Circulating cell-free messenger RNA secretome characterization of primary sclerosing cholangitis

BACKGROUND

Primary sclerosing cholangitis (PSC) is a rare chronic cholestatic liver disease characterized by multifocal bile duct strictures. To date, underlying molecular mechanisms of PSC remain unclear, and therapeutic options are limited.

METHODS

We performed cell-free messenger RNA (cf-mRNA) sequencing to characterize the circulating transcriptome of PSC and noninvasively investigate potentially bioactive signals that are associated with PSC. Serum cf-mRNA profiles were compared among 50 individuals with PSC, 20 healthy controls, and 235 individuals with NAFLD. Tissue and cell type-of-origin genes that are dysregulated in subjects with PSC were evaluated. Subsequently, diagnostic classifiers were developed using PSC dysregulated cf-mRNA genes.

RESULTS

Differential expression analysis of the cf-mRNA transcriptomes of PSC and healthy controls resulted in identification of 1407 dysregulated genes. Furthermore, differentially expressed genes between PSC and healthy controls or NAFLD shared common genes known to be involved in liver pathophysiology. In particular, genes from liver- and specific cell type-origin, including hepatocyte, HSCs, and KCs, were highly abundant in cf-mRNA of subjects with PSC. Gene cluster analysis revealed that liver-specific genes dysregulated in PSC form a distinct cluster, which corresponded to a subset of the PSC subject population. Finally, we developed a cf-mRNA diagnostic classifier using liver-specific genes that discriminated PSC from healthy control subjects using gene transcripts of liver origin.

CONCLUSIONS

Blood-based whole-transcriptome cf-mRNA profiling revealed high abundance of liver-specific genes in sera of subjects with PSC, which may be used to diagnose patients with PSC. We identified several unique cf-mRNA profiles of subjects with PSC. These findings may also have utility for noninvasive molecular stratification of subjects with PSC for pharmacotherapy safety and response studies.

Transcriptomic recurrence score improves recurrence prediction for surgically treated patients with intermediate-risk clear cell kidney cancer

BACKGROUND

Risk stratification of kidney cancer patients after nephrectomy may tailor surveillance intensity and selection for adjuvant therapy. Transcriptomic approaches are effective in predicting recurrence, but whether they add value to clinicopathologic models remains unclear.

METHODS

Data from patients with clear cell renal cell carcinoma (ccRCC) was downloaded from The Cancer Genome Atlas. Clinicopathologic variables were used to calculate SSIGN (stage, size, grade, and necrosis) scores. The 16 gene recurrence score (RS) signature was generated using RNA-seq data. Transcriptomic risk groups were calculated using the original thresholds. SSIGN groups were divided into low, intermediate, and high risk. Disease-free status was the primary endpoint assessed.

RESULTS

SSIGN and RS were calculated for 428 patients with non-metastatic ccRCC. SSIGN low-, intermediate-, and high-risk groups demonstrated 2.7%, 15.2%, and 27.5%, 3-year recurrence risk, respectively. On multivariable analysis, the RS was associated with disease-free status (sub-distribution hazard ratio (sHR) 1.43 per 25 RS [95% CI (1.00-1.43)], p = 0.05). By risk groups, RS further risk stratified the SSIGN intermediate-risk group (sHR 2.22 [95% CI 1.10-4.50], p = 0.03). SSIGN intermediate-risk patients with low and high RS had a 3-year recurrence rate of 8.0% and 25.2%, respectively. Within this risk group, the area under the curve (AUC) at 3 years was 0.69 for SSIGN, 0.74 for RS, and 0.78 for their combination.

CONCLUSIONS

Transcriptomic recurrence scores improve risk prediction even when controlling for clinicopathologic factors. Utility may be best suited for intermediate-risk patients who have heterogeneous outcomes and further refinement for clinical utility is warranted.

The IFMIF-DONES Project: Design Status and Main Achievements Within the EUROfusion FP8 Work Programme

International Fusion Materials Irradiation Facility-DEMO-Oriented NEutron Source (IFMIF-DONES) is a high-intensity neutron irradiation facility for qualification of fusion reactor materials, which is being designed as part of the European roadmap to fusion-generated electricity. Its main purpose is to study the behavior of materials properties under irradiation in a neutron flux able to simulate the same effects in terms of relevant nuclear responses as those expected in the first wall of the DEMO reactor which is envisaged to follow ITER. It is thus a key facility to support the design, licensing and safe operation of DEMO as well as of the fusion power plants that will be developed afterwards. The start of its construction is foreseen in the next few years. In this contribution, an overview of the IFMIF-DONES neutron source is presented together with a snapshot of the current engineering design status and of the relevant key results achieved within the EUROfusion Work Package Early Neutron Source (WPENS) as part of the 2014–2020 EURATOM Research and Training Programme, complementary to the EU Horizon 2020 Framework Programme (FP8). Moreover, some information on the future developments of the project are given.

Survey of extracellular communication of systemic and organ-specific inflammatory responses through cell free messenger RNA profiling in mice

Background

Inflammatory and immune responses are essential and dynamic biological processes that protect the body against acute and chronic adverse stimuli. While conventional protein markers have been used to evaluate systemic inflammatory response, the immunological response to stimulation is complex and involves modulation of a large set of genes and interacting signalling pathways of innate and adaptive immune systems. There is a need for a non-invasive tool that can comprehensively evaluate and monitor molecular dysregulations associated with inflammatory and immune responses in circulation and in inaccessible solid organs.

Methods

Here we utilized cell-free messenger RNA (cf-mRNA) RNA-Seq whole transcriptome profiling and computational biology to temporally assess lipopolysaccharide (LPS) induced and JAK inhibitor modulated inflammatory and immune responses in mouse plasma samples.

Findings

Cf-mRNA profiling displayed a pattern of systemic immune responses elicited by LPS and dysregulation of associated pathways. Moreover, attenuation of several inflammatory pathways, including STAT and interferon pathways, were observed following the treatment of JAK inhibitor. We further identified the dysregulation of liver-specific transcripts in cf-mRNA which reflected changes in the gene-expression pattern in this generally inaccessible biological compartment.

Interpretation

Using a preclinical mouse model, we demonstrated the potential of plasma cf-mRNA profiling for systemic and organ-specific characterization of drug-induced molecular alterations that are associated with inflammatory and immune responses.

Funding

Molecular Stethoscope.

NOS3 rs1799983 and rs2070744 polymorphisms and their association with advanced chronic kidney disease and coronary heart disease in Canarian population with type 2 diabetes

CONTEXT

Different polymorphisms of the endothelial nitric oxide synthase gene (NOS3) have been related to diabetic kidney disease.

OBJECTIVE

To evaluate the association between advanced diabetic chronic kidney disease (ACKD) and the rs1799983 and rs2070744 poymorphisms of NOS3 in a population from the Gran Canaria island.

DESIGN

Cross-sectional case-control study.

SUBJECTS AND METHODS

Polymorphisms were genotyped in 152 subjects with ACKD secondary to type 2 diabetes [estimated glomerular filtration rate (eGFR) <30 mL/min/1.73 m²], 110 subjects with type 2 diabetes for 20 or more years since diagnosis without ACKD (eGFR ≥45 mL/min/1.73m² and albumin/creatinine ratio <300 mg/g and/or 24-h urinary albumin excretion <300 mg) and 292 healthy controls. Association between both polymorphisms and established coronary heart disease (CHD) was also analyzed in both groups with diabetes.

RESULTS

A greater proportion of homozygous individuals for the risk allele C of rs2070744 was found among subjects with ACKD. Association between ACKD and rs2070744 was observed in a recessive genetic model, both for comparison to subjects with diabetes but no ACKD [OR 2.17 (95% CI: 1.17-4.00), p=0.014] and for comparison to healthy controls [OR 1.61 (1.03-2.52), p=0.036]. The frequency of the C allele was significantly higher among subjects with CHD, but only in the group with ACKD. No associations were found for rs1799983.

CONCLUSIONS

NOS3 rs2070744 is associated with ACKD in population with type 2 diabetes from Gran Canaria. A link between this genetic variant and CHD in Canarian subjects with type 2 diabetes could be restricted to cases with ACKD.

Noninvasive characterization of Alzheimer's disease by circulating, cell-free messenger RNA next-generation sequencing

The lack of accessible noninvasive tools to examine the molecular alterations occurring in the brain limits our understanding of the causes and progression of Alzheimer's disease (AD), as well as the identification of effective therapeutic strategies. Here, we conducted a comprehensive profiling of circulating, cell-free messenger RNA (cf-mRNA) in plasma of 126 patients with AD and 116 healthy controls of similar age. We identified 2591 dysregulated genes in the cf-mRNA of patients with AD, which are enriched in biological processes well known to be associated with AD. Dysregulated genes included brain-specific genes and resembled those identified to be dysregulated in postmortem AD brain tissue. Furthermore, we identified disease-relevant circulating gene transcripts that correlated with the severity of cognitive impairment. These data highlight the potential of high-throughput cf-mRNA sequencing to evaluate AD-related pathophysiological alterations in the brain, leading to precision healthcare solutions that could improve AD patient management.

Importance of the Second Opinion in Surgical Breast Pathology and Its Therapeutic Implications

Introduction/Objective

Histopathological diagnosis determines surgical management and complementary therapies in patients with breast cancer. There has been reported significant diagnostic divergences, between 7.8 and 26%, and in tumor markers between 3.4 and 41%. We evaluate the agreement between diagnoses of general pathologists and specialists of our center, in which serious discrepancies could have therapeutic repercussions.

Methods

Method: A retrospective study from 2012 to 2019. The cases were classified in benign and malignant. The atypical lesions were included with benign. Major disagreements were considered when there was a change in diagnosis from benign to malignant or vice versa, variation from intraepithelial to microinvasive carcinomas, infiltrating to intraductal carcinomas or vice versa. When necessary, we repeat routine stains and/or immunostains, or add new immunostains.

Material: 295 cases. 294 women and 1 man. 228 biopsies and 67 immunostains of prognostic-predictive factors.

Results

We found diagnostic differences in 46/295 cases (15.6%). Major discrepancies in 32 cases (10.8%). In morphological diagnoses 11/228 (4.8%) and in immunodeterminations 20/67 (29.9%). In diagnostic changes, they highlighted 3 cases of ductal carcinoma in situ (DCIS) to benign, 2 cases of benign lesions to DCIS, 1 benign to invasive ductal carcinoma (IDC), 1 DCIS to IDC and 1 IDC to DCIS.

Conclusion

We found serious diagnostic divergences in 32 of 295 cases, 10.8%, which could have varied the therapeutic approach. In morphological interpretation 4.8% and in immunohistochemical results 29.9%. This should motivate multidisciplinary teams to routinely use the second opinion in surgical breast disease

Ciliated Carcinoma Associated With Human Papiloma Virus: Presentation As Cervical Metastasis Of Unknown Primary

Introduction/Objective

There is a significant increase in high-risk human papilloma virus (HPV) -related carcinomas of the head and neck. Half of them debut with metastases in cervical nodes, of expansive growth, usually cystic-necrotic. Most are oropharyngeal primaries. They are non-keratinizing squamous carcinomas with mild atypia, sometimes with exceptional characteristics, such as glandular differentiation and inclusion of ciliated cells

Methods

Clinical Case: 39-year-old male patient, operated two years ago, in another institution, for cervical metastasis from HPV-related Ciliated Carcinoma (HPV-RCC), 4.5 x 2 cm. No primary cancer was found in his study. Two months ago, a new 4.3 x 2.7 cm metastasis was resected, performing a right cervical dissection, with another 36 lymph nodes without tumor. Palatine tonsils, adenoids are removed and a biopsy of the oral mucosa is taken, and no malignancy was found. In our center, biopsies of the tongue and right glosso-tonsillar fold are taken, without objectify malignancy.

Results

The metastases had macroscopic cystic-necrotic appearance. Histology corresponded to nonkeratinizing squamous carcinoma with microcystic spaces and the presence of ciliated columnar cells. The immunohistochemical study gave strong and diffuse positivity for p16. The real-time multiple PCR study detected HPV genotype 16.

Conclusion

We present an exceptional case of Ciliated Carcinoma Related to HPV, a recently described entity. These are nonkeratinizing squamous neoplasms, which include cystic spaces and ciliated columnar cells. Both components reveal HPV positivity, with p16 expression and high-risk viral typing. HPV-RCC should be considered in the differential diagnosis of well-differentiated squamous lesions of the oropharyngeal cavity and at the cervical level, with non-neoplastic cysts. Our patient will undergo radiotherapy protocol, for unknown primary

Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing

Circulating cell-free mRNA (cf-mRNA) holds great promise as a non-invasive diagnostic biomarker. However, cf-mRNA composition and its potential clinical applications remain largely unexplored. Here we show, using Next Generation Sequencing-based profiling, that cf-mRNA is enriched in transcripts derived from the bone marrow compared to circulating cells. Further, longitudinal studies involving bone marrow ablation followed by hematopoietic stem cell transplantation in multiple myeloma and acute myeloid leukemia patients indicate that cf-mRNA levels reflect the transcriptional activity of bone marrow-resident hematopoietic lineages during bone marrow reconstitution. Mechanistically, stimulation of specific bone marrow cell populations in vivo using growth factor pharmacotherapy show that cf-mRNA reflects dynamic functional changes over time associated with cellular activity. Our results shed light on the biology of the circulating transcriptome and highlight the potential utility of cf-mRNA to non-invasively monitor bone marrow involved pathologies.

Circulating cell-free mRNA holds great promise as a non-invasive diagnostic biomarker. Here the authors show that cell-free mRNA captures transcripts from the bone marrow and can be used to non-invasively monitor dynamic changes in bone marrow physiology.

PIMA: A population informative multiplex for the Americas

We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment I_n values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.

Predicting tearing paths in thin sheets

This study investigates the tearing of a thin notched sheet when two points on the sheet are pulled apart. The concepts that determine the crack trajectory are reviewed in the general anisotropic case, in which the energy of the fracture depends on the fracture direction. When observed as a flat sheet a purely geometric "tearing vector" is defined through the location of the crack tip and the pulling points. Both Griffiths's criterion and the maximum energy release rate criterion (MERR) predict a fracture path that is parallel to the tearing vector in the isotropic case. However, for the anisotropic case, the application of the MERR leads to a crack path that deviates from the tearing vector, following a propagation direction that tends to minimize the fracture energy. In the case of strong anisotropy, it is more difficult to obtain an analytical prediction of the tearing trajectory. Thus, simple geometrical arguments are provided to give a derivation of a differential equation accounting for crack trajectory, according to the natural coordinates of the pulling, and in the case that the anisotropy is sufficiently weak. The solution derived from this analysis is in good agreement with previous experimental observations.

Predicting age from the transcriptome of human dermal fibroblasts

Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.

Tpr regulates the total number of nuclear pore complexes per cell nucleus

In this study, McCloskey et al. investigated the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope. Their results show that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types and provide insight into a critical role of the nucleoporin Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.

The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.

Nucleoporin-mediated regulation of cell identity genes

Here, Ibarra et al. investigate the contribution of nuclear envelope components to the regulation of cell type-specific gene expression and show a role for NPC components in the regulation of cell type-specific gene expression The authors found that nucleoporin-associated superenhancers localize preferentially to the nuclear periphery, and, in the absence of nucleoporins, transcriptional changes of SE-associated genes were observed.

The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.

Facile production of stable silicon nanoparticles: laser chemistry coupled to in situ stabilization via room temperature hydrosilylation

Stable, alkyl-terminated, light-emitting silicon nanoparticles have been synthesized in a continuous process by laser pyrolysis of a liquid trialkyl-silane precursor selected as a safer alternative to gas silane (SiH4). Stabilization was achieved by in situ reaction using a liquid collection system instead of the usual solid state filtration. The alkene contained in the collection liquid (1-dodecene) reacted with the newly formed silicon nanoparticles in an unusual room-temperature hydrosilylation process. It was achieved by the presence of fluoride species, also produced during laser pyrolysis from the decomposition of sulfur hexafluoride (SF6) selected as a laser sensitizer. This process directly rendered alkyl-passivated silicon nanoparticles with consistent morphology and size (<3 nm), avoiding the use of costly post-synthetic treatments.

Optimization and shelf life of a low-lactose yogurt with Lactobacillus rhamnosus HN001

Lactose intolerance results in gastrointestinal discomfort and the malabsorption of certain nutrients, such as calcium. The replacement of milk with low-lactose and probiotic-enriched dairy products is an effective strategy of mitigating the symptoms of lactose intolerance. Lactobacillus rhamnosus HN001 (HN001) is a safe, immunity-stimulating probiotic. We have developed a process to increase the hydrolysis of lactose and HN001 growth in yogurt versus β-galactosidase (βG) concentration and enzymatic hydrolysis time (EHT) before bacterial fermentation. The objective of this study was to optimize the conditions by which yogurt is processed as a function of βG and EHT using a multifactorial design, with lactose content, HN001 growth, process time, and sensory quality as dependent variables. Further, the shelf life of the optimized yogurt was evaluated. In the optimization study, polynomials explained the dependent variables. Based on Pearson correlation coefficients, HN001 growth correlated positively with the hydrolysis of lactose. However, low lactose content and high HN001 count increased the fermentation time and lowered the sensory quality. The optimized conditions-using polynomials to obtain yogurt with >1 × 10(7) cfu of HN001/mL, <10 g of lactose/L, and a minimum overall sensory quality of 7 on the Karlsruhe scale-yielded a theoretical value of 910 neutral lactose units/kg for βG and 2.3h for EHT, which were validated in an industrial-scale assay. Based on a shelf-life study at 3 temperatures, the hydrolysis of lactose and the growth of HN001 continue during storage. Arrhenius equations were developed for the variables in the shelf-life study. Our results demonstrate that it is feasible to develop a low-lactose yogurt to which HN001 has been added for lactose-intolerant persons who wish to strengthen their immune system.

Neuroprotection of completely lacerated spinal cord of adult rats by homotopic and heterotopic transplantation

To evaluate the neuroprotective effect of transplants placed in the lesion zone after a complete spinal cord (SC) laceration, two independent series of experiments were carried out. In the first, allogeneic or xenogeneic fetal SC was transplanted into the gaps of the damaged lower thoracic SC of adult rats. In the transplanted rats the incidence of life-threatening complications was reduced, and the survival rate was increased compared with the control group (lesion, without implant). Histological examination showed less damage to the neighboring SC parenchyma in the transplanted rats. The measurement of this neuroprotective effect was made in a second series of experiments. Using the same model of SC injury, allogeneic fetal SC, autologous peripheral nerve and/or adipose tissue were implanted. Rats with implants of Gelfoam and damaged rats without implants were the controls. The implanted rats of all groups, including the Gelfoam group, showed a better survival rate than the nonimplanted rats. Significantly less damage to the neighboring SC parenchyma was measured in implanted rats with any of the live tissues tested compared with non-implanted rats, although no significant differences were observed between the Gelfoam group and the nonimplanted rats. Histological evidence of tissue implant survival was observed in all corresponding groups. It is concluded that the transplanted tissues tested here have a neuroprotective effect, possibly by acting as a buffer to neurotoxic substance(s) released by the stumps, and/or by exerting trophic effect(s) on the host.