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1.  Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA 
The EMBO Journal  2015;34(11):1478-1492.
There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. This interaction triggers the degradation of GcvB by RNase E, alleviating the GcvB-mediated mRNA repression of other amino acid-related transport and metabolic genes. Intriguingly, since the gltIJKL mRNA itself is a target of GcvB, the SroC sponge seems to enable both an internal feed-forward loop to activate its parental mRNA in cis and activation of many trans-encoded mRNAs in the same pathway. Disabling this mRNA cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources.
doi:10.15252/embj.201490546
PMCID: PMC4474525  PMID: 25630703
GcvB; Hfq; noncoding RNA; RNase E; SroC
2.  Synthetic viability genomic screening defines Sae2 function in DNA repair 
The EMBO Journal  2015;34(11):1509-1522.
DNA double-strand break (DSB) repair by homologous recombination (HR) requires 3′ single-stranded DNA (ssDNA) generation by 5′ DNA-end resection. During meiosis, yeast Sae2 cooperates with the nuclease Mre11 to remove covalently bound Spo11 from DSB termini, allowing resection and HR to ensue. Mitotic roles of Sae2 and Mre11 nuclease have remained enigmatic, however, since cells lacking these display modest resection defects but marked DNA damage hypersensitivities. By combining classic genetic suppressor screening with high-throughput DNA sequencing, we identify Mre11 mutations that strongly suppress DNA damage sensitivities of sae2Δ cells. By assessing the impacts of these mutations at the cellular, biochemical and structural levels, we propose that, in addition to promoting resection, a crucial role for Sae2 and Mre11 nuclease activity in mitotic DSB repair is to facilitate the removal of Mre11 from ssDNA associated with DSB ends. Thus, without Sae2 or Mre11 nuclease activity, Mre11 bound to partly processed DSBs impairs strand invasion and HR.
doi:10.15252/embj.201590973
PMCID: PMC4474527  PMID: 25899817
Mre11; Sae2; suppressor screening; synthetic viability; whole-genome sequencing
3.  Extracellular matrix elasticity and topography: material-based cues that affect cell function via conserved mechanisms 
Chemical, mechanical, and topographic extracellular matrix (ECM) cues have been extensively studied for their influence on cell behavior. These ECM cues alter cell adhesion, cell shape, and cell migration, and activate signal transduction pathways to influence gene expression, proliferation, and differentiation. ECM elasticity and topography, in particular, have emerged as material properties of intense focus based on strong evidence these physical cue can partially dictate stem cell differentiation. Cells generate forces to pull on their adhesive contacts, and these tractional forces appear to be a common element of cells’ responses to both elasticity and topography. This review focuses on recently published work that links ECM topography and mechanics and their influence on differentiation and other cell behaviors, We also highlight signaling pathways typically implicated in mechanotransduction that are (or may be) shared by cells subjected to topographic cues. Finally, we conclude with a brief discussion of the potential implications of these commonalities for cell based therapies and biomaterial design.
doi:10.1002/jbm.a.35254
PMCID: PMC4258536  PMID: 24910444
topography; matrix mechanics; cell fate; mechanotransduction; differentiation
4.  Genetic and epigenetic aberrations occurring in colorectal tumors associated with serrated pathway 
International Journal of Cancer  2015;138(7):1634-1644.
To clarify molecular alterations in serrated pathway of colorectal cancer (CRC), we performed epigenetic and genetic analyses in sessile serrated adenoma/polyps (SSA/P), traditional serrated adenomas (TSAs) and high‐methylation CRC. The methylation levels of six Group‐1 and 14 Group‐2 markers, established in our previous studies, were analyzed quantitatively using pyrosequencing. Subsequently, we performed targeted exon sequencing analyses of 126 candidate driver genes and examined molecular alterations that are associated with cancer development. SSA/P showed high methylation levels of both Group‐1 and Group‐2 markers, frequent BRAF mutation and occurrence in proximal colon, which were features of high‐methylation CRC. But TSA showed low‐methylation levels of Group‐1 markers, less frequent BRAF mutation and occurrence at distal colon. SSA/P, but not TSA, is thus considered to be precursor of high‐methylation CRC. High‐methylation CRC had even higher methylation levels of some genes, e.g., MLH1, than SSA/P, and significant frequency of somatic mutations in nonsynonymous mutations (p < 0.0001) and insertion/deletions (p = 0.002). MLH1‐methylated SSA/P showed lower methylation level of MLH1 compared with high‐methylation CRC, and rarely accompanied silencing of MLH1 expression. The mutation frequencies were not different between MLH1‐methylated and MLH1‐unmethylated SSA/P, suggesting that MLH1 methylation might be insufficient in SSA/P to acquire a hypermutation phenotype. Mutations of mismatch repair genes, e.g., MSH3 and MSH6, and genes in PI3K, WNT, TGF‐β and BMP signaling (but not in TP53 signaling) were significantly involved in high‐methylation CRC compared with adenoma, suggesting importance of abrogation of these genes in serrated pathway.
What's new?
The serrated pathway of colorectal cancer (CRC) development is characterized by the presence of saw‐toothed colonic crypts and by a high‐methylation epigenotype. Not all serrated lesions, however, give rise to CRC. Here, only sessile serrated adenoma/polyps, a potentially malignant serrated polyp subtype, were identified as precursors of high‐methylation CRC. Moreover, MLH1 expression, silencing of which previously was linked to microsatellite instability in CRC, was found to be preserved in most serrated adenoma/polyp samples. The findings suggest that the acquisition of a hypermutation phenotype in serrated CRC likely depends on extensive MLH1 methylation and mutation of additional mismatch repair genes.
doi:10.1002/ijc.29903
PMCID: PMC4737347  PMID: 26510091
colorectal cancer (CRC); sessile serrated adenoma/polyp (SSA/P); traditional serrated adenoma (TSA); DNA methylation; gene mutation
5.  The influence of neighbourhood-level socioeconomic deprivation on cardiovascular disease mortality in older age: longitudinal multilevel analyses from a cohort of older British men 
Background
Evidence from longitudinal studies on the influence of neighbourhood socioeconomic factors in older age on cardiovascular disease (CVD) mortality is limited. We aimed to investigate the prospective association of neighbourhood-level deprivation in later life with CVD mortality, and assess the underlying role of established cardiovascular risk factors.
Methods
A socially representative cohort of 3924 men, aged 60–79 years in 1998–2000, from 24 British towns, was followed up until 2012 for CVD mortality. Quintiles of the national Index of Multiple Deprivation (IMD), a composite score of neighbourhood-level factors (including income, employment, education, housing and living environment) were used. Multilevel logistic regression with discrete-time models (stratifying follow-up time into months) were used.
Results
Over 12 years, 1545 deaths occurred, including 580 from CVD. The risk of CVD mortality showed a graded increase from IMD quintile 1 (least deprived) to 5 (most deprived). Compared to quintile 1, the age-adjusted odds of CVD mortality in quintile 5 were 1.71 (95% CI 1.32 to 2.21), and 1.62 (95% CI 1.23 to 2.13) on further adjustment for individual social class, which was attenuated slightly to 1.44 (95% CI 1.09 to 1.89), but remained statistically significant after adjustment for smoking, body mass index, physical activity and use of alcohol. Further adjustment for blood pressure, high-density lipoprotein cholesterol and prevalent diabetes made little difference.
Conclusions
Neighbourhood-level deprivation was associated with an increased risk of CVD mortality in older people independent of individual-level social class and cardiovascular risk factors. The role of other specific neighbourhood-level factors merits further research.
doi:10.1136/jech-2015-205542
PMCID: PMC4680118  PMID: 26285580
DEPRIVATION; AGEING; Cardiovascular disease; INEQUALITIES; MULTILEVEL MODELLING
6.  Whole-body MRI of patients with polymyalgia rheumatica identifies a distinct subset with complete patient-reported response to glucocorticoids 
Annals of the Rheumatic Diseases  2015;74(12):2188-2192.
Objectives
To determine whether whole-body MRI defines clinically relevant subgroups within polymyalgia rheumatica (PMR) including glucocorticoid responsiveness.
Methods
22 patients with PMR and 16 with rheumatoid arthritis (RA), untreated and diagnosed by consultant rheumatologists, underwent whole-body, multiple-joint MRI, scored by two experts. Patients with PMR reported whether they felt ‘back to normal’ on glucocorticoid therapy and were followed for a median of 2 years.
Results
All patients with PMR were deemed to respond to glucocorticoids clinically. A characteristic pattern of symmetrical, extracapsular inflammation, adjacent to greater trochanter, acetabulum, ischial tuberosity and/or symphysis pubis, was observed in 14/22 of the PMR cases. In PMR, this pattern was associated with complete glucocorticoid response (p=0.01), higher pretreatment C-reactive protein (CRP) and serum interleukin-6 (IL-6), and better post-treatment fatigue and function. Only 1/14 in the extracapsular group could stop glucocorticoids within 1 year, compared with 4/7 of the others. A score derived from the five sites discriminating best between PMR and RA correlated with IL-6 (p<0.002). IL-6 levels ≥16.8 pg/mL had 86% sensitivity and 86% specificity for the extracapsular MRI pattern.
Conclusions
A subset of patients with rheumatologist-diagnosed PMR had a characteristic, extracapsular pattern of MRI inflammation, associated with elevated IL-6/CRP and with complete patient-reported glucocorticoid responsiveness.
doi:10.1136/annrheumdis-2015-207395
PMCID: PMC4680120  PMID: 26376658
Magnetic Resonance Imaging; Polymyalgia Rheumatica; Cytokines
7.  Retroviral DNA Transposition: Themes and Variations 
Microbiology spectrum  2014;2(5):MDNA3-0005-2014-.
SUMMARY
Retroviruses and LTR retrotransposons are transposable elements that encapsidate the RNAs that are intermediates in the transposition of DNA copies of their genomes (proviruses), from one cell (or one locus) to another. Mechanistic similarities in DNA transposase enzymes and retroviral/retrotransposon integrases underscore the close evolutionary relationship among these elements.
The retroviruses are very ancient infectious agents, presumed to have evolved from Ty3/Gypsy LTR retrotransposons (1), and DNA copies of their sequences can be found embedded in the genomes of most, if not all, members of the tree of life. All retroviruses share a specific gene arrangement and similar replication strategies. However, given their ancestries and occupation of diverse evolutionary niches, it should not be surprising that unique sequences have been acquired in some retroviral genomes and that the details of the mechanism by which their transposition is accomplished can vary.
While every step in the retrovirus lifecycle is, in some sense, relevant to transposition, this Chapter focuses mainly on the early phase of retroviral replication, during which viral DNA is synthesized and integrated into its host genome. Some of the initial studies that set the stage for current understanding are highlighted, as well as more recent findings obtained through use of an ever-expanding technological toolbox including genomics, proteomics, and siRNA screening. Persistence in the area of structural biology has provided new insight into conserved mechanisms as well as variations in detail among retroviruses, which can also be instructive.
doi:10.1128/microbiolspec.MDNA3-0005-2014
PMCID: PMC4383315  PMID: 25844274
8.  Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA 
The EMBO Journal  2015;34(11):1478-1492.
There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. This interaction triggers the degradation of GcvB by RNase E, alleviating the GcvB-mediated mRNA repression of other amino acid-related transport and metabolic genes. Intriguingly, since the gltIJKL mRNA itself is a target of GcvB, the SroC sponge seems to enable both an internal feed-forward loop to activate its parental mRNA in cis and activation of many trans-encoded mRNAs in the same pathway. Disabling this mRNA cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources.
doi:10.15252/embj.201490546
PMCID: PMC4474525  PMID: 25630703
GcvB; Hfq; noncoding RNA; RNase E; SroC
9.  Synthetic viability genomic screening defines Sae2 function in DNA repair 
The EMBO Journal  2015;34(11):1509-1522.
DNA double-strand break (DSB) repair by homologous recombination (HR) requires 3′ single-stranded DNA (ssDNA) generation by 5′ DNA-end resection. During meiosis, yeast Sae2 cooperates with the nuclease Mre11 to remove covalently bound Spo11 from DSB termini, allowing resection and HR to ensue. Mitotic roles of Sae2 and Mre11 nuclease have remained enigmatic, however, since cells lacking these display modest resection defects but marked DNA damage hypersensitivities. By combining classic genetic suppressor screening with high-throughput DNA sequencing, we identify Mre11 mutations that strongly suppress DNA damage sensitivities of sae2∆ cells. By assessing the impacts of these mutations at the cellular, biochemical and structural levels, we propose that, in addition to promoting resection, a crucial role for Sae2 and Mre11 nuclease activity in mitotic DSB repair is to facilitate the removal of Mre11 from ssDNA associated with DSB ends. Thus, without Sae2 or Mre11 nuclease activity, Mre11 bound to partly processed DSBs impairs strand invasion and HR.
doi:10.15252/embj.201590973
PMCID: PMC4474527  PMID: 25899817
Mre11; Sae2; suppressor screening; synthetic viability; whole-genome sequencing
10.  Platelet derived growth factor (PDGF) contained in Platelet Rich Plasma (PRP) stimulates migration of osteoblasts by reorganizing actin cytoskeleton 
Cell Adhesion & Migration  2014;8(6):595-602.
Platelet-rich plasma (PRP) is a platelet concentrate in a small volume of plasma. It is highly enriched in growth factors able to stimulate the migration and growth of bone-forming cells. PRP is often used in clinical applications, as dental surgery and fracture healing. Platelet derived growth factor (PDGF), is highly concentrated in PRP and it was shown in our previous studies to provide the chemotactic stimulus to SaOS-2 osteoblasts to move in a microchemotaxis assay. Aim of the present studies is to analyze the effects of a PRP pretreatment (short time course: 30–150 min) of SaOS-2 cells with PRP on the organization of actin cytoskeleton, the main effector of cell mobility. The results indicate that a pretreatment with PRP increases chemokinesis and chemotaxis and concomitantly induces the organization of actin microfilaments, visualized by immunocytochemistry, in a directionally elongated phenotype, which is characteristic of the cells able to move. PRP also produces a transient increase in the expression of PGDF α receptor. This reorganization is blocked by the immunoneutralization of PDGF demonstrating the responsibility of this growth factor in triggering the mechanisms responsible for cellular movements.
doi:10.4161/19336918.2014.972785
PMCID: PMC4594427  PMID: 25482626
actin; chemotaxis; cytoskeleton; migration; osteoblasts; PRP; PDGF receptor; SaOS-2
11.  Primary Care Utilization and Colorectal Cancer Incidence and Mortality Among Medicare Beneficiaries 
Annals of internal medicine  2013;159(7):437-446.
Background
Utilization of primary care may decrease colorectal cancer (CRC) incidence and death through greater receipt of CRC screening tests.
Objective
To examine the association of primary care utilization with CRC incidence, CRC deaths, and all-cause mortality.
Design
Population-based, case–control study.
Setting
Medicare program.
Participants
Persons aged 67 to 85 years diagnosed with CRC between 1994 and 2005 in U.S. Surveillance, Epidemiology, and End Results (SEER) regions matched with control patients (n = 205 804 for CRC incidence, 54 160 for CRC mortality, and 121 070 for all-cause mortality).
Measurements
Primary care visits in the 4- to 27-month period before CRC diagnosis, CRC incidence, CRC mortality, and all-cause mortality.
Results
Compared with persons having 0 or 1 primary care visit, persons with 5 to 10 visits had lower CRC incidence (adjusted odds ratio [OR], 0.94 [95% CI, 0.91 to 0.96]) and mortality (adjusted OR, 0.78 [CI, 0.75 to 0.82]) and lower all-cause mortality (adjusted OR, 0.79 [CI, 0.76 to 0.82]). Associations were stronger in patients with late-stage CRC diagnosis, distal lesions, and diagnosis in more recent years when there was greater Medicare screening coverage. Ever receipt of CRC screening and polypectomy mediated the association of primary care utilization with CRC incidence.
Limitation
This study used administrative data, which made it difficult to identify potential confounders and prevented examination of the content of primary care visits.
Conclusion
Medicare beneficiaries with higher utilization of primary care have lower CRC incidence and mortality and lower overall mortality. Increasing and promoting access to primary care in the United States for Medicare beneficiaries may help decrease the national burden of CRC.
Primary Funding Source
American Cancer Society.
doi:10.7326/0003-4819-159-7-201310010-00003
PMCID: PMC4605549  PMID: 24081284
12.  Cucurbit [7] uril encapsulated cisplatin overcomes resistance to cisplatin induced by Rab25 overexpression in an intraperitoneal ovarian cancer model 
Background
Ovarian cancer is the most fatal of gynaecological malignancies, usually detected at a late stage with intraperitoneal dissemination. Appropriate preclinical models are needed that recapitulate both the histopathological and molecular features of human ovarian cancer for drug-efficacy analysis.
Methods
Longitudinal studies comparing cisplatin performance either alone or in a novel cisplatin-based delivery-system, cucurbit[7]uril-encapsulated cisplatin (cisplatin@CB[7]) were performed on subcutaneous (s.c.) and intraperitoneal (i.p.) xenografts using the human ovarian cancer cell line A2780 stably expressing the small GTPase Rab25, which allows A2780 intraperitoneal growth; and luciferase, to allow tumour load measurement by non-invasive bioluminescent imaging.
Results
Rab25 expression induced cisplatin resistance compared to the parental cell line as assessed by the MTT assay in vitro. These findings did not translate in vivo, where cisplatin resistance was determined by the microenvironment. Subcutaneous xenografts of either parental A2780 or cisplatin-resistant Rab25-expressing A2780 cells presented similar responses to cisplatin treatment. In contrast, increased cisplatin resistance was only detected in i.p. tumours. Treatment of the cisplatin-resistant i.p. model with the novel cisplatin@CB[7] delivery system resulted in a substantial reduction of i.p. tumour load and increased necrosis.
Conclusions
Poor clinical performance of novel chemotherapeutics might reflect inappropriate preclinical models. Here we present an ovarian i.p. model that recapitulates the histopathological and chemoresistant features of the clinical disease. In addition, we demonstrate that the novel cisplatin-delivery system, cisplatin@CB[7] may have utility in the treatment of drug-resistant ovarian human cancers.
doi:10.1186/s13048-015-0189-4
PMCID: PMC4575495  PMID: 26384969
13.  The Use of Biospecimens in Population-Based Research: A Review of the National Cancer Institute's Division of Cancer Control and Population Sciences Grant Portfolio 
Biopreservation and Biobanking  2014;12(4):240-245.
Over the past two decades, researchers have increasingly used human biospecimens to evaluate hypotheses related to disease risk, outcomes and treatment. We conducted an analysis of population-science cancer research grants funded by the National Cancer Institute (NCI) to gain a more comprehensive understanding of biospecimens and common derivatives involved in those studies and identify opportunities for advancing the field. Data available for 1,018 extramural, peer-reviewed grants (active as of July 2012) supported by the Division of Cancer Control and Population Sciences (DCCPS), the NCI Division that supports cancer control and population-science extramural research grants, were analyzed. 455 of the grants were determined to involve biospecimens or derivatives. The most common specimen types included were whole blood (51% of grants), serum or plasma (40%), tissue (39%), and the biospecimen derivative, DNA (66%). While use of biospecimens in molecular epidemiology has become common, biospecimens for behavioral and social research is emerging, as observed in our analysis. Additionally, we found the majority of grants were using already existing biospecimens (63%). Grants that involved use of existing biospecimens resulted in lower costs (studies that used existing serum/plasma biospecimens were 4.2 times less expensive) and more publications per year (1.4 times) than grants collecting new biospecimens. This analysis serves as a first step at understanding the types of biospecimen collections supported by NCI DCCPS. There is room to encourage increased use of archived biospecimens and new collections of rarer specimen and cancer types, as well as for behavioral and social research. To facilitate these efforts, we are working to better catalogue our funded resources and make that data available to the extramural community.
doi:10.1089/bio.2014.0009
PMCID: PMC4150371  PMID: 25162460
14.  Assessment of DNA Encapsulation, a New Room-Temperature DNA Storage Method 
Biopreservation and Biobanking  2014;12(3):176-183.
A new procedure for room-temperature storage of DNA was evaluated whereby DNA samples from human tissue, bacteria, and plants were stored under an anoxic and anhydrous atmosphere in small glass vials fitted in stainless-steel, laser-sealed capsules (DNAshells®). Samples were stored in DNAshells® at room temperature for various periods of time to assess any degradation and compare it to frozen control samples and those stored in GenTegra™ tubes. The study included analysis of the effect of accelerated aging by using a high temperature (76°C) at 50% relative humidity. No detectable DNA degradation was seen in samples stored in DNAshells® at room temperature for 18 months. Polymerase chain reaction experiments, pulsed field gel electrophoresis, and amplified fragment length polymorphism analyses also demonstrated that the protective properties of DNAshells® are not affected by storage under extreme conditions (76°C, 50% humidity) for 30 hours, guaranteeing 100 years without DNA sample degradation. However, after 30 hours of storage at 76°C, it was necessary to include adjustments to the process in order to avoid DNA loss. Successful protection of DNA was obtained for 1 week and even 1 month of storage at high temperature by adding trehalose, which provides a protective matrix. This study demonstrates the many advantages of using DNAshells® for room-temperature storage, particularly in terms of long-term stability, safety, transport, and applications for molecular biology research.
doi:10.1089/bio.2013.0082
PMCID: PMC4128249  PMID: 24955733
15.  Factors Associated with Willingness to Participate in Biospecimen Research Among Chinese Americans 
Biopreservation and Biobanking  2014;12(2):131-138.
A paucity of information exists on the recruitment of Asian Americans for biospecimen research. Although studies show that Chinese Americans are at high risk for hepatitis B virus (HBV) infection, little is known about their willingness to participate in HBV-related biospecimen research and how knowledge, attitudes, and cultural factors impact their willingness to participate. The study was guided by Community-Based Participatory Research principles. Data were derived from an assessment study on HBV-related biospecimen research participation among Chinese Americans in the Philadelphia region. The assessment was conducted with 415 Chinese Americans recruited from eight Chinese community-based organizations. Cultural beliefs, knowledge, and attitudes toward biospecimen research were examined for associations with their willingness to participate in biospecimen banking research. Overall, 192 (46.3%) of 415 participants who completed the assessment indicated they were willing to participate if they were invited to donate blood to be frozen and stored for future HBV biospecimen studies. Cultural variables significant in bivariate analysis included collectivism, knowledge about biospecimen research, and Yin-Yang beliefs. Fatalism and individualism were not associated with participation willingness. In multivariate analysis, age, health care attitudes, and trust were significantly associated with willingness to participate in biospecimen banking research. Asian American communities have little knowledge of biospecimen banking and will benefit from educational campaigns that emphasize collective benefits and attitudes towards and trust in the health care system. Understanding cultural factors is important for improving Chinese Americans' knowledge, awareness, and intentions of participation in biospecimen research. Similar efforts need to be undertaken to develop culturally appropriate educational intervention programs to increase participation in biospecimen research among other Asian American groups.
doi:10.1089/bio.2013.0081
PMCID: PMC3995351  PMID: 24749880
16.  Introducing Research Initiatives into Healthcare: What Do Doctors Think? 
Biopreservation and Biobanking  2014;12(2):91-98.
Background: Current national and international policies emphasize the need to develop research initiatives within our health care system. Institutional biobanking represents a modern, large-scale research initiative that is reliant upon the support of several aspects of the health care organization. This research project aims to explore doctors' views on the concept of institutional biobanking and to gain insight into the factors which impact the development of research initiatives within healthcare systems.
Methods: Qualitative research study using semi-structured interviews. The research was conducted across two public teaching hospitals in Sydney, Australia where institutional biobanking was being introduced. Twenty-five participants were interviewed, of whom 21 were medical practitioners at the specialist trainee level or above in a specialty directly related to biobanking; four were key stakeholders responsible for the design and implementation of the biobanking initiative.
Results: All participants strongly supported the concept of institutional biobanking. Participants highlighted the discordance between the doctors who work to establish the biobank (the contributors) and the researchers who use it (the consumers). Participants identified several barriers that limit the success of research initiatives in the hospital setting including: the ‘resistance to change’ culture; the difficulties in engaging health professionals in research initiatives; and the lack of incentives offered to doctors for their contribution. Doctors positively valued the opportunity to advise the implementation team, and felt that the initiative could benefit from their knowledge and expertise.
Conclusion: Successful integration of research initiatives into hospitals requires early collaboration between the implementing team and the health care professionals to produce a plan that is sensitive to the needs of the health professionals and tailored to the hospital setting. Research initiatives must consider incentives that encourage doctors to adopt operational responsibility for hospital research initiatives.
doi:10.1089/bio.2013.0069
PMCID: PMC3995354  PMID: 24749875
17.  Cancer Patient Perceptions about Biobanking and Preferred Timing of Consent 
Biopreservation and Biobanking  2014;12(2):106-112.
Little is known about how cancer patients feel about donating their tissue, especially in a multiethnic population. Structured interviews were conducted with 30 patients recently diagnosed with cancer, referred to the study by six cancer surgeons and oncologists and by other patients in the study. The participants reported a variety of cancers, and the sample reflected the racial distribution of Hawai`i, including Caucasians (23%), Native Hawaiians and Pacific Islanders (27%), Asians (37%), Hispanics (7%), Native Americans (3%), and African Americans (3%). The interview questions and analysis were guided by the Framework Approach, with interview questions based on pre-set aims. Findings suggest that most cancer patients would donate cancer tissue to science, especially if informed that doing so could help researchers find causes of and cures for cancer. Patients varied on when in their cancer journey they would be most receptive to being asked for a donation, however two-thirds thought they would be more receptive if approached after surgery. Only three of the 30 patients said they would want to be re-consented each time their tissue is requested for research. They identified their physician as the preferred messenger regarding tissue donation. No obvious differences were seen by race. Findings confirm those of other researchers who have reported broad support for biobank participation if informed consent and confidentiality could be assured. Given that the physician was seen as the key messenger about biobanking, more education is needed around cancer tissue collection for physicians, as well as for cancer patients.
doi:10.1089/bio.2013.0083
PMCID: PMC3995435  PMID: 24749877
18.  Clinical Biospecimens: Reference Materials, Certified for Nominal Properties? 
Biopreservation and Biobanking  2014;12(2):113-120.
This report makes the case for clinical biospecimens to be certified for nominal properties, in particular the diagnosis, and to attain the level of Reference Materials. Clinical certified biospecimens that are collected, processed, characterized, stored, and distributed by biobanks are urgently needed to facilitate diagnostic test development, evaluation, and quality assurance. Four examples are provided to illustrate this purpose and the certification approaches that could be applied are proposed.
doi:10.1089/bio.2013.0086
PMCID: PMC3995442  PMID: 24749878
19.  Evaluation of Sericin as a Fetal Bovine Serum-Replacing Cryoprotectant During Freezing of Human Mesenchymal Stromal Cells and Human Osteoblast-Like Cells 
Biopreservation and Biobanking  2014;12(2):99-105.
A reliable, cryoprotective, xeno-free medium suitable for different cell types is highly desirable in regenerative medicine. There is danger of infection or allergic reaction with the use of fetal bovine serum (FBS), making it problematic for medical applications. The aim of the present study was to develop an FBS-free cryoprotective medium for human mesenchymal stromal cells (hMSCs; primary cells) and immortalized human osteoblasts (SAOS-2 cell line). Furthermore, we endeavored to eliminate or reduce the presence of dimethyl sulfoxide (DMSO) in the medium. Sericin, a sticky protein derived from the silkworm cocoon, was investigated as a substitute for FBS and DMSO in the freezing medium. Cell viability (24 hours after thawing, both hMSC and SAOS-2) and colony-forming ability (2 weeks after thawing, only for hMSCs) were both determined. The FBS-free medium with 1% sericin in 10% DMSO was found to be a suitable freezing medium for primary hMSCs, in contrast to immortalized human osteoblasts. Surprisingly, the storage of hMSCs in a cultivation medium with only 10% DMSO also provided satisfactory results. Any drop in DMSO concentration led to significantly worse survival of cells, with little improvement in hMSC survival in the presence of sericin. Thus, sericin may substitute for FBS in the freezing medium for primary hMSCs, but cannot substitute for DMSO.
doi:10.1089/bio.2013.0078
PMCID: PMC3995509  PMID: 24749876
20.  A Framework for Biobank Sustainability 
Biopreservation and Biobanking  2014;12(1):60-68.
Each year funding agencies and academic institutions spend millions of dollars and euros on biobanking. All funding providers assume that after initial investments biobanks should be able to operate sustainably. However the topic of sustainability is challenging for the discipline of biobanking for several major reasons: the diversity in the biobanking landscape, the different purposes of biobanks, the fact that biobanks are dissimilar to other research infrastructures and the absence of universally understood or applicable value metrics for funders and other stakeholders. In this article our aim is to delineate a framework to allow more effective discussion and action around approaches for improving biobank sustainability. The term sustainability is often used to mean fiscally self-sustaining, but this restricted definition is not sufficient for biobanking. Instead we propose that biobank sustainability should be considered within a framework of three dimensions – financial, operational, and social. In each dimension, areas of focus or elements are identified that may allow different types of biobanks to distinguish and evaluate the relevance, likelihood, and impact of each element, as well as the risks to the biobank of failure to address them. Examples of practical solutions, tools and strategies to address biobank sustainability are also discussed.
doi:10.1089/bio.2013.0064
PMCID: PMC4150367  PMID: 24620771
21.  Challenges of Biobanking in South Africa to Facilitate Indigenous Research in an Environment Burdened with Human Immunodeficiency Virus, Tuberculosis, and Emerging Noncommunicable Diseases 
Biopreservation and Biobanking  2013;11(6):347-354.
The high burden of infectious diseases and the growing problem of noncommunicable and metabolic disease syndromes in South Africa (SA) forces a more focused research approach to facilitate cutting-edge scientific growth and public health development. Increased SA research on these diseases and syndromes and the collection of associated biospecimens has ensured a plethora of biobanks created by individuals, albeit without the foresight of prospective and collective use by other local and international researchers. As the need for access to high-quality specimens in statistically relevant numbers has increased, so has the necessity for the development of national human biobanks in SA and across the Continent. The prospects of achieving sustainable centralized biobanks are still an emerging and evolving concept, primarily and recently driven by the launch of the H3Africa consortium, which includes the development of harmonized and standardized biobanking operating procedures. This process is hindered by a myriad of complex societal considerations and ethico-legal challenges. Efforts to consolidate and standardize biological sample collections are further compromised by the lack of full appreciation by national stakeholders of the biological value inherent in these collections, and the availability of high quality human samples with well-annotated data for future scientific research and development. Inadequate or nonexistent legislative structures that specifically regulate the storage, use, dispersal, and disposal of human biological samples are common phenomena and pose further challenges. Furthermore, concerns relating to consent for unspecified future uses, as well as access to information and data protection, are all new paradigms that require further consideration and public engagement. This article reviews important fundamental issues such as governance, ethics, infrastructure, and bioinformatics that are important foundational prerequisites for the establishment and evolution of successful human biobanking in South Africa.
doi:10.1089/bio.2013.0049
PMCID: PMC4076990  PMID: 24835364
22.  Advancing Microwave Technology for Dehydration Processing of Biologics 
Biopreservation and Biobanking  2013;11(5):278-284.
Our prior work has shown that microwave processing can be effective as a method for dehydrating cell-based suspensions in preparation for anhydrous storage, yielding homogenous samples with predictable and reproducible drying times. In the current work an optimized microwave-based drying process was developed that expands upon this previous proof-of-concept. Utilization of a commercial microwave (CEM SAM 255, Matthews, NC) enabled continuous drying at variable low power settings. A new turntable was manufactured from Ultra High Molecular Weight Polyethylene (UHMW-PE; Grainger, Lake Forest, IL) to provide for drying of up to 12 samples at a time. The new process enabled rapid and simultaneous drying of multiple samples in containment devices suitable for long-term storage and aseptic rehydration of the sample. To determine sample repeatability and consistency of drying within the microwave cavity, a concentration series of aqueous trehalose solutions were dried for specific intervals and water content assessed using Karl Fischer Titration at the end of each processing period. Samples were dried on Whatman S-14 conjugate release filters (Whatman, Maidestone, UK), a glass fiber membrane used currently in clinical laboratories. The filters were cut to size for use in a 13 mm Swinnex® syringe filter holder (Millipore™, Billerica, MA). Samples of 40 μL volume could be dehydrated to the equilibrium moisture content by continuous processing at 20% with excellent sample-to-sample repeatability. The microwave-assisted procedure enabled high throughput, repeatable drying of multiple samples, in a manner easily adaptable for drying a wide array of biological samples. Depending on the tolerance for sample heating, the drying time can be altered by changing the power level of the microwave unit.
doi:10.1089/bio.2013.0024
PMCID: PMC4076997  PMID: 24835259
23.  A Data Standard for Sourcing Fit-for-Purpose Biological Samples in an Integrated Virtual Network of Biobanks 
Biopreservation and Biobanking  2014;12(3):184-191.
Human tissue biobanks are at the epicenter of clinical research, responsible for providing both clinical samples and annotated data. There is a need for large numbers of samples to provide statistical power to research studies, especially since treatment and diagnosis are becoming ever more personalized. A single biobank cannot provide sufficient numbers of samples to capture the full spectrum of any disease. Currently there is no infrastructure in the United Kingdom (UK) to integrate biobanks. Therefore the National Cancer Research Institute (NCRI) Confederation of Cancer Biobanks (CCB) Working Group 3 looked to establish a data standard to enable biobanks to communicate about the samples they hold and so facilitate the formation of an integrated national network of biobanks. The Working Group examined the existing data standards available to biobanks, such as the MIABIS standard, and compared these to the aims of the working group. The CCB-developed data standard has brought many improvements: (1) Where existing data standards have been developed, these have been incorporated, ensuring compatibility with other initiatives; (2) the standard was written with the expectation that it will be extended for specific disease areas, such as the Breast Cancer Campaign Tissue Bank (BCCTB) and the Strategic Tissue Repository Alliances Through Unified Methods (STRATUM) project; and (3) biobanks will be able to communicate about specific samples, as well as aggregated statistics.
The development of this data standard will allow all biobanks to integrate and share information about the samples they hold, facilitating the possibility of a national portal for researchers to find suitable samples for research. In addition, the data standard will allow other clinical services, such as disease registries, to communicate with biobanks in a standardized format allowing for greater cross-discipline data sharing.
doi:10.1089/bio.2013.0089
PMCID: PMC4066222  PMID: 24785371
24.  How to Design Biospecimen Identifiers and Integrate Relevant Functionalities into Your Biospecimen Management System 
Biopreservation and Biobanking  2014;12(3):199-205.
Effective tracking of biospecimens within a biobank requires that each biospecimen has a unique identifier (ID). This ID can be found on the sample container as well as in the biospecimen management system. In the latter, the biospecimen ID is the key to annotation data such as location, quality, and sample processing. Guidelines such as the Best Practices from the International Society of Biological and Environmental Repositories only state that a unique identifier should be issued for each sample. However, to our knowledge, all guidelines lack a specific description of how to actually generate such an ID and how this can be supported by an IT system. Here, we provide a guide for biobankers on how to generate a biospecimen ID for your biobank. We also provide an example of how to apply this guide using a longitudinal multi-center research project (and its biobank). Starting with a description of the biobank's purpose and workflows through to collecting requirements from stakeholders and relevant documents (i.e., guidelines or data protection concepts), and existing IT-systems, we describe in detail how a concept to develop an ID system can be developed from this information. The concept contains two parts: one is the generation of the biospecimen ID according to the requirements of stakeholders, existing documentation such as guidelines or data protection concepts, and existing IT-infrastructures, and the second is the implementation of the biospecimen IDs and related functionalities covering the handling of individual biospecimens within an existing biospecimen management system. From describing the concept, the article moves on to how the new concept supports both existing or planned biobank workflows. Finally, the implementation and validation step is outlined to the reader and practical hints are provided for each step.
doi:10.1089/bio.2013.0085
PMCID: PMC4066232  PMID: 24955734
25.  Public Perspectives on Biospecimen Procurement: What Biorepositories Should Consider 
Biopreservation and Biobanking  2013;11(3):137-143.
Purpose
Human biospecimens are central to biobanking efforts, yet how members of the public think about biobank procurement strategies is not well understood. This study aimed to explore public perspectives toward the procurement of residual clinical material versus “direct” procurement strategies such as the drawing of blood.
Methods
Members of the public residing in and beyond the biobank catchment area of the University of Iowa Hospitals and Clinics were randomly selected to participate in focus groups and a telephone survey.
Results
The majority of survey participants (75%, n=559) found both residual and direct procurement strategies equally workable. Small proportions preferred either residual (15%; n=117) or direct (5%; n=40) procurement. Focus group participants (n=48) could identify benefits to both procurement strategies, but raised concerns about possible donor inconvenience/discomfort and reduced biospecimen accrual in the case of direct procurement. Residual procurement raised concerns about lower-quality samples being procured without full donor awareness.
Conclusion
Biobanks should consider that members of the public in their research programs may be willing to make specimen donations regardless of whether a residual or direct procurement strategy is employed. Limiting patient discomfort and inconvenience may make direct procurement strategies more acceptable to some members of the public. Ensuring donor awareness through effective informed consent may allay public concerns about the indirectness of donating clinical biospecimens.
doi:10.1089/bio.2013.0001
PMCID: PMC4076971  PMID: 24850089

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