Integrated Proteogenomic Analysis Reveals Distinct Potentially Actionable Therapeutic Vulnerabilities in Triple-Negative Breast Cancer Subtypes.

Triple-negative breast cancer (TNBC) is characterized by an aggressive clinical presentation and a paucity of clinically actionable genomic alterations. Here, we utilized the Cancer Genome Atlas (TCGA) to explore the proteogenomic landscape of TNBC subtypes to see whether genomic alterations can be inferred from proteomic data. We found only 4% of the protein level changes are explained by mutations, while 21% of the protein and 35% of the transcriptomics changes were determined by copy number alterations (CNAs).

A Multi-Center Clinical Study to Harvest and Characterize Circulating Tumor Cells from Patients with Metastatic Breast Cancer Using the Parsortix PC1 System.

Circulating tumor cells (CTCs) captured from the blood of cancer patients may serve as a surrogate source of tumor material that can be obtained via a venipuncture (also known as a liquid biopsy) and used to better understand tumor characteristics. However, the only FDA-cleared CTC assay has been limited to the enumeration of surface marker-defined cells and not further characterization of the CTCs. In this study, we tested the ability of a semi-automated device capable of capturing and harvesting CTCs from peripheral blood based on cell size and deformability, agnostic of cell-surface markers (the Parsortix PC1 System), to yield CTCs for evaluation by downstream techniques commonly available in clinical laboratories.

Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer.

Background: Metastatic breast cancer (MBC) and the circulating tumor cells (CTCs) leading to macrometastases are inherently different than primary breast cancer. We evaluated whether whole transcriptome RNA-Seq of CTCs isolated via an epitope-independent approach may serve as a surrogate for biopsies of macrometastases.

Methods: We performed RNA-Seq on fresh metastatic tumor biopsies, CTCs, and peripheral blood (PB) from 19 newly diagnosed MBC patients.

DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds.

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential.

Identification of putative actionable alterations in clinically relevant genes in breast cancer.

Background: Individualising treatment in breast cancer requires effective predictive biomarkers. While relatively few genomic aberrations are clinically relevant, there is a need for characterising patients across different subtypes to identify actionable alterations.

Methods: We identified genomic alterations in 49 potentially actionable genes for which drugs are available either clinically or via clinical trials.

EP300 knockdown reduces cancer stem cell phenotype, tumor growth and metastasis in triple negative breast cancer.

Background: Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype with basal features, lacking the expression of receptors targeted successfully in other breast cancer subtypes. Treatment response to adjuvant and neoadjuvant chemotherapy is often short-lived and metastatic spread occurs at higher rates than other subtypes within the first five years after diagnosis. TNBCs exhibit stem cell features and are enriched for cancer stem cell (CSC) populations.

Idiopathic Bilateral Ovarian Vein Thrombosis in a Non-Pregnant Healthy Patient: A Case Report and Review of the Literature.

Ovarian vein thrombosis (OVT) is a potentially life-threatening condition, and it is typically related to the peripartum period; however, it is also associated with pelvic inflammatory disease, recent pelvic or abdominal surgery, inflammatory bowel disease, thrombophilia, malignancy, and sepsis. Idiopathic isolated OVT is rare and is usually presented as case reports in the medical literature. In this report, we present a case of bilateral OVT in a postmenopausal female with no identifiable risk factors and normal coagulation profile workup to highlight the importance of considering it as a differential diagnosis in female patients presenting with abdominal pain.

Increased risk of disseminated cryptococcal infection in a patient with multiple sclerosis on fingolimod.

Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system (CNS), with an estimated 2.3 million people being affected globally, and is a major cause of permanent disability. About 90 % of the affected patients with MS have relapsing-remitting type.

A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer.

The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs).

Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer.

Whole exome sequencing (WES), targeted gene panel sequencing and single nucleotide polymorphism (SNP) arrays are increasingly used for the identification of actionable alterations that are critical to cancer care. Here, we compared The Cancer Genome Atlas (TCGA) and the Genomics Evidence Neoplasia Information Exchange (GENIE) breast cancer genomic datasets (array and next generation sequencing (NGS) data) in detecting genomic alterations in clinically relevant genes. We performed an in silico analysis to determine the concordance in the frequencies of actionable mutations and copy number alterations/aberrations (CNAs) in the two most common breast cancer histologies, invasive lobular and invasive ductal carcinoma.

RNA-Seq of Circulating Tumor Cells in Stage II-III Breast Cancer.

Background: We characterized the whole transcriptome of circulating tumor cells (CTCs) in stage II-III breast cancer to evaluate correlations with primary tumor biology.

Methods: CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE/FACS). CTCs, PB, and fresh tumors were profiled using RNA-seq.

Challenges in using liquid biopsies for gene expression profiling.

Circulating tumor cells (CTCs) have potential utility as a surrogate biomarker of tumor biology via a liquid biopsy. The aim of this study was to evaluate if the nCounter NanoString assay could be used for accurate gene expression profiling of CTCs using the PAM50 research-use-only CodeSet. Analysis was performed on CTCs isolated by the ANGLE Parsortix system from healthy blood spiked with the breast cancer cell lines Hs578T, SkBr3, MDA-MB-231 or MCF7.

On genome annotation of Brucellaphage Gadvasu (BpG): discovery of ORFans for integrated systems biology approaches.

Brucellaphage Gadvasu (BpG) is a lytic phage infecting Brucella spp. Brucellaphages contain dsDNA as genetic material and are short-tailed particles with host-specificity. Here, we report the challenges on annotation in the complete genome sequence of BpG when compared with that of a recent broad host-range brucellaphage Pr, an original reference genome.

Synthesis of novel antimicrobial aryl himachalene derivatives from naturally occurring himachalenes.

Five new 2,9,9-trimethyl-6,7,8,9-tetrahydro-benzocyclohepten-5-ylidene-amine derivatives (16a-16e) were synthesized from α-dehydro-ar-himachalene (11) that was originally prepared from an isomeric mixture of α, β and γ himachalenes (10), the abundant sesquiterpenes of Cedrus deodara essential oil. In addition, different aryl himachalenes derivatives (9, 12, 14 and 15) were also formed from 11. The structures of the synthesized compounds were confirmed on the basis of their NMR, IR and mass spectral data.

The epigenome as a potential mediator of cancer and disease prevention in prenatal development.

Epigenetic events establish a particular gene expression signature for each cell type during differentiation and fertilization. Disruption of these epigenetic programs in response to environmental stimuli during prenatal exposure dysregulates the fetal epigenome, potentially impacting susceptibility to disease later in life (the fetal basis of adult disease). Maternal dietary modifications during gestation and lactation play a pivotal role in the period of fetal (re)programming.

Naturally occurring limonene to cinnamyl-type gamma-butyrolactone substituted aldol condensation derivatives as antioxidant compounds.

A method has been developed for the synthesis of gamma-butyrolactone substituted cinnamyl type Aldol condensation products under milder proline and triethylamine basic conditions. The antioxidant activity of all the synthesized compounds was assessed using three different assays. The cinnamyl type derivatives of gamma-butyrolactone bearing an -OH group in the benzene ring exhibited excellent antioxidant activity.

Naturally occurring himachalenes to benzocycloheptene amino vinyl bromide derivatives: as antidepressant molecules.

A new series of benzocycloheptene amino vinyl bromide derivatives (9a-9m) were synthesized from isomeric mixture of himachalenes through two-step synthesis. The unusual structure of benzocycloheptene amino vinyl bromide derivative (9a) was confirmed by NMR and X-ray crystallography analyses. The newly synthesized amino vinyl bromide derivatives of benzocycloheptene were further evaluated for their antidepressant activities.

An efficient microwave assisted extraction of phenolic compounds and antioxidant potential of Ginkgo biloba.

Flavonoid glycosides are a significant group of compounds found in Ginkgo biloba leaves, but the long extraction procedures in existing methods are a challenging problem. In this work, a microwave-assisted extraction (MAE) method has been developed for extracting bioactive compounds from G. biloba.

Epigenetic silencing of sFRP1 activates the canonical Wnt pathway and contributes to increased cell growth and proliferation in hepatocellular carcinoma.

The Wnt pathway is a key regulator of embryonic development and stem cells, and its aberrant activation is associated with human malignancies, most notably hepatocellular carcinoma (HCC). Epigenetic deregulation of the genes encoding the secreted frizzled-related proteins (sFRPs), the Wnt signalling antagonists, has been linked with aberrant hyperactivation of the Wnt signalling in HCC cells; however, the precise underlying mechanism remains elusive. We investigated the methylation profiles of Wnt antagonists in liver samples of different stages of HCC development and liver cancer cell lines and studied the functional impact of aberrant epigenetic silencing of sFRPs on the canonical Wnt pathway and cell viability.

Spatial and temporal variation of secondary metabolite profiles in Ginkgo biloba leaves.

Terpene trilactones (TTLs) are the main bioactive constituents of Ginkgo biloba used for the preparation of drugs for several ailments. Flavonoid glycosides (FGs) are the significant group of compounds found in Ginkgo leaves used in food and healthcare products. The variation in the content of bioactive constituents, as well as antioxidant activity, with respect to change in altitude and the time of sample collection was investigated.

Chemical fingerprint analysis of phenolics of Albizia chinensis based on ultra-performance LC-electrospray ionization-quadrupole time-of-flight mass spectrometry and antioxidant activity.

Albizia species have been shown to have anti-inflammatory and anti-allergic properties. However, efficient analytical methods for identification of their active constituents are still lacking. Ultra-performance liquid chromatography coupled with electrospray ionization-quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS) was used to study the phenolic composition of the ethanolic extracts of different parts (flowers, leaves, pods and bark) of A.

Antifungal sesquiterpenes from Cedrus deodara.

Two new sesquiterpenes, (E)-(2S,3S,6R)-atlantone-2,3-diol (1) and (E)-(2S,3S,6S)-atlantone-2,3,6-triol (2), along with two known sesquiterpenes, atlantolone (3) and (E)-α-atlantone (4), were isolated from Cedrus deodara Loud. The structures of the new compounds were elucidated on the basis of UV, IR, NMR, HR‑ESI-QTOF‑MS, and EI mass spectral studies. The n-hexane and chloroformextracts of sawdust and compounds 3 and 4 from the plant exhibited antifungal activity against Aspergillus flavus, A.

Chemical composition of hydrodistilled and solvent volatiles extracted from woodchips of Himalayan Cedrus: Cedrus deodara (Roxb.) Loud.

The essential oil and extract obtained from the wood chips of Cedrus deodara by hydrodistillation and percolation respectively have been analyzed by GC-FID and GC-MS techniques. Thirty four compounds were identified from the essential oil and twenty six from the extract accounting for 98.3 and 94.