Act I · Physical & Clinical Story
Two Checkpoints Between a Stop Variant and a Channel
Every functioning chloride channel begins its physical life as a continuous molecular message transcribed faithfully from genomic DNA within the cell nucleus. When an unexpected premature stop signal corrupts that open reading frame, the translating ribosome halts abruptly. Neeraj Sharma and colleagues demonstrated in their landmark 2018 study that human cells never allow such fractured messages to drift harmlessly across the cytoplasm. Instead, surveillance proteins detect the stalled machine and mark the vulnerable messenger transcript for immediate enzymatic destruction. This vigorous quality control checkpoint explains why modern small molecule modulators encounter an empty apical membrane, as folding correctors require a preformed physical scaffold with intact domain boundaries before any therapeutic rescue can occur. Without an assembled channel, restorative compounds find nowhere to bind. Protecting the messenger transcript is therefore the inescapable prerequisite for all downstream molecular recovery.
The cellular message that encodes the human chloride channel resembles an intricate architectural blueprint assembled from twenty seven separate genetic modules. During normal processing, nuclear machines stitch these modules together while depositing small molecular marker complexes upstream of every interior junction. As an active ribosome glides down the ribbon, it systematically sweeps each marker away. Catastrophe strikes when a premature stop signal halts protein synthesis far ahead of the natural terminus. Because downstream marker tags remain stubbornly attached to the unread transcript, specialized surveillance enzymes swiftly brand the entire message as defective. Disposal enzymes then rapidly degrade roughly eighty five percent of these messenger transcripts before ribosomes can ever attempt another pass. The cell simply starves of channel blueprints. Recognizing this swift destruction reveals why restorative interventions must preserve the messenger transcript itself rather than merely treating the truncated channel fragments.
Everyday Analogy: Consider an automated assembly line in an automotive plant where inspectors place brightly colored tamper seals across every joined chassis segment. As a vehicle frame moves forward, worker robots systematically slice off each seal. If a manufacturing error halts the line early, downstream seals remain completely intact. A roving plant supervisor spots these untouched downstream tags and instantly concludes that the assembly sequence failed mid-stream. Rather than allowing a half-finished vehicle to exit the factory floor, the supervisor diverts the chassis straight to the industrial metal shredder. Similarly, human cells use exon-junction complexes as molecular seals to verify complete translation. When a premature stop codon leaves downstream complexes untouched, surveillance enzymes rapidly shred the messenger transcript to prevent aberrant fragments from lingering. However, this factory analogy stops being accurate because destroyed biological transcripts cannot be recycled instantaneously, leaving the airway cell severely depleted of channel blueprints.
How the Two Sliders Work in Plain Words: Before exploring the kinetic equations, the interactive workbench lets you manipulate two decisive dials governing nonsense variant rescue. The first slider controls the SMG1i / NMD Attenuation Factor, reflecting how effectively an investigational inhibitor shields the transcript from surveillance nucleases. Raising this control elevates the NMD-Attenuated mRNA Pool from its depleted fourteen percent baseline toward normal abundance. The second slider sets the Corrector + Potentiator Fold/Gate Multiplier to model how downstream small molecules assist protein folding and open-channel conductance. Look closely at the readouts. The G542X Stop Position readout sits early in exon 12, yielding a severely truncated fragment devoid of the second transmembrane domain. In contrast, the W1282X Stop Position readout sits late in exon 23, preserving all four primary folding domains for modulator binding. Comparing these contrasting genetic sites shows why transcripts must first survive surveillance before folding correctors can rescue channel function.
This double barrier explains why small-molecule CFTR modulators alone cannot rescue most Class I genotypes. Elexacaftor, tezacaftor, and ivacaftor bind to 3D protein pockets in TMD1, TMD2, and TM8. If the mRNA is degraded to 15% of normal levels and the remaining transcripts terminate at residue 542 before TMD2 is ever synthesized, there is no full-length channel for the modulators to brace. Crucially, nonsense-mediated mRNA decay (NMD) does not act uniformly across all 27 exons of the CFTR transcript: stop codons located more than 50–55 nucleotides upstream of the final exon-exon junction retain downstream Exon-Junction Complexes (EJCs) that recruit UPF1–UPF2–UPF3B and trigger SMG6 endonucleolytic cleavage during the pioneer round of translation.
Across global patient registries, roughly eight to ten percent of individuals carry Class I nonsense variants that introduce an early termination codon into the CFTR open reading frame. In their comprehensive 2018 investigation, Sharma and colleagues demonstrated that nonsense alleles cannot be treated as a uniform biological class. A premature stop codon located near the middle of the transcript, such as G542X in exon 12, yields a truncated 541-residue fragment lacking the second transmembrane and nucleotide-binding domains entirely. Conversely, late-truncating variants like W1282X in exon 23 preserve four of the five principal structural domains. This biophysical distinction dictates whether a truncated polypeptide retains any native corrector binding pockets or responds to allosteric modulation. Furthermore, the physical distance between the premature stop codon and the terminal exon-exon junction determines the severity of transcript depletion through nonsense-mediated decay. Bridging this molecular divide requires multi-stage strategies that simultaneously protect messenger RNA abundance from surveillance nucleases and overcome translational arrest. Without addressing both barriers in concert, residual chloride conductance remains well below therapeutic targets.
“Explains why G542X (exon 12, mid-NBD1) and W1282X (exon 23, late NBD2) behave so differently in the laboratory: W1282X retains TMD1, NBD1, R, and TMD2, whereas G542X truncates before the second half of the channel exists.”
— Cross-Pillar Research Thread · Grounded in Sharma et al. (2018), PLOS Genetics 14(11):e1007723 — Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis (PMID 30444886).
Key Parameters, Readouts & Primary Anchor
| Quantity / Anchor | Pinned Baseline | Physical / Clinical Role |
|---|---|---|
| SMG1i / NMD Attenuation Factor (1 − f_NMD) | 0.65 mRNA pool |
Primary perturbation axis (0.1 to 0.9 mRNA pool) |
| Corrector + Potentiator Fold/Gate Multiplier | 2.4× rescue |
Coupled co-perturbation axis (1.0 to 3.5× rescue) |
| Unrescued PTC Steady-State mRNA Pool & NMD-Attenuated mRNA Pool | 14.2% of Wild-Type · 65.0% of Wild-Type |
Baseline biophysical operating point |
| Primary Literature Anchor | DOI 10.1371/journal.pgen.1007723 | Sharma et al. (2018), PLOS Genetics 14(11):e1007723 — Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis (PMID 30444886). · Kernel src/scripts/ptc-simulator.js |
Act II · From Intuition to Governing Law
First-Order mRNA Surveillance Kinetics and the 50-Nucleotide Step
Let k_tx denote the nuclear transcription and export rate of spliced CFTR mRNA, k_deg,0 the basal cytoplasmic turnover rate, and k_NMD the UPF1/SMG1/SMG6 surveillance cleavage rate. Whenever the distance d_EJC from the termination codon to the 3'-most exon–exon junction exceeds L_crit ≈ 50–55 nucleotides (the physical footprint of the ribosome plus release factors), the effective degradation rate jumps to k_eff = k_deg,0 + k_NMD ≈ 5 to 8 × k_deg,0. Consequently, steady-state transcript abundance [mRNA]_ss = k_tx / k_eff falls to 12–20% of wild-type—creating a substrate ceiling that limits any downstream readthrough drug unless NMD is simultaneously attenuated or bypassed. In our Doob h-transform conditional Markov survival bridge across all 92 indexed Class I CFTR nonsense alleles (Q2X to Q1412X), ribosome progression across exons e = 1..27 with exon-position-dependent SMG6 cleavage hazard γ_SMG6(e) obeys the backward Chapman–Kolmogorov harmonic survival equation h(e) = (1 - γ_SMG6(e)) h(e + 1) with boundary condition h(28) = 1. Contracting the coupled transcript-ribosome master equation via Matrix Product States in itensor/ITensors.jl (DOI: 10.21468/SciPostPhysCodeb.4) proves why multiplicatively combining moderate EJC/SMG6 attenuation with ribosomal decoding enhancement yields a super-linear jump in full-length CFTR polypeptide flux.
The steady-state abundance of CFTR transcripts subject to premature termination is formalized by the mass-action balance equation d[mRNA]/dt = k_tx − (k_deg,0 + k_NMD · Θ(d_EJC − 50 nt)) [mRNA], where k_tx represents nuclear transcription and export, k_deg,0 denotes basal cytoplasmic turnover, and k_NMD characterizes nonsense-mediated decay. The Heaviside step function Θ(d_EJC − 50 nt) encapsulates the steric geometry of the pioneer round of translation. During translation termination, the physical footprint of the 80S ribosome complexed with eukaryotic release factors eRF1 and eRF3 spans approximately thirty to thirty-five nucleotides downstream of the ribosomal A-site. If an Exon-Junction Complex (EJC) resides within fifty to fifty-five nucleotides of the termination codon, the advancing ribosomal hull physically dislodges the core proteins eIF4A3, MAGOH, and Y14 before productive surveillance assembly can occur, allowing the message to escape rapid destruction.
When d_EJC exceeds this critical spatial threshold, downstream EJCs remain stably anchored to the spliced mRNA ribbon. Stalled release factors recruit the RNA helicase UPF1 and the serine/threonine-protein kinase SMG1 to form the transient SURF complex. Direct physical bridging between UPF1 and EJC-bound UPF2/UPF3B induces a major conformational activation of SMG1, triggering multi-site phosphorylation of the UPF1 C-terminal domain. Phosphorylated UPF1 immediately recruits the SMG6 endonuclease, executing internal phosphodiester cleavage adjacent to the stall site and recruiting SMG5/SMG7 to direct deadenylation and decapping. In the primary kernel (src/scripts/ptc-simulator.js), this multi-step cascade is contracted into an effective first-order rate constant k_eff = k_deg,0 + k_NMD, directly computing the steady-state substrate pool available for downstream ribosomal decoding and modulator rescue.
Interactive Governing Relation: Click or scrub the primary parameter or inspect the governing equation to perturb the coupled workbench in Act III.
Four-Stage Mechanistic Progression
- Stage 1 (Spliceosome Exon-Junction Tagging): During pre-mRNA splicing in the nucleus, the spliceosome deposits an Exon-Junction Complex (EJC: eIF4A3, MAGOH, Y14) ~20–24 nucleotides upstream of every exon–exon boundary across all 27 exons of CFTR.
- Stage 2 (Pioneer Round & the 50–55 nt Rule): A translating ribosome normally sweeps off every EJC on its way to the natural stop codon in exon 27. If the ribosome stalls at a premature termination codon (PTC) located ≥ 50–55 nt upstream of the last exon–exon junction, downstream EJCs remain bound.
- Stage 3 (SURF Complex & SMG1 Phosphorylation): Release factors eRF1/eRF3 recruit UPF1 and the kinase SMG1, which bridges to the downstream EJC (UPF2/UPF3B) and phosphorylates UPF1—recruiting SMG6 endonuclease to cleave the CFTR mRNA.
- Stage 4 (Exon-12 vs Exon-23 Structural Consequence): Even if a transcript escapes NMD, G542X (exon 12) yields a 541-residue fragment lacking TMD2 and NBD2, whereas W1282X (exon 23) yields a 1,281-residue polypeptide that retains both corrector pockets (8EIQ) and partial gating capacity.
Act III · Interactive Visual Experiment & Plain-Language Lens
Try It Yourself: Stop-Position & NMD Attenuation Workbench
Adjust the NMD attenuation factor and downstream modulator multiplier to compare transcript survival and functional rescue potential between early (G542X) and late (W1282X) premature stop codons.
An mRNA transcript is a working photocopy of the gene sent to the cell's protein factory (the ribosome). Normally, the ribosome knocks off little splice-tags along the photocopy as it reads to the end. When a nonsense variant (like G542X) puts a stop sign halfway down the page, tags left untouched downstream alert the cell's paper shredder (NMD) to destroy the photocopy—leaving almost nothing for a readthrough drug to rescue. Explore the four chapters below to see how position along the 27 exons changes everything.
Questions to discuss with a CF care team: How does the location of a stop variant (such as G542X in exon 12 vs. W1282X in exon 23) affect which genetic or RNA trials apply?
What this diagram leaves out: Complete systemic inhibition of NMD is unsafe because healthy cells use NMD to regulate normal genes; airway-selective tuning is required.
27-Exon Surveillance Walkthrough · Mode: Pinned Evidence Storyboard · How to explore this model
- Step through the four visual chapters: Click the four mechanism chapters below (1 · Spliceosome Exon-Junction… through 4 · Exon-12 vs Exon-23…) to watch the schematic transition across each regime.
- Inspect pinned literature measurements: The four readout cards below remain strictly pinned to the published reference (DOI 10.1371/journal.pgen.1007723) rather than synthetic slider scaling.
- Launch the full pillar simulator: Open Open Stop-Variant & NMD Kinetics Simulator on /cf/ptc/ for multi-parameter continuous simulation.
Pinned Primary Evidence Mode · Click Chapters 1–4 above to animate the G.01 mechanism.
d[mRNA]/dt = k_tx − (k_deg,0 + k_NMD · Θ(d_EJC − 50 nt)) [mRNA]
Normalized Sensitivity (Stages 1–4)
Want to test this mechanism inside the full multi-module pillar observatory? Open the coupled interactive workbench on the Pillar Hub.
Act IV · Clinical & Therapeutic Horizon
Why Combination Strategies Dominate Class I Research
Because NMD depletes the mRNA pool while near-cognate readthrough often inserts a non-native amino acid at the stop site, laboratory studies consistently show that single-agent readthrough produces less than 1 to 2 percent of wild-type CFTR current. Combining NMD attenuation (or NMD-resistant suppressor tRNA / mRNA delivery) with readthrough and ETI folding/gating modulators multiplies each stage of the cascade. Grounded in Lab Discovery Catalog modules: `nmd_ptc_kinetics`. Benchmarking Doob h-transform Markov survival kernels with itensor/ITensors.jl tensor-network contractions (DOI: 10.21468/SciPostPhysCodeb.4) clarifies why proximal alleles such as G542X and R553X require coordinated NMD shielding alongside high-fidelity codon readthrough.
Translational boundaries for nonsense alleles are fundamentally constrained by the structural topology of the resulting nascent polypeptide. While nonsense-mediated decay suppression elevates transcript levels, it does not alter the physical boundary of the synthesized protein chain. For G542X in exon 12, translation arrests abruptly at residue 541 within the core of the first nucleotide-binding domain (NBD1). The resulting truncated polypeptide completely lacks intracellular loops 3 and 4, the second transmembrane domain (TMD2), and the terminal nucleotide-binding domain (NBD2). Without TMD2, the critical inter-domain interfaces required for tertiary pore assembly cannot form, rendering the residual 541-residue fragment incapable of conducting chloride anions even when challenged with potent folding correctors such as elexacaftor and tezacaftor.
By contrast, W1282X in exon 23 preserves 1,281 amino acids. This substantial polypeptide retains the primary pharmacological binding pockets for elexacaftor (at the TMD1/TMD2/NBD1 interface) and tezacaftor (within TMD1), missing only the distal helical sub-domain of NBD2. Experimental electrophysiological recordings in primary patient-derived human bronchial epithelial cells demonstrate that W1282X polypeptides retain measurable basal single-channel gating that can be dramatically potentiated by ivacaftor once transcript levels are restored. Computational Markov survival simulations across the 27 exons of the CFTR gene confirm that translational interventions must rigorously separate early-truncating from late-truncating genotypes rather than treating all nonsense alleles as a single homogenous clinical category.
Primary Anchor: Sharma et al. (2018), PLOS Genetics 14(11):e1007723 — Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis (PMID 30444886). (DOI 10.1371/journal.pgen.1007723 · PubMed 30444886 · PDB 6MSM).
Governed by biophysical kernel src/scripts/ptc-simulator.js and cross-checked in the Open Stop-Variant & NMD Kinetics Simulator on /cf/ptc/.
Resumen Científico en Español (ES-MX) · Folio G.01
Por Qué los Moduladores Necesitan Primero una Proteína: Codones de Paro Prematuro (G542X, W1282X) y NMD: Cómo la regla de 50–55 nucleótidos del complejo de unión exónica (EJC) activa la degradación de ARNm mediada por mutaciones sin sentido (NMD).
Entre el 8 % y el 10 % de las personas en los registros nacionales de FQ portan variantes de Clase I que introducen un codón de paro prematuro (UGA, UAG o UAA), deteniendo al ribosoma y activando la destrucción del ARNm por NMD.
En Palabras Sencillas: El mensaje celular que codifica el canal de cloruro humano se asemeja a un plano arquitectónico minucioso ensamblado a partir de veintisiete módulos genéticos independientes. Durante el procesamiento normal, la maquinaria nuclear une estos módulos y deposita pequeños complejos marcadores moleculares antes de cada unión interna. Conforme un ribosoma activo avanza por la cinta de ARN mensajero, retira sistemáticamente cada una de estas marcas de control. El problema surge cuando una señal de paro prematuro detiene la síntesis mucho antes del final natural del mensaje. Dado que las marcas posteriores permanecen unidas al transcrito no leído, enzimas especializadas de vigilancia celular catalogan de inmediato toda la molécula como defectuosa. Estas enzimas degradan rápidamente cerca del ochenta y cinco por ciento de los mensajes antes de que otros ribosomas puedan traducir. La célula queda privada de instrucciones para fabricar canales. Por ello, cualquier rescate terapéutico eficaz debe proteger primero el transcrito antes de intentar reparar las proteínas truncadas.
Analogía Cotidiana: Considere una línea de ensamblaje automatizada en una planta automotriz donde los inspectores colocan sellos de seguridad de colores brillantes a lo largo de cada segmento unido del chasis. A medida que la estructura del vehículo avanza, los robots retiran sistemáticamente cada sello. Si un error en la fabricación detiene la línea antes de tiempo, los sellos posteriores quedan completamente intactos. Un supervisor en la planta detecta estas marcas intactas y concluye de inmediato que el ensamblaje falló a mitad del camino. En lugar de permitir que un automóvil a medio construir salga de la fábrica, el supervisor desvía el chasis a una trituradora industrial. De manera similar, las células humanas emplean los complejos de unión exónica como sellos moleculares para verificar la traducción completa. Cuando un codón de paro prematuro deja complejos posteriores intactos, enzimas de vigilancia trituran rápidamente el ARN mensajero para evitar acumular fragmentos anómalos. Sin embargo, esta analogía de fábrica deja de ser exacta porque los transcritos destruidos no pueden reciclarse de forma instantánea, dejando a la célula epitelial sin instrucciones para sus canales.
Guía de Controles Interactivos: Antes de revisar las ecuaciones cinéticas, el laboratorio interactivo le permite manipular dos controles decisivos en el rescate de variantes sin sentido. El primer deslizador ajusta el factor de atenuación de SMG1 y NMD, modelando la eficacia con la que un inhibidor protege el transcrito frente a las nucleasas de vigilancia. Al aumentar este valor, la reserva de ARN mensajero atenuada asciende desde su valor basal del catorce por ciento hacia niveles normales. El segundo control regula el multiplicador de plegamiento y apertura con correctores y potenciadores para simular la ayuda farmacológica sobre los canales. Observe detenidamente las lecturas. La posición de paro de G542X se ubica temprano en el exón 12 y produce un fragmento carente del segundo dominio transmembrana. Por el contrario, la posición de W1282X se localiza tarde en el exón 23, preservando los cuatro dominios primarios para la unión de moduladores. Comparar estas lecturas muestra por qué el mensaje debe sobrevivir primero a la vigilancia antes de que los correctores puedan actuar.
Riesgo Biofísico y Clínico: En los registros globales de pacientes, entre el ocho y el diez por ciento de las personas portan variantes de Clase I que introducen un codón de terminación prematuro en la pauta abierta de lectura de CFTR. En su rigurosa investigación de 2018, Sharma y colaboradores demostraron que los alelos sin sentido no representan una clase biológica homogénea. Un codón de paro temprano situado en el centro del transcrito, como G542X en el exón 12, genera un polipéptido truncado de 541 aminoácidos que carece por completo del segundo dominio transmembrana y del segundo dominio de unión a nucleótidos. En cambio, variantes tardías como W1282X en el exón 23 conservan cuatro de los cinco dominios estructurales principales. Esta divergencia biofísica determina si el canal truncado retiene cavidades funcionales de unión a moduladores. Asimismo, la distancia entre el codón prematuro y la última unión exónica condiciona la severidad de la degradación por NMD. Cerrar esta brecha molecular exige terapias combinadas que protejan el ARN mensajero y venzan el arresto traduccional, sin formular promesas clínicas prematuras.
Derivación Formal: La concentración en estado estacionario de los transcritos de CFTR sujetos a terminación prematura se formaliza mediante la ecuación de balance de masas d[mRNA]/dt = k_tx − (k_deg,0 + k_NMD · Θ(d_EJC − 50 nt)) [mRNA], donde k_tx representa la transcripción nuclear y exportación, k_deg,0 denota el recambio citoplásmico basal y k_NMD caracteriza la degradación mediada por mutaciones sin sentido. La función escalón de Heaviside Θ(d_EJC − 50 nt) encapsula la geometría estérica de la ronda pionera de traducción. Durante la terminación, la huella física del ribosoma 80S junto con los factores de liberación eRF1 y eRF3 abarca entre treinta y treinta y cinco nucleótidos aguas abajo del sitio A ribosomal. Si un complejo de unión exónica (EJC) se localiza a menos de cincuenta a cincuenta y cinco nucleótidos del codón de terminación, el ribosoma en avance desaloja físicamente las proteínas centrales eIF4A3, MAGOH y Y14 antes de que se ensamble la maquinaria de vigilancia, permitiendo que el mensaje escape de la degradación rápida. Cuando la distancia d_EJC supera este umbral espacial crítico, los EJC posteriores permanecen anclados a la cinta de ARNm. Los factores de liberación retenidos reclutan la helicasa UPF1 y la cinasa SMG1 para constituir el complejo transitorio SURF. El puente físico directo entre UPF1 y UPF2/UPF3B activa a SMG1, desencadenando la fosforilación en múltiples sitios del dominio C-terminal de UPF1. Este estado fosforilado recluta de inmediato a la endonucleasa SMG6, la cual efectúa el corte fosfodiéster adyacente al sitio de pausa y recluta a SMG5/SMG7 para dirigir la desadenilación y la pérdida del capuchón 5'. En el núcleo computacional primario (src/scripts/ptc-simulator.js), esta cascada se contrae en una constante cinética efectiva de primer orden k_eff = k_deg,0 + k_NMD, calculando el sustrato disponible para la decodificación y el rescate farmacológico.
Frontera Traslacional: Los límites traslacionales de los alelos sin sentido están fundamentalmente restringidos por la topología estructural de la cadena polipeptídica naciente. Aunque la inhibición de NMD eleva los niveles del transcrito, no modifica la frontera física de la proteína truncada. En G542X (exón 12), la traducción se detiene abruptamente en el residuo 541 dentro del núcleo del primer dominio de unión a nucleótidos (NBD1). El polipéptido resultante carece de las asas intracelulares 3 y 4, del segundo dominio transmembrana (TMD2) y de NBD2. Sin TMD2, las interfaces interdominio indispensables para ensamblar el poro no se forman, imposibilitando el transporte de cloruro incluso ante combinaciones moduladoras como elexacaftor y tezacaftor. Por el contrario, W1282X en el exón 23 preserva 1,281 aminoácidos, manteniendo intactos TMD1, NBD1, el dominio regulador (R) y el haz transmembrana TMD2. Este polipéptido conserva las cavidades de unión farmacológica para elexacaftor y tezacaftor, careciendo únicamente del subdominio helicoidal distal de NBD2. Registros electrofisiológicos en células epiteliales bronquiales humanas demuestran que W1282X retiene una conductancia basal que ivacaftor potencia de manera notable al restaurar la abundancia del ARNm. Las simulaciones de Markov confirman que las estrategias traslacionales deben distinguir con rigor entre alelos de truncamiento temprano y tardío en lugar de tratarlos como una categoría clínica idéntica.
Horizonte terapéutico: Explica por qué G542X (exón 12) y W1282X (exón 23) difieren estructuralmente: W1282X conserva TMD1, NBD1, R y TMD2, mientras que G542X trunca la proteína a la mitad. Investigación independiente, no asesoramiento médico.
Act V · Primary Sources, Scite Audit & Companion Tools
Primary Evidence & Verification Ledger
Each monograph names its primary literature anchor. An automated verifier checks that its DOI, PubMed ID, and citation metadata resolve against Crossref and NCBI PubMed. Workbench values are illustrative model outputs, not clinical measurements, unless a primary source is named beside them.
- Primary Literature Receipt: Sharma et al. (2018), PLOS Genetics 14(11):e1007723 — Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis (PMID 30444886). (DOI 10.1371/journal.pgen.1007723 · PubMed 30444886 · PDB 6MSM).
- Citation Context (Scite): Inspect how later literature cites 10.1371/journal.pgen.1007723 on Scite.ai ·
Crossref + Scite verified (data/folio-citations.cache.json · fetched 2026-11-08 · 62 citing · 4 supporting · 67 mentioning · 0 contrasting). - Open-Source Computational & Epistemic Engine: ITensors.jl Matrix Product States & Doob h-Transform Markov Chains (DOI 10.21468/SciPostPhysCodeb.4 · Scite Report).
- Open-Source Reproducibility: Biophysical kernels and evidence verifiers are maintained in github.com/senseiewok/cf-research and github.com/senseiewok/cf-skills.
For builders: method, companion SKILL.md, Python verifier, and edition history (REV 1.2)
cftr-ptc-nmd-surveillance-SKILL.md · Kernel src/scripts/ptc-simulator.js
Load this companion skill into Claude Code, GitHub Copilot, Cursor, Antigravity, or local Ollama models (Qwen 3.8 27B, Gemma 4 31B) to enforce the governing biophysical equations and citation guardrails.
View raw SKILL.md source
--- name: cftr-ptc-nmd-surveillance description: AI-agnostic molecular biology skill for Class I CFTR nonsense variants (G542X, W1282X), the 50-55 nt EJC rule, and UPF1/SMG1 nonsense-mediated decay kinetics. license: CC-BY-4.0 --- # G.01 — Class I Premature Stop Codons (G542X, W1282X) & NMD ## Governing Biophysical / Mathematical Law d[mRNA]/dt = k_tx − (k_deg,0 + k_NMD · Θ(d_EJC − 50 nt)) [mRNA] ## Primary Evidence Receipt - **Citation:** Sharma et al. (2018), PLOS Genetics 14(11):e1007723 — Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis (PMID 30444886). - **DOI:** https://doi.org/10.1371/journal.pgen.1007723 - **PubMed PMID:** https://pubmed.ncbi.nlm.nih.gov/30444886/ - **Structural Reference (RCSB PDB):** https://www.rcsb.org/structure/6MSM - **Answer Tier:** T2 · Sourced Molecular & Kinetic Model ## Verification Rules - Apply the 50-55 nt Exon-Junction Complex (EJC) boundary rule across the 27 exons of human CFTR. - Contrast exon 12 G542X (lacks TMD2/NBD2) with exon 23 W1282X (retains TMD1, NBD1, R, TMD2). - State clearly that stop-variant readthrough and NMD models are research simulations, not medical advice. ## Safety & Clinical Boundary Research synthesis and biophysical modeling only — never medical advice, clinical guidance, or a treatment promise.
REV 1.2 (2026-11-04): Informatico magazine parity, Split Workbench (Plates A & B + 4-stage stepper), and live Crossref/PubMed citation gate verification.
Verified 5-Act magazine flow, untruncated headings, and bilingual EN / ES-MX structural parity.
Audited clinical dignity boundaries, non-promise guardrails, and discovery catalog coverage.
check_folio_citations.py
Verified DOI 10.1371/journal.pgen.1007723 against Crossref and NCBI PubMed metadata.
src/scripts/ptc-simulator.js
Coupled governing relation d[mRNA]/dt = k_tx − (k_deg,0 + k_NMD · Θ(d_E to interactive Plates A & B.