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CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here, we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. Amplification of CSN5 is required for transformation of primary human breast epithelial cells by defined oncogenes. The transforming effects of CSN5 require CSN subunits for assembly of the full COP9 signalosome and the isopeptidase activity of CSN5, which potentiates the transcriptional activity of MYC. Transgenic inhibition of CSN5 isopeptidase activity blocks breast cancer progression evoked by MYC and RAS in vivo. These results highlight CSN5 isopeptidase activity in breast cancer progression, suggesting it as a therapeutic target in aggressive human breast cancers. [Cancer Res 2008;68(2):506–15]

Supplementary Figure Legends 1-2 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

Supplementary Tables 1-4 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

Supplementary Figure 1 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

Supplementary Figures 1-6 from CSN5 Isopeptidase Activity Links COP9 Signalosome Activation to Breast Cancer Progression

A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new genetic subtypes of cancers should be treated is unknown. Here, we show that a gene module map can guide the prospective identification of targeted therapies for genetic subtypes of cancer. By visualizing genome-scale gene expression in cancer as combinations of activated and deactivated functional modules, gene module maps can reveal specific functional pathways associated with each subtype that might be susceptible to targeted therapies. We show that in human breast cancers, activation of a poor-prognosis “wound signature” is strongly associated with induction of both a mitochondria gene module and a proteasome gene module. We found that 3-bromopyruvic acid, which inhibits glycolysis, selectively killed breast cells expressing the mitochondria and wound signatures. In addition, inhibition of proteasome activity by bortezomib, a drug approved for human use in multiple myeloma, abrogated wound signature expression and selectively killed breast cells expressing the wound signature. Thus, gene module maps may enable rapid translation of complex genomic signatures in human disease to targeted therapeutic strategies. [Cancer Res 2008;68(2):369–78]

Supplementary Figure 2 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

Background Telemedicine is an emerging field with numerous applications within medicine. Previous review articles describe its use within plastic surgery and otolaryngology but none, to the authors' knowledge, within dermatologic surgery. Objective To provide a review of the applications of telemedicine within dermatologic surgery. Materials and methods A PubMed search of articles published on teledermatology was conducted in July 2018. Articles were selected based on their relevance to dermatologic surgery and reviewed for their discussion of the applications of telemedicine in surgical and cosmetic dermatology. Results The initial search resulted in 156 articles. Eleven ultimately met inclusion criteria: 2 in referral and consultation, 5 in telepathology, 2 in intraoperative uses, and 2 in postprocedural care. Conclusion For preoperative consultation, teledermatology enables the surgeon to plan ahead and increases access to care by reducing the number of clinic visits. Telepathology has the potential to allow intraoperative consultation with a dermatopathologist to achieve accurate tumor clearance without delay. Smartglasses represent a promising technology for greater care coordination and a teaching tool. Postprocedural monitoring via text messaging provides convenient access to expert advice and early detection of postoperative complications. With increasing technologic advancements, telemedicine holds great potential to augment the dermatologic surgeon's daily practice.

Importance Innovative, online models of specialty-care delivery are critical to improving patient access and outcomes. Objective To determine whether an online, collaborative connected-health model results in equivalent clinical improvements in psoriasis compared with in-person care. Design, Setting, and Participants The Patient-Centered Outcomes Research Institute Psoriasis Teledermatology Trial is a 12-month, pragmatic, randomized clinical equivalency trial to evaluate the effect of an online model for psoriasis compared with in-person care. Participant recruitment and study visits took place at multicenter ambulatory clinics from February 2, 2015, to August 18, 2017. Participants were adults with psoriasis in Northern California, Southern California, and Colorado. The eligibility criteria were an age of 18 years or older, having physician-diagnosed psoriasis, access to the internet and a digital camera or mobile phone with a camera, and having a primary care physician. Analyses were on an intention-to-treat basis. Interventions Participants were randomized 1:1 to receive online or in-person care (148 randomized to online care and 148 randomized to in-person care). The online model enabled patients and primary care physicians to access dermatologists online asynchronously. The dermatologists provided assessments, recommendations, education, and prescriptions online. The in-person group sought care in person. The frequency of online or in-person visits was determined by medical necessity. All participants were exposed to their respective interventions for 12 months. Main Outcomes and Measures The prespecified primary outcome was the difference in improvement in the self-administered Psoriasis Area and Severity Index (PASI) score between the online and in-person groups. Prespecified secondary outcomes included body surface area (BSA) affected by psoriasis and the patient global assessment score. Results Of the 296 randomized participants, 147 were women, 149 were men, 187 were white, and the mean (SD) age was 49 (14) years. The adjusted difference between the online and in-person groups in the mean change in the self-administered PASI score during the 12-month study period was –0.27 (95% CI, –0.85 to 0.31). The difference in the mean change in BSA affected by psoriasis between the 2 groups was –0.05% (95% CI, –1.58% to 1.48%). Between-group differences in the PASI score and BSA were within prespecified equivalence margins, which demonstrated equivalence between the 2 interventions. The difference in the mean change in the patient global assessment score between the 2 groups was –0.11 (95% CI, –0.32 to 0.10), which exceeded the equivalence margin, with the online group displaying greater improvement. Conclusions and Relevance The online, collaborative connected-health model was as effective as in-person management in improving clinical outcomes among patients with psoriasis. Innovative telehealth delivery models that emphasize collaboration, quality, and efficiency can be transformative to improving patient-centered outcomes in chronic diseases. Trial Registration ClinicalTrials.gov Identifier:NCT02358135

Embryonic definitive endoderm (DE) generates the epithelial compartment of vital organs such as liver, pancreas, and intestine. However, purification of DE in mammals has not been achieved, limiting the molecular "definition" of endoderm, and hindering our understanding of DE development and attempts to produce endoderm from sources such as embryonic stem (ES) cells. Here, we describe purification of mouse DE using fluorescence-activated cell sorting (FACS) and mice harboring a transgene encoding enhanced green fluorescent protein (eGFP) inserted into the Sox17 locus, which is expressed in the embryonic endoderm. Comparison of patterns of signaling pathway activation in native mouse DE and endoderm-like cells generated from ES cells produced novel culture modifications that generated Sox17-eGFP⁺ progeny whose gene expression resembled DE more closely than achieved with standard methods. These studies also produced new FACS methods for purifying DE from nontransgenic mice and mouse ES cell cultures. Parallel studies of a new human SOX17-eGFP ES cell line allowed analysis of endoderm differentiation in vitro, leading to culture modifications that enhanced expression of an endoderm-like signature. This work should accelerate our understanding of mechanisms regulating DE development in mice and humans, and guide further use of ES cells for tissue replacement.

Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such activity are not known. Here we use an ultrahigh-density array that tiles the promoters of 56 cell-cycle genes to interrogate 108 samples representing diverse perturbations. We identify 216 transcribed regions that encode putative lncRNAs, many with RT-PCR–validated periodic expression during the cell cycle, show altered expression in human cancers and are regulated in expression by specific oncogenic stimuli, stem cell differentiation or DNA damage. DNA damage induces five lncRNAs from the CDKN1A promoter, and one such lncRNA, named PANDA, is induced in a p53-dependent manner. PANDA interacts with the transcription factor NF-YA to limit expression of pro-apoptotic genes; PANDA depletion markedly sensitized human fibroblasts to apoptosis by doxorubicin. These findings suggest potentially widespread roles for promoter lncRNAs in cell-growth control., National Institutes of Health (U.S.), National Institute of Arthritis and Musculoskeletal and Skin Diseases (U.S.) (NIAMS) (K08-AR054615)), National Cancer Institute (U.S.) (NIH/(NCI) (R01-CA118750)), National Cancer Institute (U.S.) (NIH/(NCI) R01-CA130795)), Juvenile Diabetes Research Foundation International, American Cancer Society, Howard Hughes Medical Institute (Early career scientist), Stanford University (Graduate Fellowship), National Science Foundation (U.S.) (Graduate Research Fellowship), United States. Dept. of Defense (National Defense Science and Engineering Graduate Fellowship)

Refined cancer models are required if researchers are to assess the burgeoning number of potential targets for cancer therapeutics in a clinically relevant context that allows a fast turnaround. Here we use tumor-associated genetic pathways to transform primary human epithelial cells from the epidermis, oropharynx, esophagus and cervix into genetically defined tumors in a human three-dimensional (3D) tissue environment that incorporates cell-populated stroma and intact basement membrane. These engineered organotypic tissues recapitulated natural features of tumor progression, including epithelial invasion through basement membrane, a complex process that is necessary for biological malignancy in 90% of human cancers. Invasion was rapid and was potentiated by stromal cells. Oncogenic signals in 3D tissue, but not 2D culture, resembled gene expression profiles from spontaneous human cancers. We screened 3D organotypic neoplasia with well-characterized signaling pathway inhibitors to distill a clinically faithful cancer gene signature. Multitissue 3D human tissue cancer models may provide an efficient and relevant complement to current approaches to characterizing cancer progression.

Large intervening non-coding RNAs (lincRNAs) are pervasively transcribed in the genome(1-3) yet their potential involvement in human disease is not well understood(4,5). Recent studies of dosage compensation, imprinting, and homeotic gene expression suggest that individual lincRNAs can function as the interface between DNA and specific chromatin remodelling activities(6-8). Here we show that lincRNAs in the HOX loci become systematically dys-regulated during breast cancer progression. The lincRNA termed HOTAIR is increased in expression in primary breast tumours and metastases, and HOTAIR expression level in primary tumours is a powerful predictor of eventual metastasis and death. Enforced expression of HOTAIR in epithelial cancer cells induced genome-wide re-targeting of Polycomb repressive complex 2 (PRC2) to an occupancy pattern more resembling embryonic fibroblasts, leading to altered histone H3 lysine 27 methylation, gene expression, and increased cancer invasiveness and metastasis in a manner dependent on PRC2. Conversely, loss of HOTAIR can inhibit cancer invasiveness, particularly in cells that possess excessive PRC2 activity. These findings indicate that lincRNAs have active roles in modulating the cancer epigenome and may be important targets for cancer diagnosis and therapy

CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here, we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. Amplification of CSN5 is required for transformation of primary human breast epithelial cells by defined oncogenes. The transforming effects of CSN5 require CSN subunits for assembly of the full COP9 signalosome and the isopeptidase activity of CSN5, which potentiates the transcriptional activity of MYC. Transgenic inhibition of CSN5 isopeptidase activity blocks breast cancer progression evoked by MYC and RAS in vivo. These results highlight CSN5 isopeptidase activity in breast cancer progression, suggesting it as a therapeutic target in aggressive human breast cancers. [Cancer Res 2008;68(2):506–15]

The 4,5-diarylated-1H-pyrrole-2-carboxylates 3-8 have each been prepared as hybrids of the potent anti-mitotic agent combretastatin A-4 (1) and the similarly active marine alkaloid lamellarin T (2). The key steps involved selective lithium-for-halogen exchange at C5 within the N-PMB protected 4,5-dibromopyrrole 22 and Negishi cross-coupling of the derived zincated species with the relevant aryl iodide. The ensuing 5-aryl-4-bromopyrrole then engaged in Suzuki-Miyaura cross-coupling with the appropriate arylboronic acid to give the 4,5-diarylated pyrroles 4, 6 and 8. TFA-promoted removal of the N-PMB group within these last compounds then gave the N-unsubstituted congeners 3, 5 and 7. Compounds 3-8 have all been evaluated for their anti-mitotic and cytotoxic properties and two of them, 3 and 5, display useful activities although they are less potent than combretastatin A-4.

The Pd0-catalysed cross-coupling of intact pyrroles with various reaction partners is reviewed. Coverage includes the Buchwald-Hartwig, carbonylation, Heck, Kumada, Negishi, Sonogashira, Stille, Suzuki-Miyaura, Tsuji-Trost, and (Pd0-catalysed) Ullmann reactions. Some emphasis is given to the application of such processes in the synthesis of pyrrole-containing natural products.

Compound 3, representing the tetra-O-methyl ether derivative of structure, 1, assigned to the cytotoxic marine alkaloid halitulin, has been assembled in a convergent manner from the readily available building blocks 5, 6 and 11.

The synthesis of ABE tricyclic analogues 18 of the alkaloid methyllycaconitine 1 is described. The analogues contain the key pharmacophore reputed to be responsible for the biological activity of methyllycaconitine 1, namely, a homocholine motif formed from a tertiary N-ethylamine in a 3-azabicyclo[3.3.1]nonane ring system and a 2-(3-methyl-2,5-dioxopyrrolin-1-yl)benzoate ester side chain. The 3-azabicyclo[3.3.1]nonane ring system 10 was assembled via a double Mannich reaction of ethyl 3-(but-3′-enyl)-2-oxocyclohexane-1-carboxylate 9 with ethylamine and formaldehyde. Attempts to append a B ring to this AE ring system via McMurray coupling of dialdehyde 5 were hampered by the inability to effect conversion of the C-9 ketone 10 to vinyl ether 6. Wittig methylenation of ketone 10 afforded diene 7, however, subsequent attempts to effect double hydroboration–oxidation of diene 7 failed to realise diol 11enroute to the key dialdehyde precursor 5 required for the McMurray coupling. Wacker oxidation of the homoallyl group of 10 afforded methyl ketone 12 which underwent intramolecular aldol condensation to form enone 13. After selective reduction of the ketone and methylation, the resultant methyl ethers 15 underwent reduction of the ester sidechain affording neopentyl substituted alcohols 16. Finally, the 2-(3-methyl-2,5-dioxopyrrolin-1-yl)benzoate ester sidechain was appended by treatment of alcohols 16 with N-(trifluoroacetyl)anthranilic acid followed by fusion of the resultant anthranilates 17 with methylsuccinic anhydride.

The title compound 1 has been prepared, for the first time, in six steps and a completely stereo-controlled fashion from the cis-1,2-dihydrocatechol 3. The starting material is a readily available and enantiopure compound that can be obtained in large quantity ia toluene dioxygenase (TDO) mediated dihydroxylation of iodobenzene.

Compound 1, the structure of which has been assigned to the marine natural product haliclorensin, was prepared by an unambiguous synthetic pathway and subjected to spectroscopic analysis. The derived data do not match those reported for the natural product.

The title compounds 1 and 2, which are effective and specific inhibitors of phosphohexomutases, have been prepared in enantiomerically pure form from toluene. The initial step of the reaction sequence involves enzymatic cis-1,2-dihydroxylation of toluene by E. coli JM109 (pDTG601) to give the cis-1,2-dihydrocatechol 3. The latter compound is then converted, ia a series of chemical oxidation and reduction steps, into compounds 1 and 2. The X-ray crystal structures of the bis-acetonide derivatives 11, 13 and 14 have been determined.

It has been hypothesized that neoplastic progression develops as a consequence of an acquired genetic instability and the subsequent evolution of clonal populations with accumulated genetic errors1. Accordingly, human cancers and some premalignant lesions contain multiple genetic abnormalities not present in the normal tissues from which the neoplasms arose2,3. Barrett oesophagus (BE) is a premalignant condition which predisposes to oesophageal adenocarcinoma (EA) that can be biopsied prospectively over time because endoscopic surveillance is recommended for early detection of cancer4,5. In addition, oesophagectomy specimens frequently contain the premalignant epithelium from which the cancer arose6. Neoplastic progression in BE is associated with alterations in TP53 (also known as p53) and CDKN2A (also known as p16) and non-random losses of heterozygosity 7−11 (LOH). Aneuploid or increased 4N populations occur in more than 90−95% of EAs, arise in premalignant epithelium and predict progression10,12,13. We have previously shown in small numbers of patients that disruption of TP53 and CDKN2A typically occurs before aneuploidy and cancer 10,11,14,15 . Here, we determine the evolutionary relationships of non-random LOH, TP53 and CDKN2A mutations, CDKN2A CpG-island methylation and ploidy during neoplastic progression. Diploid cell progenitors with somatic genetic or epigenetic abnormalities in TP53 and CDKN2A were capable of clonal expansion, spreading to large regions of oesophageal mucosa. The subsequent evolution of neoplastic progeny frequently involved bifurcations and LOH at 5q, 13q and 18q that occurred in no obligate order relative to each other, DNA-content aneuploidy or cancer. Our results indicate that clonal evolution is more complex than predicted by linear models.

The ability of cancers to grow indefinitely has fueled the idea that cancer and stem cells may have common underlying mechanisms. Detailed gene expression maps have now shown the diversity and distinctiveness in gene expression programs associated with stemness in embryonic and adult stem cells. These maps have further revealed a shared transcriptional program in embryonic stem cells (ESC) and cancer stem cells. Surprisingly, forced activation of an ESC-like gene expression program in adult epithelial cells can reprogram them into human cancer stem cells and achieve pathologic self-renewal. The ability to create induced cancer stem cells (iCSC) may provide opportunities to better define the biology of cancer stem cells in order to trace or eliminate them in human patients.

The marine natural products (±)-longamide (1), (±)-longamide B methyl ester (2), (±)-longamide B (3) and (±)-hanishin (4), each of which embodies a pyrroloketopiperazine core, have been synthesised in a concise fashion from pyrrole.

Proliferation of human mammary epithelial cells (HMEC) is limited to a few passages in culture due to an arrest in G1 termed selection or mortality stage 0, M0. A small number of cells spontaneously escape M0, continue to proliferate in culture, and then enter a second mortality stage, M1, at which they senesce. Evidence that M0 involves the Rb pathway comes from the observation that expression of human papillomavirus type 16 E7 alleviates the M0 proliferation block, and we further show that the Rb-binding region of E7 is required to allow cells to bypass M0. In contrast, E6 does not prevent HMEC from entering M0 but, rather, is involved in M1 bypass. Here we show that inactivation of the D-type cyclin-dependent kinase inhibitor p16INK4A is associated with escape from the M0 proliferation block. Early-passage HMEC express readily detectable amounts of p16 protein, whereas normal or E6-expressing HMEC that escaped M0 expressed markedly reduced amounts of p16 mRNA and protein. This initial reduction of p16 expression was associated with limited methylation of the p16 promoter region CpG island. At later passages, a further reduction in p16 expression occurred, accompanied by increased CpG island methylation. In contrast, reduction of p16 expression did not occur in E7-expressing HMEC that bypassed M0, due to inactivation of Rb. These observations in the E6-expressing HMEC correlate well with the finding that CpG island methylation is a mechanism of p16 inactivation in the development of human tumors, including breast cancer.

VOLUME 56, NO. 3, 2002 Current affiliations: Division of Gastroenterology and Hepatology, Department of Medicine, Department of Pathology, and Department of Radiology, Veterans Affairs Palo Alto Health Care System and Stanford University School of Medicine, Palo Alto, California. Reprint requests: Roy M. Soetikno, MD, Chief of Endoscopy, Veterans Affairs Palo Alto Health Care System, 3801 Miranda Ave., GI-111, Palo Alto, CA 94305. 37/4/126619 doi:10.1067/mge.2002.126619 S Friedland, A Yu, R Rouse, et al. Gastric pancreatic rest leading to pyogenic liver abscess

Little is known about genes that govern the development of the definitive endoderm in mammals; this germ layer gives rise to the intestinal epithelium and various other cell types, such as hepatocytes, derived from the gut. The discovery that the rat hepatocyte transcription factor HNF3 is similar to the Drosophila forkhead gene, which plays a critical role in gut development in the fly, led us to isolate genes containing the HNF3/forkhead (HFH) domain that are expressed in mouse endoderm develop ment. We recovered mouse HNF3β from an embryo cDNA library and found that the gene is first expressed in the anterior portion of the primitive streak at the onset of gastrulation, in a region where definitive endoderm first arises. Its expression persists in axial structures derived from the mouse equivalent of Hensen’s node, namely definitive endoderm and notochord, and in the ventral region of the developing neural tube. Expression of the highly related gene, HNF3α, appears to initiate later than HNF3P and is first seen in midline endoderm cells. Expression. subsequently appears in notochord, ventral neural tube, and gut endoderm in patterns similar to HNF3β. Microscale DNA binding assays show that HNF3 proteins are detectable in the midgut at 9.5 days p.c. At later stages HNF3 mRNAs and protein are expressed strongly in endoderm-derived tissues such as the liver. HNF3 is also the only known hepatocyte enriched transcription factor present in a highly de-dif ferentiated liver cell line that retains the capacity to re differentiate to the hepatic phenotype. Taken together, these studies suggest that HNF3α and HNF3β are involved in both the initiation and maintenance of the endodermal lineage. We also discovered a novel HFH containing gene, HFH-ES.1, that is expressed transiently in posterior ectoderm and mesoderm at the primitive streak stage, and later predominantly in the neural tube. HFH-ES.1 is highly similar in structure and expression profile to the Drosophila HFH gene FD4, suggesting that HFH family members have different, evolutionarily conserved roles in development.

The marine natural products (±)-longamide (1), (±)-longamide B methyl ester (2), (±)-longamide B (3) and (±)-hanishin (4), each of which embodies a pyrroloketopiperazine core, have been synthesised in a concise fashion from pyrrole.

The title compound 1 has been prepared, for the first time, in six steps and a completely stereo-controlled fashion from the cis-1,2-dihydrocatechol 3. The starting material is a readily available and enantiopure compound that can be obtained in large quantity ia toluene dioxygenase (TDO) mediated dihydroxylation of iodobenzene.

Major clinical issues in bladder cancer include the identification of prediction markers and novel therapeutic targets for invasive bladder cancer. In the current study, we describe the isolation and characterization of a tumor-initiating cell (T-IC) subpopulation in primary human bladder cancer, based on the expression of markers similar to that of normal bladder basal cells (Lineage-CD44 + CK5 + CK20 − ). The bladder T-IC subpopulation was defined functionally by its enriched ability to induce xenograft tumors in vivo that recapitulated the heterogeneity of the original tumor. Further, molecular analysis of more than 300 bladder cancer specimens revealed heterogeneity among activated oncogenic pathways in T-IC (e.g., 80% Gli1, 45% Stat3, 10% Bmi-1, and 5% β-catenin). Despite this molecular heterogeneity, we identified a unique bladder T-IC gene signature by gene chip analysis. This T-IC gene signature, which effectively distinguishes muscle-invasive bladder cancer with worse clinical prognosis from non-muscle-invasive (superficial) cancer, has significant clinical value. It also can predict the progression of a subset of recurring non-muscle-invasive cancers. Finally, we found that CD47, a protein that provides an inhibitory signal for macrophage phagocytosis, is highly expressed in bladder T-ICs compared with the rest of the tumor. Blockade of CD47 by a mAb resulted in macrophage engulfment of bladder cancer cells in vitro. In summary, we have identified a T-IC subpopulation with potential prognostic and therapeutic value for invasive bladder cancer.

The skin is the largest organ of the body and is critical to survival of the organism as a barrier to the environment and for thermal regulation and hydration retention. In order to serve these critical functions, the skin is constantly undergoing renewal and possesses the capacity for repair of wounds, which are dependent on the multiple types of stem cells in the skin. Engineered skin substitutes have a critical medical application to patients with extensive burn wounds. However, current skin substitutes do not restore the normal skin anatomy, lacking the normal appendages of skin including hair follicles, sebaceous glands, and sweat glands as well as the normal mechanical properties of the skin. Advances in stem cell biology and skin morphogenesis hold promise for the ability to markedly improve the engineering of skin substitutes that would ideally be indistinguishable from normal skin.

The prevention of autoimmunity requires the elimination of self-reactive T cells during their development and maturation. The expression of diverse self-antigens by stromal cells in the thymus is essential to this process and depends, in part, on the activity of the autoimmune regulator (Aire) gene. Here we report the identification of extrathymicAire-expressing cells (eTACs) resident within the secondary lymphoid organs. These stromally derived eTACs express a diverse array of distinct self-antigens and are capable of interacting with and deleting naïve autoreactive T cells. Using two-photon microscopy, we observed stable antigen-specific interactions between eTACs and autoreactive T cells. We propose that such a secondary network of self-antigen–expressing stromal cells may help reinforce immune tolerance by preventing the maturation of autoreactive T cells that escape thymic negative selection.

A major goal of cancer research is to match specific therapies to molecular targets in cancer. Genome-scale expression profiling has identified new subtypes of cancer based on consistent patterns of variation in gene expression, leading to improved prognostic predictions. However, how these new genetic subtypes of cancers should be treated is unknown. Here, we show that a gene module map can guide the prospective identification of targeted therapies for genetic subtypes of cancer. By visualizing genome-scale gene expression in cancer as combinations of activated and deactivated functional modules, gene module maps can reveal specific functional pathways associated with each subtype that might be susceptible to targeted therapies. We show that in human breast cancers, activation of a poor-prognosis “wound signature” is strongly associated with induction of both a mitochondria gene module and a proteasome gene module. We found that 3-bromopyruvic acid, which inhibits glycolysis, selectively killed breast cells expressing the mitochondria and wound signatures. In addition, inhibition of proteasome activity by bortezomib, a drug approved for human use in multiple myeloma, abrogated wound signature expression and selectively killed breast cells expressing the wound signature. Thus, gene module maps may enable rapid translation of complex genomic signatures in human disease to targeted therapeutic strategies. [Cancer Res 2008;68(2):369–78]

The title compounds 1 and 2, which are effective and specific inhibitors of phosphohexomutases, have been prepared in enantiomerically pure form from toluene. The initial step of the reaction sequence involves enzymatic cis-1,2-dihydroxylation of toluene by E. coli JM109 (pDTG601) to give the cis-1,2-dihydrocatechol 3. The latter compound is then converted, ia a series of chemical oxidation and reduction steps, into compounds 1 and 2. The X-ray crystal structures of the bis-acetonide derivatives 11, 13 and 14 have been determined.

CpG island methylation plays an important role in normal cellular processes, such as genomic imprinting and X-chromosome inactivation, as well as in abnormal processes, such as neoplasia. However, the dynamics of de novo CpG island methylation, during which a CpG island is converted from an unmethylated, active state to a densely methylated, inactive state, are largely unknown. It is unclear whether the development of de novo CpG island methylation is a progressive process, in which a subset of CpG sites are initially methylated with a subsequent increase in methylation density, or a single event, in which the initial methylation event encompasses the entire CpG island. The tumor suppressor gene p16/CDKN2a/INK4a (p16) is inactivated by CpG island methylation during neoplastic progression in a variety of human cancers. We investigated the development of methylation in the p16 CpG island in primary human mammary epithelial cell strains during escape from mortality stage 0 (M(0)) growth arrest. The methylation status of 47 CpG sites in the p16 CpG island on individual DNA molecules was determined by sequencing PCR clones of bisulfite-treated genomic DNA. The p16 CpG island was initially methylated at a subset of sites in three discrete regions in association with p16 transcriptional repression and escape from M(0) growth arrest. With continued passage, methylation gradually increased in density and methylation expanded to sites in adjacent regions. Thus, de novo methylation in the p16 CpG island is a progressive process that is neither site specific nor completely random but instead is region specific. Our results suggest that early detection of methylation in the CpG island of the p16 gene will require methylation analysis of the three regions and that the identification of region-specific methylation patterns in other genes may be essential for an accurate assessment of methylation-mediated transcriptional silencing.

The product of the p16/INK4a/CDKN2/MTS1 tumor-suppressor gene acts as a negative cell cycle regulator by inhibiting G 1 cyclindependent kinases that phosphorylate the retinoblastoma protein. p16 is inactivated in a wide range of human malignancies, including familial melanoma. However, its expression and function in sporadic melanoma has not been extensively investigated. We studied p16 expression in 62 archival melanomas and 30 archival nevi and lentigines by immunohistochemistry. Eighteen of 26 (69%) superficial spreading melanomas, 17 of 28 (61%) nodular melanomas, all of three lentigo maligna melanomas, and all of five melanoma metastases were found to harbor less than 10% p16-positive tumor cells. In contrast, only six of 24 (25%) nevi had less than 10% positive cells. No correlation between tumor thickness and loss of p16 expression was found. Using DNA from micro-dissected tumor and matched normal tissues, five of seven (71%) p16-negative melanoma cases had 9p21 loss of heterozygosity (LOH), and one of these 9p21 LOH cases had promoter region hypermethylation of the remaining p16 allele. These data demonstrate that partial or complete loss of p16 expression is prevalent in sporadic melanoma and is frequently associated with 9p21 LOH.

We have identified three new members of the olfactory receptor (OR) gene family within a large segment of DNA that is duplicated with high similarity near many human telomeres. This segment is present at 3q, 15q, and 19p in each of 45 unrelated humans sampled from various populations. Additional copies are present polymorphically at 11 other subtelomeric locations. The frequency with which the block is present at some locations varies among populations. While humans carry seven to 11 copies of the OR-containing block, it is located in chimpanzee and gorilla predominantly at a single site, which is not orthologous to any of the locations in the human genome. The observation that sequences flanking the OR-containing segment are duplicated on larger and different sets of chromosomes than the OR block itself demonstrates that the segment is part of a much larger, complex patchwork of subtelomeric duplications. The population analyses and structural results suggest the types of processes that have shaped these regions during evolution. From its sequence, one of the OR genes in this duplicated block appears to be potentially functional. Our findings raise the possibility that functional diversity in the OR family is generated in part through duplications and inter-chromosomal rearrangements of the DNA near human telomeres.

BACKGROUND: Dermatomyositis (DM) is an autoimmune disease that mainly affects the skin, muscle, and lung. The pathogenesis of skin inflammation in DM is not well understood. METHODOLOGY AND FINDINGS: We analyzed genome-wide expression data in DM skin and compared them to those from healthy controls. We observed a robust upregulation of interferon (IFN)-inducible genes in DM skin, as well as several other gene modules pertaining to inflammation, complement activation, and epidermal activation and differentiation. The interferon (IFN)-inducible genes within the DM signature were present not only in DM and lupus, but also cutaneous herpes simplex-2 infection and to a lesser degree, psoriasis. This IFN signature was absent or weakly present in atopic dermatitis, allergic contact dermatitis, acne vulgaris, systemic sclerosis, and localized scleroderma/morphea. We observed that the IFN signature in DM skin appears to be more closely related to type I than type II IFN based on in vitro IFN stimulation expression signatures. However, quantitation of IFN mRNAs in DM skin shows that the majority of known type I IFNs, as well as IFN g, are overexpressed in DM skin. In addition, both IFN-beta and IFN-gamma (but not other type I IFN) transcript levels were highly correlated with the degree of the in vivo IFN transcriptional response in DM skin. CONCLUSIONS AND SIGNIFICANCE: As in the blood and muscle, DM skin is characterized by an overwhelming presence of an IFN signature, although it is difficult to conclusively define this response as type I or type II. Understanding the significance of the IFN signature in this wide array of inflammatory diseases will be furthered by identification of the nature of the cells that both produce and respond to IFN, as well as which IFN subtype is biologically active in each diseased tissue.

The kindled-convulsion model was used to assess the development of tolerance and cross tolerance to the anticonvulsant effects of antiepileptic drugs. In Experiment 1, tolerance developed to the anticonvulsant effects of bidaily (one every 48 h) IP injections of phenobarbital, trimethadione, and clonazepam on convulsions elicited 1 h after each injection in kindled rats by amygdala stimulation. In Experiment 2, kindled rats that were tolerant to the anticonvulsant effects of phenobarbital, trimethadione, or clonazepam received bidaily IP injections of carbamazepine, each followed 1 h later by a convulsive amygdala stimulation. There was a statistically significant transfer of tolerance from phenobarbital to carbamazepine, but not from either trimethadione or clonazepam to carbamazepine. Apparently, tolerance to anticonvulsant drugs is most likely to transfer between drugs that are effective against similar kinds of clinical and experimental seizures and have similar putative mechanisms of action.

Global gene expression patterns can provide comprehensive molecular portraits of biologic diversity and complex disease states, but understanding the physiologic meaning and genetic basis of the myriad gene expression changes have been a challenge. Several new analytic strategies have now been developed to improve the interpretation of microarray data. Because genes work together in groups to carry out specific functions, defining the unit of analysis by coherent changes in biologically meaningful sets of genes, termed modules, improves our understanding of the biological processes underlying the gene expression changes. The gene module approach has been used in exploratory discovery of defective oxidative phosphorylation in diabetes mellitus and also has allowed definitive hypothesis testing on a genomic scale for the relationship between wound healing and cancer and for the oncogenic mechanism of cyclin D. To understand the genetic basis of global gene expression patterns, computational modeling of regulatory networks can highlight key regulators of the gene expression changes, and many of these predictions can now be experimentally validated using global chromatin-immunoprecipitation analysis.