Zodiac (Case 12) — HER3: the little sister of HER2 and its potential role in liquid cancer

This is the 12th-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.

HER3 is member of the human EGF receptor (HER/EGFR) family. The family is home of famous receptor tyrosine kinases such as HER2 and EGFR, which have been heavily targeted in cancer treatment. For example,Trastuzumab is Cetuximab are FDA-approved monoclonal antibodies (mAb) targetting HER2 and EGFR, respectively, among many other approved mAb’s.

A recent paper by Gaborit et al. in PNAS investigated the important role of antibody for HER3 in inhibiting tumor growth. I did a quick investigation of HER3 in Zodiac. The top co-expressed gene with HER3 in Zodiac is

FUT3 The Lewis histo-blood group system comprises a set of fucosylated glycosphingolipids that are synthesized by exocrine epithelial cells and circulate in body fluids. The glycosphingolipids function in embryogenesis, tissue differentiation, tumor metastasis, inflammation, and bacterial adhesion. They are secondarily absorbed to red blood cells giving rise to their Lewis phenotype. This gene is a member of the fucosyltransferase family, which catalyzes the addition of fucose to precursor polysaccharides in the last step of Lewis antigen biosynthesis. It encodes an enzyme with alpha(1,3)-fucosyltransferase and alpha(1,4)-fucosyltransferase activities. Mutations in this gene are responsible for the majority of Lewis antigen-negative phenotypes.

This gene seems to be related many important functions in development, cell differentiation, and tumor metastasis. Among the top genes, a few of them are related to growth factors (or their receptors) as expected. Specifically, they are either epidermal growth factor (EGF) -EGR receptor (EGFR) or hepatocyte growth factor (HGF) -HGF receptor (HGFR). They are listed below according to a descending order of statistical significance based on Zodiac.

ERBB2 (this is HER2) This gene encodes a member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. This protein has no ligand binding domain of its own and therefore cannot bind growth factors. However, it does bind tightly to other ligand-bound EGF receptor family members to form a heterodimer, stabilizing ligand binding and enhancing kinase-mediated activation of downstream signalling pathways, such as those involving mitogen-activated protein kinase and phosphatidylinositol-3 kinase. Allelic variations at amino acid positions 654 and 655 of isoform a (positions 624 and 625 of isoform b) have been reported, with the most common allele, Ile654/Ile655, shown here. Amplification and/or overexpression of this gene has been reported in numerous cancers, including breast and ovarian tumors.

MACC1 MACC1 is a key regulator of the hepatocyte growth factor (HGF; MIM 142409)-HGF receptor (HGFR, or MET; MIM 164860) pathway, which is involved in cellular growth, epithelial-mesenchymal transition, angiogenesis, cell motility, invasiveness, and metastasis. Expression of MACC1 in colon cancer (MIM 114500) specimens is an independent prognostic indicator for metastasis formation and metastasis-free survival (Stein et al., 2009 [PubMed 19098908]).

GRB7 The product of this gene belongs to a small family of adapter proteins that are known to interact with a number of receptor tyrosine kinases and signaling molecules. This gene encodes a growth factor receptor-binding protein that interacts with epidermal growth factor receptor (EGFR) and ephrin receptors. The protein plays a role in the integrin signaling pathway and cell migration by binding with focal adhesion kinase (FAK).

SPINT1 The protein encoded by this gene is a member of the Kunitz family of serine protease inhibitors. The protein is a potent inhibitor specific for HGF activator and is thought to be involved in the regulation of the proteolytic activation of HGF in injured tissues.

Inhibition of HER3 is likely to affect these important growth factors and their receptors, therefore supporting the main findings in the PNAS paper above.

What triggered me to write this blog is not these findings as they are more or less “expected”. Sure, HER3 should be associated with other growth factors and receptors, since it belongs to a family of growth factor receptor genes. Zodiac seems to confirm this general prior belief. However, since Zodiac provides interactions on several other genomic features, I took a further look and found that there is an unusual large number of interactions between HER3 ME (methylation) and other genes’ GE (gene expression). See the figure below.

HER3

I looked into the top 20 genes whose GE are associated with ME of HER3. The top 20 genes are overwhelmingly loaded with genes related to lymphocytes and immune cells such as NK and T cells. It appears that HER3 might be associated with liquid cancers and lymphocyte malignancies. The following genes are ordered from top as ranked by Zodiac. I removed genes without NCBI descriptions.

LAG3 Lymphocyte-activation protein 3 belongs to Ig superfamily and contains 4 extracellular Ig-like domains. The LAG3 gene contains 8 exons. The sequence data, exon/intron organization, and chromosomal localization all indicate a close relationship of LAG3 to CD4.

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.

PTPN7 The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is preferentially expressed in a variety of hematopoietic cells, and is an early response gene in lymphokine stimulated cells. The non-catalytic N-terminus of this PTP can interact with MAP kinases and suppress the MAP kinase activities. This PTP was shown to be involved in the regulation of T cell antigen receptor (TCR) signaling, which was thought to function through dephosphorylating the molecules related to MAP kinase pathway.

MMP25 Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMPs are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. However, the protein encoded by this gene is a member of the membrane-type MMP (MT-MMP) subfamily, attached to the plasma membrane via a glycosylphosphatidyl inositol anchor. In response to bacterial infection or inflammation, the encoded protein is thought to inactivate alpha-1 proteinase inhibitor, a major tissue protectant against proteolytic enzymes released by activated neutrophils, facilitating the transendothelial migration of neutrophils to inflammatory sites. The encoded protein may also play a role in tumor invasion and metastasis through activation of MMP2. The gene has previously been referred to as MMP20 but has been renamed MMP25.

HCST This gene encodes a transmembrane signaling adaptor that contains a YxxM motif in its cytoplasmic domain. The encoded protein may form part of the immune recognition receptor complex with the C-type lectin-like receptor NKG2D. As part of this receptor complex, this protein may activate phosphatidylinositol 3-kinase dependent signaling pathways through its intracytoplasmic YxxM motif. This receptor complex may have a role in cell survival and proliferation by activation of NK and T cell responses.

CCR7 The protein encoded by this gene is a member of the G protein-coupled receptor family. This receptor was identified as a gene induced by the Epstein-Barr virus (EBV), and is thought to be a mediator of EBV effects on B lymphocytes. This receptor is expressed in various lymphoid tissues and activates B and T lymphocytes. It has been shown to control the migration of memory T cells to inflamed tissues, as well as stimulate dendritic cell maturation. The chemokine (C-C motif) ligand 19 (CCL19/ECL) has been reported to be a specific ligand of this receptor. Signals mediated by this receptor regulate T cell homeostasis in lymph nodes, and may also function in the activation and polarization of T cells, and in chronic inflammation pathogenesis.

CYTIP The protein encoded by this gene contains 2 leucine zipper domains and a putative C-terminal nuclear targeting signal, but does not have any hydrophobic regions. This protein is expressed weakly in resting NK and T cells. The encoded protein modulates the activation of ARF genes by CYTH1. This protein interacts with CYTH1 and SNX27 proteins and may act to sequester CYTH1 protein in the cytoplasm.

GFI1 This gene encodes a nuclear zinc finger protein that functions as a transcriptional repressor. This protein plays a role in diverse developmental contexts, including hematopoiesis and oncogenesis. It functions as part of a complex along with other cofactors to control histone modifications that lead to silencing of the target gene promoters. Mutations in this gene cause autosomal dominant severe congenital neutropenia, and also dominant nonimmune chronic idiopathic neutropenia of adults, which are heterogeneous hematopoietic disorders that cause predispositions to leukemias and infections.

PTPN22 This gene encodes of member of the non-receptor class 4 subfamily of the protein-tyrosine phosphatase family. The encoded protein is a lymphoid-specific intracellular phosphatase that associates with the molecular adapter protein CBL and may be involved in regulating CBL function in the T-cell receptor signaling pathway. Mutations in this gene may be associated with a range of autoimmune disorders including Type 1 Diabetes, rheumatoid arthritis, systemic lupus erythematosus and Graves’ disease.

RHOH The protein encoded by this gene is a member of the Ras superfamily of guanosine triphosphate (GTP)-metabolizing enzymes. The encoded protein is expressed in hematopoietic cells, where it functions as a negative regulator of cell growth and survival. This gene may be hypermutated or misexpressed in leukemias and lymphomas. Chromosomal translocations in non-Hodgkin’s lymphoma occur between this locus and B-cell CLL/lymphoma 6 (BCL6) on chromosome 3, leading to the production of fusion transcripts.

These are positive ME-GE interactions, meaning that methylation of HER3 will lead to over-expression of these genes. These findings seem to suggest that HER3 has a role in liquid cancer.

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Zodiac (case 11): Are there similarities in genetic interactions between Cancer and Neurological Disorders?

This is the 11th-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.

Today I want to raise a bold question: Are genetic interactions between cancer and neurological disorders, such as Alzheimer disease (AD), similar? My current belief is that there are definitely similar genetic interactions between cancer and neurodisorders. In my previous two articles (here and here) I showed, as side notes, that some immune cancer biomarkers are related to genes with critical neurological functions. Today, I came across a Nature article published on Aug. 31, 2015, revealing a new physiological APP (this is the gene I will talk about) processing pathway, which generates proteolytic fragments capable of inhibiting neuronal activity within the hippocampus. This potentially has translational relevance for therapeutic strategies targeting APP processing in AD.

I learned from this article that APP is a critical gene for AD. So I looked up APP in Zodiac, which contains genome-wide gene-pair interactions in cancer. I did not expect to see much since Zodiac s is a database in cancer, not AD. Well, the top gene that co-express with APP is

PCDHB2 This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3′ exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections.

OK. I learned that the top gene “talks” with APP in cancer is PCDHB2, which is a member of a gene cluster related to cadherin. Cadherin is a critical protein that properly adheres cells together, so that they don’t wonder around in mature organs or tissues. Apparently, this is important physiologically. In cancer, cells do not properly bind to each other, and therefore become ill-shaped, like a tumor. Maybe when cells do not adhere to each other in brain, we get neural disorders, like Alzheimer?

Moving down the list, the second gene with top co-expression with APP is TMTC1. Humans know nothing about this gene.

The third gene is

FAT4 The protein encoded by this gene is a member of the protocadherin family. This gene may play a role in regulating planar cell polarity (PCP). Studies in mice suggest that loss of PCP signaling may cause cystic kidney disease, and mutations in this gene have been associated with Van Maldergem Syndrome 2.

It is a gene that regulate how cells shape in the space, which is called planar cell polarity. Surprisingly, FAT4 is a gene of the same protcadherin family as PCDHB2, the top gene above! This starts to give me goosebumps! Essentially the top two genes interact with APP are from the same gene family regulating spacing of cells. And neurodisorders like AD are affected by spacing of neural cells.

Moving on, the next gene is

GPRASP2 The protein encoded by this gene is a member of a family that regulates the activity of G protein-coupled receptors (GPCRs). The encoded protein has been shown to be capable of interacting with several GPCRs, including the M1 muscarinic acetylcholine receptor and the calcitonin receptor.

So it is a G protein-coupled receptor, or GPCR! What is a GPCR? It is a protein that has been awarded at least seven Nobel Prizes, including The 2012 Nobel Prize in Chemistry, awarded to Brian Kobilka and Robert Lefkowitz for their work that was “crucial for understanding how G protein–coupled receptors function.” It is apparently a very important protein and has been linked to at least the following nine physiological functions in human, among which 1, 2, 3, 4, 6, 7 are related to neural functions. Also, 5, 7 and 9 are related to cancer as well!

  1. The visual sense: The opsins use a photoisomerization reaction to translate electromagnetic radiation into cellular signals. Rhodopsin, for example, uses the conversion of 11-cis-retinal to all-trans-retinal for this purpose
  2. The gustatory sense (taste): GPCRs in taste cells mediate release of gustducin in response to bitter- and sweet-tasting substances.
  3. The sense of smell: Receptors of the olfactory epithelium bind odorants (olfactory receptors) and pheromones (vomeronasal receptors)
  4. Behavioral and mood regulation: Receptors in the mammalian brain bind several different neurotransmitters, including serotonin, dopamine, GABA, and glutamate
  5. Regulation of immune system activity and inflammation: Chemokine receptors bind ligands that mediate intercellular communication between cells of the immune system; receptors such as histamine receptors bind inflammatory mediators and engage target cell types in the inflammatory response. GPCRs are also involved in immune-modulation and directly involved in suppression of TLR-induced immune responses from T cells.[20]
  6. Autonomic nervous system transmission: Both the sympathetic and parasympathetic nervous systems are regulated by GPCR pathways, responsible for control of many automatic functions of the body such as blood pressure, heart rate, and digestive processes
  7. Cell density sensing: A novel GPCR role in regulating cell density sensing.
  8. Homeostasis modulation (e.g., water balance).[21]
  9. Involved in growth and metastasis of some types of tumors.[22]

The next top gene co-expresses with APP in Zodiac is

NDN This intronless gene is located in the Prader-Willi syndrome deletion region. It is an imprinted gene and is expressed exclusively from the paternal allele. Studies in mouse suggest that the protein encoded by this gene may suppress growth in postmitotic neurons.

NDN is related to neurons.

At this point, I am convinced that Zodiac, albeit a database computed using cancer data, can reveal relationships of genes in neural disorders as well. This seems to suggest that disease-related genetic interactions in cancer and neural disorders might have overlaps.

As I move down the list in Zodiac, genes related to neural functions continue to show up such as PTPRKPIEZO2 and HEY2. Below is a Zodiac visual summary of all the genes mentioned in this article.

APP

To avoid making an overly long article, I decide to stop here. I start to suspect that many ill-functioned inter-cellular mechanisms in cancer might be also present in neural degenerate diseases such as Alzheimer. I wonder if any cancer therapies targeting these mechansims could be tested on neurodisorders, at least in cell lines and mice.

Zodiac (case 10): PTEN and MYC — Is there a middle man?

This is the 10th-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

There has been a lot of recent work discussing the association of pTEN deletion and MYC amplification with progression of prostate cancer. Led by my colleagues at NorthShore University HealthSystem, Dr. Wennuan Liu, some pioneering work has shown the association between pTEN deletion and c-MYC amplification, and its effect on the progression of prostate cancer. In addition, other work has shown that over-expression in c-MYC is also associated with bad prognosis of prostate cancer.

I started a search of “PTEN” in Zodiac and looked for CN-CN (copy number-copy number) associations between other human gens and PTEN. Almost all the top genes reside on the same chromosome 10 of pTEN, implying  the reason that these genes are co-deleted or co-amplified with pTEN is due to segmental changes on the chromosome spanning a large region. Zodiac successfully identified these genes as the top ranked ones in the genome. Among the list of genes that have high associations with pTEN, one gene, MXI1, stood out.

MXI1 Expression of the c-myc gene, which produces an oncogenic transcription factor, is tightly regulated in normal cells but is frequently deregulated in human cancers. The protein encoded by this gene is a transcriptional repressor thought to negatively regulate MYC function, and is therefore a potential tumor suppressor. This protein inhibits the transcriptional activity of MYC by competing for MAX, another basic helix-loop-helix protein that binds to MYC and is required for its function. Defects in this gene are frequently found in patients with prostate tumors.

MXI1 ranks as the 17th gene that has the highest copy number co-change pattern in the genome (about 20,000 genes) according to Zodiac. It spans about 104K base pairs on Chromosome 10q24-q25 (note pTEN resides at Chromosome 10q23.3). So when pTEN is deleted in tumors, very likely MXI1 will also be deleted. Since MXI1 copy number positively affects MXI1 gene expression (see Zodiac Figure here), MXI1 deletion will down regulate MXI1 gene expression, which in turn will reduce the repressing effects on MYC expression (i.e., upregulate MYC expression). In other words, a hypothesis can be generated in prostate where

pTEN (deletion) —-> MXI1 (deletion) —-> MXI1 (expression down) —-> MYC (expression up)

pTEN deletion is associated with MXI1 deletion due to their proximity on the genome. MXI1 deletion leads to down regulation of MXI1 expression which then leads to up regulation of MYC expression.

Our team is currently working on a full analysis of pTEN, MXI1, and MYC in prostate cancer data of TCGA. This new hypothesis could potentially explain the association between pTEN deletion and MYC over expression. However, it does not explain the association between pTEN deletion and MYC amplification. Reasons for joint copy number changes are still mostly unknown to humans. Zodiac has all the copy number co-changes for pairs of genes and could be queried to reveal any potential patterns.

Lastly, MXI1 might be an important gene for prostate cancer progression, especially metastasis to bone. Below are a couple of genes among the top ones that have positive GE-GE association with MXI1. They are known prognosis markers for prostate cancer.

BMP6 The bone morphogenetic proteins (BMPs) are a family of secreted signaling molecules that can induce ectopic bone growth. Many BMPs are part of the transforming growth factor-beta (TGFB) superfamily. BMPs were originally identified by an ability of demineralized bone extract to induce endochondral osteogenesis in vivo in an extraskeletal site. Based on its expression early in embryogenesis, the BMP encoded by this gene has a proposed role in early development. In addition, the fact that this BMP is closely related to BMP5 and BMP7 has lead to speculation of possible bone inductive activity.
TNFRSF11B The protein encoded by this gene is a member of the TNF-receptor superfamily. This protein is an osteoblast-secreted decoy receptor that functions as a negative regulator of bone resorption. This protein specifically binds to its ligand, osteoprotegerin ligand, both of which are key extracellular regulators of osteoclast development. Studies of the mouse counterpart also suggest that this protein and its ligand play a role in lymph-node organogenesis and vascular calcification.
Unfortunately, the top gene C11ORF88 that is associated with MXI1 in terms of GE is an open read frame. This gene has much stronger association with MXI1 than any other genes, but humans know nothing about it!
I hope this blog could generate some new research direction for prostate cancer, especially its mechanism of progression and metastasis.