Use of cell-free RNA in urine sample in characterizing kidney injury

Abstract

The present disclosure is directed to (a) a method of detecting kidney injury in a subject comprising measuring the level of at least one cell-free RNA (cfRNA) in a subject urine sample that is a kidney injury signature gene; and detecting kidney injury based on the level of the cfRNA; and (b) a method of determining the underlying etiology of an acute kidney injury (AKI) in a subject undergoing an immune checkpoint inhibitor (ICI) therapy comprising: (i) measuring the level of at least one cell-free RNA (cfRNA) molecule in a urine sample from the subject, wherein the cfRNA molecule is from a gene, wherein the level of the cfRNA of the gene corresponds to an etiology of AKI; (ii) comparing the level of the cfRNA to a control; and (iii) determining that the underlying etiology of the AKI is either acute tubulointerstitial nephritis or acute tubular necrosis / hemodynamic AKI based on the level of the cfRNA as compared to the control.

Description

USE OF CELL-FREE RNA IN URINE SAMPLEIN CHARACTERIZING KIDNEY INJURYCROSS REFERENCE TO RELATED APPLICATION

[0001] This application claims the benefit of U.S. Provisional Patent Application No.63 / 733,784, filed December 13, 2024, the contents of which are incorporated herein by reference in its entirety.STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

[0002] This subject of this disclosure was made with government support under Grant Nos. DP2AI138242 and R01AI146165, awarded by the National Institutes of Health. The government has certain rights in this invention.BACKROUND

[0003] There is increasing interest in the use of circulating cell-free RNA (cfRNA) in plasma as an analyte for diagnosing and monitoring disease, with applications spanning cancer diagnosis, maternal health monitoring, and infectious disease testing. Recent studies demonstrate that cfRNA can also be isolated from urine, but the utility of urine cfRNA for patient monitoring applications remains underexplored. Given its physical connection to the urinary tract and the kidneys, urine cfRNA is in principle a promising analyte to monitor the kidney and complications of the urinary tract, but no studies have tested this concept in practice.SUMMARY OF DISCLOSURE

[0004] One aspect of the disclosure is directed to a method of detecting kidney injury in a subject, the method comprising: measuring the level of at least one cell-free RNA (cfRNA) transcript in a urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; and detecting kidney injury based on the measured level of the at least one cfRNA transcript.

[0005] In some embodiments, the method further comprises: measuring the level of at least one cfRNA transcript in a subsequent urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; detecting kidney injury based on the measured level of the at least one cfRNA transcript in the subsequent urine sample; anddetermining whether there is a change in the kidney injury. Tn some embodiments, the at least one cfRNA comprises a cfRNA of a kidney injury signature gene with an increased level as compared to control being indicative of kidney injury. In some embodiments, the at least one cfRNA comprises a cfRNA of a kidney injury signature gene with a decreased level as compared to control being indicative of AKI.

[0006] In some embodiments, measuring the level of at least one cfRNA comprises RNA sequencing. In some embodiments, measuring the level of at least one cfRNA comprises a PCR assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR). In some embodiments, measuring the level of at least one cfRNA comprises in situ hybridization, clustered regularly interspaced short palindromic repeats (CRISPR) assay, Loop-mediated isothermal amplification (LAMP), or microarray.

[0007] In some embodiments, the method further comprises a step of detecting the cells of origin of the kidney injury of the subject. In some embodiments, the cells of origin are kidney epithelial cells and the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells or a combination thereof. In some embodiments, the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney.

[0008] In some embodiments, the kidney injury is acute kidney injury (AKI).

[0009] In some embodiments, the urine sample is a longitudinally collected urine sample. In some embodiments, the longitudinally collected urine sample is obtained from the subject about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 10 days, about 15 days, about 30 days, about 45 days, about 60 days, about 75 days, about 90 days, about 105 days, and / or about 120 days after the initial urine sample is collected from the subject.

[0010] In some embodiments, when there is a kidney injury in the subject, the method further comprises treating the subject with a therapy to ameliorate the kidney injury.

[0011] In some embodiments, the subject has undergone a transplant of an organ or tissue of the urinary tract.

[0012] Another aspect of the disclosure is directed to a method of determining the underlying etiology of an acute kidney injury (AKI) in a subject undergoing an immune checkpoint inhibitor (ICI) therapy, the method comprising: (i) measuring the level of at least one cell-free RNA (cfRNA) molecule in a urine sample from the subject, wherein the at least one cfRNA molecule is a cfRNA of a gene and wherein a differential abundance of the cfRNA of the gene corresponds to an etiology of AKI; (ii) comparing the measured level of the at least one cfRNA to a control; and (iii) determining that the underlying etiology of the AKI is either acute tubulointerstitial nephritis (ATIN) or acute tubular necrosis / hemodynamic AKI (ATN) based on an increase or decrease in the level of the at least one cfRNA as compared to the control.

[0013] In some embodiments, the at least one cfRNA comprises a cfRNA of a signature gene with an increased level as compared to control being indicative of an ATIN etiology. In some embodiments, the at least one cfRNA comprises a cfRNA of a signature gene with a decreased level as compared to control being indicative of an ATIN etiology.

[0014] In some embodiments, measuring the level of at least one cfRNA comprises RNA sequencing. In some embodiments, measuring the level of at least one cfRNA comprises a PCR assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR). In some embodiments, measuring the level of at least one cfRNA comprises in situ hybridization, clustered regularly interspaced short palindromic repeats (CRISPR) assay, Loop-mediated isothermal amplification (LAMP), or microarray.

[0015] In some embodiments, the method further comprises a step of detecting the cells of origin of the kidney injury of the subject. In some embodiments, the cells of origin are kidney epithelial cells and the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells or a combination thereof. In some embodiments, the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney.

[0016] In some embodiments, the kidney injury is acute kidney injury (AKI).

[0017] In some embodiments, the urine sample is a longitudinally collected urine sample. In some embodiments, the longitudinally collected urine sample is obtained from the subject about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about10 days, about 15 days, about 30 days, about 45 days, about 60 days, about 75 days, about 90 days, about 105 days, and / or about 120 days after the initial urine sample is collected from the subject.

[0018] In some embodiments, when there is a kidney injury in the subject, the method further comprises treating the subject with a therapy to ameliorate the kidney injury.

[0019] In some embodiments, the subject has undergone a transplant of an organ or tissue of the urinary tract.BRIEF DESCRIPTION OF THE DRAWINGS

[0020] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Offce upon request and payment of the necessary fee.

[0021] FIG. 1A-D. Properties and cellular origins of urine and plasma cfRNA. (A), Study design (created with BioRender.com); (B), stacked bar plot of mean fraction of biotypes in each cohort; (C), grouped box plot of transcriptome Gini index calculated from the healthy cohort. *P < 0.05, **P < 0.01, ***P < 0.001 (2-tailed, Wilcoxon rank sum test); (D), pie charts of mean fraction of CTO of urine and plasma cell-free transcriptomes from matched healthy volunteers (n = 5).

[0022] FIG. 2A-E. Monitoring systemic changes. (A), HSCT cohort samples overview (created with BioRender.com); (B), volcano plot showing differentially expressed genes in DO vs PR and E vs DO conditions for urine and plasma cfRNA; (C), upset plots showing the mutual exclusive and overlapping genes in each condition for urine and plasma cfRNA; (D), area plot showing average cfRNA deconvolution results at each timepoint; (E), box plots showing fraction of CTO at each timepoint.

[0023] FIG. 3A-E. Monitoring kidney injury and complications of the urinary tract. (A), Illustration of location of kidney tubule epithelial cells and parietal epithelial cells (created with BioRender.com); (B), box plots showing fraction of kidney connecting tubule epithelial cells and parietal cells in patients with AKI and patients without AKI grouped by biofluid source. *P < 0.05, **P < 0.01, ***P < 0.001 (2-tailed, Wilcoxon rank sum test); (C), volcano plot showing differentially expressed genes in patients receiving ICI therapy with AKI (AKI) vs patients without AKI on ICI therapy (Control); (D), box plots showing normalized gene counts of JUN and SOX9 in patients receiving ICI therapy with AKI (AKI) vs patients without AKI on ICItherapy (Control). *P < 0.05, **P < 0.01, ***P < 0.001 (2-tailed, Wilcoxon rank sum test); (E), volcano plot showing differentially expressed genes in patients with ATIN vs patients with ATN / hemodynamic AKI. Heatmap showing hierarchical clustering of ATIN and ATN samples based on genes identified in differential abundance analysis.

[0024] FIG. 4A-D. Impact of differential centrifugation on urine cfRNA features. A) Bar plot showing biotype distribution across 3 different centrifugation methods for three donors. B) Box plot depicting the Gini index for the centrifugation methods. C) PCA plot of all samples showing clustering based on transcriptomic profile where samples are color coded based on centrifugation method and shaped based on individual donor. D) Plot showing the correlation of cell type fraction between different centrifugation methods where each point represents a cell type.

[0025] FIG. 5A-D. Impact of different preservatives on urine cfRNA features. A) Bar plot showing biotype distribution across 3 different preservative methods for three donors. B) Box plot depicting the gini index for the preservative methods. C) PCA plot of all samples showing clustering based on transcriptomic profile where samples are color coded based on preservative and shaped based on individual donor. D) Plot showing the correlation of cell type fraction between different preservative methods where each point represents a cell type.

[0026] FIG. 6A-D. Length distribution of urine cfRNA measured for different protocols. A) Electropherograms of urine cDNA libraries corresponding to different urine collection methods (RFU: relative fluorescence unit per peak). B) Fragment length distribution of cfRNA sequencing reads measured for different urine collection methods. C) Electropherograms of urine cDNA libraries corresponding to different centrifugation methods. D) Fragment length distribution of cfRNA sequencing reads measured for different centrifugation methods.

[0027] FIG. 7A-B. Biophysical properties of urine cfRNA. A) Density plot illustrating the average insert size length profiles for each cohort. B) Box plot depicting the percentage contribution of counts from the top 10 most abundant genes in each sample across all cohorts.

[0028] FIG. 8A-D. Impact of different references on cell type deconvolution: A) Pie chart showing 5 top cells of origin from urine cfRNA of 5 healthy volunteers generated using the complete Tabula Sapiens reference used for plasma. B) Pie chart showing 5 top cells of origin from urine cfRNA of 5 healthy volunteers generated using the selected cell types for urine. Boxplot showing the cell type fractions of kidney tubule epithelial cells of urine cfRNA from AKI patients and controls run on C) Plasma reference and D) Urine reference.

[0029] FIG. 9A-B. Pathways that are activated or inhibited in each condition: A) DO vs PR, and B) E vs DO as revealed by urine and plasma cfRNA.

[0030] FIG. 10A-C. Box plots showing Gini index of the cell-types of origin in urine and plasma A) for all samples and B) spread across all sampling timepoints for the HSCT cohort. C) Boxplot showing Bray-Curtis similarity index of cell -types of origin between patients and within individual patients.

[0031] FIG. 11. Box plots showing fraction bladder urothelial cells (left) and club cells of prostate epithelium hillock (right) for HSCT patients with clinical evidence of epithelial cells.

[0032] FIG. 12. Box plot showing contributions of Parietal epithelial cells and kidney tubule epithelial cells in healthy volunteer and patients with and without detectable BKV load in plasma(two tailed, Wilcoxon rank sum test).

[0033] FIG. 13. Fraction of kidney tubule epithelial cells in patient samples collected when BKV was either detected or below the limit of quantification, relative to the day of transplantation.

[0034] FIG. 14A-B. Box plot showing the normalized gene abundance of A) JUND and B) CEBPB in plasma and urine in AKI patients and ICI controls.

[0035] FIG. 15A-C. Gene signatures between AIN and ATN samples. A) Box plots showing the normalized gene abundance of CXCL9, CXCL10 and CXCL11 in urine cfRNA in AIN and ATN patient samples. B) Plots showing high abundance of APOA4 and CLCA1 in select AIN samples. C) Volcano plot showing differential abundant samples in AIN vs ATN when 3 samples highlighted in FIG. 14A are exempted (AIN=9, ATN=11).DETAILED DESCRIPTION

[0036] One aspect of the disclosure is directed to a method of detecting kidney injury in a subject, the method comprising: measuring the level of at least one cell-free RNA (cfRNA) transcript in a urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; and detecting kidney injury based on the measured level of the at least one cfRNA transcript.

[0037] In some embodiments, the method further comprises: measuring the level of at least one cfRNA transcript in a subsequent urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; detecting kidney injury based on the measured level of the at least one cfRNA transcript in the subsequent urine sample; anddetermining whether there is a change in the kidney injury. In some embodiments, the method further comprises a step of detecting the cells of origin of the kidney injury of the subject. In some embodiments, the cells of origin are kidney epithelial cells and the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells or a combination thereof. In some embodiments, the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney.

[0038] In some embodiments, the kidney injury is acute kidney injury (AKI). In some embodiments, when there is a kidney injury in the subject, the method further comprises treating the subject with a therapy to ameliorate the kidney injury. In some embodiments, the subject has undergone a transplant of an organ or tissue of the urinary tract.

[0039] Another aspect of the disclosure is directed to a method of determining the underlying etiology of an acute kidney injury (AKI) in a subject undergoing an immune checkpoint inhibitor (ICI) therapy, the method comprising: (i) measuring the level of at least one cell-free RNA (cfRNA) molecule in a urine sample from the subject, wherein the at least one cfRNA molecule is a cfRNA of a gene and wherein a differential abundance of the cfRNA of the gene corresponds to an etiology of AKI; (ii) comparing the measured level of the at least one cfRNA to a control; and (iii) determining that the underlying etiology of the AKI is either acute tubulointerstitial nephritis (ATIN) or acute tubular necrosis / hemodynamic AKI (ATN) based on an increase or decrease in the level of the at least one cfRNA as compared to the control.

[0040] Although claimed subject matter will be described in terms of certain examples, other examples, including examples that do not provide all the benefits and features set forth herein, are also within the scope of this disclosure. Various structural, logical, and process step changes may be made without departing from the scope of the disclosure.

[0041] Ranges of values are disclosed herein. The ranges set out a lower limit value and an upper limit value. Unless otherwise stated, the ranges include the lower limit value, the upper limit value, and all values between the lower limit value and the upper limit value, including, but not limited to, all values to the magnitude of the smallest value (either the lower limit value or the upper limit value).

[0042] In the description that follows, certain conventions will be followed as regards to the usage of terminology. Generally, terms used herein are intended to be interpreted consistently with the meaning of those terms as they are known to those of skill in the art. In practicing the present disclosure, many conventional techniques in molecular biology, microbiology, cell biology, biochemistry, and immunology are used, which are within the skill of the art. These techniques are described in greater detail in, for example, Molecular Cloning: a Laboratory Manual 4th edition, J.F. Sambrook and D.W. Russell, ed. Cold Spring Harbor Laboratory Press 2012; Recombinant Antibodies for Immunotherapy, Melvyn Little, ed. Cambridge University Press 2009; “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Current Protocols in Molecular Biology” (F. M. Ausubel et al., eds., 1987, and periodic updates); “PCR: The Polymerase Chain Reaction”, (Mullis et al., ed., 1994); “A Practical Guide to Molecular Cloning” (Perbal Bernard V., 1988); “Phage Display: A Laboratory Manual” (Barbas et al., 2001). The contents of these references and other references containing standard protocols, widely known to and relied upon by those of skill in the art, including manufacturers’ instructions are hereby incorporated by reference as part of the disclosure.

[0043] The term “urine sample” refers to a sample or specimen from a subject. In some embodiments, the urine sample is a clean catch urine sample. Clean catch urine sample is known in the art. Briefly, a midstream urine sample is collected by first cleaning the genital area, urinating a small amount to clear any bacteria, and then collecting the rest of the urine in a sterile cup. In some embodiments, the urine sample is 24-hour urine sample. A 24-hour urine sample is known in the art and is done by collecting a subject’s urine in a special container over a full 24-hour period.

[0044] The term “subject” refers to mammals. Non-limiting examples of mammals include but are not limited to human, horse, camel, dog. cat, pig, cow, goat, and sheep. In some embodiments, the mammal is human. In some embodiments, the subject has undergone a transplant of an organ or tissue of the urinary tract.

[0045] The terms “cell-free RNA” or “cfRNA” refer to cfRNA released by cells in the solid tissues of the urinary tract. cfRNA is primarily released by dying cells; therefore, cfRNA may provide insights into pathways of cell death and mechanisms of cellular injury. cfRNA is also released into the blood by way of active secretion, cells release cfRNA to the subject’s bodilyfluid and thus may increase the quantity of the specific cfRNA in the subject’s urine sample as compared to a healthy individual. cfRNA may include any types of RNA that are circulating in the bodily fluid of a person without being enclosed in a cell body or a nucleus.

[0046] A “gene panel” or “panel” refers to a defined collection of genes. A panel may include relevant pathogen associated genes and likely variants of selected genes. In some embodiments, the panel comprises a collection of signature genes. As used herein, the term “signature gene” refers to a gene whose expression is correlated, either positively or negatively, with disease extent or outcome or with another predictor of disease extent or outcome. In some embodiment, the gene panels are used in sequencing assays. Sequencing based assays are known in the art. Some non-limiting examples of sequencing based assays are next generation sequencing (NGS), Sanger sequencing, oxidative bisulfite sequencing, direct RNA sequencing, and others. In a next generation sequencing (NGS) panel test, only clinically important genes are examined to obtain genomic data in a timely and cost-effective manner. In some embodiments, the gene panels are used in NGS. In some embodiments, the gene panels are used in non- sequencing based assays. Non- sequencing based assays are known in the art. Non-limiting examples of non-sequencing based assays include microarrays, polymerase chain reaction (PCR), including real-time PCR, reverse transcription PCR (RT-PCR), quantitative reverse transcription PCR (RT-qPCR), quantitative PCR (qPCR), digital droplet PCR (ddPCR), and others (as described in Shemer, R. et al., Current Protocols in Molecular Biology, 127.1 (2019): e90; and Zemmour, Hai, et al., Nature Communications, 9.1 (2018): 1-9, both incorporated herein in their entirety)..

[0047] As used herein, the term “profile” generally refers to gene expression profile. A gene expression profile can be understood to mean a pattern of abundance (level) of expression of genes. In some embodiments, a gene expression profile is a measurement of the expression of multiple genes at once. In some embodiments, gene expression is measured by cfRNA in a subject, e.g., cfRNA in a serum or plasma sample, in which case, the profile is that of a subject’s cfRNA. Gene expression profiles can be characteristic or unique to a status of a subject, e.g., a healthy status or a disease status (such as cancer or infectious disease) and can therefore be used to distinguish between different statuses.

[0048] In some embodiments, the profile is a profile of genes identified in this disclosure to be associated with kidney injuries, which are also referred to herein as “kidney injury signature gene”. It is to be understood that the profile of signature genes in this disclosure have not allbeen associated with the kidney injury previously. Kidney injury signature genes of this disclosure were identified by the present inventors using the methods developed and disclosed herein. Kidney injury signature genes exhibit differential expression in subjects having the kidney injury relative to subjects without kidney injury, for example. The differential expression refers to the difference in abundance of a kidney injury signature gene in subjects having kidney injury relative to subjects without kidney injury. In some embodiments, the expression levels of signature genes may be used to predict progression of kidney injury. Measurement of expression of kidney injury signature genes refers to the absolute abundance (relative to a threshold detection limit / amount) or relative abundance (increase or decrease) in cfRNA relative to a control level (e.g., a level in a healthy subject) is indicative of kidney injury. In some embodiments, a kidney signature gene is not expressed or its expression is not detectable in a healthy control sample, then the absolute abundance and relative abundance are equivalent.

[0049] A “signature nucleic acid” is a nucleic acid comprising or corresponding to, in case of cDNA, the complete or partial sequence of a RNA transcript encoded by a signature gene, or the complement of such complete or partial sequence. A signature protein is encoded by or corresponding to a signature gene of the disclosure.

[0050] As used herein, “control” refers to a healthy subject, or a sample obtained from a healthy subject, or the level of gene expression in a sample from a healthy subject which can be either predetermined, or preestablished, or determined simultaneously with a subject under examination. In some embodiments, “control” is used to indicate the baseline or starting level of a signature gene in a sample from the subject. In some embodiments, the baseline or starting level of a signature gene is the measurement of the signature gene in the initial sample from the subject, i.e. the first sample obtained from the subject at a particular time point.

[0051] As used herein, the term “reference profile” refers to the profile of genes (e.g., the same genes identified in this disclosure to be associated with an kidney injury) in a subject not inflicted with a kidney injury.

[0052] In some embodiments, machine learning and model training is performed using R (4.0.2) with the DESeq2 (vl.34.0), Caret (v6.0.90), and pROC (vl.18.0) packages. In some embodiments, sample metadata and count matrices split 70 / 30 into a training set and a test set, controlling for disease status and cohort to minimize differences in the training and test datasets.In some embodiments, sample metadata and count matrices are split into a training set, validation set, and test set, controlling for disease status and cohort to minimize differences in the datasets.

[0053] In some embodiments, features for model training are selected by filtering and differential abundance analysis. First, differential abundance analysis was performed on the raw training counts using DESeq2. Then feature selection was conducted using the output from DESeq2 on retained genes. In some embodiments, genes are excluded that have a base-mean of less than 100 and a Benjamini-Hochberg adjusted p-value greater than 0.05. In some embodiments, genes are excluded that have a base-mean of less than 50 and a Benjamini-Hochberg adjusted p-value greater than 0.05.

[0054] In some embodiments, machine learning algorithms are trained using 5-fold cross validation and grid search hyperparameter tuning. In some embodiments, accuracy, sensitivity, specificity, and / or area under the receiver operating characteristic curve (ROC-AUC) are used to measure test performance. In some embodiments, the classification models used are generalized linear models with Ridge and LASSO feature selection (GLMNETRIDGE and GLMNETLASSO), support vector machines with linear and radial basis function kernel (SVMLin and SVMRAD), random forest (RF), random forest ExtraTrees (EXTRATREES), neural networks (NNET), linear discriminant analysis (LDA), nearest shrunken centroids (PAM), C5.0 (C5), k-nearest neighbors (KNN), naive bayes (NB), CART (RPART), and generalized linear models (GLM).

[0055] As used herein, “one, more, or all” refers to the panel of biomarkers comprising one of the listed genes, more than one of the listed genes, or all of the listed genes, respectively. In some embodiments, more than one includes at least 2 of the listed genes. In some embodiments, more than one includes at least 3 of the listed genes. In some embodiments, more than one includes at least 4 of the listed genes. In some embodiments, more than one includes at least 5 of the listed genes. In some embodiments, more than one includes at least 6 of the listed genes. In some embodiments, more than one includes at least 7 of the listed genes. In some embodiments, more than one includes at least 8 of the listed genes. In some embodiments, more than one includes at least 9 of the listed genes. In some embodiments, more than one includes at least 10 of the listed genes. In some embodiments, more than one includes at least 15 of the listed genes. In some embodiments, more than one includes at least 20 of the listed genes. In some embodiments, more than one includes at least 25 of the listed genes. In some embodiments, more than one includes atleast 30 of the listed genes. In some embodiments, more than one includes at least 40 of the listed genes. In some embodiments, more than one includes at least 50 of the listed genes. In some embodiments, more than one includes at least 60 of the listed genes. In some embodiments, more than one includes at least 70 of the listed genes. In some embodiments, more than one includes at least 80 of the listed genes. In some embodiments, more than one includes at least 90 of the listed genes. In some embodiments, more than one includes at least 100 of the listed genes.

[0056] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one skilled in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and / or materials in connection with which the publications are cited.Detection of Acute Kidney Injury in cfRNA from Urine

[0057] In this disclosure, urine cfRNA was isolated, its biophysical properties measured and its diverse molecular composition and origin demonstrated as compared to plasma cfRNA. The disclosed findings recapitulate some aspects of recent work by Hulstaert et al. (Cell Rep 2020;33 : 108552) and Vorperian et al. (Multiomics characterization of cell type repertoires for urine liquid biopsies. Genomics 2023 Oct), particularly regarding the stability and cell-types of origin of urine cfRNA. However, this disclosure is the first of its kind to systematically assess the utility of urine cfRNA relative to plasma cfRNA for the monitoring of immune dynamics and kidney injury.

[0058] While the presence of transrenal cell-free DNA (cfDNA) in urine has been suggested in the literature, using the methods disclosed within showed analyses of plasma and urine cfRNA changes in matched samples from patients that undergo HSCT show that urine and plasma cfRNA represent distinct reservoirs that are not strongly coupled. This is perhaps mostly clearly shown by the low representation of platelet-derived cfRNA in urine and the low representation of cfRNA from kidney cells in plasma. These findings suggest that there is minimal exchange of cfRNA between these two biofluids, and points to their use for distinct diagnostic applications.

[0059] In hematopoietic stem cell transplantation (HSCT), analysis herein shows that plasma cfRNA more effectively captures systemic and immune dynamics compared to urine cfRNA, as evidenced by the number of differentially abundant genes, activated and inhibited pathways from pairwise differential abundance analysis and large-scale changes in the cfRNA cell-types-of-origin. For example, a marked decrease in the contribution of immune cells to plasma cfRNA following chemotherapy and a subsequent sharp increase following stem cell engraftment was observed. In contrast, such trends were not seen for urine cfRNA which suggests that urine cfRNA is not a sensitive analyte to monitor systemic or immune related changes.

[0060] Conversely, the results using the disclosed methods show that urine cfRNA is more sensitive to changes in the urinary tract than plasma cfRNA, and that there may be distinct urinary cfRNA signatures depending on the underlying etiology of AKI. In the AKI cohort the differential contribution of kidney cortex cell types using both biofluids was explored. Parietal epithelial cells, which line the Bowman’s capsule, show no significant differences in their cfRNA contributions from both urine and plasma. However, a significant change in the contributions of kidney tubule epithelial cells in urinary cfRNA but not plasma cfRNA in patients with AKI compared to patients without AKI was observed.

[0061] One aspect of the disclosure is directed to a method of detecting kidney injury in a subject, the method comprising: measuring the level of at least one cell-free RNA (cfRNA) transcript in a urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; and detecting kidney injury based on the measured level of the at least one cfRNA transcript.

[0062] As used herein, “kidney injury” refers to the subject’s kidneys inability to filter waste products from blood. “Acute kidney injury”, or “AKI”, refers to a subject’s kidneys sudden inability to filter waste products from blood. Acute kidney injury is sometimes known as acute kidney failure. There are several known causes of AKI, including but not limited to, a slowed blood flow to the kidneys, glomerulonephritis (inflammation of glomerulus), immune system disease, tumor lysis syndrome, and urine blockage, which is caused by a number of disorders including kidney stones, enlarged prostate, urinary tract blood clots, cancer of the bladder, prostate, cervix, or colon, along with their treatments, and nerve damage to the nerves of the urinary tract. AKI is known to almost always be linked to a co-existing medical condition.

[0063] As used herein, “kidney injury signature gene” refers to a gene whose absolute abundance (relative to a threshold detection limit / amount) or relative abundance (increase or decrease) in cfRNA relative to a control level (e.g., a level in a healthy subject) is indicative of kidney injury. In some embodiments, a kidney signature gene is not expressed, or its expression is not detectable in a healthy control sample, then the absolute abundance and relative abundance are equivalent.

[0064] The inventors have recognized that cells of damaged kidney tissue release cell free RNA. Measurement of expression of kidney injury signature genes in the cfRNA can be used to determine the absolute abundance (relative to a threshold detection limit / amount) or relative abundance (increase or decrease) in cfRNA relative to a control level (e.g., a level in a healthy subject) as indicative of kidney injury.

[0065] In some embodiments, the method of detecting kidney injury in a subject comprises measuring the level of at least one cell-free RNA (cfRNA) transcript in an initial urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; and detecting kidney injury based on the measured level of the at least one cfRNA transcript. In some embodiments, the method of detecting kidney injury in a subject further comprises the measuring of a level of at least one cfRNA transcript in a subsequent urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; comparing the level of the at least one cfRNA transcript in the initial urine sample with the level of the at least one cfRNA transcript in the subsequent urine; and determining whether there is a change in the kidney injury.

[0066] In some embodiments, multiple urine samples are collected from the subject. In some embodiments, the collecting of multiple urine samples comprises a set of longitudinally collected biological samples of the subject. As used herein, “subsequent urine sample” refers to any urine sample collected from the same subject at a point in time after the initial, first, or original urine sample was collected. In some embodiments, the longitudinally collected urine sample is obtained from the subject about 1 day after the initial urine sample is collected from the subject; insome embodiments, the longitudinally collected urine sample is obtained from the subject about 2 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 3 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinallycollected urine sample is obtained from the subject about 4 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 5 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 6 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 7 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 10 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 15 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 30 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 45 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 60 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 75 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 90 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 105 days after the initial urine sample is collected from the subject; and / or the longitudinally collected urine sample is obtained from the subject about 120 days after the initial urine sample is collected from the subject.

[0067] In some embodiments, the at least one cfRNA comprises a cfRNA of a kidney injury signature gene with an increased level as compared to a control, where the increased level is indicative of kidney injury. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from: LASPI (NM_006148.4), TMEM176A (NM_018487.3), TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3), TTC22 (NM_001114108.2), CACNA2D2 (NM_006030.4), NFIX (NM_001365902.3), IL32 (NM_001376923.1), SCMH1 (NM_001394311.1), PTBP1 (NM_002819.5), LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3),SEC63 (NM_007214.5), VIM (NM_003380.5), CD44 (NM_000610.4), TMSB10 (NM_021103.4), SZRD1 (NM_001114600.3), LAMC2 (NM_005562.3), YBX3 (NM_003651.5). VMP1 (NM_030938.5), BICRA (NM_001394372.1), RPL18 (NM_000979.4), CTSA (NM_000308.4), SLC9A3R2 (NM_001130012.3), WDR18 (NM_024100.4), TLE2 (NM_003260.5), MTHFD2 (NM_006636.4), PDE4A (NM_001111307.2), PLPP1 (NM_003711.4). BCL3 (NM_005178.5), RAB27A (NM_183235.3), DAZAP1 (NM_018959.4), PTPN18 (NM_014369.4), ACTB (NM_001101.5), TPD52 (NM_001025253.3), ARAF (NM_001654.5), GNB1 (NM_002074.5), TP53INP2 (NM_021202.3), RIMS1 (NM_014989.7), RPS5 (NM_001009.4), BAX (NM_138761.4), SH3BP2 (NM_001122681.2), GNAS (NM_000516.7), EBF4 (NM_001395167.1), RPLPO (NM_001002.4), GRAMD1A (NM_020895.5). CDV3 (NM_017548.5), ALKBH5 (NM_017758.4), NUBP2 (NM_012225.4), SETD1A (NM_014712.3), CIRBP (NM_001300829.2), MKNK2 (NM_199054.3), SEC14L2 (NM_012429.5), SLC25A1 (NM_005984.5), GGA1 (NM_013365.5), CYB5R3 (NM_000398.7). TTLL12 (NM_015140.4), CTSZ (NM_001336.4). CDC25B (NM_021873.4), WFDC2 (NM_006103.4), MAP1LC3A (NM_032514.4), LPIN2 (NM_001375808.2), PLP2 (NM_002668.3), TIMP1 (NM_003254.3), MAGED2 (NM_177433.3), NUTF2 (NM_005796.3), CLCN7 (NM_001287.6), UBE2I (NM_003345.5), MAZ (NM_002383.4), TMC5 (NM_001261841.2), BL0C1S6 (NM_012388.4), PPP2CB (NM_001009552.2), MAN2B1 (NM_000528.4). NUCB1 (NM_006184.6), SF3A2 (NM_007165.5), OAZ1 (), TLE5 (NM_001130.6), SGTA (NM_003021.4), MED25 (NM_030973.4), FBL (NM_001436.4), SLC1A5 (NM_005628.3), CCDC9 (NM_015603.3), PTPRS (NM_002850.4), KDELR1 (NM_006801.3). RAB3D (NM_004283.4), PLEKHA4 (NM_020904.3), RPL18A (NM_000980.4), COPE (NM_007263.4), LSR (NM_205834.4), GSK3A (NM_019884.3), ZC3HAV1 (NM_020119.4), MOSPD3 (NMJ123948.5), IMPDH1 (NM_000883.4), ZNHIT1 (NM 006349.3). PRKAG2 (NM_016203.4), BCL7B (NM_001707.4), LIMK1 (NM_002314.4). PRUNE2 (NM_015225.3), TESK1 (NM_006285.3), EDF1 (NM_003792.4), SFXN3 (NM_030971.6), FBXW4 (NM_022039.4), CCNY (NM_145012.6), RPL28 (NM_000991.5), CASC3 (NM_007359.5), PFN1 (NM_005022.4), SLC25A11 (NM_003562.5), RASD1 (NM_016084.5), CCL2 (NM_002982.4), SLC9A3R1 (NM_004252), SLAIN2 (NM_020846.2), CRACD (NM_001393381.1), CRYAB (NM_001289808.2), MDK (NM_002391.6), FOXM1 (NM_021953.4), GAPDH (NM_002046.7), CHPT1 (NM_020244.3), ATN1 (NM_001940.4),C12orf57 (NM_138425.4), C0X6A1 (NM_004373.4), TDP2 (NM_016614.3), S0D2 (NM_000636.4), TRIM38 (NM_006355.5), PHF1 (NM_024165.3), FBRSL1(NM_001367871.1), LMNB1 (NM_005573.4), SKP1 (NM_170679.3). ERGIC1 (NM_001031711.3), GNAI2 (NM_002070.4), RPS15 (NM_001018.5), MLPH (NM_024101.7), 0DC1 (NM_002539.3), SRSF4 (NM_005626.5), SRM (NM_003132.3), Clorf21 (NM_030806.4). TSPAN1 (NM_005727.4). CTSD (NM_001909.5), SPP1 (NM_001040058.2), ELL2 (NM_012081.6), CCDC92 (NM_025140.3), NEK6 (NM_014397.6), TGFB3 (NM_003239.5), OGFRL1 (NM_024576.5), DUSP1 (NM_004417.4), EGR1 (NM_001964.3), SERP1 (NM_014445.4), CLU (NM_001831.4), TNFRSF10B (NM_003842.5), S0RBS3 (NM_005775.5), TNFSF10 (NM_003810.4), KIAA1191 (NM_020444.5), CALD1 (NM_033138.4). NR4A1 (NM_173157.3), TUBA1B (NM_006082.3), AMD1 (NM_001634.6), MXD4 (NM_006454.3), PMEPA1 (NM_020182.5), KLHDC3 (NM_057161.4), MEA1 (NM_014623.4), CDKN1A (NM_000389.5), DEK (NM_003472.4), MYRF (NM_001127392.3), MT2A (NM_005953.5). SOX9 (NM_000346.4), PPDPF (NM_024299.4), C3 (NM_000064.4). CENPB (NM_001810.6), CAPNS1 (NM_001749.4), HIVEP3 (NM_024503.5), EMC6 (NM_031298.4), YWHAH (NM_003405.4), ATF4 (NM_182810.3), CDC42EP1 (NM_152243.3), LIF (NM_002309.5), BCL2L2 (NM_004050.5), PGAP6 (NM_021259.3), PRKCSH (NM_001289104.2), ACTN4 (NM_004924.6), KLHDC7B (NM_138433.5), SSBP4 (NM_032627.5). GDF15 (NM_004864.4), JUND (NM_005354.6), UBE2M (NM_003969.4), EIF3G (NM_003755.5), SLC6A8 (NM_005629.4), UBE2D2 (NM_003339.3), TOP2A (NM_001067.4), RARA (NM_000964.4), ITGB4 (NM_000213.5), WBP2 (NM_012478.4), TRIM47 (NM_033452.3), FLOT2 (NM_004475.3), TCEAL4 (NM_001006935.3), PLAAT4 (NM_004585.5), CEP20 (NM_144600.4), BTG1 (NM_001731.3), BHLHE40 (NM_003670.3), TMEM106C (NM_001143842.2), LDHA (NM_005566.4), ETS1 (NM_001143820.2), OS9 (NM_006812.4). MAP7 (NM_003980.6), NIBAN1 (NM_052966.4), ODF2 (NM_001351578.2), KLF4 (NM_004235.6), ANP32B (NM_006401.3), FLOT1 (NM_005803.4), PARP6 (NM_001323532.2), TACC2 (NM_206862.4), PARP9 (NM_001146105.2), RNF185 (NM_152267.4), CLSTN3 (NM_014718.4), WARSI (NM_004184.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SAMD1 (NM_138352.3). AKT1 (NM_001382430.1), ZNF787 (NM_001002836.4), RPL13A (NM_012423.4), SH3BGRL3 (NM_031286.4), SYTL1 (NM_001193308.2), MGST3(NM_004528.4), HDGF (NM_004494.3), RABI 3 (NM_002870.5), ARL8A (NM_138795.4), RHOB (NM_004040.4), RPL32 (NM_000994.4), ARL6IP5 (NM_006407.4), RPS3A (NM_001006.5). TRIM41 (NM_033549.5), HIGD2A (NM_138820.4), FAM193B (NM_001190946.3), PPP1R18 (NM_133471.4), PRIM2 (NM_000947.5), PNRC1 (NM_006813.3), RPL10 (NM_006013.5), RPL7A (NM_000972.3), MKI67 (NM_002417.5), DGKZ (NM_001199267.2), ALDOA (NM_001243177.4). TMCO3 (NM_017905.6), RILPL2 (NM_145058.3), PRDM8 (NM_001099403.2), RASSF3 (NM_178169.4), UBALD1 (NM_145253.3), CMIP (NM_198390.3), CEP112 (NM_001199165.4), AD AMTS 1 (NM_006988.5), AZINI (NM_148174.4), HKDC1 (NM_025130.4), FBRS (NM_001105079.3), RBPMS (NM_001008710.3), MMP14 (NM_004995.4), FZD1 (NM_003505.2), CREB3L1 (NM_052854.4). FAIM (NM_001033031.2), SLC45A3 (NM_033102.3). NBL1 (NM_005380.8), FBXW5 (NM_018998.4), IFNGR2 (NM_005534.4), CSRP1 (NM_004078.3), UBE2Z (NMJ123079.5), PTMS (NM_002824.6), RGS12 (NM_001394154.1), ZYX (NM_003461.5). CALM3 (NM_005184.4), PDE9A (NM_002606.3). NDUFV3 (NM_021075.4), S100A1 (NM_006271.2), MGAT4B (NM_014275.5), RPL8 (NM_001317782.2), FMNL3 (NM_175736.5), CXCL16 (NM_001386809.1). RPL29 (NM.000992.3), SDC3(NM_014654.4), VCAM1 (NM_001078.4), ATF3 (NM_001674.4), Clorf 115 (NM_024709.5), KIF26B (NM_018012.4), LRATD1 (NM_145175.4), H3-3A (NM_002107.7), CCNYL1 (NM_001330218.2), FZD5 (NM_003468.4), IGFBP7 (NM_001553.3), SSR2 (NM_003145.4). ZC3H12A (NM_025079.3), MEAF6 (NM_001270875.3), DNALI1 (NM_003462.5), BAP1 (NM_004656.4), SGMS2 (NM_001375905.1), H2AZ1 (NM_002106.4), BSN (NM_003458.4), CTSB (NM_001908.5), FASTK (NM_006712.5). PCBD1 (NM_000281.4), TAF10 (NM_006284.4), CDYL2 (NM_152342.4), SEC11C (NM_033280.4), RRAD (NM_004165.3), B2M (NM_004048.4), MBD6 (NM_052897.4), TRUB2 (NM_015679.3), TPM4 (NM 003290.3). GPX4 (NM_002085.5), MIDN (NM_001388306.1), GATAD2A (NM_001384528.1), RPL13 (NM_000977.4), TUBA1C (NM_032704.5), CDC42EP5 (NM_145057.4), EEF2 (NM_001961.4). NXN (NM_022463.5), CDK2AP2 (NM_005851.5). FTH1 (NM_002032.3), RAB4A (NM_004578.4), DDIT4 (NM_019058.4), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2), RAB31 (NM_006868.4), STAT3 (NM_139276.3). CHTF8 (NM_001039690.5), TNIP2 (NM_024309.4). ATF5(NM_001193646.2), PCBP1 (NM_006196.4), MUC3A (NM_005960.2), RPS9 (NM_001013.4),NDUFA3 (NM_004542.4), MRPL36 (NM_032479.4), FBXL14 (NM_152441.3), RPS7 (NM_001011.4), MALT1 (NM_006785.4), CEBPB (NM_005194.4), PPP1CA (NM_002708.4), PPP1R14B (NM_138689.3), TNFRSF10D (NM_003840.5). EIF1 (NM_005801.4), PITPNA (NM_006224.4), RPL15 (NM_002948.5), HRAS (NM_005343.4), RAB1B (NM_030981.3), ASPHD1 (NM_181718.4), MARCKSL1 (NM_023009.7), TP53I11 (NM_006034.5), CLTB (NM 007097.5). SART1 (NM_005146.5), DRAP1 (NM_006442.4), RPS6KB2 (NM_003952.3), B3GALT6 (NM.080605.4), NUPR1 (NM_012385.3), SLC35A4 (NM_080670.4), WSB2 (NM_018639.5), JUN (NM_002228.4), CD151 (NM_004357.5), HNRNPAO (NM_006805.4), MAF (NM_005360.5), CTNNBIP1 (NM_020248.3), KCTD12 (NM_ 138444.4), CALR (NM_004343.4), ZFPM1 (NM_153813.3), MAF1 (NM_032272.5), FGD6 (NM_018351.4), MEX3D (NM_203304.4). PHLDA2 (NM_003311.4), CLN8 (NM_018941.4), KMT5A (NM_020382.7), PTP4A2 (NM_080391.4), SNRNP35 (NM_022717.4), PDE4B (NM_002600.4), SEPTIN9 (NM_001113491.2), H2BC21 (NM_003528.3), H1-1O (NM_006026.4). P4HB (NM_000918.4), ZFP36L1 (NM_004926.4), COL4A1 (NM_001845.6), PTMA (NM_002823.5), ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), FYB2 (NM_001004303.5), PLA2G2A (NM_001395463.1), H2AX (NM_002105.3), ZDHHC9 (NM_016032.4), Hl-0 (NM_005318.4), SULF2 (NM_001387048.1), VKORC1L1 (NM_173517.6), LAMB3 (NM_000228.3), FLNA (NM_001110556.2), SERPINA1 (NM_000295.5). HNRNPAB (NM_031266.3), GPAA1 (NM_003801.4), H2BC12 (NM_001312653.2), RPL12 (NM_000976.4), NRARP (NM_001004354.3), MAFK (NM_002360.4), GLMP (NM_144580.3), LDB1 (NM_001113407.3), ZNF358 (NM_018083.5), ARHGAP11A (NM_014783.6), UBE2J1 (NM_016021.3). R3HDM4 (NM_138774.4), TGM2 (NM_004613.4), VTRNA1-1 (NR_026703.1), RNY1 (NR_004391.1), RNY3 (NR_004392.1), SAMD5 (NM_001030060.3), H2BC18 (NM_001024599.5), RTL8A (NM_001078172.2), LINC00963 (NR_038955.1), TRAF3IP1 (NM_015650.4). RNF5 (NM_006913.4), NEU1 (NM_000434.4), HLA-C (NM_002117.6), HLA-E (NM_005516.6), AKT1S1 (NM_001098633.4), HMGN1 (NM_004965.7), HLA-A (NM_002116.8). SNORD17 (NR_003045.1), ZNF580 (NM_207115.2), LBH (NM_030915.4), UBXN2B (NM_001077619.2), CEBPD (NM_005195.4), HLA-DPB1 (NM_002121.6), RPL41 (NM_001035267.2), TAPBP (NM_003190.5), TMA7 (NM_015933.6), GPX1 (NM_000581.4), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2),LINGO 127 (NR_015353.2), TMEM250 (NM_152833.3), RBM14 (NM_006328.4), MIF (NM_002415.2), ARPC1A (NM_006409.4), RP11-100N21.1 (AC092597), TMEM141 (NM_032928.4). H2AJ (NM_177925.5), CDK11B (NM_033486.3), SMIM31 (NM_001352885.1), MALAT1 (NR_002819.5), RNY4 (NR_004393.1), HOXAIO(NM_018951.4), LYN (NM_002350.4), RP11-156P1.3, SRSF8 (NM_032102.4), TAF15 (NM 139215.3). CHASERR (NR_037600.1). RP11-290D2.6. ENSG00000275110 (NM_033380.3), FLJ16779, H4C5 (NM_003545.4), LHX1-DT (NR_135671.1), RP11-467J12.4 (NR_136518.1), MYO19 (NM_001163735.2), H4C2 (NM_003544.3), RPll-147L13.il, RP11-84E17.1, where the accession number for each gene is provided in the parenthesis. For purposes of this disclosure, the accession numbers provide identification of the genes and the version of the accession number of any of the kidney injury signature genes (i.e., the number following the period in the accession number) is not particularly important and does not affect the purpose of the disclosed methods.

[0068] In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from TMEM176A (NM_018487.3), TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3), TTC22 (NM_001114108.2), CACNA2D2 (NM_006030.4), NFIX (NM_001365902.3), IL32 (NM_001376923.1), SCMH1(NM_001394311.1), LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3), VIM (NM_003380.5), CD44 (NM_000610.4). SZRD1 (NM_001114600.3), LAMC2 (NM_005562.3), VMP1 (NM_030938.5), BICRA (NM_001394372.1), CTSA (NM_000308.4), SLC9A3R2 (NM_001130012.3), WDR18 (NM_024100.4), TLE2 (NM_003260.5). MTHFD2 (NM_006636.4), PDE4A (NM_001111307.2), PLPP1 (NM_003711.4), BCL3 (NM_005178.5), RAB27A (NM_183235.3), DAZAP1 (NM_018959.4), PTPN18 (NM_014369.4). TPD52 (NM_001025253.3), GNB1 (NM_002074.5), TP53INP2 (NM 021202.3). RIMS1 (NM_014989.7). BAX (NM_138761.4). SH3BP2 (NM_001122681.2), EBF4 (NM_001395167.1), GRAMD1A (NM_020895.5), CDV3 (NM_017548.5), NUBP2 (NM_012225.4), MKNK2 (NM_199054.3), SEC14L2 (NM_012429.5), SLC25A1 (NM_005984.5), GGA1 (NM_013365.5), CYB5R3 (NM_000398.7), TTLL12 (NM_015140.4), CTSZ (NM_001336.4), CDC25B (NM_021873.4), WFDC2 (NM_006103.4), MAP1LC3A (NM_032514.4). LPIN2 (NM_001375808.2), PLP2 (NM_002668.3), TIMP1 (NM_003254.3), MAGED2 (NM_177433.3), NUTF2 (NM_005796.3), CLCN7 (NM_001287.6), MAZ(NM_002383.4), TMC5 (NM_001261841.2), BL0C1S6 (NM_012388.4), MAN2B1 (NM_000528.4), SF3A2 (NM_007165.5), SGTA (NM_003021.4), MED25 (NM_030973.4), SLC1A5 (NM_005628.3), PTPRS (NM_002850.4), KDELR1 (NM_006801.3), RAB3D (NM_004283.4), PLEKHA4 (NM_020904.3), COPE (NM_007263.4), LSR (NM_205834.4), GSK3A (NM_019884.3), ZC3HAV1 (NM_020119.4), MOSPD3 (NM_023948.5), IMPDH1 (NM_000883.4), ZNHIT1 (NM_006349.3). BCL7B (NM_001707.4). LIMK1 (NM_002314.4), PRUNE2 (NM_015225.3), TESK1 (NM_006285.3), EDF1 (NM_003792.4), SFXN3 (NM_030971.6), FBXW4 (NM_022039.4), SLC25A11 (NM_003562.5), RASD1 (NM_016084.5), CCL2 (NM_002982.4), SLC9A3R1 (NM_004252), CRACD (NM_001393381.1), CRYAB (NM_001289808.2), MDK (NM_002391.6), FOXM1 (NM_021953.4), CHPT1 (NM_020244.3), C12orf57 (NM_138425.4), COX6A1 (NM_004373.4), SOD2 (NM_000636.4), PHF1 (NM_024165.3), FBRSL1 (NM_001367871.1), LMNB1 (NM_005573.4), ERGIC1 (NM_001031711.3), GNAI2 (NM_002070.4), MLPH (NM-024101.7). ODC1 (NM_002539.3), SRM (NM_003132.3), Clorf21 (NM_030806.4). TSPAN1 (NM_005727.4), CTSD (NM_001909.5), SPP1 (NM_001040058.2), ELL2 (NM_012081.6), CCDC92 (NM_025140.3), NEK6 (NM_014397.6), TGFB3 (NM_003239.5), OGFRL1 (NM_024576.5), DUSP1 (NM_004417.4), EGR1 (NM_001964.3), SERP1 (NM_014445.4), CLU (NM_001831.4), TNFRSF10B (NM_003842.5), SORBS3 (NM_005775.5). TNFSF10 (NM_003810.4), CALD1 (NM_033138.4), NR4A1 (NM_173157.3), TUBA1B (NM_006082.3), AMD1 (NM_001634.6), MXD4 (NM_006454.3), PMEPA1 (NM_020182.5), KLHDC3 (NM_057161.4), MEA1 (NM_014623.4), CDKN1A (NM_000389.5). DEK (NM_003472.4), MYRF (NM_001127392.3), MT2A (NM_005953.5), SOX9 (NM_000346.4), PPDPF (NM_024299.4), C3 (NM_000064.4), HIVEP3 (NM_024503.5), EMC6 (NM_031298.4), YWHAH (NM_003405.4), ATF4 (NM_182810.3), CDC42EP1 (NM_152243.3). LIF (NM_002309.5). PGAP6 (NM_021259.3), KLHDC7B (NM_138433.5), SSBP4 (NM_032627.5), GDF15 (NM_004864.4), JUND (NM_005354.6), UBE2M (NM_003969.4), EIF3G (NM_003755.5), SLC6A8 (NM_005629.4), TOP2A (NM_001067.4), RARA (NM_000964.4), ITGB4 (NM_000213.5), TRIM47 (NM_033452.3), PLAAT4 (NM_004585.5), CEP20 (NM_144600.4), BTG1 (NM_001731.3), BHLHE40 (NM_003670.3), TMEM106C (NM_001143842.2), LDHA (NM_005566.4), ETS1 (NM_001143820.2), MAP7 (NM_003980.6), NIBAN1 (NM_052966.4), KLF4 (NM_004235.6), ANP32B (NM_006401.3),PARP6 (NM_OO 1323532.2), TACC2 (NM_206862.4), PARP9 (NM_001146105.2), RNF185 (NM_152267.4), CLSTN3 (NM_014718.4), WARSI (NM_004184.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SAMD1 (NM_138352.3), AKT1 (NM_001382430.1), ZNF787 (NM_001002836.4), SH3BGRL3 (NM_031286.4), SYTL1 (NM_001193308.2), MGST3 (NM_004528.4), RABB (NM_002870.5). ARL8A (NM_138795.4), RHOB (NM_004040.4), ARL6IP5 (NM_006407.4), HIGD2A (NM_138820.4), FAM193B (NM_001190946.3), PPP1R18 (NM_133471.4), PRIM2 (NM_000947.5), PNRC1 (NM_006813.3), MKI67 (NM_002417.5), DGKZ (NM_001199267.2), ALDOA (NM_001243177.4), TMCO3 (NM_017905.6), RILPL2 (NM_145058.3), PRDM8 (NM_001099403.2), RASSF3 (NM_178169.4), UBALD1 (NM_145253.3), CMIP (NM_198390.3). CEP112 (NM_001199165.4), ADAMTS1 (NM_006988.5), AZINI (NM_148174.4), HKDC1 (NM_025130.4), RBPMS (NM_001008710.3), MMP14 (NM_004995.4), FZD1 (NM_003505.2), CREB3L1 (NM_052854.4), FAIM (NM_001033031.2). SLC45A3 (NM_033102.3), NBL1 (NM_005380.8). IFNGR2 (NM_005534.4), CSRP1 (NM_004078.3), UBE2Z (NM_023079.5), PTMS (NM_002824.6), RGS12 (NM_001394154.1), ZYX (NM_003461.5), PDE9A (NM_002606.3), S100A1 (NM_006271.2), MGAT4B (NM_014275.5), FMNL3 (NM_175736.5), CXCL16 (NM_001386809.1), SDC3 (NM_014654.4), VCAM1 (NM_001078.4), ATF3 (NM_001674.4), KIF26B (NM_018012.4), LRATD1 (NM_145175.4), H3-3A (NM_002107.7), CCNYL1 (NM_001330218.2), FZD5 (NM_003468.4), IGFBP7 (NM_001553.3), SSR2 (NM_003145.4), ZC3H12A (NM_025079.3), MEAF6 (NM_001270875.3), DNALI1 (NM_003462.5), SGMS2 (NM_001375905.1), H2AZ1 (NM_002106.4), BSN (NM_003458.4). CTSB (NM_001908.5), FASTK (NM_006712.5), PCBD1 (NM_000281.4), TAF10 (NM_006284.4), CDYL2 (NM_152342.4), SEC11C (NM_033280.4), RRAD (NM_004165.3), B2M (NM_004048.4), MBD6 (NM_052897.4), TRUB2 (NM_015679.3), MIDN (NM_001388306.1), TUBA1C (NM_032704.5), CDC42EP5 (NM_145057.4), NXN (NM_022463.5), CDK2AP2 (NM_005851.5), FTH1 (NM_002032.3), RAB4A (NM_004578.4), DDIT4 (NM_019058.4), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2), RAB31 (NM_006868.4), CHTF8 (NM_001039690.5), ATF5 (NM_001193646.2), MUC3A (NM_005960.2), NDUFA3 (NM_004542.4). MRPL36 (NM_032479.4), FBXL14 (NM_152441.3). MALT1 (NM_006785.4), CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), HRAS(NM_005343.4), R AB 1 B (NM_030981.3), ASPHD1 (NM_181718.4), MARCKSL1 (NM_023009.7), TP53I11 (NM_006034.5), CLTB (NM_007097.5), RPS6KB2 (NM_003952.3), B3GALT6 (NM_080605.4), NUPR1 (NM_012385.3), SLC35A4 (NM_080670.4), WSB2 (NM_018639.5), JUN (NM_002228.4), CD151 (NM_004357.5), HNRNPAO (NM_006805.4), MAF (NM_005360.5), CTNNBIP1 (NM_020248.3), KCTD12 (NM_ 138444.4), ZFPM1 (NM 153813.3). FGD6 (NM_018351.4), MEX3D (NM_203304.4), PHLDA2 (NM_003311.4), CLN8 (NM_018941.4), KMT5A (NM_020382.7), SNRNP35 (NM_022717.4), PDE4B (NM_002600.4), H2BC21 (NM_003528.3), H1-1O (NM_006026.4), P4HB (NM_000918.4), ZFP36L1 (NM_004926.4), COL4A1 (NM_001845.6), ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), FYB2 (NM_001004303.5), PLA2G2A (NM_001395463.1), H2AX (NM_002105.3). ZDHHC9 (NM_016032.4), Hl-0 (NM_005318.4), SULF2 (NM_001387048.1), VK0RC1L1 (NM_173517.6), LAMB3 (NM_000228.3), FLNA (NM_001110556.2), SERPINA1 (NM_000295.5), GPAA1 (NM_003801.4), H2BC12 (NM_001312653.2), RPL12 (NM_000976.4). NRARP (NM_001004354.3), MAFK (NM_002360.4), GLMP (NM_144580.3), ZNF358 (NM_018083.5), ARHGAP11A(NM_014783.6), UBE2J1 (NM_016021.3), R3HDM4 (NM_138774.4), TGM2 (NM_004613.4), VTRNA1-1 (NR_026703.1), RNY1 (NR_004391), RNY3 (NR_004392.1), SAMD5 (NM_001030060.3), H2BC18 (NM_001024599.5), RTL8A (NM_001078172.2), LINC00963 (NR_038955.1), RNF5 (NM_006913.4). NEU1 (NM_000434.4), HLA-C (NM_002117.6), HLA-E (NM_005516.6), AKT1S1 (NM_001098633.4), HMGN1 (NM_004965.7), HLA-A (NM_002116.8), SNORD17 (NR_003045.1), ZNF580 (NM_207115.2), LBH (NM_030915.4), CEBPD (NM_005195.4), HLA-DPB1 (NM_002121.6), TAPBP (NM_003190.5), GPX1 (NM_000581.4), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), LINC01278, TMEM250 (NM_152833.3), RBM14 (NM_006328.4), MIF (NM 002415.2), ARPC1A (NM_006409.4), RP11-100N21.1 (AC092597). TMEM141 (NM_032928.4), H2AJ (NM_177925.5), SMIM31 (NM_001352885.1), MALAT1 (NR_002819.5), RNY4 (NR_004393.1), HOXAIO (NM_018951.4), LYN (NM_002350.4), RP11-156P1.3, CHASERR (NR_037600.1), RP11-290D2.6, ENSG00000275110 (NM_033380.3), FLJ16779, H4C5 (NM_003545.4), LHX1-DT (NR_135671.1), RP11-467J12.4, MYO19 (NM_001163735.2). H4C2 (NM_003544.3), RPll-147L13.il, and RP11-84E17.1. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of kidneyinjury signature genes selected from TMEM176A (NM_018487.3), TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3), CACNA2D2 (NM_006030.4), NFIX (NM_001365902.3), IL32 (NM_001376923.1), LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3), CD44 (NM_000610.4), LAMC2 (NM_005562.3), CTSA (NM_000308.4), MTHFD2 (NM_006636.4), PDE4A (NM_001111307.2), PLPP1 (NM_003711.4). BCL3 (NM_005178.5), RAB27A (NM_183235.3), RIMS1 (NM_014989.7), EBF4 (NM_001395167.1), SEC14L2 (NM_012429.5), CDC25B (NM_021873.4), WFDC2 (NM_006103.4), MAP1LC3A (NM_032514.4). PLP2 (NM_002668.3). TIMP1 (NM_003254.3), MAZ (NM_002383.4), TMC5 (NM.001261841.2), RAB3D (NM_004283.4), MOSPD3 (NM_023948.5), PRUNE2 (NM_015225.3), SFXN3 (NM_030971.6), RASD1 (NM_016084.5), CCL2 (NM_002982.4), CRACD (NM_001393381.1), CRYAB (NM_001289808.2). MDK (NM_002391.6), FOXM1 (NM_021953.4), CHPT1 (NM_020244.3), LMNB1 (NM_005573.4), TSPAN1 (NM_005727.4), SPP1 (NM_001040058.2), TGFB3 (NM_003239.5), OGFRL1 (NM_024576.5). EGR1 (NM_001964.3), CLU (NM_001831.4), SORBS3 (NM_005775.5), TNFSF10 (NM_003810.4), PMEPA1 (NM_020182.5), MYRF (NM_001127392.3), MT2A (NM_005953.5), C3 (NM_000064.4), CDC42EP1 (NM_152243.3), LIF (NM_002309.5), KLHDC7B (NM_138433.5), SLC6A8 (NM_005629.4), TOP2A (NM_001067.4), TRIM47 (NM_033452.3), PLAAT4 (NM_004585.5), NIBAN1 (NM_052966.4), KLF4 (NM_004235.6), CLSTN3 (NM_014718.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SYTL1 (NM_001193308.2), ARL6IP5 (NM_006407.4), PPP1R18 (NM_133471.4), PRIM2 (NM_000947.5), MKI67 (NM_002417.5), PRDM8 (NM_001099403.2), AD AMTS 1 (NM_006988.5), HKDC1 (NM_025130.4). MMP14 (NM_004995.4), CREB3L1 (NM_052854.4), SLC45A3 (NM_033102.3), NBL1 (NM_005380.8), ZYX (NM_003461.5), FMNL3 (NM_175736.5), CXCL16 (NM_001386809.1), VCAM1 (NM_001078.4). ATF3 (NM_001674.4). LRATD1(NM_145175.4), FZD5 (NM_003468.4), SGMS2 (NM_001375905.1), BSN (NM_003458.4), TAF10 (NM_006284.4), RRAD (NM_004165.3), B2M (NM_004048.4), CDC42EP5 (NM_145057.4), NXN (NM_022463.5), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2), MUC3A (NM_005960.2), NDUFA3 (NM_004542.4), CEBPB (NM_005194.4). TNFRSF10D (NM_003840.5), ASPHD1 (NM_181718.4), TP53I11 (NM_006034.5), B3GALT6 (NM_080605.4), NUPR1 (NM_012385.3), JUN (NM_002228.4),CD151 (NM_004357.5), ZFPM1 (NM_153813.3), MEX3D (NM_203304.4), PHLDA2 (NM_003311.4), SNRNP35 (NM_022717.4), PDE4B (NM_002600.4), C0L4A1(NM_OO 1845.6). ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), PLA2G2A (NM_001395463.1), H2AX (NM_002105.3), LAMB3 (NM_000228.3), SERPINA1 (NM_000295.5), NRARP (NM_001004354.3), MAFK (NM_002360.4), GLMP (NM 144580.3). ARHGAP11A (NM_014783.6). TGM2 (NM_004613.4), VTRNA1-1 (NR_026703.1), RNY1 (NR_004391), SAMD5 (NM_001030060.3), HLA-C (NM_002117.6), HLA-A (NM_002116.8), SN0RD17 (NR_003045.1), ZNF580 (NM_207115.2), HLA-DPB1 (NM_002121.6), TAPBP (NM_003190.5), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), RBM14 (NM_006328.4), SMIM31 (NM_001352885.1), MALAT1 (NR_002819.5), RNY4 (NR_004393.1), HOXAIO(NM_018951.4), LYN (NM_002350.4), FLJ16779, and RP11-467J12.4. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from IL32 (NM_001376923.1). LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3), BCL3 (NM_005178.5), CDC25B (NM_021873.4), MAZ (NM_002383.4), RAB3D (NM_004283.4), PRUNE2 (NM_015225.3), RASD1 (NM_016084.5), SORBS3 (NM_005775.5), CDC42EP1 (NM_152243.3), PLAAT4 (NM_004585.5), SYTL1 (NM_001193308.2), ADAMTS1 (NM_006988.5), NBL1 (NM_005380.8), ZYX (NM_003461.5). CXCL16 (NM_001386809.1), LRATD1 (NM_145175.4), FZD5 (NM_003468.4), TAF10 (NM_006284.4), RRAD (NM_004165.3), CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), JUN (NM_002228.4), ZFPM1 (NM_153813.3), SNRNP35 (NM_022717.4), SERPINA1 (NM_000295.5), MAFK (NM_002360.4), ARHGAP11A (NM_014783.6), TGM2 (NM_004613.4), VTRNA1-1 (NR_026703.1), RNY1 (NR_004391), HLA-DPB1 (NM_002121.6), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), and RNY4 (NR_004393.1). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from RASD1 (NM_016084.5), ERGIC1 (NM_001031711.3), MLPH (NM_024101.7), ODC1 (NM_002539.3), SOX9 (NM_000346.4), PPDPF (NM_024299.4), CDC42EP1 (NM_152243.3), JUND (NM_005354.6), NBL1 (NM_005380.8), TAF10 (NM_006284.4), MIDN (NM_001388306.1), CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), JUN (NM_002228.4), HNRNPAO (NM_006805.4), RPL12 (NM_000976.4), MAFK (NM_002360.4), HLA-DPB1 (NM_002121.6), andRNY4 (NR_004393.1). In someembodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from RASD1 (NM_016084.5), CDC42EP1 (NM_152243.3), NBL1 (NM_005380.8), TAF10 (NM_006284.4). CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), JUN (NM_002228.4), MAFK (NM_002360.4), HLA-DPB1 (NM_002121.6), and RNY4 (NR_004393.1). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from RASD1 (NM_016084.5). NBL1 (NM_005380.8), CEBPB (NM_005194.4), HLA-DPB1 (NM_002121.6), and RNY4 (NR_004393.1). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CEBPB (NM_005194.4), HLA-DPB1 (NM_002121.6), and RNY4 (NR_004393.1).

[0069] In some embodiments, the at least one cfRNA comprises a cfRNA of a kidney injury signature gene with a decreased level as compared to control being indicative of AKE In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from SPAG9 (NM_001130528.3), IKZF2 (NM_001387220.1), RFC1 (NM_002913.5), ZFYVE16 (NM_001284236.3), LSG1 (NM_018385.3), CAPG (NM_001747.4), PUM2 (NM_015317.5), PKN2 (NM_006256.4), TBC1D1 (NM_001396959.1), NGEF (NM_019850.3), EML1 (NM_004434.3), KDM5A (NM_001042603.3), TOP2B (NM_001330700.2), FDFT1 (NM_004462.5), SMARCA2 (NM_003070.5), HSP90AA1 (NM_005348.4), NCOA1 (NM_003743.5), EPB41L1 (NM_012156.2), KIF9 (NM_182902.4), C20orfl94 (NM_001009984), TRPM7 (NM_017672.6), MIEF1 (NM_019008.6), GABRE (NM_004961.4). INTS6 (NM-012141.3), HERC1 (NM_003922.4), AVL9 (NM_015060.3), PIK3CG (NM_001282426.2), TAX1BP1 (NM_006024.7), ANKMY2 (NM_020319.3), KANK1 (NM_015158.5). TASOR2 (NM_001321783.2), INTS2 (NM_001351695.2). PRKAR2A (NM_004157.4), PARD3B (NM_001302769.2), CASP8AP2 (NM_001137667.2), FBXL5 (NM_012161.4), HSDL2 (NM_032303.5), DNAL1 (NM_031427.4), AFTPH (NM_203437.4), PPP1R3C (NM 005398.7). ARFGEF2 (NM_006420.3). CNOT1 (NM_016284.5), ICE2 (NM_024611.6), THEM6 (NM_016647.3), OSBPL2 (NM_144498.4), PPIL4 (NM_139126.4), DIAPH1 (NM_005219.5), EXOC4 (NM_021807.4), PPARG (NM_138711.6), KRBA1 (NM_001290187.2), CTIF (NM_014772.3), APC (NM_000038.6), MDM2 (NM_002392.6), GCC2 (NM_181453.4), EGF (NM_001963.6), ESCO1 (NM.052911.3), SHQ1 (NM_018130.3), PIK3R1 (NM_181523.3), PPIP5K2 (NM_001276277.3). MPP7 (NM_001318170.2), CCT5 (NM_012073.5), KCNJ1 (NM_153766.3), RABGAP1L (NM_001366446.1), EPG5(NM_020964.3), ZNF117 (NM_015852.5), CCDC174 (NM_016474.5), ZFYVE9 (NM_004799.4), EPB41 (NM_OO 1376013.1), CLIC6 (NM_053277.3), ACOX1 (NM_004035.7), MYSM1 (NM_001085487.3), ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), GNL3 (NM_014366.5), TASOR (NM_001365635.2), HPGD (NM_000860.6), ICE1 (NM_015325.3), ARHGAP12 (NM_018287.7), ABRAXAS2 (NM_032182.4), CLPX (NM_006660.5), SGSM1 (NM 001098497.3), TEF (NM_003216.4), SRP68 (NM_014230.4), C2CD3 (NM_001286577.2), HSPA4 (NM_002154.4), ZNF439 (NM_001348719.2), TNKS (NM_003747.3), PSMD1 (NM_002807.4), CEP97 (NM_024548.4), ZNF397 (NM_001135178.3), PLCD1 (NM_006225.4), NBR1 (NM_005899.5), PIK3R4 (NM_014602.3), ZNF420 (NM_144689.5), PEG3 (NM_006210.3), ITSN2 (NM_006277.3), TTC37 (NM_014639). CTR9 (NM_014633.5), PHACTR4 (NM_001048183.3), ASAH2B (NM_001321958.2), ZDBF2 (NM_020923.3), RNU6-36P, ZNF134 (NM_003435.5), LINC01363 (NR_110811.1), LINC02016, RP1-17K7.2 (AL035078), GAN (NM_022041.4), SRGAP2 (NM_015326.5), SYNRG (NM_007247.6), XXbac-BPG283O16.9, and RP11-157L3.14 where the accession number for each gene is provided in the parenthesis. For purposes of this disclosure, the accession numbers provide identification of the genes and the version of the accession number of any of the kidney injury signature genes (i.e., the number following the period in the accession number) is not particularly important and does not affect the purpose of the disclosed methods. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected fromIKZF2 (NM_001387220.1), LSG1 (NM_018385.3), CAPG (NM_001747.4), PKN2 (NM_006256.4), NGEF (NM_019850.3), EML1 (NM_004434.3), KIF9 (NM_182902.4). GABRE (NM_004961.4), PIK3CG (NM_001282426.2), ANKMY2 (NM_020319.3), INTS2 (NM_001351695.2), PPP1R3C (NM_005398.7), ICE2 (NM_024611.6), THEM6 (NM_016647.3), PPARG (NM_138711.6), KRBA1 (NMJ101290187.2), APC (NM 000038.6). EGF (NM_001963.6), SHQ1 (NM_018130.3). MPP7 (NM_001318170.2), KCNJ1 (NM_153766.3), ZNF117 (NM_015852.5), CLIC6 (NM_053277.3), ACOX1 (NM_004035.7), ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), HPGD (NM_000860.6), ABRAXAS2 (NM_032182.4), SGSM1 (NM_001098497.3), TEF (NM_003216.4), ZNF439 (NM_001348719.2), CEP97 (NM_024548.4), PLCD1 (NM_006225.4), PIK3R4(NM_014602.3). ZNF420 (NM_144689.5), PEG3 (NM_006210.3), ASAH2B (NM_001321958.2), ZDBF2 (NM_020923.3), RNU6-36P, ZNF134 (NM_003435.5),LINGO 1363 (NR_110811.1), LINC02016, RP1-17K7.2, GAN (NM_022041.4), SRGAP2 (NM_015326.5), XXbac-BPG283O16.9, and RP11-157L3.14. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from SPAG9 (NM_001130528.3), PKN2 (NM_006256.4), TBC1D1 (NM_001396959.1), NGEF (NM_019850.3), NCOA1 (NM_003743.5), C20orfl94, INTS2 (NM_001351695.2), FBXL5 (NM_012161.4). OSBPL2 (NM_144498.4). PPARG (NM_138711.6), CTIF (NM_014772.3), APC (NM_000038.6), EGF (NM_001963.6), ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), ICE1 (NM_015325.3), PIK3R4 (NM_014602.3), RNU6-36P, LINC02016, and RP1-17K7.2. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from NCOA1 (NM_003743.5), FBXL5 (NM_012161.4), CTIF (NM_014772.3), EGF (NM_001963.6). ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), LINC02016, and RP1-17K7.2. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from EGF (NM_001963.6), KCNJ3 (NM_002239.4), LINC02016. and RP1-17K.7.2. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from EGF (NM_001963.6) and KCNI3 (NM_002239.4).

[0070] In some embodiments, the at least one cfRNA comprises a cfRNA of at least two signature genes, where an increase in level of one signature gene as compared to a control and the decrease in the level of another signature gene as compared to control is indicative of an ATIN etiology. In such embodiments, the at least one signature gene where an increase in level is indicative of an ATIN etiology is selected from LASPI (NM_006148.4), TMEM176A (NM_018487.3), TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3). TTC22 (NM_001114108.2). CACNA2D2 (NM_006030.4). NFIX (NM_001365902.3), IL32 (NM_001376923.1), SCMH1 (NM_001394311.1), PTBP1 (NM_002819.5), LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3), SEC63 (NM_007214.5), VIM (NM_003380.5). CD44 (NM_000610.4), TMSB10 (NM_021103.4), SZRD1 (NM_001114600.3), LAMC2 (NM_005562.3), YBX3 (NM_003651.5), VMP1 (NM_030938.5), BICRA (NM_001394372.1), RPL18 (NM_000979.4), CTSA (NM_000308.4), SLC9A3R2 (NM_001130012.3), WDR18 (NM_024100.4), TLE2 (NM_003260.5), MTHFD2 (NM_006636.4), PDE4A (NM_001111307.2), PLPP1(NM-003711.4). BCL3 (NM_005178.5), RAB27A (NM_183235.3), DAZAP1 (NM_018959.4), PTPN18 (NM_014369.4), ACTB (NM_001101.5), TPD52 (NM_001025253.3), ARAF(NM_001654.5), GNB1 (NM_002074.5), TP53INP2 (NM_021202.3), RIMS1 (NM_014989.7), RPS5 (NM_001009.4), BAX (NM_138761.4), SH3BP2 (NM_001122681.2), GNAS (NM_000516.7). EBF4 (NM_001395167.1), RPLPO (NM_001002.4), GRAMD1A (NM_020895.5), CDV3 (NM_017548.5), ALKBH5 (NM_017758.4), NUBP2 (NM_012225.4), SETD1A (NM_014712.3), CIRBP (NM_001300829.2), MKNK2 (NM_199054.3), SEC14L2 (NM 012429.5). SLC25A1 (NM_005984.5), GGA1 (NM_013365.5), CYB5R3 (NM_000398.7), TTLL12 (NM_015140.4), CTSZ (NM_001336.4), CDC25B (NM_021873.4), WFDC2 (NM_006103.4). MAP1LC3A (NM_032514.4). LPIN2 (NM_001375808.2), PLP2 (NM_002668.3), TIMP1 (NM_003254.3), MAGED2 (NM_177433.3), NUTF2 (NM_005796.3), CLCN7 (NM_001287.6), UBE2I (NM_003345.5), MAZ (NM_002383.4), TMC5 (NM_001261841.2). BL0C1S6 (NM_012388.4), PPP2CB (NM_001009552.2), MAN2B1 (NM_000528.4), NUCB1 (NM_006184.6), SF3A2 (NM_007165.5), OAZ1 (), TLE5 (NM_001130.6), SGTA (NM_003021.4), MED25 (NM_030973.4), FBL (NM_001436.4), SLC1A5 (NM_005628.3), CCDC9 (NM_015603.3), PTPRS (NM_002850.4), KDELR1 (NM_006801.3), RAB3D (NM_004283.4), PLEKHA4 (NM_020904.3), RPL18A (NM_000980.4), COPE (NM_007263.4), LSR (NM_205834.4), GSK3A (NM_019884.3), ZC3HAV1 (NM_020119.4), MOSPD3 (NM_023948.5), IMPDH1 (NM_000883.4), ZNHIT1 (NM_006349.3), PRKAG2 (NM_016203.4), BCL7B (NM_001707.4), LIMK1 (NM_002314.4), PRUNE2 (NM_015225.3), TESK1 (NM_006285.3), EDF1 (NM_003792.4), SFXN3(NM-030971.6), FBXW4 (NM_022039.4), CCNY (NM_145012.6), RPL28 (NM_000991.5), CASC3 (NM_007359.5), PFN1 (NM_005022.4), SLC25A11 (NM_003562.5), RASD1 (NM_016084.5). CCL2 (NM_002982.4), SLC9A3R1 (NM_004252), SLAIN2 (NM_020846.2), CRACD (NM_001393381.1), CRYAB (NM_001289808.2), MDK (NM_002391.6), FOXM1 (NM_021953.4), GAPDH (NM_002046.7), CHPT1 (NM_020244.3), ATN1 (NM_001940.4), C12orf57 (NM_138425.4), COX6A1 (NM_004373.4), TDP2 (NM_016614.3), SOD2 (NM_000636.4), TRIM38 (NM_006355.5), PHF1 (NM_024165.3), FBRSL1(NM_001367871.1), LMNB1 (NM_005573.4), SKP1 (NM_170679.3), ERGIC1(NM-001031711.3), GNAI2 (NM_002070.4), RPS15 (NM_001018.5), MLPH (NM_024101.7), ODC1 (NM_002539.3), SRSF4 (NM_005626.5), SRM (NM_003132.3), Clorf21 (NM_030806.4). TSPAN1 (NM_005727.4), CTSD (NM_001909.5), SPP1 (NM_001040058.2), ELL2 (NM_012081.6), CCDC92 (NM_025140.3), NEK6 (NM_014397.6), TGFB3(NM_003239.5), OGFRL1 (NM_024576.5), DUSP1 (NM_004417.4), EGR1 (NM_001964.3), SERP1 (NM_014445.4), CLU (NM.001831.4), TNFRSF10B (NM_003842.5), SORBS3 (NM_005775.5). TNFSF10 (NM_003810.4), KIAA1191 (NM_020444.5), CALD1 (NM_033138.4), NR4A1 (NM_173157.3), TUBA1B (NM_006082.3), AMD1 (NM_001634.6), MXD4 (NM_006454.3), PMEPA1 (NM_020182.5), KLHDC3 (NM_057161.4), MEA1 (NM_014623.4), CDKN1A (NM_000389.5), DEK (NM_003472.4), MYRF (NM_001127392.3), MT2A (NM_005953.5), S0X9 (NM_000346.4), PPDPF (NM_024299.4), C3 (NM_000064.4), CENPB (NM_001810.6), CAPNS1 (NM_001749.4), HIVEP3 (NM_024503.5), EMC6 (NM_031298.4), YWHAH (NM_003405.4), ATF4 (NM_182810.3), CDC42EP1 (NM_152243.3), LIF (NM_002309.5), BCL2L2 (NM_004050.5), PGAP6 (NM_021259.3), PRKCSH (NM_001289104.2), ACTN4 (NM_004924.6), KLHDC7B (NM_138433.5), SSBP4 (NM_032627.5), GDF15 (NM_004864.4), JUND (NM_005354.6), UBE2M (NM_003969.4), EIF3G (NM_003755.5), SLC6A8 (NM_005629.4), UBE2D2 (NM_003339.3), TOP2A (NM_001067.4). RARA (NM_000964.4), ITGB4 (NM_000213.5), WBP2 (NM_012478.4), TRIM47 (NM_033452.3), FLOT2 (NM_004475.3), TCEAL4 (NM_001006935.3), PLAAT4 (NM_004585.5), CEP20 (NM_144600.4), BTG1 (NM_001731.3), BHLHE40 (NM_003670.3), TMEM106C (NM_001143842.2), LDHA (NM_005566.4), ETS1 (NM_001143820.2), OS9 (NM_006812.4), MAP7 (NM_003980.6), NIBAN1 (NM_052966.4), ODF2 (NM_001351578.2), KLF4 (NM_004235.6), ANP32B (NM_006401.3), FLOT1 (NM_005803.4), PARP6 (NM_001323532.2), TACC2 (NM_206862.4), PARP9 (NM_001146105.2), RNF185 (NM_152267.4), CLSTN3 (NM_014718.4), WARSI (NM_004184.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SAMD1 (NM_138352.3), AKT1 (NM_001382430.1), ZNF787 (NM_001002836.4), RPL13A (NM_012423.4), SH3BGRL3 (NM_031286.4), SYTL1 (NM_001193308.2), MGST3 (NM_004528.4). HDGF (NM_004494.3). RABB (NM_002870.5). ARL8A (NM_138795.4), RHOB (NM_004040.4), RPL32 (NM_000994.4), ARL6IP5 (NM_006407.4), RPS3A (NM_001006.5), TRIM41 (NM_033549.5), HIGD2A (NM_138820.4), FAM193B(NM_001190946.3), PPP1R18 (NM_133471.4), PRIM2 (NM_000947.5), PNRC1 (NM_006813.3), RPL10 (NM_006013.5), RPL7A (NM_000972.3), MKI67 (NM_002417.5), DGKZ (NM_001199267.2), ALDOA (NM_001243177.4), TMCO3 (NM_017905.6), RILPL2 (NM_145058.3), PRDM8 (NM_001099403.2), RASSF3 (NM_178169.4), UBALD1(NM_145253.3), CMIP (NM_198390.3), CEP112 (NM_001199165.4), ADAMTS1 (NM_006988.5), AZINI (NM_148174.4), HKDC1 (NM_025130.4), FBRS (NM_001105079.3), RBPMS (NM_001008710.3). MMP14 (NM_004995.4), FZD1 (NM_003505.2), CREB3L1 (NM_052854.4), FAIM (NM_001033031.2), SLC45A3 (NM_033102.3), NBL1 (NM_005380.8), FBXW5 (NM_018998.4), IFNGR2 (NM_005534.4), CSRP1 (NM_004078.3), UBE2Z (NM_023079.5), PTMS (NM_002824.6), RGS12 (NM_001394154.1), ZYX (NM_003461.5), CALM3 (NM_005184.4), PDE9A (NM_002606.3), NDUFV3 (NM_021075.4), S100A1 (NM_006271.2), MGAT4B (NM_014275.5), RPL8 (NM_001317782.2), FMNL3 (NM_175736.5), CXCL16 (NM_001386809.1), RPL29 (NM_000992.3), SDC3(NM_014654.4), VCAM1 (NM_001078.4), ATF3 (NM_001674.4), Clorf 115 (NM_024709.5), KIF26B (NM_018012.4), LRATD1 (NM_145175.4). H3-3A (NM_002107.7), CCNYL1 (NM_001330218.2), FZD5 (NM_003468.4), IGFBP7 (NM_001553.3), SSR2 (NM_003145.4), ZC3H12A (NM_025079.3), MEAF6 (NM_001270875.3), DNALI1 (NM_003462.5), BAP1 (NM_004656.4), SGMS2 (NM_001375905.1), H2AZ1 (NM_002106.4), BSN (NM_003458.4), CTSB (NM_001908.5), FASTK (NM_006712.5), PCBD1 (NM_000281.4), TAF10 (NM_006284.4), CDYL2 (NM_152342.4), SEC11C (NM_033280.4), RRAD (NM_004165.3), B2M (NM_004048.4), MBD6 (NM_052897.4), TRUB2 (NM_015679.3), TPM4 (NM_003290.3), GPX4 (NM_002085.5), MIDN (NM_001388306.1), GATAD2A (NM_001384528.1), RPL13 (NM_000977.4), TUBA1C (NM_032704.5), CDC42EP5 (NM_145057.4), EEF2 (NM_001961.4), NXN (NM_022463.5), CDK2AP2 (NM_005851.5), FTH1 (NM_002032.3), RAB4A (NM_004578.4), DDIT4 (NM_019058.4), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2), RAB31 (NM_006868.4), STAT3 (NM_139276.3), CHTF8 (NM_001039690.5), TNIP2 (NM_024309.4), ATF5 (NM_001193646.2), PCBP1 (NM_006196.4), MUC3A (NM_005960.2), RPS9 (NM_001013.4), NDUFA3 (NM_004542.4), MRPL36 (NM_032479.4). FBXL14 (NM_152441.3), RPS7 (NM_001011.4), MALT1 (NM_006785.4), CEBPB (NM_005194.4), PPP1CA (NM_002708.4), PPP1R14B (NM_138689.3), TNFRSF10D (NM_003840.5), EIF1 (NM_005801.4), PITPNA (NM_006224.4), RPL15 (NM_002948.5), HRAS (NM_005343.4), RAB1B (NM_030981.3), ASPHD1 (NM_181718.4), MARCKSL1 (NM_023009.7), TP53I11 (NM_006034.5), CLTB (NM_007097.5). SART1 (NM_005146.5), DRAP1 (NM_006442.4), RPS6KB2 (NM_003952.3), B3GALT6 (NM_080605.4), NUPR1 (NM_012385.3), SLC35A4 (NM_080670.4), WSB2(NM_018639.5), JUN (NM_002228.4), CD151 (NM_004357.5), HNRNPAO (NM_006805.4), MAF (NM_005360.5), CTNNBIP1 (NM_020248.3), KCTD12 (NM_ 138444.4), CALR (NM_004343.4). ZFPM1 (NM_153813.3), MAF1 (NM_032272.5). FGD6 (NM_018351.4), MEX3D (NM_203304.4), PHLDA2 (NM_003311.4), CLN8 (NM_018941.4), KMT5A (NM_020382.7), PTP4A2 (NM_080391.4), SNRNP35 (NM_022717.4), PDE4B (NM 002600.4). SEPTIN9 (NM_001113491.2), H2BC21 (NM_003528.3), H1-1O (NM_006026.4), P4HB (NM_000918.4), ZFP36L1 (NM_004926.4), COL4A1 (NM_001845.6), PTMA (NM_002823.5), ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), FYB2 (NM_001004303.5), PLA2G2A (NM_001395463.1), H2AX (NM_002105.3), ZDHHC9 (NM_016032.4), Hl-0 (NM_005318.4), SULF2 (NM_001387048.1), VKORC1L1 (NM_173517.6). LAMB3 (NM_000228.3), FLNA (NM_001110556.2), SERPINA1 (NM_000295.5), HNRNPAB (NM_031266.3), GPAA1 (NM_003801.4), H2BC12 (NM_001312653.2), RPL12 (NM_000976.4), NRARP (NM_001004354.3), MAFK (NM_002360.4). GLMP (NM_144580.3), LDB1 (NM_001113407.3), ZNF358 (NM_018083.5), ARHGAP11A (NM_014783.6), UBE2J1 (NM_016021.3), R3HDM4 (NM_138774.4), TGM2 (NM_004613.4), VTRNA1-1 (NR_026703.1), RNY1 (NR_004391.1), RNY3 (NR_004392.1), SAMD5 (NM_001030060.3), H2BC18 (NM_001024599.5), RTL8A (NM_001078172.2), LINC00963 (NR_038955.1), TRAF3IP1 (NM_015650.4), RNF5 (NM_006913.4), NEU1 (NM_000434.4), HLA-C (NM_002117.6), HLA-E (NM_005516.6), AKT1S1 (NM_001098633.4), HMGN1 (NM_004965.7), HLA-A (NM_002116.8), SNORD17 (NR_003045.1), ZNF580 (NM_207115.2), LBH (NM_030915.4), UBXN2B (NM_001077619.2), CEBPD (NM_005195.4), HLA-DPB1 (NM_002121.6). RPL41 (NM_001035267.2), TAPBP (NM_003190.5), TMA7 (NM_015933.6), GPX1 (NM_000581.4), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), LINC0127 (NR 015353.2). TMEM250 (NM_152833.3), RBM14 (NM_006328.4), MIF (NM_002415.2), ARPC1A (NM_006409.4), RP11-100N21.1 (AC092597), TMEM141 (NM_032928.4), H2AJ (NM_177925.5), CDK11B (NM_033486.3), SMIM31 (NM_001352885.1), MALAT1 (NR_002819.5), RNY4 (NR_004393.1), HOXAIO(NM_018951.4), LYN (NM_002350.4), RP11-156P1.3, SRSF8 (NM_032102.4), TAF15 (NM_139215.3). CHASERR (NR_037600.1). RP11-290D2.6. ENSG00000275110 (NM_033380.3), FLJ16779, H4C5 (NM_003545.4), LHX1-DT (NR_135671.1), RP11-467J12.4(NR_136518.1), MY019 (NM_OO 1163735.2), H4C2 (NM_003544.3), RPll-147L13.il, and RP11-84E17.1, and the at least one signature gene with a decrease in level being indicative of an ATIN etiology is selected from SPAG9 (NM_001130528.3), IKZF2 (NM_001387220.1), RFC1 (NM_002913.5), ZFYVE16 (NM_001284236.3), LSG1 (NM_018385.3), CAPG(NM_001747.4), PUM2 (NM_015317.5), PKN2 (NM_006256.4). TBC1D1 (NM_001396959.1), NGEF (NM_019850.3). EML1 (NM_004434.3), KDM5A (NM_001042603.3), TOP2B (NM_001330700.2), FDFT1 (NM_004462.5), SMARCA2 (NM_003070.5), HSP90AA1 (NM_005348.4), NC0A1 (NM_003743.5), EPB41L1 (NM_012156.2), KIF9 (NM_182902.4), C20orfl94 (NM_001009984), TRPM7 (NM_017672.6), MIEF1 (NM_019008.6), GABRE (NM_004961.4), INTS6 (NM_012141.3), HERC1 (NM_003922.4), AVL9 (NM_015060.3), PIK3CG (NM_001282426.2), TAX1BP1 (NM_006024.7). ANKMY2 (NM_020319.3), KANK1 (NM_015158.5), TASOR2 (NM_001321783.2), INTS2 (NM_001351695.2), PRKAR2A (NM_004157.4), PARD3B (NM_001302769.2), CASP8AP2 (NM_001137667.2), FBXL5 (NM_012161.4). HSDL2 (NM_032303.5), DNAL1 (NM_031427.4), AFTPH (NM_203437.4). PPP1R3C (NM_005398.7), ARFGEF2 (NM_006420.3), CNOT1 (NM_016284.5), ICE2 (NM_024611.6), THEM6 (NM_016647.3), OSBPL2 (NM_144498.4), PPIL4 (NM_139126.4), DIAPH1 (NM_005219.5), EXOC4 (NM_021807.4), PPARG (NM_138711.6), KRBA1 (NM_001290187.2), CTIF (NM_014772.3), APC (NM_000038.6), MDM2 (NM_002392.6), GCC2 (NM_181453.4), EGF (NM_001963.6), ESCO1 (NM_052911.3), SHQ1 (NM_018130.3), PIK3R1 (NM_181523.3), PPIP5K2 (NM_001276277.3), MPP7 (NM_001318170.2), CCT5 (NM_012073.5), KCNJ1 (NM_153766.3), RABGAP1L (NM_001366446.1), EPG5 (NM_020964.3). ZNF117 (NM_015852.5), CCDC174 (NM_016474.5), ZFYVE9 (NM_004799.4), EPB41 (NM_001376013.1), CLIC6 (NM_053277.3), ACOX1 (NM_004035.7), MYSM1 (NM_001085487.3), ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), GNL3 (NM_014366.5). TASOR (NM_001365635.2), HPGD (NM_000860.6), ICE1 (NM_015325.3). ARHGAP12 (NM_018287.7), ABRAXAS2 (NM_032182.4), CLPX (NM_006660.5), SGSM1 (NM_001098497.3), TEF (NM_003216.4), SRP68 (NM_014230.4), C2CD3 (NM_001286577.2), HSPA4 (NM_002154.4), ZNF439 (NM_001348719.2), TNKS (NM_003747.3), PSMD1 (NM_002807.4), CEP97 (NM_024548.4), ZNF397 (NM_001135178.3). PLCD1 (NM_006225.4), NBR1 (NM_005899.5), PIK3R4 (NM_014602.3), ZNF420 (NM_144689.5), PEG3 (NM_006210.3), ITSN2 (NM_006277.3), TTC37(NM_014639), CTR9 (NM_014633.5), PHACTR4 (NM_OO 1048183.3), ASAH2B (NM_001321958.2), ZDBF2 (NM_020923.3), RNU6-36P, ZNF134 (NM_003435.5), LINC01363 (NR_110811.1), LINC02016. RP1-17K7.2 (AL035078), GAN (NM_022041.4), SRGAP2 (NM_015326.5), SYNRG (NM_007247.6), XXbac-BPG283O16.9, and RP11-157L3.14.

[0071] In some embodiments, the step of measuring the level of at least one cfRNA comprises performing nucleotide sequencing of the cell-free RNA. Methods of sequencing are described in Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. Cell Rep. Med. 4, 101034 (2023), which is incorporated herein by reference in its entirety. In some embodiments, measuring the level of at least one cfRNA comprises a polymerase chain reaction (PCR) assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR). In some embodiments, the measuring the level of at least one cfRNA comprises RNA sequencing. In some embodiments, the measuring the level of at least one cfRNA comprises a PCR assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR).

[0072] In some embodiments, the measuring the level of at least one cfRNA comprises in situ hybridization, clustered regularly interspaced short palindromic repeats (CRISPR) assay, Loop-mediated isothermal amplification (LAMP), or microarray.

[0073] In some embodiments, the method further comprises a step of detecting the cells of origin of the kidney injury of the subject. In some embodiments, the cells of origin are kidney epithelial cells. In some embodiments, the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells, or a combination thereof.

[0074] In some embodiments, the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney. In some embodiments, the step of estimating the cfRNA cell types comprises using a reference RNA-seq data set with a deconvolution algorithm. Deconvolution algorithms are known in the art, for example, the BayesPrism and the Tabula Sapiens human cell atlas as a reference.

[0075] In some embodiments, when a kidney injury is detected, the method further comprises administering a therapeutically effective amount of treatment to the subject to treat the kidney injury. As used herein, “administration” and “treatment,” refers to contact of an exogenous pharmaceutical, therapeutic, diagnostic agent, or composition to the subject. As such, as used herein, “administration” and “treatment” refer to therapeutic and pharmacokinetic methods. As used herein, “treat” or “treatment” includes a postponement of development of the symptoms associated with disease and / or a reduction in the severity of such symptoms that will or are expected to develop with the disease. The terms further include ameliorating existing symptoms, preventing additional symptoms, and ameliorating or preventing the underlying causes of such symptoms. Thus, the terms denote that a beneficial result has been conferred on a subject in need thereof.

[0076] As used herein, the term “therapeutically effective amount” or “effective amount” refers to an amount of a treatment, that when administered alone or in combination with an additional therapeutic agent to a cell, tissue, or subject is effective to prevent or ameliorate the disease or condition to be treated. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms, e.g., treatment, healing, prevention or amelioration of the relevant medical condition, or an increase in rate of treatment, healing, prevention or amelioration of such conditions.

[0077] Treatments for AKI are known in the art. Fluid and electrolyte management is used to prevent dehydration or fluid overload. In prerenal AKI, intravenous (IV) fluids help restore blood flow to the kidneys. However, in cases of fluid retention, diuretics may be used to remove excess fluid from the body. Electrolyte imbalances, such as high potassium levels, are managed through dietary restrictions, medications, or dialysis. Medications and drug adjustments are another method to avoid further kidney damage. Drugs that are toxic to the kidneys, such as nonsteroidal anti-inflammatory drugs (NSAIDs) and certain antibiotics, may be discontinued or replaced with safer alternatives. Medications may be used to control blood pressure, manage infections, and treat complications like metabolic acidosis. In some cases, dialysis may be required to remove waste products and excess fluids from the blood. Hemodialysis or peritoneal dialysis is considered when symptoms like severe electrolyte imbalances, uremia, or fluid overload pose life-threatening risks. Lastly, effective management of underlying conditions such as diabetes, high blood pressure, infections, or autoimmune diseases is crucial for kidney recovery. Inpostrenal AKI, relieving urinary obstructions through catheterization or surgery can restore normal urine flow and prevent further complications.

[0078] In some embodiments, the subject has undergone a transplant of an organ or tissue of the urinary tract. The main organs of the urinary tract include the kidneys, ureters, bladder, and urethra.Determining Etiology of an Acute Kidney Injury

[0079] AKI is a common complication of ICI therapy, occurring in up to 15-20% of patients treated with ICIs. However, there are no clinical features that are sensitive or specific for differentiating ICI- AKI from AKI from non-ICI-related etiologies (22). Thus, patients must undergo kidney biopsy, which is an invasive procedure and is relatively contraindicated in patients with a solitary kidney or on therapeutic anticoagulation. There have been efforts to identify non-invasive biomarkers of IC1-AKI in the blood and urine; however, to date, urinary cfRNA has not been studied in this context. Using methods of the current disclosure, it was observed that CXCL-9, CXCL-10, and CXCL-11 were preferentially expressed in the urine of patients with ICI-related ATIN, but not in patients with ATN / hemodynamic AKI. These are chemokines that regulate immune cell migration, differentiation, and activation, and may be elevated in the setting of T-cell hyperactivation in the setting of ICI-AKI. CXCL-9 has been shown to be expressed in kidney biopsy tissue and in the urine of patients with ATIN (26,27). The methods of the present disclosure therefore suggest that there are distinct gene differences in the urine of patients with ICI-AKI compared to patients with non-ICI-AKI and highlight that urinary cfRNA is a useful analyte for characterizing AKI.

[0080] Another aspect of this disclosure is directed to a method of determining the underlying etiology of an acute kidney injury (AKI) in a subject undergoing an immune checkpoint inhibitor (ICI) therapy, the method comprising: (i) measuring the level of at least one cell-free RNA (cfRNA) molecule in a urine sample from the subject, wherein the at least one cfRNA molecule is a cfRNA of a gene and wherein a differential abundance of the cfRNA of the gene corresponds to an etiology of AKI; (ii) comparing the measured level of the at least one cfRNA to a control; and (iii) determining that the underlying etiology of the AKI is either acute tubulointerstitial nephritis (ATIN) or acute tubular necrosis / hemodynamic AKI (ATN) based on an increase or decrease in the level of the at least one cfRNA as compared to the control.

[0081] In some embodiments, the at least one cfRNA comprises a cfRNA of a signature gene with an increased level as compared to a control, where the increased level is indicative of an ATIN etiology.

[0082] In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), NOS2 (NM_000625.4), CYTH3 (NM 004227.4). ETV7 (NM_016135.4), LTF (NM_002343.6), CLCA1 (NM_001285.4).PHLDB1 (NM_001144758.3), CD74 (NM_001025159.3), BIRC3 (NM_001165.5), BARX2 (NM_003658.5), WDR37 (NM_014023.4), TRAF1 (NM_005658.5), LAMC2 (NM_005562.3), EPB41L2 (NM_001431.4), APOB (NM_000384.3), KIZ (NM_018474.6), ICAM1 (NM_000201.3), LYZ (NM_000239.3), CIRBP (NM_001300829.2), CERK (NM_022766.6), NFKBIA (NM_020529.3), LIPG (NM_006033.4), TMC5 (NM_001261841.2), IL4I1 (NM_152899.2), FAM83E (NM_017708.4), PLEKHA4 (NM_020904.3), ARRDC2 (NM_015683.2), ZC3HAV1 (NM_020119.4), FBXW4 (NM_022039.4), CCL2 (NM_002982.4), APOA4 (NM_000482.4), SLC15A3 (NM_016582.3), FOXM1 (NM_021953.4). FN1 (NMJ212482.4), STAT1 (NM_007315.4), KCNJ13 (NM_002242.4), GBP1 (NM_002053.3), SYF2 (NM_015484.5), IFIT3 (NM_001549.6), CD274 (NM_014143.4), CIT (NM_001206999.2), TBCC (NM_003192.3), IRF1 (NM_002198.3), TSPAN8 (NM_004616.3), SAT1 (NM_002970.4), BST2 (NM_004335.4), IDO1 (NM_002164.6), PSMC3IP (NM_016556.4), TOP2A (NM_001067.4), EPSTI1 (NM_033255.5), HNRNPA1 (NM_031157.4), CD164 (NM_006016.6), TRA2B (NM_004593.3), KLF4 (NM_004235.6), ANP32B (NM_006401.3), MMP7 (NM_002423.5), THBS1 (NM_003246.4), IFI44L (NM_006820.4). MNS1 (NM_018365.4), CXCL9 (NM_002416.3). TPM1 (NM_001018005.2), NLRC5 (NM_001384950.1), IRF8 (NM_002163.4), CCDC40 (NM_017950.4), SECTM1 (NM_003004.3), RNF157 (NM_052916.3), PMAIP1 (NM_021127.3), RABB (NM_002870.5), ARL6IP5 (NM_006407.4), PNRC1 (NM_006813.3). SLC2A13 (NM_052885.4), GBP5 (NM_052942.5), RPGR (NM_001034853.2), UBE2L6 (NM_004223.5), ETS2 (NM_005239.6), MX1 (NM_002462.5), XDH (NM_000379.4), CDC42SE2 (NM_001375635.1), IFNGR2 (NM_005534.4), CXCL16 (NM_001386809.1), CAMK2N1 (NM_018584.6), GBP2 (NM_004120.5), PIGR (NM_002644.4), SGPP2 (NM_152386.4), CTSS (NM_004079.5), FZD5 (NM_003468.4), CXCL1 (NM_001511.4), ZC3H12A (NM_025079.3). TAGAP (NM_054114.5), TNFRSF11B (NM_002546.4), REEP3 (NM_001001330.3), DENND2B(NM_213618.2), B2M (NM_004048.4), TPM4 (NM_003290.3), BATF2 (NM_138456.4), TAPI (NM_000593.6), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), MUC17 (NM_001040105.2), MUC3A (NM_005960.2), OTUD3 (NM_015207.2), EMB (NM_198449.3), PARP14 (NM_017554.3), MUC13 (NM_033049.4), CTDSP2 (NM_005730.4), KCMF1 (NM_020122.5), KCTD12 (NM_138444.4), HLA-DQB1 (NM_002123.5), H2BC4 (NM 003526.3). FRAT2 (NM_012083.3). RELL1 (NM_001085400.2), CLN8 (NM_018941.4), H2AC21 (NM_175065.3), SOCS1 (NM_003745.2), ZFP36L1 (NM_004926.4), IFITM1 (NM_003641.5), NAP1L1 (NM_004537.7), PTMA (NM_002823.5), RP5-1086D14.6, BNIP5 (NM_001010903.5), HLA-DRB1 (NM_002124.4), HLA-DQA1 (NM_002122.5), FAM177B (NM_001394345.1), HLA-DRB5 (NM_002125.4), MUC2 (NM_002457.5), H2BC18 (NM_001024599.5), PSMB8 (NM_148919.4), HLA-DRA (NM_019111.5), HLA-C (NM_002117.6), HLA-E (NM_005516.6), TRIM31 (NM_007028.5), HLA-F (NM_001098479.2), HCP5 (NR_040662), HLA-H (NR_001434.4), HLA-A (NM_002116.8), HLA-DPB1 (NM_002121.6), LINC01133 (NR_038849.1), HLA-DPA1 (NM_033554.4). HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), PSMB9 (NM_002800.5), FMN1 (NM_001277313.2), LYN (NM_002350.4), CCL5 (NM_002985.3), H2AC12 (NM_080596.3), CCL4 (NM_002984.4), FCGBP (NM_003890.3), UHRF1 (NM_001048201.3), LHX1-DT (NR-135671.1), H4C2 (NM_003544.3), CTD-3014M21.1 (NR_027412.1), and H3C3 (NM_003531.3). where the accession number for each gene is provided in the parenthesis. For purposes of this disclosure, the accession numbers provide identification of the genes and the version of the accession number of any of the kidney injury signature genes (i.e., the number following the period in the accession number) is not particularly important and does not affect the purpose of the disclosed methods. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), NOS2 (NM 000625.4). ETV7 (NM_016135.4), LTF (NM_002343.6), CD74 (NM_001025159.3). BIRC3 (NM_001165.5), WDR37 (NM_014023.4), EPB41L2 (NM_001431.4), ICAM1 (NM_000201.3), LYZ (NM_000239.3), NFKBIA (NM_020529.3), IL4I1 (NM_152899.2), FAM83E (NM_017708.4), PLEKHA4 (NM_020904.3), FN1 (NM_212482.4), STAT1 (NM_007315.4), GBP1 (NM_002053.3), CD274 (NM_014143.4), IRF1 (NM_002198.3), EPSTI1 (NM_033255.5), TRA2B (NM_004593.3). MMP7 (NM_002423.5), IFI44L (NM_006820.4), MNS1 (NM_018365.4), CXCL9 (NM_002416.3), TPM1 (NM_001018005.2),IRF8 (NM_002163.4), SECTM1 (NM_003004.3), SLC2A13 (NM_052885.4), GBP5 (NM_052942.5), CDC42SE2 (NM_001375635.1), GBP2 (NM_004120.5), PIGR (NM_002644.4), CTSS (NM_004079.5), DENND2B (NM_213618.2), B2M (NM_004048.4), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), OTUD3 (NM_015207.2), IFITM1 (NM_003641.5), BNIP5 (NM_001010903.5), HLA-DQA1 (NM 002122.5). PSMB8 (NM_148919.4), HLA-DRA (NM_01911L5), HLA-E (NM_005516.6), TRIM31 (NM_007028.5), HLA-F (NM_001098479.2), HCP5 (NR_040662), HLA-H (NR_001434.4), HLA-A (NM_002116.8), HLA-DPB1 (NM_002121.6), HLA-DPA1 (NM_033554.4), HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), PSMB9 (NM_002800.5), LYN (NM_002350.4), CCL5 (NM_002985.3), H2AC12 (NM_080596.3), CCL4 (NM_002984.4), LHX1-DT (NR_135671.1), and CTD-3014M21.1. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), NOS2 (NM_000625.4), LTF (NM_002343.6), CD74 (NM_001025159.3), IL4I1 (NM_152899.2), GBP1 (NM_002053.3), CD274 (NM_014143.4), EPSTI1 (NM_033255.5), CXCL9 (NM_002416.3), GBP5 (NM_052942.5), GBP2 (NM_004120.5), B2M (NM_004048.4), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), IFITM1 (NM_003641.5), HLA-DQA1 (NM_002122.5), HLA-DRA (NM_01911L5), HLA-F (NM_001098479.2), HLA-H (NR_001434.4), HLA-DPA1 (NM_033554.4). HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), CCL5 (NM_002985.3). CCL4 (NM_002984.4), and CTD-3014M21.1. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), CD74 (NM_001025159.3), STAT1 (NM_007315.4). GBP1 (NM_002053.3), CD274 (NM_014143.4), EPSTI1 (NM_033255.5), CXCL9 (NM_002416.3), GBP5 (NM_052942.5), GBP2 (NM_004120.5), DENND2B (NM_213618.2), BATF2 (NM_138456.4), CXCL10 (NM 001565.4). CXCL11 (NM_005409.5). PSMB8 (NM_148919.4), HLA-DRA (NM_01911L5), HCP5 (NR_040662), HLA-H (NR_001434.4), HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), and LHX1-DT (NR_135671.1). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CD274 (NM_014143.4), CXCL9 (NM_002416.3), GBP5 (NM_052942.5), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), HLA-DRA (NM_019111.5), HLA-H (NR_001434.4), and OR2I1P (NM_001396058.1). In some embodiments, the at least one cfRNAcomprises one or more or all of cfRNAs of genes selected from CXCL9 (NM_002416.3), GBP5 (NM_052942.5), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), and HLA-H (NR_001434.4). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CXCL9 (NM_002416.3), GBP5 (NM_052942.5), CXCL10 (NM_001565.4), and CXCL11 (NM_005409.5). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CXCL9 (NM_002416.3), CXCL10 (NM_001565.4), andCXCLll (NM_005409.5).

[0083] In some embodiments, the at least one cfRNA comprises a cfRNA of a signature gene with a decreased level as compared to control being indicative of an ATIN etiology. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5). CAPG (NM_001747.4), DHX8 (NM_004941.3), TOP2B (NM_001330700.2), SMARCA2 (NM_003070.5), ASCC2 (NM_032204.5), KIAA0930 (NM_001009880.2), HSPB1 (NM_001540.5), VAT1 (NM_006373.4). OSBP (NM_002556.3), FBXL5 (NM_012161.4), NAGK (NM_017567.6), SH3BP5 (NM_004844.5), KRT7 (NM_005556.4), IL1RN (NM_173842.3), LRPPRC (NM_133259.4), GOLGA4 (NM_002078.5), DAB2 (NM_001343.4), PLCD3 (NM_133373.5), FOXQ1 (NM_033260.4), TSC1 (NM_000368.5), YWHAB (NM_139323.4), KMT2D (NM_003482.4), EVPL (NM_001988.4), HSPA4 (NM_002154.4), ABLIM3 (NM_014945.5), SNCG (NM_003087.3). SOWAHB (NM_001029870.3), ZNF398 (NM.170686.3), CARD11 (NM_032415.7), HOMEZ (NM_020834.3), and RP11-7K24.3. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM_001747.4), ASCC2 (NM_032204.5), NAGK (NM_017567.6), SH3BP5 (NM_004844.5), KRT7 (NM_005556.4), IL1RN (NM_173842.3), DAB2 (NM_001343.4), PLCD3 (NM_133373.5), FOXQ1 (NM_033260.4), EVPL (NM_001988.4), ABLIM3 (NM_014945.5). SNCG (NM_003087.3), SOWAHB (NM_001029870.3), ZNF398 (NM_170686.3), CARD11 (NM_032415.7), HOMEZ (NM_020834.3), and RP11-7K24.3. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM.001747.4), ASCC2 (NM_032204.5), KRT7 (NM_005556.4), and RP11-7K24.3. In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG(NM_OO 1747.4), and ASCC2 (NM_032204.5). In some embodiments, the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4) and TOMM34 (NM_006809.5).

[0084] In some embodiments, the at least one cfRNA comprises a cfRNA of at least two signature genes, where an increase in level of one signature gene as compared to a control and the decrease in the level of another signature gene as compared to control is indicative of an ATIN etiology. In such embodiments, the at least one signature gene where an increase in level is indicative of an ATIN etiology is selected from CX3CL1 (NM_002996.6), NOS2 (NM_000625.4), CYTH3 (NM_004227.4), ETV7 (NM_016135.4), LTF (NM_002343.6), CLCA1 (NM_001285.4), PHLDB1 (NM_001144758.3), CD74 (NM_001025159.3), BIRC3 (NM_001165.5). BARX2 (NM_003658.5), WDR37 (NM_014023.4). TRAF1 (NM_005658.5). LAMC2 (NM_005562.3), EPB41L2 (NM_001431.4), APOB (NM_000384.3), KIZ(NM_018474.6), ICAM1 (NM_000201.3), LYZ (NM_000239.3), CIRBP (NM_001300829.2), CERK (NM_022766.6). NFKBIA (NM_020529.3). LIPG (NM_006033.4), TMC5 (NM_001261841.2), IL4I1 (NM_152899.2), FAM83E (NM_017708.4), PLEKHA4 (NM_020904.3), ARRDC2 (NM_015683.2), ZC3HAV1 (NM_020119.4), FBXW4 (NM_022039.4), CCL2 (NM_002982.4), APOA4 (NM_000482.4), SLC15A3 (NM_016582.3), FOXM1 (NM_021953.4), FN1 (NM_212482.4), STAT1 (NM_007315.4), KCNJ13 (NM_002242.4). GBP1 (NM_002053.3), SYF2 (NM_015484.5), IFIT3 (NM_001549.6), CD274 (NM_014143.4), CIT (NM_001206999.2), TBCC (NM_003192.3), IRF1 (NM_002198.3), TSPAN8 (NM_004616.3), SAT1 (NM_002970.4), BST2 (NM_004335.4), IDO1 (NM_002164.6). PSMC3IP (NM_016556.4), TOP2A (NM_001067.4), EPSTI1 (NM_033255.5). HNRNPA1 (NM_031157.4), CD164 (NM_006016.6), TRA2B (NM_004593.3), KLF4 (NM_004235.6), ANP32B (NM_006401.3), MMP7 (NM_002423.5), THBS1 (NM_003246.4), IFI44L (NM_006820.4), MNS1 (NM_018365.4). CXCL9 (NM_002416.3), TPM1 (NM_001018005.2), NLRC5 (NM_001384950.1), IRF8 (NM_002163.4), CCDC40(NM_017950.4), SECTM1 (NM_003004.3), RNF157 (NM_052916.3), PMAIP1(NM_021127.3), RABI3 (NM_002870.5), ARL6IP5 (NM_006407.4), PNRC1 (NM_006813.3), SLC2A13 (NM_052885.4), GBP5 (NM_052942.5), RPGR (NM_001034853.2), UBE2L6 (NM_004223.5). ETS2 (NM_005239.6). MX1 (NM_002462.5). XDH (NM_000379.4).CDC42SE2 (NM_001375635.1), IFNGR2 (NM_005534.4), CXCL16 (NM_001386809.1),CAMK2N1 (NM_018584.6), GBP2 (NM_004120.5), PTGR (NM_002644.4), SGPP2 (NM_152386.4), CTSS (NM_004079.5), FZD5 (NM_003468.4), CXCL1 (NM_001511.4), ZC3H12A (NM_025079.3), TAGAP (NM_054114.5), TNFRSF11B (NM_002546.4), REEP3 (NM_001001330.3), DENND2B (NM_213618.2), B2M (NM_004048.4), TPM4 (NM_003290.3), BATF2 (NM_138456.4), TAPI (NM_000593.6), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), MUC17 (NM_001040105.2). MUC3A (NM_005960.2), OTUD3 (NM_015207.2), EMB (NM_198449.3), PARP14 (NM_017554.3), MUC13 (NM_033049.4), CTDSP2 (NM_005730.4), KCMF1 (NM_020122.5), KCTD12 (NM_ 138444.4), HLA-DQB1 (NM_002123.5), H2BC4 (NM_003526.3), FRAT2 (NM_012083.3), RELL1 (NM_001085400.2), CLN8 (NM.018941.4), H2AC21 (NM_175065.3), SOCS1 (NM_003745.2). ZFP36L1 (NM_004926.4), IFITM1 (NM_003641.5), NAP1L1 (NM_004537.7), PTMA (NM_002823.5), RP5-1086D14.6, BNIP5 (NM_001010903.5), HLA-DRB1 (NM_002124.4), HLA-DQA1 (NM_002122.5), FAM177B (NM_001394345.1), HLA-DRB5 (NM_002125.4). MUC2 (NM_002457.5), H2BC18 (NM_001024599.5), PSMB8 (NM_148919.4), HLA-DRA (NM_019111.5), HLA-C (NM_002117.6), HLA-E (NM_005516.6), TRIM31 (NM_007028.5), HLA-F (NM_001098479.2), HCP5 (NR_040662), HLA-H (NR_001434.4), HLA-A (NM_002116.8), HLA-DPB1 (NM.002121.6), LINC01133 (NR_038849.1), HLA-DPA1 (NM_033554.4), HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), PSMB9 (NM_002800.5), FMN1 (NM_001277313.2), LYN (NM_002350.4), CCL5 (NM_002985.3), H2AC12 (NM_080596.3), CCL4 (NM_002984.4), FCGBP (NM_003890.3), UHRF1 (NM_001048201.3), LHX1-DT (NR_135671.1), H4C2 (NM_003544.3). CTD-3014M21.1 (NR_027412.1), H3C3 (NM_003531.3) and the at least one signature gene with a decrease in level being indicative of an ATIN etiology is selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM_001747.4), DHX8 (NM_004941.3). TOP2B (NM_001330700.2), SMARCA2 (NM_003070.5), ASCC2 (NM_032204.5), KIAA0930 (NM_001009880.2), HSPB1 (NM_001540.5), VAT1 (NM_006373.4), OSBP (NM_002556.3), FBXL5 (NM_012161.4), NAGK (NM_017567.6), SH3BP5 (NM_004844.5), KRT7 (NM_005556.4), IL1RN (NM_173842.3), LRPPRC (NM_133259.4), GOLGA4 (NM_002078.5), DAB2 (NM_001343.4), PLCD3 (NM_133373.5), FOXQ1 (NM_033260.4), TSC1 (NM_000368.5). YWHAB (NM_139323.4), KMT2D (NM_003482.4), EVPL (NM_001988.4), HSPA4 (NM_002154.4), ABLIM3 (NM_014945.5),SNCG (NM_003087.3), SOWAHB (NM_001029870.3), ZNF398 (NM_170686.3), CARD 11 (NM_032415.7), HOMEZ (NM_020834.3), and RP11-7K24.3.

[0085] In some embodiments, the measuring the level of at least one cfRNA comprises RNA sequencing. In some embodiments, the measuring the level of at least one cfRNA comprises a polymerase chain reaction (PCR) assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR).

[0086] In some embodiments, the measuring the level of at least one cfRNA comprises in situ hybridization, clustered regularly interspaced short palindromic repeats (CRISPR) assay, Loop-mediated isothermal amplification (LAMP), or microarray.

[0087] In some embodiments, the method further comprises a step of detecting the cells of origin of the kidney injury of the subject. In some embodiments, the cells of origin are kidney epithelial cells. In some embodiments, the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells, or a combination thereof.

[0088] In some embodiments, the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney. In some embodiments, the step of estimating the cfRNA cell types comprises using a reference RNA-seq data set with a deconvolution algorithm. Deconvolution algorithms are known in the art, for example, the BayesPrism and the Tabula Sapiens human cell atlas as a reference.

[0089] In some embodiments, the urine sample is a longitudinally collected urine sample. In some embodiments, multiple urine samples are collected from the subject. In some embodiments, the collecting of multiple urine samples comprises a set of longitudinally collected biological samples of the subject. As used herein, “subsequent urine sample” refers to any urine sample collected from the same subject at a point in time after the initial, first, or original urine sample was collected. In some embodiments, the longitudinally collected urine sample is obtained from the subject about 1 day after the initial urine sample is collected from the subject; insome embodiments, the longitudinally collected urine sample is obtained from the subject about 2 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 3 days after theinitial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 4 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 5 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 6 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 7 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 10 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 15 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 30 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 45 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 60 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 75 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 90 days after the initial urine sample is collected from the subject; in some embodiments, the longitudinally collected urine sample is obtained from the subject about 105 days after the initial urine sample is collected from the subject; and / or the longitudinally collected urine sample is obtained from the subject about 120 days after the initial urine sample is collected from the subject.

[0090] In some embodiments, when there is a kidney injury in the subject, the method further comprises treating the subject with a therapy to ameliorate the kidney injury.

[0091] In some embodiments, the subject has undergone a transplant of an organ or tissue of the urinary tract.EXAMPLES

[0092] The specific examples listed below are only illustrative of certain embodiments of the disclosure and by no means limiting.Example 1 : Materials and MethodsPatient Cohorts

[0093] HSCT patients (n=24): Matched blood (n=106) and urine (n=103) samples were collected on admission before the beginning of the conditioning chemotherapy, on the day of transplantation after completion of conditioning therapy, at engraftment (14 to 21 days following transplantation), and at months 1. 2, 3, and 6 post transplantation. Additional samples were collected at the time of presentation of complications.

[0094] Patients receiving ICIs (n=46): We prospectively collected blood (n=40) and urine (n=38) samples from patients with cancer who were treated with ICIs and developed AKI, defined as a >1.5-fold rise in serum creatinine (SCr) from baseline, where baseline is defined as the SCr closest to and preceding initiation of the ICI. Patients with ICI-related AKI had biopsy-proven acute tubulointerstitial nephritis (ATIN) (n=15) or clinically adjudicated ATIN (n=9). Patients with non-ICI-related AKI had biopsy-proven acute tubular necrosis (ATN) (n=7) or ATN adjudicated by 2 nephrologists (n=6). We also collected blood and urine samples from patients who received at least one cycle of ICIs, did not develop AKI, and had no irAEs within 30 days of sample collection (n=9).Plasma cell-free RNA isolation

[0095] Plasma samples were frozen within four hours after collection and stored at -80 °C. When required for analysis, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from the plasma supernatant (250-1500 pl). Urine cell-free RNA isolation

[0096] Urine samples were frozen within four hours after collection. When required for analysis, the samples were thawed at room temperature and centrifuged at 16,000 x g for 10 minutes at 4°C. cfRNA was extracted from (450-2000 pl) supernatant using QIAamp Circulating Nucleic Acid Kit -Purification of Circulating microRNA in serum / plasma / urine protocol (Qiagen).Extracted RNA was DNase treated and concentrated.Library preparation and sequencing

[0097] Sequencing libraries were prepared and quantified from 8 pl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara) aspreviously described (5,6). Sequencing was performed on the Illumina NextSeq 2000 platform (2 x 76 bp) or Illumina Novaseq 6000 (2x150 bp).Cells-types of origin deconvolution

[0098] Cell-types of origin deconvolution was performed using BayesPrism (v2.0) (14). Cells were subsampled to 300 cells or 1000 cells using anndata 0.9.1 and pandas 1.5.2 packages. Quantification and statistical analyses

[0099] Differential abundance analysis was carried out as previously described (5.6). All statistical methods were performed in R version 4.0.2. Groups were compared using two-sided Wilcoxon Rank-Sum tests. Boxes in the box plots indicate 25th and 75th percentile, the band in the box indicated the median and whiskers extend to 1.5 x Interquartile Range (IQR) of the hinge.Preanalytical variables of urine

[0100] Urine from healthy volunteers was collected and centrifuged using three different centrifugation protocols. Samples were either spun at 3000 x g for 30 minutes, 3200 RPM for 5 minutes at 4°C or 200 x g for 10 minutes with a second spin at 1800 x g for 10 minutes at 4°C. To study the impact of preservatives in the collection device, samples were aliquoted into tubes without preservatives, 25mM EDTA (Invitrogen, 15575-038), or Streck Urine Preserve in a 1:4 ratio (Streck, 230599) and incubated at room temperature for 1 hour.Sample Collection and Pre-processing

[0101] HSCT Patients: Blood was collected through venipuncture in ethylenediaminetetraacetic acid tubes (Becton Dickinson, ref no. 366643), centrifuged for 10 mins at 2000 rpm, and plasma was carefully pipetted out and stored at -80°C. Urine was collected via mid-stream void and within 2 hours of collection, 50 ml was centrifuged at 3000 x g for 30 minutes, and the supernatant was aliquoted and stored at -80°C.

[0102] Patients Receiving ICIs with AKI and non-AKI Controls: Blood was collected through venipuncture into EDTA tubes (Becton Dickinson, ref no. 366643), centrifuged for 10-15 min at 3200 RPM at 4°C and plasma pipetted out carefully. Plasma was then aliquoted and frozen at -80°C. Urine was collected from the needleless port of a foley catheter into a urine cup,poured into a centrifuge tube, and centrifuged for 5 minutes at 3200 RPM at 4°C. Urine supernatant was poured into a new centrifuge tube, aliquoted and frozen at -80°C.

[0103] Healthy volunteers: Blood from healthy volunteers was collected via venipuncture into a 15 mL tube and spun at 1,900 x g and 4°C. Plasma was pipetted out carefully into clean 15 mL falcon tubes and centrifuged again at 2,000 x g and 4°C. Platelet-free plasma was extracted and stored into 1 mL cryotubes. Healthy volunteers provided urine using clean catch collection protocol (1). Urine was centrifuged at 200 x g for 10 mins and decanted into new 15 mL conical tubes and further spun at 1,800 x g for 10 minutes before being aliquoted into 2mL or 15 mL tubes for storage.Bioinformatics processing and sample quality filtering

[0104] Adapter and low quality bases were trimmed using BBDuk (v38.90) (2). Reads were trimmed to 61 base pairs before alignment using cutadapt (v4.9) (3). Reads were aligned to the Gencode GRCh38 human reference genome using STAR (v2.7.0f, default parameters) (4).Aligned reads were deduplicated using UMI-tools (vl.1.2) (5) before feature quantification using featureCounts (v2.0.0.0)(6). Samples were excluded based on the quality metrics defined in Moufarrej et. al (7). Briefly, samples were removed if they met any of the following cutoff criteria. 1) Ribosomal RNA fraction > 10% 2) Intron to Exon ratio greater than 33) absolute of Z score of the 5 ’-3’ bias greater than 3 standard deviations from the mean 4) total counts less than 60000. Differential expression analysis was performed in R using DESeq2 (v 1.34.0) (8) and pathway analysis was performed using Ingenuity Pathway Analysis software (v73620684). Differential Abundance Analysis

[0105] Differential abundance analysis was carried out using DESeq2 (8). P-values were adjusted using Benjamin Hochberg method to correct for multiple hypothesis testing. DESeq2 models the data using a negative binomial distribution and a Wald test is used to estimate the significance of the fold changes. Differentially abundant genes were identified as genes with an adjusted p-value of less than 0.05. For visualization, gene counts were normalized using variance stabilizing transformation (8).Cells-types of origin deconvolution

[0106] We utilized different single cell references for the plasma cfRNA and urine cfRNA deconvolution. We used Tabula Sapiens (9) for the deconvolution of plasma cfRNA and a custom genitourinary system cell reference, which includes a subset of cells from Tabula Sapiensexpected to be found in urine, for the deconvolution of urine cfRNA. Due to the limited representation of genitourinary specific cells in Tabula Sapiens, we created custom-made single cell references by replacing kidney epithelial cells from the above references with kidney cells from the KPMP consortium (10). These references were then used for deconvolution of plasma and urine cfRNA in the AKI cohort.Example 2: Robustness of urine cfRNA to changes in preanalytical variables

[0107] First, we evaluated the impact of centrifugation and the use of different preservatives on measurements of urine cfRNA features. For this purpose, urine was collected from three volunteers using distinct centrifugation and preservative conditions with triplicates for each condition (n=27). A very strong concordance for the measured gene abundance, biotype distribution, transcriptome diversity, fragment length profiles and cell types of origin for samples collected using different centrifugation methods and preservative conditions was observed (FIG.4-3). Collectively, these data indicated the robustness of urine cfRNA profiling to differences in preanalytical variables.Example 3: Clinical study design

[0108] We isolated and sequenced cell-free RNA from a total of 297 plasma and urine samples from healthy volunteers (n=5), HSCT recipients (n=24), patients who received ICI, but did not develop AKI (non- AKI controls, n=9), and patients who developed AKI while on ICI therapy (n=37, FIG. 1A, Table 1). For the HSCT recipients, we collected matched urine and plasma samples at predetermined time points relative to transplantation: before the conditioning regimen (PR, n=13), on the day of transplantation before receiving stem cells (DO, n=13), during engraftment (E, n=15), at 1, 2, 3, and 6 months post transplantation (n=57), with additional samples taken at time of complication (urine: n=8; plasma: n=5). Of the 37 patients in the AKI cohort, 24 (64.86%) had biopsy-proven or clinically-adjudicated acute tubulointerstitial nephritis (ATIN) and 13 (35.14%) had biopsy-proven or clinically-adjudicated acute tubular necrosis (ATN).Table 1Example 4: Origins of plasma cell-free RNA and urine cell-free RNA

[0109] We first examined the properties of urine cfRNA and plasma cfRNA, focusing on RNA-seq insert size, RNA species composition, transcript diversity, and cell types of origin. The insert sizes of cfRNA in both urine and plasma were similar and exhibited a broad distribution (mean insert length 152 bp ± 30 bp and 146 bp ± 24.6 bp for plasma and urine cfRNA respectively, FIG. 7A). We quantified the representation of different RNA biotypes and found that the majority of sequenced transcripts in plasma and urine were derived from protein-coding genes (81.5% ± 5.5 % and 95.3% ± 0.6 %, in plasma and urine respectively, FIG. IB). In addition, we observed a greater proportion of mitochondrial ribosomal RNA transcripts in plasma than urine(12.5%±3.9 % vs 0.16%±0.06% in plasma vs. urine respectively), which indicates potential differences in biogenesis and stability of plasma and urine cell-free RNA. A small number of transcripts were derived from other biotypes, including miscellaneous small RNAs, long noncoding RNA (IncRNA), and unprocessed and processed pseudogenes.

[0110] To quantify the diversity of the cfRNA transcrip tomes, we calculated the Gini index which measures deviation from a uniform distribution. We observed significantly higher Gini indices for plasma compared to urine, indicating that a smaller number of genes contribute a greater number of reads in plasma cfRNA compared to urine cfRNA (two tailed, Wilcoxon rank sum test, p values < 0.001 for AKI cohort and HSCT cohort, p value = 0.016 for healthy volunteers) (FIG. 1C, FIG. 7B). The genes that occurred at the highest frequency and abundance were RN7SL1, TPT1, and FTH1 in urine, and MT-RNR2, RN7SL1, andACTB in plasma.

[0111] Next, we examined the cell types that contribute cfRNA to the mixtures in plasma and urine. BayesPrism was used for deconvolution of the cell-free transcriptomes using custom references for plasma and urine. In matched samples from healthy volunteers, we observed clear differences in the primary contributing cell types of plasma and urine cfRNA (FIG. ID). B-cells, platelets, and endothelial cells together accounted for more than 40% of the cfRNA in plasma, while more than 50% of the cfRNA in urine was derived from epithelial cells from the prostate and kidney. The deconvolution references were robust to the top cell types identified in urine (FIG. 8). Additionally, the mean fraction of platelet-derived cfRNA was high in plasma (16.1%) but very low in urine (0.7%). Conversely, kidney epithelial cell-derived cfRNA was abundant in urine (12%) but scarce in plasma (1.5%). These findings provided an initial indication that plasma and urine cfRNA represent distinct reservoirs, with minimal exchange between them. Example 5: Monitoring of immune activity using urine and plasma cell-free RNA in HSCT

[0112] We next investigated the utility of urine vs. plasma cfRNA for monitoring immune dynamics and systemic injury in the context of HSCT, a primary treatment for hematologic malignancies. HSCT recipients undergo intensive chemotherapy conditioning prior to donor stem cell infusion to reduce disease burden, suppress the recipient’s immune system, and ensure successful engraftment of donor stem cells. Here, we used longitudinally collected matched urine and plasma samples to measure the impact of conditioning therapy, subsequent engraftment of donor stem cells, and reconstitution of hematopoiesis (FIG. 2A). We first conducted differentialgene abundance analysis between sequential timepoints, focusing on the impact of conditioning therapy (day of the transplant vs. pre-conditioning, DO vs. PR) and engraftment (engraftment vs. day of the transplant, E vs. DO), and measured differentially abundant genes (DAGs, adj. p-value < 0.05; FIG. 2B). For plasma, we observed dramatic alterations in the cfRNA profiles in response to the conditioning regimen (n=1015 DAGs, DO vs PR) and subsequent stem cell engraftment (n=3074 DAGs, E vs DO), as would be expected. In contrast, for urine we observed far smaller changes (DO vs PR n=0 DAGs, E vs DO n=182 DAGs; FIG. 2C). In addition, we observed little overlap between DAGs for urine and plasma cfRNA, underscoring the distinct molecular signatures captured in each biofluid (FIG. 2C). Pathway enrichment analysis of the DAGs revealed no overlap in significantly activated or inhibited pathways between urine and plasma cfRNA (FIG. 9A, B).

[0113] We next quantified the dynamic changes in the cell-types of origin (CTO) across sampled timepoints to further examine the response to HSCT as measured by urine and plasma cfRNA. We observed dramatic changes in the CTO for plasma cfRNA but not urine cfRNA in response to conditioning therapy (PR vs. DO) and the engraftment process (E vs DO), which agrees with the differential gene abundance analysis (FIG. 2D). We observed a significant decrease in immune cell contributions in response to chemotherapy treatment and a subsequent increase post-engraftment in plasma but not in urine (FIG. 2E, Table 2). The representation of platelet derived cfRNA was high in plasma throughout the transplantation course, and very low for urine (FIG.2E, Table 2). Conversely, the burden of cfRNA derived from kidney epithelial cells was high in urine, and very low in plasma at all timepoints (FIG. 2E, Table 2). These results again demonstrate that there is minimal exchange of cfRNA between plasma and urine, and that the plasma and urine cfRNA reservoirs are distinct. We also quantified the diversity of the cell type origins of plasma and urine cfRNA and observed a more uniform contribution for urine (FIG. 10A, B). When comparing samples, we observed smaller differences for samples collected from the same patients than for samples collected from different patients for both urine and plasma (FIG. 10C).Table 2"

[0114] We next explored urinary tract related injury in the HSCT cohort and discovered similar trends. Elevated levels of urinary cfRNA from bladder urothelial cells and prostate epithelium cells in samples from patients with epithelial cells clinically detected in their urine compared to those without (p-value = 0.023 and p- value = 0.0035 respectively, FIG. 11) were observed. These differences were not observed for plasma cfRNA (data not shown). We also observed an increase in cfRNA derived from kidney tubule epithelial cells in the urine of patients with detectable BKV levels, compared to those without detectable BKV levels and healthy volunteers (FIG. 12, Table 3). This was also shown in samples collected longitudinally from patients with BKV detected over a time course (FIG. 13). This was the first indication that urine cfRNA may be useful in monitoring kidney-related complications.Table 3"Example 6: Monitoring AKI and urinary tract related complications in patients who received ICI Therapy

[0115] Given the direct relation between urine cfRNA and the kidney and urinary tract, we reasoned that urine cfRNA could be an informative analyte for detecting complications in these organs. To test this, we explored cfRNA signatures of different AKI etiologies in the context of ICI therapy. First, we compared the cell-type of origins of urine and plasma cfRNA for patients who received ICIs and developed AKI, either from the ICI or from non-ICI-related causes, alongwith controls who received ICTs and did not develop AKI. Among patients with AKI compared to patients without AKI, we observed significantly higher levels of urine cfRNA derived from kidney connecting tubule epithelial cells (p-value=0.02, FIG. 3A-B, Tables 4 and 5). On the other hand, parietal epithelial cells, which line the Bowman’s capsule, were poorly represented in urine, and we did not observe significant variation in the abundance of these cells for patients with and without AKI in urine cfRNA, in line with expectations from the anatomy of the kidney (p-valiie-0.71 , FIG. 3A-B, Tables 4 and 5). In contrast, kidney connecting tubule and parietal epithelial cells were poorly represented in plasma cfRNA and no significant differences in their abundance was observed in plasma-derived cfRNA for patients with and without AKI (kidney tubule p-value=0.9, parietal cell p-value=0.11, FIG. 3B, Tables 4 and 5).Table 4"

[0116] The cell-type of origin analysis suggested that cfRNA from kidney cells is shed in the urine, and therefore urine cfRNA biomarkers may identify AKI. To explore this, we performeddifferential abundance analysis comparing the AKI patient samples to the patients receiving ICIs without AKI. We identified 569 DAGs for the urine cfRNA comparison and 0 DAGs for plasma cfRNA (BH adjusted p-value < 0.05, FIG. 3C). Urine cfRNA samples from AKI patients were enriched with transcription factors including JUND and JUN, both part of the Ap-1 protein complex (15), CEBPB, a leucine zipper transcription factor responsible for inducing inflammatory responses, and SOX9, a transcription factor associated with cellular repair (FIG.3D, FIG. 14). The cell-type of origin and differential abundance analysis results indicate that cfRNA derived from kidney tubular epithelial cells can be robustly detected in urine but not in plasma, and that urine cfRNA profiling can distinguish patients with and without AKI.Table 5Example 7: Differentiating ICI-AKI from non-ICI-Related Causes

[0117] We next investigated whether urine cfRNA can distinguish different underlying etiologies of AKI among patients receiving ICIs. For this analysis, we classified AKI etiologies into two groups: ATIN (n=12), as determined by biopsy, versus ATN / AKI (n=ll) from hemodynamic causes. We performed differential abundance analysis and identified 185 differentially abundant genes between the two groups (BH adj p-value <0.05, FIG. 3E). Chemokine ligands, includingCXC motif chemokine ligands CXCL9, CXC 10 and CXCL11 were preferentially elevated in the urine from ATIN patients (FIG. 15). The same analysis performed for plasma cfRNA (n=12 per group) yielded no DAGs (FIG. 3E). In three samples of ATIN patients who were diagnosed to also have a bladder or urothelial cancer, we observed a very high abundance of APOA4 and CLCA1 (FIG. 15). To verify that these samples were not skewing the ATIN versus ATN / AKI comparison, we repeated the analysis excluding those samples and identified similar DAGs separating patients with ATIN versus ATN / AKI (FIG. 15). Overall, these observations indicate the urine cfRNA is a promising analyte to identify kidney injury. These findings are important, since the mechanistic underpinnings of ICI-AKI are not well-understood, and there are no clinical features that reliably differentiate ICI-AKI from non-ICI-related AKI in the absence of a kidney biopsy.

Claims

WHAT IS CLAIMED IS:

1. A method of detecting a kidney injury in a subject, the method comprising:measuring the level of at least one cell-free RNA (cfRNA) transcript in a urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene; anddetecting kidney injury based on an increase or decrease in the level of the at least one cfRNA.

2. The method of claim 1, further comprising:measuring the level of at least one cfRNA transcript in a subsequent urine sample from the subject, wherein the at least one cfRNA transcript is a cfRNA of a kidney injury signature gene;detecting kidney injury based on the measured level of the at least one cfRNA transcript in the subsequent urine sample; anddetermining whether there is a change in the kidney injury.

3. The method of claim 1 or 2, wherein the at least one cfRNA comprises a cfRNA of a kidney injury signature gene with an increased level as compared to control being indicative of kidney injury.

4. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from LASPI (NM_006148.4), TMEM176A (NM_018487.3). TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3), TTC22 (NM_001114108.2), CACNA2D2 (NM_006030.4), NFIX (NM_001365902.3), IL32 (NM_001376923.1), SCMH1 (NM_001394311.1), PTBP1 (NM_002819.5). LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3). SEC63 (NM_007214.5), VIM (NM_003380.5), CD44 (NM_000610.4), TMSB10 (NM_021103.4), SZRD1 (NM_001114600.3), LAMC2 (NM_005562.3), YBX3 (NM_003651.5), VMP1 (NM_030938.5), BICRA (NM_001394372.1), RPL18 (NM_000979.4), CTSA (NM_000308.4), SLC9A3R2 (NM_001130012.3), WDR18 (NM_024100.4), TLE2 (NM_003260.5). MTHFD2 (NM_006636.4), PDE4A (NM_001111307.2), PLPP1 (NM_003711.4), BCL3 (NM_005178.5), RAB27A (NM_183235.3), DAZAP1 (NM_018959.4), PTPN18 (NM_014369.4), ACTB (NM_001101.5), TPD52 (NM_001025253.3), ARAF(NM_001654.5), GNB1 (NM_002074.5), TP53INP2 (NM_021202.3), RIMS1 (NM_014989.7), RPS5 (NM_001009.4), BAX (NM_138761.4), SH3BP2 (NM_001122681.2), GNAS (NM_000516.7). EBF4 (NM_001395167.1), RPLPO (NM_001002.4), GRAMD1A (NM_020895.5), CDV3 (NM_017548.5), ALKBH5 (NM_017758.4), NUBP2 (NM_012225.4), SETD1A (NM_014712.3), CIRBP (NM_001300829.2), MKNK2 (NM_199054.3), SEC14L2 (NM 012429.5). SLC25A1 (NM_005984.5), GGA1 (NM_013365.5), CYB5R3 (NM_000398.7), TTLL12 (NM_015140.4), CTSZ (NM_001336.4), CDC25B (NM_021873.4), WFDC2 (NM_006103.4). MAP1LC3A (NM_032514.4). LPIN2 (NM_001375808.2), PLP2 (NM_002668.3), TIMP1 (NM_003254.3), MAGED2 (NM_177433.3), NUTF2 (NM_005796.3), CLCN7 (NM_001287.6), UBE2I (NM_003345.5), MAZ (NM_002383.4), TMC5 (NM_001261841.2). BL0C1S6 (NM_012388.4), PPP2CB (NM_001009552.2), MAN2B1 (NM_000528.4), NUCB1 (NM_006184.6), SF3A2 (NM_007165.5), OAZ1 (), TLE5 (NM_001130.6), SGTA (NM_003021.4), MED25 (NM_030973.4), FBL (NM_001436.4), SLC1A5 (NM_005628.3), CCDC9 (NM_015603.3), PTPRS (NM_002850.4), KDELR1 (NM_006801.3), RAB3D (NM_004283.4), PLEKHA4 (NM_020904.3), RPL18A (NM_000980.4), COPE (NM_007263.4), LSR (NM_205834.4), GSK3A (NM_019884.3), ZC3HAV1 (NM_020119.4), MOSPD3 (NM_023948.5), IMPDH1 (NM_000883.4), ZNHIT1 (NM_006349.3), PRKAG2 (NM_016203.4), BCL7B (NM_001707.4), LIMK1 (NM_002314.4), PRUNE2 (NM_015225.3), TESK1 (NM_006285.3), EDF1 (NM_003792.4), SFXN3(NM-030971.6), FBXW4 (NM_022039.4), CCNY (NM_145012.6), RPL28 (NM_000991.5), CASC3 (NM_007359.5), PFN1 (NM_005022.4), SLC25A11 (NM_003562.5), RASD1 (NM_016084.5). CCL2 (NM_002982.4), SLC9A3R1 (NM_004252), SLAIN2 (NM_020846.2), CRACD (NM_001393381.1), CRYAB (NM_001289808.2), MDK (NM_002391.6), FOXM1 (NM_021953.4), GAPDH (NM_002046.7), CHPT1 (NM_020244.3), ATN1 (NM_001940.4), C12orf57 (NM_138425.4), COX6A1 (NM_004373.4), TDP2 (NM_016614.3), SOD2 (NM_000636.4), TRIM38 (NM_006355.5), PHF1 (NM_024165.3), FBRSL1(NM_001367871.1), LMNB1 (NM_005573.4), SKP1 (NM_170679.3), ERGIC1(NM-001031711.3), GNAI2 (NM_002070.4), RPS15 (NM_001018.5), MLPH (NM_024101.7), ODC1 (NM_002539.3), SRSF4 (NM_005626.5), SRM (NM_003132.3), Clorf21 (NM_030806.4). TSPAN1 (NM_005727.4), CTSD (NM_001909.5), SPP1 (NM_001040058.2), ELL2 (NM_012081.6), CCDC92 (NM_025140.3), NEK6 (NM_014397.6), TGFB3(NM_003239.5), 0GFRL1 (NM_024576.5), DUSP1 (NM_004417.4), EGR1 (NM_001964.3), SERP1 (NM_014445.4), CLU (NM.001831.4), TNFRSF10B (NM_003842.5), SORBS3 (NM_005775.5). TNFSF10 (NM_003810.4), KIAA1191 (NM_020444.5), CALD1 (NM_033138.4), NR4A1 (NM_173157.3), TUBA1B (NM_006082.3), AMD1 (NM_001634.6), MXD4 (NM_006454.3), PMEPA1 (NM_020182.5), KLHDC3 (NM_057161.4), MEA1 (NM_014623.4), CDKN1A (NM_000389.5), DEK (NM_003472.4), MYRF (NM_001127392.3), MT2A (NM_005953.5), SOX9 (NM_000346.4), PPDPF (NM_024299.4), C3 (NM_000064.4), CENPB (NM_001810.6), CAPNS1 (NM_001749.4), HIVEP3 (NM_024503.5), EMC6 (NM_031298.4), YWHAH (NM_003405.4), ATF4 (NM_182810.3), CDC42EP1 (NM_152243.3), LIF (NM_002309.5), BCL2L2 (NM_004050.5), PGAP6 (NM_021259.3), PRKCSH (NM_001289104.2), ACTN4 (NM_004924.6), KLHDC7B (NM_138433.5), SSBP4 (NM_032627.5), GDF15 (NM_004864.4), JUND (NM_005354.6), UBE2M (NM_003969.4), EIF3G (NM_003755.5), SLC6A8 (NM_005629.4), UBE2D2 (NM_003339.3), TOP2A (NM_001067.4). RARA (NM_000964.4), ITGB4 (NM_000213.5), WBP2 (NM_012478.4), TRIM47 (NM_033452.3), FLOT2 (NM_004475.3), TCEAL4 (NM_001006935.3), PLAAT4 (NM_004585.5), CEP20 (NM_144600.4), BTG1 (NM_001731.3), BHLHE40 (NM_003670.3), TMEM106C (NM_001143842.2), LDHA (NM_005566.4), ETS1 (NM_001143820.2), OS9 (NM_006812.4), MAP7 (NM_003980.6), NIBAN1 (NM_052966.4), ODF2 (NM_001351578.2), KLF4 (NM_004235.6), ANP32B (NM_006401.3), FLOT1 (NM_005803.4), PARP6 (NM_001323532.2), TACC2 (NM_206862.4), PARP9 (NM_001146105.2), RNF185 (NM_152267.4), CLSTN3 (NM_014718.4), WARSI (NM_004184.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SAMD1 (NM_138352.3), AKT1 (NM_001382430.1), ZNF787 (NM_001002836.4), RPL13A (NM_012423.4), SH3BGRL3 (NM_031286.4), SYTL1 (NM_001193308.2), MGST3 (NM_004528.4). HDGF (NM_004494.3). RABB (NM_002870.5). ARL8A (NM_138795.4), RHOB (NM_004040.4), RPL32 (NM_000994.4), ARL6IP5 (NM_006407.4), RPS3A (NM_001006.5), TRIM41 (NM_033549.5), HIGD2A (NM_138820.4), FAM193B(NM_001190946.3), PPP1R18 (NM_133471.4), PRIM2 (NM_000947.5), PNRC1 (NM_006813.3), RPL10 (NM_006013.5), RPL7A (NM_000972.3), MKI67 (NM_002417.5), DGKZ (NM_001199267.2), ALDOA (NM_001243177.4), TMCO3 (NM_017905.6), RILPL2 (NM_145058.3), PRDM8 (NM_001099403.2), RASSF3 (NM_178169.4), UBALD1(NM_145253.3), CMIP (NM_198390.3), CEP112 (NM_001199165.4), ADAMTS1 (NM_006988.5), AZINI (NM_148174.4), HKDC1 (NM_025130.4), FBRS (NM_001105079.3), RBPMS (NM_001008710.3). MMP14 (NM_004995.4), FZD1 (NM_003505.2), CREB3L1 (NM_052854.4), FAIM (NM_001033031.2), SLC45A3 (NM_033102.3), NBL1 (NM_005380.8), FBXW5 (NM_018998.4), IFNGR2 (NM_005534.4), CSRP1 (NM_004078.3), UBE2Z (NM_023079.5), PTMS (NM_002824.6), RGS12 (NM_001394154.1), ZYX (NM_003461.5), CALM3 (NM_005184.4), PDE9A (NM_002606.3), NDUFV3 (NM_021075.4), S100A1 (NM_006271.2), MGAT4B (NM_014275.5), RPL8 (NM_001317782.2), FMNL3 (NM_175736.5), CXCL16 (NM_001386809.1), RPL29 (NM_000992.3), SDC3(NM_014654.4), VCAM1 (NM_001078.4), ATF3 (NM_001674.4), Clorf 115 (NM_024709.5), KIF26B (NM_018012.4), LRATD1 (NM_145175.4). H3-3A (NM_002107.7), CCNYL1 (NM_001330218.2), FZD5 (NM_003468.4), IGFBP7 (NM_001553.3), SSR2 (NM_003145.4), ZC3H12A (NM_025079.3), MEAF6 (NM_001270875.3), DNALI1 (NM_003462.5), BAP1 (NM_004656.4), SGMS2 (NM_001375905.1), H2AZ1 (NM_002106.4), BSN (NM_003458.4), CTSB (NM_001908.5), FASTK (NM_006712.5), PCBD1 (NM_000281.4), TAF10 (NM_006284.4), CDYL2 (NM_152342.4), SEC11C (NM_033280.4), RRAD (NM_004165.3), B2M (NM_004048.4), MBD6 (NM_052897.4), TRUB2 (NM_015679.3), TPM4 (NM_003290.3), GPX4 (NM_002085.5), MIDN (NM_001388306.1), GATAD2A (NM_001384528.1), RPL13 (NM_000977.4), TUBA1C (NM_032704.5), CDC42EP5 (NM_145057.4), EEF2 (NM_001961.4), NXN (NM_022463.5), CDK2AP2 (NM_005851.5), FTH1 (NM_002032.3), RAB4A (NM_004578.4), DDIT4 (NM_019058.4), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2), RAB31 (NM_006868.4), STAT3 (NM_139276.3), CHTF8 (NM_001039690.5), TNIP2 (NM_024309.4), ATF5 (NM_001193646.2), PCBP1 (NM_006196.4), MUC3A (NM_005960.2), RPS9 (NM_001013.4), NDUFA3 (NM_004542.4), MRPL36 (NM_032479.4). FBXL14 (NM_152441.3), RPS7 (NM_001011.4), MALT1 (NM_006785.4), CEBPB (NM_005194.4), PPP1CA (NM_002708.4), PPP1R14B (NM_138689.3), TNFRSF10D (NM_003840.5), EIF1 (NM_005801.4), PITPNA (NM_006224.4), RPL15 (NM_002948.5), HRAS (NM_005343.4), RAB1B (NM_030981.3), ASPHD1 (NM_181718.4), MARCKSL1 (NM_023009.7), TP53I11 (NM_006034.5), CLTB (NM_007097.5). SART1 (NM_005146.5), DRAP1 (NM_006442.4), RPS6KB2 (NM_003952.3), B3GALT6 (NM_080605.4), NUPR1 (NM_012385.3), SLC35A4 (NM_080670.4), WSB2(NM_018639.5), JUN (NM_002228.4), CD151 (NM_004357.5), HNRNPAO (NM_006805.4), MAF (NM_005360.5), CTNNBIP1 (NM_020248.3), KCTD12 (NM_ 138444.4), CALR (NM_004343.4). ZFPM1 (NM_153813.3), MAF1 (NM_032272.5). FGD6 (NM_018351.4), MEX3D (NM_203304.4), PHLDA2 (NM_003311.4), CLN8 (NM_018941.4), KMT5A (NM_020382.7), PTP4A2 (NM_080391.4), SNRNP35 (NM_022717.4), PDE4B (NM 002600.4). SEPTIN9 (NM_001113491.2), H2BC21 (NM_003528.3), H1-1O (NM_006026.4), P4HB (NM_000918.4), ZFP36L1 (NM_004926.4), COL4A1 (NM_001845.6), PTMA (NM_002823.5), ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), FYB2 (NM_001004303.5), PLA2G2A (NM_001395463.1), H2AX (NM_002105.3), ZDHHC9 (NM_016032.4), Hl-0 (NM_005318.4), SULF2 (NM_001387048.1), VKORC1L1 (NM_173517.6). LAMB3 (NM_000228.3), FLNA (NM_001110556.2), SERPINA1 (NM_000295.5), HNRNPAB (NM_031266.3), GPAA1 (NM_003801.4), H2BC12 (NM_001312653.2), RPL12 (NM_000976.4), NRARP (NM_001004354.3), MAFK (NM_002360.4). GLMP (NM_144580.3), LDB1 (NM_001113407.3), ZNF358 (NM_018083.5), ARHGAP11A (NM_014783.6), UBE2J1 (NM_016021.3), R3HDM4 (NM_138774.4), TGM2 (NM_004613.4), VTRNA1-1 (NR_026703.1), RNY1 (NR_004391.1), RNY3 (NR_004392.1), SAMD5 (NM_001030060.3), H2BC18 (NM_001024599.5), RTL8A (NM_001078172.2), LINC00963 (NR_038955.1), TRAF3IP1 (NM_015650.4), RNF5 (NM_006913.4), NEU 1 (NM_000434.4), HLA-C (NM_002117.6), HLA-E (NM_005516.6), AKT1S1 (NM_001098633.4), HMGN1 (NM_004965.7), HLA-A (NM_002116.8), SNORD17 (NR_003045.1), ZNF580 (NM_207115.2), LBH (NM_030915.4), UBXN2B (NM_001077619.2), CEBPD (NM_005195.4), HLA-DPB1 (NM_002121.6). RPL41 (NM_001035267.2), TAPBP (NM_003190.5), TMA7 (NM_015933.6), GPX1 (NM_000581.4), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), LINC0127 (NR_015353.2). TMEM250 (NM_152833.3), RBM14 (NM_006328.4), MIF (NM_002415.2), ARPC1A (NM_006409.4), RP11-100N21.1 (AC092597), TMEM141 (NM_032928.4), H2AJ (NM_177925.5), CDK11B (NM_033486.3), SMIM31 (NM_001352885.1), MALAT1 (NR_002819.5), RNY4 (NR_ 004393.1), HOXAIO(NM_018951.4), LYN (NM_002350.4), RP11-156P1.3, SRSF8 (NM_032102.4), TAF15 (NM_139215.3). CHASERR (NR_037600.1). RP11-290D2.

6. ENSG00000275110 (NM_033380.3), FLJ16779, H4C5 (NM_003545.4), LHX1-DT (NR__135671.1), RP11-467J12.4(NR_136518.1), MY019 (NM_OO 1163735.2), H4C2 (NM_003544.3), RPll-147L13.il, and RP11-84E17.1.

5. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from TMEM176A (NM_018487.3), TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3), TTC22 (NM_001114108.2), CACNA2D2 (NM_006030.4), NFIX (NM_001365902.3), IL32 (NM_001376923.1), SCMH1 (NM_001394311.1). LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3), VIM (NM_003380.5), CD44 (NM_000610.4), SZRD1 (NM_001114600.3), LAMC2 (NM_005562.3), VMP1 (NM_030938.5), BICRA (NM_001394372.1), CTSA (NM_000308.4), SLC9A3R2 (NM_001130012.3), WDR18 (NM_024100.4). TLE2 (NM_003260.5), MTHFD2 (NM_006636.4), PDE4A (NM_001111307.2), PLPP1(NM-003711.4), BCL3 (NM_005178.5), RAB27A (NM_183235.3), DAZAP1 (NM_018959.4), PTPN18 (NM_014369.4), TPD52 (NM_001025253.3). GNB1 (NM_002074.5), TP53INP2 (NM_021202.3), RIMS1 (NM_014989.7), BAX (NM_138761.4), SH3BP2 (NM_001122681.2), EBF4 (NM_001395167.1), GRAMD1A (NM_020895.5), CDV3 (NM_017548.5), NUBP2 (NM_012225.4), MKNK2 (NM_199054.3), SEC14L2 (NM_012429.5), SLC25A1 (NM_005984.5), GGA1 (NM_013365.5), CYB5R3 (NM_000398.7), TTLL12 (NM_015140.4), CTSZ (NM_001336.4), CDC25B (NM_021873.4), WFDC2 (NM_006103.4), MAP1LC3A (NM_032514.4), LPIN2 (NM_001375808.2), PLP2 (NM_002668.3), TIMP1 (NM_003254.3), MAGED2 (NM_177433.3), NUTF2 (NM_005796.3), CLCN7 (NM_001287.6), MAZ (NM_002383.4), TMC5 (NM_001261841.2), BLOC1S6 (NM_012388.4), MAN2B1 (NM_000528.4), SF3A2 (NM_007165.5), SGTA (NM_003021.4), MED25 (NM_030973.4), SLC1A5 (NM_005628.3), PTPRS (NM_002850.4), KDELR1 (NM_006801.3), RAB3D (NM_004283.4), PLEKHA4 (NM_020904.3), COPE (NM_007263.4), LSR (NM_205834.4), GSK3A (NM_019884.3), ZC3HAV1 (NM_020119.4), MOSPD3 (NM_023948.5), IMPDH1 (NM_000883.4), ZNHIT1 (NM_006349.3), BCL7B (NM_001707.4). LIMK1 (NM_002314.4), PRUNE2 (NM_015225.3), TESK1 (NM_006285.3), EDF1 (NM_003792.4), SFXN3 (NM_030971.6), FBXW4 (NM_022039.4), SLC25A11 (NM_003562.5), RASD1 (NM_016084.5). CCL2 (NM_002982.4), SLC9A3R1 (NM_004252), CRACD (NM_001393381.1), CRYAB (NM_001289808.2), MDK (NM_002391.6), FOXM1 (NM_021953.4), CHPT1 (NM_020244.3), C12orf57 (NM_138425.4), COX6A1(NM_004373.4), S0D2 (NM_000636.4), PHF1 (NM_024165.3), FBRSL1 (NM_001367871.1), LMNB1 (NM_005573.4), ERGIC1 (NM_001031711.3), GNAI2 (NM_002070.4), MLPH (NM-024101.7). 0DC1 (NM_002539.3), SRM (NM_003132.3), Clorf21 (NM_030806.4). TSPAN1 (NM_005727.4), CTSD (NM_001909.5), SPP1 (NM_001040058.2), ELL2 (NM_012081.6), CCDC92 (NM_025140.3), NEK6 (NM_014397.6), TGFB3 (NM_003239.5), OGFRL1 (NM_024576.5), DUSP1 (NM_004417.4). EGR1 (NM_001964.3), SERP1 (NM_014445.4), CLU (NM_001831.4), TNFRSF10B (NM_003842.5), SORBS3 (NM_005775.5), TNFSF10 (NM_003810.4), CALD1 (NM_033138.4), NR4A1 (NM_173157.3), TUBA1B (NM_006082.3), AMD1 (NM_001634.6), MXD4 (NM_006454.3), PMEPA1 (NM_020182.5), KLHDC3 (NM_057161.4), MEA1 (NM_014623.4), CDKN1A (NM_000389.5). DEK (NM_003472.4), MYRF (NM_001127392.3), MT2A (NM_005953.5), SOX9 (NM_000346.4), PPDPF (NM_024299.4), C3 (NM_000064.4), HIVEP3 (NM_024503.5), EMC6 (NM_031298.4), YWHAH (NM_003405.4), ATF4 (NM_182810.3), CDC42EP1 (NM_152243.3), LIF (NM_002309.5). PGAP6 (NM_021259.3), KLHDC7B (NM_138433.5), SSBP4 (NM_032627.5), GDF15 (NM_004864.4), JUND (NM_005354.6), UBE2M (NM_003969.4), EIF3G (NM_003755.5), SLC6A8 (NM_005629.4), TOP2A (NM_001067.4), RARA (NM_000964.4), ITGB4 (NM_000213.5), TRIM47 (NM_033452.3), PLAAT4 (NM_004585.5), CEP20 (NM_144600.4), BTG1 (NM_001731.3), BHLHE40 (NM_003670.3), TMEM106C (NM_001143842.2), LDHA (NM_005566.4), ETS1 (NM_001143820.2), MAP7 (NM_003980.6), NIBAN1 (NM_052966.4), KLF4 (NM_004235.6), ANP32B (NM_006401.3), PARP6 (NM_001323532.2), TACC2 (NM_206862.4), PARP9 (NM_001146105.2), RNF185 (NM_152267.4), CLSTN3 (NM_014718.4). WARSI (NM_004184.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SAMD1 (NM_138352.3), AKT1 (NM_001382430.1), ZNF787 (NM_001002836.4), SH3BGRL3 (NM_031286.4), SYTL1 (NM_001193308.2), MGST3 (NM_004528.4), RABB (NM_002870.5), ARL8A (NM_138795.4), RHOB (NM_004040.4), ARL6IP5 (NM_006407.4), HIGD2A (NM_138820.4), FAM193B (NM_001190946.3), PPP1R18 (NM_133471.4), PRIM2 (NM_000947.5), PNRC1 (NM_006813.3), MKI67 (NM_002417.5), DGKZ (NM_001199267.2), ALDOA (NM_001243177.4), TMCO3 (NM_017905.6), RILPL2 (NM_145058.3), PRDM8 (NM_001099403.2), RASSF3 (NM_178169.4). UBALD1 (NM_145253.3), CMIP (NM_198390.3), CEP112 (NM_001199165.4), ADAMTS1 (NM_006988.5), AZINI(NM_148174.4), HKDC1 (NM_025130.4), RBPMS (NM_001008710.3), MMP14 (NM_004995.4), FZD1 (NM_003505.2), CREB3L1 (NM_052854.4), FAIM (NM_001033031.2). SLC45A3 (NM_033102.3), NBL1 (NM_005380.8). IFNGR2 (NM_005534.4), CSRP1 (NM_004078.3), UBE2Z (NM_023079.5), PTMS (NM_002824.6), RGS12 (NM_001394154.1), ZYX (NM.003461.5), PDE9A (NM_002606.3), S100A1 (NM_006271.2). MGAT4B (NM_014275.5), FMNL3 (NM_175736.5). CXCL16 (NM_001386809.1), SDC3 (NM_014654.4), VCAM1 (NM_001078.4), ATF3 (NM_001674.4), KIF26B (NM_018012.4), LRATD1 (NM_145175.4), H3-3A (NM_002107.7), CCNYL1 (NM_001330218.2), FZD5 (NM_003468.4), IGFBP7 (NM_001553.3), SSR2 (NM_003145.4), ZC3H12A (NM_025079.3), MEAF6 (NM_001270875.3), DNALI1 (NM_003462.5), SGMS2 (NM_001375905.1), H2AZ1 (NM_002106.4), BSN (NM_003458.4), CTSB (NM_001908.5), FASTK (NM_006712.5), PCBD1 (NM_000281.4), TAF10 (NM_006284.4), CDYL2 (NM_152342.4), SEC11C (NM_033280.4), RRAD (NM_004165.3), B2M (NM_004048.4), MBD6 (NM_052897.4), TRUB2 (NM_015679.3), MIDN (NM_001388306.1), TUBA1C (NM_032704.5), CDC42EP5 (NM_145057.4), NXN (NM_022463.5), CDK2AP2 (NM_005851.5), FTH1 (NM_002032.3), RAB4A (NM_004578.4), DDIT4 (NM_019058.4), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2), RAB31 (NM_006868.4), CHTF8 (NM_001039690.5), ATF5 (NM_001193646.2), MUC3A (NM_005960.2), NDUFA3 (NM_004542.4). MRPL36 (NM_032479.4), FBXL14 (NM_152441.3). MALT1 (NM_006785.4), CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), HRAS (NM_005343.4), RAB1B (NM_030981.3), ASPHD1 (NM_181718.4), MARCKSL1 (NM_023009.7). TP53I11 (NM_006034.5), CLTB (NM_007097.5), RPS6KB2 (NM_003952.3), B3GALT6 (NM_080605.4), NUPR1 (NM_012385.3), SLC35A4 (NM_080670.4), WSB2 (NM_018639.5), JUN (NM_002228.4), CD151 (NM_004357.5), HNRNPAO (NM_006805.4), MAF (NM 005360.5), CTNNBIP1 (NM_020248.3). KCTD12 (NM_ 138444.4), ZFPM1 (NM_153813.3), FGD6 (NM_018351.4), MEX3D (NM_203304.4), PHLDA2 (NM_003311.4), CLN8 (NM_018941.4), KMT5A (NM_020382.7), SNRNP35 (NM_022717.4), PDE4B (NM_002600.4), H2BC21 (NM_003528.3), Hl-10 (NM_006026.4), P4HB (NM_000918.4), ZFP36L1 (NM_004926.4), COL4A1 (NM_001845.6), ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), FYB2 (NM_001004303.5), PLA2G2A (NM_001395463.1), H2AX (NM_002105.3), ZDHHC9 (NM_016032.4), Hl-0 (NM_005318.4), SULF2(NM_001387048.1), VKORC1L1 (NM_173517.6), LAMB3 (NM_000228.3), FLNA (NM_001110556.2), SERPINA1 (NM_000295.5), GPAA1 (NM.003801.4), H2BC12 (NM_001312653.2), RPL12 (NM_000976.4). NRARP (NM_001004354.3), MAFK (NM_002360.4), GLMP (NM_144580.3), ZNF358 (NM_018083.5), ARHGAP11A(NM_014783.6), UBE2J1 (NM_016021.3), R3HDM4 (NM_138774.4), TGM2 (NM_004613.4), VTRNA1-1 (NRJ126703.1), RNY1 (NR_004391). RNY3 (NR_004392.1), SAMD5 (NM_001030060.3), H2BC18 (NM_001024599.5), RTL8A (NM_001078172.2), LINC00963 (NR_038955.1), RNF5 (NM_006913.4). NEU1 (NM_000434.4), HLA-C (NM_002117.6), HLA-E (NM_005516.6), AKT1S1 (NM_001098633.4), HMGN1 (NM_004965.7), HLA-A (NM_002116.8), SNORD17 (NR_003045.1), ZNF580 (NM_207115.2), LBH (NM_030915.4), CEBPD (NM_005195.4), HLA-DPB1 (NM_002121.6), TAPBP (NM_003190.5), GPX1 (NM_000581.4), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), LINC01278, TMEM250 (NM_152833.3), RBM14 (NM_006328.4), MIF (NM_002415.2), ARPC1A (NM_006409.4), RP11-100N21.1 (AC092597). TMEM141 (NM_032928.4), H2AJ (NM_177925.5), SMIM31 (NM_001352885.1), MALAT1 (NR_002819.5), RNY4 (NR_004393.1), HOXAIO (NM_018951.4), LYN (NM_002350.4), RP11-156P1.3, CHASERR (NR_037600.1), RP11-290D2.6, ENSG00000275110 (NM_033380.3), FLJ16779, H4C5 (NM_003545.4), LHX1-DT (NR_135671.1 ), RP11-467J12.4, MYO19 (NM_001163735.2), H4C2 (NM_003544.3), RPll-147L13.il, and RP11-84E17.1.

6. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from TMEM176A (NM_018487.3). TMEM98 (NM_015544.3), CX3CL1 (NM_002996.6), TNFRSF12A (NM_016639.3), CACNA2D2 (NM_006030.4), NFIX (NM_001365902.3), IL32 (NM_001376923.1), LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3). CD44 (NM_000610.4), LAMC2 (NM_005562.3), CTSA (NM_000308.4), MTHFD2 (NM_006636.4), PDE4A(NM_001111307.2), PLPP1 (NM_003711.4), BCL3 (NM_005178.5). RAB27A (NM_183235.3), RIMS1 (NM_014989.7), EBF4 (NM_001395167.1), SEC14L2 (NM_012429.5), CDC25B (NM_021873.4), WFDC2 (NM_006103.4), MAP1LC3A (NM_032514.4), PLP2 (NM_002668.3). TIMP1 (NM_003254.3). MAZ (NM_002383.4). TMC5 (NM_001261841.2), RAB3D (NM_004283.4), MOSPD3 (NM_023948.5), PRUNE2 (NM_015225.3), SFXN3 (NM_030971.6), RASD1 (NM_016084.5), CCL2 (NM_002982.4), CRACD(NM_OO 1393381.1), CRYAB (NM_OO 1289808.2), MDK (NM_002391.6), FOXM1 (NM_021953.4), CHPT1 (NM_020244.3), LMNB1 (NM_005573.4), TSPAN1 (NM_005727.4), SPP1 (NM_001040058.2), TGFB3 (NM_003239.5), OGFRL1 (NM_024576.5), EGR1 (NM_001964.3), CLU (NM_001831.4), SORBS3 (NM_005775.5), TNFSF10 (NM_003810.4), PMEPA1 (NM_020182.5), MYRF (NM_001127392.3), MT2A (NM_005953.5), C3 (NM 000064.4). CDC42EP1 (NM_152243.3), LIF (NM_002309.5), KLHDC7B (NM_138433.5), SLC6A8 (NM_005629.4), TOP2A (NM_001067.4), TRIM47 (NM_033452.3), PLAAT4 (NM_004585.5), NIBAN1 (NM_052966.4), KLF4 (NM_004235.6), CLSTN3 (NM_014718.4), NOL3 (NM_001276309.3), ARRB2 (NM_004313.4), SECTM1 (NM_003004.3), SYTL1 (NM_001193308.2), ARL6IP5 (NM_006407.4), PPP1R18 (NM_133471.4). PRIM2 (NM_000947.5). MKI67 (NM_002417.5). PRDM8 (NM_001099403.2), ADAMTS1 (NM_006988.5), HKDC1 (NM_025130.4), MMP14 (NM_004995.4), CREB3L1 (NM_052854.4), SLC45A3 (NM_033102.3), NBL1 (NM_005380.8). ZYX (NM_003461.5). FMNL3 (NM_175736.5), CXCL16 (NM_001386809.1), VCAM1 (NM_001078.4), ATF3 (NM_001674.4), LRATD1(NM_145175.4), FZD5 (NM_003468.4), SGMS2 (NM_001375905.1), BSN (NM_003458.4), TAF10 (NM_006284.4), RRAD (NM_004165.3), B2M (NM_004048.4), CDC42EP5 (NM_145057.4), NXN (NM_022463.5), GNG4 (NM_001098722.2), NT5DC2 (NM_001134231.2). MUC3A (NM_005960.2), NDUFA3 (NM_004542.4). CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), ASPHD1 (NM.181718.4), TP53I11 (NM_006034.5), B3GALT6 (NM_080605.4), NUPR1 (NM_012385.3), JUN (NM_002228.4), CD151 (NM_004357.5), ZFPM1 (NM_153813.3), MEX3D (NM_203304.4), PHLDA2 (NM_003311.4), SNRNP35 (NM_022717.4), PDE4B (NM_002600.4), COL4A1(NM_001845.6), ISG15 (NM_005101.4), TMEM220 (NM_001004313.3), PLA2G2A (NM 001395463.1), H2AX (NM_002105.3). LAMB3 (NM_000228.3), SERPINA1 (NM_000295.5), NRARP (NM_001004354.3), MAFK (NM_002360.4), GLMP (NM_144580.3), ARHGAP11A (NM_014783.6), TGM2 (NM_004613.4), VTRNA1-1 (NR.026703.1), RNY1 (NR_004391), SAMD5 (NM_001030060.3), HLA-C (NM_002117.6), HLA-A (NM_002116.8), SNORD17 (NR_003045.1), ZNF580 (NM_207115.2), HLA-DPB1 (NM_002121.6). TAPBP (NM_003190.5), TMEM238 (NM_001190764.2), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), RBM14 (NM_006328.4), SMIM31(NM_OO 1352885.1), MALAT1 (NR_002819.5), RNY4 (NR_ 004393.1), HOXAIO (NM_018951.4), LYN (NM_002350.4), FLJ16779, RP11-467J12.

47. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from IL32 (NM_001376923.1), LTF (NM_002343.6), ELOVL5 (NM_021814.5), CD74 (NM_001025159.3), BCL3 (NM_005178.5), CDC25B (NM_021873.4), MAZ (NM_002383.4), RAB3D (NM_004283.4), PRUNE2 (NM_015225.3), RASD1 (NM_016084.5), SORBS3 (NM_005775.5), CDC42EP1 (NM_152243.3), PLAAT4 (NM_004585.5), SYTL1 (NM_001193308.2), ADAMTS1 (NM_006988.5), NBL1 (NM_005380.8), ZYX (NM_003461.5), CXCL16 (NM_001386809.1), LRATD1 (NM_145175.4), FZD5 (NM_003468.4), TAF10 (NM_006284.4), RRAD (NM_004165.3), CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), JUN (NM_002228.4), ZFPM1 (NM_153813.3), SNRNP35 (NM_022717.4), SERPINA1 (NM_000295.5), MAFK (NM_002360.4), ARHGAP11A (NM_014783.6). TGM2 (NM_004613.4), VTRNA1-1 (NR__026703.1), RNY1 (NR_004391), HLA-DPB1 (NM_002121.6), HLA-B (NM_005514.8), C12orf75 (NM_001145199.2), RNY4 (NR_004393.1).

8. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from RASD1 (NM_016084.5), ERGIC1 (NM_001031711.3). MLPH (NM_O241O1.7), ODC1 (NM_002539.3), SOX9 (NM_000346.4), PPDPF (NM_024299.4), CDC42EP1 (NM_152243.3), JUND (NM_005354.6), NBL1 (NM_005380.8), TAF10 (NM_006284.4), MIDN (NM_001388306.1), CEBPB (NM_005194.4). TNFRSF10D (NM_003840.5), JUN (NM_002228.4), HNRNPAO (NM_006805.4), RPL12 (NM_000976.4), MAFK (NM_002360.4), HLA-DPB1 (NM_002121.6), and RNY4 (NR_004393.1).

9. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from RASD1 (NM_016084.5), CDC42EP1 (NM_152243.3), NBL1 (NMJJ05380.8), TAF10 (NM_006284.4), CEBPB (NM_005194.4), TNFRSF10D (NM_003840.5), JUN (NM_002228.4), MAFK (NM_002360.4), HLA-DPB1 (NM_002121.6), RNY4 (NR.004393.1).

10. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from RASD1 (NM_016084.5), NBL1(NM_005380.8), CEBPB (NM_005194.4), HLA-DPB1 (NM_OO2121.6), andRNY4 (NR_004393.1).

11. The method of claim 3, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from CEBPB (NM_005194.4), HLA-DPB1 (NM_002121.6), and RNY4 (NR_004393.1).

12. The method of any one of claims 1-11, wherein the at least one cfRNA comprises a cfRNA of a kidney injury signature gene with a decreased level as compared to control being indicative of AKI.

13. The method of 12, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from SPAG9 (NM_001130528.3), IKZF2 (NM_001387220.1), RFC1 (NM_002913.5), ZFYVE16 (NM_001284236.3). LSG1 (NM_018385.3), CAPG(NM_001747.4), PUM2 (NM_015317.5), PKN2 (NM_006256.4), TBC1D1 (NM_001396959.1), NGEF (NM_019850.3), EML1 (NM_004434.3), KDM5A (NM_001042603.3), TOP2B (NM_001330700.2), FDFT1 (NM_004462.5), SMARCA2 (NM_003070.5), HSP90AA1 (NM_005348.4), NCOA1 (NM_003743.5), EPB41L1 (NM_012156.2), KIF9 (NM_182902.4), C20orfl94 (NM„001009984), TRPM7 (NM_017672.6), MIEF1 (NM_019008.6), GABRE (NM_004961.4), 1NTS6 (NM_012141.3), HERC1 (NM_003922.4), AVL9 (NM_015060.3), PIK3CG (NM_001282426.2), TAX1BP1 (NM_006024.7), ANKMY2 (NM_020319.3), KANK1 (NM_015158.5). TASOR2 (NM_001321783.2), INTS2 (NM_001351695.2). PRKAR2A (NM_004157.4), PARD3B (NM_001302769.2), CASP8AP2 (NM_001137667.2), FBXL5 (NM_012161.4), HSDL2 (NM_032303.5), DNAL1 (NM_031427.4), AFTPH (NM_203437.4), PPP1R3C (NM 005398.7). ARFGEF2 (NM_006420.3). CNOT1 (NM_016284.5), ICE2 (NM_024611.6), THEM6 (NM_016647.3), OSBPL2 (NM_144498.4), PPIL4 (NM_139126.4), DIAPH1 (NM_005219.5), EXOC4 (NM_021807.4), PPARG (NM_138711.6), KRBA1 (NM_001290187.2), CTIF (NM_014772.3), APC (NM_000038.6), MDM2 (NM_002392.6), GCC2 (NM_181453.4), EGF (NM_001963.6), ESCO1 (NM_052911.3), SHQ1 (NM_018130.3), PIK3R1 (NM_181523.3), PPIP5K2 (NM_001276277.3). MPP7 (NM_001318170.2), CCT5 (NM_012073.5), KCNJ1 (NM_153766.3), RABGAP1L (NM_001366446.1), EPG5 (NM_020964.3), ZNF117 (NM_015852.5), CCDC174 (NM_016474.5), ZFYVE9(NM_004799.4), EPB41 (NM_OO 1376013.1 ), CLIC6 (NM_053277.3), ACOX1 (NMJ104035.7), MYSM1 (NM_001085487.3), ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), GNL3 (NM_014366.5). TASOR (NM_001365635.2), HPGD (NM_000860.6), ICE1 (NM_015325.3). ARHGAP12 (NM_018287.7), ABRAXAS2 (NM_032182.4), CLPX (NM_006660.5), SGSM1 (NM_001098497.3), TEF (NM_003216.4), SRP68 (NM_014230.4), C2CD3 (NM_001286577.2), HSPA4 (NM_002154.4), ZNF439 (NM_001348719.2). TNKS (NM_003747.3), PSMD1 (NM_002807.4), CEP97 (NM_024548.4), ZNF397 (NM_001135178.3), PLCD1 (NM_006225.4), NBR1 (NM_005899.5), PIK3R4 (NM_014602.3), ZNF420 (NM_144689.5), PEG3 (NM_006210.3), ITSN2 (NM_006277.3), TTC37(NM..014639), CTR9 (NM_014633.5), PHACTR4 (NM_001048183.3), ASAH2B (NM_001321958.2), ZDBF2 (NM_020923.3), RNU6-36P. ZNF134 (NM_003435.5), LINC01363 (NR_110811.1), LINC02016, RP1-17K7.2 (AL035078), GAN (NM_022041.4), SRGAP2 (NM_015326.5), SYNRG (NM_007247.6), XXbac-BPG283O16.9, and RP11-157L3.14.

14. The method of claim 12, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from 1KZF2 (NM_001387220.1), LSG1 (NM_018385.3), CAPG (NM_001747.4), PKN2 (NM_006256.4), NGEF (NM_019850.3), EML1 (NM_004434.3), KIF9 (NM_182902.4), GABRE (NM_004961.4), PIK3CG(NM_001282426.2), ANKMY2 (NM_020319.3), INTS2 (NM_001351695.2), PPP1R3C (NM_005398.7), ICE2 (NM_024611.6), THEM6 (NM_016647.3), PPARG (NM_138711.6), KRBA1 (NM_001290187.2), APC (NM_000038.6), EGF (NM_001963.6), SHQ1(NM_018130.3), MPP7 (NM_001318170.2), KCNJ1 (NM_153766.3), ZNF117 (NM_015852.5), CLIC6 (NM_053277.3), ACOX1 (NM_004035.7), ACP6 (NM.016361.5), KCNJ3 (NM_002239.4), HPGD (NM_000860.6), ABRAXAS2 (NM_032182.4). SGSM1 (NM_001098497.3), TEF (NM_003216.4), ZNF439 (NM_001348719.2), CEP97 (NM_024548.4), PLCD1 (NM_006225.4), PIK3R4 (NM_014602.3), ZNF420 (NM_144689.5), PEG3 (NM_006210.3), ASAH2B (NM_001321958.2), ZDBF2 (NM_020923.3), RNU6-36P, ZNF134 (NM_003435.5), LINC01363 (NR_110811.1), LINC02016, RP1-17K7.2, GAN(NM-022041.4). SRGAP2 (NM_015326.5). XXbac-BPG283O16.9, and RP11-157L3.14.

15. The method of claim 12, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from SPAG9 (NM_001130528.3), PKN2 (NM_006256.4), TBC1D1 (NM_001396959.1), NGEF (NM_019850.3), NCOA1 (NM_003743.5), C20orfl94, INTS2 (NM_001351695.2), FBXL5 (NM_012161.4), OSBPL2 (NM_144498.4), PPARG(NM-138711.6), CTIF (NM_014772.3), APC (NM_000038.6), EGF (NM_001963.6), ACP6 (NM_016361.5). KCNJ3 (NM_002239.4), ICE1 (NM_015325.3). PIK3R4 (NM_014602.3), RNU6-36P, LINC02016, RP1-17K7.2.

16. The method of claim 12, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from NCOA1 (NM_003743.5), FBXL5 (NM-012161.4). CTIF (NM_014772.3). EGF (NM_001963.6), ACP6 (NM_016361.5), KCNJ3 (NM_002239.4), LINC02016, and RP1-17K7.2.

17. The method of claim 12, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from EGF (NM_001963.6), KCNJ3 (NM_002239.4), LINC02016, and RP1-17K7.2.

18. The method of claim 12, wherein the at least one cfRNA comprises one or more or all of cfRNAs of kidney injury signature genes selected from EGF (NM_001963.6), KCNJ3 (NM_002239.4).

19. The method according to any one of claims 1-18, wherein measuring the level of at least one cfRNA comprises RNA sequencing.

20. The method according to any one of claims 1-18. wherein measuring the level of at least one cfRNA comprises a PCR assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR).

21. The method according to any one of claims 1-18, wherein measuring the level of at least one cfRNA comprises in situ hybridization, clustered regularly interspaced short palindromic repeats (CRISPR) assay, Loop-mediated isothermal amplification (LAMP), or microarray.

22. The method of any one of claims 1-21, wherein the method further comprises a step of detecting the cells of origin of the kidney injury of the subject.

23. The method of claim 22, wherein the cells of origin are kidney epithelial cells and the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells or a combination thereof.

24. The method of any one of claims 21-23, wherein the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney.

25. The method of any one of claims 1-24, wherein the kidney injury is acute kidney injury (AKI).

26. The method of any one of claims 1-25, wherein the urine sample is a longitudinally collected urine sample.

27. The method of claim 26, wherein the longitudinally collected urine sample is obtained from the subject about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 10 days, about 15 days, about 30 days, about 45 days, about 60 days, about 75 days, about 90 days, about 105 days, and / or about 120 days after the initial urine sample is collected from the subject.

28. The method according to any one of claims 1-27, wherein when there is a kidney injury in the subject, the method further comprises treating the subject with a therapy to ameliorate the kidney injury.

29. The method according to any one of claims 1-28, wherein the subject has undergone a transplant of an organ or tissue of the urinary tract.

30. A method for determining the underlying etiology of an acute kidney injury (AKI) in a subject undergoing an immune checkpoint inhibitor (ICI) therapy, the method comprising:measuring the level of at least one cell-free RNA (cfRNA) molecule in a urine sample from the subject, wherein the at least one cfRNA molecule is a cfRNA of a gene andwherein a differential abundance of the cfRNA of the gene corresponds to an etiology of AKI;comparing the measured level of the at least one cfRNA to a control; and determining that the underlying etiology of the AKI is either acute tubulointerstitial nephritis (ATIN) or acute tubular necrosis / hemodynamic AKI (ATN) based on an increase or decrease in the level of the at least one cfRNA as compared to the control.

31. The method of claim 30, wherein the at least one cfRNA comprises a cfRNA of a signature gene with an increased level as compared to control being indicative of an ATIN etiology.

32. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), NOS2 (NM_000625.4), CYTH3 (NM_004227.4), ETV7 (NM_016135.4), LTF (NM_002343.6), CLCA1 (NM_001285.4), PHLDB1 (NM_001144758.3), CD74 (NM_001025159.3), BIRC3 (NM_001165.5), BARX2 (NM_003658.5), WDR37 (NM_014023.4), TRAF1 (NM_005658.5), LAMC2 (NM_005562.3), EPB41L2 (NM_001431.4), APOB (NM_000384.3), KIZ (NM_018474.6), ICAM1 (NM_000201.3). LYZ (NM_000239.3), CIRBP (NM_001300829.2), CERK (NM_022766.6), NFKBIA (NM_020529.3), LIPG (NM_006033.4), TMC5 (NM_001261841.2), IL4I1 (NM_152899.2), FAM83E (NM_017708.4), PLEKHA4 (NM_020904.3), ARRDC2 (NM_015683.2), ZC3HAV1 (NM_020119.4), FBXW4 (NM_022039.4), CCL2 (NM_002982.4), APOA4 (NM_000482.4), SLC15A3 (NM_016582.3), FOXM1 (NM_021953.4), FN1 (NM_212482.4). STAT1 (NM_007315.4), KCNJ13 (NM_002242.4), GBP1 (NM_002053.3). SYF2 (NM_015484.5), IFIT3 (NM_001549.6), CD274 (NM_014143.4), CIT (NM_001206999.2), TBCC (NM_003192.3), IRF1 (NM_002198.3), TSPAN8 (NM_004616.3), SAT1 (NM_002970.4), BST2 (NM_004335.4), IDO1 (NM_002164.6), PSMC3IP (NM_016556.4), TOP2A (NM_001067.4), EPSTI1 (NM_033255.5), HNRNPA1(NM_031157.4), CD164 (NM_006016.6), TRA2B (NM_004593.3), KLF4 (NM_004235.6), ANP32B (NM_006401.3), MMP7 (NM_002423.5), THBS1 (NM_003246.4), IFI44L (NM_006820.4), MNS1 (NM_018365.4), CXCL9 (NM_002416.3), TPM1 (NM_001018005.2), NLRC5 (NM_001384950.1), IRF8 (NM_002163.4), CCDC40 (NM_017950.4), SECTM1 (NM_003004.3), RNF157 (NM_052916.3), PMAIP1 (NM_021127.3), RABB (NM_002870.5),ARL6TP5 (NM_006407.4), PNRC1 (NM_006813.3), SLC2A13 (NM_052885.4), GBP5 (NM_052942.5), RPGR (NM_001034853.2), UBE2L6 (NM_004223.5), ETS2 (NM_005239.6), MX1 (NM_002462.5), XDH (NM_000379.4), CDC42SE2 (NM_001375635.1), IFNGR2 (NM_005534.4), CXCL16 (NM_001386809.1), CAMK2N1 (NM_018584.6), GBP2 (NM_004120.5), PIGR (NM_002644.4), SGPP2 (NM_152386.4). CTSS (NM_004079.5), FZD5 (NM 003468.4). CXCL1 (NM_00151L4), ZC3H12A (NM_025079.3). TAGAP (NM_054114.5), TNFRSF11B (NM_002546.4), REEP3 (NM_001001330.3), DENND2B (NM_213618.2), B2M (NM_004048.4), TPM4 (NM_003290.3), BATF2 (NM_138456.4), TAPI (NM_000593.6), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), MUC17 (NM_001040105.2), MUC3A (NM_005960.2), OTUD3 (NM_015207.2), EMB (NM_198449.3), PARP14 (NM_017554.3), MUC13 (NM_033049.4), CTDSP2 (NM_005730.4), KCMF1 (NM_020122.5), KCTD12 (NM_138444.4), HLA-DQB1 (NM_002123.5), H2BC4 (NM_003526.3), FRAT2 (NM_012083.3), RELL1 (NM_001085400.2), CLN8 (NM_018941.4), H2AC21 (NM_175065.3), SOCS1 (NM_003745.2), ZFP36L1 (NM_004926.4), IFITM1 (NM_003641.5), NAP1L1 (NM_004537.7), PTMA (NM_002823.5), RP5-1086D14.6, BNIP5 (NM_001010903.5), HLA-DRB1 (NM_002124.4), HLA-DQA1 (NM_002122.5), FAM177B (NM_001394345.1), HLA-DRB5 (NM_002125.4), MUC2 (NM_002457.5), H2BC18 (NM_001024599.5), PSMB8 (NM_148919.4), HLA-DRA (NM_019111.5), HLA-C (NM_002117.6), HLA-E (NM_005516.6), TRIM31 (NM_007028.5), HLA-F (NM_001098479.2), HCP5 (NR_040662), HLA-H (NR_001434.4), HLA-A (NM_002116.8), HLA-DPB1 (NM_002121.6), LINC01133 (NR_038849.1), HLA-DPA1 (NM_033554.4), HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), PSMB9 (NM_002800.5). FMN1 (NM_001277313.2), LYN (NM_002350.4), CCL5 (NM_002985.3), H2AC12 (NM_080596.3), CCL4 (NM_002984.4), FCGBP (NM_003890.3), UHRF1 (NM_001048201.3), LHX1-DT (NR-135671.1), H4C2 (NM_003544.3). CTD-3014M21.1 (NR_027412.1), andH3C3 (NM_00353L3).

33. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), NOS2 (NM_000625.4), ETV7 (NM_016135.4). LTF (NM_002343.6), CD74 (NM_001025159.3), BIRC3 (NM_001165.5), WDR37 (NM_014023.4), EPB41L2 (NM_001431.4), ICAM1 (NM_000201.3), LYZ (NM_000239.3), NFKBIA (NM_020529.3), IL4I1 (NM_152899.2), FAM83E (NM_017708.4),PLEKHA4 (NM_020904.3), FN1 (NM_212482.4), STAT1 (NM_007315.4), GBP1 (NM_002053.3), CD274 (NM_014143.4), IRF1 (NM_002198.3), EPSTI1 (NM_033255.5), TRA2B (NM_004593.3), MMP7 (NM_002423.5), IFI44L (NM_006820.4), MNS1(NM_018365.4), CXCL9 (NM_002416.3), TPM1 (NM_001018005.2), IRF8 (NM_002163.4), SECTM1 (NM_003004.3), SLC2A13 (NM_052885.4), GBP5 (NM_052942.5), CDC42SE2 (NM_001375635.1), GBP2 (NM_004120.5), PIGR (NM_002644.4), CTSS (NM_004079.5). DENND2B (NM_213618.2), B2M (NM_004048.4), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), OTUD3 (NM_015207.2), IFITM1 (NM_003641.5), BNIP5 (NM_001010903.5), HLA-DQA1 (NM_002122.5), PSMB8 (NM_148919.4), HLA-DRA (NM_019111.5), HLA-E (NM_005516.6), TRIM31 (NM_007028.5), HLA-F (NM_001098479.2), HCP5 (NR_040662), HLA-H (NR_001434.4). HLA-A (NM_002116.8), HLA-DPB1 (NM_002121.6), HLA-DPA1 (NM_033554.4), HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), PSMB9 (NM_002800.5), LYN (NM_002350.4), CCL5 (NM_002985.3), H2AC12 (NM_080596.3), CCL4 (NM_002984.4), LHX1-DT (NR_135671.1), and CTD-3014M21.1.

34. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), NOS2 (NM_000625.4), LTF (NM_002343.6). CD74 (NM_001025159.3), IL4I1 (NM_152899.2), GBP1 (NM_002053.3), CD274 (NM_O14143.4), EPSTI1 (NM_033255.5), CXCL9 (NM_002416.3), GBP5 (NM_052942.5), GBP2 (NM_004120.5), B2M (NM_004048.4), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), IFITM1 (NM_003641.5), HLA-DQA1 (NM_002122.5), HLA-DRA (NM_019111.5), HLA-F (NM_001098479.2), HLA-H(NR_001434.4), HLA-DPA1 (NM_033554.4), HLA-B (NM_005514.8), OR2I1P (NM_001396058.1), CCL5 (NM_002985.3), CCL4 (NM_002984.4), and CTD-3014M21.1.

35. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CX3CL1 (NM_002996.6), CD74 (NM_001025159.3), STAT1 (NM_007315.4), GBP1 (NM_002053.3), CD274 (NM_014143.4), EPSTI1 (NM_033255.5), CXCL9 (NM_002416.3), GBP5 (NM_052942.5). GBP2 (NM_004120.5), DENND2B (NM_213618.2), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), PSMB8 (NM_148919.4), HLA-DRA (NM_019111.5), HCP5 (NR_040662), HLA-H(NR_OO 1434.4), HLA-B (NM_005514.8), 0R2I1P (NM_001396058.1), and LHX1-DT (NR_135671.1).

36. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CD274 (NM_014143.4), CXCL9 (NM_002416.3), GBP5 (NM_052942.5), BATF2 (NM_138456.4), CXCL10 (NM_001565.4), CXCL11 (NM_005409.5), HLA-DRA (NM_019111.5), HLA-H (NR_001434.4), and OR2I1P (NM_001396058.1).

37. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CXCL9 (NM_002416.3), GBP5 (NM_052942.5), BATF2 (NM_138456.4). CXCL10 (NM_001565.4). CXCL11 (NM_005409.5). and HLA-H (NR_001434.4).

38. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CXCL9 (NM_002416.3), GBP5 (NM_052942.5), CXCL10 (NM_001565.4), andCXCLll (NM_005409.5).

39. The method of claim 31, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from CXCL9 (NM_002416.3), CXCL10 (NM_001565.4), and CXCL11 (NM_005409.5).

40. The method of any one of claims 30-39. wherein the at least one cfRNA comprises a cfRNA of a signature gene with a decreased level as compared to control being indicative of an ATIN etiology.

41. The method of claim 40, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM_001747.4), DHX8 (NM_004941.3), TOP2B (NM_001330700.2), SMARCA2 (NM_003070.5), ASCC2 (NM_032204.5), KIAA0930 (NM_001009880.2), HSPB1 (NM_001540.5). VAT1 (NM_006373.4), OSBP (NM_002556.3), FBXL5 (NM_012161.4), NAGK (NM_017567.6), SH3BP5 (NM_004844.5), KRT7 (NM_005556.4), IL1RN (NM_173842.3), LRPPRC (NM_133259.4). GOLGA4 (NM_002078.5), DAB2 (NM_001343.4), PLCD3 (NM_133373.5), FOXQ1 (NM_033260.4). TSC1 (NM_000368.5), YWHAB (NM_139323.4), KMT2D (NM_003482.4), EVPL (NM_001988.4), HSPA4 (NM_002154.4),ABLIM3 (NM_014945.5), SNCG (NM_003087.3), SOWAHB (NM_001029870.3), ZNF398 (NM_170686.3), CARD11 (NM_032415.7), HOMEZ (NM_020834.3), and RP11-7K24.3.

42. The method of claim 40, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM_001747.4), ASCC2 (NM_032204.5), NAGK (NM_017567.6), SH3BP5 (NM_004844.5), KRT7 (NM_005556.4), IL1RN (NM_173842.3), DAB2 (NM_001343.4), PLCD3 (NM_133373.5), FOXQ1 (NM_033260.4), EVPL (NM_001988.4), ABLIM3 (NM_014945.5), SNCG (NM_003087.3), SOWAHB (NM_001029870.3), ZNF398 (NM_170686.3), CARD 11 (NM_032415.7), HOMEZ (NM_020834.3), and RP11-7K24.3.

43. The method of claim 40, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM_001747.4). ASCC2 (NM_032204.5), KRT7 (NM_005556.4), and RP11-7K24.3.

44. The method of claim 40, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4), TOMM34 (NM_006809.5), CAPG (NM_001747.4), and ASCC2 (NM_032204.5).

45. The method of claim 40, wherein the at least one cfRNA comprises one or more or all of cfRNAs of genes selected from ALDH3B1 (NM_000694.4) andTOMM34 (NM_006809.5).

46. The method according to any one of claims 30-45, wherein measuring the level of at least one cfRNA comprises RNA sequencing.

47. The method according to any one of claims 30-45, wherein measuring the level of at least one cfRNA comprises a PCR assay such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR).

48. The method according to any one of claims 30-45, wherein measuring the level of at least one cfRNA comprises in situ hybridization, clustered regularly interspaced short palindromic repeats (CRISPR) assay, Loop-mediated isothermal amplification (LAMP), or microarray.

49. The method of any one of claims 30-48, wherein the method further comprises a step of detecting the cells of origin of the kidney injury of the subject.

50. The method of claim 49, wherein the cells of origin are kidney epithelial cells and the kidney epithelial cells are selected from kidney tubule epithelial cells, connecting tubule cells, kidney proximal epithelial cells, kidney distal epithelial cells, kidney loop of Henle ascending or descending tubule epithelial cells, kidney collecting duct epithelial cells, kidney parietal epithelial cells or a combination thereof.

51. The method of either claim 49 or 50, wherein the detecting the cells of origin of the injured tissue of the subject comprises comparing the expression profile of the cfRNAs in the urine sample to the expression profiles characteristic of cells of the kidney.

52. The method of any one of claims 30-51, wherein the urine sample is a longitudinally collected urine sample.

53. The method of claim 52, wherein the longitudinally collected urine sample is obtained from the subject about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 10 days, about 15 days, about 30 days, about 45 days, about 60 days, about 75 days, about 90 days, about 105 days, and / or about 120 days after the initial urine sample is collected from the subject.

54. The method according to any one of claims 30-53, wherein when there is a kidney injury in the subject, the method further comprises treating the subject with a therapy to ameliorate the kidney injury.

55. The method according to any one of claims 30-54, wherein the subject has undergone a transplant of an organ or tissue of the urinary tract.

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