Recent advances in molecular techniques such as targeted next-generation sequencing analyses, fusion assays, comparative genomic hybridization, and fluorescence in-situ hybridization have facilitated accurate tumor diagnosis. T- and B-cell clonality studies are essential in diagnosing lymphoproliferative disorders. This chapter will describe these molecular techniques and how they can serve as ancillary tests.

Primary cutaneous lymphomas comprise a group of B- and T-cell lymphomas that do not have extracutaneous involvement at the time of diagnosis. They are the second most common group of extranodal lymphomas. Cutaneous B-cell lymphomas are generally classified into three main subgroups: cutaneous marginal zone B-cell lymphoma, cutaneous follicle center lymphoma, and cutaneous large B-cell lymphoma, leg type. Cutaneous T-cell and NK-cell lymphomas can derive from the helper T-cells (CD4+), cytotoxic T-cells (CD8+), gamma-delta T-cells (CD56+), or follicle helper T-cells (CD279/PD1). Immunohistochemistry plays an important role in the classification of B- and T-cell lymphoid lesions. A number of immunostains have recently become commercially available and can serve as diagnostic adjuncts in cases lacking characteristic immunohistochemical staining.

Being one of the most common cutaneous epithelial neoplasms and having a diverse morphologic appearance, squamous cell carcinoma can mimic a variety of neoplasms including epithelial, lymphoid, melanocytic as well as mesenchymal neoplasms of the skin. In this chapter, the role of immunohistochemistry in the distinction of squamous cell carcinoma versus basal cell carcinoma, sebaceous carcinoma, and porocarcinoma; sarcomatoid squamous cell carcinoma versus spindle cell melanomas and sarcomas; poorly differentiated squamous cell carcinoma versus Merkel cell carcinoma; and the diagnosis of anogenital squamous intraepithelial neoplasia will be discussed. Squamous precursors of the anogenital region arise via three pathways: classical which is associated with human papillomavirus (HPV) infection, usual or the differentiated or simplex pathway which is HPV-independent and caused by TP53 mutations, and a third pathway characterized by HPV-independence and p53 wild-type status. The role of immunostains in classifying anogenital squamous precursor lesions will be discussed.

The histogenesis of a variety of tumors such as epithelioid sarcoma, alveolar soft part sarcoma, and synovial sarcoma remains unknown. Tumors of histiocytic origin include Erdheim-Chester disease and histiocytic sarcoma and dendritic cell tumors include Langerhans cell histiocytosis, follicular dendritic cell sarcoma, and interdigitating dendritic cell sarcoma. Despite their similar histopathologic appearance, tumors of histiocytic and dendritic cell origin have different immunoprofile and immunohistochemistry is essential in classifying these tumors. Leukemia cutis or granulocytic or myeloid sarcoma is comprised of immature myeloid precursor cells. Lymphoblastic lymphomas are derived from precursor B- or T-cell lymphocytes. Cutaneous involvement can be the sole manifestation of these diseases, during or after development of bone marrow leukemia. In this chapter these miscellaneous entities as well as Merkel cell carcinoma, myoepithelioma, myoepithelial carcinoma, Ewing sarcoma, and mast cell infiltrate are discussed.

Traditionally tumors derived from the cutaneous appendages are classified according to their lines of differentiation: either follicular, sebaceous, eccrine or apocrine. However, there are overlapping histologic features and the classification is far from being straight forward. Often a tumor would exhibit multiple lines of differentiation with features of both eccrine and apocrine and even sebaceous differentiation. In some instances, immunohistochemistry can be of help in distinguishing epidermal from adnexal origin, benign from malignant adnexal neoplasms, and primary adnexal carcinoma from cutaneous metastases.

Skin infections can be caused by bacteria, viruses, parasites, and fungi. While some of the infections are self-limited, others can spread beyond the skin and become systemic resulting in fatal outcome when without appropriate treatment. A crucial step toward making the etiologic diagnosis of infection is sample collection with pertinent laboratory testing. In conjunction with culture, serology, special stains, immunohistochemistry, electron microscopy, and molecular assays, a skin biopsy can provide useful diagnostic information together with clinicopathologic correlation. Using antibodies either commercially available or only at highly specialized laboratories such as the Centers for Disease Control and Prevention, immunohistochemistry can detect the presence of microbial antigens in skin biopsies. Immunohistochemistry can play an important role in determining an infectious etiology. It is useful in detecting fastidious or slow-growing organisms, is valuable for characterizing emerging infections or pathogens with high biosafety concern and provides immunolocalization of antigens facilitating correlation between the infectious pathogen and host tissue response.

Cutaneous tumors including adnexal, melanocytic, and mesenchymal lesions in the setting of multiple tumors can be associated with a hereditary syndrome. Some are of clinical importance due to the association with internal malignancy and they can be screened by immunohistochemical stains performed on the associated tumors. Early diagnosis would allow timely genetic counseling and appropriate cancer surveillance. In this chapter the role of mismatch repair proteins in the screening for Muir-Torre syndromes, BAP1 for BAP1-tumor syndrome, PTEN for Cowden syndrome/PTEN hamartoma syndrome, and 2SC and FH for hereditary leiomyomatosis and renal cell carcinoma will be discussed.

Pseudolymphomas can be comprised of a prominent infiltrate of B cells, T cells, and even plasma cells. In these settings, they can mimic a lymphoproliferative process and immunohistochemistry plays an important role in excluding cutaneous lymphoma. B-cell pseudolymphomas or cutaneous lymphoid hyperplasia can mimic cutaneous follicle center cell lymphoma and primary cutaneous marginal zone B-cell lymphoma histopathologically. T-cell pseudolymphomas include a variety of inflammatory dermatoses that exhibit epidermotropism and can mimic a T-cell lymphoproliferative disorders such as mycosis fungoides. Some examples include lymphomatoid contact dermatitis, lymphomatoid drug eruption, follicular mucinosis, lupus erythematosus panniculitis, pigmented purpuric dermatosis, pityriasis lichenoides chronica/pityriasis lichenoides et varioliformis acuta, and pseudolymphomatous folliculitis. In some instances, the infiltrate is rich in plasma cells as in IgG4-related disease in the skin. Ultimately clinical pathologic correlation and sometimes the use of molecular studies will allow the classification of these entities.

The technique of immunofluorescence, employing similar principles as immunohistochemistry, is used daily in dermatopathology. These studies include direct immunofluorescence and indirect immunofluorescence using either monkey esophagus or rat bladder or NaCl-split skin as substrate. In this chapter, the role of immunofluorescence studies in classifying immunobullous disorders and diagnosing vasculitis and connective tissue disease is outlined.

In recent years there have been several new immunohistochemical markers made available for diagnosing melanocytic lesions. Immunostains can be helpful in the distinction of benign from atypical melanocytic proliferation and of melanocytic versus non-melanocytic lesions in the appropriate clinical context. The role of immunostains in the following diagnostic settings will be discussed in this chapter: melanoma in situ/ lentigo maligna versus pigmented actinic keratosis/ solar lentigo, nevoid melanoma versus melanocytic nevus, severely atypical compound melanocytic nevus versus invasive melanoma, benign versus atypical proliferative nodule arising in a congenital nevus, atypical Spitz tumor versus Spitzoid melanoma, nodal nevus versus metastatic melanoma, desmoplastic melanoma versus mimics, melanoma versus clear cell sarcoma, melanocytic versus histiocytic, sarcoma, or Merkel cell carcinoma.

Pathologists often encounter soft tissue neoplasms while examining biopsies and excisions from the skin. Soft tissue neoplasms are classified along their line of differentiation and include fibroblastic, myofibroblastic and fibrohistiocytic tumors, smooth muscle tumors, skeletal muscle tumors, neural tumors, lipomatous tumors, vascular tumors, pericytic and perivascular tumors and tumors of uncertain differentiation. These tumors can be categorized as benign, intermediate (locally recurrent/aggressive), intermediate (rarely metastasizing) and malignant (locally recurrent/aggressive with significant metastatic potential). Histologic diagnosis, grading and staging is imperative for prognostication and treatment. The continually expanding array of molecular diagnostics techniques has identified numerous novel gene alterations in soft tissue neoplasms that has enabled identification of new diagnostic entities with accompanying diagnostic and surrogate immunohistochemical markers. In this chapter we will review many soft tissue neoplasms and highlight important immunohistochemical markers.