Microphases are targets for therapeutic intervention for neurodegenerative disorders

Genes are copied to make RNA transcripts, then the copies, or transcripts, are translated into proteins. The transcripts, known as pre-messenger-RNA (pre-mRNA) are processed in the cellular nucleus to generate bona fide mRNAs that are then translated by ribosomes. This processing, known as splicing, happens in a cellular region known as nuclear speckles. Errors in splicing, which can happen as a function of aging, during cellular stress, or during aberrant cellular responses, directly contribute to the onset and progress of various cancers and are associated with neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS).

Speckles are thought to be biomolecular condensates, where DNA, RNA and proteins are organized into distinct molecular communities that form via phase separation. Rohit V. Pappu, the Gene K. Beare Distinguished Professor of Biomedical Engineering in the McKelvey School of Engineering at Washington University in St. Louis, and Min Kyung Shinn, a former postdoctoral researcher in his lab, investigated some of the physical features of nuclear speckles that were inconsistent with the type of uniform droplets one expected to see if they formed via liquid-liquid phase separation.

Shinn and Pappu set out to reconstitute the phase transitions of various RNA-binding proteins that belong to nuclear speckles, after discussing the issue with K.V. Prasanth, professor of cell & developmental biology at University of Illinois Urbana-Champaign and an expert in nuclear speckles. Results of their research were published in Cell Dec. 19, 2025.

Right away, their microscopy images revealed that the speckle-associated proteins were distinct in the types of structures they formed.

“We realized that the RNA binding proteins, which feature distinct combinations of folded RNA recognition motifs (RRMs) and distinct types of intrinsically disordered regions (IDRs), fit the description of being unconventional block copolymers,” Pappu said. “These types of molecules, which have regions that favor versus disfavor interactions with the solvent, are known to form micelles or microphases. Within such nanometer-sized block copolymeric molecules and form assemblies that are on the order of tens of nanometers in size, encompassing tens to hundreds of molecules depending on the molecular architectures and the nature of the intermolecular and inter-block interactions.”

Their first microscopy images spurred an intense 2 ½-year-long investigation into all aspects of RRM-containing, speckle-associated proteins and added numerous researchers to the team. What emerged was rather simple, Pappu said. 

“The amino acid sequences encode protein-specific patterns of strong attractions, strong repulsions and agnostic inter-block or inter-domain interactions,” he explained. “This combination sets up an interplay such that at some specific size, the attractions and repulsions counterbalance one another, and assemblies, known as microphases, which have specific nanoscale sizes, are formed.”

Shinn found that microphases can come together and form higher-order structures such as those that are seen in cells. But they defied the definition of being macrophases because they do not ever fuse, or drip, or become rounded like drops of liquid. Instead, there is an interplay of attractions and repulsions that limits the sizes of microphases, assemblies of microphases, or even higher-order structures that can form. The upshot is the type of mottled or speckled organization one observes in cells. 

Shinn then found that the structures of microphases enable specific and preferential interactions with specific long noncoding RNAs (lncRNAs) such as MALAT1, which has been established as a regulator of speckle activities. By analyzing the RNA sequence grammars, Shinn discovered that disrupting specific motifs within the sequence of MALAT1 essentially obliterated the specificity of recognition of this lncRNA by the microphase formed by the splicing factor, SRSF1. 

“Strikingly, the protein TDP-43, which is associated with ALS pathology also forms microphases, which are precise structures encompassing precise numbers of molecules,” Shinn said. “It appears that many of the higher-order inclusions and aggregates found in motor neurons of ALS patients might be traced back to the smallest structures — microphases — that this protein forms.”

The team said the microphases seem to be the relevant targets for therapeutic intervention in specific cancers and in ALS because they have precise organizations of molecules. Their research allows others to study the structures formed by microphases and ask how they can be disrupted, stabilized or otherwise manipulated. 

Finally, Shinn and Pappu said the novel class of molecules, which they refer to as FRODOs, are likely the norm rather than the exception as organizers of biomolecular condensates.

“These FRODOs can be transformative for the design of novel biomaterials for a range of engineering applications including heterogeneous catalysis — an area that is just coming into focus for the Pappu lab,” Pappu said.

Shinn MK, Tomares DT, Liu V, Pant A, Qiu Y, Vitalis A, Song YJ, Ayala Y, Ruff KM, Strout GW, Lew MD, Prasanth KV, Pappu RV. Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases. Cell. Dec. 19, 2025. DOI:  https://doi.org/10.1016/j.cell.2025.11.026

Funding for this research was provided by the National Institutes of Health (K99GM152778, R01NS121114, R35GM124858, T32EB019944, R01GM132458); the St. Jude Children’s Research Hospital research collaborative on the biology and biophysics of RNP granules; the U.S. Air Force Office of Scientific Research (FA9550-20-1-0241); and the National Science Foundation (MCB2227268, Center for Quantitative Cell Biology); the Cancer Center at Illinois seed grant; and ARPA-H. 

The collection of all QF-DEEM images obtained for each of the constructs, computational data, and code used for analyses are available via http://doi.org/10.5281/zenodo.17096527.

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