18-03-2011, 03:28 PM
PRESENTED BY:
HARISH KUMAR.G
[attachment=10510]
INTRODUCTION
• A vast range of molecular biology, cellular biology, and advanced validation tools are available in modern medical research today, and some of these tools, capable of separating proteins on gel then identifying them using lasers, have given rise –over the last 25 years – to a novel science called proteomics. Proteomics tools are broadly applied in human disease. They allow the classification of diseases on a molecular basis, giving deep insights into the patho physiology and prognosis of disorders, and finally providing a systematic search for diagnostic and therapeutic targets. Many pharmaceutical companies have been working for years on the ap-plication of proteomics in disease, some of them having invested hundreds of mil-lions of dollars in the necessary infrastructures. Proteomics research consortia are also funded by the state in various countries, in particular in the USA, Canada,France, and Germany.
INDIVIDUAL PROTIEN PATTERNS IN CLINICAL PRACTICE
• A prerequisite for such pattern-based protein studies is access to well-characterized normal and pathological samples obtained from human patients at different stages of disease or from normal volunteers for comparison purposes, as well as access to clinical follow-up data, including treatment and outcome data.
• In practice, such access is limited by a number of boundaries. The access to normal tissues is especially difficult in the case of volunteers, who should, of course, not be put into any danger by sampling procedures. Another point is to decide if physicians have the right to use organs, tissues, and/or body fluids obtained from their patients for their own research, or if these patients remain the owners of the parts separated from their body. It is obvious that major economic interests depend on the answer to this question. Marketing of body fluids, for ex-ample blood or plasma pheresis products, or of organs such as maternal placenta.
WHAT IS HUMAN MATERIAL
• Human samples include cadavers, organs, tissues, cells, body fluids, hair, nails,and body waste products. A cadaver is defined as a dead human body. Organs mean any human organ (heart, liver, kidney, lung, pancreas, small bowel, etc.).Human tissues include normal or pathologic human tissues obtained from biop-sies or surgical specimens, including corneas
• Somatic cells are cells from any body organ, including stem cells from the umbilical cord or bone marrow, but not sperm, ovula, and embryonic stem cells. Gonadic cells include sperm and ovula. Embryonic (stem) cells are cells obtained from a human embryo. Body fluids include blood, products derived from blood and cerebrospinal fluid. Hair, nails, and body waste products (urine, stool) are components of the human body that are traditionally excluded from the categories above. It is important to note that a given sample can eventually change category (e.g. products derived from an embryonic stem cell might be used in tissue engineering or in organ transplantation).
NEW RESEARCH TOOLS, OLD PROBLEMS
• The rapid development of biotechnologies over the last 25 years has generated a number of bioethical questions, and although these questions might – at first sight – appear new, a careful analysis shows that this is not the case. The human corpse has held great symbolic significance in various civilizations. In ancient Egypt, performing an incision into the body in order to remove the organs for embalming was considered to be an injury to the integrity of the dead person; the other embalmers present would throw stones at the man who made the cut.Since they weren’t really trying to hurt him, this has to be considered as a symbolic part of the ceremony. The ancient Hebrews, in a practice that continues in orthodox Judaism, expressed concerns about the desecration of the body by “mutilation” and have shaped a long tradition of resistance to the dissection of Jews for teaching purposes. Thus, the symbolic meaning attached to human tissue is a permanent feature in history, at least since the Antiquity. In modern time, the problem has become more complex because of the vanishing frontiers in the definition and limits of “human tissues”, and because some experimental procedures now allow some human materials to be immortalized.
PROTIEN TECHNOLOGIES,DIAGNOSIS AND PROGNOSIS
• So far, most current diagnostic tests are based on the detection and quantification of single proteins in body fluids. The direct availability of these proteins in body fluids, in particular in the serum, is an important feature in clinical practice, be-cause repeated sampling is possible with minimal need for invasive tests. For ex-ample, tests such as carcino embryonary antigen (CEA) in colorectal cancer, prostate specific antigen (PSA) in prostate cancer, alpha-fetoprotein (AFP) in hepato cellular carcinoma, etc. are currently used in clinical practice. Historically, these tests– most of them based on ELISA technology – were developed only on empirical grounds based on observation and correlation of measured levels of single proteins with the diagnosis or recurrence of disease. A common characteristic is their relatively low predictive value, so that they cannot be used alone for diagnostic purposes, and they have to be complemented with other procedures, in cancer usually a biopsy.
• In the meantime, as introduced above, novel analytical tools have turned attention to possible improvements of these classical tests in order to improve their specificity and thus their potential for diagnosis, in particular for population screening. Recently, genomic, polymerase chain reaction (PCR)-based diagnostic tests have been introduced into the market. In proteomics research, patterns of protein expression have been shown to yield more biologically relevant and clinically useful information than assays of single proteins. For example, protein chips coupled with SELDI/TOF-MS (surface-enhanced laser desorption ionization/time-of-flight mass spectrometry), when coupled to a pattern-matching algorithm, haveled to the identification of biomarker patterns in pancreatic juice, urine, or serum,which correctly classified cancer and non-cancer with high sensitivity and specificity in patient populations suffering from several cancers.
THE DIMENSIONS OF PROGNOSIS
• As Hippocrates recognized more than 2000 years ago, forecasting plays a centralrole in decision making in medicine, and prognosis concerns not only the end ofdisease, but also its progression and its duration:
• “By foreseeing and foretelling, in the presence of the sick, the present, thepast, and the future ..., he (the physician) will be the more readily believedto be acquainted with the circumstances of the sick; so that men will haveconfidence to in trust themselves to such a physician. And he will managethe cure best who has foreseen what is to happen from the present state ofmatters.” (The Book of Prognosis)
• The patient’s history helps to predict prognosis. Different endpoints of interest can be evaluated, which may be multiple (for example, as Hippocrates had al-ready recognized, survival or therapy response). Prognosis also changes with the therapeutic choices made. A prognosis can vary over time. Thus, in contrast to diagnosis, prognosis is multidimensional.
• In modern, scientific medical thinking, prognosis depends on a collection of variables called prognostic factors. In cancer, for example, prognostic factors in-clude macroscopic and microscopic characteristics of diseased organs and tissues. However, prognostic factors concern not only the diseased organ, but also the patient and the treatment administered. In solid cancers, the most decisive prognostic factor is the result of the surgical resection – microscopically curative or not –information that cannot and never will be provided by a molecular pattern. Thus, and this is a significant boundary for biomedical application of proteomics, theanalysis of diseased tissues or organs alone, for example with proteomics tools, will only provide part of the prognostic information.
• As a corollary of the above, molecular data have to be linked to personalized clinical information in prognostic and therapeutic biomedical research, including validation tasks. To be able to achieve accurate forecasting or validation (e.g. therapy response studies), prospective data acquisition is necessary over many months or even years.
• In clinical practice, the number of clinical and pathological variables considered in a particular case is usually between 10 and 100. Of course, this conventional prognostic information gives the clinical framework for proteomics studies, and not the opposite. A second consequence will be detailed below, namely that the need for personalized information in proteomics studies generates a series of ethical, information, privacy, property, and consent problems.
DIAGNOSIS AND PROGNOSIS
• Two core disciplines of modern medicine are diagnosis and prognosis, which are often considered together. For example, in almost every family an unfortunate des-tiny illustrates that cancer diagnosis is associated with dismal prognosis. In medical oncology, both disciplines are also closely associated. The best proof is given by the International Union against Cancer (UICC) classification itself, which fore-casts a particular patient’s prognosis by defining the extent of disease at the time of diagnosis. Modern developments in proteomics tend to perpetuate this traditional association between diagnosis and prognosis, since molecular markers of disease can often be used for both purposes, at least when the question is discussed at the bench. However, when considered from the bedside, associating diagnosis with prognosis is an oxymoron: diagnosis is a generalization, the result of a classification that is independent of the individual case, while the prognosis de-scribes the probable course of the illness in a particular patient. Another distinction has to be made in terms of time. Diagnosis freezes the disease process, pro-viding the physician (and the patient) with a snapshot picture. In contrast, prognosis expands a momentary state into a defined time sequence, a kind of motion picture.
• In molecular medicine, a diagnosis can be made by identifying common traits between sick people. For example, common proteomics patterns can be deter-mined in cancer patients: this approach is usually called “expression proteomics”.In contrast, to forecast prognosis, only those qualitative and quantitative differ-ences in protein expression that ultimately result in dysfunction in cellular behavior and thus in clinical phenotype over time are selected (so-called functional proteomics).
USING HUMAN TISSUE IN BIOMEDICAL RESEARCH – POTENTIAL PITFALLS
• When, or preferably before, using human tissue or body fluids in biomedicine, the researcher should be aware of the potential pitfalls. Privacy for the living and for the dead and profit for biomedical researchers are two issues of importance for the patient, who is the primary supplier of human samples, and for their rela-tives. Recent scandals have highlighted the growing need to enforce patient’s consent, and to safeguard the identity and civil rights of donors and relatives. They have also underscored the potential risks for a researcher or for a physician in performing research or transferring human tissue to a third party without having obtained a formal authorization from the patient or their relatives.
• UNESCO has contributed to the elaboration of the ethical framework surrounding biomedical research by formulating the principles of the Universal Declaration on the Human Genome and Human Rights, adopted in 1998. Article 5a de-fines the rights of those who undergo “research, treatment or diagnosis” on their own genome. Article 5c affirms respect for the right of each person to decide whether or not to be informed of the results of a genetic examination. In Europe, the only binding instrument on bioethics is the Convention for the Protection of Human Rights and the Dignity of Human Being with regard to the Application of Biology and Medicine – the so-called Convention on Human Rights and Bio medicine – adopted in 1997 by the Council of Europe. Article 21 of the Convention de-clares that the human body and its parts shall not, as such, give rise to financial gain. Article 22 states that, “when in the course of an intervention any part of a human body is removed, it may be stored and used for a purpose other than that for which it was removed, only if this is done in conformity with appropriate information and consent procedures”.
SPECIFICITY OF PROTEOMICS
• As we stated at the beginning of this chapter, proteomics studies have so far played only a minor role in clinical medicine when compared with genetic stud-ies, but this role is expected to increase over the next years. Proteomics studies, more than genetic investigations, allow the investigation of disease over time, and often require repeated analyses over the course of disease. Clearly, anonymization of probes is not directly compatible with such follow-up studies, although the problem can be circumvented by contracting a third party for anonymization and follow-up tasks, so that the biological information never comes into contact with the patient’s identity.
• Genetic studies barely allow the analysis of body fluids, at least when compared with proteomics studies. Ethics committee usually deliver authorization for sampling a few milliliters of blood or serum in patients or in normal volunteers more easily than for performing biopsies. In this respect, proteomics researchers might benefit from favorable framework conditions. However, the problem of serum analysis in biomedical proteomics research is complicated by the large quantities (up to several liters) of serum that are necessary to identify certain peptides pre-sent in a very low concentration, so that the serum of hundreds of patients has to be pooled.
• Finally, another important specificity of proteomics studies is that they do not amplify genetic information, so that the data protection and privacy issues are less important than when performing, for example, genome-wide cDNA expression studies. However, researchers should not overestimate this difference since even a single but significant piece of information gained from the protein pattern might imply significant privacy issues.
CONCLUSION
• Over the last two decades, medical research has begun to make extensive use of products of human origin in diagnostics, therapeutics, and most recently, in predictive medicine. It is now expected that modern medicine will shift from a generalized, impersonal scientific knowledge to a singular, individual, personalized practice. Since proteomics analyze the functional molecules of a normal or dis-eased cell, and because proteomics take into account dynamic aspects over time, itis expected that this novel science will make a major contribution to the development of medical art.
• By analyzing tissues of human origin, linking disease and/or risk-specific molecular patterns with patient identity, the researcher is endorsing potential risks linked to protection of privacy, violation of existing or future legislation, unauthorized or unethical use of samples, financial claims on research results, non-communication of prognostic information of potential risks, etc.
• The ethical questions raised by molecular research, in particular the balancing of the interests of greater control – defended by patients’ organizations – versus wider access to human biological samples and related data – supported by industry and insurance companies – will be the subject of renewed controversy. This will challenge the ability of the researchers’ community to deliver innovation and the capacity of governments to deal ethically with the protection of the rights of patients.
• In everyday practice, in the absence of clearly established national and international frameworks these many issues can accurately be addressed by ensuring transparent informed patient consent.
HARISH KUMAR.G
[attachment=10510]
INTRODUCTION
• A vast range of molecular biology, cellular biology, and advanced validation tools are available in modern medical research today, and some of these tools, capable of separating proteins on gel then identifying them using lasers, have given rise –over the last 25 years – to a novel science called proteomics. Proteomics tools are broadly applied in human disease. They allow the classification of diseases on a molecular basis, giving deep insights into the patho physiology and prognosis of disorders, and finally providing a systematic search for diagnostic and therapeutic targets. Many pharmaceutical companies have been working for years on the ap-plication of proteomics in disease, some of them having invested hundreds of mil-lions of dollars in the necessary infrastructures. Proteomics research consortia are also funded by the state in various countries, in particular in the USA, Canada,France, and Germany.
INDIVIDUAL PROTIEN PATTERNS IN CLINICAL PRACTICE
• A prerequisite for such pattern-based protein studies is access to well-characterized normal and pathological samples obtained from human patients at different stages of disease or from normal volunteers for comparison purposes, as well as access to clinical follow-up data, including treatment and outcome data.
• In practice, such access is limited by a number of boundaries. The access to normal tissues is especially difficult in the case of volunteers, who should, of course, not be put into any danger by sampling procedures. Another point is to decide if physicians have the right to use organs, tissues, and/or body fluids obtained from their patients for their own research, or if these patients remain the owners of the parts separated from their body. It is obvious that major economic interests depend on the answer to this question. Marketing of body fluids, for ex-ample blood or plasma pheresis products, or of organs such as maternal placenta.
WHAT IS HUMAN MATERIAL
• Human samples include cadavers, organs, tissues, cells, body fluids, hair, nails,and body waste products. A cadaver is defined as a dead human body. Organs mean any human organ (heart, liver, kidney, lung, pancreas, small bowel, etc.).Human tissues include normal or pathologic human tissues obtained from biop-sies or surgical specimens, including corneas
• Somatic cells are cells from any body organ, including stem cells from the umbilical cord or bone marrow, but not sperm, ovula, and embryonic stem cells. Gonadic cells include sperm and ovula. Embryonic (stem) cells are cells obtained from a human embryo. Body fluids include blood, products derived from blood and cerebrospinal fluid. Hair, nails, and body waste products (urine, stool) are components of the human body that are traditionally excluded from the categories above. It is important to note that a given sample can eventually change category (e.g. products derived from an embryonic stem cell might be used in tissue engineering or in organ transplantation).
NEW RESEARCH TOOLS, OLD PROBLEMS
• The rapid development of biotechnologies over the last 25 years has generated a number of bioethical questions, and although these questions might – at first sight – appear new, a careful analysis shows that this is not the case. The human corpse has held great symbolic significance in various civilizations. In ancient Egypt, performing an incision into the body in order to remove the organs for embalming was considered to be an injury to the integrity of the dead person; the other embalmers present would throw stones at the man who made the cut.Since they weren’t really trying to hurt him, this has to be considered as a symbolic part of the ceremony. The ancient Hebrews, in a practice that continues in orthodox Judaism, expressed concerns about the desecration of the body by “mutilation” and have shaped a long tradition of resistance to the dissection of Jews for teaching purposes. Thus, the symbolic meaning attached to human tissue is a permanent feature in history, at least since the Antiquity. In modern time, the problem has become more complex because of the vanishing frontiers in the definition and limits of “human tissues”, and because some experimental procedures now allow some human materials to be immortalized.
PROTIEN TECHNOLOGIES,DIAGNOSIS AND PROGNOSIS
• So far, most current diagnostic tests are based on the detection and quantification of single proteins in body fluids. The direct availability of these proteins in body fluids, in particular in the serum, is an important feature in clinical practice, be-cause repeated sampling is possible with minimal need for invasive tests. For ex-ample, tests such as carcino embryonary antigen (CEA) in colorectal cancer, prostate specific antigen (PSA) in prostate cancer, alpha-fetoprotein (AFP) in hepato cellular carcinoma, etc. are currently used in clinical practice. Historically, these tests– most of them based on ELISA technology – were developed only on empirical grounds based on observation and correlation of measured levels of single proteins with the diagnosis or recurrence of disease. A common characteristic is their relatively low predictive value, so that they cannot be used alone for diagnostic purposes, and they have to be complemented with other procedures, in cancer usually a biopsy.
• In the meantime, as introduced above, novel analytical tools have turned attention to possible improvements of these classical tests in order to improve their specificity and thus their potential for diagnosis, in particular for population screening. Recently, genomic, polymerase chain reaction (PCR)-based diagnostic tests have been introduced into the market. In proteomics research, patterns of protein expression have been shown to yield more biologically relevant and clinically useful information than assays of single proteins. For example, protein chips coupled with SELDI/TOF-MS (surface-enhanced laser desorption ionization/time-of-flight mass spectrometry), when coupled to a pattern-matching algorithm, haveled to the identification of biomarker patterns in pancreatic juice, urine, or serum,which correctly classified cancer and non-cancer with high sensitivity and specificity in patient populations suffering from several cancers.
THE DIMENSIONS OF PROGNOSIS
• As Hippocrates recognized more than 2000 years ago, forecasting plays a centralrole in decision making in medicine, and prognosis concerns not only the end ofdisease, but also its progression and its duration:
• “By foreseeing and foretelling, in the presence of the sick, the present, thepast, and the future ..., he (the physician) will be the more readily believedto be acquainted with the circumstances of the sick; so that men will haveconfidence to in trust themselves to such a physician. And he will managethe cure best who has foreseen what is to happen from the present state ofmatters.” (The Book of Prognosis)
• The patient’s history helps to predict prognosis. Different endpoints of interest can be evaluated, which may be multiple (for example, as Hippocrates had al-ready recognized, survival or therapy response). Prognosis also changes with the therapeutic choices made. A prognosis can vary over time. Thus, in contrast to diagnosis, prognosis is multidimensional.
• In modern, scientific medical thinking, prognosis depends on a collection of variables called prognostic factors. In cancer, for example, prognostic factors in-clude macroscopic and microscopic characteristics of diseased organs and tissues. However, prognostic factors concern not only the diseased organ, but also the patient and the treatment administered. In solid cancers, the most decisive prognostic factor is the result of the surgical resection – microscopically curative or not –information that cannot and never will be provided by a molecular pattern. Thus, and this is a significant boundary for biomedical application of proteomics, theanalysis of diseased tissues or organs alone, for example with proteomics tools, will only provide part of the prognostic information.
• As a corollary of the above, molecular data have to be linked to personalized clinical information in prognostic and therapeutic biomedical research, including validation tasks. To be able to achieve accurate forecasting or validation (e.g. therapy response studies), prospective data acquisition is necessary over many months or even years.
• In clinical practice, the number of clinical and pathological variables considered in a particular case is usually between 10 and 100. Of course, this conventional prognostic information gives the clinical framework for proteomics studies, and not the opposite. A second consequence will be detailed below, namely that the need for personalized information in proteomics studies generates a series of ethical, information, privacy, property, and consent problems.
DIAGNOSIS AND PROGNOSIS
• Two core disciplines of modern medicine are diagnosis and prognosis, which are often considered together. For example, in almost every family an unfortunate des-tiny illustrates that cancer diagnosis is associated with dismal prognosis. In medical oncology, both disciplines are also closely associated. The best proof is given by the International Union against Cancer (UICC) classification itself, which fore-casts a particular patient’s prognosis by defining the extent of disease at the time of diagnosis. Modern developments in proteomics tend to perpetuate this traditional association between diagnosis and prognosis, since molecular markers of disease can often be used for both purposes, at least when the question is discussed at the bench. However, when considered from the bedside, associating diagnosis with prognosis is an oxymoron: diagnosis is a generalization, the result of a classification that is independent of the individual case, while the prognosis de-scribes the probable course of the illness in a particular patient. Another distinction has to be made in terms of time. Diagnosis freezes the disease process, pro-viding the physician (and the patient) with a snapshot picture. In contrast, prognosis expands a momentary state into a defined time sequence, a kind of motion picture.
• In molecular medicine, a diagnosis can be made by identifying common traits between sick people. For example, common proteomics patterns can be deter-mined in cancer patients: this approach is usually called “expression proteomics”.In contrast, to forecast prognosis, only those qualitative and quantitative differ-ences in protein expression that ultimately result in dysfunction in cellular behavior and thus in clinical phenotype over time are selected (so-called functional proteomics).
USING HUMAN TISSUE IN BIOMEDICAL RESEARCH – POTENTIAL PITFALLS
• When, or preferably before, using human tissue or body fluids in biomedicine, the researcher should be aware of the potential pitfalls. Privacy for the living and for the dead and profit for biomedical researchers are two issues of importance for the patient, who is the primary supplier of human samples, and for their rela-tives. Recent scandals have highlighted the growing need to enforce patient’s consent, and to safeguard the identity and civil rights of donors and relatives. They have also underscored the potential risks for a researcher or for a physician in performing research or transferring human tissue to a third party without having obtained a formal authorization from the patient or their relatives.
• UNESCO has contributed to the elaboration of the ethical framework surrounding biomedical research by formulating the principles of the Universal Declaration on the Human Genome and Human Rights, adopted in 1998. Article 5a de-fines the rights of those who undergo “research, treatment or diagnosis” on their own genome. Article 5c affirms respect for the right of each person to decide whether or not to be informed of the results of a genetic examination. In Europe, the only binding instrument on bioethics is the Convention for the Protection of Human Rights and the Dignity of Human Being with regard to the Application of Biology and Medicine – the so-called Convention on Human Rights and Bio medicine – adopted in 1997 by the Council of Europe. Article 21 of the Convention de-clares that the human body and its parts shall not, as such, give rise to financial gain. Article 22 states that, “when in the course of an intervention any part of a human body is removed, it may be stored and used for a purpose other than that for which it was removed, only if this is done in conformity with appropriate information and consent procedures”.
SPECIFICITY OF PROTEOMICS
• As we stated at the beginning of this chapter, proteomics studies have so far played only a minor role in clinical medicine when compared with genetic stud-ies, but this role is expected to increase over the next years. Proteomics studies, more than genetic investigations, allow the investigation of disease over time, and often require repeated analyses over the course of disease. Clearly, anonymization of probes is not directly compatible with such follow-up studies, although the problem can be circumvented by contracting a third party for anonymization and follow-up tasks, so that the biological information never comes into contact with the patient’s identity.
• Genetic studies barely allow the analysis of body fluids, at least when compared with proteomics studies. Ethics committee usually deliver authorization for sampling a few milliliters of blood or serum in patients or in normal volunteers more easily than for performing biopsies. In this respect, proteomics researchers might benefit from favorable framework conditions. However, the problem of serum analysis in biomedical proteomics research is complicated by the large quantities (up to several liters) of serum that are necessary to identify certain peptides pre-sent in a very low concentration, so that the serum of hundreds of patients has to be pooled.
• Finally, another important specificity of proteomics studies is that they do not amplify genetic information, so that the data protection and privacy issues are less important than when performing, for example, genome-wide cDNA expression studies. However, researchers should not overestimate this difference since even a single but significant piece of information gained from the protein pattern might imply significant privacy issues.
CONCLUSION
• Over the last two decades, medical research has begun to make extensive use of products of human origin in diagnostics, therapeutics, and most recently, in predictive medicine. It is now expected that modern medicine will shift from a generalized, impersonal scientific knowledge to a singular, individual, personalized practice. Since proteomics analyze the functional molecules of a normal or dis-eased cell, and because proteomics take into account dynamic aspects over time, itis expected that this novel science will make a major contribution to the development of medical art.
• By analyzing tissues of human origin, linking disease and/or risk-specific molecular patterns with patient identity, the researcher is endorsing potential risks linked to protection of privacy, violation of existing or future legislation, unauthorized or unethical use of samples, financial claims on research results, non-communication of prognostic information of potential risks, etc.
• The ethical questions raised by molecular research, in particular the balancing of the interests of greater control – defended by patients’ organizations – versus wider access to human biological samples and related data – supported by industry and insurance companies – will be the subject of renewed controversy. This will challenge the ability of the researchers’ community to deliver innovation and the capacity of governments to deal ethically with the protection of the rights of patients.
• In everyday practice, in the absence of clearly established national and international frameworks these many issues can accurately be addressed by ensuring transparent informed patient consent.