SUMMARY Gene regulatory networks (GRNs) guiding differentiation of cell types and cell assemblies in the nervous system are poorly understood because of inherent complexities and interdependence of signaling pathways. Here, we report transcriptome dynamics of differentiating rod photoreceptors in the mammalian retina. As the transcription factor NRL determines rod cell fate, we performed expression profiling of developing NRL-positive (rods) and NRL-negative (S-cone like) mouse photoreceptors. We identified a large-scale, sharp transition in the transcriptome landscape between postnatal day 6 and 10 concordant with rod morphogenesis. Rod-specific temporal DNA methylation corroborated gene expression patterns. De novo assembly and alternative splicing analyses revealed previously un-annotated rod-enriched transcripts and the role of NRL in transcript maturation. Furthermore, we defined the relationship of NRL with other transcriptional regulators and downstream cognate effectors. Our studies provide the framework for comprehensive system-level analysis of the GRN underlying the development of a single sensory neuron, the rod photoreceptor.

The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.

Increased expression of Kruppel-like factor 7 (KLF7) is an independent predictor of poor outcome in pediatric acute lymphoblastic leukemia. The contribution of KLF7 to hematopoiesis has not been previously described. Herein, we characterized the effect on murine hematopoiesis of the loss of KLF7 and enforced expression of KLF7. Long-term multilineage engraftment of Klf7 Ϫ/Ϫ cells was comparable with control cells, and self-renewal, as assessed by serial transplantation, was not affected. Enforced expression of KLF7 results in a marked suppression of myeloid progenitor cell growth and a loss of short-and long-term repopulating activity. Interestingly, enforced expression of KLF7, although resulting in multilineage growth suppression that extended to hematopoietic stem cells and common lymphoid progenitors, spared T cells and enhanced the survival of early thymocytes. RNA expression profiling of KLF7-overexpressing hematopoietic progenitors identified several potential target genes mediating these effects. Notably, the known KLF7 target Cdkn1a (p21 Cip1/Waf1 ) was not induced by KLF7, and loss of CDKN1A does not rescue the repopulating defect. These results suggest that KLF7 is not required for normal hematopoietic stem and progenitor function, but increased expression, as seen in a subset of lymphoid leukemia, inhibits myeloid cell proliferation and promotes early thymocyte survival. (Blood. 2012;120(15):2981-2989) IntroductionAlthough current therapeutic protocols have achieved a cure rate of Ͼ 85% in pediatric patients with acute lymphoblastic leukemia (ALL), outcomes for patients with persistent disease after induction chemotherapy or who have relapsed disease are much worse. Currently, more than half of children with relapsed ALL die from the disease, and a study from the Children's Oncology Group demonstrated that the 5-year survival rate for children with an early relapse (Ͻ 18 months from initial diagnosis) is only 21.0% Ϯ 1.8%. 1 The identification of patients with high-risk features and the need for intensification of therapy is crucial to the management of such persons.In an analysis of bone marrow cells of 187 children with ALL, Flotho et al showed that the expression of Kruppel-like factor 7 (KLF7) was significantly elevated in patients with minimal residual disease at day 19 of therapy and was an independent predictor of leukemic relapse in a separate cohort of 99 patients. 2 Minimal residual disease at day 19 of induction therapy is highly predictive of high-risk disease and is a reliable marker of chemotherapy-refractory leukemia. 3 In addition, a 5.5-fold increase in KLF7 expression was found in the bone marrow cells of patients with imatinib-resistant CML compared with sensitive controls. 4 The KLF family of transcription factors are involved in regulating cellular growth and differentiation in multiple tissue types. Furthermore, members of this family are involved in numerous aspects of hematopoiesis, including the regulation of erythropoiesis, lymphopoiesis, and myelopoiesis. 5-7 KLF7 is import...

Background: Patients with locally advanced or recurrent prostate cancer typically undergo androgen deprivation therapy (ADT), but the benefits are often short-lived and the responses variable. ADT failure results in castration-resistant prostate cancer (CRPC), which inevitably leads to metastasis. We hypothesized that differences in tumor transcriptional programs may reflect differential responses to ADT and subsequent metastasis. Results: We performed whole transcriptome analysis of 20 patient-matched Pre-ADT biopsies and 20 Post-ADT prostatectomy specimens, and identified two subgroups of patients (high impact and low impact groups) that exhibited distinct transcriptional changes in response to ADT. We found that all patients lost the AR-dependent subtype (PCS2) transcriptional signatures. The high impact group maintained the more aggressive subtype (PCS1) signal, while the low impact group more resembled an AR-suppressed (PCS3) subtype. Computational analyses identified transcription factor coordinated groups (TFCGs) enriched in the high impact group network. Leveraging a large public dataset of over 800 metastatic and primary samples, we identified 33 TFCGs in common between the high impact group and metastatic lesions, including SOX4/FOXA2/GATA4, and a TFCG containing JUN, JUNB, JUND, FOS, FOSB, and FOSL1. The majority of metastatic TFCGs were subsets of larger TFCGs in the high impact group network, suggesting a refinement of critical TFCGs in prostate cancer progression. Conclusions: We have identified TFCGs associated with pronounced initial transcriptional response to ADT, aggressive signatures, and metastasis. Our findings suggest multiple new hypotheses that could lead to novel combination therapies to prevent the development of CRPC following ADT.

MRI in combination with genomic markers are critical in the management of gliomas. Radiomics and radiogenomics analysis facilitate the quantitative assessment of tumor properties which can be used to model both molecular subtype and predict disease progression. In this work, we report on the Drosophila gene capicua (CIC) mutation biomarker effects alongside radiomics features on the predictive ability of CIC mutation status in lower-grade gliomas (LGG). Genomic data of lower grade glioma (LGG) patients from The Cancer Genome Atlas (TCGA) (n = 509) and corresponding MR images from TCIA (n = 120) were utilized. Following tumor segmentation, radiomics features were extracted from T1, T2, T2 Flair, and T1 contrast enhanced (CE) images. Lasso feature reduction was used to obtain the most important MR image features and then logistic regression used to predict CIC mutation status. In our study, CIC mutation rarely occurred in Astrocytoma but has a high probability of occurrence in Oligodendroglioma. The presence of CIC mutation was found to be associated with better survival of glioma patients (p < 1e−4, HR: 0.2445), even with co-occurrence of IDH mutation and 1p/19q co-deletion (p = 0.0362, HR: 0.3674). An eleven-feature model achieved glioma prediction accuracy of 94.2% (95% CI, 94.03-94.38%), a six-feature model achieved oligodendroglioma prediction accuracy of 92.3% (95% CI, 91.70-92.92%). MR imaging and its derived image of gliomas with CIC mutation appears more complex and non-uniform but are associated with lower malignancy. Our study identified CIC as a potential prognostic factor in glioma which has close associations with survival. MRI radiomic features could predict CIC mutation, and reflect less malignant manifestations such as milder necrosis and larger tumor volume in MRI and its derived images that could help clinical judgment.

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e18729 Background: Proton pump inhibitors (PPI) can disrupt the gut microbiome and thereby modulate response to immunotherapy in cancer patients. In a recently published post-hoc analysis of 757 non-small cell lung cancer (NSCLC) patients receiving atezolizumab pooled from two prospective trials, overall survival (OS) and progression-free survival were significantly lower among the 234 patients receiving PPI. We investigated the impact of PPI in a larger cohort of NSCLC patients treated with ICI within the Veterans Health Administration. Methods: We conducted a nested cohort study of Veterans who were diagnosed with NSCLC between 2010 & 2018 and treated with ICI (immune checkpoint inhibitors). Exposure was defined as receipt of a PPI prescription within 90 days of an ICI infusion. Chi-square tests were used to compare characteristics of exposed versus unexposed Veterans. OS was measured from start of ICI. Cox proportional hazard multivariate (MV) regression was used to calculate hazard ratios (HR) corresponding to variables associated with OS. Results: We identified 3,634 Veterans receiving ICI with non-exclusive exposures to nivolumab (59.3%), pembrolizumab (35.1%), durvalumab (6.9%), and atezolizumab (3.3%). Their median age was 69, and a plurality had male gender (97.0%), white race (73.0%), comorbidity count ≥1 (60.4%), adenocarcinoma (47.8%), and stage IV disease at diagnosis (40.9%). In this nested cohort, 2,159 (59.4%) were exposed to PPI, predominantly omeprazole (1,264 or 85.6% of PPI group). Patients receiving PPI were more likely to be ≤71 years of age, to be white, to reside in rural areas, to have a higher comorbidity burden, to have adenocarcinoma histology, and to receive chemotherapy (all p≤0.04). On MV analysis, PPI use was not significantly associated with detriment in OS (HR 0.96 [0.89-1.04], p= 0.35). In the matched cohort analysis, median survival did not significantly differ between the 1,389 patients taking PPI and the 1,389 without PPI (median 10 versus 10 months, HR 0.98 [0.90-1.06], p= 0.59). Conclusions: In the largest analysis to date of concurrent PPI use in patients with NSCLC receiving ICI, there were no survival differences associated with concomitant PPI use. These results suggest that PPIs do not compromise ICI efficacy.

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