Zodiac (Case 9): Zodiac Shows Potential Utility in AutoImmune Deficiency

This is the 9th-article of a blog series aiming to introduce Zodiac, a comprehensive tool that reveals genetic interactions in cancer by big-data computation. An introduction of Zodiac is in the 1st article here.

This piece will be a short one since I am stepping out of my main domain, cancer. In this piece, I will briefly talk about a recent negative trial for treating systemic lupus erythematosus (SLE), also known as Lupus. It is an autoimmune disease currently with no cure. UCB, a Belgium-based biopharmaceutical company announced a devastating statement that its phase III trials (EMBODY 1&2) failed to meet its primary endpoint. The candidate drug is a monoclonal antibody called epratuzumab, which targets CD22 in the mature B-cell, a biomarker with elevated expression in Lupus patients.

I searched CD22 in Zodiac and found that the top 5 genes might shed new light about the CD22 mechanism. The majority of these genes are related neuro-disorders. It is interesting that Zodiac, a primary database for cancer, links genes in neuro-disorders.

SYN2 This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia.

KCNH4 Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, subfamily H. This member is a pore-forming (alpha) subunit. The gene is brain-specific, and located in the neocortex and the striatum. It may be involved in cellular excitability of restricted neurons in the central nervous system.

ST3GAL5 Ganglioside GM3 is known to participate in the induction of cell differentiation, modulation of cell proliferation, maintenance of fibroblast morphology, signal transduction, and integrin-mediated cell adhesion. The protein encoded by this gene is a type II membrane protein which catalyzes the formation of GM3 using lactosylceramide as the substrate. The encoded protein is a member of glycosyltransferase family 29 and may be localized to the Golgi apparatus. Mutation in this gene has been associated with Amish infantile epilepsy syndrome.

F5 This gene encodes an essential cofactor of the blood coagulation cascade. This factor circulates in plasma, and is converted to the active form by the release of the activation peptide by thrombin during coagulation. This generates a heavy chain and a light chain which are held together by calcium ions. The activated protein is a cofactor that participates with activated coagulation factor X to activate prothrombin to thrombin. Defects in this gene result in either an autosomal recessive hemorrhagic diathesis or an autosomal dominant form of thrombophilia, which is known as activated protein C resistance. (Note: this gene is related to thrombin/prothrombin. According to Wiki, activation of prothrombin is crucial in physiological and pathological coagulation. Various rare diseases involving prothrombin have been described (e.g., hypoprothrombinemia). Anti-prothrombin antibodies in autoimmune disease may be a factor in the formation of the lupus anticoagulant also known as antiphospholipid syndrome).

HIST2H2BE Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a replication-dependent histone that is a member of the histone H2B family, and generates two transcripts through the use of the conserved stem-loop termination motif, and the polyA addition motif. The protein has antibacterial and antifungal antimicrobial activity. (Note: This is a histone gene, with essential epigenetic functions. According to KEGG, this gene is in the Lupus disease pathway. See here)

These are the top five genes found in Zodiac that are strongly associated with CD22, and they seem to be related to auto-immune deficiencies. One striking finding is that none of these genes have any cancer terms in their descriptions, even though Zodiac is generated using cancer data.

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Zodiac (Case 8): CD19-Targeting Chimeric Antigen Receptor (CAR) T-Cell Cancer Therapy — What does Zodiac know about CD19?

This is the 8th-article of a blog series aiming to introduce Zodiac, a comprehensive tool that reveals genetic interactions in cancer by big-data computation. An introduction of Zodiac is in the 1st article here.

CD19-targeting CART immunotherapy made a splash recently (see here) as a potentially revolutionary cancer therapy. So far CART targeting CD19 has shown remarkable therapeutic effects in a small group of hematological cancer patients. Due to these initial promising results, a large number of clinical trials have now been proposed or started based on CART therapies. CD19 is one of the earliest biomarkers for CART for drug development and here I describe a set of top genes that co-express with CD19 in Zodiac.

Based on a false discovery rate of 0.01 threshold, Zodiac returns 1,343 co-expressed genes with CD19. I looked at the top 20 of them.

The usual suspects: Since this is about immunotherapy, the usual suspects show up as the top genes associated with CD19. These genes are related to immune cells, functions, defense, activations, etc in the cellular system. They are

  • CD69 This gene encodes a member of the calcium dependent lectin superfamily of type II transmembrane receptors. Expression of the encoded protein is induced upon activation of T lymphocytes, and may play a role in proliferation. Furthermore, the protein may act to transmit signals in natural killer cells and platelets.
  • GPR183 This gene was identified by the up-regulation of its expression upon Epstein-Barr virus infection of primary B lymphocytes. This gene is predicted to encode a G protein-coupled receptor that is most closely related to the thrombin receptor. Expression of this gene was detected in B-lymphocyte cell lines and lymphoid tissues but not in T-lymphocyte cell lines or peripheral blood T lymphocytes. The function of this gene is unknown.
  • CD79A The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-alpha protein of the B-cell antigen component.
  • ST14 The protein encoded by this gene is an epithelial-derived, integral membrane serine protease. This protease forms a complex with the Kunitz-type serine protease inhibitor, HAI-1, and is found to be activated by sphingosine 1-phosphate. This protease has been shown to cleave and activate hepatocyte growth factor/scattering factor, and urokinase plasminogen activator, which suggest the function of this protease as an epithelial membrane activator for other proteases and latent growth factors. The expression of this protease has been associated with breast, colon, prostate, and ovarian tumors, which implicates its role in cancer invasion, and metastasis.

The grand protease gene:

More about granzymes and perforin will be described in my future blog, which I plan to put together a comprehensive map between them and other CD markers using Zodiac. Potentially, I might also leak a new gene, the function of which is unknown, but might play critical roles in immune system. I hope that the new gene could help cancer drug development.

Most interestingly to me is a gene called

KYNU Kynureninase is a pyridoxal-5’s-phosphate (pyridoxal-P) dependent enzyme that catalyzes the cleavage of L-kynurenine and L-3-hydroxykynurenine into anthranilic and 3-hydroxyanthranilic acids, respectively. Kynureninase is involved in the biosynthesis of NAD cofactors from tryptophan through the kynurenine pathway.

which is a gene related to Kynurenine. From Wikipedia, “Kynurenine is synthesized by the enzyme tryptophan dioxygenase, which is made primarily but not exclusively in the liver, and indoleamine 2,3-dioxygenase (IDO), which is made in many tissues in response to immune activation.[1] Kynurenine and its further breakdown products carry out diverse biological functions, including dilating blood vessels during inflammation[2] and regulating the immune response.[3] Some cancers increase kynurenine production, which increases tumor growth.[1] ” Here, I suspect that there is a relationship between kynurenine pathway and CD19. Interesting, a recent paper in Blood confirmed my suspicion. The authors show that enhanced kynurenine blocks CD19-CART effect in xenocraft models and preconditioning chemotherapies suppressing IDO improve the anti-tumor effects of CD19-CART. Zodiac shows that KYNU is highly positively associated with CD19 (beta-value 11.9).  This suggests that a high KYNU expression in TCGA tumor samples (which could be mixed tumor/stroma)  could reduce CD19-related-immune-cell anti-cancer effect by its silencing mechanism of CD19-immune cells. In other words, KYNU could be a co-immune blockade gene. Zodiac also shows that KYNU is positively associated with many other CD markers, most of which are being investigated for immunotherapies in cancer. Below is a picture from Zodiac showing associations between KYNU and CD markers.

KYNU

Lastly, like the previous post on CD33, I also found genes associated with CD19 possessing important neural and cognitive functions.

  • SEPT1 This gene is a member of the septin family of GTPases. Members of this family are required for cytokinesis and the maintenance of cellular morphology. This gene encodes a protein that can form homo- and heterooligomeric filaments, and may contribute to the formation of neurofibrillary tangles in Alzheimer’s disease.
  • ARHGAP9 This gene encodes a member of the Rho-GAP family of GTPase activating proteins. The protein has substantial GAP activity towards several Rho-family GTPases in vitro, converting them to an inactive GDP-bound state. It is implicated in regulating adhesion of hematopoietic cells to the extracellular matrix. (Note: GTPase is a family of proteins that plays important roles in many functions, including including recognition of taste, smell and light.)

In the press release for a successful phase I trial for a CD19-targeting CART, it was stated that “T-cell activation causes the release of inflammatory cytokines, producing symptoms including high fevers, aches, hypotension, and, more rarely, pulmonary edema and neurologic effects such as delirium.” Delirium is an organically-caused decline from a previously attained baseline level of cognitive function. It appears that the neurological side effects of CD-marker-targeting CART might be due to the association of neurologically related genes and the CD markers.

Zodiac (case 7): CD33 as A Target of Immunotherapy Myeloid Leukemia

This is the 7th-article of a blog series aiming to introduce Zodiac, a comprehensive tool that reveals genetic interactions in cancer by big-data computation. An introduction of Zodiac is in the 1st article here.

CD33 has been used as a cell surface target for treating myeloid leukemia. Lintuzumab is currently an investigational monoclonal antibody (mAB) that targets CD33 for treating myeloid leukemia. Other mABs are also being developed although efficacy has not been impressive so far. There is a renewed interest in targeting CD33, using activated Natural Killer (NK) cells, which are considered as a type of innate immune cells. I took a look at CD33 in Zodiac and found the following genes that are associated with CD33 with strong co-expression.

First, CD33 is positively associated with several other “CD” markers, namely

CD163 The protein encoded by this gene is a member of the scavenger receptor cysteine-rich (SRCR) superfamily, and is exclusively expressed in monocytes and macrophages. It functions as an acute phase-regulated receptor involved in the clearance and endocytosis of hemoglobin/haptoglobin complexes by macrophages, and may thereby protect tissues from free hemoglobin-mediated oxidative damage. This protein may also function as an innate immune sensor for bacteria and inducer of local inflammation.

CD53 The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. It contributes to the transduction of CD2-generated signals in T cells and natural killer cells and has been suggested to play a role in growth regulation. Familial deficiency of this gene has been linked to an immunodeficiency associated with recurrent infectious diseases caused by bacteria, fungi and viruses.

CD86 This gene encodes a type I membrane protein that is a member of the immunoglobulin superfamily. This protein is expressed by antigen-presenting cells, and it is the ligand for two proteins at the cell surface of T cells, CD28 antigen and cytotoxic T-lymphocyte-associated protein 4. Binding of this protein with CD28 antigen is a costimulatory signal for activation of the T-cell. Binding of this protein with cytotoxic T-lymphocyte-associated protein 4 negatively regulates T-cell activation and diminishes the immune response.

CD37 The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins and other transmembrane 4 superfamily proteins. It may play a role in T-cell-B-cell interactions.

Apparently, these CD-markers all have a role in immune defense, some directly related to NK cells. The following genes also strongly co-express with CD33 in tumor samples. Their functions are related to immune defense as well. For example, SAMHD1 directly involves in the regulation of innate immune response.

ITGAM This gene encodes the integrin alpha M chain. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This I-domain containing alpha integrin combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred to as macrophage receptor 1 (‘Mac-1’), or inactivated-C3b (iC3b) receptor 3 (‘CR3’). The alpha M beta 2 integrin is important in the adherence of neutrophils and monocytes to stimulated endothelium, and also in the phagocytosis of complement coated particles.

IFI30 The protein encoded by this gene is a lysosomal thiol reductase that at low pH can reduce protein disulfide bonds. The enzyme is expressed constitutively in antigen-presenting cells and induced by gamma-interferon in other cell types. This enzyme has an important role in MHC class II-restricted antigen processing.

SAMHD1 This gene may play a role in regulation of the innate immune response. The encoded protein is upregulated in response to viral infection and may be involved in mediation of tumor necrosis factor-alpha proinflammatory responses. Mutations in this gene have been associated with Aicardi-Goutieres syndrome.

Lastly, interestingly Zodiac showed three genes that co-express with CD33 and are related to neurological functions.

PVALB The protein encoded by this gene is a high affinity calcium ion-binding protein that is structurally and functionally similar to calmodulin and troponin C. The encoded protein is thought to be involved in muscle relaxation. See also a paper here.

ADORA3 This gene encodes a protein that belongs to the family of adenosine receptors, which are G-protein-coupled receptors that are involved in a variety of intracellular signaling pathways and physiological functions. The receptor encoded by this gene mediates a sustained cardioprotective function during cardiac ischemia, it is involved in the inhibition of neutrophil degranulation in neutrophil-mediated tissue injury, it has been implicated in both neuroprotective and neurodegenerative effects, and it may also mediate both cell proliferation and cell death. Alternative splicing results in multiple transcript variants. This gene shares its 5′ terminal exon with some transcripts from overlapping GeneID:57413, which encodes an immunoglobulin domain-containing protein.

TNFRSF1B The protein encoded by this gene is a member of the TNF-receptor superfamily. This protein and TNF-receptor 1 form a heterocomplex that mediates the recruitment of two anti-apoptotic proteins, c-IAP1 and c-IAP2, which possess E3 ubiquitin ligase activity. The function of IAPs in TNF-receptor signalling is unknown, however, c-IAP1 is thought to potentiate TNF-induced apoptosis by the ubiquitination and degradation of TNF-receptor-associated factor 2, which mediates anti-apoptotic signals. Knockout studies in mice also suggest a role of this protein in protecting neurons from apoptosis by stimulating antioxidative pathways.

In summary, Zodiac confirms the close relationship between CD33 and immune cells. The suggested genes maybe further evaluated. A few genes that co-express with CD33 also relate to neurological functions.