Question: What medication, used as chemotherapy and to suppress the immune system, is used as treatment for Autoimmune encephalitis?

Context paragraphs:
Cyclophosphamide: Cyclophosphamide (CP), also known as cytophosphane among other, is a medication used as chemotherapy and to suppress the immune system.  As chemotherapy it is used to treat lymphoma, multiple myeloma, leukemia, ovarian cancer, breast cancer, small cell lung cancer, neuroblastoma, and sarcoma.  As an immune suppressor it is used in nephrotic syndrome and following organ transplant.  It is taken by mouth or injection into a vein.

Autoimmune encephalitis: Autoimmune encephalitis (or autoimmune encephalopathy) is a diverse group of neuro-psychiatric disorders recognized recently , presenting acutely or subacutely with alteration of consciousness, cognitive decline, seizure, and abnormal movements.  Associated with systemic autoimmune disorders, CNS autoimmune disorders and paraneoplastic syndromes.  Pathogenesis is likely to be mediated by antibodies (Abs) to CNS proteins.  The Abs are directed against membrane receptors and ion channel-associated proteins that are expressed on the surface of neurons in the CNS, such as N-methyl D-aspartate receptors and leucine-rich, glioma inactivated protein and contactin-associated protein like, that are associated with voltage-gated potassium channels.  The diseases are not invariably cancer-related and are therefore different from the classical paraneoplastic neurological diseases that are associated with, but not caused by, Abs to intracellular proteins.  Diagnosis of autoimmune encephalopathy is based on the clinical course, serologic evidence of autoimmunity, severe but nonspecific slowing on electroencephalography, and evidence of intrathecal inflammation in the cerebrospinal fluid and neuroimaging by MRI.  Treatment include first-line steroids, intravenous immunoglobulins (IVIG), and plasma exchange, and second-line Rituximab and Cyclophosphamide, followed in many cases by steroid-sparing agents in the long-term.

Immunodeficiency: Immunodeficiency (or immune deficiency) is a state in which the immune system's ability to fight infectious disease and cancer is compromised or entirely absent.  Most cases of immunodeficiency are acquired ("secondary") due to extrinsic factors that affect the patient's immune system.  Examples of these extrinsic factors include HIV infection, extremes of age, and environmental factors, such as nutrition.  In the clinical setting, the immunosuppression by some drugs, such as steroids, can be either an adverse effect or the intended purpose of the treatment.  Examples of such use is in organ transplant surgery as an anti-rejection measure and in patients suffering from an overactive immune system, as in autoimmune diseases.  Some people are born with intrinsic defects in their immune system, or primary immunodeficiency.  A person who has an immunodeficiency of any kind is said to be immunocompromised.  An immunocompromised person may be particularly vulnerable to opportunistic infections, in addition to normal infections that could affect everyone.  Immunodeficiency also decreases cancer immunosurveillance, in which the immune system scans the body's cells and kills neoplastic ones.

Immunology: Immunology is a branch of biology that covers the study of immune systems in all organisms.  It was the Russian biologist Ilya Ilyich Mechnikov who boosted studies on immunology, and received the Nobel Prize in 1908 for his work.  He jabbed the thorn of a rose on a starfish and noted that, 24 hours later, cells were surrounding the tip.  It was an active response of the body, trying to maintain its integrity.  It was Mechnikov who first observed the phenomenon of phagocytosis, in which the body defends itself against a foreign body, and coined the term.  Immunology charts, measures, and contextualizes the: physiological functioning of the immune system in states of both health and diseases; malfunctions of the immune system in immunological disorders (such as autoimmune diseases, hypersensitivities, immune deficiency, and transplant rejection); the physical, chemical and physiological characteristics of the components of the immune system "in vitro", "in situ," and "in vivo".  Immunology has applications in numerous disciplines of medicine, particularly in the fields of organ transplantation, oncology, virology, bacteriology, parasitology, psychiatry, and dermatology.

Biological response modifiers: Biological response modifiers (BRMs) are substances that modify immune responses.  They can be both endogenous (produced naturally within the body) and exogenous (as pharmaceutical drugs), and they can either enhance an immune response or suppress it.  Some of these substances arouse the body's response to an infection, and others can keep the response from becoming excessive.  Thus they serve as immunomodulators in immunotherapy (therapy that makes use of immune responses), which can be helpful in treating cancer (where targeted therapy often relies on the immune system being used to attack cancer cells) and in treating autoimmune diseases (in which the immune system attacks the self), such as some kinds of arthritis and dermatitis.  Most BRMs are biopharmaceuticals (biologics), including monoclonal antibodies, interleukin 2, interferons, and various types of colony-stimulating factors (e.g., CSF, GM-CSF, G-CSF).  "Immunotherapy makes use of BRMs to "enhance" the activity of the immune system to increase the body's natural defense mechanisms against cancer", whereas BRMs for rheumatoid arthritis aim to reduce inflammation.

Antigenic variation: Antigenic variation refers to the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters its surface proteins in order to evade a host immune response.  It is related to phase variation.  Immune evasion is particularly important for organisms that target long-lived hosts, repeatedly infect a single host and are easily transmittable.  Antigenic variation not only enables immune evasion by the pathogen, but also allows the microbes to cause re-infection, as their antigens are no longer recognized by the host's immune system.  When an organism is exposed to a particular antigen (i.e. a protein on the surface of a bacterium) an immune response is stimulated and antibodies are generated to target that specific antigen.  The immune system will then "remember" that particular antigen, and defenses aimed at that antigen become part of the immune system’s acquired immune response.  If the same pathogen tries to re-infect the same host the antibodies will act rapidly to target the pathogen for destruction.  However, if the pathogen can alter its surface antigens, it can evade the host's acquired immune system.  This will allow the pathogen to re-infect the host while the immune system generates new antibodies to target the newly identified antigen.  Antigenic variation can occur by altering a variety of surface molecules including proteins and carbohydrates.  There are many molecular mechanisms behind antigenic variation, including gene conversion, site-specific DNA inversions, hypermutation, as well as recombination of sequence cassettes.  In all cases, antigenic variation and phase variation result in a heterogenic phenotype of a clonal population.  Individual cells either express the phase-variable protein(s) or express one of multiple antigenic forms of the protein.  This form of regulation has been identified mainly, but not exclusively, for a wide variety of surface structures in pathogens and is implicated as a virulence strategy.

Angela Vincent: Angela Vincent (born 1942) is a professor at Somerville College of Oxford University.  She is the head of a research group, which is located in the West Wing within the John Radcliffe Hospital, and works on a wide range of biological disciplines encompassing molecular biology, biochemistry, cellular immunology and intracellular neurophysiology.  The group's research is focused on autoimmune and genetic disorders of the neuromuscular junction, peripheral nerves and more recently the exciting field of central nervous system diseases.  The principal autoimmune diseases studied are myasthenia gravis, the Lambert-Eaton myasthenic syndrome, limbic encephalitis, other types of autoimmune encephalitis and acquired neuromyotonia.

Immune system: The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease.  To function properly, an immune system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms, and distinguish them from the organism's own healthy tissue.  In many species, the immune system can be classified into subsystems, such as the innate immune system versus the adaptive immune system, or humoral immunity versus cell-mediated immunity.  In humans, the blood–brain barrier, blood–cerebrospinal fluid barrier, and similar fluid–brain barriers separate the peripheral immune system from the neuroimmune system, which protects the brain.

Immunomics: Immunomics is the study of immune system regulation and response to pathogens using genome-wide approaches.  With the rise of genomic and proteomic technologies, scientists have been able to visualize biological networks and infer interrelationships between genes and/or proteins; recently, these technologies have been used to help better understand how the immune system functions and how it is regulated.  Two thirds of the genome is active in one or more immune cell types and less than 1% of genes are uniquely expressed in a given type of cell.  Therefore, it is critical that the expression patterns of these immune cell types be deciphered in the context of a network, and not as an individual, so that their roles be correctly characterized and related to one another.  Defects of the immune system such as autoimmune diseases, immunodeficiency, and malignancies can benefit from genomic insights on pathological processes.  For example, analyzing the systematic variation of gene expression can relate these patterns with specific diseases and gene networks important for immune functions.

Adaptive immune system: The adaptive immune system, also known as the acquired immune system or, more rarely, as the specific immune system, is a subsystem of the overall immune system that is composed of highly specialized, systemic cells and processes that eliminate pathogens or prevent their growth.  The adaptive immune system is one of the two main immunity strategies found in vertebrates (the other being the innate immune system).  Adaptive immunity creates immunological memory after an initial response to a specific pathogen, and leads to an enhanced response to subsequent encounters with that pathogen.  This process of acquired immunity is the basis of vaccination.  Like the innate system, the adaptive system includes both humoral immunity components and cell-mediated immunity components.

Supporting paragraphs: Autoimmune encephalitis Cyclophosphamide
Answer: Cyclophosphamide