Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients

Purpose

Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicities demonstrate distinct clinical behaviors. Thus, we investigated microbiome dysbiosis in Egyptian, African American (AA), and European American (EA) CRC patients.

Patients and methods

CRCs and their corresponding normal tissues from Egyptian (n = 17) patients of the Alexandria University Hospital, Egypt, and tissues from AA (n = 18) and EA (n = 19) patients at the University of Alabama at Birmingham were collected. DNA was isolated from frozen tissues, and the microbiome composition was analyzed by 16S rRNA sequencing. Differential microbial abundance, diversity, and metabolic pathways were identified using linear discriminant analysis (LDA) effect size analyses. Additionally, we compared these profiles with our previously published microbiome data derived from Kenyan CRC patients.

Results

Differential microbiome analysis of CRCs across all racial/ethnic groups showed dysbiosis. There were high abundances of Herbaspirillum and Staphylococcus in CRCs of Egyptians, Leptotrichia in CRCs of AAs, Flexspiria and Streptococcus in CRCs of EAs, and Akkermansia muciniphila and Prevotella nigrescens in CRCs of Kenyans (LDA score >4, adj. p-value <0.05). Functional analyses showed distinct microbial metabolic pathways in CRCs compared to normal tissues within the racial/ethnic groups. Egyptian CRCs, compared to normal tissues, showed lower l-methionine biosynthesis and higher galactose degradation pathways.

Conclusions

Our findings showed altered mucosa-associated microbiome profiles of CRCs and their metabolic pathways across racial/ethnic groups. These findings provide a basis for future studies to link racial/ethnic microbiome differences with distinct clinical behaviors in CRC.

Eligibility criteria to cisplatin in head and neck squamous cell carcinoma: Egyptian expert opinion

Introduction

The use of cisplatin in clinical practice in the management of head and neck squamous cell carcinoma (HNSCC) is limited by its toxicity and acquired resistance, which makes the decision-making process of its prescription multifactorial.

Methods

An Egyptian expert panel (comprising nine Egyptian oncologists) meeting was held after a comprehensive literature review on the use of cisplatin in HNSCC. The panel aimed to develop a consensus on evidence-based recommendations for receiving cisplatin in the chemoradiotherapy management of HNSCC in Egyptian clinical practice.

Results

The panel indicated that an Eastern Cooperative Oncology Group Performance Status (ECOG PS) > 2, creatinine clearance (CCR) < 50 ml/min, neuropathy grade ≥ 2, pre-existing hearing loss or tinnitus ≥2, hematological problems (platelets < 100,000/mm3, neutrophils < 1500/mm, and hemoglobin < 9 g/dl), and heart failure of New York Heart Association Classes III or IV (even if cardiovascular therapy is optimized); are all absolute contraindications to receiving cisplatin. On the other hand, relative contraindications to cisplatin according to the panel were an ECOG PS of 2, age more than 70 years, CCR between 50 and 60 ml/min, grade 1 neuropathy, grade 1 hearing loss, involuntary weight loss of ≥20% of body weight, Child-Pugh Scores B and C, previous induction chemotherapy, and heart failure of New York Heart Association Classes I or II with left ventricular ejection fraction ≤50%. The panel agreed that the socioeconomic status of patients should be considered when prescribing cisplatin to HNSCC patients.

Conclusion

Our discussion resulted in a set of evidence-based recommendations for cisplatin eligibility criteria in patients of HNSCC in Egypt.

A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients

BACKGROUND

Colorectal cancer (CRC) is the fifth most diagnosed cancer in Sub-Saharan Africa. In Kenya, CRC incidence rates tripled from 1997 to 2017. In the Moi Teaching and Referral Hospital, Moi University, there has been an increase in CRC cases, notably for younger patients. A suggested pathobiology for this increase is gut microbiome dysbiosis. Since, for the Kenyan CRC patient population, microbiome studies are rare, there is a need for a better understanding of how microbiome dysbiosis influences CRC epidemiology in Kenya. In this single-center study, the focus was on profiling the gut microbiome of Kenyan CRC patients and healthy volunteers and evaluating associations between microbiome profiles and the age of CRC patients.

METHODS

The gut mucosa-associated microbiome of 18 CRC patients and 18 healthy controls were determined by 16S rRNA sequencing and analyzed for alpha and beta diversity, differential abundance, and microbial metabolic profiling.

RESULTS

Alpha diversity metrics showed no significant differences, but beta diversity metrics showed dissimilarities in the microbial communities between CRC patients and healthy controls. The most underrepresented species in the CRC group were Prevotella copri (P. copri) and Faecalibacterium prausnitzii (F. prausnitzii), although Bacteroides fragilis (B. fragilis) and Prevotella nigrescens were overrepresented (linear discriminant analysis, LDA score >2, P<0.05). Also, for CRC patients, significant metagenomic functional alterations were evident in microbial glutamate metabolic pathways (L-glutamate degradation VIII was enriched, and L-glutamate and L-glutamine biosynthesis were diminished) (P<0.05, log2 Fold Change >1). Moreover, the microbiome composition was different for patients under 40 years of age compared to older patients (LDA score >2, P<0.05).

CONCLUSIONS

Microbiome and microbial metabolic profiles of CRC patients are different from those of healthy individuals. CRC microbiome dysbiosis, particularly P. copri and F. prausnitzii depletion and glutamate metabolic alterations, are evident in Kenyan CRC patients.

Risk of Developing Breast Reconstruction Complications: A Machine-Learning Nomogram for Individualized Risk Estimation with and without Postmastectomy Radiation Therapy

BACKGROUND

The purpose of this study was to create a nomogram using machine learning models predicting risk of breast reconstruction complications with or without postmastectomy radiation therapy.

METHODS

Between 1997 and 2017, 1617 breast cancer patients undergoing mastectomy and breast reconstruction were analyzed. Those with autologous, tissue expander/implant, and single-stage direct-to-implant reconstruction were included. Postmastectomy radiation therapy was delivered either with three-dimensional conformal photon or proton therapy. Complication endpoints were defined based on surgical reintervention operative notes as infection/necrosis requiring débridement. For implant-based patients, complications were defined as capsular contracture requiring capsulotomy and implant failure. For each complication endpoint, least absolute shrinkage and selection operator-penalized regression was used to select the subset of predictors associated with the smallest prediction error from 10-fold cross-validation. Nomograms were built using the least absolute shrinkage and selection operator-selected predictors, and internal validation using cross-validation was performed.

RESULTS

Median follow-up was 6.6 years. Among 1617 patients, 23 percent underwent autologous reconstruction, 39 percent underwent direct-to-implant reconstruction, and 37 percent underwent tissue expander/implant reconstruction. Among 759 patients who received postmastectomy radiation therapy, 8.3 percent received proton-therapy to the chest wall and nodes and 43 percent received chest wall boost. Internal validation for each model showed an area under the receiver operating characteristic curve of 73 percent for infection, 75 percent for capsular contracture, 76 percent for absolute implant failure, and 68 percent for overall implant failure. Periareolar incisions and complete implant muscle coverage were found to be important predictors for infection and capsular contracture, respectively. In a multivariable analysis, we found that protons compared to no postmastectomy radiation therapy significantly increased capsular contracture risk (OR, 15.3; p < 0.001). This was higher than the effect of photons with electron boost versus no postmastectomy radiation therapy (OR, 2.5; p = 0.01).

CONCLUSION

Using machine learning, these nomograms provided prediction of postmastectomy breast reconstruction complications with and without radiation therapy.

CLINICAL QUESTION/LEVEL OF EVIDENCE

Risk, III.

LGR5, HES1 and ATOH1 in Young Rectal Cancer Patients in Egyptian

OBJECTIVE

The study aimed to delineate the gene expression profile of LGR5, HES1 and ATOH1 in young Egyptian rectal cancer (RC) patients and investigate the correlation between expression profiles and clinical outcome.

METHODS

The study was conducted on 30 young Egyptian RC patients. Expression study of LGR5, HES1 and ATOH1 were performed by quantitative PCR (QPCR) based on comparative Cq method after normalization to adjacent non tumor tissues and ACTB as a reference gene. Patients were followed up for assessment of response to neoadjuvant chemoradiotherapy (CRT) based on revised RECIST1.1.

RESULT

The study detected overexpression of LGR5 and HES1 and down-regulation of ATOH1 in human RC tissues compared to non- tumor tissues. High expression of LGR5 was correlated with more depth of tumor invasion, lymph node (LN) metastasis, advanced cTNM stage and mesorectal fascia (MRF) involvement. More prominently, high LGR5 expression level was associated with poor response to CRT. LGR5 was suggested as unfavorable prognostic biomarker for RC. Conversely, HES1 and ATOH1 expression did not show significant association with most of the studied clinical criteria nor response to CRT. Still, HES1 and ATOH1 were significantly and inversely associated with presence of mucinous component.

CONCLUSION

High LGR5 expression is indicative of poor prognosis among young Egyptian RC patients and is proposed as a predictive marker of resistance to neoadjuvant CRT. However, HES1 and ATOH1 expressions were not prognostic nor predictive of response to CRT. Overall, LGR5, HES1 and ATOH1 gene expression patterns among young onset RC patients, are in line with patterns encountered in older age groups.

Abstract 107: Self-Reported Physical Activity Patterns among Colorectal Cancer Survivors in Egypt

Purpose: Compared to the U.S., colorectal cancer (CRC) in Egypt is more prevalent among younger individuals (under age 40) and diagnosed at an advanced stage leading to higher mortality rates. Given these higher mortality rates, focusing on tertiary prevention strategies, such as physical activity, is warranted. Our study purpose was to assess physical activity behavior in colorectal cancer survivors living in Egypt.

Methods: Egyptian study staff recruited 86 participants from the Alexandria University Oncology Department. Eligible participants were post-primary or currently undergoing treatment for CRC. Study staff administered the World Health Organization physical activity questionnaire (GPAQ; www.who.int/chp/steps/GPAQ/en/) and Godin Leisure-Time Exercise Questionnaire (GLTEQ). Both assessments were translated into Arabic.

Results: The median age of study participants was 52 years old with 43% being male, 64% reporting early stage cancer, 77% reporting one or more years of school, and 79% living in an urban location. Most participants (76%) had a normal or overweight BMI. According to the GPAQ, the median total MET mins/wk for participants was 1440 with interquartile range of 225 to 6720; 63% of participants met the GPAQ WHO recommendations of ≥600 MET mins/wk. Occupational and transportation contributed to the majority of total MET mins/wk. According to the GLTEQ, the median for weekly minutes of ≥moderate intensity physical activity was 0 with interquartile range of 0 to 23 minutes per week. Only 14% were meeting physical activity recommendations of ≥150 weekly minutes of ≥moderate intensity physical activity based on the GLTEQ.

Conclusion: The prevalence of meeting physical activity recommendations varies depending on measurement tool used. Considering sources of physical activity beyond recreational alone is important for more fully understanding physical activity behavior. The low levels of recreational or leisure exercise provides an opportunity for increasing the prevalence of sufficient physical activity in CRC survivors in Egypt.

Citation Format: Salma Mohamed Aly, Doaa Genena, James Shikany, Lori Brand Bateman, Mona Fouad, Waleed Arafat, Salah-Eldin Abdelmoneim, Sejong Bae, Isabel Scarinci, Marwa Hussein, Miriam A. Zaki, Somaia Khamess, Laura Q. Rogers. Self-Reported Physical Activity Patterns among Colorectal Cancer Survivors in Egypt [abstract]. In: Proceedings of the 9th Annual Symposium on Global Cancer Research; Global Cancer Research and Control: Looking Back and Charting a Path Forward; 2021 Mar 10-11. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2021;30(7 Suppl):Abstract nr 107.

Psychological and Sexual Health During the COVID-19 Pandemic in Egypt: Are Women Suffering More?

Introduction

Psychological consequences of the COVID-19 pandemic include pandemic triggered feelings of fear, uncertainty, and anxiety added to the effects of restricting the population's activities in lockdown.

Aim

We aimed to study the effect of COVID-19 pandemic on sexual satisfaction of females and males in Egypt and to evaluate possible predictive factors.

Methods

Married men and females in Egypt were invited to respond to an online questionnaire. The questionnaire addressed medical history, socioeconomic status, sexual performance satisfaction before and during the lockdown in addition to validated Arabic questionnaires for depression, sexual function in males and females, and sexual satisfaction (Generalized Anxiety Disorder-7, Patient Health Questionnaire-9, Female Sexual Function Index, International Index of Erectile Function-5, Index of Sexual Satisfaction, respectively).

Main outcome measure

The main outcome measures were frequency of depression, anxiety, sexual dysfunction, and sexual satisfaction in males and females during COVID-19 lockdown.

Results

A total of 479 females and 217 males completed the questionnaire. Sexual satisfaction was significantly higher before (91.2%, 73.5%) than during lockdown (70.5%, 56.2%) in both males and females, respectively. During lockdown, significantly more males (70.5%) reported being satisfied with their sexual performance than females (56.2%) (P < .001). More than half of the male subjects (68.2%) had no erectile dysfunction while 97.3% females scored ≤26.5 on the Female Sexual Function Index scale suggestive of sexual difficulties. Sexual stress was significantly greater in females (70.8%) than males (63.1%). Educational level, occupation, anxiety, and erectile dysfunction were independently associated with sexual stress in males. Being a housewife or unemployed, husband's age >35 years, marriage duration of 5-10 years, anxiety, and female sexual dysfunction were predictors of sexual relation stress in females.

Conclusion

COVID-19 pandemic was associated with lower sexual satisfaction in both genders. Females however suffered more anxiety and depression and thereby greater risk of sexual function difficulties and sexual dissatisfaction. Intervention strategies in order to lessen the suffering of affected individuals particularly after the pandemic are recommended.

Omar SS, Dawood W, Eid N, et al. Psychological and Sexual Health During the COVID-19 Pandemic in Egypt: Are Women Suffering More. Sex Med 2021;9:100295.

Abstract 6103: Absence of Mitsuokella multacida is associated with early onset of colorectal cancer

Colorectal cancer (CRC) is a global burden, with an expected 2.2 million annual cases and 1.1 million deaths by 2030. Nearly 90% of CRC cases occur in people over the age of 50. However, early onset (&lt;50 years) of CRC is increasing in Egypt. Prior studies suggest that alteration in microbiome composition (dysbiosis) disturbs the symbiotic relationship between the colorectum and resident micro-organisms and promotes CRC. We hypothesize that, for Egyptians, microbiome dysbiosis is responsible for early-onset of CRC. We further hypothesize that there is cross-talk between the microbiome, tumor molecular features, and the immune microenvironment. Thus, we investigated the molecular profiling of these patients via integrated transcriptional-microbiome analysis. We assessed the colonic microbiota and the expression of specific host response genes in normal colonic mucosal samples from 8 healthy individuals and samples from 20 Egyptian CRC patients. A retrospective convenience sample design was employed. Colonoscopy was performed on these patients at Alexandria University Hospital, Alexandria, Egypt. Microbiota composition was determined by 16S rRNA amplicon sequencing. A panel of 784 genes involved in tumor, microenvironment, and immune response were used to characterize differential expression across patient groups by the Nanostring method. This panel facilitates the estimation of immune cell abundance for 15 tumor-infiltrating immune cell types. Differential abundance and cross-talk between the relative abundance of microbiota and tumor RNA expression were evaluated using negative binomial model fitting and Wald statistics. One third of our CRC patient population was under 50 years old at the time of diagnosis with CRC, and most were female. Healthy controls were even younger than CRC cases, and most were females. There were differences in relative abundances of bacteria between healthy controls and those with CRCs. Analysis showed a low abundance of Mitsuokella multacida, a short-chain fatty acid (SCFA)-producing bacterium, in CRC patients when compared to healthy individuals. In particular, this trend was evident for older CRC patients (≥ 50 years); of note, this bacterium was absent in younger patients (&lt;50 years) (adj. p-value = 0.01). Further, there was a high abundance of Fusobacterium nucleatum in all CRC patients compared to healthy individuals (adj. p-value = 0.04). In cross-talk analysis for healthy controls, elevated abundance of M. multacida was inversely associated with macrophage abundance (global p-value =0.055).For Egyptian patients, the absence of SCFA-producing multacida in younger patients may be a reason for early onset of CRC. These findings suggest that the oncoprotective effect of Mitsuokella multacida should be further investigated. These studies are supported by the US-Egypt STDF grants (NAS 2000007148 and 144/17) and the Impact funds of University of Alabama at Birmingham.

Citation Format: Amr Elkholy, Michael Behring, Mohammed Mohsen, Prachi Bajpai, Amira Embaby, Doaa Header, Reham Abo Elwafa, Hesham Saeed, Mona Fouad, Waleed Arafat, Upender Manne. Absence of Mitsuokella multacida is associated with early onset of colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6103.

Barriers to and Facilitators of Colorectal Cancer Screening in Egypt: Examining the Perceptions of Physicians and Residents in Alexandria

PURPOSE

Colorectal cancer (CRC) screening is not routinely performed in Egypt, and more than one third of CRC cases occur in individuals age 40 and younger, with overall survival estimated at only 2 years, presumably because of late diagnoses. To lay the foundation for the development of a CRC multilevel screening program in Egypt to promote CRC prevention and early detection, this qualitative study aimed to explore the potential barriers to and facilitators of screening from the perspectives of physicians and residents in Alexandria.

METHODS

We conducted one-on-one, 1-hour, semistructured interviews with primary health care physicians and specialists—oncologists and gastroenterologists—practicing in Alexandria, Egypt. Focus groups of residents, stratified by social class and gender, were also held. Interviews and focus groups were conducted in Arabic by trained interviewers/moderator, and were audio recorded, transcribed, translated into English, and analyzed using thematic analysis.

RESULTS

Seventeen physicians participated—8 specialists and 9 primary care physicians—and 7 focus groups—7 to 8 participants each—were held. According to both interview and focus group participants, individual-level barriers to CRC screening included socioeconomic status, a lack of emphasis on prevention in the culture, fear, and cost. Provider-level barriers as mentioned by physicians included a belief that only high-risk patients should be screened and a lack of confidence in providers to perform and interpret screening tests appropriately. Structural-level barriers, discussed by physicians and focus group participants, included cost and a lack of testing availability. Potential facilitators of screening mentioned by physicians included implementing a media campaign emphasizing early detection and curability. Focus group participants focused on making screening tests free or low cost, obligatory, and convenient.

CONCLUSION

On the basis of the perceptions of physicians and residents of Alexandria, Egypt, multiple barriers to and facilitators of CRC screening exist. Addressing these would be important in designing a successful screening program.

Designing an Effective Colorectal Cancer Screening Program in Egypt: A Qualitative Study of Perceptions of Egyptian Primary Care Physicians and Specialists

BACKGROUND

In Egypt more than one-third of colorectal cancer (CRC) cases occur in individuals aged 40 years and younger, and are diagnosed at advanced stages; currently, CRC screening is not done as a routine part of preventive care. To lay the foundation for the development of a CRC multilevel screening program in Egypt, this qualitative study aimed to explore the perspectives of Egyptian physicians.

MATERIALS AND METHODS

The PRECEDE-PROCEED model, which focuses on predisposing (intrapersonal), reinforcing (interpersonal), and enabling (structural) factors inherent in health behaviors, served as our theoretical framework. Primary health care physicians, oncologists, and gastroenterologists practicing in Alexandria, Egypt, participated in 1 one-hour semistructured interview. Interviews were audio recorded, transcribed, translated into English, and analyzed by thematic analysis.

RESULTS

Seventeen physicians participated (n = 8 specialists and n = 9 primary care physicians). Barriers to CRC screening included socioeconomic status, a lack of emphasis on prevention, fear, and cost (predisposing); a belief that only high risk patients should be screened and a lack of confidence in providers to perform and interpret screening tests appropriately (reinforcing); and cost, lack of availability of the tests, and inadequate training for laboratory technicians and providers (enabling). Potential facilitators included implementing a media campaign emphasizing early detection, curability and prevention (predisposing); educating physicians and eliciting physician engagement (reinforcing); and decreasing costs, making screening tests widely available, and providing well-trained providers (enabling).

CONCLUSION

A CRC screening program is needed in Egypt, and to be successful it would likely need to address barriers at multiple levels.

IMPLICATIONS FOR PRACTICE

In Egypt, colorectal screening is not a routine part of preventive care, and colorectal cancer is often diagnosed at an advanced stage in individuals aged 40 years or younger. Screening can prevent and detect colorectal cancer in its early stages, but before designing any screening program, understanding the context is important as cultural beliefs may impact the acceptability of screening methods. By exploring the perspectives of Egyptian physicians, this study found important insights into how screening program components should be considered in the Egyptian culture and lays the foundation for the development of a multilevel colorectal screening program in Egypt.

Site of Metastases as Prognostic Factors in Unselected Population of Stage IV Non-Small Cell Lung Cancer

Background

Advanced stage non-small cell lung cancer (NSCLC) is a heterogenous disease, yet, with the exception of targeted therapies, most guidelines recommended uniform treatment irrespective of tumor burden or sites of metastases and this may explain, in part, the wide range of responses to same lines of therapy.

Aim of work

In this work we tried to explore the effect of metastatic sites in on overall survival (OS), in an unselected group of Non-small cell lung cancer patients who received different treatments line.

Methods

A retrospective analysis was performed on patients with stage IV NSCLC who received systemic treatment at UAB Cancer Center (NCI designated comprehensive cancer center) between 2002 to 2012. The details of sites of metastases, systemic therapy and overall survival were recorded for each patient.

Result

In 409 patients who received systemic treatment, there was statistically significant lower OS in those presenting with liver metastases (p<0.001), adrenal metastases (p=0.011) and metastases to abdominal lymph nodes (p=0.014). There was no statistically significance difference in OS in patient presenting with pleural metastases or effusion (p=0.908), metastases to heart or pericardium (p=0.654), metastases to bone (p=0.281), brain (p=0.717) or skin and subcutaneous tissue (p=0.642).

Conclusion

Intra-abdominal metastases confer a particularly poor prognosis in stage IV NSCLC treated with systemic therapy and may identify patients in whom aggressive treatment beyond first line therapy is not appropriate.

Novel targeted therapies and immunotherapy for advanced thyroid cancers

Thyroid cancer is a frequently encountered endocrine malignancy. Despite the favorable prognosis of this disease, 15–20% of differentiated thyroid cancer (DTC) cases and most anaplastic types, remain resistant to standard treatment options, including radioactive iodine (RAI). In addition, around 30% of medullary thyroid cancer (MTC) cases show resistance after surgery. The evolving understanding of disease-specific molecular therapeutic targets has led to the approval of two targeted therapies (Sorafenib and Lenvatinib) for RAI refractory DTC and another two drugs (Vandetanib and Cabozantinib) for MTC. These advanced therapies exert their effects by blocking the MAPK pathway, which has been widely correlated to different types of thyroid cancers. While these drugs remain reserved for thyroid cancer patients who failed all treatment options, their ability to improve patients’ overall survival remain hindered by their low efficacy and other molecular factors. Among these factors is the tumor’s ability to activate parallel proliferative signaling pathways other than the cascades blocked by these drugs, along with overexpression of some tyrosine kinase receptors (TKR). These facts urge the search for novel different treatment strategies for advanced thyroid cases beyond these drugs. Furthermore, the growing knowledge of the dynamic immune system interaction with tumor microenvironment has revolutionized the cancer immune therapy field. In this review, we aim to discuss the molecular escape mechanisms of thyroid tumors from these drugs. We also highlight novel therapeutic options targeting other pathways than MAPK, including PI3K pathway, ALK translocations and HER2/3 receptors and their clinical impact. We also aim to discuss the usage of targeted therapy in restoring thyroid tumor sensitivity to RAI, and finally turn to extensively discuss the role of immunotherapy as a potential alternative treatment option for advanced thyroid diseases.

Comparison between standard and reduced volume radiotherapy in bladder preservation trimodality protocol for muscle-invasive bladder cancer patients

Aim

Our aim is to compare the toxicity, pelvic nodal relapse, and overall survival of whole bladder irradiation only to the standard technique of whole pelvis irradiation followed by bladder boost in patients with muscle-invasive bladder carcinoma undergoing bladder preservation protocol.

Material and method

A total of 60 patients with transitional cell carcinoma, stage T2-3, N0, M0 bladder cancer were subjected to maximal transurethral resection bladder tumour (TURB). Then, the patients were randomised into two groups: group I (30 patients) to receive whole pelvis radiotherapy 44 Gy followed by 20 Gy bladder boost. While group II (30 patients) were randomised to receive whole bladder radiotherapy alone for a total dose of 64 Gy. In both groups, concomitant cisplatin and paclitaxel were given weekly throughout the whole course of radiotherapy where conventional 2 Gy/fraction were used. Additionally, four cycles of adjuvant cisplatin and paclitaxel were given after the end of the chemoradiotherapy induction course.

Results

The first assessment after the induction chemoradiotherapy showed that complete response was achieved in 73.3% of patients in group I and 76.7% of the patients in group II. After a median follow-up of 2 years, regional relapse occurred in 7.1% of patients in group I and 10.3% in group II. (p = 1). Distant metastases were detected in 17.9% of patient in group I and 13.8% in group II (p = 0.73). The 2-year disease-free survival was 60% in group I and 63.3% in group II (p = 0.79). The whole 2-year overall survival was 75% in group I and 79.3% in group II (p = 0.689). Radiation gastrointestinal (GI) acute toxicity was higher in group I than in group II (p = 0.001), while late GI radiation toxicity was comparable in both groups.

Conclusion

Treating the bladder only, without elective pelvic nodal irradiation, did not compromise pelvic control rate, but significantly decreased the acute radiation toxicity.

Role of nanotechnology and gene delivery systems in TRAIL-based therapies

Since its identification as a member of the tumour necrosis factor (TNF) family, TRAIL (TNF-related apoptosis-inducing ligand) has emerged as a new avenue in apoptosis-inducing cancer therapies. Its ability to circumvent the chemoresistance of conventional therapeutics and to interact with cancer stem cells (CSCs) self-renewal pathways, amplified its potential as a cancer apoptotic agent. Many recombinant preparations of this death ligand and monoclonal antibodies targeting its death receptors have been tested in monotherapy and combinational clinical trials. Gene therapy is a new approach for cancer treatment which implies viral or non-viral functional transgene induction of apoptosis in cancer cells or repair of the underlying genetic abnormality on a molecular level. The role of this approach in overcoming the traditional barriers of radiation and chemotherapeutics systemic toxicity, risk of recurrence, and metastasis made it a promising platform for cancer treatment. The recent first Food Drug Administration (FDA) approved oncolytic herpes virus for melanoma treatment brings forth the potency of the cancer gene therapy approach in the future. Many gene delivery systems have been studied for intratumoural TRAIL gene delivery alone or in combination with chemotherapeutic agents to produce synergistic cancer cytotoxicity. However, there still remain many obstacles to be conquered for this different gene delivery systems. Nanomedicine on the other hand offers a new frontier for clinical trials and biomedical research. The FDA approved nanodrugs motivates horizon exploration for other nanoscale designed particles’ implications in gene delivery. In this review we aim to highlight the molecular role of TRAIL in apoptosis and interaction with cancer stem cells (CSCs) self-renewal pathways. Finally, we also aim to discuss the different roles of gene delivery systems, mesenchymal cells, and nanotechnology designs in TRAIL gene delivery.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

High Throughput Kinomic Profiling of Human Clear Cell Renal Cell Carcinoma Identifies Kinase Activity Dependent Molecular Subtypes

Despite the widespread use of kinase-targeted agents in clear cell renal cell carcinoma (CC-RCC), comprehensive kinase activity evaluation (kinomic profiling) of these tumors is lacking. Thus, kinomic profiling of CC-RCC may assist in devising a classification system associated with clinical outcomes, and help identify potential therapeutic targets. Fresh frozen CC-RCC tumor lysates from 41 clinically annotated patients who had localized disease at diagnosis were kinomically profiled using the PamStation®12 high-content phospho-peptide substrate microarray system (PamGene International). Twelve of these patients also had matched normal kidneys available that were also profiled. Unsupervised hierarchical clustering and supervised comparisons based on tumor vs. normal kidney and clinical outcome (tumor recurrence) were performed and coupled with advanced network modeling and upstream kinase prediction methods. Unsupervised clustering analysis of localized CC-RCC tumors identified 3 major kinomic groups associated with inflammation (A), translation initiation (B), and immune response and cell adhesions (C) processes. Potential driver kinases implicated include PFTAIRE (PFTK1), PKG1, and SRC, which were identified in groups A, B, and C, respectively. Of the 9 patients who had tumor recurrence, only one was found in Group B. Supervised analysis showed decreased kinase activity of CDK1 and RSK1-4 substrates in those which progressed compared to others. Twelve tumors with matching normal renal tissue implicated increased PIM's and MAPKAPK's in tumors compared to adjacent normal renal tissue. As such, comprehensive kinase profiling of CC-RCC tumors could provide a functional classification strategy for patients with localized disease and identify potential therapeutic targets.

Botryoid-type of embryonal rhabdomyosarcoma of renal pelvis in a young woman

A 22-year-old woman presented with three weeks history of intermittent left loin pain, on radiological evaluation by U\S and MRI revealed left renal pelvic mass, ureterorenoscopy and biopsy taken, but couldn’t reveal definitive diagnosis other than presence of a malignant process. Left nephroureterctomy was performed. Grossly there is a polypoid mass attached to the upper pole of the kidney by stalk. Light microscopic examination and immunohistochemical staining confirm a diagnosis of Botryoid-type of embryonal rhabdomyosarcoma. Treatment and follow up to 1 year is mentioned. Reviewing the literature the presented case is the second of this tumor in adult renal pelvis.

A clinical trial to study the effect of adding cis-retinoic acid during and after conventional treatment for pediatric neuroblastoma patient

10057

Background: Neuroblastoma is predominantly a tumor of early childhood, with two thirds of the cases presenting in children younger than 5 years. Cis-retinoic acid has been used as maintenance therapy for treatment of advanced neuroblastoma after BMT. Patients who received cis-retinoic acid had significantly better 3-year event-free survival than patients receiving no maintenance therapy. However, there is no data available about usingcis-retinoic acid during induction phase of chemotherapy. The aim of this study is to evaluate the efficacy of cis-retinoic acid when used in combination with conventional chemotherapy in pediatric patient who is newly diagnosed with locally advanced neuroblastoma. Methods: Seventeen newly diagnosed children with locally advanced neuroblastoma who is candidate to receive chemotherapy were also received cis-retinoic acid starting at a dose of 160 /m2 day (day 2–15 of chemotherapy) first the 3 patients, 20% dose reduction were allowed if toxicity occurred in first cohort of patient. . Patients were giving the drugs for at least 4 cycles. RT-PCR analysis of several related genes was done from tumor, sample after treatment. Results: Median age 2.4. Male:Female ratio was 1.4:1. Patients were stage III, IV (70%), II (30%). 88% of patients were presented with abdominal mass .Most patient received at least 6 cycles of OPEC/OJEC regimen. N Myc was done to 12 of patients. Median follow up was 6 months. Maximum tolerated dose were 130mg/m2, response was seen as CR 30%VGR 40, PR 12%, and PD 18%. Median event free survival was 12 months. Toxicity: Hypercalcemia mucositis, rash, and elevated liver enzymes were the main dose limiting effect of cis-retinoic acid. Preliminary collaborative analysis showed that down regulation of N-MYC is related to response rate. Conclusions: Cis-retinoic acid at dose 130mg/m2 is a well tolerated drug with chemotherapy. Response to treatment is better than historical control. Randomized phase III trial is warranted.

No significant financial relationships to disclose.

An immunomagnetic-based method for the purification of ovarian cancer cells from patient-derived ascites

OBJECTIVE

Primary ovarian cancer cells obtained from fresh tumor have many advantages over established cell lines. Therefore, a procedure for the specific and efficient purification of such neoplastic cells is critical. We report an effective immunomagnetic method for the isolation of tumor cells from the ascitic fluid of patients diagnosed with ovarian adenocarcinoma.

METHODS

This procedure incorporates the use of monoclonal antibody (mAb) CC49, which recognizes the tumor-associated glycoprotein 72 (TAG-72). TAG-72 is highly expressed on ovarian tumor cell surfaces with little or no reactivity with normal tissues. Also used in this protocol are immunomagnetic beads, which bind to the CC49 mAb via a secondary antibody. When ovarian cancer cells adhere to the magnetic beads, a magnetic field is used to separate the tumor cells from all other cellular components.

RESULTS

Using ascitic fluid from five patients, we found that preparations before purification contained between 38 and 52% neoplastic cells. Using our method, we produced preparations that were between 63 and 96% pure for cancer cells, thus obtaining an average increase in tumor cell enrichment of 86%.

CONCLUSION

We, therefore, believe this method is preferable for producing high yields of pure ovarian neoplastic cells. We are now employing this technique in our laboratory to provide a stringent and pure template for our studies on gene transfer to primary ovarian cancer cells.

Adenoviral-mediated suicide gene therapy for ovarian cancer

The purpose of this phase I study was to determine the potential efficacy of adenoviral-mediated suicide gene therapy in women with recurrent ovarian cancer. Fourteen patients were treated intraperitoneally with herpes simplex virus-thymidine kinase (HSV-TK)-encoding adenovirus (AdHSV-TK) in dosages ranging between 1x10(9) and 1x10(11) pfu. Beginning 2 days later, ganciclovir (GCV) was administered intravenously at a dose of 5 mg/kg bid for 14 days. Transient vector-associated fever was experienced by 4 of 14 (29%) treated patients. Other possible vector-associated constitutional symptoms, abdominal pain, and gastrointestinal symptoms were experienced by 6 of 14 (43%) treated patients. No other dose-limiting vector-specific side effects were noted. Of the 13 patients evaluable for response, 5 (38%) had stable disease and 8 (62%) had evidence of progressive disease. Molecular analysis of evaluable ascites samples demonstrated the presence of transgene DNA and RNA in most patients 2 days following Ad HSV-TK administration. Ten of 11 evaluable patients had an increase in anti-adenovirus antibody titer. These results suggest that treatment with AdHSV-TK in combination with GCV is feasible in the context of human ovarian cancer and tolerated at the dosages studied.

Antineoplastic effect of anti-erbB-2 intrabody is not correlated with scFv affinity for its target

Intracellular single-chain antibodies (scFvs) have emerged as a powerful method to knock out expression of oncoproteins. We have demonstrated previously that scFvs directed against a variety of molecular targets induce specific toxicity in tumor cells. Recently, the utility of an anti-erbB-2 scFv has predicated its evaluation in a phase I gene therapy clinical trial. The utility of scFv as an intrabody is closely linked to its interaction with a target, limiting the contribution of the latter to the neoplastic phenotype. In this study, we sought to determine whether improvement in the affinity of the scFv for its cognate target could improve the efficiency of intrabody-mediated oncoprotein knockout. We compared in erbB-2-positive and -negative tumor cells the function of plasmids encoding a newly developed C6.5 anti-erbB-2 scFv, which has a 1000-fold higher affinity, with our original e23 anti-erbB-2 scFv. Intracellular scFv expression, target binding, and tumor cell cytotoxicity were found to be similar in all conditions tested, including dose-response studies with limiting dilutions of the scFv. On this basis, we have concluded that the antineoplastic effect of anti-erbB-2 intrabody is not correlated with scFv affinity for its target.

A cancer gene therapy approach utilizing an anti-erbB-2 single-chain antibody-encoding adenovirus (AD21): a phase I trial

The purpose of this Phase I study was to determine the feasibility of using an anti-erbB-2-encoding adenovirus (Ad21) to treat erbB-2-overexpressing ovarian cancer. Recurrent ovarian cancer patients were treated i.p. with Ad21 in dosages ranging from 1 x 10(9) to 1 x 10(11) pfu. Patients were monitored after treatment for evidence of clinical toxicity and efficacy. Peritoneal aspirates and serum samples were obtained to assess for evidence of gene transfer/expression, for generation of wild-type vector, and antiadenoviral humoral response. Fifteen patients were treated per study specifications. Treatment-specific grade 1/2 fever was experienced by 9 of 15 (60%) patients. Other transient grade 1/2 constitutional, pain, and gastrointestinal symptoms were also experienced. No dose-limiting vector-related toxicity was experienced. Of 13 patients evaluable for response, 5 (38%) had stable disease and 8 (61%) had evidence of progressive disease. One patient with nonmeasurable disease normalized her CA125 at the 8-week evaluation, and one patient with nonmeasurable disease remained without clinical evidence of disease for 6 months after treatment. PCR analysis of peritoneal aspirates demonstrated the presence of Ad21 in 84.6%, 84.6%, and 61.6% of evaluable specimens at days 2, 14, and 56 after treatment, respectively. No wild-type virus was detected. Reverse transcription-PCR analysis demonstrated expression of the anti-erbB-2 sFv-encoding gene in 10 of 14 evaluable patients at day 2. Five of six evaluable patients had an increase in antiadenovirus antibody titer. This study suggests that adenoviral-mediated gene therapy using an anti-erbB-2-directed intrabody is feasible in the context of human ovarian cancer.

Pro-apoptotic treatment with an adenovirus encoding Bax enhances the effect of chemotherapy in ovarian cancer

BACKGROUND

Tumor cell heterogeneity and resistance to chemotherapy-mediated cell death are major obstacles in cancer therapy. It has been reported that expression of the pro-apoptotic molecule Bax can induce cell death or sensitize tumor cells to chemotherapy in stable cell clones derived from tumor cells. However, these studies are limited in that they cannot represent the heterogeneity of cancer cells observed in vivo. In this study, we have further explored the therapeutic potential of Bax.

METHODS

Using an inducible recombinant Bax adenovirus, we screened a panel of ovarian cancer cell lines and primary patient-derived ovarian tumor cells for their sensitivity to Bax-mediated cytotoxicity. Apoptotic cell death was evaluated qualitatively with Hoechst staining and quantitatively with MTS and Annexin V-based assays. Endogenous levels of both Bcl-2 and Bax protein and p53 status were evaluated. The potential of bax to sensitize ovarian cancer lines to chemotherapy was also tested. Dose-response curves were generated to evaluate cell death.

RESULTS

Overexpression of Bax directly induced apoptosis in both ovarian cancer cell lines and the patient-derived primary cancer cells. However, the sensitivity of these cells to Bax varied and appeared to be independent of both the status of p53 and the endogenous levels of bcl-2 or Bax, critical molecules in the apoptotic pathway. Importantly, overexpression of Bax significantly enhanced chemotherapy-induced cytotoxicity in both established cell lines and primary ovarian carcinoma cells.

CONCLUSIONS

These studies suggest that overexpression of Bax alone or in combination with chemotherapy may provide a means to overcome the problems imposed by the heterogeneous nature of tumors, ultimately augmenting the efficacy of chemotherapy in patients suffering from ovarian cancer.

Gene therapy for carcinoma of the breast: Pro-apoptotic gene therapy

The dysregulation of apoptosis contributes in a variety of ways to the malignant phenotype. It is increasingly recognized that the alteration of pro-apoptotic and anti-apoptotic molecules determines not only escape from mechanisms that control cell cycle and DNA damage, but also endows the cancer cells with the capacity to survive in the presence of a metabolically adverse milieu, to resist the attack of the immune system, to locally invade and survive despite a lack of tissue anchorage, and to evade the otherwise lethal insults induced by drugs and radiotherapy. A multitude of apoptosis mediators has been identified in the past decade, and the roles of several of them in breast cancer have been delineated by studying the clinical correlates of pathologically documented abnormalities. Using this information, attempts are being made to correct the fundamental anomalies at the genetic level. Fundamental to this end are the design of more efficient and selective gene transfer systems, and the employment of complex interventions that are tailored to breast cancer and that are aimed concomitantly towards different components of the redundant regulatory pathways. The combination of such genetic modifications is most likely to be effective when combined with conventional treatments, thus robustly activating several pro-apoptotic pathways.

Genetically modified CD34+ cells as cellular vehicles for gene delivery into areas of angiogenesis in a rhesus model

To develop a cellular vehicle able to reach systemically disseminated areas of angiogenesis, we sought to exploit the natural tropism of circulating endothelial progenitor cells (EPCs). Primate CD34+ EPCs were genetically modified with high efficiency and minimal toxicity using a non-replicative herpes virus vector. These EPCs localized in a skin autograft model of angiogenesis in rhesus monkeys, and sustained the expression of a reporter gene for several weeks while circulating in the blood. In animals infused with autologous CD34+ EPCs transduced with a thymidine kinase-encoding herpes virus, skin autografts and subcutaneous Matrigel pellets impregnated with vascular growth factors underwent necrosis or accelerated regression after administration of ganciclovir. Importantly, the whole intervention was perfectly well tolerated. The accessibility, easy manipulation, lack of immunogenicity of the autologous CD34+ cell vehicles, and tropism for areas of angiogenesis render autologous CD34+ circulating endothelial progenitors as ideal candidates for exploration of their use as cellular vehicles when systemic gene delivery to those areas is required. Gene Therapy (2000) 7, 43-52.

Patulin-induced inhibition of protein synthesis in hepatoma tissue culture

Patulin is a mycotoxin produced by several species of fungi and is commonly found in fruits. It is regulated in several countries at a tolerance level of 50 micrograms/Kg. We investigated its ability to inhibit cell growth in hepatoma tissue culture and its ability to inhibit protein synthesis. It was found to be cytostatic at concentration of 1 microgram/mL (6.4 microM). It inhibits protein synthesis by two mechanisms: inhibition of amino acid uptake into the cell and their incorporation into proteins. The former mechanism appears to be more significant than the latter. This is consistent with previous work showing the ability of patulin to perturb plasma membrane function.

Inhibition of aminoacyl-tRNA synthetases by the mycotoxin patulin

The effect of patulin on tRNA aminoacylation has been determined. This mycotoxin inhibits the aminoacylation process by irreversibly inactivating aminoacyl-tRNA synthetases. At neutral and alkaline pH-values, the inactivation occurs mainly by modification of essential thiol groups of the protein, whereas at acidic pH, where the effect is the most pronounced, the modification of other amino acid residues cannot be excluded.