Citations

Background: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited disorder leading to kidney failure. Tolvaptan, the only FDA-approved therapy, modestly slows disease progression but is limited by significant adverse effects, highlighting the need for more effective and better-tolerated treatments. Ciliary polycystins are central to ADPKD pathogenesis. We previously demonstrated that a cilia base-localized pool of CDK6 restricts ciliary polycystin abundance by suppressing axonemal polyglutamylation. However, whether CDK6 inhibition can restore polycystin function and suppress ADPKD progression in vivo remains unknown. Methods: Abemaciclib was tested in in vitro 3D cyst assays and ex vivo metanephric organ cultures. In vivo efficacy of early- and late-stage intervention were assessed in F1(129/B6) Pkd1 R3277C/R3277C mice receiving daily abemaciclib. Tolvaptan served as a therapeutic control. Cyst burden, fibrosis in the kidneys, kidney function, and primary cilia of renal epithelial cells were analyzed at study endpoints. Results: CDK6 was prominently upregulated in cyst-lining cells in human and murine PKD kidneys. At doses substantially lower than those used in oncology, abemaciclib robustly suppressed cyst growth in vitro and ex vivo . In vivo , long-term early treatment arrested cyst progression more effectively than tolvaptan without detectable toxicity. Late intervention largely halted cyst growth in females and reversed cyst progression in males. Mechanistically, abemaciclib restored axonemal polyglutamylation and increased ciliary polycystin levels. Conclusions: Abemaciclib has greater therapeutic efficacy and tolerability than tolvaptan in this preclinical model, largely driven by CDK6 inhibition–mediated restoration of axonemal polyglutamylation and increased ciliary polycystin abundance.

Myelodysplastic syndromes (MDS), which are hematopoietic stem cell malignancies, are often accompanied by signs of chronic inflammation, that can in turn drive the pathogenetic process. The precise mechanisms dysregulating inflammatory and innate immune signaling in MDS hematopoietic stem and progenitor cells (HSPCs) remain under investigation. We report that mice lacking Tet2 developed a hyper-inflammatory state, which can be further fueled by LPS-induced inflammation. This chronic inflammation temporarily promotes the self-renewal and myeloid differentiation of Tet2-deficient HSPCs; however, it ultimately accelerates HSC exhaustion and triggers MDS development in chimeric mouse models. Driving this phenotype was the activation of the NLRC4 inflammasome pathway. Notably, Nlrc4 depletion in Tet2-deficient mice impaired MDS development and improved the survival of these mice. These findings uncover a novel mechanistic basis for the MDS-associated inflammation and provide new targeting opportunities in its management.

Summary Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine. 1 However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions. 1–3 It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres. 4 To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.

Key Points Inositol polyphosphate-5-phosphatase E (INPP5E) and type Ig phosphatidylinositol-4-phosphate 5-kinase (PIPKIγ) coordinated the homeostasis of phosphatidylinositol-4-phosphate and phosphatidylinositol-4,5-bisphosphate in primary cilia. Modulating INPP5E or PIPKIγ activity changed the level of polycystin-1 and polycystin-2 in primary cilia. INPP5E inhibition increased the hypomorphic PKD1 variants (PC1-R3277C) in cilia and reduced cystogenesis in the kidney in vitro . Background Autosomal dominant polycystic kidney disease is mainly caused by mutations in PKD1 and PKD2 , which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively. PC1 and PC2 assemble a cation channel complex enriched in primary cilium, a sensory organelle associated with various developmental diseases, including polycystic kidney disease (PKD). Accumulating evidence supports the necessity of functional polycystin (PC) complex in cilia to prevent cystogenesis in the kidney, indicating that improving their ciliary levels may ameliorate defects underlying PKD pathogenesis. Yet, molecular mechanisms underlying the ciliary targeting and homeostasis of the PC complex are not fully understood. Methods Indirect immunofluorescence microscopy was used to monitor ciliary levels of PC1 and PC2 in renal epithelial cells. Electrophysiology analysis in oocytes was used to determine the channel activity of the PC complex. Cystogenesis in the kidney was measured using in vitro 3D-Matrigel cell models and ex vivo mouse embryonic kidney models. Results Suppressing inositol polyphosphate-5-phosphatase E (INPP5E) or activating type Ig phosphatidylinositol-4-phosphate 5-kinase raised ciliary levels of the PC complex in both normal renal epithelial cells and cells carrying autosomal dominant polycystic kidney disease mutations that interrupt the trafficking of PCs into cilia, including GANAB inactivation and the trafficking PKD1 mutation p.Arg3277Cys (RC). PC1 RC formed a complex with PC2 and exhibited normal channel activity in vitro . An INPP5E that increases PC1 and PC2 in cilia, suppressed in vitro forskolin-induced cystogenesis of inner medullary collecting duct epithelial cell line 3 cells in 3D Matrigel and ex vivo cyst formation in embryonic Pkd1 RC/RC mouse kidneys. Conclusions Our results demonstrated that increasing the ciliary level of PCs, by manipulating a ciliary phosphoinositide signaling axis, enhanced the functionality of PCs and suppressed cystogenesis of renal epithelial cells in vitro .

Abstract Measurable residual disease (MRD) assessment by flow cytometry (FC) plays an essential role in prognosis and therapy escalation of B-cell acute lymphoblastic leukemia (B-ALL). However, the high degree of expertise and manual analysis time required limits the availability of this assay. To overcome this limitation, we developed a data-enhancing artificial intelligence (AI) pipeline that accelerates and simplifies MRD analysis. Unaltered FC files from 171 B-ALL MRD-positive and 89 MRD-negative cases were processed through an AI pipeline trained with 31 expert-gated negative controls. Cluster-informed downsampling reduced FC files from 1.2 million to 155 884 cells per case, on average, (87% cellularity reduction), whereas preserving small MRD populations (median, 100% retention for MRD of <1%) and allowing for true percentage MRD estimates using a correction factor. A deep neural network cell classifier automatically identified normal hematopoietic subsets (macro-averaged F1 score of 0.86); and an AI measure of anomaly discriminated B-ALL from benign mononuclear (area under the curve [AUC] of 0.98) or B-lymphoid cells (AUC of 0.94). Manual analysis of AI-enhanced files was completed in only 1.01 minutes per case, on average (standard deviation of ±0.57); with 100% positive agreement with conventional analysis (for MRD of ≥0.01%), 100% negative agreement, and excellent quantitative correlation (R2 = 0.92). Our cloud-based AI-enhancement solution accelerates B-ALL MRD identification without compromising test performance and has the potential of facilitating B-ALL MRD analysis by more clinical laboratories.

9009 Background: International Medical Graduates (IMGs) are a vital component of the US oncology workforce, representing nearly half of practicing medical oncologists. However, systemic barriers may influence their career trajectories differently. Understanding these challenges is essential for addressing workforce disparities and optimizing cancer care delivery across diverse geographic regions. Methods: We conducted a cross-sectional study of 13,497 medical oncologists using the 2024 Dec CMS Provider Dataset linked with the 2023 Rural-Urban Continuum Codes (RUCC). Medical oncologists were identified by their self-reported primary specialties, including Hematology/Oncology, Medical Oncology, and Hematopoietic Cell Transplant. Physicians were categorized by graduation origin (based on their self-reported medical school), career stage (early: 0–10 years, mid: 11–30 years, late: >30 years post-medical school graduation). The primary outcomes included practice at Main Campus of NCI Designated Cancer Centers (as an indicator of academic practice) and the geographical location of their practice (Metro, Non-Metro, Mixed). We employed chi-squared tests for statistical comparisons and performed stratified analyses by career stage to evaluate transition patterns over time. Results: 6920 IMGs constituted 48.7% of the oncology workforce, with similar gender distributions between IMG and non-IMG oncologists (37.9% vs 36.5% female, p=0.068). Notably, early career oncologists were less likely to be IMGs (IMG vs non-IMGs: 8.2% vs 12.5%, p<0.001). Compared to Non-IMGs, IMG oncologists are less likely to practice at main campuses of NCI Center (19.9% vs. 27.7%, p<0.001), especially as their career advances (all p<0.01). (Table). IMGs had higher representation in non-metropolitan areas than non-IMGs (11.4% vs 9.1%, p<0.001), particularly in late-career stages (14.7% vs 12.3%, p=0.033), indicating their unique role in serving underserved regions. (Table). Conclusions: Our findings reveal that, IMGs are less likely to practice at main campuses of NCI-Cancer Center than their non-IMG colleagues. Meanwhile, IMG oncologists are disproportionately serving rural communities. Supporting IMG pathways in oncology is critical to ensure a balanced cancer care delivery across the United States. Practice setting distribution and academic affiliation among international medical graduates (IMGs) and US graduates (USGs) by career stage. IMG (N=6,577) Non-IMG (N=6,920) IMG (N=6,577) Non-IMG (N=6,920) NCI Center Other NCI Center Other Metro Non-Metro/Mixed Metro Non-Metro/Mixed Total 19.9% 80.1% 27.7% 72.3% 88.6% 11.4% 90.9% 9.1% Career Stage Early (0-10y) 29.1% 70.9% 36.1% 63.9% 91.1% 8.9% 95.4% 4.6% Mid (11-30y) 21.3% 78.7% 28.8% 71.2% 90.1% 9.9% 91.6% 8.4% Senior (30+y) 15.0% 85.0% 22.0% 78.0% 85.3% 14.7% 87.7% 12.3%

Tubulin polyglutamylation is a posttranslational modification that occurs primarily along the axoneme of cilia. Defective axoneme polyglutamylation impairs cilia function and has been correlated with ciliopathies, including Joubert Syndrome (JBTS). However, the precise mechanisms regulating proper axoneme polyglutamylation remain vague. Here, we show that cyclin-dependent kinase 6 (CDK6), but not its paralog CDK4, localizes to the cilia base and suppresses axoneme polyglutamylation by phosphorylating RAB11 family interacting protein 5 (FIP5) at site S641, a critical regulator of cilia import of glutamylases. S641 phosphorylation disrupts the ciliary recruitment of FIP5 and its association with RAB11, thereby reducing the ciliary import of glutamylases. Encouragingly, the FDA-approved CDK4/6 inhibitor Abemaciclib can effectively restore cilia function in JBTS cells with defective glutamylation. In summary, our study elucidates the regulatory mechanisms governing axoneme polyglutamylation and suggests that developing CDK6-specific inhibitors could be a promising therapeutic strategy to enhance cilia function in ciliopathy patients.