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Molecular Advances in Liver Pathology Impact on Diagnosis

Sanjay Kakar, MD University of California, San Francisco

2019 HK-IAP meeting

Molecular advances: liver

Hepatocellular adenoma Genetic classification (WHO 2010)

Hepatocellular carcinoma,

cholangiocarcinoma

Genetic classification

Targeted therapy?

Metastatic poorly-

differentiated neoplasms

Identifying site of origin and histologic

subtype

Disease category Molecular alterations

Neonatal cholestatic

diseases

PFIC: FIC1, BSEP, MDR3

Alagille: JAG1

Polycystic liver diseases Renal cytic diseases: PKHD, PKD1, PKD2

Liver only: PRKCSH, SEC63

Hepatoblastoma Wnt signalling: Beta-catenin, glutamine

synthetase

Case 1: 40/F, biopsy from a 4 cm liver mass

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Diagnosis in 2004: FNH

2019: Inflammatory hepatocellular adenoma

GS: negative SAA: positive

HCA: genetic classification

HNF-1α inactivation TCF1 gene that encodes hepatocyte nuclear factor

β-catenin activation CTTNB1 exon 3 mutation (encodes β-catenin

IL-6 pathway activated IL6RT gene (encodes gp130), FRK, STAT3, GNAS

Mutation-negative No HNF-1α or β-cateninmutation

Zucman-Rossi, Hepatology, 2006

WHO blue book, 2019

HCA: WHO classification

HNF-1αinactivated

Inflammatory β-cateninactivated

35-50% 40-50% 10%

Women, OC use Women (OCs), menObesity, diabetes

40% in menAndrogens, glycogen

storage disease

Marked steatosis, no atypia

Inflammation, sinusoidal dilatation,

ductular reaction

Pseudoacinar, small cell change

HCC rare HCC rare HCC 40%

LFABP negative SAA positiveCRP positive

Nuclear β-cateninDiffuse GS

Unclassified (5-10%): no known defining features

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Case 2: 31/F with obesity

Biopsy from 5 cm liver mass

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Diffuse GS

Nuclear β-catenin

β-catenin-activated hepatocellular

neoplasms

HNF1α Inflammatory Unclassified

β-catenin mutation

HCA

Atypical

HCC

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Diagnosis

• 2004: Hepatocellular adenoma

• 2019: Atypical hepatocellular

neoplasm with beta-catenin

activation

Case 3: 38/M with 10 cm liver mass

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Triad: Oncocytic cytoplasm, prominent nucleoli,

lamellar fibrosis

Breakpart FISH assay:.

PRKACA 5' end: red probe, 3' end: green probe.

Normal: together. Deletion: loss of 5' end, only 3' green signal visible

Image provided by Dr. Torbenson, Mayo Clinic

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Diagnosis

• 2004: Well-differentiated

hepatocellular carcinoma

(?Fibrolamellar-like)

• 2019: Fibrolamellar hepatocellular

carcinoma

Case 4

• 32/M with a large liver mass detected on

work-up for abdominal pain

• Core needle biopsy from the liver was

obtained. H&E and CK7 stains provided

• Patient was put on gemcitabine-based

chemotherapy as the tumor was

considered unresectable

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CK7

CK7

Diagnosis?

A. Intrahepatic

cholangiocarcinoma

B. Metastatic carcinoma

C. Sarcomatoid

carcinoma

D. Sarcoma

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Intrahepatic cholangiocarcinomaIDH1/IDH2 mutations

• Accumulation of

2-HG (hydroxyl

glutarate)

• Inhibits histone

and DNA

methylases

• Blocks cellular

differentiation

Kipp, Hum Pathol 2012

Borger, Oncologist 2012

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IDH1 mutations

• 19-36% of ICC

• Gliomas, chondrosarcoma, AML

• IDH1 in gliomas: R132H in 90%

• IDH1 in ICC

R132H rare

R132C most common

ICC: Inactivating mutations in

chromatin remodeling genes

Gene Mutation in ICC

BAP1 (BRCA-

associated protein

7-29%

PBRM1 11-17%

ARID1A 19-36%

Farshidfar, Cell Reports 2017

Misumi, Histopathol 2017

BAP1: intact nuclear staining

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BAP1 loss in ICC

BAP1 mutation

• Melanocytic tumors

• Mesothelioma

• Rare: pancreatic, upper GI

adenocarcinoma

Weisner, J Clin Oncol 2012

Misumi, Histopathol 2017

ICC: FGFR2 translocation

• Ligand-independent

activation of the FGFR

kinase domain

• ICC: 15% (6-50%)

• Breast, prostate cancers

• Can be detected by FISH

Graham, Hum Pathol 2014

Arai, Hepatol 2014

Farshidfar, Cell Reports 2017

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FISH breakapart probeFGFR2 translocation

Graham, Hum Pathol 2014

Schulze, Nat Genetics, 2015

Zhou, Nat Commun, 2014

Moeini, Clin Cancer Res 2016

Genetic changes: ICC

Metabolic genes

IDH1

IDH2

19-36%

0-6%

Chromatin remodeling

genes

BAP1

ARID1A

PBRM1

7-29%

19-36%

11-17%

Fusion events

FGFR2

ROS1

6-50%

1-9%

Other mutations

KRAS

BRAF

24%

3-7%

Histologic-genetic correlation

Study Morphologic features

IDH mutationKipp, Hum Pathol 2012

-Organoid arrangement

-Rare to absent gland formation

less desmoplasia

-Compact small glands with little

desmoplasia

-Clear cell change

FGFR2 translocationGraham. Hum Path 2014

-Intraductal growth

-Anastomosing tubular glands with

desmoplasia

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IDH mutant ICC: 'Hepatoid' areas

FGFR fusion ICC: Anastamosing tubular pattern

ICC vs. metastatic adenocarcinoma

Genetic change

ICC BiliaryAC

GB PDAC Eso/Gastric

IDHmutations

19-36% 0-7% 0 0 0

BAP1 mutation

7-29% 0-10% 0 <1% 3%

FGFR2 fusion

6-50% 0-5% 20% 0 2-9%

PBRM1mutation

11-17% 5% 20% 4-6% 0

SMAD4mutation

0-4% 10-25% 0 35-60% 8%

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BAP1 loss in ICC

Weisner, J Clin Oncol 2012Misumi, Histopathol 2017

Cholangiocarcinoma: Albumin ISH

Ferrone, Ann Surg Oncol2016

Case 5: 68/F with 6 subcapsular liver nodule

(<1 cm) during cholecystectomy

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Angulated irregular glands

Mucinous epithelium

Alcian blue

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Adenocarcinoma

BDA vs adenocarcinomaImmunohistochemistry: p53, Ki-67

IHC Result

p53

Strong diffuse

staining

35% ICC

60% metastatic PDAC

None: bile duct adenoma (patchy weak to

moderate staining)

Ki-67 index

>10%

ICC: 88.5% (mean >20%)

BDA: none (mean 2%)

Tan, AIMM 2004

Hornick, AJSP 2005

Tsokos/Gill, Histopathol 2016

Bile duct adenoma

Study Result

Pujals, Hepatology

2015

53% had BRAF V600E mutation

Pujals, Histopathol

2015

53% positive for VE1 antibody by

immunohistochemistry

Angkathunyakul,

Histopathol 2017

87.5% had BRAF V600E mutation

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BRAF mutation in adenoca

Study Result

Goeppert, Mod

Pathol 2014

ICC: 5/159 (3%)

Extrahepatic biliary, GB: negative

Zhu, Ann Surg

Oncol 2014

ICC: 5%

Lee, JCP 2016 Extrahepatic biliary: 1%

Hong, Arch Path Lab

Med 2011

Pancreatic: 5%

VE1 antibody (BRAF V600E mutation)

BDA vs AdenocarcinomaSummary

Feature Result

Size >3 cm: likely malignant

IHC Ki-67

p53

BRAF V600E

BAP1

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Case 6: 54/M with chronic hepatitis C, no cirrhosis

Resection for 5 cm liver mass

CK19

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Hep Par 1 positive

Arginase, glypican-3, pCEA negative

Diagnosis?

A. Intrahepatic

cholangiocarcinoma

B. HCC

C. Combined HCC-CCA

Intermediate carcinoma

WHO 2019

• Rare diagnosis

• Term used only if the tumor is composed

almost entirely of intermediate cells

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Intermediate carcinoma

• Morphologic features intermediate

between hepatocytes and

cholangiocytes

• Monotonous tumor cells with scant

cytoplasm

• Typically arranged in strands in an

abundant fibrous stroma

Brunt, Hepatol 2018

Tumor component without obvious hepatocellular or

cholangiocarcinoma features

“Stem cell features” PD carcinomaIntermediate

Scirrhous HCC

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CK19Hep Par 1

GPC-3Arginase-1

Matsuura, Histopath 2005

Krings/Kakar, Mod Pathol 2013

Scirrhous HCC

ICC vs. HCC

Genetic changes Hepatocellular carcinoma

Intrahepaticcholangiocarcinoma

IDH mutations PBRM1 mutationFGFR2 fusionBAP1 mutation

RareRareRare5%

19-36%11-17%6-50%7-29%

CTNNB1 (β-catenin) mutationTERT promoter mutation

20-30%

30-50%

Uncommon

Rare

Schulze, Nat Genetics, 2015

Zhou, Nat Commun, 2014

Moeini, Clin Cancer Res 2016

Poorly diff carcinoma with IDH1 mutation, favor intrahepatic cholangiocarcinoma

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Genetic changes: liver tumors

Schulze, Nat Genetics, 2015

Zhou, Nat Commun, 2014

Moeini, Clin Cancer Res 2016

Hepatocellular carcinoma

Intrahepaticcholangiocarcinoma

β-catenin mutation (20-30%)TERT promoter mutation (30-50%)Amplification:

MET, FGF19

Metabolic genes:IDH1, IDH2 mutations (25-30%)

Chromatin remodeling:BAP1, ARID1A

Fusion events:FGFR2, ROS1

other mutations:KRAS/BRAF/EGFR

Molecular classification:Gene signatures

"At a time when oncology is moving towards

personalized medicine, the lack of tissue in a

large proportion of cases has significantly

limited this approach for HCC."

Torbenson/Schirmaker, Hepatol 2015