1. Introduction
Acute myeloid leukemia (AML) is a complex, diverse disease driven by varied genetic and epigenetic shifts in immature blood cells, resulting in wide-ranging clinical outcomes. While treatment has evolved, the prognosis remains grim for older patients or those harboring high-risk mutations like FLT3-ITD or PTPN11, who often cannot withstand the rigors of intensive chemotherapy [
1]. AML survival leans heavily on anti-apoptotic proteins, particularly BCL-2. This vulnerability established BCL-2 inhibitors, notably venetoclax (VEN), as a transformative standard-of-care for patients unfit for traditional chemo, boosting both remission rates and overall survival. Nevertheless, efficacy is not universal; roughly 35% of patients face primary resistance or eventual relapse [
2,
3]. Mechanisms of resistance are multifaceted and include the co-expression of other anti-apoptotic proteins (e.g., MCL-1, BCL-XL) not targeted by the drug [
4,
5], the plasticity of the AML cell state leading to adaptive resistance [
6,
7], and the presence of other high-risk mutations (e.g., FLT3-ITD, PTPN11) [
8,
9,
10]. Combining VEN with other agents (hypomethylating agents (HMAs) like azacitidine or decitabine, or low-dose cytarabine) has improved response rates in older, unfit AML patients [
3]. However, overcoming primary resistance and preventing relapse still remain major clinical challenges due to the complex scenarios underlying HMA/VEN treatment [
11,
12].
The neuroactive ligand–receptor interaction (NLRI) pathway serves as a fundamental signaling axis that modulates critical biological functions. While traditionally associated with neurodegenerative disorders, the NLRI pathway is increasingly recognized for its role in oncogenesis, specifically enhancing tumor aggressiveness and drug resistance in solid malignancies such as prostate and colon cancer [
13,
14,
15,
16]. These effects are often mediated through the activation of pro-survival pathways like AKT and NFκB, as well as the modulation of the tumor microenvironment [
13,
17,
18]. Despite these insights in solid tumors, the specific contribution of the NLRI pathway to hematologic malignancies—and particularly the emergence of VEN resistance in AML—remains largely unexplored.
Because NLRI signaling modulates caspase activation—a requisite for VEN-induced apoptosis, we hypothesized that the downregulation of CHRNB4 and the subsequent alteration of NLRI signaling represent a novel survival mechanism that allows AML cells to bypass BCL-2 inhibition. To investigate this, we characterized VEN-resistant AML models across diverse in vitro and in vivo contexts. Through comprehensive molecular and murine analyses, we identified the NLRI pathway as the exclusive shared signaling node significantly dysregulated across independent resistant models. Within this axis, we prioritized CHRNB4 for biological validation, as it represented the sole transcript consistently and significantly suppressed in both cell lines and tumor models. We demonstrate that resistance is mechanistically driven by CHRNB4 silencing. Furthermore, our findings indicate that CHRNB4 depletion serves as a robust predictor of shortened overall survival and diminished clinical response in venetoclax-treated patients. Conversely, enforced CHRNB4 expression—a definitive gain-of-function approach—effectively impairs the clonogenic capacity and tumorigenicity of resistant cells. Collectively, these data establish the NLRI pathway as a mediator of the VEN-resistant phenotype and position CHRNB4 as a critical biomarker for next-generation therapeutic strategies.
3. Discussion
While venetoclax (VEN) monotherapy initially showed promise, its clinical utility in AML is severely limited by the inevitable emergence of acquired resistance [
23,
24]. Although FDA-approved combinations with hypomethylating agents or low-dose cytarabine have improved remission rates and overall survival [
23,
25,
26,
27,
28], significant hurdles remain, including profound myelosuppression and persistent therapeutic evasion [
26,
29]. This study elucidates a novel molecular driver of such resistance, demonstrating that chronic VEN exposure triggers a transcriptomic rewiring of the NLRI pathway. Specifically, we identified the downregulation of CHRNB4 as a critical mediator of reduced drug sensitivity. These findings position CHRNB4 as a potential indicator for VEN response and suggest that targeting the NLRI axis offers a compelling therapeutic strategy to overcome resistance in AML.
Resistance to VEN in leukemia is inherently multifactorial, typically driven by molecular adaptations that reinforce anti-apoptotic defenses. Standard mechanisms include the upregulation of survival proteins like MCL-1 and BCL-XL, acquired mutations in BCL2 or BAX, and the activation of compensatory signaling through the PI3K/AKT axis [
30]. We prioritized the MV4-11 (VENM) model for in-depth mechanistic and in vivo studies because its FLT3-ITD mutation more accurately reflects the high-risk genetic landscape seen in clinical VEN resistance. Additionally, this model’s reliable engraftment and well-characterized growth kinetics provided a robust, reproducible system for our xenograft and molecular analyses. Consistent with previous reports [
31,
32], our data demonstrate that resistant VENM and VENK cells possess superior proliferative fitness, characterized by increased colony density and spheroid size. Furthermore, in vivo xenograft models confirmed that VENM cells harbor significantly higher tumorigenic potential than their parental counterparts. However, our mechanistic findings deviate from the classical paradigm. Rather than an increase, we observed a subtle decrease in MCL-1 and BCL-XL expression in resistant cells—a shift that, in isolation, should lower the apoptotic threshold. Paradoxically, this was accompanied by a marked reduction in cleaved caspase-9 and PARP, indicating a profound inhibition of the executioner caspase cascade. Collectively, these results suggest that VEN resistance in this context involves a compensatory shift toward BCL-2-independent survival mechanisms. This discovery provides a strong rationale for combining VEN with agents like HMAs, which can further suppress MCL-1 and BCL-XL, induce pro-apoptotic NOXA, and reverse the epigenetic silencing of genes such as GSDME to bypass intrinsic resistance.
Mutations in FLT3 and KIT are established drivers of VEN resistance in AML, frequently correlating with diminished therapeutic response and a higher propensity for clinical relapse [
8,
9,
10,
33,
34]. Our analysis reveals that CHRNB4 expression is significantly downregulated in high-risk patient cohorts—such as those harboring FLT3-ITD without NPM1 mutations—compared to those with favorable risk profiles. These data suggest a potential synergy between CHRNB4 depletion and oncogenic FLT3 or KIT signaling in the establishment of resistant leukemic populations. Notably, while the specific NLRI pathway components dysregulated in our models varied (20 genes in VENM vs. 26 in VENK), CHRNB4 emerged as the exclusive overlapping node across these genetically distinct backgrounds. This ‘pathway-level convergence’—where different genetic nodes within the same network are recruited depending on the oncogenic context—is a recognized phenomenon in cancer systems biology. The consistent suppression of CHRNB4 across both FLT3-mutated and KIT-mutated lineages suggests it may represent a critical common denominator, or ‘master regulator,’ of the resistant phenotype. Furthermore, the non-overlapping genes identified likely reflect the biological plasticity and functional redundancy inherent in AML, where complementary signals within the NLRI pathway bypass BCL-2 inhibition. While this study prioritizes the functional validation of CHRNB4, the broader transcriptomic remodeling observed underscores the complexity of this bypass mechanism. Future investigations into these secondary NLRI-associated genes will further elucidate the molecular framework of resistance and may uncover therapeutic vulnerabilities tailored to the specific genetic context of FLT3- or KIT-mutant AML.
The NLRI pathway is a critical signaling scaffold that, while primarily known for regulating neurobiological functions, is increasingly implicated in tumor progression and therapeutic evasion across diverse malignancies [
13,
14,
15,
16]. Although mechanisms such as the activation of pro-survival signaling, neuroendocrine differentiation, and epigenetic remodeling have been documented in solid tumors, a significant knowledge gap persists regarding how this pathway drives resistance in hematological malignancies, particularly against VEN in AML. To address this, we performed transcriptomic profiling of VEN-resistant (VENM and VENK) and PAR cells. Integrated KEGG and GSEA analyses identified the NLRI and apoptotic pathways as the most significantly enriched among differentially expressed transcripts. Specifically, the NLRI pathway involved 20 altered genes in VENM and 26 in VENK cells. Notably, CHRNB4 emerged as the only shared gene consistently downregulated across both resistant models and their derived tumors, suggesting a central regulatory role in VEN resistance. These resistant populations exhibited a markedly aggressive phenotype, characterized by accelerated in vitro proliferation, enhanced spheroid and colony-forming capacity, and heightened tumorigenicity in vivo. Crucially, the functional restoration of CHRNB4 in resistant cells significantly impaired both cell adhesion and colony formation. Clinical validation further underscored these findings, as lower CHRNB4 expression in AML patients predicted significantly shorter overall survival and a diminished response to VEN-based regimens. Collectively, our data establish the NLRI pathway as a primary driver of VEN resistance and identify CHRNB4 as both a potential prognostic indicator and a promising therapeutic target for overcoming resistance in AML.
Analysis of TCGA data reveals that low CHRNB4 expression correlates with poor clinical prognosis and molecular signatures of venetoclax resistance, including elevated pAKT and reduced BCL-2/MCL-1 ratios. These findings suggest that CHRNB4 downregulation facilitates both disease progression and pro-survival signaling. Conversely, our functional assays show that CHRNB4 overexpression impairs tumor formation and suppresses growth, reinforcing its role as a putative tumor suppressor.
Our overexpression experiments revealed a notable discrepancy: while CHRNB4 restoration was associated with increased survival markers like pAKT and MCL-1, it simultaneously inhibited colony formation and adhesion without inducing PARP cleavage. This suggests that despite the induction of certain survival signals, the overall fitness of these leukemic cells is significantly compromised. A possible explanation for this “signaling-to-function” divergence is that high-level CHRNB4 expression may correlate with cellular stress, such as endoplasmic reticulum (ER) stress or altered Ca
2+ homeostasis [
35,
36]. These transcriptomic signatures might reflect a state where compensatory upregulation of pAKT and MCL-1 occurs alongside a reduction in proliferative and adhesive capacity [
37,
38,
39]. In this context, the absence of cleaved PARP suggests that the cells may be undergoing functional impairment rather than immediate apoptosis. Further investigation is required to definitively characterize these stress-mediated pathways and their role in modulating the fitness of venetoclax-resistant AML.
Our study has several limitations. First, while our results highlight the impact of CHRNB4 on growth dynamics, the study is restricted to two AML cell lines. Given the limited gene-level overlap between these models, the claim of a shared NLRI-driven resistance program across diverse AML contexts must be interpreted with caution. Furthermore, “resistance” in our models was primarily defined by sustained proliferation under continuous selective pressure rather than formal IC50 or AUC shifts. While our chosen drug concentrations (0.01–0.08 nM) align with the estimated physiologically active, unbound fraction of venetoclax (~0.2 nM) [
40], future studies incorporating standard dose–response analyses and broader genomic representation are required to ensure these mechanisms are universally applicable across the heterogeneous landscape of AML.
Second, our mechanistic evidence is currently supported primarily in a single model and based on gain-of-function re-expression. The lack of complementary loss-of-function data (knockdown/knockout) in parental cells, alongside the absence of direct chemosensitivity rescue and apoptosis assays, remains a significant limitation. While CHRNB4 suppresses aggressive growth phenotypes, we have not yet definitively quantified its direct impact on the apoptotic threshold or BCL-2 dependency through biophysical assays like BH3 profiling. Moreover, the observed signaling-to-function discrepancy—where survival markers increased despite inhibited growth—suggests complex, stress-mediated contradictions that remain to be fully resolved.
Third, our in vivo and 3D Matrigel models did not evaluate tumor growth under continuous drug exposure. Because these assays were conducted without immediate post-injection drug exposure, they should be framed as exploratory rather than definitive evidence of therapeutic resistance. Investigating these kinetics with active drug pressure will be critical to precisely characterize the fitness and evolutionary trajectory of resistant clones. Additionally, as no formal blinding or randomization was applied to these procedures, a potential risk of observer bias must be acknowledged.
Finally, our patient-level validation is preliminary and utilized a cohort where CHRNB4 expression may partially reflect underlying differentiation states, such as primitive versus monocytic maturation. Larger, prospective clinical cohorts are essential to confirm the independent prognostic value of CHRNB4 and establish its utility as a robust biomarker. Collectively, these points identify the necessary trajectory for future research to refine the role of the NLRI pathway in VEN-resistant AML.
4. Experimental Methods
4.1. Cell Lines and Cell Culture
The human AML cell lines MV4-11 (CRL-9591) and Kasumi-1 (CRL-2724) were obtained from the American Type Culture Collection (ATCC). MV4-11 is a non-adherent line carrying the t(4;11) translocation (MLL-AF4 fusion) and a FLT3-ITD mutation. Kasumi-1, derived from an AML patient with the t(8;21) translocation (RUNX1-RUNX1T1/AML1-ETO fusion), harbors a c-KIT-activating mutation and exhibits myeloid and macrophage lineage characteristics. While we relied on the characterization and quality control provided by the vendor at the time of purchase, we acknowledge that additional in-house authentication (STR profiling) or mycoplasma testing was not performed for this study. To mitigate risks of contamination or misidentification, both lines were verified against the International Cell Line Authentication Committee (ICLAC) database and were not found among the registers of commonly misidentified or cross-contaminated cell lines.
Cells were cultured in RPMI-1640 medium (GE Healthcare #SH30027.01, GE Healthcare, Uppsala, Sweden) supplemented with 10% (for MV4-11) or 20% (for Kasumi-1) fetal bovine serum (FBS, Gibco by Life Technologies #16140-071, Thermo Fisher Scientific, Waltham, MA, USA) and 1% Antibiotic–Antimycotic (Gibco by Life Technologies #15240062, Thermo Fisher Scientific, Waltham, MA, USA). Cells were maintained at 37 °C in a humidified incubator with 5% CO2.
4.2. Reagents and Plasmid Constructs
The BCL-2 inhibitor Venetoclax (HY-15531) was purchased from MedChemExpress (Princeton, NJ, USA). For in vitro studies, all drugs were initially dissolved in dimethyl sulfoxide (DMSO) and stored at −80 °C. The CHRNB4 overexpression plasmid was obtained from Vector Builder (Chicago, IL, USA), and the corresponding control plasmid was acquired from Addgene (Watertown, MA, USA).
4.3. Stepwise Induction of Venetoclax Resistance
Parental MV4-11 and Kasumi-1 cells were exposed to a low, sub-lethal concentration of the BCL-2 inhibitor VEN (0.001 nM) in a stepwise manner to induce resistance. Surviving cells were cultured, and upon recovery of consistent growth rates, the venetoclax concentration was incrementally increased. Final concentrations reached 0.01 nM for MV4-11 and 0.08 nM for Kasumi-1 cells. The total selection period was 8–10 weeks. Cell viability, proliferation rate, and morphological changes were routinely monitored during the adaptation process. The ‘resistance’ in this study is defined as the sustained proliferative capacity of VENK and VENM cells under continuous VEN exposure, which resulted in the inhibition of the parental lines. Once established, resistant cell lines were routinely maintained in medium containing 0.01 nM (MV4-11) and 0.08 nM (Kasumi-1) venetoclax to preserve the resistant phenotype. For experiments requiring drug-free conditions, both parental and resistant cells were washed once with blank RPMI 1640 medium (no FBS, no antibiotics) to remove any residual venetoclax. The washed cells were then cultured in regular RPMI 1640 medium (with 10% FBS and antibiotics) for 48–72 h to allow for recovery and proliferation in a drug-free environment before use in downstream assays. The 72 h recovery period was intentionally designed to ensure that both parental and resistant cells were in a comparable physiological state at the time of injection. This brief window allows for the clearance of residual VEN, ensuring that any observed differences in growth are due to the stable, acquired phenotypes of the resistant cells rather than acute, transient drug effects.
4.4. Lentivirus Vector, Virus Production and Virus Infection
For lentivirus production, HEK-293T cells were seeded in a 10 cm culture dish at a density of 2.0 × 106 cells/dish and incubated for 24 h. Cells were subsequently transfected with 4 µg of either the target or scrambled control plasmids using a CalPhos™ Mammalian Transfection Kit (Clontech Laboratories, Inc., Mountain View, CA, USA), following the manufacturer’s protocol. Viral supernatants were collected at both 48 and 72 h post-transfection and concentrated using a Lenti-X™ Concentrator (Clontech, Cat. #631232). For infection, 2 × 106 recipient MV4-11-resistant cells were resuspended in 1 mL of medium and transduced with the harvested lentiviruses in the presence of Polybrene at a final concentration of 4 µg/mL. Stable transformants were selected by adding puromycin to a final concentration of 1 µg/mL 24 h post-transduction.
4.5. Colony-Forming Assays
Progenitor cell function was assessed via colony-forming assays using Human Methylcellulose Complete Media (R&D Systems, #HSC003, Bio-Techne Corporation, Minneapolis, MN, USA). Briefly, cells were suspended in 0.3 mL of the provided cell suspension medium and then thoroughly mixed with 3 mL of the complete methylcellulose media. This mixture was plated into 35 mm dishes and incubated. Colony number and size were evaluated and recorded after 7–14 days.
4.6. 3D Spheroid-Forming Assays
For spheroid assays, 2000 cells were suspended in 100 µL of Corning Matrigel Matrix Growth Factor Reduced (Corning #356230, Corning Life Sciences, Tewksbury, MA, USA) and seeded on the 24-well culture plate. The spheroids were then cultured for 3 to 14 days under standard conditions. Imaging was performed using a Zeiss LSM 880 confocal/multiphoton microscope (Carl Zeiss AG, Oberkochen, Germany). Two-photon excitation was achieved with an 800 nm laser, and fluorophores were spectrally separated by their emission for detection. Note that spheroid assays are intended to model the protective effects of the bone marrow niche rather than traditional epithelial spheroids.
4.7. Western Blotting
The whole cellular lysates were prepared by harvesting the cells in 1 × cell lysis buffer [20 mM HEPES (pH 7.0), 150 mM NaCl and 0.1% NP40] supplemented with 1 mM phenylmethane sulfonyl fluoride (PMSF, Sigma #10837091001, St. Louis, MO, USA), 1 × Phosphatase Inhibitor Cocktail 2 and 3 (Sigma #P5726, P0044), and 1 × protease inhibitors (protease inhibitor cocktail set III, Calbiochem–Novabiochem #539134, San Diego, CA, USA). The proteins were resolved by sodium dodecyl sulfate (SDS)–polyacrylamide gel electrophoresis, transferred onto PVDF membranes (GE Healthcare #10600023), blocked by 5% non-fat milk followed by probing with first antibodies, anti-BCL-2 (Millipore, St. Louis, MO, USA, #05-729), anti-BCL-XL (Santa Cruz, Dallas, TX, USA, #sc-7195), anti-MCL-1 (Santa Cruz, #sc-819), anti-AKT (Cell Signaling, Danvers, MA, USA, #9272), Anti-pAKT (Cell Signaling, #4060), anti-CHRNB4 (Abcam, Cambridge, UK, #ab233735), anti-β-Actin (Cell Signaling, #4967) as well as HRP-conjugated secondary antibodies, goat anti-rabbit IgG (Cell Signaling, #7074), and goat anti-mouse IgG (Cell Signaling, #7076).
4.8. RNA Isolation, cDNA Preparation and Quantitative PCR (qPCR)
Total RNA was isolated according to the manufacturer’s instructions using the miRNeasy Kit (Qiagen, Hilden, Germany, #217004). Complementary DNA (cDNA) synthesis was synthesized from the isolated RNA using SuperScript® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA, USA, #18080-051). Gene expression levels were quantified via qPCR using the SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA, #4309155). Target gene expression was normalized to 18S ribosomal RNA levels. Primer sequences are CHRNB4: F 5′-CAGCTTATCAGCGTGAATGAGC-3′, R 5′-GTCAGGCGGTAATCAGTCCAT-3′; CYSLTR2: F 5′-ACTGAGGACCGTCCACTTGA-3′, R 5′-CCCAGCAAAGTAATAGAGCAGAG-3′; QRFPR: F 5′-CAGGCGCTTAACATTACCCC-3′, R 5′-CCGGTACAGAGCGATGAACTG-3′; P2RX5: F 5′-TACCTGGTCGTATGGGTGTTC-3′, R 5′-GCCCAAGATCCGAGGTGTTG-3′; GABRD: F 5′-GCATCCGAATCACCTCCACTG-3′, R 5′-GATGAGTAACCGTAGCTCTCCA-3′; CRHR2: F 5′-CCCTTGTCGTCAACTACCTGG-3′, R 5′-ACATTTCGCAGGATAAAGGTGG-3′; 18S: F 5′-ATTAAGGGTGTGGGCCGAAG-3′, R 5′-TGGCTAGGACGTGGCTGTAT-3′.
4.9. RNA Sequencing and Data Processing
Strand-specific transcriptome library construction was completed by enriching mRNA from total RNA, and sequenced by the DNBSEQ high-throughput platform at BGI (
https://www.bgi.com). Briefly, mRNA was purified from total RNA using oligo(dT) magnetic beads, fragmented, and converted to double-stranded cDNA with dUTP incorporated into the second strand. The cDNA underwent end repair, A-tailing, and adapter ligation. UDG digestion was performed to remove the second strand before PCR amplification. After purification with XP Beads (Beckman Coulter Life Sciences, Indianapolis, IN, USA), the library was validated on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The double-stranded PCR product was heat-denatured and circularized using a splint oligo. Single-strand circular DNA libraries were amplified via rolling circle replication with phi29 polymerase to produce DNA nanoballs. These were sequenced on a patterned nanoarray using combinatorial probe-anchor synthesis, generating single-end 50 (or paired-end 100/150) base reads. Triplicate samples were sequenced.
Genes were considered significantly up- or down-regulated if they met a univariate p-value of <0.05 and had an absolute fold difference of ≥1.5. A univariate significance threshold of 0.001 was used for filtering or pre-screening genes prior to comparison. Signaling pathway analysis was performed using DAVID (Version 6.7).
Significant KEGG pathways (adjusted p-value < 0.05) were visualized as dot plots using the clusterProfiler and ggplot2 R packages (Version R.4.5.1). The top up- or down-regulated categories were identified based on their statistical significance, and the number of genes contributing to each category was illustrated.
4.10. In Vivo Tumorigenesis Assays
Female athymic nude mice (4–6 weeks old) were purchased from the Jackson Laboratory. All animal procedures were conducted in accordance with the National Institutes of Health guidelines for the care and use of laboratory animals and were approved by the Institutional Animal Care and Use Committee (IACUC) at Case Western Reserve University. Mice were monitored daily for signs of pain and distress, including significant weight loss, decreased activity, and hunched posture. All animals were provided ad libitum access to food and water throughout the study.
MV4-11 cells (parental vs. resistant; mock vs. CHRNB4 overexpression; 3 × 106) were suspended in a 3:7 mixture of serum-free medium and Matrigel® (Corning, Inc.) and subcutaneously injected into both flanks of 6-week-old female athymic nude mice. Tumor growth was monitored every 2–3 days using an electronic caliper. Tumor volume was calculated using formula 1/2 × A × B × B, where A is the length and B is the width, expressed in cubic millimeters. Tumor growth curves were generated for each treatment group by plotting the mean tumor volume over time and AUC was calculated. The study endpoint was determined per IACUC guidelines.
Upon reaching the study endpoint, mice were euthanized by CO2 inhalation followed by cervical dislocation. Excised tumors were divided for different analyses. A portion was snap-frozen and stored at −80 °C for subsequent molecular characterization. Another portion was fixed in 10% neutral buffered formalin for 24 h at 4 °C for histological analysis. After fixation, tissues were transferred to PBS, processed, and embedded in paraffin blocks for immunohistochemical and hematoxylin and eosin staining.
4.11. Hematoxylin and Eosin (H&E) and Immunohistochemical (IHC) Staining
Tumor and tissue samples were harvested from mice and immediately preserved by fixation in 10% neutral buffered formalin. Following fixation, the samples were submitted to the Department of Pathology at the MetroHealth System, Case Western Reserve University, for processing and IHC (Ki-67) or H&E staining. The prepared slides were visualized and photographed with a Leica microscope (Leica Microsystems, Wetzlar, Germany) fitted with a high-resolution spot camera, which was interfaced with Image-Pro Plus software (Media Cybernetics, Rockville, MD, USA) for image acquisition.
4.12. Gene Expression and Survival Analysis
mRNA expression data for the CHRNB4 gene were obtained from The Cancer Genome Atlas (TCGA) AML cohort (TCGA, Firehose Legacy) via the cBioPortal for Cancer Genomics (
https://www.cbioportal.org/ (accessed on 3 October 2025)). Patients were stratified into two groups based on their CHRNB4 mRNA expression levels: a low-expression group (lower 25% of expression values, i.e., the first quartile) and a high-expression group (remaining 75%). Overall survival (OS) was the primary endpoint. Survival curves were estimated using the Kaplan–Meier method, and differences between the groups were assessed using the log-rank test.
Survival analyses were conducted using the median expression value, optimal cutoff values, and a predefined 25% cutoff to stratify patients into expression groups. A multivariate Cox proportional hazards regression analysis was then performed to evaluate the prognostic impact of CHRNB4 expression alongside other relevant clinical variables. All statistical analyses were performed using JMP® Student Edition version 18 (SAS Institute Inc., Cary, NC, USA).
4.13. Statistical Analysis
Statistical analyses were performed using JMP Student Edition (Version 18). Sample sizes were not statistically predetermined to ensure a specific power but were chosen based on the established literature for functional oncology assays. While randomization and blinding were not formally applied to experimental procedures, functional assays—including spheroid and colony frequency and dimensions—were quantified using Image-J/FIJI (Version 2.14.0; 1.54f) with a 50 µm diameter threshold and validated by an independent investigator blinded to experimental conditions. In vitro experiments, such as qPCR, Western blotting, and proliferation assays, were performed in biological triplicate (n = 3) unless otherwise noted.
Data were evaluated for normality via Shapiro–Wilk tests and for homogeneity of variance to justify parametric analyses. Group means were compared using two-tailed Student’s t-tests, with non-parametric alternatives applied for unequal variances; one-way ANOVA or mixed-effects models were utilized to account for intra-subject clustering in bilateral flank studies. In vivo growth kinetics were evaluated using Area Under the Curve (AUC) to emphasize cumulative tumor burden. Transcriptomic data were aligned with STAR, normalized by DESeq2, and screened using a Benjamini–Hochberg adjusted p-value (p < 0.05) followed by a post hoc fold-change threshold (|log2FC| > 1). Clinical relevance was assessed via multivariable Cox regression models adjusted for age, sex, and ELN 2022 risk categories using complete-case analysis. Finally, the association between CHRNB4 and venetoclax resistance was examined across primitive and monocytic maturation states to account for differentiation-driven sensitivity. In all cases, p < 0.05 was considered statistically significant.