December 2022 – Renal

The patient is a 33-year-old woman who is two months post-partum. She has a past medical history of mild pregnancy-associated hypertension during her first pregnancy six years ago. During her most recent pregnancy, she was hospitalized for possible preeclampsia, and she received treatment with magnesium sulfate. Serum creatinine was noted to be elevated at 2.19 mg/dL on admission and was 2.13 mg/dL at discharge. She was non-hypertensive at discharge. On follow-up, her serum creatinine was 1.98 mg/dL, and her serum albumin was normal at 4.3 g/dL. She did not have significant proteinuria and has no family history of renal disease. 

Figure 1: Low-power view of kidney core biopsy, demonstrating a focus of fibrosis with associated moderate mononuclear inflammation. Even from low-power magnification, tubular nucleomegaly is striking (H&E, 4x). 
Figure 2: Many proximal tubular nuclei show pleomorphic and enlarged nuclei. Some nuclei have bizarre shapes (H&E 10x). 
Figure 3: Electron micrograph of the tubules shows enlarged nuclei with irregular nuclear contours. Some nuclei have prominent nucleoli (EM, 1.5kx)

What is the most probable cause of the nuclear findings in the tubules? 

  • Genetic mutation
  • Radiation therapy
  • Magnesium sulfate effect
  • Viral infection

The correct answer is ...

Genetic mutation.

This is a case of karyomegalic interstitial nephritis (KIN), also known as karyomegalic nephropathy or systemic karyomegaly, which is a rare chronic tubulointerstitial nephritis most frequently caused by a genetic mutation in the FAN1 gene. In this case, whole exome sequencing later revealed a pathogenic homozygous frameshift mutation in FAN1 resulting in premature FAN1 protein truncation. Along with the morphologic and clinical findings, this further supports a diagnosis of autosomal recessive KIN.

The kidney biopsy contains tubules with pleomorphic, bizarre, and enlarged nuclei. Multinucleation and irregular nuclear membrane contours are frequently seen. Though rare macronucleoli are seen, nucleoli are generally inconspicuous to small. The tubular nuclei are approximately 2-5x larger than usual. Viral cytopathic effect is not appreciated. Overall, there is moderate tubular atrophy and interstitial fibrosis with associated mononuclear inflammation. Immunofluorescent microscopy studies are essentially negative. Electron microscopy reiterates the nuclear irregularities and enlargement in the tubules and the absence of viral cytopathic effect. These findings are most consistent with karyomegalic interstitial nephritis (KIN).

Karyomegalic interstitial nephritis (KIN) is rare, with approximately 50 cases reported in the literature. The known cases have generally presented in young adults (median: 33 years) and mostly in individuals of European and Maori descent. Presentation is variable: early-onset end-stage kidney disease is often seen, and cases may also exhibit elevated serum markers of hepatocyte damage, mild anemia, and recurrent upper respiratory infections. Most cases have been linked to autosomal recessive mutations in FAN1, which encodes Fanconi anemia-associated nuclease-1, a protein that repairs DNA interstrand crosslink damage and controls DNA ploidy in renal tubular cells. This protein is most highly expressed in kidney, liver, and neuronal tissue. Nuclear changes can be seen in these other tissues, but the kidney is most likely to be affected pathologically by fibrosis and inflammation. Often, along with the characteristic karyomegaly, kidney biopsies will show chronic inflammatory changes — interstitial fibrosis, tubular atrophy, and mononuclear inflammation, as in this case. Ki67 expression is typically reduced, and mitotic figures are usually absent. Of note, karyomegalic cells can shed in urine and can mimic viral cytopathic effect or even carcinoma in urine cytology specimens.

Patients often slowly but inevitably progress to renal failure, likely due to inadequate DNA repair after injury. Though kidney malignancies with FAN1 mutations have not been reported, FAN1 mutations have been implicated as risk factors in colorectal and pancreatic cancers. There is no effective treatment available for KIN. At least one reported case has shown recurrence of KIN in an allograft kidney transplant, though the donor kidney was the patient’s sibling, raising the possibility of quiescent KIN present in the donor. 

Though KIN is sometimes associated with chemotherapeutic agents (particularly ifosfamide) and mycotoxins (particularly ochratoxin), there is no known association with magnesium sulfate use. This patient has no history of radiation therapy; further, radiation therapy effect tends to be more restricted in distribution. Viral cytopathic effect from adenovirus, polyomaviruses, and CMV can be somewhat similar in appearance, but electron microscopy and immunohistochemistry can help with the diagnosis in difficult cases. Viral infections also tend to have more tubulitis and can have plasma cells if longstanding. There is no known association between autoimmune disease and KIN. 


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Salvatore Mignano, D.O.

Fellow, Renal Pathology 
Mayo Clinic

Mary Fidler, M.D.

Consultant, Anatomic Pathology
Mayo Clinic
Assistant Professor of Laboratory Medicine and Pathology
Mayo Clinic College of Medicine and Science

MCL Education

This post was developed by our Education and Technical Publications Team.