Pathways Case Studies: November 2022

Chromosomal microarray was ordered on a one-day-old girl with a cardiac anomaly and respiratory insufficiency. Microarray demonstrated a 22 kilobase deletion and a 42 kilobase deletion at chromosome 7q31.2 within the CFTR gene, which is associated with cystic fibrosis (Figure 1). 

Figure 1: Chromosomal microarray signal at CFTR

Does this confirm a diagnosis of cystic fibrosis in this patient?

  • Yes, this confirms a diagnosis of cystic fibrosis.
  • No, deletions are not a disease mechanism in cystic fibrosis.
  • No, this confirms that this patient is a carrier for cystic fibrosis.
  • No, this result cannot differentiate between carrier status and diagnosis of cystic fibrosis.

The correct answer is ...

No, this result cannot differentiate between carrier status and diagnosis of cystic fibrosis.

Cystic fibrosis is an autosomal recessive disease. This means that both copies of the gene must be altered (either through mutations or structural changes such as deletions) to diagnose it. Therefore, it is important to determine if the two deletions within CFTR in this patient are in cis or in trans. If the deletions are in trans, meaning one deletion on each copy of CFTR, this would support a clinical diagnosis of cystic fibrosis or a CF-related disorder. If the deletions are in cis, this may represent carrier status for cystic fibrosis or a clinical diagnosis of cystic fibrosis, or a CF-related disorder if a second hit, such as a mutation, is found on the other allele. However, this microarray data alone does not allow us to determine the configuration of the deletions, making the correct answer this result, "cannot differentiate between carrier status and diagnosis of cystic fibrosis."

Additional follow-up testing is required to determine the configuration of these deletions and differentiate between carrier status and a diagnosis of cystic fibrosis. Chromosomal microarray or multiplex-ligation dependent probe amplification (MLPA) of the CFTR gene in the parents of this patient can provide a clue to how these deletions were inherited. If both deletions are found in a single parent, then they are likely in cis in the patient, but if one was inherited from each parent then the deletions are in trans. If both deletions are found in cis, this is suggestive that the patient is at least a cystic fibrosis carrier. However, further follow-up mutation testing in this patient can help clarify this by determining if there is a second hit within the CFTR gene.


Lauren Choate

Lauren Choate, Ph.D.

Fellow, Laboratory Genetics and Genomics
Mayo Clinic

Photo of Ross Rowsey, Ph.D.

Ross Rowsey, Ph.D.

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

A woman in her late 20s presented with multiple slow growing renal masses measuring up to 4.2 cm in greatest dimension on CT imaging. Representative images of the masses are shown in the figures below with H/E, CA-IX, and CK7 staining.

Figure 1: 4x
Figure 2: 20x
Figure 3: Carbonic Anhydrase 9 (CA-IX), 10x
Figure 4: Cytokeratin 7 (CK7), 10x

What is the most likely diagnosis?

  • Clear cell renal cell carcinoma
  • Clear cell papillary renal cell tumor
  • Renal cell carcinoma with fibromyomatous stroma
  • Papillary renal cell carcinoma

The correct answer is ...

Renal cell carcinoma with fibromyomatous stroma.

As seen on H/E, the above mass forming lesion is comprised of cells with clear cytoplasm arranged in alveolar/ acinar patterns with intersecting bands of fibromyomatous stroma (Figure 1). Immunohistochemical stains reveal that the tumor cells, exhibit membranous carbonic anhydrase 9 (Figure 3) staining and in contrast to the majority of other clear cell renal cell carcinomas are diffusely positive for CK7 (Figure 4). Taken together, the immunohistochemical and morphologic features of this tumor are consistent with what has been described as a renal carcinoma with fibromuscular stroma.1

Dense cytoplasmic condensation is commonly seen in these tumors and may be mistakenly characterized as rhabdoid change (Figure 2). Grading these as high-grade tumors with rhabdoid change may not be accurate as these are mostly indolent tumors with rare reports of metastasis to regional lymph nodes. 

Therefore, correctly diagnosing these tumors has important implications for accurate prognostication.

It is important to note that these tumors can have significant morphologic overlap with those that have alterations of TSC1, TSC2, MTOR, and/or TCEB1 (ELOC) genes.2 Unfortunately, no immunohistochemistry based surrogate markers are available to make this distinction. Next generation sequencing of the tumor and/or germline testing may be helpful in this regard. Current NCCN guidelines recommend germline testing for patients presenting with multifocal and or bilateral tumors as well as in patients with a younger age of onset (<46 years of age). A diagnosis of renal cell carcinoma with fibromyomatous stroma in the appropriate clinical context can therefore have important implications for establishing a diagnosis of tuberous sclerosis complex.3-4 


  1. Shah RB. Renal cell carcinoma with fibromyomatous stroma-the whole story. Adv Anat Pathol. 2022; 29, 168-177.
  2. Farkas DH, Trpkov K, McKenney JK. "Renal cell carcinoma with leiomyomatous stroma" harbor somatic mutations of TSC1, TSC2, MTOR, and/or ELOC (TCEB1): clinicopathologic and molecular characterization of 18 sporadic tumors supports a distinct entity. Am J Surg Pathol. 2020; 44, 571-581.
  3. Gupta S, Jimenez RE, Herrera-Hernandez L, Lohse CM, Thompson RH, Boorjian SA, Leibovich BC, Cheville JC. Renal neoplasia in tuberous sclerosis: a study of 41 patients. Mayo Clin Proc. 2021; 96, 1470-1489.
  4. Guo J, et al. Tuberous sclerosis-associated renal cell carcinoma: a clinicopathologic study of 57 separate carcinomas in 18 patients. Am J Surg Pathol. 2014 Nov;38(11):1457-67. 

Luke Cypher, M.D., Ph.D.

Fellow, Surgical Pathology
Mayo Clinic

Sounak Gupta, M.B.B.S., Ph.D.

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

A woman in her 70s presented with abnormal uterine bleeding. Imaging showed a 1.8 cm, friable cervical nodule compressing the cervical neck. Microscopic images and selected immunohistochemical stains are shown in Figure 1.

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8

Based on these findings, what would be the most likely diagnosis?

  • Diffuse large B-cell lymphoma
  • Adenosquamous carcinoma
  • Squamous cell carcinoma with a lymphoepithelioma-like morphologic pattern
  • Carcinosarcoma

The correct answer is ...

Squamous cell carcinoma with a lymphoepithelioma-like morphologic pattern.

Histologic sections showed a cellular proliferation with infiltrative borders, arranged in solid, somewhat syncytial sheets and a vaguely lobular pattern. The tumor islands were separated by minimal intervening stroma. Close examination demonstrated a distinct subset of poorly differentiated epithelioid cells with irregular nuclear contours, increased nuclear-to-cytoplasmic ratio, vesicular chromatin, and variably prominent nucleoli. Mitotic activity was increased. In addition, a dense, stromal lymphocytic infiltrate was present within and around the tumor nests.

Immunohistochemical studies were performed to further characterize this neoplastic proliferation. The epithelioid cells were positive for keratin AE1/AE3 and P40, and demonstrated no immunoreactivity for chromogranin, myogenin, and synaptophysin. BRG1 and INI1 showed retained expression. The lymphoid infiltrate was highlighted by the CD45 immunostain.

Human papillomavirus (HPV) and Epstein–Barr virus (EBV) in situ hybridization (ISH) studies showed that the epithelioid proliferation was positive for HPV family 16 ISH (HPV types included in the panel: 16, 18, 31, 33, and 55). No reactivity was noted for HPV family 6 ISH (HPV types included in the panel: 6 and 11) and EBV ISH.

Based on these findings, a diagnosis of squamous cell carcinoma (SCC) with a lymphoepithelioma-like morphologic pattern was rendered. Lymphoepithelioma-like carcinoma is a variant of HPV-associated SCC of the uterine cervix, characterized by a dense lymphocytic stromal infiltrate.1 It is relatively rare and most of the literature is based on small case studies.2-6 It generally occurs at a younger age than “conventional” cervical SCC, with the average age at diagnosis being 52.9 years according to a literature review.5 However, a wide age range has been reported.3-6 Most of the patients described in the literature are multiparous and present with an exophytic mass.

The pathogenesis of lymphoepithelioma-like SCC of the uterine cervix has not been entirely elucidated. Few studies suggest EBV as an etiologic factor; however, a well-defined association between EBV and lymphoepithelioma-like SCC of the uterine cervix has not been established (1). Most of the evidence indicates an HPV-driven etiology.1-4,6 Limited data suggest a relatively better prognosis, compared to other SCCs of the uterine cervix.3,4

Microscopic examination shows sheets of poorly differentiated cells growing in a syncytial-like growth pattern. The individual cells have large nuclei with vesicular chromatin, prominent nucleoli, and poorly defined borders.2,4 Keratinization is typically absent. The neoplastic cells are admixed with a dense peritumoral and intratumoral inflammatory infiltrate comprised of lymphocytes, with a small subset of plasma cells.5,6 The infiltrating lymphocytes were demonstrated to be predominantly CD8 (+) T cells.5     

Differential diagnosis of lymphoepithelioma-like carcinoma of the uterine cervix includes poorly differentiated adenosquamous carcinomas, formerly known as “glassy cell carcinomas.” On histopathologic examination, cells of this entity have distinct cell membranes and a high-grade cytomorphology with pleomorphic nuclei and abundant eosinophilic cytoplasm. In addition, the surrounding inflammatory infiltrate is rich in eosinophils and plasma cells in poorly differentiated adenosquamous carcinomas, in contrast to a predominance of lymphocytes in lymphoepithelioma-like carcinoma of the uterine cervix.6 Lymphoepithelioma-like SCC of the uterine cervix should also be distinguished from lymphomas involving the cervix, which are very rare. Additional studies such as flow cytometry can be utilized, if lymphoproliferative disorders remain within the differential diagnosis based on morphologic findings. 


  1. WHO Classification of Tumours Editorial Board. Female genital tumours [Internet]. Lyon (France): International Agency for Research on Cancer; 2020 [cited 2022 September 18]. (WHO classification of tumours series, 5th ed.; vol. 4). Available from:
  2. Saylam K, Anaf V, Fayt I, Noel JC. Lymphoepithelioma-like carcinoma of the cervix with prominent eosinophilic infiltrate: an HPV-18 associated case. Acta Obstet Gynecol Scand. 2002; 81:564-566.
  3. Martorell MA, Julian JM, Calabuig C, García-García JA, Pérez-Vallés A. Lymphoepithelioma-like carcinoma of the uterine cervix. Arch Pathol Lab Med. 2002; 126:1501-1505.
  4. Yun HS, Lee SK, Yoon G, et al. Lymphoepithelioma-like carcinoma of the uterine cervix. Obstet Gynecol Sci.2017; 60:118-123.
  5. Philippe A, Rassy M, Craciun L, et al. Inflammatory stroma of lymphoepithelioma-like carcinoma of the cervix: Immunohistochemical study of 3 cases and review of the literature. Int J Gynecol Pathol. 2018; 37:482-487.
  6. Pinto A, Huang M, Nadji M. Lymphoepithelioma-like carcinoma of the uterine cervix: A pathologic study of eight cases with emphasis on the association with human papillomavirus. Am J Clin Pathol. 2019; 151:231-239.
Photo of Burak Tekin, M.D.

Burak Tekin, M.D.

Resident, Anatomic and Clinical Pathology
Mayo Clinic

Amy Clayton, M.D.

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

A 63-year-old man presents with fever, night sweats, and fatigue. On examination he was found to have generalized peripheral lymphadenopathy. Excisional biopsy of his right inguinal lymph node was performed. Histology and immunohistochemical staining are shown below. In addition, the atypical small- medium-sized cells were positive for CD5, CD10, BCL6 (partial staining), and CXCL13 and were negative for CD20, PAX5, and cyclin D1. Scattered large CD20/PAX5-positive cells were EBV-positive by in situ hybridization.

Figure 1: H&E1
Figure 2: H&E2
Figure 3: CD3
Figure 4: CD21
Figure 5: CD279
Figure 6: ICOS

What is the most likely diagnosis?

  • Angioimmunoblastic T-cell lymphoma
  • Peripheral T-cell lymphoma, not otherwise specified (PCTL-NOS)
  • Reactive lymphoid hyperplasia
  • Classic Hodgkin lymphoma (CHL), mixed cellularity type

The correct answer is ...

Angioimmunoblastic T-cell lymphoma.

The lymph node architecture is partially effaced by an abnormal lymphocyte population expanding the paracortex (Figure 1: H&E1). The lymphocytes are small to medium in size and have slightly irregular nuclear contours, inconspicuous nucleoli, and abundant clear cytoplasm. They are associated with prominent vasculature and arborized high endothelial venules (HEV) (Figure 2: H&E2). The abnormal lymphocytes often form small clusters around follicles and HEV and are accompanied by a polymorphous background of small reactive lymphocytes, plasma cells, eosinophils, and histiocytes (not shown in image). They usually express the pan-T-cell antigensCD2, CD3 and, CD5, have variable loss of CD7, and are almost always CD4-positive and CD8-negative. In contrast to other types of T-cell lymphoma, loss of pan–T-cell antigen expression is an uncommon finding in AITL. The expression of T follicular helper (TFH) cell markers such as CD10, BCL6, CXCL13, CD279, and ICOS represents an important adjunct in the diagnosis of AITL and provides further evidence that AITL derives from TFH cells. In addition, they are associated with disorganized, largely disrupted, CD21-positive follicular dendritic cell meshworks surrounding the prominent vessels, which is a diagnostic hallmark of AITL. Finally, EBV is detected by in situ hybridization in 80% to 96% of lymph nodes involved by the disease. In most cases, the EBV-infected cells represent transformed B cells. These morphologic and immunoarchitectural features support the diagnosis of AITL. Per WHO5 classification this lymphoma would be classified as nodal TFH cell lymphoma, angioimmunoblastic-type. Per ICC classification this lymphoma would be classified as follicular helper T-cell lymphoma, angioimmunoblastic type.

Incorrect answers:

Peripheral T-Cell lymphoma, not otherwise specified (PCTL-NOS) encompasses all mature T-cell lymphomas lacking specific features that would allow categorization within any of the better defined “specific” subtypes of other mature T-cell lymphoma described in the WHO classifications. The presence of morphologic features typical of AITL coupled with a TFH phenotype would support the diagnosis of AITL and exclude the diagnosis of PTCL-NOS. 

Reactive lymphoid hyperplasia of lymph node can have overlapping features with early involvement by AITL. Absence of atypical T-cells with abundant clear cytoplasm that are positive for TFH cell markers and lack of disrupted follicular dendritic cell meshworks favor reactive lymphoid hyperplasia over AITL. Although absence of a T-cell receptor gene rearrangement would support reactive lymphoid hyperplasia, clonal T-cell receptor gene rearrangements can occasionally be seen in reactive conditions, so the presence of a clonal T-cell receptor gene rearrangement does not necessarily support the diagnosis of malignant lymphoma of T-cell lineage. 

Classic Hodgkin lymphoma (CHL), mixed cellularity type — In some cases of AITL, the presence of scattered EBV-positive B cells that have some overlapping features with some of which can acquire Hodgkin/Reed Sternberg (HRS) cells (variable CD15+, CD30+, variable CD20+) may mimic CHL. Because AITL cases may show minimal cytologic atypia of T cells, the distinction from CHL may be difficult. CHL lacks neoplastic T cells with clear cytoplasm and shows no increase in HEV or FDC. As above, although absence of a T-cell receptor gene rearrangement would support CHL, the presence of a clonal T-cell receptor gene rearrangement does not necessarily support the diagnosis of malignant lymphoma of T-cell lineage. 


  1. Khokhar FA, Payne WD, Talwalkar SS, et al. Angioimmunoblastic T-cell lymphoma in bone marrow: a morphologic and immunophenotypic study. Hum Pathol. 41(1):79-87, 2010
  2. Swerdlow SH, Campo E, Pileri SA, et al. The 2016 revision of the World Health Organization (WHO) classification of lymphoid neoplasms. Blood. 127:2375-90, 2016
  3. Weiss LM, O'Malley D. Benign lymphadenopathies. Mod Pathol. 26 Suppl 1: S88-96, 2013
  4. Andersen MD, Kamper P, Nielsen PS, et al: Tumour-associated mast cells in classical Hodgkin's lymphoma: correlation with histological subtype, other tumour-infiltrating inflammatory cell subsets and outcome. Eur J Haematol. 96(3):252-9, 2016
  5. Broccoli A, Zinzani PL. Peripheral T-cell lymphoma, not otherwise specified. Blood. 2017 Mar 2;129(9):1103-1112. doi:10.1182/blood-2016-08-692566. Epub 2017 Jan 23. 

Mazen Osman, M.B., B.Ch.

Fellow, Hematopathology
Mayo Clinic

Ellen McPhail, M.D.

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

A 34-year-old right-handed woman with a history of intractable epilepsy underwent a right frontal craniotomy for resection of a brain lesion.

She experienced her first seizure episode at age 23. Her seizures consisted of a fidgeting movement, speech interruption and feeling of anxiety, as well as occasional left head turn, or pacing in circles while she is standing. Interictal EEG displayed potential epileptogenic activity in the bifrontal regions (R>L), as well as infrequent right temporal activity. A brain MRI, as shown below, revealed a mildly abnormal contour in the anterior paramedian right frontal gyrus, with underlying T2 hyperintensity in the subcortical white matter, with no apparent mass effect. 

Figure 1
Figure 2
Figure 3

The micrographs above show a representative section from the lesion, including immunostains for crystallin, GFAP, IDH, and NeuN. What is incorrect about this patient’s underlying neurological condition?

  1. This lesion is characterized by cortical dyslamination, and dysmorphic neurons with balloon cells.
  2. This lesion is caused by alterations of TSC1/TSC2 genes.
  3. Activation of mTOR pathway and phosphorylation of tau plays a role in pathogenesis.
  4. Hemimegalencephaly should be in differential diagnosis.

The correct answer is ...

This lesion is caused by alterations of TSC1/TSC2 genes.

The correct diagnosis is focal cortical dysplasia, ILAE type IIb. H&E on representative sections shows portions of cerebral cortex and subcortical white matter with multifocal collections of balloon cells, which are alpha-beta crystallin immunoreactive. NeuN demonstrates focal disorganization of the laminar neuronal architecture of the background cerebral cortex, with a focal collection of dysmorphic neurons. GFAP highlights subpial and subcortical reactive gliosis. No evidence of an atypical infiltrating glial cell population is identified; IDH1 R132H immunohistochemistry is negative in tissue. These findings support the diagnosis. 

Focal cortical dysplasia (FCD) is a malformation of cortical development, which can lead to interactable focal epilepsy.2 Characterized by specific cytological and architectural abnormalities, it usually involves a small portion of one gyrus (that may be enlarged).4 Histologically, cortical lamination and organization is disrupted (choice A). In the most recent classification by the International League Against Epilepsy (ILAE) there are three main types each with several subtypes introduced with revisions to the criteria.5

FCD types I and III are characterized by dyslamination and disrupted organization of tissue architecture, but with morphologically normal neurons and glial cells.5 FCD II is distinguished from FCD I and III by dysplastic, megalocytic neurons admixed with normal neurons. Subtype IIb is further characterized by the presence of balloon cells, which express both neuronal and glial protein transcription products; hence, are considered to be from a mixed lineage.2

Balloon cells can also be present in hemimegalencephaly (HME) (choice D) and tuberous sclerosis. In fact, microscopically, FCD II and HME are identical, with both showing similar dyslaminated cortex, abnormal glial cells, dysplastic neurons, and balloon cells mixed with normal glia and neurons.5 The main difference between FCD IIb and HME is the extent of the lesion. Being derived from an earlier developmental stage, HME tends to involve much larger areas up to a lobe or even entire hemisphere.6 Similar histopathological findings can be seen in the cortical tubers of tuberous sclerosis, however, it is distinguished from FCD and HME with dystrophic calcifications, and absence of the characteristic alterations of TSC1 (tuberin) and TSC2 (hamartin) (choice B).1 However, the pathogenesis of these three disorders similarly involves the activation of mammalian target of rapamycin (mTOR) signalling pathway3 and phosphorylation of tau; hence known collectively as infantile tauopathies (choice C).8


  1. Jozwiak J. Hamartin and tuberin: working together for tumour suppression. Int J Cancer. 2006 Jan 1;118(1):1-5. doi:10.1002/ijc.21542. PMID: 16206276
  2. Lamparello P, Baybis M, Pollard J, Hol EM, Eisenstat DD, Aronica E, Crino PB. Developmental lineage of cell types in cortical dysplasia with balloon cells. Brain. 2007 Sep;130(Pt 9):2267-76. doi:10.1093/brain/awm175. PMID: 17711980
  3. Lim JS, Kim WI, Kang HC, Kim SH, Park AH, Park EK, Cho YW, Kim S, Kim HM, Kim JA, Kim J, Rhee H, Kang SG, Kim HD, Kim D, Kim DS, Lee JH. Brain somatic mutations in MTOR cause focal cortical dysplasia type II leading to intractable epilepsy. Nat Med. 2015 Apr;21(4):395-400. doi:10.1038/nm.3824. Epub 2015 Mar 23. PMID: 25799227
  4. Miyata H, Hori T, Vinters HV. Surgical pathology of epilepsy-associated non-neoplastic cerebral lesions: a brief introduction with special reference to hippocampal sclerosis and focal cortical dysplasia. Neuropathology. 2013 Aug;33(4):442-58. doi:10.1111/neup.12028. Epub 2013 Mar 27. PMID: 23530853; PMCID: PMC4120885.
  5. Najm IM, Sarnat HB, Blümcke I. Review: The international consensus classification of Focal Cortical Dysplasia - a critical update 2018. Neuropathol Appl Neurobiol. 2018 Feb;44(1):18-31. doi:10.1111/nan.12462. PMID: 29359399.
  6. Severino M, Geraldo AF, Utz N, Tortora D, Pogledic I, Klonowski W, Triulzi F, Arrigoni F, Mankad K, Leventer RJ, Mancini GMS, Barkovich JA, Lequin MH, Rossi A. Definitions and classification of malformations of cortical development: practical guidelines. Brain. 2020 Oct 1;143(10):2874-2894. doi: 10.1093/brain/awaa174. Erratum in: Brain. 2020 Dec 1;143(12): e108. PMID: 32779696; PMCID: PMC7586092.
  7. Siedlecka M, Grajkowska W, Galus R, Dembowska-Bagińska B, Jóźwiak J. Focal cortical dysplasia: Molecular disturbances and clinicopathological classification (Review). Int J Mol Med. 2016 Nov;38(5):1327-1337. doi:10.3892/ijmm.2016.2760. Epub 2016 Sep 29. PMID: 28025990
  8. Sarnat HB, Flores-Sarnat L. Infantile tauopathies: Hemimegalencephaly; tuberous sclerosis complex; focal cortical dysplasia 2; ganglioglioma. Brain Dev. 2015 Jun;37(6):553-62. doi:10.1016/j.braindev.2014.08.010. Epub 2014 Oct 19. PMID: 25451314.

Amir Nazem, M.D., Ph.D.

Resident, Anatomic/Neuropathology 
Mayo Clinic

Jorge Lopez-Trejo, M.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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