Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium

BACKGROUND

Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients while also elucidating disease heterogeneity. We sought to develop an ultra-deep plasma next-generation sequencing (NGS) assay for patients with non-small-cell lung cancers (NSCLC) that could detect targetable oncogenic drivers and resistance mutations in patients where tissue biopsy failed to identify an actionable alteration.

PATIENTS AND METHODS

Plasma was prospectively collected from patients with advanced, progressive NSCLC. We carried out ultra-deep NGS using cfDNA extracted from plasma and matched white blood cells using a hybrid capture panel covering 37 lung cancer-related genes sequenced to 50 000× raw target coverage filtering somatic mutations attributable to clonal hematopoiesis. Clinical sensitivity and specificity for plasma detection of known oncogenic drivers were calculated and compared with tissue genotyping results. Orthogonal ddPCR validation was carried out in a subset of cases.

RESULTS

In 127 assessable patients, plasma NGS detected driver mutations with variant allele fractions ranging from 0.14% to 52%. Plasma ddPCR for EGFR or KRAS mutations revealed findings nearly identical to those of plasma NGS in 21 of 22 patients, with high concordance of variant allele fraction (r = 0.98). Blinded to tissue genotype, plasma NGS sensitivity for de novo plasma detection of known oncogenic drivers was 75% (68/91). Specificity of plasma NGS in those who were driver-negative by tissue NGS was 100% (19/19). In 17 patients with tumor tissue deemed insufficient for genotyping, plasma NGS identified four KRAS mutations. In 23 EGFR mutant cases with acquired resistance to targeted therapy, plasma NGS detected potential resistance mechanisms, including EGFR T790M and C797S mutations and ERBB2 amplification.

CONCLUSIONS

Ultra-deep plasma NGS with clonal hematopoiesis filtering resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsy was inadequate for genotyping.

Insuffisances rénales aiguës : actes du 5e Séminaire de recherche translationnelle de la Société de réanimation de langue française (Paris, 4 décembre 2018)

Le séminaire annuel de la commission de recherche translationnelle de la SRLF a eu lieu à Paris le 4 décembre 2018. Ce séminaire a pour but de réunir des cliniciens et scientifiques autour de grandes thématiques de recherche en médecine intensive et réanimation. La cinquième édition a porté sur l’insuffisance rénale aiguë, problématique quotidienne importante des réanimateurs. Les interventions se sont intéressées à la physiopathologie des diverses formes d’insuffisance rénale aiguë, à la récupération rénale, aux modèles expérimentaux, à l’hémodynamique régionale ou encore aux innovations technologiques en épuration extrarénale.

Prise en charge du transplanté rénal en réanimation

La transplantation rénale est la thérapeutique de choix de l’insuffisance rénale chronique au stade ultime, son usage est de plus en plus large. Les progrès réalisés dans les traitements immunosuppresseurs ont permis une amélioration de la durée de vie du greffon, mais au prix d’une augmentation des complications cardiovasculaires et infectieuses. Environ 5 % des transplantés rénaux présentent des complications sévères qui nécessitent une prise en charge intensive. Elles sont principalement de cause infectieuse et dominées par la défaillance respiratoire aiguë. L’insuffisance rénale aiguë est commune, elle affecte la fonction du greffon à court et long termes. La prise en charge en réanimation de ces complications doit prendre en compte le terrain particulier du transplanté rénal et les effets délétères de l’immunosuppression, condition nécessaire à une amélioration de la mortalité qui reste à plus de 30 %.

Brief summary of French guidelines for the prevention, diagnosis and treatment of hospital-acquired pneumonia in ICU

Background

The French Society of Anaesthesia and Intensive Care Medicine and the French Society of Intensive Care edited guidelines focused on hospital-acquired pneumonia (HAP) in intensive care unit. The goal of 16 French-speaking experts was to produce a framework enabling an easier decision-making process for intensivists.

Results

The guidelines were related to 3 specific areas related to HAP (prevention, diagnosis and treatment) in 4 identified patient populations (COPD, neutropenia, post-operative and paediatric). The literature analysis and the formulation of the guidelines were conducted according to the Grade of Recommendation Assessment, Development and Evaluation methodology. An extensive literature research over the last 10 years was conducted based on publications indexed in PubMed™ and Cochrane™ databases.

Conclusions

HAP should be prevented by a standardised multimodal approach and the use of selective digestive decontamination in units where multidrug-resistant bacteria prevalence was below 20%. Diagnosis relies on clinical assessment and microbiological findings. Monotherapy, in the absence of risk factors for multidrug-resistant bacteria, non-fermenting Gram-negative bacilli and/or increased mortality (septic shock, organ failure), is strongly recommended. After microbiological documentation, it is recommended to reduce the spectrum and to prefer monotherapy for the antibiotic therapy of HAP, including for non-fermenting Gram-negative bacilli.

Sodium bicarbonate therapy for patients with severe metabolic acidaemia in the intensive care unit (BICAR-ICU): a multicentre, open-label, randomised controlled, phase 3 trial

BACKGROUND

Acute acidaemia is frequently observed during critical illness. Sodium bicarbonate infusion for the treatment of severe metabolic acidaemia is a possible treatment option but remains controversial, as no studies to date have examined its effect on clinical outcomes. Therefore, we aimed to evaluate whether sodium bicarbonate infusion would improve these outcomes in critically ill patients.

METHODS

We did a multicentre, open-label, randomised controlled, phase 3 trial. Local investigators screened eligible patients from 26 intensive care units (ICUs) in France. We included adult patients (aged ≥18 years) who were admitted within 48 h to the ICU with severe acidaemia (pH ≤7·20, PaCO₂ ≤45 mm Hg, and sodium bicarbonate concentration ≤20 mmol/L) and with a total Sequential Organ Failure Assessment score of 4 or more or an arterial lactate concentration of 2 mmol/L or more. We randomly assigned patients (1:1), by stratified randomisation with minimisation via a restricted web platform, to receive either no sodium bicarbonate (control group) or 4·2% of intravenous sodium bicarbonate infusion (bicarbonate group) to maintain the arterial pH above 7·30. Our protocol recommended that the volume of each infusion should be within the range of 125-250 mL in 30 min, with a maximum of 1000 mL within 24 h after inclusion. Randomisation criteria were stratified among three prespecified strata: age, sepsis status, and the Acute Kidney Injury Network (AKIN) score. The primary outcome was a composite of death from any cause by day 28 and the presence of at least one organ failure at day 7. All analyses were done on data from the intention-to-treat population, which included all patients who underwent randomisation. This study is registered with ClinicalTrials.gov, number NCT02476253.

FINDINGS

Between May 5, 2015, and May 7, 2017, we enrolled 389 patients into the intention-to-treat analysis in the overall population (194 in the control group and 195 in the bicarbonate group). The primary outcome occurred in 138 (71%) of 194 patients in the control group and 128 (66%) of 195 in the bicarbonate group (absolute difference estimate -5·5%, 95% CI -15·2 to 4·2; p=0·24). The Kaplan-Meier method estimate of the probability of survival at day 28 between the control group and bicarbonate group was not significant (46% [95% CI 40-54] vs 55% [49-63]; p=0·09. In the prespecified AKIN stratum of patients with a score of 2 or 3, the Kaplan-Meier method estimate of survival by day 28 between the control group and bicarbonate group was significant (37% [95% CI 28-48] vs 54% [45-65]; p=0·0283). [corrected] Metabolic alkalosis, hypernatraemia, and hypocalcaemia were observed more frequently in the bicarbonate group than in the control group, with no life-threatening complications reported.

INTERPRETATION

In patients with severe metabolic acidaemia, sodium bicarbonate had no effect on the primary composite outcome. However, sodium bicarbonate decreased the primary composite outcome and day 28 mortality in the a-priori defined stratum of patients with acute kidney injury.

FUNDING

French Ministry of Health and the Société Française d'Anesthésie Réanimation.

Faire face à la menace infectieuse en réanimation : de la veille épidémiologique à l’innovation. Actes du séminaire de recherche translationnelle de la Société de réanimation de langue française (5 décembre 2017)

Le séminaire annuel de la Commission de recherche translationnelle de la SRLF a pour but de réunir des cliniciens et scientifiques autour de grandes thématiques de recherche en médecine intensive et réanimation. La quatrième édition du séminaire a porté sur l’infectiologie, thématique au centre des préoccupations des réanimateurs. Les interventions se sont ainsi focalisées sur des aspects aussi divers que les relations hôtes–pathogènes, la contribution de pathogènes dans des pathologies habituellement considérées comme non infectieuses, l’émergence de nouveaux risques infectieux, les avancées technologiques du diagnostic moléculaire des infections et le développement de stratégies antibactériennes alternatives à l’antibiothérapie classique.

Risk factors for anastomotic leakage following ileosigmoid or ileorectal anastomosis

AIM

Reconstruction with an ileosigmoidal anastomosis (ISA) or ileorectal anastomosis (IRA) is a surgical option after a subtotal colectomy. Anastomotic leakage (AL) is a problematic complication and high rates have been reported, but there is limited understanding of the risk factors involved. The aim of this study was to assess the established and potential predictors of AL following ISA and IRA.

METHOD

This was a retrospective cohort study including all patients who had undergone ISA or IRA at three Swedish referral centres for colorectal surgery between January 2007 and March 2015. Data regarding clinical characteristics, treatment and outcome were collected from medical records. Univariate and multivariate logistic regression models were used to determine the association between patient and treatment related factors and the cumulative incidence of AL.

RESULTS

In total, 227 patients were included. Overall, AL was detected amongst 30 patients (13.2%). Amongst patients undergoing colectomy with synchronous ISA or IRA (one-stage procedure), AL occurred in 23 out of 120 (19.2%) compared with seven out of 107 (6.5%) after stoma reversal with ISA or IRA (two-stage procedure) (P = 0.004). In addition, the multivariate analyses revealed a statistically significantly lower odds ratio for AL following a two-stage procedure (OR 0.10, 95% CI 0.03-0.41, P = 0.001).

CONCLUSIONS

This study confirms high rates of AL following ISA and IRA. In particular, a synchronous procedure with colectomy and ISA/IRA carries a high risk of AL.

Extensions to the HISA Standard – the SynEx Computing Environment

Objectives: This paper reports on the integration work required to support the delivery of healthcare. Specifically, four elements are included being: the DHE (a standards based distributed healthcare environment), Synapses which is a patient record server, XML as a technology to deliver records, and finally two client applications that facilitate structured data entry (SDE) and the remote booking of specialist services. Methods: A general motivation for the work is presented and augmented on hand of a clinical scenario. Additionally, the adoption of a middleware approach is reviewed. The role of computerised patient records is described followed by an account of a federated record server. The approach favoured by standards bodies in utilising XML is covered and the tailoring to suit the needs of the integration is explained. The main practical challenges in achieving integration are presented, one of these being the mapping between the DHE data model and the Synapses server record architecture.

Results: The described environment has been demonstrated to provide the functionality that is required and in addition it has been shown that the engineering challenges can be met in a controlled and orderly manner.

Conclusions: The role of the DHE middleware component acting as an ‘anchor’ has been shown to be a valid one onto which other specialised components can be added to provide a richer service environment. Additionally, it has been demonstrated that XML is a good candidate technology that facilitates connectivity to client applications over an extranet. The demands inherent in both the clinical scenario and the computerised patient record can be met by the computing environment described in the paper.

Pharmacokinetic study of anidulafungin in ICU patients with intra-abdominal candidiasis

Background

Only limited pharmacokinetic data are available for anidulafungin in ICU patients, especially in patients treated for severe intra-abdominal infection (IAI).

Methods

This was a prospective multicentre observational study in ICU patients with suspected yeast IAI. All patients received an intravenous loading dose of 200 mg of anidulafungin, followed by 100 mg/day. Thirteen blood samples were drawn between day 1 and day 5 for pharmacokinetic analysis. Samples were analysed by an HPLC-tandem MS method. Demographics and SAPS2 and SOFA scores were recorded.

Results

Fourteen patients with a median age (IQR) of 62 years (48-70) and with a mean BMI of 30.5 kg/m 2 were included from three centres; 57.1% were women. Their median (IQR) SAPS2 score was 54 (45-67) and their median (IQR) SOFA score was 8 (7-12). Six patients with community-acquired IAI and eight patients with nosocomial-acquired IAI were included. Twelve yeasts were isolated: six Candida albicans , two Candida glabrata , two Candida tropicalis , one Candida parapsilosis and one Candida krusei . Pharmacokinetic parameters were as follows [mean (% coefficient of variation)]: C max (mg/L) = 6.0 (29%); T max (h) = 1.6 (25.8%); C min (mg/L) = 3.2 (36.8%); AUC 0-24 (mg·h/L) = 88.9 (38.6%); t 1/2 (h) = 42.1 (68.2%); CL (L/h) = 1.2 (42.3%); and V (L) = 72.8 (87.8%). A two-compartment model best described the anidulafungin concentrations in the population pharmacokinetic study.

Conclusions

The pharmacokinetic parameters of anidulafungin in critically ill ICU patients with complicated IAI are similar to those observed in the literature. However, an increased V and a longer t 1/2 were observed in this study. (EudraCT No. 2010-018695-25).

B-cell activating factor BAFF reflects patients' immunological risk profile after kidney transplantation

The B-cell activating factor BAFF plays an important role in the development and maturation of B-lymphocytes, which can contribute to the generation of donor-specific antibodies and thus may influence graft function and graft survival. Inconsistent data on the role of BAFF levels after renal transplantation for the formation of donor-specific antibodies and the contribution for allograft rejection exist. The aim of the current study was to determine to what extent the degree of pre-immunization is reflected by each patient's BAFF levels before transplantation and in the follow-up. Furthermore, the impact of BAFF on allograft rejection frequency as well as severity and resulting allograft function over time was analyzed. Additionally, the impact of viral infections on BAFF levels after transplantation - as a potential confounder - was examined. For this purpose, a group of pre-sensitized patients (PRA>0%, (52±24% on average), n=40) was compared with non-sensitized patients (PRA=0%, n=62) and in a subsequent analysis stratification in accordance to the detected BAFF level was performed. Pre-sensitized patients had significantly higher BAFF levels before transplantation and suffered significantly more often from early steroid-resistant, mainly antibody-mediated rejections. A result which was confirmed also in highly sensitized patients with PRA levels >50%. Additionally, in the follow-up patients with either rising BAFF levels over time or BAFF levels above the median also had significantly more often antibody mediated rejections. Additionally, patients with BAFF levels above detected median even displayed impaired creatinine values as well as an induced eGFR slope up to month 48 after transplantation. The occurrence of viral infections (CMV, BKV) was only an additional influencing factor in the absence of concomitant allograft rejections. Therefore, the B-cell proliferation factor BAFF appears not only to reflect the immunological risk profile of patients in the context of kidney transplantation, it may possibly be further developed as a predictor of patients with an increased risk profile for subsequent allograft rejection and impaired allograft function.

A diaper-embedded disposable nitrite sensor with integrated on-board urine-activated battery for UTI screening

This paper reports a low-cost solution to the early detection of urinary nitrite, a common surrogate for urinary tract infection (UTI). We present a facile method to fabricate a disposable and flexible colorimetric [1] nitrite sensor and its urine-activated power source [2] on a hydrophobic (wax) paper through laser-assisted patterning and lamination. Such device, integrated with interface circuitry and a Bluetooth low energy (BLE) module can be embedded onto a diaper, and transmit semi-quantitative UTI monitoring information in a point-of-care and autonomous fashion. The proposed nitrite sensing platform achieves a sensitivity of 1.35 ms/(mg/L) and a detection limit of 4 mg/L.

Functional characterisation and cell specificity of BvSUT1, the transporter that loads sucrose into the phloem of sugar beet (Beta vulgaris L.) source leaves

Sugar beet (Beta vulgaris L.) is one of the most important sugar-producing plants worldwide and provides about one third of the sugar consumed by humans. Here we report on molecular characterisation of the BvSUT1 gene and on the functional characterisation of the encoded transporter. In contrast to the recently identified tonoplast-localised sucrose transporter BvTST2.1 from sugar beet taproots, which evolved within the monosaccharide transporter (MST) superfamily, BvSUT1 represents a classical sucrose transporter and is a typical member of the disaccharide transporter (DST) superfamily. Transgenic Arabidopsis plants expressing the β-GLUCURONIDASE (GUS) reporter gene under control of the BvSUT1-promoter showed GUS histochemical staining of their phloem; an anti-BvSUT1-antiserum identified the BvSUT1 transporter specifically in phloem companion cells. After expression of BvSUT1 cDNA in bakers' yeasts (Saccharomyces cerevisiae) uptake characteristics of the BvSUT1 protein were studied. Moreover, the sugar beet transporter was characterised as a proton-coupled sucrose symporter in Xenopus laevis oocytes. Our findings indicate that BvSUT1 is the sucrose transporter that is responsible for loading of sucrose into the phloem of sugar beet source leaves delivering sucrose to the storage tissue in sugar beet taproot sinks.

TGFβ engages MEK/ERK to differentially regulate benign and malignant pancreas cell function

While TGFβ signals are anti-proliferative in benign and well-differentiated pancreatic cells, TGFβ appears to promote the progression of advanced cancers. To better understand dysregulation of the TGFβ pathway, we first generated mouse models of neoplastic disease with TGFβ receptor deficiencies. These models displayed reduced levels of pERK irrespective of KRAS mutation. Furthermore, exogenous TGFβ led to rapid and sustained TGFBR1-dependent ERK phosphorylation in benign pancreatic duct cells. Similar to results that our group has published in colon cancer cells, inhibition of ERK phosphorylation in duct cells mitigated TGFβ-induced upregulation of growth suppressive pSMAD2 and p21, prevented downregulation of the pro-growth signal CDK2 and ablated TGFβ-induced EMT. These observations suggest that ERK is a key factor in growth suppressive TGFβ signals, yet may also contribute to detrimental TGFβ signaling such as EMT. In neoplastic PanIN cells, pERK was not necessary for either TGFβ-induced pSMAD2 phosphorylation or CDK2 repression, but was required for upregulation of p21 and EMT indicating a partial divergence between TGFβ and MEK/ERK in early carcinogenesis. In cancer cells, pERK had no effect on TGFβ-induced upregulation of pSMAD2 and p21, suggesting the two pathways have completely diverged with respect to the cell cycle. Furthermore, inhibition of pERK both reduced levels of CDK2 and prevented EMT independent of exogenous TGFβ, consistent with most observations identifying pERK as a tumor promoter. Combined, these data suggest that during carcinogenesis pERK initially facilitates and later antagonizes TGFβ-mediated cell cycle arrest, yet remains critical for the pathological, EMT-inducing arm of TGFβ signaling.

Effects of lysophospholipid supplementation to lower nutrient diets on growth performance, intestinal morphology, and blood metabolites in broiler chickens

The purpose of this research was to investigate the effects of dietary lysophospholipid (LPL) supplementation on low-energy, crude protein, and selected amino acids on growth performance, intestinal morphology, blood metabolites, inflammatory response, and carcass traits in broiler chickens. A total of 300 one-day-old male chicks (Ross 308) were assigned to 5 treatments, with 6 replications of 10 birds each in a completely randomized design. The 5 treatments were: positive control (PC) without LPL supplementation and adequate in all nutrients, negative control (NC) without LPL, and reduced 150 kcal/kg of metabolizable energy and reduced 5 to 6% of crude protein and selected amino acids including Lys, Met, Thr, and Trp in a calculated amount relative to the PC, NC + 0.05% LPL (LPL05), NC + 0.10% LPL (LPL10), and NC + 0.15% LPL (LPL15). Feeding LPL linearly improved growth performance, feed conversion ratio, ether extract, and protein digestibility. LPL supplementation on low-energy and nitrogenous diets showed significant enhancements in metabolic profiles of blood glucose, protein utilization, and immune system functions. These improvements influenced carcass composition, especially in relative weights of pancreas and breast muscle. In contrast, LPL addition showed no significant effects on relative weights of immune organs, gizzard, and abdominal fat. The NC birds were more susceptible to inflammation via modulating the secretion of interleukin-1 (IL-1) and increasing crypt depth in the jejunal and duodenal segments. However, the inclusion of 0.05% LPL to the NC diet could alleviate inflammation with increased jejunal villi height, ratio of villi height to crypt depth, and decreased IL-1 level. Overall, LPL promotes growth performance, nutrient utilization, gut health, anti-inflammation, and muscle yields when applied to diets of broiler chickens with lower levels of energy, crude protein, and selected amino acids.