Advanced Microscopy – Zooming in on the Big Idea in Pathology

Principal Investigator: Elena Aikawa, MD, PhD, Brigham and Women’s Hospital

Rupture of vulnerable atherosclerotic plaques is the leading cause of myocardial infarct and stroke.  A major limitation in the field, which hinders current clinical practice and research progress, is the inability to identify and visualize the early processes that lead to microcalcifications. To overcome this limitation, this project used super-resolution imaging available at the HCBI along with a near-infrared calcium tracer to visualize the nucleation of microcalcifications within a recently developed controllable three-dimensional collagen hydrogel system.This approach will address areas of pathology that cannot be addressed using current technologies applied in clinical practice and provide new insights into the pathobiology of plaque rupture.

Principal Investigator: Andrew Beck, MD, PhD, Beth Israel Deaconess Medical Center

Breast cancer is a leading cause of cancer death among women. The current system for diagnosing breast cancer based on the pathological analysis of microscopic images has changed little over the past several decades.  Fluorescent lightsheet microscopy enables the rapid acquisition of high-resolution three-dimensional (3D) images directly from tissue samples up to several millimeters in thickness. The aim of this project was to determine the ability to perform fluorescent lightsheet microscopy directly on archival patient tissue samples and to use the method to identify 3D morphological hallmarks of breast carcinogenesis. 

Principal Investigator: Katie Bentley, PhD, Beth Israel Deaconess Medical Center

Retinopathies, which often cause blindness and are characterized by abnormal growth of excessive, leaky and bulbous new blood vessels.  By comparing diseased and normal tissues using light sheet microscopy, this study will help unravel how and why vessel growth degenerates in retinopathy conditions and provide a new testbed to investigate the effects of new therapeutic targets.

Principal Investigator:  David Clapham, MD, PhD, Boston Children’s Hospital

Focal cortical dysplasia (FCD) is a common pathology finding in medically refractory seizure foci. Microscopically, it is characterized by disrupted cortical layering, dysmorphic neurons, and balloon cells. Using transfected human FCD surgical samples with Brainbow adeno-associated viral vectors would label the neurons in a wide variety of colors, enabling reconstruction of dendritic and axonal arbors. The advanced microscopes at HCBI will greatly facilitate the imaging of these multicolor samples. This will mark the very first time for a type of human cortical neurons to be analyzed in a near-saturated manner, and the resulting data will provide the first structural evidence for alterations in the inhibitory circuitry in epilepsy.

Principal Investigator: Beverly Faulkner-Jones, MD, PhD, Beth Israel Deaconess Medical Center

Pathologists render a diagnosis by reading thin tissue sections mounted on glass slides.  With advances in digital methods, it is now feasible to have a new workflow in which pathologists are presented with aligned whole slide images (WSIs) of serial sections. The expectation is for faster evaluation, greater objectivity, and improved diagnostic accuracy. This project will develop and deploy web-based tools for aligning and viewing the WSI datasets and multiple WSI image datasets will be generated that can used for direct comparison with the current approach of viewing glass slides on conventional microscopes.

Principal Investigator: Susan Hagen, PhD, Beth Israel Deaconess Medical Center

Gastric cancer continues to be a global health issue but the management of gastric cancer remains limited. The discovery of molecular targets that regulate each step in the gastric cancer (GC) cascade could lead to novel therapeutic approaches and this represents an opportunity to identify biomarkers for early detection and treatment. For this, project equipment at HCBI was used to determine, in a mouse GC model, the three-dimensional high resolution pattern of cldn18 expression in stomach from archived paraffin sections.

Principal Investigator: Aldebaran Hofer, PhD, Veterans Affairs Boston Healthcare System

Autosomal dominant polycystic kidney disease (ADPKD) is a progressive disease of renal and hepatic dysfunction marked by cyst formation and organ enlargement.

Using the Zeiss Lightsheet Z.1 microscope at HCBI and 3D organ cultures allows for the interrogation, in 3D, of signaling events that take place deep within the tissue over many hours. The goal is to identify the early steps that drive cyst formation and to develop a platform for future evaluation of this process in human PKD disease variants.

Principal Investigator: Anthony Iafrate, MD, PhD, Massachusetts General Hospital

We are entering the era where chemotherapies are chosen to precisely match the unique genetic alterations in each patient’s tumor. New genomic technologies, such as next generation sequencing (NGS), are central to this approach. However, NSG is currently inferior to Fluorescence in situ hybridization (FISH) with regard to assessing copy number.

The aim of this proposal, using a highly-multiplexed FISH approach, is to develop and test image acquisition and analysis platforms that would enable the copy number analysis of 30 genes simultaneously.

The ultimate goal of this proposal is to provide a comprehensive genotype assay that will guide the choice of targeted therapies and that will impact how we identify, diagnose, and alter the clinical course of cancers.

Principal Investigator: Rakesh Karmacharya, MD PhD, Massachusetts General Hospital 

Using super-resolution light microscopy would enable the detection of differences between schizophrenia and control neurons on a nanometer scale, these studies will help develop image-based cellular assays using patient-derived cells that can be used to develop clinically-relevant disease biomarkers.

Principal Investigator: Astrid Weins, MD, PhD, Brigham and Women’s Hospital

Ultrastructural examination by electron microscopy and immunofluorescence microscopy are indispensable tools in kidney pathology. Particularly injury to the nanometric structure of the kidney filter, which is a  hallmark of proteinuria and can only be confirmed using electron microscopy. 

B7-1, a T cell molecule as a novel biomarker in the glomeruli of a subgroup of patients with nephrotic syndrome. This proposal outlines the use of superresolution microscopy on fresh frozen human kidney biopsies positive for B7-1, to determine the location of B7-1 in the glomerulus.

Principal Investigator: Leonard Zon, MD, Boston Children’s Hospital

The entire blood system is supported throughout life by a small number of cells called Hematopoietic Stem Cells (HSC). Hematologic malignancies, such as leukemia, are caused by malignant transformation of HSC. A curative treatment for these blood diseases is HSC transplantation (HSCT). To improve on current HSCT protocols, there is a need to directly track and image HSC as they engraft in a new site of hematopoiesis or “niche”. 

Using transparent zebrafish, and the advanced microscopes at the Harvard Center for Biological Imaging, will enable the direct observation of the interactions between HSC and their niche during engraftment. We believe this project will increase our understanding of HSC engraftment and have potential to improve clinical HSCT.