Faculty Bibliography

Purpose: Quantification of local metabolic tumor volume changes (DELTAMTV) after chemo-radiotherapy (CRT) would allow accurate tumor response evaluation. The purpose of this study is to measure local DELTAMTV using blended PET/CT registration and to provide an early prediction of pathologic tumor response. Method(s): 61 patients with locally advanced esophageal cancer underwent baseline, postinduction chemotherapy (follow-up) and post-CRT PET/CT. A grayscale blended PET/CT image was generated and follow-up blended PET/CT image was registered to the baseline blended PET/CT image with tumor motion correction. Jacobian map (J) was computed from the transformation which measured local MTV shrinkage (J < 1) or expansion (J > 1). Registration accuracy was evaluated by comparing the net DELTAMTV calculated by Jacobian integral [(mean J - 1) x baseline MTV] vs. semi-automatic segmentation. Radiomic features were then extracted from the Jacobian maps and PET/CT images and distinctive features were identified using a hierarchical clustering method. A logistic regression model was constructed using two distinctive features preidentified from PET/CT images (PET Kurtosis) and Jacobian map (Mean of Cluster Shade) to predict pathologic complete response (pCR). The model was evaluated using 10x5-fold crossvalidation. Result(s): Qualitatively, Jacobian map by blended PET/CT registration showed smoother local DELTAMTV than PET-PET and CT-CT registrations. Quantitatively, DELTAMTV calculated by Jacobian integral of blended PET/CT registration (-42.0%) was closer to DELTAMTV measured by the semi-automatic segmentation (-50.0%) than by PET-PET (-29.4%) and CT-CT (-8.0%) registrations. Kurtosis in follow-up PET and Jacobian Mean of Cluster Shade represented uniformity of FDG uptake and asymmetry of DELTAMTV, respectively and the logistic model built with these two features achieved a high accuracy (AUC = 0.82) in predicting pCR. Conclusion(s): The novel Blended PET/CT registration led to more accurate quantification of DELTAMTV than PET-PET and CT-CT registrations. The model with combination of PET/CT and Jacobian features showed high accuracy in predicting pCR

The bone marrow microenvironment has a key role in regulating haematopoiesis, but its molecular complexity and response to stress are incompletely understood. Here we map the transcriptional landscape of mouse bone marrow vascular, perivascular and osteoblast cell populations at single-cell resolution, both at homeostasis and under conditions of stress-induced haematopoiesis. This analysis revealed previously unappreciated levels of cellular heterogeneity within the bone marrow niche and resolved cellular sources of pro-haematopoietic growth factors, chemokines and membrane-bound ligands. Our studies demonstrate a considerable transcriptional remodelling of niche elements under stress conditions, including an adipocytic skewing of perivascular cells. Among the stress-induced changes, we observed that vascular Notch delta-like ligands (encoded by Dll1 and Dll4) were downregulated. In the absence of vascular Dll4, haematopoietic stem cells prematurely induced a myeloid transcriptional program. These findings refine our understanding of the cellular architecture of the bone marrow niche, reveal a dynamic and heterogeneous molecular landscape that is highly sensitive to stress and illustrate the utility of single-cell transcriptomic data in evaluating the regulation of haematopoiesis by discrete niche populations.

BACKGROUND:Full-term pregnancy (FTP) at an early age confers long-term protection against breast cancer. Previously, we reported that a FTP imprints a specific gene expression profile in the breast of postmenopausal women. Herein, we evaluated gene expression changes induced by parity in the breast of premenopausal women. METHODS:Gene expression profiling of normal breast tissue from 30 nulliparous (NP) and 79 parous (P) premenopausal volunteers was performed using Affymetrix microarrays. In addition to a discovery/validation analysis, we conducted an analysis of gene expression differences in P vs. NP women as a function of time since last FTP. Finally, a laser capture microdissection substudy was performed to compare the gene expression profile in the whole breast biopsy with that in the epithelial and stromal tissues. RESULTS:Discovery/validation analysis identified 43 differentially expressed genes in P vs. NP breast. Analysis of expression as a function of time since FTP revealed 286 differentially expressed genes (238 up- and 48 downregulated) comparing all P vs. all NP, and/or P women whose last FTP was less than 5 years before biopsy vs. all NP women. The upregulated genes showed three expression patterns: (1) transient: genes upregulated after FTP but whose expression levels returned to NP levels. These genes were mainly related to immune response, specifically activation of T cells. (2) Long-term changing: genes upregulated following FTP, whose expression levels decreased with increasing time since FTP but did not return to NP levels. These were related to immune response and development. (3) Long-term constant: genes that remained upregulated in parous compared to nulliparous breast, independently of time since FTP. These were mainly involved in development/cell differentiation processes, and also chromatin remodeling. Lastly, we found that the gene expression in whole tissue was a weighted average of the expression in epithelial and stromal tissues. CONCLUSIONS:Genes transiently activated by FTP may have a role in protecting the mammary gland against neoplastically transformed cells through activation of T cells. Furthermore, chromatin remodeling and cell differentiation, represented by the genes that are maintained upregulated long after the FTP, may be responsible for the lasting preventive effect against breast cancer.

Background/UNASSIGNED:Two primary histologic subtypes, superficial spreading melanoma (SSM) and nodular melanoma (NM), comprise the majority of all cutaneous melanomas. NM is associated with worse outcomes, which have been attributed to increased thickness at presentation, and it is widely expected that NM and SSM would exhibit similar behavior once metastasized. Herein, we tested the hypothesis that primary histologic subtype is an independent predictor of survival and may impact response to treatment in the metastatic setting. Methods/UNASSIGNED:We examined the most recent Surveillance, Epidemiology, and End Results (SEER) cohort (n = 118 508) and the New York University (NYU) cohort (n = 1621) with available protocol-driven follow-up. Outcomes specified by primary histology were studied in both the primary and metastatic settings with respect to BRAF-targeted therapy and immunotherapy. We characterized known driver mutations and examined a 140-gene panel in a subset of NM and SSM cases using next-generation sequencing. All statistical tests were two-sided. Results/UNASSIGNED:NM was an independent risk factor for death in both the SEER (hazard ratio [HR] = 1.55, 95% confidence interval [CI] = 1.41 to 1.70, P < .001) and NYU (HR = 1.47, 95% CI = 1.05, 2.07, P = .03) cohorts, controlling for thickness, ulceration, stage, and other variables. In the metastatic setting, NM remained an independent risk factor for death upon treatment with BRAF-targeted therapy (HR = 3.33, 95% CI = 1.06 to 10.47, P = .04) but showed no statistically significant difference with immune checkpoint inhibition. NM was associated with a higher rate of NRAS mutation (P < .001), and high-throughput sequencing revealed NM-specific genomic alterations in NOTCH4, ANK3, and ZNF560, which were independently validated. Conclusions/UNASSIGNED:Our data reveal distinct clinical and biological differences between NM and SSM that support revisiting the prognostic and predictive impact of primary histology subtype in the management of cutaneous melanoma.

The extent of PTEN loss that confers clinical and biological impact in melanoma is unclear. We evaluated the clinical and biologic relevance of PTEN dosage in melanoma, and tested the postulate that partial PTEN loss is due to epigenetic mechanisms. PTEN expression was assessed by immunohistochemistry in a stage III melanoma cohort (n=190) with prospective follow up. 21/190 (11%) of tumors had strong PTEN expression, 51/190 (27%) had intermediate PTEN, 44/190 (23%) had weak PTEN, and 74/190 (39%) had absent PTEN. Both weak and absent PTEN expression predicted shorter survival in multivariate analyses (HR 2.13, p<0.01). We demonstrate a continuous negative correlation between PTEN and activated Akt in melanoma cells with titrated PTEN expression and in two additional independent tumor datasets. PTEN genomic alterations (deletion, mutation), promoter methylation, and protein destabilization did not fully explain PTEN loss in melanoma, whereas PTEN levels increased with treatment of melanoma cells with the histone deacetylase inhibitor LBH589. Our data indicate that partial PTEN loss is due to modifiable epigenetic mechanisms and drives Akt activation and worse prognosis, suggesting a potential approach to improve the clinical outcome for a subset of advanced melanoma patients.

In this paper, we discuss adjusted cumulative incidence in multiple treatment groups with unbalanced samples. In a nonrandomized experiment or an observational study, the observed data may be unbalanced in covariates when multiple treatments are administered differently based on patients' characteristics. In the case of multiple survival outcomes, clinical researchers are often interested in estimating the cumulative incidence within a specific treatment group, and this approach is subject to a potential bias with unbalanced samples. Using extensive simulation analyses, we demonstrate that a naïve approach to the estimation of a cumulative incidence curve may yield misleading results, unless patients' characteristics are fully considered. To achieve an unbiased estimation from unbalanced data, we propose an adjusted cumulative incidence based on the inverse probability of a treatment weighting. In a series of simulations, the proposed method shows robust performance when estimating cumulative incidence under various scenarios, including balanced and unbalanced samples. Lastly, we explain how to apply the proposed method using an example based on real data.

Chronic inflammation drives many obesity-associated conditions, including atherosclerosis. GlycA, a marker of systemic inflammation with lower intraindividual variability than hsCRP, is independently associated with incident cardiovascular events and mortality. Although GlycA is elevated in obesity, correlations with anthropometric measures are modest and the effect of weight loss on GlycA is untested. Obese (BMI 44.6±6.6kg/m² ), non-diabetic women (33.7±8.2 years) undergoing Roux-en-Y gastric bypass (n=23) or sleeve gastrectomy (n=31) were prospectively studied at baseline, 6 and 12 months post-procedure. Women with normal BMI (n=14) served as controls. Bariatric surgery significantly reduced GlycA by 6 months (451±47umol/L vs 383±50umol/L; p<0.001) with further reduction at 12 months (348±41umol/L; p<0.001) and no difference between procedures. At 12 months, despite 41% of surgical subjects maintaining BMI >30kg/m² , GlycA levels did not differ between surgical and control subjects (p=0.13). Increased HDL particle size was strongly associated with reduced GlycA (r=-0.49; p<0.001) and was found to mediate up to 43% of its weight-loss-associated fall. This is the first study to demonstrate that surgical weight loss markedly reduces levels of GlycA.