Pathways Case Studies: January 2023

A 15-year-old girl diagnosed with multiple sulfatase deficiency (MSD) was referred to Mayo Clinic for severe headaches, worsening musculoskeletal pain, and management of congenital heart disease. 

Her complex clinical history is remarkable for short stature, progressive scoliosis, multiple contractures, coarse facial features, hearing and vision loss, bilateral corneal opacities, absent puberty, abnormal echocardiogram, and hepatosplenomegaly. She has normal intelligence without progressive loss of cognitive function and does not have ichthyosis. 

Her diagnosis of MSD, established before age 1, was based on low enzymatic activities of arylsulfatases A and B.

Due to suspicion of misdiagnosis, a series of biochemical tests were performed. Analysis of glycosaminoglycans (GAGs) in urine showed increased excretion of dermatan sulfate; heparan sulfate and keratan sulfate were normal. Urine sulfatide excretion was within the normal range, and the enzymatic activities of several sulfatases were either low or normal (Table 1).

Table 1

Which statement is correct?

  • The biochemical results are inconclusive; they could point to either metachromatic leukodystrophy (MLD) or MSD.
  • The clinical and biochemical profiles are suggestive of MPS VI.
  • The biochemical results are suggestive of MPS IVA.
  • The clinical and biochemical profiles are indicative of MSD.

The correct answer is ...

The clinical and biochemical profiles are suggestive of MPS VI.

MPS VI (Maroteaux-Lamy syndrome) is an autosomal recessive lysosomal storage disorder caused by pathogenic variants in ARSB, the gene that encodes for arylsulfatase B.

The clinical features of MPS VI include short stature, dysostosis multiplex, contractures, corneal clouding, hepatosplenomegaly, cardiorespiratory insufficiencies, and hearing loss. Notably, cognitive and behavioral abnormalities are rare.

The enzyme defect in MPS VI leads to elevated urinary excretions of dermatan sulfate and chondroitin-4-sulfate with normal levels of both heparan sulfate and keratan sulfate. Since the enzyme is not directly involved in sphingolipid metabolism, sulfatide excretion is expected to be normal.1

Incorrect — The clinical and biochemical profiles are indicative of MSD.

MSD is a rare autosomal recessive disorder caused by pathogenic variants in SUMF1, resulting in reduced or absent formylglycine-generating enzyme (FGE) activity. FGE catalyzes a post-translational modification necessary to activate all cellular sulfatases — the generation of formylglycine, a unique amino acid residue found only in the catalytic domains of sulfatases.

Most sulfatases are lysosomal enzymes involved in GAG and sulfated sphingolipid (sulfatide) catabolism. Genetic defects in the lysosomal sulfatases are associated with distinct subtypes of lysosomal storage disorders, in particular, mucopolysaccharidosis (MPS) types II, III, IV, and VI, and metachromatic leukodystrophy (MLD).

FGE deficiency leads to diminished activities of all or multiple sulfatases and consequently to a progressive multisystem disorder with combined clinical features of single sulfatase deficiencies. 

Individuals with MSD invariably have neurological complications, the majority presenting with developmental regression and hypotonia. Epilepsy, sensorineural hearing loss, and spasticity are also frequently observed. Brain MRI findings, including leukodystrophy and cerebral atrophy, can be similar to those observed in MLD and may lead to a misdiagnosis.

Common non-neurological signs overlap with those frequently observed in several MPS subtypes, e.g., growth restriction, dysostosis multiplex, hepatosplenomegaly, coarse facies, and corneal clouding. In contrast, most individuals with MSD present with ichthyosis, which is not commonly observed in MPS.

Biochemical investigations are expected to reveal decreased activities of multiple sulfatases, elevated urinary excretion of all GAGs, and increased excretion of sulfatides.2,3

Incorrect — The biochemical results are inconclusive; they could point to either metachromatic leukodystrophy (MLD) or MSD.

MLD results from a low or absent activity of arylsulfatase A, an enzyme involved in lysosomal sulfatide catabolism, caused by either deficiency of the enzyme itself or its activation protein, sphingolipid activator protein B (sapB). Clinically, MLD is characterized by progressive motor and cognitive impairment due to damage to myelin sheaths in the central and peripheral nervous systems. 

Besides low arylsulfatase A activity, the biochemical hallmark of MLD is the accumulation of sulfatides in tissues, particularly in myelin sheaths, and their elevated excretion in urine.4

Of interest, a disease-causing sapB deficiency does not result in low enzyme activity in vitro but can be detected by elevated sulfatide excretion. Conversely, relatively common polymorphisms in ARSA cause decreased arylsulfatase A activity in vitro but no detectable clinical symptoms — a phenomenon referred to as pseudodeficiency.

Incorrect — The biochemical results are suggestive of MPS IVA.

MPS IVA (Morquio A syndrome) results from a deficiency of N-acetylgalactosamine-6-sulfate sulfatase, an enzyme necessary for keratan sulfate and chondroitin 6-sulfate catabolism. 

The syndrome is characterized by severe skeletal dysplasia, e.g., short stature with short trunk and neck, kyphoscoliosis, platyspondyly, and odontoid hypoplasia. Hearing loss, corneal clouding, hypermobile joints, as well as cardiac and respiratory complications are common. Most individuals with MPS IVA have normal intelligence. 

Biochemically, MPS IVA is distinguished by elevated keratan sulfate and chondroitin 6-sulfate in blood and urine.5 


The case presented here was diagnosed with MSD at an early age based on low activities of arylsulfatases A and B. Her clinical symptoms at an older age were atypical for the syndrome, particularly the normal intelligence and absence of cognitive regression and ichthyosis. This incongruity between the clinical picture and diagnosis prompted further biochemical and genetic (see below) testing. 

The biochemical results were unambiguous — sulfatide excretion was normal, only the excretion of dermatan sulfate was elevated, and of all sulfatases tested, only the activity of arylsulfatase B was consistently low.

Molecular testing was performed using a NGS lysosomal storage disease panel (74 genes) and no pathogenic variants or VUSs were detected in SUMF1. However, a homozygous variant was detected in ARSB, not previously reported but predicted to be pathogenic. 

Interestingly, a polymorphism in ARSA was detected involving the same amino acid change as a known pseudodeficiency allele, which might explain the reduced activity measured in arylsulfatase A.

This case illustrates that extensive biochemical testing is often necessary to establish a correct diagnosis in the complex landscape of biochemical genetic diseases confounded by frequent pseudo deficiencies, VUSs, and variable clinical expressions.


  1. D'Avanzo F, Zanetti A, De Filippis C, Tomanin R. Mucopolysaccharidosis type VI, an updated overview of the disease. Int J Mol Sci. 2021;22.
  2. Dierks T, Schmidt B, Borissenko LV, et al. Multiple sulfatase deficiency is caused by mutations in the gene encoding the human C(alpha)-formylglycine generating enzyme. Cell. 2003;113:435-444.
  3. Adang LA, Schlotawa L, Groeschel S, et al. Natural history of multiple sulfatase deficiency: Retrospective phenotyping and functional variant analysis to characterize an ultra-rare disease. J Inherit Metab Dis. 2020;43:1298-1309.
  4. Shaimardanova AA, Chulpanova DS, Solovyeva VV, et al. Metachromatic leukodystrophy: diagnosis, modeling, and treatment approaches. Front Med (Lausanne). 2020;7:576221.
  5. Peracha H, Sawamoto K, Averill L, et al. Molecular genetics and metabolism, special edition: Diagnosis, diagnosis and prognosis of Mucopolysaccharidosis IVA. Mol Genet Metab. 2018;125:18-37.

Freyr Johannsson, Ph.D.

Fellow, Clinical Biochemical Genetics
Mayo Clinic

Silvia Tortorelli, M.D., Ph.D.

Consultant, Biochemical Genetics
Mayo Clinic
Associate Professor of Laboratory Medicine and Pathology
Mayo Clinic College of Medicine and Science

Linda Hasadsri, M.D., Ph.D.

Consultant, Laboratory Genetics & Genomics
Mayo Clinic
Assistant Professor of Laboratory Medicine and Pathology
Mayo Clinic College of Medicine and Science

A 24-year-old woman presented with a right leg mass. A needle core biopsy revealed a round cell neoplasm composed of relatively bland cells arranged in sheets and separated by thick fibrous septae. Microcystic spaces and thin vessels with hyalinized walls were identified. The mitotic count was low, and necrosis was absent. By immunohistochemistry, the tumor's cells were positive for S100, desmin, MYOD1, GFAP, and rare cells stained with keratin AE1/AE3. 

Figure 1: 4X_EWSR1::PATZ1
Figure 2: 10X_EWSR1::PATZ1

What is the most likely diagnosis?

  • Alveolar rhabdomyosarcoma
  • EWSR1::PATZ1-rearranged sarcoma
  • Ewing sarcoma
  • Desmoplastic small round cell tumor

The correct answer is ...

EWSR1::PATZ1-rearranged sarcoma.

Malignant mesenchymal tumors harboring EWSR1::PATZ1 gene fusions are currently classified by the WHO as “round cell sarcomas with EWSR1-non-ETS fusions.” The majority of tumors harboring EWSR1::PATZ1 gene fusions share common morphologic features, including relatively bland cytology, low mitotic activity, and absent necrosis; however, a minor percentage of tumors can show unusual morphology, high mitotic activity, or necrosis. Although they occur commonly in the torso, they may also occur in other regions, such as the leg and head and neck region. They display an unusual immunoprofile, with co-expression of epithelial, skeletal muscle, and nerve sheath-associated antigens. So far, only a limited number of cases have been reported with short follow-up, which makes judgement of clinical behavior somewhat difficult; however, preliminary studies suggest that these tumors may behave in a somewhat indolent fashion after complete excision.

Desmoplastic small round cell tumor: This is an uncommon tumor, usually occurring in the abdominal cavity of young male patients. By histology they are characterized by nests, sheets, and cords of relatively monomorphic cells intervened by abundant desmoplastic fibrous stroma. Mitoses and necrosis are very common. These tumors stain diffusely for keratin and desmin, while they are usually negative for GFAP and S100. The most common fusion identified in these tumors is EWSR1::WT1.

Alveolar rhabdomyosarcoma: This sarcoma is a high-grade malignant neoplasm presenting predominantly in the head and neck region or the extremities of adolescents and young adults. Histologically, it shows a highly cellular tumor composed of nests and sheets of primitive-appearing rounded cells separated by variably prominent fibrous septae, often forming an alveolar-like (pseudoalveolar) spaces. The lesional cells usually have scant cytoplasm and rhabdomyoblasts may be seen. By immunohistochemistry, these tumors show usually diffuse desmin, myogenin, and MYOD1 expression, occasional keratin positive cells and variable expression for neuroendocrine markers. Molecular testing reveals a fusion between FOXO1 and PAX3 or PAX7 in the majority of cases. 

Ewing sarcoma: This tumor presents as a small, round, blue cell tumor and might histologically be the most similar neoplasm to EWSR1::PATZ. In fact, previously some of these new tumors were likely classified as Ewing sarcoma before we had fusion testing. Histologically, Ewing sarcoma shows a uniform population of small, round, blue cells with abundant vacuolated cytoplasm secondary to deposition of glycogen. Necrosis is fairly common and may present in a peritheliomatous pattern characterized by a sheath of viable tumor cells closely surrounding central vessels. These tumors are highlighted diffusely by CD99 in a membranous fashion; FLI1 and NKX2.2 are usually positive, too. Focal keratin staining is seen in about a third of cases. The most classic fusion of Ewing sarcoma is EWSR1::FLI1; however, EWSR1::ERG or other rearrangements between members of the FET family (most commonly EWSR1, also FUSTAF15) with the ETS family (FLI1ERGETV1ETV4 and FEV) may occur. 


  1. Michal M, Rubin BP, Agaimy A, et al. EWSR1-PATZ1-rearranged sarcoma: a report of nine cases of spindle and round cell neoplasms with predilection for thoracoabdominal soft tissues and frequent expression of neural and skeletal muscle markers. Mod Pathol. 2021;34(4):770–785.
  2. Bridge JA, Sumegi J, Druta M, Bui MM, Henderson-Jackson E, Linos K, Baker M, Walko CM, Millis S, Brohl AS. Clinical, pathological, and genomic features of EWSR1-PATZ1 fusion sarcoma. Mod Pathol. 2019 Nov;32(11):1593-1604. doi:10.1038/s41379-019-0301-1. Epub 2019 Jun 12. PMID: 31189996.

Carina Dehner, M.D., Ph.D.

Fellow, Bone and Soft Tissue
Mayo Clinic

Jorge Torres-Mora, M.D.

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

A 70-year-old man presents with sudden-onset mental status change progressing to unconsciousness. He hikes and fishes regularly and had some recent “insect” bites. Lyme disease (caused by Borrelia burgdorferi) antibody screening by an enzyme immunoassay and immunoblots were positive (IgM: 3 proteins detected and IgG: 6 proteins detected; Figure 1). Anaplasma phagocytophilum IgG testing by immunofluorescence was also ordered and positive at a titer of 1:1024 (Figure 2).

Figure 1: Lyme
Figure 2: HGA

What is the best interpretation of these results?

  • Cross-reactive B. burgdorferi and A. phagocytophilum antibodies.
  • Recent/current Lyme disease and A. phagocytophilum infections.
  • Recent/current Lyme disease and remote A. phagocytophilum infection.
  • Recent/current A. phagocytophilum infection and remote Lyme disease.

The correct answer is ...

Recent/current Lyme disease and A. phagocytophilum infections.

Coinfection with tick-borne pathogens is a relatively common yet under-recognized occurrence. It is estimated that between 2% and 10% of patients with Lyme disease are concurrently affected by human granulocytic anaplasmosis (HGA). This is because the causative agents of Lyme disease (Borrelia burgdorferi, B. mayonii, etc.) and HGA (Anaplasma phagocytophilum) are transmitted by the same tick species (Ixodes scapularis). 

Lyme disease and HGA share overlapping symptoms, and therefore differentiating them on purely clinical grounds can be difficult. Infection with B. burgdorferi can be distinguished from HGA by the presence of erythema migrans (EM; target rash) and central nervous system involvement (neuroborreliosis). HGA, on the other hand, is more likely to cause transaminitis and cytopenias. In many cases, however, coinfections likely go undiagnosed.

Lyme disease can be diagnosed clinically based on tick exposure and EM, which is largely pathognomonic for the infection. Laboratory testing is principally serologic, and importantly, not necessary in patients with EM. For other suspected cases, a two-tiered testing approach is taken, including a screening test usually based on an enzymatic immunoassay (EIA). Positive screens are confirmed either using an EIA to detect antibodies to B. burgdorferi antigens different from the first EIA, or by immunoblot for IgM and IgG. An immunoblot is considered positive if either IgM (within 30 days of symptoms) or IgG (at any time) are positive. IgM and IgG immunoblots are considered positive if antibodies are detected to at least two out of a possible three antigens, and five out of a possible 10 antigens, respectively. Serology cannot reliably differentiate recent from remote infection, as IgM can persist beyond 30 days. Onset of symptoms must be used in conjunction with serologic results.

HGA can be diagnosed by polymerase chain reaction (PCR) during an acute infection. After the initial infection clears, however, serology by immunofluorescence assay (IFA) is the preferred method. Recent infection is suggested in patients with high IgG IFA titers (≥1:256) or by a fourfold increase in titers upon repeat testing.

1. Recent/current Lyme disease and remote A. phagocytophilum infection.

A recent or current Lyme disease infection, alongside remote Anaplasma infection would be indicated by a positive Lyme disease EIA screen and immunoblot results, with a low A. phagocytophilum IgG titers that do not increase with time. The A. phagocytophilum titer of 1:1024 is indicative of a very recent infection.

2. Recent/current A. phagocytophilum infection and remote Lyme disease.

In this patient’s case, a current or recent Lyme disease infection is suggested by confirmed two-tier serologic test results, recent symptoms, and CNS involvement. HGA infection alone would not account for the mental status change in this patient. Confirmation testing can be performed for neuroborreliosis performing a B. burgdorferi antibody index, which compares pathogen antibody levels in both CSF and serum.

3. Cross-reactive B. burgdorferi and A. phagocytophilum antibodies.

Antibodies to these two pathogens have not been shown to cross-react. 


  1. Hansmann Y, Jaulhac B, Kieffer P, et al. Value of PCR, serology, and blood smears for human granulocytic anaplasmosis diagnosis, France. Emerg Infect Dis. 2019;25(5):996-998.
  2. Horowitz HW, Aguero-Rosenfeld ME, Holmgren D, et al. Lyme disease and human granulocytic anaplasmosis coinfection: impact of case definition on coinfection rates and illness severity. Clin Infect Dis. 2013;56(1):93-99.
  3. Sanchez-Vicente S, Tagliafierro T, Coleman JL, Benach JL, Tokarz R. Polymicrobial nature of tick-borne diseases. mBio. 2019;10(5):e02055-19. Published 2019 Sep 10.
  4. Theel ES. The past, present and (possible) future of serologic testing for Lyme disease. J Clin Microbiol. 2016; May;54(5):1191-1196.

Jonathan Wilcock, D.O.

Fellow, Clinical Microbiology
Mayo Clinic

Photo of Elitza Theel, Ph.D.

Elitza Theel, Ph.D.

Consultant, Clinical Microbiology
Mayo Clinic
Professor of Laboratory Medicine and Pathology
Mayo Clinic College of Medicine and Science

A 68-year-old woman with a past medical history of atrial fibrillation and upper GI bleeding presented with a 10-month history of slowly progressive abdominal fullness and right upper-quadrant pain. An MRCP revealed a 7.6 cm by 6.8 cm infiltrative nodular lesion in the hepatic hilum with dilation of the left intrahepatic bile duct. The patient underwent resection of the lesion. Gross and histologic images are shown. 

Figure 1
Figure 2

What is the most common mutation associated with this diagnosis?

  • TP53
  • SMAD4
  • KRAS
  • GNAS

The correct answer is ...


The patient’s initial presentation is highly concerning for cholangiocarcinoma arising above the level of the common bile duct as indicated by the lack of obstructive jaundice and the location of post-obstructive bile duct dilation.  

The gross and histologic findings demonstrate an interesting presentation of colloidal carcinoma (mucinous adenocarcinoma) arising from perihilar bile ducts. Colloidal carcinoma is a rare histologic subtype of cholangiocarcinoma that most often arises in association with intraductal papillary neoplasia of the bile ducts (IPNB). Colloidal bile duct carcinomas may be widely disseminated at the time of diagnosis; however, in this case, the lesion showed minimal invasion into the bile duct wall and adventitial fat. 

Cholangiocarcinomas share many molecular features with pancreatic ductal adenocarcinomas (PDAC), with several common alterations factoring prominently into the mutational landscapes of both tumors. Of note, FGFR2 and FGFR3 rearrangements can act as driver mutations in cholangiocarcinomas, while FGFR rearrangements have not been reported in PDAC. FGFR aberrations represent an alternative pathway of oncogenesis, and as a result, the frequency of KRAS mutations is diminished at the population level to a level below that of TP53, the most commonly mutated tumor suppressor gene in both malignancies and most commonly mutated gene in cholangiocarcinoma.

It is important to note that there may be significant differences in mutational frequencies depending on intra vs. extrahepatic locations. In general, it appears that extrahepatic cholangiocarcinomas have a more diverse profile of driver mutations than intrahepatic carcinomas; however, this remains difficult to assess due to the relatively low frequency with which cholangiocarcinomas occur. As a whole, GNAS mutations in PDAC and cholangiocarcinoma are rare; however, in the subset of cancers arising from intraductal papillary neoplasms, GNAS mutations are more frequent. Fewer than half of IPNBs carry a GNAS mutation, and a small minority of these cases progress to cholangiocarcinoma. SMAD4 is frequently mutated in cholangiocarcinoma as well. In this capacity, it functions as driver mutation; however, at a frequency of 10%, SMAD4 mutations are far less common than both KRAS and TP53. 


  1. Nakamura, H Arai, Y Totoki, Y et al. Genomic spectra of biliary tract cancer. Nature Genetics. 2015; 47(9):1003-10.
  2. Arend MJ, Fukayama M, Klimstra DS, et al. WHO Classification of Tumours of the Digestive System. Lyon, France: IRAC; 2019.
  3. The Cancer Genome Atlas Network. Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell; 32(2):185-203. 

Andrew Cannon, M.D., Ph.D.

Resident, Anatomic and Clinical Pathology
Mayo Clinic

Charles Sturgis, M.D.

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

A comprehensive genetic evaluation of five genes linked to hereditary hemorrhagic telangiectasia (HHT) was performed on a 64-year-old man with recurrent nosebleeds (two times/week). Targeted next-generation sequencing and supplemental Sanger sequencing did not identify any single nucleotide variants or small insertions/deletions. Evaluation of the data for copy number revealed a full gene deletion of ENG, encoding endoglin. Quantitative PCR of ENG confirmed a heterozygous deletion in the patient.

Figure 1: Text

Based upon these results, what is the most appropriate interpretation?

  • This data confirms a heterozygous full gene deletion of ENG, which is pathogenic, but not sufficient for a diagnosis of hereditary hemorrhagic telangiectasia, type 1.
  • This data confirms a heterozygous full gene deletion of ENG but is not pathogenic.
  • This data confirms a heterozygous full gene deletion of ENG, which is pathogenic and sufficient for a diagnosis of hereditary hemorrhagic telangiectasia, type 1.
  • This data does not confirm a full gene deletion of ENG. Additional confirmation studies are needed.

The correct answer is ...

This data confirms a heterozygous full gene deletion of ENG, which is pathogenic and sufficient for a diagnosis of hereditary hemorrhagic telangiectasia, type 1.

Hereditary hemorrhagic telangiectasis (HHT) is a highly penetrant, autosomal dominant disorder that is thought to be underdiagnosed. It is characterized by the abnormal development of blood vessels with recurrent nosebleeds (epistaxis) known to be a common clinical manifestation. While other clinical features supporting a diagnosis of HHT were unavailable in this case, the identification of a heterozygous, pathogenic variant in a disease-associated gene establishes the diagnosis. Based upon intrafamilial variability of clinical symptoms associated with this phenotype, evaluation of this variant in at-risk relatives would be recommended.

Approximately 44% of all pathogenic variants identified in HHT reside in ENG, encoding endoglin, and lead to the diagnosis of HHT, type 1. Endoglin is a transmembrane protein that forms homodimers expressed primarily on endothelial cells and is known to be important for the maintenance of vessel wall integrity. ENG has a haploinsufficiency score of 3, defined as providing sufficient evidence for dosage sensitivity of this gene, which confirms that a single copy of this gene is not adequate to meet the needs of the cell. Indeed, heterozygous loss-of-function variants are an established mechanism of disease for ENG. To date, a wide spectrum of pathogenic variants has been identified in ENG, ranging from single nucleotide variants to copy number variants, including full gene deletions. 


  1. McDonald J, Stevenson DA. Hereditary Hemorrhagic Telangiectasia. 2000 Jun 26 [updated 2021 Nov 24]. In: Adam MP, Everman DB, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2022. PMID: 20301525.
  2. Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum, MJ, Ledbetter DH, Maglott DR, Martin CL, Nussbaum RL, Plon SE, Ramos EM, Sherry ST, Watson, MS, for ClinGen. ClinGen The Clinical Genome Resource. June 4, 2015. N Engl J Med 2015; 372:2235-2242. PMID: 26014595. 

Jeanne Theis, Ph.D.

Fellow, Laboratory Genetics & Genomics
Mayo Clinic

Linnea Baudhuin, Ph.D.

Consultant, Laboratory Genetics & Genomics
Mayo Clinic
Professor of Laboratory Medicine and Pathology
Mayo Clinic College of Medicine and Science

The decedent is a 52-year-old man with a history of atherosclerotic cardiovascular disease, diabetes mellitus type 2, and hypertension who was witnessed to become unresponsive and was pronounced shortly after arrival to the emergency department. 

Figure 1

What do the lesions of the brainstem most likely represent?

  • Unilateral subdural hematoma
  • Rapid sodium correction
  • Fixation artifact
  • Internal capsule infarct

The correct answer is ...

Internal capsule infarct.

The image provided shows atrophy of the right cerebral peduncle, pons, and medulla. The decedent in this case had a history of a large remote infarct with right middle cerebral artery (MCA) distribution, which involved the right posterior limb of the internal capsule, causing a residual left motor deficit. The atrophy seen in our picture is a consequence of Wallerian degeneration of the corticospinal tract (CST), later highlighted on histology with LBF-PAS stains.

The corticospinal tract is the major pathway providing voluntary motor function. It originates primarily from the frontoparietal cortices, including the primary motor cortex, secondary motor area, and somatosensory cortex, which come together to form bundles that travel through the internal capsule and cerebral peduncles. The bundles then travel ipsilaterally down to the brainstem. As the corticospinal tract continues to travel down into the medulla, 75% to 90% of the fibers decussate to the contralateral side via the pyramidal decussation, and then continue to travel down the spinal cord to provide innervation to the distal extremities and muscle groups.

It has been shown that the extent of the infarct’s injury to the hemispheric course of the CST predicts the extent of remote tissue loss in the ipsilateral cerebral peduncle and distally, likely resulting primarily from axonal degeneration of the CST distal to the site of injury.

The distribution and gross appearance of the lesion in our picture makes the other choices less likely.


  1. Mark VW, Taub E, Perkins C, Gauthier LV, Uswatte G, Ogorek J. Poststroke cerebral peduncular atrophy correlates with a measure of corticospinal tract injury in the cerebral hemisphere. AJNR Am J Neuroradiol. 2008 Feb;29(2):354-8. doi:10.3174/ajnr.A0811. Epub 2007 Nov 16. PMID: 18024577; PMCID: PMC8119009. 
  2. Natali AL, Reddy V, Bordoni B. Neuroanatomy, Corticospinal Cord Tract. [Updated 2022 Aug 22]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2022 Jan-. Available from:
  3. Ellison, D. (2013) Neuropathology: A reference text of CNS pathology. Edinburgh: Mosby. 

Fabiola Righi, D.O.

Resident, Anatomic and Clinical Pathology
Mayo Clinic

R. Ross Reichard, M.D.

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

A 40-year-old man who was a lifetime nonsmoker presented with shortness of breath for one month. Imaging revealed a large left upper lobe mass, for which he underwent endobronchial biopsy and eventual resection. H&E photomicrographs of the mass are pictured below. Immunohistochemistry revealed the tumor cells stained focally positive for cytokeratin AE1/AE3, p40, and synaptophysin, with punctate nuclear positivity for NUT. The neoplastic cells stained negative for TTF1, CD45, CD99, and SALL4. BRG1 and INI-1 were retained. 

Figure 1: H&E 100x original magnification
Figure 2: H&E 400x original magnification

Which of the following genetic abnormalities is most likely to be identified in this tumor?

  • t(11;22) (EWSR1::FLI1)
  • 17p13 (TP53) mutation
  • t(15;19) (BRD4::NUTM1)
  • Isochromosome 12p

The correct answer is ...

t(15;19) (BRD4::NUTM1).

Nuclear protein in testis (NUT) carcinoma is a rare and aggressive poorly differentiated carcinoma. Though initially described in midline structures, NUT carcinomas have been reported in many locations, most commonly in the thoracic cavity. Morphologically, these tumors are characterized by sheets or nests of primitive-appearing cells, sometimes with abrupt foci of squamous differentiation. They are characterized by speckled nuclear positivity with NUT immunohistochemistry and/or NUT gene rearrangements (most commonly BRD4::NUTM1).1 By immunohistochemistry, NUT carcinomas can display variable positivity for keratin, squamous markers, and neuroendocrine markers.

The differential diagnosis for NUT carcinoma includes other small round blue cell tumors, such as Ewing sarcoma and desmoplastic small round cell tumor (DSRCT). Unlike NUT carcinoma, Ewing sarcoma and DSRCT lack foci of squamous differentiation, and commonly contain EWSR1::FLI1 fusion products by FISH.2 NUT carcinomas may also morphologically resemble lymphoma, but typically stain negative for CD45. 

Primitive germ cell tumors may also resemble NUT carcinoma by morphology. Germ cell tumor immunohistochemical markers such as SALL4, OCT4, and glypican 3 can be useful in ruling out these entities. In contrast to NUT carcinoma, metastatic testicular germ cell tumors most commonly display abnormalities involving chromosome 12.3

Given the variable positivity for neuroendocrine markers in NUT carcinomas, small cell carcinoma is often on the differential. However, the clinical presentation of small cell carcinoma differs from NUT carcinoma, mainly affecting older patients who smoke. Chromosome 17p, which encodes the TP53 gene, is implicated in the genetic basis of many carcinomas, including small cell lung carcinoma.4


  1. French, C. Demystified molecular pathology of NUT midline carcinomas. J Clin Pathol. 2010;63(6):492-6.
  2. Yamaguchi U, Hasegawa T, et al. J Clin Pathol. 2005;58(10):1051-1056. 
  3. Sheikine Y, Genega E, et al. Molecular genetics of testicular germ cell tumors. Am J Cancer Res. 2012;2(2):153-167.
  4. Semenova E, Nagel R, et al. Genes Dev. 2015;29(14)1447-1462.

Allison Kerper, MD

Resident, Anatomic and Clinical Pathology 
Mayo Clinic

Ying-Chun Lo, M.D., Ph.D.

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

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