Inflammation

This topic page reorganises the 42 source notes filed under inflammation into reading-order axes. It does not replace the by-photo Markdown; every claim links back to a source note or the canonical transcription. Where a source carries Uncertain Spans, that uncertainty is preserved here rather than smoothed out.

Overview

The corpus treats inflammation as a Pipeline of Inflammation arc with seven overlapping problems. (1) The foundational pyroptosis / NLRP3 / IL-1 biology, including the NLRP3 structure, toxicity, and Tx tables (20240722_183118, 20240722_183132, 20240722_183144, 20240722_183147). (2) CAPS and inflammation-related disease-model framing as the clinical proof-of- concept anchor (20240722_183138, 20240722_183141, 20240722_183150). (3) The NLRP3 inhibitor (Marianthi) program (PFR-4231-100), an internal small- molecule effort with executive summary, AD evidence, competitor map, in- vivo strategy, microglial imaging, PK/PD postmortem assays, safety, and ShareFolder pages (20240722_183153 onward, collected on the entity page nlrp3-inhibitor). (4) Imaging neuroinflammation as a translational PD biomarker via 3rd- generation TSPO tracers (20240722_183104, 20240722_183108). (5) Cytokine / chemokine / inflammasome biomarker omics across CSF, blood, PBMC, and AD postmortem cohorts (20240722_183203, 20240722_183208, 20240722_183212, 20240722_183215). (6) Competitor / KOL / In Vivo strategy material around Havrda and Katy (20240722_183225, 20240722_183228, 20240722_183234, 20240722_183238, 20240722_183241). (7) The Complement / C5aR1 strand (Woodruff, Innomedica/Haven) as a parallel neuroinflammation MOA (20240722_183332, 20240722_183335, 20240722_183342). Stratification, postmortem, and adjacent strands (20240722_183348, 20240722_183354, 20240722_183521, 20240722_184310, 20240722_184357, 20240722_184743) sit alongside these as related, often loosely-linked, evidence.

Source Coverage

42 source notes are assigned to the inflammation section. They sit across 19 first-level nav_path clusters; the topic axes below collapse those clusters as follows:

nav root (first nav_path entry)sourcescovered axis
Pipeline of Inflammation14umbrella heading; rows are split by sub-path into NLRP3 biology / CAPS / NLRP3 inhibitor program / Complement-C5aR1 / Postmortem-iron axes
Inflammation5NLRP3 biology, NLRP3 inhibitor competitor/Havrda, In Vivo strategy/Katy, 기타 MOA Greenamyre Lab
Assays of pyroptosis2biomarker / assay strand (CSF/plasma/PBMC)
Imaging neuroinflammation2DPA714 / 3rd-generation TSPO axis
In Vivo strategy2Katy in-vivo strategy (Atuka mouse, longitudinal)
NLRP32NLRP3 structure and toxicity
NLRP3 inhibitor (Marianthi) (P...)2NLRP3 inhibitor program (AD/Assays of pyroptosis, Pipeline/Competitors)
Stratification strategy on...2Stratification strategy on Mitochondria, Pathogenicity-of-variant scales
[GT]1adjacent AAV / Capsid (serotype) page
Assays of pyroptosis (cytokine / chemokine omics)1NLRP3 inhibitor program AD omics block
Background1Pipeline C5aR1 / Innomedica (Haven) / In Vivo Calibration
Comp Bio1NLRP3 inhibitor program clinical / multi-modal biomarker / Somascan interleukins
Cryopyrin-Associated Periodic Syndromes (CAPS)1CAPS classification, genetics, MOA, IL-1β
Havrda1NLRP3 inhibitor program competitor/HED/IHC strand
Minee Choi1Kv1.3 / Muna Tx / Lipid MAPS lipid category
Pipeline CAPS1Pipeline CAPS limitations / outcome measures / registry / animal model
Pyroptosis evidence/MOA...1KOL / FOX-1 Marios Politis / K-BIOX
Pyroptosis MOA1foundational Pyroptosis MOA
Stratification strategy on neuroinflammation1RNA-Seq (Daria) / C5aR1 (Woodruff) postmortem

For exact nav_path strings and headings see inflammation and the matching by-nav indexes under pipeline-of-inflammation and the cluster slugs listed in related_topics_by_nav.

Across the 42 sources, the source-note frontmatter records 172 uncertain_span_count entries and 0 body-embedded figure assets. The zero-figure count is consistent with the 2026-04-29 body-purity decision (docs/decisions/2026-04-29-body-purity-and-figure-only-embeds.md): the inflammation pages embed scatter plots, decision-flow diagrams, Gantt-style planning grids, and dosing-cartoon figures inside crops that also carry table or label text, so they are kept as evidence and not embedded. The 172 uncertain spans are retained as review targets and not resolved here.

NLRP3 / Inflammasome / Pyroptosis Biology

20240722_183118 opens the Pipeline of Inflammation arc with a Pyroptosis MOA block that references low CSHL (cold spring harbor) 2020 Abstract253 MOA and a ptosis evidence/MOA/Correction in PD heading. The page records 5 Uncertain Spans for clipped section labels and the lower-table boundary into 20240722_183132.

20240722_183121, 20240722_183125, and 20240722_183128 carry the multi-page Pyroptosis evidence/MOA/Correction in PD table whose rows span human plasma / brain models / Korean summary block; row content is captured but the cross-page logical grid was preserved in related_photos rather than reconciled into a single block. These three pages together carry 12 Uncertain Spans (3 + 5 + 4) for clipped row boundaries and table-split markers. The trailing 20240722_183351 carries the Pyroptosis evidence/MOA... KOL block (FOX-1: Marios politis:, K-BIOX, KOLs); it is the page where the pyroptosis-evidence axis folds into KOL/site-recruiting notes and is flagged with 5 Uncertain Spans.

20240722_183132 is the NLRP3 > Structure page with IL-1β, IL-1 Receptors, Toxicity, NLRP3 Structure, and the start of an Uncertain Spans review table (5 entries). 20240722_183144 extends into NLRP3 > Toxicity > Tx with 4 Uncertain Spans for clipped treatment-comparison rows; the page is the bridge between the NLRP3 biology block and the NLRP3 inhibitor program executive-summary tables that follow. 20240722_183147 sits under Inflammation > NLRP3 > Tx and carries the clinical-outcome-table continuation to 20240722_183159; it is flagged with 5 Uncertain Spans for clipped outcome rows.

The CAPS arc grounds the NLRP3 inhibitor program in its FCAS / MWS / NOMID / DIRA clinical proof-of-concept space. 20240722_183138 is the Cryopyrin-Associated Periodic Syndromes (CAPS) overview page with Questions / Classification / Genetics / Inheritance / MOA / IL-1β sub-headings and 3 Uncertain Spans (Agostini / Rodriguez / Smith table rows). 20240722_183141 extends into Pipeline of Inflammation > CAPS > WBC > Dx > ARP > Sx with sub-headings WBC, Dx, f. Dx criteria, ARP, Sx and the papilledema / conjunctivitis / audiogram row continuation to 20240722_183144. Pipeline CAPS framing is on 20240722_183150 (Pipeline CAPS with Limitations, Outcome measures, Registry, Animal model, TM); 4 Uncertain Spans for clipped registry / animal-model row labels.

NLRP3 Inhibitor (Marianthi) — Program Distribution

The 11 sources whose nav_path references the program nav root in any position (with any of the variant spellings NLRP3 inhibitor (Marianthi) (P...), NLRP3 inhibitor (Marianthi), or NLRP3 inhibitor (Marianthi) (PFR-4231-100)) are the canonical input for the program-level entity page at nlrp3-inhibitor; this section only summarises how that program material is distributed across the topic sources. Per-axis narrative for the program lives on the entity page, not here. (Only 2 of the 11 sources carry the program as the first nav_path entry — see the entity page’s Source Scope And Boundary Notes for the breakdown.)

The introductory page is 20240722_183153, which opens NLRP3 inhibitor (Marianthi) (PFR-4231-100) with an Executive summary status table (LGE (202102), PE (Dec, 2021), CN (202210), PDE 3/21, CS (202409) RSLT, CDE (PRC) Dec2023→ 202402? → 202507, IND (202508 ← 202410), pH? (202509 / 202411)) and a Pipeline CAPS Gantt-style grid keyed by Feb-Dec / 1-5 columns and rows TR06693098, TR06698660, 2nd atuka, Bz-ATP Rat, series 5c TR06798980, RAT formulation pk study. The In vitro / TR06802042 (5c) acieved cell carries the typo acieved (preserved verbatim) and the trailing IND (202508) / pH? (202411) tokens are flagged as uncertain. The page records 5 Uncertain Spans.

20240722_183156 holds the program’s TR847 deprioritization discussion, a TSPO/VMAT2 readout grid (WB / IHC / ARG / PET columns), the AD In vivo plan (Tau P301L (=rTg4510 일걸) at ReMynd, systemic LPS vs local BzATP), the NBB project number 1513 sample inventory (50 CSF / 21 plasma / 17 frozen hippocampus / 42 paraffin hippocampus AD donors; matched dementia and control rows), and an Assays of pyroptosis cell-pellet/CSF/blood/PBMC table referencing (Luo, 2019 #1852), (Peng, 2019 #1853), (Chatterjee, 2020 #1263), (Fan, 2020 #657), the Havrda MSD detection range 0.78 ng/mL (Sebastian LLOQ to 16.2+ ng/mL (%) — 90th percentile, the Cusabio ELISA (CSB E15885h) LLOQ 0.039 ng/mL, Detection Range 0.156-10 ng/mL, and the SMCxPro buffer LLOQ 44 pg/mL with S/B 829. The program’s low recovery (CSF & plasma), no MRD set up (CSF) issue line is flagged.

20240722_183159 continues the Inflammation > NLRP3 inhibitor (Marianthi) > AD > Assays of pyroptosis strand, 20240722_183206 holds Quanterix: and Progress sub-blocks (Page 695 of 701; 4 Uncertain Spans), and 20240722_183218 holds the AD evidence overall block (no human genetic link to AD; NLRP3 not differentially expressed in AD brain but GSDMD, IL18 and PYCARD up-regulated in parahippocampal gyrus; NLRP3-pathway is up-regulated in immune-activated patient group), the MSBB / ROSMAP / scRNAseq / Emory Mount Sinai per-region table, the Molecular subtypes AD (A / B1 / B2 / C1 / C2) classification with Jonghun: NLRP3 (Limitation is that there is no biomarker for discriminating the subgroups...) annotation, and the Competitor table ((Genali) / Inzomelid (Inflazome / Roche) / NCT04015076 / Dapansutrile (Olatec) / Neumora (£2.1M from Parkinson's UK) / Novartis DFV890 / Ventyx VTX-2735). The Roche Inzomelid row shows Ph 1b for PD withdrawn 'strategic decision by sponsor', Ph 2b for CAPS terminated. 20240722_183222 is the Pipeline / Competitors continuation (Ventus VENT-02 P1 ongoing, Roche RO7486967 / RG6418 / Selnoflast Kp,uu: 0.06~0.1, NodThera NT-0796 P1b/2a HV→PD with the Healthy elderly control levels set to 100% biomarker grid showing IL-1β, IL-6, IL-8, CCL2, CXCL1, NFL, sTREM2 from Day 1 / Day 7 / Day 28, and the Halia / MCC950 NACHT-domain binding note); 5 Uncertain Spans.

The program then runs through:

  • 20240722_183231: In Vivo strategy > Havrda > HED > IHC with Compounds, In vivo strategy details, and Cell numbers in AAV1/2 + pSyn mice; 4 uncertain spans.
  • 20240722_183244: the Katy > Longitudinal > Metabolomics > Microglial Imaging cohort evaluation table (NET PD FS-ZONE, LCC, PARS, PPMI, SURE-PD 2, BioFind) and the [18F]DPA714 / [18F]FEPPA tracer comparison plan; 4 uncertain spans.
  • 20240722_183255: the Microglial Imaging > NHP > PDE > PE > PET Summary tracer-experiment table (Bmax / Invicro / 6OHDA rat / [3H]MCC950 / [3H]TR06616126 / [3H]PBR28) with the Triaging compounds / Anne Kanta DMPK email and the LPS-rat Dosing regimen sub-table; 5 uncertain spans.
  • 20240722_183308: the PK/PD > PK/PD Strategy > Postmortem > Proteina Pablo Pelegrin / Roche speck-bound NLRP3-ASC-caspase-1-GSDMD assay matrix and the Proteina vs Charles River Co-IP / WB / Mass spec / Pull-down comparison; 4 uncertain spans.
  • 20240722_183321: the Reactome / Safety di-22:6-BMP phospholipidosis biomarker block and the Established NLRP3 Inhibitor Screening Flow figure (CHEMISTRY → THP-1-hNLRP3 Caspase-1 → IL-1β → cytotox / selectivity / binding / mouse PK/PD → in-vivo efficacy with parallel ADMET / Cyp / Promiscuity / Na / Solubility / Safety47 / Genotox tracks); 4 uncertain spans.

The screening flow figure (20240722_183321) is the single best one-page program schematic; the executive-summary status table on 20240722_183153 is the single best timeline anchor.

Imaging Neuroinflammation And TSPO

20240722_183104 opens the Imaging neuroinflammation axis with Imaging neuroinflammation, DPA714, 3<sup>rd</sup> Generation TSPO headings; 4 Uncertain Spans recorded. 20240722_183108 continues the Imaging neuroinflammation > DPA714 > 3rd Generation TSPO comparison table with 3 Uncertain Spans. These two pages set up the TSPO / DPA714 / FEPPA tracer choice that the NLRP3 inhibitor program’s Microglial Imaging axis later picks up on 20240722_183244 and 20240722_183255.

Biomarker / Cytokine / Omics Workstreams

20240722_183203 is the Assays of pyroptosis page following Pipeline CAPS and continuing the multi-row gasdermin D / αSyn-fragment evidence comparison; 5 Uncertain Spans recorded. 20240722_183208 holds the Assays of pyroptosis > Budget & FTE > Ceri > Chemistry block with sub- headings CBID (BST):, Summary of NLRP3 biomarker detection methods in the literature, Budget & FTE, Ceri, Chemistry, TSD Chemistry Goals; 4 Uncertain Spans. 20240722_183212 is the Comp Bio page (Clinical, Combining MBMs Multi-Modal Biomarkers and Biomarker Panels, Comp Bio, PD, Somascan Interleukins (Protein level: 20230803 excel (somascan.ppmi_assoc_summary-8-3-23.xlsx, 20230804 ppt))); 5 Uncertain Spans. 20240722_183215 carries the Assays of pyroptosis (cytokine / chemokine omics) > AD axis with sub- headings Interleukins, AD, Overall; 5 Uncertain Spans. These four pages should be re-checked rather than re-quoted; specific Somascan columns and AD subgroup sample sizes are image-primary on the source pages.

Competitor / In Vivo Strategy / KOL (Havrda, Katy)

The Havrda / Katy strand sits adjacent to the NLRP3 inhibitor program but the source notes’ nav_path does not place it under the program nav root, so the topic page hosts it rather than the entity page.

  • 20240722_183225: Inflammation > Competitor > Havrda with sub-headings Competitor, Havrda, Clinical, Subpopulation strategy, Preclinical; 2 Uncertain Spans.
  • 20240722_183228: Havrda with Tamoxifen-inducible Nlrp3 allele., HED, IHC, In Vivo strategy headings; 4 Uncertain Spans.
  • 20240722_183234: In Vivo strategy > Katy with Biomarkers measurements for planned in vivo studies, Subchronic, Katy; 6 Uncertain Spans.
  • 20240722_183238: Inflammation > In Vivo strategy > Katy with Atuka aSyn / BzATP rat dose grid, 098: 2ND ATUKA mouse, 10 mpk, (vs AAV+veh) TH ↓ Putamen / NBB / Imperial; 4 Uncertain Spans.
  • 20240722_183241: In Vivo strategy > Katy > Longitudinal with Workflow, Longitudinal; 5 Uncertain Spans.

The Katy in-vivo strand uses ATUKA aSyn / BzATP rat models; the Havrda strand uses the tamoxifen-inducible Nlrp3 allele and IHC readouts. The program-level strategic role of these strands is folded into nlrp3-inhibitor.

Complement / C5aR1

20240722_183332 sits under Stratification strategy on neuroinflammation > RNA-Seq (Daria) > C5aR1 (Woodruff, Univ of Queensland) with sub-headings Stratification strategy on neuroinflammation, Postmortem study, RNA-Seq (Daria), C5aR1 (Woodruff, Univ of Queensland); 4 Uncertain Spans. 20240722_183335 is the program-style Pipeline of Inflammation > Complement / C5aR1 > MOA > Woodruff's study plan > Screening > DD page with Woodruff's study plan with C5aR1 inhibitors, Screening, DD headings; 4 Uncertain Spans. 20240722_183342 extends the strand into Background > Pipeline C5aR1 > Innomedica (Haven) > In Vivo Clibration (Background, Pipeline C5aR1, Innomedica (Haven), In Vivo Clibration headings; 3 Uncertain Spans). The Complement / C5aR1 arc parallels the NLRP3 inhibitor program as a separate neuroinflammation MOA candidate; the source note is the canonical place for in-vivo model and screening detail rather than this topic.

Stratification, Postmortem, And Adjacent Strands

The remaining six pages are loosely linked to the inflammation topic through nav-path adjacency rather than direct mechanism overlap:

  • 20240722_183348: Pipeline of Inflammation > Postmortem > Imaging of Iron > IT > Jaya with sub-headings Postmortem, Imaging of Iron, IT, Jaya, Hardy; 4 Uncertain Spans. Postmortem / iron-imaging KOL block (Jaya / Hardy).
  • 20240722_183354: Minee Choi > Kv1.3 > Kyoko Yoshikawa > Lee Jonghun with sub-headings Minee Choi, Kv1.3, Pipeline [Muna Tx], Kyoko Yoshikawa, Lee Jonghun, Lipid category (eight, by Lipid MAPS consortium); 2 Uncertain Spans. Kv1.3 / Muna Tx microglia KOL adjacency and lipid classification.
  • 20240722_183521: Stratification strategy on...Stratification strategy on Mitochondria page; 5 Uncertain Spans.
  • 20240722_184310: Stratification strategy on... > Pathogenicity of variant with a long heading list including Sleep, Ataxia, SARA, NPI, PDQ39, SCOPA-AUT, Table 1 Unified PD Rating Scale subscores, Schwab and England ADL, UDRS, Oxidative stress biomarkers, PADD, Pathogenicity of variant, Figure 1. Evidence Framework; 3 Uncertain Spans. Clinical-scale review adjacent to stratification.
  • 20240722_184357: Inflammation > 기타 MOA들 > Pittsburgh University > Greenamyre Lab with sub-headings Pittsburgh University, Greenamyre Lab, INTERESTS, Burton Lab, Berman Lab; 3 Uncertain Spans. University collaboration / KOL block.
  • 20240722_184743: [GT] > AAV > Capsid (serotype) with sub-headings Keytruda / LoD- LLOQ / [GT] AAV / Capsid (serotype), [GT], Scheme of a CMV virus, AAV, Capsid (serotype), Tissue tropism; 4 Uncertain Spans. Adjacent AAV / capsid / tropism reference block.

Source Table

All 42 sources, in capture-time order, with the per-page uncertain-span and embedded-image counts copied from front matter. nav path is the full nav_path recorded in the source note.

stemnav path / headingsource notecanonicaluncertain spansembedded images
20240722_183104Imaging neuroinflammationnotemd40
20240722_183108Imaging neuroinflammation > DPA714 > 3rd Generation TSPOnotemd30
20240722_183118Pyroptosis MOAnotemd50
20240722_183121Pipeline of Inflammation > Pyroptosis MOA > Pyroptosis evidence/MOA/Correction in PDnotemd30
20240722_183125Pipeline of Inflammation > Pyroptosis MOAnotemd50
20240722_183128Pipeline of Inflammation > Pyroptosis MOA > Pyroptosis evidence/MOAnotemd40
20240722_183132NLRP3 > Structurenotemd50
20240722_183138Cryopyrin-Associated Periodic Syndromes (CAPS)notemd30
20240722_183141Pipeline of Inflammation > CAPS > WBC > Dx > ARP > Sxnotemd40
20240722_183144NLRP3 > Toxicitynotemd40
20240722_183147Inflammation > NLRP3 > Txnotemd50
20240722_183150Pipeline CAPSnotemd40
20240722_183153Pipeline of Inflammation > Pipeline CAPS > Animal model > TM > NLRP3 inhibitor (Marianthi) (PFR-4231-100)notemd50
20240722_183156NLRP3 inhibitor (Marianthi) (P…) > AD > Assays of pyroptosisnotemd40
20240722_183159Inflammation > NLRP3 inhibitor (Marianthi) > AD > Assays of pyroptosisnotemd30
20240722_183203Assays of pyroptosisnotemd50
20240722_183206Pipeline of Inflammation > Pipeline CAPS > NLRP3 inhibitor (Marianthi) (PFR-4231-100) > AD > Assays of pyroptosisnotemd40
20240722_183208Assays of pyroptosis > Budget & FTE > Ceri > Chemistrynotemd40
20240722_183212Comp Bionotemd50
20240722_183215Assays of pyroptosis (cytokine / chemokine omics) > ADnotemd50
20240722_183218Pipeline of Inflammation > NLRP3 inhibitor (Marianthi) > AD > Chemistry > Clinical > Comp Bio > Competitornotemd40
20240722_183222NLRP3 inhibitor (Marianthi) (P…) > Pipeline / Competitorsnotemd50
20240722_183225Inflammation > Competitor > Havrdanotemd20
20240722_183228Havrdanotemd40
20240722_183231Pipeline of Inflammation > NLRP3 inhibitor (Marianthi) > In Vivo strategy > Havrda > HED > IHCnotemd40
20240722_183234In Vivo strategy > Katynotemd60
20240722_183238Inflammation > In Vivo strategy > Katynotemd40
20240722_183241In Vivo strategy > Katy > Longitudinalnotemd50
20240722_183244Pipeline of Inflammation > NLRP3 inhibitor (Marianthi) > Katy > Longitudinal > Metabolomics > Microglial Imagingnotemd40
20240722_183255Pipeline of Inflammation > NLRP3 inhibitor (Marianthi) > Microglial Imaging > NHP > PDE > PE > PETnotemd50
20240722_183308Pipeline of Inflammation > NLRP3 inhibitor (Marianthi) > PK/PD > PK/PD Strategy > Postmortem > Proteinanotemd40
20240722_183321Pipeline of Inflammation > NLRP3 inhibitor (Marianthi) > Reactome > Safety > Screening flow > ShareFoldernotemd40
20240722_183332Stratification strategy on neuroinflammation > RNA-Seq (Daria) > C5aR1 (Woodruff, Univ of Queensland)notemd40
20240722_183335Pipeline of Inflammation > Complement / C5aR1 > MOA > Woodruff’s study plan > Screening > DDnotemd40
20240722_183342Background > Pipeline C5aR1 > Innomedica (Haven) > In Vivo Clibrationnotemd30
20240722_183348Pipeline of Inflammation > Postmortem > Imaging of Iron > IT > Jayanotemd40
20240722_183351Pyroptosis evidence/MOA…notemd50
20240722_183354Minee Choi > Kv1.3 > Kyoko Yoshikawa > Lee Jonghunnotemd20
20240722_183521Stratification strategy on…notemd50
20240722_184310Stratification strategy on… > Pathogenicity of variantnotemd30
20240722_184357Inflammation > 기타 MOA들 > Pittsburgh University > Greenamyre Labnotemd30
20240722_184743[GT] > AAV > Capsid (serotype)notemd40

Totals across the 42 sources: uncertain_span_count = 172, embedded_image_count = 0. These are review surface area; the zero-figure-embed count reflects the 2026-04-29 body-purity decision (docs/decisions/2026-04-29-body-purity-and-figure-only-embeds.md) under which mixed text-and-figure crops on these pages are kept as evidence rather than embedded.

Uncertainties Carried Forward

This page deliberately does not paraphrase Pyroptosis evidence-table cell values, NLRP3 structural detail, CAPS classification rows, NLRP3 inhibitor program Gantt cells, executive-summary date tokens, competitor-table notes, AD MSBB / ROSMAP cohort cells, NodThera Day- 1/7/28 percentages, NHP imaging Bmax tracer matrix cells, Proteina / Charles River Co-IP method comparison cells, Established NLRP3 Inhibitor Screening Flow node labels, Somascan interleukin columns, or Stratification strategy on... Pathogenicity-of-variant scale tables. Specific uncertainty hot spots worth checking before any downstream extraction:

Per-page program-level uncertainty for the NLRP3 inhibitor program is maintained on nlrp3-inhibitor under Uncertainties Carried From Source.