Evidence map›Paper›PMID 38370828›Full record

ArticlebioRxiv : the preprint server for biology2024

DNA density is a better indicator of a nuclear bleb than lamin B loss.

Samantha Bunner, Kelsey Prince, Karan Srikrishna, Emily Marie Pujadas, Antonia Amonu McCarthy, Anna Kuklinski, Olivia Jackson, Pedro Pellegrino, Shrushti Jagtap, Imuetiyan Eweka and 15 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 5 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

25 authors at 3 institutions in 2 countries.

Samantha BunnerBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Kelsey PrinceBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Karan SrikrishnaBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Emily Marie PujadasDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Antonia Amonu McCarthyBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Anna KuklinskiBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Olivia JacksonBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Pedro PellegrinoBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Shrushti JagtapBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Imuetiyan EwekaBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Colman LawlorBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Emma EastinBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Griffin YasBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Julianna AielloBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Nathan LaPointeBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Isabelle Schramm von BlucherBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Jillian HardyBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Jason ChenBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Vadim BackmanDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Anne JanssenSchool of Biological Sciences, University of Cambridge, Cambridge, United Kingdom.
Mary PackardBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Katherine DorfmanBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
Luay AlmassalhaDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Michael Seifu BahiruBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.
A D StephensBiology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA.ORCID 0000-0001-5474-7845
Amherst College · USNorthwestern University · USUniversity of Cambridge · GB

Funding

Center for 3D Structure and Physics of the GenomeUM1HG011536 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2020 to 2024
$11.8M
Technology Development UnitU54CA268084 · NCI · NORTHWESTERN UNIVERSITY · PI Vadim Backman, Daniela E Matei · 2022 to 2026
$10.0M
Studying E-cadherin dynamics during extravasation and metastatic colonizationU54CA261694 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI ROGER D KAMM · 2021 to 2026
$9.1M
Reducing Cancer Transcriptional Heterogeneity through Regulation of Chromatin StructureR01CA228272 · NCI · NORTHWESTERN UNIVERSITY · PI BACKMAN, VADIM, ROY, HEMANT K. · 2018 to 2022
$3.2M
Analyzing the role of chromatin compaction in nuclear mechanics, structure, and functionR00GM123195 · NIGMS · UNIVERSITY OF MASSACHUSETTS AMHERST · PI STEPHENS, ANDREW DANIEL · 2020 to 2022
$745k
NCI NIH HHS R01 CA228272NCI NIH HHS U54 CA261694NCI NIH HHS U54 CA268084NHGRI NIH HHS UM1 HG011536NIGMS NIH HHS R00 GM123195
6 · The paper itself

Abstract

Nuclear blebs are herniations of the nucleus that occur in diseased nuclei that cause nuclear rupture leading to cellular dysfunction. Chromatin and lamins are two of the major structural components of the nucleus that maintain its shape and function, but their relative roles in nuclear blebbing remain elusive. Lamin B is reported to be lost in blebs by qualitative data while quantitative studies reveal a spectrum of lamin B levels in nuclear blebs dependent on perturbation and cell type. Chromatin has been reported to be decreased or de-compacted in nuclear blebs, but again the data are not conclusive. To determine the composition of nuclear blebs, we compared the immunofluorescence intensity of lamin B and DNA in the main nucleus body and nuclear bleb across cell types and perturbations. Lamin B nuclear bleb levels varied drastically across MEF wild type and chromatin or lamins perturbations, HCT116 lamin B1-GFP imaging, and human disease model cells of progeria and prostate cancer. However, DNA concentration was consistently decreased to about half that of the main nucleus body across all measured conditions. Using Partial Wave Spectroscopic (PWS) microscopy to measure chromatin density in the nuclear bleb vs body we find similar results that DNA is consistently less dense in nuclear blebs. Thus, our data spanning many different cell types and perturbations supports that decreased DNA is a better marker of a nuclear bleb than lamin B levels that vary widely.

Identifiers

PMID38370828
PMCPMC10871186
OpenAlexW4391616153

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.