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US-20260125765-A1 - KIDNEY CANCER SCREENING METHODS

US20260125765A1US 20260125765 A1US20260125765 A1US 20260125765A1US-20260125765-A1

Abstract

Device and methods for detection of kidney cancer using urine samples are disclosed herein. The device and methods enable isolation and quantification of kidney tumor cells in urine samples from a subject in need thereof.

Inventors

  • WEN CHEN BURNS

Assignees

  • Cicadea Biotech, LLC

Dates

Publication Date
20260507
Application Date
20251222

Claims (20)

  1. 1 . A method for detecting a target analyte in cancer cells in a urine sample, the method comprising: (a) obtaining or having obtained the urine sample from a subject; (b) passing the urine sample through a filtration member to obtain a retentate, wherein the retentate is enriched in cancer cells, and wherein the filtration member is disposed concentrically within a first container member of a device; the filtration member comprising a clog-resistant filter disposed therein, the filter having a pore size of about 8 to about 12 microns; and (c) detecting the target analyte in the retentate; wherein the cancer cells are selected from kidney cancer cells, bladder cancer cells, urinary tract cancer cells, prostate cancer cells, and testicular cancer cells.
  2. 2 . The method of claim 1 , wherein the method further comprises: (d) quantifying the target analyte of (c).
  3. 3 . The method of claim 2 , wherein the method of quantification comprises a method selected from quantitative Polymerase chain reaction (qPCR), Reverse-Transcription PCR (RT-PCR), Multiplex PCR, Nested PCR, High Fidelity PCR, Fast PCR, Hot Start PCR, Long-range PCR, Arbitrary Primed PCR, Digital PCR, Droplet Digital PCR (ddPCR), isothermal amplification PCR, and Endpoint PCR (qualitative PCR).
  4. 4 . The method of claim 2 , wherein the target analyte comprises a discerning nucleic acid sequence or a housekeeping gene or a fragment thereof.
  5. 5 . The method of claim 4 , wherein the housekeeping gene is GAPDH.
  6. 6 . The method of claim 2 wherein the quantification of target analyte is used to: (a) estimate a tumor cell density in urine; (b) identify the tumor cells in urine; or (c) characterize the phenotype of the tumor cells.
  7. 7 . The method of claim 1 , further subjecting the retentate to disruption of the cancer cells in the retentate and centrifugation to produce a filtrate comprising DNA from the cancer cells.
  8. 8 . The method of claim 1 , wherein the filtration member comprises a membrane with a pore size of about 8 microns.
  9. 9 . The method of claim 1 , wherein the subject is at risk of having, suspected of having, undergoing screening, or has a current or prior diagnosis of kidney cancer, bladder cancer, urinary tract cancer, prostate cancer, or testicle cancer.
  10. 10 . The method of claim 6 , further comprising indicating the subject as having cancer when the level of the target analyte the retentate or the tumor cell density in the urine sample is elevated compared to a reference level.
  11. 11 . A device of claim 1 , the device comprising: (a) the container member having a bottom surface having a center point; and (b) the filtration member having a center point, the filtration member concentrically positioned adjacent to the container member.
  12. 12 . A method of treating a subject suspected of, at risk of having, or undergoing screening for a cancer, comprising: (a) obtaining or having obtained a urine sample from the subject; (b) passing the urine sample through a filtration member to obtain a retentate, wherein the retentate is enriched in cancer cells; and wherein the filtration member comprises a clog-resistant filter disposed therein, the filter having a pore size of about 8 to about 12 microns; (c) lysing or disrupting the cells in the retentate to form a lysed/disrupted cell mixture comprising nucleic acid from lysed/disrupted cells; (d) filtering the lysed/disrupted cell mixture from (c) through the filtration membrane to form a filtrate comprising the nucleic acid from the lysed/disrupted cells; (e) quantifying the level of a target analyte present in the retentate; (f) comparing the level of the target analyte in the urine sample to a reference level of the target analyte in a control sample; determining the tumor cell density of the urine sample in the retentate; or characterizing the phenotype of the tumor cells; (g) indicating the subject as having cancer when the level of the target analyte or the tumor cell density in the urine sample is elevated compared to the reference level; and (h) administering a treatment to the subject identified as having cancer; wherein the cancer is selected from kidney cancer, bladder cancer, urinary tract cancer, prostate cancer, and testicular cancer.
  13. 13 . The method of claim 12 , wherein the target analyte comprises a housekeeping gene or a fragment thereof.
  14. 14 . The method of claim 13 , wherein the target analyte is GAPDH DNA or a fragment thereof.
  15. 15 . The method of claim 12 , wherein the filtration member comprises a membrane with a pore size of about 8 microns.
  16. 16 . The method of claim 12 , wherein (c) or (d) comprises: (a) isolating a nucleic acid from the cancer cells in the retentate; and (b) conducting a qPCR analysis using primers and probe targeting a discerning nucleic acid sequence, sequences, or a fragment thereof.
  17. 17 . The method of claim 12 , wherein the filtration member is disposed concentrically within a container member of a device, the container member having a bottom surface having a center point; and the filtration member having a center point, the filtration member concentrically positioned adjacent to the container member.
  18. 18 . The method of claim 12 , further comprising subjecting the subject identified as having cancer to in-depth clinical workup or imaging prior to step (a) or subsequent to step (g).
  19. 19 . The method of claim 12 , wherein the treatment comprises administering the subject identified as having cancer a treatment selected from a chemotherapeutic agent, an immunomodulatory drug, an anti-inflammatory agent, an anti-angiogenic agent, a checkpoint inhibitor, an immunotherapy, ablation, radiation, and surgery.
  20. 20 . The method of claim 12 , wherein the method of (e) is selected from quantitative Polymerase chain reaction (qPCR), Reverse-Transcription PCR (RT-PCR), Multiplex PCR, Nested PCR, High Fidelity PCR, Fast PCR, Hot Start PCR, Long-range PCR, Arbitrary Primed PCR, Digital PCR, Droplet Digital PCR (ddPCR), isothermal amplification PCR, and Endpoint PCR (qualitative PCR).

Description

CROSS-REFERENCE TO RELATED APPLICATIONS The present application is a divisional of U.S. patent application Ser. No. 18/449,442, filed Aug. 14, 2023, which claims the benefit of U.S. Provisional Patent Application No. 63/397,618, filed Aug. 12, 2022, the contents of each of which is hereby incorporated by reference in its entirety. SEQUENCE LISTING The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety for all purposes. The XML copy, created on Dec. 19, 2025, is referred to as 111315-865714_Sequence_Listing.xml and is 3,682 bytes in size. FIELD The present disclosure provides methods, devices, and kits for diagnosing kidney cancer from urine samples in a subject in need thereof. BACKGROUND The American Cancer Society's estimates that about 81,800 new cases of kidney cancer (52,360 in men and 29,440 in women) will be diagnosed in the US for 2023 and about 14,890 people (9,920 men and 4,970 women) will die from this disease each year. Renal cell carcinomas (RCC) are the most common form of kidney cancer, however other forms of kidney cancers include transitional cell carcinomas, Wilms tumors, and renal sarcomas. Renal cell carcinoma is found mostly in high-risk groups of patients over the age of 65 in US. An estimated 18.2% of renal cancer cases are fatal. Most early-stage renal cancer patients do not present with symptoms and are incidentally found during a CT-scan for other purposes. If treated when the disease is localized to the kidney (stage 1-2), 5-year survival rates for renal cancer are 93%. However, the survival rate drops significantly, to as low as 15%, with locally advanced or metastatic disease. Even if treated, renal cancer may have a recurrence rate of 20% to 40% after removal of a kidney (nephrectomy). Early diagnosis is therefore key to favorable outcomes for a subject suffering from kidney cancer. However, currently methods for detecting kidney cancer are limited in ability to detect the cancer early. Detection also often occurs after the cancer has already metastasized to other locations and the patient is experiencing symptoms. These diagnoses preferentially use CT Scan imaging, which exposes the patient to harmful radiation. Moreover, such testing is costly which deters referring a patient for screening unless the patient presents with specific symptoms (such as blood in urine, unexplained flank pain, cough, bone pain, or other symptoms of advanced or metastatic disease) that are deemed to warrant CT scan analysis. Current methods are not sufficiently sensitive for early detection of kidney cancer from urine samples. Additionally, blood testing for genetic markers is limited by the fact that no single biomarker is validated for rapid screening of all mutations of kidney cancer genes. An urgent need exists for a simple, non-invasive, effective screening method for early detection of primary and recurrent renal cancer in the urinary tract. SUMMARY In some aspects the current disclosure encompasses a method for screening for a target analyte in a urine sample from a subject in need thereof, the method comprising the steps of: obtaining or having obtained the urine sample; passing the urine sample through a filtration member to obtain a retentate, wherein the retentate is enriched in urine tumor cells (UTCs), and detecting the target analyte present in the retentate. In some aspects, the subject is at risk of having, suspected of having, or has a current or prior diagnosis of kidney cancer. In some aspects, the method further comprises quantifying the target analyte. In some aspects, the method of quantification comprises quantitative Polymerase chain reaction (qPCR). In some aspects, the target analyte comprises a discerning sequence or a housekeeping gene or a fragment thereof. In some aspects, the housekeeping gene is GAPDH. In some aspects, the quantification of target analyte is used to estimate the tumor cell density in urine. In some aspects, the tumor cells are kidney cancer cells, bladder cancer cells, urinary tract cancer cells, prostate cancer cells, or testicle cancer cells. In some aspects, the filtration member comprises a membrane with a pore size of about 8 microns. In further aspects, provided herein is a method for classifying a subject suspected or at risk of having kidney cancer, comprising: (a) obtaining or having obtained a urine sample from the subject;(b) passing the urine sample through a filtration member to obtain a retentate, wherein the retentate is enriched in kidney tumor cells;(c) lysing or disrupting the intact cells in the retentate to form a lysed/disrupted cell mixture comprising nucleic acid from lysed/disrupted cells;(d) filtering the lysed/disrupted cell mixture from (c) through the filtration membrane to form a filtrate comprising the nucleic acid from the lysed/disrupted cells;(e) subjecting the filtrate from (d) to a quantitative polymerase chain