Abstract
The monoclonal gammopathies of renal significance (MGRS) are defined by the presence of a nephrotoxic monoclonal protein in the absence of a well-defined malignant entity. Mechanistically it has been postulated that, across the varied subtypes of MGRS, abnormal plasma cell or B-cell clones in the marrow produce nephrotoxic proteins; however, in many cases, no paraprotein is detected by conventional laboratory methods and the bone marrow can be morphologically normal. The genomic underpinnings of MGRS are unexplored and, due to the rarity of this disease, clinicians are often left to unable to determine the exact nature of the clonal cell populations. We carried out a pilot study to characterize ctDNA in MGRS patients (pts). The first phase of the protocol sought to collect peripheral blood samples and, when possible, matched bone marrow aspirates, from MGRS pts to evaluate the feasibility of ultra-low pass whole genome sequencing (ULP-WGS) from peripheral blood to identify and characterize ctDNA.
We report ULP-WGS results from peripheral blood samples in the initial phase of the study. Peripheral blood samples were collected from renal biopsy proven non-amyloidosis MGRS pts prior to the initiation of treatment. Cell free DNA (cfDNA) was extracted and quantified. A total of 5-20 ng of cfDNA input was used for ULP-WGS. Libraries were pooled and sequenced using 100-bp paired-end runs to an average genome-wide coverage of 0.5x. After deconvolution and alignment, fragments with size 90-150bp were extracted using samtools. IchorCNA was utilized to calculate tumor fraction based on a panel of normals derived from three plasma samples from healthy controls. Model parameters were optimized for low tumor fraction and a threshold of 3% ctDNA was used to identify positive samples. Renal responses were assessed based on International Kidney and Monoclonal Gammopathy (IKMG) group criteria.
Nine pts and were consented and gave samples for the study along with 3 healthy controls. Seven pts were sequenced, 4 of which were females and 3 were males. Median age was 58 years. Among sequenced pts, 5 presented with proliferative glomerulonephritis with monoclonal immune deposition (PGNMID) and 2 with light chain deposition disease (LCDD). Both patients with LCDD were kappa predominant and showed detectable plasma clones (8% and 3%). One of these pts displayed t(11:14) on bone marrow FISH testing. Among the 5 pts with PGNMID, 3 had IgG kappa deposition and only one had a detectable plasma clone (5%), which harbored trisomy 9 by FISH. Bone marrow flow cytometry was positive in 2 pts.
Median 24-hour urine protein content was 7.11g (0.92 – 10.58), median serum albumin 3.20 g/dL (2.90 – 4.90) and median serum creatinine at the time of diagnosis was 2.15 mg/dL (1.30-6.40). CKD was present in 6 of 7 pts at the time of diagnosis. Four pts had known hypertension. One exhibited a history of malignancy and one had a history of autoimmune disease.
ctDNA was detectable at a threshold of > 3.0% of cfDNA in 5 of 7 pts. Median ctDNA content was 4.0% (3.18% - 14.97%) of cfDNA. Four of the 5 samples containing ctDNA were hyperdiploid. Chromosome 19 was the most common site of copy number increase whereas chromosomes 6, 10, and 18 exhibited the most frequent decreases in copy number. Two pts with PGNMID had detectable ctDNA without evidence of a serological or marrow-based clone.
All pts received daratumumab, cyclophosphamide, bortezomib and dexamethasone as initial treatment. Five pts responded to therapy. Two patients ultimately underwent autologous stem cell transplant and a single patient received venetoclax as second line therapy. Of the patients exhibiting detectable ctDNA, three did not exhibit renal response to initial treatment. Both pts without ctDNA had PGNMID and responded to frontline treatment.
Mass spectrometry analysis and deep targeted sequencing of bone marrow aspirates and peripheral blood will be presented.
To our knowledge, this is the first study to detect ctDNA in MGRS. ULP-WGS, when combined with targeted sequencing and diagnostic modalities such as mass spectrometry, has the potential to not only to aid in diagnosis and treatment selection on a practical basis, but also to begin to unravel the underlying genomics of this rare disease. This approach has potential to serve as a platform for further genomic exploration and biomarker development in MGRS.
