medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata

MOTIVATION

Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software.

RESULTS

We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019).

AVAILABILITY AND IMPLEMENTATION

The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A retrospective comparison of neoadjuvant chemoradiotherapy regimens for locally advanced esophageal cancer

Preoperative chemoradiotherapy (CRT) with carboplatin/paclitaxel has been shown to increase survival in patients with esophageal cancer, including gastroesophageal junction (GE) junction cancer, over surgery alone; however, there have been no studies comparing the different neoadjuvant CRT regimens. We retrospectively evaluated the long-term results of trimodality therapy for patients with locally advanced esophageal cancer treated on several chemotherapy regimens. Between 1999 and 2014, 215 patients with locally advanced esophageal cancer underwent neoadjuvant CRT followed by surgical resection. The median age was 62 years (range 21-84), 80.5% were men and 86% had adenocarcinoma. The following chemotherapy regimens were administered: cisplatin/5FU (14.9%), cisplatin/irinotecan (35.8%), carboplatin/paclitaxel (35.8%), and other (9.7%). The majority of patients (92.1%) received a radiation dose of 50.4 Gy. Predictors of toxicities and surgical complications were assessed using logistic regression. Overall survival (OS) and recurrence-free survival (RFS) were estimated using the Kaplan-Meier method and proportional hazards regression was used to model time-to-event outcomes. The median follow-up among surviving patients was 4.1 years (range 0.4,13). The median OS was 3.0 years from time of diagnosis and OS was 36.8% at 5 years. RFS was 34.9% at 5 years. After neoadjuvant CRT, 34.7% of patients achieved a pathologic complete response including 60.7% of squamous cell carcinoma patients and 18.4% of adenocarcinoma patients (P < 0.001) and 66% were downstaged. Of the variables examined, pathologic stage, preoperative baseline cardiac comorbidity, postoperative cardiac or pulmonary complications, and chemotherapy regimen were associated with OS. Using cisplatin and 5FU as the reference regimen, patients treated with carboplatin/paclitaxel had significantly improved OS (HR = 0.47, P = 0.017 after adjusting for surgery type, radiation modality, baseline cardiac comorbidity, and preoperative stage) with 5-year OS rate of 66%. The most common surgical complications were cardiac in 61 patients (28.5%) and pulmonary in 52 patients (24.3%). Cardiac complications were associated with age (OR 1.05, P = 0.007) and cardiac comorbidity (OR 2.6, P = 0.02) and pulmonary complications with female gender (OR 3.98, P < 0.001). Forty-four patients (20.5%) required readmission within 30 days of discharge, and readmission was associated with cardiac comorbidity (OR 2.7, P = 0.017). Three patients died within 30 days of surgery. We observed an association between neoadjuvant carboplatin/paclitaxel and improved overall survival that requires confirmation in a prospective randomized trial.

AQUA and FISH analysis of HER-2/neu expression and amplification in a small cell lung carcinoma tissue microarray

AIMS

Most small cell lung carcinoma (SCLC) patients have metastatic disease at the time of diagnosis and are faced with poor prognosis and limited treatment options. Reports of HER-2/neu gene amplification and overexpression in this malignancy have raised the possibility of applying targeted immunotherapy with trastuzumab, the monoclonal antibody used to treat metastatic breast cancer. However, a review of the studies measuring HER-2/neu gene amplification and protein expression in SCLC reveals discordant results. The aim of the present study was to re-examine HER-2/neu expression in SCLC in relation to gene copy number using the new, highly sensitive, immunofluorescence automated quantitative analysis (AQUA) technology.

METHODS AND RESULTS

Fluorescence in situ hybridization (FISH) was used to measure HER-2/neu gene copy number and amplification status and AQUA was used to measure protein expression in a series of 23 SCLC tumours on a tissue microarray. None of the 17 SCLC specimens assessable by FISH exhibited HER-2/neu gene amplification as defined by a HER-2/neu/chromosome 17 ratio = or > 2. Twelve of 17 (70.1%) SCLC samples were polysomic for chromosome 17 with corresponding increases in HER-2/neu gene copy numbers. Intermediate levels of protein expression corresponding to AQUA scores in the range of 4-24 were detected in all 23 specimens. High protein expression levels corresponding to AQUA scores up to 83, observed previously in association with gene amplification and poor prognosis in breast cancer cases, were not detected in the present study. No statistically significant association was observed between absolute chromosome 17 or HER-2/neu gene copy numbers and protein expression levels in tumour cells (P > 0.45).

CONCLUSIONS

The lack of gene amplification and robust HER-2/neu protein expression in SCLC tumour cells in this series does not suggest a prominent role for the HER-2/neu gene in SCLC tumour progression and does not support the general applicability of targeted immunotherapy with trastuzumab to this malignancy.

The Mouse Genome Database (MGD): integrating biology with the genome

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Ductal lavage for detection of cellular atypia in women at high risk for breast cancer

BACKGROUND

Breast cancer originates in breast epithelium and is associated with progressive molecular and morphologic changes. Women with atypical breast ductal epithelial cells have an increased relative risk of breast cancer. In this study, ductal lavage, a new procedure for collecting ductal cells with a microcatheter, was compared with nipple aspiration with regard to safety, tolerability, and the ability to detect abnormal breast epithelial cells.

METHODS

Women at high risk for breast cancer who had nonsuspicious mammograms and clinical breast examinations underwent nipple aspiration followed by lavage of fluid-yielding ducts. All statistical tests were two-sided.

RESULTS

The 507 women enrolled included 291 (57%) with a history of breast cancer and 199 (39%) with a 5-year Gail risk for breast cancer of 1.7% or more. Nipple aspirate fluid (NAF) samples were evaluated cytologically for 417 women, and ductal lavage samples were evaluated for 383 women. Adequate samples for diagnosis were collected from 111 (27%) and 299 (78%) women, respectively. A median of 13,500 epithelial cells per duct (range, 43-492,000 cells) was collected by ductal lavage compared with a median of 120 epithelial cells per breast (range, 10-74,300) collected by nipple aspiration. For ductal lavage, 92 (24%) subjects had abnormal cells that were mildly (17%) or markedly (6%) atypical or malignant (<1%). For NAF, corresponding percentages were 6%, 3%, and fewer than 1%. Ductal lavage detected abnormal intraductal breast cells 3.2 times more often than nipple aspiration (79 versus 25 breasts; McNemar's test, P<.001). No serious procedure-related adverse events were reported.

CONCLUSIONS

Large numbers of ductal cells can be collected by ductal lavage to detect atypical cellular changes within the breast. Ductal lavage is a safe and well-tolerated procedure and is a more sensitive method of detecting cellular atypia than nipple aspiration.

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the gastric mucosa, where it appears to persist throughout the host's life unless the patient is treated. Colonization induces chronic gastric inflammation which can progress to a variety of diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer and mucosal-associated lymphoma. Strain-specific genetic diversity has been proposed to be involved in the organism's ability to cause different diseases or even be beneficial to the infected host and to participate in the lifelong chronicity of infection. Here we compare the complete genomic sequences of two unrelated H. pylori isolates. This is, to our knowledge, the first such genomic comparison. H. pylori was believed to exhibit a large degree of genomic and allelic diversity, but we find that the overall genomic organization, gene order and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite similar. Between 6 to 7% of the genes are specific to each strain, with almost half of these genes being clustered in a single hypervariable region.

Repeat expansion detection analysis of (CAG)n tracts in tumor cell lines, testicular tumors, and testicular cancer families

The mutational expansion of triplet repeat microsatellite sequences underlies the transmission of a number of heritable neurological disorders. However, this form of microsatellite instability has not previously been observed in association with malignant disease. Because trinucleotide expansions can dramatically alter gene expression and protein function, we hypothesized that they might occur in neoplastic cells as a mechanism through which to alter cancer genes. Accordingly, we used the repeat expansion detection technique to determine whether (CAG)n triplet repeat expansions were present in DNA from malignant cells. No expansions were observed in a survey of 20 tumor cell lines derived from neoplasms of the breast, ovary, cervix, endometrium, lung, colon, placenta, or hematopoietic system. However, we did observe expanded (CAG)n tracts in DNA from 5 of 11 testicular tumor cell lines and in 1 of 11 sporadic testicular tumors. Examination of the corresponding normal DNA, when available, revealed that some of the expansions were germline in nature. To assess the possibility that (CAG)n expansions underlie some cases of inherited testicular cancer, we also analyzed germline DNA from members of five kindreds predisposed to this malignancy. An increase in (CAG)n tract size was observed in all five families and was particularly striking in one large pedigree in which expansions were observed in three of four affected siblings. These observations raise the possibility that the germline transmission of expanded (CAG)n tracts may play a role in testicular tumorigenesis.

Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors

Structure-based drug design requires the development of efficient computer programs for exploring the structural compatibility of various flexible ligands with a given receptor. While various algorithms are available for finding docked conformations, selecting a target function that can reliably score the conformations remains a serious problem. We show that the use of an empirical free energy evaluation method, originally developed to characterize protein-protein interactions, can substantially improve the efficacy of search algorithms. In addition to the molecular mechanics interaction energy, the function takes account of solvation and side chain conformational entropy, while remaining simple enough to replace the incomplete target functions used in many drug docking and design procedures. The free energy function is used here in conjunction with a simple site mapping-fragment assembly algorithm, for docking the MVT-101 non-peptide inhibitor to HIV-1 protease. In particular, we predict the bound structure with an all atom RMSD of 1.21 A, compared to 1.69 A using an energy target function, and also accurately predict the free energy shifts obtained with a series of five trimeric hydroxyethylene isostere analogs.

Microsatellite instability in ovarian neoplasms

Microsatellite instability has been observed in a variety of sporadic malignancies, but its existence in sporadic ovarian cancer has been the subject of conflicting reports. We have performed a polymerase chain reaction-based microsatellite analysis of DNAs extracted from the neoplastic and non-neoplastic tissues of 41 ovarian cancer patients. Tumour-associated alterations were observed in seven (17%) of these cases. Clinicopathological correlations revealed that: (1) alterations among tumours classified as serous adenocarcinomas occurred with relatively low frequency (2/24 or 8%); (2) most of the tumours with microsatellite alterations (5/7 or 71%) were of less common histopathological types (epithelial subtypes such as endometrioid and mixed serous and mucinous, or non-epithelial types such as malignant mixed Müllerian or germ cell tumours); (3) tumour-associated alterations were observed in 3/4 (75%) of the patients with stage I tumours vs 4/37 (11%) of the patients with stage II, III and IV tumours (P = 0.01); (4) tumour-associated microsatellite instability was found to occur with similar frequencies among patients with and without clinical features suggestive of familial disease, including positive family history, early onset, or multiple primary tumours. In summary, we have observed microsatellite alterations in the neoplastic tissues of ovarian cancer patients with diverse genetic backgrounds and clinicopathological features. The pattern of alterations is consistent with the possibility that multiple mechanisms may be responsible for microsatellite instability in ovarian neoplasms.

A polymerase chain reaction-based microsatellite typing assay used for tumor cell line identification

In this report we describe the application of a polymerase chain reaction (PCR)-based DNA typing assay to the analysis of tumor cell line identity. We have applied the technique to analyze four tumor cell lines purchased from the American Type Culture Collection (SK-OV-3, SK-BR-3, OVCAR, HeLa) and four lines isolated from the ascites fluids of ovarian cancer patients (YAOVBIX1, YAOVBIX3, OC194, and OC346). In this assay, three polymorphic tetranucleotide microsatellite loci (GABARB1, TH01, and HPRTB) were amplified from tumor cell line DNAs in radioactive PCR-reactions. The products were resolved in polyacrylamide gels and exposed to film to produce individual-specific patterns for five of the cell lines (HeLa, SK-BR-3, OVCAR, YAOVBIX3, and OC194). However, three of the cell lines, SK-OV-3, YAOVBIX1, and OC436 had identical "fingerprints" at all three loci. The probability that the observed profile match could occur between three randomly selected heterologous cell lines was calculated to be 1.32 x 10(-13). On the basis of this analysis, we have identified two independent cross-contamination events involving the SK-OV-3 ovarian adenocarcinoma cell line. The PCR-based analysis of tetranucleotide microsatellite loci is technically straightforward and produces discrete allelic bands associated with known population frequencies, allowing for the unequivocal interpretation of typing patterns.

Alcohol and other drug abuse among social work colleagues and their families: impact on practice

This article presents data from a 1987 random sample survey mailed to the membership of the New York City chapter of the National Association of Social Workers. The purpose of the study was to determine the prevalence of alcohol and other drug problems as perceived by social workers among their colleagues and their family members and friends. Forty-three percent of the 198 respondents said that they had known at least one social worker who had a problem with alcohol or other drugs. The large number of social workers with close personal involvement with substance abuse was significant: 60 percent had close friends or family members with a problem, 39 percent had a nuclear family member with a problem, and 11 percent were adult children of alcoholics. The latter group reported a significantly higher impact on job functioning than did the other groups. Implications of these findings and recommendations for dealing with them are discussed.

Graphical representations of the class I MHC cleft

We describe computer graphics and computer aided manufacture of three-dimensional models designed specifically to elucidate the cleft in the class I human leukocyte antigen. The models evolve from computer graphical representations and provide a geometrically and chemically concise and detailed view of the antigen binding site. The techniques provide a new approach to representations of binding sites. The model provides sufficient detail to support binding specificities analysis of active sites involved in protein and DNA binding.

NEU protein overexpression in benign, borderline, and malignant ovarian neoplasms

In situ hybridization (ISH) analysis of 24 benign, borderline, and malignant ovarian tumor specimens revealed NEU transcript expression by epithelial elements in approximately two-thirds of the samples and high-level expression in 3 grade 3 adenocarcinomas. Immunohistochemical staining (IHC) of a total of 86 specimens (including 17 of those studied by ISH) localized NEU antigen expression to epithelial cells in 36 of 86 samples with strong membrane staining observed in 12, including 1 benign, 1 borderline serous carcinoma, 3 clear cell/endometrioid carcinomas, and 7 predominantly papillary serous carcinomas with areas of clear cell/endometrioid histology. Clinical correlation of the IHC results for the 72 Stage I-IV invasively malignant neoplasms revealed no statistically significant association of the intensity of NEU IHC staining with either relapse-free or overall survival. However, more of the patients whose tumors showed strong membrane staining for NEU antigen suffered relapses of disease by 3 and 4 years than did patients whose tumors showed weak or no membrane staining. These results suggest a role for the NEU gene product in the physiology of benign ovarian surface epithelium and the neoplastic epithelium of preinvasive borderline and some invasively malignant adenocarcinomas.

Neu proto-oncogene amplification and expression in ovarian adenocarcinoma cell lines

In this communication, the authors summarize their characterization of eight ovarian adenocarcinoma-derived cell lines for level of neu gene amplification, expression of neu transcripts and protein, and intraperitoneal tumorigenicity in nude mice. Two of the eight cell lines in our study (SKOV3 and YAOVBIX1) exhibited five- to ninefold neu DNA sequence amplification, accompanied by up to 200-fold overexpression of transcripts and protein (p185). Both of these cell lines expressed a major approximately 7.5 kb neu-complementary transcript not previously reported in other neu-positive tumor cell lines. One pair of cell lines (YAOVBIX1 and YAOVBIX3), isolated from a single ovarian carcinoma patient's ascites sample differed dramatically in regard to level of neu gene amplification and expression. Immunohistochemical staining of the primary ovarian tumor from which these two lines were derived demonstrated populations of both neu-positive and neu-negative malignant epithelial cells. Seven of the eight ovarian carcinoma lines produced intra-abdominal tumors after intraperitoneal injection into nude mice, irrespective of level of neu gene expression. This study demonstrates tumor cell heterogeneity with regard to neu gene amplification and expression in an ovarian adenocarcinoma, reveals the overexpression of novel neu-complementary transcripts in two independently isolated ovarian adenocarcinoma cell lines, and suggests that neu gene expression is not required for intraperitoneal tumorigenicity of ovarian carcinoma xenografts in a nude mouse model system.

FMS (CSF-1 receptor) and CSF-1 transcripts and protein are expressed by human breast carcinomas in vivo and in vitro

The expression in vivo of FMS transcripts and antigen by neoplastic epithelial cells was demonstrated immunohistochemically or by in situ hybridization in sixteen of seventeen human breast carcinoma specimens and one case of sclerosing adenosis. Expression of CSF-1 receptor (FMS) transcripts and protein was also observed in vitro in two or three breast carcinoma-derived cell lines and was dramatically increased by dexamethasone, a potent glucocorticoid and inducer of mammary epithelial cell differentiation. Immunohistochemical staining with an anti-CSF-1 antibody identified neoplastic epithelial cell co-expression of fms and CSF-1 antigens in more than one-third of the fms-positive invasive carcinoma specimens. These results suggest that autocrine and paracrine interactions of the lymphohematopoietic cytokine CSF-1 and its receptor may participate in the biology of human mammary neoplasms.