Mendelian Inheritance in Man (OMIM): (database of human genetic diseases and genetic variants)

See also DNA

Introduction/Definitions:

When defining the number of chromosomes necessary to define  a species, geneticits count the haploid (n) number of chromosomes. For humans and many other species, the total number of chromosomes in a cell is called the diploid (2n) number, which is twice the hapoid number. For humans, the haploid number is 23 and the diploid number is 46. Diploid chromosomes reflect the equal genetic contribution that each parent makes to offspring. Materal and paternal chromosomes are referred to as being homologus, and each oe of the pair is termed a homologue.

Humans have 23 paired chromosomes. 22 of these pairs are non-sex (autosomes or chromosomes inherited symmetrically from both parents, regardless of sex) and 1 pair are sex chromosomes (X and Y in males and XX in females) to bring the total number of chromosomes in a human somatic (non-germ line) to a total of 46. Thus at conception, every human inherits a half set of her mother’s genetic information, consisting of 23 chains of DNA with 20k genes, and also a half set of her father’s genetic information, consisting of another 23 chains of DNA 20k genes. During gestation, that information is conveyed into every cell in the humn being’s body and thus results in two instances of every gene. 

Chromosomes have two arms, the so called long arm (“q”) and the short arm (“p) which are separated by a centromere.

Although the Mendelian model explains a lot of inheritance, there are exceptions. Primiarly, these are due to the presence of DNA in organelle genomes, specifically mitochondria and chloroplasts. Another prominent exception found in flowering plants and mammals involves parent of origin effects called imprinting. 

Organisms also generally have many more genes that assort independently than the number of chromosomes. This means that independent assortment cannot be due only to the random alignment of different chromosomes during meiosis. The reason for this is crossing over of homologues during meiosis. 

Gene 

a Gene is any DNA sequence that is transcribed as a single unit and encodes one set of closely related polypeptide chains. In eucaryotes, protein coding genes are usually composed of a string of alternating introns (non-coding regions) and exons (coding regions). The complete set of information contained in an organism’s DNA is sometimes called its “genome”. In humans, the genome is about 20,000-30,000 proteins since our DNA is capable of coding for that many proteins. Humans, mice and puffer fish all have about the same number of genes. Thus, organismal complexity is not a simple funcito of either genome size or gene number. DNA in humans is distributed over 24 different chromosomes.

Allele: 

An allele is one of a pair, or series, of forms of a gene or non-geneic region that occur at a given locus in a chromosome. Alleles are symbolized with the same basic symbol (e.g., B for dominant and b for recessive; B1, B2, Bn for n additive alleles at a locus). In a normal diploid cell there are two alleles of any one gene (one from each parent), which occupy the same relative position (locus) on homologous chromosomes. Within a population there may be more than two alleles of a gene. Small nucleotide polymorphisms (SNPs) also have alleles (i.e., the two (or more) nucleotides that characterize the SNP.

Alleles do not always have a clear dominant and recessive relationship; in some cases, alleles can be co-dominant, meaning both alleles are expressed equally in the phenotype, and neither is considered dominant over the other. In humans, for example, the A and B alleles for blood type are codominant, so someone with one A allele and one B allele will have blood type AB.

The existence of small RNAs encoded by dominant alleles have been shown to prevent the expression of recessive alleles. In one model, a small RNA encoded by the frist allele recognises a specific sequence on the second allele and blocks its expression. (“Dominant and recessive gene expression, chapter Two: the molecualr mechanism for dominance”. Agroecology, December 17, 2014)

Introns: 

Introns are non-coding regions of the DNA. Traditionally they were referred to as “junk DNA” because at least historically they appeared to serve no function.  US Patent No. 5,612,179 discloses that certain DNA sequences in coding reigons (exons) of certain genes are correlated with non-coindg regions (introns) within the same gene, non-coding regions in different genes, or non-coding regions of the genome that are not part of any gene. The correlated coding and non-coding regions tend to be inherited together, with only rare shuffling. In other words, the regions are in “linkage disequilibrium” meaning that the coding and non-coidng regions appear “linked” together in individuals’ genomes more often that probability would dictate. Linkdage disequilibrium is a condition in which certain alleles at two linked loci are non-randomly assocaited with each other. The correlated coding and non-coding regions may be linked even though the two sequences are located far apart form one another on the chromosome. 

GeneMaps: are defined as groups of gene(s) that are directly or indirectly involved in at least one phenotype of a trait.

Genotype: set of alleles at a specified locus or loci.

Epigentic inheritance: An epigentic change is defined as a mitotically and/or meiotically stable change in gene funciton that does not involve a change in DNA sequence. An example is X-chromosome inactivation (see below) where an entire chromosome is silenced, and the effect is inherited through many mitotic dividsions. In some mouse and rat models, this even includes effects of materianl diet on F2 animals. 

Epigenetic mechniasms include changes in DNA methylation and histone modifications. Noncoding RNAs and nuclear organization have aso been implicated. Alternations in chromatin structure and the accessibility of DNA seem to be a point of convergence for multiple epigentic mechanisms. 

–Genomic impriting: is an example of epigenetic inheritance.  In genomic imprinting, the phenotype caused by a mutant allele is exhibited when the allele comes form one parent, but not when it comes from the other. Some imprinted genes are inactivated in the paternal germ line and therefore not expressed in the zygote. Other imprinted genes are inactivated in the maternal germ line, with the same result. This makes the zygote effectively haploid for an imprinted gene, and thus the effect of mutant alleles depends on the parent of origial Imprinted genes also seem to be concenetrated in particular regions of the genome, with genes that are both maternally and paternally imprinted. 

An example of genetic imprinting the igf 2 gene in the mouse. Mutant igf 2 leads to dwarf mice. However, only the paternal allele is expressed. Thus when normal mice (homozygous, green normal) were crossed with drawf mice (red homozygous for a recessive mutant allele of igf2), the phenotypes of the hterozygous offspring were deifferent depending on which parent contirbuted the mutant allele. For example, a paternal (green) with materinal red mutant mouse would appear normal since the maternal mutant allele is not expressed. However, a paternal red with materinal green would appear drarf since materinal green is not expressed. 

Haplotype: The allelic pattern of a group of (usually contiguous) DNA markers or other polymorphic loci along an individual chromosome or double helical DNA segment. Haplotypes identify individual chromosomes or chromosome segments. The presence of shared haplotype patterns amoung a group of individuals implies that the locus defined by the haplotype has been inerited, identical by descent froma common ancestor. Detection of identical by descent haplotypes is the basis of linkage disequilibrium (LD) mapping.

Noncoding DNA: A huan gene is made up of numerous pieces of coding DNA (exons) interspeersed with lenghs of noncoding DNA (introns). Introns comprise about 24% of the human genome, whereas the exons comprise less than 1.5%. However, this noncoding DNA is important. MicroRNA genes (miRNA), for example, are hidden in the noncoding DNA. Tehy are a mechanism for controlling gene expression. Long, noncoding RNA is also not translated into protein but serve a regulatory role and likely regulate gene expression. 

sex-linked or X-linked: A trait determined by a gene on the X chromosome is said to be sex-linked or X-linked because it will segragate with the sex chromosomes. From ancient times, people noted conditions taht seem to affect males to a greater degree than females. This can be explained if the genes responsbiel are located on the X chromosome. Red-green color blindness for example is a condition that is more common in males becasue the gene affected is carried on the X chromosome. Anotehr example is hemophilia, a disease that affects a single protein in a casade of proteins involved in the formation of blood clots. 

Dosage compensation, epistasis and X inactivation: Although males have only one X chromosome and females have two, female cells do not produce twice the amount of the proteins encoded by genes on the X chromosome. Instead, one of the X chromosomes in females is inactivated early in embronic devellpment, shortly after the embryo’s sex is determined. This inactivation is an example of dosage compensation which ensures an equal level of expression from the sex chromosomes despite a differing number of sex chromosomes in males and females. In Drosophila, by contrast, dosage compensation is acheived by increasing the level of expression on the male X chromosome. Which X chromosome is inactivated in human females varies randomly from cell to cell. If a female is heterozygous for a sex linked trait, some of the cells will express one allele and some the other. Females that are heterozgous for X chromosome alleles are genetic mosaics in that their individual cells may express different alleles depending on which chromosome is inactivated. The calico cat, for example, is a female that has a patchy distribution of dark fur, organge fur and white fur. The dark fur and organe fur are due to heterozygosity for a gene on the X chromosome that detemrines pigment color. One allele results in dark fur, and another allele results in organe fur. Which of these colors is observed in any particular patch is due to inactivaiton of one X chromosome. If the chromosome containing the organe allele is inactivated, then the fur will be dark and vice versa. The patchy distribution of colr, and the presence of white fur, is due to a second gene that is epistatic to the fur color gene. That is, the presence of this second gene produces a patchy distribution of pignment with some areas totally lacking pignment. In the areas that lack pigment, the effect of either fur color allele is masked. This is an example of both epistasis and X inactivation. 

Maternal Inheritance: is a mode of uniparental (one-parent) inheritance form the mother. For example, organelles are usually inherited from usually the mother. When a zygote is formed, it received an equal contribution of the nuclear genome from each parent, but it gets all of the mitochondia from the egg cell, which contains a great deal more cytoplasm and thus organelles. As the zygote divides, these original mitchondia divide as well and are partitioned randomly. As a result, the mitochondria in every cell of an adult organism can be traced back tot he original maternal mitochondia present in the egg. 

In humans, the diease Leber’s hereditary optic neuropathy shows maternal inheritance. The genetic basis of this disease is a mutant allele for a subunit of NADH dehydrogenase. The mutant allele reduces the efficiency of electron flow in the elctron transport chain in mitochondria, in turn reducing overall ATP produciton. Some nerve cells in the optic system are particularly sensitive to reduction in ATP production, resulting in neural degeneration. A mother with this disease will pass it on to all of ther progency, whereas a father wih the disease will not pass it on to any of this progeny. Note that unlike ex-linked inheritance above, in maternal inheritance males and females are equally affected. 

Crossing over of homologues during Meiosis: In prophase I of meiosis, homologues appear to physically exchange material by crossing over. As the distance separating loci increases, the probability of recombination occurring between them during meiosis also increases. Genetic maps are constructed based on recombination frequency. 1 map unit is 1% recombinant progeny. 

Short tandem repeats (STRs): are short repeats of 2-4 bases that can differ in repeat number between individuals. These have been sued in genetic mapping, and also form the basis for databases used in forensic anlysis of DNA. 

Single-nucleotide polymorphisms (SNPs): Using data form sequencing the human genome allows the identificaiton and mapping of single base differences between individuals. Any differences between individuals in populations are termed polymorphisms: polymorphisms affecting a single base of a gene locus are called SNPs. It is possible to start with a complex disease phenotype, for example, coronary artery disease, then look for SNPs assocaiated with this phenotype in a population. As the locaiton of each SNP is known, one can then look for candidate genes in that region of the genome. This is an example of forward genetics, going from a known phenotype to an unknown genotype. There are over 650 million SNV entries in a databse devoted to genetic variation. There is also massive variation in short repetitive regions that difficult to sequence accurately. 

DNA fingerprinting uses short tandem repeats (STRs) that vary in number between individuals. The CODIS database stores data on 13 different STR loci. 

Chromosome Structure:

Each chromosome consists of a long DNA molecule associated with proteins that fold the DNA into a more compact structure. This complex of DNA and protein is sometimes referred to as chromatin. The proteins that bind to the DNA are typically referred to as the histones and the nonhistone proteins.

Chromatin is organized into nucleosomal subunits. Each nucleosome consists of 146 bp of DNA wrapped around two molecules each of the histone proteins H2A, H2B, H3 and H4 and a single linker protein, H1. Histones are responsible for the most basic level of chromosome organization, the nucleosome, which is DNA and histone proteins. Histone dimers form a compact octamer core.  The lenght of the DNA wound around the core has been shown to be about 150 nucleotide pairs wrapped twice around 8 histone molecules (two each of H2A, H2B, H3, and H4). Nucleosomes are separated by about 50 bp of DNA.

Many hydrogen bonds are formed between DNA (phosphodiester backbone) and the histone core (amino acid backbone). Numerous hydrophobic interactions interactions also hold DNA and protein together in the nucleosome. All the core histones are rich in lysine and arginine (2 amino acids with basic side chains) and their positive charges can neutralize the negatively charged DNA backbone. Each of the core histones has a long N-terminal amino acid tails which extends out from the DNA-histone core. The N-terminal tails of each of the histones are subject to different types of covalent modification which are crucial in regulating chromatin structure which can regulate gene expression. The domains are lysine rich are are targets of a class of enzymes termed histone acetyl transferases.

Although long strings of nucleosomes form on most chromosomal DNA, chromatin in a cell probably rarely adopts an extended beads on a string form. Instead, it is seen to be in the form of a fiber about 30 nm thick. This represents nucleosomes which are packed on top of one another, generating arrays in which the DNA is even more condensed. Such highly packed chromatin is sometimes referred to as euchromatin. The 30 nm euchromatin is not conducive to transcription (2nm and 11 nm would be compatible).

There is even a more condensed form of chromatin that is sometimes called heterochromatin which is included in certain regions of the chromosomes such as the telemores and centromeres. Covalent modification of the nucleosome core histones as by methylation of specifc lysines by histone methl transferases play a critical role in the formation of heterochromatin. One protein, Sir2, also has a role in creating a pattern of histone underacetylation unique to heterchromatin.

Sex chromosomes: 

In males, the single X chromosome paris in meiosis with a disimilar partner called the Y Chromosome. The X and Y chromosomes are terms sex chromosomes because of their association with sex. The defulat setting in human embronic development leads to female development. Some of the active genes of the Y chromosome are responsible for the masculinization of genitalia and secondary sex organs, producing features, associated with “maleness” in humans. Consequently, any individual with at last one Y chromosome is normally male. In vertebrates, this form of sex determination is seen in mammals and birds and is called chromosomal sex determination.

The structure and number of sex chromosomes vary in idfferent species. In the fruit fly, Drosophila, females are XX and males XY, which is also the case for humans and other mammals. However, in birds, the male has two Z chromosemes, and the female has a Z and a W chromosome. Some insects, such as grasshoppers, have no Y chromosome; females are XX and males are characterized as XO (O indicates the absence of a chromosome)

Humans have 46 chrosomes (23 paris). One pair consists of the sex chromosomes, which are dissiimilar wehreas the other 22 paris, which are similar are called autosomes. 

The Y chromosome in males is highly condensed. Becasue few genes on the Y chromosome are expressed, recessive alleles on a male’s single X chromosome have not active counterpart of the Y chromosome. 

Although males have only one X chromosome and females have two, female cells do not produce twice the amount of the proteins encoded by genes on the X chromosome. Instead, one of the X chromosomes in females is inactivated early in embryonic development, shortly after the embryo’s sex is determeind. Tis inactivaiton is an example of dosage compensation, which ensures an equal level of expression from the sex chromsomes despite a differing number of sex chromosomes in amles and females. In Drosophila, by contrast, dosage compensation is acheived by increasing the level of expression on the male X chromsome. 

The X chromosome inactviation mechanism of dosage compensation is true of all mammals. Females that are heterozygous for X chromosome alleles are egentic mosaics in that their individual cells may express different alleles, depending on which chromosome is inactivated. An example is the calico cat, a female that has a patchy distribution of dark fur, orange fur and white fur. The dark and orange fur are due to heterozygosity for a gene on the X chromosome that determines pigment color. One allele results in dark fur, and another allele results in orange fur. Which of these colors is observed in any particular patch is due to inactivaiton of one x chromsome. If the chromosome containing the orange allele is inactivated, then the fur will be dark and vice versa. In addition, the patchy distribution of colr and the rpesence of white fur is due to a second gene that is epistatic to the fur color gene. The presence of this second gene produces a patchy distribution of pigment, which some areas totally lacking pigment. In the areas that lack pigment, the effect of either fur color allele is masked. Thus the caolico cat is an exaple of both epistasis and X inactivation. 

Aneuploidies:

The particular array of chromosomes an individual organism possesses is called its Karyotype. In the human karyotype, the 23 pairs of chromosomes differ widely in size and in centromere position. 

The failure of homologues or sister chromatids to separate properly during meiosis is called nondisjunction. This failure leads to the gain or loss of a chromosome, a condition called aneuploidy. The frequency of aneuploidy in humans has been estimated at 7010% of clincially recognized conceptions. Inidivduals who have lost one copy of an autosome are said to be monosomic, and generally do not survive embryonic development. In all but a few cases, individuals who have gained an extra autosome (called trisomics) also do not survive. Data from linically recognized spontaneous abortions indicate levels of aneuploidy as high as 35%. 

Embryos trisomic for 5 of the smallest human autosomes (numbers 13, 15, 18, 21 and 22) can develop and survive to live . Trisomy for 13, 15 or 18 casues severe developmenal defects and infants with such a genetic makeup die within a few months. In constrast, individuals trisomic for chromosome 21 or mroe rarely #22, usually survive to adjultood. In these individuals, the matruation of the skeletal system is delayed, so they generally are short and have poor muslce tone. Their mental devleopment is also affected, and children with trisomy 21 show dome degree of intellectual disability. 

Aneuploidy:

The presence of a variation in the number of chromosomes from the usual complement of 46 is referred to as aneuploidy. The absence of a single chromosome from a usual pair is referred to as monosomy, and presence of an additional copy of a single chromosome to the usual pair is referred to as trisomy.

Aneuploidy refers to the state where the wrong number of chromosomes (e.g., the wrong number of full chromosomes or the wrong number of chromosome segments, such as presence of deletions or duplications of a chromosome segment) is present in a cell. In the case of a somatic human cell it may refer to the case where a cell does not contain 22 pairs of autosomal chromosomes and one pair of sex chromosomes. in the case of a human gamete, it may refer to the case where a cell does not contain one of each of the 23 chromosomes. In the case of a single chromosome tyype, it may refer to the case where more or less than two homologous but non-identical chromosome copies are present, or where there are two chromosome copies present that originate from the same parent.  (Natera, US 10,262,755)

Nondisjunction of sex-chromosomes:

Aneuploidy for the sex chromosomes has less severe consequences than autosomal aneuploidy. Nondisjunction of sex chromosomes can occur in either male or female meiosis. In fmale meiosis, this will produce oocytes with either two X chromosmes, or no X chromosome. In male meiosis, the cutcome depends on whether the nondisjunction occurs during meiosis I or II, and can produce XY sperm, YY sperm and sperm with no sex chromosomes. Variousombinations of these gametes and normal gametes leads to zygotes with sex chromosome aneuploidies: XXX, XXY, XO, OY and YYY. The most extreme case is the complete lack of an X chromosome (OY), which resutls in embryonic lethality. At the other end of the spectrum, XXX individuals develop into females with one funcitonal X chromosome. They may be taller in stature, but are otherwise indistinguishable from XX females. An XXXY individual develops as a male with many female body characteristics and in some, but not all cases, diminished mental capcity. This condition, called Klinefelter syndrome, occurs in about 1-1000 male births. 

Copy number variation (CNVs) are often assigned to one of two main categoreis, based on the lengh of the affected sequence. The first category include copy number polymorphisms (CNPs) which are commin in the general population, occurring with an overall frequency of greater than 1%. CNPs are tpically small (most are less than 10 kilbases in lengh) and they are often enriched for genes that encode proteins important in drug detoxification and immunity. A subset of the CNPs is highly variable with respect to copy number. As a result, different human chromosomes can have a wide range of copy number (e.g., 2-5) for a particular set of genes. CNPs associated with immune response genes have recently been associated with susceptibility to complex genetic diseases, including psoriasis, Crohn’s diease and glomerulonephritis. The seocnd class of CNV include realtively rare varints that are much longer than CNPs, ranging in size form hundreds of thousands of base pairs to over 1 million base pairs in lenght. In some cases, these CNVs may have arisen druing production of the sperm or egg that gave rise to an individual or they may have been passed down fro only a few generations. (Natera, US 10,262,755)

Gene copy number and Diseases:

Gene copy number can also be altered in cancer cells. For instance, dupolicaiton of Chrlp is common in breast cancer and the EGFR copy number can be higher than normal in non-small cell lung cancer. (Natera, US 10,262,755)

A higher copy number of CCL3L1 has been associated with lower susceptibility to HIV infection, and a low copy nmber of FCGR3B (the CD16 cell surface immuoglobulin receptor) can increase susceptibility to systemic lupus erythematosus and similar inflammatory autoimmune disorders. (Natera, US 10,262,755)

Aneuloides in autosomal and sex chromosomes are responsible for a number of genetic conditions including Down syndrom (trisomy of chromosome 21), Edwards syndrome (trisomy of chromosomes 18), Patau syndrome (trisomy of chromosome 13)., Turner syndrome (full or partial monosomy of X), Klinefeiter syndrom (XXY), XYY syndrome, XXYY syndrome and Triple X syndrome. 

The most commo viable autosomal trisomies are trisomies of chromosomes 21, 18 and 13. Trisomy 13 and trisomy 18 often result in miscarriage, stillbirth or in the case of viable birth, neonatal death. Trisomy 21 is not usually life threatening but can result in significant physical and mental disability. Fetuses with aneuploidies of multiple chromosomes are unlikely to survive past the early stages of pregnancy. The additional chromosomes found in cases of trisomy may be paternally or maternally inherited. In trisomies 13, 18 and 21, the extra copy of the relevant chromosomes is inherited form the mother in the majority of cases. 

Detection of Deletions and Duplications of chromosome segments or entire chromosomes:

(Natera, US 10,262,755) disclsoes determing whether an aneuploidy mutation is present by analyzing a sample of blood to dtermine a level of allelic imblance fourality of chromosomes or chromosome segments known to exhibit aneuploidy in cancer by generating nucleic acid sequence data for a set of polymorphic loci on each of the plurality of chromosomes or chromosome segments, using the nucleic acid sequence date to generate phased allelic data fot teh set of polymorphic loci on each of the pourality of chromosomes or chromosome segmetns and termeing the level of allelic imbalance prsent for each of the plurality of chromosomes or segments using the phased allelic data, wherein a detectable allelic imbalance is indicative of an aneuploidy mutation in the solid tumor for each of the plurality of chromosomal segments. Allelic data refers to a set of genotypic data concerning a set of one or more alleles. It can refer to the phased, haplotypic data. it may also refer to SNP identities and it may refer to the sequence data of teh DNA, including insertions, deletions, repeats and mutations. 

The plasma membrane of all electrically excitable cells such as neurons contain voltage gated cation channels which are responsible for generating an action potential which is a traveling wave of electrical excitation. An action potential is generated by a depolorization or shift in the membrane potential of the plasma membrane to a less negative value.

In nerve and skeletal muscle cells, a stimulus that causes sufficient depolarization promptly causes voltage gated Na+channels to open, allowing a small amount of Na+ to enter the cell down its electrochemical gradient. The influx of + charge depolarizes the membrane thereby opening more Na+ channels causing further depolarization. This process continues within a fraction of a millisecond until the electrical potential has shifted from its resting value of about -70 mV to almost as far as the Na+ equilibrium potential of about +50 mV. At this point, when the net electrochemical driving force for the flow of Na+ is almost zero, the cell would come to a new resting state but this does not occur because Na+ channels are inactivated and K+channels are opened. When K+ channels are opened, the transient influx of Na+ is overwhelmed by the efflux of K+ which quickly drives the membrane back toward the K+ equilibrium potential.

How do Na+ channels go from an initial closed to an open and then inactivated state? One model proposed is the so called “ball-and-chain” model. When the membrane is at rest (highly polarized), the closed conformation has the lowest free energy and is therefore most stable. When the membrane is depolarized, the energy of the open conformation is lower so the channel has a high probability of opening. The free energy of the inactivated conformation is even lower so that after a randomly variable period spent in the open state, the channel becomes inactivated. The model is called “ball and chain” because the occlusion of the channel is thought to occur by a ball like structure that is linked to the channel through a chain.

Introduction:

Cell membranes are not permeable to all molecules. Small molecules like oxygen and carbon dioxide diffuse rapidly across membranes. Small uncharged polar molecules like water or urea diffuse more slowly (but large uncharged polar molecules like glucose can not readily diffuse). In contrast, lipid bilayers are highly impermeable to charged molecules (ions) due to their charge and high degree of hydration. For these ions, special transport proteins are required.

The process by which a carrier protein transfers a solute molecule across the lipid bilayer resembles an enzyme-substrate reaction in that when the carrier is saturated (all solute binding sites are occupied), the rate of transport is maximal (Vmax).

There are different types of transmembrane transport (also called “carrier-mediated transport”):

Facilitated or Passive Diffusion: 

Passive Transport: Many substances can move in and out of the cell without the cell’s having to expend energy. This type of movement is temred “passive transport”. Some ions and molecuels can pass thorugh the membrane failry easily and do so because of a concentraiton gradient inside the membrane versus outside.

Facilitated or “passive” diffusion: In the case of an uncharged molecule, this mechanism simply uses the concentration gradient or the difference in concentration on the two sides of a membrane. If the solute carries a net charge, both its concentration gradient and the electrical potential difference across the membrane which when combined constitutes theelectrochemical gradient for the solute.

–Facilitated diffusion of ions through channels: (see also ion channels):

Some substances also move in resonse to a concentration gradient, but do so through specific protein channels in the membrane. Channel proteins have a hydrophilic interior that provides an aqueous channel through which polar molecuels can pass when the channel is open. (carrier proteins on the other hand, bind specifically to the molecule they assist).

–Facilitated Diffusion by Carrier Proteins:

Carriar proteins:bind specifically to a molecule that they assit, much like an enzyme binds to the substrate. Thus in contrast to ion channels, carrier proteins bind specifically to the molecule they assist. Carriers must bind to teh molecule they transport, so as concetnration increases, more of the carriers are bound to the transported molecule until all carriers are occupate wehre hte rate of trnasport will be constant.

Vetebrate red blood cells (RBCs) provide an example of facilitated diffusion. One RBC carreir protein transprot a different molecule in each direction: chloride ion (Cl-) in one direction and bicarbonate ion (HCO3-) in the opposite direction. This carrier is also important in the uptake and rlease of carbon dioxide.

Glucose is also transported in RBCs by facilitated diffusion through a sepcifi carrier protein. When glucose binds to the transporter, this alters the shape of the carrier, pulling glucose through the bilayer and releasing it inside the plasma mebrane. Releasing glucose causes the transporter to revert to its orginal shape so it can bind another glucose molecule outside the cell.

Osmosis:

Osmosis is the movement of water across membranes.

Water molecuels interact with dissolved solutes by forming hydration shells around the cahrged solute molecuels. The concetnration of cell solutes in a solution determines the osmotic concentraiton of the solution. If two solutions have unqueal osmotic concentraitons, the solution with the higher concentration is hypertonic and the solution with lower concetnraiton is hypotonic. A plasma membrane separates two solutions; the cytoplams and the extracellualr fluid. The direction and extent of any diffusion of water across the plasma membrane is determined by comparing the osmotic strenght of these solutions. Water diffuses out of a cell in a hypertonic solution (where the cytoplasm of the cell is hypotonic compared with the extracellular fluid). Thes loss of water causes the cell to shrink until the osmotic concentraiton of the cytoplasm and the extrcellular fluid become equal.

In a hypotonic solution (the cell’s cytoplasm is hypertonic relative to the extracellular fluid), water diffuses into the cell causing the cell to swell. As water enters the cell form a hypotonic solution, pressue is applied to the plasma membrane until it bursts. It is important for animal cells, which only ahve a plasma mebrane, to maintain osmotic balance. Blood contains a high concetnraiton of the protein albumin which elevates the solute concetnraiton of the blood to match that of one’s cell’s cytoplasm. Cells of prokaryotes, fungi, plants and many protists are surrounded by strong cell walls, which can withstand high internal pressures without bursting.

Aquaporins: Water channels:

Studies on artifical membranes show that water, despite its polarity, can cross the membrane, but this flow is limited. Water flow in living cells is faciltiated by aquoporins which are specialized channels for water. More than 11 different kinds of aquaporins have been found in mammals. Tehse fall into two classes; those that are specific for only water and those that allow other small hydrophilic molecules, such as glycerol or urea, to cross the membrane as well. The human genetic disease hereditary (nephrogenic) diabetes insipidus (NDI) has been shown to be caused by a nonfunctional aquaporin protein. This diesase causes the excretion of large olumes of dilute urine.

Active transport: 

Active transportrequires a source of metabolic energy such as ATP.

Na+/K+ ATPase:

A prime example of such active transport is the Na+/K+ ATPase which moves 3 Na+ out of the cell and 2 K+ into the cell. Since this pump drives 3 positively charged ions out and 2 in, it tends to create an electrical potential with the cell’s inside negative relative to the outside (the pump, however, does not contribute more than 10% to the membrane potential).

One model for how this pump works is that binding of Na+ and the subsequent phosphorylation by ATP of the cytoplasmic face of the pump induces the protein to undergo a conformational change that transfers Na+ across the membrane and releases it on the outside where K+ then binds and the subsequent dephosphorylation returns the protein to its original conformation which transfers K+ across the membrane and into the cytosol.

Although this pump contributes no more than 10% to the membrane potential of the cell, it is extremely important in regulating osmolarity of the cell. Cells contain a high concentration of solutes like negatively charged organic molecules on the inside of the cell and their accompanying cations which creates a large osmotic gradient. This effect is counteracted by an opposite osmotic gradient due to a high concentration of inorganic ions, mainly Na+ and Cl- in the extracellular fluid. The Na+/K+ maintains this balance by pumping out Na+ that leaks in down its steep electrochemical gradient. Cl- is kept out by the membrane potential of the cell.

Ca2+ ATPase:

Another transport ATPase is the Ca2+ ATPase which moves  Ca2+ from the cytosol back into the sarcoplasmiic reticulum after an action potential depolarizes a muscle cell and releases Ca2+ from the SR. This is important for muscle contraction. Muscles are stimulated to contract by motor neurons. When a somatic motor neuron delivers electrochemical impuses, it stimulates contraction of the muscle fibers; it innervates (makes synapses with) through the following steps: (1) the motor neuron, at the neuromuscular junction, releases the neurotransmitter acetylcholine (ACh). ACh binds to receptors in the muscle cell membrane to 0pen Na+ channels. The influx of Na+ ions depolarizes the muscle cell membrane. (2) the impulses spread along the membrane of the muscle fiber and are carried into the muscle fibers through T tubules. (3) the T tubules conduct the impulses toward the sarcoplasmic reticulum, opening Ca2+ channels and releasing Ca2+. The Ca2+ binds to troponin, exposing the myosin-binding sites on the actin myofilaments and stimulating muscle contraction. (4) When the motor neuron stops sending electrical impulses, it also ceases releasing ACh, in turn stopping the production of impulses in the muscle fiber. Another membrane protein in the SR then uses energy from ATP hydrolysis to pump Ca2+ back into the SR by active transport. Tropinin is no longer bound to Ca2+, so tropomyosin returns to its inhibitory position, allowing the muscle to relax. When a muslce is relaxed, its mysin heads are in the activated conformation bound to ADP and Pi, but they are unable to bind to actin. In the relaxed state, the attachment site for the myosin heads on the actin are physically blocked by tropomyosin, in the thin filaments. Cross-bridges therefore cannot form and the filaments cannot slide. For contraction to occur, the tropomyosin must be moved out of the way so that the myosin heads can bind to the uncovered actin-binding sites. This requires the aciton of troponin, a regulatory protein complex that holds tropomyosin and actin together. The regulatory interactions between troponin and tropomyosin are controled by the Ca2+ concentraiton of the muscle fiber. When the ca2+ cocentraiton of the cytoplams is low, tropomyosin inhibts cross-bridge formation. When the Ca2+ rises, Ca2+ binds to troponin, altering its conformation and shfiting the troponin-tropomyosin complex. This shift in conformation exposes the myson binding sites on teh actin. Cross-bridges can thus form, undergo power strokes and produce muscle contraction.

ABC transporters:

A family of transport ATPases of great clinical importance are ABC transporters which have 2 ATP binding domains. ATP binding leads to dimerization of these 2 domains  Eucaryotes seem to use ABC transporters mostly for export such as hydrophobic drugs. This makes the control of malaria difficult because the protist responsible for causing this disease has amplified a gene encoding an ABC transporter that pumps out drugs used against it. In most vertebrate cells, an ABC transporter in the ER membrane transports a variety of peptides produced by protein degradation from the cytosol into the ER. The transported fragments are eventually carried to the cell surface where they are displayed for scrutiny by cytotoxic T lymphocytes. The disease cystic fibrosis is also caused by a mutation in a gene encoding an ABC transporter.

Secondary active transport: 

Some moleuels are moved against their concentration gradient by using the energy stored in a gradient of a different molecule. In this process called “coupled transport” the energy released as one molecule moves down its concentraiton gradient is captured and used to move a different molecule against its gradient.

As noted above, the energy stored in ATP moelcuels can be used to create a gradient of Na+ and K+ across the membrane. These gradeints can then be used to pwoer the transport of other molecuels across the membrane.

The active glucose transpoter uses the Na+ gradient produced by the Na+/K+ pump as a source of energy to power the movement of glucose into the cell. In this system, both glucose and Na+ bind to the transport protein, which allows Na+ to pass into the cell down its concetnraiton gradient, capturing the energya nd using it to move glucose into the cell. In this kind of cotransport, both molecuels are moving in teh same direction across the membrane, therefore the transporter is a symporter.

Na+ is the typical co-transported ion in the plasma cells of animals whose electrochemical gradient provides a driving force for the transport of a second molecule. The Na+ that enters the cell is subsequently pumped out by the ATP driven Na+ pump in the PM which by maintaining the Na+ gradient indirectly drives the transport. This is why such ion driven carriers are said to mediate “secondary active transport” whereas ATP driven carriers are said to mediate “active transport.” Secondary active transport can be coupled transport in the same direction (symporters). Examples of symporters include glucose carrier that is driven by a Na+ gradient. Epithelial cells pump glucose into the cell through the apical domain using a Na+ powered glucose symport (glucose then passes down its concentration gradient by passive transport by a different glucose carrier protein in the basal membrane domains). Secondary active transport can also be coupled transport in the opposite direction (antiporters). Most cells have one or more types of Na+ driven antiporters in their PM that help to maintain the cytosolic pH at around 7.2. These proteins use the energy stored in the Na+ gradient to pump out excess H+.

Cell membranes consist of a continuous double layer of lipid molecules in which membrane proteins are embedded. Lipids constitute about 50% of the mass of most animal cell membranes with the rest of the mass being protein. All of the lipid molecules are amphipathic in that they have a hydrophilic or polar end and a hydrophobic or nonpolar end. 

Most lipids in the CM are randomly mixed in the lipid monolayer in which they reside. The van der Waals attractive forces between neighboring fatty acid tails are not selective enough to hold these lipids together. Some lipid molecules, however, that have long and saturated fatty hydrocarbon chains (like sphingolipids) are able to be held together transiently in small microdomains or lipid rafts. Membrane proteins with unusually long transmembrane domains also accumulate in the rafts. Because the hydrocarbon chains of the lipids concentrated in lipid rafts are longer and straighter than the fatty acid chains of most membrane lipids, the rafts are thicker and thus tend to accumulate certain membrane proteins.

Some type of lipid microdomains include 1) caveolae which accumulate the protein caveolin, 2) nanodomains which are rich in cholesterol and are located in the outer leaf of the PM. 

The lipid compositions of the 2 monolayers of the lipid bilayer in many cell membranes is also very different. This lipid asymmetry has functional significance. For example, many cytosolic proteins bind to specific lipid head groups found in the cytosolic monolayer of the lipid bilayer. As an example, the enzyme protein kinase C (PKC) is activated in response to various extracellular signals and then binds to the cytosolic face of the PM where phosphatidylserine (a phospholipid discussed below) is found. As another example, when animal cells undergo programed cell death (), phosphatidylserine rapidly translocates to the extracellular monolayer which serves as a signal to induce cells like macrophages to phagocytose the dead cell. This would not occur with phosphatidylserine on the cytosolic monolayer. This translocation is accomplished with the help of scramblase. 

Membrane Lipids

There are 3 main types of membrane lipids; 1. Phosphlipids, 2. cholesterol and 3. glycolipids.

1) Phospholipids are the most abundant membrane lipids. Phospholipids are composed of glyerol linked to two fatty acids and a phosphate group. The phosphate group can have additional molecules attached, such as the positively charged choline . Phosphatidylcholine is a common component of membranes. In the fluid mosaic model, a mosaic of proteins floats in or on the fluid lipid bilayer like botas on a pond. Carbohydrate chains are often bound to the extracellular portion of these proteins forming glycoproteins. Inside the cell, actin filaments and intermediate filaments interact with membrane proteins. Outside the cell, amny animal cells have an elaborate extracellular matrix ocmposed primarily of glycoproteins. 

Phospholipds have a polar head group and 2 hydrocarbon tails which are usually fatty acids which can differ in lenght. One tail usually has one or more cis-double bonds (unsaturated) each of which creates a small kink in the tail. These bonds increase the fluidity of the cell membrane because it makes it more difficult to pack the hydrocarbon chains together. Thus the lipid bilayers containing them are thinner than bilayers formed exclusively from saturated lipids. In addition, the double bonds make it more difficult to freeze.

There are a variety of phospholipids in eucaryotic membranes which act as a type of solvent for the proteins in the membrane. Some membrane proteins can function only in the presence of specific phospholipid head groups. Some important phospholipids in the plasma membrane of cells are the following.

• phosphoglycerides are derived from glycerol. Phosphatidylserine as well as well as phosphatidylethanolamine contain a terminal primary amino groups and are found in the inner monoloayer of the lipid bilayer. Phosphatidylcholine has choline in its head group and is found in the outer monolayer. Out of the phosphoglycerides, only phosphatidylserine carries a net negative charge. 

• sphingomylin is derived from serine. As with phosphatidylcholine (above), it has choline in its head group and is thus found in the outer monolayer of the plasmid membrane.

• inositol phosphlipids have a crucial role in cell signalling. Phosphatidylinositol is concentrated in the cytosolic monolayer. A variety of lipid kinases can add phosphate groups at distinct position on its inositol ring. The phosphoyrlated inositol phospholipids then act as binding sites that recruit specific proteins from the cytosol such as the phosphatidylinositol kinase (PI 3-kinase). 

2) Cholesterol is also a major constituent in the eucaryotic cell membranes. Cholesterol is a steroid with a polar hydroxyl group (-OH). They orientate themselves in the lipid bilayer with their hydroxyl groups close to the polar head groups of phospholipids where their rigid steroid rings interact with the hydrocarbon chains closest to the polar heads on phospholipids. In this position, cholesterol makes the lipid bilayer less deformable in this region and thereby decreases the permeability to small water soluble molecules.

3) glycolipids are sugar containing lipid molecules where they are found in the outer monolayer (noncytosolic side) of the PM. Some important glycolipids include:

• Gangliosides have a net negative charge and are thought to function in cell recognition processes in which membrane bound carboyhdrate binding proteins called lectins binds to the sugar groups on glycolipids in cell-cell adhesion. Some glycolipids provide entry points for bacterial toxins. For example, the ganglioside GM1 acts as a cell surface receptor for the toxin that causes cholera which leads to an increase in cAMP which in turn causes a large efflux of Na+ and water in the intestine.

• cerebrosides

Membrane Vesicles

Membrane vesicles are essentially spherical vesicles, generally less than 130 nm in diameter, composed of a lip bilayer containing a cytosolic fraction. Particular membrane vesicles are more specifically produced by cells, from intracellular compartments through fusion with the plasmic membrane of a cell, resulting in their release in biological fluids or in th supernatant of cells in culture.

Exosomes: are between about 300-120 nm in diameters and advantageously carry membrane proteins, particularly major histocompatility complex proteins and other others which directly or indirectly participate in antigen presentation. Depending on their origin, exosomes may also have proteins such as MHC I, MHC II, CD63, CD81 and/or HSP70 and have no endoplasmic reticulum or Golgi apparatus. Exosomes are essentially void of nucleic acids such as DNA or RNA. 

Exosome release has been demonstrated from different cell types in varied physiological contexts. For example, B lymphocytes have been shown to release exosomes carrying class II MHC which play a role in antigenic presentation. Similarly, DCs produce exosomes (i.e., dexosomes, Dex) and play a role in immune response mediation, particularly in cytotoxic T lymphocyte stimulation. Tumor cells have also been shown to secrete specific exosomes (i.e., texosomes, Tex) carrying tumor antigens and capable of presenting these antigen or transmitting them to APCs. 

Lamparski (WO 01/82958) discloses methods of preparing membrane visciles by obtaining a population of cells such as DCs, optionally sensitizing the DCs to antigen(s) culturing the DCs under conditions which allow them to release membrane vesicles, clarificaiton of the culture supernatant, concentraiton of the supernatant, diafiltraiton of the concentrated supernatant, isolation of the memrane vesicles using density cusion centrifugation, contacting the membrane viscles with a peptide to produce peptide loaded membrane vesicles , optionally a diafiltration buffer exchange step and sterile filtraiton of these membrane vesicles. 

Membrane Proteins

Membrane proteins can be purified with detergents which are small amphipathic molecuels that tend to form micelles in water. When mixed with membranes, the hydrophobic ends of detergents bind to the hydrophobic regions of the membrane proteins, thereby displacing the lipid molecules. Since the other end of the detergent is polar, this binding tends to bring the membrane proteins into solution as detergent-protein complexes. The polar ends of detergents can be either charged (ionic), as in sodiuim dodecyl sulfate (SDS) or uncharged as in triton detergents. With strong ionic detergents like SDS, even the most hydrophobic membrane proteins can be solubilized. Many hydrophobic membrane proteins can be solubilized and then purified in an active form by the use of mild detergents like triton X-100. Membrane proteins can be broadly classified as follows:

• Transmembrane proteins are amphipathic proteins that extend through the entire lipid bilayer of the PM. Their hydrophobic regions interact with the hydrophobic tails of the lipids while their hydrophilic regions are exposed to water on either side of the membrane.  In most transmembrane proteins the polypeptide chain crosses the lipid bilayer in an  because hydrogen bonding between the peptide bonds (which are polar) of these proteins is maximized if the polypeptide chain forms an alpha helix as it crosses the bilayer.

• Proteins containing about 20-30 amino acids with a high degree of hydrophobicity are long enough to span a lipid bilayer as an alpha helix and can often be identified by means of a hydropathy plot. In single pass transmembrane proteins, the polypeptide crosses the bilayer only once whereas in multipass transmembrane proteins, the polypeptide chain crosses multiple times. One such multipass transmembrane protein that can also satisfy the hydrogen bonding requirements of the polypeptide is the so called B barrel. In this conformation, the multiple transmembrane strands of the protein are arranged as a B sheet in the form of a closed barrel. 

  Most transmembrane proteins in animal cells are glycosylated. The sugar residues are added in the lumen of the ER and Golgi apparatus. Because of this, the oligosaccharide chains are always present on the noncytosolic (inside the cell) side of the PM. Disulfide bonds also form between cysteine residues on the noncytosolic side of the PM where they stablize the protein. Such bonds can not form on the cytosolic side due to the reducing environment of the cytosol of the cell.

  The 3 major transmembrane proteins responsible for cellular communication are 1) , 2) and 3) .

  • peripheral membrane proteins do not extend into the lipid bilayer but are rather bound to the face of the membrane by noncovalent interactions with other membrane proteins. 

  • GPI anchored proteins are linked via an oligosaccharid linker to phosphatidylinositol in the noncytosolic bilayer. GPI linked proteins are made as single pass transmembrane proteins in the ER. While still in the ER, the transmembrane segment of the protein is cleaved off and a glycosylphosphatidylinositol (GPI) anchor is added.

See also the Cell Cycle See also Cancer Disease Mechanisms

See also signal transduction

Controling the process of cell division is critical. Loss of this control can lead to cancer. 

The G1/S checkpoint is the primary point at which the cell decides to divide. This checkpoint is thus the primary point at which external signals can influence events of the cell cycle. As the G1/S checkpoint is approached, the triggering signal in yeast appears to be the accumulation of G1 cyclins. These form a complex with Cdc2 to create the active G1/S Cdk, which phosphoryaltes a number of targets that bring about the increased enzyme activity for DNA replciation. 

The primary molecular mechanism of cell cycle control is phosphorylation. The enzymes that accomplish this phosphorylation are the Cdks. Cdk is a protein kinase that activates numerous cell proteins by phosphorylating them. Cyclin is a regulatory protein required to activate Cdk. This complex is also called mitosis-promoting factor (MPF). The activity of Cdk is also controlled by the pattern of phosphorylation. Phosphorylation at one stie inactivates the Cdk, and phosphorylation at another site activates the Cdk. 

Mammalian cells answer to a wide range of extracellular growth factors, mitogen antagonists, differentiation inducers and spatial cues in exercising their commitment to enter S phase. Key regulators of G1 progression include three D-type cyclins (D1, D2, and D3) which assemble into holoenzymes with either cdk4 or cdk6 and cyclin E which combines later in G1 with cdk2.

Growth factors act by triggering intracellular signaling systems. Fibroblasts, for example, possess numerous receptors on their plasms membrane for platelet-derived growth factor (PDGF). The PDGF receptor is a receptor tyrosine kinase (RTK) that initiates a MAP kinase cascade to stimulate cell division. PDGF was discovered when investigaors found that fibroblasts would grwo and divide in tissue culture only if the growth medicum contained PDGF. 

Specific Regulators of the Cell Cycle:

Cyclins/Cdks

–D type cyclins/ Cdk4 & Cdk6: phosphorylate and inactivate pRB in response to mitogenic signals. 

–CDK4-CDK6 and the cell cycle: 

CDK4 and CDK6 are particularly relevant to oncogenesis because together with D type cyclins, they promote progression of the cell cycle from G1 phase to S phas.e One decade after their discovery, the small molecule palbociclib emerged as the first CDK4/CDK6 inhibitors to gain approval by the FDA. 

–CyclinE/Cdk2: activity is present briefly in the late G1 and early S phases and is critical for S-phase entry.

Protein kinases and protein phosphatases that modify Cdks

–Cdk-activating kinase (CAK) phosphorylates an activating site in Cdks 

–Wee1 kinase phosphorylates inhibitory sites in Cdks, primarily involved in controlling entry into mitosis

–Cdc25 phosphatases remove inhibitory phosphates from Cdks; 3 family members (Cdc25A, B, C) in mammals; Cdc25C is the activator of Cdk1 at the onset of mitosis

Cyclin-dependent Kinase Inhibitors (CdkIs) 

Sic1 (budding yeast) suppresses Cdk activity in G1; phosporylation by Cdk1 triggers its destruction

p27 is the product of the p27Kip1 gene. It suppresses G1/S-Cdk and S-Cdk activities in G1; helps cells to withdraw from cell cycle when they terminally differentiate; phosphorylation by cdk2 triggers its ubiquitylation by SCF

p21 is the product of the p21waf1/cip1 gene. It is a cdk inhibitor that suppresses G1/S-Cdk and S-Cdk activities following DNA damage in G1; Loss of cyclin-cdk activity in G1 phase prevents phosphorylation of pRb, and the hypophosphorylated pRb retains its ability to sequester E2F and prevents initiation of DNA synthesis. After DNA damage in cells with wild-type p53, pRb is found predominantly in the hypophosphorylated form. Abrogation of pRb activity by   prevents G1 arrest.

Modulation of expression of p21waf1/cip1 can be P53-dependent or P53-independent. p21 synthesis is increased when p53 is induced after DNA damage by ionizing radiation. By indirectly inhibiting cdk activity, p53 induction thereby prevents pRb phosphorylation and the release of E2F.

p16 is the product of the ink-4a gene. p16 suppresses G1-Cdk activity in G1; p16 is a which is frequently inactivated in cancer

Ubiquitin ligases and their activators

SCF catalyzes ubiquitylation of regulatory proteins involved in G1 control, including CKIs (Sic1 in buddying yeast, p27 in mammals); phosphorylation of target protein usually required for this activity)

Gene regulatory proteins

SCB and MCB yeast transcription factors that are activated by the G1 cyclins which in turn activate transcription genes required for S phase entry

Myc activates transcription of D type cyclins, SCF and E2F leading to increase E2F activity and S phase entry

E2Fs are a family of heterodimeric transcription regulators which can transactivate genes whose products are importnt for S phase entry. E2Fs promotes transcription of genes required for G1/S progression, including genes encoding G1/S cyclins, S-cyclins, and proteins required for DNA synthesis; stimulated by G1 Cdk; phosphorylates in response to extracellular mitogens

p53 promotes transcription of genes that induce cell cycle arrest (especially p21) or in response to DNA damage or other cell stress. Its expression is often elevated subsequent to induction of p53 activity. The TP53 gene, which is a tumor-suppressor gene, encods the p53 protein. Theis gene has been called the “guardian of the genome” because it is involved in the G/1S checkpoint, hwere damaged DNA causes p53 to pause the cell cycle to give the cell time to repair the damage. If the damage is severe enoguh, p53 will casue the cell to initiate apoptosis 

Mdm2 is the major negative regulatory of p53. Mdm2 promotes p53 degradation. It is a ubiquitin ligase that targets 053 to proteasomal degradation, thus defining a negative feedback loop to regulate p53 levels. Downregulation of Mdm2 trnascript by the catechin EGCG might preserve intact p53 protein. Mdm2 is itself a positive transcriptional target of p53. 

The transforming proteins of , including adenovirus E1B 55 kD protein, SV40 T antigen, and , also bind to p53 and prevent .

Growth Factors: Over 300 different peptides that appear to ahve grwoth factor activity have been identified. These can be grouped into mroe than 30 families of related peptides. A specific cell surface receptor recognizes each growth factor, its binidng site fitting that grwoth factor precisely. Tehse receptors often initiate MPA kinase cascades in which the final kinase enters the nucleus and activates transcription factors by phosphorylation. These transcription factors timulate the production of g1 cyclins and the proteins that are necessary for cell-cycle progression. 

The cellular selectivity of a particular grwoth factor depends on which target cells bear its unique receptor. Some grwoth factors, such as PDGF and EGF affect a broad range of cell types, but others affect only specific types. For example, nerve growth factor (NGF) promotes the growth of certain classes of neurons, and erythropoietin tiggers cell division in red blood cell precursos. Most animla cells need a comibnaiton of several different growth factors to overcome the various controls that inhibit cell division. 

Cytokines

TGF-B is the prototype member of a large superfamily of cytokines that exhibit diverse effects on cell proliferation. TGFB1 is the most extesnively studies member of the family and its antiprolifertive effects on many types of cells has been well documented. When administered in the G1 phase of the cell cycle, TGFB1 reversibly arrests cells in late 5!, by preventing phosphorylation of by cylin-cdk complexes. After progression from G1 to S phse, cells become unresponsive to the growth-inhibitory effects of TGFB1. Cell-cycle arest is primarily accomplished by either inhibition of cdk4 expression or induction of p15INK4B.

See also cell cycle control

Introduction/Definitions:

Progression through the cell cycle requires the coordination of  variety of macromolecular syntheses, assemblies and movements. The chromosomes must be replicated, condensed, segregated, and decondensed. The spindle poles must duplicate, separated, and migrate to opposite ends of the nucleus. Coordination of these complex processes is thought to be achieved by  series of changes in the cyclin-dependent kinases (CDKs). The active forms of the CDKs are a complex of at lest two proteins,  kinase and  cyclin. These complexes undergo changes in the kinase and cyclin components that are believed to drive the cell from one stage of the cell cycle to another. According to this paradigm, cell cycle stage is determined by the constellation of proteins activated or inactivated by phosphorylation as  result of the activity of the CDKs during that stage.

The phases of the cell cycle are gap 1 (G1), synthesis (S1), gap 2 (G2), mitosis and cytokinesis (C). G1, S and G2 are collectivley called interphase and mitosis and cytokinesis together are called M phase. 

Mitosis: is the phase of the cell cycle in which the spindle apparatus assembles, binds to the chromosomes, and moves the sister chromatids apart. Chromosomes become highly condensed and then are separated and distributed to the two daughter nuclei. The condensation of interphase chromosomes into mitotic chromosomes requires a class of proteins called condensins which are large protein complexes that contain SMC proteins; these are long, dimeric protein molecules that use the energy of ATP hydrolysis to make large right handed loops in DNA. When the 46 human chromosomes at mitosis are stained with dyes, one can see a reproducible banding patter. The centromere attaches to the duplicated chromosomes to the mitotic spindle so that one copy is distributed to each daughter cell. 

Cytokinesis: is the phase of the cell cycle when the cytoplasm divides, creating two daughter cells. 

Interphase:  

The period when the cell is not in mitosis is referred to as “interphase”. most of th cell cycle is spent in interphase. Chromosomes are replicated beginning at the origins of replication and proceed bidirectionally from the origins across the chromosome.  

Interphase contains the G1, S and G2 phases of the cell cycle. During interphase, the cell grows, replicates chrosomes, organelles and centrioles and syntehsizes components needed for mitosis., including tubulin. Cohesin proteins hold chromatids togetehr at the centromere of each chromosome. :

• G1 (gap phase 1): is the phase between M phase (below) and S phase. For most cells, this is the longest phase. Unlike transit through the S, G2, and M phases, G1 progression normally relies on sitmulation by mitogens and can be blocked by antiproliferative cytokines. Cells often pause in G1 before DNA replication and enter a resting state called the Go phase. some cells, such as muslce and nerve cells, remain there permanently, others, such as liver cells, can resume G1 phase in response to factors released druing injury. The ability to enter Go accounts for the incredible diversity seen in the lenght of the cell cycle in different tissues. Epithelial cells lining the human gut divide more than twice a day, constantly renewing this lining. By contrast, liver cells divide only once every year or two, spending most of their time in the Go phase. Mature neurons and muslces cells as stated usually never leave Go. 

• S (syntehsis): In contrast to bacteria which replicate their DNA continually, DNA replication in most eucaryotic cells occurs only during a specific part of the cell division cycle, called the DNA synthesis phase or S phase. In a mammalian cell, the S phase typically lasts for around 8 hours. 

• G2 (gap phase 2): is the phase between S phase and mitosis. 

M Phase: (Mitosis and Cytokinesis)

Mitosis and cytokineses (below) are usually referred to collectivley as M phase. 

In late interphase (G2), the cytoplasms contains two centrosomes. Within the nucleus, the chromosomes are duplicated, but cannot yet be distinguished individually because they are still in the form of loosely pakced chromatin fibers.

After the chromosomes duplicate during interphase, a series of stages occurs during mitosis: prophase, metaphase, anaphase and telophase as described below. Cytokinesis then divides the cytoplasm, yielding two genetically dientical daugher cells. 

Prophase: In the nucleus, the chromatin fibers coil, so that the chromosomes become thick enough to be seen individually with a light microscope. Each chromosome exsits as two identical sister chromatids joined together at the centromere. In the tyoplasms, the mitotic spindle begins to form. Late in prophase, the nuclear envelope breaks into pieces, the spindle tracks attach to the centromeres of the chromosomes and move toward the center of the cell.

Metaphase: The mitotic spindle is now fully formed. The centromeres of all the chromosomes line up between the two poles of the spindle. For each chromosome, the tracks of the mitotic spindle attached to the two sister chromatids pull toward opposite poles. 

Anaphase: The sister chromatids of each chromosomes separate and move toward opposite poles of the cell. Separation of sister chromatids during mitosis depends on microtubules attaching to proteins found in the kinetochore. 

Telophase: The nuclear envelope forms, the chromosomes uncoil and the spindle disappears. Cytokineses, the division of the cytoplasms occurs. In animals, a cleavage furrow pinches the cell in two, producing two daughter cells. 

Meiosis

Both somatic cells (nonrerpdouctive cells) and germ-line cells are diploid. The cirtical difference is that somatic cells undergo mitosis to form genetically idnetical, diploid daughter cells, but germ-line cells can undergo meiosis to produce haploid gamets. Germ-line cells contained in the sexual organs of the male and female can undergo meiosis to produce haploid gametes (eggs and sperm). As only one set of chromosomes are present in the gametes, they are haploid. Germ cells are diploid at the beginning of their development, but become haploid during the process of gametogenesis.Subsequent to feritzation of the sperm and egg to become diploid, with one set 23 chromosomes from the father and one set of 23 chromosomes form the mother in the human. 

The process of cell division that produces haploid gametes in diploid organisms, resembles mitosis, but with two important differences. First, the number of chromosomes is cut in half. In meiosis, a cell that has duplicated its chromosomes undergoes two consecutive divisions called meiosis I and meiosis II. Because one duplication of the chromosomes is followed by two divisions, each of the 4 daugters cells resulting from meiosis has a haploid set of chromosomes -half as many chromosomes as the starting cell. In other words, meiosis entails two nucler and cytoplasmic divisions (duplication, division in half, then division in half again), yielding four haploid cells. 

Meiosis I: Homologous Chromosomes Separate

–Interphase: As with mitosis, meiosis is preceded by an interphase during which the chromosomes duplicate. Each chromosomes then consists of two identical sister chromatids. 

–Prophase I: As the chromosomes coil up, special proteins cause the homologous chromsomes to stick together in pairs. The resulting struture has 4 chromatids. Within each set, chromatids of the homologous chromosomes exchange corresponding segments -they “cross over“. Crossing over rearranges genetic information. The exchange of segments between nonsister chromatids –one maternal chromatid and one paternal chromatid of a homologous par adds to the genetic variety resulting from sexual reproduction. 

–Methaphase I: The homologous paairs are aligned in the middle of the cell. The sister chromatids of each chromosomes are still attached at their centromeres. 

–Anaphase I: The attachment between the homologous chromosomes of each pair breaks, the chromosomes now migrate toward the poles of the cell. In contrast to mitosis, the sister chromatids migrate as a pair instead of splitting up. They are separated not from each other but from their homologous partners. 

–Telophase I and Cytokinesis: In telophase I, the chromosomes arrive at the poles of the cell. Usually cytokineses occurs along with telophase I, and two haploid daughter cells are formed. 

Meiosis II: is like a mitotic division without DNA replication. 

Meiosis II is essentially the same as mitosis. The important difference is that meiosis II starts with a haploid cell that has not undergone chromosome duplication during the preceding interphase. 

–Prophase II: a spindle forms and moves the chromosomes toward the middle of the cell. 

–Metaphase II: the chromosomes are aligned as they are in mitosis, with the tracks attached to the sister chromatids of each chromosomes coming from opposite poles. 

–Anaphase II: The centromeres of sister chromatids separate and the sister chromatids of each pair move toward opposite poles of the cell.

–Telophase II: nucleus form at the cell poles and cytokinesis occurs. There are now four haplid daughter cells each with single chromosomes. 

The caspases, comprising a family of cysteine proteases, have been firmly established as major mediators of the execution phase of apoptosis. While most of the known CASPs are involved in apoptosis, others function as proinflammatory caspases, leading to the maturation of proinflammatory cytokines. Cross-linking of death receptors (TNFR1, Fas, and death receptor 3) can directly activate caspases, whereas most other apoptotic stimuli lead to mitochodnrial changes and a subsequent activation of the caspase cascade. 

Caspases have cysteine at their active site and cleave target proteins at specific aspartic acids.  All caspases share similarities in amino acid sequence. They are expressed as proenzymes that contain 3 domains; an N-terminal prodomain, a large subunit containing the active site cysteine and a C-terminal small subunit. Processing of caspases to a mature product occurs following different apoptotic stimuli, and requires cleavage at specific aspartic acid residues located between the different subdomains. Two types of proteases have been shown to perform this type of aspartic acid specific maturation: the caspases themselves and the serine protease granzyme B. 

Once activated, caspases cleave and thereby activate other procaspases, resulting in an amplifying proteolytic cascade. Some of the activated caspases then cleave other proteins in the cell like nuclear lamins and a protein that normally holds a DNAse in an inactivative form thereby paving the way for the DNAse to cut up the DNA in the cell nucleus. 

–Caspase 3 activation is said to be a critical initial event in the apoptosis enactment caspase cascade. In this cascade, cytochrome c, normally sequestered in the mitochondrial intermembrane space, is released through the mitochondrial outer membrane early during apoptosis and interacts with Apaf-1, dATP (or ATP), and procaspase 9, culminating in the proteolytic activation of the caspase 9 zymogen. Activated caspase 9 activates procaspase 3, and caspase 3, in turn, activates a DNA fragmentation factor (DFF)/caspase-activated DNase (CAD), which finally induces DNA fragmentation. 

—Inhibitors of Caspases

• Viral inhibitors of caspases: Several viruses encode proteins which inhibit caspases.

• p21 has been reported to inhibit caspase 3

Apaf-1: is a cell-death effector that acts with cytochrome c and caspase-9 to mediate p53 dependent apoptosis. It is a potential tumor suppressor.

Cytochrome c is normally sequestered in the mitochondria, but it is released into the cytosol on treatment with certain apoptotic stimuli. There, cytochrome c triggers oligomerization of Apaf-1, which then binds and activates Casp9. 

Caspase 12: is polymorphic which means that its sequence varies in different people.

Pathways for apoptosis induction or inhibition originate from both extrinsic and intrinsic signalling systems.

Extrinsic Activation of Apoptosis:The extrinsic pathway is initiated by ligand binding to cell surface death receptor, and this binding induces the assembly of a death-inducing signlaing complex that facilitates activation of initiator caspase-8.

Extrinsic signalling pathways are initiated by ligand binding to cell-surface receptors (e.g., Fas ligand binding to Fas/Apo1/CD95). Intrinsic signalling involves the activation and oligomerization of proteins (e.g., BAX) that are capable of binding and destablizing mitochondrial membranes. In most cases, both extrinsic and intrinsic apoptosis require the activation of a family of proteases (CASPASES) and culminate in the participation of nucleases and other destructive enzymes that eliminate cells without eliciting inflammation. Both apoptotic pathways converge on the activation of caspase-3 which is the executioner of apoptosis.

• : The extrnsic pathway is mediated by ligation of a death receptor upon its binding to a death-inducing ligand that results in the activation of caspase-8, which activates caspase3. Extrinsic initiation of apoptosis occurs by stimulation of sets of surface receptors (e.g.,  or TNFR) by their cognate ligands. This results in trimerization and docking of proteins containing so-called death domains which in turn activate large amounts of caspase 8, an initiator caspase, followed directly by cleavage of downstream effector caspases in Type I cells. By contrast, Type II cells produce little activate caspase 8 and therefore relay on a mitochondrial amplification step.

The extrinsic pathway can be induced by interactions between  (such as , interferon-gamma and TGF-B) and death receptors, resulting in activation of Casp-8.  : 

Intrinsic Activation of Apoptosis: The intrinsic pathway involves induced permeabilization of the outer mitochondrial membrane, leading to the release of several proapoptotic factors, including cytochrome C and SMAC, that cooperate to faciliate activation of initiator caspase-9, which in turn, leads to activation of effector caspases such as caspase-3.

• : The instrinsic pathway is mediated by agents such as stress stimuli and toxins that cause the release of cytochrome c from mitochondria into the cytoplasms and result in activation of caspase-9 which activates caspase-3. The Intrinsic induction of apoptotis starts within the cell and can occur by direct activation of caspases or a variety of stress-related mechanisms. The intrinsic pathway is triggered in response to a variety of apoptotic stimuli including anticancer agents, oxidative damage, UV irradiation and growth factor withdrawal and is mediated through mitochondria. These stimuli induce the loss of mitochondrial membrane integrity and result in the critical event — release of multiple molecules, including cytochrome c (cyt c), which associates with Apaf-1 and Casp-9 to promote caspase activation.

The release of cytochrome c is largely controlled by members of proteins of the Bcl-2 family, which can act to promote or to inhibit this release. On a molecular level, free cytosolic cytochrome c initiates the formation of a signaling complex (called the apoptosome) that encompasses the molecules Apaf-1 and the proteases caspase-9 and caspase-3. In the formation of this complex, caspase-9 is activated with in turn activates caspase-3. Active caspase-3 then cleaves cellular substrates to bring about the morphological changes of apoptosis such as nuclear condensation.

• granzyme B pathway, where the cytotoxic cell protease granzyme B is delivered to sensitive target cells.

Although apoptosis through death receptors does not appear to require the involvement of mitochondria, several levels of cross-talking exist between these two pathways. For example, the Bcl-2 family plays an important role in this cross-talking by acting on mitochondria. Active capase-8, the downstream effector caspase of the extrinsic pathway can cleave the cytosolic Bid into the BH3-only domain-containing, proapoptotic, truncated tBid fragment which can translocate into mitochondria, where it binds to its mitochondrial proapoptotic partner Bax or Bak to trigger the release of cyt c into the cytosol. In certain cell lines, overexpression of Bcl-2/Bcl-xl prevents the efflux of cyt c from the mitochondria, and can prevent cell death receptor-induced apoptosis.

Apoptosis, or programmed cell death, is a process fundamental to the normal development and homeostasis of multicellular organisms. Deregulation of programmed cell death leads to a number of human diseases, including cancer, neurodegenerative disorders, and acquired immunodeficiency syndrome. The cell death machinery comprises effectors, activators, and negative regulators.

Apotosis should be distinguished from the more random process of necrotic cell death, which is closely associated with the inflammatory responses that are commonly observed during an infectious diesease. Necrosis elicits inflammation, whereas the recognition of apoptotic cells leads not only to phagocytosis but also to downregulation of inflammation via the anti-inflammatory cytokines TGF-? and IL-10 due to interaction of the phosphatidylserine (PS) phagocyte receptor with apoptotic cells.

See also  Apoptosis Assays

Apoptosis is necessary in Human Development and Maintenance

Apoptosis is vital in the following processes:

• (1) T lympocytes development: Most immature T cells are useless (incorrect rearrangement of the T cell receptor) or potentially detrimental (self-reactive) to the organisms. More than 95% of thymocytes that immigrate into the thymus are eliminated by positive and negative selection during their development. 

• (2) Killing of target cells by and NK cells: 

• (3) Immune privilege: Cellular immune response reactions and their associated inflammatory responses can cause nonspecific damage to nearby tissues. Although most organs can tolerate such inflammation, some, such as the eye and testis, cannot. These organs have mechanisms to protect themselves against unwanted immune reactions. Although inflammatory cells can enter these organs, they are killed by FasL expressed in the organs. This suggests a use for FasL as an immunosuppressive agent to target activated effector cells in transplantation. Interestingly, several groups have found that some tumor cells become resistant to Fas-induced apoptosis and constitutively express FasL. FasL expressed on tumor cells then counterattacks CTL and NK cells by binding Fas on their surfaces to cause apoptosis. This mechanism may account for the ability of tumor cells to evade immune destruction.

• • (4) Infectious Disease: It is clear that apoptosis has a direct role in many infectious diseases, especially those caused by viruses, intracellular protozoans and intracellular bacteria.

  Inducing Signals 

  Multiple physiologic and pathologic signals are capable of inducing apoptosis in disparate cell types, and multiple signal transduction processes result in apoptosis in different tissues. The process of apoptosis can be triggered by pleiotropic ways, including the following:

  • physical agents such as X-ray, y-irradiation

  • chemical agents such as cellular toxins, hormones, and natural signaling molecules such as tumor necrosis factor (TNF), transforming growth factor beta (TGF-B), and Fas ligand (FasL, CD95).

  • Growth factor withdrawl such as nerve growth factor withdrawal from neurons

  Signaling Pathways in Apoptosis

  Most forms of apoptosis converse on caspases as downstream effectors, and a significant body of work indicates that caspases are activated by one of tow main pathways, either the intrinsic or extrinsic pathway.

  Effector or Execution Pathways in Apoptosis

  The signals which induce apoptosis and the signalling traduction processes appear to be transduced to common effector or execution pathways. For example, each of the pathways above converges to a common execution phase of apoptosis that requires activation of caspases 3 and 7 from their inactive zymogen form to their processed, activate form. In apoptosis, caspases function in both initiation and execution of cell disassembly in response to apoptotic signal. 

  The activation of the cell death pathway depends on both the triggering stimulus and the cell type, and in many forms of apoptosis cytochrome c release from mitochondria is important for activation of downstream caspases. Programmed death of cells is affected by many of the same gene products controlling .

• Despite the large role which caspases play in apoptosis, noncapse proteases such as cathepsins D and B, calpains and various serine proteases have been reported as essential downstream effectors of caspases, for instance, in TNF-mediated apoptosis. Apoptosis can even occur in the complete absence of caspase activation. 

  Cathepsin D: has been proposed to mediate a regulated type of programmed cell death, initiated by various cytokines. 

  The known signaling pathways induced by various apoptotic stimuli converge into a common death pathway either at a mitochondrial step or finally at a step at which Asp-Glu-Val-Asp (DEVD)-specific caspase-3-like cysteine proteases are activated. Active caspase 3 like proteases cleave a limited set of cellular proteins, and the resulting inactivation/activation of substrates leads to the typical apoptotic morphology of the dying cell. Although the activation of a caspase cascade has been considered a hallmark of apoptosis, apoptotic pathways not requiring known caspases have been reported. For example, a proapoptotic protein Bax, which targets mitochondrail membranes; a topoisomerase I poison, camptothesin; and nitric oxide have been reported to induce apoptosis-like cell death with caspase activation. 

  Topoisomerase poisonsparticularly topoisomerase I inhibitors, induce apoptosis in many cells that lack functional . are ubiquitous enzymes that modulate the topographic structure of DNA by transiently introducing breaks in the DNA backbone. 

  Use of Apoptosis in the Treatment of Human Disease

  Not surprisingly, agents that induce apoptosis in cancer cells have attracted a great deal of attention. This makes sense, because if you can induce cancer cells to undergo programmed cell death, you can potentially eliminate the cancer.

  Morphological Changes Associated with Apoptosis

  In apoptosis a cell shrinks and condenses. The cytoskeleton collapses, the nuclear envelope disassembles and the nuclear DNA breaks up into fragments. The cell surface also displays a ) that cause the dying cell to be rapidly phagocytosed. All of these changes are v

• ery different from what happens in cell necrosis which is where a cell wells and bursts due to acute injury.

  Markers of Apoptosis

  • Cleavage of poly-(ADP-rebose) polymerase has been used as a surrogate marker for the entry of cells into the irreversible execution phase of apoptosis, even though this event appears likely to be an epiphenomenon

  • cleavage of the nuclear matrix protein lamin B is thought to be related to nuclear chromatin changes that occur during apoptosis.

Integrins are widely expressed cell surface adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. Integrins are the principal receptors on animal cells for binding most  like collagens, fibronectin and laminins. T cells have little apparent adhesion to integrin ligands. However, upon activation through T cell receptor or chemokine receptors, a cascade of signaling events leads to enhanced integrin functionality, known as “inside-out” signaling. it involves the translocation of proteins to integrin cytoplasmic domains and the assembly of multiprotin complexes. The formation of these complexes results in activation and clustering of integrins, thus enhancing both affinity and avidity of integrins for their ligands.

Integrins are cell adhersion receptors that transmit bidirectional signals across the plasma membrane and link the extracellular enviornment of a cell to the actin cytoskeleton. The conformation of the integrin extracellular domain and its affinity for ligand are dynamically regulated by a process termed “inside-out signaling”. Rapid upregulation of adhesiveness of integrins on platelets and white blood cells mediates homostasis and luekocyte trafficking to sies of inflammation. By coupling to the actin cytoskeleton, integrins promote firm adhesion and provide traction for laeml-lipodium protrusion and locamotion. (US 2010/0167418). 

Structure:

Integrins are transmembrane alpha-beta heterodimers and at least 18 alpha and eight beta subunits are knonw in human, generating 24 heterodimers. The alpha and beta subunits have distinct domain structures, with extracellular domains from each subunit contributing to the ligand-binding site of the hterodimer. Examples of integrins include alpha4beta7. (Singh, US 16/536, 777, published as US 2020/0088749). 

Integrins are composed of 2 noncovalently associated transmembrane glycoprotein subunits called alpha and beta. Integrins have been organized into eight distinct subfamilies based on beta subunit assocations. Members of the beta 1 subfamily (also called VLA proteins) each contain the beta1 subunit in association with one of at least nine difference alpha subunits. In the beta2 subfamily, there are 3 distinct alpha subunits which associate with beta2 (CD11/CD18). The other groups associated with the beta3-beta8 subfamilies have various roles and functions.

Alpha-4 Integrin family: 

The α4 integrin family includes one of the most broadly expressed integrins, α4β1, and two of the most specialized integrins, α4β7 and α9β1. Unique among integrins, α4β7 is a homing receptor that targets lymphocytes and specific leukocyte subsets in the bloodstream to mucosal tissues, especially the gut. The primary ligand for α4β7-mediated homing is mucosal adhesion molecule-1 (MAdCAM-1), an addressin with two immunoglobulin superfamily (IgSF) domains and a mucin-like stalk that is specifically expressed on Peyer’s patch high endothelial venules and postcapillary venules in lamina propria. (J. Cell Biol. 2012, 196(1)). 131-146). 

Regulation of Integrin Expression: 

Integrin binding to their ligands depend on extracellular divalent cations like Ca2+ reflecting the presence of divalent cation binding domains in the extracellular part of the subunits. 

Integrins bind to a matrix protein outside the cell and to the  via an anchor protein inside the cell. The binding to their ligands is of low affinity but high capacity. (binding depends on a large number of weak adhesions). The clustering of integrins at sites of contact with the matrix can activate intracellular signaling pathways. Many of the signaling functions of integrins depend on a cytoplasmic protein tyrosine kinase called focal adhesion kinase (FAK). When integrins cluster at sites of cell-matrix contact, FAK is recruited to focal adhesions by intracellular anchor proteins such as talin or paxillin. The clustered FAK molecules cross phosphorylate each other on a specific tyrosine for members of the Src family of cytoplasmic .

A cell can also control integrin ligand interactions from within (inside out signaling) which allows regulated adhesion. This is important for example with T lymphocytes where the weak binding of a T lymphocyte to its specific antigen on the surface of an antigen presenting cell triggers intracellular signaling pathways that activate its integrins. The activated integrins enable the T cell to remain in contact long enough to become fully stimulated.

Integrins and Disease: 

During adhesion and transmigration, integrins of the beta1 and beta2 family, such as VLA4 (alpha4-beta1) or LFA-1 (alphaLbeta2), bind to their endothelial counter-receptors vascular cell adhesion molecule (VCAM)-1 and intercellular adhesion molecule (ICAM)-1, respectively. EAE: Numerous studies have shown that adhesion of lymphocytes to inflamed brain vessels during EAE is mainly mediated by the VLA-4-VCAM-1 system, although there is also evidence pointing to the role of the LFA-1-ICAM-1 interaction. 

Atherosclerosis: Vascular cell adhesion molecules determine which type of luekocytes are recruited by selectively expressing specific adhesion molecules uch as vascular cell adhesion molecule-1 (VCAM-1), intracellular adhesion molecule-1 (ICAM-1) and E-selectin. Subsequent conversion of leucocytes to foramy macrophages results in the synthesis of a wide variety of inflammatory cytokines, growth factors and chemoattractants that help popagate the leukocyte and platelet recruitment, smooth muscle cell proliferation, endothelial cell activation and extracellular matrix synthesis characteristic of maturing atherosclerotic plaque. 

HIV: The HIV cell surface glycoprotein, gp120, was shown to directly bind alpha4beta7 potentially facilitating HIV entrance into CD4 T cells. Several but not all integrin blocking antibodies reduced viral replication in CD4 T cell cultures.

Therapeutics: 

Natalizumab is a humanized anti-alpha4 integrin antibody that is approved for treatment of both MS and Crohn’s disease.

Vedolizumab is a gut-specific, alpha4beta7 integrin neutralizing mAb which does not affect peripheral blood cell counts and appears to lack systemic effects. 

(Singh, US 16/536, 777, published as US 2020/0088749).