Frequency of HER2 Expression, MMR Deficiency, and PI3KCA Mutation in Pretreated Surgical Specimens of Patients with Esophageal Squamous Cell Carcinoma in Iran Cancer Institute.

Background & Objective: Iran is located in the esophageal cancer geographical belt. As multiple genetic alterations are responsible for the molecular pathogenesis of esophageal squamous cell cancer (ESCC), the role and frequency of HER2 expression, MMR deficiency, and PI3KCA mutation are not well defined. Methods: We carried out HER2/neu expression, dMMR/MSI high, and PI3KCA mutation analysis in specimens of patients with ESCC. We accessed archival tissue blocks related to specimens of 68 ESCC cases at the time of surgery following neoadjuvant chemoradiation. These patients underwent surgery during 2013-2018 at the Cancer Institute of Iran affiliated with the Tehran University of Medical Sciences in Tehran. Results: None of the patients showed HER2 expression, dMMR/MSI high, or PI3K mutations. Conclusion: dMMR/MSI-H and PI3KCA mutation and HER2 expression may not be reliable andfrequent targets for systemic therapy in patients with esophageal SCC.

Malignant transformation of tailgut cyst to squamous cell carcinoma, a rare case with poor outcome.

Tailgut cyst, a type of retro-rectal cyst, is a rare condition requiring evaluation for malignant transformation. We report a case of squamous cell carcinoma arising in the retro-rectal cyst, in a 51-year-old female who underwent incomplete resection of the cyst and chemo-radiotherapy, subsequently became locally recurred and metastatic.

Challenging Issues in Diagnosis and Screening of BK Virus Nephropathy in Kidney Transplant Recipients, A Multicenter Experience in Iranian Population.

INTRODUCTION: BK virus nephropathy (BKVN) is an important complication of kidney transplantation and kidney biopsy remains the gold standard for its diagnosis. Urine/serum polymerase chain reaction (PCR) is a more sensitive diagnostic method, although it has some potential limitations. METHODS: This study enrolled all kidney transplant recipients who underwent kidney transplant biopsy, collected from three medical centers. Urine and serum PCR results of the patients were also collected from the molecular laboratories. The cut-off value for positive viral DNA load in serum and urine were > 104 and > 107 copies/mL, respectively. Sensitivity, specifity, positive and negative predictive values (PPV, NPV) and cut off values for PCR results were compared with pathologic diagnosis among laboratories. RESULTS: Among 369 biopsy samples, 33 (8.9%) had definite diagnosis of BKVN. PCR results were available for 138 cases. Three patients with definite BKVN had negative PCR results. In 22 patients, PCR was positive without evidence of BKVN. The overall sensitivity, specificity, PPV and NPV of PCR for detecting BKVN, based on a unique cut-off value, were 88, 81, 51, and 97%; respectively. The overall accuracy of PCR in all laboratories was high (82 to 86%), however significant inter-laboratory differences in sensitivity and specificity was found . A 2-log difference in threshold value for positive results was observed in one laboratory. CONCLUSION: PCR may show a significant variability between different laboratories. Interpretation of PCR results using a single cut-off value for all laboratories, may decrease the sensitivity for the diagnosis and screening of BKVN.  DOI: 10.52547/ijkd.7143.

A case report of the sustained and rapid response of bevacizumab in a TP53-positive breast cancer and liver metastatic patient through personalized medicine.

HER2-positive metastatic breast cancer is much less frequent than other subgroups of breast cancer. Treatment options for this cancer are mostly limited to systemic chemotherapy, which leads to moderate improvements. Targeted therapy against malignant breast cancer requires the identification of reliable biomarkers for personalized medicine to obtain the maximum benefit of this therapy. Any mutations in the TP53 signaling pathway can be considered as a significant causative factor of breast cancer, for which the identification of target genes plays an important role in selecting the appropriate treatment. The use of personalized gene expression profiling could be valuable to find the direct target of the treatment in this case. The present study assessed the genetic profile of an HER2-positive metastatic breast cancer patient (with a liver metastasis) and figured out a complete and sustained response to bevacizumab. According to the results of next-generation sequencing (NGS) analysis, the patient's genetic profile showed an increased expression of p4EBP1 and PTEN and the activation of the mTOR signaling pathway with a mutation in the TP53 gene. Based on the common treatment of similar profiling, we administrated bevacizumab/Taxol/Gemzar chemotherapy up to six courses. Accordingly, as the response to treatment was revealed by reducing the volume of the liver metastasis from 4 to 1.4 cm, metastasectomy was performed as a complementary treatment. Hence, personalized gene expression profiling not only is useful for targeted therapy but also could be recommended to avoid prescription of non-responsive drugs.

Evaluation of the Relationship Between Expression of Villin and Gelsolin Genes and Axillary Lymph Node Metastasis in Patients with Breast Cancer.

BACKGROUND & OBJECTIVE: Nowadays, actin-binding proteins such as Villin and Gelsolin have been considered to be associated with aggressive tumors. This study mainly aims to determine the relationship between Gelsolin and Villin genes expression and metastasis of axillary lymph nodes in patients with breast cancer. METHODS: The included population consisted of 40 confirmed cases of female breast cancer (including 20 patients with breast cancer along with axillary lymph node metastasis and 20 patients without axillary lymph node metastasis). Expression of Villin and Gelsolin genes was evaluated using Real-time PCR and pre-designed primers. RESULTS: The mean expression level of Villin in groups with and without axillary lymph node metastasis was 3.33±1.35 and 0.87±0.88, respectively (P<0.001). The mean Gelsolin expression levels in both groups (with and without axillary lymph node metastasis) were 4.13±2.40 and 1.00±0.35, respectively (P<0.001). The significant relationships were independent of individuals' age. CONCLUSION: Patients with axillary lymph node metastasis may express significant higher level of Villin and Gelsolin genes.

Human papilloma virus infection and fascin over-expression in squamous cell carcinoma of the cervix.

Background: Human papilloma virus (HPV) is involved in development of almost all cervical cancers, mainly through the subversion of cellular mechanisms of growth control. Fascin plays central role in subsequent cell transformation events. Fascin mediates stabilization of parallel actin bundles where cellular protrusions are formed; this represents primary stages of cell migration and metastasis. Immunohistochemical assays have shown up-regulation of fascin expression in many epithelial and non-epithelial neoplasms. Therefore, the aim of this study was to investigate HPV infection and fascin expression in samples of cervical cancer. Methods: Of 66 patients with confirmed SCC, formalin-fixed specimens, embedded in paraffin blocks were evaluated for HPV infection with nested multiplex polymerase chain reaction (NM-PCR) and for fascin expression with immunohistochemical assays. Statistical analysis was performed using Wilcoxon rank-sum test and SPSS software. A p<0.05 was considered for statistical significance. Results: Of 66 samples, 52 (78.7%) were found positive for HPV infection and fascin over-expression was shown in all squamous cell carcinoma samples. Conclusion: This study showed fascin overexpression in squamous cell carcinoma of the cervix which might be involved in metastasis of cancers induced by some types of HPV, hypothetically through attenuation of inter-cellular adhesions, and induction of cell motility.

Angiotensin-Converting Enzyme Gene Polymorphism in Children with Idiopathic Nephrotic Syndrome, Effect on Biopsy Findings.

OBJECTIVE: Angiotensin converting enzyme (ACE) converts angiotensin I into angiotensin II. The ACE gene shows an I/D polymorphism, which correlates with ACE concentrations. The aim of this study is to evaluate the distribution of the ACE I/D genotype in children with idiopathic nephrotic syndrome (INS) and healthy controls and study the effect of this polymorphism on clinical and pathologic findings. METHODS: ACE gene I/D polymorphism of 104 patients with INS and 119 controls were determined. RESULTS: The DD, ID, and II genotypes were found in 58.7%, 22.1%, and 19.2% of the patients, and in 79.8%, 2.5%, and 17.6% of controls, respectively (p > 0.05). The ID genotype was seen more frequently in patients resistant to treatment. CONCLUSION: The observed differences with previous reports suggest the influence of the genetic background on disease course. The ACE I/D gene polymorphism's role seems to be more important in renal disease progression than susceptibility.

Prevalence of adeno-associated virus and human papillomavirus DNA in Iranian women with and without cervical cancer.

There is plenty of substantial evidence to support anti-tumor activity of viruses. Adeno-associated virus (AAV) may interact with human papillomavirus (HPV) to modify the risk of cervical neoplasia. The seroprevalence of AAV among women with cervical cancer has been reported to be lower than healthy ones. In spite of this finding, detection of AAV DNA in cervical biopsies does not entirely support the inverse association between AAV seropositivity and cervical cancer. This association is still controversial and requires more thorough evaluation in different countries. The aim of this case-control study was to find the prevalence of AAV and HPV DNA sequences in Iranian women with and without cervical cancer to assess the probable association of AAV infection and cervical cancer. In this study, paraffin-embedded tissue samples of 61 cervical cancer cases and 50 healthy controls (HCs) were investigated for AAV and HPV DNA by semi-nested and nested PCRs respectively. AAV DNA was detected in 7 cases (14%) of HCs and 9 specimens (14.8%) of case group. According to the branching in the phylogenetic tree, AAV2 was the only type detected in this study. Moreover, HPV DNA was detected in 8 cases (16%) of HCs and 44 specimens (72.13%) of case group. In conclusion, a low proportion of cervical biopsies from Iranian women contained AAV-2 genome. No significant difference in correlation between HPV and cervical cancer in presence or absence of AAV genome in cervix was found.

Validation of a next generation sequencing panel for detection of hotspot cancer mutations in a clinical laboratory.

Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform. Important parameters for somatic mutations including the threshold for differentiation of a positive and a negative result, coverage, sensitivity, specificity, and limit of detection (LoD) were analyzed. Variant calls with coverage of <100x were found to be inaccurate. The limit of detection for identifying hotspot mutations was determined to be 4.3%. The sensitivity and specificity of the method were 96.1% and 97.8% respectively. No statistically significant difference was found between different gene targets in terms of performance of hotspot frequency measurement for the subset tested. In every validation study, the number of samples, the manner of sample selection, and the number and type of variants play a role in the outcome. Therefore, these parameters should be assessed according to the clinical needs of each laboratory undertaking the validation.

Detection and Typing of Human Papilloma Viruses by Nested Multiplex Polymerase Chain Reaction Assay in Cervical Cancer.

BACKGROUND: Cervical cancer is the leading cause of death from cancer in under-developed countries. Human papilloma virus (HPV) 16 and 18 are the most prevalent types associated with carcinogenesis in the cervix. Conventional Polymerase Chain Reaction (PCR), type-specific and consensus primer-based PCR followed by sequencing, Restriction Fragment Length Polymorphism (RFLP) or hybridization by specific probes are common methods for HPV detection and typing. In addition, some researchers have developed a multiplex PCR for simultaneous detection and typing of different HPVs. OBJECTIVES: The aim of the present study was to investigate the prevalence of HPV infection and its types in cervical Squamous Cell Carcinoma (SCC) using the Nested Multiplex PCR (NMPCR) assay. PATIENTS AND METHODS: Sixty-six samples with histologically confirmed SCC were evaluated. Total DNA was isolated by phenol-chloroform extraction and ethanol precipitation. Nested multiplex PCR was performed with first-round PCR by GP-E6/E7 consensus primers for amplification of the genomic DNA of all known mucosal HPV genotypes and second-round PCR by type-specific multiplex PCR primer cocktails. RESULTS: Human papilloma virus infection was detected in 78.8% of samples, with the highest prevalence of HPV 16 (60.6%) while concurrent infections with two types was detected in 10.6%. CONCLUSIONS: The NMPCR assay is more convenient and easy for analysis of results, which is important for fast diagnosis and patient management, in a type-specific manner.

Priority Setting for Improvement of Cervical Cancer Prevention in Iran.

BACKGROUND: Cervical cancer is the fourth most common cancer among women worldwide. Organized cervical screening and vaccination against human papilloma virus (HPV) have been successful interventions for prevention of invasive cervical cancer (ICC). Because of cultural and religious considerations, ICC has low incidence in Iran and many other Muslim countries. There is no organized cervical screening in these countries. Therefore, ICC is usually diagnosed in advanced stages with poor prognosis in these countries. We performed a priority setting exercise and suggested priorities for prevention of ICC in this setting. METHODS: We invited experts and researchers to a workshop and asked them to list important suggestions for ICC prevention in Iran. After merging similar items and removing the duplicates, we asked the experts to rank the list of suggested items. We used a strategy grid and Go-zone analysis to determine final list of priorities for ICC prevention in Iran. RESULTS: From 26 final items suggested as priorities for prevention of ICC, the most important priorities were developing national guidelines for cervical screening and quality control protocol for patient follow-up and management of precancerous lesions. In addition, we emphasized considering insurance coverage for cervical screening, public awareness, and research priorities, and establishment of a cervical screening registry. CONCLUSION: A comprehensive approach and implementation of organized cervical screening program is necessary for prevention of ICC in Iran and other low incidence Muslim countries. Because of high cost for vaccination and low incidence of cervical cancer, we do not recommend HPV vaccination for the time being in Iran.

Human papilloma virus and esophageal squamous cell carcinoma.

Human papillomavirus (HPV) has also been suggested as an etiology of esophageal squamous cell carcinoma (SCC). The aim of this study was to investigate the prevalence of HPV infection in esophageal SCCs in our region with strict contamination control to prevent false positive results. Thirty cases of esophageal squamous cell carcinomas were chosen by simple random selection in a period of two years. PCR for target sequence of HPV L1 gene was performed on nucleic acid extracted from samples by means of GP5+/GP6+ primers. All tissue samples in both case and control groups were negative for HPV-DNA. Although the number of cases in this study was limited, the contribution of HPV in the substantial number of esophageal SCCs in our region is unlikely.

Lithium protects against spinal cord injury in rats: role of nitric oxide.

OBJECTIVE: Lithium improves locomotor scores after spinal cord injury (SCI) in rats. However, the underlying mechanisms are unknown. Herein, we assess the role of nitric oxide (NO) in this action. METHODS: The first set of experiments were performed to determine a dose of lithium that effectively improves locomotor scores in rats with SCI. Therefore, rats received different doses of lithium chloride (1, 4, 10, and 20 mg/kg intraperitoneally) or saline 1 hour before SCI. In the next step, the role of NO in the effect of lithium on SCI was investigated. For this purpose, rats were co-treated with an effective dose of lithium (20 mg/kg 1 hour before SCI) and a noneffective dose of Nω-nitro-L-arginine methyl ester (L-NAME, a nonselective NO synthase inhibitor; 15 mg/kg intraperitoneally 30 minutes before SCI). SCI was induced by compressing the T9 spinal segment with an aneurysmal clip for 60 seconds in anesthetized rats. Locomotor scores were determined at 1, 3, 5, 7, 14, 21, and 28 days after SCI. Plasma lithium levels were measured 12 hours after SCI. Spinal histopathologies were examined 30 days after SCI. RESULTS: Lithium (20 mg/kg) significantly improved locomotor scores and decreased histopathologic spinal damage. l-NAME (15 mg/kg) reversed the beneficial effects of lithium. The 20-mg/kg dose of lithium resulted in a 0.68 ± 0.02 mEq/L plasma lithium concentration, which is lower than the therapeutic level in humans (0.8-1.2 mEq/L). CONCLUSION: Lithium protects against SCI through an NO-dependent mechanism.

Contributory role of viral infection in congenital tumour development.

Congenital tumours are a group of distinct infrequent disorders whose exact aetiologies have not clearly been understood so far. Viral infection seems to be one of the key factors involved in the carcinogenesis of certain tumours. This study was performed to assess whether viral DNAs are present in the congenital tumours or not. Nucleic acid from 31 congenital tumours was extracted. Detection of Epstein-Barr virus, Cytomegalovirus (CMV), adenovirus, Herpes simplex virus 1 (HSV1) and 2, Human herpes virus 6 (HHV6), and BK virus was performed using polymerase chain reaction. Viral nucleic acid was detected in eight subjects (25.8%), mostly adenovirus, CMV, and HHV6. Despite their low frequencies, a possible role could be identified for viral infections in tumour development or progression.

Lack of detection of the mouse mammary tumor-like virus (MMTV) Env gene in Iranian women breast cancer using real time PCR.

BACKGROUND: Mouse mammary tumor virus (MMTV) is the major cause of mammary tumors in mice. There is limited controversial evidence about the probable etiologic role of MMTV- like virus in human breast cancer. MATERIALS AND METHODS: A total of 40 Formalin fixed paraffin embedded samples with diagnosis of breast cancer were collected in a period of 3 years from cancer institute of Iran. We selected both pre-menopausal and post-menopausal patients with different histologic grades and different ethnic groups. We evaluated presence of MMTV-like virus env gene through real time PCR method. RESULTS: Forty patients (20 pre and 20 post- menopausal women) were evaluated with the mean age of 49.67. The average tumor size was 39 mm. None of the studied samples were positive for MMTV-like virus env gene target sequences. CONCLUSIONS: We found no evidence on the potential role of MMTV-like virus in the carcinogenicity of breast cancer among Iranian women.

Human papilloma virus and esophageal squamous cell carcinoma.

Human papilloma virus (HPV) has been suggested as an etiology of esophageal squamous cell carcinoma (SCC). The aim of this study was to investigate the prevalence of HPV infection in esophageal SCCs in our region with strict contamination control to prevent false positive results. Thirty cases of esophageal squamous cell carcinomas were chosen by simple random selection in a period of two years. PCR for target sequence of HPV L1 gene was performed on nucleic acid extracted from samples by means of GP5+/GP6+ primers. All tissue samples in both case and control groups were negative for HPV-DNA. Although the number of cases in this study was limited, the contribution of HPV in substantial number of esophageal SCCs in our region is unlikely.

Alpha 1 antitrypsin deficiency in infants with neonatal cholestasis.

OBJECTIVE: Alpha1-antitrypsin deficiency (A1ATD) is the most important indication for liver transplantation in children. The gene frequencies vary in different ethnic groups. In the present study, we attempt to determine the frequencies of the most common defective alleles, Z and S, in Iranian children suffering from idiopathic neonatal cholestasis. Eighty-seven infants were typed for Z and S alleles. METHODS: In a single center study, 87 consecutive liver biopsies from infants with cholestasis were reviewed and patients with neonatal cholestasis enrolled in the study and cases with confirmed biliary tract atresia excluded. Formalin fixed paraffin embedded blocks were used for DNA extraction. AAT genotype was determined by polymerase chain reaction (PCR) assay and amplification of the two most common deficiency variants, S and Z alleles, and then sequencing of PCR products. FINDINGS: There were 48 (55.2%) males and 39 (44.8%) females, with a median age of 60 days. Out of 87 of the study subject, 2 (2.2%) were heterozygous for the S allele, and no ZZ, SS or MZ individual was found in the patients. No other polymorphism was found in the sequencing results. CONCLUSION: In comparison to other populations, AAT deficiency seems not to be an important etiologic factor for neonatal cholestatic liver disease in Iran; however, further studies are recommended to estimate the true mutant gene frequencies.

Human papillomavirus genotypes in Iranian patients with cervical cancer.

The aim of this study was to determine the frequency of HPV genotypes isolated from cervical intra-epithelial neoplasia grade III and invasive carcinomas of Iranian patients. A total of 94 cases were selected in five years from 2003 to 2007. After nucleic acid purification, real-time PCR was performed by means of GP5+/GP6+ primers. Subsequently, PCR products were sequenced, on the basis of which a phylogenetic tree was constructed. Negative samples and twelve randomly selected positive samples were also typed by reverse hybridization to increase the sensitivity and to confirm the results. Of 94 evaluated samples, 7 were negative for internal control gene and were excluded from the study. The overall genotyping results of phylogenetic analysis and hybridization methods were as follows: HPV 16: 75% (65/87); HPV 18: 3% (2/87); HPV 31: 1% (1/87); HPV 45: 1% (1/87). High frequency of HPV 16 and low frequency of HPV 18 were found in this study. Information about HPV genotype distribution is important in cervical cancer screening and prevention.

Malignant ovarian germ cell tumours in gonadal Y chromosome mosaicism.

AIMS: Previous studies have shown that two partially overlapping mechanisms are responsible for the development of malignant ovarian germ cell tumours (MOGCT): either spontaneous mutations, mostly in KIT gene, or the presence of Y chromosome material, in dysgenetic gonads. While unilateral oophorectomy and preservation of fertility is favourable in most cases, presence of whole or part of Y chromosome in dysgenetic ovaries is associated with a risk of bilateral germ cell tumour development. The aim of this study was to evaluate the frequency of Y chromosome material in these tumours. METHODS: A total of 47 cases with histopathologic diagnosis of malignant germ cell tumour were selected in a period of 9 years. A relative quantitative PCR (RQ-PCR) method was designed and validated to detect testis-specific protein Y-encoded (TSPY) gene on Y chromosome. After DNA extraction, TSPY gene was sought as a surrogate of Y chromosome. RESULTS: Significant amounts of TSPY gene were found in seven cases, two of which had gonadoblastoma and one had cytogenetic proof of Y chromosome presence. CONCLUSIONS: Some MOGCTs develop on the background of gonadal mosaicism and gonadal dysgenesis. Bilateral oophorectomy may be indicated in patients with these disorders because they are at risk of developing an MOGCT on the contralateral gonad. Moreover, this chromosomal abnormality is hardly found by routine methods, and the abnormality is more easily sought in MOGCT cells by means of RQ-PCR.