UNat Med | Indlela yokusebenzisa imifanekiso emininzi ye-omics yokwenza imephu yethumba elihlanganisiweyo

UNat Med | Indlela ye-multi-omics yokumakisha imeko ye-tumor edibeneyo, i-immune kunye ne-microbial yomhlaza we-colorectal ityhila ukusebenzisana kwe-microbiome nenkqubo yomzimba yokuzikhusela
Nangona ii-biomarkers zomhlaza wekoloni oyintloko ziye zafundwa kakhulu kwiminyaka yakutshanje, izikhokelo zeklinikhi zangoku zixhomekeke kuphela kwisigaba se-tumor-lymph node-metastasis kunye nokufumanisa iziphene zokulungiswa kwe-DNA mismatch (MMR) okanye ukungazinzi kwe-microsatellite (MSI) (ukongeza kuvavanyo oluqhelekileyo lwe-pathology) ukumisela iingcebiso zonyango. Abaphandi baphawule ukungabikho konxibelelwano phakathi kweempendulo zomzimba ezisekelwe kwi-gene expression-based, iiprofayili ze-microbial, kunye ne-tumor stroma kwi-Cancer Genome Atlas (TCGA) colorectal cancer cohort kunye nokusinda kwesigulana.

Njengoko uphando luye lwaqhubeka, iimpawu zobungakanani bomhlaza oyintloko we-colorectal, kubandakanya uhlobo lomhlaza olufana nolweseli, i-immune, i-stromal, okanye uhlobo lwe-microbial lomhlaza, ziye zaxelwa ukuba zihambelana kakhulu neziphumo zeklinikhi, kodwa kusekho ukuqonda okuncinci malunga nendlela ukusebenzisana kwazo okuchaphazela ngayo iziphumo zesigulana.
Ukuze kuhlalutywe ubudlelwane phakathi kobunzima be-phenotypic kunye nesiphumo, iqela labaphandi abavela kwiSidra Institute of Medical Research eQatar kutshanje baphuhlise kwaye baqinisekisa amanqaku adibeneyo (mICroScore) achaza iqela lezigulana ezinezinga elihle lokusinda ngokudibanisa iimpawu ze-microbiome kunye ne-immune rejection constants (ICR). Iqela lenze uhlalutyo olubanzi lwe-genomic lweesampuli eziqandisiweyo ezintsha ezivela kwizigulana ezingama-348 ezinomhlaza we-colorectal oyintloko, kubandakanya ukulandelelana kwe-RNA yeethumba kunye nezicubu ze-colorectal ezinempilo ezifanayo, ukulandelelana kwe-exome epheleleyo, i-deep T-cell receptor kunye nokulandelelana kwe-16S bacterial rRNA gene, eyongezelelwa lulandelelwano lwe-tumor genome epheleleyo ukuze ichaze ngakumbi i-microbiome. Olu phononongo lupapashwe kwiNature Medicine njenge-"An integrated tumor, immune and microbiome atlas of colon cancer".

Inqaku elipapashwe kwiNature Medicine

Isishwankathelo se-AC-ICAM

Abaphandi basebenzise iqonga le-orthogonal genomic ukuhlalutya iisampuli ze-tumor eziqandisiweyo ezintsha kunye nokudibanisa izicubu ze-colon ezisempilweni ezikufutshane (ii-tumor-normal pairs) ezivela kwizigulana ezine-histologic diagnosis yomhlaza we-colon ngaphandle konyango lwenkqubo. Ngokusekelwe kulandelelwano lwe-whole-exome (WES), ulawulo lomgangatho wedatha ye-RNA-seq, kunye nokuhlolwa kwemigangatho yokubandakanywa, idatha ye-genomic evela kwizigulana ezingama-348 yagcinwa kwaye yasetyenziselwa uhlalutyo olusezantsi kunye nokulandelela okuphakathi kweminyaka eyi-4.6. Iqela lophando lathiya le mithombo i-Sidra-LUMC AC-ICAM: Imephu kunye nesikhokelo sokusebenzisana kwe-immune-cancer-microbiome (Umfanekiso 1).

Ukwahlulwahlulwa kweemolekyuli kusetyenziswa i-ICR

Bethatha iseti yeempawu zemfuza zomzimba ezisetyenziswa rhoqo ukuze kuhlolwe umhlaza rhoqo, ezibizwa ngokuba yi-immune constant of rejection (ICR), iqela lophando liphucule i-ICR ngokuyinciphisa ibe yiphaneli ye-20-gene egubungela iintlobo ezahlukeneyo zomhlaza, kubandakanya i-melanoma, umhlaza wesinyi, kunye nomhlaza webele. I-ICR ikwanxulunyaniswa nempendulo ye-immunotherapy kwiintlobo ezahlukeneyo zomhlaza, kubandakanya umhlaza webele.

Okokuqala, abaphandi baqinisekisile utyikityo lwe-ICR lweqela le-AC-ICAM, besebenzisa indlela ye-ICR gene-based co-classification ukuze bahlukanise iqela libe zii-clusters ezintathu/ii-immune subtypes: i-ICR ephezulu (ii-hot tumors), i-ICR ephakathi kunye ne-ICR ephantsi (ii-cold tumors) (Umfanekiso 1b). Abaphandi bachaze ukuthambekela komzimba okunxulunyaniswa ne-consensus molecular subtypes (CMS), udidi olusekelwe kwi-transcriptome lomhlaza wamathumbu. Iindidi ze-CMS ziquka i-CMS1/immune, i-CMS2/canonical, i-CMS3/metabolic kunye ne-CMS4/mesenchymal. Uhlalutyo lubonise ukuba amanqaku e-ICR ayenxulumene kakubi neendlela ezithile zeeseli zomhlaza kuzo zonke ii-CMS subtypes, kwaye ubudlelwane obuhle neendlela ezithintela ukhuseleko kunye ne-stromal-related pathways bubonwe kuphela kwii-CMS4 tumors.

Kuzo zonke ii-CMS, ubuninzi beeseli zendalo ezibulala abantu (NK) kunye neeseli ze-T babuphezulu kwiintlobo ze-ICR eziphezulu zokuzikhusela, kunye nokwahluka okukhulu kwezinye iinxalenye ze-leukocyte (Umfanekiso 1c). Iintlobo ze-ICR immune zazine-OS kunye ne-PFS ezahlukeneyo, kunye nokwanda okuqhubekayo kwe-ICR ukusuka kwizantsi ukuya phezulu (Umfanekiso 1d), okuqinisekisa indima yokuxela kwangaphambili ye-ICR kumhlaza we-colorectal.

Umfanekiso 1. Uyilo lophando lwe-AC-ICAM, uphawu lwe-gene olunxulumene nomzimba, iintlobo ezahlukeneyo zomzimba kunye nokusinda.
I-ICR ibamba iiseli ze-T ezityebiswe ziithumba, ezikhuliswe ngokwe-clonal
Kuye kwaxelwa ukuba zimbalwa kakhulu iiseli ze-T ezingenela kwizicubu ze-tumor ezichanekileyo kwii-antigen ze-tumor (ngaphantsi kwe-10%). Ke ngoko, uninzi lweeseli ze-T ezingaphakathi kwe-tumor zibizwa ngokuba ziiseli ze-T ezizimeleyo (iiseli ze-T ezizimeleyo). Ulwalamano oluqinileyo nenani leeseli ze-T eziqhelekileyo ezinee-TCR ezivelisayo lubonwe kwi-stromal cell kunye ne-leukocyte subpopulations (ezifunyenwe yi-RNA-seq), ezinokusetyenziselwa ukuqikelela iiseli ze-T subpopulations (Umfanekiso 2a). Kwi-ICR clusters (ngokubanzi kunye nokuhlelwa kwe-CMS), i-clonality ephezulu yee-immune SEQ TCRs ibonwe kwi-ICR-high kunye ne-CMS subtype CMS1/immune groups (Umfanekiso 2c), kunye nenani eliphezulu lee-tumor ezikumgangatho ophezulu we-ICR. Ukusebenzisa i-transcriptome iyonke (ii-genes ezili-18,270), ii-genes ezintandathu ze-ICR (IFNG, STAT1, IRF1, CCL5, GZMA, kunye ne-CXCL10) beziphakathi kwee-genes ezilishumi eziphezulu ezinxulumene ne-TCR immune SEQ clonality (Umfanekiso 2d). I-ImmunoSEQ TCR clonality inxulumene kakhulu neejini ezininzi ze-ICR kunee-correlations ezibonwe kusetyenziswa ii-CD8+ markers ezisabela kwi-tumor (Umfanekiso 2f kunye no-2g). Ukuqukumbela, uhlalutyo olungentla lubonisa ukuba uphawu lwe-ICR lubamba ubukho beeseli ze-T ezityebileyo kwi-tumor, ezikhuliswe yi-clonally kwaye lunokuchaza imiphumo yalo yokuxela kwangaphambili.

Umfanekiso 2. Iimetrikhi ze-TCR kunye nolwalamano kunye ne-immune-related genes, i-immune kunye ne-molecular subtypes.
Ukwakheka kwe-microbiome kwizicubu ezisempilweni kunye nomhlaza wamathumbu amakhulu
Abaphandi benze ukulandelelana kwe-16S rRNA besebenzisa i-DNA ekhutshwe kwi-tumor ehambelanayo kunye ne-colon tissue enempilo kwizigulane ezingama-246 (Umfanekiso 3a). Ukuqinisekisa, abaphandi bahlalutye idatha yokulandelelana kwe-16S rRNA gene evela kwiisampulu ezongezelelweyo ze-tumor ezingama-42 ezazingafanelanga i-DNA eqhelekileyo ekhoyo ukuze zihlalutywe. Okokuqala, abaphandi bathelekisa ubuninzi bezityalo phakathi kwe-tumor ehambelanayo kunye ne-colon tissue enempilo. I-Clostridium perfringens yanda kakhulu kwi-tumor xa ithelekiswa ne-samples enempilo (Umfanekiso 3a-3d). Akukho mahluko mkhulu kulwahluko lwe-alpha (ukwahluka kunye nobuninzi beentlobo kwisampulu enye) phakathi kwe-tumor kunye ne-cell tissue enempilo, kwaye ukuncipha okuncinci kolwahluko lwe-microbial kwabonwa kwi-tumor ephezulu ye-ICR xa kuthelekiswa ne-tumor ephantsi kwe-ICR.
Ukuze kufunyanwe unxulumano olufanelekileyo ngokwezonyango phakathi kweeprofayili ze-microbial kunye neziphumo zeklinikhi, abaphandi bajolise ekusebenziseni idatha yokulandelelana kwe-16S rRNA gene ukuchonga iimpawu ze-microbiome ezixela kwangaphambili ukusinda. Kwi-AC-ICAM246, abaphandi basebenzise imodeli yokuguqulwa kwe-OS Cox ekhethe iimpawu ezingama-41 ezinee-coefficients ezingezizo zero (ezinxulunyaniswa nomngcipheko wokufa owahlukileyo), ezibizwa ngokuba zii-MBR classifiers (Umfanekiso 3f).
Kule cohort yoqeqesho (ICAM246), amanqaku aphantsi e-MBR (MBR<0, i-MBR ephantsi) adibene nomngcipheko ophantsi kakhulu wokufa (85%). Abaphandi baqinisekisile unxibelelwano phakathi kwe-MBR ephantsi (umngcipheko) kunye ne-OS ende kwii-cohorts ezimbini eziqinisekisiweyo ngokuzimeleyo (ICAM42 kunye ne-TCGA-COAD). (Umfanekiso 3) Olu phononongo lubonise unxibelelwano oluqinileyo phakathi kwe-endogastric cocci kunye namanqaku e-MBR, afanayo kwi-tumor nakwizicubu ze-colon eziphilileyo.

Umfanekiso 3. I-Microbiome kwi-tumor nakwizicubu eziphilileyo kunye nolwalamano ne-ICR kunye nokusinda kwesigulana.
Isiphelo
Indlela yokusebenzisa i-multi-omics esetyenzisiweyo kolu phononongo ivumela ukufunyanwa nokuhlalutywa ngokupheleleyo kwe-molecular signature yempendulo yomzimba kumhlaza we-colorectal kwaye ityhila ukusebenzisana phakathi kwe-microbiome kunye nenkqubo yomzimba yokuzikhusela. Ukulandelelana okunzulu kwe-TCR yethumba kunye nezicubu eziphilileyo kubonise ukuba isiphumo sokuxela kwangaphambili se-ICR sinokubangelwa kukukwazi kwayo ukubamba ii-T cell clones ezityebileyo ze-tumor kwaye mhlawumbi i-tumor antigen-specific.

Ngokuhlalutya ukwakheka kwe-tumor microbiome kusetyenziswa ukulandelelana kwe-16S rRNA gene kwiisampuli ze-AC-ICAM, iqela lichonge isiginitsha ye-microbiome (i-MBR risk score) enexabiso eliqinileyo lokuxela kwangaphambili. Nangona olu siginitsha luthathwe kwiisampuli ze-tumor, bekukho unxibelelwano oluqinileyo phakathi kwe-colorectum esempilweni kunye ne-tumor MBR risk score, nto leyo ebonisa ukuba olu siginitsha lunokubamba ukwakheka kwe-gut microbiome yezigulana. Ngokudibanisa amanqaku e-ICR kunye ne-MBR, bekunokwenzeka ukuchonga nokuqinisekisa i-biomarker yabafundi be-multi-omic eqikelela ukusinda kwizigulana ezinomhlaza we-colon. Idatha ye-multi-omic yolu phononongo inika isixhobo sokuqonda ngcono ibhayoloji yomhlaza we-colon kunye nokunceda ekufumaneni iindlela zonyango ezenzelwe wena.

Isalathiso:
Roelands, J., Kuppen, PJK, Ahmed, EI et al. I-tumor edibeneyo, i-immune kunye ne-microbiome atlas yomhlaza wekoloni. UNat Med 29, 1273-1286 (2023).