in euchromatin is faster than that in heterochromatin in early G1, but surprisingly, heterochromatin loading accelerates relative to euchromatin loading in middle and late G1. This differential acceleration allows both chromatin types to begin S phase with similar concentrations of loaded MCM. The different loading dynamics require ORCA-dependent differences in origin recognition complex distribution. A consequence of heterochromatin licensing dynamics is that cells experiencing a truncated G1 phase from premature cyclin E expression enter S phase with underlicensed heterochromatin, and DNA damage accumulates preferentially in heterochromatin in the subsequent S/G2 phase. Thus, G1 length is critical for sufficient MCM loading, particularly in heterochromatin, to ensure complete genome duplication and to maintain genome stability.
MeSH term(s)	Animals ; Cell Cycle ; Cell Cycle Proteins/metabolism ; Chromatin/metabolism ; DNA Replication ; Euchromatin ; Eukaryotic Cells ; Heterochromatin ; Humans ; Minichromosome Maintenance Proteins/metabolism ; Origin Recognition Complex/metabolism ; Replication Origin
Chemical Substances	Cell Cycle Proteins ; Chromatin ; Euchromatin ; Heterochromatin ; Origin Recognition Complex ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
Language	English
Publishing date	2022-01-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
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/gkac003
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Article ; Online: Cell biology: The persistence of memory.

Kedziora, Katarzyna M / Purvis, Jeremy E

Nature

2017 Volume 549, Issue 7672, Page(s) 343–344

Language	English
Publishing date	2017-09-21
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature23549
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Article ; Online: Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells.

Zikry, Tarek M / Wolff, Samuel C / Ranek, Jolene S / Davis, Harris M / Naugle, Ander / Luthra, Namit / Whitman, Austin A / Kedziora, Katarzyna M / Stallaert, Wayne / Kosorok, Michael R / Spanheimer, Philip M / Purvis, Jeremy E

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 7, Page(s) e2309261121

Abstract: The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage ... ...

Abstract	The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage of tumor cells continues to divide in the presence of palbociclib-a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcomes. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant cells in both cultured and primary breast tumor samples resected from patients. Resistant cells showed premature accumulation of multiple G1 regulators including E2F1, retinoblastoma protein, and CDK2, as well as enhanced sensitivity to pharmacological inhibition of CDK2 activity. Using trajectory inference approaches, we show how plasticity among cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.
MeSH term(s)	Humans ; Female ; Cell Cycle ; Cell Division ; Piperazines/pharmacology ; Piperazines/therapeutic use ; Breast Neoplasms/drug therapy ; Cyclin-Dependent Kinase 4/metabolism ; Cyclin-Dependent Kinase 6/metabolism ; Protein Kinase Inhibitors/pharmacology ; Pyridines
Chemical Substances	palbociclib (G9ZF61LE7G) ; Piperazines ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22) ; Cyclin-Dependent Kinase 6 (EC 2.7.11.22) ; Protein Kinase Inhibitors ; Pyridines
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2309261121
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Article ; Online: Fluorescence resonance energy transfer microscopy (FRET).

Kedziora, Katarzyna M / Jalink, Kees

Methods in molecular biology (Clifton, N.J.)

2015 Volume 1251, Page(s) 67–82

Abstract: FRET (Förster Resonance Energy Transfer) microscopy breaks the resolution limit of light to let us investigate the conformation and function of proteins within living cells. Intensity-based methods are the most popular and direct approach to detect FRET. ...

Abstract	FRET (Förster Resonance Energy Transfer) microscopy breaks the resolution limit of light to let us investigate the conformation and function of proteins within living cells. Intensity-based methods are the most popular and direct approach to detect FRET. Among them, detection of sensitized emission signals and ratio imaging of specially designed FRET sensors are routinely used in modern cell biology laboratories. In this chapter, we provide protocols for both these techniques. We guide the reader through the mathematical corrections necessary to calculate the sensitized emission image. We illustrate this approach with an example of studying the interaction of nexin (SNX1) proteins. In the ratio FRET protocol, we focus on monitoring changes in cellular concentration of cAMP with an EPAC-based FRET sensor.
MeSH term(s)	Cyclic AMP/analysis ; Filtration ; Fluorescence Resonance Energy Transfer/instrumentation ; Fluorescence Resonance Energy Transfer/methods ; HEK293 Cells ; Humans ; Microscopy, Fluorescence/instrumentation ; Microscopy, Fluorescence/methods ; Sorting Nexins/ultrastructure
Chemical Substances	Sorting Nexins ; Cyclic AMP (E0399OZS9N)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-2080-8_5
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Article ; Online: Bistable switches as integrators and actuators during cell cycle progression.

Stallaert, Wayne / Kedziora, Katarzyna M / Chao, Hui Xiao / Purvis, Jeremy E

FEBS letters

2019 Volume 593, Issue 20, Page(s) 2805–2816

Abstract: Progression through the cell cycle is driven by bistable switches-specialized molecular circuits that govern transitions from one cellular state to another. Although the mechanics of bistable switches are relatively well understood, it is less clear how ... ...

Abstract	Progression through the cell cycle is driven by bistable switches-specialized molecular circuits that govern transitions from one cellular state to another. Although the mechanics of bistable switches are relatively well understood, it is less clear how cells integrate multiple sources of molecular information to engage these switches. Here, we describe how bistable switches act as hubs of information processing and examine how variability, competition, and inheritance of molecular signals determine the timing of the Rb-E2F bistable switch that controls cell cycle entry. Bistable switches confer both robustness and plasticity to cell cycle progression, ensuring that cell cycle events are performed completely and in the correct order, while still allowing flexibility to cope with ongoing stress and changing environmental conditions.
MeSH term(s)	Animals ; Cell Cycle/drug effects ; Cell Cycle/genetics ; Cell Cycle Checkpoints/drug effects ; Cell Cycle Checkpoints/genetics ; Cyclin-Dependent Kinases/genetics ; Cyclin-Dependent Kinases/metabolism ; DNA Damage/drug effects ; DNA Repair/drug effects ; DNA Replication/drug effects ; E2F Transcription Factors/genetics ; E2F Transcription Factors/metabolism ; Eukaryotic Cells/cytology ; Eukaryotic Cells/drug effects ; Eukaryotic Cells/metabolism ; Gene Expression Regulation ; Humans ; Intercellular Signaling Peptides and Proteins/pharmacology ; Mitogens/pharmacology ; Retinoblastoma Protein/genetics ; Retinoblastoma Protein/metabolism ; Signal Transduction
Chemical Substances	E2F Transcription Factors ; Intercellular Signaling Peptides and Proteins ; Mitogens ; Retinoblastoma Protein ; Cyclin-Dependent Kinases (EC 2.7.11.22)
Language	English
Publishing date	2019-10-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13628
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Article ; Online: AGS3 antagonizes LGN to balance oriented cell divisions and cell fate choices in mammalian epidermis.

Descovich, Carlos P / Lough, Kendall J / Jena, Akankshya / Wu, Jessica J / Yom, Jina / Spitzer, Danielle C / Uppalapati, Manuela / Kedziora, Katarzyna M / Williams, Scott E

eLife

2023 Volume 12

Abstract: Oriented cell divisions balance self-renewal and differentiation in stratified epithelia such as the skin epidermis. During peak epidermal stratification, the distribution of division angles among basal keratinocyte progenitors is bimodal, with planar ... ...

Abstract	Oriented cell divisions balance self-renewal and differentiation in stratified epithelia such as the skin epidermis. During peak epidermal stratification, the distribution of division angles among basal keratinocyte progenitors is bimodal, with planar and perpendicular divisions driving symmetric and asymmetric daughter cell fates, respectively. An apically restricted, evolutionarily conserved spindle orientation complex that includes the scaffolding protein LGN/Pins/Gpsm2 plays a central role in promoting perpendicular divisions and stratification, but why only a subset of cell polarize LGN is not known. Here, we demonstrate that the LGN paralog, AGS3/Gpsm1, is a novel negative regulator of LGN and inhibits perpendicular divisions. Static and ex vivo live imaging reveal that AGS3 overexpression displaces LGN from the apical cortex and increases planar orientations, while AGS3 loss prolongs cortical LGN localization and leads to a perpendicular orientation bias. Genetic epistasis experiments in double mutants confirm that AGS3 operates through LGN. Finally, clonal lineage tracing shows that LGN and AGS3 promote asymmetric and symmetric fates, respectively, while also influencing differentiation through delamination. Collectively, these studies shed new light on how spindle orientation influences epidermal stratification.
MeSH term(s)	Animals ; Cell Cycle Proteins/metabolism ; Carrier Proteins/metabolism ; Cell Division ; Epidermis/metabolism ; Cell Differentiation/genetics ; Spindle Apparatus/metabolism ; Cell Polarity ; Mammals/metabolism
Chemical Substances	Cell Cycle Proteins ; Carrier Proteins
Language	English
Publishing date	2023-04-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.80403
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Article ; Online: Antibiotic-induced accumulation of lipid II synergizes with antimicrobial fatty acids to eradicate bacterial populations.

Sidders, Ashelyn E / Kedziora, Katarzyna M / Arts, Melina / Daniel, Jan-Martin / de Benedetti, Stefania / Beam, Jenna E / Bui, Duyen T / Parsons, Joshua B / Schneider, Tanja / Rowe, Sarah E / Conlon, Brian P

eLife

2023 Volume 12

Abstract: Antibiotic tolerance and antibiotic resistance are the two major obstacles to the efficient and reliable treatment of bacterial infections. Identifying antibiotic adjuvants that sensitize resistant and tolerant bacteria to antibiotic killing may lead to ... ...

Abstract	Antibiotic tolerance and antibiotic resistance are the two major obstacles to the efficient and reliable treatment of bacterial infections. Identifying antibiotic adjuvants that sensitize resistant and tolerant bacteria to antibiotic killing may lead to the development of superior treatments with improved outcomes. Vancomycin, a lipid II inhibitor, is a frontline antibiotic for treating methicillin-resistant
MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Vancomycin/pharmacology ; Methicillin-Resistant Staphylococcus aureus ; Fatty Acids ; Gram-Positive Bacterial Infections/microbiology ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents ; Vancomycin (6Q205EH1VU) ; Fatty Acids ; muramyl-NAc-(pentapeptide)pyrophosphoryl-undecaprenol
Language	English
Publishing date	2023-03-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.80246
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Article: Bistable switches as integrators and actuators during cell cycle progression

Stallaert, Wayne / Kedziora, Katarzyna M. / Chao, Hui Xiao / Purvis, Jeremy E.

FEBS letters. 2019 Oct., v. 593, no. 20

2019

Abstract: Progression through the cell cycle is driven by bistable switches—specialized molecular circuits that govern transitions from one cellular state to another. Although the mechanics of bistable switches are relatively well understood, it is less clear how ... ...

Abstract	Progression through the cell cycle is driven by bistable switches—specialized molecular circuits that govern transitions from one cellular state to another. Although the mechanics of bistable switches are relatively well understood, it is less clear how cells integrate multiple sources of molecular information to engage these switches. Here, we describe how bistable switches act as hubs of information processing and examine how variability, competition, and inheritance of molecular signals determine the timing of the Rb‐E2F bistable switch that controls cell cycle entry. Bistable switches confer both robustness and plasticity to cell cycle progression, ensuring that cell cycle events are performed completely and in the correct order, while still allowing flexibility to cope with ongoing stress and changing environmental conditions.
Keywords	cell cycle ; mechanics ; plasticity
Language	English
Dates of publication	2019-10
Size	p. 2805-2816.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13628
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