Search

Readout-segmented echo-planar diffusion-weighted imaging (RS-EPI) can improve image quality and signal-to-noise ratio, the resulting apparent diffusion coefficient (ADC) value acts as a more sensitive biomarker to characterize tumors. However, data regarding the differentiation of breast cancer (BC) receptor statuses using RS-EPI are limited.To determine whether RS-EPI improves the differentiation of receptor statuses compared with conventional single-shot (SS) EPI in breast MRI.Retrospective.A total of 151 BC women with the mean age of 50.6 years.A 3 T/ RS-EPI and SS-EPI.The ADCs of the lesion and normal background tissue from the two sequences were collected by two radiologists with 15 years of experience working of breast MRI (M.H.Z. and X.F.C.), and a normalized ADC was calculated by dividing the mean ADC value of the lesion by the mean ADC value of the normal background tissue.Agreement between the ADC measurements from the two sequences was assessed using the Pearson correlation coefficient and Bland-Altman plots. One-way analysis of variance, Kruskal-Wallis test, and median difference were used to compare the ADC measurements for all lesions and different receptor statuses. A P value less than 0.05 indicated a significant result.The ADC measurements of all lesions and normal background tissues were significantly higher on RS-EPI than on SS-EPI (1.82 ± 0.33 vs. 1.55 ± 0.30 and 0.83 ± 0.11 vs. 0.79 ± 0.10). The normalized ADC was lower on RS-EPI than on SS-EPI (0.47 ± 0.11 vs. 0.53 ± 0.12, a median difference of -0.04 [95% CI: -0.256 to 0.111]). For both diffusion methods, only the ADC measurement of RS-EPI was higher for human epidermal growth factor receptor-2 (HER-2)-positive tumors than for HER-2-negative tumors (0.87 ± 0.10 vs. 0.81 ± 0.11), and this measurement was associated with HER-2 positive status (adjusted odds ratio [OR] = 654.4); however, similar results were not observed for the ADC measurement of SS-EPI (0.80 ± 0.10 vs. 0.78 ± 0.11 with P = 0.199 and adjusted OR = 0.21 with P = 0.464, respectively).RS-EPI can improve the distinction between HER-2-positive and HER-2-negative breast cancer, complementing the clinical application of diffusion imaging.3 TECHNICAL EFFICACY: Stage 1.

Context.— Repeated surgery is necessary for 20% to 40% of breast conservation surgeries owing to the unavailability of any adjunctive, accurate, and objective tool in the surgeon's hand for real-time margin assessment to achieve the desired balance of oncologic and cosmetic outcomes. Objective.— To assess the feasibility of using a multispectral autofluorescence imaging device for discriminating malignant neoplasm from normal breast tissue in pathology as a critical step in the development of a device for intraoperative use, and to demonstrate the device's utility for use in processing and prioritizing specimens during frozen section and in the pathology grossing room. Design.— We performed a preliminary assessment of our device, called the TumorMAP system, on 172 fresh tissue blocks from 115 patients obtained from lumpectomy specimens at the time of initial gross examination and compared the device results with gold standard pathology evaluation. Results.— The preliminary results demonstrate the potential of our device in detecting breast cancer in fresh tissue samples with a sensitivity of 82%, a specificity of 91%, a positive predictive value of 84%, and a negative predictive value of 89%. Conclusions.— Our results suggest that the TumorMAP system is suitable for the detection of malignant neoplasm in freshly excised breast specimens and has the potential to evaluate resection margins in real time.

Context.—Recent advances in comprehensive genomic profiling by next-generation sequencing have uncovered the genomic alterations at the molecular level for many types of tumors; as such, numerous small specific molecules that target these alterations have been developed and widely used in the management of these cancers.Objective.—To provide a concise molecular genomic update in solid, bone and soft tissue tumors, hematopoietic as well as lymphoid malignancies; discuss its clinical applications; and familiarize practicing pathologists with the emerging cancer biomarkers and their diagnostic utilities.Data Sources.—This review is based on the National Comprehensive Cancer Network guidelines and peer-reviewed English literature.Conclusions.—Tumor-specific biomarkers and molecular/genomic alterations, including pan-cancer markers, have been significantly expanded in the past decade thanks to large-scale high-throughput technologies and will continue to emerge in the future. These biomarkers can be of great value in diagnosis, prognosis, and/or targeted therapy/treatment. Familiarization with these emerging and ever-changing tumor biomarkers will undoubtedly aid pathologists in making accurate and state-of-the-art diagnoses and enable them to be more actively involved in the care of cancer patients.

Introduction/Objective Beta catenin plays an important role in cancer tumorigenesis and have been found to be associated with metastasis in a variety of tumors. Analyzing TCGA data, we found that 30% of endometrial endometrioid carcinoma cases have beta-catenin mutations. We hypothesize that beta-catenin mutation may be associated with metastasis of endometrial endometrioid carcinoma. ER and PR expression was also compared to determine any changes after metastasis. Methods Retrospective institutional review of all endometrial endometrioid carcinoma (192 cases) between 2011 to 2018 was performed, including 149 cases of FIGO grade I, 38 cases of FIGO grade II and 5 cases of FIGO grade III. 19 cases with paired primary and metastatic specimen were identified. Immunohistochemistry staining (IHC) was carried out for ER, PR and beta-catenin. Results Median patient age was 56 years. The most common metastatic site was vagina, accounting for 68% of metastasis (14/19), followed by bladder (3/19), lung (2/19) and rectum (1/19). The primary and metastatic carcinoma of all 19 cases exhibit very similar morphology. All of those cases were positive and concordant for ER and PR in primary and metastatic endometrioid carcinoma. On the other hand, nuclear beta-catenin staining caused by mutation was positive in 5 metastatic carcinoma but not in primary carcinoma. Conclusion IHC expression of ER and PR remains unchanged between primary and metastatic carcinoma, demonstrating the reliability of ER and PR to confirm the origin of metastatic carcinoma. 26% of the metastatic carcinoma (5/19) exhibit nuclear beta-catenin staining but not in primary carcinoma, suggesting the possible role of beta-catenin in metastasis of endometrial endometrioid carcinoma.

Trophoblastic neoplasms involving the ovary are uncommon and include gestational tumors, which are either metastatic from the uterus or ectopic and nongestational tumors, which include those of germ cell type/origin and somatic tumors with trophoblastic differentiation; in all these types, most are pure choriocarcinoma. Intermediate trophoblastic tumors, which include placental site trophoblastic tumor (PSTT) and epithelioid trophoblastic tumor (ETT), are rare in the ovary, with most assumed to be gestational; this is the only category formally recognized in 2014 World Health Organization (WHO) classification, likely due to few well-documented nongestational examples. We report the clinicopathologic features of 6 ovarian intermediate trophoblastic tumors, including 3 PSTTs, 2 ETTs, and 1 ETT with choriocarcinomatous differentiation. DNA-based short tandem repeat genotyping identified 4 of these as nongestational (3 PSTTs and 1 ETT), as evidenced by sharing of alleles between tumor and normal tissue at all informative loci. Interestingly, all 3 of the nongestational PSTTs coexisted with mature cystic teratoma. The remaining 2 tumors (1 ETT and 1 ETT with some choriocarcinomatous differentiation) were gestational (likely ectopic due to lack of evidence of a uterine tumor), as evidenced by the presence of both maternal and novel/nonmaternal alleles at informative loci in tumor compared with normal tissue. It is important to recognize a distinct category of primary ovarian nongestational intermediate trophoblastic tumors of germ cell type/origin, including PSTT and ETT, in classification systems to guide clinical management, as gestational and nongestational tumors have different genetic origins and may require different therapy. Genotyping is useful for classification as nongestational versus gestational, particularly as traditional clinicopathologic findings cannot always predict the nature of a trophoblastic tumor.

We are reporting a novel sequencing technology, RepSeq (Repetitive Sequence), that has high sensitivity, specificity and quick turn-around time. This new sequencing technology is developed by modifying traditional Sanger sequencing technology in several aspects. The first, a homopolymer tail is added to the PCR primer(s), which makes interpreting electropherograms a lot easier than that in traditional Sanger sequencing. The second, an indicator nucleotide is added at the 5’end of the homopolymer tail. In the presence of a deletion, the position of the indicator nucleotide in relation to the wild type confirms the deletion. At the same time, the indicator of the wild type serves as the internal control. Furthermore, the specific design of the PCR and/or sequencing primers will specifically enrich/select mutant alleles, which increases sensitivity and specificity significantly. Based on serial dilution studies, the analytical lower limit of detection was 1.47 copies. A total of 89 samples were tested for EGFR exon 19 deletion, of which 21 were normal blood samples and 68 were samples previously tested by either pyrosequencing or TruSeq Next Generation Sequencing Cancer Panel. There was 100 % concordance among all the samples tested. RepSeq technology has overcome the shortcomings of Sanger sequencing and offers an easy-to-use novel sequencing method for personalized precision medicine.

Objectives The most common genetic alterations in prostate cancer are fusions of ERG and other members of the E26 transformation-specific (ETS) family of transcription factors, including ETV1, ETV4, and FLI1. Analyzing TCGA data, we found that similar to ERG fusion, FLI1 fusion-associated FLI1 mRNA level increases. ERG IHC stain has been a surrogate test for ERG fusion. Therefore, we hypothesize that FLI IHC stain could also be used to detect FLI1 fusion in prostate cancer. Methods In total, 111 primary prostate adenocarcinoma (>10% by volume) cases from our institute were selected for tissue microarray (TMA) construction. The regular full section slides and TMA slides were subject to IHC stain of ERG and FLI1 (Santa Cruz, SC-113). The criteria for positive FLI1 are (1) nuclear staining; (2) only in tumor cells, not in nontumor cells; and (3) FLI1-positive cells should be negative for ERG IHC staining. Results For prostate TMA slides, ~50% of cases were positive for ERG; ~30% of cases were weakly positive for FLI1. However, all of the FLI1 weakly positive cases were positive for ERG as well possibly due to cross-reactivity between ERG and FLI1, which was demonstrated in other studies. Conclusion Overall, we conclude that the cross-reactivity between FL1 and ERG precluded the detection of FLI1 fusion in prostatic adenocarcinoma under current conditions. We are in the process of selecting some cases to detect FLI1 fusion by next-generation sequencing (NGS) and FISH.

We are presenting an evaluation of Allele Specific Multiplex Sequencing (ASMS) to detect two EGFR somatic mutations (L858R, T790M). Late stage lung cancer samples were tested for both EGFR mutations and were compared to either pyrosequencing or TruSeq. The analytical lower limit of detection (LLOD) for the ASMS-L858R assay was found to be 36 copies, and 72 copies for the ASMS-T790M assay. The forty-one FFPE samples that were tested for T790M showed 100% concordance with the respective comparative method. The forty-five FFPE samples tested previously by Truseq for L858R showed 100% concordance with ASMS. Out of the twenty L858R samples previously tested by pyrosequencing, there was 95% concordance with ASMS. Additionally, twenty-one normal blood samples were tested by ASMS were found to be negative for L858R and T790M. In conclusion, the detection of L858R and T790M by ASMS are in acceptable concordance with both pyrosequencing and TruSeq in detecting EGFR mutations from late stage lung cancer. Further, ASMS was able to detect EGFR (L858R) with 10 picograms (3 copies gDNA) of FFPE extracted DNA, and hence could be used to detect mutations from samples carrying low copy numbers.

Recent studies link synaptojanin 1 (synj1), the main phosphoinositol (4,5)-biphosphate phosphatase (PI(4,5)P2-degrading enzyme) in the brain and synapses, to Alzheimer disease. Here we report a novel mechanism by which synj1 reversely regulates cellular clearance of amyloid-β (Aβ). Genetic down-regulation of synj1 reduces both extracellular and intracellular Aβ levels in N2a cells stably expressing the Swedish mutant of amyloid precursor protein (APP). Moreover, synj1 haploinsufficiency in an Alzheimer disease transgenic mouse model expressing the Swedish mutant APP and the presenilin-1 mutant ΔE9 reduces amyloid plaque load, as well as Aβ40 and Aβ42 levels in hippocampus of 9-month-old animals. Reduced expression of synj1 attenuates cognitive deficits in these transgenic mice. However, reduction of synj1 does not affect levels of full-length APP and the C-terminal fragment, suggesting that Aβ generation by β- and γ-secretase cleavage is not affected. Instead, synj1 knockdown increases Aβ uptake and cellular degradation through accelerated delivery to lysosomes. These effects are partially dependent upon elevated PI(4,5)P2 with synj1 down-regulation. In summary, our data suggest a novel mechanism by which reduction of a PI(4,5)P2-degrading enzyme, synj1, improves amyloid-induced neuropathology and behavior deficits through accelerating cellular Aβ clearance. Background: Recent studies have linked synaptojanin 1 (synj1) with Alzheimer disease (AD). Results: We report that synj1 reduction decreases amyloid plaque burden and attenuates cognitive deterioration in an AD mouse model. These effects are mediated through accelerating endosomal/lysosomal degradation of Aβ. Conclusion: Our data suggest a novel mechanism by which synj1 reduction promotes Aβ clearance. Significance: These studies implicate a therapeutic strategy for AD.

Objectives: Renal cell carcinoma (RCC) is a heterogeneous neoplasm with different morphology and molecular changes. Recently, a study investigated panmetabolomic profiles and metabolic genes of more than 600 clear cell RCC (ccRCC) tumors showed the rate-limiting gluconeogenic enzyme fructose-1,6-bisphosphatase 1 (FBP-1) was inhibited in almost 100% of ccRCCs. Here, we …

Translocation renal cell carcinoma is a newly recognized subtype of renal cell carcinoma (RCC) with chromosomal translocations involving TFE3 (Xp11.2) or, less frequently, TFEB (6p21). Xp11 translocation RCC was originally described as a pediatric neoplasm representing 20% to 40% of pediatric RCCs, with a much lower frequency in the adult population. TFEB translocation RCC is very rare, with approximately 10 cases reported in the literature. Here, we describe the clinicopathologic features of adult translocation RCC from a single institution. Using tissue microarray, immunohistochemistry, cytogenetic examination, and fluorescence in situ hybridization, we identified 6 (∼5%) cases of TFE3 translocation RCC and 1 (1%) case of TFEB translocation RCC in 121 consecutive adult RCC cases between 2001 and 2009. Our results suggest that weak TFE3 staining of a significant proportion of RCC cases may be because of expression of the full-length TFE3 protein rather than the chimeric fusion protein resulting from chromosomal translocation.

Both Xp11.2 translocation renal cell carcinoma (RCC) and alveolar soft part sarcoma (ASPS) are characterized by various translocations disrupting chromosome Xp11.2, which result in gene fusions involving the TFE3 transcription factor gene. Diagnostic tools to detect translocations involving the TFE3 gene on chromosome X would be valuable in the evaluation of these tumors. We developed a dual-color, break-apart fluorescence in situ hybridization (FISH) assay to identify the chromosomal break point in paraffin-embedded tissue. This assay was validated using 4 cases of Xp11.2 RCC [proven by karyotype and/or reverse-transcriptase polymerase chain reaction (RT-PCR)], 2 cases of ASPS (proven by karyotype or RT-PCR), the UOK109 cell line carrying the inv(X) (p11;q12), and several negative controls (both neoplastic and non-neoplastic). This break-apart FISH assay is a relatively quick procedure for detecting Xp11.2 RCC and ASPS translocations and can be applied to archival paraffin-embedded tissue.

Xp11 translocation cancers include Xp11 translocation renal cell carcinoma (RCC), Xp11 translocation perivascular epithelioid cell tumor (PEComa), and melanotic Xp11 translocation renal cancer. In Xp11 translocation cancers, oncogenic activation of TFE3 is driven by the fusion of TFE3 with a number of different gene partners; however, the impact of individual fusion variant on specific clinicopathologic features of Xp11 translocation cancers has not been well defined. In this study, we analyze 60 Xp11 translocation cancers by fluorescence in situ hybridization using custom bacterial artificial chromosome probes to establish their TFE3 fusion gene partner. In 5 cases RNA sequencing was also used to further characterize the fusion transcripts. The 60 Xp11 translocation cancers included 47 Xp11 translocation RCC, 8 Xp11 translocation PEComas, and 5 melanotic Xp11 translocation renal cancers. A fusion partner was identified in 53/60 (88%) cases, including 18 SFPQ (PSF), 16 PRCC, 12 ASPSCR1 (ASPL), 6 NONO, and 1 DVL2. We provide the first morphologic description of the NONO-TFE3 RCC, which frequently demonstrates subnuclear vacuoles leading to distinctive suprabasal nuclear palisading. Similar subnuclear vacuolization was also characteristic of SFPQ-TFE3 RCC, creating overlapping features with clear cell papillary RCC. We also describe the first RCC with a DVL2-TFE3 gene fusion, in addition to an extrarenal pigmented PEComa with a NONO-TFE3 gene fusion. Furthermore, among neoplasms with the SFPQ-TFE3, NONO-TFE3, DVL2-TFE3, and ASPL-TFE3 gene fusions, the RCCs are almost always PAX8 positive, cathepsin K negative by immunohistochemistry, whereas the mesenchymal counterparts (Xp11 translocation PEComas, melanotic Xp11 translocation renal cancers, and alveolar soft part sarcoma) are PAX8 negative, cathepsin K positive. These findings support the concept that despite an identical gene fusion, the RCCs are distinct from the corresponding mesenchymal neoplasms, perhaps due to the cellular context in which the translocation occurs. We corroborate prior data showing that the PRCC-TFE3 RCCs are the only known Xp11 translocation RCC molecular subtype that are consistently cathepsin K positive. In summary, our data expand further the clinicopathologic features of cancers with specific TFE3 gene fusions and should allow for more meaningful clinicopathologic associations to be drawn.

The apolipoprotein E4 (ApoE4) allele is the strongest genetic risk factor for developing sporadic Alzheimer's disease (AD). However, the mechanisms underlying the pathogenic nature of ApoE4 are not well understood. In this study, we have found that ApoE proteins are critical determinants of brain phospholipid homeostasis and that the ApoE4 isoform is dysfunctional in this process. We have found that the levels of phosphoinositol biphosphate (PIP2) are reduced in postmortem human brain tissues of ApoE4 carriers, in the brains of ApoE4 knock-in (KI) mice, and in primary neurons expressing ApoE4 alleles compared with those levels in ApoE3 counterparts. These changes are secondary to increased expression of a PIP2-degrading enzyme, the phosphoinositol phosphatase synaptojanin 1 (synj1), in ApoE4 carriers. Genetic reduction of synj1 in ApoE4 KI mouse models restores PIP2 levels and, more important, rescues AD-related cognitive deficits in these mice. Further studies indicate that ApoE4 behaves similar to ApoE null conditions, which fails to degrade synj1 mRNA efficiently, unlike ApoE3 does. These data suggest a loss of function of ApoE4 genotype. Together, our data uncover a previously unidentified mechanism that links ApoE4-induced phospholipid changes to the pathogenic nature of ApoE4 in AD.

We report experiments that infer a radical reorientation of tyrosine-phosphorylated parallel STAT1 dimers to an antiparallel form. Such a change in structure allows easy access to a phosphatase. With differentially epitope-tagged molecules, we show that the two monomers of a dimer remain together during dephosphorylation although they most likely undergo spatial reorientation. Extensive single amino acid mutagenesis within crystallographically established domains, manipulation of amino acids in an unstructured tether that connects the N-terminal domain (ND) to the core of the protein, and the demonstration that overexpressed ND can facilitate dephosphorylation of a core molecule lacking an ND all support this model: When the tyrosine-phosphorylated STAT1 disengages from DNA, the ND dimerizes and somehow assists in freeing the reciprocal pY–SH2 binding between the monomers of the dimer while ND ⋅ ND dimerization persists. The core of the monomers rotate allowing reciprocal association of the coiled:coil and DNA-binding domains to present pY at the two ends of an antiparallel dimer for ready dephosphorylation.

Presenilin (PS1/PS2) is a major component of gamma-secretase, the activity that mediates proteolysis of beta-amyloid precursor protein to generate beta-amyloid (Abeta). Here we demonstrate that PS1, through its loop region, binds to phospholipase D1 (PLD1), thereby recruiting it to the Golgi/trans-Golgi network. Overexpression of wild-type PLD1 reduces Abeta generation. Conversely, down-regulation of endogenous PLD1 by small hairpin RNA elevates Abeta production. The Abeta-lowering effect of PLD1 is independent of its ability to promote vesicular budding of beta-amyloid precursor protein. The data indicate that overexpression of PLD1 decreases, and down-regulation of PLD1 increases, the catalytic activity, and the association of the subunits, of gamma-secretase.

3Y1 rat fibroblasts overexpressing the tyrosine kinase c-Src (3Y1(c-Src) cells) become transformed by downregulation of protein kinase C delta (PKC delta). However, when 3Y1(c-Src) cells were subjected to serum withdrawal, they underwent apoptosis via a cytochrome c/caspase 9 pathway. In contrast, neither parental nor v-Src-transformed 3Y1 cells underwent apoptosis when subjected to serum withdrawal. If PKC delta was downregulated, the apoptotic phenotypes induced by serum withdrawal in the 3Y1(c-Src) cells were suppressed. The apparent survival signal generated by PKC delta downregulation was independent of the phosphatidylinositol-3-kinase (PI3K)/Akt survival pathway. Collectively, these data indicate that (1) c-Src overexpression renders cells sensitive to apoptotic stress, and (2) that downregulation of PKC delta provides a novel PI3K/Akt-independent survival signal capable of suppressing apoptotic signals.

Background: In clinical practice of complex diseases such as cancer it is a challenging task to correctly identify driving factors and specific interactions between multitudes of genomic and clinical variables. In cancer where patterns are heterogeneous and involve highly complex interactions of biological pathways, this is by far a non-trivial task. Using novel approaches in machine learning, we demonstrate the ability to quantitatively and accurately reveal and describe patterns in genomic and clinical data. Method: We developed a computational framework based on a number of interacting learners performing extensive pattern search and data characterization. This framework is multilevel and involves steps of relevant data transformations. We formulate and apply contextually relevant criteria to distinguish and rank iteratively obtained findings and identify hidden relations between features and characteristic connections to the clinical outcome. Summary: We successfully tested our method on the public data of Glioblastoma Multiforme (GBM) from The Cancer Genome Atlas (TCGA). We identify interacting sets of genomic variables to represent clinically relevant subgroups of samples. We observe a dense presence of interacting known cellular processes in GBM such as EGFR, FGFR, ERK, RAS, MAPK, P53, as well as novel such as calcium signaling, kinesin motor and protein kinase pathways, tubulin and microtubule binding, phorbol esters/diacylglycerol binding domain (C1 domain), purine ribonucleoside triphosphate binding, positive regulation of phospholipase activity and others. The top ranking pathways recap the well-known and new biology. In addition, compared to known genes in the literature, we also observe involvement of novel genes in GBM subtype characterization. Finally, we propose two-fold solution: identification of distinctive patterns in the input genomic and output clinical data, and specific format of their interactions. Citation Format: Nevenka Dimitrova, Konstantin Volyanskyy, Vlado Menkovski, Yee Him Cheung, Minghao Zhong, John T. Fallon, Eric Vail. Identification of clinically relevant patterns in complex genomic interactions of glioblastoma multiforme [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4549. doi:10.1158/1538-7445.AM2017-4549

TERT promoter mutations were recently discovered in melanoma by next generation sequencing. Subsequently, several malignancies including urothelial carcinoma were also found to be associated with the same TERT promoter mutations. Small cell carcinoma (SCC) of the urinary bladder is a rare subtype with an aggressive clinical course. Despite the frequent occurrence of TERT promoter mutations in urothelial carcinoma, the incidence of the mutations in SCC of the urinary bladder is unknown. In addition, as a potential molecular marker to distinguish SCC of the urinary bladder from SCC of the prostate, lung (SCLC) and other origins, this information may be clinically useful. We collected a total of 11 cases of SCC of the urinary bladder (10 cases are primary SCC of the urinary bladder; 1 case has primary SCC of the urinary bladder and liver metastasis). We also included 20 cases of SCLC, 2 cases of SCC of the prostate, 5 cases of Merkel cell carcinoma, and 6 cases of SCC from other sites (cervical, GE junction, breast, and soft tissue). In addition, 3 cases of non-neoplastic tissue from the matched SCC of bladder patient and 14 cases of benign urinary bladder were also included. All tumor sections have been examined to confirm the diagnosis and to make sure more than 20% are of tumor content. Genomic DNA was isolated from FFPE tissue and a fragment of the TERT promoter (145 bp) was amplified by PCR. The TERT promoter mutations are determined by bi-directional Sanger sequencing. All (11/11) SCC of the urinary bladder bear TERT promoter mutation C228T. Neither of SCC from all other origins nor matched non-neoplastic tissue contains the TERT promoter mutations. We demonstrated a high frequency TERT promoter mutation in SCC of the urinary bladder, but not in SCC of other origin, such as the prostate. The findings further illustrate molecular differences between SCC of the urinary bladder and SCC of other origins, despite their shared morphologic and immunophenotypic similarities. The TERT promoter mutation may be a biomarker differentiating SCC of the urinary bladder from SCC of other origins.

Downregulation of protein kinase C delta (PKC delta) by treatment with the tumor-promoting phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA) transforms cells that overexpress the non-receptor class tyrosine kinase c-Src (Z. Lu et al., Mol. Cell. Biol. 17:3418-3428, 1997). We extended these studies to cells overexpressing a receptor class tyrosine kinase, the epidermal growth factor (EGF) receptor (EGFR cells); like c-Src, the EGF receptor is overexpressed in several human tumors. In contrast with expectations, downregulation of PKC isoforms with TPA did not transform the EGFR cells; however, treatment with EGF did transform these cells. Since TPA downregulates all phorbol ester-responsive PKC isoforms, we examined the effects of PKC delta- and PKC alpha-specific inhibitors and the expression of dominant negative mutants for both PKC delta and alpha. Consistent with a tumor-suppressing function for PKC delta, the PKC delta-specific inhibitor rottlerin and a dominant negative PKC delta mutant transformed the EGFR cells in the absence of EGF. In contrast, the PKC alpha-specific inhibitor Go6976 and expression of a dominant negative PKC alpha mutant blocked the transformed phenotype induced by both EGF and PKC delta inhibition. Interestingly, both rottlerin and EGF induced substantial increases in phospholipase D (PLD) activity, which is commonly elevated in response to mitogenic stimuli. The elevation of PLD activity in response to inhibiting PKC delta, like transformation, was dependent upon PKC alpha and restricted to the EGFR cells. These data demonstrate that PKC isoforms alpha and delta have antagonistic effects on both transformation and PLD activity and further support a tumor suppressor role for PKC delta that may be mediated by suppression of tyrosine kinase-dependent increases in PLD activity.

Glomerular sparing (GS) is defined as a unique growth pattern in which tumor cells replace the majority of renal tubes and overrun intact glomeruli. This phenomenon has been well recognized by pathologists as a typical infiltrative pattern and some studies suggested it was an independent risk factor. Here, we study the clinical, pathological, and immunohistochemical features of primary kidney neoplasms with glomerular sparing pattern. We searched the archives of our pathology department for nephrectomy specimens and reviewed all pathology reports from 2009-2013. We selected cases with tumor and collected clinicopathological information, focusing on re-evaluation of cases with glomerular sparing pattern. To facilitate our study we performed immunohistochemical stains of PAX-8, p63, and InI-1 on selected cases. We selected a total of 204 nephrectomy cases in this study, including 163 cases of renal cell carcinoma; 37 cases of urothelial carcinoma; 4 cases from other categories (Wilms tumor, primary diffuse large B-cell lymphoma, angiolipoma, rhabdoid tumor). Finally, we identified 7 cases of primary kidney tumors with glomerular sparing pattern: 2 cases of clear cell renal cell carcinomas (ccRCC), 1 case of collecting duct carcinoma, 2 cases of urothelial carcinoma (UC), 1 case of diffuse large B-cell lymphoma and 1 case of malignant rhabdoid tumor. The primary kidney tumors with glomerular sparing pattern are rare and incidence in our study is

Xp11 translocation renal cell carcinomas harbor chromosome translocations involving the Xp11 breakpoint, resulting in gene fusions involving the TFE3 gene. The most common subtypes are the ASPSCR1-TFE3 renal cell carcinomas resulting from t(X;17)(p11;q25) translocation, and the PRCC-TFE3 renal cell carcinomas, resulting from t(X;1)(p11;q21) translocation. A formal clinical comparison of these two subtypes of Xp11 translocation renal cell carcinomas has not been performed. We report one new genetically confirmed Xp11 translocation renal cell carcinoma of each type. We also reviewed the literature for all published cases of ASPSCR1-TFE3 and PRCC-TFE3 renal cell carcinomas and contacted all corresponding authors to obtain or update the published follow-up information. Study of two new, unpublished cases, and review of the literature revealed that 8/8 patients who presented with distant metastasis had ASPSCR1-TFE3 renal cell carcinomas, and all but one of these patients either died of disease or had progressive disease. Regional lymph nodes were involved by metastasis in 24 of the 32 ASPSCR1-TFE3 cases in which nodes were resected, compared with 5 of 14 PRCC-TFE3 cases (P=0.02).; however, 11 of 13 evaluable patients with ASPSCR1-TFE3 renal cell carcinomas who presented with N1M0 disease remained disease free. Two PRCC-TFE3 renal cell carcinomas recurred late (at 20 and 30 years, respectively). In multivariate analysis, only older age or advanced stage at presentation (not fusion subtype) predicted death. In conclusion, ASPSCR1-TFE3 renal cell carcinomas are more likely to present at advanced stage (particularly node-positive disease) than are PRCC-TFE3 renal cell carcinomas. Although systemic metastases portend a grim prognosis, regional lymph node involvement does not, at least in short-term follow-up. The tendency for PRCC-TFE3 renal cell carcinomas to recur late warrants long-term follow-up.

Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) is a subtype of RCC characterized by translocations involving a breakpoint at the TFE3 gene (Xp11.2). Moderate to strong nuclear TFE3 immunoreactivity has been recognized as a specific diagnostic marker for this type of tumor. However, exclusive cytoplasmic localization of a TFE3 fusion protein was reported in UOK 145 cells, a cell line derived from an Xp11.2 RCC harboring the PSF-TFE3 translocation. If reproducible using immunohistochemistry (IHC), this finding would have important implications for pathologists in the diagnosis of Xp11.2 RCC, calling into question the specificity of nuclear immunoreactivity for TFE3 in these tumors. The purpose of this study was to determine whether the above-noted cytoplasmic localization of the TFE3 fusion protein could be reproduced using IHC. UOK 145 cells and fresh frozen tissue from 2 clinical cases of Xp11.2 RCC found to harbor the PSF-TFE3 gene rearrangement (by cytogenetic testing) were collected. All samples were subjected to histopathologic evaluation by board-certified pathologists, TFE3 IHC, reverse transcription polymerase chain reaction, and Sanger sequencing analysis. A strong nuclear TFE3 immunoreactivity was demonstrated in all samples including the UOK 145 cell line. No cytoplasmic immunoreactivity was seen. Reverse transcription polymerase chain reaction and Sanger sequencing confirmed the previously reported PSF-TFE3 gene fusion between exon 9 of PSF and exon 6 of TFE3 in the UOK 145 cell line and in one of 2 clinical cases of Xp11.2 RCC. A novel PSF-TFE3 gene fusion between exon 9 of PSF and exon 5 of TFE3 was detected in the second clinical case of Xp11.2 RCC.

The B-Raf protein is a key signaling molecule in the mitogen activated protein kinase (MAPK) signaling pathway and has been implicated in the pathogenesis of a variety of cancers. An important V600E mutation has been identified and can cause constitutive B-Raf activation. Recent studies have evaluated a variety of small molecule inhibitors targeting B-Raf, including PLX4032/vemurafenib, dabrafenib, LGX818, GDC0879, XL281, ARQ736, PLX3603 (RO5212054), and RAF265. Therapeutic resistance has been identified and various mechanisms described. This review also discussed the current understanding of B-Raf signaling mechanism, methods of mutation detection, treatment strategies as well as potential methods of overcoming therapeutic resistance.

Context.—Glandular lesions of the urinary bladder include a broad spectrum of entities ranging from completely benign glandular lesions to primary and secondary malignancies. Common benign bladder lesions that exhibit glandular differentiation include cystitis cystica, cystitis glandularis, von Brunn nests, nephrogenic adenoma, intestinal metaplasia, urachal remnant, endometriosis, and prostatic-type polyp. The World Health Organization defines primary adenocarcinoma of the bladder as an epithelial malignancy with pure glandular differentiation without evidence of typical urothelial carcinoma. Malignant lesions that should be included in the differential diagnosis of a primary adenocarcinoma of the bladder include noninvasive and invasive urothelial carcinoma with glandular differentiation and secondary malignancies involving the bladder by direct extension or metastasis. The recognition and distinction of these different entities may be a challenge for pathologists, but they are of great clinical importance. Objective.—To review features of primary bladder adenocarcinoma as well as those entities that need to be differentiated from primary bladder adenocarcinoma, with emphasis on clinical findings, pathologic characteristics, and immunoprofiles. Data Sources.—Selected original articles published in the PubMed service of the US National Library of Medicine. Conclusions.—The accurate diagnosis of adenocarcinoma of the urinary bladder is important and challenging. It has to prompt an extensive clinical workup to rule out other glandular lesions in the urinary bladder, especially the possibility of secondary involvement of the bladder by an adenocarcinoma from a different site.

Background: In clinical practice it is a common challenge to correctly classify disease against normal cases and to identify disease subtypes. In complex diseases such as cancer where patterns are heterogeneous, highly complex interaction of pathways are involved, and continuous multi-level genomic changes occur, this is a challenging task. Using genomics data, analyzed by un-supervised and supervised machine learning tools, we demonstrate the ability to quantitatively and accurately describe a patient's tumor. Design: We used Level III RNASeq gene expression data from 20531 genes in 889 tumor samples of RCC across three subtypes - clear cell renal cell carcinoma (CCRCC), papillary renal cell carcinoma (PRCC), chromophobe carcinoma (ChRCC) and 129 normal samples from the Cancer Genome Atlas (TCGA). We developed a computational framework for feature (gene/transcript) selection and subtype predictive model construction. This framework relies on a well-known “random forest” (RF) method with iterative feature selection and 10-fold cross-validation. We performed a series of (1) tumor vs normal tissue experiments for each subtype; (2) pairwise subtype comparison, and finally (3) all three subtypes comparison and predictive genes identification. Results: In each computational run our method detected 2054 (10%) top varying genes, and estimated the predictive power of each of the selected genes using RF. On average this method demonstrated 93-97% accuracy. We identified genes known to play a role in renal cell carcinoma for example, CA9, LOX, SFRP1, SLC4A1, CDKN2A, KISS1R, EGF and others. In addition, our analysis uncovered genes that may represent characteristic patterns for subtyping and differentiation from normal renal tissue cells, for example TCF21, IRX1, STC2, UMOD, AQP2, ANGPTL4, BSND and FABP7, genes not previously associated with renal cell carcinoma. In three different experiments we differentiated each of the three subtypes from normal tissue, and performed enrichment analysis for the top most significant genes in each case. We observed that both CCRCC and PRCC have genes involved in the “glycosaminoglycan biosynthesis - heparan sulfate” (HS6ST2, HS6ST3) and “riboflavin metabolism” (ACPP) pathways. Whereas ChRCC is more strongly associated with the “glycosphingolipid biosynthesis - lacto and neolacto series” pathway (B3GNT3, FUT6) and have five genes (B3GNT3, CYP2B6, CYP2J2, FUT6, UGT2A3) involved in other metabolic pathways. Changes in glycosaminoglycan and glycolipid were also previously reported for associations with RCC. Conclusions: We demonstrate the effectiveness of a computational framework and predictive power of gene expression data for tumor subtyping in RCC. Our framework is generic and can be applied in combination with other types of data such as different modalities of genomic data (copy number variations, methylation) as well as clinical data. Citation Format: Konstantin Volyanskyy, Yong Mao, Yee Him Cheung, Balaji Santhanam, Vlado Menkovski, Zharko Aleksovski, Minghao Zhong, John T. Fallon, Nevenka Dimitrova. Normal versus tumor and subtype prediction in renal cell carcinoma TCGA data sets. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3651.

Presenilins (PS1/PS2) regulate proteolysis of beta-amyloid precursor protein (betaAPP) and affect its intracellular trafficking. Here, we demonstrate that a PS1-interacting protein, phospholipase D1 (PLD1), affects intracellular trafficking of betaAPP. Overexpression of PLD1 in PS1wt cells promotes generation of betaAPP-containing vesicles from the trans-Golgi network. Conversely, inhibition of PLD1 activity by 1-butanol decreases betaAPP trafficking in both wt and PS1-deficient cells. The subcellular localization of PLD1 is altered, and PLD enzymatic activity is reduced in cells expressing familial Alzheimer's disease (FAD) PS1 mutations compared with PS1wt cells. Overexpression of wt, but not catalytically inactive, PLD1 increases budding of betaAPP-containing vesicles from the trans-Golgi network in FAD mutant cells. Surface delivery of betaAPP is also increased by PLD1 in these cells. The impaired neurite outgrowth capacity in FAD mutant neurons was corrected by introducing PLD1 into these cells. The results indicate that PLD1 may represent a therapeutic target for rescuing compromised neuronal function in AD.

IFN-γ treatment of cells leads to tyrosine phosphorylation of signal transducer and activator of transcription (STAT) 1 followed by dimerization through a reciprocal Src homology 2–phosphotyrosine interaction near the –COOH end of each monomer, forming a parallel structure that accumulates in the nucleus to drive transcription. Prompt dephosphorylation and return to the cytoplasm completes the activation–inactivation cycle. Nonphosphorylated STATs dimerize, and a previously described interface between N-terminal domain (ND) dimers has been implicated in this dimerization. A new crystal structure of nonphosphorylated STAT1 containing the ND dimer has two possible configurations for the body of STAT1, one of which is antiparallel. In this antiparallel structure, the Src homology 2 domains are at opposite ends of the dimer, with the coiled:coil domain of one monomer interacting reciprocally with the DNA-binding domain of its partner. Here, we find that mutations in either the coiled:coil/DNA-binding domain interface or the ND dimer interface block dimerization of nonphosphorylated molecules and cause a resistance to dephosphorylation in vivo and resistance to a tyrosine phosphatase in vitro . We conclude that a parallel STAT1 phosphodimer not bound to DNA most likely undergoes a conformational rearrangement (parallel to antiparallel) to present the phosphotyrosine efficiently for dephosphorylation.

3Y1 rat fibroblasts overexpressing the epidermal growth factor (EGF) receptor (EGFR cells) become transformed when treated with EGF. A common response to oncogenic and mitogenic stimuli is elevated phospholipase D (PLD) activity. RalA, a small GTPase that functions as a downstream effector molecule of Ras, exists in a complex with PLD1. In the EGFR cells, EGF induced a Ras-dependent activation of RalA. The activation of PLD by EGF in these cells was dependent upon both Ras and RalA. In contrast, EGF-induced activation of Erk1, Erk2, and Jun kinase was dependent on Ras but independent of RalA, indicating divergent pathways activated by EGF and mediated by Ras. The transformed phenotype induced by EGF in the EGFR cells was dependent upon both Ras and RalA. Importantly, overexpression of wild-type RalA or an activated RalA mutant increased PLD activity in the absence of EGF and transformed the EGFR cells. Although overexpression of PLD1 is generally toxic to cells, the EGFR cells not only tolerated PLD1 overexpression but also became transformed in the absence of EGF. These data demonstrate that either RalA or PLD1 can cooperate with EGF receptor to transform cells.