Showing posts with label carcinogenesis. Show all posts
Showing posts with label carcinogenesis. Show all posts

Monday, January 22, 2018

Announcement: Precision Medicine and the Reinvention of Human Disease

In January, 2018, Academic Press is publishing my latest book, Precision Medicine and the Reinvention of Human Disease

Here is the book description, from the back cover:

Despite what you may have read in the popular press and in social media, Precision Medicine is not devoted to finding unique treatments for individuals, based on analyzing their DNA. To the contrary, the goal of Precision Medicine is to find general treatments that are highly effective for large numbers of individuals who fall into precisely diagnosed groups.

We now know that every disease develops over time, through a sequence of defined biological steps, and that these steps may differ among individuals, based on genetic and environmental conditions. We are currently developing rational therapies and preventive measures, based on our precise understanding of the steps leading to the clinical expression of diseases.

Precision Medicine and the Reinvention of Human Disease explains the scientific breakthroughs that have changed the way that we understand diseases, and reveals how medical scientists are using this new knowledge to launch a medical revolution.

Key Features
  • Clarifies the foundational concepts of Precision Medicine, distinguishing this field from its predecessors such as genomics, pharmacogenetics, and personalized medicine.
  • Gathers the chief conceptual advances in the fields of genetics, pathology, and bioinformatics, and synthesizes a coherent narrative for the field of Precision Medicine.
  • Delivers its message in plain language, and in a relaxed, conversational writing style, making it easy to understand the complex subject matter.
  • Guides the reader through a coherent and logical narrative, gradually providing expertise and skills along the way.
  • Covers the importance of data sharing in Precision Medicine, and the many data-related challenges that confront this fragile new field.

Table of Contents
Preface.                                                                 

Chapter 1. Introduction: Seriously, What is Precision Medicine?                     
  Glossary
  References


Chapter 2. Redefining Disease Causality                                            
  Section 2.1 Causality and Its Paradoxes                              
  Section 2.2 Why We Are Confident that Diseases Develop in Steps                  
  Section 2.3 Cause of Death                                           
  Section 2.4 What Is a Disease Pathway?                                              
  Section 2.5 Does Single Event Pathogenesis Ever Happen?      
  Glossary
  References


Chapter 3. Genetics: Clues, Not Answers, to the Mysteries of Precision Medicine         
  Section 3.1 Inscrutable Genes                                               
  Section 3.2 Inscrutable Diseases                                            
  Section 3.3 Recursive Epigenomic/Genomic Diseases                                              
  Section 3.4 Why a Gene-based Disease Classification Is a Bad Idea           
  Glossary
  References


Chapter 4. Disease Convergence
  Section 4.1 Mechanisms of Convergence                                       
  Section 4.2 Phenocopy Diseases: Convergence Without Mutation        
  Section 4.3 The Autoantibody Phenocopies                                      
  Section 4.4 Pathway-Directed Treatments for Convergent Diseases             
  Glossary
  References


Chapter 5. The Precision of the Rare Diseases                                          
  Section 5.1 The Biological Differences Between Rare Diseases and Common Diseases   
  Section 5.2 Precision Medicine's First Benefit: Cures for Rare Diseases            
  Section 5.3 What the Rare Diseases Tell Us About the Common Diseases               
  Section 5.4 Treatments for Rare Diseases are Effective Against the Common Diseases 
  Glossary
  References


Chapter 6. Precision Organisms                                                        
  Section 6.1 Modern Taxonomy of Infectious Diseases                                    
  Section 6.2 Our Genome Is a Book Titled "The History of Human Infections"           
  Section 6.3 Inflammatory Diseases: Collateral Damage in the War on Human Infection    
  Section 6.4 Revising Koch's Postulates in the Era of Precision Diagnostics      
  Section 6.5 Diseases-in-waiting                                              
  Section 6.6 Precision Taxonomy                                               
  Glossary
  References


Chapter 7. Reinventing Diagnosis                                                  
  Section 7.1 The Principles of Classification               
  Section 7.2 Superclasses                                                     
  Section 7.3 Classifications Cannot Be Based on Similarities                       
  Section 7.4 The Horrible Consequences of Class Blending                
  Section 7.5 What Is Precision Diagnosis?                                   
  Glossary
  References


Chapter 8. Precision Data                                                              
  Section 8.1 What Are the Minimal Necessary Properties of Good Data?              
  Section 8.2 Data Identification and Data Deidentification                      
  Section 8.3 What Do We Do With Non-quantitative, Descriptive Data?    
  Section 8.4 Incredibly Simple Methods to Understand Precision Medicine Data         
  Section 8.5 Data Reanalysis: More important than the Original Data Analysis      
  Section 8.6 What Is Data Sharing, and Why Don't We Do More of It?              
  Glossary
  References


Chapter 9. The Alternate Futures of Precision Medicine                               
  Section 9.1 Hypersurveillance                           
  Section 9.2 Do It Yourself Medicine                                   
  Section 9.3 Eugenics                                          
  Section 9.4 Public Health                                                
  Section 9.5 The Data Analyst of Tomorrow                           
  Section 9.6 Fast, Cheap, Precise Clinical Trials              
  Section 9.7 Animal Experimentation                 
  Glossary
  References

Friday, January 9, 2015

More on Luck and Cause

Earlier this week, I posted a blog criticizing the conclusions reached in a highly publicized paper written by a group of scientists at Johns Hopkins Medical Center. The authors conclude that "bad luck", rather than environmental or genetic causes, is responsible for the bulk of human cancers. My prior blog post explained why Hopkins is wrong.

After the blog was written, I received some very interesting feedback from a LinkedIn group (Science writers), much of which centered on the different ways that people use the words "luck" and "cause". Though mathematicians will despair, the word "good luck" is routinely applied to just about anything that has desirable outcome. So if a high school student gets a perfect score on the SAT exam, he or she was very very lucky. If you would interject to say that luck had nothing to do with it ("It was all due to student's high intelligence!"), you would be informed that the intelligence was a matter of luck, being as the student had done nothing to earn his or her intelligence. If you were to suggest that the "cause" of the high score was hard work, you would be told that "hard work" was just one of many conditions that led to the high score (e.g., "lucky" intelligence, a good night's sleep the night before, growing up in a stable living environment where current events, history and literature are discussed). There being many different "causes," it wouldn't make much sense to think in terms of any specific cause, and you might as well chalk it up to just plain good luck.

Getting back to biology and disease, consider these hypotheticals:

If you have 5 people living with an Ebola patient, and three of the five come down with the disease, would you say that these three came down with Ebola because they were "unlucky"? Or would you say that these three came down with Ebola because they were infected with the virus [and the other two were not]?

Would you say that the Ebola virus caused the infection in these three individuals? Or would you say that many factors, such as "luck", the environment, low innate viral resistance, poor nutrition, all set the stage for their infections, and that the Ebola virus was just one of many ingredients in the brew?

There's a real danger with using "luck" to describe events that we do not understand or cannot predict. Likewise, causation can be deceptive when dealing with a multi-step process that plays out over years or decades (like cancer).

When I think about "cause" I'm usually applying the "but-for" criteria ("but-for" this, that would not have happened). So, for me, Ebola virus causes Ebola hemorrhagic fever, and infections are not a matter of luck. Likewise, for me, there are "but-for" causes of cancer (e.g., chemicals, viruses, predisposing genes), and many important modifying factors that probably don't rise to the level of "but-for" causes (e.g., cell proliferation, DNA repair, genomic and epigenomic influences, regression-causing events, immune status); and cancer is not caused by bad luck.

Today, cancer has become the quintessential "bad luck" disease. In a prior blog, I described examples of "bad luck" cancers that transformed into "specific cause" cancers, when we studied the data. My personal opinion is that most cases of cancer are associated with known "but-for" causes. As we learn more and more about the different types of cancers, particularly the huge variety of rare cancers, we continue to find specific causes for specific cancers. I just assume, perhaps incorrectly, that every cancer has a cause.

I urge everyone reading this blog to also read my prior blog, which provides a full rebuttal to the Johns Hopkins "bad luck" cancer hypothesis.

- Jules Berman

tags: johns hopkins, press release, cancer news, bad luck, data repurposing, opinion, criticism, carcinogenesis, rare cancer, rare diseases, cancer incidence, comparative carcinogenesis, Jules J. Berman, Ph.D., M.D., cancer research, new findings, mutation rate, rebuttal, stem cell renewal, probabilistic models, data modeling, randomness, chance, misfortune, accident, unpredictable, causation, causative role, but-for, but for, sine qua non

Monday, January 5, 2015

Human diseases are not caused by bad luck

Earlier this week, I posted a blog criticizing the conclusions reached in a highly publicized paper written by a group of scientists at Johns Hopkins Medical Center. The authors conclude that "bad luck", rather than environmental or genetic causes, is responsible for the bulk of human cancers. My prior blog post explained why Hopkins is wrong.

After the blog was written, I got some very interesting feedback from a LinkedIn group (Science writers). Much of the discussion centered on the meaning of "luck", as it applies to biological processes.

Terms such as "luck", "accident", "misfortune", and "unpredictable" are often used, inappropriately, to describe complex events that we do not fully understand. For example, we speak in terms of "motor vehicle accidents" to describe vehicular crashes, even when we have discovered non-accidental causes (e.g., driving while intoxicated, driving on the wrong side of the road, failure to yield). We use the term "cerebrovascular accident" to describe strokes, even in individuals who have abundant risk factors (e.g., high blood pressure, e.g., occluded carotid artery). When we come down with a cold, we often say that it was our bad luck or our misfortune to get sick, even when we know that the cold was caused by a virus.

When we flip a coin, we like to think that the outcome occurs randomly, because there is a 50% chance of heads or of tails. But we all know, at some level, that the outcome of the toss is predetermined at the moment that the coin flips into the air. The laws of physics come into play, with a complexity that defies human prediction. Coin tosses, and roulette spins, are examples of processes that can be modeled, mathematically and intuitively, as probabilistic events. But we shouldn't confuse a probabilistic model with a physical reality.

Biology and medicine are replete with examples of phenomena that were attributed to "bad luck" until we finally determined their causes. For example, until the dawn of the twentieth century, the cause of malaria was unknown. There must have been something in the air (mala aria = bad air in medieval Italian). In 1880, Laveran identified the causative agent, a protozoan, in the blood of affected patients, for which he was awarded the Nobel prize in 1907. Through the centuries, people suffering from infectious diseases, vitamin deficiencies, and environmental toxins were considered "unfortunate", meaning "without luck."

Do not presume that modern-day scientists are too enlightened to be taken in by "chance" phenomenon. For many years, medical scientists sought a cause for sudden infant death syndrome (SIDS). Children were dying in their cribs, unpredictably, as though they had the bad luck to just stop breathing. In the past half century, we have learned that the majority of cases of SIDS are associated with sleeping conditions that limit the infants ability to breathe (e.g., sleeping on stomach, in hot room, with overabundance of soft bedding, etc.).

Today, cancer has become the quintessential "bad luck" disease. The literature gives us lots of examples of "bad luck" cancers that transformed into "specific cause" cancers, when we studied the data.

For example, In a landmark paper published in 1971 by Herbst and coworkers, the authors found an increase in the number of young women who developed an extremely rare cancer: clear cell adenocarcinoma of the cervix or of the vagina. The mothers of these young women had ingested a nonsteroidal synthetic estrogen (diethylsilbestrol, DES) during their pregnancies. In utero exposure to the drug caused a specific rare tumor to occur in the daughters. The offspring were classic "bad luck" cancer victims, having done nothing to put themselves at risk. Herbst had to go back a generation to find the real cause.

Women who developed mesotheliomas, a very rare cancer, in the 1970s and 1980s, were also the victims of "bad luck", until cancer epidemiologists found the common factor that linked these cases. These women had washed the asbestos-laden clothes of their fathers or husbands, who worked in the shipyards during World War II. Their brief exposure to asbestos resulted in mesotheliomas 20+ years later.

Much of what we observe in biology and medicine looks exactly like luck... until we understand the cause. The effect of "bad luck" hypotheses, as they apply to biology and medicine, is to halt scientific progress. Why would scientists waste their time looking for the causes of cancer, if cancers are caused by "bad luck"? The U.S. Environmental Protection Agency certainly can't protect us from bad luck!

I urge everyone reading this blog to also read my prior blog, which provides a rebuttal to the Johns Hopkins "bad luck" cancer hypothesis.

- Jules Berman

tags: johns hopkins, cancer news, bad luck, data repurposing, opinion, criticism, carcinogenesis, rare cancer, rare diseases, cancer incidence, comparative carcinogenesis, Jules J. Berman, Ph.D., M.D., cancer research, new findings, mutation rate, rebuttal, stem cell renewal, probabilistic models, data modeling, randomness, chance, misfortune, accident, unpredictable

Friday, January 2, 2015

Hopkins is wrong. Role of bad luck in cancer not shown!

Amidst much fanfare, Johns Hopkins issued a news release, dated Jan. 1, 2015, under the banner, “Bad Luck of Random Mutations Plays Predominant Role in Cancer, Study Shows" The subtitle to the banner is, "Statistical modeling links cancer risk with number of stem cell divisions.”

Whoever wrote the Hopkins news report doesn't seem to understand that the subtitle contradicts the title. The title implies that the authors have proven an assertion (i.e., that bad luck causes cancer). The subtitle indicates that they have only established an association (i.e., there is a statistical link between cancer incidence and random mutations occurring as stem cells divide). It seems like a quibble, but there is an immense conceptual gulf between a "link" and a "cause". It's easy to find a correlation, but it's hard to prove a causal role. In many cases, correlations simply disappear when the original data is reanalyzed with different analytic methods, or when some of the original assumptions are changed, or when new data is obtained, or when information from some other study provides better results that support an opposing hypothesis.

The Hopkins researchers reviewed the literature to find, "the cumulative total number of divisions of stem cells among 31 tissue types during an average individual’s lifetime." These numbers for the different tissues, correlated closely with the risk of cancer occurring in those tissues. Having arrived at the correlation, "using statistical theory, the pair calculated how much of the variation in cancer risk can be explained by the number of stem cell divisions, which is 0.804 squared, or, in percentage form, approximately 65 percent." Of the 31 tissues they studied, the tumor incidence in 9 of the tissues did not fit their "bad luck" correlation. Tumor incidence in these tissues, according to the news report, must come from some other source, such as environmental carcinogens. The 22 tissues that fit their model were deemed the "bad luck" tumors.

The bad luck hypothesis is not new. Cancer researchers have been trying to titrate the various suspected causes of cancer for decades. In the 1970s, when there was a large push to find chemicals in the environment that cause cancer, it was widely accepted that about 85% of cancers were caused by environment agents; 15% were caused by other things, such as genes, and this last 15% would also include "bad luck" mutations. These numbers were based on statistical inferences from data on the geographic variations in cancer incidence, looking at how the types of cancers occurring in populations changed in different locations on earth and in response to identified carcinogens.

Back in the early '70s, there was an awareness of the special place of "rare cancers" in the discussion. The common cancers (i.e., skin, lung, colon), were all presumed to be caused by environmental toxins (e.g., UV light, cigarettes, food and water contaminants, chronic infections, etc). More than 90% of the burden of cancer in the U.S. is accounted for by just a handful of cancer types (namely, basal cell carcinoma of skin, squamous cell carcinoma of skin, bronchogenic lung cancer, adenocarcinoma of colon, adenocarcinoma of breast, adenocarcinoma of prostate, adenocarcinoma of pancreas, ovarian carcinoma, esophageal cancer, and maybe one or two others). There are over 6,000 different kinds of cancer. All but a half dozen or so of these 6,000 varieties of cancer are rare, accounting in the aggregate for fewer than 10% of the tumors occurring in humans. Many of the rare cancers have well-studied patterns of inheritance. Because there are so many known inherited rare cancers, we tend to assume (perhaps incorrectly) that the bulk of rare cancers are caused by inherited genes (i.e., not caused by random mutations occurring in individuals with cancer).

OK, so lessons learned through the history of cancer research seems to be at odds with the conclusions drawn by the Hopkins team. Let's ignore history, for a moment. Here is a list of present-day concerns that should, at the very least, tone down the conclusions reached by the Hopkins study.

1. There are animals with much higher stem cell renewal than that seen in humans. Consider the whale. Whales have tons of intestines with trillions of dividing cells. If stem cell division and random mutation account for cancer, then you would expect every whale to be chock full of intestinal cancers. They are not. Please, spare me the argument that whales are different from humans and the two species cannot be compared. If you assert that random mutations in the DNA of stem cells is the cause of cancer, then your assertion should apply equally to any organisms that contains DNA and stem cells.

2. Carcinogenesis (i.e., the biological process that leads to cancer) is known to be a multi-step phenomenon. Mutation may be the first step, but many additional steps, leading to cancer, must occur, sometimes playing out over decades. In a multi-step process, you cannot expect any single event (e.g., a random bad luck mutation) to account, by itself, for the incidence of cancer.

3. There is a high cancer rate in mice and rats, both relatively short-lived animals. Wouldn't you expect a low accumulation of random bad mutations in animals that only live a year or two? The rapid evolution of cancers in short-lived animals (i.e., weeks or months) suggests that something in addition to random bad luck mutations must account for carcinogenesis in these animals.

4. Biological systems are complex, and causation is seldom a meaningful concept when many events contribute to a single observed phenomenon. For example, random mutation may occur more frequently in tissues with rapidly dividing stem cells, but rapid division of cells may occur in response to some toxic effect or chronic condition that causes a subpopulation of cells to die. Hence, rapid division of stem cells may be the result of some other "cause". Likewise, chronic toxicity and subsequent stem cell renewal in various tissues may result from higher rates of activation of carcinogens (i.e., metabolism) in those tissues. Hence, stem stem cell renewal may be tightly coupled with a variety of biological influences other than "bad luck".

In summary, the correlation observed by the Hopkins scientists is interesting, and it probably deserves further investigation. But the assertion that "bad luck" causes most human cancers is pretty much meaningless, at the moment.

- Jules J. Berman

p.s. The topic of today's blog is covered in depth in several of my published books, particularly Neoplasms: Principles of Development and Diversity, and expanded in my next blog post.

tags: johns hopkins, cancer news, bad luck, data repurposing, opinion, criticism, carcinogenesis, rare cancer, rare diseases, cancer incidence, comparative carcinogenesis, Jules J. Berman, Ph.D., M.D., cancer research, new findings, mutation rate, rebuttal, stem cell, stem cell renewal

Tuesday, July 15, 2014

Relationship between Hamartoma and Cancer

In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



The book has an extensive glossary, that explains the meaning and relevance of medical terms appearing throughout the chapters. The glossary can be read as a stand-along document. Here is an example of one term, "hamartoma", excerpted from the glossary.
Hamartoma - Hamartomas are benign tumors that occupy a peculiar zone lying between neoplasia (i.e., a clonal expansion of an abnormal cell) and hyperplasia (i.e., the localized overgrowth of a tissue). Some hamartomas are composed of tissues derived from several embryonic lineages (e.g., ectodermal tissues mixed with mesenchymal tissue). This is almost never the case in cancers, which are clonally derived neoplasms wherein every cell is derived from a single embryonic lineage. Tuberous sclerosis is an inherited hamartoma syndrome. The pathognomonic lesion in tuberous sclerosis is the brain tuber, from which the syndrome takes its name. Tubers of the brain consist of localized but poorly demarcated malformations of neuronal and glial cells. Like other hamartoma syndromes, the germline mutation in tuberous sclerosis produces benign hamartomas as well as carcinomas, indicating that hamartomas and cancers are biologically related. Hamartomas and cancers associated with tuberous sclerosis include cortical tubers of brain, retinal astrocytoma, cardiac rhabdomyoma, lymphangiomyomatosis (very rarely), facial angiofibroma, white ash leaf-shaped macules, subcutaneous nodules, cafe-au-lait spots, subungual fibromata, myocardial rhabdomyoma, multiple bilateral renal angiomyolipoma, ependymoma, renal carcinoma, subependymal giant cell astrocytoma [62].

Another genetic condition associated with hamartomas is Cowden syndrome, also known as multiple hamartoma syndrome. Cowden syndrome is associated with a loss of function mutation in PTEN, a tumor suppressor gene. Features that may be encountered are macrocephaly, intestinal hamartomatous polyps, benign hamartomatous skin tumors (multiple trichilemmomas, papillomatous papules, and acral keratoses), dysplastic gangliocytoma of the cerebellum, and a predisposition to cancers of the breast, thyroid and endometrium.

I urge you to read more about my book. There's a good preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

- Jules J. Berman, Ph.D., M.D. tags: rare disease, common disease, orphan disease, orphan drugs, types of cancer, cancer types, tumor types, tumor biology, rare cancers, common cancers, hyperplasia, tissue overgrowth, disease genes, genetic disease, carcinogenesis, glossary

Aneuploidy and Carcinogenesis

In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



The book has an extensive glossary, that explains the meaning and relevance of medical terms appearing throughout the chapters. The glossary can be read as a stand-along document. Here is an example of one term, "aneuploidy", excerpted from the glossary.
Aneuploidy - The presence of an abnormal number of chromosomes (for the species) in a cell. Most cancers contain aneuploid cells; an observation that holds true for virtually every poorly differentiated cancer. Aneuploidy is seen less often in benign tumors and well-differentiated tumors. Aneuploidy is also found in epithelial precancers and other growing lesions that can sometimes regress spontaneously (e.g., keratoacanthoma). These observations have prompted speculation that chromosomal instability and the acquisition of aneuploidy is an underlying cause of the cancer phenotype (i.e., tumor growth, invasion into surrounding tissues, and metastases).

Such causal associations invite skepticism, particularly in the realm of cancer biology, as virtually every cellular process and constituent of cancer cells has been shown to deviate from the norm. Nonetheless, there is good reason to suspect that aneuploidy is at least a factor in tumor development, as mutations that cause aneuploidy are associated with a heightened risk of cancer (e.g., Brca1 gene mutations [13] and mutations of mitotic checkpoint genes [14]). Cancer researchers have warned that aneuploidy, by itself, may not cause cancer [15]. Aneuploidy may need to be accompanied by other factors associated with genetic instability, such as the accumulation of DNA damage, specific cancer-causing mutations, epigenomic and cytogenetic abnormalities, and reduced cell death [15].

As usual, a rare disease helps to clarify the role of aneuploidy in carcinogenesis. Mosaic variegated aneuploidy syndrome-1 (MVA1) is caused by a homozygous or compound heterozygous mutation in the BUB1B gene, which encodes a key protein in the mitotic spindle check point. This disease is characterized by widespread aneuploidy in more than 25% of the cells of the body, and a heightened risk of developing childhood cancers (e.g., rhabdomyosarcoma, Wilms tumor, and leukemia). Because the underlying cause of mosaic variegated aneuploidy syndrome-1 is a gene that produces aneuploidy, and because such aneuploidy is an early event (i.e., congenital) that precedes the development of cancer and that is found in the developed cancer cells, then it is reasonable to infer that aneuploidy is closely associated with events that lead to cancer. See Mutator phenotype, Carcinogenesis, Cytogenetics, and Karyotype.

I urge you to read more about my book. There's a good preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

- Jules J. Berman, Ph.D., M.D. tags: rare disease, common disease, orphan disease, orphan drugs, types of cancer, cancer types, tumor types, tumor biology, rare cancers, common cancers, aneuploidy, cytogenetics, euploidy, carcinogenesis, glossary

Wednesday, July 9, 2014

Rare Cancer are Subsets of Common Cancers

In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



One of the key ideas developed in the book is that each common diseases is actually an aggregate of cellular processes that are present, individually, in rare diseases. In the case of the common cancers, we can find specific rare diseases that are subsets of the common diseases.

Here is an excerpt from Chapter 8:

8.3.3 Inherited syndromes that cause rare cancers are often associated with increased risk for developing common cancers; hence, the causes of rare cancers are related to the causes of common cancers. Many of the greatest advances in our understanding of common cancers have come through the study of rare familial cancer syndromes in which common types of cancer occur. Here are a few common cancers and the familial syndromes that account for a small percentage of cases.

Colon tumors (benign and malignant)
- Colorectal cancer hereditary non-polyposis
- Polyposis syndrome, mixed hereditary
- Turcot syndrome (central nervous system cancer and familial polyposis of the colon)
- Mismatch repair gene pmsl1 colorectal cancer hereditary, non-polyposis type 3 included
- Checkpoint kinase 2 S. pombe homologue of breast and colorectal cancer susceptibility
- Colorectal adenomatous polyposis autosomal recessive
- Oligodontia–colorectal cancer syndrome
- Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome
- Adenomatous polyposis of the colon (APC)
- Peutz–Jeghers syndrome
- Colorectal cancer hereditary non-polyposis type 2
- Colorectal cancer susceptibility on chromosome 9
Lung cancer
- Lung cancer 1
- Lung cancer, alveolar cell carcinoma included
Breast cancer
- Brca1 breast cancer type 1
- Breast cancer 11–22 translocation associated
- Brca2 breast cancer type 2
- Brca3 breast cancer type 3
Basal cell carcinoma of skin (see Glossary item, Basal cell carcinoma)
- Basal cell carcinomas with milia and coarse sparse hair
- Basal cell nevus syndrome
- Basal cell carcinoma, multiple
- Basaloid follicular hamartoma syndrome (see Glossary item, Hamartoma)
- Basal cell carcinoma with follicular differentiation
- Xeroderma pigmentosum complementation group b
- Xeroderma pigmentosum 1
Renal cell carcinoma
- Renal carcinoma, familial associated 1 included
- Renal cell carcinoma, papillary
- Non-papillary renal carcinoma 1
- Renal cell carcinoma, papillary 3
- Leiomyomatosis and renal cell cancer hereditary
Thyroid cancer
- Thyroid carcinoma, familial medullary
- Familial non-medullary thyroid cancer
- Papillary thyroid microcarcinoma
- Thyroid carcinoma, papillary with papillary renal neoplasia
- Thyroid carcinoma, non-medullary 1
- Thyroid carcinoma, Hürthle cell
- Thyroid carcinoma, follicular
Ovarian cancer
- Epithelial ovarian cancer
- Ovarian cancer, epithelial, susceptibility to
Melanoma
- Melanoma, cutaneous malignant 4
- Melanoma, cutaneous malignant 3
- Familial atypical multiple mole melanoma-pancreatic carcinoma syndrome
- Dysplastic nevus syndrome, hereditary b-k mole syndrome
Prostate cancer
- Prostate cancer, hereditary x-linked
- Prostate cancer, hereditary 1
- Prostate cancer, hereditary 20
- Prostate cancer, hereditary 7
- Prostate cancer, hereditary 3
- Prostate cancer/brain cancer, susceptibility
When we look at individual inherited cancer syndromes, we see that both rare and common cancers may result. Here is the list of different types of cancer associated with the Li–Fraumeni syndrome [15]. The syndrome-associated cancers are divided into common and rare cancers.

Common tumors associated with Li-Fraumeni syndrome
- Breast cancer
- Lung adenocarcinoma
- Colon cancer
- Pancreatic cancer
- Prostate cancer
Rare tumors associated with Li-Fraumeni syndrome
- Soft tissue sarcomas
- Osteosarcomas
- Brain tumors
- Acute leukemias
- Adrenocortical carcinomas
- Wilms tumor
- Phyllodes tumor of breast
It is worth noting that the common cancers associated with rare cancer syndromes have a similar morphologic appearance as their sporadic counterparts. This suggests that regardless of underlying genetic cause, the pathogenesis of each named common cancer tends to converge to its characteristic phenotype.

I urge you to read more about this book. There's a good preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

- Jules J. Berman, Ph.D., M.D. tags: rare disease, common disease, orphan disease, orphan drugs, carcinogenesis, common cancers, rare cancers, cancer syndromes, familial cancer syndromes

Tuesday, June 17, 2014

Biological Differences between Rare Cancers and Common Cancers

In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. This book builds the case that the best way to advance our understanding of the common diseases is to focus our attention on the rare diseases.


Chapter 8 covers the topic of rare cancers. The rare cancers are biologically different from the common cancers. Chapter 8 explores the biological basis of these differences, and why research into the rare cancers has given us major breakthroughs in the prevention and treatment of all cancers.

Here are some of the biological differences between rare cancers and common cancers:
1. Just a few types of common cancers account for the majority of occurrences of cancer.

2. Most of the different types of cancers are rare cancers. Specifically, there are several thousand rare cancers, and only a few dozen common cancers.

3. Virtually every common cancer is composed of cells derived from the ectodermal or the endodermal layers of the embryo (see Glossary items, Ectoderm, Endoderm). Rare cancers derive from all three germ layers, but the majority of rare cancers derive from the mesoderm.

4. All of the childhood cancers are rare cancers.

5. All the advanced stage cancers that we can currently cure are rare cancers, and most of the curable rare cancers are cancers that occur in children.

6. Inherited syndromes that cause rare cancers are often associated with increased risk for developing common cancers; hence, the causes of rare cancers are related to the causes of common cancers.

7. Rare cancers are genetically simpler than common cancers (i.e., have fewer mutations). In many cases, we know the underlying mutation that leads to the development of rare cancers. We do not know the underlying mutation(s) that leads to common cancers.

8. Common cancers are genetically heterogeneous and may contain one or more rare types of cancer having the same clinical phenotype as the common cancer.

9. Most of what we know about the pathogenesis of cancer has come from observations on rare cancers.

10. The rare cancers serve as sentinels for environmental agents that can cause various types of cancer; either rare or common. Common cancers cannot serve as sentinels.

11. Treatments developed for the rare cancers will almost certainly apply to the common cancers.


I urge you to read more about this book. There's a good preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

- Jules Berman, Ph.D., M.D.

Sunday, September 26, 2010

Tumor speciation revisited

"Things that are new are wont to be set forward rudely and formlessly, and then must be polished and perfected in succeeding centuries."
  - Pappus, a Helenistic mathematician (circa 350-300 B.C.E.)

Regular readers of this blog all know that I have a keen interest in the tumor speciation (why we encounter a the set of tumor types that are familiar to all pathologists, and no others). Some examples of different types of tumors are: follicular lymphomas, glioblastomas, oligodendrogliomas, seminomas, hepatocellular carcinomas, etc.)

I find the question of tumor speciation to be profound for the following reason: Research in the genetics of tumors has found that tumors are incredibly complex, with some tumors having thousands of genetic mutations, making each tumor unique from every other tumor that has ever occurred in humans. If every tumor is unique, and if many tumors are genetically complex (many mutations) and internally heterogeneous (a tumor cell may be genetically separable from another tumor cell from the same tumor), then why are there only a finite number of different kinds of tumors? Shouldn't there be a near-infinite number of tumor types?

In a prior post, I tried to answer this question, drawing an analogy from animal speciation, and though the argument seems valid, I can see how it might confuse readers. I spent much of a chapter in my Neoplasms book explaining tumor speciation, but I can't help but wonder if there's a shorter explanation.

Here's my third try:

Basically, cancer is caused by alterations in the genome. Tumor speciation is restricted to a relatively small set of patterns in the epigenome.

That's it! Here's the explanation of what it means and why it makes sense.

When oncogenic mutations occur in cells, a malignant phenotype can only arise in cells that have a specific type of differentiation. The type of differentiation that a cell manifests is determined by the epigenome (the non-sequence modifications to DNA). There are about 200 different cell types in the body. Each cell type within an individual animal has the same exact genome (DNA sequence) as every other cell type in the same animal. Neutrophils, enterocytes, neurons, thyroid cells differ from one another because of differences in their epigenomes.

Because we only observe about 200 different cell types in the body, it's likely that only a finite set of epigenomic patterns "work"; i.e., sustain cell viability. In the case of cancer, the cancer genotype can only manifest itself within a finite set of epigenomic patterns. Specific types of genetic alterations are found in specific types of epigenomic patterns (e.g., the bcr/abl mutation is seen in myeloid lineage cells). Even when cancer mutations become complex, their malignant phenotype can only occur in a restricted epigenomic background.

What happens during the process of carcinogenesis (the period following a carcinogenic mutation and leading to the emergence of an invasive cancer, often years later)? Maybe carcinogenesis requires epigenomic accommodation of the cancer genotype. Over multiple cell generations, the epigenome continuously changes until a stable epigenomic pattern is selected. Because most epigenomic patterns are not viable, most cancer mutations never lead to the emergence of a tumor.

This argument hardly constitutes proof of anything, but in my Neoplasms book, I provide many examples of how tumors develop within the constraints of allowable epigenomic patterns (i.e., the observed differentiated cell types).

Jump to the next Specified Life blog

- © 2010 Jules Berman

In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



I urge you to read more about my book. There's a generous preview of the book at the Google Books site.

tags: biology of rare diseases, common diseases, genetic disease, disease genetics, orphan diseases, orphan drugs, rare disease organizations, rare disease research, rare diseases, rare disease funding, rare disease research, funding for rare diseases, importance of rare diseases, funding opportunities, books about rare diseases, books about orphan drugs, orphan drug development, pathology of rare diseases, complex diseases, carcinogenesis, neoplasia, neoplasms, oncogenes, cancer development, epigenome, genome, cancer diversity, cancer phenotype, cancer genotype, cancer epigenotype, tumor development, tumour development

Friday, September 24, 2010

Melanoma and the precancer time machine

In an earlier post, I explained the precancer time machine phenomenon. Basically, when you successfully treat precancers, you don't see an immediate drop in the incidence of invasive cancers; you see a drop in invasive cancers at some point in the future, corresponding to the time at which the treated precancers would have developed into invasive cancers.

In the earlier post, I demonstrated that the precancer time machine seemed to apply in the case of dcis and invasive breast cancer.

In today's post, I've used the latest SEER (The U.S. National Cancer Institute's Surveillance Epidemiology and End Results) cancer data to show that there seems to be the same phenomenon going on for melanoma precancers.

The topic of treating melanoma precancers has been somewhat controversial. It would seem to be a no-brainer that we can reduce the incidence of invasive melanomas by treating melanoma precancers (dysplastic nevi and in situ melanomas). Unfortunately, there is no epidemilogiic evidence to support this assertion. Basically, the incidence of invasive melanoma seems to be rising every year, despite our best efforts to stem the tide (through the use of sunscreens, avoiding exposure to strong sunlight, and treating precancers).

The latest SEER data (which covers cancer cases from 1973 to 2007) seems to offer some hope that conditions might be improving.

Here's the graph of invasive melanome incidence in the U.S. SEER population.



The tallest bars (blue) are the crude numbers of occurrences of invasive malignant melanoma. The middle bars (maroon) are the occurrences of invasive melanoma expressed as a proportion of the total number of SEER cases. The bottom bars (white), are the occurrences of melanoma expressed as a proprotion of the total population of the U.S. in the perspective years.

Here are the numbers:

crude of SEER of U.S. Pop
1973 001062 001916 000501
1974 001305 001938 000610
1975 001559 002116 000721
1976 001601 002116 000734
1977 001791 002337 000813
1978 001829 002347 000821
1979 001973 002460 000876
1980 002190 002645 000963
1981 002298 002690 001001
1982 002352 002714 001015
1983 002350 002617 001005
1984 002462 002638 001043
1985 002795 002864 001174
1986 002947 002942 001227
1987 003050 002879 001258
1988 002948 002743 001205
1989 003194 002896 001294
1990 003272 002816 001311
1991 003518 002853 001395
1992 003569 002786 001399
1993 003611 002860 001400
1994 003904 003097 001499
1995 004189 003283 001594
1996 004438 003641 001673
1997 004627 003668 001728
1998 004739 003663 001753
1999 004893 003704 001794
2000 005105 003832 001814
2001 005380 003911 001886
2002 005377 003857 001867
2003 005514 003993 001898
2004 005859 004062 001998
2005 006451 004431 002180
2006 006431 004335 002152
2007 006325 004172 002097

In the last two years studied (2006, 2007), the incidence of invasive malignant melanoma has dropped. Is this just a fluke, or does it indicate a real trend? There's no way to be sure, but inspection of the graph would indicate that it's the first time since 1973 when incidence has dropped two years running.

What about the corresponding incidence of in situ melanoma (the non-invasive precursor for invasive melanoma)?

Here's the graph for in situ melanoma.


Here are the numbers.

crude of SEER of U.S. Pop
1973 000035 000063 000016
1974 000059 000087 000027
1975 000081 000109 000037
1976 000096 000126 000044
1977 000155 000202 000070
1978 000177 000227 000079
1979 000177 000220 000078
1980 000263 000317 000115
1981 000276 000323 000120
1982 000326 000376 000140
1983 000384 000427 000164
1984 000466 000499 000197
1985 000638 000653 000268
1986 000723 000721 000301
1987 000782 000738 000322
1988 000824 000766 000337
1989 000976 000885 000395
1990 001127 000970 000451
1991 001192 000966 000472
1992 001373 001072 000538
1993 001375 001089 000533
1994 001599 001268 000614
1995 001920 001504 000730
1996 002091 001715 000788
1997 002258 001790 000843
1998 002533 001957 000937
1999 002765 002093 001013
2000 003202 002404 001137
2001 003508 002550 001230
2002 003656 002622 001269
2003 003429 002483 001180
2004 003604 002499 001229
2005 004060 002788 001372
2006 004048 002728 001354
2007 004291 002831 001422

The incidence of in situ melanoma keeps going up and up. That's as it should be. When we successfully cure more and more in situ melanomas, we reduce the incidence of invasive melanomas.

The lag between the rise in incidence of the in situ lesions and the drop in incidence of the invasive lesions is due to the precancer time machine phenomenon.

Can we be sure? Not yet. Hopefully, over the next five years or so, the data will become a little more convincing.

- © 2010 Jules Berman

key words: precancer, precancerous, skin cancer, dysplastic nevi, dysplastic nevus, dysplastic naevus, dysplastic naevi, cancer mortality, cancer prevention, carcinogenesis
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases.



I urge you to read more about my book. There's a generous preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.

Tuesday, June 19, 2007

"Precancer" versus "early cancer"

Precancers are the lesions from which cancers grow. Some people question why we need to specify some lesions as precancers when we know that carcinogenesis is a multistep process and that every cancer traverses many un-named biological states as it develops into a fully malignant lesion. Why can't we recognize that precancers are just an early form of cancer and refer to the precancers by the name of its developed cancer? Can't we just use adjectives like "early stage" squamous carcinoma or "non-invasive" pancreatic carcinoma? Wouldn't that make life a lot easier than inventing names for the pre-invasive stage of every cancer?

Much as I like data simplification, it just can't be done in the case of the precancers. Precancers have specific, characteristic properties that separate them from cancers. Because of these properties, the treatment of precancers may be very different from the treatment of cancers. In fact, if we take full advantage of the biologic features that separate the precancers from the cancers, we may actually find that we can eliminate deaths from cancer.

What are these special properties of the precancers?

1. Precancers, unlike cancers, tend to regress. Cancers tend to grow and only rarely regress. Furthermore, it some cases, we can influence the rate of regression of the precancers with relatively non-toxic drugs. Understanding the biology of regression is something that we can only learn from the precancers.

2. When a precancer progresses, it progresses to cancer. But not all precancers progress. Many precancers just stay precancers indefinitely, as far as we can tell. Why should we think of a precancer as an early stage of a cancer if it never becomes a cancer?

3. Precancers that progress to cancer can apparently progress into more than one type of cancer. Consequently, there are more types of cancers than there are types of precancers. For instance, in the lung, squamous metaplasia/dysplasia of bronchial epithelium may give rise to bronchogenic squamous cell carcinoma, bronchogenic adenocarcinoma, bronchogenic small cell carcinoma, or bronchogenic mixed carcinoma. If a lesion can progress into any of several different lesions, it is impossible to pretend that the lesion is just an early form of one named cancer.

4. Precancers can be cured. When a precancer is cured, the cancer never develops. The treatments that we use for precancers are likely to be different from (and much less toxic than) the treatments that we use for cancers.

Because the biology of precancer is distinguishable from the biology of cancer, and because there are clinically useful reasons (i.e., treatment and prevention of cancer) to make these distinctions, the precancers should be curated as designated entities.

Jules Berman