Table 1 Types and functions of genetic markers of prostate cancer

SChLAP1

(lncRNAs)

RNA

Plasma

lncRNAs regulate epigenetic modification and transcription by modulating histone or DNA

[96]

PCA3

Prostate cancer antigen 3

Urine

This gene is prostate-specific noncoding mRNA, it is assessed in a urine sample to determine the stage, grading, and aggressiveness of PCa

[97]

PCAT-1

RNA Gene

Blood

PCAT-1 is involved in cancer. It regulates proliferation, cell cycle, apoptosis, metastasis, DNA repair, and homologous recombination

[98]

AMACR

Gene

Blood

This gene encodes an enzyme called α-methylacyl-CoA racemase (AMACR)

[99]

CDKN2A

Gene

Tissue

Cyclin-dependent kinase inhibitor 2A located at chromosome 9

[100]

GOLPH2

cis-Golgi-localised protein

Tissue

In more than 90% of cases, Golgi membrane antigen is produced by an overexpressed gene

[101]

TMPRSS2-ERG

Prostate-specific and androgen-response gene

Urine sample

TMPRSS2 is a serine protease encoding prostate-specific and androgen-responsive gene involved in prostate carcinogenesis, and the ERG gene encodes a protein that serves as a transcriptional regulator

[102]

CCND2

Cell cycle regulatory gene

Tissue

This gene encodes proteins belonging to the cyclin family

[103]

PIM1

Gene

Blood

PIM1 is a protein kinase-encoding gene. Its expression level is significantly high in advanced prostate cancer cases

[104]

PTEN

Gene

Blood

The gene encodes an enzyme found in almost all tissues

[105]

p14b

Gene

Urine

Methylation of this tumor suppressor gene link with the degree of malignancy

[106]

PDLIM4

A protein coding gene

Whole blood

Reduced expression levels of PDLIM4 occur by hypermethylation which is helpful in the detection of prostate tumorigenesis

[107]

NKX3A

The protein encoded by the NKX3-1 gene

Whole blood

Transcription factor helps in the development of prostate epithelium. Mutation or losses in this gene may lead to the development of prostate cancer

[108]

GSTP1

Hypermethylation

An isozyme encoded by the GST pi gene

Urine

Hypermethylation inactivates the GSTP1, which plays a role in liver cancer

[109]

GSTP-1

(Glutathione S-transferase P1)

Ubiquitous enzymes cause detoxification

Whole blood

A tumor suppressor in PCa

[110]

RB1

Gene

Whole blood

In advanced cancer stages, allelic loss or mutation leads to loss of function of tumor suppressor

[111]

CNA of Genome

Copy number variations (CNVs)

Whole blood

CNVs in the specific genomic regions in somatic cells

[112]

TP53

Gene

Whole blood

In advanced cancer stages, allelic loss or mutation leads to loss of function of tumor suppressor

[113]

ASC/TMS1 (PYCARD)

An adaptor protein activating caspase-1

Plasma

The immune response regulator encoded by this gene and its hypermethylation is found in 40% of cases

[114]

ASPM, ASF1B, BUB1B, BIRC5, CENPF, CDC20, CDCA8, CDC2, CDCA3, CDKN3, DLGAP5, DTL, CEP55,C18orf24,FOXM1, PLK1, MCM10, NUSAP1, KIF20A, KIAA0101, PRC1, RRM2, PBK, TOP2A, TK1, RAD51, RAD54L, PTTG1, CENPM, and ORC6L

Genes

Whole blood

Genes to predict metastatic risk and treatment outcomes

[115]

EPB41L3

A protein coding gene

Whole blood

This gene encodes a cortical cytoskeleton protein in more than 70% of prostate cancer cases

[116]

CpG islands

Genomic regions containing a large number of CpG dinucleotide repeats

Whole blood

Progression and development of PCa occur due to hypermethylation in these regions, disrupting the normal function of various genes

[117]

APC, GSTP1 or GSTP1, RASSF1A, RARB2, MDR1

Genes

Whole blood

Combined hypermethylation assays can determine benign and cancerous alterations in the prostate

[118]

RASSF1A

Gene

Serum

In benign prostate, hypermethylation is observed in the gene's promoter region. While in the promoter region, a patchy pattern of hypermethylation is indicative of carcinomas

[119]

RNASEL

Gene

Whole blood

DNA hypomethylation acts as the hallmark of the hereditary prostate cancer gene

[120]

TNFSR10D/DCR2

Gene

Whole blood

Gene down-regulates in PCa by hypermethylation. This gene encodes DR4 and DR5 receptors of the intracellular death domain (DD)

[121]

Polycomb components (PcG proteins)

Transcriptional repressor

Whole blood

Increased expression of polycomb complexes and chromatin modification may reveal prostate cancer's progression

[121]

HDAC1

Gene

Whole blood

TMPRSS2-ERG gene fusion caused by a histone deacetylase is involved in prostate cancer

[122]

DLC1

Gene

Whole blood

Methylation leads to gene repression that occurs extensively in prostates of older men; it may be the marker for early-stage prostate cancer

[123]

LINE-1 retrotransposons

Class I

transposable elements in DNA

Whole blood

In metastatic cases, hypomethylation occurs in these sequences, while hypermethylated retrotransposons are observed in normal conditions

[124]

CDKN1C

Gene

Whole blood

Hypermethylation causes the inactivation of the gene in prostate cancer

[125]

Ki-67

Nuclear protein

Whole blood

It is associated with Cell-cycle-proliferation and is a predictive marker for PCa

[126]

PSCA

Prostate Stem Cell Antigen

Whole blood

Increased PSCA expression linked with capsular invasion in prostate cancer

[127]

IGF2

Gene

Whole blood

The IGF2 gene encodes for insulin-like growth factor 2, which controls the growth and division of cells. Differential methylation loss before manifesting carcinomas and methylation change in IGF2 is a pre-neoplastic condition in the prostate

[128]

MME

Membrane metalloendopeptidase

Whole blood

Biomarker linked with the progression of PCa

[129]

H3K4

DNA packaging protein Histone H3

Whole blood

The poor prognosis of PCa is linked with increased dimethylation at lysine residue

[130]

H3K18

DNA packaging protein Histone H3

Plasma

The poor prognosis of PCa is also linked with increased acetylation activation of the marker

[131]

JMJD3

Histone demethylase

Cell/tissue extract

The overexpression of demethylase is found in metastatic prostate cancer

[132]