Suzanne Manning - Academia.edu (original) (raw)

Papers by Suzanne Manning

PLoS ONE, 2013

Somatic mutation calling from next-generation sequencing data remains a challenge due to the diff... more Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, subclonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.

Laboratory investigation; a journal of technical methods and pathology, 1994

Mutations in the p53 tumor suppressor gene have been identified in breast and many other carcinom... more Mutations in the p53 tumor suppressor gene have been identified in breast and many other carcinomas. It is not clear, however, when these mutations occur during breast carcinogenesis. Overexpression of 53 protein has been reported in some ductal carcinoma in situ (DCIS) lesions. To further study the overexpression of p53 in DCIS of the breast and correlate these findings with changes at the molecular level, we performed p53 immunostaining and direct sequencing in noncomedo and comedo DCIS. Archival blocks were obtained on cases of noncomedo DCIS, (including encysted, noninvasive papillary carcinoma) and comedo DCIS. Immunohistochemical staining with the p53 antibody DO7 was performed on all cases. Polymerase chain reaction (PCR) amplification of exons 5, 6, and 7 of the p53 gene was performed and the PCR products were directly sequenced. Four comedo DCIS cases that were p53 immunopositive were further screened for p53 mutations by PCR/single strand conformation polymorphism in exons...

During tumorigenesis, a heterotypic interface exists between cancer and stromal cells that can bo... more During tumorigenesis, a heterotypic interface exists between cancer and stromal cells that can both support and repress tumor growth. In the breast, studies have demonstrated a pro-tumorigenic role for adipocytes. However, the molecular mechanisms by which breast cancer cells coopt adipocytes remain elusive. Studying breast tumors and normal adjacent tissue (NAT) from several patient cohorts and mouse models, we show that lipolysis and lipolytic signaling are activated in NAT. We investigate the tumor-adipocyte interface and find that functional gap junctions form between breast cancer cells and adipocytes. As a result, cAMP, a critical lipolysis-inducing signaling molecule, is transferred from breast cancer cells to adipocytes and activates lipolysis in a gap junction-dependent manner; a fundamentally new mechanism of lipolysis activation in adipocytes. We find that gap junction formation depends upon connexin 31 (Cx31), and that Cx31 is essential for breast tumor growth and activa...

Molecular and Cellular Biology, 1988

Several genes which are deactivated on the initiation of development of Dictyostelium discoideum ... more Several genes which are deactivated on the initiation of development of Dictyostelium discoideum were identified by differential screening of various cDNA libraries. These genes have in common a decrease in the steady-state levels of their corresponding mRNAs on the onset of development and as development proceeds. When development was carried out in the absence of protein synthesis by inhibition with cycloheximide, the decrease in mRNA levels for most genes (V genes) was normal or slightly accelerated. For about 5% of the genes (H genes), however, cycloheximide caused an apparent induction of expression, as revealed by a slight or dramatic increase in mRNA levels, instead of the normal decrease. This effect was due to inhibition of protein synthesis and not to cycloheximide per se. The induction was found to be due to an enhancement of the transcription rate; normal rates of transcription for the H genes were dependent on continued protein synthesis during vegetative growth and dev...

American journal of physiology. Lung cellular and molecular physiology, 2002

We examined gene and surface expression and activity of the endothelin (ET)-1 receptors (ETA and ... more We examined gene and surface expression and activity of the endothelin (ET)-1 receptors (ETA and ETB) in subendothelial (L1) and inner medial (L2) cells from the main pulmonary artery of sheep with continuous air embolization (CAE)-induced chronic pulmonary hypertension (CPH). According to quantitative real-time RT-PCR, basal gene expression of both receptors was significantly higher in L2 than L1 cells, and hypertensive L2 cells showed significantly higher gene expression of ETB than controls. Expression of both genes in hypertensive L1 cells was similar to controls. Fluorescence-activated cell sorter analysis confirmed the increased distribution of ET(B) in hypertensive L2 cells. Although only the ETA receptors in control L2 cells showed significant binding of [125I]-labeled ET-1 at 1 h, both receptors bound ET-1 to hypertensive cells. Exposure to exogenous ET-1 for 18 h revealed that only the L2 cells internalized ET-1, and internalization by hypertensive L2 cells was significant...

Cancer research, 2003

Changes in expression of arachidonic acid (AA) metabolizing enzymes are implicated in the develop... more Changes in expression of arachidonic acid (AA) metabolizing enzymes are implicated in the development and progression of human prostate carcinoma (Pca). Transgenic mouse models of Pca that progress from high-grade prostatic intraepithelial neoplasia (HGPIN) to invasive and metastatic carcinoma could facilitate study of the regulation and function of these genes in Pca progression. Herein we characterize the AA-metabolizing enzymes in transgenic mice established with a prostate epithelial-specific long probasin promoter and the SV40 large T antigen (LPB-Tag mice) that develop extensive HGPIN and invasive and metastatic carcinoma with neuroendocrine (NE) differentiation. Murine 8-lipoxygenase (8-LOX), homologue of the 15-LOX-2 enzyme that is expressed in benign human prostatic epithelium and reduced in Pca, was not detected in wild-type or LPB-Tag prostates as determined by enzyme assay, reverse transcription-PCR, and immunohistochemistry. The most prominent AA metabolite in mouse pro...

Nucleic Acids Research, 1989

We have examined the expression and structure of several genes belonging to two classes of vegeta... more We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 hours. In contrast, when cells were grown in axenic broth, the mRNA levels remained constant until a dramatic drop occurred around 10 to 12 hours. Thus, regulation of both classes of genes during the first several hours of development is dependent upon the prior growth conditions. Analysis of genomic clones has resulted in the identification of two V genes, VI and V18, as ribosomal protein genes. Several other V genes were not found to be ribosomal protein genes, suggesting that

Neoplasia, 2001

Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic... more Recent studies in prostate tissues and especially cell lines have suggested roles for arachidonic acid (AA) metabolizing enzymes in prostate adenocarcinoma (Pca) development or progression. The goal of this study was to more fully characterize lipoxygenase (LOX) and cyclooxygenase-2 (COX-2) gene expression and AA metabolism in benign and malignant prostate using snap-frozen tissues obtained intraoperatively and mRNA analyses and enzyme assays. Formation of 15-hydroxyeicosatetraenoic acid (15-HETE) was detected in 23 / 29 benign samples and 15-LOX-2 mRNA was detected in 21 / 25 benign samples. In pairs of pure benign and Pca from the same patients, 15-HETE production and 15-LOX-2 mRNA were reduced in Pca versus benign in 9 / 14 (P = .04) and 14 / 17 (P = .002), respectively. Under the same conditions, neither 5-HETE nor 12-HETE formation was detectable in 29 benign and 24 tumor samples; with a more sensitive assay, traces were detected in some samples, but there was no clear association with tumor tissue. COX-2 mRNA was detected by nuclease protection assay in 7 / 16 benign samples and 5 / 16 tumors. In benign and tumor pairs from 10 patients, COX-2 was higher in tumor versus benign in only 2, with similar results by in situ hybridization. Paraffin immunoperoxidase for COX-2 was performed in whole mount sections from 87 additional radical prostatectomy specimens, with strong expression in ejaculatory duct as a positive control and corroboration with in situ hybridization. No immunostaining was detected in benign prostate or tumor in 45% of cases. Greater immunostaining in tumor versus benign was present in only 17% of cases, and correlated with high tumor grade (Gleason score 8 and 9 vs. 5 to 7). In conclusion, reduced 15-LOX-2 expression and 15-HETE formation is the most characteristic alteration of AA metabolism in Pca. Increased 12-HETE and 5-HETE formation in Pca were not discernible. Increased COX-2 expression is not a typical abnormality in Pca in general, but occurs in high-grade tumors. Neoplasia (2001) 3, 287-303.

Developmental Genetics, 1991

We have examined the expression and structure of vegetative specific genes belonging to the V and... more We have examined the expression and structure of vegetative specific genes belonging to the V and H gene classes. Both classes o f genes are deactivated at the onset of development by a reduction in the rate of transcription. Thus, the genes must be reactivated when the terminally differentiated spores germinate and the resulting amebae return to the vegetative state. During germination, activation of expression of most members of the V gene class was found to parallel the emergence of amaebae from the spore coats. The activation o f the V genes did not occur when protein synthesis was inhibited. The timiny uf activation of the H genes was more heterogeneous and did not parallel emergence. H gene activation occurred even when protein synthesis was inhibited. V4 was found to be the only vegetative specific gene that was responsive to the presence of bacteria. V4 expression was induced by 25-100 fold via transcriptional activation when bacteria were added to amebae growing axenically. Isolation and sequence analysis of the corresponding genomic clones revealed that two V genes, V18 and V1, encode ribosomal proteins. Promoter analysis has delineated the sequences necessary for expression and regulation for several of the V and H genes. In all cases, expression was determined 6, sequences within the first several hundred base pairs of the transcription start site. For V18 and V14, a positive constitutive element was identified in addition to the sequences involved in regulation. Finally, all of the characterizations and findings are discussed in terms of postulated models for V and H gene expression and regulation.

Developmental Genetics, 1988

Several genes that are deactivated upon the initiation of development of Dictyostelium discoideum... more Several genes that are deactivated upon the initiation of development of Dictyostelium discoideum have been identified by differential screening of various cDNA libraries. These genes have in common a decrease in the steady-state levels of their Corresponding'mRNAs as development proceeds. When development was carried out in the absence of protein synthesis by inhibition with cycloheximide, the decrease in mRNA levels for most genes (V genes) was normal or slightly accelerated. However, for about 5% of the genes (H genes), cycloheximide caused an apparent induction of expression, as revealed by a slight or dramatic increase in mRNA levels instead of the normal decrease. This effect was due to inhibition of protein synthesis and not to cycloheximide per se. The induction was found to be due to an enhancement of the trascription rate; normal rates of transcription for the H genes were dependent upon continued protein synthesis during vegetative growth and during development. Thus, two general regulatory classes exist for deactivation of gene expression upon initiation of development, one dependent and one independent of protein synthesis. Models concerning the control of expression of these two classes of genes are discussed here. Analysis of expression of these genes in mutant strains that are aggregationdeficient has also been performed, and the results lead to subdivisions of the classes.

Developmental Biology, 1988

We have identified and characterized three genes, the I genes (I for induced), which are induced ... more We have identified and characterized three genes, the I genes (I for induced), which are induced during the preaggregative phase of the developmental program of Dictyostelium discoideum None of these genes are expressed in cells growing vegetatively on bacteria or in axenic broth, and their induction during early development is due to transcriptional activation. Developmental expression of 16, 18, and Ill occurs even in the absence of protein synthesis. Their induction is very rapid and occurs essentially at the onset of development. The expression is transient, peaking between 2 and 4 hr followed by a rapid loss of expression. These characteristics suggest that the induction of 16,18, and Ill is a primary result of the initiation of development, and thus they represent the first such genes isolated. Although their expression behavior shares these characteristics, examination of their expression under various conditions of development and in a variety of aggregation-deficient mutant strains reveals that the details of the regulation and developmental control of these three genes are distinct.

Cancer research, Jan 15, 2001

15-Lipoxygenase (15-LOX)-2 is expressed in benign prostate secretory cells and benign prostate pr... more 15-Lipoxygenase (15-LOX)-2 is expressed in benign prostate secretory cells and benign prostate produces 15S-hydroxyeicosatetraenoic acid (15S-HETE) from exogenous arachidonic acid (AA). In contrast, 15S-LOX-2 and 15S-HETE formation are reduced in prostate carcinoma (Pca). The mechanisms whereby reduced 15-LOX-2 may contribute to Pca development or progression are not known. We investigated the expression of peroxisome proliferator-activated receptor (PPAR) gamma in benign and malignant prostate tissues and the ability of 15S-HETE to activate PPARgamma-dependent transcription and modulate proliferation of the Pca cell line PC3. In contrast to benign prostate and similar to most Pca tissues, 15-LOX-2 mRNA was not detected in PC3 cells, and they did not produce detectable 15-HETE from [14C]AA. By reverse transcription-PCR, PPARgamma mRNA was present in 18 of 18 benign and 9 of 9 tumor specimens. The PPARgamma ligand BRL 49653 and 15S-HETE caused a dose-dependent inhibition of PC3 proli...

Human Pathology, 1998

The rate of parvovirus B19 (PV) infection in cases of &amp;quot;idiopathic&amp;qu... more The rate of parvovirus B19 (PV) infection in cases of &amp;quot;idiopathic&amp;quot; nonimmune hydrops fetalis (NIHF) is reported to be approximately 16% with polymerase chain reaction (PCR)-based methods. Antibodies for use in paraffin-embedded tissue have not been systematically compared with PCR or with the presence of inclusions at varying gestational ages. All autopsy cases of NIHF and those with effusions of multiple serous membranes examined between 1991 and 1996 (n = 29) were evaluated for the presence of PV DNA by PCR analysis of paraffin-embedded liver tissue. PCR-positive cases and &amp;quot;idiopathic&amp;quot; cases were examined for the presence of inclusions in routine histological sections and for PV protein using a monoclonal antibody (NovoCastra R92F6). Among the four clinically idiopathic cases, one (25%) was positive for PV using PCR. The three negative idiopathic cases had no inclusions and were negative for PV by PCR and immunohistochemistry (IHC); all were third-trimester gestations (28, 31, and 32 weeks). Identifiable risk factors for NIHF other than PV in the remaining 25 cases included cystic hygroma, seven (three 45,X; two 46,XX; two no growth); complex cardiac anomaly, six; infection, three (two CMV, one chlamydia); twin-twin transfusion, two; lymphangiectasia, two; diaphragmatic hernia, tracheal atresia, trisomy 21, congenital cystic adenomatoid malformation, one each. One of these nonidiopathic cases, a fetus with cystic hygroma and a 45,X karyotype, was positive for PV DNA only on the blot, consistent with a low titer; no inclusions were present, and IHC was negative in multiple organs in this instance. One of four (25%) cases of idiopathic NIHF cases contained PV DNA by PCR analysis; there were abundant inclusions in multiple organs, and IHC was strongly positive as well. Of 25 cases of nonidiopathic NIHF, one (4%) was also positive for PV DNA by PCR. PV protein was detected by IHC only in the presence of inclusions; IHC thus may be useful for highlighting sparse inclusions. No second-trimester case of NIHF was unexplained. Late (third-trimester) cases of &amp;quot;idiopathic&amp;quot; NIHF are likely to be negative by all methods, either because they are not attributable to PV infection or because PV protein and DNA are below detectable levels or are no longer present. Maternal serology for PV and TORCH agents may be the best method for investigating third-trimester losses to otherwise unexplained NIHF.

Circulation Research, 2005

We show that 1 of the type II bone morphogenetic protein (BMP) receptor ligands, BMP4, is widely ... more We show that 1 of the type II bone morphogenetic protein (BMP) receptor ligands, BMP4, is widely expressed in the adult mouse lung and is upregulated in hypoxia-induced pulmonary hypertension (PH). Furthermore, heterozygous null Bmp4 lacZ/+ mice are protected from the development of hypoxia-induced PH, vascular smooth muscle cell proliferation, and vascular remodeling. This is associated with a reduction in hypoxia-induced Smad1/5/8 phosphorylation and Id1 expression in the pulmonary vasculature. In addition, pulmonary microvascular endothelial cells secrete BMP4 in response to hypoxia and promote proliferation and migration of vascular smooth muscle cells in a BMP4-dependent fashion. These findings indicate that BMP4 plays a dominant role in regulating BMP signaling in the hypoxic pulmonary vasculature and suggest that endothelium-derived BMP4 plays a direct, paracrine role in promoting smooth muscle proliferation and remodeling in hypoxic PH.

Breast Cancer Research and Treatment, 1998

Human Pathology, 2000

BACKGROUND After long-term androgen deprivation therapy, 25-30% prostate cancer (PCa) acquires an... more BACKGROUND After long-term androgen deprivation therapy, 25-30% prostate cancer (PCa) acquires an aggressive neuroendocrine (NE) phenotype. Dysregulation of YAP1, a key transcription coactivator of the Hippo pathway, has been related to cancer progression. However, its role in neuroendocrine prostate cancer (NEPC) has not been assessed. METHODS Immunohistochemistry was used to evaluate YAP1 protein levels during PCa initiation and progression. YAP1 knockdown and luciferase reporter assays were used to evaluate the ability of YAP1 to modulate Wnt/beta-Catenin signaling. RESULTS YAP1 expression was present in the basal epithelial cells in benign prostatic tissues, lost in low grade PCa, but elevated in high grade prostate adenocarcinomas. Interestingly, the expression of YAP1 was reduced/lost in both human and mouse NEPC. Finally, YAP1 knockdown in PCa cells activates Wnt/beta-Catenin signaling, which has been implicated in NE differentiation of PCa, supporting a functional involvement of the loss of YAP1 expression in NEPC development. CONCLUSIONS The expression of YAP1 is elevated in high grade prostate adenocarcinomas while lost in NEPC. Reduced YAP1 activates Wnt/beta-Catenin signaling in PCa cells. These results suggest that when applied to PCa patients, YAP1 inhibitors shall be used with caution.