Era of Molecular Diagnostics Techniques before and after the COVID-19 Pandemic.

Despite the growth of molecular diagnosis from the era of Hippocrates, the emergence of COVID-19 is still remarkable. The previously used molecular techniques were not rapid enough to screen a vast population at home, in offices, and in hospitals. Additionally, these techniques were only available in advanced clinical laboratories.The pandemic outbreak enhanced the urgency of researchers and research and development companies to invent more rapid, robust, and portable devices and instruments to screen a vast community in a cost-effective and short time. There has been noteworthy progress in molecular diagnosing tools before and after the pandemic. This review focuses on the advancements in molecular diagnostic techniques before and after the emergence of COVID-19 and how the pandemic accelerated the implantation of molecular diagnostic techniques in most clinical laboratories towardbecoming routine tests.

Potency of Moringa oleifera leaf extract and silver nanoparticles against immune, microbial and HT-29 colon cancer cells growth modulation.

Moringa oleifera plant grows in many countries worldwide and being utilized as a customary medication. The current study aimed to investigate the biological effect of Moringa oleifera leaf extract (MOE) alone or in combination with silver nanoparticles (AgNPs) on colon cancer, microbial cell growth. MOE was utilized in the green synthesis of AgNPs. The characterization of AgNPs was done by UV-Vis-spectrophotometry, X-ray diffraction (XRD) and scanning electron microscopy (SEM). MOE was tested for their sugars, active biomolecules, ROS, protein contents. Results revealed that created AgNPs are about 61 nm in diameter. There were no detectable sugar and protein in MOE, but it contains ROS and active biomolecules. MOE and MOE+AgNPs exerted mild antibacterial action and increased the number of apoptotic cells and p53 protein expression of HT-29 colon cancer cells. MOE and MOE+AgNPs could arrest HT-29 cells at G2/M phase and stimulate splenic cell growth. Both extract preparations showed antioxidant activities. Because MOE and MOE+AgNP stimulated immune cells and activated apoptosis in cancer cells, these preparations can be utilized as anticancer agents.

High-intensity focused ultrasound (HIFU) therapy for benign thyroid nodules: a 3-year retrospective multicenter follow-up study.

BACKGROUND: Outcomes of high-intensity focused ultrasound (HIFU), as a non-surgical treatment option for benign symptomatic thyroid nodules, has mainly been based on single-center studies and short-term follow-up. Therefore, we assessed the safety, and long-term efficacy of HIFU in benign thyroid nodules among four centers with expertise in thyroid mini-invasive procedures. PATIENTS AND METHODS: Retrospective three year follow-up study in four European centers, treating solid benign thyroid nodules causing pressure symptoms and/or cosmetic concerns. Nodule volume reduction was assessed at 1, 3, 6, 12, 24, and 36 months post-treatment. Technical efficacy, defined as a volume reduction rate (VVR) >50% was evaluated at 6, 12, 24 and 36 months. Predictive factors of efficacy were assessed using logistic models. Complications and side effects were classified according to the Interventional Radiology Guidelines and changes in local symptoms were scored on a visual-analog scale. RESULTS: Sixty-five patients (mean age 51.1 ± 14.0 years; 86.2% women) with a single thyroid nodule and a mean baseline nodule volume of 9.8 ± 10.3 mL were treated with a mean energy of 7.1 ± 3.1 kJ (range: 2.0 to 15.5 kJ). Median nodule volume reduction was 31.5% (IQR: -38.6% to -23.1%) at 12 months and 31.9% (IQR: -36.4% to -16.1%) at 36 months. Technical efficacy was obtained in 17.2% of cases at 6 months, 17.8% at 12 months, 3.4% at 24 months, and 7.4% at 36 months. The number of treated pixels and the mean energy delivered were positively correlated to VRR at 1, 6 and 12 months. The risk of treatment failure decreased by 4.3% for each additional unit of energy delivered. The procedure duration was inversely correlated with treatment failure (OR 1.043, 95% CI: 1.011-1.083; p = 0.014). Improvement of cervical pressure symptoms or cosmetic complaints were observed in less than 15% of the cases at 12, 24 and 36 months. Horner's syndrome occurred in one case (1.5%) and minor complications, not requiring treatment, in three (4.6%) patients. No change in thyroid function was registered. CONCLUSIONS: HIFU carried a low risk of complications. A single treatment resulted in a 30-35% thyroid nodule volume decrease within one year, reduction that remained stable for 2 years. Outcomes varied significantly between centers with different HIFU expertise. Focus on improved HIFU technology, adequate training, and appropriate selection of patients is needed to achieve efficacy comparable to other thermal ablation procedures.

Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase overexpressing mice defines an immune-associated gene signature linked to tamoxifen resistance.

Response to breast cancer chemoprevention can depend upon host genetic makeup and initiating events leading up to preneoplasia. Increased expression of aromatase and estrogen receptor (ER) is found in conjunction with breast cancer. To investigate response or resistance to endocrine therapy, mice with targeted overexpression of Esr1 or CYP19A1 to mammary epithelial cells were employed, representing two direct pathophysiological interventions in estrogen pathway signaling. Both Esr1 and CYP19A1 overexpressing mice responded to letrozole with reduced hyperplastic alveolar nodule prevalence and decreased mammary epithelial cell proliferation. CYP19A1 overexpressing mice were tamoxifen sensitive but Esr1 overexpressing mice were tamoxifen resistant. Increased ER expression occurred with tamoxifen resistance but no consistent changes in progesterone receptor, pSTAT3, pSTAT5, cyclin D1 or cyclin E levels in association with response or resistance were found. RNA-sequencing (RNA-seq) was employed to seek a transcriptome predictive of tamoxifen resistance using these models and a second tamoxifen-resistant model, BRCA1 deficient/Trp53 haploinsufficient mice. Sixty-eight genes associated with immune system processing were upregulated in tamoxifen-resistant Esr1- and Brca1-deficient mice, whereas genes related to aromatic compound metabolic process were upregulated in tamoxifen-sensitive CYP19A1 mice. Interferon regulatory factor 7 was identified as a key transcription factor regulating these 68 immune processing genes. Two loci encoding novel transcripts with high homology to human immunoglobulin lambda-like polypeptide 1 were uniquely upregulated in the tamoxifen-resistant models. Letrozole proved to be a successful alternative to tamoxifen. Further study of transcriptional changes associated with tamoxifen resistance including immune-related genes could expand our mechanistic understanding and lead to biomarkers predictive of escape or response to endocrine therapies.

In silico Screening and Validation of Achyranthes aspera as a Potential Inhibitor of BRAF and NRAS in Controlling Thyroid Cancer.

BACKGROUND: Thyroid carcinoma (THCA) is one of the most prevalent endocrine tumors, accounting for 3.4% of all cancers diagnosed annually. Single Nucleotide Polymorphisms (SNPs) are the most prevalent genetic variation associated with thyroid cancer. Understanding thyroid cancer genetics will enhance diagnosis, prognosis, and treatment. METHODS: This TCGA-based study analyzes thyroid cancer-associated highly mutated genes through highly robust in silico techniques. Pathway, gene expression, and survival studies were performed on the top 10 highly mutated genes (BRAF, NRAS, TG, TTN, HRAS, MUC16, ZFHX3, CSMD2, EIFIAX, SPTA1). Novel natural compounds from Achyranthes aspera Linn were discovered to target two highly mutated genes. The natural compounds and synthetic drugs used to treat thyroid cancer were subjected to comparative molecular docking against BRAF and NRAS targets. The ADME characteristics of Achyranthes aspera Linn compounds were also investigated. RESULTS: The gene expression analysis revealed that the expression of ZFHX3, MCU16, EIF1AX, HRAS, and NRAS was up-regulated in tumor cells while BRAF, TTN, TG, CSMD2, and SPTA1 were down-regulated in tumor cells. In addition, the protein-protein interaction network demonstrated that HRAS, BRAF, NRAS, SPTA1, and TG proteins have strong interactions with each other as compared to other genes. The ADMET analysis shows that seven compounds have druglike properties. These compounds were further studied for molecular docking studies. The compounds MPHY012847, IMPHY005295, and IMPHY000939 show higher binding affinity with BRAF than pimasertib. In addition, IMPHY000939, IMPHY000303, IMPHY012847, and IMPHY005295 showed a better binding affinity with NRAS than Guanosine Triphosphate. CONCLUSION: The outcomes of docking experiments conducted on BRAF and NRAS provide insight into natural compounds with pharmacological characteristics. These findings indicate that natural compounds derived from plants as a more promising cancer treatment option. Thus, the results of docking investigations conducted on BRAF and NRAS substantiate the conclusions that the molecule possesses the most suited drug-like qualities. Compared to other compounds, natural compounds are superior, and they are also druggable. This demonstrates that natural plant compounds can be an excellent source of potential anti-cancer agents. The preclinical research will pave the road for a possible anti-cancer agent.

Evaluation of Cytotoxicity of the Methanolic Extract of Red Sea Marine Sponge Xestospongia Testudinaria and Its Related Compounds Against MCF-7 Human Breast Cancer Cells.

Background: Breast cancer is a leading cause of death and one of the most common fatal medical conditions in the world. Chemical compounds of various types have been identified in the Red Sea marine sponge Xestospongia testudinaria, including sterol esters, sterols, indole alkaloids, and brominated polyunsaturated fatty acids. These compounds have demonstrated promising biological features, which in cludes anti-inflammatory, cancer preventive, and antioxidant capacities. Methods: The cytotoxic potential of Xestospongia testudinaria was assessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and morphological alterations in MCF-7 cell line. Furthermore, the flow cytometry was also utilized to assess apoptosis and identify changes in the cell cycle; besides, cell migration was assessed by scratch wound-healing assay. Results: A significant dose-dependent decrease in the percentage of MCF-7 cell viability was observed with IC50 39.8 ug/mL. Functional studies were performed on MCF-7 to show that Xestospongia testudinaria raises apoptotic cell death and induces growth arrest at the G1/G0 while inhibiting cell migration in scratch assay. Conclusion: These results demonstrated that Xestospongia testudinaria extract has an inhibitory effect on breast cancer cells proliferation, migration and induce apoptosis. Thus, it holds great promise as a potential treatment for breast cancer.

Risk association of RANKL and OPG gene polymorphism with breast cancer to bone metastasis in Pashtun population of Khyber Pakhtunkhwa, Pakistan.

INTRODUCTION: The receptor activator NF-κB ligand (RANKL) and Osteoprotegrin (OPG) single nucleotide polymorphisms (SNPs) have been associated with the risk of breast cancer to bone metastasis. This study was designed to investigate the association of RANKL and OPG gene polymorphisms with breast to bone metastasis in Pashtun population of Khyber Pakhtunkhwa, Pakistan. MATERIALS AND METHODS: A total of 215 participants were enrolled containing 106 breast cancer patients, 58 breast to bone metastasis and 51 age and gender matched healthy controls. RANKL (rs9533156) and OPG (rs2073618, rs3102735) polymorphisms were genotyped in genomic DNA, using Tetra-ARMS PCR protocol. The results were analyzed among the three groups and P-value less then 0.05 were considered statistically significant. RESULTS: Our results displayed significant association of OPG (rs3102735) risk allele and corresponding genotypes in breast cancer vs healthy controls, bone metastasis vs healthy controls and breast cancer vs breast to bone metastasis as a disease risk. However, there was no association observed for OPG (rs2073618) risk allele and corresponding genotypes with the diseases risk. Similarly, RANKL (rs9533156) risk allele and corresponding genotypes in breast cancer vs healthy controls, bone metastasis vs healthy controls and breast cancer vs breast to bone metastasis exhibited significant association except for the risk allele carrying genotypes in breast to bone metastasis. CONCLUSION: OPG (rs3102735) and RANKL (rs9533156) exhibited significant association with breast to bone metastasis while OPG (rs2073618) didn't show significant association with breast to bone metastasis in Pashtun population of Pakistan. However, this study unlocks more questions to investigate the exact scenario of genetic predisposition of breast to bone metastasis.

Haematological Traits in Symptomatic and Asymptomatic COVID-19 Positive Patients for Predicting Severity and Hospitalization.

Objective: The present investigation aims on the clinical attributes and haematological parameters between symptomatic (COVID-19 ICU) and asymptomatic (COVID-19 homes isolation) patients as predisposing sign for COVID-19 related mortality. Materials and Methods: A retrospective cohort research was conducted of admitted patients to ICU, who were suffering from severe COVID-19 in Aseer Central Hospital, Abha, Kingdom of Saudi Arabia (KSA) from July 2020 until September 2020. The study included individuals with COVID -19 and ICU admission as symptomatic group and others who are COVID-19 positives with quarantine as asymptomatic group. Epidemiological, clinical and haematological laboratory data were retrospectively collected, analysed with control subjects. Results: Of the 38 ICU patients studied, the most common symptoms were fever and respiratory distress (100%), cough (86.8%). Majority were of Saudi origin (78.9%). Eighteen (47.4%) COVID-19 ICU patients showed leukocytosis, 6 (15.8%) had severe thrombocytopenia (with most having thrombocytopenia), 18 (47.4%) were anaemic. A significant correlation was observed between the WBC, RBC, Hb, platelets, neutrophil and lymphocyte count between ICU inmates compared with quarantine (p < 0.001) and RBC, Hb, neutrophil and lymphocyte count with control groups (p < 0.001). Conclusion: From the observations it is evident that, the blood tests have potential clinical value in predicting COVID-19 progression. Further, patient characteristics including age, leukocyte count, RBC, platelets and differential leukocyte counts may be significant predictors for monitoring the progression of the critical illness observed in SARS-COV-2 patients. Also, treatment procedures can be re-defined further to reduce COVID-19 mortalities in more critically ill COVID-19 individuals.

Evaluation of participation and performance indicators in a breast cancer screening program in Saudi Arabia.

OBJECTIVES: To evaluate early performance indicators for breast cancer screening at the King Abdulaziz University Hospital in Saudi Arabia. METHODS: This study retrospectively evaluated data from women who underwent their first breast cancer screening program in Jeddah, Saudi Arabia between 2012 and 2019. Data on screening results were used to estimate performance indicators and generate descriptive statistics. RESULTS: Of the 16000 women invited from 2012 to 2019, a total of 1911 (11.9%) participated. The majority of women (68.8%) were between 40 and 55 years old. Based on the screening process results, 26.6%, 40.1%, 9.7%, 1.3%, 0.7%, and 5.2% of women had BI-RADS scores of R1, R2, R3, R4, R5, and R0 respectively. The remaining 16.3% did not have mammogram records. The recall rate, or the percentage of women who underwent further evaluation, was 19.9%; 18.9% underwent a biopsy procedure. In addition, 1.6% of women had cancer screen-detected, although only 0.7% were diagnosed with breast cancer. CONCLUSION: In light of the low participation and high recall rates, it is essential that the screening program utilizes performance indicators to optimize resource utilization and ensure the quality of the service provided. Additionally, a national framework and standardized performance indicators could mitigate this problem for other cancer screening programs.

Long-Term Results of Ultrasound-Guided Radiofrequency Ablation of Benign Thyroid Nodules: State of the Art and Future Perspectives-A Systematic Review.

Background: Nearly 20 years after the first feasibility study, minimally invasive ultrasound (US)-guided therapeutic techniques are now considered as a safe and effective alternative to surgery for symptomatic benign thyroid nodules. Radiofrequency ablation (RFA) is one of the most widely used treatment in specialized thyroid centers but, due to the relatively recent introduction into clinical practice, there are limited long-term follow-up studies. Aim of our work was to review the outcomes of RFA on solid nonfunctioning and on autonomous thyroid nodules (AFTN) on a long-time period for assessing the results in term of efficacy, complications, and costs and to compare them to the current indications of RFA. Methods: A systematic review was performed using EMBASE and Medline library data between 2008 and 2021. Seventeen studies evaluated RFA for the treatment of benign solid (nonfunctioning or autonomous) thyroid nodules, with an at least 18 months of follow-up. Data extraction and quality assessment were performed by two endocrinologist according to PRISMA guidelines. Anthropometric data, safety and efficacy parameters were collected. Results: The majority of the studies was retrospective study and reported 933 nodules, mostly solid. Baseline volume ranged between 6.1 ± 9.6 and 36.3 ± 59.8 ml. Local analgesia was used and the time duration of the treatment was between 5 ± 2 and 22.1 ± 10.9 min. The volume reduction rate at 12 months ranged from 67% to 75% for the nodule treated with a single procedure and reached to 93.6 ± 9.7% for nodules treated with repeat ablations. The regrowth rate at 12 months ranged from 0% to 34%. Conclusion: All the studies under examination consistently validated the long-term clinical efficacy and the substantial safety of RFA for the treatment of benign thyroid nodules. Thermal ablation, however, is an operator-dependent technique and should be performed in centers with specific expertise. The selection of the patients should be rigorous because the nodule size and the structural and functional characteristics influence the appropriateness and the outcomes of the treatment. Future perspectives as the treatment of micro-papillary thyroid cancer or cervical recurrence need further investigations.

Severe Graves' disease-associated orbitopathy: A rare case of frontal bone hemangioma.

Graves' orbitopathy might be severe, requiring treatment with high-dose glucocorticoids. A lytic bone lesion, malignant lesions, and diseases resulting from bone remodeling processes (eg, Paget's disease) must be excluded by markers and imagery. Outcomes of high-dose glucocorticoids and thyrotoxicosis must be screened and prevented.

The Role of Cerebral CT Angiogram in Subacute Ischemic Cerebrovascular Events.

BACKGROUND: Stroke is a spectrum of medical emergencies resulting from a direct insult to the cerebral blood flow. Cerebral computed tomography angiogram (CTA) plays an important role in the diagnostic algorithm of acute stroke. However, the role of CTA in the subacute phase is not well-established. This study aimed to assess the diagnostic role of CTA in subacute ischemic stroke and transient ischemic attack (TIA) in identifying underlying etiology. It also aimed to describe the commonly encountered CTA findings in the subacute phase of ischemic events. METHODS: This is a retrospective study in which we evaluated the radiologic records of all patients who had a cerebral CTA for subacute stroke and TIA during the period from January 1, 2010 to May 30, 2018. RESULTS: The study included 104 cases diagnosed with subacute ischemic stroke or TIA. Patients' ages ranged from 8 to 96 years with a mean age of 52.9 (18.1) years. Most of the patients were males (68.3%; 71). CTA findings were abnormal in 86 cases (82.7%). Stenosis was diagnosed in 34 (32.7%) cases, followed by acute arterial thrombosis (25; 24%) and chronic occlusion (17; 16.3%). The internal carotid artery was the most affected (57.6%), followed by the vertebrobasilar arteries. CONCLUSION: The current study revealed that CTA has a high diagnostic yield in the subacute phase of ischemic cerebrovascular events, with an important role in detecting clinically relevant findings in this group of patients.

Synergistic efficacies of thymoquinone and standard antibiotics against multi-drug resistant isolates.

OBJECTIVES: To explore the antibacterial activity of thymoquinone (TQ), a quinone extracted from Nigella sativa. METHODS: This study was conducted from May 2019 to March 2020 at the Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia. The antimicrobial activity, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of TQ were determined using an agar well diffusion method and broth microdilution assays, and the synergistic effect was evaluated using antibiotics in parallel. The disruptive effect of TQ on bacterial cell membranes was determined using scanning electron microscopy. The antivirulence properties of TQ, which include adherence and biofilm formation, were also investigated using adherence and biofilm formation assays, respectively. RESULTS: Thymoquinone demonstrated bactericidal efficacy against 4/14 bacterial strains, with MIC range of 1.04-8.3 µg/mL and and MBC range of 10.41-66.66 µg/mL. Thymoquinone showed synergism against Klebsiella pneumoniae, Staphylococcus epidermidis (American Type Culture Collection 12228), Staphylococcus aureus, and Staphylococcus epidermidis in combination with the tested antibiotics. Thymoquinone inhibited bacterial adhesion by 39%-54%, 48%-68%, and 61%-81% at 0.5 × MIC, 1 × MIC, and 2 × MIC, respectively. The tested bacterial strains significantly inhibited biofilm formation after treatment with various concentrations of TQ for 24 and 48 hours. CONCLUSION: The combinatory effect of TQ with antimicrobials should be considered when developing new antimicrobial therapy regimens to overcome multidrug-resistant.

IOX-101 Reverses Drug Resistance Through Suppression of Akt/mTOR/NF-κB Signaling in Cancer Stem Cell-Like, Sphere-Forming NSCLC Cell.

Drug discovery research to fight lung cancer is incessantly challenged by drug resistance. In this study, we used drug-resistant lung cancer stem like cells (A549-CS) to compare the efficacy of standard drugs like cisplatin (DDP) and gemcitabine (GEM) with a novel arylidene derivative IOX-101. A549-CS was derived from regular A549 cells by growing in special media. Resistance proteins were detected using Western blotting. Cell proliferations were assessed by MTT assay. Cytokine release was enumerated using enzyme-linked immunosorbent assay. The effect of drugs on apoptosis and cell cycle was studied with flow cytometry protocols. Apoptosis-related proteins, caspases, and other signaling protein expressions like Akt and mammalian target of rapamycin (mTOR) were assessed by Western blotting. Expression of CD133 and nuclear factor κB (NF-κB) phosphorylation was assessed using flow cytometry. A549-CS showed significant increase in CD133 expression in comparison with A549 cells. Expression of resistance markers like MDR-1, lung resistance protein (LRP), and GST-II were detected in A549-CS. While DDP and GEM had relatively lower efficacy in A549-CS, IOX-101 inhibited the proliferation of both A549 and A549-CS with GI50 values of 268 and 296.5 nM, respectively. IOX-101 increased the sub-G0 phase in the cell cycle of A549-CS and increased the percentage of apoptotic cells. Western blot analysis revealed activation of caspases, Bax, and reduction in Bcl-2 levels. Further mechanistic investigation revealed IOX-101 to deactivate Akt, mTOR, and NF-κB signaling in A549-CS cells. Additionally, IOX-101 treatment to A549-CS also reversed MDR-1 and LRP expressions. Collectively, our results demonstrate efficacy of IOX-101 in A549-CS, which was resistant against the tested standard drugs. The activity was mediated by suppressing Akt/mTOR/NF-κB signaling.

Expanding primary cells from mucoepidermoid and other salivary gland neoplasms for genetic and chemosensitivity testing.

Restricted availability of cell and animal models is a rate-limiting step for investigation of salivary gland neoplasm pathophysiology and therapeutic response. Conditionally reprogrammed cell (CRC) technology enables establishment of primary epithelial cell cultures from patient material. This study tested a translational workflow for acquisition, expansion and testing of CRC-derived primary cultures of salivary gland neoplasms from patients presenting to an academic surgical practice. Results showed that cultured cells were sufficient for epithelial cell-specific transcriptome characterization to detect candidate therapeutic pathways and fusion genes, and for screening for cancer risk-associated single nucleotide polymorphisms (SNPs) and driver gene mutations through exome sequencing. Focused study of primary cultures of a low-grade mucoepidermoid carcinoma demonstrated amphiregulin-mechanistic target of rapamycin-protein kinase B (AKT; AKT1) pathway activation, identified through bioinformatics and subsequently confirmed as present in primary tissue and preserved through different secondary 2D and 3D culture media and xenografts. Candidate therapeutic testing showed that the allosteric AKT inhibitor MK2206 reproducibly inhibited cell survival across different culture formats. By contrast, the cells appeared resistant to the adenosine triphosphate competitive AKT inhibitor GSK690693. Procedures employed here illustrate an approach for reproducibly obtaining material for pathophysiological studies of salivary gland neoplasms, and other less common epithelial cancer types, that can be executed without compromising pathological examination of patient specimens. The approach permits combined genetic and cell-based physiological and therapeutic investigations in addition to more traditional pathologic studies, and can be used to build sustainable bio-banks for future inquiries.This article has an associated First Person interview with the first author of the paper.

Fluorescence In Situ Hybridization of Cells, Chromosomes, and Formalin-Fixed Paraffin-Embedded Tissues.

Fluorescence in situ hybridization (FISH) with DNA probes allows the visualization of gene copy number and localization of specific DNA targets with fluorescence microscopy. Cells in culture, metaphase chromosomes, and tissue sections are fixed and prepared on glass slides. Both the DNA in the cells and fluorescently labeled probe are denatured, and the labeled probe is allowed to hybridize to the cellular DNA. The slides are washed, counterstained, and viewed via fluorescence microscopy. We describe the basic method for preparing slides and probes for studies involving DNA copy number changes and structural chromosome rearrangements in formalin-fixed paraffin-embedded (FFPE) tissue sections and cell culture preparations.

Primary cancer cell culture: mammary-optimized vs conditional reprogramming.

The impact of different culture conditions on biology of primary cancer cells is not always addressed. Here, conditional reprogramming (CRC) was compared with mammary-optimized EpiCult-B (EpiC) for primary mammary epithelial cell isolation and propagation, allograft generation, and genome-wide transcriptional consequences using cancer and non-cancer mammary tissue from mice with different dosages of Brca1 and p53 Selective comparison to DMEM was included. Primary cultures were established with all three media, but CRC was most efficient for initial isolation (P<0.05). Allograft development was faster using cells grown in EpiC compared with CRC (P<0.05). Transcriptome comparison of paired CRC and EpiC cultures revealed 1700 differentially expressed genes by passage 20. CRC promoted Trp53 gene family upregulation and increased expression of epithelial differentiation genes, whereas EpiC elevated expression of epithelial-mesenchymal transition genes. Differences did not persist in allografts where both methods yielded allografts with relatively similar transcriptomes. Restricting passage (<7) reduced numbers of differentially expressed genes below 50. In conclusion, CRC was most efficient for initial cell isolation but EpiC was quicker for allograft generation. The extensive culture-specific gene expression patterns that emerged with longer passage could be limited by reducing passage number when both culture transcriptomes were equally similar to that of the primary tissue. Defining impact of culture condition and passage on the transcriptome of primary cells could assist experimental design and interpretation. For example, differences that appear with passage and culture condition are potentially exploitable for comparative studies targeting specific biological networks in different transcriptional environments.

Trp63 is regulated by STAT5 in mammary tissue and subject to differentiation in cancer.

Transformation-related protein 63 (Trp63), the predominant member of the Trp53 family, contributes to epithelial differentiation and is expressed in breast neoplasia. Trp63 features two distinct promoters yielding specific mRNAs encoding two major TRP63 isoforms, a transactivating transcription factor and a dominant negative isoform. Specific TRP63 isoforms are linked to cell cycle arrest, apoptosis, survival, and epithelial mesenchymal transition (EMT). Although TRP63 overexpression in cultured cells is used to elucidate functions, little is known about Trp63 regulation in normal and cancerous mammary tissues. This study used ChIP-seq to interrogate transcription factor binding and histone modifications of the Trp63 locus in mammary tissue and RNA-seq and immunohistochemistry to gauge gene expression. H3K4me2 and H3K4me3 marks coincided only with the proximal promoter, supporting RNA-seq data showing the predominance of the dominant negative isoform. STAT5 bound specifically to the Trp63 proximal promoter and Trp63 mRNA levels were elevated upon deleting Stat5 from mammary tissue, suggesting its role as a negative regulator. The dominant negative TRP63 isoform was localized to nuclei of basal mammary epithelial cells throughout reproductive cycles and retained in a majority of the triple-negative cancers generated from loss of full-length Brca1. Increased expression of dominant negative isoforms was correlated with developmental windows of increased progesterone receptor binding to the proximal Trp63 promoter and decreased expression during lactation was correlated with STAT5 binding to the same region. TRP63 is present in the majority of triple-negative cancers resulting from loss of Brca1 but diminished in less differentiated cancer subtypes and in cancer cells undergoing EMT.