Inference on differences between classes using cluster-specific contrasts of mixed effects.

The detection of differentially expressed (DE) genes, that is, genes whose expression levels vary between two or more classes representing different experimental conditions (say, diseases), is one of the most commonly studied problems in bioinformatics. For example, the identification of DE genes between distinct disease phenotypes is an important first step in understanding and developing treatment drugs for the disease. We present a novel approach to the problem of detecting DE genes that is based on a test statistic formed as a weighted (normalized) cluster-specific contrast in the mixed effects of the mixture model used in the first instance to cluster the gene profiles into a manageable number of clusters. The key factor in the formation of our test statistic is the use of gene-specific mixed effects in the cluster-specific contrast. It thus means that the (soft) assignment of a given gene to a cluster is not crucial. This is because in addition to class differences between the (estimated) fixed effects terms for a cluster, gene-specific class differences also contribute to the cluster-specific contributions to the final form of the test statistic. The proposed test statistic can be used where the primary aim is to rank the genes in order of evidence against the null hypothesis of no DE. We also show how a P-value can be calculated for each gene for use in multiple hypothesis testing where the intent is to control the false discovery rate (FDR) at some desired level. With the use of publicly available and simulated datasets, we show that the proposed contrast-based approach outperforms other methods commonly used for the detection of DE genes both in a ranking context with lower proportion of false discoveries and in a multiple hypothesis testing context with higher power for a specified level of the FDR.

Progression from Prediabetes to Diabetes in a Diverse U.S. Population: A Machine Learning Model.

Objective: To date, there are no widely implemented machine learning (ML) models that predict progression from prediabetes to diabetes. Addressing this knowledge gap would aid in identifying at-risk patients within this heterogeneous population who may benefit from targeted treatment and management in order to preserve glucose metabolism and prevent adverse outcomes. The objective of this study was to utilize readily available laboratory data to train and test the performance of ML-based predictive risk models for progression from prediabetes to diabetes. Methods: The study population was composed of laboratory information services data procured from a large U.S. outpatient laboratory network. The retrospective dataset was composed of 15,029 adults over a 5-year period with initial hemoglobin A1C (A1C) values between 5.0% and 6.4%. ML models were developed using random forest survival methods. The ground truth outcome was progression to A1C values indicative of diabetes (i.e., ≥6.5%) within 5 years. Results: The prediabetes risk classifier model accurately predicted A1C ≥6.5% within 5 years and achieved an area under the receiver-operator characteristic curve of 0.87. The most important predictors of progression from prediabetes to diabetes were initial A1C, initial serum glucose, A1C slope, serum glucose slope, initial HDL, HDL slope, age, and sex. Conclusions: Leveraging readily obtainable laboratory data, our ML risk classifier accurately predicts elevation in A1C associated with progression from prediabetes to diabetes. Although prospective studies are warranted, the results support the clinical utility of the model to improve timely recognition, risk stratification, and optimal management for patients with prediabetes.

p-21-Activated kinase-1, -4 and -6 and estrogen receptor expression pattern in normal placenta and gestational trophoblastic diseases.

OBJECTIVES: To delineate the potential role of p21-activated kinases (PAKs) in the pathogenesis of gestational trophoblastic diseases (GTD) by defining the expression pattern of PAK-1, -4 and -6 and their potential implication in estrogen receptor (ER) regulation of normal placental tissue and GTD. METHODS: We evaluated immunohistochemically 10 normal first-trimester placentas (NP), 10 partial moles (PM), 15 complete moles (CM) and 3 choriocarcinomas (CCA) for PAK-1, PAK-4, PAK-6 and ER expression intensity and localization. Staining outcomes were assessed utilizing non-parametric Kruskal-Wallis one-way analysis of variance test followed by pairwise Wilcoxon Rank Sum tests. Statistical significance was determined by two-sided p-value of <0.05. RESULTS: In NP, PAK-6 immunoreactivity was predominantly cytoplasmic. Compared to NP, PM and CM demonstrated significant increase of cytoplasmic PAK-6 in cytotrophoblast (p=0.012, p=0.033 respectively), accompanied by significantly increased nuclear immunoreactivity in cytotrophoblast (p=0.008, p=0.045 respectively) and intermediate trophoblast (p=0.003, p=0.015 respectively). PAK-4 was found significantly upregulated in both cytoplasmic and nuclear compartments of cytotrophoblast and syncytiotrophoblast in PM (p=0.004 and p=0.002 for cytotrophoblast; p=0.018 and p=0.002 for syncytiotrophoblast, respectively) and CM (p=0.001 and p=0.001 for cytotrophoblast; p=0.002 and p=0.001 for syncytiotrophoblast, respectively) when compared to NP, whereas PAK-1 expression was significantly reduced in the syncytiotrophoblast of PM (p=0.025 for cytoplasm and p=0.008 for nucleus). Nuclear expression of ER was undetectable in all stained samples. CONCLUSION: Our results reveal PAK-6 upregulation in GTD compared to NP. The absence of nuclear expression of ER might stem in part from the repressive effect of PAK-6 in trophoblastic tissue.

Vascular endothelial growth factors and their receptors and regulators in gestational trophoblastic diseases and normal placenta.

OBJECTIVE: To study the expression of vascular endothelial growth factors (VEGFs), placental growth factor (PLGF) and their receptors (VEGFR-1, -2, -3) and their regulators (IL-6, CD147) in normal placenta and gestational trophoblastic disease (GTD) in order to evaluate their potential role in the biology of GTD. STUDY DESIGN: Paraffin sections of 10 normal, first-trimester placentas, 10 partial moles, 10 complete moles, 5 choriocarcinomas and 5 placental site trophoblastic tumors (PSTTs) were studied immunohistochemically for expression of VEGFR-1, VEGFR-2, VEGFR-3, IL-6, PLGF and CD147. Immunolocalization of VEGF, Angiopoietin-1 and Angiopoietin-2 was performed on 5 choriocarcinomas and 5 PSTTs. The levels of VEGF and VEGFR-2 were determined in supernatants and lysates of normal trophoblast, JEG-3 and JAR choriocarcinoma cells with electrochemiluminescence assays. RESULTS: The normal placenta had significantly stronger expression of VEGFR-2 than did those of partial and complete mole (p = 0.001, p = 0.003). VEGF, Angiopoietin-1 and Angiopoietin-2 expression in PSTT were significantly higher than those in choriocarcinoma (p = 0.002, p= 0.01, p = 0.038). Choriocarcinoma showed stronger intensity of staining for VEGFR-3 than did normal placenta, partial and complete mole (p = 0.036, p = 0.038, p = 0.05). Choriocarcinoma had significantly stronger staining of CD147 than did partial and complete mole (p<0.01, p<0.01). PSTT exhibited significantly stronger staining for IL-6 than did choriocarcinoma (p = 0.03). CONCLUSION: PSTTs exhibited strong staining for VEGF, and choriocarcinoma showed strong staining for VEGFR-3. Agents that inhibit the activity of VEGF and VEGF receptors may prove to be useful in the therapy of gestational trophoblastic neoplasia.

Matrix metalloproteinases and their inhibitors and inducer in gestational trophoblastic diseases and normal placenta.

OBJECTIVES: This study aimed to investigate the expression of recently identified matrix metalloproteinases (MMPs), their inhibitors (TIMPs), and inducer (CD147) in a wide range of gestational trophoblastic diseases (GTD) thereby expanding our understanding of the potential role of MMPs in GTD. METHODS: Paraffin sections of 10 normal first-trimester placentas (NP), 10 partial moles (PM), 10 complete moles (CM), 5 choriocarcinomas (CCA) and 5 placental site trophoblastic tumors (PSTT) were studied immunohistochemically for expression of MMP-7, MMP-14, MMP-21, MMP-28, TIMP-3, TIMP-4 and CD147. Immunolocalization of MMP-1, MMP-2, MMP-3, MMP-9, MMP-13 and TIMP-1 was performed on 5 CCA and 5 PSTTs. RESULTS: CCA showed stronger intensity for MMP-14 and MMP-28 than PSTT (p<0.05, p<0.05). CCA and PSTT had stronger expression of MMP-21 than NP, PM and CM (p<0.05, p<0.05, p<0.01). PSTT (p<0.05, p<0.05), NP (p<0.01, p<0.01) and CM (p<0.01, p<0.05) showed stronger staining for TIMP-3 and TIMP-4 than CCA. CONCLUSION: Choriocarcinoma's high expression of MMPs and low expression of MMP inhibitors may contribute to its invasiveness and metastatic potential. Similarly, PSTT's lower expression of MMPs and high expression of MMP inhibitors may partly explain its lower invasiveness. Agents that inhibit MMP may prove useful in treating GTD.

Age related cellular immune response against complete molar pregnancy.

OBJECTIVE: Advanced maternal age may result in a weaker immune response against complete molar pregnancy, therefore increasing the risk of gestational trophoblastic neoplasia due to ineffective elimination of the trophoblastic cells after evacuation. The present study was undertaken to investigate the cellular immune response against complete molar pregnancy at the implantation site in younger and older patients. STUDY DESIGN: Immunolocalization of CD8, granzyme B (GrB), FoxP3 and CD56 was performed on histologic tissue sections prepared from 18 patients aged < or = 40 years and 10 patients aged > 40 years to characterize effector (GrB+CD8+) cytotoxic T cells, GrB positive and negative natural killer cells (CD56) and regulatory T cells (FoxP3+) at the implantation site in complete molar pregnancies. RESULTS: The number of the different immune cell types did not show significant differences in the implantation sites of complete molar pregnancies between the 2 age groups or between persistent and nonpersistent cases. CONCLUSION: Immunosenescence of the natural killer and T cells most likely does not play a role in the increased incidence of gestational trophoblastic neoplasia in older patients with complete moles.

30 years' experience in the treatment of low-risk gestational trophoblastic neoplasia in Hungary.

OBJECTIVE: To review the clinical experience in the treatment of patients with low-risk gestational trophoblastic neoplasia (GTN) over the past 30 years in a national trophoblastic disease center. STUDY DESIGN: Between January 1, 1977, and December 31, 2007, 302 patients with low-risk GTN were treated. The patients were directed to our institution from all parts of Hungary. The patients were 14 to 53 years of age with an average age of 28.3 years. Methotrexate (MTX)/folinic acid or actinomycin-D (Act-D) primary chemotherapy was selected based upon the patient's stage and prognostic score of GTN. RESULTS: Among 218 low-risk patients, 210 (96.3%) achieved remission as a result of MTX therapy. In 8 patients (3.7%), MTX-Act-D-cyclophosphamide (MAC) combination chemotherapy was needed to achieve complete remission, in some cases assisted by operation. Among 84 patients, 81 (96.4%) achieved remission as a result of Act-D therapy. In 3 cases (3.6%) complete remission was achieved by MAC combination chemotherapy. We detected metastases in 22.8% (69/302) of our low-risk patients. Chemotherapy, surgical intervention or other supplementary treatments resulted in 100% remission in cases of low-risk nonmetastatic and metastatic disease. CONCLUSION: Our data indicate that MTX/folinic acid or Act-D should be the primary treatment in patients with nonmetastatic or metastatic low-risk GTN. Importantly, patients with resistance to single-agent chemotherapy regularly achieve complete remission with MAC combination chemotherapy. Results show that patient care under the direction of experienced clinicians serves to optimize the opportunity for cure and minimize morbidity.

Increased HLA-DMB expression in the tumor epithelium is associated with increased CTL infiltration and improved prognosis in advanced-stage serous ovarian cancer.

PURPOSE: To evaluate the possible mechanisms influencing the infiltration of CD8 T lymphocytes into the tumor epithelium of advanced-stage serous ovarian cancers. EXPERIMENTAL DESIGN: Immunohistochemical localization of CD8 T lymphocytes was done on a homogeneous population of 184 high-grade, advanced-stage serous ovarian cancer tissue specimens. Microarray analysis was done on microdissected tumor epithelium from 38 specimens to identify genes up-regulated or down-regulated in specimens with differing numbers of tumor-infiltrating CD8 T lymphocytes. Quantitative real-time PCR and immunohistochemistry were used to validate a candidate gene. Univariate and multivariate survival analyses were done combining CD8 T lymphocyte number and HLA-DMB expression with standard prognostic factors. RESULTS: Marked CD8 T lymphocyte infiltration of the tumor epithelium is associated with a 20-month improvement in median overall survival. Additionally, when combined with cytoreduction status and age, CD8 T lymphocyte status is an independent prognostic factor for survival. Microarray analysis showed HLA-DMB, a component of the MHC II antigen presentation machinery, to be differentially expressed in specimens with an abundance of tumor-infiltrating CD8 T lymphocytes. This relationship was validated at both mRNA and protein levels. As well, high HLA-DMB expression in the tumor epithelium was associated with a significant improvement in median overall survival in both univariate and multivariate analyses. CONCLUSIONS: Tumor cell expression of HLA-DMB is associated with increased numbers of tumor-infiltrating CD8 T lymphocytes and both are associated with improved survival in advanced-stage serous ovarian cancer.

Overexpression of laminin receptor 1 on decidual cells in partial and complete mole.

OBJECTIVES: Laminin receptor 1 (LR1), a non-integrin-type laminin receptor, has been described in several tumors and may play a role in tumor invasion. It is well known that LR1 can modify the conformation and degradation of laminin thus enhancing tumor cell invasion. LR1 may play a role in controlling trophoblast invasion in normal and molar pregnancies. MATERIALS AND METHODS: Real-time polymerase chain reaction (RT-PCR) was performed on total cDNA from 17 gestational age-controlled normal placentas, 10 complete moles (CM), and 4 partial moles (PM). Immunolocalization of LR1 was performed on paraffin sections prepared from 17 age-controlled placentas, 17 PM, and 19 CM. RESULTS: RT-PCR demonstrated a 13-fold increase in LR1 mRNA expression in molar tissues (PM and CM combined) versus normal placentas (p=0.012). Immunohistochemical analysis revealed LR1 localized to the decidual cells. In normal placenta LR1 localized to the decidual cell membrane. However, in PM and CM, LR1 was additionally noted in the cytoplasm of decidual cells. Interestingly, with immunohistochemistry method, we found that PM demonstrated higher protein expression of LR1 than either normal placenta or CM (p=0.001 and p=0.024, respectively). CONCLUSION: LR1 is expressed in both the decidual cells of normal placenta and mole (CM and PM). Decidual cells in CM and PM express LR1 significantly greater than the decidual cells in placenta. The underlying mechanism of how molar tissue may be associated with enhanced expression of LR1 in the maternal endometrium is unclear.

Immune cell profiling in intraplacental and postmolar choriocarcinomas.

OBJECTIVE: To determine the level of infiltration and antigen profile of immune cells and explore their relationship in intraplacental and postmolar choriocarcinoma to better understand the immunobiology of choriocarcinoma. STUDY DESIGN: Immunolocalization of CD8, Granzyme B (GrB) and FoxP3 was performed on sections prepared from 5 intraplacental and 7 postmolar choriocarcinomas to characterize effector Tc cells (GrB+, CD8+) and GrB- (GrB-, CD8+) Tc cells, GrB+ NK cells (GrB+, CD8-) and Treg (FoxP3+) cells. RESULTS: In the case of intraplacental choriocarcinoma, immune cell infiltration was not detected in the surrounding villi or in the tumor. Immune cell infiltration into the implantation site of the placenta with intraplacental choriocarcinoma did not differ from that into the normal pregnancy implantation site. In postmolar choriocarcinoma the immune cell infiltration of the adjacent tissue was vigorous and involved all types of immune cells (Tc, NK, Treg). In 6 of 7 cases of postmolar choriocarcinoma, in spite of the vigorous immune response, immune cells could not be seen in the choriocarcinoma tissue. A sharp infiltration border of immune cells was noted at the edge of the postmolar choriocarcinoma tissue. CONCLUSION: Intraplacental choriocarcinoma is not associated with a vigorous immune cell response. In contrast, postmolar choriocarcinoma is associated with a vigorous immune cell response in adjacent tissues but not the choriocarcinoma tissue itself.

Antigen-specific T cell immune response detected by skewed T cell receptor usage in normal placenta and complete molar pregnancy.

OBJECTIVE: To investigate the antigenicity of normal placenta and complete molar trophoblastic tissue. STUDY DESIGN: T cell receptor (TCR) variable beta chain (VBC) gene expression was analyzed utilizing fresh frozen tissues. Real-time polymerase chain reactions (RT-PCR) were performed on cDNA samples from 10 normal buffy coats (BC), 7 normal placentas (NP) and 14 complete molar pregnancies (CM) using a TCR beta chain and 25 variable TCR beta chain primers. Relative expressions were calculated for each individual gene. RESULTS: Significant changes were noted in most of the gene expressions in NP and CM as compared to the buffy coat samples. The relative expression of most genes was significantly decreased in NP and CM, but VBC gene number 4 was increased in both NP and CM; however, a significant difference was noted only between BC and CM (p = 0.023). Comparing NP to CM, 5 other VBC gene expressions were decreased significantly in the CM tissues (p < 0.05). CONCLUSION: In normal placenta and CM pregnancies, T cells appear to express certain TCR VBC genes in a different manner than in BC. These genes and the VBC gene profile difference found between NP and CM may play an important role in the immunobiology of CM pregnancy.

Vascularization and expression of angiogenic factors in partial and complete molar pregnancies.

OBJECTIVE: To determine the microvessel density (MVD) at the implantation site of normal placenta (NP) and molar pregnancies and to correlate MVD with clinical data and underlying angiogenic factors. STUDY DESIGN: Immunolocalization of CD31, vascular endothelial growth factor and angiopoietin 1 and 2 were performed on NPs, nonpersistent partial moles, persistent partial moles (PPM), nonpersistent complete moles and persistent complete moles (PCM). RESULTS: Significant differences were identified in the MVD between NP and complete mole (CM), and PM and CM (p < 0.001 and p < 0.035, respectively). MVD in PPM and PCM was significantly higher (p = 0.036 and p < 0.001, respectively) when compared to NP. MVD > 100 per high-power field was associated with an increased risk of persistence (p < 0.04). MVD showed a strong correlation with immediate postevacuation hCG levels (p < 0.03). Angiopoietin 2 staining was more heterogeneous, with lower overall expression in molar pregnancies as compared to more homogeneous expression in NP (p < 0.05). CONCLUSION: MVD is highly correlated with hCG levels, suggesting that hCG may act as an angiogenic factor during implantation of molar pregnancy. MVD at the implantation site may be associated with excessive trophoblastic proliferation or reflect high hCG levels, which places patients at increased risk of persistent neoplasia.

Immune cell profiling in normal pregnancy, partial and complete molar pregnancy.

OBJECTIVES: Cytotoxic T cells (Tc) and natural killer (NK) cells may play a role in controlling trophoblast invasion. This study was undertaken to determine the level of infiltration and antigen profile of immune cells and explore their relationship in normal placenta (NP) and molar tissues to better understand the biology of gestational trophoblastic diseases. MATERIALS AND METHODS: Immunolocalization of CD8, Granzyme B (GrB), and FoxP3 was performed on sections prepared from 11 gestational age-matched NP, 19 partial moles (PM), and 18 complete moles (CM) to characterize effector (GrB+CD8+) and GrB- (GrB-CD8+) Tc cells, GrB+ NK cells (GrB+CD8-), and Treg (FoxP3+) cells. RESULTS: Immune cells infiltrated into the implantation site of normal placenta, PM, and CM with increasing frequency. Effector and GrB- Tc, GrB+ NK and Treg infiltration in the CM were significantly stronger than seen in the normal placenta (p=0.002, p=0.007, p=0.002, respectively). Immune cell infiltration was not detected in the villi or trophoblast of gestational tissues. Treg infiltration in the implantation site was only observed in PM and CM. In CM and PM Tc infiltration positively correlated with Treg infiltration (p=0.035), but Treg infiltration did not correlate with the Tc effector ratio (effector Tc cells/all Tc cells). CONCLUSION: In CM the cellular immune response in the implantation site was significantly more vigorous than seen in normal placenta. These observations demonstrate that in the implantation site of CM, the number of effector Tc and GrB+ NK cells are increased and Treg cells may negatively regulate T lymphocyte activation.

Immunohistochemistry for 2-Succinocysteine (2SC) and Fumarate Hydratase (FH) in Cutaneous Leiomyomas May Aid in Identification of Patients With HLRCC (Hereditary Leiomyomatosis and Renal Cell Carcinoma Syndrome).

Hereditary leiomyomatosis and renal cell carcinoma syndrome (HLRCC) is caused by germline mutations in the fumarate hydratase (FH) gene and predisposes to cutaneous and uterine leiomyomas and renal cell carcinoma (RCC). HLRCC-associated renal tumors are clinically aggressive, and patients would benefit from surveillance and early detection. Cutaneous leiomyomas that occur in association with HLRCC typically present early and are multiple. Thus far, the presence of certain morphologic features (large eosinophilic macronucleoli surrounded by halos and eosinophilic cytoplasmic inclusions) in RCC and uterine leiomyomas has been shown to correlate with FH mutations. Immunohistochemistry (IHC) for 2-succinocysteine (2SC) and FH has also been shown to correlate well with FH gene mutation status in RCC and uterine leiomyomas. The aim of this study was to assess the effectiveness of morphologic features and IHC at predicting FH gene mutations in cutaneous leiomyomas. We identified 22 patients with multiple cutaneous leiomyomas (40 total MCLs) and 25 patients with single leiomyomas (25 SCLs). Mutations in the FH gene were detected in 11 of 13 (85%) sequenced MCLs and 1 of 11 (9%) SCLs. A strong association was observed between 2SC positivity by IHC and presence of FH gene mutation (P=0.0028 for 2SC) but not with FH loss by IHC (P=0.4 for FH). All 11 MCLs with an FH mutation showed positive staining for 2SC, whereas 6 of 11 showed complete loss of FH staining. Our study suggests that the presence of MCLs should raise the possibility of HLRCC. IHC for FH and 2SC is helpful in detection of FH gene mutations and should be considered in all newly diagnosed cutaneous leiomyomas.

ARID1A is a useful marker of malignancy in peritoneal washings for endometrial carcinoma.

BACKGROUND: ARID1A (AT-rich interactive domain 1A gene) has recently been identified as a novel tumor suppressor gene and one of the driver genes in endometrial carcinogenesis. Approximately 30% to 40% of endometrial carcinomas harbor mutations in the ARID1A gene, which results in complete loss of ARID1A protein expression. Although ARID1A aberrations are not restricted to endometrial cancer, the authors hypothesized that it might be a useful marker of malignancy in peritoneal washings for patients with endometrial cancer. METHODS: The cytology archive of Brigham and Women's Hospital was searched to identify cell blocks from peritoneal washings that contained malignant or benign endometrial epithelium. From 2006 through 2013, 17 cases of endometrial carcinoma (EMCA) and 16 cases of endometriosis were identified. Surgical pathology reports and follow-up data were used to confirm the diagnoses. Immunohistochemistry for ARID1A was performed, and slides were scored as 0 (complete loss of staining) or 1 (retained staining) by 2 independent pathologists. The discordant cases were resolved by consensus. The two-tailed Fisher exact probability test was used to calculate statistical significance. RESULTS: Complete loss of ARID1A expression was found in 8 of 17 EMCA cases (47%) and none of the 16 endometriosis cases (0%) (P = .024). The concordance among the pathologists on first review was high (96.7%). CONCLUSIONS: The results of the current study demonstrated that ARID1A can be used in peritoneal washings to confirm malignancy in patients with EMCA. Complete loss of ARID1A expression by immunohistochemistry is highly specific for carcinoma, but retained expression is not informative.