PARKN GT (PFR-4249-100)

PARKN GT is the AAV9-Parkin gene-therapy program led by Takeshi Hioki under program code PFR-4249-100. The corpus material covers in-vivo delivery literature, an executive-summary expression timeline, codon-optimized PRKN constructs, a decision tree and draft timeline, biomarker expected-change matrices, NHP studies, sample-size logic for a PRKN natural-history study, the bioanalytical method to differentiate human and monkey Parkin, the multi-year Parkin-binding-assay HTS log up to termination, the PE I Imaging GBA plan, and TM-level assay tables.

This page only collects sources whose nav_path is rooted in or sits under PARKN GT (Takeshi Hioki, PFR-4249-100) (or its trailing-tail Parkin, > TM > Assays > ... > PINK-1). Topic-level cross-program context for Parkin, Parkin PD, and pS65-Ub lives at parkin.

Program Overview

The development timeline recorded across the executive-summary pages is LGE 2020 Oct → PE 2021/12 → CN 2023/10 → CS 2024/06 → IND 2025/86 → P1 start ?, with the trailing 2025/86 token flagged as uncertain (20240722_182011). 20240722_182014 lists the gates separately as PE Feb 2022 / CN Mar 2023 / CS Mar 2024 / IND Aug 2025 and records that 2 promoters (PGK1 and Syn1) and 3 codon-optimized PRKN cDNAs (CpG5-2, CpG5-4, CpG0-3) were prioritized in 202203, with AAV9 vectors carrying the three codon-optimized PRKN cDNA sequences in evaluation. Cassette nomenclature in source includes PK012 (WT reference), PK022/023/024/025/026, PK030/031, PK041, PK044, PK045, PK046.

The strategic decision spine is 20240722_182021: a decision tree contrasting an ICM/neurosurgery with established AAVs primary scenario against a Novel capsids / iCP-Parkin contingency plan, with mouse POC criteria >=20% recovery of mitochondria function (WB, Seahorse), neuroprotection of DA neurons (IHC) in SN, or symptomatic function (DA by HPLC) by local AAV injection over vehicle control and NHP transgene-expression criteria >=20% of DA neurons expressing Parkin protein in SN by IHC (or alternative ISH plus protein expression by LC-MS). The biomarker expected-change matrices give per-row predictions for CSF Parkin protein, CSF Parkin mRNA, CSF pS65-Ub, and Brain MC1 proteins in MPTP and Parkin-KO mouse models.

The competitor / strategy comparison on 20240722_182018 names Cellivery iCP-Parkin (Chung 2020 #1378), MISSION Therapeutic / NysnoBio USP30 inhibitor / MTX115325 / AAV5 / ASO (Fang 2023 #2558), MitoCoP (mitophagy inducer / ASO / 40 candidate hit-genes), and the DBS+PRkn discussion (Treatment timelines are different, Treatment targets are different (DBS: STN/GP/PN; Prkn: P/SN/SN+P), Dual treatment doubles several risks, Even for Ph1/2, it may impossible to find trial patients in a reasonable time frame).

The clinical / TE / PD / IMG biomarker plan on 20240722_182029 is explicit that Target Engagement: CSF Parkin protein and Parkin PET are co-deployed; Pharmacodynamic: pS65-Ub; Imaging: MC1 PET is proposed as the translatable in-vivo brain imaging biomarker of mitochondrial integrity in Parkin-PD; Disease Related: DaTScan; and a-Syn pathology is rarely observed in the target population, so aSyn-related biomarkers are not planned for this project.

The PRKN longitudinal observational study proposed in 20240722_182033 targets N ~ 25 (10 HC, 15 symptomatic PD within 2 years of symptom onset), biallelic confirmed LOF PRKN mutation carriers, 3-5 years follow-up; endpoints span UPDRS / digital motor / 7T MRI (volumetric, NM, DTI) / DaT SPECT or VMAT2 PET / 31P MRS / Parkin PET if available / MC1 PET / FDG-PET / plasma NfL, dopamine metabolites, lactate, pyruvate, creatine-kinase, sphingomyelins / CSF pS65-Ub, VDAC, phosphorylated Parkin, TOM40/20, mtDNA, cytochrome C, IL-6. Sample- size cells worth checking before re-quoting include the partial heatmap figures and the line 20% reduction and 50% CV results in a sample size of 21 at 80% power, one-sided alpha = 0.10.

NHP plan is in 20240722_182040 (1M NHP biodistribution at NBR 047-052, Injection Feb/Mar 2023, Necropsy Mar/Apr 2023, IHC/ISH report Jun 2023; AAV9 PK044 with PGK1 priority; Neurochase vs Clear Point device choice; CSF sampling Days -15, 15, 29 with 1.0 mL or as much as possible, centrifuge 4°C, 2000g, 5 minutes, aliquoting into Eppendorf Protein LoBind, shipment to TSHO; NBB / PrecisionMed correlation plan with target normal CSF Parkin ≈ 1 pg/mL).

The bioanalytical-method comparison on 20240722_182043 and 20240722_182046 compares HA-Tag, In situ hybridization (RNAScope), LCMS (DMPK), SMCxPro (NSTM), IHC of HA-PRKN, and an Apomorph? column. Homology between human and NHP Parkin is 97%. Three pairs of species-specific peptides were identified for LC/MS measurement of parkin proteins, with material ordered 20220801. SMCxPRO LLOQ for CSF Parkin protein is 1.22 pg/mL in 100 μL neat CSF and 0.12 pg/mL in 1 mL CSF (10x concentration). The buffer-LLOQ row gives ELISA 125 (pg/mL), MSD 24.4 (pg/mL), and SMCxPRO 0.61.

The Parkin binding-assay HTS history runs across 20240722_182053, 20240722_182057, and 20240722_182100: a 11- candidate list was sent to TCAL on 20210709; the development log spans 20210615 → 20220715, including ASMS results, Biogen’s compound exploration, ADDP E000-25157 parkin binding assay development with the 20221215 termination memo and 20230331 ASMS assay-development result PDF. After termination, the program proposes RDDU's PE I Imaging GBA Plan (20240722_182100, 20240722_182103) with a PK/PD strategy and a [Benchmark] FA GT PRC1 PE narrative.

Safety and TM-level assay tables are at 20240722_182106 (Safety de-risking strategy, Sharefolder, PGRN resources, Assays table) and 20240722_182110 (TM Assays summary, NBB LLOQ tables, brain/CSF comparison, pS65-Ub reagents, ubiquitin linkage, IVC, Parkin activity assay). 20240722_182113 trails into Parkin activity assay? > TMQB > TPP/TCP > Unmet Needs > Vector production > PINK-1 and is the bridge from the PARKN GT TM/Assay strand to the PINK-1 page in the corpus.

Evidence Package

evidence area	source-captured detail	source
In-vivo Parkin gene/protein delivery literature	MPTP mice (Paterna 2007, Yasuda 2011), 6OHDA rat/mice (Vercammen 2006, Chung 2020 / Cellivery iCP-Parkin), Bian 2012 Parkin Tg, Manfredsson 2007 6OHDA rat + AAV Parkin (provisional).	20240722_182011
Cassette / capsid in vitro program	12 expression cassettes tested in plasmid → 9 nominated as LGE candidates; in-vivo POC with AAV9 in 4-month Parkin KO mice, ICM, single injection, n=7 per cassette; codon optimization with CpG5-2, CpG5-4, CpG0-3 and PGK1 / Syn1 promoters.	20240722_182011, 20240722_182014
Executive summary, AAV9-Parkin expression comparisons	Y-axis Parkin protein (% of PK012); bars for PK012, PK044, PK045, PK046; iPSC-DA infection plot for PK044/045/046 vs PK012 (WT).	20240722_182014
Decision tree and draft timeline	Mouse POC and NHP capsid-profiling gates with >=20% criteria; established AAV path (Decision 2-1 / 2-2 Feb 2023); iCP-Parkin path (Cellivery agreement Dec 2022); best-case Aug 2025 IND; alternative Dec 2023 path with May 2026 IND.	20240722_182021
Biomarker expected-change matrix (MPTP and Parkin KO)	CSF Parkin protein/mRNA: =/None at baseline → ↑↑ on Tx; CSF pS65-Ub: very low at baseline → ↑ on Tx; Brain MC1 proteins: ↓ at baseline → ↑ on Tx (per Palacino).	20240722_182021, 20240722_182025
In-vivo MPTP / 6-OHDA / α-Syn PFF / R275W tables	rAAV9 hSYN1-coPRKN (PK041) and hPGK1-coPRKN (PK044) at 1x10^8-1x10^10 vg/brain; ~20% DA-neuron recovery (IHC), ~30% recovery (WES); α-Syn PFF 1M ~23% DA-neuron recovery; LPS Iba1 trend; naive R275W STR DA unaltered at 25M.	20240722_182025
KOL inputs	Hattori (PRKN-PD astrocyte immaturity / lactate consumption / dancing-feet dyskinesia / R275W KI mouse), Schlossmacher (anti-oxidant Parkin function, ↑ H2O2 and GSH:GSSG ratio in Parkin-PD), Christine Klein (31P MRS, RT-QuIC aSyn seeding, neuromelanin imaging, vit K2 PINK1 fly model, ↓ parkin → ↑ STING → ↑ IL-6).	20240722_182025, 20240722_182029
PRC1 dataset and FXN GT benchmark	PRC1 Candidates Of In Vivo Disease-relevant/Function Model data criteria; FXN benchmark for NHP biodistribution and ROA after capsid selection.	20240722_182025
Externalization (publication / IP)	Brain Parkin assay publication planned with Juntendo-U (no IP); pS65Ub publication will (no IP, since assistance from Mitokinin).	20240722_182021, 20240722_182025
FY22 goals	Set preliminary target CSF parkin protein level via NBB CSF and brain-CSF correlation (NBB and NHP biodistribution); confirm transgene protein expression in monkey CSF.	20240722_182025
Biomarker plan	TE: CSF Parkin protein (SMC); Parkin PET (Paul McQuade & Makoto Fusimi); PD: pS65-Ub; IMG: MC1 PET with [18F]BCPP-EF; DR: DaTScan; aSyn pathway not pursued.	20240722_182029
Natural-history strategy	MJFF / PPMI MC1 PET proposal, Leuven Koen Van Laere collaboration, PDGene (PRKN homo/compound 45; hetero 79), GP2 (Christine Klein), ROPAD/Centogene (>200), PPMI (6 (?) by Jaya), Arndt Rolfs / Arcensus.	20240722_182029, 20240722_182033
PRKN longitudinal observational study	N ~ 25 (10 HC, 15 PD within 2 years of onset), 3-5 years yearly assessments, multi-modality endpoints; sample-size partial figures 20% reduction and 50% CV → N=21 at 80% power one-sided alpha 0.10.	20240722_182033
NHP study plan	ROA neurosurgery pilot (Oct 2022 - Mar 2023), 1M NHP biodistribution slot at NBR (047-052), Injection Feb/Mar 2023, Necropsy Mar/Apr 2023, Report Jun 2023; AAV9 PK044 PGK1 priority; pilot device Neurochase vs Clear Point; route/dose table for SN, SN+Putamen, Putamen.	20240722_182036, 20240722_182040
CSF / blood sample handling	CSF Day-15/15/29; 1.0 mL target; 4°C 2000g 5 min centrifuge; Eppendorf Protein LoBind; shipment to TSHO Fujisawa.	20240722_182040, 20240722_182043
NBB / PrecisionMed and NHP BD correlation plan	Six-step plan to set normal CSF/brain Parkin levels, brain-CSF correlation in HC and PD samples, then NHP BD vehicle vs AAV groups. Target normal human CSF Parkin ≈ 1 pg/mL.	20240722_182040
Bioanalytical method comparison	HA-Tag / ISH (RNAScope) / LCMS (DMPK) / SMCxPro (NSTM) / IHC (of HA-PRKN); 97% human-NHP homology; 3 pairs of species-specific peptides identified for LC/MS; SMCxPRO LLOQ CSF parkin 1.22 pg/mL neat (100 μL) / 0.12 pg/mL 10x-concentrated (1 mL).	20240722_182043, 20240722_182046
Quantitative BM criteria / target validation	20220119 / 20220130 drafts; Target validation / Postmortem plan; Questions / Needs / criteria / timeline.	20240722_182050
Parkin binding assay HTS log	PE I planning, HTS history rows 20210615 / 20210708 quick memo / 20210709 11-candidate list to TCAL; full ASMS / SPR development log 20210615 → 20220715; ADDP E000-25157 development.	20240722_182053, 20240722_182057
Parkin binding assay termination	20221215 ADDP termination memo; 20230331 ADDP ASMS assay-development result PDF; controversial-binders summary.	20240722_182100
RDDU’s PE I Imaging GBA plan	PK/PD strategy, 20201007 / 2021005 DMPK meetings, AAV/PK rationale, PRC1 Parkin team considerations, [Benchmark] FA GT PRC1 PE narrative.	20240722_182100, 20240722_182103
Safety / Sharefolder / PGRN	Disease-model questions, Safety de-risking strategy, Sharefolder, Parkin protein notes, Assays table.	20240722_182106
TM Assays / NBB LLOQ / pS65-Ub reagents / IVC / Parkin activity	TM Assays summary table, NBB LLOQ tables, brain/CSF comparison, pS65-Ub reagents, ubiquitin linkage notes, IVC, start of Parkin activity assay.	20240722_182110
Vector production / TMQB / TPP/TCP / Unmet Needs / PINK-1 transition	Trailing-tail page covering Parkin / pS65-Ub assays / IVC / Parkin activity assay? / TMQB / TPP/TCP / Unmet Needs / Vector production / PINK-1.	20240722_182113

Source Table

stem	nav path	source note	canonical	uncertain spans	embedded images
20240722_182011	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100)	note	md	4	0
20240722_182014	Parkin > PARKN GT (Takeshi Hioki, PFR-…) > Executive summary	note	md	3	1
20240722_182018	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100) > Clinical strategy	note	md	2	1
20240722_182021	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100)	note	md	2	2
20240722_182025	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100)	note	md	1	0
20240722_182029	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100)	note	md	2	0
20240722_182033	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100) > Natural Hx study > Sample size estimation	note	md	2	2
20240722_182036	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100) > Natural Hx study > Sample size estimation > NHP Studies > Current plan	note	md	2	2
20240722_182040	Parkin > PARKN GT (Takeshi Hioki, PFR-4249-100) > NHP Studies > Current plan	note	md	0	0
20240722_182043	PARKN GT (Takeshi Hioki, PFR-4249-100) > NHP Studies > Bioanalytical method to differentiate human and monkey Parkin	note	md	1	0
20240722_182046	PARKN GT (Takeshi Hioki, PFR-4249-100) > NHP Studies > Bioanalytical method to differentiate human and monkey Parkin	note	md	2	0
20240722_182050	PARKN GT (Takeshi Hioki, PFR-4249-100) > Natural Hx study > Quantitative BM criteria / Target validation	note	md	0	0
20240722_182053	PARKN GT (Takeshi Hioki, PFR-4249-100) > PE > PET	note	md	0	0
20240722_182057	PARKN GT (Takeshi Hioki, PFR-4249-100) > PE > PET	note	md	2	0
20240722_182100	PARKN GT (Takeshi Hioki, PFR-4249-100) > PE > PET	note	md	3	0
20240722_182103	PARKN GT (Takeshi Hioki, PFR-4249-100) > RD DDU’s PET Imaging GBA > PK/PD Strategy	note	md	4	0
20240722_182106	PARKN GT (Takeshi Hioki, PFR-4249-100) > Safety > Sharefolder	note	md	2	0
20240722_182110	PARKN GT (Takeshi Hioki, PFR-4249-100) > TM > Assays	note	md	1	0
20240722_182113	Parkin, > TM > Assays > IVC > Parkin activity assay? > TMQB > TPP/TCP > Unmet Needs > Vector production > PINK-1	note	md	4	0

19 sources; uncertain_span_count totals 37; embedded_image_count totals 8.

Source Scope And Boundary Notes

The 19-source set deviates from a strict “first nav_path entry = PARKN GT (Takeshi Hioki, PFR-4249-100)” rule in two specific places. Both are recorded here so the entity scope can be revisited if needed.

• 20240722_182103 is filed under gba-pd-asyn rather than sections/parkin because the discovery layer assigned it to the GBA-PD cluster from its body’s GBA PET / PRC1 PE narrative content. The source-note nav_path first entry, however, is PARKN GT (Takeshi Hioki, PFR-4249-100) > RD DDU's PET Imaging GBA > PK/PD Strategy. Including it here keeps the PE I imaging GBA plan in the same program file as 20240722_182100 (its immediate predecessor).
• 20240722_182113 carries the Parkin, (trailing-comma typo) first nav root rather than PARKN GT (Takeshi Hioki, PFR-4249-100), so it does not show up in the per-nav-root index at parkn-gt-takeshi-hioki-pfr-4249-100. It is included here because (a) its page_label is Page 144 of 150, the same Word page as the surrounding PARKN GT TM/Assays sources (20240722_182106, 20240722_182110) and (b) its body is a direct continuation of the PARKN GT TM/Assays content (Parkin / pS65-Ub assay reagent tables, ubiquitin linkage notes, IVC, Parkin activity assay, TMQB, TPP/TCP, Unmet Needs, Vector production) that ends with a single boundary line transitioning into PINK-1. The PINK-1 page itself (20240722_182116) is not included in this entity page; it is a distinct topic and belongs to the broader Parkin topic at parkin.

Key Source Interpretations

interpretation	source
The program prioritizes ICM / neurosurgery with established AAVs as the primary scenario and treats novel capsids and iCP-Parkin as contingency plans, with Dec 2022 mouse POC framed as the first VIP.	20240722_182021
Decision criteria are explicit: >=20% mitochondria-function recovery in mouse POC and >=20% of DA neurons expressing Parkin in NHP SN by IHC (or alternative ISH plus LC-MS).	20240722_182021
The biomarker plan deliberately decouples target engagement (CSF Parkin protein, Parkin PET) from pharmacodynamic readout (pS65-Ub) and from imaging (MC1 PET), and explicitly excludes aSyn-related biomarkers because aSyn pathology is rarely observed in the target population.	20240722_182029
A single SMCxPro CSF Parkin assay is used across the natural-history → NHP path; SMCxPRO LLOQ in CSF is 1.22 pg/mL neat / 0.12 pg/mL 10x-concentrated, and target normal human CSF Parkin is approximately 1 pg/mL.	20240722_182040, 20240722_182043
Differentiating human and monkey Parkin in NHP is the source-level critical bioanalytical question; the source compares HA-Tag / ISH (RNAScope) / LCMS / SMCxPro / IHC and notes that 97% homology and only 6 aa differences make differentiation hard.	20240722_182043, 20240722_182046
The Parkin binding assay HTS effort was terminated on 20221215 (ADDP E000-25157), with the 20230331 ADDP ASMS assay-development result PDF as the closing artifact; PE I imaging GBA is the proposed downstream path.	20240722_182100, 20240722_182103
The PRKN longitudinal observational study targets N ~ 25 over 3-5 years; sample-size partial figures suggest detection of a 20% reduction at 50% CV requires roughly N=21 per arm at 80% power, one-sided alpha 0.10.	20240722_182033
Externalization plan: brain Parkin assay publication is planned with Juntendo-U; pS65Ub will publish; neither pursues IP because the assay method is not core IP and Mitokinin assistance was used for pS65-Ub.	20240722_182021, 20240722_182025

Figure / Asset Groups In Source

source	figure group
20240722_182014	AAV9-Parkin expression comparisons (PK012 / PK044 / PK045 / PK046); iPSC-DA neuron infection plot.
20240722_182018	GBA expression evaluation by imaging schematic (Mutant vs Normal GBA1 across Control / GBA-PD / GBA-PD + GT).
20240722_182021	PARKIN GT decision tree; PARKIN GT draft timeline (Mar 9, 2022) with PE / CN / CS / IND gates.
20240722_182033	Sample-size 90% power and 80% power partial heatmaps.
20240722_182036	Sample-size estimation continuation and Wilson 2020 MC1 statistics.

Uncertainties Carried From Source

issue	source
IND 2025/86 may be 2025/8?, 2025/6?, or another date-like notation; preserved verbatim.	20240722_182011
In-vivo expression vector dose appears as (1x10**) vg/10 uL with the exponent not safely readable.	20240722_182011
AAV9-Parkin expression dose annotation 1.6x 10^? VG/injection is not safely readable.	20240722_182014
The GBA PET schematic at the bottom of 20240722_182014 is truncated; confirm with the adjacent capture before extracting full schematic logic.	20240722_182014
Decision-tree gate logic and draft-timeline schedule fields are image-primary; use the embedded asset before extracting exact gate criteria.	20240722_182021
Sample-size heatmap cell values and exact per-CV detection thresholds are image-primary.	20240722_182033
Bioanalytical method LLOQ table cells, peptide-alignment figure labels, and yellow-highlighted CSF Biomarker block include small-print fields; values should be re-checked before reuse.	20240722_182043, 20240722_182046
Parkin binding assay log entries refer to dated meeting fragments and ADDP / ASMS / SPR development steps that span multiple pages; 20221215 termination memo and 20230331 ADDP PDF are the final artifacts, but intermediate dose / activity values are image- or text-primary on the source pages.	20240722_182057, 20240722_182100
20240722_182025 Manfredsson 2007 row is provisional (미저장으로 인해, 추후 작성) and should be treated as not finalized.	20240722_182025
20240722_182103 is filed under sections/gba-pd-asyn; the page covers the PE I Imaging GBA plan and a [Benchmark] FA GT PRC1 PE narrative whose detailed cells are uncertain.	20240722_182103

Related Pages

• parkin - topic-level synthesis across the 46 Parkin section sources
• parkin - section index for Parkin / PARKN GT / PINK1
• parkn-gt-takeshi-hioki-pfr-4249-100 - per-nav-root index for PARKN GT (Takeshi Hioki, PFR-4249-100)
• parkin - per-nav-root index for Parkin and Parkin,
• source-catalog - all 447 sources in capture order
• pr001 - PR001 (GBA gene-therapy comparator, same modality class)