Integrative molecular profiling of routine clinical prostate cancer specimens

BACKGROUND

Comprehensive molecular profiling led to the recognition of multiple prostate cancer (PCa) molecular subtypes and driving alterations, but translating these findings to clinical practice is challenging.

PATIENTS AND METHODS

We developed a formalin-fixed paraffin-embedded (FFPE) tissue compatible integrative assay for PCa molecular subtyping and interrogation of relevant genetic/transcriptomic alterations (MiPC). We applied MiPC, which combines capture-based next generation sequencing and quantitative reverse transcription PCR (qRT-PCR), to 53 FFPE PCa specimens representing cases not well represented in frozen tissue cohorts, including 8 paired primary tumor and lymph node metastases. Results were validated using multiplexed PCR based NGS and Sanger sequencing.

RESULTS

We identified known and novel potential driving, somatic mutations and copy number alterations, including a novel BRAF T599_V600insHT mutation and CYP11B2 amplification in a patient treated with ketoconazole (a potent CYP11B2 inhibitor). qRT-PCR integration enabled comprehensive molecular subtyping and provided complementary information, such as androgen receptor (AR) target gene module assessment in advanced cases and SPINK1 over-expression. MiPC identified highly concordant profiles for all 8 tumor/lymph node metastasis pairs, consistent with limited heterogeneity amongst driving events. MiPC and exome sequencing were performed on separately isolated conventional acinar PCa and prostatic small cell carcinoma (SCC) components from the same FFPE resection specimen to enable direct comparison of histologically distinct components. While both components showed TMPRSS2:ERG fusions, the SCC component exclusively harbored complete TP53 inactivation (frameshift variant and copy loss) and two CREBBP mutations.

CONCLUSIONS

Our results demonstrate the feasibility of integrative profiling of routine PCa specimens, which may have utility for understanding disease biology and enabling personalized medicine applications.

Next-Gen Sequencing Exposes Frequent MED12 Mutations and Actionable Therapeutic Targets in Phyllodes Tumors

Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a small subset of all breast neoplasms, yet little is known about the genetic alterations that drive tumor initiation and/or progression. Here, targeted next-generation sequencing (NGS) was used to identify somatic alterations in formalin-fixed paraffin-embedded (FFPE) patient specimens from malignant, borderline, and benign cases. NGS revealed mutations in mediator complex subunit 12 (MED12) affecting the G44 hotspot residue in the majority (67%) of cases spanning all three histologic grades. In addition, loss-of-function mutations in p53 (TP53) as well as deleterious mutations in the tumor suppressors retinoblastoma (RB1) and neurofibromin 1 (NF1) were identified exclusively in malignant tumors. High-level copy-number alterations (CNA) were nearly exclusively confined to malignant tumors, including potentially clinically actionable gene amplifications in IGF1R and EGFR. Taken together, this study defines the genomic landscape underlying phyllodes tumor development, suggests potential molecular correlates to histologic grade, expands the spectrum of human tumors with frequent recurrent MED12 mutations, and identifies IGF1R and EGFR as potential therapeutic targets in malignant cases.

IMPLICATIONS

Integrated genomic sequencing and mutational profiling provides insight into the molecular origin of phyllodes tumors and indicates potential druggable targets in malignant disease. Visual Overview: http://mcr.aacrjournals.org/content/early/2015/04/02/1541-7786.MCR-14-0578/F1.large.jpg.

Acute mesenteric ischaemia

Acute Mesenteric Ischaemia (AMI) is an uncommon vascular emergency where the diagnosis is often difficult and overlooked and delay in diagnosis results in a grave outcome. Although extravascular events like intussusception, volvulus, strangulated hernia and adhesive obstruction in neglected cases can result intestinal gangrene, this contribution will be limited to acute mesenteric ischaemia as a primary event. AMI consists of four pathologic processes (arterial thrombosis, arterial embolism, Non Occlusive Mesenteric Ischaemia (NOMI) and mesenteric venous thrombosis (MVT)) with similar clinical presentation and one potentially fatal pathological endpoint- intestinal gangrene. The clinical setting and the patient's risk profile often give the clue to the etiological process while the presentation is dominated by severe unrelenting abdominal pain out of proportion to the physical findings. The key to the successful management depends on the surgeon's ability to suspect the diagnosis, pursue appropriate investigations and institute aggressive treatment. The mortality remains high due to difficulty and delay in the diagnosis.

Diffuse malignant mesothelioma of the peritoneum following abdominal radiotherapy

Two cases of diffuse malignant mesothelioma of the peritoneum are described in 65 and 54-year-old patients a long time following abdominal radiotherapy treatment for testicular tumour in addition to orchidectomy.

Composition of gallstones and sequential events in biliary lithogenesis--is it different in south India compared to north?

AIMS

This study was carried out to determine the gross type and composition of gallstones from South India in order to compare it with published results from the North to see whether the sequential events in biliary lithogenesis are different in these two geographical areas. MATHODOLOGY: A total of 76 stones collected from various hospitals in South India including JIPMER were analysed using X-ray crystallography. Patient characteristics were recorded. Gross typing was done according to Bockus' morphological criteria.

RESULTS

Patients with gallstones in South India were found to be older in age with near equal gender distribution. Pigment calcium stones accounted for 56.5%, pigment stones for 17.2% and mixed stones for 14.2% of gallstones. Bilirubin and its salts were the most frequently identified class of compounds by crystallography. Analysis of gallstones layer by layer revealed equal distribution of bilirubin compounds between the centre and outer layers except crystalline bilirubin which was found only in outer layers. Vaterite, a polymorph of calcium carbonate was found in the nucleus, whereas vaterite and aragonite were found in the outer layers. Combination of anhydrous cholesterol and cholesterol II were found in the nucleus. Epitaxial relationship were found to hold good except for vaterite and aragonite.

CONCLUSION

Gallstones from South India are probably due to infection rather than supersaturation as evidenced by predominance of pigment calcium stones and various types of bilirubin and calcium carbonate compounds. Vaterite is important for nucleation. Further growth of stones is influenced by epitaxial relationship. These findings are dissimilar to that reported from North India indicating a different stimulus for stone precipitation in these two areas.

Dieulafoy's lesion: an obscure cause of GI bleeding

Dieulafoy's lesion is an uncommon cause of major gastrointestinal bleeding and may be difficult to recognise. It consists of an arteriole that protrudes through a tiny mucosal defect, usually within 6 cm of the gastroesophageal junction on the lesser curve of the stomach. Similar lesions have also been described in the distal oesophagus, small intestine, colon, and rectum. Awareness of the condition and experience in endoscopy are the mainstay of diagnosis. Therapeutic endoscopy is the first line of treatment. It is safe, effective and has very good long term results.

The quantitative buffy coat capillary tubes versus thin and thick blood films in the diagnosis of malaria in Saudi Arabia

The Quantitative Buffy Coat (QBC) capillary tube was compared with both the thin and thick films in the diagnosis of malaria among three groups of hospitalized patients. Group (1) comprised subjects with no symptoms or signs, group (2) comprised patients with fever and rigors of unknown cause, and group (3) comprised treated malarial patients consulting the hospital for a follow up. The QBC test showed more sensitivity than the two conventional methods in the three groups as follows: in group (1) the QBC was positive in 14.2% compared to 9% only in either thin or thick blood films. In group (2) the positivity was 95.1% compared to 79.3% & 76.8% in the thin and thick blood films respectively. In group (3) the sensitivity was 22.9% compared to only 5.7% in both of the thin and thick blood films. The authors found that the QBC technique in addition to its high sensitivity is very practical, reliable, simple and easy to perform. No doubt, the thin blood film still the method of choice in species identification of malaria parasites.

The histopathological picture of the liver of hamsters experimentally infected with Leishmania D. infantum on top of Schistosoma mansoni infection

No doubt, double and triple infection in a patient is not an uncommon phenomenon in the Old World. Consequently, the histopathological picture of the liver of Syrian golden hamsters experimentally infected with Leishmania. d. infantum on top of pre-infection with S. mansoni was studied. The results showed that the liver was markedly affected by the concomitant infection than infection with either parasite alone. The superadded Leishmania infection caused the early appearance of cell necrosis and fatty changes. The schistosomal granulomas were rounded in shape and well circumscribed. However, they were smaller in size and less in number when compared with schistosomal control. Also, there was a comparative decrease in the number of their cellular constitutions but without changing in the cell types. The schistosomal granulomas were surrounded with a rim of amastigotes laden macrophages. On the other hand, the leishmanial granulomas, were irregular in shape but comparatively increased in size and in number on the behalf of the schistosomal granulomas. Their cellular constitutions comparatively increased as well. So, it is concluded that the L.d. infantum infection on the top of S. mansoni infection suppressed the schistosomal pathological picture in the liver of hamsters.

In vitro effect of ivermectin on the larvae of Lucilia sericata meigen in Saudi Arabia

Myiasis or the infestation of the living, necrotic or dead tissues of the body of man or animals by the dipterous fly larvae is a world wide welfare problem. Consequently, control of these larvae attracted the attention of many authors. In this paper, the broad spectrum antiparasitic drug, ivermectin was used in-vitro against the larvae of the green bottle fly, Lucilia sericata. The LC 50 was found to be 9 ppm (0.76-1.5) and the slope function was 0.59. This means that ivermectin is a safe and very effective larvicide for L. sericata.

Blastocystis hominis among apparently healthy food handlers in Jeddah, Saudi Arabia

A prospective study was carried out to investigate the prevalence of Blastocystis hominis among random sample of apparently healthy food handlers. A total of 250 non Saudi males over 21 years of age were examined. Ninety (36%) had pathogenic and non pathogenic intestinal parasites. A total of 143 parasites were detected in their stool specimens. Twenty were B. hominis (13.99%) while other parasites were 123 (86.01%). B. hominis was found in 20 positive cases (22.22%) with an overall rate of 8%. Of these twenty cases, two had B. hominis as a sole parasite, twelve as a double infection and six as a triple infection. Other intestinal parasites were found, Giardia lamblia (16.8%), Entamoeba histolytica (10%), E. coli (6.4%), Chilomastix mesnili (5.6%), Trichomonas hominis (1.2%), and Endolimax nana (0.8%). The helminths were represented by Ascaris lumbricoides (4%), Hymenolepis nana (3.2%), Enterobius vermicularis (1.2%) and Trichocephalus trichiura (0.8%). No doubt, B. hominis should be in mind of parasitologists and physicians when dealing with patients with gastrointestinal troubles.

Histopathological studies of Syrian golden hamsters experimentally infected with Leishmania D. infantum

In the 1980s, infantile visceral leishmaniasis was documented in Al Agamy (Alexandria). The causative agent is Leishmania d. infantum and the insect vector is Phlebotomus langeroni. In this paper, Syrian golden hamsters were chosen as a model animal for histopathological studies of L. d. infantum. Twenty four male hamsters were experimentally infected with L.d. infantum. Every week, two hamsters were sacrificed and parts from the liver, heart, lung, spleen, small intestine and kidney were paraffin sectioned and stained with haematoxylin and eosin or with Giemsa stain. The leishmanial granuloma was the main histopathological changes and the liver was the main organ affected. Leishmanial granulomas were common in the liver, but few in lung and small intestine. The hepatic granulomas increased in surface areas and in number in the late stage of the infection (< 6 weeks). They were formed mainly of histiocytes, less lymphocytes and very few eosinophils with necrosis inside and bridging in between granulomas mainly occurred in the late stage of infection. Neither fibrosis nor peripheral delimitation was seen. Kupffer cell hyperplasia was seen throughout the experimental period (12 weeks). The spleen showed expansion of the red pulp and atrophy of the white pulp. The kidney showed mesangial cell proliferation and the mesangial matrix increased accompanied with amyloid deposition. All the tissue sections were photographed and the results were discussed.

Anti-toxoplasma antibodies in butchers and slaughtered sheep and goats in Jeddah Municipal abattoir, Saudi Arabia

Toxoplasma gondii is a zoonotic parasite of world-wide distribution. It is more or less endemic in all countries of the Middle East. In Jeddah Municipal abattoir, anti-Toxoplasma IgG was found to be 39% in sheep and 28% in goats as indicated by IHAT. On the other hand, anti-Toxoplasma IgG and IgM in butchers were 80% and 20% respectively, as indicated by the micro-ELISA. The risk of Toxoplasma transmission particularly, from meat inadequately cooked was discussed.

The effect of Schistosoma mansoni infection on testicular lipid in mice

This study was performed to establish the changes in the level of some serum hormones (Follicle stimulating hormone "FSH", Leutinizing hormone "LH" and testosterone) as well as to determine the changes in the concentrations of some testicular lipid parameters (viz., total cholesterol and total triacylglycerols) of infected mice with Schistosoma mansoni for different periods of time. Electron microscopical studies were also performed to define any histological changes in the testis upon infection with S. mansoni. The serum levels of gonadotropins (FSH, LH) showed no significant changes in infected as compared to control mice. On the other hand, the serum level of testosterone showed a significant decrease (P < 0.001) in infected as compared to control mice starting form the 14th week post infection. Testicular lipids showed a significant increase (P < 0.01) in the concentration of total cholesterol and a significant decrease (P < 0.005) in the concentration of total triacylglycerols in infected as compared to control mice especially at late stages on infection (14-20 weeks post infection). However, electron microscopical studies showed non significant histological changes in the testicular tissues of infected mice at different stages of infection. It is concluded that schistosomiasis has an important metabolic effect on testicular lipids as well as on the serum level of testosterone, whereas structural changes and spermatogenesis might require a longer period of infection and/or severe infection with higher number of cercariae.

Changes in serum lipids of mice experimentally infected with Schistosoma mansoni

Serum samples of mice infected with 80 cercariae of Schistosoma mansoni for different time periods (2-20 weeks) were used in this study. It was observed that the concentrations of serum total cholesterol and triacylglycerol decreased significantly (P < 0.001, P < 0.0001 respectively) in infected as compared to control mice starting from the fourth week post infection. Similarly, the concentration of serum high density lipoprotein-cholesterol (HDL-C) decreased significantly (P > 0.001) in infected as compared to control mice. However, the serum lipoproteins profile was variable at different stages of infection. On the other hand, the liver weight increased significantly (P < 0.0001) in infected as compared to control mice starting from the sixth week post infection. These changes might be attributed to several metabolites released by S. mansoni which affect the host hepatic tissue resulting in decreased synthesis of these parameters and their release into the circulation.

Effect of schistosomiasis mansoni on open-field exploratory behavior in mice

The response of mice infected with Schistosoma mansoni to a novel environment has been investigated in an attempt to study the effects of the disease on brain cognitive function by using opto-varimix instrument and autotrack computer program. Two to 18 weeks infected mice showed lower ambulatory activities than their matched controls with the largest reduction occurring between weeks 6 to 10. Maximum effects were observed in week 8. The first 5 minutes of ambulatory activities, designated as the "first session", were 22.3% lower in infected mice as compared with controls. The decline in the first session activities of infected mice was slower than the controls. Infected mice showed fewer stereotype movements with maximum reduction in week 16 of infection. There was no correlation between mice ambulatory activities or stereotype movements and infection duration. The importance of these findings in relation to the course of the disease and the underlying mechanism(s) are discussed.

Experimental schistosomiasis mansoni: electrophoretic studies on serum proteins before and after administration of oxamniquine

By means of electrophoresis quantitative estimation of serum protein components were made at various intervals before and after treatment with oxamniquine. During infection of mice with S. mansoni serum protein fractions showed marked alterations. Significant increase of total protein, alpha-2 globulin and beta globulin started at week 4 and alpha-1 globulin and gamma globulin at week 6. The significant decrease of globulins at week 6 resulted in reduced albumin globulin ratios. Some of these changes developed during maturation of worms and became more evident with initiation of egg deposition. The possible cause of these variations and their significance were discussed. Oxamniquine treatment of infected mice inhibited such alterations. Administration of the drug to normal mice was followed by temporary increase of serum albumin.

Schistosoma mansoni: tegumental surface alterations following oxamniquine treatment of infected mice

The in vivo effects of oxamniquine on the tegumental surface of adult Schistosoma mansoni were studied using scanning electron microscopy. Pronounced tegumental alterations were observed in all worms including marked oedema, wrinkling and distortion, atrophy, loss of tone and complete disorganization of suckers, blebbing, destruction of tubercles, collapse of sensory papillae and erosion or peeling of the surface layer. The amount of damage was more marked in males than females and varied considerably among worms recovered from the same host and even in different regions of the same worm. Damage was irreversible and all worms were eventually eliminated.

Susceptibility of Schistosoma mansoni prevalent in Saudi Arabia to oxamniquine in experimentally infected mice

The therapeutic efficiency of oxamniquine against the local strain of Schistosoma mansoni was investigated in experimentally infected mice. The drug was administered orally using a human-equivalent dose of 20 mg kg-1 day-1 for 3 consecutive days (total dose of 60 mg kg-1). Oxamniquine proved to be very effective as indicated by hepatic shift, oogram changes, complete elimination of adult worms and eradication of faecal eggs.

Immunohistochemical localization of catechol methyltransferase in normal and cancerous breast tissues of mice and rats

The immunocytochemical localization of catechol methyltransferase was determined in normal and cancerous breast tissues of inbred female Swiss-Webster mice and in normal, lactating, and cancerous breast tissues of inbred Sprague-Dawley rats. The enzyme was found to be cytoplasmically localized in ductal epithelial cells of secretory tubules in both inactive and stimulated mammary glands, in endothelial cells lining blood vessels, in fibroblasts in the connective tissue matrix, and, especially, in tumor cells. Adipose cells were nonreactive. The intensity of the immunocytochemical reaction in tumor cells was stronger than that in lactating tissues, which, in turn, was more reactive than that in normal, unstimulated breast tissues.

Immunoperoxidase localization of catechol-o-methyl transferase (COMT) in human breast cancer

Immunoperoxidase reaction of appropriately fixed tissue with an antiserum to catechol-o-methyl transferase (COMT), as the primary step in the peroxidase-immunoglobulin bridge technique, has been utilized for the localization of COMT in biopsy specimens of human breast neoplasm and its metastases. Our immunocytochemical identification of a strong activity of COMT in all cases studied might have a diagnostic implication in breast cancer.

Cytofluorescence localization of adriamycin-binding sites of cardiac tissue

A study of the cardiotoxicity induced by adriamycin (ADR) was done on the heart tissue of Sprague-Dawley rats receiving a single intravenous dose (15 mg/kg). Condensed bright orange-red fluoresced chromatin was observed in the nuclei of the myocardial cells of the left ventricle 2 h after drug injection. Just then, the intensity of the fluorescence emission started to decrease until it reached its minimum after 21 days, and disappeared completely 28 days after drug injection.

Studies of estrogen induced renal tumours in male Syrian hamsters. I. Cytochemical studies of lysosomal enzymes acid phosphatase and beta-glucuronidase

The localization and concentration of lysosomal enzymes acid phosphatase and beta-glucuronidase in kidney cells of Syrian hamsters after DES administration were studied. A positive cytoplasmic reaction was demonstrated for both enzymes. Increased activity of these enzymes were observed in renal tumour in contrast to normal homologous cells. These results can be explained on the basis that lysosomal enzymes were synthesized in tumour cells at a higher rate or it may be due to the invasion of tumour tissue by hydrolase rich microphages.