A novel pathway of levodopa metabolism by commensal Bifidobacteria

The gold-standard treatment for Parkinson's disease is levodopa (L-DOPA), which is taken orally and absorbed intestinally. L-DOPA must reach the brain intact to exert its clinical effect; peripheral metabolism by host and microbial enzymes is a clinical management issue. The gut microbiota is altered in PD, with one consistent and unexplained observation being an increase in Bifidobacterium abundance among patients. Recently, certain Bifidobacterium species were shown to have the ability to metabolize L-tyrosine, an L-DOPA structural analog. Using both clinical cohort data and in vitro experimentation, we investigated the potential for commensal Bifidobacteria to metabolize this drug. In PD patients, Bifidobacterium abundance was positively correlated with L-DOPA dose and negatively with serum tyrosine concentration. In vitro experiments revealed that certain species, including B. bifidum, B. breve, and B. longum, were able to metabolize this drug via deamination followed by reduction to the compound 3,4-dihydroxyphenyl lactic acid (DHPLA) using existing tyrosine-metabolising genes. DHPLA appears to be a waste product generated during regeneration of NAD +. This metabolism occurs at low levels in rich medium, but is significantly upregulated in nutrient-limited minimal medium. Discovery of this novel metabolism of L-DOPA to DHPLA by a common commensal may help inform medication management in PD.

Rapidly rising cases with omicron In Senegal

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Omicron variant continues to progress in Senegal with the appearance of new contaminations.

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IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.

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Since this date, the number of Omicron variant infections has increased over the weeks.

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Molecular surveillance of the Omicron variant is carried out in real time to inform the medical authorities.

The transcriptional landscape of the clustered protocadherins in the cardiovascular system

Background

The alpha, beta and gamma clustered protocadherins (cPcdhs) genes encode homotypic cell adhesion molecules that are highly expressed in the brain. They are well described to be expressed in a combinatorial fashion to specify neuronal identity for coding synaptic connectivity. Unexpectedly, we recently uncovered evidence from studies in mice and human showing PCHDA variants can cause congenital heart defects. As all the genes of the alpha or gamma PCDH cluster share a common 3' end and are highly homologous, the expression of these gene clusters has been underestimated or overlooked due to multimapping issues. This is especially problematic in single cell RNAseq (scRNA) data generated using 3' based amplification protocols.

Methods and results

We constructed a modified bioinformatic pipeline for analyzing the cPcdhs transcripts (Fig. 1a). Raw data of Publicly available scRNA datasets were downloaded and re-processed and analyzed for expression of the cPCDH transcripts using our custom pipeline. Integrating 10 scRNA datasets of mouse heart tissues from embryonic 7.75 (E7.75) to postnatal 30 months (PM30) were performed by Harmony and Seurat. This showed Pcdhg had the highest expression among the three Pcdh gene clusters, with next being Pcdhb and then Pcdha (Fig. 1b). Pcdhb and Pcdhg were enriched in endocardial cells and fibroblasts (Fig. 1b). Unlike gene expression in neurons, expression of the cPcdhs in cardiac cell types did not shown the stochastic, sparse, combinatorial expression patterns seen in neurons (Fig. 1b). Despite the relatively low level of Pcdha expression in all cardiac cell types, it is intriguing that independent scRNA datasets showed Pcdha is expressed most highly in the atrium in the early embryo, possibly due to known atrial dominance in the early embryo (Fig. 1c). Pcdhb is highly expressed in the OFT and atrioventricular canal of both human and mouse heart, suggesting its perturbation may contribute to outflow tract or AV valve abnormalities (Fig. 1c-d). Consistent with our previous finding of an important role for the Pcdha gene cluster in left ventricular outflow obstructive (LVOTO) lesions, we observed expression of Pcdhg was broadly upregulated in the Adamts19 homozygous knockout mice exhibiting aortic valve dysfunction, a CHD phenotype in the LVOTO spectrum (Fig. 1e).

Conclusions

Using a new bioinformatics pipeline, we systematically mapped the transcriptional landscapes of cPcdhs during heart development using scRNA data. This revealed cell type-specific and anatomical characteristics in the expression of the different cPcdhs. These findings show the cPcdhs are transcriptionally regulated very differently in the cardiovascular system from regulation observed in the brain. The single cell transcriptional profile for the cPcdhs in the cardiovascular system can serve as the foundation for future investigations into the broader role of the cPcdhs in cardiovascular development and disease.

Funding Acknowledgement

Type of funding sources: None.

Single-cell transcriptome analysis yields new insights into the pathogenic mechanisms and possible genetic etiology of cardiomyopathies

Background

Inherited cardiomyopathies (CM) represent a clinically heterogeneous group of primary cardiac muscle disorders with a strong genetic underpinning. Recent rapid genomic advances have led to the identification of numerous disease-causing genes for both non-syndromic (nsCM) and syndromic (sCM) cardiomyopathies. This has greatly facilitated molecular genetic testing, thus enabling accurate disease diagnosis needed for the practice of precision medicine and the optimization of patient outcome. However, many cardiomyopathies remain unexplained with the known genes and dominant genetic model of disease.

Purpose

To reassess the genetic features of known CM genes as a strategy to recover novel candidate CM genes.

Methods

Known hypertrophic CM (HCM), dilated CM (DCM) and pediatric CM genes were curated from the literature and from 23 commercial CM diagnostic panels. They were classified as non-syndromic and syndromic, and further annotated using two constraint metrics, the missense Z score and pLI score obtained from the GnomAD database. Publicly available mouse (n=6) and human (n=3) single-cell RNA (scRNA) datasets were downloaded and cardiomyocyte specific differentially expressed genes (DEGs) (fold change >0.1; adjusted P<0.0001) were recovered. Genes identified as DEGs in at least 4 mouse or 3 human scRNA datasets were recovered as nsCM candidate genes.

Results

Analyses of 9 scRNA datasets showed the majority of known nsCM genes are cardiomyocyte specific (Fig. 1a-b). nsCM and sCM genes have distinct expression and genetic profile. nsCM genes are associated with higher heart expression and lower loss intolerance (Fig. 1c). In contrast, syndromic CM genes mostly showed lower expression with high loss intolerance, consistent with their higher clinical impact. However, interestingly some of the nsCM genes (MYLK2, TMPO and KLF10) show low or even no detectable expression in mouse and human cardiac cells. Using the scRNA data, we assessed cellular expression of genes in the 23 commercial CM diagnostic panels. This analysis showed some of the CM genes with high cardiomyocytes expression have low coverage on the current commercial CM panels (Fig. 1d). Using human and mouse scRNA data, we recovered 224 mouse and 157 human nsCM candidate genes. MTUS2 (microtubule-associated tumor suppressor candidate 2) was identified as a strong nsCM candidate gene supported by evidence from both mouse and human studies (Fig. 1e-f).

Conclusions

Our analysis showed many of the nsCM genes have differential cardiomyocyte expression with low loss intolerance, while the reverse was observed for many sCM genes. We propose increasing commercial panel coverage of cardiomyocytes-specific expressed genes may help increase disease diagnostic yield. Additionally, novel candidate genes uncovered trained on cardiomyocyte expression profile may help accelerate elucidation of unsolved cardiomyopathy cases.

Funding Acknowledgement

Type of funding sources: None.

420 Impact of Surgical Training on Long-Term Patient Outcomes in Sleeve Gastrectomy

Aim

Although few studies have examined the impact of surgical training on early postoperative outcomes in bariatric surgery, there is limited data on longer-term outcomes in trainee-performed cases. Our aim was to evaluate the effect of surgical training on weight loss outcomes following laparoscopic sleeve gastrectomy (LSG).

Method

Data was prospectively collated on patients undergoing primary LSG at a Quaternary Bariatric London teaching Hospital between 2016-2017. Inclusion criteria was BMI≥35. Exclusion criteria were BMI<35 or > 60, planned HDU admission and LSG with concomitant hiatus hernia repair. Operative time, length of stay, complications and longer-term excess weight loss was recorded with outcomes of consultant and trainee cases compared.

Results

76 LSG patients were included; 44 performed by consultants, 32 by trainees. There was no difference in age, gender, pre-operative weight, BMI and number of obesity-related comorbidities between groups. Operative time (trainee105±10.0 vs consultant91±18.1 mins) and length of stay (trainee2.6±0.4 vs consultant2.8±0.9 days) were similar between groups. There were 3 complications in the trainee group (intra-abdominal collection requiring drainage, wound infection, hypokalaemia); and 2 with consultants (wound infection, intra-operative bleeding with ICU admission). Excess Weight Loss(%) at 2 years was 55.9%±7.5% for trainee cases and 52.4%±6.7% for consultant cases(p=0.49). Excess Weight Loss(%) at 3.5 years was 54.9%±9.9% for trainee cases and 50.7%±9.9% for consultant cases(p=0.54).

Conclusions

Outcomes in trainee performed LSG are comparable to those performed by consultants. Surgical training in a high-volume teaching hospital does not appear to have detrimental effect on patient outcomes following LSG.

The BC ADPKD Network: A Comprehensive Provincial Approach to Support Specialized and Locally Delivered Multidisciplinary ADPKD Care

Purpose:

With evolving evidence around the progression, assessment, and management of autosomal dominant polycystic kidney disease (ADPKD), care of the disease has become increasingly complex. Needs assessments in British Columbia (BC) described variability in knowledge and comfort with incorporating these new aspects of ADPKD care into clinical practice. Undercapture of early-stage ADPKD patients in existing renal databases was also identified as an unmet need.

Sources of Information:

A multidisciplinary group of clinicians and patient partners with interest and expertise in ADPKD and/or multidisciplinary kidney care informed the project work. An existing provincial renal database was used to support the provincial ADPKD registry.

Methods:

A formalized, comprehensive provincial ADPKD Network was created within the existing infrastructure of multidisciplinary kidney clinics (MDCs) in BC. The Network is coordinated provincially and implemented locally. It incorporates robust data collection, education, creation, and dissemination of dedicated clinical tools; collaboration between clinics and clinicians across the province; and ongoing evaluation and continuous quality improvement.

Key Findings:

Over the 5 years since its inception, the BC ADPKD Network has enabled increased and earlier identification of British Columbians living with ADPKD and a shift in practice toward increased and earlier enrollment of ADPKD patients into MDCs. A host of tailored ADPKD clinical tools have been created and implemented in all MDCs across the province to support existing MDC staff in the delivery of more standardized and specialized ADPKD care. A collaborative provincial clinician network founded on Local Clinical Champions has been established to support ongoing experience sharing between clinics. An evaluation framework has been established to evaluate outcomes and enable ongoing refinement of the Network.

Limitations:

The provincial ADPKD registry is undergoing enhancements to enable more comprehensive capture of APDKD-specific information such as total kidney volume and genetic results, but at present, this remains a limitation. It remains to be seen whether the activities of the ADPKD Network will improve long-term clinical outcomes and care experiences of patients living with ADPKD, and a long-term sustainability assessment of this model of care will be required.

Implications:

The structure, tools, and coordinated and collaborative clinician network established through this comprehensive provincial ADPKD Network may be valuable in addressing the variability and gaps in existing ADPKD care while allowing patients and families across BC to receive enhanced care locally, in their usual kidney care environments.

Virgibacillus doumboii sp. nov., a halophilic bacterium isolated from the stool of a healthy child in Mali

A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).

Virgibacillus ihumii sp. nov., a new bacterium isolated from the stool of healthy African children

During a case–control study on severe acute malnutrition, strain Marseille-Q1233 was isolated. It is a Gram-positive, rod-shaped and halophilic bacillus isolated from a stool sample of Malian child under the age of 5. The fatty acid profile of the strain consisted of C15:0-anteiso and C14:0-iso as major components. Digital DNA-DNA hybridization and average nucleotide identity calculation showed 23.10% and 80.81% similarity respectively between strain Marseille-Q1233 and Virgibacillus siamensis strain Marseille-P2607, the phylogenetically closely related species with standing in nomenclature. On the basis of these results, we report the description of Virgibacillus ihumii sp. nov. strain Marseille-Q1233 as a new bacterial species.

Description of Clostridium cagae sp. nov., Clostridium rectalis sp. nov. and Hathewaya massiliensis sp. nov., new anaerobic bacteria isolated from human stool samples

Using culturomics methods, three strains were isolated, identified and characterized following the taxonogenomics concept. Clostridium cagae strain Marseille-P4344T (=CSURP4344), Clostridium rectalis strain Marseille-P4200T (=CSURP4200) and Hathewaya massiliensis strain Marseille-P3545T (=CSURP3545) were isolated from human stool samples. The phylogenetic reconstruction, phenotypic criteria and genomic analyses were carried out and demonstrated that these three bacteria are different from previously known bacterial species with standing in nomenclature and were classified as new members of the Clostridiaceae family.

Taxonogenomics description of Bacillus dakarensis sp. nov., Bacillus sinesaloumensis sp. nov. and Bacillus massiliogabonensis sp. nov., three new species isolated from human stools

Using microbial culturomics, three Bacillus strains were isolated, identified and characterized following the taxonogenomics strategy. Bacillus dakarensis strain Marseille-P3515^T (=CSURP3515), Bacillus sinesaloumensis strain Marseille-P3516^T (=CSURP3516), and Bacillus massiliogabonensis strain Marseille-P2639^T (=CSURP2639) were isolated from human stool samples. The phylogenetic analysis, phenotypic characteristics and genotypic data presented here prove that these three bacteria are different from previously known bacterial species with standing in nomenclature and represent new Bacillus species.

Anaerococcus marasmi sp. nov., a new bacterium isolated from human gut microbiota

Anaerococcus marasmi sp. nov. strain Marseille-P3557^T is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557^T was 2 130 060 bp long (35.4% G + C content). The closest species based on 16S ribosomal RNA sequence was Anaerococcus prevotii strain 20548, with 97.6% sequence similarity. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-P3557^T as the type strain of Anaerococcus marasmi sp. nov., a new species within the genus Anaerococcus.

Taxono-genomics and description of Gordonibacter massiliensis sp. nov., a new bacterium isolated from stool of healthy patient

Using the taxono-genomics concept, we describe here a strictly anaerobic Gram-positive bacillus. This strain was isolated from the stool sample of a 50-year-old healthy Bedouin woman. The 16S rRNA gene sequence analysis and the whole-genome sequencing showed that this isolate belonged to the genus Gordonibacter in the family Eggerthellaceae. Based on these criteria, we propose the creation of Gordonibacter massiliensis sp. nov., strain Marseille-P2775^T (= CSUR P2775).

Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen

Parabacteroides massiliensis sp. nov., strain Marseille-P2231^T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It was isolated from a stool specimen of a 25-year-old healthy woman. Its genome was 5 013 798 bp long with a 45.7 mol% G+C content. The closest species based on 16S rRNA sequence was Parabacteroides merdae strain JCM 9497^T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231^T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides.

Corynebacterium senegalense sp. nov. and Arthrobacter senegalensis sp. nov., two new Actinobacteria isolated from skin swab from the palm of hand

Corynebacterium senegalense strain Marseille-P4329^T (= CSURP4329) and Arthrobacter senegalensis strain Marseille-P4329^T (= CSURP4198) are new species first isolated from human skin. A culturomics approach and taxonogenomics methods were used for these new bacterial species.

Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child

Based on our phenotypic and genotypic analyses, Brachybacterium massiliense strain Marseille-P2240T (= CSURP2240; = DSM 101766) is a new species isolated from stool of a healthy subject. The strain was stained Gram-positive. It was aerobic, catalase-positive and oxidase-negative. Its optimal growth occurs at 37°C in aerobic condition. The 16S ribosomal RNA sequence analysis revealed that strain Marseille-P2240T shown 98.18% similarity with Brachybacterium saurashtrense strain JG 06, the more closely related species with standing in nomenclature.

Corynebacterium pacaense sp. nov., Alistipes megaguti sp. nov., Alistipes provencensis sp. nov., 3 new bacteria isolated from fresh human stool specimens

Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417^T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997^T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431^T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens.

Varibaculum timonense sp. nov., a new bacterial species isolated from human stool sample

Varibaculum timonense sp. nov. strain Marseille-P3369^T (= CSURP3369) is a new species from the order Actinomycetales that has been isolated from a fresh stool sample of a healthy French woman.

Attachment security and existential distress among patients with advanced cancer

BACKGROUND

Felt security in close relationships may affect individual adaptation responses to existential threat in severe illness. We examined the contribution of attachment security to demoralization, a state of existential distress involving perceived pointlessness and meaninglessness in advanced cancer.

METHOD

A mixed cross-sectional sample of 382 patients with advanced cancer (mean age 59, 60% female) was recruited from outpatient oncology clinics. Participants completed self-report measures of attachment security, demoralization, depression, and physical symptom burden. We used multiple linear regression to analyze the association between attachment security and demoralization, controlling for demographic factors and symptom burden and tested whether attachment security moderated the association of symptom burden with demoralization. Separate analyses compared the contribution of the dimensions of attachment anxiety and attachment avoidance.

RESULTS

The prevalence of clinically relevant demoralization was 35%. Demoralization was associated with lower attachment security (β = -0.54, 95%CI: -0.62 to 0.46). This effect was empirically stronger for attachment anxiety (β = 0.52, 95%CI: 0.44 to 0.60) compared to attachment avoidance (β = 0.36, 95%CI: 0.27 to 0.45). Attachment security also significantly moderated the association of physical symptom burden with demoralization, such that with less attachment security, there was a stronger association between symptom burden and demoralization.

CONCLUSION

Attachment security may protect from demoralization in advanced cancer. Its relative lack, particularly on the dimension of attachment anxiety, may limit adaptive capacities to deal with illness burden and to sustain morale and purpose in life. An understanding of individual differences in attachment needs can inform existential interventions for severely ill individuals.

Two-year follow-up of patients with septic shock presenting with low HDL: the effect upon acute kidney injury, death and estimated glomerular filtration rate

BACKGROUND

Sepsis is associated with decreased levels of high-density lipoprotein (HDL) cholesterol. HDL has anti-inflammatory properties, and the use of Apo A-I mimetic peptides is associated with renal function improvement in animal models of sepsis. However, it is not known whether decreased HDL level results in impaired renal function in human sepsis. We investigated whether low levels of HDL conferred an increased risk of sepsis-associated acute kidney injury (AKI) or long-term decreased estimated glomerular filtration rate (eGFR) after sepsis.

METHODS

HDL concentration (mg dL^-1 ) was measured in plasma samples from 180 patients with septic shock at admission to the Emergency Department (ED). We divided the patients using median HDL as a cut-off value and assessed the frequency of sepsis-associated AKI and long-term decreased eGFR after sepsis. Univariate and multivariate analyses were performed.

RESULTS

Patients with low HDL had a significantly greater frequency of KDIGO 2 or 3 sepsis-associated AKI [39/90 (43.3%) vs. 12/90 (13.3%), P < 0.001] and decreased long-term eGFR [24/58 (41.4%) vs. 11/57 (19.3%), P = 0.018] compared to those with high HDL. The adjusted OR for sepsis-associated AKI and decreased eGFR after sepsis in the lower HDL group was 2.80 (95% CI 1.08-7.25, P = 0.033) and 5.45 (95% CI 1.57-18.93, P = 0.008), respectively.

CONCLUSION

Low HDL levels during sepsis are associated with increased risk of sepsis-associated AKI, and/or subsequent decreased eGFR. These results suggest that HDL may be involved and/or may be a marker of kidney injury during and after sepsis.

Impact of early palliative care on caregivers of patients with advanced cancer: cluster randomised trial

Background

Early palliative care improves the quality of life (QoL) and satisfaction with care of patients with advanced cancer, but little is known about its effect on caregivers. Here, we report outcomes of caregiver satisfaction with care and QoL from a trial of early palliative care.

Patients and methods

Twenty-four medical oncology clinics were cluster-randomised, stratified by tumour site (lung, gastrointestinal, genitourinary, breast and gynaecological), to early palliative care team referral, or to standard oncology care with palliative care only as needed. Caregivers of patients with advanced cancer (clinical prognosis of 6-24 months, Eastern Cooperative Oncology Group 0-2) in both trial arms completed validated measures assessing satisfaction with care (FAMCARE-19) and QoL [SF-36v2 Health Survey; Caregiver QoL-Cancer (CQoL-C)], at baseline and monthly for 4 months. We used a multilevel linear random-intercept mixed-effect model to test whether there was improvement in the intervention group relative to the control group over 3 and 4 months.

Results

A total of 182 caregivers completed baseline measures (94 intervention, 88 control); 151 caregivers (77 intervention, 74 control) completed at least one follow-up assessment. Satisfaction with care improved in the palliative intervention group compared with controls over 3 months (P = 0.007) and 4 months (P = 0.02). There was no significant improvement in the intervention group compared with controls for CQoL-C (3 months: P = 0.92, 4 months: P = 0.51), Physical Component Summary of the SF-36v2 Health Survey (3 months: P = 0.83, 4 months: P = 0.20), or Mental Component Summary of the SF-36v2 Health Survey (3 months: P = 0.87, 4 months: P = 0.60).

Conclusion

Early palliative care increased satisfaction with care in caregivers of patients with advanced cancer.

ClinicalTrials.gov identifier

NCT01248624.

Gaps and barriers in health-care provision for co-morbid diabetes and chronic kidney disease: a cross-sectional study

BACKGROUND

Patients with diabetes and chronic kidney disease (CKD) are a complex subset of the growing number of patients with diabetes, due to multi-morbidity. Gaps between recommended and received care for diabetes and chronic kidney disease (CKD) are evident despite promulgation of guidelines. Here, we document gaps in tertiary health-care, and the commonest patient-reported barriers to health-care, before exploring the association between these gaps and barriers.

METHODS

This cross-sectional study recruited patients with diabetes and CKD (eGFR < 60 mL/min/1.73 m2) across 4 large hospitals. For each patient, questionnaires were completed examining clinical data, recommended care, and patient-reported barriers limiting health-care. Descriptive statistics, subgroup analyses by CKD stage and hospital, and analyses examining the relationship between health-care gaps and barriers were performed.

RESULTS

308 patients, of mean age 66.9 (SD 11.0) years, and mostly male (69.5%) and having type 2 diabetes (88.0%), participated. 49.1% had stage 3, 24.7% stage 4 and 26.3% stage 5 CKD. Gaps between recommended versus received care were evident: 31.9% of patients had an HbA1c ≥ 8%, and 39.3% had a measured blood pressure ≥ 140/90 mmHg. The commonest barriers were poor continuity of care (49.3%), inadequate understanding/education about CKD (43.5%), and feeling unwell (42.6%). However, barriers associated with a failure to receive items of recommended care were inadequate support from family and friends, conflicting advice from and poor communication amongst specialists, the effect of co-morbidities on self-management and feeling unmotivated (all p < 0.05).

CONCLUSIONS

Barriers to health-care varied across CKD stages and hospitals. Barriers associated with a deviation from recommended care were different for different items of care, suggesting that specific interventions targeting each item of care are required.

Abstract P2-03-11: Genomic pattern of breast carcinomas carrying mutations of non-BRCA homologous recombination genes

Background

BRCA1 and BRCA2 are involved in the homologous recombination (HR) double-strand DNA break repair and genomic patterns of breast tumors with defective BRCA are characterized by increased genomic instability. The pre-clinical and clinical studies show that tumors with defective BRCA or other HR genes can response to platinum and PARP inhibitors. However, the genomic pattern of tumors carrying mutations of non-BRCA HR genes are not investigated.

Methods

Genomic patterns of breast carcinomas were performed by comparative genomic hybridization (CGH) array containing 60000 probes covering the whole genome with an average spacing of 40kb. The frequency of gains and losses for each regions detected by probes was calculated by ratio thresholds of 0.25 and -0.25, respectively. Large-scale genomic structural aberration was defined as the region of gains and losses of at least 10Mb. We analyzed the difference of large-scale aberration, including numbers, length and specific regions, between tumors with BRCA mutation (mtBRCA), non-BRCA HR mutation (mtHR) and wild type.

Results

We examined 41 breast carcinomas, including 15 cases with BRCA mutations, 14 with non-BRCA HR gene mutations and 12 without mutations (control). The 14 non-BRCA HR gene were 1 ATM, 1 BRIP1, 1 BARD1, 1 FANCA, 2 FANCB, 1 FANCI, 1 PALB2, 2 RAD50, 2 RAD51C and 2 RAD51D. The number and length of large-scale genomic structural aberration of mtBRCA tumors were significantly higher than wild type tumors (number p=0.005; length p=0.005), indicating CGH can distinguish the mtBRCA from control tumors. We then checked the mtHR tumors, which also revealed significantly increased number and longer length of structural aberrations compared to wild type tumors (number p=0.035; length p=0.022), but were not different from mtBRCA tumors (number p=0.204; length p=0.425). Among the specific regions on chromosomes, mtBRCA and mtHR tumors contained similar genomic aberration regions but different from wild type tumors. The most frequent aberration regions of mtBRCA and mtHR tumors are chromosome 6p22.1-p25, 6q21-q27, 8q11.1-q24, 11p11.2-p14.1, 11q, 12p and 19p, which are less revealed in the wild type (all p value &lt;0.05).

Conclusions

Our study demonstrated a direct evidence that increased genomic instability were the common characteristics of mtBRCA and non-BRCA mtHR tumors. In addition, we identify the specific genomic patterns of mtBRCA and mtHR tumors, which can be a biomarker indicating HR deficiency and response to platinum and PARP inhibitors.

Citation Format: Lin P-H, Kuo W-H, Wang M-Y, Lo C, Lin C-H, Lu Y-S, Chiu C-F, Huang C-S. Genomic pattern of breast carcinomas carrying mutations of non-BRCA homologous recombination genes [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-03-11.

Population-based cohort study of variation in the use of emergency cholecystectomy for benign gallbladder diseases

Background

The aims of this prospective population-based cohort study were to identify the patient and hospital characteristics associated with emergency cholecystectomy, and the influences of these in determining variations between hospitals.

Methods

Data were collected for consecutive patients undergoing cholecystectomy in acute UK and Irish hospitals between 1 March and 1 May 2014. Potential explanatory variables influencing the performance of emergency cholecystectomy were analysed by means of multilevel, multivariable logistic regression modelling using a two-level hierarchical structure with patients (level 1) nested within hospitals (level 2).

Results

Data were collected on 4744 cholecystectomies from 165 hospitals. Increasing age, lower ASA fitness grade, biliary colic, the need for further imaging (magnetic retrograde cholangiopancreatography), endoscopic interventions (endoscopic retrograde cholangiopancreatography) and admission to a non-biliary centre significantly reduced the likelihood of an emergency cholecystectomy being performed. The multilevel model was used to calculate the probability of receiving an emergency cholecystectomy for a woman aged 40 years or over with an ASA grade of I or II and a BMI of at least 25·0 kg/m2, who presented with acute cholecystitis with an ultrasound scan showing a thick-walled gallbladder and a normal common bile duct. The mean predicted probability of receiving an emergency cholecystectomy was 0·52 (95 per cent c.i. 0·45 to 0·57). The predicted probabilities ranged from 0·02 to 0·95 across the 165 hospitals, demonstrating significant variation between hospitals.

Conclusion

Patients with similar characteristics presenting to different hospitals with acute gallbladder pathology do not receive comparable care.

High-quality genome sequence and description of Bacillus ndiopicus strain FF3(T) sp. nov

Strain FF3^T was isolated from the skin-flora of a 39-year-old healthy Senegalese man. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not allow any identification. This strain exhibited a 16S rRNA sequence similarity of 96.8% with Bacillus massiliensis, the phylogenetically closest species with standing nomenclature. Using a polyphasic study made of phenotypic and genomic analyses, strain FF3^T was Gram-positive, aeroanaerobic and rod shaped and exhibited a genome of 4 068 720 bp with a G+C content of 37.03% that coded 3982 protein-coding and 67 RNA genes (including four rRNA operons). On the basis of these data, we propose the creation of Bacillus ndiopicus sp. nov.

Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov

Strain FF8^T (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8^T was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov.