Posts Tagged ‘Pathology’

Cancer detection and therapeutics

Curator: Larry H. Bernstein, MD, FCAP



Kurzweill Reports

Machine learning rivals human skills in cancer detection

Two announcements yesterday (April 21) suggest that deep learning algorithms rival human skills in detecting cancer from ultrasound images and in identifying cancer in pathology reports.

Samsung Medison RS80A ultrasound imaging system (credit: Samsung)

Samsung Medison, a global medical equipment company and an affiliate of Samsung Electronics, has just updated its RS80A ultrasound imaging system with a deep learning algorithm for breast-lesion analysis.

The “S-Detect for Breast” feature uses big data collected from breast-exam cases and recommends whether the selected lesion is benign or malignant. It’s used in in lesion segmentation, characteristic analysis, and assessment processes, providing “more accurate results.”

“We saw a high level of conformity from analyzing and detecting lesion in various cases by using the S-Detect,” said professor Han Boo Kyung, a radiologist at Samsung Medical Center.

“Users can reduce taking unnecessary biopsies and doctors-in-training will likely have more reliable support in accurately detecting malignant and suspicious lesions.”

Deep learning is better than humans in extracting meaning from cancer pathology reports

Meanwhile, researchers from the Regenstrief Institute and Indiana University School of Informatics and Computing at Indiana University-Purdue University Indianapolis say they’ve found that open-source machine learning tools are as good as — or better than — humans in extracting crucial meaning from free-text (unstructured) pathology reports and detecting cancer cases. The computer tools are also faster and less resource-intensive.

(U.S. states require cancer cases to be reported to statewide cancer registries for disease tracking, identification of at-risk populations, and recognition of unusual trends or clusters. This free-text information can be difficult for health officials to interpret, which can further delay health department action, when action is needed.)

“We think that its no longer necessary for humans to spend time reviewing text reports to determine if cancer is present or not,” said study senior author Shaun Grannis*, M.D., M.S., interim director of the Regenstrief Center of Biomedical Informatics.

Awash in oceans of data

“We have come to the point in time that technology can handle this. A human’s time is better spent helping other humans by providing them with better clinical care. Everything — physician practices, health care systems, health information exchanges, insurers, as well as public health departments — are awash in oceans of data. How can we hope to make sense of this deluge of data? Humans can’t do it — but computers can.”

This is especially relevant for underserved nations, where a majority of clinical data is collected in the form of unstructured free text, he said.

The researchers sampled 7,000 free-text pathology reports from over 30 hospitals that participate in the Indiana Health Information Exchange and used open source tools, classification algorithms, and varying feature selection approaches to predict if a report was positive or negative for cancer. The results indicated that a fully automated review yielded results similar or better than those of trained human reviewers, saving both time and money.

Major infrastructure advance

“We found that artificial intelligence was as least as accurate as humans in identifying cancer cases from free-text clinical data. For example the computer ‘learned’ that the word ‘sheet’ or ‘sheets’ signified cancer as ‘sheet’ or ‘sheets of cells’ are used in pathology reports to indicate malignancy.

“This is not an advance in ideas; it’s a major infrastructure advance — we have the technology, we have the data, we have the software from which we saw accurate, rapid review of vast amounts of data without human oversight or supervision.”

The study was published in the April 2016 issue of the Journal of Biomedical Informatics. It was conducted with support from the Centers for Disease Control and Prevention.

Co-authors of the study include researchers at the IU Fairbanks School of Public Health, the IU School of Medicine and the School of Science at IUPUI.

* Grannis, a Regenstrief Institute investigator and an associate professor of family medicine at the IU School of Medicine, is the architect of the Regenstrief syndromic surveillance detector for communicable diseases and led the technical implementation of Indiana’s Public Health Emergency Surveillance System — one of the nation’s largest. Studies over the past decade have shown that this system detects outbreaks of communicable diseases seven to nine days earlier and finds four times as many cases as human reporting while providing more complete data.

Yann Lecun is Director of AI Research, Facebook and a noted deep-learning expert. 


Toward better public health reporting using existing off the shelf approaches: A comparison of alternative cancer detection approaches using plaintext medical data and non-dictionary based feature selection

Suranga N. Kasthurirathnea, , Brian E. Dixonb, cJudy GichoyadHuiping XucYuni XiadBurke Mamlinb, dShaun J. Grannisb, d


• Cancer cases can be identified in unstructured clinical data to support public health reporting.
• Such cancer detection methods do not require complex external ontologies or human intervention.
• Such approaches can identify cases with sensitivity, specificity, PPV, accuracy, and AUC exceeding 80–90%.
• Automated cancer detection methods perform as well as approaches that require costly clinician input.
• These approaches may be generalized for other health analytics applications and healthcare domains.



Increased adoption of electronic health records has resulted in increased availability of free text clinical data for secondary use. A variety of approaches to obtain actionable information from unstructured free text data exist. These approaches are resource intensive, inherently complex and rely on structured clinical data and dictionary-based approaches. We sought to evaluate the potential to obtain actionable information from free text pathology reports using routinely available tools and approaches that do not depend on dictionary-based approaches.

Materials and methods

We obtained pathology reports from a large health information exchange and evaluated the capacity to detect cancer cases from these reports using 3 non-dictionary feature selection approaches, 4 feature subset sizes, and 5 clinical decision models: simple logistic regression, naïve bayes, k-nearest neighbor, random forest, and J48 decision tree. The performance of each decision model was evaluated using sensitivity, specificity, accuracy, positive predictive value, and area under the receiver operating characteristics (ROC) curve.


Decision models parameterized using automated, informed, and manual feature selection approaches yielded similar results. Furthermore, non-dictionary classification approaches identified cancer cases present in free text reports with evaluation measures approaching and exceeding 80–90% for most metrics.


Our methods are feasible and practical approaches for extracting substantial information value from free text medical data, and the results suggest that these methods can perform on par, if not better, than existing dictionary-based approaches. Given that public health agencies are often under-resourced and lack the technical capacity for more complex methodologies, these results represent potentially significant value to the public health field.

Graphical abstract
 Image for unlabelled figure

Scientists shoot anticancer drugs deep into tumors

Ultrasonic vibrations cause gas microbubbles to explode, releasing nanoparticles containing anticancer drugs

Schematic of a magnetic microbubble used in the study, containing gas core (blue) and shell of magnetic iron-oxide nanoparticles (red) that form a dense shell (center) around drug-containing nanoparticles. When stimulated by ultrasound at resonant frequencies, the microbubbles explode, releasing the nanoparticles, which can travel hundreds of micrometers into tumor tissue to deliver anticancer drugs and can also be imaged on an MRI machine. (credit: Yu Gao et al./NPG Asia Materials)


Scientists at Nanyang Technological University (NTU Singapore) have invented a new way to deliver cancer drugs deep into tumor cells.

They created micro-sized gas bubbles coated with anticancer drug particles embedded in iron oxide nanoparticles and used MRI or other magnetic sources to direct these microbubbles to gather around a specific tumor. Then they used ultrasound to vibrate the microbubbles, providing the energy to direct the drug particles into a targeted kill zone in the tumor. The magnetic nanoparticles also allow for imaging in an MRI machine.

The microbubbles were successfully tested in mice and the study has been published by the Nature Publishing Group in Asia Materials.

Overcoming limitations of chemotherapy

This innovative technique was developed by a multidisciplinary team of scientists led by Asst Prof C. J. Xu from the School of Chemical and Biomedical Engineering and Assoc. Prof Claus-Dieter Ohl from the School of Physical and Mathematical Sciences.

Xu, who is also a researcher at the NTU-Northwestern Institute for Nanomedicine, said their new method may solve some of the most pressing problems faced in chemotherapy used to treat cancer.

The main problem is that current chemotherapy drugs cannot be easily targeted. The drug particles flow in the bloodstream, damaging both healthy and cancerous cells. Typically, these drugs are flushed away quickly in organs such as the lungs and liver, limiting their effectiveness.

The remaining drugs are also unable to penetrate deep into the core of the tumor, leaving some cancer cells alive, which could lead to a resurgence in tumor growth.

Delivering anticancer drugs deep into tumors

Schematic of the apparatus used to investigate magnetic microbubble oscillation and nanoparticle release (credit: Yu Gao et al./NPG Asia Materials)

The microbubbles are magnetic, so after injecting them into the bloodstream, they can be clustered around the tumor using magnets to ensure that they don’t kill the healthy cells, explains Xu, who has been working on cancer diagnosis and drug delivery systems since 2004.

“More importantly, our invention is the first of its kind that allows drug particles to be directed deep into a tumor in a few milliseconds. They can penetrate a depth of 50 cell layers or more (about 200 micrometers) — twice the width of a human hair. This helps to ensure that the drugs can reach the cancer cells on the surface and also inside the core of the tumor.”

According to Clinical Associate Professor Chia Sing Joo, a Senior Consultant at the Tan Tock Seng Hospital’s Endoscopy Centre and the Urology & Continence Clinic, “For anticancer drugs to achieve their best effectiveness, they need to penetrate into the tumor efficiently in order to reach the cytoplasm of all the cancer cells that are being targeted without affecting the normal cells.

“Currently, this can [only] be achieved by means of a direct injection into the tumor or by administering a large dosage of anticancer drugs, which can be painful, expensive, impractical and might have various side effects. If successful, I envisage [the new drug-delivery system] can be a good alternative treatment in the future, one which is low cost and yet effective for the treatment of cancers involving solid tumors, as it might minimize the side effects of drugs.” Joo is a surgeon experienced in the treatment of prostate, bladder and kidney cancer and a consultant for this study.

According to Ohl, an expert in biophysics who has published previous studies involving drug delivery systems and bubble dynamics, “most prototype drug delivery systems on the market face three main challenges before they can be commercially successful: they have to be non-invasive, patient-friendly, and yet cost-effective. We were able to come up with our solution that addresses these three challenges.”

The 12-person study team included scientists from City University of Hong Kong and Technion – Israel Institute of Technology (Technion). The team plans to use this new drug delivery system in studies on lung and liver cancer using animal models, and eventually clinical studies.

They estimate that it will take another eight to ten years before it reaches human clinical trials.


Abstract of Controlled nanoparticle release from stable magnetic microbubble oscillations

Magnetic microbubbles (MMBs) are microbubbles (MBs) coated with magnetic nanoparticles (NPs). MMBs not only maintain the acoustic properties of MBs, but also serve as an important contrast agent for magnetic resonance imaging. Such dual-modality functionality makes MMBs particularly useful for a wide range of biomedical applications, such as localized drug/gene delivery. This article reports the ability of MMBs to release their particle cargo on demand under stable oscillation. When stimulated by ultrasound at resonant frequencies, MMBs of 450 nm to 200 μm oscillate in volume and surface modes. Above an oscillation threshold, NPs are released from the MMB shell and can travel hundreds of micrometers from the surface of the bubble. The migration of NPs from MMBs can be described with a force balance model. With this technology, we deliver doxorubicin-containing poly(lactic-co-glycolic acid) particles across a physiological barrier bothin vitro and in vivo, with a 18-fold and 5-fold increase in NP delivery to the heart tissue of zebrafish and tumor tissue of mouse, respectively. The penetration of released NPs in tissues is also improved. The ability to remotely control the release of NPs from MMBs suggests opportunities for targeted drug delivery through/into tissues that are not easily diffused through or penetrated.



Artificial protein controls first self-assembly of C60 fullerenes

New discovery expected to lead to new materials with properties such as higher strength, lighter weight, and greater chemical reactivity, resulting in applications ranging from medicine to energy and electronics
Buckminsterfullerene (C60), aka fullerene and buckyball (credit: St Stev via / CC BY-NC-ND)

A Dartmouth College scientist and his collaborators* have created the first high-resolution co-assembly between a protein and buckminsterfullerene (C60), aka fullerene and buckyball (a sphere-like molecule composed of 60 carbon atoms and shaped like a soccer ball).

“This is a proof-of-principle study demonstrating that proteins can be used as effective vehicles for organizing nanomaterials by design,” says senior author Gevorg Grigoryan, an assistant professor of computer science at Dartmouth and senior author of a study discussed in an open-access paper in the journal in Nature Communications.

Proteins organize and orchestrate essentially all molecular processes in our cells. The goal of the new study was to create a new artificial protein that can direct the self-assembly of fullerene into ordered superstructures.

COP, a stable tetramer (a polymer derived from four identical single molecule) in isolation, interacts with C60 (fullerene) molecules via a surface-binding site and further self-assembles into a co-crystalline array called C60Sol–COP (credit: Kook-Han Kim et al./Nature Communications)

Grigoryan and his colleagues show that that their artificial protein organizes a fullerene into a lattice called C60Sol–COP. COP, a protein that is a stable tetramer (a polymer derived from four identical single molecules), interacted with fullerene molecules via a surface-binding site and further self-assembled into an ordered crystalline superstructure. Interestingly, the superstructure exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating.

Grigoryan says that if we learn to do the programmable self-assembly of precisely organized molecular building blocks more generally, it will lead to a range of new materials with properties such as higher strength, lighter weight, and greater chemical reactivity, resulting in a host of applications, from medicine to energy and electronics.

Fullerenes are currently used in nanotechnology because of their high heat resistance and electrical superconductivity (when doped), but the molecule has been difficult to organize in useful ways.

* The study also included researchers from Dartmouth College, Sungkyunkwan University, the New Jersey Institute of Technology, the National Institute of Science Education and Research, the University of California-San Francisco, the University of Pennsylvania, and the Institute for Basic Science.

Abstract of Protein-directed self-assembly of a fullerene crystal

Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design.


Protein-directed self-assembly of a fullerene crystal

Kook-Han KimDong-Kyun KoYong-Tae KimNam Hyeong Kim,….., Yong Ho Kim Gevorg Grigoryan
Nature Communications 2016;7,(11429)

Programmable self-assembly of molecular building blocks is a highly desirable way of achieving bottom-up control over novel functions and materials. Applications of molecular assemblies are well explored in the literature, ranging from optoelectronic1, 2, magnetic3, and photovoltaic4 devices to chemical and bioanalytical sensing5, and medicine6. However, it has been a daunting challenge to quantitatively describe and control the driving forces that govern self-assembly, particularly given the broad range of molecular building blocks one would like to organize. In this respect, nature’s self-assembling macromolecules hold considerable promise as standard chassis for encoding precise organization. By learning to engineer the assembly of these molecules, myriad other molecular building blocks can be co-organized in desired ways through non-covalent or covalent attachment. The protein polymer is a particularly attractive candidate for a standard assembly chassis given its rich chemical alphabet, diversity of available assembly geometries, broad ability to engage other molecular moieties, and the possibility of engineered function. Considerable progress has been made in the area of engineering protein assemblies7, 8, using either computational9, 10,11, 12, 13, 14 or rational approaches15, 16, 17, 18, but the problem remains a grand challenge. A major difficulty lies in accounting for the enormous continuum of possible assembly geometries available to proteins to engineer a sequence that predictably prefers just one. General design principles, which provide predictive rules of assembly, are thus of enormous utility in limiting the geometric search space and enabling robust design11, 19.

In this work, we demonstrate the first ever high-resolution structure of co-assembly between a protein and buckminsterfullerene (C60), which suggests a simple structural mode for protein–fullerene co-organization. Three separate crystal structures, resolved to 1.67, 1.76 and 2.35Å, reveal a protein lattice with C60 groups occupying periodic sites wedged between two helical segments, each donating a Tyr residue. A half site of the motif is estimated to have nM-scale affinity for C60, such that binding of fullerene appears to direct the organization of protein units in the co-crystal. The assembly exhibits a nm-spaced helical arrangement of fullerenes along a crystallographic axis, endowing the crystal with electrical conductance properties. We closely investigate the interfacial geometry of the C60-binding motif, finding it to be common among protein crystal lattices. C60 and its derivatives have been previously reported to interact with several proteins20, 21, 22, 23, 24, 25, although a high-resolution structure of a protein–C60 has been lacking. Still, prior evidence of interaction indicates that fullerenes and proteins are compatible as materials. This, together with the simple (and naturally recurrent) geometry of the C60-binding motif we discover, suggests that it may be possible to use the structural principles emergent from our study to generate a variety of C60–protein co-assemblies to further explore and exploit the properties of fullerenes26.


The aim of programmable self-assembly is to anticipate and harness unique collective properties that arise from precisely organized molecular building blocks. To this end, achieving atomic-level precision is crucial. This work demonstrates the first atomic resolution structures of a fullerene–protein assembly, establishing the feasibility of creating such objects, and further suggests a possible design principle for engineering such assemblies in general. How robust the discovered C60-binding motif is towards designing novel assemblies will need to be tested through a number of future design studies. However, the straightforward manner in which self-organization arose in our case, the simplicity of the C60-organizing motif in the lattice, together with its high affinity and the ubiquity of associated interfaces in natural protein lattices, are certainly promising with respect to the general applicability of the design principle. Our work also demonstrates the potential utility of exploring C60/protein co-organization, as derived supercrystals already showed synergistic charge conductance properties. Taken together, these results point to an exciting direction of inquiry towards generating protein–fullerene assemblies for the study and design of novel properties.


Scientists turn skin cells into heart and brain cells using only drugs — no stem cells required

Closer to the natural regeneration that happens in animals like newts and salamanders and no medical-safety and embryo concerns
Neurons created from chemically induced neural stem cells. The cells were created from skin cells that were reprogrammed into neural stem cells using a cocktail of only nine chemicals. This is the first time cellular reprogramming has been accomplished without adding external genes to the cells. (credit: Mingliang Zhang, PhD, Gladstone Institutes)

Scientists at the Gladstone Institutes have used chemicals to transform skin cells into heart cells and brain cells, instead of adding external genes — making this accomplishment a breakthrough, according to the scientists.

The research lays the groundwork for one day being able to regenerate lost or damaged cells directly with pharmaceutical drugs — a more efficient and reliable method to reprogram cells and one that avoids medical concerns surrounding genetic engineering.

Instead, in two studies published in an open-access paper in Science and in Cell Stem Cell, the team of scientists at the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone used chemical cocktails to gradually coax skin cells to change into organ-specific stem-cell-like cells and ultimately into heart or brain cells.

“This method brings us closer to being able to generate new cells at the site of injury in patients,” said Gladstone senior investigator Sheng Ding, PhD, the senior author on both studies. “Our hope is to one day treat diseases like heart failure or Parkinson’s disease with drugs that help the heart and brain regenerate damaged areas from their own existing tissue cells. This process is much closer to the natural regeneration that happens in animals like newts and salamanders, which has long fascinated us.”

Chemically Repaired Hearts

A human heart cell that was chemically reprogrammed from a human skin cell (credit: Nan Cao/Gladstone Institutes)

Transplanted adult heart cells do not survive or integrate properly into the heart and few stem cells can be coaxed into becoming heart cells.

Instead, in the Science study, the researchers used a cocktail of nine chemicals to change human skin cells into beating heart cells. By trial and error, they found the best combination of chemicals to begin the process by changing the cells into a state resembling multipotent stem cells (cells that can turn into many different types of cells in a particular organ). A second cocktail of chemicals and growth factors then helped transition the cells to become heart muscle cells.

With this method, more than 97% of the cells began beating, a characteristic of fully developed, healthy heart cells. The cells also responded appropriately to hormones, and molecularly, they resembled heart muscle cells, not skin cells. What’s more, when the cells were transplanted into a mouse heart early in the process, they developed into healthy-looking heart muscle cells within the organ.

“The ultimate goal in treating heart failure is a robust, reliable way for the heart to create new muscle cells,” said Srivastava, co-senior author on the Science paper. “Reprogramming a patient’s own cells could provide the safest and most efficient way to regenerate dying or diseased heart muscle.”

Rejuvenating the brain with neural stem cell-like cells

In the second study, authored by Gladstone postdoctoral scholar Mingliang Zhang, PhD, and published in Cell Stem Cell, the scientists created neural stem-cell-like cells from mouse skin cells using a similar approach.

The chemical cocktail again consisted of nine molecules, some of which overlapped with those used in the first study. Over ten days, the cocktail changed the identity of the cells, until all of the skin-cell genes were turned off and the genes of the neural stem-cell-like cells were gradually turned on.

When transplanted into mice, the neural stem-cell-like cells spontaneously developed into the three basic types of brain cells: neurons, oligodendrocytes, and astrocytes. The neural stem-cell-like cells were also able to self-replicate, making them ideal for treating neurodegenerative diseases or brain injury.

With their improved safety, these neural stem-cell-like cells could one day be used for cell replacement therapy in neurodegenerative diseases like Parkinson’s disease and Alzheimer’s disease, according to co-senior author Yadong Huang, MD, PhD, a senior investigator at Gladstone. “In the future, we could even imagine treating patients with a drug cocktail that acts on the brain or spinal cord, rejuvenating cells in the brain in real time.”


Gladstone Institutes | Chemically Reprogrammed Beating Heart Cell

Abstract of Conversion of human fibroblasts into functional cardiomyocytes by small molecules

Reprogramming somatic fibroblasts into alternative lineages would provide a promising source of cells for regenerative therapy. However, transdifferentiating human cells to specific homogeneous, functional cell types is challenging. Here we show that cardiomyocyte-like cells can be generated by treating human fibroblasts with a combination of nine compounds (9C). The chemically induced cardiomyocyte-like cells (ciCMs) uniformly contracted and resembled human cardiomyocytes in their transcriptome, epigenetic, and electrophysiological properties. 9C treatment of human fibroblasts resulted in a more open-chromatin conformation at key heart developmental genes, enabling their promoters/enhancers to bind effectors of major cardiogenic signals. When transplanted into infarcted mouse hearts, 9C-treated fibroblasts were efficiently converted to ciCMs. This pharmacological approach for lineage-specific reprogramming may have many important therapeutic implications after further optimization to generate mature cardiac cells.

Abstract of Pharmacological Reprogramming of Fibroblasts into Neural Stem Cells by Signaling-Directed Transcriptional Activation

Cellular reprogramming using chemically defined conditions, without genetic manipulation, is a promising approach for generating clinically relevant cell types for regenerative medicine and drug discovery. However, small-molecule approaches for inducing lineage-specific stem cells from somatic cells across lineage boundaries have been challenging. Here, we report highly efficient reprogramming of mouse fibroblasts into induced neural stem cell-like cells (ciNSLCs) using a cocktail of nine components (M9). The resulting ciNSLCs closely resemble primary neural stem cells molecularly and functionally. Transcriptome analysis revealed that M9 induces a gradual and specific conversion of fibroblasts toward a neural fate. During reprogramming specific transcription factors such as Elk1 and Gli2 that are downstream of M9-induced signaling pathways bind and activate endogenous master neural genes to specify neural identity. Our study provides an effective chemical approach for generating neural stem cells from mouse fibroblasts and reveals mechanistic insights into underlying reprogramming processes.


Ultrafast laser technique identifies brain tumors in real time

04/19/2016  Posted by Lee DubayAssociate Editor, BioOptics World

A research group at VU University Amsterdam (The Netherlands) has shown that an ultrafast laser technique can reveal exactly where brain tumors are, producing images in less than a minute and enabling surgeons to removetumors without compromising healthy tissue.

Related: OCT-based approach facilitates brain cancer surgery

Pathologists typically use staining methods, in which chemicals like hematoxylin and eosin turn different tissue components blue and red, revealing its structure and whether there are any tumor cells. But for a definitive diagnosis, this process can take up to 24 hours—which means surgeons may not realize some cancerous tissue has escaped from their attention until after surgery, requiring a second operation and more risk.

But the research team’s new ultrafast laser technique is label-free—instead, they fire short, 20-fs-long laser pulses into the tissue, and when three photons converge at the same time and place, the photons interact with the nonlinear optical properties of the tissue. Through well-known phenomena in optics called second- and third-harmonic generation, these interactions produce a single photon.

The key is that the incoming and outgoing photons have different wavelengths. The incoming photons are at 1200 nm, long enough to penetrate deep into the tissue. The single photon that is produced, however, is at 600 or 400 nm, depending on if it’s second- or third-harmonic generation. The shorter wavelengths mean the photon can scatter in the tissue. The scattered photon thus contains information about the tissue, and when it reaches a detector—in this case, a high-sensitivity gallium arsenide phosphide (GaAsP) photomultiplier tube—it reveals what the tissue looks like inside.

Tissue from a patient diagnosed with low-grade glioma. The green image is taken with the new method, while the pink uses conventional hematoxylin and eosin staining. Going from the upper left to the lower right, both images show increasing cell density because of more tumor tissue. The insets reveal the high density of tumor cells. (Credit: N.V. Kuzmin et al, VU University Amsterdam, The Netherlands)

The research team used the technique to analyze glial brain tumors, which are particularly deadly because it’s hard to get rid of tumor cells by surgery, irradiation, and chemotherapy without substantial collateral damage to the surrounding brain tissue. They tested their method on samples of glial brain tumors from humans, finding that the histological detail in these images was as good—if not better—than those made with conventional staining techniques. They were able to make most images in under a minute. The smaller ones took less than a second, while larger images of a few square millimeters took five minutes—making it possible to do it in real time in the operating room, according to Marloes Groot of VU University Amsterdam, who led the work.

Now that they’ve shown their approach works, the researchers are developing a handheld device that a surgeon can use to identify a tumor’s border during surgery. The incoming laser pulses can only reach a depth of about 100 µm into the tissue. To reach farther, Groot envisions attaching a needle that can pierce the tissue and deliver photons deeper, allowing diagnosis during an operation and possibly before surgery begins.

Full details of the work appear in the journal Biomedical Optics Express; for more information, please visit

Third harmonic generation imaging for fast, label-free pathology of human brain tumors

N. V. Kuzmin, P. Wesseling, P. C. de Witt Hamer, D. P. Noske, G. D. Galgano, H. D. Mansvelder, J. C. Baayen, and M. L. Groot
Biomedical Optics Express > Volume 7 > Issue 5 > Page 1889

In brain tumor surgery, recognition of tumor boundaries is key. However, intraoperative assessment of tumor boundaries by the neurosurgeon is difficult. Therefore, there is an urgent need for tools that provide the neurosurgeon with pathological information during the operation. We show that third harmonic generation (THG) microscopy provides label-free, real-time images of histopathological quality; increased cellularity, nuclear pleomorphism, and rarefaction of neuropil in fresh, unstained human brain tissue could be clearly recognized. We further demonstrate THG images taken with a GRIN objective, as a step toward in situ THG microendoscopy of tumor boundaries. THG imaging is thus a promising tool for optical biopsies.




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A step forward in diagnostics

Larry H. Bernstein, MD, FCAP, Curator



3D Imaging of Cancer Cells Could Lead to Improved Ability of Pathologists and Radiologists to Plan Cancer Treatments and Monitor Cell Interactions

DARK DAILY   4/8/2016


Imaging research is one step closer to giving clinicians a way to do high-resolution scans of malignant cells in order to diagnose cancer and help identify useful therapies. If this technology were to prove successful in clinical studies, it might change how anatomic pathologists and radiologists diagnose and treat cancer.

Researchers at the University of Texas Southwestern Medical Center developed a way to create near-isotropic, high-resolution scans of cells within their microenvironments. The process involves utilizing a combination of two-photonBessel beams and specialized filtering.

New Imaging Approach Could be Useful to Both Pathologists and Radiologists

In a recent press release, senior author Reto Fiolka, PhD, said “there is clear evidence that the environment strongly affects cellular behavior—thus, the value of cell culture experiments on glass must at least be questioned. Our microscope is one tool that may bring us a deeper understanding of the molecular mechanisms that drive cancer cell behavior, since it enables high-resolution imaging in more realistic tumor.”

In a study in Developmental Cell, Erik S. Welf, PhD, et al, described the new microenvironmental selective plane illumination microscopy (meSPIM). When developing the technology, the team outlined three goals:

1. The microscope design must not prohibitively constrain microenvironmental properties.

2. Spatial and temporal resolution must match the cellular features of interest.

3. Spatial resolution must be isotropic to avoid spatial bias in quantitative measurements.

This new technology offers pathologists and medical laboratory scientists a new look at cancer cells and other diseases. The study notes that meSPIM eliminates the influence of stiff barriers, such as glass slide covers, while also allowing a level of control over both mechanical and chemical influences that was previously impossible.

Early meSPIM Research Reveals New Cell Behaviors

Early use of meSPIM in observing melanoma cells is already offering new insights into the relationship between the cell behavior of cellular- and subcellular-scale mechanisms and the microenvironment in which these cells exist. The study notes, “The ability to image fine cellular details in controllable microenvironments revealedmorphodynamic features not commonly observed in the narrow range of mechanical environments usually studied in vitro.”

One such difference is the appearance of blebbing. Created by melanoma cells and lines, these small protrusions are thought to aid in cell mobility and survival. Using meSPIM, observers could follow the blebbing process in real-time. Formation of blebs on slides and within an extracellular matrix (ECM) showed significant differences in both formation and manipulation of the surrounding microenvironment.

The team is also using meSPIM to take a look at membrane-associated biosensorand cytosolic biosensor signals in 3D. They hope that investigation of proteins such as phosphatidylinositol 3-kinase (PI3K) and protein kinase C will help to further clarify the roles these signals play in reorientation of fibroblasts.



meSPIM combined with computer vision enables imaging, visualization, and quantification of how cells alter collagen fibers over large distances within an image volume measuring 100 mm on each side. (Photo Copyright: Welf and Driscoll et al.)×300.jpg


Seeing cancer cells in 3-D (w/ Video)

February 22, 2016

Cancer in 3-D

Extracted surfaces of two cancer cells. (Left) A lung cancer cell colored by actin intensity near the cell surface. Actin is a structural molecule that is integral to cell movement. (Right) A melanoma cell colored by PI3-kinase activity near the cell surface. PI3K is a signaling molecule that is key to many cell processes. Credit: Welf and Driscoll et al.

Cancer cells don’t live on glass slides, yet the vast majority of images related to cancer biology come from the cells being photographed on flat, two-dimensional surfaces—images that are sometimes used to make conclusions about the behaviour of cells that normally reside in a more complex environment. But a new high-resolution microscope, presented February 22 in Developmental Cell, now makes it possible to visualize cancer cells in 3D and record how they are signaling to other parts of their environment, revealing previously unappreciated biology of how cancer cells survive and disperse within living things.

“There is clear evidence that the environment strongly affects cellular behavior—thus, the value of cell culture experiments on glass must at least be questioned,” says senior author Reto Fiolka, an optical scientist at the University of Texas Southwestern Medical Center. “Our is one tool that may bring us a deeper understanding of the molecular mechanisms that drive cancer cell behavior, since it enables high-resolution imaging in more realistic tumor environments.”

In their study, Fiolka and colleagues, including co-senior author Gaudenz Danuser, and co-first authors Meghan Driscoll and Erik Welf, also of UT Southwestern, used their microscope to image different kinds of skin cancer cells from patients. They found that in a 3D environment (where cells normally reside), unlike a glass slide, multiple melanoma cell lines and primary melanoma cells (from patients with varied genetic mutations) form many small protrusions called blebs. One hypothesis is that this blebbing may help the survive or move around and could thus play a role in skin cancer cell invasiveness or drug resistance in patients.

The researchers say that this is a first step toward understanding 3D biology in tumor microenvironments. And since these kinds of images may be too complicated to interpret by the naked eye alone, the next step will be to develop powerful computer platforms to extract and process the information.

“When we conceived of this project, we first asked what we wanted to measure and then designed a microscope and analytical platform to achieve this goal,” says co-first author Erik Welf, a cell biologist. “We hope that now instead of asking what we can measure, scientists will ask what we must measure in order to make meaningful contributions to cancer cell biology.”

The microscope control software and image analytical code are freely available to the scientific community.

More information: Developmental Cell, Welf and Driscoll et al.: “Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments”

Read more at:

Quantitative Multiscale Cell Imaging in Controlled 3D Microenvironments

Erik S. Welf4, Meghan K. Driscoll4, Kevin M. Dean, Claudia Schäfer, Jun Chu, Michael W. Davidson, Michael Z. Lin, Gaudenz Danusercorrespondence , Reto Fiolkacorrespondence
Dev Cell  22 Feb 2016;  Volume 36, Issue 4:462–475     DOI:
  • meSPIM allows microenvironmentally conscious 3D imaging/analysis of subcellular biology
  • Precisely controlled microenvironments reveal diverse morphological phenotypes
  • Isotropic resolution and high speed enable the quantification of 3D cell signaling and morphodynamics
  • Multiscale quantification of microenvironmental reorganization by cells


The microenvironment determines cell behavior, but the underlying molecular mechanisms are poorly understood because quantitative studies of cell signaling and behavior have been challenging due to insufficient spatial and/or temporal resolution and limitations on microenvironmental control. Here we introduce microenvironmental selective plane illumination microscopy (meSPIM) for imaging and quantification of intracellular signaling and submicrometer cellular structures as well as large-scale cell morphological and environmental features. We demonstrate the utility of this approach by showing that the mechanical properties of the microenvironment regulate the transition of melanoma cells from actin-driven protrusion to blebbing, and we present tools to quantify how cells manipulate individual collagen fibers. We leverage the nearly isotropic resolution of meSPIM to quantify the local concentration of actin and phosphatidylinositol 3-kinase signaling on the surfaces of cells deep within 3D collagen matrices and track the many small membrane protrusions that appear in these more physiologically relevant environments.

Read more: 3D Imaging of Cancer Cells Could Lead to Improved Ability of Pathologists and Radiologists to Plan Cancer Treatments and Monitor Cell Interactions | Dark Daily

The research team believes this opens new possibilities for studying diseases at a subcellular level, saying, “Cell biology is necessarily restricted to studying what we can measure. Accordingly, while the last hundred years have yielded incredible insight into cellular processes, unfortunately most of these studies have involved cells plated onto flat, stiff surfaces that are drastically different from the in vivo microenvironment …

“Here, we introduce an imaging platform that enables detailed subcellular observations without compromising microenvironmental control and thus should open a window for addressing these fundamental questions of cell biology.”

Limitations of meSPIM

One significant issue associated with the use of meSPIM is the need to process the large quantity of data into useful information. Algorithms currently allow for automatic bleb detection. However, manual marking, while time consuming, still provides increased accuracy. Researchers believe the next step in improving the quality of meSPIM scans lie in computer platforms designed to extract and process the scan data.

Until this process is automated, user bias, sample mounting, and data handling will remain risks for introducing errors into the collected data. Yet, even in its early stages, meSPIM offers new options for assessing the state of cancer cells and may eventually provide pathologists and radiologists with additional information when creating treatment plans or assessments.


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Outstanding Achievement in Pathology

Curator: Larry H Bernstein, MD, FCAP


Olympus America Honors Outstanding Pathologists During First Annual “Unsung Heroes” Awards

Melville, Ny—Tracey Corey Handy, M.D., Chief Medical Examiner of Kentucky, and Matthew Zarka, M.D., affiliated with the University of Vermont and the Fletcher Allen Health Center, were recognized as the 1999 winners of the “Unsung Heroes” Awards. The awards, sponsored by Olympus America Inc., a world leading manufacturer of microscopes, in cooperation with the College of American Pathologists (CAP), were presented at a ceremony during the Fall CAP Conference in New Orleans.

The awards are the first in the on-going “Unsung Heroes” program sponsored by Olympus for the purpose of increasing public awareness of the vital and often invisible role pathologists have in saving lives. In addition to their expertise with a microscope, pathologists are the doctors who ensure that clinical laboratory testing is reliable and that diseases are accurately diagnosed. They are on the front lines whenever the public is threatened with disease. Their role in forensic science is crucial in helping prevent people from falling prey to abuse or avoidable illness. As Dan Biondi, Olympus Senior Vice President, points out, “Olympus is committed to supporting the work of the world’s pathologists and to advocating an educated patient population.”

Dr. Tracey Corey Handy is recognized as an “Unsung Hero” for her role in upgrading the well-being of children as Kentucky’s Chief Medical Examiner. Along with several colleagues, Dr. Handy founded the state’s “Living Forensics” team in 1991. Since its inception, the team has consulted on more than 700 cases of suspected child abuse. This effort has led to an increased conviction rate of abuse perpetrators and helps to reduce further cases of child abuse. In addition, Dr. Handy has initiated a program of routine screening for metabolic defects apparent in victims of Sudden Infant Death Syndrome (SIDS), which has resulted in the correct diagnosis of conditions that would have otherwise been attributed to SIDS. Dr. Handy has also chaired the state’s first child mortality review group that has resulted in the initiation of prevention programs, particularly in the event of accidental child death. A frequent speaker and contributor of her expertise to organizations throughout the country, she also teaches forensic pathology and has been published in more than a dozen peer-reviewed journals and books.

Dr. Matthew Zarka is recognized as an “Unsung Hero” for his efforts in aiding the extremely poor Mexican-Indian population in the remote mountain regions of Oaxaca, Mexico. Over the last two years Dr. Zarka has volunteered his time and services to bring much needed medical care to these impoverished communities. He and his OB/GYN team have been setting up the very first clinics throughout the area, enjoining the coffee companies of Mexico to spread word of the clinics to the local population and to help transport patients to the clinics. After each female patient underwent a gynecological examination, Dr. Zarka stained and read her Pap test. When needed, more extensive evaluations, biopsies, treatment and counsel were provided. Overwhelmingly successful, Dr. Zarka’s outreaching medical mission has grown to include additional professional staff. By volunteering his time and expertise, Dr. Zarka provides the only real access most people of the region have to modern medical care. His contribution has undoubtedly saved lives that might otherwise have been lost.

Stanford University

Benjamin Pinsky, MD, PhD, Assistant Professor of Pathology and Medicine (Infectious Diseases) is the recipient of the 2014 Siemens Healhcare Diagnostics Young Investigator Award.  This award “honors outstanding laboratory research in clinical microbiology or antimicrobial agents and is intended to further the career development of a young clinical scientist and promote awareness of clinical microbiology as a career.”

Stephen J. Galli, MD, Chair of Pathology, Professor of Pathology and Microbiology and Immunology, and the Mary Hewitt Loveless, MD Professor, is the recipient of the 2014 ASIP (American Society of Investigative Pathology) Rouse Whipple Award.  This award is presented to a senior scientist with a distinguished career in research who has advanced the understanding of disease and has continued productivity at the time of this award.

Dr. Raffick Bowen, Clinical Associate Professor and Associate Medical Director of SHC’s Clinical Chemistry and Immunology Laboratory is the recipient of the American Association of Clinical Chemistry’s Outstanding Speaker Award for 2013. This award recognizes his achievement in earning a speaker evaluation rating of 4.5 or higher during a 2013 continuing education activity accredited by AACC. The title of Dr. Bowen’s presentation is “Implementation of Autoverification in a Clinical Chemistry Laboratory: Theory to Practice”

Richard Kempson, MD,

Emeritus Professor of Pathology, is the recipient of the 2014 United States and Canadian Academy of Pathology (USCAP) President’s Award. The USCAP President’s Award is given annually to recognize an individual for outstanding service to the field of pathology.

Dr. Kempson is richly deserving of this award. Dr. Kempson has not only contributed substantially to the surgical pathology literature, particularly in gynecologic and soft tissue pathology but also, with Dr. Ronald Dorfman, he trained a substantial percentage of this and the next generation’s academic and community leaders in surgical pathology.

Dr. Kempson’s affiliation with Stanford University began in 1968 when he and Dr. Ronald Dorfman were recruited to Stanford to develop a program in surgical pathology. In short order, they established an internationally recognized residency and clinical fellowship program which went on to train more than 275 pathologists in the art and science of diagnostic surgical pathology. Dr. Kempson developed a distinctive teaching style that emphasized precise diagnostic criteria, approaching diagnosis with a broad morphologic differential diagnosis, and most importantly, always highlighting the relevance to patient management of the morphologic distinctions being made.

Prior to his recruitment to Stanford, Dr. Kempson was an Assistant Professor of Pathology and Surgical Pathology at Washington University. Dr. Kempson served as an Associate Professor of Pathology at Stanford from 1968 to 1974 and a Professor of Pathology from 1974 to 2001. In addition to his academic duties, he served as Co-Director of Surgical Pathology from 1968 until 2001. He also has served as President of the Association of Directors of Surgical Pathology (1993-1995), the United States and Canadian Academy of Pathology (1996) and the Arthur Purdy Stout Society (1996) and the California Society of Pathologists. The Richard Kempson, MD, Professorship in Surgical Pathology was established by the Department of Pathology in 2002 to honor him and his remarkable contributions to surgical pathology.

University of California, San Diego

A new era in diagnostics has emerged within the concept of Personalized Medicine. Imagine selecting cancer chemotherapy drugs based on knowledge of the precise mutations in a cancer. Can we predict who may have an adverse response to a medication based on that individual’s genetic blueprint? At UCSD, we are dedicated to making these resources available to our patients in the very near future. This is why we recently established the Pathology Center for Personalized Medicine. The goal of the Center is to conduct leading research necessary to form the foundation for advanced personalized medicine diagnostic testing and then to make this testing available in the CALM. For more information on the Center for Personalized Medicine, click here.

The research enterprise in Pathology at UCSD has grown dramatically in the past five years, and we are now amongst the top 15 programs in the country. Basic and translational research laboratories in the UCSD Pathology Department tackle important problems concerning cancer development and progression, angiogenesis, stem cell biology, neurodegenerative diseases, peripheral neuropathy, inflammation, infectious diseases, and wound healing. Our laboratories provide excellent environments for learning cell biology, molecular genetics, biochemistry, and animal physiology. Our faculty includes many active participants in the Biomedical Sciences (BMS) Graduate Program. For more information on this program, click here. We also have excellent opportunities for postdoctoral researchers. Please click here to visit our web page on summarizing the Pathology Department research enterprise. Then visit individual web pages for each of our faculty member to view specific research interests.

The Department of Pathology is home to both an outstanding Comparative Pathology and Medicine Program (for more information, click here) and the UCSD Research Ethics Program. We provide major educational support to the School of Medicine and the Skaggs School of Pharmacy and Pharmaceutical Sciences. For further information on these training opportunities, click here.

The La Jolla/San Diego community is a fertile environment for research and the pharmaceutical industry. The Sanford Burnham Medical Research Institute, the Scripps Research Institute, the Sidney Kimmel Cancer Center, the Salk Institute for Biological Studies, and the La Jolla Institute for Allergy and Immunology house exciting scientific programs and provide for numerous scientific collaborations. We also boast a plethora of biotechnology companies, located nearby on the La Jolla mesa.

The overall theme and focus of the Department of Pathology is to elucidate the molecular basis and pathology of human disease.  The faculty is comprised of basic, translational and physician scientists that utilize the latest techniques in genomics, proteomics, cell biology, molecular biology and physiology to develop new diagnostic and therapeutic approaches for a wide range of diseases, including cancer, neurological disease, microbial infection, and inflammatory disease.

Steven L. Gonias, M.D., Ph.D.

Our laboratory is interested in identifying and characterizing novel pathways by which proteases and their cell-surface receptors regulate cell physiology. We are particularly interested in the function of proteases in cancer but also have active projects related to peripheral nerve injury, Alzheimer’s disease and cardiovascular biology. One focus involves urokinase-type plasminogen activator (uPA), a serine protease and plasminogen activator that binds with high affinity to a GPI-anchored receptor called uPAR. This event activates multiple cell-signaling pathways that affect cell migration, survival, and phenotype. We are actively working to elucidate mechanisms by which uPAR-initiated cell-signaling promotes cancer metastasis. We are particularly interested in breast cancer, but also work on prostate cancer and cancers of the central nervous system.

The complex of uPA with its inhibitor, PAI-1, is a ligand for a receptor called LRP-1. LRP-1 also is the receptor for other ligands, including extracellular matrix proteins, growth factors and foreign toxins. Our laboratory elucidated a pathway in which LRP-1 regulates cell-signaling indirectly, by regulating the cell-surface level of uPAR. However, recent studies suggest that LRP-1 also directly regulates cell-signaling by binding adaptor proteins, such as Shc and JIP. By this mechanism, LRP-1 regulates cell survival and gene transcription. Our current re­search is aimed at determining the role of LRP-1 in cancer and peripheral nerve injury, using in vitro and in vivomodel systems. Using proteomics approaches, we also are actively investigating the ability of LRP-1 to model the composition of the plasma membrane.

Our third area of focus concerns the plasma protease inhibitor, alpha2M. Our laboratory has demonstrated that this protein functions as a conformation-dependent carrier of growth factors. Alpha2M may also function in cell-signaling by binding to LRP-1. By site-directed mutagenesis, we have iso­lated and individually modified various functional sites in this multifunc­tional protein.

David Bailey, MD, PhD

David N. Bailey received his Bachelor of Science degree in Chemistry “with high distinction” from Indiana University and his Doctor of Medicine degree from Yale University.  He completed a National Institutes of Health postdoctoral fellowship in Laboratory Medicine and a residency in Clinical Pathology, both at Yale, serving as Chief Resident in his final year.  He is certified in Clinical Pathology and Chemical Pathology by the American Board of Pathology.

Dr. Bailey joined the University of California (UC) San Diego faculty in 1977 and served as Director of the Toxicology Laboratory of UC San Diego Medical Center (1977-2007), Head of the Division of Laboratory Medicine (1983-1989, 1994-1998), Acting Chair (1986-1988) and permanent Chair of the Department of Pathology (1988-2001),  Director of the Pathology Residency Program (1986-1999), Director of Clinical Laboratories of UCSD Medical Center (1982-1999), Interim Vice Chancellor for Health Sciences and Dean of the UC San Diego School of Medicine (1999-2000 and 2006-2007), Deputy Vice Chancellor for Health Sciences (2001-2007), and Dean for Faculty & Student Matters in UC San Diego School of Medicine (2003-2007).  From 2007 to 2009, he was Vice Chancellor for Health Affairs, Dean of the School of Medicine, and Professor of Pathology and Laboratory Medicine at the University of California, Irvine.

Dr. Bailey was recognized by the Institute of Scientific Information as one of the world’s ten most cited authors in forensic sciences (1981-93). He received the Gerald T. Evans Award from the Academy of Clinical Laboratory Physicians and Scientists in 1993 for his leadership and service to the Academy.  Dr. Bailey has served as President of the California Association of Toxicologists (1981-1982), President of the Academy of Clinical Laboratory Physicians and Scientists (1988-89), and Secretary-Treasurer of the Association of Pathology Chairs (1996-99).  He has also served on the Chemical Pathology Test Development and Advisory Committee of the American Board of Pathology; the Editorial Boards of Clinical Chemistry, the Journal of Analytical Toxicology, and the American Journal of Clinical Pathology; the Doris A. Howell Foundation for Women’s Health Research Board of Directors; the Board of Directors of the George G. Glenner Alzheimer’s Family Centers, Inc.; the Board of Directors of the Children’s Hospital of Orange County; the Board of Directors of Children’s Healthcare of California; the Board of Directors of the Rady Children’s Hospital of San Diego; the Board of Directors of the Veterans Medical Research Foundation (San Diego); and the Executive Committee and Governing Board of the California Institute of Telecommunications and Information Technology, among others.

David A. Herold, M.D., Ph.D.

My laboratory research interests are in the area of mass spectrometry application to clinical diagnostics. This includes prostaglandins, trace metal and steroids. Additionally, we has been involved in the development and validation of “classical” clinical chemistry diagnostic tests. The application of the mass spectrometry to determine the validity of endocrine tests, in particular testosterone, has been of particular interest. We have been using GC-MS, LC-MS, and MS-MS techniques for these investigations. At the present time, we are involved with the use of Accelerator Mass Spectrometry for the determination of calcium flux in serum and urine using 41Ca as a marker. The purpose of these studies is to better understand bone remodeling in normal and diseased patients. We have also investigated the use of microfluidics for the application to clinical diagnostics to measure selected proteins in a rapid and accurate manner.


David Cheresh, Ph.D.

Tumor growth, invasion, stem cells and drug resistance. Molecular regulation of tumor growth and angiogenesis. Drug development targeting molecular pathways involved in tumor growth metastasis and angiogenesis.

The Cheresh laboratory focuses on the discovery of molecular pathways involved in the progression of cancer. Cheresh’s earlier work identified integrin αυβ3 as a biomarker of tumor angiogenesis and tumor progression, and was involved in the discovery of a drug called cilentigide which targets integrins αυβ3 and αυβ5.

The Cheresh laboratory has identified a series of critical microRNAs that regulate the growth of blood vessels.  These microRNAs control the angiogenic switch that occurs during the earliest stages of tumor growth and neovascularization in the retina.  As such one of these microRNAs may have therapeutic application as it is capable of maintaining blood vessels in the quiescent state.

Cheresh and colleagues have identified integrin αυβ3 as a biomarker of tumor stem cells during intrinsic or acquired resistance of a wide range of tumors including: cancer of the lung, pancreas, breast, and colon.   Cheresh and his lab discovered that αυβ3 expression is both necessary and sufficient to account for tumor stemness and drug resistance based on its ability to drive a molecular pathway regulating these processes.  This has led to the development of new therapeutic strategies to resensitize patients to drugs such as erlotinib and lapatinib that target EGFR.

The Cheresh laboratory has identified RAF kinase as an important target involved in tumor growth and angiogenesis.  They have developed a new drug design strategy to target RAF and other relevant kinases by designing allosteric inhibitors of these targets.  This is based on the use of defined chemical scaffolds to dock into an allosteric pocket on these kinases to render them inactive.  The combined use of in silico and biological screening has yielded drugs with nM anti-tumor activity that produce strong anti-tumor growth in mouse models following once a day oral dosing.   This approach appears to yield drugs that target tumors that are resistant to ATP mimetic inhibitors of RAF, Kit or PDGFR

John Lowe

Senior Director, Pathology

I joined Genentech in 2008 as Senior Director of Pathology, after having spent more than 18 years as an HHMI Investigator at the University of Michigan and then 3 years as Chair of Pathology at Case Western Reserve University School of Medicine. The role of Senior Director of Pathology in Research at Genentech offered attractive opportunities to do research in an outstanding, disease-focused scientific environment, while also helping to lead the scientific and research support activities of the Pathology department. These latter efforts help Genentech continue to make a major positive difference to the health and well being of a large number of patients afflicted with cancer, autoimmune syndromes, neurodegenerative diseases and other illnesses for which therapies are unsatisfactory or nonexistent.

An exceptional team of pathologists, laboratory managers, scientific associates and administrative staff in the department collaborate with me in these efforts. Additional outstanding pathologists, scientists, and managers continue to be recruited to assist us in ensuring that the department performs at the highest level. Our task is made more straightforward by the environment at Genentech, which is characterized by exceptionally bright, motivated and collaborative colleagues at every level, spectacular facilities, and workplace philosophies that are conducive to the highest levels of achievement.

Postdoctoral Mentor

The opportunity to mentor postdoctoral fellows at Genentech has been a stimulating and gratifying experience for me. This derives in part from the freedom afforded by the program to pursue research directions that are deemed to be important and interesting, even if these have no immediate therapeutic relevance. The special mentoring experience also derives from extraordinary breadth and quality of the core laboratories at Genentech, and the spectacular intellectual environment. Together, these circumstances provide an unparalleled opportunity for postdoctoral fellows, and their mentors, to engage in biomedical discovery of the highest caliber.

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Identification of Biomarkers that are Related to the Actin Cytoskeleton

Curator and Writer: Larry H Bernstein, MD, FCAP

This is Part I in a series of articles on Calcium and Cell motility.

The Series consists of the following articles:

Part I: Identification of Biomarkers that are Related to the Actin Cytoskeleton

Larry H Bernstein, MD, FCAP

Part II: Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

Larry H. Bernstein, MD, FCAP, Stephen Williams, PhD and Aviva Lev-Ari, PhD, RN

Part III: Renal Distal Tubular Ca2+ Exchange Mechanism in Health and Disease

Larry H. Bernstein, MD, FCAP, Stephen J. Williams, PhD
 and Aviva Lev-Ari, PhD, RN

Part IV: The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia, Similarities and Differences, and Pharmaceutical Targets

Larry H Bernstein, MD, FCAP, Justin Pearlman, MD, PhD, FACC and Aviva Lev-Ari, PhD, RN

Part V: Ca2+-Stimulated Exocytosis:  The Role of Calmodulin and Protein Kinase C in Ca2+ Regulation of Hormone and Neurotransmitter

Larry H Bernstein, MD, FCAP
Aviva Lev-Ari, PhD, RN

Part VI: Calcium Cycling (ATPase Pump) in Cardiac Gene Therapy: Inhalable Gene Therapy for Pulmonary Arterial Hypertension and Percutaneous Intra-coronary Artery Infusion for Heart Failure: Contributions by Roger J. Hajjar, MD

Aviva Lev-Ari, PhD, RN

Part VII: Cardiac Contractility & Myocardium Performance: Ventricular Arrhythmias and Non-ischemic Heart Failure – Therapeutic Implications for Cardiomyocyte Ryanopathy (Calcium Release-related Contractile Dysfunction) and Catecholamine Responses

Justin Pearlman, MD, PhD, FACC, Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

Part VIII: Disruption of Calcium Homeostasis: Cardiomyocytes and Vascular Smooth Muscle Cells: The Cardiac and Cardiovascular Calcium Signaling Mechanism

Justin Pearlman, MD, PhD, FACC, Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

Part IXCalcium-Channel Blockers, Calcium Release-related Contractile Dysfunction (Ryanopathy) and Calcium as Neurotransmitter Sensor

Justin Pearlman, MD, PhD, FACC, Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

Part X: Synaptotagmin functions as a Calcium Sensor: How Calcium Ions Regulate the fusion of vesicles with cell membranes during Neurotransmission

Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

Part XI: Sensors and Signaling in Oxidative Stress

Larry H. Bernstein, MD, FCAP

Part XII: Atherosclerosis Independence: Genetic Polymorphisms of Ion Channels Role in the Pathogenesis of Coronary Microvascular Dysfunction and Myocardial Ischemia (Coronary Artery Disease (CAD))

Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN


In this article the Author will cover two types of biomarker on the function of actin in cytoskeleton mobility in situ.

  • First, is an application in developing the actin or other component, for a biotarget and then, to be able to follow it as

(a) a biomarker either for diagnosis, or

(b) for the potential treatment prediction of disease free survival.

  • Second, is mostly in the context of MI, for which there is an abundance of work to reference, and a substantial body of knowledge about

(a) treatment and long term effects of diet, exercise, and

(b) underlying effects of therapeutic drugs.

1.  Cell Membrane (cytoskeletal) Plasticity

Refer to … Squeezing Ovarian Cancer Cells to Predict Metastatic Potential: Cell Stiffness as Possible Biomarker

Reporter/curator: Prabodh Kandala, PhD

New Georgia Tech research shows that cell stiffness could be a valuable clue for doctors as they search for and treat cancerous cells before they’re able to spread. The findings, which are published in the journal PLoS One, found that highly metastatic ovarian cancer cells are several times softer than less metastatic ovarian cancer cells. This study used atomic force microscopy (AFM) to study the mechanical properties of various ovarian cell lines. A soft mechanical probe “tapped” healthy, malignant and metastatic ovarian cells to measure their stiffness. In order to spread, metastatic cells must push themselves into the bloodstream. As a result, they must be highly deformable and softer. This study results indicate that cell stiffness may be a useful biomarker to evaluate the relative metastatic potential of ovarian and perhaps other types of cancer cells.

Comparative gene expression analyses indicate that the reduced stiffness of highly metastatic HEY A8 cells is associated with actin cytoskeleton remodeling and microscopic examination of actin fiber structure in these cell lines is consistent with this prediction.   The results suggest either of two approaches. Atomic Force Microscopy is not normally used by pathologists in diagnostics. Electron microscopy requires space for making and cutting the embedded specimen, and a separate room for the instrument. The instrument is large and the technique was not suitable for anything other than research initially until EM gained importance in Renal Pathology. It has not otherwise been used.  This new method looks like it might be more justified over a spectrum of cases.

A.  Atomic Force Microscopy

So the first point related to microscopy is whether AFM has feasibility for routine clinical use in the pathologists’ hands. This requires:

  1. suitable size of equipment
  2.  suitable manipulation of the specimen
  3. The question of whether you are using overnight fixed specimen, or whether the material is used unfixed
  4. Nothing is said about staining of cells for identification.
  5. Then there is the question about whether this will increase the number of Pathologist Assistants used across the country, which I am not against.   This would be the end of “house” trained PAs, and gives more credence to the too few PA programs across the country. The PA programs have to be reviewed and accredited by NAACLS (I served 8 years on the Board). A PA is represented on the Board, and programs are inspected by qualified peers.   There is no academic recognition given to this for tenure and promotion in Pathology Departments, and a pathologist is selected for a medical advisory role by the ASCP, and must be a Medical Advisor to a MLS accredited Program.   The fact is that PAs do gross anatomic dictation of selected specimens, and they do autopsies under the guidance of a pathologist. This is the reality of the profession today. The pathologist has to be in attendance at a variety of quality review conferences, for surgical morbidity and mortality to obstetrics review, and the Cancer Review. Cytopathology and cytogenetics are in the pathology domain.   In the case of tumors of the throat, cervix, and accessible orifices, it seems plausible to receive a swab for preparation. However, sampling error is greater than for a biopsy. A directed needle biopsy or a MIS specimen is needed for the ovary.

B.  identification of biomarkers that are related to the actin cytoskeleton

The alternative to the first approach is the identification of biomarkers that are related to the actin cytoskeleton, perhaps in the nature of the lipid or apoprotein isoform that gives the cell membrane deformability. The method measuring by Atomic Force Microscopy is shown with the current method of cytological screening, and I call attention to cells clustered together that have a scant cytoplasm surrounding nuclei occupying 1/2 to 3/4 of the cell radius.  The cells are not anaplastic, but the clumps are suggestive of glnad forming epithelium.

English: Animation showing 3-D nature of clust...

English: Animation showing 3-D nature of cluster. Image:Serous carcinoma 2a – cytology.jpg (Photo credit: Wikipedia)

The cell membrane, also called the plasma memb...

The cell membrane, also called the plasma membrane or plasmalemma, is a semipermeable lipid bilayer common to all living cells. It contains a variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes. It also serves as the attachment point for both the intracellular cytoskeleton and, if present, the cell wall. (Photo credit: Wikipedia)

English: AFM bema detection

AFM non contact mode

AFM non contact mode (Photo credit: Wikipedia)

C.  The diagnosis of ovarian cancer can be problematic because it can have a long period of growth undetected.

On the other hand, it is easily accessible once there is reason to suspect it. They are terrible to deal with because they metastasize along the abdominal peritoneum and form a solid cake. It is a problem of location and silence until it is late. Once they do announce a presence on the abdominal wall, there is probably a serous effusion. It was not possible to rely on a single marker, but when CA125 was introduced, Dr. Marguerite Pinto, Chief of Cytology at Bridgeport Hospital-Yale New Haven Health came to the immnunochemistry lab and we worked out a method for analyzing effusions, as we had already done with carcinoembryonic antigen.       The use of CEA and CA125 was published by Pinto and Bernstein as a first that had an impact.  This was followed by a study with the Chief of Oncology, Dr. Martin Rosman, that showed that the 30 month survival of patients post treatment is predicted by the half-life of disappearance of CA125 in serum.  At the time of this writing, I am not sure of the extent of its use 20 years later. History has taught us that adoption can be slow, depending very much on dissemination from major academic medical centers.  On the other hand, concepts can also be stuck at academic medical centers because of a rigid and unprepared mindset in the professional community.  The best example of this is the story of Ignaz Semmelweis, the best student of Rokitansky in Vienna for discovering the cause and prevention of childbirth fever at a time that nursemaids had far better results at obstetrical delivery than physicians.  Contrary to this, Edward Jenner, the best student of John Hunter (anatomist, surgeon, and physician to James Hume), discovered vaccination from the observation that milkmaids did not get smallpox (cowpox was a better alternative).
Only this year a Nobel Prize in Physics was awarded to an Israeli scientist who, working in the US, was unable to convince his associates of his discovery of PSEUDOCRYSTALS. – Diagnostic efficiency of carcinoembryonic antigen and CA125 in the cytological evaluation of effusions. M M Pinto, L H Bernstein, R A Rudolph, D A Brogan, M Rosman Arch Pathol Lab Med 1992; 116(6):626-631 ICID: 825503 Article type: Review article – Immunoradiometric assay of CA 125 in effusions. Comparison with carcinoembryonic antigen. M M Pinto, L H Bernstein, D A Brogan, E Criscuolo Cancer 1987; 59(2):218-222 ICID: 825555 Article type: Review article – Carcinoembryonic antigen in effusions. A diagnostic adjunct to cytology. M M Pinto, L H Bernstein, D A Brogan, E M Criscuolo Acta Cytologica 1987; 31(2):113-118 ICID: 825557

Predictive Modeling

Ovarian Cancer a plot of the CA125 elimination half-life vs the Kullback-Liebler distance

Ca125 half-life vs Kullback Entropy                                                          HL vs Survival KM plot 

Troponin(s) T, I, C  and the contractile apparatus  (contributed by Aviva Lev-Ari, PhD, RN)


For 2012 – 2013 Frontier Contribution in Cardiology on Gene Therapy Solutions for Improving Myocardial Contractility, see

Lev-Ari, A. 8/1/2013 Calcium Cycling (ATPase Pump) in Cardiac Gene Therapy: Inhalable Gene Therapy for Pulmonary Arterial Hypertension and Percutaneous Intra-coronary Artery Infusion for Heart Failure: Contributions by Roger J. Hajjar, MD

For explanation of Conduction prior to Myocardial Contractility, see

Lev-Ari, A. 4/28/2013 Genetics of Conduction Disease: Atrioventricular (AV) Conduction Disease (block): Gene Mutations – Transcription, Excitability, and Energy Homeostasis

The contraction of skeletal muscle is triggered by nerve impulses, which stimulate the release of Ca2+ from the sarcoplasmic reticulum—a specialized network of internal membranes, similar to the endoplasmic reticulum, that stores high concentrations of Ca2+ ions. The release of Ca2+ from the sarcoplasmic reticulum increases the concentration of Ca2+ in the cytosol from approximately 10-7 to 10-5 M. The increased Ca2+ concentration signals muscle contraction via the action of two accessory proteins bound to the actin filaments: tropomyosin and troponin (Figure 11.25). Tropomyosin is a fibrous protein that binds lengthwise along the groove of actin filaments. In striated muscle, each tropomyosin molecule is bound to troponin, which is a complex of three polypeptides: troponin C (Ca2+-binding), troponin I (inhibitory), and troponin T (tropomyosin-binding).

  • When the concentration of Ca2+ is low, the complex of the troponins with tropomyosin blocks the interaction of actin and myosin, so the muscle does not contract.
  • At high concentrations, Ca2+ binding to troponin C shifts the position of the complex, relieving this inhibition and allowing contraction to proceed.

Figure 11.25

Association of tropomyosin and troponins with actin filaments. (A) Tropomyosin binds lengthwise along actin filaments and, in striated muscle, is associated with a complex of three troponins: troponin I (TnI), troponin C (TnC), and troponin T (TnT). In (more…)
Contractile Assemblies of Actin and Myosin in Nonmuscle Cells

Contractile assemblies of actin and myosin, resembling small-scale versions of muscle fibers, are present also in nonmuscle cells. As in muscle, the actin filaments in these contractile assemblies are interdigitated with bipolar filaments of myosin II, consisting of 15 to 20 myosin II molecules, which produce contraction by sliding the actin filaments relative to one another (Figure 11.26). The actin filaments in contractile bundles in nonmuscle cells are also associated with tropomyosin, which facilitates their interaction with myosin II, probably by competing with filamin for binding sites on actin.

Figure 11.26

Contractile assemblies in nonmuscle cells. Bipolar filaments of myosin II produce contraction by sliding actin filaments in opposite directions.

Two examples of contractile assemblies in nonmuscle cells, stress fibers and adhesion belts, were discussed earlier with respect to attachment of the actin cytoskeleton to regions of cell-substrate and cell-cell contacts (see Figures 11.13 and 11.14). The contraction of stress fibers produces tension across the cell, allowing the cell to pull on a substrate (e.g., the extracellular matrix) to which it is anchored. The contraction of adhesion belts alters the shape of epithelial cell sheets: a process that is particularly important during embryonic development, when sheets of epithelial cells fold into structures such as tubes.

The most dramatic example of actin-myosin contraction in nonmuscle cells, however, is provided by cytokinesis—the division of a cell into two following mitosis (Figure 11.27). Toward the end of mitosis in animal cells, a contractile ring consisting of actin filaments and myosin II assembles just underneath the plasma membrane. Its contraction pulls the plasma membrane progressively inward, constricting the center of the cell and pinching it in two. Interestingly, the thickness of the contractile ring remains constant as it contracts, implying that actin filaments disassemble as contraction proceeds. The ring then disperses completely following cell division.

Figure 11.27

Cytokinesis. Following completion of mitosis (nuclear division), a contractile ring consisting of actin filaments and myosin II divides the cell in two.

2.  Use of Troponin(s) in Diagnosis

Troponins T and I are released into the circulation at the time of an acute coronary syndrome (ACS).  Troponin T was first introduced by Roche (developed in Germany) for the Roche platform as a superior biomarker for identifying acute myocardial infarction (AMI), because of a monoclonal specificity to the cardiac troponin T.  It could not be measured on any other platform (limited license patent), so the Washington University Clinical Chemistry group developed a myocardiocyte specific troponin I that quickly became widely available to Beckman, and was adapted to other instruments.  This was intended to replace the CK isoenzyme MB, that is highly elevated in rhabdomyolysis associated with sepsis or with anesthesia in special cases.

The troponins I and T had a tenfold scale difference, and the Receiver Operator Curve Generated cutoff was accurate for AMI, but had significant elevation with end-stage renal disease.  The industry worked in concert to develop a high sensitivity assay for each because there were some missed AMIs just below the ROC cutoff, which could be interpreted as Plaque Rupture.  However, the concept of plaque rupture had to be reconsidered, and we are left with type1 and type 2 AMI (disregarding the case of post PCI or CABG related).   This led to the current establishment of 3 standard deviations above the lowest measureable level at 10% coefficient of variation.  This has been discussed sufficiently elsewhere.  It did introduce a problem in the use of the test as a “silver bullet” once the finer distinctions aqnd the interest in using the test for prognosis as well as diagnosis.   This is where the use of another protein associated with heart failure came into play – either the B type natriuretic peptide, or its propeptide, N-terminal pro BNP.  The prognostic value of using these markers, secreted by the HEART and acting on the kidneys (sodium reabsorption) has proved useful.  But there has not been a multivariate refinement of the use of a two biomarker approach.  In the following part D, I illustrate what can be done with an algorithmic approach to multiple markers.

Software Agent for Diagnosis of AMI

Isaac E. Mayzlin, Ph.D., David Mayzlin, Larry H. Bernstein, M.D. The so called gold standard of proof of a method is considered the Receiver-Operating Characteristic Curve, developed for detecting “enemy planes or missiles”, and adopted first by radiologists in medicine.  This matches the correct “hits” to the actual calssification and it is generally taught as a plot of sensitivity vs (1 – specifity).  But what if you had no “training” variable?  Work inspired by Eugene Rypka’s bacterial classification led to Rosser Rudolph’s application of the Entropy of Shannon and Weaver to identify meaningful information, referring to what was Kullback-Liebler distance as “effective information”.  This allowed Rudolph and Bernstein to classify using disease biomarkers obtaing the same results as the ROC curve using an apl program.  The same data set was used by Bernstein, Adan et al. previously, and was again used by Izaak Mayzlin from University of Moscow with a new wrinkle.  Dr. Mayzlin created a neural network (Maynet), and then did a traditional NN with training on the data, and also clustered the data using geometric distance clustering and trained on the clusters.  It was interesting to see that the optimum cluster separation was closely related to the number of classes and the accuracy of classification.  An earlier simpler model using the slope of the MB isoenzyme increase and percent of total CK activity was perhaps related to Burton Sobel’s work on CK-MB disappearance rate for infarct size. The main process consists of three successive steps: (1)       clustering performed on training data set, (2)       neural network’s training on clusters from previous step, and (3)       classifier’s accuracy evaluation on testing data. The classifier in this research will be the ANN, created on step 2, with output in the range [0,1], that provides binary result (1 – AMI, 0 – not AMI), using decision point 0.5. Table  1.  Effect  of  selection  of  maximum  distance  on  the  number  of  classes  formed  and  on  the accuracy of recognition by ANN

Clustering Distance Factor F(D = F * R) Number ofClasses Number of Nodes in The Hidden Layers Number of Misrecognized Patterns inThe TestingSet of 43 Percent ofMisrecognized 2414135 1,  02,  03,  01,  02,  03,  0 3,  2 3,  2 121121 1 1 2.3 2.3

Creatine kinase B-subunit activity in serum in cases of suspected myocardial infarction: a prediction model based on the slope of MB increase and percentage CK-MB activity. L H Bernstein, G Reynoso Clin Chem 1983; 29(3):590-592 ICID: 825549 Diagnosis of acute myocardial infarction from two measurements of creatine kinase isoenzyme MB with use of nonparametric probability estimation. L H Bernstein, I J Good, G I Holtzman, M L Deaton, J Babb.  Clin Chem 1989; 35(3):444-447 ICID: 825570 – Information induction for predicting acute myocardial infarction. R A Rudolph, L H Bernstein, J Babb. Clin Chem 1988; 34(10):2031-2038 ICID: 825568

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  • Redberg’s conclusions are correct for the initial screening. The issue has been whether to do further testing for low or intermediate risk patients.
  • The most intriguing finding that is not at all surprising is that the CCTA added very little in the suspect group with small or moderate risk.
  • The ultra sensitive troponin threw the ROC out the window
  • The improved assay does pick up minor elevations of troponin in the absence of MI.

Critical Care | Abstract | Cardiac ischemia in patients with septic …
Aviva Lev-Ari  6/26/2013

  • refer to:  Cardiac ischemia in patients with septic shock randomized to vasopressin or norepinephrine

Mehta S, Granton J,  Gordon AC, Cook DJ, et al.
Critical Care 2013, 17:R117
Troponin and CK levels, and rates of ischemic ECG changes were similar in the VP and NE groups. In multivariable analysis

  • only APACHE II was associated with 28-day mortality (OR 1.07, 95% CI 1.01-1.14, p=0.033).

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