cxxv) We also tried to measure PGRN levels in GBA-PD patients. However, only one sample had pathogenic GBA mutation, which failed to conclude the link of GBA mutation and PGRN.
cxxvi) Meanwhile, in PD, GRN SNP rs5848 that lowers PGRN levels is said to be associated with PD risk. When I previously communicated with Rene, Gil, and Akhil, they said this is an ongoing effort at Denali although it takes a while.
I don’t know about MJFF, but If I have found out something, I will let you know.
MJF
| Animal | https://www.michaeljfox.org/grant/delayed-start-assessment-program-progranulin-progressive-rodent-model-parkinsons-disease | Neurodyn Inc |
| https://www.michaeljfox.org/grant/assessment-therapeutic-efficacy-progranulin-sub-chronic-animal-model-pd |
Prophylactic vs Therapeutic
| Midbrain | ISF | CSF | prophylactic | Therapeutically | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| pros | Cons | pros | Cons | |||||||
| Can look at, cleared pre-existing aSyn pathology | Can look at, normalization of TH ie baseline, required for replacement Tx? | |||||||||
| succss | NLRP3, TAK-341: | Mice, | LV-A53T (hippocampus) → 2w (1w in paper) after, Tx (13w, ip) | No TH data | NA | |||||
| rat | Pff | O | ||||||||
| IONIS ASO BIIB101/ION464 | RAT | Therapeutic: Pff (Striatum) → (3w after) Tx (ICV) | {Cole, 2021 #2235} ↓50% aSyn → ↓ >70% paSyn → ↑ TH cell (1.3-2 fold increase vs vehicle-treated animal, but don't know relative improvement vs baseline ie normalization) | |||||||
| Prophylactic model | ||||||||||
| BIIB054 (=cinpanemab) | Prophylactic | {Weihofen, 2019 #2236} in all three models, chBIIB054 treatment started prior to intrastriatal PFF inoculation: ↓ truncated aSyn in contralateral cortex. no TH data | ||||||||
| Therapeutic | {Weihofen, 2019 #2236} No theraptueic model used | |||||||||
| prasinezumab | Prophylactic | |||||||||
| Therapeutic | {Games 2014}(mThy1—syn, line 61) SN: =TH cell, striatum: ↑ TH {Masliah, 2011 #2240} PDGF-b promoter (Line D), TH data 없는 듯? | |||||||||
Protein tags
| category | purpose | examples |
|---|---|---|
| Affinity tag | appended to proteins so that they can be purified from their crude biological source using an affinity technique. | chitin binding protein (CBP), maltose binding protein (MBP), Strep-tag[2] and glutathione-S-transferase (GST) |
| Solubilization tag | are used, especially for recombinant proteins expressed in chaperone-deficient species such as E. coli, to assist in the proper folding in proteins and keep them from precipitating. | thioredoxin (TRX) and poly(NANP). Some affinity tags have a dual role as a solubilization agent, such as MBP, and GST. |
| Chromatography tag | used to alter chromatographic properties of the protein to afford different resolution across a particular separation technique. | FLAG-tag. |
| Epitope tag | short peptide sequences which are chosen because high-affinity antibodies can be reliably produced in many different species. These are usually derived from viral genes, which explain their high immunoreactivity. These tags are particularly useful for western blotting, immunofluorescence and immunoprecipitation experiments, | ALFA-tag, V5-tag, Myc-tag, HA-tag, Spot-tag, T7-tag and NE-tag. |
| Fluorescence tag | used to give visual readout on a protein. | GFP BFP (BLUE FLUORESCENT PROTEIN) eg: Atuka MOUSE nlrp3, published in 1996, derived from Aequorea victoria, 1 MSKGEELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKFICTT GKLPVPWPTL VTTFSHGVQC 71 FSRYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK 141 LEYNFNSHNV YIMADKQKNG IKVNFKIRHN IEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSALSKD 211 PNEKRDHMVL LEFVTAAGIT HGMDELYK |
| Many recombinant proteins are expressed as fusion proteins, meaning that they contain an affinity/epitope tag (e.g. His or GST). A tag is a short sequence of DNA that codes for a specific amino acid, which is frequently inserted into a target gene at the point of coding for expression at either the N or C terminal of the protein required. One of the most commonly used tags is the polyhistidine tag, also known as His-Tag, which is a string of usually between six and nine histidine residues (see Figure 1 below). This method of tagging is especially useful as it allows for easy purification and detection of the recombinant protein. he fusion tag is routinely left attached to the protein when carrying out experiments, with the assumption that the addition has no effect on structure or function | ||
| These data show that, although function was not altered for any of the proteins studied, the structure of one of the His-tagged proteins was different from the native form of that protein. In Most Cases, the Presence of His-Tag Decreased Thermal Stability |
PRS
| PRS inhouse | pathway-specific PRSes, collaboration with Scripps, epistasis was not accounted for | ||||||||||||||||||||||||||||||||||||||||||||||
| (rasuhn et al., 2019, PMID 33324897) |
Table 2 SNPs taken a genome-wide association study on PD used for stratification of patients (omics+/- groups)
| ||||||||||||||||||||||||||||||||||||||||||||||
| (inger, 2021 #1651) PRS with feature (LASSO) | 47 SNPs leads to AUC of 0.85 and can be found in the Supplementary Information |
Proteomics
Data Presentation
{Wessner, 2022 #2572} good review
Issues and Solving
| Primary Reason | problem | How to solve/normalize |
|---|---|---|
| inevitable differences in sample processing and experimental runs that may be separated by hours or weeks. | Intersample variation | normalization within and between experiments,
|
| missing data problem" ( |
PD Proteomics
| Brain | CSF | blood | Fibroblast |
|---|
Uncertain Spans
- The “succss” label in the first row of the Prophylactic vs Therapeutic table is reproduced as printed (likely a typo for “success” in the source).
- The third Therapeutically pros/cons header row text overlaps the first content row in the source layout; whether it is intended as a sub-header of the columns or a sticky annotation row could not be unambiguously determined from this photo alone.
- The “Atuka MOUSE nlrp3” annotation next to the BFP/GFP row appears to be a handwritten-style note overlaid on the printed example; reproduced verbatim but its exact spelling (“Atuka”) was not cross-verified against any other photo.