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Cancer Research Society · Oct 4 Meeting
Introduction to Pathology& Literature Review Masterclass
Part I — Pathology  ·  Part II — Literature Reviews
The subfieldsSlide workflowA real metastatic casePubMed mastery
Part One
Introduction
to Pathology

The study of disease itself — and the microscope work behind nearly every cancer diagnosis on earth.

The Field

Pathology is the study of disease itself.

Not one organ, not one treatment — the mechanisms. Pathology asks four questions about any illness: what causes it (etiology), how it develops (pathogenesis), what it does to cells and tissues (morphology), and what that means for the patient.

It's the bridge between the basic science of the lab and the decisions made at the bedside. Almost every cancer diagnosis starts with a pathologist looking at tissue.

The four questions
  • Etiology — what caused it?
  • Pathogenesis — how did it develop?
  • Morphology — what changed in the tissue?
  • Clinical meaning — what does it do to the patient?
First Look · Normal Tissue
Normal lung histology
H&E · ~100×
Healthy lung tissue. Note the open, lace-like air spaces and thin, orderly walls.
Yale Rosen / Wikimedia Commons · CC BY-SA 2.0

This is what order looks like.

Normal lung is mostly air. The alveoli — the tiny sacs where oxygen crosses into blood — show up as open white spaces framed by delicate pink walls just one or two cells thick. Everything is spacious, regular, and repeating.

Hold this image in your head. In a few slides you'll see what happens when cancer fills those spaces in — and the contrast is the whole point.

Open air spacesThin wallsRegular pattern
The Role

The "doctor's doctor."

Pathologists rarely meet the patient — but their report drives what happens next. When a surgeon removes a tumor, the pathologist determines whether it's cancer, what type, how aggressive, and whether it was fully removed. Oncologists can't choose a therapy until that report lands.

Diagnose

Benign or malignant? And what exactly is it?

Characterize

Grade, stage, margins, and molecular markers that guide therapy.

Guide

The report becomes the roadmap for the whole care team.

The Map

Two great branches.

Anatomic Pathology

Diagnosis by examining the structure of tissues and cells — what the disease looks like under the microscope and to the naked eye. The world of biopsies, tumors, and slides.

SurgicalCytologyAutopsyForensic

Clinical Pathology

Diagnosis through laboratory analysis of body fluids — blood, urine, marrow. Measuring, counting, and detecting rather than looking. Also called laboratory medicine.

ChemistryHematologyMicrobiologyBlood bank

Molecular & computational pathology cuts across both — and it's where cancer research is moving fastest.

Subfields · Anatomic

Where structure tells the story.

Surgical Pathology

The largest subfield. Examines tissue removed in surgery or biopsy — the engine of cancer diagnosis.

Histopathology

Microscopic study of stained tissue sections. The core skill you'll practice in the lab.

Cytopathology

Diagnosis from individual cells — Pap smears, fine-needle aspirates. Faster, less invasive.

Autopsy Pathology

Post-mortem exam to establish cause of death and advance medical understanding.

Forensic Pathology

Autopsy in a legal context — trauma, toxicology, time and manner of death.

Neuropathology

Specialized study of nervous-system tissue — brain tumors, neurodegeneration.

Subfields · Clinical

Where measurement tells the story.

Clinical Chemistry

Chemical analysis of blood and fluids — glucose, enzymes, hormones, tumor markers.

Hematopathology

Diseases of blood and marrow — leukemias, lymphomas, anemias.

Medical Microbiology

Identifying bacteria, viruses, fungi, parasites — and what will treat them.

Transfusion Medicine

Blood typing, cross-matching, and the safe management of the blood supply.

Immunopathology

Disorders of the immune system — autoimmunity, allergy, immunodeficiency.

Molecular Pathology

Detecting disease at the level of DNA, RNA, and protein. Coming up next.

The Frontier · Where CRS Lives
Immunohistochemistry TTF-1 nuclear staining
IHC · TTF-1
Immunohistochemistry: an antibody against TTF-1 turns the brown stain on in lung adenocarcinoma nuclei — molecular identity made visible.
Mikael Häggström / Wikimedia Commons · CC0

Molecular & computational pathology.

Modern diagnosis isn't just "what does it look like" — it's "what is it made of, genetically." Immunohistochemistry (IHC) stains for specific proteins. Sequencing reads the tumor's mutations. And increasingly, algorithms read the slides.

IHC

Antibodies tag a target protein so it shows up in color — is the tumor expressing this marker?

NGS / Digital AI

Sequencing finds actionable mutations (EGFR, KRAS, ALK); ML models grade whole-slide images. The thread tying pathology to everything CRS docks, screens, and models.

The Workflow · The Heart of It

From patient to diagnosis.

Every slide you'll look at in the lab traveled this exact path. When you look down the microscope, you're seeing the end of a nine-step journey.

01
Specimen
Biopsy or resection taken from the patient.
02
Accessioning
Logged, numbered, tracked.
03
Grossing
Examined by eye, measured, cut to size.
04
Fixation
Formalin preserves tissue, stops decay.
05
Processing
Water out, wax in.
06
Embedding
Set into a paraffin block.
07
Microtomy
Sliced ~4 µm thin — thinner than a cell.
08
Staining
H&E brings colorless tissue to life.
09
Microscopy
Read the slide → sign out the report.
The Workflow · Microtomy
Microtome cutting paraffin ribbon
A microtome shaves a continuous ribbon of 5-µm sections from the paraffin block. Each one becomes a slide.
Wikimedia Commons · CC BY-SA 2.0

A slice thinner than a single cell.

Sections are cut to about 4–5 micrometers — so thin that light passes through and you see a single flat layer of cells rather than a confusing stack. The paraffin block makes it possible: wax turns soft, wet tissue into something firm enough to shave cleanly.

Fixation matters just as much. The moment tissue leaves the body it begins to break down. Formalin cross-links the proteins and freezes the architecture — so what you see is the disease, not decay.

~4µm
Section thickness
24h+
Specimen to sign-out
The Workflow · Staining

Why everything is pink and purple.

Raw tissue is nearly colorless. The H&E stain — hematoxylin and eosin — is the most-used stain in all of medicine, and it's what gives histology its signature look.

Hematoxylin → purple
Binds DNA — stains the nucleus. Dark, crowded nuclei are a classic warning sign.
Eosin → pink
Binds proteins — stains the cytoplasm and the tissue around the nuclei.
H&E stained tissue showing purple nuclei and pink cytoplasm
H&E
Purple dots (nuclei) scattered in a pink field (cytoplasm). Read the balance and you're reading the tissue.
Kirstein et al. / Wikimedia Commons · CC BY 4.0
Reading the Slide · Signs of Trouble
Carcinoma with nuclear pleomorphism and mitoses
H&E · high power
High-grade carcinoma: nuclei of wildly different sizes, darkly stained, with cells caught mid-division.
Wikimedia Commons · CC BY 3.0

What makes a pathologist lean in.

Train your eye on these five features — they're what separates a benign slide from a malignant one, and what you'll hunt for in the lab.

  • Pleomorphism — cells varying wildly in size and shape
  • High N:C ratio — the nucleus crowding out the cell
  • Hyperchromasia — dark, dense nuclei
  • Mitoses — too many cells caught dividing
  • Lost architecture — orderly tissue turning chaotic
Reading the Slide · Grade & Stage

Two different questions.

Grade — how abnormal?

How far the cells have drifted from normal. Well-differentiated still looks almost like the original tissue; poorly differentiated is barely recognizable. Higher grade usually means more aggressive.

Stage — how far spread?

How much territory the cancer has taken. Size of the tumor (T), lymph node involvement (N), and whether it has metastasized to distant organs (M). The TNM system.

A tumor can be high-grade but early-stage, or low-grade but widespread. You need both numbers to know what you're dealing with.

The Case · Your Real Slides
Lung adenocarcinoma histology
H&E · adenocarcinoma
Lung adenocarcinoma: malignant cells forming irregular gland-like structures, crowding out the normal open air spaces.
Yale Rosen / Wikimedia Commons · CC BY-SA 2.0

Lung adenocarcinoma, metastatic.

Two slides in the lab aren't teaching samples — they come from an actual patient at MD Anderson Cancer Center with late-stage lung adenocarcinoma that has metastasized. Compare this against the normal lung from slide 04.

Adeno- = gland

Cancer of glandular, secretory cells — the most common lung cancer type.

-carcinoma

Arises from epithelial (lining) cells. Most human cancers are carcinomas.

Metastasis

Broken free and seeded a distant organ. This is what makes cancer lethal.

Spot it

Irregular glands where they don't belong; crowded dark nuclei; lost architecture.

A Second Way to See · Cytology

Sometimes you don't need a slice.

Not every diagnosis requires cutting tissue. In cytopathology, loose cells — scraped, brushed, or drawn out with a fine needle — are spread on a slide directly. It's faster and far less invasive, the approach behind the Pap smear and many first-pass cancer checks.

The trade-off: you see cells in isolation, losing the tissue architecture that histology preserves. Often it's the first look that decides whether a biopsy is needed.

Fine-needle aspirationPap smearFluid cytology
Adenocarcinoma cytology preparation
Cytology · 100×
Adenocarcinoma cells in a cytology preparation — diagnosis from loose cells, no tissue section required.
Wikimedia Commons · CC BY-SA
MD Anderson Traineeship · Firsthand

Scoring real slides — and becoming the study.

This past summer I trained at MD Anderson Cancer Center through the DPLM ONCORE Youth Summer Program, in the Department of Pathology & Laboratory Medicine. The project turned our own learning into the experiment: could pathology-naïve high school students, after hands-on teaching, reliably score FOLR1 immunohistochemistry — the companion biomarker that decides mirvetuximab eligibility in platinum-resistant high-grade ovarian / fallopian-tube / peritoneal cancer?

Scored 100 cases — 50 biopsies + 50 resections of high-grade serous carcinoma — on both glass and digital slides, with a 2-week washout between.
Measured agreement vs. faculty using Fleiss' κ and Gwet's AC1; student concordance was substantial (κ≈0.71).
Found digital slides cut resection reading time by more than half — an objective framework for training new readers.
Abstract submitted — USCAP 2027, Vancouver · primary presenter
MD Anderson traineeship — cohort, campus, and badge
Summer 2026 — DPLM ONCORE cohort at MD Anderson, Houston.
Personal photos
The Lab · What You'll Do

Hands on the microscope.

This deck was the warm-up. In the lab, you put it to work.

100
Prepared disease slides across a range of pathologies
2
Real MD Anderson slides — late-stage lung adenocarcinoma, metastatic
1:1
Microscopes provided — see it yourself, no screen between
Part Two
The Literature
Review Masterclass

The same rigor you brought to the microscope, aimed at the page. How to search PubMed like a researcher, read a paper without drowning, and tell good science from bad.

Why It Matters

Every project starts here.

Before you dock a molecule, run a screen, or design a study, you have to know what's already been done — what's settled, what's contested, and where the gap is that your work could fill. A literature review is how you find the edge of human knowledge before trying to push it.

Orient

Learn the field's language, key players, and landmark papers fast.

Avoid reinventing

Don't spend months on a question already answered in 2019.

Find the gap

The unanswered question is your research opportunity.

Know the Difference

Narrative vs. systematic.

Narrative review

A broad, expert summary of a topic. Flexible, readable, good for orientation — but the author chooses what to include, so it can carry bias. This is what most student "lit reviews" actually are.

Systematic review

A reproducible method: a pre-defined question, an explicit search protocol, and strict inclusion/exclusion criteria applied to every paper found. Meta-analyses pool their numbers. The gold standard — and much more work.

Start narrative to learn a field. Go systematic when you need an answer you can defend.

Step 1 · Define the Question

A fuzzy question gets fuzzy results.

"Lung cancer treatment" returns half a million papers. Narrow it until it's answerable. In clinical research the PICO frame helps structure it:

P — Population

Who? e.g. EGFR-mutant NSCLC patients

I — Intervention

What? e.g. osimertinib

C — Comparison

Versus? e.g. first-gen TKIs

O — Outcome

Measuring? e.g. progression-free survival

Those four pieces become your search terms. The question writes the query.

Step 2 · PubMed

PubMed is not Google.

PubMed indexes 37+ million biomedical citations from MEDLINE and beyond, maintained by the NIH's National Library of Medicine. Searching it like a search engine wastes its real power. The payoff is in structured search: MeSH terms, boolean logic, and field tags.

Free to search. Many results link to free full text via PubMed Central (PMC).

pubmed.ncbi.nlm.nih.gov37M+ citationsNIH / NLM
The three tools that change everything
  • MeSH — the controlled vocabulary that finds a concept no matter how authors worded it
  • Boolean — AND / OR / NOT to combine concepts precisely
  • Field tags — [ti], [au], [dp] to target where a term must appear
PubMed · MeSH Terms

One concept, every synonym.

Authors might write "heart attack," "myocardial infarction," or "MI." MeSH — Medical Subject Headings — is a standardized vocabulary where all of those map to a single official term. Search the MeSH term and you catch every paper on the concept, no matter the wording.

"Carcinoma, Non-Small-Cell Lung"[MeSH] AND "Protein Kinase Inhibitors"[MeSH]
→ Catches every indexed paper on NSCLC + kinase inhibitors, however the authors phrased it. Look terms up first in the MeSH Database (linked from PubMed).

MeSH also has a hierarchy — searching a broad term can automatically include its narrower children ("explode").

PubMed · Boolean + Field Tags

Build the query like a circuit.

Boolean logic (capitalize them)
  • AND — both must appear (narrows)
  • OR — either appears (widens; group synonyms)
  • NOT — exclude a term (use carefully)
Useful field tags
  • [tiab] — title or abstract
  • [au] — specific author
  • [dp] — date of publication
  • [ta] — journal title
(EGFR OR "epidermal growth factor receptor") AND docking[tiab] AND 2020:2026[dp]
→ Parentheses group the OR; the result is recent papers with "docking" in title/abstract on EGFR, under any name.
PubMed · Filters & Other Sources

Trim the pile, then widen the net.

PubMed filters (left sidebar)

Free full text · publication date · article type (Review, RCT, Meta-Analysis) · species. One click each — huge time savers. Use "Review" to find existing lit reviews that hand you a reading list.

Beyond PubMed

Google Scholar — widest net, catches preprints & citations. Connected Papers — visual map of what cites what. Scopus / Web of Science — citation tracking. bioRxiv/medRxiv — preprints (unreviewed).

Citation chasing: found one great paper? Read its references (backward) and see what cited it (forward). Often faster than any search.

Step 3 · Screen

You will not read them all.

A good search returns dozens to hundreds of hits. Triage in layers — spend seconds before you spend hours.

1
Title
Obviously irrelevant? Discard in 2 seconds.
2
Abstract
Does it actually address your question?
3
Full text
Only the survivors earn a full read.
4
Keep / cut
Apply inclusion criteria consistently.

Decide your inclusion/exclusion criteria up front (years, study type, language) so you're not deciding case-by-case and drifting.

Step 4 · Read Strategically

The three-pass method.

Never read a paper front to back on the first go. Make three increasingly deep passes — most papers get cut after pass one.

Pass 1 · ~5 min

Title, abstract, figures, conclusion. What did they do and find? Decide if it's worth more time.

Pass 2 · ~1 hr

Read the body, skim the math. Grasp the methods and whether the evidence supports the claims.

Pass 3 · deep

Reconstruct it. Could you reproduce it? Where would it break? For papers central to your work.

Read figures first. In a good paper the figures tell the whole story — often faster and more honestly than the prose.

Step 5 · Judge the Quality

Not all published science is good science.

Peer review is a filter, not a guarantee. Read with these questions live — the same critical eye behind CRS's meta-research work on reporting quality.

Red flags
  • Tiny sample size, no power calculation
  • No control group / weak comparison
  • Claims far bigger than the data support
  • No code, no data, no way to reproduce
  • Predatory journal; undisclosed conflicts
Green flags
  • Pre-registered; methods you could repeat
  • Data and code openly shared
  • Limitations stated honestly
  • Results replicated by others
  • Reputable, indexed journal
Step 6 · Stay Organized

A system beats your memory.

Reference manager

Zotero (free, excellent) grabs citations in one click, stores PDFs, and generates your bibliography in any style. Alternatives: Mendeley, EndNote. Set this up before paper #5, not after #50.

Synthesis matrix

A simple table: one row per paper, columns for question, method, sample, key finding, limitations. Fill it as you read. When it's done, your review almost writes itself — you read across rows, not down.

Capture the citation the moment you decide to keep a paper. Re-finding a lost source is the single biggest time sink in any review.

Step 7 · Synthesize & Write

Synthesis, not a book report.

A review isn't a list of summaries ("Smith found X. Jones found Y."). It's an argument organized by theme: here's what the field agrees on, here's where it conflicts, here's the gap — and here's where my work fits.

Group by idea

Organize around themes and debates, not one-paper-at-a-time.

Cite everything

Every claim that isn't yours gets a citation. Paraphrase; never copy. Quote rarely.

Land the gap

End by naming the open question your research will take on.

On AI tools: fine for finding and summarizing — never trust a citation you haven't opened yourself. Models invent plausible-looking references. Verify every one.

Thanks for coming
See you next
meeting.

You can now trace a specimen from patient to microscope — and a research question from a vague idea to a defensible review. Next up: the pathology lab, and your own literature search.

Next meeting — Oct 26 · Radiation Oncology

Cancer Research Society · slcancerresearch.org · @slhscrs