Patent Application
20180282809
The present invention relates to the field of medicine and RNA biology, in particular it relates to the field of diagnosis of a disease using circRNAs, more particular the present invention relates to the field of diagnosis of a neurodegenerative disease, e.g. Alzheimer's disease.
Many diseases are associated with deregulation of gene expression. Such deregulation is in many cases detectable at early stages of the disease. In fact, detection of deregulated expression often serves as a biomarker for a disease or the risk for acquiring a disease before the disease manifests in terms of symptoms. However, diagnosis is often restricted to samples of the diseased tissue. In some cases, diagnosis also aims at the detection of biomarkers in easily accessible samples, such as blood. However, these methods are restricted to protein biomarkers and require cumbersome preparation of the samples, e.g. serum or plasma samples. The direct readout of expression, i.e. RNA, is in most cases not feasible in blood samples, as RNAs are prone to degradation. Hence, RNA nowadays is a poor biomarker in blood, in particular for diseases manifesting in tissues others than blood.
Regulatory RNAs such as microRNAs (miRNAs) or long non-coding RNAs (lncRNAs) have been implicated in many biological processes and human diseases such as cancer (reviewed in Batista P J, Chang H Y. Long Noncoding RNAs: Cellular Address Codes in Development and Disease. Cell. 2013; 152(6):1298-1307; and Cech T R, Steitz J A. The Noncoding RNA Revolution Trashing Old Rules to Forge New Ones. Cell. 2014; 157(1):77-94). Recent studies have drawn attention to a new class of RNA that is endogenously expressed as single-stranded, covalently closed circular molecules (circRNA, reviewed in Jeck W R, Sharpless N E. Detecting and characterizing circular RNAs. Nature Biotechnology. 2014; 32(5):453-461). Most circRNAs are probably products of a ‘back-splice’ reaction that joins a splice donor site with an upstream splice acceptor site (see Ashwal-Fluss R, Meyer M, Pamudurti N R, et al. circRNA Biogenesis Competes with Pre-mRNA Splicing. MOLCEL. 2014; 1-12; and Starke S, Jost I, Rossbach O, et al. Exon Circularization Requires Canonical Splice Signals. Cell Reports. 2015; 10(1):103-111). Circular RNA is known for several decades from viroids, viruses and plants, but until recently only few mammalian circRNAs were reported. Sequencing based studies lately revealed that circRNAs are abundantly and prevalently expressed across life, oftentimes in a tissue and developmental-stage specific manner (see Danan M, Schwartz S, Edelheit S, Sorek R. Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res. 2012; 40(7):3131-3142; Salzman J, Gawad C, Wang P L, Lacayo N, Brown P O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE. 2012; 7(2):e30733; Jeck W R, Sorrentino J A, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013; 19(2):141-157; Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338; Salzman J, Chen R E, Olsen M N, Wang P L, Brown P O. Cell-Type Specific Features of Circular RNA Expression. PLoS Genetics. 2013; 9(9):e1003777; Wang P L, Bao Y, Yee M-C, et al. Circular RNA is expressed across the eukaryotic tree of life. PLoS ONE. 2014; 9(3):e90859; Guo J U, Agarwal V, Guo H, Bartel D P. Expanded identification and characterization of mammalian circular RNAs. Genome Biology. 2014; 1-14; and You X, Vlatkovic I, Babic A, et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci. 20117-25). The vast majority of circRNAs consists of 2-4 exons of protein coding genes, but they can also derive from intronic, non-coding, antisense, 5′ or 3′ untranslated or intergenic genomic regions (see Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338; and Zhang Y, Zhang X-O, Chen T, et al. Circular Intronic Long Noncoding RNAs. MOLCEL. 2013; 1-15). Although not fully understood, the biogenesis of many mammalian circRNAs depends on complementary sequences within flanking introns (see Ashwal-Fluss R, Meyer M, Pamudurti N R, et al. circRNA Biogenesis Competes with Pre-mRNA Splicing. MOLCEL. 2014; 1-12; Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. MOLCEL. 2015; 1-17; Zhang X-O, Wang H-B, Zhang Y, et al. Complementary Sequence-Mediated Exon Circularization. Cell. 2014; Liang D, Wilusz J E. Short intronic repeat sequences facilitate circular RNA production. Genes and Development. 2014; Conn S J, Pillman K A, Toubia J, et al. The RNA Binding Protein Quaking Regulates Formation of circRNAs. Cell. 2015; 160(6):1125-1134; and Ivanov A, Memczak S, Wyler E, et al. Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals. CellReports. 2015; 10(2):170-177) and their expression can be modulated by antagonistic or activating trans-acting factors such as ADAR and Quaking (see Ivanov A, Memczak S, Wyler E, et al. Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals. Cell Reports. 2015; 10(2):170-177; and Conn S J, Pillman K A, Toubia J, et al. The RNA Binding Protein Quaking Regulates Formation of circRNAs. Cell. 2015; 160(6):1125-1134; respectively). Although the function of animal circRNAs is largely unknown, it was demonstrated that the circRNAs CDR1as (ciRS-7) and SRY can act as antagonists of specific miRNAs by functioning as miRNA sponges (see Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338; and Hansen T B, Jensen T I, Clausen B H, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013; 495(7441):384-388). Moreover, stable knockdown of CDR1as caused a migration defect in cell culture and a circRNA produced from the muscleblind transcript can bind muscleblind protein and likely regulate its expression levels (see Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338; and Ashwal-Fluss R, Meyer M, Pamudurti N R, et al. circRNA Biogenesis Competes with Pre-mRNA Splicing. MOLCEL. 2014; 1-12). Besides these specific functions for the few in-depth analyzed circRNAs, a recent study uncovered a putatively more general competition mechanism between linear RNA splicing and co-transcriptional circular RNA splicing (see Ashwal-Fluss R, Meyer M, Pamudurti N R, et al. circRNA Biogenesis Competes with Pre-mRNA Splicing. MOLCEL. 2014; 1-12). The lack of free ends, i.e. its circularity, renders circRNAs resistant to exonucleolytic activities within cells and in extracellular environments. Thus, circRNAs are stable molecules as demonstrated by their long half lives in cells a feature that distinguishes them from canonical linear RNA isoforms (see Cocquerelle C, Daubersies P, Majérus MA, Kerckaert J P, Bailleul B. Splicing with inverted order of exons occurs proximal to large introns. EMBO J 1992; 11(3):1095-1098; Jeck W R, Sorrentino J A, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013; 19(2):141-157; and Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338).
The inventors now for the first time show the presence of a plurality of ten thousands of circRNAs in standard clinical whole blood specimen of diseased subjects and thereby show that circRNAs function as biomarkers in human disorders, in particular neurodegenerative disorders, as exemplified by Alzheimer's disease. Strikingly, the mRNA transcripts which give rise to circRNAs were in hundreds of cases almost not detectable while the corresponding circRNAs were highly expressed, underlining the significance of circRNAs as novel biomarkers. Approaches have been performed to detect circRNAs as biomarkers in blood. However, these approaches use processed blood. Blood-exosomes have been postulated as comprising circRNAs (Li, Yan et al. (2015); Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis; Cell Res, 25(8): 981-984). However, blood-exosomes are difficultly obtainable and the cumbersome procedure renders the procedure susceptible to errors and the significance of the so obtained circRNA levels questionable. The present inventors however showed that circRNAs in unprocessed samples, e.g. whole blood, are detectable and are surprisingly well suited as biomarkers.
Alzheimer's disease (also referred to as “AD”), is the cause for 60% to 70% of cases of dementia. It is a chronic neurodegenerative disease starting slowly and getting worse over time. One of the first symptoms is a short-term memory loss. As the disease advances, symptoms can include problems with language, disorientation (including easily getting lost), mood swings, loss of motivation, not managing self care, and behavioural issues. As a person's condition declines, she or he often withdraws from family and society. Gradually, bodily functions are lost, ultimately leading to death. Although the speed of progression can vary, the average life expectancy following diagnosis is three to nine years. The cause of Alzheimer's disease is poorly understood. About 70% of the risk is believed to be genetic with many genes usually involved. Other risk factors include a history of head injuries, depression, or hypertension. The disease process is associated with plaques and tangles in the brain.
Currently, the diagnosis of Alzheimer's disease is based on the history of the illness and cognitive testing. These tests are often substituted by medical imaging and blood tests to rule out other possible causes. Initial symptoms are often mistaken for normal ageing. Today, examination of brain tissue is needed for a definite diagnosis. However, brain tissue is not easily accessible and the surgical intervention causes severe dangers. Mental and physical exercise, and avoiding obesity may decrease the risk of AD.
In 2010, there were between 21 and 35 million people worldwide with AD. It most often begins in people over 65 years of age, although 4% to 5% of cases are early-onset Alzheimer's which begin before this. It affects about 6% of people 65 years and older. In 2010, dementia resulted in about 486,000 deaths. In developed countries, AD is one of the most financially costly diseases. There is a long felt need for a direct, easy and reliable diagnosis of Alzheimer's disease to allow intervention and prevention of adverse effects of the beginning or progressing mental degeneration.
The molecular underpinnings of AD are controversially debated; although substantial research efforts were made and are currently ongoing (annual budget for AD of the NIH in 2015 is $566 million). In particular there is an urgent need for biomarkers for AD since it is believed that the molecular alterations involved in the disease precede the symptoms years or even decades, hindering therapeutic interventions.
The present invention provides for a method that overcomes the above outlined drawbacks. The inventors have found that it is possible to detect circRNAs in samples of a bodily fluid in a great amount. The inventors further have proven that the circRNAs are indicative for a disease that is not a disease of the bodily fluid. Thereby, a tool is given to directly diagnose a disease by determining presence or absence of one or more circRNAs in a bodily fluid. The invention therefore provides for a new class of biomarkers in bodily fluids, e.g. blood.
Hence, the present invention relates to a method for diagnosing a disease of a subject, comprising the step of:
wherein the presence or absence of said one or more circRNA is indicative for the disease. Preferably, said disease is not a disease of said bodily fluid.
As has been shown by the inventors, certain circRNAs may be present in samples of a diseased subject at differing levels as compared to samples from healthy subjects. Hence, it may be desirable to decide on “presence” or “absence” of a circRNA when compared to a control level. Hence, in a preferred embodiment of the method according to the present invention the determination step comprises:
wherein differing levels between the determined and the control level are indicative for the disease. Hence, the invention also relates to a method for diagnosing a disease of a subject, comprising the step of:
wherein differing levels between the determined and the control level are indicative for the disease.
In a preferred embodiment of the present invention, the method is a method for diagnosing a neurodegenerative disease in a subject. Hence, the invention also relates to a method for diagnosing the neurodegenerative disease, preferably Alzheimer's disease, in a subject comprising the steps of:
The inventors, furthermore, identified circRNAs that were not previously known to be present in blood. These novel blood circRNAs are listed in Table 1. Hence the present invention also relates to a nucleic acid probe specifically hybridizing to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of SEQ ID NO:1 to 910, and a RNA sequence encoded by a sequence of SEQ ID NO:1 to 910, or specifically hybridizing to a reverse complement sequence thereof; preferably specifically hybridizing to a sequence selected from the group consisting of SEQ ID NO:1 to 910, and a RNA sequence encoded by a sequence of SEQ ID NO:1 to 910, or specifically hybridizing to a reverse complement sequence thereof.
Furthermore, the invention relates to a kit for diagnosing a neurodegenerative disease, comprising means for specifically detecting one or more nucleic acid sequence encoded by a sequence selected from the group consisting of SEQ ID NO:1 to 910 or SEQ ID NO:911 to SEQ ID NO:1820.
The invention, furthermore, provides an array for determining the presence or level of a plurality of nucleic acids, comprising a plurality of probes, wherein the plurality of probes specifically hybridize to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, and a RNA sequence encoded by a sequence of SEQ ID NO:1 to 910, or to a reverse complement sequence thereof; preferably the plurality of probes comprises probes specifically hybridizing to the sequence of nucleotide 11 to 30 of at least 100, preferably at least 150 more preferably at least 200 nucleic acid sequences selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, and a RNA sequence encoded by a sequence of SEQ ID NO:1 to 910; or specifically hybridize to the reverse complement sequences thereof, preferably the plurality of probes comprises probes specifically hybridizing to the sequence of nucleotide 11 to 30 of SEQ ID NO:1 to SEQ ID NO:200, or a RNA sequence encoded by a sequence of SEQ ID NO:1 to 200, or the reverse complement sequences thereof.
The invention in particular relates to the use of a nucleic acid probe specifically hybridizing to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910; and a RNA sequence encoded by a sequence of SEQ ID NO:1 to 910, or hybridizing to the reverse complement thereof, a kit according to the invention, or an array according to the invention for the diagnosis of a neurodegenerative disease, preferably for the diagnosis of Alzheimer's disease.
As outlined herein and exemplified in the Examples, the inventors for the first time provide evidence that circular RNAs (circRNA) is present in whole blood in great amounts and suited as biomarker for diseases in a subject. Hence, the invention relates to a method for diagnosing a disease of a subject, comprising the step of determining the presence or absence of one or more circular RNA (circRNA) in a sample of a bodily fluid of said subject; wherein the presence or absence of said one or more circRNA is indicative for the disease.
It was unexpectedly possible to show a correlation of differing levels of RNAs and a disease in a tissue other than the sample tissue, i.e. other than the bodily fluid tested. Hence, in a preferred embodiment said disease is not a disease of said bodily fluid. The gist of the present invention is that circRNAs in bodily fluids like blood are unexpectedly suited as biomarkers.
The term “biomarker” (biological marker) was introduced in 1989 as a Medical Subject Heading (MeSH) term: “measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc.” In 2001, an NIH working group standardized the definition of a biomarker as “a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention” and defined types of biomarkers. A biomarker may be measured on a biosample (as a blood, urine, or tissue test), it may be a recording obtained from a person (blood pressure, ECG, or Holter), or it may be an imaging test (echocardiogram or CT scan). Biomarkers can indicate a variety of health or disease characteristics, including the level or type of exposure to an environmental factor, genetic susceptibility, genetic responses to exposures, markers of subclinical or clinical disease, or indicators of response to therapy. Thus, a simplistic way to think of biomarkers is as indicators of disease trait (risk factor or risk marker), disease state (preclinical or clinical), or disease rate (progression). Accordingly, biomarkers can be classified as antecedent biomarkers (identifying the risk of developing an illness), screening biomarkers (screening for subclinical disease), diagnostic biomarkers (recognizing overt disease), staging biomarkers (categorizing disease severity), or prognostic biomarkers (predicting future disease course, including recurrence and response to therapy, and monitoring efficacy of therapy). The biomarkers of the present invention are preferably antecedent or screening biomarkers. Hence, the methods are methods for diagnosing the presence or the risk for acquiring a disease.
Biomarkers may also serve as surrogate end points. Although there is limited consensus on this issue, a surrogate end point is one that can be used as an outcome in clinical trials to evaluate safety and effectiveness of therapies in lieu of measurement of the true outcome of interest. The underlying principle is that alterations in the surrogate end point track closely with changes in the outcome of interest. Surrogate end points have the advantage that they may be gathered in a shorter time frame and with less expense than end points such as morbidity and mortality, which require large clinical trials for evaluation. Additional values of surrogate end points include the fact that they are closer to the exposure/intervention of interest and may be easier to relate causally than more distant clinical events. An important disadvantage of surrogate end points is that if the clinical outcome of interest is influenced by numerous factors (in addition to the surrogate end point), residual confounding may reduce the validity of the surrogate end point. It has been suggested that the validity of a surrogate end point is greater if it can explain at least 50% of the effect of an exposure or intervention on the outcome of interest.
A “sample” in the meaning of the invention can be all biological fluids of the subject, such as lymph, saliva, urine, cerebrospinal fluid or blood. The sample is collected from the patient or subjected to the diagnosis according to the invention. The sample of the bodily fluid is in a preferred embodiment selected from the group consisting of blood, cerebrospinal fluid, saliva, serum, plasma, and semen, the most preferred embodiment of the sample is a whole blood sample. A “sample” in the meaning of the invention may also be a sample originating from a biochemical or chemical reaction such as the product of an amplification reaction. Liquid samples may be subjected to one or more pre-treatments prior to use in the present invention. Such pre-treatments include, but are not limited to dilution, filtration, centrifugation, concentration, sedimentation, precipitation or dialysis. Pre-treatments may also include the addition of chemical or biochemical substances to the solution, e.g. in order to stabilize the sample and the contained nucleic acids, in particular the circRNAs. Such addition of chemical or biochemical substances include acids, bases, buffers, salts, solvents, reactive dyes, detergents, emulsifiers, or chelators, like EDTA. The sample may for instance be taken and directly mixed with such substances. In a particularly preferred embodiment of the invention the sample is a whole blood sample. The whole blood sample is preferably not pre-treated by means of dilution, filtration, centrifugation, concentration, sedimentation, precipitation or dialysis. It is, however, preferred that substances are added to the sample in order to stabilize the sample until onset of analysis. “Stabilizing” in this context means prevention of degradation of the circRNAs to be determined. Preferred stabilizers in this context are EDTA, e.g. K2EDTA, RNase inhibitors, alcohols e.g. ethanol and isopropanol, agents used to salt out proteins (such as RNAlater).
“Whole blood” is a venous, arterial or capillary blood sample in which the concentrations and properties of cellular and extra-cellular constituents remain relatively unaltered when compared with their in vivo state. In some embodiments, anticoagulation in vitro stabilizes the constituents in a whole blood sample.
In a preferred embodiment the sample comprises a nucleic acid or nucleic acids. The term “nucleic acid” is here used in its broadest sense and comprises ribonucleic acids (RNA) and deoxyribonucleic acids (DNA) from all possible sources, in all lengths and configurations, such as double stranded, single stranded, circular, linear or branched. All sub-units and sub-types are also comprised, such as monomeric nucleotides, oligomers, plasmids, viral and bacterial nucleic acids, as well as genomic and non-genomic DNA and RNA from the subject, circular RNA (circRNA), messenger RNA (mRNA) in processed and unprocessed form, transfer RNA (tRNA), heterogeneous nuclear RNA (hn-RNA), ribosomal RNA (rRNA), complementary DNA (cDNA) as well as all other conceivable nucleic acids. However, in the most preferred embodiment the sample comprises circRNAs.
“Presence” or “absence” of a circRNA in connection with the present invention means that the circRNA is present at levels above a certain threshold or below a certain threshold, respectively. In case the threshold is “0” this would mean that “presence” is the actual presence of circRNA in the sample and “absence” is the actual absence. However, “presence” in context with the present invention may also mean that the respective circRNA is present at a level above a threshold, e.g. the levels determined in a control. “absence” in this context then means that the level of the circRNA is at or below the certain threshold. Hence, it is preferred that the method of the present invention comprises determining of the level of one or more circRNA and comparing it to a control level of said one or more circRNA. In a preferred embodiment of the invention the determination step comprises: (i) determining the level of said one or more circRNA; and (ii) comparing the determined level to a control level of said one or more circRNA; wherein differing levels between the determined and the control level are indicative for the disease. In other words, the invention relates to a method for diagnosing a disease of a subject, comprising the step of (i) determining the level of said one or more circRNA; and (ii) comparing the determined level to a control level of said one or more circRNA; wherein differing levels between the determined and the control level are indicative for the disease.
The term “control level” relates to a level to which the determined level is compared in order to allow the distinction between “presence” or “absence” of the circRNA. The control level is preferably the level which is determinant for the deductive step of making the actual diagnose. Control level in a preferred embodiment relates to the level of the respective circRNA in a healthy subject or a population of healthy subjects, i.e. a subject not having the disease to be diagnosed, e.g. not having a neurodegenerative disease, such as Alzheimer's disease. The skilled person with the disclosure of the present application is in the position to determine suited control levels using common statistical methods.
In the context of the present invention, the levels of the one or more circRNA may be analyzed in a number of fashions well known to a person skilled in the art. For example, each assay result obtained may be compared to a “normal” or “control” value, or a value indicating a particular disease or outcome. A particular diagnosis/prognosis may depend upon the comparison of each assay result to such a value, which may be referred to as a diagnostic or prognostic “threshold”. In certain embodiments, assays for one or more diagnostic or prognostic indicators are correlated to a condition or disease by merely the presence or absence of the circRNAs in the assay. For example, an assay can be designed so that a positive signal only occurs above a particular threshold level of interest, and below which level the assay provides no signal above background.
The sensitivity and specificity of a diagnostic and/or prognostic test depends on more than just the analytical “quality” of the test, they also depend on the definition of what constitutes an abnormal result, i.e. when a level may be regarded as differing from a control level. In practice, Receiver Operating Characteristic curves (ROC curves), are typically calculated by plotting the value of a variable versus its relative frequency in “normal” (i.e. apparently healthy individuals not having ovarian cancer) and “disease” populations. For any particular marker, a distribution of marker levels for subjects with and without a disease will likely overlap. Under such conditions, a test does not absolutely distinguish normal from disease with 100% accuracy, and the area of overlap indicates where the test cannot distinguish normal from disease. A threshold is selected, below which the test is considered to be abnormal and above which the test is considered to be normal. The area under the ROC curve is a measure of the probability that the perceived measurement will allow correct identification of a condition. ROC curves can be used even when test results don't necessarily give an accurate number. As long as one can rank results, one can create a ROC curve. For example, results of a test on “disease” samples might be ranked according to degree (e.g. 1=low, 2=normal, and 3=high). This ranking can be correlated to results in the “normal” or “control” population, and a ROC curve created. These methods are well known in the art. See, e.g., Hanley et al. 1982. Radiology 143: 29-36. Preferably, a threshold is selected to provide a ROC curve area of greater than about 0.5, more preferably greater than about 0.7, still more preferably greater than about 0.8, even more preferably greater than about 0.85, and most preferably greater than about 0.9. The term “about” in this context refers to +/−5% of a given measurement.
The horizontal axis of the ROC curve represents (1-specificity), which increases with the rate of false positives. The vertical axis of the curve represents sensitivity, which increases with the rate of true positives. Thus, for a particular cut-off selected, the value of (1-specificity) may be determined, and a corresponding sensitivity may be obtained. The area under the ROC curve is a measure of the probability that the measured marker level will allow correct identification of a disease or condition. Thus, the area under the ROC curve can be used to determine the effectiveness of the test.
In other embodiments, a positive likelihood ratio, negative likelihood ratio, odds ratio, or hazard ratio is used as a measure of a test's ability to predict risk or diagnose a disease. In the case of a positive likelihood ratio, a value of 1 indicates that a positive result is equally likely among subjects in both the “diseased” and “control” groups; a value greater than 1 indicates that a positive result is more likely in the diseased group; and a value less than 1 indicates that a positive result is more likely in the control group. In the case of a negative likelihood ratio, a value of 1 indicates that a negative result is equally likely among subjects in both the “diseased” and “control” groups; a value greater than 1 indicates that a negative result is more likely in the test group; and a value less than 1 indicates that a negative result is more likely in the control group.
In the case of an odds ratio, a value of 1 indicates that a positive result is equally likely among subjects in both the “diseased” and “control” groups; a value greater than 1 indicates that a positive result is more likely in the diseased group; and a value less than 1 indicates that a positive result is more likely in the control group.
In the case of a hazard ratio, a value of 1 indicates that the relative risk of an endpoint (e.g., death) is equal in both the “diseased” and “control” groups; a value greater than 1 indicates that the risk is greater in the diseased group; and a value less than 1 indicates that the risk is greater in the control group.
The skilled artisan will understand that associating a diagnostic or prognostic indicator, with a diagnosis or with a prognostic risk of a future clinical outcome is a statistical analysis. For example, a marker level of lower than X may signal that a patient is more likely to suffer from an adverse outcome than patients with a level more than or equal to X, as determined by a level of statistical significance. For another marker, a marker level of higher than X may signal that a patient is more likely to suffer from an adverse outcome than patients with a level less than or equal to X, as determined by a level of statistical significance. Additionally, a change in marker concentration from baseline levels may be reflective of patient prognosis, and the degree of change in marker level may be related to the severity of adverse events. Statistical significance is often determined by comparing two or more populations, and determining a confidence interval and/or a p value. See, e.g., Dowdy and Wearden, Statistics for Research, John Wiley & Sons, New York, 1983. Preferred confidence intervals of the invention are 90%, 95%, 97.5%, 98%, 99%, 99.5%, 99.9% and 99.99%, while preferred p values are 0.1, 0.05, 0.025, 0.02, 0.01, 0.005, 0.001, and 0.0001.
Suitable threshold levels for the diagnosis of the disease can be determined for certain combinations of circRNAs. This can e.g. be done by grouping a reference population of patients according to their level of circRNAs into certain quantiles, e.g. quartiles, quintiles or even according to suitable percentiles. For each of the quantiles or groups above and below certain percentiles, hazard ratios can be calculated comparing the risk for an adverse outcome, i.e. a “disease” or “Alzheimer's disease”, between those patients who have a certain disease and those who have not. In such a scenario, a hazard ratio (HR) above 1 indicates a higher risk for an adverse outcome for the patients. A HR below 1 indicates beneficial effects of a certain treatment in the group of patients. A HR around 1 (e.g. +/−0.1) indicates no elevated risk for the particular group of patients. By comparison of the HR between certain quantiles of patients with each other and with the HR of the overall population of patients, it is possible to identify those quantiles of patients who have an elevated risk and those who benefit from medication and thereby stratify subjects according to the present invention.
In some cases presence of the disease will not affect patients with levels (e.g. in the fifth quintile) of a circRNA different from the “control level”, while in other cases patients with levels similar to the control level will be affected (e.g. in the first quintile). However, with the above explanations and his common knowledge, a skilled person is able to identify those groups of patients having a disease, e.g. a neurodegenerative disease as Alzheimer's disease. Exemplarily, some combinations of levels of circRNAs are listed for Alzheimer's disease in the appended examples. In another embodiment of the invention, the diagnosis is determined by relating the patient's individual level of marker peptide to certain percentiles (e.g. 97.5th percentile (in case increased levels being indicative for a disease) or the 2.5th percentile (in case decreased levels being indicative for a disease)) of a healthy population.
Kaplan-Meier estimators may be used for the assessment or prediction of the outcome or risk (e.g. diagnosis, relapse, progression or morbidity) of a patient.
“Equal” level in context with the present invention means that the levels differ by not more than ±10%, preferably by not more than ±5%, more preferably by not more than ±2%. “Decreased” or “increased” level in the context of the present invention mean that the levels differ by more than 10%, preferably by more than 15%, preferably more than 20%.
The term “subject” relates to a subject to be diagnosed, preferably a subject suspected to have or to have a risk for acquiring a disease, preferably a neurodegenerative disease, more preferably a subject suspected to have or to have a risk for acquiring Alzheimer's disease. The subject is preferably an animal, more preferably a mammal, most preferably a human.
The inventors have found that differential abundance of circRNA in samples of a bodily fluid is suited as a biomarker. It has been found that differing levels of circRNAs are correlating with a disease. This has been proven for Alzheimer's disease, a disease of neuronal tissue. Without being bound by reference, the correlation may be due to a passage of the circRNAs through the blood-brain-barrier, i.e. the circRNAs detected in the method according to the present invention are differentially expressed in the tissue of the disease, i.e. the tissue of interest. In case of the neurodegenerative disease (e.g. Alzheimer's disease) the tissue of interest is neuronal tissue, e.g. the brain. Hence, in one embodiment of the present invention said one or more circRNA, the differing levels of which in the bodily fluid are attributed to the presence of the disease, is differentially expressed between the diseased and non-diseased state in the tissue of interest. Alternatively, the circRNA levels may be of secondary nature, e.g. arise due to an immune response in the bodily fluid. Hence, in a further embodiment said one or more circRNA, the differing levels of which in the bodily fluid are attributed to the presence of the disease, is not differentially expressed between the diseased and non-diseased state in the tissue of interest.
Circular RNA” (circRNA) has been previously described. However, not in connection with their detection in a bodily fluid, e.g. blood. The skilled person is able to determine whether a detected RNA is a circular RNA. In particular, a circRNA does not contain a free 3′-end or a free 5′ end, i.e. the entire nucleic acid is circularized. The circRNA is preferably a circularized, single stranded RNA molecule. Furthermore, the circRNA according to the present invention is a result of a head-to-tail splicing event that results in a discontinuous sequence with respect to the genomic sequence encoding the RNA. This means that a first sequence being present 5′-upstream of a second sequence in the genomic context, on the circRNA said first sequence at its 5′-end is linked to the 3′ end of said second sequence and thereby closing the circle. The consequence of this arrangement is that at the junction where the 5′-end of said first sequence is linked to the 3′-end of said second sequence a unique sequence is build that is neither present in the genomic context nor in the normally transcribed RNA, e.g. mRNA. It has been found by the inventors that these junctions in all identified circRNAs, in the genomic context, are flanked by the canonical splice sequence, the GT/AG splice signal known by the skilled person. Hence, the circRNAs according to the present invention preferably contain an exon-exon junction in a head-to-tail arrangement, as visualized in
Further, in a preferred embodiment RNA sequences which map continuously to the genome by aligning without any trimming (end-to-end mode) are neglected. Reads not mapping continuously to the genome are preferably used for circRNA candidate detection. The terminal sequences (anchors) from the sequences, e.g. 20 nt or more, may be extracted and re-aligned independently to the genome. From this alignment the sequences may be extended until the full circRNA sequence is covered, i.e. aligned. Consecutively aligning anchors indicate linear splicing events whereas alignment in reverse orientation indicates head-to-tail splicing as observed in circRNAs (see
The circRNAs according to the present invention may be detected using different techniques. As outlined herein, the exon-exon junction in a head-to-tail arrangement is unique to the circRNAs. Hence, the detection of these is preferred. Nucleic acid detection methods are commonly known to the skilled person and include probe hybridization based methods, nucleic acid amplification based methods, and nucleic acid sequencing, or combinations thereof. Hence, in a preferred embodiment of the present invention circRNA is detected using a method selected from the group consisting of probe hybridization based methods, nucleic acid amplification based methods, and nucleic acid sequencing.
Probe hybridization based method employ the feature of nucleic acids to specifically hybridize to a complementary strand. To this end nucleic acid probes may be employed that specifically hybridize to the exon-exon junction in a head-to-tail arrangement of the circRNA, i.e. to a sequence spanning the exon-exon junction, preferably to the region extending from 10 nt upstream to 10 nt downstream of the exon-exon junction, preferably to the region from 20 nt upstream to 20 nt downstream of the exon-exon junction, or even a greater region spanning the exon-exon junction. The skilled person will recognize that hybridization probes specifically hybridizing to the respective sequence of the circRNA may be used, as well as hybridization probes specifically hybridizing to the reverse complement sequence thereof, e.g. in case the circRNA is previously reverse transcribed to cDNA and/or amplified.
Hybridization can also be used as a measure of homology between two nucleic acid sequences. A nucleic acid sequence hybridizing specifically to an exon-exon junction in a head-to-tail arrangement according to the present invention may be used as a hybridization probe according to standard hybridization techniques. The hybridization of the probe to DNA or RNA from a test source (e.g., the bodily fluid, like whole blood, or amplified nucleic acids from the sample of the bodily fluid) is an indication of the presence of the relevant circRNA in the test source.
Hybridization conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 6.3.1-6.3.6, 1991. Preferably, specific hybridization refers to hybridization under stringent conditions. “Stringent conditions” are defined as equivalent to hybridization in 6× sodium chloride/sodium citrate (SSC) at 45° C., followed by a wash in 0.2×SSC, 0.1% SDS at 65° C.; or as equivalent to hybridization in commercially available hybridization buffers (e.g. ULTRAHyb, ThermoScientific) for blotting techniques and 5×SSC 0.5% SDS (750 mM NaCl, 75 mM sodium citrate, 0.5% sodiumdodecylsulfate, pH 7.0) for array based detection methods at 65° C.
The means and methods of the present invention preferably comprise the use of nucleic acid probes. A nucleic acid probe according to the present invention is an oligonucleotide, nucleic acid or a fragment thereof, which is substantially complementary to a specific nucleic acid sequence. “substantially complementary” refers to the ability to hybridize to the specific nucleic acid sequence under stringent conditions.
The skilled person knows means and methods to determine the levels of nucleic acids in a sample and compare them to control levels. Such methods may employ labeled nucleic acid probes according to the invention. “Labels” include fluorescent or enzymatic active labels as further defined herein below. Such methods include real-time PCR methods and microarray methods, like Affimetrix®, nanostring and the like.
The determination of the circRNAs or their level may also be detected using sequencing techniques. The skilled person is able to use sequencing techniques in connection with the present invention. Sequencing techniques include but are not limited to Maxam-Gilbert Sequencing, Sanger sequencing (chain-termination method using ddNTPs), and next generation sequencing methods, like massively parallel signature sequencing (MPSS), polony sequencing, 454 pyrosequencing, Illumina (Solexa) sequencing, SOLiD sequencing, or ion torrent semiconductor sequencing or single molecule, real-time technology sequencing (SMRT).
The detection/determination of the circRNAs and the respective level may also employ nucleic acid amplification method alone or in combination with the sequencing and/or hybridization method. Nucleic acid amplification may be used to amplify the sequence of interest prior to detection. It may however also be used for quantifying a nucleic acid, e.g. by real-time PCR methods. Such methods are commonly known to the skilled person. Nucleic acid amplification methods for example include rolling circle amplification (such as in Liu, et al., “Rolling circle DNA synthesis: Small circular oligonucleotides as efficient templates for DNA polymerases,” J. Am. Chem. Soc. 118:1587-1594 (1996).), isothermal amplification (such as in Walker, et al., “Strand displacement amplification—an isothermal, in vitro DNA amplification technique,” Nucleic Acids Res. 20(7):1691-6 (1992)), ligase chain reaction (such as in Landegren, et al., “A Ligase-Mediated Gene Detection Technique,” Science 241:1077-1080, 1988, or, in Wiedmann, et al., “Ligase Chain Reaction (LCR)—Overview and Applications,” PCR Methods and Applications (Cold Spring Harbor Laboratory Press, Cold Spring Harbor Laboratory, N Y, 1994) pp. S51-S64.)). Nucleic-acid amplification can be accomplished by any of the various nucleic-acid amplification methods known in the art, including but not limited to the polymerase chain reaction (PCR), ligase chain reaction (LCR), transcription-based amplification system (TAS), nucleic acid sequence based amplification (NASBA), rolling circle amplification (RCA), transcription-mediated amplification (TMA), self-sustaining sequence replication (3SR) and Qβ amplification. It will be readily understood that the amplification of the circRNA may start with a reverse transcription of the RNA into complementary DNA (cDNA), optionally followed by amplification of the so produced cDNA.
It may be desirable to reduce or diminish non circRNA prior to the determination or the presence or level of the circRNAs. To this end RNA degrading agents may be added to the sample and/or the isolated total nucleic acids, e.g. total RNA, thereof, wherein said RNA degrading agent does not degrade circRNAs or does degrade circRNAs only at lower rates as compared to linear RNAs. One such agent is RNase R. RNase R is a 3′-5′ exoribonuclease closely related to RNase II, which has been shown to be involved in selective mRNA degradation, particularly of non stop mRNAs in bacteria (see Cheng; Deutscher, M P et al. (2005). “An important role for RNase R in mRNA decay”. Molecular Cell 17(2):313-318; and Venkataraman, K; Guja, K E; Garcia-Diaz, M; Karzai, A W (2014). “Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue.”; Frontiers in microbiology 5:93. Suzuki H1, Zuo Y, Wang J, Zhang M Q, Malhotra A, Mayeda A; Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing; Nucleic Acids Res. 2006 May 8; 34(8):e63.). RNase R has homologues in many other organisms. When a part of another larger protein has a domain that is very similar to RNase R, this is called an RNase R domain. Hence, in a preferred embodiment the sample is treated with RNase R before determination of the circRNA to deplete linear RNA isoforms from the total RNA preparation and thereby increase detection sensitivity.
As outlined herein, the diagnostic or prognostic value of a single circRNA may not be sufficient in order to allow a diagnosis or prognosis with a reliable result. In such case it may be desirable to determine the presence or level of more than one circRNA in the sample and optionally comparing them to the respective control level. The skilled person will acknowledge that these more than one circRNAs may be chosen from a predetermined panel of circRNAs. Such panel usually includes the minimum number of circRNAs necessary to allow a reliable diagnosis or prognosis. The number of circRNAs of the panel may vary depending on the desired reliability and/or the prognostic or diagnostic value of the included circRNAs, e.g. when determined alone. Hence, the method according to the present invention in a preferred embodiment determines more than one circRNA from a panel of circRNAs, e.g. their presence or absence, or level, respectively.
The panel for obtaining the desired may be chosen according to the needs. In particular the skilled person may apply statistical approaches as outlined herein in order to validate the diagnostic and/or prognostic significance of a certain panel. The inventors have herein shown for a neurodegenerative disease the development of a certain panel of circRNAs giving a reasonable degree of certainty. The skilled person may apply common statistical techniques in order to develop a panel of circRNAs. Such statistical techniques include cluster analysis (e.g. hierarchical or k-means clustering), principle component analysis or factor analysis.
In principle, the statistical methods aim the identification of circRNAs or panels of circRNAs that exhibit differing presence and/or levels in samples of diseased and healthy/normal subjects. As outlined, the panel is preferably a panel of more than one circRNA, i.e. a plurality. In a preferred embodiment of the invention said panel comprises a plurality of circRNAs that have been identified as being present at differing levels in bodily fluid samples of patients having the disease and patients not having the disease. The panel of circRNAs has been preferably identified by principle component analysis or clustering.
The “principle component analysis” (PCA) (as also used exemplified herein) regards the analysis of factors differing between diseased and healthy subjects. PCA is known to the skilled person (see Pearson K., “On lines and planes of closest fit to systems of points in space”, The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science 2.11 559-572 (1901), and Hotelling H., “Analysis of a complex of statistical variables into principal components” Journal of educational psychology 24.6 417 (1933)). The circRNAs to be chosen for the principle component analysis may be those previously determined in samples of healthy and/or diseased subject. Thresholds may be incorporated in order to consider a circRNA for further analysis, in a preferred embodiment only circRNAs having an expression value of at least 6.7 after variance stabilizing transformation of raw read counts in one of the samples. PCA may be performed on circRNAs included in the analysis using the prcomp function of the standard package “stats” of the “R” programming language (R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0). Depending on the circRNAs chosen, the disease and other factors, the weights can vary. However, the skilled artisan will acknowledge that these circRNAs with the highest weight as regards the principle component of interest, i.e. disease/healthy state, shall be chosen in order to obtain the circRNAs with the highest predictive absolute values. PCA is used to visualize and measure the amount of variation in a data set. Mathematically, PCA is an orthogonal linear transformation that transforms the data to a new coordinate system such that the greatest variance by some projection of the data lies on the first coordinate which is called Principal Component 1 (PC1) and so on. The before mentioned calculated weight represents the distance of each circular RNA to this specific projection. Thus, the higher the absolute value the more relevant is for this projection.
“Hierarchical Clustering” (also referred to herein as “clustering”) may be performed as known in the art (reviewed in Murtagh, F and Conteras, P “Methods of hierarchical clustering” arXiv preprint arXiv:1105.0121 (2011)). Samples may be clustered on log2 transformed normalized circRNA expression profiles (log2(ni+1)). Hierarchical, agglomerative clustering may be performed with complete linkage and optionally by further using Spearman's rank correlation as distance metric (1−{corr [log(ni+1)]}). “The goal of cluster analysis is to partition observations (here circRNA expression) into groups (“clusters”) so that the pairwise dissimilarities between those assigned to the same cluster tend to be smaller than those in different clusters” (see Friedman J, Hastie T, and Tibshiriani R, “The elements of statistical learning”, Vol. 1. Soringer, Berlin: Springer series in statistics (2001)). Here, the measure for dissimilarity is defined as the Spearman's rank correlation. A visualization and complete description of the hierarchical clustering is provided by a dendrogram.
The inventors have exemplified the method outlined above for a neurodegenerative disease, in particular Alzheimer's disease. A neurodegenerative disease in context with the present invention is to be understood as a disease associated with neurodegeneration. Neurodegeneration means a progressive loss of structure or function of neurons, including death of neurons. Many neurodegenerative diseases including ALS, Parkinson's, Alzheimer's, and Huntington's occur as a result of neurodegenerative processes. Nowadays, many similarities exist that relate these diseases to one another on a sub-cellular level. There are many parallels between different neurodegenerative disorders including atypical protein assemblies (protein misfolding and/or agglomeration) as well as induced cell death. Neurodegeneration can be found in many different levels of neuronal circuitry ranging from molecular to systemic. Hence, in a preferred embodiment of the present invention the disease is a neurodegenerative disease, preferably selected from the group of Alzheimer's, ALS, Parkinson's, and Huntington's.
In a particularly preferred embodiment the disease is Alzheimer's disease. Alzheimer's disease has been identified as a protein misfolding disease (proteopathy), causing plaque accumulation of abnormally folded amyloid beta protein, and tau protein in the brain. Plaques are made up of small peptides, 39-43 amino acids in length, called amyloid beta (Aβ). AP is a fragment from the larger amyloid precursor protein (APP). APP is a transmembrane protein that penetrates through the neuron's membrane. APP is critical to neuron growth, survival, and post-injury repair. In Alzheimer's disease, an unknown enzyme in a proteolytic process causes APP to be divided into smaller fragments. One of these fragments gives rise to fibrils of amyloid beta, which then form clumps that deposit outside neurons in dense formations known as senile plaques. AD is also considered a tauopathy due to abnormal aggregation of the tau protein. In AD, tau undergoes chemical changes, becoming hyperphosphorylated; it then begins to pair with other threads, creating neurofibrillary tangles and disintegrating the neuron's transport system. A patient, is classified as having Alzheimer's disease according to the criteria as set by the National Institute of Neurological and Communicative Disorders and Stroke (NINCDS) and the Alzheimer's disease and Related Disorders Association (ADRDA, now known as the Alzheimer's Association), the NINCDS-ADRDA Alzheimer's Criteria for diagnosis in 1984, extensively updated in 2007 (see McKhann G, Drachman D, Folstein M, et al. Clinical Diagnosis of Alzheimer's disease: Report of the NINCDS-ADRDA Work Group under the Auspices of Department of Health and Human Services Task Force on Alzheimer's disease. Neurology. 1984; 34(7):939-44; and Dubois B, Feldman H H, Jacova C, et al. Research Criteria for the Diagnosis of Alzheimer's disease: Revising the NINCDS-ADRDA Criteria. Lancet Neurology. 2007; 6(8):734-469). These criteria require that the presence of cognitive impairment, and a suspected dementia syndrome, be confirmed by neuropsychological testing for a clinical diagnosis of possible or probable Alzheimer's disease. A histopathologic confirmation including a microscopic examination of brain tissue is required for a definitive diagnosis. Good statistical reliability and validity have been shown between the diagnostic criteria and definitive histopathological confirmation (see Blacker D, Albert M S, Bassett S S, et al. Reliability and validity of NINCDS-ADRDA criteria for Alzheimer's disease. The National Institute of Mental Health Genetics Initiative. Archives of Neurology. 1994; 51(12):1198-204). Eight cognitive domains are most commonly impaired in AD memory, language, perceptual skills, attention, constructive abilities, orientation, problem solving and functional abilities. These domains are equivalent to the NINCDS-ADRDA Alzheimer's Criteria as listed in the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR) published by the American Psychiatric Association.
In a particular preferred embodiment of the present invention, it relates to a method for diagnosing a neurodegenerative disease in a subject comprises the steps of:
wherein differing levels between the determined and the control level are indicative for the disease. The neurodegenerative disease is most preferably Alzheimer's disease.
The inventors have identified specific circRNAs that have a predictive or diagnostic value as regards the neurodegenerative disease. In particular 910 highly expressed circRNAs have been identified that are differentially present in samples of patients with a neurodegenerative disease as compared to the healthy controls. These 910 circRNAs are particularly characterized by their exon-exon junction in a head-to-tail arrangement, as outlined herein above. The sequences encoding the 20 nucleotides upstream and 20 nucleotides downstream of said exon-exon junction in the respective circRNAs are given in SEQ ID NOs: 1 to 910. However, it may be sufficient to determine only 10 nucleotides upstream and 10 nucleotides downstream of the junction in order to detect the circRNAs specifically. Hence, in a preferred embodiment said one or more circRNA in the method for diagnosing the neurodegenerative disease comprises a sequence encoded by a sequence selected from the group consisting of nucleotides 11 to 30 of any of the sequences of SEQ ID NO:1 to SEQ ID NO:910. The circRNA may for instance be detected through determining the presence or levels of RNA comprising the respective sequences, e.g. by hybridization, sequencing and/or amplification methods as outlined herein. SEQ ID NO:1 to 1820 list the DNA sequences encoding the sequences of the exon-exon junctions or the complete sequences of the circRNAs of the present invention. “Encoded” in this regard means that the RNA encoded by the DNA sequence has the sequence of nucleotides as set out in the DNA sequence with the thymidines “T” being exchanged by uracils “U”, the backbone being ribonucleic acid instead of deoxyribonucleic acid. X
The inventors found that the circRNAs are indicative for the presence or the risk of acquiring a neurodegenerative disease when present at increased or decreased levels. Whether the presence of the specific circRNA at decreased or increased levels is indicative for the neurodegenerative disease is given in Table 1. Hence, in a particular preferred embodiment the presence of increased or decreased levels as defined in Table 1 under “diseased” for the circRNA comprising the respectively encoded sequence are indicative for the presence of or risk of acquiring a neurodegenerative disease, preferably for Alzheimer's disease. As outlined in the Table's legend, “+” denotes that increased levels and/or the presence of the respective circRNA are indicative for the presence or risk of acquiring Alzheimer's disease, while “−” denotes that decreased levels and/or the absence of the respective circRNA are indicative for the presence or risk of acquiring Alzheimer's disease.
As mentioned, the circRNAs may be detected through the unique sequences occurring at the exon-exon junction in the head-to-tail arrangement. However, in one embodiment the circRNA may be detected through detection of a larger portion of their sequence. In one embodiment of the method for diagnosing a neurodegenerative disease, preferably Alzheimer's disease, said one or more circRNA has a sequence as encoded by a sequence selected from the group consisting of SEQ ID NO:911 to SEQ ID NO:1820. Preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for the circRNA having the respective encoded sequence are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease.
As outlined herein, it may be desirable to determine the presence or absence, or the level of more than on circRNA in order to increase the diagnostic significance of the method according to the present invention. Hence, in a preferred embodiment of the method for diagnosing a neurodegenerative disease the levels of more than one circRNA comprising a sequence encoded by a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, or a sequence having at least 70% identity thereto, are determined and compared to the respective control level. The identity is preferably at least 80%, more preferably at least 90%, more preferably at least 95%. In a preferred embodiment the levels of at least 100 circRNAs comprising a sequence encoded by a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, or a sequence having at least 70% identity thereto, are determined in a sample of a bodily fluid of said subject and controlled to the respective control level; preferably the levels of at least 150 circRNAs and more preferably the levels of at least 200 circRNAs comprising a sequence encoded by a sequence selected from the group consisting of nt 11 to 30 of any one of SEQ ID NO:1 to SEQ ID NO:910, or a sequence having at least 70% identity thereto, are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. The identity is preferably at least 80%, more preferably at least 90%, more preferably at least 95% to the respective sequences in the SEQ ID NO:.
In one embodiment the circRNAs comprising a sequence encoded by SEQ ID NOs:1 to 910 have the sequence as determined by the inventors, i.e. have a sequence encoded by the sequence of any of SEQ ID NOs: 911 to 1820. Hence, in one embodiment of the method for diagnosing a neurodegenerative disease the levels of more than one circRNAs having a sequence being at least 70% identical to any of the sequences as encoded by SEQ ID NO: 911 to 1820 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. Particularly preferred the levels of at least 100 circRNAs having a sequence being at least 70% identical to any of the sequences as encoded by SEQ ID NOs: 911 to 1820 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level, preferably the levels of at least 150, and more preferably the levels of at least 200 circRNAs having a sequence being at least 70% identical to any of the sequences as encoded by SEQ ID NOs: 911 to 1820 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. In more preferred embodiments said sequence identity is at least 80%, preferably at least 90%, more preferably at least 95%, yet more preferably at least 99% to the outlined sequences. In a further preferred embodiment the circRNAs have the sequences as encoded by any one of SEQ ID NOs: 911 to 1820. The levels are preferably detected by using hybridization probes specifically hybridizing the sequences of nt 11 to 30 of SEQ ID NO:1 to 910 or specifically hybridizing to the sequences of SEQ ID NO:1 to 910, or an RNA sequence encoded by these sequences, or the respective reverse complements thereof.
The inventors found that the first 200 circRNAs as encoded by SEQ ID NO:1 to 910 have particular suited predictive and diagnostic values. Hence, in a preferred embodiment of the method for diagnosing a neurodegenerative disease said at least 100, preferably at least 150 more preferably at least 200 circRNAs comprise a sequence as encoded by any of SEQ ID NO:1 to SEQ ID NO:200, or a sequence having at least 70% identity thereto, or the circRNAs have a sequence as encoded by any of SEQ ID NO: 911 to 1110, or a sequence having at least 70% identity thereto. The identity is preferably at least 80%, more preferably at least 90%, more preferably at least 95%. In a preferred embodiment of the method for diagnosing a neurodegenerative disease the levels of more than one circRNA comprising a sequence encoded by a sequence being at least 70% identical to a sequence selected from the group consisting of the sequence of nt 11 to nt 30 of any one of SEQ ID NO: 1 to 200 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. Particularly preferred the levels of at least 100 circRNAs comprising a sequence encoded by a sequence being at least 70% identical to a sequence selected from the group consisting of the sequence of nt 11 to nt 30 of any one of SEQ ID NO: 1 to 200 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level, preferably of at least 150 and more preferably the levels of all 200 circRNAs comprising a sequence encoded by a sequence being at least 70% identical to a sequence selected from the group consisting of the sequence of nt 11 to nt 30 of any one of SEQ ID NO: 1 to 200 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. The identity is preferably at least 80%, more preferably at least 90%, more preferably at least 95%, yet more preferred 100%. The levels are preferably detected by using hybridization probes specifically hybridizing the sequences of nt 11 to 30 of SEQ ID NO:1 to 200 or specifically hybridizing to the sequences of SEQ ID NO:1 to 200, or an RNA sequence encoded by these sequences, or the reverse complements thereof
In one embodiment the circRNAs comprising a sequence encoded by any of the SEQ ID NOs:1 to 200 have the sequence as determined by the inventors, i.e. a sequence encoded by any of the SEQ ID NOs: 911 to 1110. Hence, in one embodiment of the method for diagnosing a neurodegenerative disease the levels of more than one circRNA having a sequence encoded by a sequence being at least 70% identical to any of the sequences of SEQ ID NO: 911 to 1110 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. Particularly preferred the levels of at least 100 circRNAs having a sequence encoded by a sequence being at least 70% identical to any of the sequences of SEQ ID NOs: 911 to 1110 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level, preferably the levels of at least 150, and more preferably the levels of at least 200 circRNAs having a sequence encoded by a sequence being at least 70% identical to any of the sequences of SEQ ID NOs: 911 to 1110 are determined in a sample of a bodily fluid of said subject and controlled to the respective control level. In more preferred embodiments said sequence identity is at least 80%, preferably at least 90%, more preferably at least 95%, yet more preferably at least 99% to the outlined sequences. In a further preferred embodiment the circRNAs have the sequences encoded by the sequences as set out in any one of SEQ ID NOs: 911 to 1110. The levels are preferably detected by using hybridization probes specifically hybridizing the sequences of nt 11 to 30 of SEQ ID NO:1 to 200 or specifically hybridizing to the sequences of SEQ ID NO:1 to 200, or an RNA sequence encoded by these sequences, or the reverse complements thereof.
The determination of percent identity between two sequences is accomplished using the mathematical algorithm of Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5877. Such an algorithm is incorporated into the BLASTN and BLASTP programs of Altschul et al. (1990) J. Mol. Biol. 215: 403-410. BLAST nucleotide searches are performed with the BLASTN program, score=100, word length=12, to obtain nucleotide sequences homologous to the nucleic acid sequences outlined herein. BLAST protein searches are performed with the BLASTP program, score=50, wordlength=3, to obtain amino acid sequences homologous to the EPO variant polypeptide, respectively. To obtain gapped alignments for comparative purposes, Gapped BLAST is utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25: 3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs are used.
In order to improve the diagnostic value, it may be desirable to determine the number of circRNAs showing increased or decreased levels being indicative for the neurodegenerative disease as outlined in Table 1. In a preferred embodiment the number of circRNAs showing increased or decreased levels being indicative for the neurodegenerative disease as outlined in Table 1 is above the 80% percentile of a control population, more preferably above the 90% percentile, yet more preferred above the 95% percentile. In a preferred embodiment of the method for diagnosing a neurodegenerative disease the presence of increased or decreased levels as defined in Table 1 under “disease” for the respective circRNA for at least 10, preferably at least 50, more preferably at least 100 circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease.
In one particular embodiment of the method for diagnosing a neurodegenerative disease the levels of all circRNAs comprising a sequence encoded by a sequence selected from the group consisting of nt 11 to 30 of any of SEQ ID NO:1 to SEQ ID NO:200, or a sequence having at least 70% identity thereto; wherein preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for at least 10, preferably at least 50, more preferably at least 100 of the respective circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease. Preferably, said method comprises the determination of the levels of all circRNAs comprising a sequence encoded by a sequence selected from the group consisting of any of SEQ ID NO:1 to SEQ ID NO:200 or a sequence having at least 70% identity thereto, wherein preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for at least 10, preferably at least 50, more preferably at least 100 of the respective circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease. Further preferred, all circRNAs with a sequence encoded by a sequence having at least 70% identity to a sequence selected from the group consisting of SEQ ID NO:911 to SEQ ID NO:1110 are detected, wherein preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for at least 10, preferably at least 50, more preferably at least 100 of the respective circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease. In more preferred embodiments said sequence identity is at least 80%, preferably at least 90%, more preferably at least 95%, yet more preferably at least 99% to the outlined sequences, yet more preferred the identity is 100%.
In one particular embodiment of the method for diagnosing a neurodegenerative disease the levels of all circRNAs comprising a sequence encoded by a sequence selected from the group consisting of nt 11 to 30 of any of SEQ ID NO:1 to SEQ ID NO:910, or a sequence having at least 70% identity thereto; wherein preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for at least 10, preferably at least 50, more preferably at least 100 of the respective circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease. Preferably, said method comprises the determination of the levels of all circRNAs comprising a sequence encoded by a sequence selected from the group consisting of any of SEQ ID NO:1 to SEQ ID NO:910 or a sequence having at least 70% identity thereto, wherein preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for at least 10, preferably at least 50, more preferably at least 100 of the respective circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease. Further preferred, all circRNAs with a sequence encoded by a sequence having at least 70% identity to a sequence selected from the group consisting of SEQ ID NO:911 to SEQ ID NO:1820 are detected, wherein preferably the presence of increased or decreased levels as defined in Table 1 under “disease” for at least 10, preferably at least 50, more preferably at least 100 of the respective circRNAs are indicative for the presence of a neurodegenerative disease, preferably Alzheimer's disease. In more preferred embodiments said sequence identity is at least 80%, preferably at least 90%, more preferably at least 95%, yet more preferably at least 99% to the outlined sequences, yet more preferred the identity is 100%.
As outlined herein above, the circRNAs may be specifically detected through their unique sequence at the exon-exon junction in the head-to-tail arrangement. Hence, the invention also relates to a nucleic acid probe specifically hybridizing to a sequence of nucleotide (nt) 11 to nt 30 of any of the sequences of SEQ ID NO:1 to 910, or specifically hybridizing to a RNA sequence encoded by these sequences, or specifically hybridizing to a reverse complement sequences thereof, preferably specifically binding to any of the sequences of SEQ ID NO:1 to 910, or specifically hybridizing to a RNA sequence encoded by these sequences, or specifically hybridizing to a reverse complement sequences thereof. In a very preferred embodiment the nucleic acid probe spans the sequence of nt 15 to nt 35 of the respective SEQ ID NO: 1 to 910, of RNA sequence encoded by these sequences, or the reverse complement sequences thereof.
Nucleic acid probes may be prepared using any suitable method, such as, for example, the phosphotriester and phosphodiester methods or automated embodiments thereof. In one such automated embodiment diethylophosphoramidites are used as starting materials and may be synthesized as described by Beaucage et al., Tetrahedron Letters, 22:1859-1862 (1981), which is hereby incorporated by reference. One method for synthesizing oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,006, which is hereby incorporated by reference. It is also possible to use a nucleic acid probes which has been isolated from a biological source (such as a restriction endonuclease digest). Preferred nucleic acid probes have a length of from about 15 to 500, more preferably about 20 to 200, most preferably about 25 to 60 bases.
The nucleic acid probe according to the present invention may be hybridization probe or as a primer for amplification reactions. In both cases the nucleic acid probe may comprise fluorescent dyes. Such fluorescent dyes may for example be FAM (5- or 6-carboxyfluorescein), VIC, NED, fluorescein, FITC, IRD-700/800, CY3, CY5, CY3.5, CY5.5, HEX, TET, TAMRA, JOE, ROX, BODIPY TMR, Oregon Green, Rhodamine Green, Rhodamine Red, Texas Red, Yakima Yellow, Alexa Fluor, PET and the like (see e.g. https://www.micro-shop.zeiss.com/us/us_en/spektral.php). In the context of the present invention, fluorescent dyes may for example be FAM (5- or 6-carboxyfluorescein), VIC, NED, fluorescein, fluorescein isothiocyanate (FITC), IRD-700/800, cyanine dyes, auch as CY3, CY5, CY3.5, CY5.5, Cy7, xanthen, 6-carboxy-2′,4′,7′,4,7-hexachlorofluorescein (HEX), TET, 6-carboxy-4′,5′-dichloro-2′,7′-dimethodyfluorescein (JOE), N,N,N′,N′-Tetramethyl-6-carboxyrhodamine (TAMRA), 6-carboxy-X-rhodamine (ROX), 5-Carboxyrhodamine-6G (R6G5), 6-carboxyrhodamine-6G (RG6), Rhodamine, Rhodamine Green, Rhodamine Red, Rhodamine 110, BODIPY dyes, such as BODIPY TMR, Oregon Green, coumarines such as Umbelliferone, benzimides, such as Hoechst 33258; phenanthridines, such as Texas Red, Yakima Yellow, Alexa Fluor, PET, ethidium bromide, acridinium dyes, carbazol dyes, phenoxazine dyes, porphyrin dyes, polymethin dyes, and the like.
In a preferred embodiment, the nucleic acid probe specifically hybridizing to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of the sequences listed in Table 1, or specifically hybridizing to a RNA sequence encoded by these sequences, or specifically hybridizing to a reverse complement sequences thereof; preferably specifically hybridizing to a sequence selected from the group consisting of the sequences listed in Table 1, or specifically hybridizing to a RNA sequence encoded by these sequences, or specifically hybridizing to a reverse complement sequences thereof.
The invention furthermore relates to a kit for specifically detecting one or more, preferably more than one nucleic acids comprising a sequence selected from the group consisting of nt 11 to nt 30 of any one of SEQ ID NO: 1 to 910, or a sequence selected from the group consisting of SEQ ID NO:1 to 910, or SEQ ID NO:911 to SEQ ID NO:1820, or an RNA sequence encoded by any of these sequences. The kit is preferably a kit for diagnosing a neurodegenerative disease, comprising means for specifically detecting one or more nucleic acid sequence selected from the group consisting of SEQ ID NO:1 to 910 or SEQ ID NO:911 to SEQ ID NO:1820, or an RNA sequence encoded by any of these sequences. In a preferred embodiment the kit comprises means for specifically detecting at least 100, preferably at least 150 more preferably at least 200 nucleic acid sequences selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910 or SEQ ID NO:911 to SEQ ID NO:1820, or an RNA sequence encoded by any of these sequences.
The means for detecting preferably are one or more of the nucleic acid probes according to the invention. Hence, in one embodiment the kit comprises one or more nucleic acid probes, preferably more than one nucleic acid probe specifically hybridizing to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, or an RNA sequence encoded by these sequences, or the reverse complements thereof; preferably the kit comprises a plurality of nucleic acid probes specifically hybridizing to the sequence of nucleotide 11 to 30 of at least 100, preferably at least 150, more preferably at least 200 nucleic acid sequences selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, or a RNA sequence encoded by these sequences, or the reverse complements thereof. In a particular preferred embodiment the kit comprises a plurality of nucleic acid probes hybridizing to the sequence of nucleotide 11 to 30 of at least 100, preferably at least 150, more preferably at least 200 nucleic acid sequences selected from the group consisting of SEQ ID NO:1 to 200, or the RNA sequences encoded by these sequences, or the reverse complements thereof; preferably the kit comprises a plurality of nucleic acid probes hybridizing to the sequence of nucleotide 11 to 30 of all of the sequences of SEQ ID NO:1 to 200, or the RNA sequences encoded by these sequences, or the reverse complements thereof.
In a further particular preferred embodiment the kit comprises a plurality of nucleic acid probes hybridizing to the sequence of at least 100, preferably at least 150, more preferably at least 200 nucleic acid sequences selected from the group consisting of SEQ ID NO:1 to 200, or an RNA sequence encoded by these sequences, or the reverse complements thereof; preferably the kit comprises a plurality of nucleic acid probes hybridizing to the sequence of all of the sequences of SEQ ID NO:1 to 200, or the RNA sequences encoded by these sequences, or the reverse complements thereof.
The kit may further comprise means for handling and/or preparation of a bodily fluid sample, preferably for cerebrospinal fluid or whole blood. In a preferred embodiment the kit comprises a container for collecting whole blood, said container comprising stabilizing agents, preferably selected from the group consisting of chelating agents, EDTA, K2EDTA, formulations like RNAlater (Qiagen) or such, or combinations thereof. In a particular preferred embodiment the kit comprises a K2EDTA coated container.
As used herein, a kit is a packaged combination optionally including instructions for use of the combination and/or other reactions and components for such use.
Furthermore, the invention relates to an array for determining the presence or level of a plurality of nucleic acids, said array comprising a plurality of probes, wherein the plurality of probes specifically hybridize to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, or an RNA sequence encoded by these sequences, or the reverse complements thereof, preferably the plurality of probes comprises probes specifically hybridizing to the sequence of nucleotide 11 to 30 of at least 100, preferably at least 150 more preferably at least 200 nucleic acid sequences selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, or the RNA sequences encoded by these sequences, or the reverse complements thereof. Preferably the plurality of probes comprises probes specifically hybridizing to the sequence of nucleotide 11 to 30 of SEQ ID NO:1 to SEQ ID NO:200, or the RNA sequences encoded by these sequences, or the reverse complements thereof.
Herein an “array” is a solid support comprising one or more nucleic acids attached thereto. Arrays, such as microarrays (e.g. from Affimetrix®) are known in the art Schena MI, Shalon D, Davis R W, Brown P O (1995); Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467-70. The solid support may be made of different nature including, but not limited to, those made of plastics, resins, polysaccharides, silica or silica-based materials, functionalized glass, modified silicon, carbon, metals, inorganic glasses, membranes, nylon, natural fibers such as silk, wool and cotton, and polymers. hi some embodiments, the material comprising the solid support has reactive groups such as carboxy, amino, hydroxy, etc., which are used for attachment of, e.g. nucleic acid probes. Polymers are preferred, and suitable polymers include, but are not limited to, polystyrene, polyethylene glycol tetraphthalate, polyvinyl acetate, polyvinyl chloride, polyvinyl pyrrolidone, polyacrylonitrile, polymethyl methacrylate, polytetrafluoroethylene, butyl rubber, styrenebutadiene rubber, natural rubber, polyethylene, polypropylene, (poly)tetrafluoroethylene, (poly)vinylidenefluoride, polycarbonate and polymethylpentene. Preferred polymers include those outlined in U.S. Pat. No. 5,427,779, hereby expressly incorporated by reference. The nucleic acid probes are preferably covalent attachment to the solid support of the array. Attachment may be performed as described below. As will be appreciated by those in the art, either the 5′ or 3′ terminus may be attached to the support using techniques known in the art. The arrays of the invention comprise at least two different covalently attached nucleic acid probes, with more than two being preferred. By “different” oligonucleotide herein is meant an oligonucleotide that has a nucleotide sequence that differs in at least one position from the sequence of a second oligonucleotide; that is, at least a single base is different, preferably their hybridization specificity is as outlined herein above.
Furthermore, the invention particularly relates to the use of a nucleic acid probe specifically hybridizing to the sequence of nucleotide 11 to 30 of a sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:910, and the RNA sequences encoded by these sequences, or hybridizing to the reverse complement thereof for the diagnosis of a neurodegenerative disease, preferably for the diagnosis of Alzheimer's disease The invention also relates to the use of a kit according to the invention for the diagnosis of a neurodegenerative disease, preferably for the diagnosis of Alzheimer's disease. Also encompassed by the invention is the use of an array according to the invention for the diagnosis of a neurodegenerative disease, preferably for the diagnosis of Alzheimer's disease.
The present invention also relates to the following items:
It will be apparent that the methods and components of the present invention, as well as the uses as substantially described herein or illustrated in the description and the examples, are also subject of the present invention and claimed herewith. In this respect, it is also understood that the embodiments as described in the description and/or any one of the examples, can be independently used and combined with any one of the embodiments described hereinbefore and claimed in the appended claims set. Thus, these and other embodiments are disclosed and encompassed by the description and examples of the present invention.
The invention is further illustrated by the following non-limiting Examples and Figures.
1. Methods
1.1 Whole Blood Sample Collection
Blood sampling was approved by the Charité ethics committee, registration number EA4/078/14 and all participants gave written informed consent. 5 mL blood were drawn from subjects by venipuncture and collected in K2EDTA coated Vacutainer (BD, #368841) and stored on ice until used for RNA preparation. For downstream RNA analysis by sequencing or qPCR assays presented here, 100 μL blood (>1 μg total RNA) is sufficient.
1.2 RNA Isolation and RNase R Treatment
Total RNA was isolated from fresh whole blood samples. Blood was diluted 1:3 in PBS and 250 μL of the dilution were used for RNA preparation using 750 μL Trizol LS reagent (Life Technology). Samples were homogenized by gentle vortexing and 200 μL chloroform was added. After centrifugation at 4° C., 15 min at full speed in a table top centrifuge, the aqueous phase was collected to a new tube (typically 400 μL). RNA was precipitated by adding an equal volume of cold isopropanol and incubation for ≥1 hour at −80° C. RNA pellets were recovered by spinning at 4° C., 30 min at full speed in a table top centrifuge. RNA pellets were washed with 1 mL 80% EtOH and subsequently air dried at room temperature for 5 min. The RNA was resuspended in 20 μL RNase-free water and treated with DNase I (Promega) for 15 min at 37° C. with subsequent heat inactivation for 10 min at 65° C. HEK293 total RNA was prepared in the same way but using 1 mL Trizol on cell pellets. For sequencing experiments the RNA preparations were additionally subjected to two rounds of ribosomal RNA depletion using a RiboMinus Kit (Life Technologies K1550-02 and A15020). Total RNA integrity and rRNA depletion were monitored using a Bioanalyzer 2001 (Agilent Technologies). For qPCR analysis the samples were treated with RNase R (Epicentre) for 15 min at 37° C. at a concentration of 3 U/μg RNA. After treatment 5% C. elegans total RNA was spiked-in followed by phenol-chloroform extraction of the RNA mixture. For controls the RNA was mock treated without the enzyme.
1.3 cDNA Library Preparation for Deep Sequencing
cDNA libraries were generated according to the Illumina TruSeq protocol. Sample RNA was fragmented, adaptor ligated, amplified and sequenced on an Illumina HiSeq2000 in 1×100 cycle runs.
1.4 Quantitative PCR (qPCR)
Total RNA was reverse transcribed using Maxima reverse transcriptase (Thermo Scientific) according to the manufacturer's protocol. qPCR reactions were performed using Maxima SYBR Green/Rox (Thermo Scientific) on a StepOne Plus System (Applied Biosystems). Primer sequences are available in the Table 7. RNase R assays were normalized to C. elegans RNA spike-in RNA.
1.5 Sanger Sequencing
PCR products were size separated by agarose gel electrophoresis, amplicons were extracted from gels and Sanger sequenced by standard methods (Eurofins).
1.6 Detection and Annotation of circRNAs
The detection of circular RNA was based on a previously published method (see Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338) with the following details. Human reference genome hg19 (February 2009, GRCh37) was downloaded from the UCSC genome browser (see Kent W J, Sugnet C W, Furey T S, et al. The human genome browser at UCSC. Genome Research. 2002; 12(6):996-1006) and was used for all subsequent analysis. bowtie2 (version 2.1.0 (see Langmead B, Salzberg S L. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012; 9(4):357-359) was employed for mapping of RNA sequencing reads. Reads were mapped to ribosomal RNA sequence data downloaded from the UCSC genome browser. Reads that do not map to rRNA were extracted for further processing. In a second step, all reads that mapped to the genome by aligning the whole read without any trimming (end-to-end mode) were neglected. Reads not mapping continuously to the genome were used for circRNA candidate detection. From those 20 nucleotide terminal sequences (anchors) were extracted and re-aligned independently to the genome. The anchor alignments were then extended until the full read sequence was covered. Consecutively aligning anchors indicate linear splicing events whereas alignment in reverse orientation indicates head-to-tail splicing as observed in circRNAs (
1.7 circRNA Annotation
Genomic coordinates of circRNA candidates were intersected with published gene models (ENSEMBL, release 75 containing 22,827 protein coding genes, 7484 lincRNAs and 3411 miRNAs). circRNAs were annotated and exon-intron structure predicted as previously described (see Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338). Known introns in circRNAs were assumed to be spliced out. Each circRNA was counted to a gene structure category if it overlaps fully or partially with the respective ENSEMBL feature (
1.8 Published RNA Data Sets
In this study rRNA depleted RNA-seq data from whole blood samples (own data), fetal cerebellum (ENCODE accession: ENCSR000AEW) fetal liver (ENCODE accession: ENCSR000AFB) and HEK293 (Table 1; see Ivanov A, Memczak S, Wyler E, et al. Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals. CellReports. 2015; 10(2):170-177) was used. Expression values, coordinates and other details of the circRNAs reported here and all associated scripts will be made available at www.circbase.org (see Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014; 20(11):1666-1670).
1.9 Quantification of circRNA and Host Gene Expression
The number of reads that span a particular head-to-tail junction were used as a measure for circRNA expression. To allow comparison of expression between samples, raw read counts were normalized to sequencing depth by dividing by the number of reads that map to protein coding gene regions and multiply by 1,000,000 (
Circular-to-linear ratios were calculated for each circRNA by dividing raw head-to-tail read counts by the median number of reads that span linear spliced junctions of the respective host gene. For both measures one pseudo count was added to avoid division by zero. CircRNAs from host genes without annotated splice junctions according to the ENSEMBL gene annotation, were not considered in this analysis.
For analysis in
1.10 Principal Component Analysis and Clustering
To perform principal component analysis (PCA) of circRNA expression in whole blood samples of different donors, variance stabilizing transformation was first performed on raw head-to-tail spliced read counts using the R package DESeq2 (see Love M I, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014; 15(12):550). Only circRNAs with a transformed expression value of at least 6.7 (n=910,
2. Results
2.1 Thousands of circRNAs are Reproducibly Detected in Human Peripheral Whole Blood
First it was determined whether circRNAs are present in standard clinical blood specimen. To this end, total RNA was prepared from two biologically independent human peripheral whole blood samples and depleted ribosomal RNAs (see Methods, supra). The samples were reverse transcribed using random primers to allow for circRNA detection and sequencing libraries were produced (
From the RNA of two human donors we identified 4550 and 4105 unique circRNA candidates, respectively, by at least two independent reads spanning a head-to-tail splice junction (FIG. 1B). In both datasets the number of total reads and linear splicing events were respectively similar, indicating reproducible sample preparation (Table 2, Table 5). When considering RNAs found in both samples, we observed a high correlation of expression for both linear (R=0.98) as well as circRNAs (R=0.80,
The predicted spliced length of blood circRNAs of 200-800 nt (median=343 nt) is similar to that in liver or cerebellum (median=394/448 nt) and previous observations in HEK293 cell cultures and other human samples (
To assess the reproducibility of the sequencing results we designed divergent, circRNA specific primers and measured relative abundances of the top eight expressed circRNAs compared to linear control genes in qPCR (
2.2 Circular-to-Linear RNA Expression is High in Blood
When inspecting the read coverage in blood sequencing data, it was noticed that oftentimes the expression of circularized exons was outstandingly high compared to the coverage of neighboring exons expressed in linear RNA isoforms of the same gene. For example, it was observed that the two exons of circRNA candidate 5, which is product of the PCNT locus were densely covered with sequencing reads in the blood samples, while the upstream and downstream exons were barely detected (
Thereafter, comparison of the blood data to published ENCODE project datasets from cerebellum, representative of neuronal tissues that in general have high circRNA expression (see Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. MOLCEL. 2015; 1-17) and to a non-neuronal primary tissue, liver (Table 2) was performed. Approx. 30% of blood circRNAs are also found in cerebellum while this fraction was around 10% for liver with higher fractions for both cases when constraining the analysis to highly expressed blood circRNAs (
The relative circular to linear RNA isoform abundance on a transcriptome wide scale was then analyzed. To this end, read counts that span head-to-tail junctions and are therefore indicative of circRNAs were compared to the median number of read counts on linear splice site junctions on the same gene, the latter serving as a proxy for linear RNA expression (see Methods, supra). We observed that many blood circRNAs are highly expressed while corresponding linear RNAs show average or low abundances (
2.3 circRNAs are Putative Biomarkers in Alzheimer's Disease
The results show that circRNAs are reproducibly and easily detected in clinical standard blood samples and therefore are well suited to serve as a new class of biomarker for human diseases, like neurodegenerative diseases. Taking into account the high expression of circRNAs in neuronal tissues (see Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. MOLCEL. 2015; 1-17) and the urgent need for biomarkers in neurological diseases, circular RNA expression in blood samples from Alzheimer's diseases patients and control subjects (see Methods, supra, Table 2, Table 4) was investigated. To this end, sequencing libraries from whole blood RNA from five individuals of each group were generated. In total 22,644 distinct circRNAs were detected in all samples combined. Then putative disease-specific circRNA expression were identified. Therefore, subsets of all detected circRNA candidates were defined and used these in a principle component analysis to detect expression differences between the two groups. Sorting of all circRNAs by expression and definition of sets for PCA analysis by increasing expression cut-offs was performed. In a range of the top 500 to top 900 circRNAs, a clear separation of control and diseased subjects was detected (
3. Discussion
Recent publications show that circRNAs can be detected in plasma and saliva samples (see Koh W, Pan W, Gawad C, et al. Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proceedings of the National Academy of Sciences. 2014; 111(20):7361-7366; and Bahn J H, Zhang Q, Li F, et al. The Landscape of MicroRNA, Piwi-Interacting RNA, and Circular RNA in Human Saliva. Clinical Chemistry. 2014). However, in both specimens only few (10-70) circular RNAs with canonical splice sites were reported, which dramatically limits any further analysis. The circular transcriptome of whole blood presented here, demonstrates that the search for putative circRNA biomarker in peripheral blood is much more suitable to yield informative results. Using RNA-Seq of clinical standard samples showed reproducible detection of around 2400 circRNA candidates that are present in human whole blood. It will be interesting to determine the origin of blood circRNAs. Accumulating evidence suggests that circRNAs are specifically expressed in a developmental stage- and tissue-specific manner, rather than being merely byproducts of splicing reactions (see Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495(7441):333-338; and Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed. MOLCEL. 2015; 1-17). Previously analyzed circRNA from neutrophils, B-cells and hematopoietic stem cells suggest that many circRNAs are constituents of hematocytes (see Salzman J, Gawad C, Wang P L, Lacayo N, Brown P O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE. 2012; 7(2):e30733). However, there is also the intriguing possibility of circRNA excretion into the extracellular space, e.g. by vesicles such as exosomes. Likewise, aberrant circRNA expression in disease may reflect, either a condition-specific transcriptome change in blood cells themselves, or a direct consequence of active or passive release of circRNA from diseased tissue.
Further, we demonstrated that many circRNAs have a high expression compared to linear RNA isoforms from the same locus, a feature that distinguishes blood circRNAs from other primary tissues such as cerebellum or liver. Considering that this was observed for hundreds of blood circRNA candidates (
After reproducibly detecting thousands of oftentimes highly expressed circRNAs in blood, it was asked whether these might be instrumental in diagnosis of human disease. Therefore measurement of putatively specific circRNA abundances in Alzheimer's disease and control samples was performed.
It was observed that analyzing specific subsets of blood circular RNAs allows distinguishing Alzheimer's disease from control samples in a principal component analysis and unsupervised clustering. This distinction was not possible when analyzing linear RNA isoforms from the same genomic loci, demonstrating that circRNA expression data bear specific information.
Given the urgent need for non-invasive biomarker detection for many disease states, these findings show a way for biomarker detection in easily accessible bodily fluid samples; like whole blood and cerebrospinal fluid. These are not being limited to Alzheimer's disease or neurological condition in general, since blood circRNA expression might be specifically altered in many disorders and therefore exploitable as diagnostic tool in human diseases.
Summary of RNA-Sequencing Results
Sequencing results for blood RNA from five controls (H), five Alzheimer patients (AD), cerebellum and liver control RNA samples. If not noted otherwise sample datasets were produced for this study.
| Number | Date | Country | Kind |
|---|---|---|---|
| 15187446.8 | Sep 2015 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2016/073321 | 9/29/2016 | WO | 00 |
