The thoughts and sights of André Lametti — just a pathologist

Acquisition of pathology whole-slide images (WSI) generates confidential patient metadata which must be handled appropriately for non-clinical purposes. Free software with multi-vendor support to remove identifying metadata from WSI is available but may be difficult to use by teams with varying information technology comfort. This post describes my design of a cross-platform file drag-and-drop interface to help resolve this challenge.

André Lametti

Background   Patients expect that their privacy will be treated with the utmost care when they generously consent to the use of their medical data in research. This is particularly intuitive for image data, including photographs of faces and external anatomy, but other medical imaging data including microscopic images need to be handled carefully as well. Sometimes, these images contain metadata such as names, places, and dates;

paw: Parse and Anonymize Whole-slide images

Is digital pathology heading the same way as music streaming? For most labs, the financial and human cost of keeping the infrastructure and delivery of digital pathology in-house is probably too high. But what this will mean for research and teaching activities that rely on easy and unfettered access to data is a tricky problem. Choosing to keep some things small and local is a tool to future-proof our transition into modernity.

Every so often, I stumble upon some variation of the graph displaying American music industry revenues by format: vinyl is replaced by cassettes, which are replaced by CDs, which are (briefly) replaced by digital downloads and ringtones, which are finally replaced by streaming services [1]. Today, essentially all casual music listening happens through streaming (and mostly through giants like Spotify, Apple Music, or YouTube).  Why would it be

Saving Digital Pathology

The list of tumours with fusions involving the FET (

 EWSR1

,

 FUS

) and CREB (

 CREB1

,

 ATF1

, or

 CREM

) families of genes is ever-expanding. These are promiscuous genes that drive neoplasia in a wide variety of anatomical sites, often without being recognized as such – but that doesn’t mean tumours with these molecular lesions are always primary to the location where they are found!

FET::CREB fusion in a lung nodule

Most thyroid fine-needle aspirates fit neatly into one of the 6 categories of the Bethesda classification. But sometimes, cases are not so easy and it is worth thinking outside the boxes! This case was one of the latter. Although the targeted nodule was located in the thyroid gland in a patient with a history of thyroid nodules, something didn’t quite fit.

A rare “thyroid” nodule

Although

 Thoracic SMARCA4-deficient undifferentiated tumour

(SD-UT) is a recognized entity in the 5th edition of the WHO classification of thoracic tumors, this alteration occurs in garden-variety lung cancer as well (and in many other tumors too!) In fact, it is likely SD-UT exists on a continuum with

 SMARCA4

-deficient lung cancer. I recently came across an interesting case that demonstrated this phenomenon.

SMARCA4-deficiency: a continuum

I collaborated on this study that Mark Sorin and colleagues published in Cancer Treatment and Research Communications, detailing the molecular profile of a large (n=997) cohort of patients at the McGill University Health Centre, the institution where I am undergoing residency training.

NGS in a Québec NSCLC cohort

I gave a presentation on Sir William Osler’s presence at McGill in the 21

 st

century at a symposium organized by McGill’s department of Social Studies of Medicine on February 3, 2021. You can find the recording here. In this brief presentation, I address three issues around Osler and his legacy at McGill.

Osler and McGill

The findings in the image above were seen in the anteroseptal left ventricular myocardium of an adult woman who died unexpectedly in non-suspicious circumstances. She was known for coronary artery disease and a remote myocardial infarct.

Calcified ventricular aneurysm

These photomicrographs belong to the adrenal taken at autopsy of an older adult who died in hospital of renal failure and resistant shock. He had been recently diagnosed with AA amyloidosis. The cause of his resistant shock was thought to be due to sepsis, although no organisms were ever detected and he did not respond to antimicrobial therapy.

Adrenal amyloidosis

Diagnosing follicular neoplasms in thyroid fine-needle aspiration specimens can be difficult, and for good reason: it is a diagnostic category intended for a family of lesions for whom it is generally not possible to determine whether they are benign or not. This unfortunately means that most patients end up getting surgery to remove at least the half of their thyroid where the nodule is present despite the absence of a firm diagnosis.

A review of follicular neoplasm of the thyroid

I collaborated on this study by Dilhan Perera and colleagues, under the direction of Momar Ndao. The article, published in iScience, explores the effects of prior BCG exposure on the effectiveness in mice of an intranasal adenovirus-based vaccine against SARS-Cov-2, the virus that causes COVID-19.  I was involved in the scoring of lung damage seen in sacrificed mice from the various experimental groups.

BCG and SARS-CoV2 vaccination in mice

In 2017, I wrote an essay about a manuscript comment on the

 Aphorisms

of Hippocrates by the 15th-century physcian Ugo Benzi (also known as Hugo of Sienna). This paper, under the direction of Prof. Faith Wallis at McGill University’s Department of History and Classical studies, analyzes the

 incipit

of the manuscript and the insights it provides on Ugo’s conception of medicine and the role of the physician.

André's slide box

Adrenal amyloidosis

Ars uero longa