Citations

ABSTRACT Evidence indicates that the integrity of in utero development influences late life healthy or unhealthy aging; however, specific links between them are unclear. Histone chaperone HIRA is thought to play a role in both life stages, and here, we explore this role using the murine pigmentary system by investigating and comparing the effects of its lineage‐specific knockout, either conditionally during embryogenesis or postnatally. Embryonic knockout of Hira in tyrosinase+ neural crest‐derived lineages, including melanoblasts, led to reduced melanoblast numbers during embryogenesis, with single‐cell RNA sequencing analysis indicating evidence of lineage‐specificity defects. This was supported in an in vitro model using melb‐a melanoblasts in which Hira knockdown affected lineage identity and melanoblast differentiation potential, with ATAC‐seq data indicating a role of HIRA in orchestrating chromatin accessibility. Interestingly, however, newborn Hira knockout mice had wild type numbers of differentiated melanocytes, albeit functionally defective, as demonstrated by very mild hypopigmentation of the first hair coat, increased melanocyte telomere‐associated DNA damage foci, and impaired response to proliferative challenge. Moreover, as they aged, mice with embryonic melanoblast Hira knockout displayed marked defects in melanocyte stem cell maintenance and premature hair graying. Importantly, this phenotype was not observed after postnatal inducible knockout, indicating an essential role for HIRA at embryonic stages that is transmitted to adulthood, rather than a direct postnatal requirement within the pigmentary system. This genetic model shows that HIRA function during early development lays a foundation for maintaining lineage identity and subsequent maintenance of adult tissue‐specific stem cells during aging.

ABSTRACTBackgroundSkip lesions in bone sarcoma are a poorly described entity. Reports on skip lesions in osteosarcoma and Ewing sarcoma suggest that whole bone MRI should be obtained to evaluate for additional tumor foci given the association with worse outcomes. However, there is limited evidence to support whole bone imaging in chondrosarcoma.MethodsBetween 1995 and 2022, 129 patients with long bone chondrosarcoma were evaluated at our institution. Lesions were located most commonly in the femur in 64 patients and the humerus in 54 patients. All imaging studies and pathology reports were reviewed to determine the presence of skip lesions, defined as an area of histology‐confirmed chondrosarcoma that was separated from the primary lesion by normal bone on pathology.ResultsWhole bone imaging was obtained during initial staging in 107 patients with two‐thirds of patients receiving MRI, CT, or bone scan. Five patients (3.9%) were found to have skip lesions in the same bone as the primary tumor. There were no transarticular skip lesions. Skip lesions were detected in three patients with low grade chondrosarcoma (4.6%) and two patients with high grade chondrosarcoma (3.2%). All lesions were within 2 cm of the primary tumor. All were visible on MRI and CT of the primary site and one was visible on plain radiographs. The presence of skip lesions did not alter the type of surgical treatment in any patients.ConclusionSkip lesions in long bone chondrosarcoma are rare. All skip lesions in this study were in close proximity to the primary tumor and the same grade as the main lesion. Our results suggest that advanced imaging of the whole bone may be of low utility for evaluating the presence of skip lesions. The clinical significance of skip lesions in chondrosarcoma remains unclear, however, their presence did not impact the treatment plan in this series.

Abstract Background: Diffuse pulmonary meningotheliomatosis (DPM) is a rare, benign proliferation of minute meningothelial-like nodules ranging from 100mm – 11mm.1 The condition presents primarily in women (9:1) in middle age.2 Discovered incidentally or with mild symptoms such as dyspnea and dry cough, the imaging findings can be concerning for miliary metastatic, atypical infectious, and immune mediated diffuse parenchymal lung disease thereby complicating the diagnostic process. Case Description: A 70-year-old female never smoker presented to our pulmonary clinic for evaluation of dyspnea and dry cough. She described evaluation roughly 20 years prior that had revealed innumerable small ground glass pulmonary nodules on CT imaging. Pulmonary function testing at that time was unremarkable, and laboratory studies had only revealed a weakly (+) SSA antibody. She was referred for a right mini-thoracotomy wedge resection, with pathology demonstrating small nodules partially involving the pleura, suspected to represent hypersensitivity pneumonitis (HP), as well as, several incidentally noted pulmonary “chemodectomas”. She was trialed on inhaled therapies, antibiotics, and even a two-year course of steroids for suspected HP without notable clinical or radiologic improvement. Interestingly, she was subsequently found to have an intracranial meningioma which was treated with external beam radiation. Upon presentation at our institution, a repeat high resolution chest CT showed mosaic attenuation with innumerable groundglass nodules and micronodules in a centrilobular and peri-lymphatic distribution. There was no significant change in appearance or distribution from prior imaging (Figure 1, A-B). Rigid bronchoscopy with transbronchial lung cryobiopsy was performed with pathology showing multiple meningothelial-like nodules (Figure 1, C). This pathologic finding, in conjunction with her clinical history, including past surgical biopsy, led to a diagnosis of DPM. Discussion: This case adds to about 50 cases of DPM and the clinical significance of diffuse perivenular and interstitial meningothelial-like cell proliferations in the lung without clear malignant potential. Additionally, it provides another case to a notable collection of cases with metachronous intracranial meningioma, suggesting possible shared pathogenesis or genetic predisposition.2 While the clinical course of DPM is generally indolent, it poses diagnostic challenges due to overlapping imaging characteristics with more aggressive pulmonary pathologies. The differential may include sarcoidosis, miliary infectious and malignant etiologies, DIPNECH, and follicular bronchiolitis. Conclusions: A systematic approach to this patient's ground-glass nodules with clinical re-evaluation given ineffective empiric treatment ultimately led to the correct diagnosis. It highlights the importance of biopsy for the diagnosis of pulmonary nodules of unclear etiology even with benign clinical progression.

Abstract Rationale: The 1-year double-blind period of the MANDARA trial (NCT04157348) demonstrated non-inferiority of benralizumab to mepolizumab for achieving remission, in adults with relapsing/refractory eosinophilic granulomatosis with polyangiitis (EGPA). Here, we report the 2-year combined double-blind and ongoing open-label extension (OLE) data. Methods: On completion of the double-blind period (n=136/140) comparing benralizumab 1x30mg versus mepolizumab 3x100mg subcutaneously every 4 weeks, patients were invited to enter the OLE where they continued benralizumab (benra/benra) or switched from mepolizumab to benralizumab (mepo/benra). Endpoints included remission (Birmingham Vasculitis Activity Score=0 and oral glucocorticoid [OGC[ dose ≤4 mg/day), OGC use, relapse, blood eosinophil count (bEOS), Asthma Control Questionnaire (ACQ-6), pre-bronchodilator forced expiratory volume in 1 second (pre-BD FEV1), and safety. Results: In total, 128 patients entered the OLE (n=66 benra/benra, n=62 mepo/benra; mean age 52.8 years; 60.2% female), and 119 completed OLE Year 1. Baseline characteristics of those entering the OLE were similar to the double-blind period. At Week 104, over 60% in both groups (41 [62.1%] benra/benra and 42 [67.7%] mepo/benra patients) achieved remission. During the OLE, 51 (77.3%) benra/benra and 42 (67.7%) mepo/benra patients had no relapses. The percentage of benra/benra patients who discontinued OGCs was similar at Weeks 49-52 (27 [40.9%]) and Weeks 101-104 (29 [43.9%]), while the percentage increased for mepo/benra patients between Weeks 49-52 (16 [25.8%]) and Weeks 101-104 (27 [43.5%]; Figure). The median (IQR) OGC dose at Weeks 101-104 was 0.5 (0,5) in benra/benra and 1.36 (0,5) mg/day in mepo/benra patients. The median (IQR) bEOS in benra/benra patients was 20 (10,40) cells/µL at both Weeks 52 and 100; bEOS were depleted in mepo/benra patients from 70 (40,90) cells/µL to 20 (10,50) cells/µL by 4 weeks after switching. Mean (SD) ACQ-6 scores were 0.64 (0.78) in benra/benra patients and 0.60 (0.76) in mepo/benra patients at Week 104 compared with 1.39 (1.18) and 1.11 (0.95) at baseline. Mean (SD) pre-BD FEV1 was 2.59 (0.90) L versus 2.62 (0.84) L in benra/benra versus mepo/benra patients at Week 52, and 2.61 (0.90) versus 2.63 (0.81) L, at Week 100. Safety of mepolizumab and benralizumab was consistent with their known profiles. Conclusions: In patients with EGPA receiving benralizumab, remission rates, OGC discontinuation, and bEOS depletion were durable over 104 weeks with low relapse rates, and without loss of asthma control or lung function decline. Additional bEOS depletion and OGC sparing was observed in patients switching from mepolizumab to benralizumab.

Abstract Chronic obstructive pulmonary disease (COPD) and pulmonary emphysema were the third-leading cause of death globally in 2019. Besides alpha-1 antitrypsin deficiency, emphysema lacks disease-modifying medications due to its heterogeneity and there remains a need to further investigate emphysema subtypes to advance its diagnosis and treatment. Recent unsupervised machine learning of the texture and anatomical location of emphysema on computed tomography (CT) images of the lung defined six quantitative CT emphysema subtypes uniquely associated with specific gene variants, environmental exposures, symptoms, physiology and clinical events. We aim to identify associations of plasma proteins with each CT emphysema subtype cross-sectionally in a multi-ethnic general population sample. MESA is a prospective cohort study that recruited 6,814 participants from six communities who self-identified as White, Black, Hispanic, or Asian race/ethnicity, ages 45-84 years old and free of clinical cardiovascular disease in 2000-02. The MESA Lung Study performed CT scans among 3,137 participants in 2010-12, which were labeled with previously described (PMID: 37268414) CT emphysema subtypes. Proteomics was assessed using SomaScan version 4.1 assay (7,596 plasma proteins). Linear regression models were adjusted for age, height, weight, sex, race, educational attainment, smoking status, pack years, urine cotinine level, body-mass index (BMI), estimated glomerular filtration rate (eGFR), CT scanner manufacturer and other CT emphysema subtypes. Results were adjusted to reflect a False Discovery Rate (FDR) p-value of less than 5% using the Benjamini-Hochberg method. Among 2,343 participants with both CT and proteomic data (mean age 69.5 years, 52.3% women, 23.7% with COPD), we identified statistically significant associations of proteins with the vanishing lung subtype (42 proteins; top hit Natural cytotoxicity triggering receptor 3 ligand 1, q = 2.9[asterisk]10-9), restrictive combined pulmonary fibrosis/emphysema (CPFE) subtype (11 proteins; top hit Integrin alpha-2/b1, q=1.0[asterisk]10-5), the combined bronchitis-apical emphysema subtype (9 proteins; top hit Desmoglein-2, q=8.8[asterisk]10-13), and the diffuse emphysema subtype (4 proteins; top hit Pulmonary surfactant-associated protein D, q=5.7[asterisk]10-3). No significant proteins were associated with the obstructive CPFE or senile subtypes after FDR correction. Most proteins were uniquely associated with one CT emphysema subtype, while a few proteins were associated with more than one subtype. This study identified specific proteins for different CT emphysema subtypes, many of which have been related less specifically to emphysema, including pulmonary surfactant production, anti-inflammatory pathways, and mitochondrial deregulation, amongst others. Validation of these proteomic associations can provide insight into further pathway assessment, clinical biomarker discovery, and targeted prevention of emphysema in the general population.

Abstract RATIONALE: Mesenchymal progenitor cells (MPCs) in the lungs of individuals with Idiopathic Pulmonary Fibrosis (IPF) show intrinsic fibrogenic properties, possessing a distinct transcriptomic profile and maintaining fibrogenic activity, which contributes to the fibroblast population in IPF. We hypothesize that IPF MPCs are distinguished from control MPCs by a unique gene interaction network. METHODS: We analyzed bulk RNA-seq data, available on the Gene Expression Omnibus (GEO) under accession numbers GSE97038 and GSE276568. In these experiments, CD44hi MPCs were isolated through flow cytometry from mesenchymal cell lines derived from IPF patients (explanted lungs from live IPF patients after lung transplant) and control subjects (lobectomy for clinical reasons) using antibodies against CD44 and SSEA4. The pooled dataset comprises nine IPF and nine control MPC lines. We identified differentially expressed genes (DEGs) in IPF MPCs compared to controls using DESeq and performed pathway enrichment analysis on DEGs using Gene Ontology (GO). We also conducted Gene Set Enrichment Analysis (GSEA) with gene sets related to stemness, pluripotency, and self-renewal. Weighted gene co-expression network analysis (WGCNA) identified functional modules specifically associated with IPF MPCs. RESULTS: Applying an adjusted p-value threshold of 0.05, we identified 134 DEGs in IPF MPCs compared to controls. GO analysis showed significant enrichment in pathways associated with leukocyte migration, extracellular matrix organization, and cell differentiation and growth. GSEA highlighted significant enrichment in two gene sets related to stemness, with adjusted p-values of 0.002 and 0.048. Using WGCNA, we identified 16 functional modules, one of which reached significance based on an adjusted p-value threshold of 0.05 and a correlation coefficient cutoff of 0.45. This significant module demonstrated a positive correlation with IPF status (correlation coefficient of 0.69, adjusted p-value 0.0085). CONCLUSION: This study is the first to characterize a distinct gene expression profile in IPF MPCs compared to controls, highlighting enriched biological processes relevant to IPF pathogenesis. GSEA results further support the hypothesis that IPF MPCs display stem cell-like gene expression patterns, including genes associated with pluripotency and self-renewal. Additionally, we identified functional gene modules that significantly correlate with the fibrogenic properties of IPF MPCs, including hub genes that may play critical roles in promoting fibrosis in IPF. These findings deepen our understanding of IPF MPC biology and identify potential targets for future research. We plan to expand this approach by increasing the sample size to enhance statistical power, aiming to identify more robust functional modules and their highly connected hub genes.

Abstract RATIONALE: Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of mortality worldwide. We previously published the polygenic transcriptome risk score (PTRS) which uses the cumulative effect of predicted gene expression to construct genetic predictors for complex diseases, and we demonstrated the value of PTRS for COPD built on Genotype-Tissue Expression (GTEx) Lung tissue with significantly improved cross-ancestry portability. However, the postmortem collection and lack of lung disease status on GTEx samples likely affect results. We hypothesized that the performance of PTRS will be improved by using disease-relevant expression quantitative trait loci (eQTLs) to construct the score. Here, we aimed to improve performance of PTRS by leveraging disease-relevant eQTLs. METHODS: We constructed two transcriptome prediction models, Elastic Net (EN) and Prediction Using Models Informed by Chromatin conformation and Epigenomics (PUMICE), using TOPMed lung RNA-seq data from the Lung Tissue Research Consortium (LTRC), which included COPD patients undergoing lung surgery. We compared their performance with two published models built on RNA-seq from GTEx Lung tissue, GTEx-EN and GTEx-PUMICE. We first integrated each of four transcriptome models with multi-ancestry GWAS of FEV1/FVC ratio (Shrine et al. 2023) to generate transcriptome-wide association study (TWAS) results, which produced trait-associated genes. Pathway analysis was then conducted on significant TWAS genes. Finally, the PTRS was computed on TWAS genes that were included in the top 20 significantly enriched pathways. We tested performance of PTRS in race-stratified analysis for moderate-to-severe and severe COPD in COPDGene. RESULTS: Our models produced more significant TWAS genes (FDR<0.05) and had more overlaps with genes identified for FEV1/FVC ratio from Shrine et al. 2023 compared to two GTEx models (Fig. A). Additionally, our models had significantly higher AUC for predicting both moderate-to-severe and severe COPD in race-stratified analysis. The mean AUC from LTRC-EN for predicting severe COPD was 0.57 and 0.55 respectively for EUR and AFA, which was significantly higher than mean AUC of 0.54 and 0.51 from GTEx-EN (Delong p-value=8.15x10-10 for EUR and 1.42x10-3 for AFA) (Fig. B). Similarly, the PTRS derived from our models produced higher Odds Ratios (OR) per standard deviation. The mean OR from LTRC-PUMICE for moderate-to-severe COPD was 1.25 and 1.18 respectively for EUR and AFA, while it was 1.17 and 1.12 from GTEx-PUMICE (Fig. C). CONCLUSIONS: Our study demonstrates the value of leveraging disease-relevant RNA-seq to construct transcriptome prediction models and their improvement on identifying lung function genes and predicting COPD across ancestries.

Gastric cancer is the fifth leading cause of cancer-related deaths worldwide. Over 95% of gastric cancers are adenocarcinomas, which are typically classified based on anatomic location and histologic type. Gastric cancer generally carries a poor prognosis because it is often diagnosed at an advanced stage. Systemic therapy can provide palliation, improve survival, and enhance the quality of life in patients with locally advanced or metastatic disease. The implementation of biomarker testing has had a significant impact on clinical practice and patient care. Targeted therapies have demonstrated encouraging results in clinical trials for the treatment of patients with locally advanced or metastatic disease. This selection from the NCCN Clinical Practice Guidelines in Oncology for Gastric Cancer highlights recommendations for biomarker testing and discusses updates for the treatment of advanced disease, including peritoneal carcinoma as only disease and unresectable locally advanced, recurrent, or metastatic disease.

Importance Use of modern neoadjuvant chemotherapy (NAC) regimens has markedly increased rates of pathologic complete response (pCR) in breast cancer, raising the question of whether surgical removal of the primary tumor is required for patients with pCR. For surgery to be omitted, one must be able to accurately predict pCR before surgery. Objective To investigate if adding post-NAC core needle biopsy of the tumor bed to trimodality imaging in patients who have clinical complete response (cCR) will predict pCR (resolution of both invasive disease and ductal carcinoma in situ) in 90% or more cases. Design, Setting, and Participants This was a phase 2, prospective, nonrandomized clinical trial. Patients were enrolled from August 2017 to June 2019. This is the final analysis, which was completed in December 2023. The setting included academic and community hospital center members of NRG (ie, the National Surgical Adjuvant Breast and Bowel Project, the Radiation Therapy Oncology Group, and the Gynecologic Oncology Group) in the US and Canada. Patients with operable (T1-T3, stage I-III) invasive ductal carcinoma who completed NAC and achieved cCR and radiological complete response (rCR) or near rCR by mammography (mass ≤1 cm and no malignant microcalcifications), ultrasound (mass ≤2 cm), and magnetic resonance imaging (no mass with rapid rise or washout kinetics). Interventions Patients underwent marker-directed stereotactic multiple-core needle biopsy of the tumor bed with marker placement before breast-conservation surgery. Main Outcomes and Measures End points were negative predictive value (NPV) and sensitivity of the biopsy. Results A total of 105 patients were enrolled with 101 evaluable (mean [SD] age, 52.8 [10.5] years); 77 patients (76.2%) were younger than 60 years, and all breast cancer subtypes were represented with 32 (31.7%) triple-negative breast cancer, 21 (20.8%) hormone receptor–positive/epidermal growth factor receptor 2 ( ERBB2 ; formerly HER2 )–negative ( ERBB2 −) breast cancer, and 46 (45.5%) ERBB2 -positive ( ERBB2 +) breast cancer. In 101 evaluable patients, 36 had residual disease at surgery (pCR = 64%). With imaging criteria, NPV of the biopsy was 78.3% (95% CI, 67.9%-86.6%), and the sensitivity of the biopsy was 50% (95% CI, 32.9%-67.1%). In an exploratory subset analysis, the NPV in patients with ERBB2 + breast cancer was 90% (95% CI, 76.3%-97.2%). On retrospective central review, 62 of 101 enrolled patients met imaging eligibility criteria. In this exploratory post hoc analysis, NPV in these patients was 86.8% (95% CI, 74.7%-94.5%). Conclusions and Relevance These findings do not support breast conservation treatment without surgery based on the study criteria for cCR and rCR/near rCR by trimodality imaging and negative tumor-bed biopsy. Strict adherence to imaging criteria may be required to achieve acceptable predictive values. TRIAL Registration ClinicalTrials.gov Identifier: NCT03188393