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Murphy, Z. R.

Publications and source records attributed to Murphy, Z. R..

2 recordsLinked to original sources

BAG3 coordinates astrocytic proteostasis of Alzheimer's disease-linked proteins via proteasome, autophagy, and retromer complex interactions

BackgroundBcl-2-associated athanogene 3 (BAG3) is a mediator of chaperone assisted selective autophagy, and in the brain, most highly expressed in astrocytes. However, its role in astrocytes remains poorly defined. Given the genetic and pathological links of BAG3 to proteostasis and neurodegenerative diseases, we investigated how BAG3 contributes to astrocyte function and Alzheimers disease (AD). MethodsSnRNA-seq of the human brain determined cell type expression of BAG3. CRISPR/Cas9 gene editing in human iPSCs, followed by tandem mass tag-mass spectrometry and RNA-sequencing was performed to assess proteomic and transcriptomic changes following BAG3 loss. Co-immunoprecipitation of BAG3 in human astrocytes defined the interactome, with top interactors being validated by western blot (WB), AlphaFold modeling, and proximity ligation assays. In astrocytes, autophagic flux, lysosomal phenotypes, proteasome activity, and endocytic uptake were measured in BAG3 KO and BAG3 WT. Finally, BAG3 expression was assessed in postmortem AD brain by WB and snRNA-seq, and its functional relevance to amyloid-{beta} (A{beta}) degradation was tested in co-cultures of BAG3 KO iAs with familial AD neurons. ResultsIn human brain and iPSC models, BAG3 was most highly expressed in astrocytes. Further, BAG3 loss caused greater proteomic disruption in astrocytes than in neurons. In the absence of BAG3, astrocytes showed reduced autophagy, diminished lysosome abundance and activity, and decreased proteasome function. To uncover molecular binding partners of BAG3 that might influence these phenotypes, we performed co-immunoprecipitation, revealing interactions with HSPB8 and other heat shock proteins, proteasome regulators (PSMD5, PSMF1), and the retromer component, VPS35. Integration of BAG3 KO transcriptomic and proteomic datasets pinpointed AD-relevant proteins under post-translational control of BAG3, which included GFAP, BIN1, and HSPB8. HSPB8 levels were markedly reduced in BAG3-deficient astrocytes with overexpression partially rescuing its levels. Loss of astrocytic BAG3 impaired A{beta} clearance in co-culture with APP/PSEN1 mutant neurons, directly linking BAG3 to a disease-relevant astrocyte function. Finally, analysis of postmortem brain tissue revealed BAG3 marks a stress-responsive astrocyte subtype in the brain of aged individuals with AD. ConclusionsBAG3 binds to key regulators of autophagy, proteasome activity, and retromer function to coordinate astrocyte proteostasis, lysosomal function, and A{beta} clearance. These findings position BAG3 as a potential therapeutic target and coordinator of glial protein quality control in neurodegeneration.

neuroscience↗

Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases1-4. Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prior to becoming double-strand mutations if unrepaired or misrepaired5. However, current DNA sequencing technologies cannot resolve these initial single-strand events. Here, we developed a single-molecule, long-read sequencing method that achieves single-molecule fidelity for single-base substitutions when present in either one or both strands of the DNA. It also detects single-strand cytosine deamination events, a common type of DNA damage. We profiled 110 samples from diverse tissues, including from individuals with cancer-predisposition syndromes, and define the first single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. Since the double-strand DNA mutations interrogated by prior studies are only the endpoint of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable new studies of how mutations arise in a variety of contexts, especially in cancer and aging.

genomics↗