Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy

. 2025 Jul 17;5(9):100928. doi: 10.1016/j.xgen.2025.100928

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Brilliant Violet 650 anti-human CD3	Biolegend	Cat#317324; RRID: AB_2563352
FITC anti-human CD45	Biolegend	Cat#304005; RRID: AB_314393
Brilliant Violet 570 anti-human CD4	Biolegend	Cat#300533; RRID: AB_10896788
Brilliant Violet 421 anti-human CD137 (4-1BB)	Biolegend	Cat#309819; RRID: AB_10895902
PE-Cy7 Anti-Human CD8a	Biolegend	Cat#300913; RRID: AB_314117
Fixable Viability Dye eFluor 780	Invitrogen	Cat#65-0865-14; RRID: AB_3113075
PE anti-human CD11c	Biolegend	Cat#337205; RRID: AB_1236439
FITC anti-human CD83	Biolegend	Cat#305305; RRID: AB_314513
Brilliant Violet 421 anti-human CD80	Biolegend	Cat#305221; RRID: AB_10899567
APC anti-human CD86	Biolegend	Cat#374207; RRID: AB_2721448
7-AAD Viability Staining Solution	Biolegend	Cat#420404; RRID: AB_408812
PE HLA-A2 Monoclonal Antibody (BB7.2)	Invitrogen	Cat#MA1-80303; RRID: AB_931640
Monoclonal ANTI-FLAG M2 antibody	Sigma-Aldrich	Cat#F1804; RRID: AB_262044
GAPDH Mouse Monoclonal antibody (2BB)	Biodragon	Cat#B3029

Chemicals, peptides, and recombinant proteins

Fetal Bovine Serum	Gibco	Cat#10091-148
Penicillin-Streptomycin	Gibco	Cat#15070-063
Trypsin-EDTA	Gibco	Cat#25200-056
DMEM	Gibco	Cat#C11995500BT
RPMI-1640	Gibco	Cat#C11875500BT
FcR Blocking Reagent human	Milteny	Cat#130-059-901
DPBS	Gibco	Cat#C14190500BT
Elispot Medium	Dakewei	Cat#6115012
SODIUM DODECYL SULFATE (SDS)	AMRESCO	Cat# 0227-1KG
RIPA buffer	Solarbio	Cat#R0010
Proteinase K	TIANGEN	Cat#RT403
Q5 HiFi DNA polymerase	NEB	Cat#M0491L
Glycine	AMRESCO	Cat#0167-1KG
HEPES free acid	AMRESCO	Cat#0511-1KG
Sodium chloride (NaCl)	SIGMA	Cat#S7653
0.5M EDTA PH = 0.8	Invitrogen	Cat#AM9260G
Amicon Ultra-0.5ML Centrifuge Filters	Millipore	Cat#UFC5010BK
Pur-A-Lyzer Midi Dialysis Kits	Sigma-Aldrich	Cat#PURD35100-1KT
SM-102 (8-[(2-hydroxyethyl)[6-oxo-6-(undecyloxy)hexyl]amino]-octanoic acid, 1-octylnonyl ester; CAS:2089251-47-6)	SINOPEG	Cat#06040008800
DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine; CAS:816-94-4)	SINOPEG	Cat#06030001100
Cholesterol	SINOPEG	Cat#06040010300
DMG-PEG2000(1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol-2000; CAS:160743-62-4)	SINOPEG	Cat#06020112402
KOD One PCR Master Mix	Toyobo	Cat#KMM-201
ClonExpress II One Step Cloning Kit	Vazyme	Cat#C112-02
T7 High Yield RNA Transcription Kit (Nl-Me-Pseudo UTP)	Vazyme	Cat#DD4202-01
EasyCap GAG m7G(5′)ppp(5')(2′OMeA)pG	Synthgene	Cat#CAP3011

Critical commercial assays

DNA Clean & Concentrator-25 Kit	Zymo	Cat#D4006
Human IFN-γ ELISpot plus kit	MABTECH	Cat#3420-4HST-2

Deposited data

120-mammals whole-genome alignments	Hecker et al.⁵²	https://bds.mpi-cbg.de/hillerlab/120MammalAlignment/
Primate net alignments	UCSC Genome Browser GRCh38/hg38 assembly	https://hgdownload.soe.ucsc.edu/goldenPath/hg38/
Annotated proteomes of 14 representative outgroup species	Ensembl	https://ensembl.org/biomart/martview
GTEx RNA sequencing data for 27 normal tissue types	dbGAP	phs000424.v10.p2
RNA sequencing data for 6 organs (forebrain, hindbrain, heart, kidney, liver and testis) across developmental stages	Cardoso-Moreira et al.⁶³	ArrayExpress: E-MTAB-6814
TCGA RNA sequencing data for 22 tumor types	Genomic Data Commons	phs000178.v11.p8
RNA sequencing data for 5 cell lines (U87, SW480, HeLa, Cal62, and OS-RC-2)	This paper	SRA: PRJNA1196182
Ribosome profiling sequencing data for multiple human tissues	Chothani et al.³⁸	PRJNA756018: SRR15513148-SRR15513226
Ribosome profiling sequencing data for human brain, liver and testis	Wang et al.⁸⁵	ArrayExpress: E-MTAB-7247
Ribosome profiling sequencing data for human embryonic stem cell neuronal cultures and human cortex	Duffy et al.⁸⁶	PRJNA743949: SRR15175563-SRR15175568, SRR19165065-SRR19165070, SRR15906422-SRR15906494
Ribosome profiling sequencing data for human kidney and kidney tumors	Loayza-Puch et al.⁸⁷	PRJNA256316: SRR1528686-SRR1528697
Raw in-house-generated mass spectrometry data	This paper	iProX: IPX0008436003
Peptide-spectrum matches identified in MassIVE	MassIVE	https://massive.ucsd.edu/ProteoSAFe/massive_search.jsp (released in 11/30/2023)
Peptide-spectrum matches identified in PeptideAtlas	PeptideAtlas	https://peptideatlas.org/builds/human/202401/APD_Hs_all.fasta
TCGA whole-genome sequencing data for BLCA samples	Genomic Data Commons	phs000178.v11.p8
Raw CRISPR/Cas9 screening data	This paper	SRA: PRJNA1196182
FANTOM enhancer annotation	Andersson et al.⁸⁸	https://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/enhancer/F5.hg38.enhancers.bed.gz
GBM cell line and NHA cell line raw Hi-C data	Wang et al.⁸⁹	GSE162976
BLCA cell line raw Hi-C data	Iyyanki et al.⁹⁰	GSE148079
BRCA cell line raw Hi-C data	Kim et al.⁹¹	GSE167150
PAAD cell line raw Hi-C data	Du et al.⁹²	GSE185069
COAD & ESCA cell line raw Hi-C data	Akdemir et al.⁹³	GSE116694
STAD primary sample raw Hi-C data	Ooi et al.⁹⁴	GSE118391
ecDNA annotations from eccDNA Atlas	Zhong et al.⁷¹	https://lcbb.swjtu.edu.cn/eccDNAatlas/download/Homo%20sapiens.xlsx

Experimental models: Cell lines

HEK293T cells	From Laboratory of Dr. Ying Liu	CL-0063
CAL62 cell	Procell Life Science & Technology Co.,Ltd.	CL-0618
HeLa cell	Procell Life Science & Technology Co.,Ltd.	CL-0101
SW480 cell	Procell Life Science & Technology Co.,Ltd.	CL-0223
OS-RC-2 cell	Procell Life Science & Technology Co.,Ltd.	CL-0177
U-87 MG cell	Procell Life Science & Technology Co.,Ltd.	CL-0238

Experimental models: Organisms/strains

Mouse: huHSC-NKG-ProF	Cyagen Biosciences Co.,Ltd	N/A

Oligonucleotides

CRISPR screening 1^st-F	TSINGKE	This paper
CRISPR screening 1^st-R	TSINGKE	This paper
CRISPR screening 2^nd-F	TSINGKE	This paper
CRISPR screening 2^nd-R-index1	TSINGKE	This paper
CRISPR screening 2^nd-R-index2	TSINGKE	This paper
CRISPR screening 2^nd-R-index3	TSINGKE	This paper
CRISPR screening 2^nd-R-index4	TSINGKE	This paper
CRISPR screening 3^rd-F	TSINGKE	This paper
CRISPR screening 3^rd-F	TSINGKE	This paper

Recombinant DNA

Plasmid: LentiCrispr-V2	From Laboratory of Dr. Shaokun Shu	N/A

Software and algorithms

PHAST v1.4	Cold Spring Harbor Laboratory	http://compgen.cshl.edu/phast/
PRANK v170427	Löytynoja lab	https://ariloytynoja.github.io/prank-msa/
featureCounts v2.0.2	Liao et al.⁹⁵	http://subread.sourceforge.net/
maSigPro v1.70.0	Nueda et al.⁹⁶	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html
fastp v0.23.4	Chen et al.⁹⁷	https://github.com/OpenGene/fastp
Trimmomatic v0.39	Bolger et al.⁹⁸	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
Cutadapt v4.5	Martin⁹⁹	https://cutadapt.readthedocs.io/en/stable/installation.html
Bowtie2 v.2.5.3	Langmead et al.¹⁰⁰	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
STAR v2.7.9a	Dobin et al.¹⁰¹	https://github.com/alexdobin/STAR/releases
RiboTISH v0.2.7	Zhang et al.¹⁰²	https://github.com/zhpn1024/ribotish
pFind v3.2	Chi et al.¹⁰³	http://pfind.org/downloads.html
AIUPred v0.9	Erdos et al.¹⁰⁴	https://aiupred.elte.hu/download
RUVSeq v.1.31.0	Risso et al.¹⁰⁵	https://github.com/drisso/RUVSeq
Peptides v2.4.6	Osorio et al.¹⁰⁶	https://github.com/dosorio/Peptides/
AmpliconSuite-pipeline v1.3.4	Luebeck et al.¹⁰⁷	https://github.com/AmpliconSuite/AmpliconSuite-pipeline
CycleViz v0.2.0	From Jens Luebeck	https://github.com/AmpliconSuite/CycleViz
runHiC v0.8.7	From Xiaotao Wang	https://github.com/XiaoTaoWang/HiC_pipeline
JuicerTools v1.13.02	From aidenlab	https://github.com/aidenlab/JuicerTools
FAN-C v0.9.26	Kruse et al.¹⁰⁸	https://github.com/vaquerizaslab/fanc
Peakachu v1.2.0	Salameh et al.¹⁰⁹	https://github.com/tariks/peakachu
HiCPeaks v0.3.7	From Xiaotao Wang	https://github.com/XiaoTaoWang/HiCPeaks
BEDTools v2.26.0	Quinlan et al.¹¹⁰	https://bedtools.readthedocs.io/en/latest/
SAMtools v1.16.1	Danecek et al.¹¹¹	https://github.com/samtools/samtools
MAGeCK v0.5.9.5	Li et al.¹¹²	https://sourceforge.net/p/mageck/wiki/install/
survival v3.5.8	From Terry M. Therneau	https://github.com/therneau/survival
NetMHCIIpan 4.1	The Immune Epitope Database	http://tools.iedb.org/mhcii/
Python v3.9.18	Python Software Foundation	https://www.python.org/
R v4.2.1	The R Foundation for Statistical Computing	https://www.r-project.org/