entity

cytoplasm

Entity Detail — Knowledge Graph Node

Understanding Entity Pages

This page aggregates everything SciDEX knows about cytoplasm: its mechanistic relationships (Knowledge Graph edges), hypotheses targeting it, analyses mentioning it, and supporting scientific papers. The interactive graph below shows its immediate neighbors. All content is AI-synthesized from peer-reviewed literature.

5Connections

13Hypotheses

4Analyses

0Outgoing

5Incoming

0Experiments

4Debates

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Wiki Pages (6)

Knowledge base pages for this entity

Outgoing (0)

Target	Relation	Type	Str
No outgoing edges

Incoming (5)

Source	Relation	Type	Str
NPM1	transports	protein	0.90
TDP-43	accumulates	protein	0.90
Chmp2Bwt	expressed_in	protein	0.90
CHMP2BΔ10	expressed_in	variant	0.90
DNAJB6b	regulates	protein	0.70

Targeting Hypotheses (13)

Hypotheses where this entity is a therapeutic target

Hypothesis	Score	Disease	Analysis
C9orf72 Hexanucleotide Repeat Dipeptide Repeat Proteins Inhi	0.738	neurodegeneration	Legacy Pre-Pipeline Hypothesis Import
TDP-43 condensation thermodynamics as a therapeutic target a	0.724	neuroscience	How can subcellular compartmentalization
RNA-binding protein condensate maturation from reversible ph	0.626	neurodegeneration	Causal Sequence of TDP-43 Nuclear Cleara
Cell-state stratification is required to resolve Causal Sequ	0.612	neurodegeneration	Causal Sequence of TDP-43 Nuclear Cleara
Perturbation-first validation should precede therapeutic cla	0.608	neurodegeneration	Causal Sequence of TDP-43 Nuclear Cleara

C9orf72 Nucleocytoplasmic Transport Rescue for ALS/FTD	0.597	neurodegeneration	Test
RNA Metabolism and Nucleocytoplasmic Transport Defects	0.580	neurodegeneration	Cross-disease neurodegeneration mechanis
Nucleocytoplasmic Transport Disruption	0.520	neurodegeneration	What mechanisms underlie TDP-43's contri
SASP-Secreted MMP-9 from Senescent Microglia Disrupts TDP-43	0.511	als	What are the mechanisms by which microgl
Nuclear Pore and Nucleocytoplasmic Transport Machinery as Ga	0.500	neurodegeneration	What determines the specificity of RNA-p
TDP-43 Phase Separation Destabilization Drives Cytoplasmic A	0.500	neurodegeneration	Test
Nuclear Export Sequestration and Cytoplasmic Depletion	0.475	-	How does the intron-retained RNA isoform
SASP-Secreted MMP-9 from Senescent Microglia Disrupts Nuclea	0.361	als	What are the mechanisms by which microgl

Mentioning Analyses (4)

Scientific analyses that reference this entity

Causal Sequence of TDP-43 Nuclear Clearance to Cytoplasmic Aggregation in ALS Mo

neurodegeneration | 2026-04-27 | 4 hypotheses Top: 0.760

What molecular mechanisms enable functional recovery and muscle re-innervation a

neurodegeneration | 2026-04-14 | 2 hypotheses Top: 0.683

Does DNAJB6 directly inhibit cross-seeding between tau, α-synuclein, and TDP-43

neurodegeneration | 2026-04-12 | 0 hypotheses

What are the specific design principles for small molecules that can selectively

medicinal chemistry | 2026-04-10 | 0 hypotheses

Experiments (0)

Experimental studies targeting or related to this entity

Experiment	Type	Disease	Score	Feasibility	Model	Status	Est. Cost
No experiments found

Related Papers (4)

Scientific publications cited in analyses involving this entity

Title & PMID	Authors	Journal	Year
Loss of Nuclear TDP-43 Impairs Lipid Metabolism in Microglia-Like Cells. [PMID:41000837]	Unknown	bioRxiv	2025
Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopat [PMID:34412701]	Unknown	Acta Neuropathol Commun	2021
Reduction of matrix metalloproteinase 9 (MMP-9) protects motor neurons from TDP- [PMID:30458231]	Unknown	Neurobiology of disease	2019
TDP-43 Depletion in Microglia Promotes Amyloid Clearance but Also Induces Synaps [PMID:28669544]	Unknown	Neuron	2017

Debates (4)

Multi-agent debates referencing this entity

What is the precise causal sequence of molecular events linking TDP-43 nuclear c

closed · Rounds: 4 · Score: 0.67 · 2026-04-28

The debate identified that TDP-43 undergoes both normal and pathological phase s

closed · Rounds: 4 · Score: 0.43 · 2026-04-21

The debate revealed that DNAJB6 evidence is limited to polyglutamine aggregation

closed · Rounds: 4 · Score: 0.79 · 2026-04-16

The study shows dramatic functional recovery and muscle re-innervation after cyt

closed · Rounds: 4 · Score: 0.85 · 2026-04-15

Related Research

Hypotheses and analyses mentioning cytoplasm in their description or question text

C9orf72 Nucleocytoplasmic Transport Rescue for ALS/FTD

Score: 0.597 · neurodegeneration · 2026-05-06

C9orf72 intronic GGGGCC repeats produce dipeptide repeat proteins and RNA foci that sequester nuclear import factors (TN

RNA Metabolism and Nucleocytoplasmic Transport Defects

Score: 0.580 · neurodegeneration · 2026-04-28

Impaired RNA processing and disrupted nucleocytoplasmic transport represent a convergent molecular phenotype, but most c

Nucleocytoplasmic Transport Disruption

Score: 0.520 · neurodegeneration · 2026-04-21

## Mechanistic Overview Nucleocytoplasmic Transport Disruption starts from the claim that modulating NUP107 within the d

SASP-Secreted MMP-9 from Senescent Microglia Disrupts TDP-43 Nuclear Retention L

Score: 0.511 · als · 2026-04-27

The hypothesis proposes that MMP-9 (matrix metalloproteinase-9), secreted via the senescence-associated secretory phenot

Nuclear Pore and Nucleocytoplasmic Transport Machinery as Gatekeepers

Score: 0.500 · neurodegeneration · 2026-04-21

## Mechanistic Overview Nuclear Pore and Nucleocytoplasmic Transport Machinery as Gatekeepers starts from the claim that

TDP-43 Phase Separation Destabilization Drives Cytoplasmic Aggregation

Score: 0.500 · neurodegeneration · 2026-05-03

Aberrant arginine methylation prevents TDP-43 liquid-liquid phase separation, promoting pathogenic aggregation. PRMT5-me

Nuclear Export Sequestration and Cytoplasmic Depletion

Score: 0.475 · unknown disease · 2026-04-26

Retained intronic sequences contain cryptic nuclear retention elements that recruit export inhibitory complexes (PHAX, A

SASP-Secreted MMP-9 from Senescent Microglia Disrupts Nuclear-Cytoplasmic Transp

Score: 0.361 · als · 2026-04-26

This hypothesis proposes that MMP-9 secreted by senescent microglia in the SASP drives ALS pathology through disruption