Memory  consolidation during a  learning  experience depends on the rapid expression of a set of IEGs in  brain   neurons . [ 14 ]   In general,  expression of genes  often can be epigenetically repressed by the presence of 5-methylcytosine in the  DNA promoter  regions of the genes.  However, in the case of IEGs associated with memory consolidation  demethylation  of  5-methylcytosine  to form the normal base  cytosine  can induce rapid gene expression.  Demethylation appears to occur by a  DNA repair  process involving the  GADD45G  protein. [ 14 ]


IEGs are used as markers in animal models of depression. Affected mice have altered levels of  Arc , affecting synaptic activity, and  EGR1 ,  involved in memory trace encoding. [ 1 ]  Other neuropsychiatric illnesses such as schizophrenia also exhibit altered IEG expression, with recent studies showing a correlation of low expression of  EGR3 , a transcription factor downstream of  NMDARs , in patients exhibiting schizophrenia. [ 15 ]  As such, IEGs are crucial markers in evaluating neuronal activity in the context of psychiatric illness with its expression pattern shaped by environmental and genetic factors. [ 15 ]


Human cytomegalovirus  (HCMV) is a prevalent beta herpesvirus that remains in the latent state, going unnoticed in healthy individuals but having serious consequences if the individual is immunocompromised. The virus cycles in and out of the latent state and is characterized by different gene expression regions: immediate-early (IE), early, and late. [ 16 ]  Conventional anti-viral treatments such as  Ganciclovir  use nucleoside analogs to target the early events of the viral replication cycles, however, these approaches are prone to developing resistance. [ 17 ]  Targeting IE1 and IE2 are thought to be crucial in regulating the pathogenesis of HCMV and retaining the virus in the latent state. Viral proteins derived from IE1 and IE2 regulate viral latency by controlling subsequent expression of early and late genes. [ 2 ]  Silencing of IE gene expression through  antisense oligonucleotides ,  RNA interference , and gene-targeting ribosomes have been investigated for therapeutic applications. [ 2 ] [ 17 ]  Alternatively, the rise of  CRISPR  technology allows for precise DNA editing that can knockout HCMV genes responsible for IE transcription. DNA targeting is more effective in latent infections, in which viral mRNA is absent or at a low concentration. [ 2 ]  Small molecule chemical inhibitors are also being investigated that target epigenetic factors and signaling proteins involved in IE expression. [ 2 ]


NM_001350962 NM_001350963 NM_001350964


NP_001337891 NP_001337892 NP_001337893


Inner mitochondrial membrane peptidase subunit 2  ( IMMP2L ) is an  enzyme  that in humans is encoded by the  IMMP2L   gene  on  chromosome 7 . [ 5 ] [ 6 ]  This  protein  catalyzes the removal of  transit peptides  required for the  targeting  of proteins from the  mitochondrial matrix , across the  inner membrane , into the  intermembrane space . IMMP2L processes the nuclear encoded protein  DIABLO .


The gene  IMMP2L  encodes protein inner mitochondrial membrane  peptidase  subunit 2 in human. The human IMMP2L gene has 18  exons  and locates at chromosome band 7q31. [ 6 ]


The human protein inner mitochondrial membrane peptidase subunit 2 has two  isoforms  due to alternative splicing. One isoform is 19.7  kDa  in size and composed of 175  amino acids . The calculated theoretical  pI  of this protein isoform is 8.66. The other isoform is 12.3 kDa in size and composed of 110 amino acids. The calculated theoretical pI of this protein isoform is 9.42. [ 7 ] [ 8 ]


As a peptidase, this protein catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the intermembrane space. it is known to process the nuclear encoding DIABLO protein.


Tourette's syndrome  is a complex neuropsychiatric disorder characterized by multiple motor and phonic  tics . In the clinical characterization of a patient with Tourette's, Petek et al. discovered a breakpoint in chromosome region 7q31. Additional characterization identified that IMMP2L, a novel gene coding for the apparent human homologue of the yeast mitochondrial inner membrane peptidase subunit 2, was found to be disrupted by both the breakpoint in the duplicated fragment and the insertion site in 7q31. It is the first association of IMMP2L gene to Tourette syndrome. [ 5 ]
Recent investigation by Bertelsen et al. further indicated that IMMP2L was one of the genes as a susceptibility factor in disease pathogenesis. Tourette syndrome is often accompanied by comorbidities such as  attention deficit hyperactivity disorder  and  obsessive–compulsive disorder . Tourette syndrome has a complex  etiology , and the underlying environmental and genetic factors responsible for this disease are still largely unknown. [ 9 ]


Immunoglobulin heavy constant alpha 1  is a immunoglobulin gene with symbol  IGHA1 . [ 3 ]  It encodes a constant (C) segment of  Immunoglobulin A   heavy chain . Immunoglobulin A is an  antibody  that plays a critical role in immune function in the  mucous membranes . IgA shows the same typical structure of other antibody classes, with two heavy chains and two light chains, and four distinct domains: one variable region, and three variable regions. As a major class of  immunoglobulin  in body secretions, IgA plays a role in defending against  infection , as well as preventing the access of foreign  antigens  to the immunologic system.


IGHA1 was first described in detail in 1975, when the  primary structure  (the amino acid sequence) of IgA was elucidated through the sequencing of tryptic and chymotryptic peptides. [ 4 ]  Similarly, the primary sequence was determined independently for the alpha-2 chain of the protein in 1979. [ 5 ]  Complete  nucleotide sequences  for the alpha-1 heavy chain constant region and the  allelic  alpha-2 heavy chain regions were published in 1984, and showed the genes were contained in three  exons , each of which encodes a single region of the protein domain. [ 6 ]


The genes encoding IGHA1 are found on  human chromosome 14 . [ 7 ]  The sequence encoding IGHA1 is 1,497 nucleotides long and is found between loci 105,707,168 and 105,708,664. [ 8 ]  The annotated chromosome location is also given as 14q32.33. [ 9 ]


The Ig alpha-1 chain C region is contained on the first of the constant regions of IgA, and is composed of an  amino acid  sequence 353 residues long. [ 10 ]  The  secondary structure  contained within this region is dominated by  beta strands , which define four antiparallel  beta sheets . These antiparallel beta-sheets are then sandwiched to form two beta-sandwiches, a typical  tertiary structure  of the immunoglobulin fold class. [ 11 ]  The two beta sheets that comprise each beta-sandwich are joined by an  alpha helix  on one side. These alpha helices define the  binding site  for this protein, with the binding site incorporating one antiparallel beta strand on either side of the helix. [ 10 ]  In addition to the binding sites, the opposite side of the beta-sandwich is connected by a series of loops, which define a hypervariable loop system, that may have a role in determining the specificity of an interaction between IgA and an antigen. [ 12 ]


IGHA1  has been implicated in a  chromosomal abnormality  identified in  multiple myeloma  lines. [ 13 ]  The abnormality has been identified as a  translocation  event, where translocation between  IGHA1  (found on chromosome 14), and  FCRL4  (the gene sequence encoding for an inhibitory receptor, found on chromosome 1) leads to the production of a  fusion protein . [ 14 ]


Interferon-induced transmembrane protein 2  is a  protein  that in humans is encoded by the IFITM2  gene . [ 5 ]  IFITM1 is a member of the IFITM family (Interferon-induced transmembrane protein) which is encoded by IFITM genes.


As the name implies, these genes are induced by  interferon  and form part of its  signaling pathway . In the absence of interferon stimulation, IFITM proteins can express broadly in tissues and cell lines. In humans, IFITM1, IFITM2 and IFITM3 are able to express in different tissues and cells while the expression of IFITM5 is limited to osteoblasts. [ 6 ]


IFITM proteins have been identified as antiviral  restriction factors  that block the early stages of viral replication. [ 7 ]  They inhibit  influenza A  virus replication, [ 8 ]  and infection with a wide range of other  enveloped viruses [ 9 ]


KIAA0753  is a protein that in humans is encoded by the  gene   KIAA0753 . The gene is located on chromosome 17p13.1, on the reverse strand spanning bases 6578141 to 6641744. [ 1 ]  The  KIAA0753  gene contains 18  exons , 19  introns  (in humans), and has no known aliases. [ 2 ]


Human KIAA0753 does not have any  paralogs , but has a wide variety of  orthologous  species. [ 3 ]  These species range from close primate relatives, to further relatives such as  amphibians  and various fish species. The most distant orthologs of human KIAA0753 were discovered to be the  giant owl limpet  and a species of  acorn worm .


The human KIAA0753 protein is 976  amino acids  in length, and contains two notable domains. [ 4 ]  The first is a domain of unknown function, designated as DUF3498, which spans from amino acid 508 to 663. The second is designated  Cdt1_m , which is a member of a  protein superfamily  located from amino acid 45 to 123. DUF3498 is reasonably well conserved in orthologous species, but the Cdt1_m region is not.


There are various predicted  post-translational modifications . These include  N-glycosylation  sites,  phosphorylation  sites,  C-mannosylation  sites,  acetylation sites , and location of protein export. A large number of phosphorylation sites are predicted with high confidence and provide evidence that, in humans, KIAA0753 is located inside the cell rather than exported out. [ 5 ]  The KIAA0753 protein does not contain any transmembrane domains. [ 6 ] [ 7 ]


The secondary structure of the protein is predominantly  alpha-helices  and coiled regions, with a small number of  beta sheet  regions. [ 8 ]


The human  KIAA0753  gene experiences  alternative splicing . Therefore, there are four main transcriptional variants of KIAA0753. Three of them, including variant 1, are similar, while variant 4 has a truncated 5’ (beginning) region. Other transcript variants are merely fragments of the original. [ 9 ]


The  promoter  region for KIAA0753 is 876 nucleotides in length, and is located between bases 6543872 to 6544747. [ 10 ]  A large number of  transcription factors  bind to the promoter region.


KIAA0753 is ubiquitously expressed throughout the human body at moderate to high levels. [ 11 ]  The majority of results show that conditional changes (disease, cancer, etc.) in general do not change the expression levels of the gene.


Researchers have studied the regulation of centriole duplication by centrosome components. [ 12 ]  The individuals conducting this experiment have identified that centrosome duplication is regulated by the following proteins: PLK4, CEP192, CEP152, CEP63, and CPAP. Among these, they found that CEP63 interacts with satellite proteins, namely KIAA0753 and another protein called CCDC14, to play a role in regulating centriole duplication. Their findings conclude that KIAA0753 positively regulates CEP63 centrosome localization and centriole duplication.


A second study has to do with the identification of hepatic microvascular adhesion-related genes of human colon cancer cells. [ 13 ]  This experiment was conducted with a variety of genes using a method called random homozygous gene perturbation.  KIAA0753  was identified as a gene in a silenced state when screening for nonadherent cells. The article concludes that the identified genes, including  KIAA0753 , may contribute to understand the metastatic process of colon cancer and possible treatments.


Ubiquitin C  has shown an interaction with KIAA0753 in humans. Further analysis of this interaction reveals that it is not due to neighboring or co-occurrence, but has been discovered experimentally. The study in question showed there to be a potential for binding between the two proteins. [ 14 ]


The following two proteins have been predicted, with high confidence, to interact with KIAA0753 through physical/neighboring interactions: WRD19, C2CD3. [ 15 ]
KIAA0753, KIAA1609, and SAV1 were found to interact with KIAA0753, determined through  textmining  methods. [ 16 ] [ 17 ]


NM_001033347 NM_001368844


KIAA1549-like  is a  protein  that in humans is encoded by the KIAA1549L  gene .
 [ 5 ]


Lysine-rich nucleolar protein 1  (KNOP1) is a  protein  which in human's is encoded by the KNOP1  gene . Aliases for KNOP1 include TSG118, C16orf88, and FAM191A. [ 1 ]


KNOP1 is located on the  negative DNA strand  of chromosome 16 at 16p12.3. It spans 15.21 kb, from 19729556 to 19714347 and has 6  exons  which are alternatively spliced in the RNA to create three main transcript isoforms. [ 2 ]   Two of the KNOP1  isoforms , B and C, lack exon 1, shifting the start codon used to the one found in exon 2, and so the proteins encoded by these lack sequence at  N-terminus . Isoform C also does not contain exon 4, which encodes the  C-terminal  DUF5595 domain.


The genes surrounding KNOP1 are  VPS35L  which is upstream and  IQCK  which is downstream of KNOP1. The IQCK gene was identified to be a potential candidate for  obsessive-compulsive disorder  in a genome-wide association study. [ 3 ]  The VPS35L encodes the protein VPS35L that acts as a component of the retriever complex. [ 4 ]


KNOP1 has high levels of expression in the  superior cervical ganglion , [ 6 ]  testis, placenta, and in early stages of hear and lung development. [ 7 ]  KNOP1 showed low levels of expression in the liver and pancreas.


There are many orthologs of KNOP1 in many different species of animals but not in the other  kingdoms . No paralogs of KNOP1 were found. Table 1 lists select KNOP1 orthologs.


The exact function of KNOP1 is not yet understood it is hypothesized to mimic nucleostemin, a nucleolar protein linked to the proliferation potential of stem cells. [ 10 ]  The protein is 518  amino acids  long, [ 11 ]  Isoform B is 458 amino acids, [ 12 ]  and Isoform C is 435 amino acids. [ 13 ]  It has a molecular weight of 58 kdal and an  isoelectric point  of 9.92  [ 14 ]  The protein is rich in lysine [ 15 ]  and has a lysine-rich region from amino acid 123–355. [ 16 ]  There is a region of the protein that interacts with the protein ZNF106. [ 17 ]  Some papers have associated it with the surface of the condensed chromosomes. [ 18 ]


KNOP1 has two domains Duf5595 (Not found in isoform C) and SMAP located at the end of the protein. [ 20 ]  DUF5595 is found in Nude C 80 ( Ndc80 ) proteins which can be found in species such as Homo sapiens. Ndc80 protein complexes are a core component of the end-on attachment sites for kinetochore microtubules. [ 21 ]  SMAP (Small acidic protein family) is found in  eukaryotes , and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important at G441  [ 22 ]


KNOP1 has been shown to interact with ZNF106 [ 23 ]  and has been confirmed by Grasberger, H., & Bell, G. I. [ 24 ]  This study concluded that the rapid downregulation of KNOP1 expression during  in vitro   terminal differentiation  coincides with a loss of nucleolar ZFP106.


NM_001034873 NM_001114545 NM_001312914


KSR2  is a  gene  which encodes  Kinase Suppressor of Ras 2  in humans.  [ 5 ]


The encoded protein plays a role in energy homeostasis, including  fatty acid oxidation ,  glucose metabolism  and  basal metabolic rate  (BMR). As a result, subsequent mutations in this gene, albeit rare, have been linked to the development of early on-set  obesity  and  insulin resistance .


Variations within the gene and its expression are hypothesized to play a key role in the phenotype of individuals with  metabolic disease , alongside  leptin -deficiency induced  hyperphagia . While the exact mechanism is unclear, it is believed that KSR2 variations result in a disruption of the  MAPK/ERK pathway , which can in turn lower the body's BMR. Since this normally accounts for about 70% of the total energy expenditure, a decrease results in excess energy storage, compared to an individual with a normal BMR on an isocaloric diet. [ 6 ]


Besides human metabolism, KSR2 is also crucial for ovarian development in the cabbage beetle  Colaphellus bowringi . [ 7 ]


Laccase (multicopper oxidoreductase) domain containing 1  is a  protein  in humans that is encoded by the LACC1  gene .
 [ 1 ]


Lactamase, beta 2  is a  protein  that in humans is encoded by the LACTB2  gene . [ 5 ]


LACTB2 is located on the 8th chromosome, with its specific location being 8q13.3. The gene contains 7 exons. [ 5 ]


The  LACTB2 protein  has a metallo β-lactamase (MBL) fold, with two zinc ions in the active site.


The metallo beta-lactamases were first identified in bacteria; they give some strains antibiotic resistance by degrading beta-lactam antibiotics (such as penicillins). However, the protein family includes many members that are ribonucleases (RNases), deoxyribonucleases (DNases) and other metabolic enzymes  [ 6 ]  MBL ribonucleases are responsible for RNA processing, generating the 3' end of tRNA,( RNase Z [ 7 ] ) eukaryotic mRNA ( CPSF-73 ) and  snRNA molecules  [ 8 ]  LACTB2 is a mitochondrial endoribonuclease which may have a role in degrading mitochondrial mRNAs. [ 9 ]


A tumor-specific LACTB2-NCOA2 fusion originating from intra-chromosomal rearrangement of chromosome 8 has been identified at both DNA and RNA levels. Unlike conventional oncogenic chimeric proteins, the fusion product lacks functional domain from respective genes, indicative of an amorphic rearrangement. This chimeric LACTB2-NCOA2 transcript was detected in 6 out of 99 (6.1%) colorectal cancer (CRC) cases, where NCOA2 was significantly downregulated. Enforced expression of wild-type  NCOA2  but not the LACTB2-NCOA2 fusion protein impaired the pro-tumorigenic phenotypes of CRC cells, whereas knockdown of endogenous NCOA2 in normal colonocytes had opposite effects. Mechanistically, NCOA2 inhibited Wnt/β-catenin signaling through simultaneously upregulating inhibitors and downregulating stimulators of Wnt/β-catenin pathway. NCOA2 is a novel negative growth regulatory gene repressing the Wnt/β-catenin pathway in CRC, where recurrent fusion with LACTB2 contributes to its disruption. [ 10 ]


NM_001161528 NM_001045475 NM_001384932 NM_001384933 NM_001384934


Leucine-rich repeats and death domain containing 1  is a  protein  that in humans is encoded by the LRRD1  gene .
 [ 5 ]


NM_001031772 NM_001033152


Lin-28 homolog B  is a  protein  that in humans is encoded by the LIN28B  gene .
 [ 5 ]


The protein encoded by this gene belongs to the  lin-28  family, which is characterized by the presence of a  cold-shock domain  and a pair of CCHC  zinc finger  domains. This gene is highly  expressed  in testis, fetal liver, placenta, and in primary human tumors and  cancer cell  lines. It is negatively regulated by  microRNAs  that target sites in the  3' UTR , and overexpression of this gene in primary tumors is linked to the repression of let-7 family of microRNAs and derepression of let-7 targets, which facilitates  cellular transformation .


The following is a  list of intestinal stem cell marker genes,  including their name and known function.


In the adult  intestine , the  crypts of Lieberkühn  are the niche for  epithelial   stem cells  and contain all proliferative stem and progenitor cells. Differentiating cells exit the cell cycle and migrate out of the crypts and onto the surface epithelium of the intestine, where they perform their physiological role (e.g., nutrient absorption by enterocytes; mucous secretion by goblet cells) and are eventually shed into the lumen. [ 1 ]  Intestinal stem cells were first identified as such in the 1970s. Cheng and Leblond used autoradiography of phagosomes to track the fate of cells at the base of the crypts, and determined that slender cells interspersed among Paneth cells at the crypt base could give rise to all of the other cell types that constituted the intestinal epithelium. [ 2 ]   Due to their narrow shape and location, these cells were called crypt base columnar cells (CBCs). Potten and colleagues used a combination of DNA labeling and assessment of the response of the epithelium to high-dose radiation to identify label-retaining cells (LRCs) as putative stem cells, which were typically located around four cell positions above the bottom of the crypt, and were therefore also called "+4 cells". [ 3 ] [ 4 ]  Later work suggested that these "+4 cells" may function as reserve or back-up stem cells, and further suggested that they divide slowly relative to the other progenitor cells in the crypt. Thus, these cells are also called quiescent stem cells. [ 5 ]


The stem cell zone model states that the CBC stem cells reside in a stem-cell-permissive environment. These cycling stem cells regularly generate progeny, which subsequently exit the niche and pass through the “common origin of differentiation” around position +5, where they commit toward the various individual lineages. Progenitors mature as they migrate upward onto the villus. Maturing Paneth cell progenitors migrate downward, with the oldest Paneth cells residing at the very base of the crypt. [ 6 ]  In accordance with the stem cell zone model proposing that, during their upward migration, CBC stem cells would only gradually lose their self-renewal capacity, it was shown in vivo that transient amplifying cells can revert to Lgr5+ CBC stem cells after damage, presumably by direct contact with Paneth cells. [ 6 ]


More recently modern genetics techniques, primarily using transgenic mice, have been used to identify genes that are specifically expressed or highly enriched in the intestinal stem cells. Below, a table of intestinal stem cell  "marker" genes  is given, along with a notation if this marks active of CBC stem cells, or quiescent/reserve/+4 stem cells.


Additional possible markers:
CD24
CD44v6
Active beta-catenin
Pcdh8  21419747


Lung cancer susceptibility 5  is a  protein  that in humans is encoded by the LNCR5  gene .
 [ 2 ]


LOC101059915  is a  protein , which in  humans  is encoded by the LOC101059915  gene . It is located on the X chromosome and has restricted expression in the testis.


The LOC101059915 gene has two aliases known as chromosome X  open reading frame  49-like and BX276092.6. [ 3 ]


LOC101059915 is located on the  X chromosome  at locus Xq13.1. It is 1,831  base pairs  long and the gene sequence has 6  exons . [ 4 ]  LOC101059915 also has one protein coding transcript.


The  promoter  region of LOC101059915 is located on the sense strand of DNA, and between base pair 71666098 and 71667904 on the X chromosome. It spans up to 1.806 bp. [ 5 ]  Expression of LOC101059915, however, is relatively low in human cells, and is primarily limited to the testis. [ 6 ]


The protein has 518  amino acids  and a molecular mass of 55.1 kDa. [ 7 ]  The  isoelectric point  is 8.15. Compared to other human proteins LOC101059915 is  glycine -,  proline -rich, and  serine -rich but the protein has lower levels of  tyrosine . [ 8 ]


The  domain of unknown function , DUF4641 covers almost the entire protein. It is a part of pfam15483. [ 9 ]  It is 410 amino acids long, from amino acid 85 until amino acid number 495. [ 10 ]


The secondary structure of LOC101059915 has been shown to consist of primarily alpha helices as determined by models made on I-TASSER and analysis using ExPASy tools. [ 11 ]


LOC101055915 is predicted to contain many different post-translational modifications. This include sites for phosphorylation (NetPhos 2.0 [ 12 ] ) and sumoylation (SUMOplot Analysis Program [ 13 ] ).


The LOC101059915 protein has been predicted to be located in the  cell nucleus  (PSORT II). [ 14 ]


CXorf49  and CXorf49B are paralogs of LOC101059915. They share upwards of 78% similarity with LOC101059915 and likely went through a  gene duplication  event relatively recently, in evolutionary terms, due to the high degree of conservation between all three sequences.


CXorf49 is especially interesting due it being shown to be involved as one of the components of a small group of the  HL-60  cell  proteome  that are most prone to form  4-Hydroxy-2-nonenal (HNE) adducts, upon exposure to nontoxic (10 μM) HNE concentrations, along with heat shock 60 kDa protein 1. [ 15 ]


Using BLAST [ 16 ]  no orthologs for LOC101059915 are found in single celled organisms, fungi or plants whose genomes have been sequenced. For multi-cellular organisms, orthologs are found in mammals, excluding  Monotremes . The table below shows a representative sample of 20 of the orthologs for LOC101059915. The table is organized based on the time of divergence from humans in millions of years (MYA). In cases where the divergence time-frame is the same the orthologs are sorted by identity (%).


anubis


Colobus


Capuchin


Marmoset


Night Monkey


boliviensis


Squirrel Monkey


tridecemlineatus


Ground Squirrel


The most distant ortholog for LOC101059915 is from the species  Sarcrophilus harrisii  which is commonly known as the  Tasmanian Devil  dating from more than 159.0 million years ago.


LRRC3B  is a  gene  frequently epigenetically inactivated in several epithelial malignancies and inhibits  cell growth  and replication. Data suggest that the LRRC3B gene could be involved in the process of  carcinogenesis  as a tumor suppressor gene. [ 1 ]


Leucine-Rich Single-Pass Membrane Protein 1 (LSMEM1)  is a  protein  that, in humans, is encoded by the LSMEM1  gene .


In humans, LSMEM1 is located on  chromosome 7q31.1 . [ 1 ] [ 2 ]  LSMEM1 neighbors the gene  IFRD1  in humans. Aliases for LSMEM1 include C7orf53, chromosome 7  open reading frame  53, and FLJ39575. [ 3 ]  The human  mRNA  is 1686 base pairs long and the gene contains 5  exons . [ 4 ]  The human mRNA also has a  5' UTR  and a  3' UTR . The 5' UTR goes from mRNA position 1 to 341, and the 3' UTR goes from mRNA position 738 to 1686.


The protein LSMEM1 encodes in humans is 131  amino acids  long [ 5 ]  and has a molecular weight ranging from 14.2 to 14.5  kDal . [ 6 ]  Its  isoelectric point  in humans is about 5, making it slightly acidic. LSMEM1 is an  integral membrane protein  and a  transmembrane protein  Besides its transmembrane segment, it is mainly made up of coils and relatively few  beta strands . As its name implies, LSMEM1 only has one transmembrane segment. The predicted  post-translational modifications  to the human LSMEM1 protein are  glycation [ 7 ]  and  phosphorylation . [ 8 ]  There is no predicted  signal peptide  for the human protein. [ 9 ]


There are no known  paralogs  in humans for LSMEM1. [ 10 ]  Orthologous proteins exist mainly in  mammals ,  birds , and  reptiles . There are also more distant orthologs in  amphibians  and  sarcopterygii . LSMEM1 does not show up in  invertebrates ,  fungi , or  prokaryotes . LSMEM1 also contains a conserved  domain of unknown function  DUF4577. [ 3 ]  When the human protein encoded by LSMEM1 is compared to a known quickly evolving protein ( fibrinopeptides ) and a known slowly evolving protein ( cytochrome c ), LSMEM1 appears to be slowly evolving.


In humans, LSMEM1 is very highly expressed in skeletal muscle. [ 11 ]  In humans, LSMEM1 also shows high expression in nerve tissue, moderate expression in the uterus, testis, bone marrow, heart, and intestines, and low expression in the brain and pancreas. [ 12 ]  It also shows expression in both the fetal and adult stages of life in humans.


LSMEM1 is predicted to have a 615 base pair  promoter  in humans just upstream of its transcriptional start site. [ 13 ]


Some  transcription factors  that are predicted to bind to the promoter of LSMEM1 in humans are:  SRF ,  EVI1 ,  SOX ,  ETS , LTSM, and TALE transcription factors. [ 13 ]  Many of the transcription factors thought to bind to the LSMEM1 promoter in humans have activity in biological processes like cell differentiation, cell cycle, cell growth, and development.


There are 3 main proteins thought to interact with the human protein encoded by the gene LSMEM1 that were determined via  two-hybrid screening  (LSMEM2 and MAL) and reconstituted complex (APP) experiments. A reconstituted complex experiment detects interactions between purified proteins  in vitro . The 3 proteins thought to interact with LSMEM1 are:  MAL ,  APP , and LSMEM2. [ 14 ]  All three of these interacting proteins are integral membrane proteins, just as LSMEM1 is.


LSMEM1 expression levels in humans are greatly decreased in  septic  skeletal muscle. [ 15 ]  For humans, the LSMEM1 protein has 17  SNP   missense mutations  within its coding sequence. [ 16 ]  The LSMEM1 protein has been shown to be prevalent in the serum of patients with  Parkinson's disease  and that it binds to diagnostic biomarkers of Parkinson's Disease as a protein  antigen . [ 17 ]


The  MADS box  is a conserved  sequence motif . The genes which contain this motif are called the MADS-box gene family. [ 1 ]  The MADS box encodes the DNA-binding MADS domain. The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T] 6 GG termed the CArG-box. [ 2 ]  MADS-domain proteins are generally  transcription factors . [ 2 ] [ 3 ]   The length of the MADS-box reported by various researchers varies somewhat, but typical lengths are in the range of 168 to 180 base pairs, i.e. the encoded MADS domain has a length of 56 to 60 amino acids. [ 4 ] [ 5 ] [ 6 ] [ 7 ]  There is evidence that the MADS domain evolved from a sequence stretch of a  type II topoisomerase  in a common ancestor of all extant eukaryotes. [ 8 ]


The first MADS-box gene to be identified was  ARG80  from budding yeast,  Saccharomyces cerevisiae , [ 9 ]  but was at that time not recognized as a member of a large gene family. The MADS-box gene family got its name later as an acronym referring to the four founding members, [ 1 ]  ignoring  ARG80 :


In  A. thaliana ,  A. majus , and  Zea mays  this motif is involved in floral development. Early study in these model angiosperms was the beginning of research into the  molecular evolution  of floral structure in general, as well as their role in nonflowering plants. [ 11 ]


MADS-box genes have been detected in nearly all eukaryotes studied. [ 8 ]  While the genomes of animals and fungi generally possess only around one to five MADS-box genes, genomes of  flowering plants  have around 100 MADS-box genes. [ 12 ] [ 13 ]
Two types of MADS-domain proteins are distinguished; the SRF-like or Type I MADS-domain proteins and the MEF2-like (after  MYOCYTE-ENHANCER-FACTOR2 ) or Type II MADS-domain proteins. [ 8 ] [ 13 ]  SRF-like MADS-domain proteins in animals and fungi have a second conserved domain, the SAM (SRF, ARG80, MCM1) domain. [ 14 ]  MEF2-like MADS-domain proteins in animals and fungi have the  MEF2  domain as a second conserved domain. [ 14 ]  In plants, the MEF2-like MADS-domain proteins are also termed MIKC-type proteins referring to their conserved domain structure, where the MADS (M) domain is followed by an Intervening (I), a Keratin-like (K) and a  C-terminal domain . [ 12 ]  In plants, MADS-domain protein form tetramers and this is thought to be central for their function. [ 15 ] [ 16 ]  The structure of the tetramerisation domain of the MADS-domain protein SEPALLATA3 was solved illustrating the structural basis for tetramer formation [ 17 ]


A  geneticist  intensely investigating MADS-box genes is  Günter Theißen  at the  University of Jena . For example, he and his coworkers have used these genes to show that the  order   Gnetales  is more closely related to the  conifers  than to the  flowering plants . [ 18 ]


MADS-box is under-studied in wheat as of 2021 [update] . [ 19 ]


In  Zea mays  the mutant  Tunicate1  produces  pod corn .  Tunicate1  is a mutant of  Z. mays MADS19  ( ZMM19 ), in the  SHORT VEGETATIVE PHASE  gene family.  ZMM19  can be  ectopically expressed . [ 19 ]


Such ectopic expression of  ZMM19  in  A. thaliana  enlarges  sepals , suggesting  conservation . [ 19 ]


MADS-box genes have a variety of functions. In animals, MADS-box genes are involved in muscle development and  cell proliferation  and differentiation. [ 14 ]  Functions in fungi range from pheromone response to  arginine  metabolism. [ 14 ]


In plants, MADS-box genes are involved in controlling all major aspects of development, including male and female  gametophyte  development, embryo and seed development, as well as root, flower and fruit development. [ 12 ] [ 13 ]


Some MADS-box genes of flowering plants have homeotic functions like the  HOX genes  of animals. [ 1 ]  The floral homeotic MADS-box genes (such as  AGAMOUS  and  DEFICIENS ) participate in the determination of floral organ identity according to the  ABC model of flower development . [ 20 ]


Another function of MADS-box genes is flowering time determination. In  Arabidopsis thaliana  the MADS box genes  SOC1 [ 21 ]  and  Flowering Locus C [ 22 ]  ( FLC ) have been shown to have an important role in the integration of molecular flowering time pathways. These genes are essential for the correct timing of  flowering , and help to ensure that fertilization occurs at the time of maximal reproductive potential.


The MADS box protein structure is characterized by four domains. At the  N terminal end  is the highly conserved MADS  DNA binding domain . [ 23 ]  Next to the MADS domain is the moderately conserved Intervening (I) and  Keratin -like (K) domains, which are involved in specific  protein-protein interactions . [ 23 ]  The  carboxyl terminal  (C) domain is highly variable and is involved in transcriptional activation and assemblage of  heterodimers  and  multimeric protein  complexes. [ 24 ]


Major gene  is a gene with pronounced  phenotype  expression, in contrast to a  modifier gene . Major gene characterizes common expression of  oligogenic series , i.e. a small number of genes that determine the same trait.


Major genes control the discontinuous or qualitative characters in contrast of  minor genes  or  polygenes  with individually small effects. Major genes segregate and may be easily subject to  mendelian  analysis. The gene categorization into major and minor determinants is more or less arbitrary. Both of the two types are in all probability only end points in a more or less continuous series of gene action and gene  interactions . [ 1 ] [ 2 ]


The term major gene was introduced into the science of inheritance by  Keneth Mather  (1941). [ 3 ]


In  biology , a  marker gene  may have several meanings. In  nuclear biology  and molecular biology, a  marker gene  is a  gene  used  to determine if a  nucleic acid sequence  has been successfully inserted into an organism's  DNA . In particular, there are two sub-types of these marker genes: a  selectable marker  and a  marker for screening . In  metagenomics  and  phylogenetics , a  marker gene  is an  orthologous gene group  which can be used to delineate between taxonomic lineages. [ 1 ]


A selectable marker protects the organism from a  selective agent  that would normally kill it or prevent its growth. In a transformation reaction, depending on the  transformation efficiency , only one in several million to billion cells may take up DNA. Rather than checking every single cell, scientists use a selective agent to kill all cells that do not contain the foreign DNA, leaving only the desired ones.


Antibiotics  are the most common selective agents. In bacteria, antibiotics are used almost exclusively. In plants, antibiotics that kill the  chloroplast  are often used as well, although tolerance to salts and growth-inhibiting hormones is becoming more popular. In mammals, resistance to antibiotics that would kill the  mitochondria  is used as a selectable marker.


A screenable marker will make cells containing the gene look different. There are three types of screening commonly used:


The  mobilized colistin resistance  ( mcr ) gene confers  plasmid-mediated   resistance  to  colistin ,  one of a number of  last-resort antibiotics  for treating  Gram-negative  infections.  mcr-1 , the original variant, is capable of  horizontal transfer  between different strains of a bacterial species. After discovery in November 2015 in  E. coli  (strain SHP45) from a  pig  in  China  it has been found in  Escherichia coli ,  Salmonella enterica ,  Klebsiella pneumoniae ,  Enterobacter aerogenes , and  Enterobacter cloacae . As of 2017 [update] , it has been detected in more than 30 countries on 5 continents in less than a year.


The "mobilized colistin resistance" ( mcr-1 ) gene confers  plasmid-mediated   resistance  to  colistin , a  polymyxin  and one of a number of  last-resort antibiotics  for treating infections. [ 1 ] [ 2 ]   The gene is found in no less than ten species of the  Enterobacteriaceae :  Escherichia coli ,  Salmonella ,  Klebsiella pneumoniae ,  Enterobacter aerogenes ,  Enterobacter cloacae ,  Cronobacter sakazakii ,  Shigella sonnei ,  Kluyvera  species,  Citrobacter  species, and  Raoultella ornithinolytica . [ citation needed ]


The mechanism of resistance of the MCR gene is a  lipid A phosphoethanolamine transferase . The enzyme transfers a phosphoethanolamine residue to the  lipid A  present in the  cell membrane  of gram-negative bacteria. The altered lipid A has much lower affinity for colistin and related polymyxins resulting in reduced activity of the antimicrobial. This type of resistance is known as target modification. [ 3 ]  Although the same mechanism has been observed before with enzymes like  eptA , [ 4 ]   mcr-1  is the first polymyxin resistance gene known to be capable of  horizontal transfer  between different strains of a bacterial species. [ 1 ]


mcr-1  also provides resistance to host  antimicrobial peptides . Bacteria carrying the gene were better at killing infected caterpillars. [ 5 ]


The gene was first discovered in  E. coli  (strain SHP45) from a  pig  in  China  April 2011 and published in November 2015. [ 6 ] [ 7 ]
It was identified by independent researchers in human samples from Malaysia, China, [ 1 ]  England, [ 8 ] [ 9 ]  Scotland, [ 10 ]  and the United States. [ 11 ]


In April 2016, a 49-year-old woman sought medical care at a  Pennsylvania  clinic for  UTI  symptoms.  PCR  of an  E. coli  isolate cultured from her urine revealed the  mcr-1  gene for the first time in the  United States , [ 12 ]  and the  CDC  sent an alert to health care facilities. In the following twelve months, four additional people were reported to have infections with mcr-1 carrying bacteria. [ 13 ]


As of February 2017 [update]  mcr-1 has been detected in more than 30 countries on 5 continents in less than a year, [ 14 ]  and it appears to be spreading in hospitals in China. [ 15 ]  The  prevalence  in five Chinese provinces between April 2011 and November 2014 was 15% in raw meat samples and 21% in food animals during 2011–14, and 1% in people hospitalized with infection. [ 1 ]


Using genetic analysis, researchers believe that they have shown that the origins of the gene were on a Chinese pig farm where  colistin  was routinely used. [ 16 ] [ 17 ]


Given the importance of  mcr-1  in enabling bacteria to acquire polymyxin resistance, MCR-1 (the protein that is encoded by  mcr-1 ) is a current inhibition target for the development of new antibiotic adjuvants. [ 18 ] [ 19 ]  For example,  ethylenediaminetetraacetic acid  (EDTA), a metal-chelating agent and common food additive, was shown to inhibit MCR-1 as it is a zinc-dependent enzyme. [ 3 ]  Substrate analogues, such as  ethanolamine  and  glucose , were also shown to inhibit MCR-1. [ 20 ]  The use of a combined antibiotics regime has shown to be able to overcome the resistance that is caused by  mcr-1 , and the mechanism of action may be directly or indirectly targeting the MCR-1 protein. [ 21 ]  Recently, a couple of studies showed that peptide nucleic acids (PNAs), a class of antisense molecules, when conjugated with cell-penetrating peptides, may inhibit the translation of MCR to turn off polymyxin resistance. [ 22 ] [ 23 ]


As of April 2021 [update] , ten mobilized colistin resistance genes termed  mcr-1  through  mcr-10  have been identified. They are  homologous  to each other, and work in similar ways. [ 24 ]  The  mcr-2  gene is a rare variant of  mcr-1  and is found only in  Belgium . The less-related  mcr-3 ,  mcr-4 , and  mcr-5  were identified in  E. coli  and  Salmonella . [ 25 ]


On the  phylogenic  tree, the various clusters of  mcr  genes are scattered between immobile resistance genes of the same type, suggesting a history of multiple transfer to plasmids. [ 26 ] [ 27 ] [ 20 ] [ 28 ]


NM_004991 NM_005241 NM_001366466 NM_001366467 NM_001366468 NM_001366469 NM_001366470 NM_001366471 NM_001366472 NM_001366473 NM_001366474


NM_007963 NM_021442 NM_001361034 NM_001370768 NM_001370769


NP_004982 NP_005232 NP_001353395 NP_001353396 NP_001353397 NP_001353398 NP_001353399 NP_001353400 NP_001353401 NP_001353402 NP_001353403 NP_004982.2


MDS1 and EVI1 complex locus protein EVI1  (MECOM) also known as  ecotropic virus integration site 1 protein homolog  (EVI-1) or  positive regulatory domain zinc finger protein 3  (PRDM3) is a  protein  that in humans is encoded by the  MECOM   gene . EVI1 was first identified as a common  retroviral  integration site in AKXD murine myeloid tumors. It has since been identified in a plethora of other organisms, and seems to play a relatively conserved developmental role in embryogenesis. EVI1 is a nuclear transcription factor involved in many signaling pathways for both coexpression and coactivation of cell cycle genes.


The EVI1 gene is located in the human genome on chromosome 3 (3q26.2). The gene spans 60 kilobases and encodes 16 exons, 10 of which are protein-coding. The first in-frame ATG start codon is in exon 3. [ 5 ]


A large number of transcript variations exist, encoding different isoforms or chimeric proteins. Some of the most common ones are:


The MECOM is primarily found in the nucleus, either soluble or bound to DNA. The 145kDa isoform is the most-studied, encoding 1051 amino acids, [ 7 ]  although there are many EVI1 fusion products detectable in cells expressing EVI1.


The MECOM protein contains 2 domains characterized by 7 zinc finger motifs followed by a proline-rich transcription repression domain, 3 more zinc finger motifs and an acidic C-terminus. [ 6 ]


EVI1 is a proto-oncogene conserved across humans, mice, and rats, sharing 91% homology in nucleotide sequence and 94% homology in amino acid sequence between humans and mice. [ 7 ]  It is a transcription factor localized to the nucleus and binds DNA through specific conserved sequences of GACAAGATA  [ 8 ]  with the potential to interact with both corepressors and coactivators.


EVI1 has been described as a proto-oncogene since its first discovery in 1988. [ 9 ]  Overexpression and aberrant expression of EVI1 has been associated with human  acute myelogenous leukemia  (AML),  myelodysplastic syndrome  (MDS) and  chronic myelogenous leukemia  (CML), and more recently has been shown as a poor prognostic indicator. Its function in these cells may be regulated by phosphorylation of serine196, in its N-terminal DNA binding domain. [ 10 ]  All of these involve erratic cellular development and differentiation in the bone marrow leading to dramatic alterations in the normal population of blood cells. EVI1 has also been found to play a role in solid ovarian and colon tumors, [ 11 ]  although it is not yet well characterized in this context. It has been hypothesized that it acts as a survival factor in tumor cell lines, preventing therapeutic-induced apoptosis and rendering the tumor cells more resistant to current treatments. [ 12 ]


EVI1 has been shown to be involved in the downstream signaling pathway of  transforming growth factor beta (TGF-β) . TGF-β, along with other TGF-β family ligands such as  bone morphogenic protein (BMP)  and  activin  are involved in regulating important cellular functions such as proliferation, differentiation, apoptosis, and matrix production. [ 13 ]  These biological roles are not only important for cellular development, but also in understanding oncogenesis.


TGF-β signaling induces transcription of the cyclin-dependent kinase (CDK) inhibitors p15 Ink4B  or p21 Cip1 , which, as a consequence, act to halt the cell cycle and stop proliferation. This inhibition can lead to cellular differentiation or apoptosis, and therefore any resistance to TGF-β is thought to contribute in some way to human leukemogenesis. [ 14 ]  The downstream effectors of TGF-β are the Smad receptors (also known as  receptor-activated Smads ).  Smad2  and  Smad3  are phosphorylated in response to TGF-β ligand binding, and translocate into the nucleus of the cell, where they can then bind to DNA and other transcription factors. [ 13 ]  Stable binding to promoters occurs through a conserved MH1 domain, and transcription activation occurs through an MH2 domain, and involves accompanying coactivators such as CBP/p300 and Sp1. [ 13 ]


The majority of literature discusses the interaction between EVI1 and Smad3, however there have been some experiments done showing that EVI1 interacts with all of the Smad proteins at varying levels, indicating a potential involvement in all of the pathways that include Smads as downstream effectors. [ 13 ]  The translocation of phosphorylated Smad3 into the nucleus allows for direct interaction with EVI1, mediated by the first zinc finger domain on EVI1 and the MH2 domain on Smad3. [ 13 ] [ 14 ]  As the Smad3 MH2 domain is required for transcription activation, EVI1 binding effectively prevents transcription of the TGF-β induced anti-growth genes through structural blocking, and also leads to recruitment of other transcriptional repressors (see Epigenetics). By inhibiting an important checkpoint pathway for tumor suppression and growth control, overexpression or aberrant expression of EVI1 has characteristic oncogenic activity.


As an additional confirmation of the role of EVI1 expression on cell cycle progression, it has been shown that high EVI1 expression is correlated with the well-known tumor suppressor and cell cycle mediator Retinoblastoma, remaining in a hyperphosphorylated state, even in the presence of TGF-β. [ 15 ]


c-Jun N-terminal kinase  (JNK) is a MAP kinase activated by extracellular stress signals such as gamma-radiation, ultraviolet light, Fas ligand, tumor necrosis factor α (TNF-α), and interleukin-1. [ 16 ]  Phosphorylation on two separate residues, Thr183 and Tyr185, cause JNK to become activated and translocate to the nucleus to phosphorylate and activate key transcription factors for the apoptotic response. [ 16 ]


Experiments co-expressing EVI1 and JNK have shown that levels of JNK-phosphorylated transcription factors (such as c-Jun) are drastically decreased in the presence of EVI1. Binding of EVI1 and JNK has been shown to occur through the first zinc finger motif on EVI1, and that this interaction does not block JNK phosphorylation and activation, but blocks JNK binding to substrate in the nucleus. [ 16 ]  Subsequent  in vitro  assays showed that stress-induced cell death from a variety of stimuli is significantly inhibited by EVI1 and JNK binding. [ 16 ]


EVI1 does not bind other MAP kinases such as p38 or ERK. [ 16 ]


Among the many other observed defects, EVI1 −/−   mouse embryos have been shown to have defects in both the development and proliferation of hematopoietic stem cells (HSCs). It is presumed that this is due to direct interaction with the transcription factor GATA-2, which is crucial for HSC development. [ 17 ]  It has subsequently been shown many times  in vitro  that EVI1 upregulation can induce proliferation and differentiation of HSCs and some other cell types such as rat fibroblasts. [ 6 ]


However, existing data is inconclusive regarding the absolute role of EVI1 in cell cycle progression. It appears to depend on the specific cell type, cell line and growth conditions being used as to whether EVI1 expression induces growth arrest or cell differentiation/proliferation, or whether it has any effect at all. [ 6 ]  The data showing direct interaction of EVI1 with the promoters for a diverse array of genes supports the theory that this is a complex transcription factor associated with many different signalling pathways involved in development and growth.


Although the literature is limited on the subject, the well-documented effects on HSCs imply that there is a potential indirect effect of aberrant EVI1 expression on tumoral angiogenesis. HSCs secrete angiopoietin, and its receptor molecule Tie2 has been implicated in angiogenesis of tumors in both humans and mice. [ 18 ]  Upregulation of Tie2 has been shown to occur under hypoxic conditions, and to increase angiogenesis when coinjected with tumor cells in mice. [ 18 ]  Observations that EVI1 −/−   mutants have substantially downregulated Tie2 and Ang-I expression, therefore, hints at an interesting role of high EVI1 expression in tumor progression. This is likely, at least in part, a reason for the widespread hemorrhaging and minimal vascular development in EVI1 deleted embryos, [ 17 ]  and has potential to indicate yet another reason for poor prognosis of EVI1 positive cancers.


EVI1 has also been shown to directly interact with C-terminal-binding protein (CtBP, a known transcriptional repressor) through  in vitro  techniques such as  yeast 2-hybrid  screens and  immunoprecipitation . [ 14 ]  This interaction has been specifically shown to rely on amino acids 544-607 on the EVI1 protein, a stretch that contains two CtBP-binding consensus motifs. [ 15 ]  This binding leads to recruitment of histone deacetylases (HDACs) as well as many other corepressor molecules leading to transcription repression via chromatin remodelling. [ 14 ]


EVI1 interaction with Smad3 followed by recruitment of corepressors can inhibit transcription and de-sensitize a cell to TGF-β signaling without ever displacing Smad3 from a gene's promoter. [ 13 ]  The epigenetic modification is clearly enough to make the DNA inaccessible to the transcription machinery.


Although EVI1 has mainly been implicated as a transcription repressor, there is some data that has shown a possible dual role for this protein. Studies show that EVI1 also binds to known coactivators cAMP responsive element binding protein (CBP) and p300/CBP-associated factor (P/CAF). [ 13 ]  These both have histone acetyltransferase activity, and lead to subsequent transcription activation. In addition, structural changes have been visualized within the nucleus of a cell, depending on the presence of corepressors or coactivators, leading researchers to believe that EVI1 has a unique response to each kind of molecule. In approximately 90% of cells, EVI1 is diffuse within the nucleus; however, when CBP and P/CAF are added, extensive nuclear speckle formation occurs. [ 19 ]  The complete physiological repercussions of this complex role of EVI1 have yet to be elucidated, however, could provide insight into the wide variety of results that have been reported regarding the effect of EVI1 on  in vitro  cell proliferation. [ 6 ]


Interaction with corepressors and coactivators appears to occur in distinct domains, [ 19 ]  and there are theories that EVI1 exists in a periodical, reversible acetylated state  [ 7 ]  within the cell. Contrasting theories indicate that the interplay between different EVI1 binding proteins acts to stabilize interactions with different transcription factors and DNA, leading to a response of EVI1 to a diverse set of stimuli. [ 13 ]


Since it was first identified in murine myeloid leukemia as a common site of retroviral integration into the chromosome, EVI1 and its surrounding DNA have been a site of many identified chromosomal translocations and abnormalities. [ 20 ]  This can lead to aberrant expression of EVI1, and,  as shown in the figure below , commonly involved chromosomal breakpoints have been mapped extensively. One major cause of EVI1 activation and consequent overexpression is a clinical condition called  3q21q26 syndrome  from inv(3)(q21q26) or t(3;3)(q21;q26). [ 7 ]  The result is the placement of a strong enhancing region for the housekeeping gene  Ribophorin  1 ( RPN1 ) [ 21 ]   next to the EVI1 coding sequence, resulting in a dramatic increase of EVI1 levels in the cell. [ 7 ]


A summary of common chromosomal abnormalities involving EVI1 and its fusion genes can be found in a review by Nucifora  et al. . [ 22 ]


The most common circumstance involves chromosomal translocations in human  AML  or  MDS , leading to constitutive expression of EVI1 and eventually to cancer. [ 22 ]  Not only are these abnormalities in the 3q26 region associated with very poor patient prognosis they are also commonly accompanied by additional karyotypic changes such as chromosome 7 monosomy, deletion of the short arm of chromosome 7, or partial deletions of chromosome 5. [ 23 ]  In addition, it has been shown that development of  acute myelogenous leukemia  is likely due to several sequential genetic changes, and that expression of EVI1 or its chimeric counterparts ME and AME alone is not enough to completely block myeloid differentiation. [ 24 ]   BCR-Abl , a fusion gene caused by t(9;22)(q34;q11)is thought to have a cooperative effect with EVI1 during the progression of AML and CML. [ 24 ]  Together, these two systems disrupt tyrosine kinase signaling and hematopoietic gene transcription.


Despite the extensively studied chromosomal abnormalities at the EVI1 locus, in anywhere from 10-50% of identified cases, EVI1 overexpression is detectable without any chromosomal abnormalities, indicating that there are other not-yet-understood systems, likely epigenetic, leading to EVI1 promoter activation. [ 6 ]  In many of these cases, it is noted that a variety of 5' transcript variants are detectable at relatively high levels. Clinical studies have shown that these variants (EVI1_1a, EVI1_1b, EVI1_1d, EVI1_3L) as well as the MDS1-EVI1 fusion transcript are all associated with poor prognosis and increased likelihood of rapid remission in cases of  de novo  AML. [ 25 ]


Very little research has been done in an attempt to therapeutically target EVI1 or any of its chimeric counterparts. However, since it has become an established fact that overexpression of EVI1 derivatives is a bad prognostic indicator, it is likely that the literature will begin to examine specific targeting within the next few years.


One very promising therapeutic agent for myelogenous leukemia and potentially other forms of cancer is  arsenic trioxide  (ATO). One study has been done showing that ATO treatment leads to specific degradation of the AML1/MDS1/EVI1 oncoprotein and induces both apoptosis and differentiation. [ 11 ]  As an atypical use of traditional pharmacogenomics, this knowledge may lead to an increased ability to treat EVI1 positive leukemias that would normally have poor prognoses. If it is established that a clinical cancer case is EVI1 positive, altering the chemotherapeutic cocktail to include a specific EVI1 antagonist may aid to increase lifespan and prevent potential relapse. Arsenic is a fairly ancient human therapeutic agent, [ 11 ]  however it has only recently returned to the forefront of cancer treatment. It has been observed that it not only induces apoptosis but can also inhibit the cell cycle, and has marked anti-angiogenesis effects. [ 26 ]  As of 2006, Phase I and II clinical trials were being conducted to test this compound on a wide variety of cancer types, and currently (2008) a number of publications are showing positive outcomes in individual case studies, both pediatric and adult. [ citation needed ]


The important and essential role of EVI1 in embryogenesis clearly indicates a close association with hormonal fluctuations in developing cells. However, to date, the presence of EVI1 in cancer has not been linked to aberrant production of any hormones or hormone receptors. It is likely that EVI1 is far enough downstream of hormonal signaling that once overproduced, it can function independently.


Areas where retroviral integration into the human genome is favored such as EVI1 have very important implications for the development of  gene therapy . It was initially thought that delivery of genetic material through a non-replicating virus vector would pose no significant risk, as the likelihood of a random incorporation near a proto-oncogene was minimal. By 2008 it was realised that sites such as EVI1 are "highly over-represented" when it comes to vector insertions. [ 5 ]


EVI1 has been shown to  interact  with:


NM_001310338 NM_001310339 NM_052865 NM_001363738


NM_001289630 NM_001289631 NM_028984 NM_001355688


NP_001297267 NP_001297268 NP_443097 NP_001350667


NP_001276559 NP_001276560 NP_083260 NP_001342617


Mitochondrial genome maintenance exonuclease 1 , abbreviated as  MGME1 , is an  enzyme  that in humans is encoded by the  MGME1  gene. [ 5 ] [ 6 ]  MGME1 is a 344  amino acids  long  protein  belonging to the PD-(D/E)XK family of nucleases. [ 5 ] [ 6 ]  It localizes to  mitochondria  where it is important for maintenance of the mitochondrial genome. Loss of function mutations in MGME1 lead to defects in mitochondrial DNA, including mitochondrial DNA depletion, duplications, deletions and increased replication intermediates. [ 6 ] [ 5 ] [ 7 ]  Also, there is an accumulation of 7S DNA, a short single stranded linear DNA strand. MGME1 deficiency in humans leads to multisystemic  mitochondrial disease . [ 5 ]


The activity of MGME1 has been studied using the purified protein in cell-free  in vitro  assays. Together these studies suggest that MGME1 functions to remove single stranded nucleotide flaps that arise during  mitochondrial DNA  replication and/or  DNA repair . MGME1 has a strong preference for cutting single stranded DNA, with weak activity on duplex DNA, and no activity on  RNA . [ 5 ] [ 6 ]  It acts as an endo-/exonuclease, requiring a free 5´or 3´ end for cleavage. [ 5 ] [ 6 ]  MGME1 can cut 5´ flap substrates that mimic primer/repair intermediates. [ 5 ] [ 8 ]  Moreover, MGME1 removes single stranded 5´-flaps in reconstituted mitochondrial DNA replication assays where it is required to enable  ligation  of the newly synthesized strand. [ 8 ]


MHC class I molecules  are one of two primary classes of  major histocompatibility complex  (MHC) molecules (the other being  MHC class II ) and are found on the  cell surface  of all  nucleated  cells in the bodies of  vertebrates . [ 1 ] [ 2 ]  They also occur on  platelets , but not on  red blood cells . Their function is to display peptide fragments of proteins from within the cell to  cytotoxic T cells ; this will trigger an immediate response from the immune system against a particular non-self antigen displayed with the help of an MHC class I protein. Because MHC class I molecules present  peptides  derived from  cytosolic  proteins, the pathway of MHC class I presentation is often called  cytosolic  or  endogenous pathway . [ 3 ]


In humans, the  HLAs  corresponding to MHC class I are  HLA-A ,  HLA-B , and  HLA-C .


Class I MHC molecules bind  peptides  generated mainly from the degradation of cytosolic proteins by the  proteasome . The MHC I: peptide complex is then inserted via the endoplasmic reticulum into the external plasma membrane of the cell. The epitope peptide is bound on extracellular parts of the class I MHC molecule. Thus, the function of the class I MHC is to display intracellular proteins to  cytotoxic T cells  (CTLs). However, class I MHC can also present peptides generated from exogenous proteins, in a process known as  cross-presentation .


A normal cell will display peptides from normal cellular protein turnover on its class I MHC, and CTLs will not be activated in response to them due to central and peripheral tolerance mechanisms. When a cell expresses foreign proteins, such as after viral infection, a fraction of the class I MHC will display these peptides on the cell surface. Consequently, CTLs specific for the MHC:peptide complex will recognize and kill presenting cells.


Alternatively, class I MHC itself can serve as an inhibitory ligand for  natural killer cells  (NKs). Reduction in the normal levels of surface class I MHC, a mechanism employed by some viruses [ 4 ]  and certain tumors to evade CTL responses, activates NK cell killing.


Paired-immunoglobulin-like receptor B (PirB), an MHCI-binding receptor, is involved in the regulation of visual  plasticity . [ 5 ]  PirB is expressed in the  central nervous system  and diminishes  ocular dominance   plasticity  in the developmental  critical period  and adulthood. [ 5 ]   When the function of PirB was abolished in mutant mice,  ocular dominance   plasticity  became more pronounced at all ages. [ 5 ]  PirB loss of function mutant mice also exhibited enhanced  plasticity  after monocular deprivation during the  critical period . [ 5 ]  These results suggest that PirB may be involved in the modulation of  synaptic plasticity  in the  visual cortex .


MHC class I molecules are heterodimers that consist of two polypeptide chains, α and  β 2 -microglobulin  (B2M). The two chains are linked noncovalently via interaction of B2M and the α 3  domain. Only the α chain is polymorphic and encoded by a  HLA gene , while the B2M subunit is not polymorphic and encoded by the  Beta-2 microglobulin  gene. The α 3  domain is plasma membrane-spanning and interacts with the  CD8  co-receptor of  T-cells . The α 3 -CD8 interaction holds the MHC I molecule in place while the  T cell receptor  (TCR) on the surface of the cytotoxic T cell binds its α 1 -α 2  heterodimer ligand, and checks the coupled peptide for antigenicity. The α 1  and α 2  domains fold to make up a groove for peptides to bind. MHC class I molecules bind peptides that are predominantly 8-10 amino acid in length (Parham 87), but the binding of longer peptides have also been reported. [ 6 ]


While a high-affinity peptide and the B2M subunit are normally required to maintain a stable  ternary complex  between the peptide, MHC I, and B2M, under subphysiological temperatures, stable, peptide-deficient MHC I/B2M  heterodimers  have been observed. [ 7 ] [ 8 ]  Synthetic stable, peptide-receptive MHC I molecules have been generated using a  disulfide bond  between the MHC I and B2M, named "open MHC-I". [ 9 ]


The peptides are generated mainly in the  cytosol  by the  proteasome . The proteasome is a macromolecule that consists of 28 subunits, of which half affect  proteolytic  activity. The proteasome degrades intracellular proteins into small peptides that are then released into the cytosol. Proteasomes can also ligate distinct peptide fragments (termed spliced peptides), producing sequences that are noncontiguous and therefore not linearly templated in the genome. The origin of spliced peptide segments can be from the same protein (cis-splicing) or different proteins (trans-splicing). [ 10 ] [ 11 ]  The peptides have to be translocated from the cytosol into the  endoplasmic reticulum  (ER) to meet the MHC class I molecule, whose peptide-binding site is in the  lumen  of the ER. They have membrane proximal  Ig fold


The peptide translocation from the cytosol into the lumen of the ER is accomplished by the  transporter associated with antigen processing  (TAP). TAP is a member of the  ABC transporter  family and is a heterodimeric multimembrane-spanning polypeptide consisting of  TAP1  and  TAP2 . The two subunits form a peptide binding site and two ATP binding sites that face the cytosol. TAP binds peptides on the cytoplasmic side and translocates them under  ATP  consumption into the lumen of the ER. The MHC class I molecule is then, in turn, loaded with peptides in the lumen of the ER.


The peptide-loading process involves several other molecules that form a large multimeric complex called the  Peptide loading complex [ 12 ]  consisting of TAP,  tapasin ,  calreticulin ,  calnexin , and  Erp57  ( PDIA3 ). Calnexin acts to stabilize the class I MHC α chains prior to β2m binding. Following complete assembly of the MHC molecule, calnexin dissociates. The MHC molecule lacking a bound peptide is inherently unstable and requires the binding of the chaperones calreticulin and Erp57. Additionally, tapasin binds to the MHC molecule and serves to link it to the TAP proteins and facilitates the selection of peptide in an iterative process called peptide editing, [ 13 ] [ 14 ] [ 15 ]  thus facilitating enhanced peptide loading and colocalization.


Once the peptide is loaded onto the MHC class I molecule, the complex dissociates and it leaves the ER through the  secretory pathway  to reach the cell surface. The transport of the MHC class I molecules through the secretory pathway involves several  posttranslational modifications  of the MHC molecule. Some of the posttranslational modifications occur in the ER and involve change to the  N-glycan  regions of the protein, followed by extensive changes to the N-glycans in the  Golgi apparatus . The N-glycans mature fully before they reach the cell surface.


Peptides that fail to bind MHC class I molecules in the lumen of the endoplasmic reticulum (ER) are removed from the ER via the  sec61  channel into the cytosol, [ 16 ] [ 17 ]  where they might undergo further trimming in size, and might be translocated by TAP back into ER for binding to a MHC class I molecule.


For example, an interaction of sec61 with bovine  albumin  has been observed. [ 18 ]


MHC class I molecules are loaded with peptides generated from the degradation of  ubiquitinated  cytosolic proteins in  proteasomes . As viruses induce cellular expression of viral proteins, some of these products are tagged for degradation, with the resulting peptide fragments entering the endoplasmic reticulum and binding to MHC I molecules. It is in this way, the MHC class I-dependent pathway of antigen presentation, that the virus infected cells signal T-cells that abnormal proteins are being produced as a result of infection.


The fate of the virus-infected cell is almost always induction of  apoptosis  through  cell-mediated immunity , reducing the risk of infecting neighboring cells. As an evolutionary response to this method of immune surveillance, many viruses are able to down-regulate or otherwise prevent the presentation of MHC class I molecules on the cell surface. In contrast to cytotoxic T lymphocytes,  natural killer  (NK) cells are normally inactivated upon recognizing MHC I molecules on the surface of cells. Therefore, in the absence of MHC I molecules, NK cells are activated and recognize the cell as aberrant, suggesting that it may be infected by viruses attempting to evade immune destruction. Several human cancers also show down-regulation of MHC I, giving transformed cells the same survival advantage of being able to avoid normal immune surveillance designed to destroy any infected or transformed cells. [ 19 ]


The MHC class I genes originated in the most  recent common ancestor  of all  jawed vertebrates , and have been found in all living jawed vertebrates that have been studied thus far. [ 2 ]  Since their emergence in jawed vertebrates, this gene family has been subjected to many divergent evolutionary paths as  speciation  events have taken place. There are, however, documented cases of trans-species  polymorphisms  in MHC class I genes, where a particular  allele  in an evolutionary related MHC class I gene remains in two species, likely due to strong pathogen-mediated  balancing selection  by  pathogens  that can infect both species. [ 20 ]   Birth-and-death  evolution is one of the mechanistic explanations for the size of the MHC class I gene family.


Birth-and-death evolution asserts that  gene duplication  events cause the genome to contain multiple copies of a gene which can then undergo separate evolutionary processes. Sometimes these processes result in  pseudogenization  (death) of one copy of the gene, though sometimes this process results in two new genes with divergent function. [ 21 ]  It is likely that human MHC class Ib loci (HLA-E, -F, and -G) as well as MHC class I pseudogenes arose from MHC class Ia loci (HLA-A, -B, and -C) in this birth-and-death process. [ 22 ]


MHC Class II molecules  are a class of  major histocompatibility complex  (MHC) molecules normally found only on  professional antigen-presenting cells  such as  dendritic cells ,  macrophages , some  endothelial cells ,  thymic epithelial cells , and  B cells . These cells are important in initiating  immune responses .


Antigens  presented by MHC class II molecules are exogenous, originating from extracellular proteins rather than cytosolic and endogenous sources like those presented by  MHC class I .


The loading of a MHC class II molecule occurs by  phagocytosis . Extracellular proteins are  endocytosed  into a  phagosome , which subsequently fuses with a  lysosome  to create a  phagolysosome . Within the phagolysosome, lysosomal enzymes degrade the proteins into  peptide fragments . These fragments are then loaded into the peptide-binding groove of the MHC class II molecule. Once loaded, the MHC class II-peptide complexes are transported to the  plasma membrane  via  vesicular transport , where they present the  antigens  to the extracellular environment. [ 1 ]


In humans, the MHC class II protein complex is encoded by the  human leukocyte antigen gene complex (HLA) . HLAs corresponding to MHC class II are  HLA-DP ,  HLA-DM ,  HLA-DOA ,  HLA-DOB ,  HLA-DQ , and  HLA-DR .


Mutations in the HLA gene complex can lead to  bare lymphocyte syndrome  (BLS), which is a type of MHC class II deficiency.


Like  MHC class I  molecules, class II molecules are also  heterodimers , but in this case consist of two homogenous peptides, an α and β chain, both of which are encoded in the MHC. [ 2 ]  The subdesignation α1, α2, etc. refers to separate domains within the  HLA  gene; each domain is usually encoded by a different exon within the gene, and some genes have further domains that encode leader sequences, transmembrane sequences, etc. These molecules have both extracellular regions as well as a transmembrane sequence and a cytoplasmic tail. The α1 and β1 regions of the chains come together to make a membrane-distal peptide-binding domain, while the α2 and β2 regions, the remaining extracellular parts of the chains, form a membrane-proximal immunoglobulin-like domain. The antigen binding groove, where the antigen or peptide binds, is made up of two α-helixes walls and β-sheet. [ 3 ]


Because the antigen-binding groove of MHC class II molecules is open at both ends while the corresponding groove on class I molecules is closed at each end, the antigens presented by MHC class II molecules are longer, generally between 15 and 24  amino acid  residues long.


These molecules are constitutively expressed in professional, immune  antigen-presenting cells , but may also be induced on other cells by  interferon γ . [ 4 ]  They are expressed on the epithelial cells in the thymus and on APCs in the periphery. MHC class II expression is closely regulated in APCs by  CIITA , which is the MHC class II transactivator. CIITA is solely expressed on professional APCs; however, non-professional APCs can also regulate CIITA activity and MHC II expression. As mentioned interferon γ  (IFN γ) triggers the expression of CIITA and is also responsible for converting  monocytes  which are MHC class II negative cells into functional APCs that express MHC class II on their surfaces. [ 5 ]


MHC class II is also expressed on group 3  innate lymphoid cells .


Having MHC class II molecules present proper peptides that are bound stably is essential for overall immune function. [ 6 ]   Because class II MHC is loaded with extracellular proteins, it is mainly concerned with presentation of extracellular pathogens (for example, bacteria that might be infecting a wound or the blood).  Class II molecules interact mainly with immune cells, like the  T helper cell  ( CD4 + ). The peptide presented regulates how T cells respond to an infection. [ 6 ]  Stable peptide binding is essential to prevent detachment and degradation of a peptide, which could occur without secure attachment to the MHC molecule. [ 6 ]  This would prevent T cell recognition of the antigen, T cell recruitment, and a proper immune response. [ 6 ]  The triggered appropriate immune response may include localized  inflammation  and swelling due to recruitment of phagocytes or may lead to a full-force antibody immune response due to activation of  B cells .


During synthesis of class II MHC in the endoplasmic reticulum, the α and β chains are produced and complexed with a special polypeptide known as the  invariant chain . [ 7 ]  The nascent MHC class II protein in the rough ER has its peptide-binding cleft blocked by the invariant chain (Ii; a trimer) to prevent it from binding cellular peptides or peptides from the endogenous pathway (such as those that would be loaded onto class I MHC).


The invariant chain also facilitates the export of class II MHC from the ER to the  Golgi apparatus , followed by fusion with a late endosome containing endocytosed, degraded proteins. The invariant chain is then broken down in stages by proteases called  cathepsins , leaving only a small fragment known as  CLIP  which maintains blockage of the peptide binding cleft on the MHC molecule. A MHC class II-like structure,  HLA-DM , facilitates  CLIP  removal and allows the binding of peptides with higher affinities. The stable class II MHC is then presented on the cell surface.


After MHC class II complexes are synthesized and presented on APCs they are unable to be expressed on the cell surface indefinitely, due to the internalization of the  plasma membrane  by the APCs(antigen presenting cells). In some cells, antigens bind to recycled MHC class II molecules while they are in the early  endosomes , while other cells such as dendritic cells internalize antigens via receptor-mediated endocytosis and create MHC class II molecules plus peptide in the endosomal-lysosomal antigen processing compartment which is independent of the synthesis of new MHC class II complexes. These suggest that after the antigen is internalized, already existent MHC class II complexes on mature  dendritic cells  can be recycled and developed into new MHC class II molecules plus peptide. [ 5 ]


Unlike MHC I, MHC II is meant to present extracellular pathogens rather than intracellular. Furthermore, the first step is to acquire the pathogen through phagocytosis. The pathogen is then broken down in a lysosome and a desired component is then acquired and loaded onto a MHC II molecule. The MHC II molecule then travels to the surface to present the antigen to a  helper T cell . MHC II activates helper T cells which help release cytokines and other things which will help induce other cells which help to combat the pathogens outside the cells.


Several molecules are involved in this pathway. [ 8 ]


PIK3R2 and PIP5K1A are two  kinases  that phosphorylate  Phosphatidylinositol  (PIP) providing PSD4 with substrates for its GTP loading ability. PSD4 as a  guanine exchange factor , loads ARL14/ARF7 with GTP. Subsequently, ARF7EP interacts with  MYO1E  which binds itself to  actin  myofibers. Altogether, this complex contributes to maintain  MHC-II  loaded vesicles within the immature  dendritic cell , impeding its translocation to the cell membrane.


One type of MHC class II deficiency, also called  bare lymphocyte syndrome , is due to mutations in the genes that code for transcription factors that regulate the expression of the MHC class II genes. [ 16 ]  It results in the depletion of  CD4  T cells and some immunoglobulin isotypes even though there are normal levels of both  CD8  Cells and  B cells  present. Deficient MHC class II molecules are unable to present antigens to T cells and properly activate T cells. T cells are then unable to proliferate, and secrete  cytokines  which normally participate in the immune response. Not only do the deficient MHC class II molecules affect the activation and proliferation of T cells but also the rest of the immune response cascade which includes B cells. Therefore, with this decrease in the number of T cells, the T cells cannot interact and activate the B cells. Normally when B cells are activated they divide, proliferate and differentiate, which includes the differentiation of these cells into plasma cells which are responsible for producing antibodies. [ 17 ]  However, when there is a deficiency in MHC class II molecules B cells are not activated and cannot differentiate into  plasma cells  which causes them to be deficient in  antibodies  which are unable to perform as they are expected. The only current form of treatment is a bone-marrow transplant however even this does not cure the disease and most patients do not live past age ten. [ 18 ]


MHC class II genes and molecules are related to a multitude of different diseases, one of which being  Type I diabetes . HLA class II genes are the most important genes associated with the risk of inheriting Type I diabetes, accounting for about 40-50% of  heritability .  Alleles  of these genes that affect peptide binding to the MHC class II molecules seem to impact Type I diabetes risk the most.  Specific allele  polymorphisms  have been identified to increase the risk (such as DRB1 and DQB1).  Others have been associated with a resistance to the disease. [ 19 ]


Migration inducting gene 7  ( Mig-7  or  Mig7 ) is a  gene  that corresponds to a  cysteine -rich protein localized to the  cell membrane  and  cytoplasm . [ 2 ]  It is the first-in-class of novel proteins translated from what are thought to be long  Non-coding RNAs . [ 3 ]


Induction of Mig-7  expression  occurs downstream of  Epidermal growth factor / Epidermal growth factor receptor ,  Cox-2 /PGE-2 or  Hepatocyte growth factor / c-Met  activation and signalling. [ 4 ] [ 5 ] [ 6 ]  Data has shown that Mig-7 expression is specific to human embryonic/fetal  cytotrophoblast  cells [ 5 ] [ 7 ]  and epithelial type cancer cells, while not expressed in normal cells. [ 4 ] [ 5 ] [ 6 ] [ 7 ] [ 8 ] [ 9 ] [ 10 ]  Data demonstrate that targeting of Mig-7 simultaneously inhibits more than one cancer-progressing pathway while likely sparing normal cells. [ 4 ] [ 5 ] [ 6 ] [ 7 ] [ 10 ] [ 11 ]


Mig-7 expression is found on, as well as in, epithelial  tumor cells  at the primary site, secondary (metastatic) sites, and blood from cancer patients. It is not produced by cells of normal human tissues or by cells from patients with inflammation but is expressed by epithelial precancerous and  malignant cells . [ 4 ] [ 5 ] [ 6 ] [ 10 ]   It is also expressed in fetal/embryonic cytotrophoblast cells of early  placenta . [ 5 ] [ 7 ]


Mig-7 expression increases in malignant cancers. There is a high sensitivity and specificity of Mig-7 detection in breast (98% n=48 of 49), uterine (100% n=49), gastric (94.5% n=104 of 110) and lung (100% n=89) cancers. [ 4 ] [ 6 ] [ 9 ] [ 10 ]


Mig-7 is thought to promote  carcinoma  cell invasion, metastasis and tumor growth through  vasculogenic mimicry , [ 11 ]  a process where tumor cells form channels for fluids to flow through. [ 12 ]  It also promotes  epithelial–mesenchymal transition  (EMT), a key developmental program that is often activated during, and required for, cancer invasion/metastasis. Mig-7 induces EMT through  hyperactivation  of  Akt  and extracellular regulated Kinase  ERK1/2  by inhibiting the tumor suppressor  protein phosphate 2A . [ 4 ] [ 6 ] [ 13 ]


Mig-7 has been associated with signaling pathways downstream of epithelial type cancer-promoting kinases.  It is expressed prior to  TWIST , [ 14 ]  the previously named “master regulator” of EMT. [ 15 ]  It has also been shown to promote tumor  neovascularization . [ 5 ] [ 8 ] [ 9 ] [ 11 ]


Cancer cell metabolism (also known as oxidative glycolysis or the  Warburg effect ) is a proposed cancer target and is likely regulated by Mig-7 through its hyperactivation of Akt. [ 6 ]


Targeting of Mig-7 with Mig-7-specific peptides significantly stimulates  breast cancer  patients’ immune cells’ killing of breast carcinoma cells  ex vivo . [ 6 ]  Targeting with  antibody  generated to the peptide representing the first nine amino acids of Mig-7 detects cells expressing this protein and significantly inhibits carcinoma cell invasion in vitro. Targeting with short  hairpin RNA , specific to decrease Mig-7 protein levels, inhibits carcinoma cell invasion and metastasis as well as returns ERK1/2, Akt, GSK, and S6 kinase to normal  phosphorylation  states through reactivation of PP2A. [ 4 ] [ 5 ] [ 6 ]


ENSG00000186594 ENSG00000282800


NM_001001870 NM_032895


MIR22HG  (MIR22 host gene), also known as   C17orf91 , [ 3 ]   MGC14376 , [ 4 ]   MIRN22, hsa-mir-22,  and  miR-22 [ 5 ]  is a human  gene  that  encodes  a  noncoding RNA  (ncRNA).This  RNA  molecule is not translated into a protein but nonetheless may have important functions.


MIR22HG ncRNA is greater than 200  nucleotides  in length and therefore informally classified as a  long non-coding RNA , i.e. lncRNA. The  MIR22HG  gene is located at  band  13.3 on the  short (or "p") arm  of  chromosome 17 . It is expressed in each of the 27 human tissues tested. [ 3 ]


Many lncRNAs regulate diverse processes including cellular metabolism, proliferation, movement,  differentiation  (i.e. change of a cell from one type to another, usually more mature, cell type),  apoptosis  (i.e. programmed cell death), and  the expression of various genes  through  chromatin remodeling ,  genomic imprinting , modulating the actions of other RNAs, and various other ways. [ 6 ]  The normal actions and functions of the  MIR22HG  gene are complex and have not been fully elucidated, but its primary function may be as a  tumor suppressor gene . [ 7 ]  It is involved in the regulation of several signaling pathways including  Wnt/β-catenin ,  epithelial-mesenchymal transition  (EMT),  notch , and  STAT3 . [ 7 ]


When overexpressed, it acts as a  tumor suppressor gene  in many cancer types but in a few cancer types it acts as an  oncogene , i.e. a tumor promotor gene:  MIR22HG  gene's impact on various cancers is strictly dependent on the type of cancer in which it operates. [ 8 ]


The roles or the  MIR22HG  gene in cancers have generally been evaluated by:  a)   next-generation sequencing  to quantify the levels of MIR22HG RNA in cancer samples, samples of nearby normal tissue of the same type as the cancer, and  cultured cancer cells  of the same type as the cancers;  b)  comparing MIR22HG lncRNA levels in patients with the same cancer to the severity (e.g. aggressiveness, recurrence rate, and survival rate) of their cancers;  c)  determining the potential mechanisms for the MIR22HG lncRNA's actions, generally by defining the effects of varying the levels of this lncRNA on various cancer-promoting or cancer-inhibiting  cell signaling pathways  in cultured cancer cells; and  d)  determining the activity of these cell signaling pathways in cancer tissues. These studies are important because they established the levels of MIR22HG lncRNA as  prognosis indicators  and suggest that this lncRNA and the implicated cancerous signaling pathways are therapeutic targets for treating these cancers. [ 7 ]


Some of the cancer types that have been associated with the  MIR22HG  gene and its lncRNA product acting to suppress the cancer are:


Some reports have suggested that the  MIR22HG  gene acts as a tumor suppressor based on examining the effects of MIR22HG lncRNA levels on cultured cancer cell function and/or and tumor spread in animal models and/or the levels of MIR22HR lncRNA in cancer versus normal nearby tissues. However, these reports did not determine the relationship of MIR22HG levels in patients' cancer tissues to their prognoses. These reports include those on:  osteosarcoma , [ 24 ]   cancer of the uterus endometrium , [ 25 ]  and  cancer of the larynx . [ 26 ]


The  MIR22HG  gene acted as a tumor promotor in  squamous cell carcinoma of the esophagus  based on studies showing that suppressing its levels in various types of cultured esophagus squamous-cell carcinoma cells inhibited their proliferation, invasiveness, and ability to form  colonies  and also increased their  apoptosis . The cell culture studies suggested that decreasing MIR22HG lncRNA levels produced these results by decreasing the expression of  STAT3 ,  c-Myc , and  PTK2 . [ 7 ] [ 28 ]


MicroRNA 95  is a small  non-coding RNA  that in humans is encoded by the MIR95  gene .
 [ 1 ] [ 2 ]


microRNAs  (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in  post-transcriptional regulation  of  gene expression  in  multicellular organisms  by affecting both the stability and  translation  of  mRNAs . miRNAs are transcribed by  RNA polymerase II  as part of capped and  polyadenylated   primary transcripts  (pri-miRNAs) that can be either  protein -coding or non-coding. The primary transcript is cleaved by the  Drosha   ribonuclease III  enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic  Dicer  ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a  RNA-induced silencing complex  (RISC), which recognizes target mRNAs through imperfect  base pairing  with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009].


MicroRNA 194-1  is a  non-coding RNA  that in humans is encoded by the MIR194-1  gene . [ 3 ]


microRNAs  (miRNAs) are short (20–24 nt) non-coding RNAs that are involved in post-transcriptional regulation of  gene expression  in multicellular organisms by affecting both the stability and translation of  mRNAs . miRNAs are transcribed by  RNA polymerase II  as part of capped and polyadenylated  primary transcripts  (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the  Drosha  ribonuclease III enzyme to produce an approximately 70-nt  stem-loop  precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic  Dicer  ribonuclease to generate the mature miRNA and  antisense  miRNA star (miRNA*) products. The mature miRNA is incorporated into a  RNA-induced silencing complex  (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [ 3 ]


MicroRNA 3648  is a  microRNA  that in humans is produced by  MIR3648   gene . This gene was recently shown to be specific to humans by  Nathan H. Lents  and colleagues. [ 3 ]
 [ 4 ]


microRNAs  (miRNAs) are short (20-24 nt)  non-coding RNAs  that are involved in  post-transcriptional regulation  of gene expression in  multicellular organisms  by affecting both the stability and  translation  of  mRNAs . miRNAs are transcribed by  RNA polymerase II  as part of  capped  and  polyadenylated   primary transcripts  (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the  Drosha  ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic  Dicer ribonuclease  to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a  RNA-induced silencing complex  (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009].


MORT  (Mortal Obligate RNA Transcript (also known as  ZNF667-AS1 )) is a  long non-coding RNA  (lncRNA) of the intergenic type ( lincRNA ) that is specific to  humans  and  great apes . [ 3 ]  The  MORT  transcript is produced in all mortal cell types, but is lost in a large fraction of the most common human cancers and therefore might have a  tumor suppressive  function.


The  MORT  gene is located on  human chromosome 19 , at position 56,989,000–57,007,000 ( hg19 ) within a cluster of zinc finger genes (ZNF genes). The  MORT  gene consists of 2  exons , 260 and 1270 bp, respectively, that are separated by a 16 kbp  intron . A large portion of the second  MORT  exon is formed by repetitive elements – two LINEs and an LTR element. [ 3 ]
The  MORT   promoter  is located in a  CpG island  that is shared with the  ZNF667  gene; the two genes reside in a head to head orientation with one another.  Despite the  MORT  gene's location inside a cluster of ZNF genes, the  MORT  gene is not homologous to any ZNF genes.  While the  MORT  gene is in a head to head orientation with  ZNF667 ,  MORT  does not overlap the  ZNF667  gene, nor does it share any antisense homology to  ZNF667 , so the officially used symbol  ZNF667-AS1  is somewhat misleading.


MORT  has orthologs only in  great apes  –  chimpanzees ,  gorillas  and  orangutans , and the RNA expression data indicates that the  MORT  transcript is expressed in these species. [ 3 ]  Thus, from a phylogenetic point view,  MORT  is likely a young lincRNA gene that emerged during evolution of great  apes . It is possible that the long life span of the great apes required evolution of additional genes with tumor suppressive activity, and that  MORT  is such an example.


MORT  is expressed in all 16 normal human tissues reported in the  Illumina  body map data, [ 4 ]  as well as all  in vitro  cultured, finite lifespan, human cell strains that have been analyzed.  In contrast,  MORT  gene expression is lost in a large percentage of human cancers and human cancer cell lines.  Using data from human cancers curated in  TCGA ,  MORT  RNA expression and  DNA methylation  state were evaluated in the 10 most common male cancers and the 10 most common female cancers [ 5 ]  (totalling 17 different cancer types based on TCGA classification). Analysis shows that the  MORT  gene expression is silenced by DNA hypermethylation of its CpG island promoter in a majority of human tumor samples in 15 of these 17 human cancers. [ 3 ]


The 15 tumor types where  MORT  is frequently silenced are  acute myeloid leukemia ,  bladder urothelial carcinoma ,  breast invasive carcinoma ,  colon adenocarcinoma ,  head and neck squamous-cell carcinoma ,  kidney renal clear cell carcinoma ,  kidney renal papillary cell carcinoma ,  liver hepatocellular carcinoma ,  lung adenocarcinoma ,  lung squamous cell carcinoma ,  lymphoid neoplasm diffuse large B-cell lymphoma ,  pancreatic adenocarcinoma ,  rectum adenocarcinoma ,  skin cutaneous melanoma , and  Uterine Corpus Endometrial Carcinoma . [ 3 ]  MORT is silenced in cervical cancer and therefore may serve as an independent  prognostic factor  with low MORT expression be associated with a decreased overall survival. [ 6 ]


Since cell immortality is an obligate feature of the cancer cell and  MORT  was discovered as a target of epigenetic silencing at the boundary where finite lifespan human cells transition from mortal to immortal,  MORT’s  epigenetic inactivation may create a cellular state permissive to cell immortalization and suggests a possible tumor suppressive mechanism of  MORT ’s action.  If this prediction is true, then epigenetic silencing of  MORT  should be an early identifiable lesion during human carcinogenesis and predicted to occur in premalignant lesions where cells have acquired pathologic immortality on their route to malignant transformation.  Indeed, recent work has shown that  MORT  is epigenetically silenced in both  DCIS , a premalignant lesion of invasive breast cancer, and colonic adenomas, a premalignant lesion of colon adenocarcinoma. [ 7 ]   Furthermore epigenetic silencing of  MORT  is associated with luminal, hormone receptor positive breast cancer, overexpression of the oncogene  CCND1 , and  GATA3  mutations, but is negatively correlated with  p53  mutations. [ 7 ]  In summary, aberrant DNA hypermethylation-mediated epigenetic silencing of  MORT  occurs early during human  carcinogenesis  apparently coincident with when a mortal cell pathologically transitions to an immortal cell.


The precise molecular function of  MORT  remains enigmatic; however, it is known that  MORT  is found preferentially in the cell cytoplasm with differential density centrifugation showing that  MORT  is enriched in the 100,000 g fraction, which contains polysomes, microsomes, endoplasmic reticulum, and the plasma membrane. [ 8 ]   Evidence is mounting that  MORT  acts as a regulator of protein translation through interactions with RNA binding proteins.


NM_001256267 NM_001256268 NM_032578


NP_001243196 NP_001243197 NP_115967


Myopalladin  is a  protein  that in humans is encoded by the  MYPN   gene . Myopalladin is a muscle protein responsible for tethering proteins at the  Z-disc  and for communicating between the  sarcomere  and the  nucleus  in  cardiac  and  skeletal muscle [ 5 ] [ 6 ] [ 7 ]


Myopalladin is a 145.2 kDa protein composed of 1320 amino acids. [ 8 ] [ 9 ]  Myopalladin has five  Ig -like repeats within the protein, and a  proline -rich domain. Myopalladin binds the Src homology domain of  nebulette  and  nebulin  and tethers it to  alpha-actinin  via its  C-terminal  domain binding to the  EF hand  domains of  alpha-actinin . The  N-terminal  region of myopalladin binds to the nuclear protein  CARP , known to regulate  gene expression  in muscle. [ 5 ]  It also has been shown to bind  ANKRD23 . [ 10 ]


Myopalladin has dual subcellular localization, residing in both the  nucleus  and  sarcomere / I-bands  in muscle. Accordingly, myopalladin has functions in both sarcomere assembly and in control of gene expression. [ 5 ]  Specifics of these functions were gleaned from studies involving  MYPN  mutants associated with various  cardiomyopathies . The Q529X myopalladin mutant demonstrated incompetence in recruiting key binding partners such as  desmin ,  alpha-actinin  and  CARP  to the  Z-disc  during myofibrilogenesis. In contrast, the Y20C mutant resulted in decreased expression of binding partners. [ 11 ]


Mutations in  MYPN  have been linked to  nemaline myopathy ,  dilated cardiomyopathy ,  hypertrophic cardiomyopathy  and  restrictive cardiomyopathy . [ 11 ] [ 12 ]
 [ 13 ]


N-Acetylated Alpha-Linked Acidic Dipeptidase Like 2  (NAALADL2) is a protein, encoded by the gene  NAALADL2  in humans.  NAALADL2  shares 25%–26% sequence identity and 45% sequence similarity with the  glutamate carboxypeptidase II  family which includes prostate cancer marker PSMA ( FOLH1 / NAALAD1 ). [ 2 ]  The NAALADL2 gene is a giant gene spanning 1.37 Mb which is approximately 49 times larger than the average gene size of 28 kb. [ 2 ] [ 3 ]  Gene length is correlated with the number of transcript variants of a gene, as such,  NAALADL2  undergoes extensive alternative splicing and has 12 splice variants as defined by Ensembl. [ 4 ] [ 5 ]


The current function of NAALADL2 is unknown.  NAALADL2  shows significant homology to N-acetylated alpha-linked acidic dipeptidase and  transferrin receptors . While sharing some homology with the M28B metallopeptidase family,  NAALADL2  does not possess favoured amino acids at certain key positions that are highly conserved, and important for metallopeptidase function, which may imply it is catalytically inactive. [ 2 ]


NAALADL2  has been shown to be severed by a  Cornelia De Lange -associated  translocation   breakpoint  at  3q26.3 . [ 2 ]


The rs17531088  SNP  in  NAALADL2  was shown to be associated with Kawasaki disease in a large  GWAS  comprising two independent cohorts totalling 893 KD cases plus population and family controls. [ 6 ]


NAALADL2 has been shown to have a role in  prostate cancer . [ 7 ]  NAALADL2 protein expression is associated with prostate tumour stage and  grade  with mRNA expression predicting poor survival following radical prostatectomy in a small cohort. [ 7 ]  Overexpression of NAALADL2 in  cell lines  subsequently altered binding to extracellular matrix (ECM) components and enhanced the invasive capacity of prostate cancer  cells . [ 7 ]   When NAALADL2 expression was artificially increased in cell lines, genes involved in the  cell cycle ,  cell adhesion ,  epithelial to mesenchymal transition  and  cytoskeletal  remodelling were altered. [ 7 ]  These results suggest NAALADL2 may act to drive aggressive prostate cancer. [ 7 ]


A  genome-wide association study (GWAS)  of 12,518 prostate cancer cases found a SNP; rs78943174, within the 3q26.31 ( NAALADL2 ) locus associated with high  Gleason sum score . [ 8 ]  A second study of SNPs occurring within common transcription factor binding sites identified the SNP; rs10936845 within a GATA2 motif. [ 9 ]  This SNP increased the expression of  NAALADL2  expression in prostate cancer patients, with increased expression also predicting biochemical recurrence. [ 9 ]


In prostate cancer, somatic  copy-number gains  in  NAALADL2  are present in around 16% of patients with localised disease, increasing to 30% of  Gleason grade  5 disease, and 50% of T stage 4 disease. [ 10 ]  co-occurring with adjacent oncogene  TBL1XR1 . [ 10 ]  The frequency of  CNA  gains in  NAALADL2  associate with a number of clinical hallmarks of aggressive prostate cancer including Gleason grade, tumour stage, positive  surgical margins  and cancer which has spread to the  lymph nodes . [ 10 ]  The frequency of copy-number gains in this genetic region also increase in  castrate resistant  and  neuroendocrine prostate cancer . [ 10 ]  The region surrounding  NAALADL2  is rich in oncogenes. [ 11 ]  Copy-number gains in  NAALADL2  often co-occur with neighbouring oncogenes including:  BCL6, ATR  and PI3K family members. [ 10 ]  Copy-number gains at the DNA level associate with mRNA expression changes in more than 450 known oncogenes, suggesting this region may be important in driving aggressive prostate cancer. [ 10 ]


A study of metastatic castrate resistant prostate cancer (mCRPC) has found the antisense strand of  NAALADL2  (NAALADL2-AS2) to be more than 2-fold higher in patients with mCRPC compared with healthy volunteers. [ 12 ]  Patients with higher  NAALADL2-AS2  expression had an improved response to enzalutamide compared to those with lower expression. [ 12 ]