Epilogue: Envisioning New Insights in Cancer Translational Biology
Author and Curator: Larry H Bernstein, MD, FCAP
The foregoing summary leads to a beginning as it is a conclusion. It concludes a body of work in the e-book series,
Series C: e-Books on Cancer & Oncology
Series C Content Consultant: Larry H. Bernstein, MD, FCAP
VOLUME ONE
Cancer Biology and Genomics for Disease Diagnosis
2014
Stephen J. Williams, PhD, Senior Editor
sjwilliamspa@comcast.net
tildabarliya@gmail.com
ritu.uab@gmail.com
Leaders in Pharmaceutical Business Intelligence
that has been presented by the cancer team of professional experts, e-Book concept was conceived by Aviva Lev-Ari, PhD, RN, e-Series Editor-in-Chief and Founder of Leaders in Pharmaceutical Business Intelligence
and the Open Access Online Scientific Journal
http://pharmaceuticalintelligence.com
Stephen J. Williams, PhD, Senior Editor, and other notable contributors in various aspects of cancer research in the emerging fields of targeted pharmacology, nanotechnology, cancer imaging, molecular pathology, transcriptional and regulatory ‘OMICS’, metabolism, medical and allied health related sciences, synthetic biology, pharmaceutical discovery, and translational medicine.
This volume and its content have been conceived and organized to capture the organized events that emerge in embryological development, leading to the major organ systems that we recognize anatomically and physiologically as an integrated being. We capture the dynamic interactions between the systems under stress that are elicited by cytokine-driven hormonal responses, long thought to be circulatory and multisystem, that affect the major compartments of fat and lean body mass, and are as much the drivers of metabolic pathway changes that emerge as epigenetics, without disregarding primary genetic diseases.
The greatest difficulty in organizing such a work is in whether it is to be merely a compilation of cancer expression organized by organ systems, or whether it is to capture developing concepts of underlying stem cell expressed changes that were once referred to as “dedifferentiation”. In proceeding through the stages of neoplastic transformation, there occur adaptive local changes in cellular utilization of anabolic and catabolic pathways, and a retention or partial retention of functional specificities.
This effectively results in the same cancer types not all fitting into the same “shoe”. There is a sequential loss of identity associated with cell migration, cell-cell interactions with underlying stroma, and metastasis., but cells may still retain identifying “signatures” in microRNA combinatorial patterns. The story is still incomplete, with gaps in our knowledge that challenge the imagination.
What we have laid out is a map with substructural ordered concepts forming subsets within the structural maps. There are the traditional energy pathways with terms aerobic and anaerobic glycolysis, gluconeogenesis, triose phosphate branch chains, pentose shunt, and TCA cycle vs the Lynen cycle, the Cori cycle, glycogenolysis, lipid peroxidation, oxidative stress, autosomy and mitosomy, and genetic transcription, cell degradation and repair, muscle contraction, nerve transmission, and their involved anatomic structures (cytoskeleton, cytoplasm, mitochondria, liposomes and phagosomes, contractile apparatus, synapse.
Then there is beneath this macro-domain the order of signaling pathways that regulate these domains and through mechanisms of cellular regulatory control have pleiotropic inhibitory or activation effects, that are driven by extracellular and intracellular energy modulating conditions through three recognized structures: the mitochondrial inner membrane, the intercellular matrix, and the ion-channels.
What remains to be done?
- There is still to be elucidated the differences in patterns within cancer types the distinct phenotypic and genotypic features that mitigate anaplastic behavior. One leg of this problem lies in the density of mitochondria, that varies between organ types, but might vary also within cell type of a common function. Another leg of this problem has also appeared to lie in the cell death mechanism that relates to the proeosomal activity acting on both the ribosome and mitochondrion in a coordinated manner. This is an unsolved mystery of molecular biology.
- Then there is a need to elucidate the major differences between tumors of endocrine, sexual, and structural organs, which are distinguished by primarily a synthetic or primarily a catabolic function, and organs that are neither primarily one or the other. For example, tumors of the thyroid and paratnhyroids, islet cells of pancreas, adrenal cortex, and pituitary glands have the longest 5 year survivals. They and the sexual organs are in the visceral compartment. The rest of the visceral compartment would be the liver, pancreas, salivary glands, gastrointestinal tract, and lungs (which are embryologically an outpouching of the gastrointestinal tract), kidneys and lower urinary tract. Cancers of these organs have a much less favorable survival (brain, breast and prostate, lymphatic, blood forming organ, skin). The case is intermediate for breast and prostate between the endocrine organs and GI tract, based on natural history, irrespective of the available treatments. Just consider the dilemma over what we do about screening for prostate cancer in men over the age of 60 years age who have a 70 percent incident silent carcinoma of the prostate that could be associated with unrelated cause of death. The very rapid turnover of the gastric and colonic GI epithelium, and of the subepithelial B cell mucosal lymphocytic structures is associated with a greater aggressiveness of the tumor.
- However, we have to reconsider the observation by NO Kaplan than the synthetic and catabolic functions are highlighted by differences in the expressions of the balance of the two major pyridine nucleotides – DPN (NAD) and TPN (NADP) – which also might be related to the density of mitochondria which is associated with both NADP and synthetic activity, and with efficient aerobic function. These are in an equilibrium through the “transhydrogenase reaction” co-discovered by Kaplan, in Fritz Lipmann’s laboratory. There does arise a conundrum involving the regulation of mitochondria in these high turnover epithelial tissues that rely on aerobic energy, and generate ATP through TPN linked activity, when they undergo carcinogenesis. The cells replicate and they become utilizers of glycolysis, while at the same time, the cell death pathway is quiescent. The result becomes the introduction of peripheral muscle and liver synthesized protein cannabolization (cancer cachexia) to provide glucose from proteolytic amino acid sources.
- There is also the structural compartment of the lean body mass. This is the heart, skeletal structures (includes smooth muscle of GI tract, uterus, urinary bladder, brain, bone, bone marrow). The contractile component is associated with sarcomas. What is most striking is that the heart, skeletal muscle, and inflammatory cells are highly catabolic, not anabolic. NO Kaplan referred tp them as DPN (NAD) tissues. This compartment requires high oxygen supply, and has a high mechanical function. But again, we return to the original observations of enrgy requirements at rest being different than at high demand. At work, skeletal muscle generates lactic acid, but the heart can use lactic acid as fuel,.
- The liver is supplied by both the portal vein and the hepatic artery, so it is not prone to local ischemic injury (Zahn infarct). It is exceptional in that it carries out synthesis of all the circulating transport proteins, has a major function in lipid synthesis and in glycogenesis and glycogenolysis, with the added role of drug detoxification through the P450 system. It is not only the largest organ (except for brain), but is highly active both anabolically and catabolically (by ubiquitilation).
- The expected cellular turnover rates for these tissues and their balance of catabolic and anabolic function would have to be taken into account to account for the occurrence and the activities of oncogenesis. This is by no means a static picture, but a dynamic organism constantly in flux imposed by internal and external challenges. It is also important to note the the organs have a concentration of mitochondria, associated with energy synthetic and catabolic requirements provided by oxygen supply and the electron transport mechanism for oxidative phosphorylation. For example, tissues that are primarily synthetic do not have intermitent states of resting and high demand, as seen in skeletal muscle, or perhaps myocardium (which is syncytial and uses lactic acid generated from skeletal muscle when there is high demand).
- The existence of lncDNA has been discovered only as a result of the human genome project (HGP). This was previously known only as “dark DNA”. It has become clear that lncDNA has an important role in cellular regulatory activities centered in the chromatin modeling. Moreover, just as proteins exhibit functionality in their folding, related to tertiary structure and highly influenced by location of –S-S- bridges and amino acid residue distances (allosteric effects), there is a less studied effect as the chromatin becomes more compressed within the nucleus, that should have a bearing on cellular expression.
According to Jose Eduardo de Salles Roselino , when the Na/Glucose transport system (for a review Silvermann, M. in Annu. Rev. Biochem.60: 757-794(1991)) was found in kidneys as well as in key absorptive cells of digestive tract, it should be stressed its functional relationship with “internal milieu” and real meaning, homeostasis. It is easy to understand how the major topic was presented as how to prevent diarrheal deaths in infants, while detected in early stages. However, from a biochemical point of view, as presented in Schrödinger´s What is life?, (biochemistry offering a molecular view for two legs of biology, physiology and genetics). Why should it be driven to the sole target of understanding genetics? Why the understanding of physiology in molecular terms should be so neglected?
From a biochemical point of view, here in a single protein. It is found the transport of the cation most directly related to water maintenance, the internal solvent that bath our cells and the hydrocarbon whose concentration is kept under homeostatic control on that solvent. Completely at variance with what is presented in microorganisms as previously mentioned in Moyed and Umbarger revision (Ann. Rev42: 444(1962)) that does not regulates the environment where they live and appears to influence it only as an incidental result of their metabolism.
In case any attempt is made in order to explain why the best leg that supports scientific reasoning from biology for medical purposes was led to atrophy, several possibilities can be raised. However, none of them could be placed strictly in scientific terms. Factors that bare little relationship with scientific progress in general terms must also be taken into account.
One simple possibility of explanation can be found in one review (G. Scatchard – Solutions of Electrolytes Ann. Rev. Physical Chemistry 14: 161-176 (1963)). A simple reading of it and the sophisticated differences among researchers will discourage one hundred per cent of biologists to keep in touch with this line of research. Biochemists may keep on reading. However, consider that first: Complexity is not amenable to reductionist vision in all cases. Second, as coupling between scalar flows such as chemical reactions and vector flows such as diffusion flows, heat flows, and electrical current can occur only in anisotropic system…let them with their problems of solvents, ions and etc. and let our biochemical reactions on another basket. At the interface, for instance, at membrane level, we will agree that ATP is converted to ADP because it is far from equilibrium and the continuous replenishment of ATP that maintain relatively constant ATP levels inside the cell and this requires some non-stationary flow.
Our major point must be to understand that our biological limits are far clearer present in our limited ability to regulate the information stored in the DNA than in the amount of information we have in the DNA as the master regulator of the cells.
The amazing revelation that Masahiro Chiga (discovery of liver adenylate kinase distinct from that of muscle) taught me (LHB) is – draw 2 circles that intersect, one of which represents what we know, the other – what we don’t know. We don’t teach how much we don’t know! Even today, as much as 40 years ago, there is a lot we need to get on top of this.
The observation is rather similar to the presentations I (Jose Eduardo de Salles Rosalino) was previously allowed to make of the conformational energy as made by R Marcus in his Nobel lecture revised (J. of Electroanalytical Chemistry 438:(1997) p251-259. His description of the energetic coordinates of a landscape of a chemical reaction is only a two-dimensional cut of what in fact is a volcano crater (in three dimensions) ( each one varie but the sum of the two is constant. Solvational+vibrational=100% in ordinate) nuclear coordinates in abcissa. In case we could represent it by research methods that allow us to discriminate in one by one degree of different pairs of energy, we would most likely have 360 other similar representations of the same phenomenon. The real representation would take into account all those 360 representation together. In case our methodology was not that fine, for instance it discriminate only differences of minimal 10 degrees in 360 possible, will have 36 partial representations of something that to be perfectly represented will require all 36 being taken together. Can you reconcile it with ATGC? Yet, when complete genome sequences were presented they were described as we will know everything about this living being. The most important problems in biology will be viewed by limited vision always and the awareness of this limited is something we should acknowledge and teach it. Therefore, our knowledge is made up of partial representations.
Even though we may have complete genome data for the most intricate biological problems, they are not so amenable to this level of reductionism. However, from general views of signals and symptoms we could get to the most detailed molecular view and in this case the genome provides an anchor. This is somehow, what Houssay was saying to me and to Leloir when he pointed out that only in very rare occasions biological phenomena could be described in three terms: Pacco, the dog and the anesthetic (previous e-mail). The non-coding region, to me will be important guiding places for protein interactions.
I like the first sentence of the second paragraph “The greatest difficulty in preparing such a book is to determine if one wants merely a collection of organ system cancer or to develop a conceptual framework which encompasses what we know and what we don’t know and how, as we investigate further, we uncover the increased complexity of the origins and development of the disease.
In point #2 I am assuming cancer arising from sexual tissue you would mean germ cell not necessarily from reproductive organs, which has sources of germ cells but the epithelial/mesenchymal cell is the origin of many solid tumors of reproductive origin.
Also point 4,5, and 6 are similar, highlighting our current understanding of the tumor metabolism is not comlete or do you suggest to classify certain tumors not just by their genetic but also by their metabolic differences as well. This would be a striking difference from the past where tumors were classified according to histologic differences and treatment options decided based on the findings from the pathologist.
It became clear in the 1980s and 90’s that metabolic differences would not be enough to explain all of the tumorigenicity phenotype and a genetic picture must be developed, including the current understanding of the importance of “dark DNA”. This shift in thinking was monumental in shifting strategies for diagnosis and treatment.
The shift in thinking was monumental, but it through away any concern about true phenotypic behavior. I moved some of that from the epilogue to the discussion, but I am working on this development further in the Prologue (preface).
1. highlighting our current understanding of the tumor metabolism is not complete
2. classify certain tumors not just by their genetic but also by their metabolic differences as well
Both are the case. Look at the emergence of bacterial resistant strains. Look again at the development of tumor resistance. Look again at significant differences in the rates and aggressiveness of neoplastic cells. Just in hematology – taking only the lymphomas – there have been at least 4 reclassifications of these tumors.
I didn’t mshow two pediatricians who made great contributions – Sidney Farber (Boston) and the physician in Minneapolis who identified T-cell immunity.
The work in genomics and cancer is proceeding at a rapid pace, and what is being uncovered is that tumors that we thought were the same based on histology are not all alike if we look at clusters of introns and exons (I hope my terms are used correctly). This part is challenging, just as proteomics is also because for offering diagnostics at low cost it will be necessary to go much further in automation.
Systematic classification in bacteriology currently used relies on feature extraction and combinatorial classes based on bacterial metabolism. It was commercially incorporated into laboratory diagnostic microbiology, which was not available when I trained under Abraham Braude. Braude was the first that I know to use agar diffusion plates to measure antibiotic sensitivities. He was a very strong influence on the 2012 Nobelist who was awarded for his work on G-proteins, and whose father was a fabulous hematologist, credited with G6PD, AK, and other enzyme-linked hemolytic anemias.
Eugene Rypka was a recently deceased microbiologist who actually developed feature extraction and classification, and it is notable that microbiology was the last of the disciplines to be automated.
My own work for many years owes as much to Rypka as to Braude, and in a strange way. Braude was my mentor, but I met Rosser Rudolph at a meeting and he was carrying out algorithms he had written on the first IBM computer based on Rypka’s work, but elegantly improved with apl software. I met an IBM engineer at the airport and he said – you can only do apl on the large computer! I published a series of papers using Kullback entropy to determine the best diagnostic cutoffs. Mas Chiga called me and said he couldn’t get it why it hasn’t caught on.
Then I met a former Soviet mathematician from Moscow University and he wrote a neural network that we didn’t publish. The reviewer was trying to steal the work, and better software came out. Izaak Mayzlin wrote the software himself. It came to the attention of IJ Good, the Chairman of Statistics at VPI, and it took his group two years to work up the heart atytacvk data I sent him. He called me when I was recovering from multiple fractures at Bridgeport Hospital to tell me it was done and clean. I was getting on the elevator at the CAP meeting when the CAP President saw me and complemented me on the recently published paper.
That was then, but when I retired, left Brooklyn Methodist, where I loved working with residents and college and Midwood High School students, I worked with Raphy Coifman and his postdoc. Raphy is a member of NAS, and he is recipient of the National Medal of Science award for his work on spectroscopy, and is now mostly focused on the EEG. It was just breathtaking.
What is happening in the patient is really a dynamic story. The metabolic expression, under genetic control is the more complete story. It requires good clean data, extraction of all of the meaningful features, or if you prefer signatures. But what is a signature? A signature is a collection of features that belongs to a biologically meaningful group. It could decide two different treatments for a malignancy that is not yet progressing vs an aggressive lesion that will metastasize widely.