Mass spectrometry (MS) has gained importance in the anlytics of biopharmaceuticals, taking different complementary approaches ranging from peptide-based sequencing to direct analysis fo intact proteins and protein assmeblies. (Rosati, Nature Protocols, 9(4), 20140)p

A variety of “hyhenated chromatography-mass spectrometry” methods have demonstrated the capability of detecting low-abundance impurities in mAb products and providing highly detailed analyses that cannot be acheived by either SDS-PAGE or CE-SDS methods.  (Wang, US 16/223,463, published as US 2019/0194298).

Hydrophilic interaction chromatography (HILIC) + MS:

for characterization of glycosylation:

Glycosylation is one of the most common postranslational modifications of proteins. Protein heterogeneity introduced by glycosylation includes differences in the nature and structure of the attached oligosacharides, and the number and position of the glycans. Common methods to study glycosylation involve glycan release or protein digestion, followed by analysis of the reuslting glycans or clycopeptides. These methods offer detailed information about the sites of clycosylation and/or the carbohydrate composition. Electrospray ionization mass spectrometry (ESI-MS) enalbes the precise mass determination and characterization of intact (glyco) proteins. However, seperation prior to MS detection often is essential to acheive reliable assignment of intact glycoproteins and detection of low abundant glycoforms. HILIC-MS has shown highly useful for the analysis of a wide range of compounds including metabolites and pepties. (Somsen, “high-resolution glycofrom profiling of intact therapeutic proteins by hydrophilic interaction chromatography-mass spectrometry” Talanta 184 (2018) 375-381). 

Glycosylation is a post-translational modificaiton of proteins that occurs in all eukaryotic cells. The sugar chains on glucoproteins can mediate biologial activity, play a role in receptror-mediated recognition, increase solubility, regulate half-life and exert a stabilizing influence upon conformation. (Gillece-castro, “N-linked glycans of glycoproteins: a new column for improved resolution” Water Corporation (2009) .ueous mobile phase used in HILIC, which overcomes the drawbacks of the poor solubility often encounted in NP-LC. Expensive ion pair reagents are not required in HILIC, and it can be conveniently coupled to mass spectromtry (MS). (Busewski, “Hydrophilic interaction liquid chromatogrpahy (HILIC) – a powerful spearation technique, Anal Bioanal Chem (2012) 402: 231-247). 

HILIC has many specific advantages over conventional NP-LC and RP-LC. For example, it is suitable for anlyzing compounds in complex systems that always elute near the void in reserved-phase chromatography. Polar samples always show good solubility in the aq

D’Atri (Hydrophilic Interaction Chromatography hyphenated with mass spectrometry: a powerful analytical tool for the comparison of originator and biosimilar therapeutic monocloanl antibodies at the middle-up level of analysis” Anal. Chem 2017, 89, 2086-2092) discloses that using a sationary phase in combination with a highly organic mobile phase, HILIC is fully compatible with electrospray ionization mass spectrometry (ESL-MS) and offers a complementary retntion mechaism compared to RPLC, since analytes are eluted based on their hydrophilicity. 

Lauber (US 2015/0316515) discloses characterization of large biological molecules modified with polar groups such as antibody glycorms by hydrophilic interaction chromatography (HILIC) which further includes the step of identifying the glycopeptie with mass spectrometry. In one embodiment the sample is first prepared by reductyion, enzymatic digeston, denaturation, fragmentation, ehmical cleavage or a combination thereof. In another emobdiment the method for analyzing a glycosylated protenaceous sample, the chromatographic material is a porous material which includes at least one hydrophilic monomer and a poly-amide bonded pahse. In certain embodimetns, the method includes the step of denaturing the glycosylated proteinaceous sample at a temperature 80C or greater and deglycosylating the denatured sample. In certain embodiments, the method includes a mobile phase eluent such as acetonitrile, isopropanol or ethanol. 

Wang (J Pharmaceutical and Biomedical Analysis, 154: 468-476 (2018) disclsoes that hydrophilic interaction chromatography (HILIC) coupled with mass spectrometry analysis can characterize LMW impurites present within a purified mAb drug product sample. After mreoval of N-linked glycans, the HILIC method separates mAb related LMW impurites with asize based elution order. Free ligh chains, half-antibody, H2L species (antibody possessing a single light chain) and protein backbone truncated species can all be confidently identifed and elucidatesd in great detal, including the truncation sites and associated post translational modificaitons. 

Wang, (US 16/223,463, published as US 2019/0194298) discloses methods for charaterizing low molecular weight (LMW) protein drug product impurities which uses hydrophilic interaction chromatography (HILIC) coupled to mass spectrometry analysis. After removal of the N-linked glycans from teh protein drug product, for example an antibody drug product, the elution of LMW impurities from the HILIC column is determend by the size of the molecular weight species. 

IEX + Mass Spectrometry: 

Cation exchange (CEX) + MS:

Wang (Anal Cehm 87: 914-921 (2015) disclsoes drug product related impurities of an anti-Clostridium difficile IgG1 mAb were profiled by CEX liquid chromatogrpahy followed by teh CEX peaks being fraction collected for MS characterization. A reversed-phase liquid chromatography/mass spectrometry (LC/MS) methology was developed on a Thermo Q-Exactive orbitrap mass spectrometer for mass measurements of the mAb, its CEX fractioanted impurties and their respective H and L chains. 

Wang (US 16/259095, published as US 2019/0234959) discloses using IEX, preferably strong CEX  with an aqueous mobile phase coupled with native mass spectrometry analysis to detect and characterize size variant protein drug product imprities. In one embodiment the protein is first deglycosylated such as by treating the sample with IdeS.

SEC + Mass Spectrometry:

Kukrer (Pharm Res, 27: 2197-2204 (2016) discloses mass spectrometric analysis (MS of mAg aggregates fractionated by size-exclusion chromatography (SEC). IgG aggregates (dimers, trimers, tetramers and HMW oligomers) were created by subjecting an IgG formulation to several pH jumps. Protein oligomer fractions were isolated by high performance size exclusion chromatogrpahy (HP-SEC) dialyzed agaisnt ammonium acetate pH 6.0 and analyzed by native electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS). 

Wang (US 16/259095, published as US 2019/0234959) discloses using SEC with an aqueous mobile phase coupled with native mass spectrometry analysis to detect and characterize size variant protein durg product imprities. In one embodiment the protein is first deglycosylated such as by treating the sample with IdeS. 

Wollacot (mAbs, 5(6): 925-935 (2013) discloses using seize exclusion high-performance liquid chromatogrpahy (SE-HPLC) analysis of a hmAb to identify a mAb species that eluted between the monomeric and dimeric species. 

 

Websites:  ClinicalTrials.gov  (lists many active CART trials). 

See also Enzymes and CRISP

Introduction to CARs/CARTs and TCRs

A very promising immunotherapy is the use of a chimeric antigen receptor (CAR) on T cells to reprogram the T cells to recognize proteins such as CD19 and CD22 found on cancer cells. This has had considerable success with acute lymphoblastic leukemia (ALL). Patients are infused with their own T cells which have been genetically modified for the CAR. CAR-T cell therapy targetting the B cell antigen CD19 was approved by the FDA for child hood acute lymphoblastic leukimia in 2017 (Hu, “Toward personalized, tumour-speciic, therapeutic vaccines for cancer” 2018). Today, 70-90% of pateints with B-cell acute lymphblastic leukemia (R/R B-ALL) who are treated with CD19 directed CAR T cells can acheive complete remission. (Klichinsky, “A milestone in macrophage-based cancer treatment” BioProcess International, 22(4), April 2024), 

Chimeric antigen receptors are protein which graft the specificity of, for example, a monoclonal antibody (mAb) to the effector function of a T-cell. Their usual form is that of a type I transmembrane domain protein with an antigen recognizing amino terminus, a spacer, a transmembrane domain all connected to a compound endodomain which transmits T-cell survival and activaiton siganls. The most common form of these moleules are fusions of single-chain variable fragments (scFv) derived from mAbs which recognize a target antigen, fused via a spacer and a trans-membrane domain to a signaling endodomain. Such molecules result in activaiton of the T-cell in response to recognition by the scFv of its target. When T cells express such a CAR, they recognize and kill target cells that express the target antigen. Several CARS have been developed against tumour assoicated antigens, and adoptive transfer approaches using such CAR-expressing T cells are currenlty in clinical trial for the treamtent of various cancers. (Thomas (WO 2016/102965)

T cells require multiple signals for optimal function; CD28 on teh T cell which interacts with B-7 (CD80); CTLA-4 (CD152) with B72 (CD86), TCR with MHC, PD-1 with PD-L1 (B7-H1). (“Next Generation of engineered T cells for immunotherapy” Maus, Cancer Crosslinks, January 18, 2018)

CARs are synthetic receptors that are comprised of extracellular ligand-binding domains fused to intracellular co-stimulatory and activation domains. First-generation CARs lack co-stimulatory signalling domains and have limited efficacy owing to insufficient signalling strenght and durability; thus second-generation and subsequent CAR designs have incorproated one or more co-stimulatory domains to enhance and sustain T cell activaiton signalling.  Hou, Nature Reviews, Drug Discovery, 29, July 2021)

CARS are not MHC restricted:

CARs are not MHC restricted but only see surface proteins. (“Next Generation of engineered T cells for immunotherapy” Maus, Cancer Crosslinks, January 18, 2018).

Both chimeric antigen receptor (CAR) and T cell receptor (TCR) engineering can direct T cell cytoxicity towards tumour cells. Conventional CARs derive their antigen-targeting moiety from antibodies and, unlike TCRs, which are restricted to major histocompatibility complex (MHC), recognize peptides in an MHC -independent manner. Although conventional CARS derive their signalling component from the CD3 complex, they have signalling properties distinct from those of TCRs. Despite the fact that the ligand binding comain of CARs frequently has substantially higher binding affinity for its target ligand compared with TCRs, TCRs can respond to a single protien-MHC whereas CARs can require substantially higher anitgen densities to induce a robust T cell response. These unique characteristics of binding a signalling preclude head to head clinical comparisons of T cells engineered with CARs versus TCRs, and the idea choice of receptor may depend on properties of the target antigen, including antigen density and ease of surface presentation. (Hou, Nature Reviews, Drug Discovery, 29, July 2021). 

Chimeric antigen receptor (CAR) T cell therapy involves isoalting a patient’s T cells; reprogramming those T cells to produce a specific, targeted receptor (a CAR) on each T cell’s surface; and infusing the patient with the reprogrammed cells. The reprogramming involves introducing genetic material  containing a nucleotide sequence encoding for a CAR into the T cell so that the cell produces the CAR on its surface. This CAR allows the T cell to recognize the specific antigen for which it was programmed. U.S. Patent No. 7,446,190 (latter held invalid for lack of written description in Juno therapeutics v. Kite Pharma (Fed. Cir, 2021) was one of the earliest patents on this technology. It claims priority to a provisional applicaiton filed on May 28, 2002 and relates to a nucleic acid polymer encoding a three-part CAR for a T cell. 

Structure:

CARs used in two T cell therapies approved to date share a commn basic design. On their extracellular side single-chain variable region termed scFv (which is a fusion of the heavy chain and light chain variable regions of an immunogloublin) recognizes a specific antigen (such as CD19). This scFv is followed by a spacer and transmembrane domain fused to an intracellular co-stimulatory domain, such as CD28 or 4-1 BB, followed by the y-chain or epsilon chian of CD3. Various other modificaitons to the CAR desgin are being investigated to enhance efficacy and/or safety. Kimbrel “Next-generation stem cells — ushering in a new era of cell-based therapies” Nature Reviews: Drug Discovery, 19, July 2020).

1) Intracellular domain: The first portion of the three-part CAR is the intracellular domain of the human CD3 (zeta) chain. It is a signaling domain that, when the T cell binds to an antigen, is actived to create an initial immune response.

First-generation CARs typically had the intracellular domain form the CD#epison chain, which is the primary transmitter of signals from endogenous TCRs. Second generation CARs added intracellular signaling domain from various costimulatoyr protein receptors (e.g., CD28, 41 BB, ICOS) to the endodomain of the CAR to provide additional signals to the T cells. More recent, third-generation CARs combine multiple signlaing domain to further augment potentcy. Chen, (WO/2021/034689)

2) costimulatory region: The second porition is a costimulatory region that includes a specific amino acid sequence that is part of a naturally occurring T cell protein called CD28. When activated, the costimulatory region creates a second signal to augment or prolong the immune response, for example, directing the T cells to multipoly. 

3) binding element: the third porition of a CAR is the binding element, which is the portion of teh CAR that determiend what target molecule or antigen the CAR can recognize and bind to. One type of binding element is a single-chain antibody (scFV). A scFV is made by taking two pieces of an antibody, one from the heavy cahin of the antibody’s variable region and one from the light chain of the variable region, and linking them together with a linker sequence. 

Engineering Techniques:

The design of the CAR construct is critical to the optimal function and presistence of CAR T cells. Key features including the target binding motif, the linker, the hinge, and the transmembrane and the cytoplasmic signaling domains, can all have a substantial impact on the activation, profieration, target-cell killing and exhaustion of CAR T cells. (Hege, “Context matters in CAR T cell tonic signaling” Nature Medicine, Vo. 27, June 2021). 

Chimeric antigen receptors (CARs) are hybrid molecules comprising three essential units: (1) an extracellular antigen-binding motif; (2) linking/transmembrane motifs and (3) intracellular T-cell signaling motifs. Teh antigen-binding motif of a CAR is commonly fashioned after a single chain fragment variable (scFv), the minimual binding domain of an immunoglobulin (Ig) molecule. Alternate antigen binding motifs, such as receptor ligands (ie, IL-13 has been engineered to bind tumor expressed IL-13 receptor, intact immune receptors , library derived peptides and innate immune system effector molecuels (such as NKG2D) also have been engineered. Alternate cell targets for CAR expression (such as NK or gamma-delta T cells) are also in development. To date the signaling motifs used in CARs always include the CD3-epsilon chain because this core motif is the key signal for T cell activation. (Krueger, WO 2016/201394). 

Bispecific CARS (tandem CARS or TanCARs):

Bispecific CARS (tandem CARS or TanCARs) have been developed to target multiple cancer specific markers simultaneously. In a TanCAR, the extracellular domain includes two antigen binding specificities in tandem, joined by a linker. The two binding specificities (scFvs) are thus both linked to a single transmembrane portion; one scFv being juxtaposed to the membrane and the other being in a distal position. For example, Grade (2013, Mol Ther Nucleic Acids 2: e105) describes a TanCAR which includes CD19-specific scFv, followed by a Gly-Ser linker and then a HER2-specific scFv. HER2-scFv was in the jxta-membrane position and the CD19-scFV in the distal position. The Tan CAR was shown to induce dsitinct T cell reactivity against each of the two tumour restricted antigens. Thomas (WO 2016/102965) describes a CAR T cell which expresses two CARs at the cell surface, one specific for CD19 and one specific for CD22. The fact that one CAR binds CD19 and the other binds CD22 is advantageous because some lymphomas and leukaemias become CD19 negative after CD19 targeting so it gives a back-up antigen, should this occur. 

Enhancers of CAR-T cells: 

CAR-enhancer (CAR-E):

Dana-Farber Research Institute has developed a “CAR-E therapeutic platform” wehre a target antigen is fused with a low-affinity enhancer olecule (“A CAR enhancer increases the activity and persistence of CAR-T cells” Nature Biotechnoloy). For example, a B-cell maturation antgien (BCMA) can be fused with a low-affinity IL-2. The BCMA CAR-E seelctively binds to CAR-T cells, leading to their proliferation, effective clearance of tumor cells and promotion of teh development of memory CAR-T cells with diverse pehnotypes. The BCMA antigen by itself does not affect CAR-T cells, but, together, they ahve a synergy. 

Hybrid Receptors

Emerging strategies aim to combine the benefits of MHC independent recognition of antigens by CARS and robust signaling from TCRs. In one strategy, an antibod-TCR (ABTCR) was desigend by fusing a Fab with TCR daomins. In another strategy, TCR fusion constructs (TRuCs) were engineered by fusing an antibody based binding domain to various TCR subunits, which reconstittued complete TCR complexes. A third strategy introduces T cell antigen couplers (TACs) which combine extravellular co-receptor domain. All three CAR-TCR hybrid receptors conferred greater antitumour efficacy than their conventional CAR counterparts in leukaemia, lymphoma and ovarian carcinoma xenograft models, with lower cytokine release levels. (Hou, Nature Reviews, Drug Discovery, 29, July 2021).

Senolytic CAR T cells (Clearing Senescent Cells)

a uPAR-specific CAR comprising an anti-mouse uPAR single-chain variable fragement linked to human CD28 costimulatory and CD3 signalling domains, and transducted human T cells has been shown to efficeinty eliminate uPAR expressing senescent cells. The acculation of senescent cells promotes inflammation and chronic tissue damage, thereby contributing to several ageing assocaited diseases. 

CAR NK Therapy

A new type of immunotherapy called CAR NK therapy uses Natural killer cells (NK) cells isolated from umbilical cord blood which have a CAR added to the cells. With the CAR, the cells can recognize an antigen on cancer cells. MD Anderson Cancel cells has been working with this type of therapy. 

Although traditional cellular immunothepary strategies are dominated by T cell expressed CARs, NK cells have more recently gained traction as an alternative cell therapy platform. NK cells possess a cytotoxic potential similar to T cells but unlike T cells, NK cells intrinsically lack alloreactivity and do not trigger side effects common to CAR-T adminsitratio such as cytokine release syndrom and immune effecotr cell associated neurotoxicity syndrome. Lamothe, “Novel CRISPR-Associated gene-editing systems discovered in metagenomic samples enable efficient and specific genome engeering”, CRISPR Journal, 6(3), 2023)

CAR Macrophages:

Companies: Carisma Therapeutics (oroginally Carma Therapeutics). 

Another promising permutation of the CAR concept invovles genetically engineered marcophages. While CART-T has treated leukemia successfully, and the modality is beginning to show promise against some lymphomas and myelomas, solid tumors remain an intractable problem regardelss of indication, target antigen, CAR design and treatment regimen. Tumors devote consdierable energy to recruting macrophages, whereas they generally try to exclude T cells. The reason for this is that T cells can recognize new antigens and thus pose a threat to tumor growth. On the other hand, macrophages can function as immunosuppressive cells when appropriately polarized toa suppressive phenotype, promoting tumor growth and immune escape. The company Carisma provisions the cells that tumors like to recruit with CARs. When a CAR-M binds with a target antgien, the cell is designed to activate as it would during typical antiboy-driven immune resposnes. It will phagocytose the bound cancer cell, induce inflammatory cytokine release, and then present tumor-derived antigens to T cells. The CAR is essentially a sense-and-response system. The receptor binds to a target antigen (eg., HER2) and emits a signal to activate a cascade that leads to further immune cell activaiton and killing of cancer cells. The cells are also polirized to the M1 phenotype so that tumors cannot make them immnosuppressive. (Klichinsky, “A milestone in macrophage-based cancer treatment” BioProcess International, 22(4), April 2024)

Antigens Targeted

BCMA (expressed on MM cells)

Poseida Therapeutics 

EBV Allogeneic CARTS:

Atara Bio 

HER2 (Human Epidermal Growth Factor 2):

Bellicum Pharmaceuticals

PSCA (Prostate Stem Cell Antigen):

Bellicum Pharmaceuticals

Delta-like ligand 3 (DLL3):

Stull (WO2016138038) discloses chimeric antigen recetpors (CARs) that include a DLL3 binding domain that specifically binds to human DLL3 prtoein which is expressed on tumor initiating cells. When the anti-DLL3 bidning domains are incorproated in a chimeric antigen recetpor expressed on lymphocytes, the resulting DLL3 lymphocytes (e.g., NK cels or T cells) are able to mount an immune response directed to aberrant DLL3 positive cells including cancer stemp cells. The CARS include an extracellular domain that includes a DLL3 binding domain, a transmembrane domain and an intracellular signaling domain that activates certain lymphocytes and generates an immune response directed to DLL3 postive tumor cells. 

Applications and Diseases Treated

CARs are synthetic, MHC independent receptors that possess the capability to redirect immune cells such as T cells toward target cells expressing antigens. Given their ability to induce remissionwith otherwise-untreatable tumors, the number of CAR-T cell clinical trials has reisen dramatically over the past decade. Creation of CAR-T cells by gene editing of the TRCR (TRAC) locus is particularly attractive because it allows combination of TCR knockout with high efficiency CAR transgene integration.  Ablation of the TCR prevents therapeutic cells form attakcing their host. Reciprocally, effective allogeneic cell therapy in immmuno-oncology requires that the body does not attack the transplanted cells, that is, that the cells persist in the recipient. Adoptively transferred T cells will disply endogenous peptides in class I HLA receptors. Natural human genetic variation within such peptides willl result in donor cells being perceived as foreign. Removal of beta2-microglobulin (B2M), a structural component of all class I HLA complexes, effectively prevents foreign cell antigen display and rejection of donor cells by the adaptive immune system. (Lamothe, “Novel CRISPR-Associated gene-editing systems discovered in metagenomic samples enable efficient and specific genome engeering”, CRISPR Journal, 6(3), 2023)

Large B-cell Lymphoma/ B-cell precursor acute lymphoblastic leukemia (AML/relapsed or refractor mantel cell lymphoma):

–Breyanzi (lisocabtagene maraleucel): is approved for treatment of adults with large C cell lymphoma, including diffuse large B cell lymphoma not otherwise specified (including diffuse large B cell lymphoma arising from indolent lymphoma), high grade B cell lymphoma, primary mediastinal large B cell lymphoma, and follicular lymphoma grade 3B who have refractory disease to first line chemoimmunotherapy or relapse within 12 monhts of the first line chemoimmunotherapy, or refractory disease to frist line chemoimmunotherapy or relpase after first line chemoimmunotherapy and are not eligible for hematopoietic stem cell tranplantation due to comorbidities or age, or relapased or refractory disease after two or mroe lines of systemic therapy.It is also indicated for treatment of adult patients with relpased or refractory chrnoic lymphocytic leukemia or small lymphocytic lymphoma who have received at least two prior lines of therapy, including a Bruton’s tyrosine kinase inhibitor and a B cell lymphoma 2 inhibitor. 

–Yescarta (axicabtagene ciloleucel)(Kite, a Gilead Company): is approved for treatment of adults with large C-cell lymphoma that is refractory to first-line chemoimmunotherpay or that relapses within 12 months of the first line chemoimmunotherpy. Also, treatment of adults with relapsed or refractory large B-cell lymphoma after two or more lines of systemic therapy, including diffuse large B-cell lymphoma not otherwise specified, primary mediatinal large b-cell lympoma, high grade B-cell lymphoma and diffuse alrge B cell lymphoma arising from follicular lymphoma. YESCARTA is a CD19-directed genetically modified autologous T cell immunotherapy.

–Kymriah (tisagenlecleucel): 

Kymriah (tisagenlecleucel) is approved for treatments of patients up to 25 years of age with B cell precursor Acute Myeloid Leukemia (AML) that is refractory or in second or later replase; adult pateints with relapsed or refractory (r/r) large B cell lympoma after two or more lines of systemic therapy; including diffuse alrge B cell lymphoma not otherwise specified, high grade B cell lymphoma and diffuse large B cell lympoma arising from follicular lymphoma; and adult pateints with replpsed or refratory follicular lymphoma after two or more lines of systemic therapy. 

–Tecartus (brexucabtagene autoleucel) (Kite, a Gilead Company): is approved for adults with replased or refractory mantle cell lymphoma. Also, treatment of adults with relapsed or refractory B cell precurosr acute lymphoblastic leukemia. 

Mantle cell lymphoma (MCL) is a rare form of cancerous B-cell non-Hodgkin’s lymphoma which usually occurs in middle or older aged adults. 

Celgene

Metastatic Melonma

Lovance

Multiple Myeloma (MM)

 BlueBird Bio   Celgene . 

–Abecma (Idecabtagene vicleucel) (Bristol Myers Squibb and 2seventy bio): is a CAR T cell therapy for the treatment of adult patients with replased or refractory multiple myeloma after two or mroe prior lines of therapy including an immunomodulatory agent, a protease inibitor, and an anti-CD38 monoclonal antibody. 

–Carvykti (citacabtagene autoieucel) (Johnson & Johnson): Carvykti is approved for treatment of adult patients with relapsed or refractory multiple myeloma after four or mroe prior lines of therapy, including a protease inhibitor, an immunomodulatory agent, and an anti-CD38 monoclonal antibody. It works by by changing your own T cells to recognize and attack a target on the surface of multiple myeloma cells and certain other healthy cells after a single infusion. The entire process generally takes about 2 to 3 months.

Factors to Consider in Therapy

Target antigen: is a major determinant of safety and efficacy for CART cell therapy. The CAR redirects T cell cytotoxicity towards it cognate antigen, irrespective of the identity of the cell that presents it. Consequently, healthy cells that share target antigen expression are at risk of on-target, off-tumour bystandinger killing. In principle, the ideal tumour antigen should be highly and uniformly expressed on tumour cells but absent on healthy tissue. Somtimes these consequences can be managed. For example, CAR-T cell therapeis targeting the pan B cell marker CD19 have demonstrated impressive clinical resposnes for the treatment of haematological malignancies, but succesful treatment by CD19 CART cells also invariably results in B cell apiasis, which is a predictable consequence of targeting CD19 that can be clinically managed by immunoglobulin transfusion. (Hou, Nature Reviews, Drug Discovery, 29, July 2021)

 Cancel cells has been working with this type of therapy. 

See also medically important gram + bacteria organisms and Medically Important Gram Negative Bacteria

Differences between Gram Negative and Gram Positive Bacteria

Gram-negative bacteria organisms have thinner cell walls which differ in composiiton from their Gram-positive counterparts. As a result, they lose the crystal violet stain (and take the color of the red counterstain) in Gram’s method of staining. Gram negative bacteria can be distinguished from gram-positive according to the following:

  • Cell Envelope: Outer membrane (gram – only): Gram negative bacteria are covered by an outer membrane which contains lipopolysaccharide (LPS) and porins. The LPS is a major antigenic component and functions as a mitogen. Mitogens are agents that are able to induce cell division in a large percentage of T or B cells. Unlike immunogens, which activate only lymphocytes bearing specific receptors, mitogens activate many clones of T or B cells irrespective of their antigen specificity. Porins form pores through the outer membrane and allow diffusion of hydrophilic molecules. Endotoxins, which are part of the lipopolysaccharide complex that forms the outer envelope of gram-ngegative bacteria, are released during the lysis of a microorganism or cell division. An essential part of quality assurance and quality control invovles testing end-product injectable drugs, medical devices, and raw materials for endotoxins. The importance of testing for endotoxins in humans cannot be emphasized enough because of the pyrogenic or immunorespeonsive reactions that can occur after exposure to bacterial pyrogens. Humans are particularly sensitive to minute amounts of endotoxins, and mild gram-negative bacterial infections can often casue a pyrogenic response. The presence of endotoxin in the bloostream can cause fever, inflammation and often irreversible shock. (Joiner, “comparison of endotoxin testing methods for pharmaceutical products” J Pharm Compd 6; 408-409 (2002)
  • Higher Lipid content: Gram – bacteria have a higher lipid content due to their outer membrane
  • Less peptidoglycan (sometimes called “cell wall”): Gram – have a thinner peptidoyglycan layer than Gram-positive cell walls in what is called the periplasmic space (the area between the internal face of the outer membrane and the external surface of the cytoplasmic membrane). The linker between the N-acetylglucosamine-N-acetylmuramic acid disaccharide units include DAP rather than a pentaglycine chain as with gram + bacteria. This thin layer fails to retain the crystal violet dye but does retain a pinkish red safranin dye.

 Gram-positive bacteria can be distinguished from gram-negative according to the following:

  • thick cells wall composed largely of peptidoglycan, which consists of repeating N-acetylglucosamine-N-acetylmuramic acid disaccharide units that are linked via short peptide bonds. In gram + bacteria, this linkage has a pentaglycine chain which is lacking in gram – bacteria.

This thick cell wall retains crystal violet dye. Thus gram-positive bacteria will stain purple in comparison with gram-negative bacterial which stain red by the counterstain safranin. 

Since the peptidoglycan layer is a target for penicillin, this drug works better for gram-positive bacteria.

  • Scaffolding proteins like teichoic and lipoteichoic acids are also associated with the peptidoglycan layer in gram positive bacteria.
  • No lipopolysaccharide (LPS) as with gram-negative bacteria.
  • No outer membrane

Classes of Leukocytes

White blood cells or “leukocytes” combat infection and in some cases phagocytose and digest debris. White blood cells are traditionally grouped into three major categories based on their appearance in the light microscope. These classes are the following:

1) Lymphocytes:

Out of all the leukocytes, only lymphocytes possess the attributes of specificity, memory and self/nonself recognition. All the other leukoctyes play accessory roles, serving to activate lymphocytes, to increase the effectiveness of antigen clearance by phagocytosis, or to secret various immune effector molecules. 

2) granulocytes and 

3) monocytes

New leukocytes enter the blood from the bone marrow (innate immune cells and B cells) or thymus (naive T cells) and express characteristic trafficking molecule patterns that enable and restrict their migration to certain regions. 

Leukocyte Migration:

Leukocytes circulate into inflammed tissues and peripheral lymphoid organs by passing between endothelial cells lining the walls of blood vessels (diapedesis). Leukocytes possess receptors which bind to leukocytes-specific on endothelial cells in this extravasation mechanism. Some of these CAMS are expressed constitutively whereas others are expressed in response to localized concentrations of cytokines produced during an inflammatory response.  Most CAMS belong to the following 4 families of proteins:

  • Integrins; 
  • Selectins
  • mucins are a group of serine and threonine rich proteins that are heavily glycosylated. 
  • ICAMs contain a variable number of immunoglobulin like domains and thus are classified in the immunoglobulin superfamily. 

Selectins and mucin-like CAMs interact with each other, and members of each family are expressed on both leukocytes and endothelial cells. Integrins which are expressed on leukocytes, interact with ICAMS expressed on endothelial cells.

As an example of CAM function, activated endothelial cells express adhesion molecules of the which interact with mucin-like cell-adhesion molecules on the neutrophil membrane. As roll over the endothelial cells, they are activated by various chemoatractants like and platelet activating factor (PAF) which triggers an activating signal mediated by  associated with receptors on the neutrophil membrane This signal induces a conformational change in the integrin molecules in the neutrophil membrane, increasing their affinity for the Ig-super family adhesion molecules on the endothelium.

Human Effector cells:

“Human effector cells” are leukocytes which epxr3ess one or more FcRs and perform effector fucntions. Preferably, the cells express at least FcyRIII and perofrm ADCC effector funciton. Exampels of human luekocytes which meidate ADCC include peripheral blood monoculcear cells (PBMC), natural Killer (NK) cells, monocytes, cytotoxic T cells and neutrophiles; with PBMC and NK cells. Presta (US 6,737,056). 

Protozoa are a subset of protists which are eukaryotes that are not classified as animals, plants, or fungi.

Protozoa constitute a large genus (some 12,000 species) that although single-celled, have a great deal of complexity with respect ot movement, feeding and behavior. Although most members are harmless, free living inhabitants of water and soil, a few species are pathogens which are collectively responsible for hundreds of millions of infections of humans each year. Protozoa are called “trophozoites” when they are in their motile feeding stage. A large number of species are also capable of entering into a dormant, resting stage called a “cyst” when conditions in the environment become unfavorable for growth and feeding. Cycsts can be dispersed by air currents and may even be important factor in the spread of diseases such as amoebic dysentery. If provided with moisture and nutrients, a cyst breaks opena dn releases the active trophozoite.

Protozoan parasites were the most frequently identified etiologic agents in waterborne disease outbreak from 1991 to 1994. The waterborne parasites Giardia lamblia, Naegleria fowleri, Acanthamoeba spp., Entamoeba histolytica, Cryptosporidium parvum, Cyclospora cayetanesis, Isospora belli. See Sterling

Affecting Blood, the Cardiovascular and Lymphatic System

Babesiosis: Babesia is a protozoan that infectes red blood cells. It is carreid by ticks and found in the upper Great Lakes region as well as in the northeast U.S. It is often diagnosed via a blood smear; the protozoan is visible inside red blood cells. A combined therapy of either atovaquone (an antiprotozoal) plus azithromycin or clindamycin plus quinine (another antiprotozoal) is recommended.

Chagas Disease (the American trypanosomiasis”): Chagas disease is named after the Brazilian physician Carlos Chagas, who discovered the disease in 1909. It is caused by the flagellated protozoan Trypanosoma cruzi, which is transmitted to animals and people by insect vectors (triatomine bug) and is found only in the Americas (mainly, in rural areas of Latin America where poverty is widespread). The bug is found in dwellings constructed form materials such as mud, adobe and straw. The insect bites the host and while feeding on its blood deposits feces. The parasite can then enter the body of the host from the insect’s feces when the host scratches and breaks the skin, or transfers the parasite to a mucous membrane. The disease can also be passed from mother to child during childbirth, during blood transfusions, and from organ transplants. Chagas disease can lead to severe cardiac and digestive problems in humans and domestic animals, but it appears to be tolerated in wild mammals. Tsetse fly-transmitted trypanosomes have evolved an elaborate genetic mechanism for repeatdly changing the antigenic nature of their protetive glycoprotein coat. Only a single gene out of some 1000 variable surface glyoprotein genes is expressed at a time. The variable surface glyscoprotein is usually duplicated and moved to 1-20 expression sites enar the end of the chromosome where it is transcribed. In the guts of the flies that spread them, trypanosomes are noninfective. When they are ready to transfer to the skin or bloodstream of their host, trypanosomes migrate to the salivary glands and acquire the thick coat of glycoprotein antigens that protect them form the host’s antibodies. Later, when they are taken up by a tsetse fly, the trypanosomes again shed their coats. The producitoh of vaccines against such a system is accordingly complex. Rleasing sterilzied flies to iimpede the rproduction of populations is another technique. Traps made of dark cloth and scented like cows but poisoned with insecticides have likewise proved effective.

A different trypanosome, T. brucei causes sleeping sickness on the African continent. It has a long incubation time and is very difficult to cure. Once the trypanosomes are transmitted by a group of insects called the triatomines, they multiply in muscle and blood cells. From time to time, the blood cells rupture and large numbers of trypanosomes are released into the bloodstream. The disease manifestations are divided into acute and chronic phases. In the acute phase, symptoms are nondescript and range form mild to severe fever, nausea and fatigue. A swelling called a “chagoma” at the site of the bug bite may be present. If the bug bite is close to the eyes, a distinct condition called Romana’s sign, swelling of the eyelids, may appear. The acute phase lasts for weeks or months after which the condition becomes chronic, which is virtually asymptomatic for a period of years or indefinitely. Eventually the trypanosomes are found in numerous sites around the body and in later years may lead to inflammation and disruption of function in organs such as the heart, the brain and the intestinal tract. Estimates put the prevalence at 8 million, 300,000 of whom live in the U.S. Chagas disease is a neglected parasitic infection in the U.S. Drugs for treatment are only available through the CDC. Recently, the U.S. begain screening all donated blood for Chagas Disease. See CDC

Plasmodium are blood and tissue protozoa. These parasites require two hosts; (1) a mosquito for sexual reproduction and (2) animals for asexual reproduction. Infection is by bite of the anopheles mosquito. Human pathogens include the following:

–Malaria:

—-Signs and Symptoms: after a 10-16 day incubation period, the first symptoms are malaise, fatigue, vaue aches and nausea with or without diarrhea, followed by bouts of chills, fever and sweating. These syptomes occur at 48-72 hour intervals, as a result of the synchronized rupturing of red blood cells.

Patients with falciparum malaria, the most virulent type, often display persistent fever, cough and weekenss for weeks without relief. Complications of malaria are hemoytic anemia from lysed blood cells and organ enlargement and rupture due to cellular debris that accumulates in the spleen, liver and kidneys. A serius complication of falciparum malaria is “cerebral malaria” where small blood vessels in the brain become obstructed due to the increased ability of red blood cells to adhere to veseel walls. The resulting decrease in oxxygen in brain tissue can result in coma and death.  See Mayo Clinic  See CDC

—-causative agent: 

Five species of over 200 species of the genus Plasmodium are known to commonly infect humans. They are P. malariaeP. vivxP, knowleskiP. ovale and P. falciparum.  The five species show variations in the pattern and severity of disease. For example, P. falciparum is responsible for the vast majority of deaths.

—-Pathogenesis and Virulence factors:

The invasion of the merozoites into RBCs leads to the release of fever inducing chemicals into the bloodstream. Plasmodium also metabolizes glucose at a high rate, leading to hypoglycemia. The damage ot RBCs results in anemia.

—-Transmission:

All forms of malaria are spread primarly by the female Anopheles mosquito. About 200 million new cases are reported each year, about 90% in Africa. The most frequent vitims are children and young adults, of whom between 500k to 1 million die annually.

—-Diagnosis:

Malaria can be diagnosed defininitevely by the discovery of a typical stage of Plasmodium in stained blood smears. Newer serological proecdures are available. Other indications are knowledge of the patient’s residence or travel in endemic areas and symptoms such as recurring chills, fever, and sweating.

—-Prevention:

Abatement includes elimination of standing water that can serve as a breeding site and spraying of insecticides to reduce populations of adult mosquitoes, especially in or near human dwellings.

Serile male mosequitos have also been introduced into endemic areas.

One can reduce their risk of infections considerably by using netting, screens and repellants, by remaining indoors at night and by taking weekly doses of prophylactic drugs.

A vaccine callaed “RTS.S, is effective against P. faciparum (the most deadly and most common strain in Africa) in children.

—-Treatment:

——Quinine with chloroquine being the least toxic type is used in nonresistant forms of Malaria. By 1820, the active ingredient in the bark of Cinchona trees, quinine, had been identified. In the 19th century, British soldiers in India used quinine-containing tonic water to fight malaria. In 1944, American chemists synthesized quinine. Qyinine can affect DNA replication and also, when P. falciparum breaks down hemoglobin from red blood cells in the digestive vacuole, an intermediary toxic form of heme is released. Quinine may itnerfer with the subsequent polymerization of these hemes, leading to a buildup of toxic hemes that poison the parasite. Now several other synthetic drugs are available to treat maleria. 

A drug called “artemisinin, derived from a plant, is recommended in many situations.

Affecting the Reproductive Tract

Vaginitis: is an inflammation of the vagina.

–signs and sumptoms: in clude some degree of vaginal itching, depending ont he etiologic agent. Sumptoms may also include burning and sometimes a discharge.

–Causative agents: While a varienty of bacteria and even protozoa can cause vaginitis, the must well known agent is the fugus Candida albicans. C albicans is a dimorphic fungus that is noraml biota in the majority of humans, living in low numbers on many mucosal surfaces such as the mouth, gastrointestinal tract and vagina. In otherwise healthy people, the fugus is not invasisive.

—-Trichomonas vaginglis: Another possible cause of vaginitis is Trichomonas which are small, pear-shaped protozoa. Trichomonas is a common sexually transmitted infeciton. Because it does not form cysts, it is more delicate and must be transmitted by intimate contact between sexual parrtners. see CDC

–Transmission and epidemilogy: Vaginal infections are nearly always opporutnistics. Disruptions of the normal bacterial biota or even minor damage to the mucosal epithelium in the vagina canlead to overgrowth by this fungus. Disruptions may be mechanical such as trauma to the vagina or they may be chemical as wehn broad spectrum antibiotics taken for some other purpose temperarily diminish the vaginal bacterial population.

–Prevention and treatment: no vaccine is available for C. albicans. Topical and oral azole drugs are used to treat vaginal candidiasis and many of them are available over hte counter.

Affecting the Gastrointestinal Track

Amoebiasis is the second leading cause of death from parasitic disease worldwide. The causative protozoan parasite, Entamoeba histolytica, is a potent pathogen. Secreting proteinases that dissolve host tissues, killing host cells on contact, and engulfing red blood cells, E histolytica trophozoites invade the intestinal mucosa, causing amoebic colitis. In some cases amoebas breach the mucosal barrier and travel through the portal circulation to the liver, where they cause abscesses consisting of a few E histolytica trophozoites surrounding dead and dying hepatocytes and liquefied cellular debris. See Stanley  Amoebiasis is a common infection of the human gastro-intestinal tract.  Amoebiasis is more closely related to poor sanitation and socioeconomic status than to climate. It has worldwide distribution. It is a major health problem in China, South East and West Asia and Latin America, especially Mexico. Only about 10% to 20% of people who are infected with E. histolytica become sick from the infection. The clinical spectrum ranges from asymptomatic infection, diarrhoea and dysentery to fulminant colitis and peritonitis as well as extra-intestinal amoebiasis. Acute amoebiasis can present as diarrhoea or dysentery with frequent, small and often bloody stools. Chronic amoebiasis can present with gastrointestinal symptoms plus fatigue, weight loss and occasional fever. Extra-intestinal amoebiasis can occur if the parasite spreads to other organs, most commonly the liver where it causes amoebic liver abscess. Amoebic liver abscess presents with fever and right upper quadrant abdominal pain. Other organs can also be involved, including pleuropulmonary, cardiac, cerebral, renal, genitourinary, peritoneal, and cutaneous sites. In developed countries, amebiasis primarily affects migrants from and travellers to endemic regions, men who have sex with men, and immunosuppressed or institutionalized individuals. The use of night soil for agricultural purposes favours the spread of the disease. Epidemic/ outbreaks (occurrence of more cases of a disease than would be expected in a community or region during a given time period) are usually associated with sewage seepage into the water supply. See AIMU

Balantidium coli: is an intestinal protozoan parasite that causes the infection “balantidiasis”. It is most prevalent in tropical and subtropical regions. It is rare in the U.S. It is transmitted by the fecal-oral route. Humans can become infected by eats fruits and vegetables that have come into contact with fecal matter from an infected animal, as well as drinking and washing food with contaminated matter. Most people experience no symptoms. It infects the large intestine of humans and the cysts are then passed into the feces. It can be serious for immunocompromised people. Symptoms in these people include persistent diarrhea, weight loss, nausea and vomiting. It is treated with tetracycline, metronidazole, and iodoquinol. See CDC website

Cryptosporidium: is an intestinal protozoan that infects a vareity of mammals, birds and reptiles. For many eyars, it was considered an intestinal ailment exclusive to calves, pigs, chickens and other puoltry but it is ceraly a zoonosis as well. Humans accidentally ingest the oocysts with water or food that has been contaminated by feces form infected animals. The organism penetrates the intestinal cells and lives intracellularly in them. It undergoes asexual and sexual reproduction in these cells, produces more oocysts which are released into the gut lumen, excreted form the host and after a short time become infective again. The oocysts are highly infectious and extremely resistant to treatment with chlorine and other disnfectants. Half of the outbreaks of diarrhea associated with swimming pools are casued by Crytosporidium. Because chlorination is not entirely successful in eradicating the cysts, most treatment plants use filtraiton to remove them, but even this method can fail. Treatment is not usually required for otherwise healthy patietns. Antidiarrheal agents (antimotility drugs) may be used. Although no curative antimicrobial agent exists for Cryptosporidium, physicians will often try nitazoxanide, which can be effective agaisnt protozoa in immunocompetent patients. See K-State (outlines many potential treatments) for Cryptosporidium parvum)

Cystoisosporiasis is an intestinal disease caused by the microscopic parasite Cystoisospora belli. This is the same parasite that used to be called Isospora belli. The parasite can be spread by ingesting food or water that was contaminated with feces (stool) from an infected person. People become infected by swallowing mature parasites, for example, by ingesting contaminated food or water. Infected people shed the immature form of the parasite in their feces. The parasite usually needs about 1 or 2 days in the environment (outside of people) to mature enough to infect someone else. In some settings, the parasite might mature in less than a day. Cystoisospora usually is spread indirectly, such as through contaminated food or water. This is because the parasite needs time to mature. However, oral-anal contact with an infected person might pose a risk for transmission. The infection is treated with prescription antibiotics. The usual treatment is with trimethoprim-sulfamethoxazole, which is also known as Bactrim*, Septra*, or Cotrim*. People who have diarrhea should also rest and drink plenty of fluids. See CDC

Giardiasis: Giardiasis is a diarrheal disease caused by the microscopic parasite Giardia. A parasite is an organism that feeds off of another to survive. Once a person or animal (for example, cats, dogs, cattle, deer, and beavers) has been infected with Giardia, the parasite lives in the intestines and is passed in feces (poop). Once outside the body, Giardia can sometimes survive for weeks or months. Giardia can be found within every region of the U.S. and around the world. See CDC

Giardia lamblia (syn.Giardia intestinalis, Giardia duodenalis) is a flagellated unicellular eukaryotic microorganism that commonly causes diarrheal disease throughout the world. It is the most common cause of waterborne outbreaks of diarrhea in the United States . It is occasionally seen as a cause of food-borne diarrhea. In certain areas of the world, water contaminated with G. lamblia cysts commonly causes travel-related giardiasis in tourists. Giardia species have two major stages in the life cycle. Infection of a host is initiated when the cyst is ingested with contaminated water or, less commonly, food or through direct fecal-oral contact. The cyst is relatively inert, allowing prolonged survival in a variety of environmental conditions. After exposure to the acidic environment of the stomach, cysts excyst into trophozoites in the proximal small intestine. The trophozoite is the vegetative form and replicates in the small intestine, where it causes symptoms of diarrhea and malabsorption. After exposure to biliary fluid, some of the trophozoites form cysts in the jejunum and are passed in the feces, allowing completion of the transmission cycle by infecting a new host. See Adam

The greatest clinical experience is with the nitroimidazole drugs, i.e., metronidazole, tinidazole, and ornidazole, which are highly effective. A 5- to 7-day course of metronidazole can be expected to cure over 90% of individuals, and a single dose of tinidazole or ornidazole will cure a similar number. Quinacrine, which is no longer produced in the United States, has excellent efficacy but may be poorly tolerated, especially in children. Furazolidone is an effective alternative but must be administered four times a day for 7 to 10 days. Paromomycin may be used during early pregnancy, because it is not systematically absorbed, but it is not always effective. Patients who have resistant infection can usually be cured by a prolonged course of treatment with a combination of a nitroimidazole with quinacrine. See Gardner

 Affecting the Nervous System

Amoebas:

Amoebae are unicellular microorganisms which are trophozoites in that they have 2 stages; an active motile feeding stage that is non infectious and a cyst stage that is infectious. Important amoebae include the following:

–Naegleria fowleri:

Naegleria fowleri is an ameboflagellate found in freshwater lakes and ponds and is the casative agent of primary amebic meningoencephalitis, a rapidly fatal disease of the central nervous system. The determinants of virulence for this ameba are unkown, but resitance to complement lysis appears to play a major role in its pathogenicity. While both pathogenic and nonpathonic Naegleria species activate AP, pathogenic N. fowleri amebae are resistance to the lytic effect of complement. Fritzinger (Infection and Immunity, 2006, 74 (2) pp. 1189-1195) demonstrate a CD59-like protein which could bind human C9 on the surface of pathogenic N. fowleri amebae and that the ability of a pathogenic species of Naegleria to synthesize a protein which protects the amebae from lytic molecules, such as MAC of complement (C5b-C9), may serve as an important virulence factor.

Naegleria fowleri occurs in people who have been swimming in warm, natural bodies of freshwater. Infection can begin when amoebas are forced into human nasal passages as a result of swimming, diving, or other aquatic activities. Once the amoeba is inoculated into the favorable habitat of the nasal mucosa, it burrows in, multiples and uses the olfactory nerve to migrate into the brain and surrounding structures. The result in primary ameibic meningo-encephalitis is a rapid massive destruction of brain and spinal tissue that causes hemorrhage and coma and invariable ends in death within a week or so. Early therapy with amphotericin B, sulfadiazine or tetracyline in some cominbation can be of some benefit. Becasue of the wide distribution of the amoeba and its hardiness, no general method of control exists. Public swimming pools and baths must be adequately chlorinated and checked periodically for the amoeba.

–Acanthamoeba: differs from Naegleria below in its portal of entry. It invades broken skin, the conjunctiva, and occasionally the lungs and urogentical epithelia. It causes a meningoencephalitis somewhat similar to that of Naegleria. The course of infection is lenghthier but nearly as deadly with only a 2-3% survival rate. At special risk for infection rare people with traumatic eye injuries, contact lens wearers and AIDS patients exposed to contaminated water.

acanthamoebae are a potential pathogen in ocular keratitis. Improper contact lense maintenance can result in infection. Incubation time is longer than naegleria.

Giardia lambia is a flagellate. Symptoms can be mild to severe (particularly for those with immunocompetency like AIDS patients).

Balantidium coil is the only member of the ciliate group which is pathogenic for humans, particularly for AIDS patients.

cryptosporidium typically caues watery diarrhea with abdominal pain that lasts for 1-4 weeks or more. Children, the elderly and immunosuppresed are particularly susceptible to severe or protracted disease. It can be spread when the feces of an infected animal is deposited in the water supply. One of the largest breakouts occurred in Milwaukee in 1992. Crytosporidium can be particularly severe in  patients. Crytosporidium belongs to the group coccidia.

isospora belli also belong to the coccidia. It reproduces in the intestinal epithelium and results in tissue damage.

enterocytozoan is a species of the microsporidia and causes chronic diarrhea in AIDS patients. 

pneumocystis carinii is an important cause of pneumonia in immunocompromised people and is transmitted by inhalation (but not from person to person). Untreated P. carinii mortality is almost 100%.

entamoeabae histolytica: have a highest infection rate in tropical and sub-tropical (which includes Florida and Southern California) area. 

naegleria:  The genus Naegleria consists of a group of free living ameboflagellates found in diverse habitats through the world. Naelgeria have been isolated from freshwater lakes, ponds, domestic water supplies, swimming pools, thermal pools, soil and dust Although over 30 species of Naegleria have been isolated, only Naegleria fowleri has been isolated from humans. (Marciano-Cabral, “The immune response to Naegleria fowleri amebae and pathogensis of infection”. FEMS Immunol. Med Microbiol 51 (2007) 243-259.)

Toxoplasma gondii: is a protozoal infection in the fetus and in immmunodeficient people, espcially those with AIDS. It is severe and often fatal. In otehrs, most cases of toxoplasmosis are asymptomatic or marked by mild symptoms such as sore throat, lumph node enlgargemetn,a nd low grade fever. Toxoplasma is an obligate intravellular parasite, making its ability to invade host cells an important factor for virulence. T. gondii is a very successful parasite iwth so little host specificity that it can attack at least 200 species of birds and mammals. However, the parasite udnergoes a sexual phase in the intestine of cats and is then released in feces, wehre it becomes an infective oocyst that survives in moist soil for several months. These forms eventually enter an asexula cyst state in tissues, called a psuedocyte. Most of the time, the parasite does not cycle in cats alone and is spread by oocysts to intermediate hosts, including rodents and birds. The cycle returns to cats when they eat these infected prey animals. Cattle and sheep can also be infected. Humans appear to be constantly exposed to the pathogen. The rate of infection can be as high as 90% in some populations. Many cases are casued by ingesting pseudocysts in undercooked contaminated meat, and other source s include contact with other mammals or even dirt and dust contamated with oocysts. In view of the fact that the oocysts are so widespread and resistant, hygiene is of paramount importance in controlling toxoplasmosis. Adequate cooking or freezing below -20C destroys both oocysts and tissue cysts. Oocysts can also be aovided by washing the ahnds after handling cats or soil possible contaimianted with cat feces, especially sandboxes and litter boxes.

Mitogen-activated protein kinases (MAPKs) are Ser/Thr kinases which act as intermediates within the signaling cascades of both growth/survival factors, such as EGF, and death receptors, such as the TNF receptor.  via mitogen-activated protein (MAP) kinases plays an important role in cellular responses including growth factor-induced cell proliferation, differentiation, and survival. The MAPK proteins are important upstream regulators of transcription factor activities and their signaling is critical to the transduction of a wide variety of extracellular stimuli into intracellular events. MAPKs such as extracellular receptor kinase (ERK), p38, and the c-Jun NH2-terminal kinase (JNK) mediate leukocyte responses to diverse stimuli. Among the four MAP kinase pathways (Erk, Jnk, p38 and Erk5 or BMK), the Jnk and p38 pathways are closely linked with inflammation. 

MAPKs act by phosphorylating and activating downstream effector nuclear kinases. The MAPK may be present in both cytosolic and nuclear compartment, where they phosphorylate transcription factors such as Elk-1, C/EBP?, activating transciption factor (ATF)-2, C-jun, and . 

MAPK Activation:

In response to different stimuli, including , growth factors, and cellular stress, MAP kinase pathways transmit signals through a stepwise series of kinases. In each of these pathways, an upstream MAP kinase kinase kinase (MKKK) becomes phosphorylated and in turn phosphorylates a downstream MAP kinase kinase (MKK), which in turn phosphorylates a MAP kinase. The activated MAP kinase then phosphorylates transcription factors or other protein kinases to alter cellular function. 

Each of the three major MAP kinase pathways is named for the terminal MAP kinase, i.e., ERK (extracellular signal-regulated kinase)p38 and JNK/SAPK (c-Jun NH2-terminal kinase/stress-activated protein kinase). These kinases are activated by MAP kinase kinases (MKKs) which phosphorylate threonine and tyrosine residues in the Thr-X-Tyr activation motif. Upon activation, MAP kinases can migrate to the nucleus where they phosphorylate and activate transcription factors such as . Each MAP kinase family targets a different set of transcription factors. 

Extracellular signal-regulated protein kinases (ERKs)

The ERK pathway appears mainly to respond to mitogens and growth factors that regulated cell proliferation and differentiation. ERKs are believed to be strongly activated and to play a critical role in transmitting signals initiated by growth-inducing tumor promoters, including 12-O-tetradecanoyl-phorbol-13-acetate (TPA), epidermal growth factor (EGF) and platelet-derived growth factor (PDGF). 

Blockage of the ERK pathway through pharmacological inhibition has previously been shown to induce apoptotic cell death in endothelial cells.

Activation of ERK1/2 is associated with pro-survival signalling. 

The ERK pathway has been reported to stabilize granulocyte/macrophage colony stimulating factor mRNA. 

MEK1/2 is an upstream activator of ERK 1/2. The MAP kinase (MEK) inhibitor: PD98059

It has been reported that ERK along with  negatively regulate the phenotypic and functional maturation of MoDCs and that inhibition of ERK or PI3K by selective inhibitors (PD98059 or LY294002) significantly enhance the phenotypic and functional matural of human MoDCs. Unexpectedly, PD98059 treatment of a macrophage cell line increased rather than decreased mTLR2 mRNN, suggesting that ER activation may inhibit TLR2 mRNA expression.

LPS Activation of ERK is reportedly little affected and even enhanced by EGCG in murine peritonela exudate cells from BAL/c mice. Interestingly, EGCG reported inhibited phosphorylation of p38 MAP kinases with a concomitant downregulation of IL-12p40 production. In contrast, activation of ERK MAP kianses weas inhibited little or rather enhanced by EGCG in murine macrophages.

ERK inhbitors: PD98059 (Calbiochem), is an inhibitor of ERK phosphorylation; U0126 

C-Jun N terminal kinases (JNKs)

JUN amino-terminal kinase (JNK) is a MAP kinase known to be crucial for T-cell function. Jun is a nuclear proto-oncogene, which constitutes a part of the transcription factor . JNK regulates activator protein-1 (AP-1) transcription in response to environmental stress such as UV exposure.The JNK pathway increases transcriptional activity of AP-1 by binding to and phosphorylating c-Jun.  Increased AP-1 activity has been shown to be involved in the promotion and progression of various types of cancers and also other processes such as inflammation, invasion, metastasis and angiogenesis. 

The JNK and p38SAPK pathways are predominantly activated by stress, such as osmotic changes and heat shock, but also by inflammatory cytokines such as IL-1? and TNF-?. 

JNK activation has been strongly linked to apopoptic signalling through phosphorylation of c-Jun. 

ATF-2 is a member of the ATF/CREB (cyclin AMP response element binding protein) family of transcription factors which associates with c-Jun to form the leucine-zipper hterodimer, c-Jun/ATF-2, that preferentially binds the TNFalppha promoter at the -106 to -99 bp site.

NK Activators: anisomycin

JNK inhibitors: SP600125 (Bennett et al., 2001)

p38 stress-activated protein kinases (p38SAPKs)

The p38SAPK pathway is involved in many aspects of immune cell function, being important in the innate immune response as well as in the adaptive immune response. In addition, p38SAPK may play an important role in T-cell development because it is found to be activated in T cells in the thymus. The cytokines IL-2 and IL-7 also activate p38SAPK in T cells. 

p38 is a master regulator of NF-kB recruitment to a subset of genes activated in cells exposed to inflammatory stimuli. Under one proposed model, NF-kB dimers translocated to the nucleus in response to stimulus bind to constitutively accessible NF-kB sites and contribute to the activation of these promoters. In some cases the p38 pathway, at least in part through the induction of H3 phosphorylation and phosphoacetylation, orchestrates the modifications that lead to enhanced accessibility of NF-kB sites. 

P38 stablizlies mRNA containing AU repeats, including genes that encode for TNF.

In some situations the p38 MAPK pathway appears to be needed for translation of an mRNA because blocking the pathway inhibits production of protein without causing disappearance of the mRNA. For example, blocking p38 MAPK in murine macrophages stimulated with LPS almost completely inhibits production of TNF? protein, but only partially inhibits induction of its mRNA. LPS also induces TNF? mRNA in the MAPKAPK-2 knockout mouse, but little or no protein is produced.

p38 Activator: Anisomycin 

P38 Inhibitors: SB-203580 (Alexis), SB202190

Regulation of MAPs

MAP kinases are themselves regulated by kinases and phosphatases, such as members of the MAP kinase phosphatase (MKP) family. MAPKs can be inactivated by removal of either their threonine or tyrosin phophates. A large number of phosphatases may be involved.

MAP involvement in Cancer immune evasion

MAPK signalling pathway can play a role in cancer immune evasion by augmenting the expression of the immunoregulatory cytokines IL-6 and IL-10. The impact of this signalling pathway on a tumour’s immunological status is particularly relevant in melanoma, where aobut half of tumours carry a mutation in the MAPK BRAF, the BRAF-V600E activating mutation, and wehre immune checkpoint blockage is a first line therapy. 

Peroxisomes get their name from the hydrogen peroxide produced as a by-product of the activites of oxidative nezymes. Hydrogen peroxide is dangerous to cells becasue of its violent chemical reactivity. However, peroxisomes also contain the enzyme catalase, which ctalyzes the decomposition of hydrogen peroxide into water and oxgen. 

Unlike mitochondria, peroxisomes do not contain DNA or ribosomes. Thus all of their proteins must be imported from the cytosol. As with mitochondria and the ER, new perosisomes arise from fission from preexisting peroxisomes.

Peroxisomes can form from the fusion of ER dervied visciles. These vesicles then import peroxisomal proteins to form a mature peroxisome. 

Function of Peroxisomes:

Peroxisomes are microbodies that contain enzymes used to oxidze fatty acids. If these oxidative enzymes were free in the cytoplasm, they could short circuti cellular metabolism, which often involves adding hydrogen atoms to oxygen. 

Peroxisomes catalyze the first reactions in the formation of plasmalogens which are the most abundant class of phosphlipids in myelin. Deficiency of plasmalogens causes profound abnormalities in the myleination of nerve cells. In addition to an ethanolamine head group, plasmalogens contain a glycerol phosphate backbone which is attached to a fatty acid which contains an ether linkage.

Peroxisomes also contain enzyme(s) that use molecular oxygen to remove hydrogen atoms in an oxidative reaction that produces hydrogen peroxide (H2O2) which is then used in the liver and kidney cells to oxidize other substrates to detoxify other molecules.

Peroxisome Signal Sequences:

SKL Sequence: A specific sequence, SKL (serine, lysine, leucine) at the C terminus of many peroxisomal proteins serves as an import signal to peroxisomes.

Peroxins: There are soluble receptor proteins called peroxins. A peroxin pex receptor for example accompanies its cargo all the way into peroxisomes much like protein transport into the nucleus. Thus the protein folds as it is transported just as with nuclear transport and ATP is required.

Genetic Diseaes related to Peroxisomes:

Some 32 genes thta econde prtoeins involved in biogenesis and maintenace of peroxisomes.

Peroxisome biogenesis disorders (PBMDs) can be caused by mutation in some of the genes known to be involved in biogenesis and maintenance of peroxisomes. 

A superantigen is an antigen bound by antibodies found in the preimmune repertoire without the requirement of adaptive maturation of antibody variable domains.

A bacterial toxin that is capable of stimulating multiple T lymphocytes, leading to the release of relatively large quantities of cytokines is a superantigen. Superantigens bind simultaneously to the VB domain of the T cell receptor and  molecule, activating all T cells bearing a particular VB domain. Because of this binding ability, superantigens can activate large numbers of T cells irrespective of their antigenic specificity. Although less than 0.01% of T cells respond to a given conventional antigen, up to 25% can respond to a given superantigen. The large number of T cells activated results in excessive production of .

Encounter with antigens generally stimulates B cell proliferation. SAg binding to the B cell receptor, on the other hand, is thought to induce cellular apoptosis (Paul, US 11988761). 

Both exogenous and endogenous superantigens have been identified. Crosslinkage of a T cell receptor and class II MHC molecule by either type of superantigen produces an activating signal that induces T-cell activation and proliferation.

Exogenous Superantigens

Exogenous superantigens are soluble proteins secreted by bacteria. Each of these exogenous superantigens binds particular V beta sequences in T cell receptors and crosslinks the TCR to a Class II MHC molecule.Some of these toxins include:

  • staphylococcal enterotoxins

  • toxic shock syndrome toxin which induces high levels of TNF and IL-1 which can induce systemic reactions that include fever, widespread blood clotting and shock.

  • exfoliative dermatitis toxin

Bacterial Superantigens:

Bacterial sueprantigens (Sags) are a well described family of 40 secrected protein toxins produced by Staphylococcus aureus and Streptococcus pyogenes with orthologues exisiting in group C Streptococcus equi and group G Streptococcus disgalactiae. Two quite unrelated Sags are also produced by Mycoplasma arthriditis mitigen (MAM) and Yersina pseudotuberculosis mitogen (YPM). MAM is unrelated by amino acid sequence homology to members of the staphylococcal/streptococcal Sag family. Systemic intoxication by a Sag can lead to the life-threatening condition toxic shock syndrome (TSS) caused by a sudden cytokine storm when large numbers of T cells are sitmulated by the Sag cross-linking MHC class II antigens and T-cell receptors (TCR). Scarlet fever is caused by pharyngeal infection of group A streptococcus (GAS) and was a common childhood illness world wide during the first half of the 20th centure. Sags are thus virulence factors that target the adaptive response through the immunological synapse. They are noted for their extreme potenecy with some members stimulating human T cells in vitro at 1 gemtogram/ml, a feature that highlights the ezquisite sensitivity of T cell recognition of MHC bound antigen. Fraser “The bacterial superantigen and superantigen-like protein” Immunological Reviews, 2008). 

Endogenous Superantigens

Endogenous superantigens are cell membrane proteins encoded by certain viruses that infect mammalian cells.

Examples of of endogenous superantigens are the HIV coat protein gp120, HIV Tat and Staphylococcal Protein A. gp120 contains an antigenic site recognized by Abs present in the preimmune repertoire of humans free of HIV infection. This qualified gp120 for designation as a B cell Sag because it is an antigen bound by Abs without the requirement of adaptive sequence diversification of Ab V domains. Synthetic peptide studies suggest that the gp120 SAg site is a conformational epitope composed of peptide determinants 231-260, 331-360 and 421-440 (Paul, US 11988761). 

Companies:

Fountain Life

Omegal Therapeutics: takes advantage of the organization of genes and regualtory elements into conserved 3D chromatin lopps. There are about 15k of these loops which they call “insualted genomic domains” each of which contains single or multiple genes together with their regulatory elements. The regulatory elements have unique genomic sequences, which makes them attractive therapeutic targets. They have mapped these regulatory elements and created a database of targets, called “EpiZips”. These EpiZips or epigenomic ZIP codes can be targeted by programmable, modular mRNA based epigenomic drugs called “epigenomic controlers”. The epigenomic controllers are delivered into cells using lipid nanopartcile technologies which are translated on the ribosomes into the respective therapeutic proteins. The fusion proteins contain a highy specific DNA binding domain, which is connected through a linker to an epigenomic effector domain that contols gene expression regulators at target insulated genomic domains. 

Life Biosciences is inducing cellular rejuvenation through parital epigenetic reprogramming. Starting with a mature injured cell, they are trying to turn back the clock to convert that cell to a more youthfull state, but wihtout going all the way back to a stem cell. Four transcirptions factors (Oct4, Sox2, Klf4 and c-Myc) together can covnert  mature cell into an induced pluripotent stem cell. Later it was discovered that c-Myc, an oncogene that can have tetratogenic effects is dispensable for this process. 

Introduction:

The ultimate goal of regenerative research is to replace damanged cells in response to injuries and agning. Transdifferentiation (or cell reprogramming), a process thorugh which a mature somatic cell transforms into a new type of mature somatic cell can acheive this gold. In vitro reprogramming of somatic cells has proven to be a powerful too and has allowed the ientificiton of some of the genetic factors required to change identity. The discovery of reverse development in the cridarian Turritopsis dohmii (class Hydrozoa) represents a promising new research system. Faced with unfavorable circumstances, the medusa naturally undergoes cellular reprogramming to revert to a younger life cycle state (the polype) thous avoiding death indefinitely. 

Aging is marked by the gradual decline of a multitude of physiological functions leading to an increasing probability of death. Recent work has begun to uncover molecular mechanisms that specify lifespan and to identify alternations in cellular physiology that occur at the end of life. For example, oxidative damage caused by the generation of free radicals in the mitochondria has been found to hasten aging by causing an accumulation of damaged cellular components. The identificaiton of biomarkers for human aging are of key interest to scientists. In this respect, many studies describe genes that provide human age signatures (see US 2007/0161022A1).usaid become reproductively mature, release gamets, and die. medusae of T. dohmii that are stressed, damaged or senescent settle on a surface and transoform into a cyst state that in 24-72 h, metamorphoses back into a single juvenile polyp. By asexual reproduction, the polyp can develop into a large colony (i.e., colonial polyp) that can then release new medusae. Because of its unique life cycle, T. dohmii has been popularized as the “immortal jellyfish”. Aging and lifespan-related genes, serine racemase and MsrA, have been shown to be enriched in the cyst. Supression of serine racemase activity can cause aging-related cognitive dysfunctions in mammals., whereas MsrA has a role in protecting cells from oxidative damages by destroying reactive intermediates or repearing damaged DNA. (Miglietta “Cellular reprogramming and immortality: expression profiling reveals putative genes involved in Turritopsis dohrnii’s life cycle reversal”. Genome Biol. Evol. 13(7). 2021).

Age Related Diseases:

Alzheimer’s disease: Transcriptomic data from microglia in AD conditions reveal an accelerated agining phenotype. It is conceivable that microglial surfveillance response is comproomised with agen, which would lead to a slow accumulation of insults to the CNS potentially leading to neurdegenerative diseases like AD. Genome-Wide Associattion studies from large European and American consortia identified common genetic polymorphisms at loci harboring gnes with microglia-specific epxrewssion pattern in the CNS, such as ABC7, CD33 and members of the MS4A genes cluster as genetic determinatns of AD risk. (Rhinn, “Shifting paradigms: The central role of microglia in Alzheimer’s disease” Neurobiology of Disease 143 (2020))

Obesity: afflict more than 1 in 3 adults in teh US and is responsible for an overall decrease in health and increased risks for cancer, heart disease and neurological deterioration among many others. 

Kidney failure and renal fibrosis: are a major concern regarding the aging opulation in the US with ore than 661,000 people either on dialysis or recipients of a kidney transplant. Davidsohn “A single combination gene therapy treats multiple age-related diseases” PNAS, 116 (47) 2019)

Heart Failure: is responsible for 425,000 deaths per year in teh US with a prevalence of over 5.8 million people Davidsohn “A single combination gene therapy treats multiple age-related diseases” PNAS, 116 (47) 2019)

Abnormalities associated with Aging

The gadual deterioration in immune fuction that occurs with aging has been termed immune senescenceThis is manifest both as reduced in vitro immune responsiveness and impaired immune response to vacination and acute infection.  The following abnormalities have been associated with aging.

Telomere Shortening

CD8+ T cells which lack CD28: A major feature of immune senescence is the accumulation of clonally expanded memory CD8 T cells characterized by the lack of CD28 expression. The proportion of CD8+ T cells that lack surface expression of CD28 increases with age so that in adulthood, 25-50% of CD8+ T cells are CD28-. In acute viral infections, there is often considerable rapid expansion of CD8+CD28- antiviral effector T cells. Upon antigenic stimulation, these CD8+CD28- T cells produce interferon gamma, but not IL-2 and proliferate poorly.

The phenotype CD57+CD28- T cell subset observed in old age donors may reflect increases in CMV specific CD 8 T cell fequencies. This phenotype has also been reported in other setting such as rheumatoid arthritis and HIV-1 infection.

Abnormalities in CMV positive Elderly:

Polarization towards Effector Memory Cells in CMV elderly: CMV specific CTL have a highly polarized membrane phentoype that is typical of effector memory cells (CD28-, CD57+, CDR7-)

Restricted TCR in CMV sepcific CTL: TCR has shown that CMV specific CTL have highly restricted clonality with greater restriction in the larger expansions. 33% more clonal expansion were observed in CMV seropositive donors compared with negative individuals. These data implicate CMV a major factor in driving oligoclonal expansions in old age. Such an accumulation might impair the ability to respond to heterologous infection and may underlie the negative influcucne of CMV eropositivity on survival in the very elderly.

bcl-2+ CMV specific T cells: It was reproted that CMV specific T cells are uniformly bcl-2+, indicating resistance to apoptosis, which is reminiscent of cells that have reached replicative senescence in cell culture.

Age-associated B cells: have been discovered in mice, which are uniquely responsive to innate stimuli and refractory to CD40 and BCR stimulation. They appear to be generated from mature B cells that exhaustively expand during the inidivual’s lifetime and thus may represent an “exhausted” lymphocyte cell population. Moreover, an IgG- CD27- population, possibly corresponding to exhausted membory B cells acculates in elderly humans. (Hayday 14/368,749)

Epigentic Abnormalities:

Agiging is accompanied by the accuulation of epigenetic changes, such as DNA hypermethylation at promoters. 

Epigenome remoding, including widespread changes to DNA methylation adn 3D chromatic structure, is also increasinly recognized as an important mechanism of gene deregulation in cancer. 

Abnormalities in Skeletal Muscle:

Ageing is accompanied by decrements in the size and function of skeletal muscle that compromises independence and quality of life in older adults. 

–Myosin: Surprisingly, most studies observe that the size and contractile function of fibres expressing slow myosin heavy chain (MHC) I are well-preserved with ageing. In contrast, there are profound age-related decrements in the size and contractile function of the fibres expressing the MHC II isoforms. Notably, lifelong aerobic exercise training is unable to prevent most of the decrements in fast fibre contractile function, which have been implicated as a primary mechanism for the age-related loss in whole-muscle power output. (Sunberg, “Single Muscle Fibre Contractile Function with Ageing” J. Physiol, 600(2023), 20222). 

Treatment Strategies:

Gene therapies:

fibroblast growth factor 21 (FGF21)alpha Kotho, and transforming growth factor-beta1. FGF21 combination therapy:

Davidson “A single combination gene therapy treats multiple age-related diseases” PNAS, 116 (47) 2019) discloses traditional methods largely ignore the relation between age related diseases, narrowly influencing a particular pathway involved in the pathogenesis of a single disease. Targeting gene therapy to a single patholoy cannot correct or prevent the deterioration of health span that results form ultiple age-related diseases. In this respect, they developed and tested 3 AAV based gene therapies and adminsitered them to adult nontransfenic mice for the treatment of 4 age-related diseases. The 3 genes involved were fibroblast growth factor 21 (FGF21), alpha Kotho, and transforming growth factor-beta1. FGF21 has established roles in metabolism and glucose handling, alphaKlotho is a known regulator of intracellular calcium and provides protection in heart and kidney pathologies and TGFbeta1 signaling plays an important role in age related hypertrophic cardiomyopathy, immune recruitment and extracellular matrix formation. Begining with the obesity model, AAV-FgF21 together with either 1 or both of the other 2 gene therapies was able to mitigate the obesity phenotype in a HFD model as well as an aged ND model, although with a slightly diminished (nonsignificant) effect. Proceeding to the type II diabetes model, they observed that all therapeutic combiantions that included AAV-FGF21 rescued the HOMA-IR levels in the treated HFD mice. 

 

 

 

ProPred (graphical web tool for predicting MHC class II binding regions in antigenic protein sequences). 

The MHC comprises tightly linked genes that encode proteins associated with intercellular recognition and antigen presentation to . The MHC plays a crucial role in the development of both humoral and cell mediated immune responses because MHC molecules function as antigen presenting structures. It is well established that binding of a peptide to an MHC molecule is a prequisite for activaiton of antigen specific T-cells. The set of MHC molecules expressed by an individual influences the antigens to which that individual’s TH and Tccells can respond since T cells can only recognize antigen when it is associated with a self MHC molecule. As only certain peptides can bind to a given MHC molecule, the identification of these peptides is one of the bottlenecks in subnit vaccine design. 

HLA molecuels are membrane bound glycoproteins that bind processed antigenic peptides and present them to T cells. The essential role of the HLA antigens lies in the control of self-recognition and thus defense against microorganisms. Based on the structure of the antigens produced and their function, there are two classes of HLA antigens, HLA Class I and Class II. HLA Class I antigens are expressed on all nucleated cells of the body. Additionally, they are found in soluble form in plasma and adsorbed onto the surface of platelets. Erythrocytes also adsorb HLA class I antigens. The tissue distribution of HLA class II antigens is confined to the “immune competent cells, including B lymphocyes, macrophages, endothelial cells and activated T lymphocytes. The expression of HLA class II on cells that would not normally express them is stimulated by cytokines like interferon gamma and is associated with acute graft rejection in the setting of transplantation. (Frey, US Patent Applicaiton No: 16/340,453, published as US 2019/0276524).

Genes of the MHC: 

There is a tremendous amount of diversity exhibited by MHC molecules within a species and within individuals. The diversity is due to polymorphism or the presence of multiple alleles at a given genetic locus with a species. These alleles differ in their DNA sequences from one individual to another by as much as 10%. Each different set of alleles that have been found are referred to as a haplotype, and an individual inherits one haplotype from the mother and one from the father. The strains of various types of mice are designated by an italic superscript to note such different haplotypes (i.e., H-2a, H-2b). Inbred mouse strains are syngeneic or identical at all genetic loci and allogeneic if they are genetically different. Congenic or strains which are genetically identical except at a single region can be bred by a series of crosses. 

Unlike with the source of diversity of antibodies and T cells which is generated by a continual process of random gene rearrangements which changes over time within an individual, the MHC molecules expressed by an individual do not change over time. But they may differ significantly from those expressed by another individual of the same species due to recombination events during crossover. This diversity creates problems with respect to matching MHC molecules for successful organ transplants. Peptide binding by class I and II molecules does not exhibit the fine specificity of antigen binding by antibodies and T-cell receptors. Instead, a given MHC molecule can bind numerous different peptides and is often referred to as “promiscuous.”

The MHC genes are contained are contained on chromosome 6 and referred to as the HLA complex in humans and on chromosome 6 and referred to as the H-2 complex in mice. The genes are organized into regions encoding the following 3 classes of molecules:

  • Class I MHC genes encode glycoproteins expressed on the surface of nearly all nucleated cells and are recognized on receptors on CD8+ killer T cells and natural killer cells. In humans, the MHC class I cell surfaced expressed molecules are referred to as HLA-A, -B or -C. 

  • Class II MHC In humans, MHC class II cell surface molecules are referred to as HLA-DR, -DP and DQ.

  • Class III MHC genes encode components of the complement system and molecules involved in inflammation such as tumor necrosis factor (TNF) and heat-shock proteins. 

Regulation

The expression of MHC molecules is also regulated by various cytokines. The interferons (alpha, beta, and gamma), for example, and  have each been shown to increase expression of class I MHC molecules on cells. IFN-?, for example, may do this by inducing the formation of a specific transcription factor that binds to the promoter sequence flanking the class I MHC genes. 

MHC expression is also influenced by various viruses. For example, HIV decreases Class I MHC expression whereas it increases Class II MHC expression. As another example, cytomegalovirus binds to the ?2-microglobulin, preventing assembly of class I MHC molecules and their transport to the plasma membrane. Decreased expression of class I MHC molecules helps viruses evade the immune response by reducing the likelihood that virus infected cells will become targets for CTL mediated destruction.

Involvement in Disease: Susceptibility to a significant number of human diseases, mostly autoimmune in nature, is assocaited with genes in the MHC. In particular, strong associations have been found between rheumatoid arthritis and a 126-kb region in the MHC class II region, between BAT2 and CLIC1, which includes five Lymphocyte Antigen (Ly-6) members.

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